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1. MIRIAM Identifiers and Resources / 2. Existing Identifier Schemes
Provedor de dados: 17
Autores: Nick  Juty; Camille Laibe; Nicolas Le Novere.
(1) An overview of the MIRIAM identifier scheme is presented, together with a description of the supporting tools and resources which allow its use as a robust cross-referencing framework.&amp;#xd;&amp;#xa;(2) An overview of existing identifier schemes within the life sciences is presented, describing the status of each scheme, the prerequisites that a user must meet to use them, and their limitations.
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6154/version/1

*100 Semi-supercentenarians and older as a proposed sample set for the Archon Genomics X PRIZE Validation Protocol*
Provedor de dados: 17
Autores: Thomas Perls; Nir Barzilai.
The &amp;#x22;Archon Genomics X PRIZE Validation Protocol&amp;#x22;:http://precedings.nature.com/documents/5731/version/1 has been posted in part to solicit comments from the scientific community. Here, we suggest 100 subjects age &amp;#x3e;=105 years as the source of DNAs for the competition.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5756/version/1

11-amino-5-N-methyl-7-fluorine- quindoline derivatives: The Potential Anti-angiogenic Agents Targeting G-quadruplex Structure in Vascular Endothelial Cell Growth Factor
Provedor de dados: 17
Autores: Tian-miao Ou; Yu-jing Lu; Xiao-dong Wang; Zeng-yun An; Yan-ping Li; Zhi-shu Huang; Lian-quan Gu.
Vascular endothelial growth factor (VEGF), a pluripotent cytokine and angiogenic growth factor, plays crucial roles in embryonic development and tumour progression, and is over-expressed in many types of cancer and generally associated with tumour progression and survival rate. The polypurine/polypyrimide sequence located upstream (-89 to -43) of the promoter region of the human VEGF gene that can form specific G-quadruplex structures and raise the possibility for transcriptional control of the VEGF gene by G-quadruplex ligands. In the present study, we investigated the interaction between the 5-N-methyl-7-fluorine-quindoline derivatives (11-amino-5-N-methyl-7-fluorine- quindoline derivatives) and the G-rich sequence in VEGF&amp;#x27;s promoter and the...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/1946/version/1

11[beta]-hydroxysteroid dehydrogenase-type 2 evolved from an ancestral 17[beta]-hydroxysteroid dehydrogenase-type 2
Provedor de dados: 17
Autores: Michael E. Baker.
11[beta]-hydroxysteroid dehydrogenase type-2 (11[beta]-HSD2) regulates the local concentration of cortisol that can activate the glucocorticoid receptor and mineralocorticoid receptor, as well as the concentration of 11-keto-testosterone, the active androgen in fish.  Similarly, 17[beta]-HSD2 regulates the levels of testosterone and estradiol that activate the androgen receptor and estrogen receptor, respectively.  Interestingly, although human 11[beta]-HSD2 and 17[beta]-HSD2 act at different positions on different steroids, these enzymes are paralogs.  Despite the physiological importance of 11[beta]-HSD2 and 17[beta]-HSD2, details of their origins and divergence from a common ancestor are not known.  An opportunity to understand their evolution is...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4649/version/1

12x coverage 454/Sanger Hybrid Assembly of Cucumber (Cucumis sativus L. cv.Borszczagovski) genome - the most efficient way to begin post genomic era
Provedor de dados: 17
Autores: Rafa&amp;#x142; W&amp;#xf3;ycicki; Justyna Witkowicz; Magdalena Pawe&amp;#x142;kowicz; Ewa Siedlecka; Wojciech Gutman; Wojciech Pl&amp;#x105;der; Anna Seroczy&amp;#x144;ska; Mieczys&amp;#x142;aw &amp;#x15a;miech; Katarzyna Niemirowicz-Szczytt; Stanis&amp;#x142;aw Karpi&amp;#x144;ski; Stefan Malepszy; Zbigniew Przybecki.
New sequencing technologies make it possible to achieve genome sequence fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects. &amp;#xd;&amp;#xa;We present here approaches undertaken on the way to the draft assembly the cucumber (Cucumis sativus L. cv. Borszczagowski) genome done with the use of 8x unpaired and 4x paired (3 Kbp) pyrosequenced 454 XLR Titanium reads, together BAC library ends fragments (12,7x physical coverage). Two different assembly approaches, namely Celera and Celera/Arachne were finally used. The Celera result was 15&amp;#x2019;196 contigs of 197 Mbp length and N50 27&amp;#x2019;086 bp and 4&amp;#x2019;157 scaffolds of 224 Mbp length...
Tipo: Poster
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5466/version/1

14-3-3&amp;#x3b6; is Amplified, Overexpressed and Possesses Oncogenic Activities in Head and Neck Squamous Cell Carcinoma
Provedor de dados: 17
Autores: Mauting Lin; Carl D. Morrison; Susie Jones; Nehad Mohamed; Jason Bacher; Christoph Plass.
Gene amplification, a common mechanism for oncogene activation in cancers, has been used in the discovery of novel oncogenes. DNA amplification is frequently observed in head and neck squamous cell carcinomas (HNSCCs) where numerous amplification events and potential oncogenes have already been reported. Recently, we applied restriction landmark genome scanning (RLGS) to study gene amplifications in HNSCC and located novel amplified and uncharacterized regions in primary tumor samples. DNA amplification on 8q22.3, the location of 14-3-3[zeta] (YWHAZ, KCIP-1) is found in 30-40% HNSCC cases. Data obtained from fluorescent in-situ hybridization (FISH) and immunohistochemistry on HNSCC tissue microarrays confirmed frequent low-level 14-3-3[zeta] copy number...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/1953/version/1

16S rRNA based identification of _Aeromonas sp. kumar_ by constructing phylogenetic tree and identification of regulatory elements from the harmful Red Tide bloom, Gulf of Mannar
Provedor de dados: 17
Autores: P. Kumar; C. M. Ramakritinan; A. K. Kumaraguru.
A bacterial strain, designated _Aeromonas sp. kumar_, was isolated from a water sample collected from Red tide Bloom occurred in the region of Gulf of Mannar region, Puthumadam Coast, India and the strain was identified using 16S rRNA based identification. During the sample collection, microbiology analysis was done to study the morphology of the bacteria. Pure culture of strain was maintained through out the study. DNA was isolated and sequenced using 16S rRNA primers. A length of 1452 nucleotide was sequenced and was put in public data base for obtaining accession number. The sequence was studied using MEGA 4, to estimate the evolutionary distances and to construct the Phylogenetic tree. Along with that Regulatory elements and Transcription factors were...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3898/version/1

17 years of integrated research, monitoring, and management of HWA and hemlock ecosystems at Delaware Water Gap National Recreation Area
Provedor de dados: 17
Autores: Richard Evans.
Delaware Water Gap National Recreation Area (&amp;#x201c;the park&amp;#x201d;) covers 28,000 ha along the Delaware River in Pennsylvania and New Jersey. Eastern hemlock forests cover 2,200 ha (8%) of the park, and are often associated with trout streams and scenic waterfalls. Activities like trout fishing, bird watching, and hiking are concentrated in hemlock forests, and many of these areas are officially designated as &amp;#x201c;Outstanding Natural Features&amp;#x201d; having &amp;#x201c;high intrinsic or unique values.&amp;#x201d; In 1989 hemlock woolly adelgid (HWA) was detected in the park, and since 1993 the park has conducted a program to address the threats that hemlock woolly adelgid and hemlock decline poses to park resources. This program...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/5520/version/1

1st INCF Workshop on Genetic Animal Models for Brain Diseases
Provedor de dados: 17
Autores: Olaf Riess; Holm Graessner.
The INCF Secretariat organized a workshop to focus on the &amp;#x201c;role of neuroinformatics in the processes of building, evaluating, and using genetic animal models for brain diseases&amp;#x201d; in Stockholm, December 13&amp;#x2013;14, 2009. Eight scientists specialized in the fields of neuroinformatics, database, ontologies, and brain disease participated together with two representatives of the National Institutes of Health and the European Union, as well as three observers of the national INCF nodes of Norway, Poland, and the United Kingdom.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5909/version/1

1st INCF Workshop on Global Portal Services for Neuroscience
Provedor de dados: 17
Autores: Jaap van Pelt; Gordon  Shepherd.
The goal of this meeting was to map out existing portal services for neuroscience, identify their features and future plans, and outline opportunities for synergistic developments. The workshop discussed alternative formats of future global and integrated portal services.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1779/version/1

1st INCF Workshop on Needs for Training in Neuroinformatics
Provedor de dados: 17
Autores: David Willshaw.
The INCF workshop on Needs for Training in Neuroinformatics was organized by the INCF National Node of the UK. The scope of the workshop was to provide as overview of the current state of neuroinformatics training and recommendations for future provision of training. The report presents a summary of the workshop discussions and recommendations to the INCF.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2563/version/1

1st INCF Workshop on Neuroanatomical Nomenclature and Taxonomy
Provedor de dados: 17
Autores: Mihail Bota; Larry Swanson.
The goal of this workshop was to agree on a general strategy for developing a systematic, useful, and scientifically appropriate framework for neuroanatomical nomenclature. The workshop focused on general principles that will serve as a basis for future decisions on implementation strategies. The report discusses the problems arising from the use of different parcellation schemes and use of different terminologies and highlights the need of a universal vocabulary for describing the structural organization of the nervous system. Workshop participants encourage the creation of an International Coordinating Committee for Neuroanatomical Nomenclature and propose short- and long-term goals for such a committee.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/1780/version/1

1st INCF Workshop on NeuroImaging Database Integration
Provedor de dados: 17
Autores: Lars  Forsberg; Per Roland.
The goal of this meeting was to map existing neuroimaging databases, particularly databases containing primary data, and to identify mechanisms that could facilitate integrated use of such databases, including possible fusion of databases. The report provides an overview of existing neuroimaging databases that were discussed during the workshop and examines the feasibility of database federations. The report includes several recommendations for future developments.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/1781/version/1

1st INCF Workshop on Sustainability of Neuroscience Databases
Provedor de dados: 17
Autores: Jack Van Horn; Jaap van Pelt.
The goal of the workshop was to discuss issues related to the sustainability of neuroscience databases, identify problems and propose solutions, and formulate recommendations to the INCF. The report summarizes the discussions of invited participants from the neuroinformatics community as well as from other disciplines where sustainability issues have already been approached. The recommendations for the INCF involve rating, ranking, and supporting database sustainability.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/1983/version/1

2011 German Escherichia coli O104:H4 outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles
Provedor de dados: 17
Autores: Man Kit Cheung; Lei Li; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 10 isolates from the current German E. coli outbreak against 30 existing E. coli genomes as well as that of a historical EHEC isolate using the alignment-free feature frequency profile method. Our results revealed a high similarity among E. coli isolates from the current outbreak and the historical EHEC being the most closely related isolate sequenced thus far.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6109/version/2

2011 German Escherichia coli outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles
Provedor de dados: 17
Autores: Man Kit Cheung; Lei LI; Wenyan Nong; Hoi Shan Kwan.
Accuracy of SNP-based whole-genome phylogeny reconstruction relies heavily on quality of sequence alignment which is particularly hindered by poorly assembled genomes. Alignment-free methods might provide additional insights. Here, we constructed a whole-genome phylogeny of 9 E.coli isolates from the 2011 German outbreak against existing E. coli genomes using the alignment-free feature frequency profile method. In addition, we looked for gene elements that distinguish the outbreak group from the other E. coli strains and possibly accounted for the emergence of the outbreak isolates using the distinguishing feature analysis.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6109/version/1

2011 German Escherichia coli outbreak: Prophage analysis of close-assembled TY2482 against 55989 using PHAST
Provedor de dados: 17
Autores: Man Kit Cheung; Lei LI; Wenyan Nong; Hoi Shan Kwan.
Using the Hiseq data of the German E. coli outbreak isolate TY2482, preliminary prophage analyses have been performed by some researchers previously. With the closed assembly of the same isolate being available, another round of analysis might help in resolving questions that remain unclear due to the incompleteness of the dataset.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6110/version/1

21 Tesla Micro-MRI of Rat Skin
Provedor de dados: 17
Autores: Rakesh Sharma; Suniket  Fulzele; Kiran Shetty; Mandeep Sachdeva; Bruce R. Locke.
*Aim:* A rapid ultra high resolution ex vivo MRI imaging method was evaluated to visualize rat skin structure. The main objectives were:1.qualitative assessment of viable epidermis, hair, oil and fat-rich skin features by multi-contrast approach;2.achievement of spatial resolution up to 15 microns; 3.comparison of skin histology with MRI skin features obtained by 21 Tesla magnetic resonance imaging (MRI) imager. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Introduction:* The ultrawide bore 900 MHz magnet has high resolution NMR magnet has a central field of 21.1 T. The high resolution MRI technique has potential for both quantitative and non-invasive morphological evaluation at micrometer level. The MRI signal was sensitive to water protons and glycolipid...
Tipo: Poster
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2639/version/1

21 Tesla MRI Microimaging of Rat Heart by Superparamagnetic Antimyoglobin Bound Nanoparticles
Provedor de dados: 17
Autores: Rakesh Sharma.
Superparamagnetic iron-oxide bound antimyoglobin (SPIOM) characteristics were analyzed at different pH.  After injecting SPIOM in heart, ex vivo magnetic resonance microimaging (MRM) technique was used to visualize microvasculature of rat heart including cardiac arteries, veins, cordate tendons attached with valves.  The measurement accuracy of ventricles, aorta, vasculature and dimensions of cordate tendons were close to coregistered histology measurements.
Tipo: Poster
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/2643/version/2

21 Tesla MRI Microimaging of Rat Heart by Superparamagnetic Antimyoglobin Bound Nanoparticles
Provedor de dados: 17
Autores: Rakesh Sharma.
Superparamagnetic iron-oxide bound antimyoglobin (SPIOM) characteristics were analyzed at different pH.  After injecting SPIOM in heart, ex vivo magnetic resonance microimaging (MRM) technique was used to visualize microvasculature of rat heart including cardiac arteries, veins, cordate tendons attached with valves.  The measurement accuracy of ventricles, aorta, vasculature and dimensions of cordate tendons were close to coregistered histology measurements.
Tipo: Poster
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2643/version/1

21 Tesla MRI Microscopy of Mice Kidney, Heart and Skin: Quantitation of MRI Visible Features
Provedor de dados: 17
Autores: S Sharma; Rakesh Sharma.
Excised mice kidney, heart and skin MRI visible features were quantitated using ex vivo 21 Tesla MRI microimager. The fast MRI acquisition protocols of FLASH, gradient echo flow compensated (GEFC) techniques were used to visualize microvasculature of mice kidney, mice heart including cardiac arteries, veins, cordate tendons and mice skin epidermis with hair follicle features.
Tipo: Presentation
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3484/version/1

21 Tesla Rat Heart Magnetic Resonance Microimaging by Paramagnetic Anti-Troponin Bound Polyethylene Based Iron-Oxide Nanoparticles and Image Processing
Provedor de dados: 17
Autores: Rakesh Sharma.
21T MR microimaging with the first use of troponin nanoparticles enhances the visualization of cardiac muscle fibers and offers technical advancement for the future. Diffusion weighting offers fiber tracking and functional analysis. Image processing offers heart probabilistic atlas and maps.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;http://www.ismrm.org/10/program/ELECTRONICPOSTERS.htm
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6650/version/1

26Al/10Be Age of Peking Man
Provedor de dados: 17
Autores: Guanjun Shen; Xing Gao; Bin Gao; Darryl Granger.
The chronological position of Peking Man, or Homo erectus pekinensis, has long been pursued, but has remained problematic due to lack of a suitable dating method^1-7^. Here we report cosmogenic ^26^Al/ ^10^Be burial dating of quartz sediments and artifacts from the lower strata of Zhoukoudian Locality 1 where the remains of early members of the Peking Man family were discovered. This study marks the first radioisotopic dating of any early hominin site in China beyond the range of mass spectrometric U-series dating. The weighted mean of six meaningful measurements, 0.75 +/-; 0.09 (0.11) Ma (million years), provides the best age estimate for lower cultural Layers ^7-10^. Together with previously reported U-series^3^ and paleomagnetic^4^ data, as well as...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2275/version/1

3D computer modeling in micropalaeontology &amp;#x2013; Late Paleozoic conodonts and foraminifers as example
Provedor de dados: 17
Autores: Andrey V. Zhuravlev; Yadviga A. Vevel.
Three-dimension modeling of fossils is one of the branches of computer using in palaeontology. The branch has wide perspectives but it is hardly developed, especially in micropalaeontology. Proposed method of 3D modelling of microfossils demands no unique and expansive equipment and can be realized practically in any palaeontological laboratory. Lower accuracy of the models developed is not critical for most the fields of their utilization: for teaching purposes, construction of illustrated databases and virtual atlases, and for the display of microfossils to a general audience.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1632/version/1

3D model of amphioxus steroid receptor complexed with estradiol
Provedor de dados: 17
Autores: Michael E. Baker; David J. Chang.
The origins of signaling by vertebrate steroids are not fully understood.  An important advance was the report that an estrogen-binding steroid receptor [SR] is present in amphioxus, a basal chordate with a similar body plan as vertebrates.  To investigate the evolution of estrogen binding to steroid receptors, we constructed a 3D model of amphioxus SR complexed with estradiol.  This 3D model indicates that although the SR is activated by estradiol, some interactions between estradiol and human ER[alpha] are not conserved in the SR, which can explain the low affinity of estradiol for the SR.  These differences between the SR and ER[alpha] in the steroid-binding domain are sufficient to suggest that another steroid is the physiological regulator of the SR....
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3316/version/1

3D model of lamprey estrogen receptor with estradiol and 15[alpha]-hydroxy-estradiol
Provedor de dados: 17
Autores: Michael E. Baker; David J. Chang; Charlie Chandsawangbhuwana.
Lamprey, a basal vertebrate, contains orthologs of the estrogen receptor (ER), progesterone receptor and corticoid receptor.  A perplexing property of lamprey is that 15[alpha]-hydroxy-steroids are active steroids.  For example, 15[alpha]-hydroxy-estradiol [15[alpha]-OH-E2] is the estrogen, instead of estradiol (E2).  To investigate how 15[alpha]-OH-E2 binds lamprey ER, we constructed a 3D model of the lamprey ER with E2 and 15[alpha]-OH-E2.  Our 3D model shows that S[delta] on Met-409 can form a hydrogen bond with the 15[alpha]-hydroxyl on 15[alpha]-OH-E2.  In human ER[alpha], the corresponding residue Ile-424 has a van der Waals contact with 15[alpha]-OH-E2.  BLAST analysis of GenBank indicates that among vertebrate ERs, only lamprey ER contains a...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2768/version/1

3D models of lamprey corticoid receptor complexed with 11-deoxycortisol and deoxycorticosterone
Provedor de dados: 17
Autores: Michael E. Baker; Kayla Y. Uh; Paiyuam Asnaashari.
The serum of Atlantic sea lamprey, a basal vertebrate, contains two corticosteroids, 11-deoxycortisol and deoxycorticosterone.  Only 11-deoxycortisol has high affinity [Kd~3 nM] for the corticoid receptor [CR] in lamprey gill cytosol.  To investigate the binding of 11-deoxycortisol to the CR, we constructed 3D models of lamprey CR complexed with 11-deoxycortisol and deoxycorticosterone.  These 3D models reveal that Leu-220 and Met-299 in lamprey CR have contacts with the 17[alpha]-hydroxyl on 11-deoxycortisol.  Lamprey CR is the ancestor of the mineralocorticoid receptor [MR] and glucocorticoid receptor [GR].  Unlike human MR and human GR, the 3D model of lamprey CR finds a van der Waals contact between Cys-227 in helix 3 and Met-264 in helix 5.  Mutant...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6216/version/1

3D Structure Development of Chikungunya Virus and its Structural Characterization &amp;#x2013; an In silico approach
Provedor de dados: 17
Autores: Anuraj Nayarisseri; Mukesh Yadav; Dowlathabad Muralidhara Rao; Sonam Kukreja; Sheaza  Ahmed; Pooja  Singh.
The 3 Dimensional structure of a protein is an expedient for structure based drug design and identifying the conformational epitopes that are foremost for designing the vaccines. Chikungunya (CHIKV) is a heat sensitive RNA virus which causes a viral disease which is transmitted in humans by human-mosquito-human transmission. Disease mostly found in the tropic and subtropical countries mainly in South India and in few other Asian countries. The primary transmission agents of Chikungunya Virus are yellow fever mosquito (_Aedes aegypti_) and forest day mosquito (_Aedes albopictus_). The forest day mosquito bites during day time and hence day time mosquito bite is the main reason for transmission. The main distinctive of the disease is a fever along with an...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5143/version/1

3DScape: three dimensional visualization plug-in for Cytoscape
Provedor de dados: 17
Autores: Qi Wang.
3DScape is the first plug-in which enables three-&amp;#xd;&amp;#xa;dimensional network visualization in Cytoscape. The extra dimension is useful in accommodating, visualizing, and distinguishing larger networks with multiple crossing connections.&amp;#xd;&amp;#xa;Special features in 3DScape include 3D layout algorithms, mapping onto 3D models and animation effects on a series of expression data. 3DScape is available at  http://www.rendware.com
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6094/version/1

9aaTAD Prediction result (2006)
Provedor de dados: 17
Autores: Martin Piskacek.
Recently reported, 9aaTAD transcription factors p53, VP16, MLL/ALL, E2A, HSF1, NF-IL6, NFAT1 and NF-kB interact directly with the general coactivator CBP/p300 aside from already referred TAF9. All four domains of CBP/p300 - KIX, TAZ1, TAZ2 and IBiD provide multiple interactions with 9aaTADs, e.g. p53. Annotation of predicted 9aa TAD using Pattern search ScanProsite on ExPASy and relevant experimental data are listed.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3984/version/1

9aaTADs mimic DNA to interact with a pseudo-DNA Binding Domain KIX of Med15 (Molecular Chameleons)
Provedor de dados: 17
Autores: martin piskacek.
The KIX-domain of Gal11/MED15 was shown to interact with short transactivation domain of Pdr1 and Oaf1 (12 and 9 amino acids respectively) annotated to 9aaTAD family. Reported NMR data revealed a surprising sequence similarity of KIX domain and basic-leucine zipper (bZIP).
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3939/version/1

A Bacterial Enzyme Catalyzing Double Reduction of a &amp;#x3b2;,&amp;#x3b4;-Diketo Ester with Unprecedented Stereoselectivity
Provedor de dados: 17
Autores: Xuri Wu; Nan Liu; Yunmian He; Yijun Chen.
Various ketoreductases exclusively participate in all common biological events, and they are a class of important biocatalysts for the production of chiral alcohols. While many types of ketoreductase have been extensively studied and their functions, properties and utilities have been well known, the capability of stereoselectively reducing two carbonyl groups in the same diketohexanoate ester molecule to form a dihydroxy product by a single ketoreductase has not been evidently characterized. Here we show that a unique and novel enzyme, diketoreductase, was cloned from Acinetobacter baylyi, heterogeneously expressed in _Escherichia coli_ and purified to homogeneity. The diketoreductase is up to 78% homologous to bacterial 3-hydroxyacyl coenzyme-A...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/1697/version/1

A Bacterial Enzyme Catalyzing Double Reduction of a &amp;#x3b2;,&amp;#x3b4;-Diketo Ester with Unprecedented Stereoselectivity
Provedor de dados: 17
Autores: Xuri Wu; Nan Liu; Yunmian He; Yijun Chen.
Various ketoreductases exclusively participate in all common biological events, and they are a class of important biocatalysts for the production of chiral alcohols. While many types of ketoreductase have been extensively studied and their functions, properties and utilities have been well known, the capability of stereoselectively reducing two carbonyl groups in the same diketohexanoate ester molecule to form a dihydroxy product by a single ketoreductase has not been evidently characterized. Here we show that a unique and novel enzyme, diketoreductase, was cloned from Acinetobacter baylyi, heterogeneously expressed in _Escherichia coli_ and purified to homogeneity. The diketoreductase is up to 78% homologous to bacterial 3-hydroxyacyl coenzyme-A...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/1697/version/2

A Bayesian Framework for Parameter Estimation in Dynamical Models with Applications to Forecasting
Provedor de dados: 17
Autores: Fl&amp;#xe1;vio Code&amp;#xe7;o Coelho; Claudia T. Code&amp;#xe7;o.
Mathematical models in Biology are powerful tools for the study and exploration of complex dynamics. Nevertheless, bringing theoretical results to an agreement with experimental observations involves acknowledging a great deal of uncertainty intrinsic to our theoretical representation of a real system.&amp;#xd;&amp;#xa;Proper handling of such uncertainties, is key to the successful usage of models to predict experimental or &amp;#xfb01;eld observations. This problem has been addressed over the years by many tools for model calibration an parameter estimation. In this article we present a general framework for uncertainty analysis and parameter estimation which is designed to handle uncertainties associated with the modeling of dynamic biological systems...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4044/version/1

A Bayesian Hierarchical Model to Derive Novel Gene Networks from Gene Ontology Fingerprints
Provedor de dados: 17
Autores: Tingting Qin; Lam Tsoi; Andrew Lawson; Jim Zheng.
We developed a Bayesian hierarchical model to identify gene networks based on the similarity score generated from comparing the gene ontology fingerprints of gene pairs. Genes in this network were assumed to have similar biological functions that can be indicated by their ontology fingerprints. Our results indicate that different pathways show consistent score threshold that allow us to distinguish biological relevant gene&amp;#x2014;gene connections in the network.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3511/version/1

A bestiary of non-linear functions for growth analysis
Provedor de dados: 17
Autores: C. E. Timothy Paine; Toby Marthews; Deborah Vogt; Drew Purves; Mark Rees; Andy Hector; Lindsay Turnbull.
Plant growth is an essential ecological process, integrating across scales from physiology to community dynamics. Predicting the growth of plants is essential to understand a wide range of ecological issues, including competition, plant-herbivore interactions and ecosystem functioning.&amp;#xd;&amp;#xa;A challenge in modeling plant growth is that growth rates almost universally decrease with increasing size, for a variety of reasons. Traditional analyses of growth are hampered by the need to remain within the structures of linear models, which handle this slowing poorly. We demonstrate the implementation of a variety of non-linear models that are more appropriate for modeling plant growth than are the traditional, linear,...
Tipo: Presentation
Palavras-chave: Ecology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5257/version/1

A Biomimetic Model of the Outer Plexiform Layer by Incorporating Memristive Devices
Provedor de dados: 17
Autores: Andras Gelencser; Themistoklis Prodromakis; Christofer Toumazou; Tamas Roska.
In this paper we present a biorealistic model for the first part of the early vision processing by incorporating memristive nanodevices. The architecture of the proposed network is based on the organisation and functioning of the outer plexiform layer (OPL) in the vertebrate retina. We demonstrate that memristive devices are indeed a valuable building block for neuromorphic architectures, as their highly non-linear and adaptive response could be exploited for establishing ultra-dense networks with similar dynamics to their biological counterparts. We particularly show that hexagonal memristive grids can be employed for faithfully emulating the smoothing-effect occurring at the OPL for enhancing the dynamic range of the system. In addition, we employ a...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6664/version/1

A bizarre Jurassic maniraptoran from China with elongate ribbon-like feathers
Provedor de dados: 17
Autores: Fucheng Zhang; Zhonghe Zhou; Xing Xu; Xiaolin Wang; Corwin Sullivan.
Recent coelurosaurian discoveries have greatly enriched our knowledge of the dinosaur-bird transition, but all reported taxa close to this transition are from relatively well-known coelurosaurian groups^1-3^. Here we report a new basal avialan, Epidexipteryx hui gen. et sp. nov., from the Middle-Late Jurassic of Inner Mongolia, China. This new species is characterized by an unexpected combination of characters seen in several different theropod groups, particularly the Oviraptorosauria. Phylogenetic analysis shows it to be the sister taxon to Epidendrosaurus^4,5^, forming a new clade at the base of Avialae^6^. Epidexipteryx also possesses two pairs of elongate ribbon-like tail feathers (ETFs), and its limbs lack contour feathers for flight. This finding...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2326/version/1

A call for disruptive innovation in science publishing with a new open data-sharing platform for the life sciences
Provedor de dados: 17
Autores: Donald  C. Cooper.
&amp;#x201c;A disruptive innovation is an innovation that helps create a new market and value network, and eventually goes on to disrupt an existing market and value network (over a few years or decades), displacing an earlier technology. The term is used in business and technology literature to describe innovations that improve a product or service in ways that the market does not expect.&amp;#x201d; -Wikipedia&amp;#xd;&amp;#xa;On April 3rd, 2012 Nature Precedings, Nature Publishing Group&amp;#x2019;s experiment in free pre-print publishing was shut down and no longer accepts submissions. According to the Nature Precedings website it was created in 2007 as &amp;#x201c;a place for researchers to share documents, including presentations, posters, white...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7151/version/1

A Case For Killing Humpback Whales?
Provedor de dados: 17
Autores: Nicholas J. Gales; Phillip J. Clapham; C. Scott Baker.
During the austral summer of 2007/08, hunting of Southern Hemisphere (SH) humpback whales will recommence after almost half a century of protection. The stated rationale for this hunt, by the Government of Japan (GoJ), is to gather important scientific information for use in management. If the scientific need were defensible, and the proponents had accommodated reasonable conservation concerns, then criticisms of the hunt would be limited to philosophical issues. This is not the case. The program&amp;#x2019;s research objectives are unlikely to be achieved by lethal methods and do not address the principal research needs for SH humpback whales identified by the International Whaling Commission (IWC).
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1313/version/1

A century of warfare shoots holes in anti-Caulerpa campaign
Provedor de dados: 17
Autores: John R. M. Chisholm; Pavel P. Povinec; Valerie Briet; Janine Gastaud; Jean M. Jaubert; Sang-Han Lee; Isabelle Levy-Palomo; Manuel Marchioretti; Audrey Minghelli-Roman.
Effort to have all varieties of the marine alga Caulerpa taxifolia listed as noxious weeds hinges on the argument that the alga&amp;#x27;s proliferation in the Mediterranean Sea is a cause and not a consequence of environmental degradation. Until now, the occurrence of two populations in a pristine part of the northern Mediterranean near the island of Porquerolles has upheld this claim. Here we show that the alga&amp;#x27;s development at Porquerolles is indeed a consequence of environmental degradation caused by military weapons&amp;#x27; impacts on seagrass beds during the last century. The available data show that substratum enrichment plays a key role in fostering development of Caulerpa, irrespective of whether this results directly from pollution or...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1240/version/1

A common subcortical oscillatory network contributes to recovery after spinal cord injury
Provedor de dados: 17
Autores: Yukio Nishimura; Yosuke Morichika; Tadashi Isa.
Recent studies in monkeys showed that when the direct cortico-motoneuronal connection was transected at mid-cervical segments, remaining, indirect cortico-motoneuronal pathways compensated for finger dexterity within one to three months. To elucidate the changes in dynamic properties of neural circuits during the recovery, we investigated the cortico-muscular and inter-muscular couplings of activities throughout the recovery course. Activities of antagonist muscle pairs showed co-activation during the second postoperative week, and oscillated coherently at frequencies of 30-46 Hz (gamma-band) by one month postoperatively. Such gamma-band inter-muscular coherence was not observed preoperatively, but became prominent and distributed widely over proximal and...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1937/version/1

A community of biocurators
Provedor de dados: 17
Autores: Pascale Gaudet.
Biocuration is a difficult mission: biological data is highly heterogeneous, and there are few areas where guidelines for data preservation and exchange exist. This has hampered the speed, quantity and diversity of data possible to capture. Hence, a major challenge for the biocuration community is to explore innovative ways to capture, represent and display information. It is also essential to increase the involvement of researchers, publishers and funding agencies in this process. I will discuss the work of the International Society for Biocuration to build a community of biocurators to achieve these goals.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5134/version/1

A comparative analysis of 21 literature search engines
Provedor de dados: 17
Autores: Kshitish  K. Acharya; Greta Kasliwal; Haritha Haridas.
With increasing number of bibliographic software, scientists and health professionals either make a subjective choice of tool(s) that could suit their needs or face a challenge of analyzing multiple features of a plethora of search programs. There is an urgent need for a thorough comparative analysis of the available bio-literature scanning tools, from the user&amp;#x2019;s perspective. We report results of the first time semi-quantitative comparison of 21 programs, which can search published (partial or full text) documents in life science areas. The observations can assist life science researchers and medical professionals to make an informed selection among the programs, depending on their search objectives. &amp;#xd;&amp;#xa;Some of the important...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2101/version/1

A comparative assessment of octanol-water partitioning and distribution constant estimation methods for perfluoroalkyl carboxylates and sulfonates
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
New experimental data is available in the literature regarding the octanol-water distribution behavior of representative straight chain perfluoroalkyl carboxylate (PFCA) and sulfonate (PFSA) congeners. The current study provides the first investigation into the predictive ability of various software programs for estimating the corresponding octanol-water partitioning (log P) and distribution (log D) constants of PFCAs and PFSAs. Wide predictive variation was found within and between the various methods. Several programs were able to accurately estimate the log P/D fragmental contributions of a -CF~2~- group for PFCAs, as well as the associated Gibbs free energies for partitioning into octanol from water due to the hydrophobic character of the...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3282/version/1

A comparative assessment of octanol-water partitioning and distribution constant estimation methods for perfluoroalkyl carboxylates and sulfonates
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
New experimental data is available in the literature regarding the octanol-water distribution behavior of representative straight chain perfluoroalkyl carboxylate (PFCA) and sulfonate (PFSA) congeners. The current study provides the first investigation into the predictive ability of various software programs for estimating the corresponding octanol-water partitioning (log P) and distribution (log D) constants of PFCAs and PFSAs. Wide predictive variation was found within and between the various methods. Several programs were able to accurately estimate the log P/D fragmental contributions of a -CF~2~- group for PFCAs, as well as the associated Gibbs free energies for partitioning into octanol from water due to the hydrophobic character of the...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3282/version/2

A Comparative Study of the Magnitude, Frequency and Distribution of Intense Rainfall in the United Kingdom
Provedor de dados: 17
Autores: John C. Rodda; Max A. Little; Harvey J. E. Rodda; Patrick E. McSharry.
During the 1960s, a study was made of the magnitude, frequency and distribution of intense rainfall over the UK, employing data from more than 120 daily-read rain gauges covering the period 1911 to 1960. Using the same methodology, that study was recently updated utilizing data for the period 1961 to 2006 for the same gauges, or from those nearby. This paper describes the techniques applied to ensure consistency of data and statistical modelling. It presents a comparison of patterns of extreme rainfalls for the two periods and discusses the changes that have taken place. Most noticeably, increases up to 20% have occurred in the north west of the country and in parts of East Anglia. There have also been changes in other areas, including decreases of the...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3847/version/1

A comparative study on the production of ethanol from lignocellulosic biomass by chemical and biological method
Provedor de dados: 17
Autores: Shaheed SM; Rohit JP; Madhan R; Selvakumar K.
Ethanol derived from non-edible biomass is renewable and a clean source of energy. It is independent of the food industry and it is economically feasible. The first generation biofuel or bioethanol is still not a very convenient source of energy as it prominently depends on the availability of grains. The main objective of this work is to develop an industrious efficient process to produce ethanol from lignocellulosic biomasses like wood and leaf in a lab scale. Two processes were compared. The first process involved an alkaline pre-treatment of the powdered biomass followed by dilute acid hydrolysis. The second process involved an alkaline treatment followed by direct hydrolysis of the biomass by use of a fungal species obtained from rotting wood....
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/6579/version/1

A conceptual framework for the evolutionary selection of biologically &amp;#x27;essential&amp;#x27; elements
Provedor de dados: 17
Autores: Mark Conyers.
Standard texts dutifully list 16 essential elements for plant growth, yet the literature indicates that the boundary between essential and nonessential nutrients for plants is not always clear. When animals and &amp;#x27;lower&amp;#x27; organisms are considered, the team of 16 is considerably expanded and the notion of essentiality is blurred. Why are some elements more important than others to plants and to organisms in general? Here I propose three criteria by which elements might have been selected in the development of organisms: low atomic weight, at least modest abundance, and ease of assembly into complex structures. Assembly of the structural elements C, N, S, P, and O is based on valency and ionic potential. The selection of monovalent elements...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3223/version/1

A condition of cooperation. Games on network
Provedor de dados: 17
Autores: Tomohiko Konno.
Natural selection is often regarded as a result of severe competition. Defect seems beneficial for a single individual in many cases.However, cooperation is observed in many levels of biological systems ranging from single cells to animals, including human society. We have yet known that in unstructured populations, evolution favors defectors over cooperators. On the other hand, there have been much interest on evolutionary games^1,2^ on structured population and on graphs^3-16^. Structures of biological systems and societies of animals can be taken as networks. They discover that network structures determine results of the games. Together with the recent interest of complex networks^17,18^, many researchers investigate real network structures. Recently...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3028/version/1

A coordinated phosphorylation cascade initiated by MSK1 directs RAR alpha recruitment to target gene promoters
Provedor de dados: 17
Autores: Nathalie Bruck; Dominique Vitoux; Christine Ferry; Vanessa Duong; Annie Bauer; Hughes de The; Cecile Rochette-Egly.
The nuclear retinoic acid (RA) receptor alpha (RAR&amp;#x3b1;) is a transcriptional transregulator that controls the expression of specific gene subsets through binding at response elements and dynamic interactions with coregulators, which are coordinated by the ligand. Here, we highlighted a novel paradigm in which the transcription of RAR&amp;#x3b1;-target genes is controlled by phosphorylation cascades initiated by the rapid RA activation of the p38MAPK/MSK1 pathway. We demonstrate that MSK1 phosphorylates RAR&amp;#x3b1; at S369 located in the Ligand Binding Domain, allowing the binding of TFIIH and thereby phosphorylation of the N-terminal domain at S77 by cdk7/cyclin H. MSK1 also phosphorylates Histone H3 at S10. Finally, the phosphorylation cascade...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2107/version/1

A Critical Evaluation of Clinical Trials in Cancer and Pharmacogenomics
Provedor de dados: 17
Autores: I. C. Baianu.
A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7052/version/1

A Database for TSSs of Human MicroRNAs
Provedor de dados: 17
Autores: Malay Bhattacharyya; Sanghamitra Bandyopadhyay.
MicroRNAs (miRNAs) are small endogeneous non-coding RNAs of about 22nt length. These short RNAs regulate the expression of mRNAs by hybridizing with their 3&amp;#x27;-UTRs or by translational repression. They have been shown to take crucial roles in many biological processes. Many of the current studies are focused over how mature miRNAs regulate mRNAs, even though there is very limited knowledge about their transcriptional loci. Primary miRNAs (pri-miRs) are first transcribed from the DNA, followed by the formation of precursor miRNA (pre-miR) by endonucleases activity, which finally produces mature miRNAs. Unfortunately, the identification of the loci of pri-miRs, and the associated information about transcription start sites (TSSs) and promoters is...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6832/version/1

A database of naturally occurring human urinary peptides and proteins for use in clinical applications
Provedor de dados: 17
Autores: Petra Z&amp;#xfc;rbig; Joshua Coon; Hartwig Bauer; Georg Behrens; Mohammed Dakna; Anna Dominiczak; Stephane Decramer; Jochen Ehrich; Danilo Fliser; Moritz Frommberger; Arnold Ganser; Mark Giolami; Igor Golovko; David Good; Wilfried Gwinner; Marion Haubitz; Stefan Herget-Rosenthal; Holger Jahn; George Jerums; Bruce Julian; Markus Kellmann; Volker Kliem; Walter Kolch; Andrzej Krolewski; Mario Luppi; Ziad Massy; Michael Melter; Christian Neus&amp;#xfc;ss; Jan Novak; Karlheinz Peter; Kasper Rossing; Harald Rupprecht; Joost Schanstra; Eric Schiffer; Jens-Uwe Stolzenburg; Lise Tarnow; Dan Theodorescu; Visith Thongboonkerd; Raymond Vanholder; Eva Weissinger; Harald Mischak; Philippe Schmitt-Kopplin.
Owing to its availability, ease of collection and correlation with (patho-) physiology, urine is an attractive source for clinical proteomics. However, the lack of comparable datasets from large cohorts has greatly hindered development in this field. Here we report the establishment of a high resolution proteome database of naturally occurring human urinary peptides and proteins - ranging from 800-17,000 Da - from over 3,600 individual samples using capillary electrophoresis coupled to mass spectrometry, yielding an average of 1,500 peptides per sample. All processed data were deposited in an SQL database, currently containing 5,010 relevant unique urinary peptides that serve as classifiers for diagnosis and monitoring of diseases, including kidney and...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2007
URL: http://precedings.nature.com/documents/1219/version/1

A database of orthologous exons in primates for comparative analysis of RNA-seq data
Provedor de dados: 17
Autores: Ran Blekhman.
RNA-seq technology facilitates the study of gene expression at the level of individual exons and transcripts. Moreover, RNA-seq enables unbiased comparative analysis of expression levels across species. Such analyses typically start by mapping sequenced reads to the appropriate reference genome before comparing expression levels across species. However, this comparison requires prior knowledge of orthology at the exon level. With this in mind, I constructed a database of orthologous exons across three primate species (human, chimpanzee, and rhesus macaque). The database facilitates cross-species comparative analysis of exon- and transcript-level regulation. A web application allowing for an easy database query: http://giladlab.uchicago.edu/orthoExon/
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7054/version/1

A decline in pollinator dependent vegetable crop productivity in India indicates pollination limitation and consequent agro-economic crises.
Provedor de dados: 17
Autores: Parthiba Basu; Ritam Bhattacharya; Pietro Ianetta.
Approximately 70% of the tropical crop species depend on pollinators for optimum yields (Roubik, 1995, Klein 2007). The economic value of such pollinated crops to India is $726 million and India is the world&amp;#x27;s second largest vegetable producer (Sidhu, 2005). This status has been underpinned by large-scale changes in land-use and pesticide dependency (Fazal, 2000; Shaw &amp;#x26; Satish, 2007). A method (c.f. Aizen et al. 2008) that partitions crops into categories depending on their relative pollinator dependence (Index of pollinator dependence, DI) was applied to analysis of vegetable yields for India over 45 years (1963-2008) using FAO data. This has revealed that since 1993, relative yields of crop production has either flattened or declined,...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6044/version/1

A Discrete State Model for Kinesin-1 with Rate Constants Modulated by Neck Linker Tension
Provedor de dados: 17
Autores: Steven J. Koch; Lawrence J. Herskowitz.
Kinesin-1 is a homodimeric molecular motor protein that uses ATP and a hand-over-hand motion to transport cargo along microtubules. How kinesin converts chemical energy into directed motion is a question that has been actively studied since its discovery. Even at the most coarse-grained level of chemical kinetics, understanding is still lacking. Minimal kinetic models are often developed to both explain kinesin&amp;#x2019;s hand-over-hand forward-stepping behavior and to infer important kinetic rate constants from experimental data. These minimal models are often limited to a handful of two-headed states on a core cycle and have been essential for the current level of understanding. However, it is not always clear how to evolve these core-cycle models to...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5038/version/1

A Draft Sequence of the Puerto Rican Parrot Genome (Amazona vittata) &amp;#x2013; a Genome Project funded by a Local Community Effort
Provedor de dados: 17
Autores: Taras K. Oleksyk.
The genome of the Puerto Rican parrot (Amazona vittata) has been sequenced and assembled in an international collaboration supported by many individual donations from the people of Puerto Rico.  This is a critically endangered endemic bird, the only surviving native parrot species in the territory of the United States, and the first parrot belonging to the large genus Amazona to have its genome sequenced and assembled.  A genome of one A. vittata female was sequenced resulting in a total of almost 42.5 billion nucleotide bases equivalent to 26.89X average coverage depth. After filtering out the short fragments (&amp;#x3c;500bp), the assembly resulted in 259,423 short fragment library contigs, half of them (N50) of at least 6,983 bp in length, with a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6552/version/1

A Drosophila systems model of withdrawal from chronic pentylenetetrazole relevant in post-epileptogenesis
Provedor de dados: 17
Autores: Priyanka Singh; Farhan Mohammad; Abhay Sharma.
Rodent kindling induced by pentylenetetrazole (PTZ) is an established model of epileptogenesis and antiepileptic drug (AED) testing. Recently, a Drosophila systems model has been described in which chronic PTZ causes a decreased climbing speed in adult males on 7th day. Some AEDs ameliorate development of this locomotor deficit. Time-series of microarray expression profiles of heads of flies treated with PTZ has been found to resemble transcriptomic alterations associated with epileptogenesis. In the fly model, withdrawal from seven day long PTZ treatment causes an increased climbing speed on 7th consequent day. Here, we present a systems model of the post-PTZ withdrawal regime. Unlike AED-untreated individuals, flies treated with any of the five AEDs...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3447/version/1

A dynamical model of genetic networks describes cell differentiation
Provedor de dados: 17
Autores: Roberto Serra; Villani Marco; Alessia Barbieri.
Cell differentiation is a complex phenomenon whereby a stem cell becomes progressively more specialized and eventually gives rise to a specific cell type. Differentiation can be either stochastic or, when appropriate signals are present, it can be driven to take a specific route. Induced pluripotency has also been recently obtained by overexpressing some genes in a differentiated cell. Here we show that a stochastic dynamical model of genetic networks can satisfactorily describe all these important features of differentiation, and others. The model is based on the emergent properties of generic genetic networks, it does not refer to specific control circuits and it can therefore hold for a wide class of lineages. The model points to a peculiar role of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4741/version/1

A few remarks on the relationship between visuo-spatial attention deficits and dyslexia
Provedor de dados: 17
Autores: John Skoyles; Bernt C. Skottun.
Dyslexia and attentional problems are often comorbid. This raises the question whether reading deficits might etiologically follow from attentional difficulties, a hypothesis that has been proposed in regard to visuo-spatial attention deficits. This visuo-spatial attention deficit hypothesis would  predict that attention deficits should be specific to dyslexia. However, it is here estimated that at the population level there are more non-dyslexic individuals than dyslexic individuals with visuo-spatial attention deficits. The reason for this is that in the overall population level there are far more individuals without dyslexia than with dyslexia. Thus, a relatively modest percentage presence of attention problems in the non-dyslexic population can result...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5525/version/1

A Formal Ontology of Sequences
Provedor de dados: 17
Autores: Robert Hoehndorf; Janet Kelso; Heinrich Herre.
The Sequence Ontology is an OBO Foundry ontology that provides categories of sequences and sequence features that are applied to the annotation of genomes.  To facilitate interoperability with other domain ontologies and to provide a foundation for automated inference, we provide here an axiom system for the Sequence and Junction categories in first- and second-order predicate logics.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3537/version/1

A Framework for BioCuration Workflows (part II)
Provedor de dados: 17
Autores: Martin Krallinger.
This is the second part of the talk &amp;#x2018;A Framework for BioCuration Workflows&amp;#x2019;, given by Martin Krallinger from the Spanish National Cancer Research Centre at the &amp;#x27;Text Mining for the BioCuration Workflow&amp;#x27; workshop. The first part was held by Gully APC Burns (USC Information Sciences Institute, USA). This presentation covered some of the main general tasks often shared by existing literature biocuration workflows: Identification of relevant articles, identification and normalization of the actual bio-entities, the extraction of the annotation event and the identification of some evidential support (e.g. experimental evidence). Some of the important aspects, bottlenecks and potential text mining approaches were briefly...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3126/version/1

A Fresh Look at Energy, Materials, and Labor in Agriculture
Provedor de dados: 17
Autores: Aaron W. Baum; Tadeusz Patzek; Martin Bender; Steve Renich; Wes Jackson.
An understanding of agriculture&amp;#x27;s energy, material, and labor requirements is essential for achieving economic and ecological sustainability, and for assessing the effectiveness of relevant policy decisions (biofuel subsidies, regulations, labeling, etc.). Previous studies of energy, materials, and labor use in farming have been based on either unverified voluntary reporting or test plots, rather than on the high-resolution measurements of mass and energy flows. Here we present a recursive analysis of 1.25 million data points describing in unprecedented detail the resource transactions on a 60 ha farm functioning for over 6 years. This analysis highlights the importance of accounting for all types of materials, as well as capital equipment,...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4291/version/1

A functional dissociation of conflict processing within anterior cingulate cortex
Provedor de dados: 17
Autores: Chobok Kim; James Kroger; Jeounghoon Kim.
Goal-directed behavior requires cognitive control to regulate neural processing when conflict is encountered. The dorsal anterior cingulate cortex (dACC) has been associated with detecting response conflict during conflict tasks. However, recent findings have indicated not only that two distinct subregions of dACC are involved in conflict processing but also that the conflict occurs at both perceptual and response levels. We clarified a functional dissociation of the caudal dACC (cdACC) and the rostral dACC (rdACC) in responding to different sources of conflict. The cdACC was selectively engaged in perceptual conflict whereas the rdACC was more active in response conflict. Further, the dorsolateral prefrontal cortex (DLPFC) was coactivated not with cdACC...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2505/version/1

A G4MP2 theoretical study on the gas phase enthalpies of formation for various polycyclic aromatic hydrocarbons (PAHs) and other C~10~ through C~20~ unsaturated hydrocarbons
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase enthalpies of formation at 298.15 and 1 atm (&amp;#x394;~f~H~(g),298K~) were calculated using the atomization approach at the G4MP2 composite method level of theory for 86 polyaromatic hydrocarbons (PAHs) and other C~10~ through C~20~ unsaturated hydrocarbons. Where available, good agreement with prior experimental data and/or high level theoretical estimates was obtained. Linear regressions between semiempirical MNDO, MNDO-d, AM1, PM3, RM1, and PM6 estimated &amp;#x394;~f~H~(g),298K~ and the corresponding G4MP2 values were employed to obtain G4MP2 corrected semiempirical &amp;#x394;~f~H~(g),298K~ for a suite of 156 C~11~ through C~42~ unsaturated hydrocarbons and PAHs.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6450/version/1

A G4/W1BD theoretical study into the gas phase enthalpies of formation for potential high energy materials
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Enthalpies of formation (&amp;#x394;~f~H~(g)~) at 298.15 K and 0 K were calculated for various potential high energy materials (HEMs) using the high-level Gaussian-4 (G4) and W1BD methods with the atomization approach. Where prior high level estimates are available in the literature, the G4 and W1BD &amp;#x394;~f~H~(g)~ are in good agreement. The results presented herein represent the highest level calculations performed to date on this suite of HEMs. These G4/W1BD enthalpies of formation should provide utility among the research community as a benchmark set of values against which to assess future experimental and/or theoretical data.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6461/version/1

A general model of continuous character evolution
Provedor de dados: 17
Autores: Carl Boettiger.
I present a general model for continuous character evolution, review some of the common challenges that emerge in such complex methods and review strategies for handling them.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6080/version/1

A generic approach for representing complex structures in biological models
Provedor de dados: 17
Autores: Robert I. Muetzelfeldt.
Increasingly, the biological modelling community is looking for ways of handling complex and possibly dynamic structures in their models.   On the one hand, the pathway-modelling groups (SBML and CellML) seek to move up levels of organisation, while on the other hand the &amp;#x22;Virtual X&amp;#x22; communities (where X is some organism or organ) need to represent the organisational structure within their object of study.   To date, various approaches have been proposed, such as  the SBML Level 3 &amp;#x27;comp&amp;#x27;, &amp;#x27;spatial&amp;#x27;, &amp;#x27;array&amp;#x27; and &amp;#x27;dyn&amp;#x27; extension packages, and domain-specific elements in languages such as NeuroML, but there is no generic approach intended to be adopted by the various...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5188/version/1

A Genome-Wide Analysis Reveals Significant Overlap of Transcription and DNA Repair in Stationary Phase Yeast
Provedor de dados: 17
Autores: Aviv de Morgan; Leonid  Brodsky; Yefim Ronin; Eviatar Nevo; Abraham Korol; Yechezkel Kashi.
The association between transcription and DNA repair is acknowledged as a player in the generation of mutations in a non-random fashion in prokaryotes and eukaryotes. Previous studies demonstrated that the transcription complex is capable of directing DNA repair to sites of transcription. This process is especially important to growth-arrested cells, in which many DNA repair capacities are diminished; it may also lead to mutations preferentially in transcribed genes. Using microarray analysis of growth-arrested yeast cultures, we demonstrated on a genomic scale, the co-localization of a DNA-turnover marker, indicative of DNA-repair-associated DNA synthesis, with genes persistently transcribed during stationary phase. This may serve as a clue regarding the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1543/version/1

A global assessment of deep-sea basalt sites for carbon sequestration
Provedor de dados: 17
Autores: David Goldberg; Angela L. Slagle.
In recent years, the debate over the most effective means to stabilize greenhouse gas concentrations in the atmosphere has endorsed multiple approaches and a variety of technologies. Assuring secure storage of anthropogenic carbon dioxide is one of our most pressing global scientific challenges that may contribute to achieving a stable solution over the next several decades. Geological sequestration by injection into deep-sea basalt formations provides unique and significant advantages over other potential storage options, including: (a) vast reservoir capacities with high porosity and permeability, sufficient to accommodate centuries-long U.S. production of fossil fuel CO~2~ at locations within a few hundreds of kilometers of populated areas; (b) chemical...
Tipo: Poster
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2640/version/1

A Handy Script to Implement Genetic Models in R
Provedor de dados: 17
Autores: Wei Zhang.
Genome-wide associations between genotypic and phenotypic data often assume certain genetic models. A handy script in R was written to implement three commonly used genetic models: additive, dominant and recessive models. This script can be easily inserted into more complicated programs to facilitate high-throughput association studies.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1537/version/1

A Handy Script to Implement Genetic Models in R
Provedor de dados: 17
Autores: Wei Zhang.
Genome-wide associations between genotypic and phenotypic data often assume certain genetic models. A handy script in R was written to implement three commonly used genetic models: additive, dominant and recessive models. This script can be easily inserted into more complicated programs to facilitate high-throughput association studies.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1537/version/2

A hydrometric analysis of the Moose Jaw River near Burdick (05JE006): Temporal trends and frequency analyses for mean, minimum, and maximum flows
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
A hydrometric analysis over the available historical record (1973-2010) was conducted for the Moose Jaw River station near Burdick in south-central Saskatchewan, Canada. Frequency analyses on mean monthly, average annual, monthly minimum/maximum, and annual minimum flows generally yielded poor fits, and problems with negative flow predictions for mid- to long-term return periods regardless of distribution type. The annual maximum streamflow time series is reasonably well-described by linear and log Pearson Type III distributions, although both distribution types underestimate extreme maximum flows. Mann-Kendall linear time series analysis on mean monthly and annual streamflows reveals no trend in annual water yields, nor in mean monthly flows between March...
Tipo: Poster
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6697/version/1

A Hyperstable Miniprotein: Additive Effects of D- and L-Ala Substitutions
Provedor de dados: 17
Autores: D. V. Williams; Bipasha Barua; Niels H. Andersen.
The effects of alanine substitutions in each helical segment of the structure, and Gly to D-Ala mutations at sites where glycines have positive phi angles in the Trp-cage miniprotein are reported. The effects of the stabilizing mutation were additive, yielding a 20-residue construct (Tm = 83^o^C). Gly to L-Ala substitutions were uniformly destabilizing ([DELTA][DELTA]G~F~ &amp;#x3e; 11 kJ/mol): the preference for a D-Ala can be as large as 16 kJ/mol. Glycine to D-Ala mutations are validated as a strategy for the design of hyperstable miniprotein scaffolds suitable for stereospecific pharmacophore display.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/2074/version/1

A Hypothetic Mechanism of Ordering  and Shaping Cells within Discrete Regions
Provedor de dados: 17
Autores: Yaroslav Strokovskyy.
We propose a hypothetic mechanism of ordering and shaping cells during _C. elegans_ embryogenesis. The mechanism is based on the assumption that during each round of division of cells, daughter cells acquire electric charges from its mother cells (charge conservation law is taken into account). Between the acts of division, the total electric field, generated by a system of charged cells, change relative positions of the charged cells within the region. In one&amp;#x2019;s turn, the positions of the charged cells determine the pattern of the electrostatic field. A mathematical model of such self-consistent mechanism is developed. The process of developing the sixteen-cell structure starting with one cell is simulated. The results correspond to the known...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4277/version/1

A Latent Variable Approach to Multivariate Quantitative Trait Loci
Provedor de dados: 17
Autores: Bob O&amp;#x27;Hara; P&amp;#xe4;ivi  Komulainen; Outi  Savolainen; Mikko J. Sillanp&amp;#xe4;&amp;#xe4;.
A novel approach based on latent variable modelling is presented for the analysis of multivariate quantitative and qualitative trait loci. The approach is general in the sense that it enables the joint analysis of many kinds of quantitative and qualitative traits (including count data and censored traits) in a single modelling framework. In the framework, the observations are modelled as functions of latent variables, which are then affected by quantitative trait loci.  Separating the analysis in this way means that measurement errors in the phenotypic observations can be included easily in the model, providing robust inferences. The performance of the method is illustrated using two real multivariate datasets, from barley and Scots pine.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4137/version/1

A Lateralized Brain Network for Visuo-Spatial Attention
Provedor de dados: 17
Autores: Michel Thiebaut de Schotten; Flavio Dell&amp;#x27;Acqua; Stephanie Forkel; Andrew Simmons; Francesco Vergani; Declan G.M. Murphy; Marco Catani.
Looking for a friend in the crowd, avoiding a sudden danger or contemplating a work of art are some examples of actions based on the efficiency of our visuo-spatial attention system. The specialization of the right brain hemisphere for visuo-spatial attention is a characteristic of most humans, but its anatomical basis remains largely unknown. Our study is the first to report in humans the existence of a bilateral parieto-frontal network whose hemispheric lateralization predicts the degree of specialization of the right hemisphere for visuo-spatial attention. Our results also suggest that this specialization is associated with an unbalanced speed of visuo-spatial processing between the two hemispheres. This lateralization may be predictive of visuo-spatial...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5549/version/1

A Linguistic Approach to Aligning Representations of Human Anatomy and Radiology
Provedor de dados: 17
Autores: Pinar Wennerberg; Manuel M&amp;#xf6;ller; Sonja Zillner.
To realize applications such as semantic medical image search different domain ontologies are necessary that provide complementary knowledge about human anatomy and radiology. Consequently, integration of these different but nevertheless related types of medical knowledge from disparate domain ontologies becomes necessary. Ontology alignment is one way to achieve this objective. Our approach for aligning medical ontologies has three aspects: (a) linguistic-based, (b) corpus-based, and (c) dialogue-based. We briefly report on the linguistic alignment (i.e. the first aspect) using an ontology on human anatomy and a terminology on radiology.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3521/version/2

A Linguistic Approach to Aligning Representations of Human Anatomy and Radiology
Provedor de dados: 17
Autores: Pinar Wennerberg; Manuel M&amp;#xf6;ller; Sonja Zillner.
To realize applications such as semantic medical image search different domain ontologies are necessary that provide complementary knowledge about human anatomy and radiology. Consequently, integration of these different but nevertheless related types of medical knowledge from disparate domain ontologies becomes necessary. Ontology alignment is one way to achieve this objective. Our approach for aligning medical ontologies has three aspects: (a) linguistic-based, (b) corpus-based, and (c) dialogue-based. We briefly report on the linguistic alignment (i.e. the first aspect) using an ontology on human anatomy and a terminology on radiology
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3521/version/1

A Linked Data Approach to Help Identify Therapeutic Targets for Cancer
Provedor de dados: 17
Autores: Helena Deus.
Cancer is still one of the leading causes of death in the developed world. To address this problem, the US National Institutes of Health (NIH) has launched The Cancer Genome Atlas (TCGA), a large scale systematic approach to characterize tumor samples from 20 cancer types and approximately 10,000 donor patients by using multiple high-throughput approaches. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Multidisciplinary projects such as TCGA and related projects across Europe aim at identifying cancer &amp;#x201c;driver&amp;#x201d; mutations to be used as therapeutic targets or diagnostic tests. Extracting and aggregating the knowledge necessary to identify such mutations remains a challenge primarily due to the need to reliably integrate the experimental datasets...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6169/version/1

A logistic regression model for microalbuminuria prediction in overweight male population
Provedor de dados: 17
Autores: BaoDe Chen; WeiYi Xu; Chen Yu; ZhenYun Ni; XueFen Li; DaWei Cui.
Background: Obesity promotes progression to microalbuminuria and increases the risk of chronic kidney disease. Current protocols of screening microalbuminuria are not recommended for the overweight or obese.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Design and Methods: A cross-sectional study was conducted. The relationship between metabolic risk factors and microalbuminuria was investigated. A regression model based on metabolic risk factors was developed and evaluated for predicting microalbuminuria in the overweight or obese.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: The prevalence of MA reached up to 17.6% in Chinese overweight men. Obesity, hypertension, hyperglycemia and hyperuricemia were the important risk factors for microalbuminuria in the overweight....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5372/version/1

A Long-Term Analysis of the Moose Jaw Climate Station (4015322/4015320): Temporal Trends and Frequency Analyses for Temperatures, Precipitation, and Wind Speed
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
A long-term analysis of temporal trends and frequency analyses for temperatures (1913-2010), precipitation (1909-2010), and wind speed (1954-1996) was conducted on the Moose Jaw climate station in south-central Saskatchewan, Canada. Average annual and springtime temperatures are increasing over time, as are daily mean temperatures during March. Mean daily maximum temperatures are increasing on an annual basis and during the spring period, whereas mean daily minimum temperatures are increasing during February, March, August, and September, as well as on an annual basis and during spring and summer. There are significant positive time trends for growing degree days base 8C (GDD~8~) and 10C (GDD~10~). Rainfall has been increasing during March as well as...
Tipo: Poster
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6703/version/1

A Mathematical Model of a Neuron with Synapses based on Physiology
Provedor de dados: 17
Autores: Xiaolin Zhang.
The neuron, when considered as a signal processing device, itsinputs are the frequency of pulses received at the synapses, and its output is the frequency of action potentials generated- in essence, a neuron is a pulse frequency signal processing device. In comparison, electrical devices use either digital or analog signals for communication or processing, and the mathematics behind these subjects is well understood. However, in regards to pulse frequency processing devices, there has not yet been a clear and persuasive mathematical model to describe the functions of neurons. It goes without saying that such a model is very important, not only for understanding neuron and neural system behavior, but also for undeveloped potential applications in industry....
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1703/version/1

A memoryless, stochastic mechanism of timing of phases of behavior by a neural network controller
Provedor de dados: 17
Autores: Saaniya Contractor; Nataliya Kozlova; Vladimir Brezina.
For a sensorimotor network to generate adaptive behavior in the environment, the phases of the behavior must be appropriately timed.  When the behavior is driven simply by the sensory stimuli from the environment, these can supply the timing.  But when the behavior is driven by an internal &amp;#x22;goal&amp;#x22; that ignores and perhaps even opposes the immediate sensory stimuli, the timing must be generated internally by the network.  We have modeled a realistic behavioral scenario that requires such internal timing.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;When the sea slug Aplysia feeds, it incrementally ingests long strips of seaweed, driven by ingestive stimuli emanating from the seaweed.  But if, having ingested a strip, the animal fails to break the...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2817/version/1

A Meta-analysis of Studies on Plant Growth Rate and Allocation to Roots and Shoots
Provedor de dados: 17
Autores: Daniel R. Taub.
I performed a meta-analysis of studies examining the relationships among nutrient availability, plant growth rate and allocation to roots vs. shoots. Species characteristic of high fertility habits grew faster than species characteristic of less fertile habitats. While species were highly plastic in root/shoot ratio, there was a strong correlation in root/shoot across fertility levels when plants were grown across fertility gradients. This suggests that the proportional mass allocation to roots is a consistent characteristic of individual species relative to other species. There was no consistent relationship between allocation to roots and either growth rate or the fertility of habitats that species typically are found in.
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/185/version/1

A Meteorite Ablation Debris: Testing and Analysis
Provedor de dados: 17
Autores: Saheeb Ahmed Kayani.
In this research report, X-ray diffraction (XRD) and X-ray fluorescence (XRF) spectrometry have been used to determine the mineralogical and elemental composition of a stone sample recovered from a location near village Lehri in district Jhelum, Pakistan. The test data is compared with previous findings (as reported in literature and included in references) to identify this sample stone as part of a prehistoric meteorite ablation debris.&amp;#xd;&amp;#xa;Further to this, carbon content of a specimen of the meteorite debris has been determined through combustion analysis. This carbon abundance has been compared with carbon wt% value of a certain type of meteorites to establish the origin and nature of the parent body of this particular meteorite debris.
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5450/version/1

A Micropropagation, Molecular and Physiochemical Analysis of Canola Brassica napus L. From Seeds
Provedor de dados: 17
Autores: Israr  Khan; Muhammad Shuaib; Sikandar Khan; Muhammad Amir Zia; Haji Akbar.
Canola is important for its oil, anticarcinogenic phytochemicals and low saturated fat content and has wide scope for further improvement through genetic transformations. Micropropagation is the practice of rapidly multiplying stock plant material to produce a large number of disease free progeny plants, using modern asceptic plant tissue culture methods and also to conserve germ plasm. A combination of auxin and cytikinin and a shock on growth regulator free medium is used for micropropagation. Molecular and physiochemical analysis done to know variation in seeds protein content and electric conductivity.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4781/version/2

A model explaining  some bryozoan colonies
Provedor de dados: 17
Autores: Dawid Mazurek.
Although the colonialism surely developed independently in Graptolithoidea and Bryozoa, both groups share  similar patterns of astogeny. One of the common features is the presence of morphological gradients. Many attempts at its explanation were made for more than a half of the century. This paper discusses a new model of the  late astogeny in some bryozoan colonies, showing a cyclic reappearance of secondary zones of astogenetic change and astogenetic repetition that cannot be explained by the single morphogen gradient theory.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1585/version/1

A modelling study of beta-amyloid induced change in hippocampal theta rhythm
Provedor de dados: 17
Autores: Xin Zou; Damien Coyle; KongFatt Wong-Lin; Liam Maguire.
Many dementia cases, such as Alzheimer&amp;#x2019;s disease (AD), are characterized by an increase in low frequency field potential oscillations. However, a definitive understanding of the effects of the beta-Amyloid peptide, which is a main marker of AD, on the low frequency theta rhythm (4-7Hz) is still unavailable. In this work, we investigate the neural mechanisms associated with beta-Amyloid toxicity using a conductance-based neuronal network model of the hippocampus CA1 region. We simulate the effects of beta-Amyloid on the A-type fast inactivating K+ channel by modulating the maximum conductance of the current in pyramidal cells, denoted by gA. Our simulation results demonstrate that as gA decreases (through A[beta]&amp;#xd;&amp;#xa;blockage), the...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6004/version/1

A Modular Semantic Annotation Framework: CellML Metadata Specifications 2.0
Provedor de dados: 17
Autores: Michael T. Cooling.
In the last decade or so, model encoding efforts such as CellML and SBML have greatly facilitated model availability. But, as the complexity of models increases, the utility of these models can vary. The addition of semantic information is crucial to transforming mathematical models from esoteric to informative resources. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We have developed a metadata specification framework to better enable the annotation of CellML models with metadata. The framework consists of a core specification describing, in general terms, how annotations should be attached using RDF/XML, and satellite specifications covering several domains of immediate interest, using elements from the Dublin Core, FOAF (Friend-Of-A-Friend), BIBO (Bibliographic...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6391/version/1

A multiple-instance scoring method to predict tissue-specific cis-regulatory motifs and regions
Provedor de dados: 17
Autores: Jin Gu.
Transcription is the central process of gene regulation. In higher eukaryotes, the transcription of a gene is usually regulated by multiple cis-regulatory regions (CRRs). In different tissues, different transcription factors bind to their cis-regulatory motifs in these CRRs to drive tissue-specific expression patterns of their target genes. By combining the genome-wide gene expression data with the genomic sequence data, we proposed multiple-instance scoring (MIS) method to predict the tissue-specific motifs and the corresponding CRRs. The method is mainly based on the assumption that only a subset of CRRs of the expressed gene should function in the studied tissue. By testing on the simulated datasets and the fly muscle dataset, MIS can identify true...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4038/version/1

A network-based signaling mechanism of cancer development and progression
Provedor de dados: 17
Autores: Edwin Wang.
We conducted a comprehensive analysis of a manually curated human signaling network containing 1634 nodes and 5089 signaling regulatory relations by integrating cancer-associated genetically and epigenetically altered genes. We find that cancer mutating genes are enriched in positive signaling regulatory loops, whereas the cancer-associated methylating genes are enriched in negative signaling regulatory loops. We further characterized an overall picture of the cancer-signaling architectural and functional organization. From the network, we extracted an oncogene-signaling map, which contains 326 nodes, 892 links and the interconnections of mutated and methylated genes. The map can be decomposed into 12 topological regions or oncogene-signaling blocks,...
Tipo: Presentation
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2238/version/1

A neural model for the visual tuning properties of action-selective neurons
Provedor de dados: 17
Autores: Martin A. Giese; Vittorio Caggiano; Falk Fleischer.
SUMMARY: The recognition of actions of conspecifics is crucial for survival and social interaction. Most current models on the recognition of transitive (goal-directed) actions rely on the hypothesized role of internal motor simulations for action recognition. However, these models do not specify how visual information can be processed by cortical mechanisms in order to be compared with such motor representations. This raises the question how such visual processing might be accomplished, and in how far motor processing is critical in order to account for the visual properties of action-selective neurons.&amp;#xd;&amp;#xa;We present a neural model for the visual processing of transient actions that is consistent with physiological data and that accomplishes...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5862/version/1

A new approach to generating research-quality data through citizen science: The USA National Phenology Monitoring System
Provedor de dados: 17
Autores: Ellen G. Denny; Abraham J. Miller-Rushing; Brian P. Haggerty; Lisa Benton; Theresa M. Crimmins; Mark Losleben; Andrew D. Richardson; Alyssa Rosemartin; Mark D. Schwartz; Kathryn A. Thomas; Jake F. Weltzin; Bruce E. Wilson.
Phenology is one of the most sensitive biological responses to climate change, and recent changes in phenology have the potential to shake up ecosystems. In some cases, it appears they already are. Thus, for ecological reasons it is critical that we improve our understanding of species&amp;#x2019; phenologies and how these phenologies are responding to recent, rapid climate change. Phenological events like flowering and bird migrations are easy to observe, culturally important, and, at a fundamental level, naturally inspire human curiosity&amp;#x2014; thus providing an excellent opportunity to engage citizen scientists. The USA National Phenology Network has recently initiated a national effort to encourage people at different levels of...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3695/version/1

A new approach to generating research-quality phenology data: The USA National Phenology Monitoring System
Provedor de dados: 17
Autores: Ellen G. Denny; Abraham J. Miller-Rushing; Brian P. Haggerty; Bruce E. Wilson; Jake F. Weltzin; the rest of the USA-NPN Protocol Development Team.
The USA National Phenology Network (www.usanpn.org) has recently initiated a national effort to encourage people at different levels of expertise&amp;#x2014;from backyard naturalists to professional scientists&amp;#x2014;to observe phenology and contribute to a national database that will be used to greatly improve our understanding of spatio-temporal variation in phenology and associated phenological responses to climate change. Many phenological observation protocols identify speci&amp;#xfb01;c single dates at which individual phenological events are observed, but the scienti&amp;#xfb01;c usefulness of long-term phenological observations can be improved with a more carefully structured protocol. At the USA-NPN we have developed a new approach that...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/3695/version/2

A new approach to the spatio-temporal pattern identification in neuronal multi-electrode registrations
Provedor de dados: 17
Autores: Federico Esposti; Jacopo Lamanna; Maria Gabriella Signorini.
A lot of methods were created in last decade for the spatio-temporal analysis of multi-electrode array (MEA) neuronal data sets. All these methods were implemented starting from a channel to channel analysis, with a great computational effort and  onerous spatial pattern recognition task. &amp;#xd;&amp;#xa;Our idea is to approach the MEA data collection from a different point of view, i.e. considering all channels simultaneously. We transform the 2D plus time MEA signal in a mono-dimensional plus time signal and elaborate it as a normal 1D signal, using the Space-Amplitude Transform method. &amp;#xd;&amp;#xa;This geometrical transformation is completely invertible and allows to employ very fast processing algorithms. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1306/version/1

A New Behavior of Nuclei during Mitosis of Lilium Hybrids
Provedor de dados: 17
Autores: Zheng Sixiang; Liu  Feihu; Zhang  Chaojun; Chen Zhilin; Ma Yuhua; Meng Pinghong; Zhao Yan.
Mitosis is nuclear division plus cytokinesis,and produces two identical daughter cells during prophase, prometaphase, metaphase, anaphase, and telophase. However, a new nucleus behavior in interspecific hybrid progenies of Lilium was observed in our experiment. Very unusual behaviors of nuclei surprisingly presented during the mitosis, such as sprouting or germination, tube-like elongation, penetrating cell membrane into a neighbor cell, the top of nuclei tube expanding, intruding and splitting of the tube-like nucleus, and micronucleus formation, and so on. Furthermore, the tetrad of meiosis was founded in mitosis of root.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Routine of the unusual nucleus behaviors observed in our experiment may be summarized as nucleus...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4631/version/1

A new dynamic property of human consciousness
Provedor de dados: 17
Autores: UnCheol  Lee; Seunghwan Kim; Gyu-Jeong Noh; Byung-Moon Choi.
As pointed out by William James, &amp;#x22;the consciousness is a dynamic process, not a thing&amp;#x22; , during which short term integration is succeeded by another differentiated neural state through the continual interplay between the environment, the body, and the brain itself. Thus, the dynamic structure underlying successive states of the brain is important for understanding human consciousness as a process. In order to investigate the dynamic property of human consciousness, we developed a new method to reconstruct a state space from electroencephalogram(EEG), in which a trajectory, reflecting states of consciousness, is constructed based on the global information integration of the brain. EEGs were obtained from 14 subjects received an intravenous...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1244/version/1

A new functional role for lateral inhibition in the striatum: Pavlovian conditioning
Provedor de dados: 17
Autores: Patrick Connor; Thomas Trappenberg.
The striatum has long been implicated in reinforcement learning and has been suggested by several neurophysiological studies as the substrate for encoding the reward value of stimuli. Reward prediction error (RPE) has been used in several basal ganglia models as the underlying learning signal, which leads to Pavlovian conditioning abilities that can be simulated by the Rescorla-Wagner model.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Lateral inhibition between striatal projection neurons was once thought to have a winner-take-all function, useful in selecting between possible actions. However, it has been noted that the necessary reciprocal connections for this interpretation are too few, and the relative strength of these synaptic connections is weak. Still,...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5986/version/1

A New General Allometric Biomass Model
Provedor de dados: 17
Autores: Wei Sheng Zeng; Shou Zheng Tang.
To implement monitoring and assessment of national forest biomass, it is becoming the trend to develop generalized single-tree biomass models suitable for large scale forest biomass estimation. Considering that the theoretical biomass allometric model developed by West et al. [1,2] was statistically different from the empirical one, the two parameters in the most commonly used biomass equation M=aDb were analyzed in this paper. Firstly, based on the knowledge of geometry, the theoretical value of parameter b was deduced, i.e., b=7/3(~2.33), and the comparison with many empirical studies conducted throughout the globe indicated that the theoretical parameter could describe soundly the average allometric relationship between aboveground biomass M and D...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6704/version/2

A New General Allometric Biomass Model
Provedor de dados: 17
Autores: Wei Sheng Zeng; Shou Zheng Tang.
To implement monitoring and assessment of national forest biomass, it is becoming the trend to develop generalized single-tree biomass models suitable for large scale forest biomass estimation. Considering that the theoretical biomass allometric model developed by West et al. [1,2] was statistically different from the empirical one, the two parameters in the most commonly used biomass equation M=aDb were analyzed in this paper. Firstly, based on the knowledge of geometry, the theoretical value of parameter b was deduced, i.e., b=7/3(&amp;#x2248;2.33), and the comparison with many empirical studies conducted throughout the globe indicated that the theoretical parameter could describe soundly the average allometric relationship between aboveground biomass M...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6704/version/1

A new mathematical model for radiation cell killing mechanism: Target cumulating model
Provedor de dados: 17
Autores: Zhao Liang; Wu Shixiu; Xie Congyin; Zhang Li.
There are numerous mathematical or statistical models have been given out for radiation cell killing mechanism. Unfortunately, none of the model could explain the mechanism perfectly. The more advanced model for it is still necessary to be researched. Following common assumption, a new theoretical model named &amp;#x22;target cumulating&amp;#x22; model is induced from the molecular and particle physics level. The result of theoretical calculation gives the equation of cell survival rate corresponding to delivered dose and other sensitivity parameters. In addition to fit the cell survival curve well, the new model showed advantages with comparing to previous models. Also, the new model predicts or explains some phenomenon that had been observed in...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/2880/version/1

A New Method for Characterization of Natural Zeolites and Organic Nanostructure using Atomic Force Microscopy
Provedor de dados: 17
Autores: Domenico P. R. O. F. Fuoco.
In order to study and develop an economic solution to environmental pollution in water, a wide variety of materials were investigated. Natural zeolites emerge from that research as the best in class of this category. Zeolites are natural materials relatively abundant and non biodegradable, economic and good to perform processes of environmental remediation. This paper contains a full description of a new method to characterize superficial properties of natural zeolites of exotic provenience (Caribbean Islets) with atomic force microscopy (AFM). AFM works with the optical microscope simplicity and the high resolution typical of a transmission electron microscope (TEM). Structural information of mesoporous material is obtained using scanning and transmission...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/6828/version/1

A new multicompartmental reaction-diffusion modeling method links transient membrane attachment of E. coli MinE to E-ring formation
Provedor de dados: 17
Autores: Satya N. V. Arjunan; Masaru Tomita.
Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3845/version/1

A new outlook towards kidney injuries
Provedor de dados: 17
Autores: Mahesh Satwekar; Abhijeet Satwekar.
Acute and chronic progression of injury to the kidney leads to the failure of the renal system and has become an increasingly important cause of morbidity and mortality. Present diagnosis detects the condition only after irreversible loss of 70 percent of kidney function. Current research is focused only on the clinical manifestations after the kidney injuries and not towards the exact cause of the condition. Here we propose a new outlook- that there is an involvement of a pathogen in the pathogenesis of kidney injuries. Basis for our proposal is given by the similarity of the pathogenesis events occurring between a classical example of hepatitis and kidney injuries. Furthermore, literature regarding the role of early kidney injury biomarkers in innate...
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Microbiology.
Ano: 2012
URL: http://precedings.nature.com/documents/7021/version/1

A new phylogenetic comparative method: detecting niches and transitions with continuous characters
Provedor de dados: 17
Autores: Carl Boettiger.
Traditional information criteria approaches can lead to misleading model choice in comparative phylogenetics. I present examples of these weaknesses using a classic data set on Anoles lizards.  I describe a more robust comparison by likelihood ratio. I then discuss a new class of models to capture the transition process between evolutionary regimes.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4615/version/1

A new potential  radiosensitizer: ammonium persulfate modified WCNTs
Provedor de dados: 17
Autores: Jian-She Yang; Bo-Zhang Yu; Wen-Xin Li.
Radiotherapy plays a very important role in cancer treatment. Radiosensitizers have been widely used to enhance the radiosensitivity of cancer cells at given radiations. Here we fabricate multi-walled carbon nanotubes with ammonium persulfate, and get very short samples with 30-50 nanometer length. Cell viability assay show that f-WCNTs induce cell death significantly. We hypothesize that free radicals originated from hydroxyl and carbonyl groups on the surface of f-WCNTs lead cell damage.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry.
Ano: 2007
URL: http://precedings.nature.com/documents/1421/version/1

A normalization technique for next generation sequencing experiments
Provedor de dados: 17
Autores: G&amp;#xfc;nter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS&amp;#x27; cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such random read count variations subsequently read counts from different experiments are comparable. Especially after normalization the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong deviations of...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4710/version/1

A normalization technique for next generation sequencing experiments
Provedor de dados: 17
Autores: G&amp;#xfc;nter Klambauer; Karin Schwarzbauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) are these days one of the key technologies in biology. NGS&amp;#x27; cost effectiveness and capability of finding the smallest variations in the genome makes them increasingly popular. For studies aiming at genome assembly, differences in read count statistics do not affect the outcome. However, these differences bias the outcome if the goal is to identify structural DNA characteristics like copy number variations (CNVs). Thus a normalization step must removed such random read count variations subsequently read counts from different experiments are comparable. Especially after normalization the commonly used assumption of Poisson read count distribution in windows on the chromosomes is more justified. Strong deviations of...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4710/version/2

A Note on Measures of Single Timeseries Activity in Resting-State fMRI Studies
Provedor de dados: 17
Autores: Xi-Nian Zuo.
In statistics, signal processing and mathematical finance, a time series  is a sequence of data points, measured typically at successive times spaced at uniform time intervals. Here, I only focus on the discrete time series. The motivation of writing this methodology note is to clarify the relationship between the measures to quantify activity of an observed timeseries. Particularly, focus one several measures used in recently emerged field of resting-state fMRI studies. Although all these measures have been extensively developed in EEG or other timeseries studies, many researchers focusing on various applications in or new comers to this new field need to know existed measures and the relationships among these measures.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4379/version/1

A Note On The Denisova Cave mtDNA Sequence
Provedor de dados: 17
Autores: Niccolo Caldararo.
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5360/version/1

A Note On The Denisova Cave mtDNA Sequence
Provedor de dados: 17
Autores: Niccolo Caldararo; Michael Guthrie.
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5360/version/3

A Note On The Denisova Cave mtDNA Sequence
Provedor de dados: 17
Autores: Niccolo Caldararo; Michael Guthrie.
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/5360/version/4

A Note On The Denisova Cave mtDNA Sequence
Provedor de dados: 17
Autores: Niccolo Caldararo; Michael Guthrie.
The recently published Altai fossil sequence from Denisova Cave was purported to be so different from anatomically modern humans, yet have the physiological landmarks of that species designation. When the published sequence was examined it was found that segments in the mtDNA hypervariable regions could be found to align with that of anatomically modern humans if one introduced an insertion at a position found in Neanderthals. Some other points of interest arise from a reconsideration of the sequences for other published samples and Neanderthals from the same perspective.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5360/version/2

A novel alveolar Krebs cycle-triggered CO2 sensing mechanism regulates regional pulmonary ventilation.
Provedor de dados: 17
Autores: Rainer Kiefmann; Paula Keller; Oliver Tritt; Kai Heckel; Sascha Tank; Martina Kiefmann; Leoni Schulte-Uentrop; Alwin Goetz.
Pulmonary perfusion disorders provoke atelectasis in order to minimize ventilation/perfusion mismatch. However, the underlying mechanisms remain unknown. Because intraalveolar CO2 concentration ([CO2]iA) declines as a consequence of poor pulmonary perfusion we postulated the existence a novel alveolar CO2-sensing mechanism which adapts the ventilation to perfusion. Real-time fluorescence imaging of rat lungs revealed that low [CO2]iA decreased cytosolic and increased mitochondrial Ca2+ in alveolar epithelial cells (AEC), leading to reduction of surfactant secretion and alveolar ventilation. Mitochondrial inhibition by ruthenium red or rotenone blocked the hypocapnia-induced responses. In cultured Type 2 AEC hypocapnia decreased cytosolic Ca2+ independently...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6185/version/1

A novel apparatus/protocol designed for optogenetic manipulation and recording of individual neurons during a motivation and working memory task in the rodent
Provedor de dados: 17
Autores: Samuel Dolzani; Donald C. Cooper.
Innovative molecular tools allow neuroscientists to study neural circuitry associated with specific behaviors. Consequently, behavioral methods must be developed to interface with these new molecular tools in order for neuroscientists to identify the causal elements underlying behavior and decision-making processes. Here we present an apparatus and protocol for a novel Go/No-Go behavioral paradigm to study the brain attention and motivation/reward circuitry in awake, head-restrained rodents. This experimental setup allows: (1) Painless and stable restraint of the head and body; (2) Rapid acquisition to simple or complex operant tasks; (3) Repeated electrophysiological single and multiple unit recordings during ongoing behavior; (4) Pharmacological and...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7152/version/1

A novel class of endogenous shRNAs in human cells
Provedor de dados: 17
Autores: Tongjun Gu; James Q. Yin; Yanwei Xu; ZhengHua Dai; Zhengge Qiu; Shenzhong Feng; Xiang Yi; Ling Jiang; Hongjie Zhang.
Until now it is still not clear how many types and amounts of small RNAs (sRNAs) exist in humans. Here we report the identification of 1258 distinct sRNAs derived from intronic regions of protein-coding genes in human with a new approach. These endogenous short hairpin RNAs (shRNAs) appear to be similar to exogenous shRNAs in structure, have a broad distribution in the stem length, and function as microRNAs (miRNAs), small interfering RNAs (siRNA) and/or piwi-interacting RNAs (piRNAs). Except for a few shRNAs, the majority of shRNAs are not phylogenetically conserved. They are differentially expressed in different cells and at diverse developmental stages. Overall, their expression levels are lower than miRNAs&amp;#x27;, but can be detected by quantitative...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/1531/version/1

A novel _Drosophila_ post-genomic CNS drug discovery model detects tetraethylammonium chloride with therapeutic potential
Provedor de dados: 17
Autores: Priyanka Singh; Farhan Mohammad*; Abhay Sharma.
A _Drosophila_ behavioral and transcriptomic model of locomotor plasticity induced by chronic pentylenetetrazole (PTZ) has recently been developed. In this model, two of the five antiepileptic drugs (AEDs) tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic PTZ induced locomotor alteration. Transcriptomic effect of the AEDs and PTZ in fly head has been described. Here, we analyze microarray expression profile of heads of flies treated with the convulsants tetraethylammonium chloride (TEA) and pilocarpine hydrochloride (PILO). Strikingly, microarray clustering placed TEA, not PILO, with LEV and NaVP in one group that was distinct from the other one...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3418/version/1

A novel Drosophila transcriptomic and behavioral model detects potassium chloride with therapeutic potential
Provedor de dados: 17
Autores: Farhan Mohammad; Priyanka Singh; Abhay Sharma.
In a newly described _Drosophila_ model, two of the five antiepileptic drugs (AEDs) tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic pentylenetetrazole (PTZ) induced locomotor alteration. To further characterize the model, we analyze here the microarray expression profile of heads of flies treated with depolarizing compound potassium chloride (KCl). Surprisingly, microarray clustering showed unexpected similarity among KCl, LEV and NaVP. Further, like the two effective AEDs in the fly model, KCl regulated genes overrepresented ribosomal pathway. Interestingly, KCl also ameliorated development of locomotor deficit in the chronic PTZ model. Both...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3429/version/1

A novel mathematical tool for generating highly conserved protein domain via different organismal genomic landscapes
Provedor de dados: 17
Autores: Arunava Goswami; Pabitra Pal Choudhury; Rajneesh Singh; Sk. Sarif Hassan.
Darwinian evolution hypothesizes that a short stretch of DNA was first constructed and then it expanded to give rise to a long strand. This long strand then produced a mix of exons, introns and repetitive DNA sequence. The order of production of above three kinds of DNA sequence is unknown. Reshuffling of stretches of DNA like above within organisms has given rise to different chromosomes. Till date it is not known how this process is governed. In this paper we show that starting with a sixteen base-pair human olfactory DNA sequence one can form a highly conserved protein domain. Once this domain is formed repetitive DNA sequences of a particular kind starts generating which signifies that this particular conserved protein domain will be unique in nature....
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4850/version/1

A Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for  Composition Improvements-  (v.4)
Provedor de dados: 17
Autores: Valentin  Prisecaru; I. C. Baianu.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions.  Conventional &amp;#x201c;wet chemistry&amp;#x201d; analytical methods are time-consuming and costly.  As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry.  Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6231/version/4

A novel predicted calcium-regulated kinase family  implicated in neurological disorders
Provedor de dados: 17
Autores: Ma&amp;#x142;gorzata Dudkiewicz; Anna Lenart; Krzysztof Paw&amp;#x142;owski.
Protein kinases are essential effectors of cellular signaling. Surprisingly, using bioinformatics tools, we predicted protein kinase structure and function for proteins of unknown function (FAM69 family) coded by five related human genes and their Metazoan homologues. Analysis of three-dimensional structure models and conservation of the classic catalytic motifs of protein kinases in four of human FAM69 proteins suggests they might have retained catalytic phosphotransferase activity. The FAM69 genes, FAM69A, FAM69B, FAM69C, C3ORF58 and CXORF36, are by large uncharacterized molecularly, yet linked to several neurological disorders in genetics studies. An EF-hand Ca2+-binding domain in FAM69A and FAM69B proteins, inserted within the structure of the kinase...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7015/version/1

A novel regulator of the p53-mediated mitochondrial apoptotic pathway
Provedor de dados: 17
Autores: Bo Young Ahn; Diane Trinh; Laura Zajchowski; Sung-Woo Kim.
The p53 tumor suppressor protein induces apoptosis in response to genotoxic and environmental stress. Recent studies have revealed the existence of a transcription-independent mitochondrial p53 apoptosis pathway, however the mechanism regulating p53 translocation to mitochondria and subsequent initiation of apoptosis was not known. Here, we show that Tid1, also known as mtHsp40 or Dnaja3, interacts with p53 and directs its translocation to mitochondria in cells exposed to hypoxia. Overexpression of Tid1 in tumor cells promoted mitochondrial localization of both wildtype and mutant forms of p53 and was able to restore the pro-apoptotic activity of mutant p53 proteins that were otherwise unable to induce apoptosis. Tid1&amp;#x27;s mitochondrial signal...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1892/version/1

A novel strategy for the targeted analysis of protein and peptide metabolites
Provedor de dados: 17
Autores: Nicholas A. Williamson; Charles Reilly; Chor-Teck Tan; Sri-Harsha Ramarathinam; Alun Jones; Christie L. Hunter; Francis R. Rooney; Anthony W. Purcell.
The detection and quantitation of exogenously administered biological macromolecules (e.g. vaccines, peptide and protein therapeutics) and their metabolites is frequently complicated by the presence of a complex endogenous mixture of closely related compounds. We describe a method that incorporates stable isotope labeling of the compound of interest allowing the selective screening of the intact molecule and all metabolites using a modified precursor ion scan. This method involves monitoring the low molecular weight fragment ions produced during MS/MS that distinguish isotopically labelled material from related endogenous compounds. All isotopically labelled substances can be selected using this scanning technique for further analysis whilst other...
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3812/version/1

A novel superior factor widely controlling the rice grain quality
Provedor de dados: 17
Autores: Kao-Chih She; Hiroaki Kusano; Kazuyoshi Koizumi; Hiromoto Yamakawa; Makoto Hakata; Tomohiro Imamura; Masato Fukuda; Natsuka Naito; Yumi Tsurumaki; Ken&amp;#x27;ichiro Matsumoto; Mari Kudoh; Eiko Itoh; Shoshi Kikuchi; Naoki Kishimoto; Junshi Yazaki; Tsuyu Ando; Masahiro Yano; Takashi Aoyama; Tadamasa Sasaki; Hikaru Satoh; Hiroaki Shimada.
Synthesis of storage starch and protein accumulation is the main action of endosperm organogenesis in term of the economic importance of rice. This event is strongly disturbed by abiotic stresses such as high temperature; thus, the upcoming global warming will cause a crisis with a great impact on food production^1,2^. The enzymes for the protein storage and starch synthesis pathway should work in concert to carry out the organogenesis of rice endosperm^3-5^, but the regulatory mechanism is largely unknown. Here we show that a novel regulatory factor, named OsCEO1, acts as the conductor of endosperm organogenesis during the rice grain filling stage. The physiological properties of _floury-endosperm-2_ (_flo2_) mutants showed many similarities to symptoms...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3283/version/1

A novel therapeutic strategy for pancreatic neoplasia using a novel RNAi platform targeting PDX-1
Provedor de dados: 17
Autores: Shi-He Liu; Donald Rao; John Nemunaitis; Neil Senzer; David Dawson; Marie-Claude Gingras; Zhaohui Wang; Richard Gibbs; Michael Norman; Nancy Templeton; Francesco DeMayo; Kelly Stehling; William Fisher; Charles Brunicardi.
Bi-functional shRNA (bi-shRNA), a novel RNA interference (RNAi) effector platform targeting PDX-1 utilizing a systemic DOTAP-Cholesterol delivery vehicle, was studied in three mouse models of progressive pancreatic neoplasia. Species-specific bi-functional PDX-1 shRNA (bi-shRNAPDX-1) lipoplexes inhibited insulin expression and secretion while also substantially inhibiting proliferation of mouse and human cell lines via disruption of cell cycle proteins in vitro. Three cycles of either bi-shRNA&amp;#x3c;sup&amp;#x3e;mousePDX-1&amp;#x3c;/sup&amp;#x3e; or shRNA&amp;#x3c;sup&amp;#x3e;mousePDX-1&amp;#x3c;/sup&amp;#x3e; lipoplexes administered intravenously prevented death from hyperinsulinemia and hypoglycemia in a lethal insulinoma mouse model. Three cycles of...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6047/version/1

A Novel Thermodynamic Method For Quantifying Ligand-Receptor Interactions: The IC (1/3) Standard Vs IC (50)
Provedor de dados: 17
Autores: Dr Sudarsan Prasad.
A method based on the Concentration Derivative Product (CDP) is proposed to analyze the thermodynamics of Drug-Receptor interactions. CDP is defined as the product of the fractional inhibition f and it&amp;#x2019;s concentration derivative. Assuming Michaelis-Menten kinetics, it is shown that for a number of drug-receptor systems (HIV protease, ACE, HMG-CoA, Opioid receptor inhibitors, etc.) f max  = 0.333, irrespective of the nature of bonding interactions and Ki.   The CDP max = [4 / ( 27 Ki ) ], and gives a measure of the drug potency directly. CDP also gives thermodynamic information about the ratio of the gradients of the inhibitor chemical potential in the free and bound states.
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6006/version/1

A Paradigm for Biology&amp;#x27;s Next Revolution
Provedor de dados: 17
Autores: Fredric D. R. Young.
A recent essay on biology&amp;#x27;s next revolution described attributes of a future theory of biology that would replace post hoc modeling with an interplay between quantitative prediction and experimental test, more characteristic of the physical sciences1. The article suggested that flux from the environment whether it be energy, chemicals metabolites, or genes is a defining characteristic of life. The essay also suggests that an interdisciplinary approach to collective phenomena centered on statistical mechanics and dynamical systems theory will be required to make use of this perspective. Over the last 30 years we have developed an approach to drug discovery and translational research that is based on a paradigm for complex systems modeling that fits...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/1770/version/1

A periodic pattern of SNPs in the human genome
Provedor de dados: 17
Autores: Bo Eskerod Madsen; Palle Villesen; Carsten Wiuf.
By surveying all validated SNPs in the human genome we have found that SNPs positioned 1, 2, 4, 6 or 8 bp apart are more frequent than SNPs 3, 5, 7 or 9 bp apart. This holds even when we correct for nucleotide frequencies and site dependencies in nucleotide usage in the genome. The observed pattern is not restricted to any of the genomic regions that might give sequencing or alignment errors; i.e. transposable elements (SINE, LINE and LTR), tandem repeats and large duplicated regions. However we can define periodic DNA, which virtually capture the entire pattern. Periodic DNA is defined as small DNA sequences (16.9 bp average length) with a high degree of periodicity in nucleotide usage. Periodic DNA is widely distributed in the genome, underrepresented in...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics.
Ano: 2007
URL: http://precedings.nature.com/documents/435/version/1

A Physiological Role for Amyloid Beta Protein: Enhancement of Learning and Memory
Provedor de dados: 17
Autores: John Morley; Susan Farr; William Banks; Steven N. Johnson; Kelvin A. Yamada; Lin Xu.
Amyloid beta protein (A[beta]) is well recognized as having a significant role in the pathogenesis of Alzheimer&amp;#x27;s disease (AD). The reason for the presence of A[beta] and its physiological role in non-disease states is not clear. In these studies, low doses of A[beta] enhanced memory retention in two memory tasks and enhanced acetylcholine production in the hippocampus _in vivo_. We then tested whether endogenous A[beta] has a role in learning and memory in young, cognitively intact mice by blocking endogenous A[beta] in healthy 2-month-old CD-1 mice. Blocking A[beta] with antibody to A[beta] or DFFVG (which blocks A[beta] binding) or decreasing A[beta] expression with an antisense directed at the A[beta] precursor APP all resulted in impaired...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2119/version/1

A PI3K-mediated negative feedback regulates Drosophila motor neuron excitability
Provedor de dados: 17
Autores: Eric Howlett; Curtis C. J. Lin; William Lavery; Michael Stern.
Negative feedback can act as a homeostatic mechanism to maintain neuronal activity at a particular specified value. At the Drosophila neuromuscular junction, a mutation in the type II metabotropic glutamate receptor gene (mGluRA) increased motor neuron excitability by disrupting an autocrine, glutamate-mediated negative feedback. We show that mGluRA mutations increase neuronal excitability by preventing PI3 kinase (PI3K) activation and consequently hyperactivating the transcription factor Foxo. Furthermore, glutamate application increases levels of phospho-Akt, a product of PI3K signaling, within motor nerve terminals in an mGluRA-dependent manner. In humans, PI3K and type II mGluRs are implicated in epilepsy, neurofibromatosis, autism, schizophrenia and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1767/version/1

A population-based study of glutathione-S-transferase M1, T1 and P1 genotypes
Provedor de dados: 17
Autores: Monika Sivo&amp;#x148;ov&amp;#xe1;; Iveta Waczul&amp;#xed;kov&amp;#xe1;; Du&amp;#x161;an Dobrota; Tatiana Mat&amp;#xe1;kov&amp;#xe1;; Jozef Hatok; Peter Ra&amp;#x10d;ay; J&amp;#xe1;n Kliment.
A retrospective study on healthy, unrelated subjects was conducted in order to estimate population glutathione-S-transferases (GST) genotype frequencies in Slovak population of men and compare our results with already published data (GSEC project)^1^. A further aim of the study was to evaluate frequencies of the _GST_ polymorphisms also in patients with prostate cancer in order to compare the evaluated proportions with those found in the control subjects. Analysis for the _GST_ gene polymorphisms was performed by PCR and PCR-RFLP. We found that the proportions are not significantly different from those estimated in a European multicentre study or from the results published by another group in Slovakia. We found significantly increased age-standardized...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2559/version/1

A Possible Solution to the Etiological Paradox that Ties Anti-Social Personality Disorder to Major Depression
Provedor de dados: 17
Autores: Alvaro Machado Dias.
Abstract. Antisocial personality disorder (ASPD) is a pervasive condition among youngsters around the globe, which has particular pungency in countries where the socioeconomic context favors delinquency. Several behavioral genetics studies have linked the disorder to the presence of copies of a polymorphic variation of the MAO-A gene that leads to enzymatic hypofunction.  An emerging tendency in this literature is to also associate it to the presence of short variations of the 5-HTTLPR polymorphism, which is well-known for its possible role in the vulnerability to major depression of individuals that were exposed to early-life stress. The current paper argues that the association of these findings introduce a theoretical problem that is not trivial...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6308/version/1

A potential cyanobacterial ancestor of Viridiplantae chloroplasts
Provedor de dados: 17
Autores: Wriddhiman Ghosh; Prabir Haldar; Sabyasachi Bhattacharya; Jaideb Chatterjee; Prosenjit Pyne; Masrure Alam.
The theory envisaging the origin of plastids from endosymbiotic cyanobacteria is well-established but it is difficult to explain the evolution (spread) of plastids in phylogenetically diverse plant groups. It is widely believed that primordial endosymbiosis occurred in the last common ancestor of all algae^1^, which then diverged into the three primary photosynthetic eukaryotic lineages, viz. the Rhodophyta (red algae), Glaucocystophyta (cyanelle-containing algae) and Viridiplantae (green algae plus all land plants)^2^. Members of these three groups invariably have double membrane-bound plastids^3^, a property that endorses the primary endosymbiotic origin of the organelles. On the other hand, the three or four membrane-bound plastids of the evolutionary...
Tipo: Manuscript
Palavras-chave: Microbiology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6607/version/1

A potential diagnostic biomarker: Proteasome LMP2/b1i-differential expression in human uterus neoplasm
Provedor de dados: 17
Autores: Takuma Hayashi; Akiko Horiuchi; Hiroyuki Aburatani; Nobuo Yaegashi; Susumu Tonegawa; Ikuo Konishi.
Uterine leiomyosarcoma (ULMS) develops more often in the muscle tissue layer of the uterine body than in the uterine cervix. The development of gynecologic tumors is often correlated with female hormone secretion; however, the development of uterine ULMS is not substantially correlated with hormonal conditions, and the risk factors are not yet known. Importantly, a diagnostic-biomarker which distinguishes malignant ULMS from benign tumor leiomyoma (LMA) is yet to be established. Accordingly, it is necessary to analyze risk factors associated with uterine ULMS, to establish a treatment method. Proteasome low-molecular mass polypeptide 2(LMP2)/b1i-deficient mice spontaneously develop uterine LMS, with a disease prevalence of ~40% by 14 months of age. We...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2012
URL: http://precedings.nature.com/documents/7082/version/1

A potential role for Dkk-1 in the pathogenesis of osteosarcoma predicts novel diagnostic and treatment strategies.
Provedor de dados: 17
Autores: Carl Gregory; Narae Lee; Angela Smolarz; Scott Olson; Odile David; Jacob Reiser; Robert Kutner; Najat Daw; Darwin Prockop; Edwin Horwitz.
Canonical Wnt signaling is an osteo-inductive signal that promotes bone repair through acceleration of osteogenic differentiation by progenitors. Dkk-1 is a secreted inhibitor of canonical Wnt signaling and thus inhibits osteogenesis. To examine a potential osteo-inhibitory role of Dkk-1 in osteosarcoma (OS), we measured serum Dkk-1 in pediatric patients with OS (median age, 13.4 years) and found it to be significantly elevated. We also found that Dkk-1 was maximally expressed by the OS cells at the tumor periphery and _in vitro_ Dkk-1 and RANKL are co-expressed by rapidly proliferating OS cells. Both Dkk-1 and conditioned media from OS cells reduces osteogenesis by human mesenchymal cells and by immuno-depletion of Dkk-1, or by adding a GSK3[beta]...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer.
Ano: 2007
URL: http://precedings.nature.com/documents/130/version/1

A prelude report on molecular docking of HER2 protein towards comprehending anti-cancer properties of saponins from Solanum tuberosum
Provedor de dados: 17
Autores: Puneet  K. Singh; Pratyoosh Shukla.
Saponins are extensively known for many biological activities e.g. antimicrobial, anti-palatability, anti-cancer and hemolytic. As cancer cells have a more cholesterol-like compound in their membrane structure the saponins bind cholesterol due to their natural affinity to bind cancer cell membrane. This prevents them from entering the body through the intestinal tract, where they have the ability to attach themselves to vital organs and grow. This study reports the effective use of lower dose saponins like immunotoxin so that they can inhibit the proliferation of cancerous pancreatic cells. The investigation of pancreatic cancer metabolic pathway it was found that proteins 3H3B produced by genes HER-2 are involved in the enhancement of this type of cancer....
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7147/version/1

A probabilistic model of plasmid replication regulation by a combination of handcuffing, iteron number and dimerization of RepA protein.
Provedor de dados: 17
Autores: Milind Watve; Gauri Tendulkar; Ketaki Ghate.
Plasmids are small circular DNA molecules in bacteria which replicate sharing the replication machinery with the bacterial chromosome. Since plasmids are much smaller than the chromosome, unless their replication is tightly regulated, their copy numbers can escalate quickly. A number of mechanisms of plasmid replication regulation are known in P1 plasmid of E. coli. Mechanisms such as autorepression of the replication initiator protein (RepA) and its dimerization are unable to explain copy number regulation by themselves. The number of RepA binding sites (iterons) is inversely related to copy numbers. Handcuffing of plasmids by RepA dimer is believed to be the main mechanism of arresting replication. We show here with a probabilistic model that for the...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5421/version/1

A Proposal of Genomic Analytical Workflow in a Bacterial Pathogen Outbreak Investigation
Provedor de dados: 17
Autores: Hoi Shan Kwan; Chun Hang Au; Chi Keung Cheng; Man Kit Cheung; Qianli Huang; Lei Li; Wenyan Nong; Man Chun Wong.
The German Escherichia coli O104:H4 outbreak causing Hemolytic Uremic Syndrome (HUS) started in early May 2011. Conventional typing methods including serotyping, multi-locus sequence typing (MLST) and pulse-field gel electrophoresis (PFGE) seemed to yield only limited information about the causative agent. The advantages of the Genome sequencing approach are apparent compared to conventional methods. Genome sequencing and analyses with an appropriate workflow would be the new paradigm in bacterial outbreak investigation.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/6663/version/1

A Quality Evaluation Framework for Bio-Ontologies
Provedor de dados: 17
Autores: Jesualdo Tomas Fernandez-Breis; Mikel  Ega&amp;#xf1;a Aranguren; Robert Stevens.
Over the past few years the number of bio-ontologies  has rapidly increased. The evaluation of ontologies has long been a problematic issue. The growing number of ontologies makes the need for a strategy for evaluating quality more urgent. We propose a framework for evaluating the quality of bio-ontologies. This framework is inspired by a well-known software quality standard, which has been adapted to the needs of ontology evaluation. An example of how to use the framework, comparing two versions of the Open Biomedical Ontologies&amp;#x27; Cell Type Ontology, is included as an illustration.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3478/version/1

A Quality Evaluation Framework for Bio-Ontologies
Provedor de dados: 17
Autores: Jesualdo Tomas Fernandez-Breis; Mikel Ega&amp;#xf1;a Aranguren; Robert Stevens.
Over the past few years the number of bio-ontologies  has rapidly increased. The evaluation of ontologies has long been a problematic issue. The growing number of ontologies makes the need for a strategy for evaluating quality more urgent. We propose a framework for evaluating the quality of bio-ontologies. This framework is inspired by a well-known software quality standard, which has been adapted to the needs of ontology evaluation. An example of how to use the framework, comparing two versions of the Open Biomedical Ontologies&amp;#x27; Cell Type Ontology, is included as an illustration.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3479/version/1

A Quantitative Approach to Investigating the Hypothesis of Prokaryotic Intron Loss
Provedor de dados: 17
Autores: Robert M. Sinclair.
Using a novel method, we show that ordered triplets of motifs usually associated with spliceosomal intron recognition are underrepresented in the protein coding sequence of complete Thermotogae, archaeal and bacterial genomes. The underrepresentation observed does not extend to the noncoding strand, suggesting that the cause of the asymmetry is related to mRNA rather than DNA. Our data do not suggest that the underrepresentation is due to gene transfer from eukaryotes. We speculate that one possible explanation for these observations is that the protein coding sequence of Thermotogae, Archaea and Bacteria was at some time in the past subjected to selection against certain motifs appearing in an order which might initiate splicing in environments harboring...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5770/version/1

A quantitative model for efficient construction of lentiviral vectors with a unique clone site
Provedor de dados: 17
Autores: Gang Zhang; Anurag  Tandon.
Lentiviral vectors (LVs) were a powerful tool for transgene expression in vivo and in vitro. However, the construction of LVs is of low efficiency, due to the large sizes and lack of proper clone sites. Therefore, it is critical to develop efficient strategies for cloning LVs. Here, we reported a combinatorial strategy to efficiently construct LVs using EGFP, hPlk2 wild type (WT) and mutant genes as inserts. Firstly, site-directed mutagenesis (SDM) was performed to create BamH I site for the inserts; secondly, pWPI LV was dephosphorylated after BamH I digestion; finally, the amounts and ratios of the insert and vector DNA were optimized to increase monomeric ligation. Our results showed that the total percentage of positive clones was approximately...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2012
URL: http://precedings.nature.com/documents/6876/version/1

A Quantitative Model for Human Olfactory Receptors
Provedor de dados: 17
Autores: Sk. Sarif  Hassan; Pabitra  Pal Choudhury; Aritra Bose.
A wide variety of chemicals having distinct odors are smelled by humans. Odor perception initiates in the nose, where it is detected by a large family of olfactory receptors (ORs). Based on divergence of evolutionary model, a sequence of human ORs database has been proposed by D. Lancet et al (2000, 2006).  It is quite impossible to infer whether a given sequence of nucleotides is a human OR or not, without any biological experimental validation. In our perspective, a proper quantitative understanding of these ORs is required to justify or nullify whether a given sequence is a human OR or not. In this paper, all human OR sequences have been quantified, and a set of clusters have been made using the quantitative results based on two different metrics. Using...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6967/version/2

A Quantitative Model for Human Olfactory Receptors
Provedor de dados: 17
Autores: Sk. Sarif  Hassan; Pabitra  Pal Choudhury; Aritra Bose.
A wide variety of chemicals having distinct odors are smelled by humans. Odor perception initiates in the nose, where it is detected by a large family of olfactory receptors (ORs). Based on divergence of evolutionary model a sequence of human ORs database has been proposed by D. Lancet et al (2000, 2006).  It is quite impossible to infer whether a given sequence of nucleotides is a human OR or not, without any biological experimental validation. In our perspective, a proper quantitative understanding of these ORs is required to justify or nullify whether a given sequence is a human OR or not. In this paper, all human OR sequences have been quantified, and a set of clusters have been made using the quantitative results based on two different metrics. Using...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6967/version/1

A quick trip through openness, freedom and transparency
Provedor de dados: 17
Autores: Konrad U. Foerstner.
This talk aims to give scientists an introduction to the concepts of openness, freedom and transparency and their applications (not only) for science. It covers the topics of open source, open formats, Creative Commons, open access, and open science/knowledge. A video of the talk is available on the author&amp;#x27;s website.&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1225/version/1

A randomised controlled trial of an intervention to promote early presentation of breast cancer in older women: effect on breast cancer awareness
Provedor de dados: 17
Autores: Louise Linsell; Lindsay  J. L. Forbes; Marcia  Kapari; Caroline  Burgess; Lynne  Omar; Lorraine  Tucker; Amanda J. Ramirez.
There is virtually no evidence for the effectiveness of interventions to promote early presentation in breast cancer. We tested the efficacy of an intervention to equip older women with the knowledge, skills, confidence and motivation to detect symptoms and seek help promptly, with the aim of promoting early presentation with breast cancer symptoms. We randomised 867 women aged 67 to 70 attending for their final routine appointment on the UK NHS Breast Screening Programme to receive: a scripted ten-minute interaction with a radiographer plus a booklet; a booklet alone; or usual care. The primary outcome was whether or not a woman was breast cancer aware based on knowledge of breast cancer symptoms and age-related risk; and reported breast checking. At one...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3816/version/1

A Rate Distortion approach to protein symmetry
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry breaking argument is applied to the problem of protein folding, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein molten globule. In the &amp;#x27;energy&amp;#x27; picture, the average distortion between codon message and protein structure, under constraints driven by evolutionary selection, serves as a temperature analog, so that low values limit the possible distribution of protein forms, producing the canonical folding funnel. A dual &amp;#x27;developmental&amp;#x27; perspective sees the rate distortion function itself as the temperature analog, and permits incorporation of chaperons or toxic exposures as catalysts, driving the system to different possible outcomes or...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4280/version/2

A Rate Distortion approach to protein symmetry
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry breaking argument is applied to the problem of protein form, via a Rate Distortion analysis of the relation between genome coding and the final condensation of the protein &amp;#x27;molten globule&amp;#x27;. The Rate Distortion Function, under coding constraints, serves as a temperature analog, so that low values act to drive proteins to simple symmetries. The Rate Distortion Function itself is significantly constrained by the availability of metabolic free energy. This work extends Tlusty&amp;#x27;s (2007) elegant exploration of the evolution of the genetic code, suggesting that rate distortion considerations may play a critical role across a broad spectrum of molecular expressions of evolutionary process.
Tipo: Manuscript
Palavras-chave: Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4280/version/1

A Reaction Route Approach to Flux Balance Analysis
Provedor de dados: 17
Autores: Ilie  Fishtik.
Background: Flux balance and network-based pathway analyses are theoretical tools aimed to find optimal steady state flux distributions in a metabolic network subject to additional constraints on the rates of the reaction steps. Although these methods are mathematically accurate, there are several physicochemical and computational aspects that are questionable and misleading. In particular, it is well known that the flux balance analysis may result in multiple flux distributions for the same objective function.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: The flux balance and network-based pathway analyses are reformulated in terms of reaction routes (RRs), a theoretical framework that has been developed by Horiuti over 50 years ago. Not only does the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2788/version/1

A reassessment of the Carnot cycle and the concept of entropy
Provedor de dados: 17
Autores: Sosale Chandrasekhar.
It is argued that the Carnot cycle is a highly inaccurate representation of a steam engine, and that the net work obtained in its operation would be zero. This conclusion is also supported by an elementary mathematical approach, which re-examines the work done in the four individual steps of the cycle. An important consequence of this is that the concept of entropy, originally proposed on the basis of the Carnot theorem, may not be a fundamentally valid thermodynamic quantity. Also, the experimental approach generally adopted in the determination of entropy is questionable, and the importance of increasing randomness in natural processes not universally valid. In fact, a more viable basis, at least vis-&amp;#xe0;-vis chemical reactions, appears to be the...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1852/version/1

A Report of the Mosquito Host Range of Pythium guiyangense Su
Provedor de dados: 17
Autores: Xiaoqing Su.
Mosquito causes problems in both disease transmission and disturbance to people&amp;#x27;s daily life. The controlling methods used now are mainly application of chemical pesticides which result in serious harm to environment. Biological control of the pest is one of the ideal ways. But, lack of suitable agent makes it difficult to extend this technique in wider scope. _Pythium guiyangense_ Su is a newly found fungal pathogen of mosquitoes and is promising for practical use. Here we summarize a list of mosquitoes that can be infected by the fungus so far, which shows the potential significance of the application of the fungus in the future.
Tipo: Manuscript
Palavras-chave: Microbiology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1875/version/1

A review of journal policies for sharing research data
Provedor de dados: 17
Autores: Heather A. Piwowar; Wendy W. Chapman.
*Background:*  Sharing data is a tenet of science, yet commonplace in only a few subdisciplines.  Recognizing that a data sharing culture is unlikely to be achieved without policy guidance, some funders and journals have begun to request and require that investigators share their primary datasets with other researchers.  The purpose of this study is to understand the current state of data sharing policies within journals, the features of journals which are associated with the strength of their data sharing policies, and whether the strength of data sharing policies impact the observed prevalence of data sharing. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Methods:*  We investigated these relationships with respect to gene expression microarray data in the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1700/version/1

A Roadmap of Cancer Systems Biology
Provedor de dados: 17
Autores: Edwin  Wang.
What is cancer systems biology? Why should we conduct systems biology research in cancer? What is the relationships between systems biology and personalized medicine? How do we conduct cancer systems biology research? This paper illustrates strategies, procedures and computational techniques for the study of cancer systems biology by focusing on network reconstruction, network analysis and modeling. Finally, certain challenges and hurdles in cancer systems biology will also be discussed.
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4322/version/1

A Roadmap of Cancer Systems Biology
Provedor de dados: 17
Autores: Edwin  Wang.
What is cancer systems biology? Why should we conduct systems biology research in cancer? What is the relationships between systems biology and personalized medicine? How do we conduct cancer systems biology research? This paper illustrates strategies, procedures and computational techniques for the study of cancer systems biology by focusing on network reconstruction, network analysis and modeling. Finally, certain challenges and hurdles in cancer systems biology will also be discussed.
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4322/version/2

A schistosome [beta] subunit remodels inactivation of a calcium channel _via_ an N-terminal polyacidic motif
Provedor de dados: 17
Autores: Vicenta Salvador-Recatala; Robert M. Greenberg.
The beta subunit of high voltage-activated Ca (Cav) channels targets the pore forming [alpha]~1~ subunit to the plasma membrane and defines the biophysical phenotype of the Cav channel complex. Cav channel inactivation following activation and opening is tightly regulated and is an essential property that not only prevents excessive entry of Ca^2+^ into the cell but may also have functions in signal transduction. The [beta] subunit modulates Ca^2+^-dependent and voltage-dependent components of Cav channel inactivation via its interaction with the I-II linker of the [alpha]~1~ subunit. Here, using Cav2.3 and whole-cell patch-clamp, we show that a [beta] subunit from the human parasite _Schistosoma mansoni_ ([beta]~Sm~) accelerates inactivation via a unique,...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4230/version/1

A science metrics based citation for tagging the biomedical researchers
Provedor de dados: 17
Autores: Adeilton Brandao.
With the thousands of scientific papers being produced every month, picking an authors name, associate it to a research field and right evaluate his or her performance is in most of times a cumbersome task. I am proposing here that science indexes as h-index, g-index, total citations and published papers  could be added to biomedical bibliographic citation in order to create a unique identifier for a given researcher.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/794/version/1

A Secret of Hypnosis: A Dynamic Rubber Hand Illusion
Provedor de dados: 17
Autores: Tomohisa Asai; Eriko Sugimori; Yoshihiko Tanno.
Presenting a suggestion of heaviness to a person in a hypnotic trance (e.g., &amp;#x22;your arm is getting heavier and heavier&amp;#x22;) tends to result in a corresponding change in the person&amp;#x27;s body position (e.g., the arm lowers). This phenomenon may be a result of activation of the mirror neuron system, which leads the subject to anticipate actual weight on the arm. The mirror system underlies people&amp;#x27;s ability to sense, in the absence of actual sensory input, experiences of other people. Perhaps this system allows the same anticipatory experience regarding non-human objects. In this study, we showed participants a picture of a rubber hand holding what appeared to be a lightweight rubber ball. In reality, the ball was weighted with...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2276/version/1

A Semantic Model for Federated Queries Over a Normalized Corpus
Provedor de dados: 17
Autores: Samuel Croset; Christoph Grabm&amp;#xfc;ller; Dietrich Rebholz-Schuhmann.
We present here a model implemented in OWL which improves information retrieval and data integration of the corpus. The model is populated with entities from CALBC and some simple queries over it are presented.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5823/version/2

A Semantic Model for Federated Queries Over a Normalized Corpus
Provedor de dados: 17
Autores: Samuel Croset.
We present here a model implemented in OWL which improves information retrieval and data integration of the corpus. The model is populated with entities from CALBC and some simple queries over it are presented.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5823/version/1

A sensorimotor area (NIf) is required for the production of learned vocalizations
Provedor de dados: 17
Autores: Sharon M. H. Gobes; Bence P. &amp;#xd6;lveczky.
Sensory feedback is essential for the acquisition of complex motor behaviors, including birdsong. In zebra finches, auditory feedback is relayed to the descending motor pathway primarily through the nucleus interfacialis nidopalii (NIf). NIf projects to HVC - a premotor region essential for song, which projects to RA, a motor cortex analogue brain area that drives muscle activity required for vocalizations. NIf is also essential for &amp;#x2018;sleep replay&amp;#x2019;, a recapitulation of song-related neural dynamics in the motor pathway during sleep. Despite being one of the major inputs to the song control pathway, there is no known role for NIf in the production of zebra finch song. To address this, we reversibly inactivated NIf using TTX or Muscimol...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5856/version/1

A set of ontologies to drive tools for the control of vector-borne diseases
Provedor de dados: 17
Autores: Pantelis Topalis; Emmanuel Dialynas; Elvira Mitraka; Elena Deliyanni; Inga Siden-Kiamos; Christos Louis.
We are developing a set of ontologies that deal with vector-borne diseases and the arthropod vectors that transmit them. For practical reasons (application priorities), we initiated this project with an ontology of insecticide resistance followed by a series of ontologies that describe malaria as well as physiological processes of mosquitoes that are relevant to, and involved in, disease transmission. These will be expanded to encompass other vector-borne diseases as well as non-mosquito vectors. The aim of the whole undertaking, which is worked out in the frame of the international IDO (Infectious Disease Ontology) project, is to provide the community with a set of ontological tools that can be used both in the development of specific databases and, most...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3464/version/1

A similarity criterion for forest growth curves
Provedor de dados: 17
Autores: Georgii A. Alexandrov; Georgy S. Golitsyn.
Comparison of forest growth curves has led many to the conclusion that there is a similarity between forest stands growing in different conditions. Here we treat the same subject from the viewpoint of similarity theory. Our goal is to form a dimensionless ratio of biophysical entities that could parameterize the diversity of forest growth curves. (Such ratios are called similarity criteria.)  Pursuing this goal, we focus on the analogy between tree crown growth and atomic explosion. A blast wave is formed when the rate of energy release is much higher than the rate of energy dissipation. The difference between the rates of energy release and dissipation is the essence of this phenomenon. The essential feature of crown growth is the difference between the...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6561/version/1

A simple clustering of the BioModels database using semanticSBML
Provedor de dados: 17
Autores: Falko Krause; Wolfram Liebermeister.
The BioModels database contains biochemical network models in SBML format, in which the biochemical meaning of elements is specified by MIRIAM-compliant RDF annotations. We used these annotations to define a similarity measure for models, scoring the overlap of the biochemical systems described. Based on this score, we used two-way clustering to detect groups of similar models and groups of co-occuring model elements. To recognize and compare biochemical elements, we used routines from the software semanticSBML. A Python script extracts all MIRIAM annotations (regardless of their qualifiers) using the semanticSBML annotation classes. The result is a matrix in which the rows represent the models (e.g. BioModel 001), while the columns represent specific...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3444/version/1

A Simple Nested Simulation for SED-ML
Provedor de dados: 17
Autores: Frank T. Bergmann.
This document describes a simple nested Simulation Experiment for SED-ML [1] that is easy to implement and will help to broaden what SED-ML is able to encode.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4257/version/1

A Simple, Rapid Method for Extracting Large Plasmid DNA from Bacteria
Provedor de dados: 17
Autores: Spencer D. Heringa; Jonathan D. Monroe; James B. Herrick.
We are studying the lateral transfer of transmissible antibiotic resistance plasmids among stream bacteria impacted by fecal runoff from poultry and cattle. Such plasmids are typically large (ca. 40 &amp;#x2013; 100 kb) and occur in low copy numbers in the cell and have therefore typically been difficult to isolate and therefore to study. Traditional protocols, based upon variations of the standard alkaline-lysis method, are long (ca. 1 1/2 to 2 days) and difficult. Commercial kits designed for the isolation of Baterial Artificial Chromosomes (BACs) can be used and are an improvement; however, these are expensive and still require hours of sustained effort. We have adapted a method published by Rondon et al. (1999), originally designed for the isolation of...
Tipo: Poster
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology.
Ano: 2007
URL: http://precedings.nature.com/documents/1249/version/1

A simulation study on different STDP models concerning localized gamma oscillations
Provedor de dados: 17
Autores: Florian Hauser; Andreas Knoblauch; G&amp;#xfc;nther Palm.
Gamma oscillations are a prominent feature in experimental as well as theoretical descriptions of brain activity. One of the network models which has the capability to generate such oscillations is what we call a local cell assembly (CA), i.e. a group of neighboring neurons which are strongly interconnected in an excitatory manner. Postulated by experimenters and extensively used in theoretical studies, these local networks seem to be a good candidate for investigating the impact of biological constraints given by models of spike-timing-dependent plasticity (STDP) on local gamma oscillating structures in the mammalian brain. Therefore we fi&amp;#xc;tted a two-compartment neuron model with AMPA- and NMDA-receptor mediated synaptic currents to desired...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5802/version/1

A snake of a different color: physiological color change in Arizona black rattlesnakes
Provedor de dados: 17
Autores: Melissa Amarello; Jeffrey J. Smith.
Coloration may serve a variety of behavioral (e.g., crypsis, communication) and physiological (e.g., thermoregulation, protection) functions for terrestrial ectotherms.  However, optimal coloration for a given function may vary over environments (spatial or temporal) or conflict with other functions.  Physiological color change (rapid change due to movement of pigment granules within chromatophores) may be an adaptation to resolve conflicting selective pressures on coloration.  The proximate factors related to physiological color change are well known in many animals, but few studies have investigated the ecological or evolutionary implications of this behavior.  Here, we present alternative hypotheses for physiological color change and discuss biotic and...
Tipo: Poster
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6711/version/1

A sorites paradox in the conventional definition of amount of substance
Provedor de dados: 17
Autores: Nigel Wheatley.
The conventional definition of amount of substance _n_ is as a quantity proportional to number of entities _N_. This implies that n is discrete for small _N_ while _n_ is considered to be continuous at the macroscopic scale, leading to a sorites paradox. A practical criterion is proposed for distinguishing between amount of substance and number of entities, and the implications for the conventional definition of amount of substance are discussed.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/5568/version/1

A stable backbone for the fungi
Provedor de dados: 17
Autores: Ingo Ebersberger; Matthias Gube; Sascha Strauss; Anne Kupczok; Martin Eckart; Kerstin Voigt; Erika Kothe; Arndt von Haeseler.
Fungi are abundant in the biosphere. They have fascinated mankind as far as written history goes and have considerably influenced our culture. In biotechnology, cell biology, genetics, and life sciences in general fungi constitute relevant model organisms. Once the phylogenetic relationships of fungi are stably resolved individual results from fungal research can be combined into a holistic picture of biology. However, and despite recent progress, the backbone of the fungal phylogeny is not yet fully resolved. Especially the early evolutionary history of fungi and the order or below-order relationships within the ascomycetes remain uncertain. Here we present the first phylogenomic study for a eukaryotic kingdom that merges all publicly available fungal...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2901/version/1

A stem-cell ageing hypothesis on the origin of Parkinson&amp;#x27;s disease
Provedor de dados: 17
Autores: Andr&amp;#xe9; Valente; Jorge Sousa; Tiago Outeiro; Lino Ferreira.
A transcriptome-wide blood expression dataset of Parkinson&amp;#x2019;s disease (PD) patients and controls was analyzed under the hypothesis-rich mathematical framework. The analysis pointed towards differential expression in blood cells in many of the processes known or predicted to be disrupted in PD. We suggest that circulating blood cells in PD patients can be in a full-blown PD-expression state. We put forward the hypothesis that sporadic PD can originate as a case of hematopoietic stem cell/differentiation process expression program defect and suggest this research direction deserves further investigation.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4263/version/1

A stem-cell ageing hypothesis on the origin of Parkinson&amp;#x27;s disease
Provedor de dados: 17
Autores: Andr&amp;#xe9;  X. C. N. Valente; Jorge Sousa; Tiago Outeiro; Lino Ferreira.
A transcriptome-wide blood expression dataset of Parkinson&amp;#x2019;s disease (PD) patients and controls was analyzed under the hypothesis-rich mathematical framework. The analysis pointed towards differential expression in blood cells in many of the processes known or predicted to be disrupted in PD. We suggest that circulating blood cells in PD patients can be in a full-blown PD-expression state. We put forward the hypothesis that sporadic PD can originate as a case of hematopoietic stem cell/differentiation process expression program defect and suggest this research direction deserves further investigation.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4263/version/2

A Study of prevalence of malnutrition in government School children in the field area of Azad nagar Bangalore, India
Provedor de dados: 17
Autores: Izhar Hasan.
Malnutrition is a problem at varying proportions in developing countries, and anthropometry is a simple tool to assess its magnitude in children. This study was aimed at identifying the prevalence of malnutrition among 500 children of govt schols of Azad Nagar, bangalore south Asia. The value of using various field based formulae and of various anthropometric indicators used for classification of malnutrition was also studied. The study was focused on children aged 8-14 years studying in class 1st to 8th in govt schools. Anthropometric data and eating practices of children were collected with the help of a pretested questionnaire and food intake diary. Selected anthropometric measurements were taken using standard techniques. Their Body Mass Index (B.M.I)...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5009/version/1

A Study of the Mechanism of Action of Zervamicin IIB Peptide Antibiotic by Molecular Dynamics Simulation
Provedor de dados: 17
Autores: Konstantin Shaitan; Olga V. Levtsova; Vladimir Makarov; Mikhail P. Kirpichnikov.
We model mechanism of action of a channel-forming peptide antibiotic, zervamicin IIB, by molecular dynamics (MD) simulation. Interaction of this peptide with neutral and negatively charged lipid bilayers is investigated. It is found that charge of membrane surface influences the orientation of zervamicin IIB molecule, that may in turn effect its permeation into the membrane. On this basis we propose modifications to ZrvIIB structure that may increase its affinity towards the prokaryotic cellular membrane. Zervamicin IIB transmembrane channels are modeled as bundles consisting of 4, 5 and 6 individual peptide monomers. Our results suggest that four monomers don&amp;#x2019;t form a stable water-filled ion channel. Thus the channel with the least number of...
Tipo: Manuscript
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3624/version/1

A Study on the Origin of Peroxisomes: Possibility of Actinobacteria Symbiosis
Provedor de dados: 17
Autores: Duhita Narendra; Saruhashi Satoshi; Hamada Kazuo; Miyata Daisuke; Horiike Tokumasa; Shinozawa Takao.
The origin of peroxisomes as having developed from the endoplasmic reticulum (ER) was proposed on the basis of the similarity between some peroxisomal proteins and ER proteins, and the localization of some peroxisomal proteins on the ER. To study the evolutionary distance between peroxisomes and ER and Prokaryotes, we carried out a phylogenetic analysis of CDC48 (cell division control 48) and its homologs, including ER-localized CDC48, CDC48 homologs in Prokaryotes and peroxisome-localized PEX1 and PEX6. A similarity search analysis of peroxisomal protein sequences to prokaryotic protein sequences using BLAST at several thresholds (E-values) was also done. We propose Actinobacteria symbiosis for the origin of peroxisomes based on the following evidence:...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1866/version/1

A Study on the Origin of Peroxisomes: Possibility of Actinobacteria Symbiosis
Provedor de dados: 17
Autores: Duhita Narendra; Saruhashi Satoshi; Hamada Kazuo; Miyata Daisuke; Horiike Tokumasa; Shinozawa Takao.
Withdrawn
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/1866/version/2

A subset of co-expressed genes in Slug-based cancer mesenchymal transition signature remains coexpressed in normal samples in a tissue-specific manner
Provedor de dados: 17
Autores: Weiyi Cheng; Dimitris Anastassiou.
A recently identified gene expression signature of EMT markers containing the transcription factor Slug was found present in samples from many publicly available cancer gene expression datasets of multiple cancer types except leukemia. We also found many of these genes co-expressed in human cancer xenografted cells, but not in mouse stroma cells, suggesting that the signature is largely produced by cancer cells undergoing some type of EMT. Here we report that a partial signature consisting of a subset of the co-expressed genes of the full signature, including at least Slug (SNAI2), collagens COL1A1, COL1A2, COL3A1, COL6A3 and genes DCN and LUM, is also present in leukemia, in which case it is also strongly associated with the chemokine CXCL12 (aka SDF1)....
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6813/version/1

A Systematic Approach to Identifying Protein-Ligand Binding Profiles on a Proteome Scale
Provedor de dados: 17
Autores: Li Xie; Nancy  Buchmeier; Lei Xie; Philip Bourne.
Identification of protein-ligand interaction networks on a proteome scale is crucial to address a wide range of biological problems such as correlating molecular functions to physiological processes and designing safe and efficient therapeutics. We have developed a novel computational strategy to identify ligand binding profiles of proteins across gene families and applied it to predicting protein functions, elucidating molecular mechanisms of drug adverse effects, and repositioning safe pharmaceuticals to treat different diseases.
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2207/version/1

A system-level neural model of the     brain mechanisms underlying     instrumental devaluation in rats
Provedor de dados: 17
Autores: Francesco Mannella; Marco Mirolli; Gianluca Baldassarre.
Goal-directed behaviours are defined by the presence of two kinds of effect on instrumental learning. First, degrading the contingencies between produced actions and desired outcomes diminishes the number of instrumental responses; second, devaluing a reward results in a lower production of instrumental actions to obtain it. We present a computational model of the neural processes underlying instrumental devaluation in rats. The model reproduces the interaction between the basolateral complex of the amygdala (BLA) and the limbic, associative and somatosensory striato-cortical loops. Firing-rate units are used to abstract the activity features of neural populations. Learning is reproduced through the use of dopamine-dependent simple and differential hebbian...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5849/version/1

A Systems Biology Approach to the Evolution of Codon Use Pattern
Provedor de dados: 17
Autores: Ines Thiele; Ronan M. T. Fleming; Richard Que; Aarash Bordbar; Bernhard O. Palsson.
The genetic code is redundant as amino acids are encoded by synonymous codons that are unequally used.This codon usage bias (CUB) affects gene expression and cellular functions yet the underlying mechanisms have not been elucidated. We used a sequence-specific, stoichiometric model of metabolism and macromolecular synthesis for Escherichia coli K12 MG1655 to test the effect of randomly changed CUB on growth maximization under various environmental conditions. Amongst CUB mutant strains, we identified reduced growth phenotypes, which were caused by tRNA supply shortage. We propose, supported by computations and bibliomic data, that expansion of tRNA gene content or tRNA reading is a mechanism to respond to changes in CUB. Our systems biology modelling...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6312/version/1

A Systems Biology Approach towards Deciphering the Unfolded Protein Response in Huntington&amp;#x27;s Disease
Provedor de dados: 17
Autores: Kameshwar R. Ayasolla; Ravi K. R. Kalathur; Matthias  E. Futschik.
Although the disease causing gene huntingtin has been known for some time, the exact cause of neuronal cell death during _Huntington&amp;#x27;s disease_ (HD) remains unknown. One potential mechanism contributing to the massive loss of neurons in HD brains might be the _Unfolded Protein Response_ (UPR) which is activated by accumulation of misfolded proteins in the endoplasmic reticulum (ER). As an adaptive response, UPR upregulates transcription of chaperones, temporarily attenuating new translation and activates protein degradation via the proteasome. However, at high levels of ER stress, UPR signalling can contribute to neuronal apoptosis.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Our primary aims include (a) construction of the UPR signalling network, (b)...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7078/version/1

A Target Restricted Assembly Method (TRAM) for Phylogenomics
Provedor de dados: 17
Autores: Kevin P. Johnson; Kimberly K. O. Walden; Hugh M. Robertson.
While next generation sequencing technology can produce sequences covering the entire genome, assembly and annotation are still prohibitive steps for many phylogenomics applications.  Here we describe a method of Target Restricted Assembly (TRAM) of a single lane of Illumina sequences for genes of relevance to phylogeny reconstruction, i.e. single copy protein-coding genes.  This method has the potential to produce a data set of hundreds of genes using only one Illumina lane per taxon.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4612/version/1

A Targeted Therapeutic Rescues Botulinum Toxin-A Poisoned Neurons
Provedor de dados: 17
Autores: Prabhati Ray; Bal Ram Singh; Radharaman Ray; Peng Zhang; Dan Li; James Keller; Michael Adler.
Botulinum neurotoxin (BoNT), a Category A biothreat agent, is the most potent poison known to mankind. Currently no antidote is available to rescue poisoned synapses. BoNT acts specifically by blocking neurotransmission primarily at peripheral nerve-muscle junctions causing severe flaccid muscle paralysis, which is fatal if proper medical care is not provided. The neurotoxin acts by specifically entering the presynaptic nerve endings where it interferes with the biochemical machinery involved in the process of neurotransmitter release, i.e., neuroexocytosis. Most serotypes of BoNT are known to remain active for weeks to months after entering the nerves, but BoNT/A is the most potent and long lasting in causing muscle paralysis. An effective medical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2149/version/1

A test of _psbK-psbI_ and _atpF-atpH_ as potential plant DNA barcodes using the flora of the Kruger National Park (South Africa) as a model system
Provedor de dados: 17
Autores: Renaud R. Y. Lahaye; Vincent Savolainen; Sylvie Duthoit; Olivier  Maurin; Michelle van der Bank.
A DNA barcode consists of a standardized short sequence of DNA (400-800bp) used to identify the taxonomic species a small organic fragment belongs to. Even though it has been easy to discriminate animal species by using the mitochondrial gene _cox1_, this is still difficult for plants seeing that the mitochondrial genome is not variable enough on the species level. During the Second International Barcode of Life Conference in Tapei (September 2007), different plastid regions were proposed as potential plant DNA barcodes, such as _atpF-atpH_ and _psbK-psbI_, but no consensus on which region to use was reached during the meeting. The largest plant DNA barcoding study to date proposed _matK_ as the best candidate and suggested that in combination with...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1896/version/1

A theory for the tissue specificity of BRCA1/2 related and other hereditary cancers
Provedor de dados: 17
Autores: Bernard Friedenson.
Women who inherit a defective BRCA1 or BRCA2 gene have risks for breast and ovarian cancer that are so high and seem so selective that many mutation carriers choose to have prophylactic surgery.   There has been much conjecture to explain such apparently striking tissue specificity.  All these suggestions share the assumption that some disabled function of normal tumor suppressor genes leads to a tissue specific cancer response.  Here the idea is proposed and tested that major determinants of where BRCA1/2 hereditary cancers occur are related to tissue specificity of the cancer pathogen, the agent that causes chronic inflammation or the carcinogen.  The target tissue may have receptors for the pathogen, become selectively exposed to an inflammatory process...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Immunology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4881/version/1

A Therapeutically Relevant Difference in Leukemia and Normal Stem Cell Self Renewal
Provedor de dados: 17
Autores: Soledad Negrotto; Zhenbo Hu; Kevin A. Link; Kwok Peng Ng; Juraj Bodo; Hien Duong; Andrew Schade; Eric Hsi; Daniel Lindner; Jaroslaw Maciejewski; James Mulloy; Yogen Saunthararajah.
Abnormal self-renewal and differentiation are defining features of acute myeloid leukemia (AML).  Using models of hematopoiesis, we show that persistent self-renewal that ignores differentiation signals can be produced through two distinct pathways.  One pathway prevents repression of stem cell genes, producing daughter cells that resemble parental stem cells despite differentiation inducing lineage-specifying factor or cytokines.  Runx1 deficiency, a frequent abnormality in AML, demonstrates the second pathway, which allows cytokine/lineage-specifying factor mediated repression of stem cell genes but impairs subsequent activation of differentiation genes that terminate transit-amplification, producing self-renewal in daughter cells that do not resemble...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3044/version/1

A Thoracic Mechanism of Mild Traumatic Brain Injury Due to Blast Pressure Waves
Provedor de dados: 17
Autores: Amy Courtney; Michael Courtney.
The mechanisms by which blast pressure waves cause mild to moderate traumatic brain injury (mTBI) are an open question. Possibilities include acceleration of the head, direct passage of the blast wave via the cranium, and propagation of the blast wave to the brain via a thoracic mechanism.  The hypothesis that the blast pressure wave reaches the brain via a thoracic mechanism is considered in light of ballistic and blast pressure wave research.  Ballistic pressure waves, caused by penetrating ballistic projectiles or ballistic impacts to body armor, can only reach the brain via an internal mechanism and have been shown to cause cerebral effects. Similar effects have been documented when a blast pressure wave has been applied to the whole body or focused on...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2169/version/1

A Three dimesional stochastic spatio-temporal model of cell spreading
Provedor de dados: 17
Autores: Yuguang P. Xiong; Padmini Rangamani; Benjamin Dubin-Thaler; Michael  Sheetz; Ravi Iyengar.
Cell motility is important for many physiological processes and the underlying&amp;#xd;&amp;#xa;biochemical reactions motility have been well-characterized. Mathematical models, using&amp;#xd;&amp;#xa;the biochemical reactions and focused on different types of spreading behavior have been&amp;#xd;&amp;#xa;constructed and analyzed. In this study, we build on these previous models to develop a&amp;#xd;&amp;#xa;three-dimensional stochastic model of isotropic spreading of mammalian fibroblasts. The model is composed of three actin remodeling reactions that occur stochastically in space and time and are regulated by membrane resistance forces. Numerical simulations indicate that the model qualitatively captures the experimentally observed isotropic cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/62/version/1

A three-dimensional stochastic spatio-temporal model of cell spreading
Provedor de dados: 17
Autores: Yuguang P. Xiong; Padmini Rangamani; Benjamin Dubin-Thaler; Michael  Sheetz; Ravi Iyengar.
Cell motility is important for many physiological processes and the underlying&amp;#xd;&amp;#xa;biochemical reactions motility have been well characterized. Mathematical models, using&amp;#xd;&amp;#xa;the biochemical reactions and focused on different types of spreading behavior have been&amp;#xd;&amp;#xa;constructed and analyzed. In this study, we build on these previous models to develop a&amp;#xd;&amp;#xa;three-dimensional stochastic model of isotropic spreading of mammalian fibroblasts. The model is composed of three actin remodeling reactions that occur stochastically in space and time and are regulated by membrane resistance forces. Numerical simulations indicate that the model qualitatively captures the experimentally observed isotropic cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/62/version/2

A Tobacco Homolog of DCN1 is Involved in Cellular Reprogramming and in Developmental Transitions
Provedor de dados: 17
Autores: Julia Hosp; Alexandra Ribarits; Katarzyna Szaszka; Yongfeng Jin; Alisher Tashpulatov; Marina Baumann; Tatiana Resch; Christina Friedmann; Elisabeth Ankele; Viktor Voronin; Klaus Palme; Alisher Touraev; Erwin Heberle-Bors.
Plant proteomes show remarkable plasticity in reaction to environmental challenges and during developmental transitions. Some of this adaptability comes from ubiquitin-mediated protein destruction regulated by cullin-RING E3 ubiquitin ligases (CRLs). CRLs are activated through modification of the cullin subunit with the ubiquitin-like protein RUB/NEDD8 by an E3 ligase called defective in cullin neddylation 1 (DCN1). Here we show that tobacco DCN1 binds ubiquitin and RUB/NEDD8, and associates with cullin. When knocked down by RNAi, tobacco pollen formation stopped and zygotic embryogenesis was blocked around the globular stage. Additionally, we found that RNAi of DCN1 inhibited the stress-triggered reprogramming of cultured microspores from their intrinsic...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5728/version/1

A transgenic rat model for reducing adult neurogenesis.
Provedor de dados: 17
Autores: Jason S. Snyder; Laura Grigereit; Michelle Brewer; Jim Pickel; Heather A. Cameron.
The function of adult neurogenesis remains unclear. While many tools for manipulating neurogenesis have been developed for mice, there are fewer tools for rats. Radiological and chemical strategies have been used to inhibit adult neurogenesis in rats but these methods may also have undesired side effects. Since rats have a larger brain and can perform complex behaviors, it would be useful to have additional rat models for studying neurogenesis. To address this gap we therefore developed a transgenic GFAP-TK rat in which adult neurogenesis can be specifically inhibited. Preliminary results suggest that, as in mice, reduced adult neurogenesis leads to anhedonia.
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6592/version/1

A Unified Approach for Representing Structurally-Complex Models in SBML Level 3
Provedor de dados: 17
Autores: Robert Muetzelfeldt.
The aim of this document is to explore a unified approach to handling several of the proposed extensions to the SBML Level 3 Core specification.   The approach is illustrated with reference to Simile, a modelling environment which appears to have most of the capabilities of the various SBML Level 3 package proposals which deal with model structure.   Simile (http://www.simulistics.com) is a visual modelling environment for continuous systems modelling which includes the ability to handle complex disaggregation of model structure, by allowing the modeller to specify classes of object and the relationships between them.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The note is organised around the 6 packages listed on the SBML Level 3 Proposals web page...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4372/version/1

A unified mechanistic model of niche, neutrality and violation of the competitive exclusion principle
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The origin of species richness is one of the most widely discussed questions in ecology. The absence of unified mechanistic model of competition makes difficult our deep understanding of this subject. Here we show such a two-species competition model that unifies (i) a mechanistic niche model, (ii) a mechanistic neutral (null) model and (iii) a mechanistic violation of the competitive exclusion principle. Our model is an individual-based cellular automaton. We demonstrate how two trophically identical and aggressively propagating species can stably coexist in one stable homogeneous habitat without any trade-offs in spite of their 10% difference in fitness. Competitive exclusion occurs if the fitness difference is significant (approximately more than 30%)....
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7089/version/1

A Unifying Scenario on the Origin and Evolution of Cellular and Viral Domains
Provedor de dados: 17
Autores: Claudiu I. Bandea.
The cellular theory on the nature of life has been one of the first major advancements in biology. Viruses, however, are the most abundant life forms, and their exclusion from mainstream biology and the Tree of Life (TOL) is a major paradox in biology. This article presents a broad, unifying scenario on the origin and evolution of cellular and viral domains that challenges the conventional views about the history of life and supports a TOL that includes viruses. Co-evolution of viruses and their host cells has led to some of the most remarkable developments and transitions in the evolution of life, including the origin of non-coding DNA as a genomic protective device against viral insertion damage. However, one of the major fundamental evolutionary...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3888/version/1

A unique avenue to control drug resistant pathogens: Experimental evidences
Provedor de dados: 17
Autores: Sribir Sen.
Drug resistant bacterial pathogens are increasing in the environment due to multiple reasons. If any drug resistant pathogen grows in a host, the host will face death treat because there is no way to resist their growth in the host system. Eventuality is death in almost all cases. Reports on the mechanisms of drug resistance in bacteria are many. However, there is no solution for these cases. The present work is providing an important understanding to fight against drug resistant pathogens and that can be used in gastrointestinal diseases.
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4934/version/1

A Universal Carrier Test for the Long Tail of Mendelian Disease
Provedor de dados: 17
Autores: Balaji S. Srinivasan; Jason Flannick; A. Scott Patterson; Christopher C. Chang; Tuan Pham; Sharon Young; Amit Kaushal; James J. Lee; Pasquale Patrizio; Eric A. Evans.
*Background:* &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Mendelian disorders are individually rare but collectively common, forming a &amp;#x22;long tail&amp;#x22; of genetic disease. More than 20 million people worldwide suffer from a disease in this long tail before the age of 25, with minorities and developing countries at highest risk and with the number of carriers far in excess of this figure. Importantly, the Jewish community&amp;#x2019;s campaign for universal Tay-Sachs screening shows that these incurable diseases can nevertheless be prevented if carrier status is known before conception. A single highly-accurate assay for the long tail of Mendelian disease would allow us to scale this successful campaign up to the general population, thereby improving...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4192/version/1

A visual sense of number
Provedor de dados: 17
Autores: David Burr; John Ross.
Evidence exists for a non-verbal capacity to apprehend number, in humans^1^ (including infants^2,3^) and in other primates^4-6^. Here we show that perceived numerosity is susceptible to adaptation, along with primary visual properties of a scene like colour, contrast, size and speed. Apparent numerosity was decreased by adapting to large numbers of dots and increased by adapting to small numbers, the effect depended entirely on the numerosity of the adapter, not on contrast, size, orientation or pixel density, and occurred with very low adapter contrasts. We suggest that numerosity is also an independent primary visual property, not reducible to others like spatial frequency or density of texture^7^.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1353/version/1

A war-prone tribe migrated out of Africa to populate the world.
Provedor de dados: 17
Autores: Eduardo  Moreno.
Of the tribal hunter gatherers still in existence today, some lead lives of great violence, whereas other groups live in societies with no warfare and very little murder^1,2,3,4,5^. Here I find that hunter gatherers that belong to mitochondrial haplotypes L0, L1 and L2 do not have a culture of ritualized fights. In contrast to this, almost all L3 derived  hunter gatherers have a more belligerent culture that includes ritualized fights such as wrestling, stick fights or headhunting expeditions. This appears to be independent of their environment, because ritualized fights occur in all climates, from the tropics to the arctic. There is also a correlation between mitochondrial haplotypes and warfare propensity or the use of murder and suicide to resolve...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4303/version/1

AAD-2004, a potent spin trapping molecule and microsomal prostaglandin E synthase-1 inhibitor, shows safety and efficacy in a mouse model of ALS
Provedor de dados: 17
Autores: Jin Shin; Young Lee; Jae Lee; Yong Lee; Woong Cho; Doo Im; Jin Lee; Bok Yun; Sun Son; Sun Park; Soo Byun; Joe Springer; Byoung Gwag.
While free radicals and inflammation constitute major routes of neuronal injury occurring in neurodegenerative diseases, neither antioxidants nor nonsteroidal anti-inflammatory drugs (NSAIDs) have shown significant efficacy in human clinical trials. To explore the possibility that concurrent blockade of free radicals and PGE2-mediated inflammation might constitute a safe and effective therapeutic approach to certain neurodegenerative diseases, we have developed 2-hydroxy-5-[2-(4-trifluoromethylphenyl)-ethylaminobezoic acid (AAD-2004) as a derivative of aspirin. AAD-2004 completely removed free radicals at 50 nM as a potent spin trapping molecule and inhibited microsomal prostaglandin E synthase-1 (mPGES-1) with an IC50 of 230 nM. Oral administration of...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5237/version/1

ABC for ancestral inference
Provedor de dados: 17
Autores: Richard  Wilkinson; Simon  Tavare.
ABC for ancestral inference
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5963/version/1

ABC for Temporally Sampled Genetic Data
Provedor de dados: 17
Autores: Mark A. Beaumont.
ABC for Temporally Sampled Genetic Data
Tipo: Presentation
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5953/version/1

ABC Methods for Bayesian Model Choice
Provedor de dados: 17
Autores: Christian P. Robert.
Approximate Bayesian computation (ABC), also known as likelihood-free  methods, have become a standard tool for the analysis of complex models, primarily in population genetics but also for complex financial models. The development of new ABC methodology is undergoing a rapid increase in the past years, as shown by multiple publications, conferences and even software. While one valid interpretation of ABC based estimation is connected with nonparametrics, the setting is quite different for model choice issues. We examined in Grelaud et al. (2009, Bayesian Analysis) the use of ABC for Bayesian model choice in the specific of Gaussian random fields (GRF), relying on a sufficient property only enjoyed by GRFs to show that the approach was legitimate. Despite...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5961/version/1

ABC SMC for parameter estimation and model selection with applications in systems biology
Provedor de dados: 17
Autores: Tina Toni.
Approximate Bayesian Computation (ABC) methods can be used in situations where the evaluation of the likelihood is computationally prohibitive. They are thus ideally suited for analyzing the complex dynamical models encountered in systems biology, where knowledge of the full (approximate) posterior is often essential.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This talk gives an overview of an ABC algorithm based on Sequential Monte Carlo (ABC SMC). Different uses of the algorithm will be presented, depending on the application question of interest. The first is the general parameter estimation framework, where the interest lies in estimating the posterior parameter distribution from available experimental data. In the second context we ask whether the model can...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5964/version/1

Ablation of smooth muscle myosin heavy chain SM2 increases smooth muscle contractility and results in postnatal death in mice
Provedor de dados: 17
Autores: Mei Chi; Yingbi Zhou; Srikanth Vedamoorthyrao; Gopal Babu; Muthu Periasamy.
The smooth muscle myosin heavy chains (SMHC) are motor proteins powering smooth muscle contraction. Alternate splicing of SHMC gene at the C-terminus produces SM1, and SM2 myosin isoforms; SM2 (200 kDa) contains a unique 9-amino-acid sequence at the carboxyl terminus, whereas SM1 (204 kDa) has a 43 amino acid non-helical tail region. To date the functional difference between C-terminal isoforms has not been established; therefore, we used an exon-specific gene targeting strategy and generated a mouse model specifically deficient in SM2. Deletion of exon-41 of the SMHC gene resulted in a complete loss of SM2 in homozygous (_SM2^-/-^_) mice, accompanied by a concomitant down-regulation of SM1 in bladders. While heterozygous (_SM2^+/-^_) mice appeared normal...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1643/version/1

ABO and Rh Blood Group Distribution Among Kunbis (Maratha) population of Amravati District, Maharashtra
Provedor de dados: 17
Autores: NANDKISHOR E. WARGHAT; NAVIN R. SHARMA; MUMTAZ M. BAIG; A. R. Yadav; S. H. Sharma; G. S. Pachalore.
The present study reports the distribution of ABO and Rh blood groups among the Kunbis (Maratha) population of Amravati district. The phenotypic frequency of blood group B is observed highest (33.06) percent, O (31.04), A (27.02) and AB is lowest (08.33) percent. The phenotypic frequency of Rh negative is (04.26) percent. TheKunbis (Maratha) population shows close genetic relationship with the Gujratis.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4868/version/1

Aboveground Net Primary Productivity in Grazed and Ungrazed pastures: Grazing Optimisation Hypothesis or Local Extinction of Vegetation Species
Provedor de dados: 17
Autores: Silvanus G. Otieno; Jesse T. Njoka; Truman P. Young; Stephen M. Mureithi; Robinson K. Ngugi.
The controversy that has surrounded herbivory studies in the last few decades prompted our investigation to establish the extent to which herbivore optimisation hypothesis or compensatory growth evidence is real. We used the traditional movable cage method to collect primary productivity data on herbage, functional groups and key individual grass species in various controlled large herbivore treatments in an east African savanna. The herbivore treatments in triplicate blocks included cattle, wild herbivores with and without mega herbivores and combinations of cattle and wild herbivores also with and without mega herbivores. The findings revealed that at herbage level, most grazed treatments (four out of five) had higher productivity than the ungrazed...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3452/version/1

Absence of historical temporal trends in monthly, seasonal, and annual streamflows for the Okanagan and Similkameen Rivers in south-central British Columbia, Canada
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Potential historical temporal trends in monthly, seasonal, and annual mean, minimum, and maximum streamflows and date of the spring freshet runoff peak were investigated for the Okanagan and Similkameen Rivers in south-central British Columbia, Canada. There appears to be no compelling evidence that streamflow patterns in the Okanagan and Similkameen Rivers have changed over the available hydrometric record, nor does there appear to be evidence that future changes in streamflow patterns are imminent or likely.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6584/version/1

Absolute Aqueous Redox Potentials ( via a new link between aqueous and gaseous properties)
Provedor de dados: 17
Autores: Raji Heyrovska.
The new finding here, that the conventional standard potentials (based on S.H.E.) are linearly dependent on ionization potentials, has yielded the absolute values of aqueous standard potentials.
Tipo: Presentation
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3395/version/1

Absolute Potentials of Standard Reference Electrodes at 25 C
Provedor de dados: 17
Autores: Raji Heyrovska.
Aqueous standard redox potentials are conventionally referred to that of the standard hydrogen electrode (SHE) as zero (IUPAC definition), in the absence of the knowledge of its absolute value. Recently, the author obtained its value (4.20 V) from a newly found linear dependence of redox potentials on ionization potentials. This has enabled now to express the potentials of standard reference electrodes in terms of the absolute values.
Tipo: Presentation
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4354/version/1

Abundance and Composition of Zooplankton (Copepoda, Cladocera, Rotifera) in Lake Taal: Potential Impact of Intensive Size-Selective Predation by the Freshwater Sardine, Sardinella tawilis (Herre 1927)
Provedor de dados: 17
Autores: Rey Donne Papa; Roberto Pagulayan; Alicia Ely Pagulayan.
Zooplankton are considered to be important members of the lake ecosystem.  The abundance and composition of which are due to several factors, for example, the impact of intensive size-selective predation by planktivorous fishes residing in the lake.  In this study, the abundance and composition of zooplankton found in the vicinity of Isla Napayun - a known fishing ground of the freshwater sardine, Sardinella tawilis (Herre 1927) was analyzed using samples taken from vertical plankton tows from the 10 and 20 m depths in 2 sampling sites from the said area.  These were then compared with the stomach contents of S. tawilis taken during the same period.  Results show that there were 4 genera of Copepoda, 4 genera of Cladocera and 2 genera of Rotifera found in...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/684/version/1

Abundance of intrinsic disorder in SV-IV, a multifunctional androgen-dependent protein secreted from rat seminal vesicle
Provedor de dados: 17
Autores: Silvia  Vilasi; Raffaele Ragone.
The potent immunomodulatory, anti-inflammatory and procoagulant properties of the&amp;#xd;&amp;#xa;protein no. 4 secreted from the rat seminal vesicle epithelium (SV-IV) have been&amp;#xd;&amp;#xa;previously found to be modulated by a supramolecular monomer-trimer equilibrium.&amp;#xd;&amp;#xa;More structural details that integrate experimental data into a predictive framework&amp;#xd;&amp;#xa;have recently been reported. Unfortunately, homology modelling and fold-recognition&amp;#xd;&amp;#xa;strategies were not successful in creating a theoretical model of the structural&amp;#xd;&amp;#xa;organization of SV-IV. It was inferred that the global structure of SV-IV is not similar&amp;#xd;&amp;#xa;to any protein of known three-dimensional structure. Reversing...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1394/version/1

ACAT1, Cav-1, and PrP expression in brains and skin fibroblasts from Sarda breed sheep with scrapie-resistant and scrapie-susceptible genotype.
Provedor de dados: 17
Autores: Alessandra Pani; Marirosa Putzolu; Claudia Mulas; Cristina D. Orr&amp;#xf9;; Claudia Abete; Claudia Norfo; M. Dolores Cannas; Sergio Laconi; Paolo La Colla; Sandra Dess&amp;#xec;.
Scrapie is an infective ovine neurodegenerative disease; the only identified component of the infectious agent being an aberrant isoform (PrPSc) of the cellular prion protein (PrPC). So far, no means for ante-mortem diagnosis are available for Scrapie as well as for any other mammal Transmissible Spongiform Encephalopaties. We recently found a strong relationship between cell susceptibility to scrapie-infection and intracellular cholesterol homeostasis alterations. In brain tissues as well as in ex vivo cultures of skin fibroblasts and PBMCs from healthy and scrapie-affected sheep carrying a scrapie-susceptible (ARQ/ARQ) genotype, the levels of cholesterol esters were consistently higher than in tissues and cultures derived from animals with a...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1211/version/1

ACBD: Database for Ascidian Chemical Genomics
Provedor de dados: 17
Autores: Yuichiro Hira; Jun Terai; Mitsuru Nakamura; Etsu Tashiro; Masaya Imoto; Kotaro Oka; Kohji Hotta.
Chemical biology approach enables us to understand the complex biological systems,using small molecules such as a specific activator or inhibitor of protein, a hormone-likeinducer, or a neurotransmitter etc. When such approach is performed genome-widely, that research is especially called &amp;#x22;chemical genomics&amp;#x22;. We are planning to make a new start of chemical genomics using one of chordate model animal, ascidian. As a first step, we constructed a database called ACBD (Ascidians Chemical Biology Database).&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;First, we reviewed and annotated past articles which describe the uses of small chemicals in the field of ascidians biology. In ACBD, chemical information and effects on ascidian are manually extracted...
Tipo: Poster
Palavras-chave: Developmental Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5087/version/2

ACBD: Database for Ascidian Chemical Genomics
Provedor de dados: 17
Autores: Yuichiro Hira; Jun Terai; Masaya Imoto; Etsu Tashiro; Kohji Hotta.
Chemical biology approach enables us to understand the complex biological systems, using small molecules such as a specific activator or inhibitor of protein, a hormone-like inducer, or a neurotransmitter. When such approach is performed genome-widely, that research is especially called &amp;#x22;chemical genomics&amp;#x22;. We are planning to make a new start of chemical genomics using one of chordate model animal, ascidian. As a first step, we constructed a database called ACBD (Ascidians Chemical Biology Database). &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;  First, we reviewed and annotated past articles which describe the uses of small chemicals in the field of ascidians biology.  In ACBD, chemical information and effects on ascidian are manually extracted...
Tipo: Poster
Palavras-chave: Developmental Biology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/5087/version/1

Accelerated Macromolecular Solution Structure Recovery
Provedor de dados: 17
Autores: Petrus Zwart; Haiguang Liu.
Small Angle X-ray Scattering (SAXS) is a standard technique for the determination of low-resolution shapes of macromolecules and their complexes, adding important insights in understanding biological function. We present a novel and computationally efficient method for shape reconstruction from SAXS data. High-quality molecular shapes are calculated in less than two minutes, providing real-time feedback during SAXS experiments.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6521/version/1

Accounting for molecular stochasticity in systematic revisions: species limits and phylogeny of Paroaria
Provedor de dados: 17
Autores: Liliana M. D&amp;#xe1;valos; Ana L. Porzecanski.
Different frameworks have been proposed for using molecular data in systematic revisions, but there is ongoing debate on their applicability, merits and shortcomings. In this paper we examine the fit between morphological and molecular data in the systematic revision of Paroaria, a group of conspicuous songbirds endemic to South America. We delimited species based on examination of &amp;#x3e; 600 specimens, and developed distance-gap, and distance- and character-based coalescent simulations to test species limits with molecular data. The morphological and molecular data collected were then analyzed using parsimony, maximum likelihood, and Bayesian phylogenetics. The simulations were better at evaluating the new species limits than using genetic distances....
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3357/version/1

Accumulation of Neural Activity in the Posterior Insula Encodes the Passage of Time
Provedor de dados: 17
Autores: Marc Wittmann; Alan N. Simmons; Jennifer L. Aron; Martin P. Paulus.
The experience of time, i.e. the estimation of duration, is fundamental for perception and behavior and, therefore, essential for the survival of the individual organism. Over the last decades, neuroimaging, neurophysiological and clinical neuropsychological studies have pointed to many different brain areas involved in the processing of time. However, the core neural substrates and the processes accounting for the encoding of duration, which could form a timekeeping mechanism (essentially, a neural clock), are still unknown. Here we present evidence of neurophysiological activity in circumscribed areas of the human brain that is involved in the encoding of duration. Time-activity curves of neural activation derived from event-related functional magnetic...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2062/version/1

Accuracy of computational solvation free energies for neutral and ionic compounds: Dependence on level of theory and solvent model
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas to aqueous phase standard state (1 atm to 1 mol/L; 298.15 K) free energies of solvation ([DELTA]G^o^~solv~) were calculated for a range of neutral and ionic inorganic and organic compounds using various levels and combinations of Hartree-Fock and density functional theory (DFT) and composite methods (CBS-Q//B3, G4MP2, and G4) with the IEFPCM-UFF, CPCM, and SMD solvation models in Gaussian 09 (G09). For a subset of highly polar and generally polyfunctional neutral organic compounds previously identified as problematic for prior solvation models, we find significantly reduced [DELTA]G^o^~solv~ errors using the revised solvent models in G09. The use of composite methods for these compounds also substantially reduces their apparent [DELTA]G^o^~solv~...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4864/version/1

Accurate estimation of homologue-specific DNA concentration-ratios in cancer samples allows long-range haplotyping
Provedor de dados: 17
Autores: Scott L. Carter; Matthew Meyerson; Gad Getz.
Interpretation of allelic copy measurements at polymorphic markers in cancer samples presents distinctive challenges and opportunities. Due to frequent gross chromosomal alterations occurring in cancer (aneuploidy), many genomic regions are present at homologous-allele imbalance. Within such regions, the unequal contribution of alleles at heterozygous markers allows for direct phasing of the haplotype derived from each individual parent. In addition, genome-wide estimates of homologue specific copy- ratios (HSCRs) are important for interpretation of the cancer genome in terms of fixed integral copy-numbers. We describe HAPSEG, a probabilistic method to interpret bi- allelic marker data in cancer samples. HAPSEG operates by partitioning the genome into...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6494/version/1

Accurate modeling of confounding variation in eQTL studies leads to a great increase in power to detect trans-regulatory effects
Provedor de dados: 17
Autores: Nicolo Fusi; Oliver Stegle; Neil Lawrence.
Expression quantitative trait loci (eQTL) studies are an integral tool to investigate the genetic component of gene expression variation. A major challenge in the analysis of such studies are hidden confounding factors, such as unobserved covariates or unknown environmental influences.  These factors can induce a pronounced artifactual correlation structure in the expression profiles, which may create spurious false associations or mask real genetic association signals.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Here, we report PANAMA (Probabilistic ANAlysis of genoMic dAta), a novel probabilistic model to account for confounding factors within an&amp;#xd;&amp;#xa;eQTL analysis. In contrast to previous methods, PANAMA learns hidden factors jointly with the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5995/version/1

Accurate Reconstruction of Molecular Phylogenies for Proteins Using Codon and Amino Acid Unified Sequence Alignments (CAUSA)
Provedor de dados: 17
Autores: Xiaolong Wang; Yu  Fu; Yue  Zhao; Qi  Wang; Chandra Sekhar  Pedamallu; Shuang-yong  Xu; Yingbo  Niu; Jingjie  Hu.
Based on molecular clock hypothesis, and neutral theory of molecular evolution, molecular phylogenies have been widely used for inferring evolutionary history of organisms and individual genes. Traditionally, alignments and phylogeny trees of proteins and their coding DNA sequences are constructed separately, thus often different conclusions were drawn. Here we present a new strategy for sequence alignment and phylogenetic tree reconstruction, codon and amino acid unified sequence alignment (CAUSA), which aligns DNA and protein sequences and draw phylogenetic trees in a unified manner. We demonstrated that CAUSA improves both the accuracy of multiple sequence alignments and phylogenetic trees by solving a variety of molecular evolutionary problems in...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6730/version/1

Accurate telemonitoring of Parkinson&amp;#x2019;s disease progression by non-invasive speech tests
Provedor de dados: 17
Autores: Athanasios Tsanas; Max A. Little; Patrick E. McSharry; Lorraine O. Ramig.
Tracking Parkinson&amp;#x27;s disease (PD) symptom progression often uses the Unified Parkinson&amp;#x2019;s Disease Rating Scale (UPDRS), which requires the patient&amp;#x27;s presence in clinic, and time-consuming physical examinations by trained medical staff. Thus, symptom monitoring is costly and logistically inconvenient for patient and clinical staff alike, also hindering recruitment for future large-scale clinical trials. Here, for the first time, we demonstrate rapid, remote replication of UPDRS assessment with clinically useful accuracy (about 7.5 UPDRS points difference from the clinicians&amp;#x2019; estimates), using only simple, self-administered, and non-invasive speech tests. We characterize speech with signal processing algorithms,...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3920/version/1

Acknowledging contributions to online expert assistance
Provedor de dados: 17
Autores: Andra Waagmeester; Gareth  Palidwor; Pawel Szczesny; Istvan Albert; Mary Mangan; Chris Miller; Simon  Cockell; Pierre Lindenbaum; Daniel A. M. M. Silvestre; Giovanni Marco Dall&amp;#x2019;Olio; Chris Evelo.
We present a poster which contains a sequence of a question, answers to this question and comments regarding acknowledging content on BioStar. Biostar.stackexchange.com is a website where questions about Bioinformatics can be asked and answered. Users can also comment on both the questions and the answers. The site is modelled after www.stackoverflow.com (see description from Joel Spolsky), a comparable site for programmers.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;Users find the site valuable both for answers to questions they have and as a reference. Since the content can also be viewed without registration the site likely reaches a larger audience. For instance, BioStar questions are often referenced on Twitter and FriendFeed. This leads to the question of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6041/version/1

Acknowledging contributions to online expert assistance
Provedor de dados: 17
Autores: Andra Waagmeester; Gareth  Palidwor; Pawel Szczesny; Istvan Albert; Mary Mangan; Chris Miller; Simon Cockell; Pierre Lindenbaum; Daniel A. M. M. Silvestre; Giovanni Marco Dall&amp;#x2019;Olio; Chris Miller.
We present a poster which contains a sequence of a question, answers to this question and comments regarding acknowledging content on BioStar. Biostar.stackexchange.com is a website where questions about Bioinformatics can be asked and answered. Users can also comment on both the questions and the answers. The site is modelled after www.stackoverflow.com (see description from Joel Spolsky), a comparable site for programmers.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Users find the site valuable both for answers to questions they have and as a reference. Since the content can also be viewed without registration the site likely reaches a larger audience. For instance, BioStar questions are often referenced on Twitter and FriendFeed. This leads to...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6043/version/1

Activation of an Estrogen/ Estrogen Receptor Signaling by BIG3 Through Its Inhibitory Effect on Nuclear Transport of PHB2/REA in Breast Cancer
Provedor de dados: 17
Autores: Jung-Won Kim; Miki Akiyama; Jae-Hyun Park; Meng-Lay Lin; Arata Shimo; Tomomi Ueki; Yataro Daigo; Tatsuhiko Tsunoda; Toshihiko Nishidate; Yusuke Nakamura; Toyomasa Katagiri.
Breast cancer is known to be a hormone-dependent disease, and estrogens through an interaction with estrogen receptor (ER) enhance the proliferative and metastatic activity of breast tumor cells. Here we show a critical role of transactivation of BIG3, brefeldin A-inhibited guanine nucleotide-exchange protein 3, in activation of the estrogen/ER signaling in breast cancer cells. Knocking-down of BIG3 expression with small-interfering RNA (siRNA) drastically suppressed the growth of breast cancer cells. Subsequent co-immunoprecipitation and immunoblotting assays revealed an interaction of BIG3 with prohibitin 2/repressor of estrogen receptor activity (PHB2/REA). When BIG3 was absent, stimulation of estradiol caused the translocation of PHB2/REA to the...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/2834/version/1

Activation of Ras-ERK pathway by Fgf8 and its downregulation by Sprouty2 for the isthmus organizing activity
Provedor de dados: 17
Autores: Asuka Suzuki-Hirano; Tatsuya Sato; Harukazu Nakamura.
In the previous studies, we showed that strong Fgf8 signaling activates the Ras-ERK pathway to induce cerebellum. Here, we show importance of negative regulation of this pathway. &amp;#x27;Prolonged&amp;#x27; activation of ERK by misexpression of _Fgf8b_ and dominant-negative _Sprouty2_ (_dnSprouty2_) did not change the fate of the mesencephalic alar plate. Downregulation of ERK activity using a MEK inhibitor, U0126, or by tetracycline dependent Tet-off system after co-expression of _Fgf8b_ and _dnSprouty2_, forced the mesencephalic alar plate to differentiate into cerebellum. We then paid attention to Mkp3. After misexpression of _dnMkp3_ and _Fgf8b_, slight downregulation of ERK activity occurred, which may be due to Sprouty2, and the mesencephalon...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2089/version/1

Activation of TRF3 Transcription Factor by Small Interfering RNAs
Provedor de dados: 17
Autores: Stephan Persengiev.
RNA interference (RNAi) is a conserved biological response to double-stranded RNAs that results in posttranscriptional silencing of target gene expression. Double-stranded processed RNAs of 21-23 nt were found to affect in a non-specific manner a number of signaling and transcription pathways, including interferon and PKR cascades. We report here that siRNAs induce the expression of general transcription factor TRF3, which can trigger an interferon response in mammalian cells.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1206/version/1

Activity of Exoenzymes in Treated Wastewater Irrigated Soils
Provedor de dados: 17
Autores: Elisabeth J&amp;#xfc;schke; Bernd Marschner.
The reuse of reclaimed wastewater for irrigation of agricultural fields greatly influences the activity of soil microorganisms through the input of organic compounds. Due to the production of exoenzymes by microorganisms for the decomposition of substrates it can be assumed that the irrigation with treated wastewater (TWW) has a strong influence on the soil enzyme pool. In this study the activity of ten exoenzymes, which catalyses processes in C, N and P nutrient cycles, were determined in 3 different soils in 0-10, 10-20, 20-30, 30-50, 50-70 and 70-100 cm soil depth. The soils were used for agriculture and irrigated with reclaimed wastewater reused after a secondary treatment step. Additionally a control after freshwater irrigation was studied. Due to the...
Tipo: Presentation
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6278/version/1

Acute Toxicity of Perfluorooctane Sulfonic Acid on Early Life Stages of Daphnia Magna, Siriella Armata, Paracentrotus Lividus Sea Urchin, and Turbot (Scophthalmus Maximus L.).
Provedor de dados: 17
Autores: Lazhar Mhadhbi; Sara P&amp;#xe9;rez Fernandez; Diego Real Conde; Moncef Boumaiza; Ricardo Beiras.
Perfluorooctane sulfonate (PFOS) is a persistent organic pollutant whose potential toxicity is causing great concern. In the present study, we used two crustaceans (_Daphnia magna_, _Siriella armata_), echinoid embryos (_Paracentrotus lividus_) and turbot (_Scophthalmus maximus L._) embryos and larvae to investigate the acute toxicity of this compound. The marine species _S. armata_ exhibited greater sensitivity than the freshwater species _D. magna_. In the 48-h acute toxicity test the median lethal concentration was 10.96 mg/L for _S. armata_ and 87.46 mg/L for _D. magna_. In the 96h toxicity test, turbot showed the lowest EC50 (0.155 mgL-1), whilst the EC50 for _S. armata_ was 7.92 mgL-1 which was approximately three times lower than that for sea urchin...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4657/version/1

Adapting natural resource management to climate change on the Olympic Peninsula
Provedor de dados: 17
Autores: Jessica Halofsky; David L. Peterson.
Climate change presents a major challenge to natural resource managers both because of the magnitude of potential effects of climate change on ecosystem structure, process, and function, and because of the uncertainty associated with those potential ecological effects. Concrete ways to adapt to climate change are needed to help natural resource managers take the first steps to incorporate climate change into management and take advantage of opportunities to balance the negative effects of climate change. We initiated a climate change adaptation case study at Olympic National Forest and Olympic National Park to determine how to adapt management of federal lands on the Olympic Peninsula to climate change. As a part of the case study process, we conducted a...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5239/version/1

Adaptive evolution and then what?
Provedor de dados: 17
Autores: Richard Svanb&amp;#xe4;ck; Mario Pineda-Krch; Michael Doebeli.
Traits determining ecological interactions and dynamics are generally subject to natural selection. That genetically based individual variation in ecological traits can influence population dynamics has interested population biologist from various perspectives. Population ecologists recognized the need to incorporate individual variation in models of population regulation, while evolutionary biologists wish to understand genetic and evolutionary dynamics, e.g. of life history traits, in density-regulated populations. But how does adaptation in ecological traits affect population dynamics? In this project we investigated how ecological dynamics changes as a consequence of adaptive evolution in ecological traits using an individual-based predator-prey model.
Tipo: Poster
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/57/version/1

Adding automated data analysis and biological evaluation to affyanalysisQC
Provedor de dados: 17
Autores: Anwesha Dutta.
Almost every cell in the body contains a full set of chromosomes and identical genes. However, only a fraction of these genes are turned on, at any given time and it is this subset of genes that are expressed, which confers unique properties to each cell type.  Gene expression is the term used to describe the transcription of the information contained within the DNA into messenger RNA (mRNA) molecules that are then translated into proteins which perform most of the critical functions of cells. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Gene expression is a highly complex and tightly regulated process that allows a cell to respond dynamically both to environmental stimuli and to its own changing needs. This mechanism acts as both an on/off switch to control which...
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5969/version/1

Adenovirus-mediated transfer of siRNA against survivin enhances the radiosensitivity of human non-small cell lung cancer cells
Provedor de dados: 17
Autores: Cheng-Ta Yang; Jhy-Ming Li; Hsu-Huei Weng; Ya-Chin Li; Miao-Fen Chen.
Expression of survivin has been reported to be correlated with shorter survival in patients with non-small cell lung cancer (NSCLC), and overexpression of survivin may lead to radioresistance in various human cancers. In this study, we inhibited survivin expression by using an adenoviral vector (AdsiSurvivin)-mediated RNAi to elucidate the combined effect of survivin-targeting gene therapy and radiotherapy on the NSCLC cells. Our data revealed that AdsiSurvivin exerted survivin gene silencing, induced apoptosis, and significantly attenuated the growth potential in NSCLC cells within 72 hours after infection. The combined treatment modalities with AdsiSurvivin infection and radiation were significantly more potent on cell-growth inhibition than monotherapy....
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2589/version/1

Adherence to cancer screenings: Is the telephone survey a good method of investigation?
Provedor de dados: 17
Autores: Alessandro Cucchi; Mauro Bergamini.
*INTRODUCTION* - In order to define subjective variables, the methodology on the assessment of the women participation to screening programs to prevent cervical cancer is presented.&amp;#xd;&amp;#xa;*MATERIALS AND METHODS* - The study was conducted using a structured questionnaire administered by telephone to a sample of women invited to screening, regardless of their real participation to the Pap test. The phone calls were made within 2 days prior to the Pap test session. The questionnaire contained 12 closed questions.&amp;#x9;&amp;#xd;&amp;#xa;*RESULTS* - We contacted a total of 1206 women: a total of 1100 women (93.70%) received the invitation letter and answered to the questionnaire.&amp;#x9;&amp;#xd;&amp;#xa;*CONCLUSIONS* - The chosen procedure...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3016/version/1

ADME/Tox WEB in silico predictions of longer chain perfluoroalkyl carboxylic acid pKa values are more accurate than other computational methods
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Perfluoroalkyl carboxylates are contaminants whose environmental fate and toxicological effects are of broad interest within the academic, industrial, and governmental science and regulatory communities. In addition, coupled perfluoroalkyl and carboxylate moieties are often used in medicinal chemistry as part of the drug design process. However, to date there has been a notable absence of reliable acidity constant estimation programs for these compounds. Here we report that the ADME/Tox WEB method for in silico pKa value predictions is more accurate than the PM6, SPARC, and COSMOtherm methods for the longer chain perfluoroalkyl carboxylic acids, suggesting this may be a good general acidity constant estimation approach for these compounds.
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2936/version/1

Adopting Nrf2 and NF-&amp;#x3ba;B from cancer: Is there any role of the duo in diabetes?
Provedor de dados: 17
Autores: Geeta Negi; Ashutosh Kumar; Shyam S. Sharma.
Oxidative stress and inflammation are two well-recognized events occurring in normal cells during cancer chemotherapy. Several antioxidant and anti-inflammatory agents have therefore been tried as rational and effective strategies for chemoprotection. Elaborate studies on antioxidants and anti-inflammatory agents in various experimental models of cancer revealed that these agents act by modulating the expression and/or activity of the transcription factors nuclear factor erythroid 2-related factor 2 (Nrf2) and nuclear factor-kappa B (NF-&amp;#x3ba;B). Nrf2 is considered the main sentinel of antioxidant defense as it induces many antioxidant and phase 2 enzymes in response to stressful conditions. Likewise, NF-&amp;#x3ba;B is considered as a denominator of...
Tipo: Manuscript
Palavras-chave: Cancer; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6581/version/1

Adoption of simultaneous different strategies against different  opponents enhances cooperation
Provedor de dados: 17
Autores: Lucas Wardil; Jafferson  K. L. da Silva.
The emergence of cooperation has been widely studied in the context of game theory on  structured populations. Usually the individuals adopt one strategy against all their neighbors. The structure can provide reproductive success for the cooperative strategy, at least for low values of defection tendency. Other mechanisms, such punishment, can also be responsible for  cooperation emergence. But what happens if the players adopt simultaneously different strategies against each one of their opponents, not just a single one? Here we study this question in the prisoner dilemma scenario structured on a square lattice and on a ring. We show that if an update rule is defined in which the players replace the  strategy that furnishes the smallest payoff,  a...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3035/version/1

ADP-ribose polymer - a novel and general biomarker of human cancers of head &amp;#x26; neck, breast, and cervix
Provedor de dados: 17
Autores: Rennie O. Lakadong; Amal C. Kataki; Rajeshwar N. Sharan.
Background: Poly-ADP-ribosylation (PAR), a reversible post-translational modification of cellular proteins, is involved in various cellular and molecular processes including carcinogenesis (Althaus &amp;#x26; Richter, 1987; Jacobson &amp;#x26; Jacobson, 1989; Poirier &amp;#x26; Moreau, 1992; Boulikas, 1993; Sharan, 2009). ADP-ribose polymer adducts are added onto target cellular proteins by this metabolic process. We hypothesize that a decrease in the concentration of total poly-ADP-ribose adducts of peripheral blood lymphocyte (PBL) proteins strongly correlates with incidence of human cancer. &amp;#xd;&amp;#xa;Methods: A novel, sensitive and convenient immunoprobe assay of poly-ADP-ribose adducts of cellular proteins has been employed using slot blots of...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2010
URL: http://precedings.nature.com/documents/4650/version/1

Adsorption of uranium and thorium on new adsorbent prepared from Moroccan oil shale impregnated with phosphoric acid
Provedor de dados: 17
Autores: El Hassane Khouya; Khadija Legrouri; Said Fakhi; Hassan Hannache.
Attention has been focused recently on the production of new adsorbents from Moroccan oil shale of Tarfaya (layer R3) by chemical activation with phosphoric acid and its application in wastewaters treatment. The optimal conditions for the preparation were searched and the tests of adsorption of uranium and thorium ions were affected. The best product was obtained by used of the ratio of activated agent/precursor equal 3 and activation of the mixture in air at 250&amp;#xb0;C during two hours after prepocessing at 120&amp;#xb0;C in air. Under these conditions the maximal adsorption capacity of methylene blue and specific area (SBET) of the new adsorbent were 526 mg/g and 630 m2/g, respectively. A batch mode experiment was used to explore the performances of...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5098/version/1

Advanced thermodynamic and processing modelling integration for amine scrubbing in post-combustion CO~2~ capture
Provedor de dados: 17
Autores: Niall Mac Dowell; Amparo Galindo; Claire S. Adjiman; George Jackson.
The reduction in CO~2~ emissions from anthropogenic sources has become a topic of widespread interest over the past number of years. As the power generation sector is by far the largest stationary-point-source of CO~2~, being responsible for approximately 35% of total global CO~2~ emissions^1^ this question has special relevance for this industry. As the inclusion of carbon capture facilities incurs a significant energy penalty on the efficiency coal-fired power-stations, there is a strong requirement for the improvement of these systems in terms of the minimisation of operation and maintenance costs, capital costs and the maximisation of efficiency and flexibility. This last issue has relevance for start-up times and ramp-rates. Post-combustion capture...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2638/version/1

Advancing transcriptome platforms
Provedor de dados: 17
Autores: Shuobo Shi.
During the last decade of years, remarkable technological innovations have emerged that allow the direct or indirect determination of the transcriptome at unprecedented scale and speed. Studies using these methods have already altered our view of the extent and complexity of transcript profiling, which has advanced from one-gene-at-a-time to a holistic view of the genome. Here, we outline the major technical advances in transcriptome characterization, including the most popular used hybridization-based platform, the well accepted tag-based sequencing platform, and the recently developed RNA-Seq (RNA sequencing) based platform. Importantly, these next-generation technologies revolutionize assessing the entire transcriptome via the recent RNA-Seq technology.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5894/version/1

Adverse Effects of Trichothiodystrophy DNA Repair and Transcription Gene Abnormalities on Human Fetal Development
Provedor de dados: 17
Autores: Roxana  Moslehi; Caroline Signore; James Troendle; Amiran Dzutsev; James L. Mills.
The effects of DNA repair and transcription genes in human prenatal life have never been studied. Trichothiodystrophy (TTD) is a rare (affected frequency of 10^-6^) recessive disorder caused by mutations in genes involved in the nucleotide excision repair (NER) pathway and in transcription. Based on our clinical observations, we conducted a genetic epidemiologic study to investigate gestational outcomes associated with TTD. We compared pregnancies resulting in TTD-affected offspring (N=24) with respect to abnormalities in their antenatal and neonatal periods to pregnancies resulting in their unaffected siblings (N=18), accounting for correlation, and to population reference values. Significantly higher incidence of several severe gestational complications...
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3582/version/1

Adversity and sex differences in social and emotional sensitivity in children; a possible mechanism for sex differences in psychiatric disorders
Provedor de dados: 17
Autores: Jonathan Hill; Helen Sharp; Lynne Murray.
Females are superior to males on a range of tasks indexing social sensitivity, the capacity to infer others&amp;#x27; mental states and respond with appropriate behaviours and emotions(1-3). There are also sex differences in psychiatric disorders in children and adolescents. Boys have higher rates of psychiatric disorders before puberty, but disorders increase markedly in girls after puberty (4). The causes of the commonest forms of disorder, antisocial behaviour problems in boys, and depression in girls, entail altered brain function caused by genetic variations and psychosocial adversities mainly arising in the family, and the interaction between the two (5;6). This may be explained by sex differences in social and emotional sensitivity provided they...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4553/version/1

Aetiology and treatment of epidermal depigmentory disorder in humans
Provedor de dados: 17
Autores: S. S. Sawhney.
The epidermal depigmentary trigger in humans at post-natal level may occur with the toxification of skin organ with the endogenously produced melanocytotoxic hydrogen peroxide and subsequent formation of hydrogen peroxide- melanolipoprotein conjugate involving the hydrogen bonding of complementary hydroxyl and carbonyl molecular surfaces of these biosignitures respectively. The condition is multifactorial but reversible. The structural and functional degeneration of melanocytes under the acquired condition never occur. The molecular conjugation theory on the aetiology and line of treatment of the epidermal depigmentary disorder (recoined as hepato-epidermal syndrome HES) has been proposed. The inherent sulfoxides of Allium cepa have been found as the...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/7025/version/1

Affordances of distractors and compatibility effects: a study with the computational model TRoPICALS
Provedor de dados: 17
Autores: Daniele Caligiore; Anna M. Borghi; Domenico Parisi; Rob Ellis; Angelo Cangelosi; Gianluca Baldassarre.
Seeing an object activates in the brain both visual and action codes. Crucial evidence supporting this view is offered by compatibility effect experiments (Ellis et al. (2007). J Exp Psychol: Hum Percept Perform): perception of an object can facilitate or interfere with the execution of an action (e.g. grasping) even when the viewer has no intention of interacting with the object. TRoPICALS (Caligiore et al. (2010). Psychol Rev) is a computational model developed to study compatibility effects. It provides a general hypothesis about the brain mechanisms underlying compatibility effects, suggesting that the top-down bias from prefrontal cortex (PFC), and its agreement or disagreement with the affordances of objects, plays a key role in such phenomena....
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5848/version/1

Affymetrix probes containing runs of contiguous guanines are not gene-specific
Provedor de dados: 17
Autores: Graham J. Upton; William B. Langdon; Andrew P. Harrison.
High Density Oligonucleotide arrays (HDONAs), such as the Affymetrix HG-U133A GeneChip, use sets of probes chosen to match specified genes, with the expectation that if a particular gene is highly expressed then all the probes in the designated probe set will provide a consistent message signifying the gene&amp;#x27;s presence. However, we demonstrate by data mining thousands of CEL files from NCBI&amp;#x27;s GEO database that 4G-probes (defined as probes containing sequences of four or more consecutive guanine (G) bases) do not react in the intended way. Rather, possibly due to the formation of G-quadruplexes, most 4G-probes are correlated, irrespective of the expression of the thousands of genes for which they were separately intended. It follows that...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1825/version/1

African wild ungulates compete with or facilitate cattle depending on season
Provedor de dados: 17
Autores: Wilfred O. Odadi; Moses Karachi; Shaukat Abdulrazak; Truman Young.
Savanna ecosystems are vital for both economic and biodiversity values. In savannas worldwide, management decisions are based on the concept that wildlife and livestock compete for grassland resources[1-4], yet there are virtually no experimental data to support this assumption[1]. Specifically, the critical assessment of whether or not wild ungulates alter livestock performance (e.g., weight gain, reproduction or survival) has rarely been carried out, although diminished performance is an essential prerequisite for inferring competition[1]. Here we use a large-scale experiment in a semi-arid savanna in Kenya to show that wild ungulates do depress cattle performance (weight gain) during the dry season, indicating a competitive effect, but enhance cattle...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4828/version/1

Age and origin of enigmatic megaherbs from the subantarctic islands
Provedor de dados: 17
Autores: Steven J. Wagstaff; Ilse Breitwieser; Christopher Quinn; Motomi Ito.
Biogeographic relationships in the southern hemisphere have puzzled biologists for the last two centuries. Once joined to form the supercontinent Gondwana, Africa, Antarctica, Australia, New Zealand and South America are widely separated by the Pacific and Indian oceans. Sir Joseph Hooker was the first to suggest that Antarctica served as a corridor for plant migration not unlike the land-bridges in the northern hemisphere. While the Antarctic flora was largely erased by glaciation during the Pleistocene, at least some of these Antarctic plant communities found refuge on the subantarctic islands. Here we provide support for the hypothesis that giant herbs persisted in the subantactic islands prior to the onset of Pleistocene glaciation, then dispersed...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1272/version/1

Ageing as a price of cooperation and complexity: Self-organization of complex systems causes the ageing of constituent networks
Provedor de dados: 17
Autores: Huba J. M. Kiss; &amp;#xc1;goston Mihalik; Tibor N&amp;#xe1;n&amp;#xe1;si; B&amp;#xe1;lint &amp;#x150;ry; Zolt&amp;#xe1;n Spir&amp;#xf3;; Csaba S&amp;#x151;ti; Peter Csermely.
The analysis of network topology and dynamics is increasingly used for the description of the structure, function and evolution of complex systems. Here we summarize key aspects of the evolvability and robustness of the hierarchical network-set of macromolecules, cells, organisms, and ecosystems. Listing the costs and benefits of cooperation as a necessary behaviour to build this network hierarchy, we outline the major hypothesis of the paper: the emergence of hierarchical complexity needs cooperation leading to the ageing of the constituent networks. Local cooperation in a stable environment may lead to over-optimization developing an &amp;#x2018;always-old&amp;#x2019; network, which ages slowly, and dies in an apoptosis-like process. Global cooperation...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2610/version/1

Agenda of the &amp;#x201c;BioSharing workshop - Unifying Bio-Resources Descriptors&amp;#x201d;
Provedor de dados: 17
Autores: Susanna-Assunta Sansone; Philippe Rocca-Serra; Pascale Gaudet; Dawn Field.
Organized by members of the BioSharing initiative (www.biosharing.org) and the International Society for Biocuration (ISB, www.biocurator.org), this workshop brought together developers, curators, journal editors and researchers to discuss the growing number of (closely related efforts) developing to catalogues of tools, databases, related data and publications.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The focus on the workshop was a strawman uniform system for describing these bio-resources (www.biodbcore.org), in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement (www.biosharing.org/standards).&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Location: ISMB/ECCB,...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6148/version/1

Agenda of the  &amp;#x22;BioSharing workshop -  Bringing catalogues of bio-resource and standards together&amp;#x22;
Provedor de dados: 17
Autores: Susanna-Assunta Sansone; Philippe Rocca-Serra; Dawn Field; Pascale Gaudet.
This workshop has brought together representatives of groups developing catalogues of bio-resources and its aims were twofold:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;1. Ensure that BioSharing (www.biosharing.org), a catalogue of minimal information checklists, terminologies and exchange formats (hereafter called standards) and policies, complements and links to existing catalogues of tools and databases, and also to publications and related material;&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;2. Outline the technical implementations of the bioDBcore checklist (www.biodbcore.org), the proposed uniform system for describing the catalogues of tools and databases, in particular, how to ensure (bi-directional) linking to the BioSharing catalogue....
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6145/version/1

Aggregation of Single Nucleotide Polymorphisms in a Human H5N1 Clade 2.2 Hemagglutinin
Provedor de dados: 17
Autores: Henry L. Niman; Magdi D. Saad; Jeffery Tjaden; Kenneth C. Earhart; Marshall R. Monteville; Mona M. Aly; Moustafa M. Mansour; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M. Esmat; Emad M. Labib; Ehab A. Ayoub; Abdelattar Arafa; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
The rapid evolution of the H5N1 serotype of avian influenza has been explained by a mechanism involving the selection of single nucleotide polymorphisms generated by copy errors.  The recent emergence of H5N1 Clade 2.2 in fifty countries, offered a unique opportunity to view the acquisition of new polymorphism in these evolving genomes.  We analyzed the H5N1 hemagglutinin gene from a fatal human case from Nigeria in 2007.  The newly emerged polymorphisms were present in diverse H5N1 isolates from the previous year.  The aggregation of these polymorphisms from clade 2.2 sub-clades was not supported by recent random mutations, and was most easily explained by recombination between closely related sequences.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/743/version/2

Aggregation of Single Nucleotide Polymorphisms in a Human H5N1 Clade 2.2 Hemagglutinin
Provedor de dados: 17
Autores: Henry L. Niman; Magdi D. Saad; Jeffery Tjaden; Kenneth C. Earhart; Marshall R. Monteville; Mona M. Aly; Moustafa M. Mansour; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M. Esmat; Emad M. Labib; Ehab A. Ayoub; Abdelattar Arafa; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
The evolution of H5N1 has attracted significant interest 1-4 due to linkages with avian 5,6 and human infections 7,8.  The basic tenets of influenza genetics 9 attribute genetic drift to replication errors caused by a polymerase complex that lacks a proof reading function.  However, recent analysis 10 of swine influenza genes identifies regions copied with absolute fidelity for more than 25 years.  In addition, polymorphism tracing of clade 2.2 H5N1 single nucleotide polymorphisms identify concurrent acquisition 11 of the same polymorphism onto multiple genetic backgrounds in widely dispersed geographical locations.  Here we show the aggregation of regional clade 2.2 polymorphisms from Germany, Egypt, and sub-Sahara Africa onto a human Nigerian H5N1...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/743/version/1

Aging as a consequence of misrepair -- A novel theory of aging
Provedor de dados: 17
Autores: Jicun Wang; Thomas Michelitsch; Arne Wunderlin; Ravi Mahadeva.
It is now increasingly realized that the underlying mechanisms which govern aging is a complex interplay of genetic regulation and damage accumulation. Aging as a result of accumulation of &amp;#x2018;faults&amp;#x2019; on cellular and molecular levels, has been proposed in the damage (fault)-accumulation theory by Kirkwood 2006. However, this theory fails to explain some aging phenotypes such as fibrosis and premature aging, since terms such as &amp;#x2018;damage&amp;#x2019; and &amp;#x2018;fault&amp;#x2019; are not specified. Therefore we introduce here a specification of the underlying mechanism of aging and arrive at a novel theory: aging of the body is a result of the accumulation of Misrepair of tissue. It emphasizes: a) it is Misrepair, not the...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2988/version/2

Aging as a consequence of misrepair -- A novel theory of aging
Provedor de dados: 17
Autores: Jicun Wang; Thomas Michelitsch; Arne Wunderlin; Ravi Mahadeva.
It is now increasingly realized that the underlying mechanisms which govern aging is a complex interplay of genetic regulation and damage accumulation. Aging as a result of accumulation of &amp;#x2018;faults&amp;#x2019; on cellular and molecular levels, has been proposed in the damage (fault)-accumulation theory by Kirkwood 2006. However, this theory fails to explain some aging phenotypes such as fibrosis and premature aging, since terms such as &amp;#x2018;damage&amp;#x2019; and &amp;#x2018;fault&amp;#x2019; are not specified. Therefore we introduce here a specification of the underlying mechanism and arrive at a novel theory: aging of the body is a result of the accumulation of Misrepair of tissue. It emphasizes: a) it is Misrepair, not the original...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2988/version/1

Aging as a consequence of misrepair -- A novel theory of aging
Provedor de dados: 17
Autores: Jicun Wang; Thomas Michelitsch; Arne Wunderlin; Ravi Mahadeva.
It is now increasingly realized that the underlying mechanisms which govern aging is a complex interplay of genetic regulation and damage accumulation. Aging as a result of accumulation of &amp;#x2018;faults&amp;#x2019; on cellular and molecular levels, has been proposed in the damage (fault)-accumulation theory by Kirkwood 2006. However, this theory fails to explain some aging phenotypes such as fibrosis and premature aging, since terms such as &amp;#x2018;damage&amp;#x2019; and &amp;#x2018;fault&amp;#x2019; are not specified. Therefore we introduce here a specification of the underlying mechanism of aging and arrive at a novel theory: aging of the body is a result of the accumulation of Misrepair of tissue. It emphasizes: a) it is Misrepair, not the...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2988/version/3

Aging-associated Alteration in the Cardiac MIF-AMPK Cascade in Response to Ischemic Stress
Provedor de dados: 17
Autores: Heng Ma; Jingying Wang; Erin Lane; Lin Leng; Wenkui Wang; Jun Ren; Richard Bucala; Ji Li.
An important role for a macrophage migration inhibitory factor (MIF)-AMP-activated protein kinase (AMPK) signaling pathway in ameliorating myocardial damage following ischemia/reperfusion has been described. An aging-associated reduction in AMPK activity may be associated with a decline in the ability of cardiac cells to activate the MIF-AMPK cascade, thereby resulting in reduced tolerance to ischemic insults. To test this hypothesis, _in vivo_ regional ischemia was induced by occlusion of the left anterior descending (LAD) coronary artery in young (4-6 months) and aged (24-26 months) mice. The ischemic AMPK activation response was impaired in aged hearts compared to young ones (p&amp;#x3c;0.01). Notably, cardiac MIF expression in aged hearts was lower...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2466/version/1

AGMAAS: a GIS integrated tool for modelling wind-borne spreading of FMD virus
Provedor de dados: 17
Autores: Judit S&amp;#xe1;bitz; Zolt&amp;#xe1;n Barcza Solymosi; Norbert Solymosi.
The aim of our work was to develop a tool integrated into Quantum GIS (QGIS) that can help&amp;#xd;&amp;#xa;the user estimate and visualize the possible infective areas around an outbreak based on HYbrid Single-Particle Lagrangian Integrated Trajectory (HYSPLIT) model.
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/7022/version/1

Agriculture: Nanotechnology&amp;#x2019;s Green Field
Provedor de dados: 17
Autores: Siddhartha Sankar Mukhopadhyay.
Natural agricultural production functions in open system, where energy and matter are exchanged freely between geosphere (especially pedosphere), biosphere, and atmosphere. The self regulation of biophysical processes in these spheres is crucial for global sustainability. However, modern farming practices have stressed the system to the extent that damaged C, N, and P cycles are threatening catastrophic consequences. High food-wastage coupled with high food price, high soil fertility zones but low crop productivity, and highly productive irrigated farming marred with ecological disasters are examples of global paradoxes associated with modern farming. High incidence of pesticide residues in soil and water bodies, low use efficiency of agricultural inputs,...
Tipo: Presentation
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/6900/version/1

Ajuvant effect of a Synthetic Aluminium - Magnesium Silicate on chloroquine phosphate, against Plasmodium berghei.
Provedor de dados: 17
Autores: madike ezeibe; obianuju obianuju Okoroafor; nnenna elendu-eleke; Augustine Ngene.
Abstract effect of a synthetic Aluminium - Magnesium Silicate (AMS) on antiplasmodial activity of chloroquine was tested. Plasmodium berghei-infected mice were treated with 7 mg/kg, 5 mg/kg and 3 mg/kg chloroquine, respectively. The two subgroups in each experiment were treated with chloroquine alone and with chloroquine in AMS respectively. Parasitaemia (%) of the group treated with 7 mg/kg was higher than that of the control. At 5 mg/kg, chloroquine treatment significantly reduced parasitaemia from 3.60 to 2.46 (P =0.01). Incorporating chloroquine in AMS significantly improved its ability to reduce P. berghei parasitaemia at 5 mgkg and at 3 mg/kg, from 2.46 0.21 to 1.57 0.25 (P = 0.01) and from 3.82 0.06 to 2.12 0.08 (P =0.01 ). It also increased...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6749/version/1

Aligning the top-level of SNOMED-CT with Basic Formal Ontology
Provedor de dados: 17
Autores: William Hogan.
Effective translational research requires automated analysis of large datasets collected by multiple researchers working at multiple locations.  Reliable, machine interpretation of-&amp;#x2014;and reasoning with&amp;#x2014;-large datasets assembled at different times and places by different researchers requires standard representations of data.  These representations are controlled, structured vocabularies also known as ontologies.  By far, the most successful ontology is the Gene Ontology (GO), used by bioinformatics researchers to annotate genomics data.  However, to address the phenotype side of translational research will require annotation of electronic medical record data and clinical research data with a clinical-phenotype ontology analogous to GO....
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2373/version/1

Alignment of Linear Biochemical Pathways Using Protein Structural Classification
Provedor de dados: 17
Autores: Sridhar Hariharaputran; Thoralf T&amp;#xf6;pel; Timm Oberwahrenbrock; Ralf Hofest&amp;#xe4;dt.
Metabolic, signaling and regulatory pathways form the basis of biological processes and are important for the analysis of cellular behavior and evolution. This paper presents an approach of aligning biochemical pathways on the basis of the structure of involved proteins and their classification. The suitable information is retrieved from an integrated database system.&amp;#xd;&amp;#xa;SIGNALIGN is available at: http://agbi.techfak.uni-bielefeld.de/signalign/index.jsp  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1943/version/1

Allele-specific primer based identification of dimeric alpha-amylase inhibitor
Provedor de dados: 17
Autores: Pradeep Sharma; Pooja Sharma; Manoj Saini; S. S. Singh.
Wheat is one of the most important staple food crops cultivated over 200 mha in the range of environment throughout the world. Wheat production must continue to increase by 2% annually, more particularly in developing world including south-east Asia. Besides increasing the inherent productivity of wheat, it is important to minimize the losses caused to production by various abiotic and biotic factors. Alpha&amp;#x2013;amylase inhibitors are attractive candidates for the control of seed weevils as these insects are highly dependent on starch as the energy source. They play an important role in the carbohydrate metabolism of many heterotrophic and autotrophic organisms. In this study, we aimed to make sequence comparison and phylogenetic relationship among...
Tipo: Poster
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/5596/version/1

Allelic Frequency of ABO And Rh D Blood Group Among The Banjara Backward Caste of Yavatmal District, Maharashtra , India
Provedor de dados: 17
Autores: Aravind B. Chavhan; Santosh S. Pawar; Mumtaz M. Baig.
The distribution of ABO blood groups and Rh(D) factor has been studied among the Banjara of Backward population of Yavatmal (Maharashtra). The A, B, O and AB blood group percentage were recorded as 24.54%, 33.82%, 29.64% and 12% respectively. The allele frequencies of O, A, B and AB groups in the combined data were found to be 0.5354, 0.2022 and 0.2624 respectively. The distribution of  Rh(D) group varies among the ABO blood groups. The Rh(D) positive allelic frequency was 0.8405 and the Rh(D) negative incidence was recorded as 02.55% in the studied population.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5482/version/1

Allelic Frequency of ABO And Rh D Blood Group Among The Banjara Caste Population of Akola District, Maharashtra , India
Provedor de dados: 17
Autores: Aravind B. Chavhan.
The distribution of ABO blood groups and Rh (D) factor has been studied among the Banjara Caste population of Akola District (Maharashtra). The O, A, B, and AB blood group percentage were recorded as 27.64%, 22.91%, 37.45% and 12% respectively. The Rh negative incidence was recorded as 02.55%. The allele frequencies of O, A, B and AB groups in the combined data were found to be 0.5196, 0.2880, and 0.1924 respectively and Rh (D) positive allelic frequency was 0.8405.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5771/version/1

Allergies, Asthma, and Eczema: Response to Disturbance of the Microbiota of the Newborn Gut
Provedor de dados: 17
Autores: Debra L. Wohl; William J. Curry.
*Background/Question/Methods*&amp;#xd;&amp;#xa;The birth of a child may include routine use of antibiotics or a delivery by cesarean section.  We applaud these medical advances for their direct benefits.  However, birthing practices have been shown to disrupt the colonization of the microbial gut in newborns, which may have long term consequences on the development of a child&amp;#x2019;s immune system resulting in atopies (i.e., asthma, allergies, and eczema).  Animal models and other research have been used to demonstrate that not only the presence, but also the community composition of the gut microbiota, is essential for normal immune development.  Furthermore, it has been established that there are differences in the intestinal microbiota of children...
Tipo: Presentation
Palavras-chave: Ecology; Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/3685/version/1

Allergological and toxicological risk assessment of genetically modified (GM) plants - Development of a model system
Provedor de dados: 17
Autores: Alain  Steinmann; Kristin  Entzian; Birgit  Gr&amp;#xfc;mmer; Udo  Meyer.
Technical advances in biotechnology lead to a rising number of genetically modified plants and derived food and feed. Therefore, the international interest in adequate and standardized analytical methods increases to assess health risks in a rapid and low cost manner.&amp;#xd;&amp;#xa;To address this issue a decision support system (DSS), which will be based on baseline data and thresholds of key parameters, is going to be established in the framework of a joint project (BioOK). Determination of the potential allergenicity or toxicity of novel proteins caused by the genetic modification compared to near isogenic variants (NIV) is a key issue in this context. For the development of DSS the model plant &amp;#x201c;potato&amp;#x201d; was used to compare...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4441/version/1

Allicin from garlic suppresses TNF-&amp;#x3b1; and augments IFN-&amp;#x3b3; expressions in monocyte cultures from patients with Vaginitis
Provedor de dados: 17
Autores: Najmul Islam; Jawed Iqbal; Nazarul Hasan; Zeeshan Fatima; Hamida Thakur; Nazia Hasan; Abbas Ali Mahdi; Tamkin Khan; Farzana Bano; Irfan Ahmad Ansari.
Objective: We tried to explore beneficial effects of allicin- a natural antioxidant from garlic in the possible management of vaginitis. &amp;#xd;&amp;#xa;Methods: Peripheral blood mononuclear cells (PBMC&amp;#x2019;s) were isolated from blood of patients having vaginal infections as well as normal healthy subjects as per our published protocol. Monocytes (MN&amp;#x2019;s) from above PBMC&amp;#x2019;s were adhered, rested overnight and cultured without or with varying doses of allicin (0-500 ng/ml). Some cultures received SN50 and SN50M (100 ug/ml). After 24 hrs cultures, the cells were harvested and the supernatants subjected to secreted TNF-&amp;#x3b1; and sIFN-&amp;#x3b3; assays by ELISA. Treated/untreated harvested cells were subjected to glutathione...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1560/version/1

Allosteric modulation of beta1 integrin function induces lung repair in animal model of emphysema.
Provedor de dados: 17
Autores: Rehab J. Al-Jamal; Linda Wilson; Chris J. Armit; Susan McIntyre; Mark Marsden; Steven D. Shapiro; David J. Harrison.
Emphysema is a progressive lung disease characterised by loss of lung parenchyma with associated functional changes including decreased tissue elastance. Here we report beta1 integrin is a novel target for tissue repair and regeneration in emphysema. We show a single dose of a monoclonal antibody against beta1 integrin induced both functional and structural reversal of elastase-induced lung injury in vivo, and we found that similar matrix remodelling changes occurred in human lung tissue. We also identified a potential mechanism of action as this  allosteric modulation of beta1 integrin inhibited elastase-induced caspase activation, F-actin aggregate formation and changes in cellular ATP levels. This was accompanied by maintenance of beta1?integrin levels...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/437/version/1

Alpha band oscillations track temporal orienting of attention
Provedor de dados: 17
Autores: Gustavo Rohenkohl; Anna Christina Nobre.
Introduction: Recent investigations using field-potential recordings in visual and auditory cortices have shown that oscillatory activity in neuronal ensembles become entrained to the timing of rhythmically presented stimuli according to their modality and location (Lakatos, Chen et al. 2007; Lakatos, Karmos et al. 2008; Lakatos, O&amp;#x27;Connell et al. 2009). In spite of the evidence showing the role of brain oscillations on forming predictions about forthcoming sensory events (for a review (Engel, Fries et al. 2001), little is known about the role of such oscillations in the temporal orienting of attention (Nobre 2001; Coull and Nobre 2008). To test the effect of temporal orienting of attention on early perceptual processing, motor selection, and...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4509/version/1

Altered cholesterol ester cycle in _ex vivo_ skin fibroblasts from Alzheimer patients
Provedor de dados: 17
Autores: Alessandra Pani; Sandra Dessi; Giacomo Diaz; Claudia Abete; Claudia Mulas; Claudia Norfo; Marirosa Putzolu; Maria Dolores Cannas; Christina Doriana Orru; Alessandra Mocali; Pier Luigi Cocco; Paolo La Colla; Francesco Paoletti.
Recent studies in both animal and cell models of Alzheimer&amp;#x27;s disease (AD) indicated that sub-cellular cholesterol distribution seems to regulate amyloid-beta (A[beta]) generation in the brain. In particular, cholesterol-esters (CE), rather than total cholesterol levels, appear directly correlated with A[beta] production. Here we observed that, similarly to brain cells, skin fibroblasts obtained from AD patients produce and accumulate more CE than skin fibroblasts from age-matched healthy controls do. AD fibroblasts also exhibited a 2 fold increase in the expression of ACAT1, in addition to lower levels of SREBP2, nCEH, Caveolin-1 and ABCA1 mRNA levels, all of which are involved in the CE cycle. HMGCoA-reductase and LDL-receptor mRNAs levels did...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1602/version/1

Altered copy gene function in plants following total intron replacement in precursor RNA
Provedor de dados: 17
Autores: Drew Schwartz.
Evidence is presented for two novel genetic mechanisms: total intron replacement in transcribedprecursor RNA by multiple short sequences and reverse transcription of the precursor RNA followedby incorporation into the genome as copy genes, some of which have acquired an altered function.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4307/version/1

Altruism among relatives and non-relatives
Provedor de dados: 17
Autores: Howard Rachlin; Bryan A. Jones.
The amount of their own monetary reward that undergraduate participants claimed they were willing to forgo, in order to give $75 to another person, decreased hyperbolically as social distance increased between the participant and the other person. Relatives tended to be ranked at closer social distances than were non-relatives. However, even at the same social distance, participants were willing to forgo significantly more money for the benefit of relatives than for the benefit of non-relatives. These results imply that altruism is determined by factors in addition to social distance.
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1565/version/1

Aluminium - Magnesium Silicate enhances antibacterial activity of Ampicillin trihydrate, against Salmonella gallinarum
Provedor de dados: 17
Autores: Madike Ezeibe; George Anosa; Okechi Okorie; Nnenna Elendu-Eleke; Obianuju Okoroafor; Augustine Ngene; Ogechukwu Chikelu.
Solutions of different concentrations, of Ampicillin trihydrate (AT) and of a formulation of AT in Aluminium Magnesium Silicate (AMS), were used for sensitivity test on Salmonella gallinarum cultures. Also, S. gallinarum-infected chicks were treated with; 10 mg / Kg (AT), 10 mg / Kg (AT in AMS), 7.5 mg / Kg ( AT), 7.5 mg /Kg (AT in AMS). Mean inhibition area, 28.39 mm produced by AT did not vary significantly (P ) from 26.36 mm produced by AT in AMS. However, 17.5 105 Salmonella gallinarum culture forming units per ml of bile of the untreated chicks and 3.4 105 (80.58 % reduction), 2.5 105 (85.7 % reduction) , 5.4 105 (69.2 % reduction ) and 0.38 105 (97.8 % reduction ) of the respective treated groups, showed AMS significantly (P 0.01) improved AT`s...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6814/version/1

Alzheimer&amp;#x27;s disease is TH17 related autoimmune disease against misfoded beta amyloid
Provedor de dados: 17
Autores: Wan-Jiung(Wan-Chung) Hu.
Alzheimer&amp;#x27;s disease is a common neurodegenerative disorder. However, its exact etiology is still unknown. There were several mechanisms proposed such as the tau hypothesis and amyloid hypothesis. However, there is evidence challenging the above two hypotheses. Here, I propose the immune-amyloid hypothesis as a mechanism for Alzheimer&amp;#x27;s disease. Th17 related autoimmunity contributes to the disease pathogenesis. Accumulation of misfolded beta amyloid can trigger heat shock protein which in turn induces TH17 immunity. By microarray analysis of peripheral blood mononuclear cells, there is up-regulation of many TH17 related molecules after Alzheimer&amp;#x27;s disease. After knowing the exact disease pathogenesis, we can develop new...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5934/version/1

Alzheimer&amp;#x27;s disease is TH17 related autoimmune disease against misfolded beta amyloid
Provedor de dados: 17
Autores: Wan-Jiung(Wan-Chung) Hu.
Alzheimer&amp;#x27;s disease is a common neurodegenerative disorder. However, its exact etiology is still unknown. There were several mechanisms proposed such as the tau hypothesis and amyloid hypothesis. However, there is evidence challenging the above two hypotheses. Here, I propose the immune-amyloid hypothesis as a mechanism for Alzheimer&amp;#x27;s disease. Th17 related autoimmunity contributes to the disease pathogenesis. Accumulation of misfolded beta amyloid can trigger heat shock protein which in turn induces TH17 immunity. By microarray analysis of peripheral blood mononuclear cells, there is up-regulation of many TH17 related molecules after Alzheimer&amp;#x27;s disease. After knowing the exact disease pathogenesis, we can develop new...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5934/version/2

Alzheimer&amp;#x27;s disease is TH17 related autoimmune disease against misfolded beta amyloid
Provedor de dados: 17
Autores: Wan-Jiung(Wan-Chung) Hu.
Alzheimer&amp;#x27;s disease is a common neurodegenerative disorder. However, its exact etiology is still unknown. There were several mechanisms proposed such as the tau hypothesis and amyloid hypothesis. However, there is evidence challenging the above two hypotheses. Here, I propose the immune-amyloid hypothesis as a mechanism for Alzheimer&amp;#x27;s disease. Th17 related autoimmunity contributes to the disease pathogenesis. Accumulation of misfolded beta amyloid can trigger heat shock protein which in turn induces TH17 immunity. By microarray analysis of peripheral blood mononuclear cells, there is up-regulation of many TH17 related molecules after Alzheimer&amp;#x27;s disease. After knowing the exact disease pathogenesis, we can develop new...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5934/version/3

Ambiguous Dependence Of Minimal Plant Generation Time On Nuclear DNA Content
Provedor de dados: 17
Autores: Victor B. Ivanov.
AMBIGUOUS DEPENDENCE OF MINIMAL PLANT GENERATION TIME ON NUCLEAR DNA CONTENT Victor B. Ivanov The minimum generation time (MGT) of plant development was suggested to depend on nuclear DNA content, which varies in plants over wide limits1. In ephemeral species with the shortest MGT, the average C values were significantly lower than in annual species, whereas the average C values in annual species were lower than those in perennial plants. However, nobody has paid attention to the ratio of annual to perennial species number as a function of C values. Here I show that with increasing C the ratio of annual to perennial species increases to C values equal to 7-8 pg (monocots) and 6-7 pg (eudicots) and then decreases and that the fraction of annuals is abundant...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4943/version/1

Amino acid features: a missing compartment of prediction of protein function
Provedor de dados: 17
Autores: Esmaeil Ebrahimie; Mansour  Ebrahimi; Mahdi  Ebrahimi.
Enormous computational efforts have been carried out to predict structure and function of protein. However, nearly all of these efforts have been focused on prediction of function based on primary nucleic acid sequence or modeling 3D structure of protein from its nucleic acid sequence. In fact, it seems that amino acid attributes, which is an intermediate phase between DNA/RNA and advanced protein structure, has been missed.&amp;#xd;&amp;#xa;From 2010, we examined the possibility of precise prediction of structural protein function based on amino acid features by improving the following three aspects of amino acid research: (1) Increasing the number of computationally calculated amino acid features, (2) Testing different feature selection (attribute...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6693/version/1

AMIS, The Article Minimum Information Standard
Provedor de dados: 17
Autores: Delphine Dauga.
The curation process is significantly slowed down by missing information in the articles analyzed (for example, the identity of the clones used to generate ISH probes, the precise sequences tested in reporter assays, etc..). To help authors ensure in the future that necessary information is present in their article, we defined the Article Minimum Information Standard (AMIS) guidelines. This standard describes for each experiment the mandatory information that should be mentioned in literature articles to facilitate the curation process. These guidelines extend the minimal information defined by the MISFISHIE format (Deutsch at al. 2008, _Nature Biotechnology_). This standard was deduced from the ANISEED curation pipeline (Tassy, Dauga, Daian, Sobral et al....
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5054/version/1

&amp;#x2206;N-p63 functions as an invasion, migration, and metastasis suppressor
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
The tumor suppressor p53 homologues, TA-p73, and p63 have been shown to function as tumor suppressors.  However, how they function as tumor suppressors remains elusive.  Expression of p63 is controlled by two distinct promoters.  Consequently, this results in two different gene products such as TA-(transactivation domain containing NH2 terminus) p63 and &amp;#x2206;N-(lacks NH2 terminus) p63.  It is generally thought that the TA-p63 functions as a tumor suppressor, while the &amp;#x2206;N-p73 functions as a proto-oncogene.  However, careful interpretation of the data concerning &amp;#x2206;N-p63 suggests that it could function as an invasion and metastasis/tumor suppressor in a cell context dependent manner.
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/4771/version/1

&amp;#x2206;N-p63 functions as an invasion, migration, and metastasis suppressor
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
The tumor suppressor p53 homologues, TA-p73, and p63 have been shown to function as tumor suppressors.  However, how they function as tumor suppressors remains elusive.  Expression of p63 is controlled by two distinct promoters.  Consequently, this results in two different gene products such as TA-(transactivation domain containing NH2 terminus) p63 and &amp;#x2206;N-(lacks NH2 terminus) p63.  It is generally thought that the TA-p63 functions as a tumor suppressor, while the &amp;#x2206;N-p73 functions as a proto-oncogene.  However, careful interpretation of the data concerning &amp;#x2206;N-p63 suggests that it could function as an invasion and metastasis/tumor suppressor in a cell context dependent manner.
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/4771/version/2

&amp;#x22;Dark Mediators&amp;#x22; of Proteins as Revealed by NMR in Water: Residue-selective Anion Bindings that are Masked by Pre-existing Buffer
Provedor de dados: 17
Autores: Jianxing Song; Linlin Miao; Haina Qin.
Ions are commonly believed to impose their effects on proteins by unspecific electrostatic screening. Here, by NMR we reveal that in water sulfate, chloride and thiocyanate are able to bind a well-folded WW domain at distinctive residues and affinities, which is surprisingly masked by the pre-existing buffer. Our study reveals that the specific anion binding is so ubiquitous and consequently no longer negligible in establishing &amp;#x22;postreductionist framework&amp;#x22; for protein biochemistry.
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6769/version/1

&amp;#x22;Ribopepzymes&amp;#x22; are probably a link from ribozymes to protein enzymes
Provedor de dados: 17
Autores: Yongjie Sheng; Dazhi Jiang; Zhen Zeng; Feng Pan; Jin Zhang.
The evolutionary relationship between RNA- and protein-based biocatalysts was key to the evolution of living systems. This relationship is thought to have depended upon the transfer of both genetic information and catalytic function in living systems. We investigated whether ribozymes could transfer genetic information and catalytic function at the chemical level. We identified a family of peptides encoded by ribozymes: 13-residue peptide encoded by the hammerhead ribozyme, a 19-residue peptide encoded by the genomic hepatitis delta virus (HDV+) ribozyme, a 25-residue peptide encoded by the antigenomic HDV (HDV-) ribozyme, a 15-residue peptide encoded by the smallest trans-acting genomic HDV (SHDV) ribozyme, and a 22-residue peptide encoded by an open...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1708/version/1

&amp;#x27;Kuthiru&amp;#x27; and &amp;#x27;Orkayama&amp;#x27; &amp;#x2013; Newly Identified Genetic Resources from Kerala, India for Salinity Tolerance in Indica Rice
Provedor de dados: 17
Autores: Vanaja Taliyil; K P. Mammootty.
Existence of genetic variability for salt tolerance within species is of paramount importance in crop improvement program. Pokkali land race of Kerala, India is the international  donor parent of most of the salinity tolerance breeding programs in rice. Here we report two new genetic resources, &amp;#x2018;Kuthiru&amp;#x2019; and &amp;#x2018;Orkayama&amp;#x2019; for salinity tolerance, from  Kaipad saline tracts of Kerala. They differ in their  morphological, physico-chemical characteristics and cooking qualities.  Panicles of these cultivars are long with bold grains. Duration of &amp;#x2018;Kuthiru&amp;#x2019; is 110 -120 days, and that of &amp;#x2018;Orkayama&amp;#x2019; is 135 -140 days. Molecular analysis revealed that the salinity tolerance mechanism...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4561/version/1

&amp;#x27;Magnetized&amp;#x27; brains are slower: The cognitive effects of fMRI
Provedor de dados: 17
Autores: Jack R. Foucher; Daniel Gounot; Bich-Thuy Pham; Corinne Marrer; Andre Dufour.
MRI is generally thought to have no impact on cognition. Although safety experiments have shown that MRI is not harmful, its finer effects have not been investigated. Because we repeatedly observed delayed response time during functional MRI (fMRI), we designed an experiment to confirm this effect and to identify its causal factor(s), including environment, noise, static magnetic field and/or gradient switch. Here we show that the participants had increased response times of +70 ms (up to +30%) in two different detection tasks, with most of this effect due to the 2 Tesla static magnetic field. The latter also specifically accounted for the longer time interval needed to detect two stimuli as occurring successively rather than simultaneously. These...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2443/version/1

An Advanced Clinical Ontology
Provedor de dados: 17
Autores: Riichiro Mizoguchi; Kouji Kozaki; Hiroko Kou; Ken Imai; Kazuhiko Ohe.
This article discusses a fundamental issues of medical ontology based on ontological theory. We focus on &amp;#x22;anatomical structure of organs&amp;#x22; and &amp;#x22;abnormal states in the human body&amp;#x22;. On the basis of the investigation, we distinguish organ-specific types from those independent of any organ to maximize the explicitness of ontology. The next feature of our ontology is to allow on-demand reorganization of is-a hierarchy of diseases instead of one fixed hierarchy to cope with various viewpoints which physician might have. We also take care of the notorious issue related to conflict of is-a and part-of relations.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3506/version/1

An Advanced Clinical Ontology
Provedor de dados: 17
Autores: Riichiro Mizoguchi; Hiroko Kou; Jun Zhou; Kouji Kozaki; Ken Imai; Kazuhiko Ohe.
This article discusses a fundamental issues of medical ontology based on ontological theory. We focus on &amp;#x22;anatomical structure of organs&amp;#x22; and &amp;#x22;abnormal states in the human body&amp;#x22;. On the basis of the investigation, we distinguish organ-specific types from those independent of any organ to maximize the explicitness of ontology. The next feature of our ontology is to allow on-demand reorganization of is-a hierarchy of diseases instead of one fixed hierarchy to cope with various viewpoints which physician might have. We also take care of the notorious issue related to conflict of is-a and part-of relations.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3498/version/1

An albumin-derived peptide scaffold capable of binding and catalysis
Provedor de dados: 17
Autores: Immacolata Luisi; Silvia Pavan; Giampaolo Fontanive; Alessandro Tossi; Fabio Benedetti; Adriano Savoini; Elisa Maurizio; Riccardo Sgarra; Daniele Sblattero; Federico Berti.
We have identified a 101-amino-acid polypeptide derived from the sequence surrounding the IIA binding site of human albumin. The polypeptide contains residues that make contact with ligands as warfarin in the parent protein, and eight cysteine residues to form disulfide bridges, which stabilize the polypeptide structure. Seventy-four amino acids are located in six [alpha]-helical regions, with the remaining amino acids forming six connecting coil/loop regions. Codon usage optimization was used to express a GST fusion protein in E. coli in yields as high as 4 mg/l. This fusion protein retains its structural integrity and aldolase activity, the ability to direct the stereochemical outcome of a diketone reduction, and its binding capacity to warfarin and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/6894/version/1

An ancient adaptive episode of convergent molecular evolution confounds phylogenetic inference
Provedor de dados: 17
Autores: Todd A. Castoe*; A.P. Jason de Koning*; Hyun-Min Kim; Wanjun Gu; Brice P. Noonan; Zhi J. Jiang; Christopher L. Parkinson; David D. Pollock.
Convergence can mislead phylogenetic inference by mimicking shared ancestry, but has been detected only rarely in molecular evolution. Here, we show that significant convergence occurred in snake and agamid lizard mitochondrial genomes. Most evidence, and most of the mitochondrial genome, supports one phylogenetic tree, but a subset of mostly amino acid-altering mitochondrial sites strongly support a radically different phylogeny. These sites are convergent, probably selected, and overwhelm the signal from other sites. This suggests that convergent molecular evolution can seriously mislead phylogenetics, even with large data sets. Radical phylogenies inconsistent with previous evidence should be treated cautiously.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2123/version/1

An apparent medieval stereogram incorporating a symbol for optical illusion
Provedor de dados: 17
Autores: John L. Cisne.
Stereograms mark a threshold in understanding visual perception. Modern study of stereopsis began with Wheatstone&amp;#x27;s invention of the stereogram and stereoscope (~ 1832), important tools in vision research and technical imagery ever since. Stereoscopic images formed with frieze and wallpaper patterns in illuminated Insular manuscripts such as the Book of Durrow (~ 680 CE), Lindisfarne Gospels (~ 700-720), and Book of Kells (~ 800) show that, long before spectacle-quality magnifying lenses (~ 1286), illuminators somehow copied multicolored, microscopically detailed designs _freehand_ with an accuracy unsurpassed in scientific instruments until the Renaissance (but well within the power of normally sighted humans&amp;#x27; stereoscopic...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3994/version/1

An approach able to escape the most common problem during protein Crystallization i.e. formation of salt crystal
Provedor de dados: 17
Autores: K. Awaneesh Singh; Patrick Celie; G. R. K. Rao; M. V. Jagannatham.
Formation and differentiation of salt crystal is a most common as well as challenging problem during protein crystallography. Although there are some methods used for their differentiation i.e. physical manipulation, birefringence, dye absorption and run a gel but all of them are totally depends on own perception and expertise as well as also require a good crystal (final stage crystal). To escape this problem the screening was done with PACT, JCSG and other automated screens as everyone do. But during optimization the additives/salts were ignored at first and optimization screen was made just based on different buffers and precipitant. After selecting suitable buffer, the type and percentage of precipitant was optimized. We got some ugly crystals and with...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4725/version/1

An artificial spiking synapse made of molecules and nanoparticles
Provedor de dados: 17
Autores: Fabien Alibart; Stephane Pleutin; David Guerin; Christian Gamrat; Dominique Vuillaume.
Molecule-based devices are envisioned to complement silicon devices by providing new functions or already existing functions at a simpler process level and at a lower cost by virtue of their self-organization capabilities, moreover, they are not bound to von Neuman architecture and this may open the way to other architectural paradigms. Here we demonstrate a device made of conjugated molecules and metal nanoparticles (NPs) which behaves as a spiking synapse suitable for integration in neural network architectures. We demonstrate that this device exhibits the main behavior of a biological synapse. These results open the way to rate coding utilization of the NOMFET in perceptron and Hopfield networks. We can also envision the NOMFET as a building block of...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3031/version/1

An assessment of organic solvent based equilibrium partitioning methods for predicting the bioconcentration behavior of perfluorinated sulfonic acids, carboxylic acids, and sulfonamides
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
SPARC, KOWWIN, and ALOGPS octanol-water partitioning (log K~ow~) and distribution (log D) constants were calculated for all C~1~ through C~8~ and the straight chain C~9~ through C~15~ perfluoroalkyl sulfonic acids (PFSAs) and carboxylic acids (PFCAs). Application of five established models for estimating bioconcentration factors (BCFs) were applied to the PFSA and PFCA log K~ow~ and log D data and compared to available field and laboratory BCF data. Wide variability was observed between the methods for estimating log K~ow~ and log D values, ranging up to several log units for particular congeners, and which was further compounded by additional variability introduced by the different BCF equations applied. With the exception of n-perfluorooctanecarboxylic...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3256/version/1

An attempt to understand Barstar, Barnase and Olfactory receptor protein folding problems using mathematical biological approach
Provedor de dados: 17
Autores: Arunava Goswami; Sk Sarif Hassan; Pabitra  Pal Choudhury.
Protein folding problem as attracted structural biologists immensely (1). Till date, correlation between X-ray crystallographic and NMR data are considered to be the best methods for determining structure of intra-cellular proteins. Generating crystals and finding correct experimental conditions for NMR are largly a gamble and resultant data processing highly time consuming. Even if, a large number of laboratories around the world and India make crystals of protein but majority of them fail to generate crystallographic data less than or equal to 10A resolution with currently available instruments. This means that X-ray crystallographic data have been generated from protein crystals with non-uniform lattices. We believe that a large portion of (chain of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4891/version/1

An emerging protagonist: Sodium Glucose Co-transporters (SGLTs) as a burgeoning target for the treatment of diabetes mellitus
Provedor de dados: 17
Autores: Danish Ahmed; Manju Sharma; Vikas  Kumar; Pankaj S Yadav.
Contemporary therapies to rationalize the hyperglycaemia in type 2 diabetes mellitus (T2DM) generally involve insulin-dependent mechanisms and lose their effectiveness as pancreatic b-cell function decreases to a greater extent. The kidney emerges out as a novel and potential target to trim down the T2DM. The filtered glucose is reabsorbed principally through the sodium glucose co-transporter-2 (SGLT2), a low affinity transport system, which is present at the luminal surface cells that cover the first segment of proximal tubules. Competitive inhibition of SGLT2 therefore represents an innovative therapeutic strategy for the treatment of hyperglycaemia and/or obesity in patients with type 1 or type 2 diabetes by enhancing glucose and energy loss through the...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7057/version/1

An evaluation of taxonomic name finding &amp;#x26; next steps in Biodiversity Heritage Library (BHL) developments
Provedor de dados: 17
Autores: Chris Freeland.
The Biodiversity Heritage Library (BHL) is an international consortium of natural history libraries that are actively scanning scientific literature from their collections and publishing the digitized content online at http://www.biodiversitylibrary.org. The presentation will cover updates on BHL progress thus far, including a review of the BHL portal application and services developed for bibliographic data exchange, as well as a roadmap of features scheduled for design and development. Of interest to taxonomists and bioinformaticians, the presentation will also cover a recently completed evaluation of taxonomic name finding algorithms, including TaxonFinder and FAT. Discussion will include a review of successes and failures in extracting taxonomic name...
Tipo: Presentation
Palavras-chave: Bioinformatics; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3372/version/1

An evolutionary approach to Function
Provedor de dados: 17
Autores: Phillip Lord.
The distinction between function and role is a vexed and difficult one. While the distinction appears to be useful, in practice it is hard to apply; this can be even worse when applying this distinction to biology. In this paper, I take an evolutionary approach, considering a series of examples, to develop and generate definitions for these concepts. I test them in practice against work performed on the Ontology for Biomedical Investigations (OBI). Finally, I give an axiomatisation and discuss methods for applying these definitions in practice.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3228/version/1

An exercise on developing an ontology-epistemology about schizophrenia and neuroanatomy
Provedor de dados: 17
Autores: Rodolpho Freire; Danilo Nunes Santos; Marcos  Vinicius dos Santos; Paulo Eduardo Santos.
This paper describes preliminary ideas on formalizing some concepts of neuroanatomy into ontological and epistemological terms. We envisage the application of this ontology on the assimilation of facts about medical knowledge about neuroimages from schizophrenic patients.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3483/version/1

An experimental and modelling exploration of the host-sanction hypothesis in legume-rhizobia mutualism
Provedor de dados: 17
Autores: Diana Marco; Juan Carbajal; Sergio Cannas; Rebeca Perez-Arnedo; Angeles Hidalgo-Perea; Jose Olivares; Jose  Ruiz-Sainz; Juan Sanju&amp;#xe1;n.
Despite the importance of mutualism as a key ecological process, its persistence in nature is difficult to explain since the existence of exploitative, &amp;#x27;cheating&amp;#x27; partners that could erode the interaction is common. By analogy with the proposed policing strategy stabilizing intraspecific cooperation, host sanctions against non N2 fixing, cheating symbionts have been proposed as a force stabilizing mutualism in legume-Rhizobium symbiosis. Following this proposal, penalizations would include decreased nodular rhizobial viability and/or early nodule senescence in nodules occupied by cheating rhizobia. In this work, we analyze the stability of Rhizobium-legume symbiosis when &amp;#x22;cheating&amp;#x22; strains are present, using an...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1964/version/1

An illusion induced by an illusion -perceptual filling-in of coloured negative afterimages
Provedor de dados: 17
Autores: Adam Geremek; Kai Hamburger; Lothar Spillmann.
Visual filling-in relates to a perceptual phenomenon in which a stimulus pattern apparently undergoes dynamic changes assuming an attribute such as colour, texture, or brightness from the surround. This perceptual completion effect has up to now been shown only for real images. Here, we present filling-in in negative afterimages, a phenomenon not yet reported. Using coloured disk-ring patterns for stimuli, we demonstrate that afterimage filling-in arises independently, and is not simply a replica of filling-in observed in real images. Such filling-in does not occur when the afterimage is elicited dichoptically, suggesting its emergence within the monocular visual pathway. In this way, our findings indicate that filling-in under certain conditions may...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3789/version/1

An innovative method for the biological control of Alternanthera philoxeroides
Provedor de dados: 17
Autores: Yusong Cao; Huiming Wang.
Biological invasion has become a serious global environmental problems and been considered as an important component of global change^1-2^. Invasions by alien species can have an impact at several levels of ecological complexity from genes to ecosystems^3-4^. Invasive alien species had seriously threated the biodiversity and natural ecosystems in China^5^, and caused economic losses by more than US$7 billion every year^6^. Alternanthera philoxeroides, commonly known as Alligator weed, is an invasive amphibious plant^7^. The effect of physical methods such as mechanical or artificial salvage, removal of A. philoxeroides were very limited. Moreover, these measure should be carried out very carefully or would easy lead to its rebound^8^. The mainly biological...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5267/version/1

An insight into the kinships of the fungi
Provedor de dados: 17
Autores: Riddhi Datta; Joy Sarkar; Krishnendu  Acharya.
The evolutionary origin of fungi is important in determining the phylogenetic relationships between fungi, animals and plants. However, determining the true relationship of fungi has been somewhat difficult owing to their simple morphology and presence of convergent characters. With the advent of newer molecular techniques, analysis of conserved protein sequences, cytochrome systems, mitochondrial and nuclear genetic material and rRNAs are being employed in elucidating   phylogenetic kinships among the eukaryotes. These emerging evidences suggest that the derivation of the fungi from plants or algae would require more evolutionary changes than its derivation from protozoa, the unicellular ancestor of the animals. To gain an overview of the current state of...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7095/version/1

An Integrated IGCC-CSS Design Course for Graduate Students in Petroleum Engineering
Provedor de dados: 17
Autores: Gioia Falcone; Behnam Jafarpour; Maria Barrufet.
A new graduate course on CO2 Capture and Uses was offered for the first time at Texas A&amp;#x26;M, Pet. Eng., in Fall 2008. &amp;#xd;&amp;#xa;A multidisciplinary team of instructors from the Pet. Eng. &amp;#x26; Chem. Eng. departments was assembled to ensure the appropriate expertise.&amp;#xd;&amp;#xa;The objective of the course is to let the students understand the need for / potential of Carbon Capture and Storage (CCS) &amp;#x26; Enhanced Oil Recovery (EOR).
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2627/version/1

An integrated solution for rapid biosensing combining linker free binding, freeze drying and high sensitivity ellipsometric detection
Provedor de dados: 17
Autores: Yongbai Yin; David R. McKenzie; Keith Fisher; Chuan Guo; Neil Nosworthy; Marcela M. Bilek.
A novel integrated biosensor methodology is proposed and demonstrated. The methodology utilizes a nitrogen-containing plasma polymer to achieve linker-free binding of biorecognition molecules that allows the sensor surface to be freeze dried for long shelf life under ambient conditions. The sensor is configured for single wavelength ellipsometric detection providing a low cost, versatile, and rapid sensing and diagnosis platform suitable for a wide range of applications and end-users. The merits of the methodology were demonstrated using three antigen-antibody pairs.
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2012
URL: http://precedings.nature.com/documents/6764/version/1

An intelligent liposome that may deliver drug molecules in a well controlled fashion
Provedor de dados: 17
Autores: Dumitru Popescu; Alin Gabriel Popescu.
The passage of molecules, especially large ones, through the cellular membrane is a very important problem for some biotechnological applications, such as drug delivery. The appearance of pores in the lipid bilayer following some controlled mechanisms may be an adequate and interesting way. Some pores, named stochastic pores, can appear due to structural and dynamic properties of lipid bilayer, but others may be favored by mechanical tension induced by different ways. Recently, a sequence of 30-40 pores was observed in the same vesicle, a pore at a time, which can appear in vesicles stretched by optical induced mechanical tension. There are two very interesting biotechnological applications that require the increase of membrane permeability: gene therapy...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2007
URL: http://precedings.nature.com/documents/1220/version/1

An offside position in football cannot be detected in zero milliseconds
Provedor de dados: 17
Autores: Francisco Belda Maruenda.
Errors when judging an offside position in football are very frequent. In the last years, several scientific papers have tried to explain the causes for human errors. When a referee or an assistant referee misjudges an offside position, it is thought to be caused by a human error. A human error means to carry out incorrectly an action we are physiologically qualified for. The hypothesis to be studied in this paper is if when judging an offside position it is possible to attribute errors to humans or to the fact that human physiology and the technical media are not capable of detecting an offside position. The offside rule has to be applied in real time, in zero milliseconds, in the precise moment when the ball is being passed, never 1 millisecond or even 1...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3835/version/1

An Olfactory Receptor Pseudogene whose Function emerged in Humans
Provedor de dados: 17
Autores: Peter Lai; Gautam Bahl; Maryse Gremigni; Valery  Matarazzo; Olivier Clot-Faybesse; Catherine Ronin; Chiquito J. Crasto.
Human olfactory receptor, hOR17-210, is identified as a pseudogene in the human genome. Experimental data has shown however, that the gene product of cloned hOR17-210 cDNA was able to bind an odorant-binding protein and is narrowly tuned for excitation by cyclic ketones. Supported by experimental results, we used the bioinformatics methods of sequence analysis, computational protein modeling and docking, to show that functionality in this receptor is retained due to sequence-structure features not previously observed in mammalian ORs. This receptor does not possess the first two transmembrane helical domains (of seven typically seen in GPCRs). It however, possesses an additional TM that has not been observed in other human olfactory receptors. By...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1290/version/1

An Ontology for Designing Models of Epidemics
Provedor de dados: 17
Autores: Geoffrey Frank; William Wheaton; Vesselina Bakalov; Phillip Cooley; Diane Wagener.
Models of epidemics allow decision makers to explore the consequences of different interventions. The Models of Infectious Disease Agent Study (MIDAS) project has been collecting studies, models, data supporting the models, and publications providing historical evidence about epidemics.&amp;#xd;&amp;#xa;An ontology has been developed for MIDAS to support the collection, documentation, and dissemination of models. It uses relations to link taxonomies (including a subset of the infectious disease ontology) that define the scope of its models and supporting documentation.&amp;#xd;&amp;#xa;The ontology is used to aid in the navigation process that is part of the user interface for identifying which studies and publications are available in the MIDAS repository...
Tipo: Presentation
Palavras-chave: Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3555/version/1

An Ontology To Represent Knowledge On Animal Testing Alternatives
Provedor de dados: 17
Autores: Thomas W&amp;#xe4;chter; Ursula G. Sauer; Andreas Doms; Barbara Grune; Michael R. Alvers; Horst Spielmann; Michael Schroeder.
EU Directive 86/609/EEC for the protection of laboratory animals obliges scientists to consider whether a planned animal experiment can be replaced, reduced or refined (3Rs principle). To meet this regulatory obligation, scientists must consult the relevant scientific literature prior to any experimental study using laboratory animals. More than 50 million potentially 3Rs relevant documents are spread over the World Wide Web, biomedical literature and patent databases. In April 2008, the beta version of Go3R (&amp;#x22;www.Go3R.org&amp;#x22;:http://www.Go3R.org), the first knowledge-based semantic search engine for alternative methods to animal experiments, was released. Go3R is free of charge and enables scientists and regulatory authorities involved in...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3148/version/1

An Ontology-Based Framework for Clinical Research Databases
Provedor de dados: 17
Autores: Richard H. Scheuermann; Megan Kong; Carl Dahlke; David Karp.
The Ontology-Based eXtensible data model (OBX) was developed to serve as a framework for the development of a clinical research database in the Immunology Database and Analysis Portal (ImmPort) system.  OBX was designed around the logical structure provided by the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI).  By using the logical structure provided by these two well-formulated ontologies, we have found that a relatively simple, extensible data model could be developed to represent the relatively complex domain of clinical research.  In addition, the common framework provided by the BFO should make it straightforward to utilize OBX database data dictionaries based on reference and application ontologies from the OBO...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3482/version/1

An open source LABVIEW platform for simulating image series of   fluorescent microtubules in gliding assays
Provedor de dados: 17
Autores: Lawrence J. Herskowitz; Steven J. Koch.
We describe an open-source LabVIEW software platform for generating simulated images of microtubules in gliding motility assays.  We describe how the software works and how to obtain the software.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4374/version/1

An optimized energy potential can predict SH2 domain-peptide interactions
Provedor de dados: 17
Autores: Zeba Wunderlich; Leonid Mirny.
Peptide recognition modules (PRMs) are used throughout biology to mediate protein-protein interactions, and many PRMs are members of large protein domain families.  Members of these families are often quite similar to each other, but each domain recognizes a distinct set of peptides, raising the question of how peptide recognition specificity is achieved using similar protein domains.  The analysis of individual protein complex structures often gives answers that are not easily applicable to other members of the same PRM family.  Bioinformatics-based approaches, one the other hand, may be difficult to interpret physically.  Here we integrate structural information with a large, quantitative data set of SH2-peptide interactions to study the physical origin...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1881/version/1

An OWL-DL Ontology for Classification of Lipids
Provedor de dados: 17
Autores: Hong-Sang Low; Christopher  J. O. Baker; Alexander Garcia; Markus R. Wenk.
Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids.
Tipo: Presentation
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3590/version/2

An OWL-DL Ontology for Classification of Lipids
Provedor de dados: 17
Autores: Hong Sang Low; Christopher J. O. Baker; Alex Garcia; Markus R. Wenk.
Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids.
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3542/version/1

An OWL-DL Ontology for Classification of Lipids
Provedor de dados: 17
Autores: Hong-Sang Low; Christopher  J. O. Baker; Alexander Garcia; Markus R. Wenk.
Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids.
Tipo: Presentation
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3590/version/1

An RNA _cis_-element upstream of the HMGA1a binding site affects exon exclusion caused by HMGA1a
Provedor de dados: 17
Autores: Kenji Ohe; Takayuki Manabe; Taiichi  Katayama; Masaya Tohyama; Akila Mayeda.
In addition to its characteristics as a DNA binding transcription factor, HMGA1a is known to bind RNA, sequence specifically and regulate aberrant splicing of the _Presenilin-2_ gene in sporadic Alzheimer&amp;#x2019;s disease^1,2^. We show here that an RNA _cis_-element, immediately upstream the HMGA1a binding site, induces exon inclusion upon mutating a GU sequence to CA. Psoralen mediated UV crosslinking showed U1 snRNP did not bind this sequence but oligonucleotide-mediated RNase H digestion showed it important for U1 snRNP to recognize the authentic 5&amp;#x2019; splice site. This sequence (5&amp;#x2019;-AAGUAC-3&amp;#x2019;) was tested for hnRNPA1 binding and function. Coimmunoprecipitation of endogenous HMGA1a and hnRNPA1 in HeLa nuclear extract,...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4119/version/1

An uncultured human-associated bacterium model
Provedor de dados: 17
Autores: Jorge M. Dinis; David E. Barton; Jamsheed Ghadiri; Deepa Surendar; Kavitha Reddy; Fernando Velasquez; Carol M. Chaffee; Wendy Lee; Helen Gavrilova; Hazel Ozuna; Samuel A. Smits; Cleber C. Ouverney.
The Bacteria Domain experienced an explosion of novel lineages identified within the last decade, especially of lineages made entirely of uncultured members. Since numerous cultivable bacteria have been shown to be instrumental in human development, health, and diseases, it is reasonable to speculate that strains from uncultured groups, which comprise nearly 80% of the human gut and 68% of human oral microbial consortia, participate in similar functions. The study of human-associated uncultured bacteria, however, has many practical limitations, such as access to patient samples, unpredictable microbial composition, and low relative abundance, all of which challenge experimental promptness and reproducibility. We propose that uncultured bacteria from...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/5757/version/1

Analysis and visualisation of RDF resources in Ondex
Provedor de dados: 17
Autores: Catherine Canevet; Artem Lysenko; Andrea Splendiani; Matthew Pocock; Chris Rawlings.
An increasing number of biomedical resources provide their information on the Semantic Web and this creates the basis for a distributed knowledge base which has the potential to advance biomedical research [1].  This potential, however, cannot be realized until researchers from the life sciences can interact with information in the Semantic Web. In particular, there is a need for tools that provide data reduction, visualization and interactive analysis capabilities.&amp;#xd;&amp;#xa;Ondex is a data integration and visualization platform developed to support Systems Biology Research [2]. At its core is a data model based on two main principles: first, all information can be represented as a graph and, second, all elements of the graph can be annotated with...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5430/version/1

Analysis of acceptance of bacillus to various heavy metals and antibiotics
Provedor de dados: 17
Autores: Yamini Singh  Sisodia; Vivek  Bajpai; Deeksha  Gaur; Pankaj Kumar  Jain.
The present study was carried out to systematically examine the pathogenic microorganisms in sewage samples isolated from the Shekhawati region of Rajasthan. In this survey, 26 bacterial strains were isolated and identified using biochemical and molecular methods. Molecular identification of isolates was done by DNA isolation, PCR amplification using 16S rDNA primer and partial sequencing of purified product after sequencing, out of 26, 10 sequences were submitted to NCBI. Out of these 10 isolates Bacillus pumilis, Bacillus subtilis and Bacillus licheniformis were taken for further studies. There is growing awareness of the need for development of new antimicrobial agents for the treatment of human, animal and plant diseases. Keeping this fact in mind, we...
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology; Molecular Cell Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7073/version/1

Analysis of Antarctic Ice Core Data (EPICA Dome C) with Flicker-Noise Spectroscopy
Provedor de dados: 17
Autores: Yuriy Polyakov; Jean Robert Petit; Serge Timashev.
Evolution of Earth&amp;#x2019;s climate system over the past 800,000 years represents a complex process with successions of uneven glacial and interglacial periods. The length, amplitudes, and development of each climate cycle depend on a number of different factors, including the orbital parameters attributed to insolation and the complex responses of the Earth system to solar radiation primarily through the amplification by Earth&amp;#x2019;s albedo and greenhouse gas and secondarily through a system of heat reservoirs, such as ice sheet and deep ocean, distributed throughout our planet. The purpose of this study is to analyze the transitions related to climate cycles in Antarctic ice core data (EPICA Dome C) of  deuterium composition and dust...
Tipo: Poster
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3341/version/1

Analysis of binding properties of VP2 protein of Human parvovirus B19 through in silico molecular docking
Provedor de dados: 17
Autores: Praneetha Amburu; Dibyabhaba  Pradhan; Vani  Priyadarshini; Munikumar Manne; Umamaheswari  Amineni.
Human parvovirus B19, a member of the Parvoviridae family, is a pathogen associated with a wide variety of diseases. Most commonly, it causes childhood rash erythema infectiosum, but in some cases more serious symptoms such as persistent arthropathy, critical failures of red cell production causing transient aplastic crisis, this infection in pregnancy causes hydrops fetalis and myocarditis. Traditional immunosuppressive therapy being unsuccessful, anti-viral therapy might be worthy of consideration. Functional annotation would provide role of viral proteome in its survival and pathogenic mechanisms. SVMProt functional family annotations of VP2 protein had deciphered its zinc-binding, coat protein, outer membrane, chlorophyll biosynthesis, DNA repair and...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5289/version/1

Analysis of Cancer Omics Data In A Semantic Web Framework
Provedor de dados: 17
Autores: Matthew Holford; James P. McCusker; Kei Cheung; Michael Krauthammer.
Our work concerns the elucidation of the cancer (epi)genome, transcriptome and proteome to better understand the complex interplay between a cancel cell&amp;#x27;s molecular state and its response to anti-cancer therapy.  To study the problem, we have previously focused on data warehousing technologies and statistical data integration.  In this paper, we present recent work on extending our analytical capabilities using Semantic Web technology.  A key new component presented here is a SPARQL endpoint to our existing data warehouse.  This endpoint allows the merging of observed quantitative data with existing data from semantic knowledge sources such as Gene Ontology (GO).  We show how such variegated quantitative and functional data can be integrated and...
Tipo: Presentation
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5391/version/1

Analysis of circadian pattern reveals tissue-specific alternative transcription in leptin signaling pathway
Provedor de dados: 17
Autores: Andrey Ptitsyn; Jeffrey Gimble.
*Background*&amp;#xd;&amp;#xa;It has been previously reported that most mammalian genes display a circadian oscillation in their baseline expression. Consequently, the phase and amplitude of each component of a signal transduction cascade has downstream consequences. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Results*&amp;#xd;&amp;#xa;We report our analysis of alternative transcripts in the leptin signaling pathway which is responsible for the systemic regulation of macronutrient storage and energy balance. We focused on the circadian expression pattern of a critical component of the leptin signaling system, suppressor of cytokine signaling 3 (SOCS3). On an Affymetrix GeneChip 430A2 microarray, this gene is represented by three probe sets targeting different...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/858/version/1

Analysis of DNA structure as a 2D random walk by complex wavelet transform
Provedor de dados: 17
Autores: Eugene B. Postnikov; Alexander Y. Loskutov; Sergey A. Larionov; Evgeny V. Ryadchenko; Roman V. Kiseliov.
We propose the original method of the time-scale wavelet analysis of DNA sequence represented as a 2D walk on a complex plane. Namely, we consider the mapping of two irreducible A &amp;#x2212; T and G &amp;#x2212; C  sequences into a walk trajectory in the plane AGTC (firstly proposed by M. Gates) as a unique complex-valued function. &amp;#xd;&amp;#xa;    This function is processed with the new algorithm of the continuous wavelet transform with the Morlet wavelet. This method is based on the representation of the transform&amp;#x2019;s result as a solution of the specific Cauchy problem for the system of PDE. &amp;#xd;&amp;#xa;    As an example, we applied the described algorithm to a part of the telomer region of the 22 human chromosome and demonstated...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1461/version/1

Analysis of DTC nutrigenetic services in Italy: state of the art, agreement to the ESHG statement and future outlooks
Provedor de dados: 17
Autores: Vincenzo Cinque; Fabio Acquaviva; Paola Vergara; Alessandra Cianflone; Imma Castaldo; Antonella Monticelli; Sergio Cocozza; Michele Pinelli.
Background: In both USA and Europe operate companies selling Direct-to-consumer genetic tests (DTC). These tests are offered to healthy people aiming to identify predispositions to complex diseases and to take preventive measures. Several DTC-nutrigenetic tests (DNTs) are available on the market. They propose the definition of a personalized diet, on the basis of the investigated genetic variants, which would reduce the risk of developing those diseases which have been associated to specific genetic markers. However, the risk/benefit balance of exposing unselected population to genetic testing without any medical surveillance is far from be established. Furthermore, it lacks an accepted procedure to select which genetic markers needs to be investigated, to...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2012
URL: http://precedings.nature.com/documents/7135/version/1

Analysis of Endocrine Disruption in Southern California Coastal Fish using an Aquatic Multi-Species Microarray
Provedor de dados: 17
Autores: Michael E. Baker; Barbara Ruggeri; James Sprague; Colleen Eckhardt; Jennifer Lapira; Ivan Wick; Laura Soverchia; Massimo Ubaldi; Alberta M. Polzonetti-Magni; Doris Vidal-Dorsch; Steven Bay; Joseph R. Gully; Jesus A. Reyes; Kevin M. Kelley; Daniel Schlenk; Ellen C. Breen; Roman &amp;#x160;&amp;#xe1;&amp;#x161;ik; Gary Hardiman.
BACKGROUND:  Endocrine disruptors include plasticizers, pesticides, detergents and pharmaceuticals.  Turbot and other flatfish are used to characterize the presence of chemicals in the marine environment.  Unfortunately, there are relatively few genes of turbot and other flatfish in GenBank, which limits the use of molecular tools such as microarrays and qRT-PCR to study disruption of endocrine responses in sentinel fish captured by regulatory agencies.&amp;#xd;&amp;#xa;OBJECTIVES:  A multi-gene cross species microarray was fabricated as a diagnostic tool to screen the effects of environmental chemicals in fish, for which there is minimal genomic information.  The array included genes that are involved in the actions of adrenal and sex steroids, thyroid...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Genetics &amp; Genomics; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2823/version/1

Analysis of feral pig (Sus scrofa) movement in a Hawaiian forest ecosystem using GPS satellite collars
Provedor de dados: 17
Autores: Lasha-Lynn  H. Salbosa; Dr. Christopher A. Lepczyk.
The ecosystem altering impacts of feral pigs have been widely documented around the world.  However, a general framework for their control and management has been lacking, especially in island ecosystems.  One reason for this lack of management is that we have little knowledge of how pigs move through different island ecosystems, especially ones that are topographically challenging such as Hawai&amp;#x201b;i.  With recent advances in telemetry and movement modeling, it is now becoming practical to understand where these large introduced animals are moving and how they are using habitat.  Hence, the primary goal of this study is to understand feral pig movement in terms of terrain, slope restrictions, and distance traveled beyond a natal site, within an...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3903/version/1

Analysis of Genetic Interaction Maps Reveals Functional Pleiotropy
Provedor de dados: 17
Autores: Shuye Pu; Karen Ronen; James Vlasblom; Jack Greenblatt; Shoshana J. Wodak.
Epistatic or genetic interactions, representing the effects of mutations on the phenotypes caused by other mutations, can be very helpful for uncovering functional relationships between genes. Recently, the Epistasis Miniarray Profile (E-MAP) method has emerged as a powerful approach for identifying such interactions systematically. As part of this approach, hierarchical clustering is used to partition genes into groups on the basis of the similarity between their global interaction profiles.  Here we present an original biclustering algorithm for identifying groups of functionally related genes from E-MAP data in a manner that allows individual genes to be assigned to more than one functional group. This enables investigation of the pleiotropic nature of...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2182/version/1

Analysis of Human Spleen Contamination
Provedor de dados: 17
Autores: Martin Kopani; Martin Weis; Jan Jakubovsky.
Besides carbon, oxygen and nitrogen, numerous other elements and their compounds are significant in the body of humans and other animals. Accumulation of some elements and their compounds is recognized by clinical and biochemical evaluation. The physical-chemical properties and topical characteristics of elements in tissues may play a crucial role in evaluation their effect on human body. The ^57^Fe M&amp;#xf6;ssbauer measurement was used for evaluation of iron&amp;#x2013;oxide biomagnetic nanoparticles composition and properties. Absorption spectra of the powdered spleen recorded at 77K and 300K were measured and subsequently analyzed. From fitted data it is possible to obtain material composition as well as discuss the mean particle size (received from...
Tipo: Poster
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1408/version/1

Analysis of Nebivolol hydrochloride and Valsartan in Pharmaceutical Dosage Form by High Performance Thin Layer Chromatographic Method
Provedor de dados: 17
Autores: Shradhanjali Singh; Anil K. Singh; Shanti B. Mishra; Alok Mukerjee; Mrinalini C. Damle.
A simple, accurate and precise high performance thin layer chromatographic method has been developed for the estimation of Valsartan and Nebivolol hydrochloride simultaneously from a tablet dosage form. The method employed silica gel 60 F254 pre-coated plates as stationary phase and a mixture of Ethyl acetate: Methanol: Ammonia (6.5:2.5:0.5 %v/v/v) as mobile phase. Densitometric scanning was performed at 280 nm using a Camag TLC scanner 3. Beer&amp;#x2019;s law was obeyed in the concentration range of 800ng/spot-2400ng/spot for Nebivolol hydrochloride and 200ng/spot-1000ng/spot for Valsartan. The Retention factor for Nebivolol hydrochloride is 0.75 &amp;#xb1; 0.04 and is 0.27 &amp;#xb1; 0.01 for Valsartan . The method was validated as per ICH Guidelines,...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6134/version/1

Analysis of N-Glycosylation Sites in HIV glycoprotein 160
Provedor de dados: 17
Autores: Rajendra Mandage.
HIV infection is a condition caused by the human immunodeficiency virus. The condition gradually destroys the immune system, which makes it harder for the body to fight infections. HIV presents a complex knot for scientists to unravel. An envelope protein of the human HIV that is encoded by the env gene contains numerous glycosylation sites. It serves as a precursor for both the GP120 and the GP41. Here statistical investigation was done to study the sequential aspects of amino acids around the N-glycosylated protein from HIV virus. Sequences containing N-glycosylated asparagine were selected from the uniprot database of N-glycosylated proteins. The frequency of occurrence of amino acid residues around the glycosylated asparagine showed that there are...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5571/version/1

Analysis of plant metabolites &amp;#x2013; the baseline-threshold principle
Provedor de dados: 17
Autores: Katja  Neubauer; Jenny Bandomir; Anett  Grunenberg; Andreas  M&amp;#xfc;ller; Udo  Kragl; Kerstin  Schmidt.
With the environmental risk assessment (ERA) for genetically modified plants (GMP) the identification of equivalence or differences in the composition of ingredients of GMPs and non-GMPs has to be investigated. The strategy is based upon the idea that traditionally cultivated crops have been used safely for many years, thus every divergence within the compounds of a GMP in contrast to its non-GMP counterpart could refer to a risk and has to be further analysed.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The BioOK company offers the opportunity to analyse very different aspects from the ERA of GMPs in one hand. Beside toxicological analysis and the determination of environmental effects via soil analysis, we can look into several plant metabolites to identify...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4439/version/2

Analysis of plant metabolites &amp;#x2013; the baseline-threshold principle
Provedor de dados: 17
Autores: Katja  Neubauer; Jenny Bandomir; Anett  Grunenberg; Andreas  M&amp;#xfc;ller; Udo  Kragl; Kerstin  Schmidt.
With the environmental risk assessment (ERA) for genetically modified plants (GMP) the identification of equivalence or differences in the composition of ingredients of GMPs and non-GMPs has to be investigated. The strategy is based upon the idea that traditionally cultivated crops have been used safely for many years, thus every divergence within the compounds of a GMP in contrast to its non-GMP counterpart could refer to a risk and has to be further analysed.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The BioOK company offers the opportunity to analyse very different aspects from the ERA of GMPs in one hand. Beside toxicological analysis and the determination of environmental effects via soil analysis, we can look into several plant metabolites to identify...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4439/version/1

Analysis of Sustainable Water Resources Management (SWRM) in Agriculture
Provedor de dados: 17
Autores: Ahmad Reza Ommani; Mohammad Chizari.
The purpose of this research was analysis Sustainable Water Resources Management (SWRM) in agriculture of Khouzestan Province of Iran. The research method was quantitative research. Total population of experts in the study included all agricultural extension experts (N=96) of Agricultural-Jihad Organization of Khuzestan Province, Iran. Based on frequency of respondents about importance rate of supportive policies regarding SWRM in agriculture, 70.8% of respondents stated that encouraging farmers for using sustainable methods had very high importance. In reference to the frequency of respondents about extension system roles on realization of SWRM dimensions in agriculture, 52.8% of respondents stated conservation of water resources had very high importance...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/4046/version/1

Analyzing local image statistics via maximum-entropy constructions
Provedor de dados: 17
Autores: Jonathan D. Victor; Daniel J. Thengone; Mary M. Conte.
Because the space of signals that the visual system encounters is high-dimensional, investigations of visual processing and perception must utilize a sampling strategy.  One kind of approach begins with a class of models for input-output relations, and then chooses a stimulus ensemble such as white noise that enables efficient determination of model parameters.  A second kind of approach begins with the explicit recognition that it is important to understand the visual system in the context of the inputs under which it functions and evolves; this motivates the use of naturalistic stimulus ensembles.  Neither approach alone is sufficient: models built from ensembles such as white noise provide only a fair account of responses to natural scenes, and the...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5794/version/1

Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are
Provedor de dados: 17
Autores: Shi Huang.
There exists a remarkable correlation between genetic distance and time of species divergence as inferred from fossil records.  This observation has provoked the molecular clock hypothesis. However, data inconsistent with the hypothesis have steadily accumulated in recent years from studies on extant organisms.  Here the published DNA and protein sequences from ancient fossil specimens were examined to see if they would support the molecular clock hypothesis.  The hypothesis predicts that ancient specimens cannot be genetically more distant to an outgroup than extant sister species are.  Also, two distinct ancient specimens cannot be genetically more distant than their extant sister species are.  The findings here did not support these predictions....
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1676/version/1

Ancient fossil specimens of extinct species are genetically more distant to an outgroup than extant sister species are
Provedor de dados: 17
Autores: Shi Huang.
There exists a remarkable correlation between genetic distance as measured by protein or DNA dissimilarity and time of species divergence as inferred from fossil records.  This observation has provoked the molecular clock hypothesis. However, data inconsistent with the hypothesis have steadily accumulated in recent years from studies of extant organisms.  Here the published DNA and protein sequences from ancient fossil specimens were examined to see if they would support the molecular clock hypothesis.  The hypothesis predicts that ancient specimens cannot be genetically more distant to an outgroup than extant sister species are.  Also, two distinct ancient specimens cannot be genetically more distant than their extant sister species are.  The findings...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1676/version/2

Ancient Trephinations in Neolithic People - Evidence for Stone Age Neurosurgery?
Provedor de dados: 17
Autores: Juergen Piek; Gundula Lidke; Thomas Terberger.
The authors present the case of a late neolithic skull (14C dating: 1940 calBC) found 1921 at B&amp;#xf6;lkendorf, 60 km north-easterly of Berlin. It shows a left frontal trephination (53 x 50 mm) and additionally a left temporo-occipital depressed skull fracture (both survived). Microscopic and 3D-CT analyses strongly suggest that the trephination has been performed for medical purposes.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1615/version/1

Androgen Receptor and Vasopressin Receptor (AVPR1a) Genetic Polymorphisms are not associated with Marital Status or Fertility among Ariaal Men of Northern Kenya
Provedor de dados: 17
Autores: Peter B. Gray; Dan T. A. Eisenberg; Benjamin C. Campbell.
A growing body of scholarship implicates testosterone and vasopressin in male reproductive behavior, including in humans. Since hormones exert their effects through their respective receptors, an open question has been whether genetic polymorphisms in the androgen receptor and vasopressin 1a receptor (AVPR1a) impact human male social behavior. Here, we sought to test for associations between polymorphisms in the coding region of the androgen receptor and promoter region of AVPR1a in relation to marital status and fertility among pastoralist Ariaal men of northern Kenya. None of the three polymorphisms were related to marital status (single, monogamously married, polygynously married) or fertility (number of current living children). We discuss these null...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3208/version/1

Angiogenesis and Vasculogenesis at 7-Day of Reperfused Acute Myocardial Infarction
Provedor de dados: 17
Autores: Sheng  Kang; Yue-jin Yang; Qing-zhi Wang; Yue L. I. Li; Yi Tian; Yu-tong Cheng; Wei-feng Shen.
Objectives &amp;#xd;&amp;#xa;This study is to investigate the angiogenesis and vasculogenesis at the first week of reperfused acute myocardial infarction (AMI).&amp;#xd;&amp;#xa;Methods &amp;#xd;&amp;#xa;16 of mini-swines (20 to 30 Kg) were randomly assigned to the sham-operated group and the AMI group. The acute myocardial infarction and reperfusion model was created and the pig tail catheter was performed to monitor hemodynamics before left anterior descending coronary artery (LAD) occlusion, 90 min of LAD occlusion and 120 min of LAD reperfusion. Pathologic myocardial tissue was collected at 7-day of LAD reperfusion and further assessed by immunochemistry, dual immunochemistry, in-situ hybridization, real-time quantitative polymerase chain reaction and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2066/version/1

Angiogenesis in Chronic Obstructive Pulmonary Disease
Provedor de dados: 17
Autores: Alessandro Matarese; Gaetano Santulli.
Angiogenesis is a crucial component of lung pathophysiology, not only in cancer but also in other disorders, such as chronic obstructive pulmonary disease (COPD). In COPD angiogenesis is definitely able to control and orchestrate the progression of airway remodeling. Herein, we provide several remarkable translational aspects of angiogenesis in COPD, exploring both basic and clinical research in this field. Indeed, we present a number of pro- and anti-angiogenic factors, which can be also used as potential biomarkers to monitor disease progression. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This pre-print has subsequently been published at http://www.unisa.it/uploads/7100/06.pdf
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7112/version/1

Angiotensinergic innervation of rat and human mesenteric resistant blood vessels
Provedor de dados: 17
Autores: Jaspal Patil; Eva Heiniger; Thomas Schaffner; Oliver Muhlemann; Hans Imboden.
In contrast to the current believe that angiotensin II (Ang II) only interacts with the sympathetic nervous system (SNS) as a circulating hormone, we document here the existence of an endogenous renin-angiotensin system (RAS) in the sympathetic coeliac ganglion and the angiotensinergic innervation with mesenteric resistant blood vessels. Our findings indicate that Ang II is synthesized inside the neurons of sympathetic coeliac ganglion and may act as an endogenous neurotransmitter locally on the mesenteric resistant blood vessels.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/354/version/1

Anhedonia in the shadow of chronic social defeat stress, or When the experimental context matters
Provedor de dados: 17
Autores: Natalia P. Bondar; Irina L. Kovalenko; Damira F. Avgustinovich; Dmitry A. Smagin; Natalia N. Kudryavtseva.
One of the core symptoms of major depression in human is anhedonia. For that reason, one of the main requirements towards experimental depression models is that they be able to demonstrate anhedonia in animals, that have been exposed to stressful events, and other behavioral changes attributable to a depression-like state. However, the results presented in the literature are contradictory: sweet solution intake, which is considered as a parameter of hedonic/anhedonic behavior in animals, responds quite differently to stressful situations in that it is either unaffected or increased or decreased. Different experimental designs used for the study of anhedonia in male mice exposed to chronic social defeat stress were tried to understand the reasons for so...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2682/version/1

Animal emergence during Snowball Earths by thermosynthesis in submarine hydrothermal vents
Provedor de dados: 17
Autores: Anthonie W. J. Muller.
Darwin already commented on the lateness in the fossil record of the emergence of the animals, calling it a valid argument against his theory of evolution^1^. This emergence of the animals (metazoans: multicellular animals) has therefore attracted much attention^2-5^. Two decades ago it was reported that extensive global glaciations (Snowball Earths) preceded the emergence^6-7^. Here we causally relate the emergence and the glaciations by invoking benthic sessile^8-11^ thermosynthesizing^12-13^ protists that gained free energy as ATP while oscillating in the thermal gradient between a submarine hydrothermal vent^14^ and the ice-covered ocean. During a global glaciation their size increased from microscopic to macroscopic due to the selective advantage of a...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3333/version/2

Animal emergence during Snowball Earths by thermosynthesis in submarine hydrothermal vents
Provedor de dados: 17
Autores: Anthonie W. J. Muller.
Darwin already commented on the lateness in the fossil record of the emergence of the animals, calling it a valid argument against his theory of evolution^1^. This emergence of the animals (metazoans: multicellular animals) has therefore attracted much attention^2-5^. Two decades ago it was reported that extensive global glaciations (Snowball Earths) preceded the emergence^6-7^. Here we causally relate the emergence and the glaciations by invoking benthic sessile^8-11^ thermosynthesizing^12-13^ protists that gained free energy as ATP while oscillating in the thermal gradient between a submarine hydrothermal vent^14^ and the ice-covered ocean. During a global glaciation their size increased from microscopic to macroscopic due to the selective advantage of a...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3333/version/1

ANN Based Virtual Classification Model for Discriminating Active and Inactive Withanolide E Analogs against  Human Breast Cancer Cell Line MCF-7
Provedor de dados: 17
Autores: Om Prakash; Feroz Khan; R.S. Sangwan.
Withanolides are a group of natural C-28 steroids built on an ergostane skeleton and classified into two major groups according to their structural skeleton: (a) compounds with a beta-oriented side chain and (b) compounds with an alpha-oriented side chain. Withanolide E represents one of the members of the latter group. Classification of active compounds on the basis of pharmacophore against specific cancer cell line poses a serious concern at the primary stage of virtual screening. To overcome this problem we have developed an artificial neural network based virtual screening model for discriminating active and non-active Withanolide-E-like derivatives or analogs against human breast cancer cell line MCF-7. In the present work, a 2D chemical descriptors...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6616/version/1

Annotated Manhattan plots and QQ plots for GWAS using R, Revisited
Provedor de dados: 17
Autores: Stephen D. Turner.
This manuscript provides software and a tutorial for creating manhattan plots and QQ plots for genome-wide association studies using the R statistical computing environment.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6070/version/1

Annotating Whole Genome Sequencing in COSMIC (The Catalogue of Somatic Mutations in Cancer)
Provedor de dados: 17
Autores: C Y Kok; S A Forbes; N Bindal; S Bamford; C G Cole; M Jia; D Breare; R Shepherd; A Menzies; K Leung; J Teague; M R Stratton; P A Futreal.
&amp;#x22;COSMIC, the Catalogue Of Somatic Mutations In Cancer&amp;#x22;:http://www.sanger.ac.uk/cosmic is designed to store and display somatic mutation information relating to human cancers, combining detailed information on publications, samples and mutation types. The information is curated both from the primary literature and the laboratories at the Cancer Genome Project, Sanger Institute, UK, and then semi-automatically entered into the COSMIC database. The v47 release (May 2010) contained the curation of 9202 papers describing 116,977 mutations across 466,851 samples. In order to provide consistent annotation of the data, COSMIC has developed a classification system for cancer histology and tissue ontology, and adapted HGVS mutation nomenclature...
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5106/version/1

Annotation and Curation of the Protein Data Bank
Provedor de dados: 17
Autores: Jasmine Young; RCSB PDBj PDBe  Protein Data Bank.
The Protein Data Bank (PDB) is the worldwide repository for experimentally determined 3D structures of biological macromolecules. Established in 1971 with just seven structures, it presently includes more than 56,000 entries. To maintain the highest standards in curation and processing, the members of the worldwide Protein Data Bank (wwPDB) collaborate in data annotation and the development of procedures, tools, and resources. Annotation-related issues, particularly those impacted by new developments&amp;#xd;&amp;#xa;in structural biology, are critically reviewed at in-person and virtual meetings regularly and frequently. Comprehensive documentation of the procedures, formats, and related data dictionaries used in data annotation are available at the wwPDB...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3379/version/1

Annotation of SBML Models Through Rule-Based Semantic Integration
Provedor de dados: 17
Autores: Allyson L. Lister; Phillip Lord; Matthew  Pocock; Anil Wipat.
*Motivation:* The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Here, we present a method using off-the-shelf semantic web technology which enables this process: the heterogeneous data sources are first syntactically converted into ontologies; these are then aligned to a small domain ontology by applying a rule base. Integrating resources in this way can accommodate multiple formats with different semantics; it provides...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3286/version/1

Annotation-based meta-analysis of microarray experiments
Provedor de dados: 17
Autores: Jie Zheng; Junmin Liu; Elisabetta Manduchi; Christian J. Stoeckert, Jr.
We are developing software applications to perform meta-analysis of microarray experiments based on standardized experiment annotations aiming to identify similar experiments and cluster experiments. The applications were tested on files obtained from the ArrayExpress public repository. Annotation terms were used to compute experiment dissimilarities to find experiments related to a query experiment. These applications may motivate efforts of bench biologists to better annotate experiments.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3569/version/1

Annual cycle of aerosol backscatter coefficient and aerosol mixed layer height above Neuch&amp;#xe2;tel (Switzerland, 47.00&amp;#xb0;N, 6.95&amp;#xb0;E)
Provedor de dados: 17
Autores: Manoj K Srivastava; Max Frioud; Renoud Matthey; Valentin  Mitev.
Due to the complexity of the direct and indirect effects of the atmospheric aerosols on the air quality and atmospheric radiation balance, complementary methods are necessary to assess the aerosol optical properties. In this sense the backscatter lidar methods are critical in aerosol vertical distribution study. This work presents the annual cycle of aerosol backscatter coefficient (ABC) and aerosol mixed layer (AML) height over Neuch&amp;#xe2;tel, Switzerland (47.00 N; 6.950 E, 485 m asl). The study is performed by a ground based backscatter lidar operating at 532 nm wavelength as part of  EARLINET program of EU. Atmospheric layering for this study is based on a classification of lower atmosphere from 1 km to 2 km above sea level (asl) and from 2 km to 5...
Tipo: Poster
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6425/version/1

Annual population rhythm of Anopheles mosquitoes in Indian subcontinent
Provedor de dados: 17
Autores: Mohit Bhardwaj; Leena Bharadwaj; Kritika Trigunayat; Madan Mohan Trigunayat.
Several organism show a rhythm based behavior in their life. Mosquitoes are surviving successfully since ancient time on earth while lots of biological creatures have been extinct. Thus it is interesting to study their population load. Climatic conditions affect mosquito population significantly so on the basis of malaria cases their population is estimated in present study in Indian geographical scenario. In this study it was found that their annual population load show a scientific rhythm. A schematic wave form representation is also presented here to show mosquito population load. This study will be helpful in malaria vector eradication and health care policies. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4569/version/1

Annual population rhythm of Anopheles mosquitoes in Indian subcontinent
Provedor de dados: 17
Autores: Mohit Bhardwaj; Leena Bharadwaj; Kritika Trigunayat; Madan Mohan Trigunayat.
Several organisms show a rhythm based behavior in their life. Mosquitoes are surviving successfully since ancient time on earth while lots of biological creatures have been extinct. Thus it is interesting to study their population load. Climatic conditions affect mosquito population significantly so on the basis of malaria cases their population is estimated in present study in Indian geographical scenario. In this study it was found that their annual population load show a scientific rhythm. A schematic wave form representation is also presented here to show mosquito population load. This study will be helpful in malaria vector eradication and health care policies. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4569/version/2

Ant Species Richness Around Amravati City Maharashtra, India
Provedor de dados: 17
Autores: Aravind B. Chavhan; Santosh S. Pawar; Mumtaz M. Baig.
Ants deserve a special place in the study of ecology, including behavior, given their species richness, social habits, and high densities, contributing to much of the animal biomes on earth (Gadagkar et.at. 1993). As ants can be studied virtually everywhere from forest interiors below ground, right up to the kitchen, we attempted a study to assess the ant species richness in a variety of habitats in and around Amravati city. The prime objective of this study is to prepare a partial checklist of ants of Amravati and to compare species richness between selected study sites. Eight study sites with different levels and types of vegetation were selected for the study.&amp;#xd;&amp;#xa;We employed an &amp;#x201c;all out search&amp;#x201d; method for collection...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5491/version/1

AntEpiSeeker2.0: extending epistasis detection to epistasis-associated pathway inference using ant colony optimization
Provedor de dados: 17
Autores: Yupeng Wang; Xinyu Liu; Romdhane Rekaya.
Genome-wide association studies (GWAS) have become a standard method for finding genetic variations that contribute to common, complex diseases. Recently, it is suggested that these diseases may be caused by epistatic interactions of multiple genetic variations. Although tens of software tools have been developed for epistasis detection, few are able to infer pathway importance from the identified epistatic interactions. AntEpiSeeker is originally an algorithm for detecting epistatic interactions in case-control studies, using a two-stage ant colony optimization (ACO) algorithm. We have developed AntEpiSeeker2.0, which extends the AntEpiSeeker algorithm to inference of epistasis-associated pathways, based on a natural use of the ACO pheromones. By looking...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6994/version/1

Anterior Olfactory Nucleus
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Beth M. Solan; Lydia L. Ng; Angela L. Guillozet-Bongaarts.
This report contains a gene expression summary of the anterior olfactory nucleus (AON), derived from the Allen Brain Atlas (ABA) in situ hybridization mouse data set. The structure&amp;#x27;s location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the AON were compared to the values of the macro/parent-structure, in this case the olfactory areas, for the purpose of extracting regionally selective gene expression data. The genes with the highest ranking selectivity ratios were manually curated and verified. 50 genes were then selected and compiled for expression characterization. The experimental data for each gene may be...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2093/version/1

Anthropogenic Renourishment Feedback on Shorebirds: a Multispecies Bayesian Perspective
Provedor de dados: 17
Autores: Matteo  Convertino; Joseph Donoghue; Ma Librada Chu-Agor; Gregory Kiker; Rafael  Munoz-Carpena; Richard  Fischer; Igor Linkov.
In this paper the realized niche of the Snowy Plover (Charadrius alexandrinus), a primarily resident Florida shorebird, is described as a function of the scenopoetic and bionomic variables at the nest-, landscape-, and regional-scale. We identified some possible geomorphological controls that influence nest-site selection and survival using data collected along the Florida Gulf coast. In particular we focused on the effects of beach replenishment interventions on the Snowy Plover (SP), and on the migratory Piping Plover&amp;#x9;(PP)&amp;#x9;(Charadrius&amp;#x9;melodus )&amp;#x9;and&amp;#x9;Red&amp;#x9;Knot&amp;#x9;(RK)&amp;#x9;(Calidris&amp;#x9;canutus ).&amp;#x9;Additionally, we investigated the potential differences between the SP breeding and wintering...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5872/version/1

Antibodies targeting Cancer stem cells, A novel pattern in Immunotherapy
Provedor de dados: 17
Autores: Sarfaraz Alam.
Antibody targeting of cancer is showing clinical and commercial success after deep research and development over the last 3 decades. They have the great potential to deliver long-term cures but a shift in thinking towards a cancer stem cell (CSC) model for tumour development is certain to have an impact on how antibodies are selected and developed, the targets they bind to and the drugs used in combination with them. CSCs have been identified from many human tumours and share many of the characteristics of normal stem cells such as the ability to renew and metabolically or physically protect themselves from xenobiotic and DNA damage. Targeting CSCs could be a strategy to improve the outcome of cancer therapy. Monoclonal antibodies are clinically and...
Tipo: Presentation
Palavras-chave: Cancer; Immunology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5428/version/1

Antibody responses to a Cryptosporidium parvum rCP15/60 vaccine
Provedor de dados: 17
Autores: Alexandra J. Burton; Daryl V. Nydam; Gary Jones; Jennifer Zambriski; Thomas C. Linden; Graham Cox; Randy Davis; Alicia Brown; Dwight D. Bowman.
Cryptosporidium parvum is a zoonotic apicomplexa-protozoan pathogen that causes gastroenteritis and diarrhoea in mammals worldwide. The organism is transmitted by ingestion of oocysts, which are shed in faeces, and completes its lifecycle in a single host.^1^ C. parvum is ubiquitous on dairy operations worldwide and is one of the leading causes of diarrhoea in calves on these farms.^2,3^ Here, for the first time, we describe the antibody response in a large group of cows to a recombinant C. parvum oocyst surface protein (rCP15/60) vaccine and the antibody response in calves fed rCP15/60-immune colostrum produced by these vaccinated cows. Results of recent genotype surveys indicate that calves are the only major reservoir for C. parvum infections in...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2009
URL: http://precedings.nature.com/documents/3988/version/1

Antibody-antigen interactions: What is the required time to equilibrium?
Provedor de dados: 17
Autores: Karl Andersson; Hanna Bj&amp;#xf6;rkelund; Magnus Malmqvist.
The use of antibodies is widespread in many areas including in-vivo and in-vitro diagnostics, quantitative analysis in research laboratories and as therapeutic substances. Since the methods for generation of antibodies has improved and regularly results in high-affinity interactions, the standard assays used for quantification of the interaction properties should be revisited because they do not necessarily produce accurate results. Here we show that in several cases, the affinity determination of strongly binding antibodies will be inherently difficult when using standard procedures, due to impractically long incubation times. Real-time kinetic analysis is often the only realistic alternative for affinity determination.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/5218/version/1

Anticancer efficacy of phenolics based structurally related compounds and their radical scavenging action
Provedor de dados: 17
Autores: Vijaya Dubey; Nusrat Masood; Suaib  Luqman; Arvind  S. Negi.
Cancer, one of the leading causes of death worldwide, is an abnormal cell proliferation that fails to respond to the normal signals.  In an effort to eradicate the growing menace of cancer, a clear understanding of fundamental biology and molecular mechanism of carcinogenesis is essential for targeted therapies. Among the devised strategies in use for cancer treatment, the one that is of immense interest is the development of plant based novel anticancer agents. Due to their tremendous availability, biological activity and efficacy, the phytochemicals deemed a gibbous future in chemoprevention. In the present study, several phenolics based structurally related compounds of steroidal and non-steroidal skeleton were synthesized and tested for their...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6644/version/1

Antidepressant suppression of REM and spindle sleep impairs hippocampus-dependent learning and memory but fosters striatal-dependent strategies
Provedor de dados: 17
Autores: Alain Watts; Howard Gritton; Jamie Sweigart; Gina Poe.
REM sleep enhances hippocampus-dependent associative memory but has little impact on striatal-dependent procedural learning. Antidepressant medications like desipramine (DMI) inhibit rapid-eye-movement (REM) sleep but it is little understood how antidepressant treatments affect learning. We found that DMI strongly suppressed REM sleep in rats for several hours and impaired reconsolidation of a familiar maze and consolidation of moved baited positions (reversal learning) in a sleep-dependent fashion. Unexpectedly, DMI also reduced the spindle-rich transition-to-REM sleep state (TR) and spatial memory changes were more related to TR than to REM sleep. Working memory was unaffected, but overnight reference memory was significantly impaired and subjects...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6524/version/1

Antidiabetic, Anti-hyperlipidemic &amp;#x26; Hepatoprotective effect of a Polyherbal Unani formulation &amp;#x201c;Qurs Tabasheer&amp;#x201d; in STZ-diabetic wistar rats
Provedor de dados: 17
Autores: Danish  Ahmed; Manju Sharma; Alok  Mukerjee; Raja Kamal Kant; Vikas  Kumar.
The present study was undertaken to evaluate the antihyperglycemic, antihyperlipidemic and hepatoprotective effect of a traditional unani formulation &amp;#x201c;Qurs Tabasheer&amp;#x201d; in streptozotocin (STZ) induced diabetic wistar rats. Up until now, no study was undertaken to appraise the efficacy of &amp;#x201c;Qurs Tabasheer&amp;#x201d; in the diabetic rats. Qurs Tabasheer is a unani formulation restraining preparations from six various herbs namely Tukhme Khurfa (Portulaca oleracea seed), Gule Surkh (Rosa damascena flower), Gile armani (Arminium bole), Gulnar (Punica granatum flower), Tabasheer (Bambusa arundinasia dried exudate on node), Tukhme Kahu (Lactuca sativa Linn seed). The effect of Qurs Tabasheer was assessed in STZ (60 mg/kg, i.p...
Tipo: Manuscript
Palavras-chave: Pharmacology; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7056/version/1

Anti-HIV therapy: pipeline approaches and future directions
Provedor de dados: 17
Autores: Lavkush Dwivedi; Mansi Shrivastava.
Human immunodeficiency virus (HIV), with about 30 million deaths and double infections (in developing countries), is an open challenge today for global scientists. Developing safe and effective measurements against it has become the prime need of hour. Though, putting it at health priority, various efforts like chemotherapy, vaccines and others are attempted globally over last decade. Consequently, highly active antiretroviral therapy was introduced but fails to completely block the viral replication due to drug resistance and various other severe side effects. The antigenic variability and lack of appropriate experimental models is the major obstacle in the development of an ever effective treatment against HIV. However, to overcome the present hurdles...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2011
URL: http://precedings.nature.com/documents/5540/version/1

Antimicrobial activity of skin secretions isolated from Indian toad, Bufo melanostictus Schneider 1799
Provedor de dados: 17
Autores: Abhishek Dinkarnath Garg; Dattatrey V. Kanitkar; Rajshekhar V. Hippargi; Amit N. Gandhare.
Amphibians like toads have been known to secrete antimicrobial secretions outside their body into their environments, through skin pores and parotid glands. Toad skin-secretions contain four types of compounds namely, biogenic amines, bufadienolides, alkaloids &amp;#x26; steroids and peptides &amp;#x26; proteins. Bulk of research relating to amphibian antimicrobial secretions has been done on frogs. In toads, such research has only been done in South America, Europe and China. Antimicrobial secretions vary considerably from specie-to-specie and drastically across various biomes. This prompted us to examine and confirm presence of antimicrobial activity (if any) in Indian Common Toad (Bufo melanostictus Schneider 1799) skin secretions since; no such...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2007
URL: http://precedings.nature.com/documents/1204/version/1

Antimicrobial and Phytochemical Analysis of Centella asiatica (L.)
Provedor de dados: 17
Autores: Ramar Perumal Samy; Vincent  TK Chow.
In vitro antibacterial studies were carried out using hexane, dichloromethane and methanol extract of leaves of Centella asiatica by disc-diffusion method against gram-positive and gram-negative bacteria. The methanol and dichloromethane extracts of leaf showed a broad spectrum antibacterial activity. Thus the results substantiate the traditional usage of this plant as a medicine.
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6033/version/1

Antioxidant response of overwintering conifers suggest species specific strategies for coping with excess excitation energy
Provedor de dados: 17
Autores: Kim Hughes; Amy Verhoeven; Alex Kokula.
Background/Question/Methods:&amp;#xd;&amp;#xa;Evergreen plants, growing in seasonally cold environments, must cope with a severe imbalance between light absorption and its utilization, as low temperatures during winter inhibit photosynthetic carbon reduction. In such conditions photoprotective mechanisms are critical, including the leaf antioxidant systems of plants. In a previous study examining _Taxus cuspidata_, we found significant increases in the enzyme glutathione reductase (GR) and the metabolite glutathione (GSH) during winter, but no increases in the enzymes superoxide dismutase, ascorbate peroxidase (APX) or the metabolite ascorbate (ASC). These results led to the hypothesis that GR and GSH serve an important role during winter stress that was...
Tipo: Poster
Palavras-chave: Earth &amp; Environment; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5324/version/1

Antiviral activity of (E)-cinnamaldehyde revisited with nanoscience tools
Provedor de dados: 17
Autores: Arunava Goswami; Ayesha Rahman.
Contradictory results have been reported regarding the anti-viral activity of (E)-cinnamaldehyde, a major constituent (~69%) of cinnamon. Here we show that (E)-cinnamaldehyde alone has very low antiviral property contrary to the belief of commoners. There are early sporadic reports in ancient medicinal practices that fine sand was used for increasing the efficacy of antiviral drugs. Can we increase the efficacy of (E)-cinnamaldehyde marginally by using one of the major constituents of sand like silica? Yes, when nanosilica is used as a carrier during (E)-cinnamaldehyde administration, the antiviral efficacy of the resultant cocktail increases marginally. Therefore, (E)-cinnamaldehyde consumed for centuries in tribal therapy as well as in alternative...
Tipo: Manuscript
Palavras-chave: Biotechnology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/5043/version/1

Antiviral Effects of a Synthetic Aluminium-Magnesium Silicate on Avian Influenza Virus
Provedor de dados: 17
Autores: Madike Ezeibe; Anthony Egbuji; Obianuju Okoroafor; James Eze; Omadi Ijabo; Augustine Ngene; Ikechukwu Eze; Joeseph Ugonabo; Mary Sanda; Ijeoma Mbuko.
Effects of a synthetic Aluminium-Magnesium Silicate (AMS) on Avian Influenza Virus (AIV) were tested. Equal amounts of H5N1 AIV samples and of AMS were mixed, left one hour, at room temperature before centrifuging. The supernatants were remeasured and tested for viral titre, for Mean Death Time (MDT) and Embryo Mortality Rate (EMR) of chicken eggs. Volumes of the viral samples reduced at rate of 23.4 &amp;#xb1; 5.48 %. Viral titres reduced significantly (P from HA, 73 &amp;#xb1; 32.72 to 1.4 &amp;#xb1;0.43). Also, mortality of infected embryos reduced from 100 % to 65% while MDT of those that died, increased significantly (P = 0.001) from 76 &amp;#xb1; 4.38 to 130 &amp;#xb1;17.27 hours.  When incubation with AMS was repeated on portions of the same sample,...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/6509/version/1

Apellicon: a web-based tool for constructing and curating Textpresso databases.
Provedor de dados: 17
Autores: William M. Urbanski; Brian  G. Condie.
As more research literature in the biological sciences is made available in electronic format, text mining systems are increasingly being used to improve the ability of investigators to retrieve relevant information. Through the use of advanced indexing techniques that utilize biological ontologies, semantic databases, and other formal representations of biological concepts text mining systems have been able to effectively parse biological literature. While text mining systems are increasingly effective at creating the linkages required to provide context-specific search results, the systems themselves are difficult to set up and use by novice computer users due to the highly technical nature of the applications. Because most researchers in the biological...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4927/version/1

Apoptotic gene expression in neuropathic pain
Provedor de dados: 17
Autores: Dario Siniscalco; Catia Giordano; Carlo Fuccio; Livio Luongo; Annalucia Migliozzi; Francesco Rossi; Sabatino Maione.
Pain initiated or caused by a primary lesion or dysfunction in the nervous system is defined as neuropathic pain. It results from direct injury to nerves in the peripheral or central nervous system and is associated with several clinical symptoms. Neuropathic pain treatment is extremely difficult, as it is a very complex disease, involving several molecular pathways. Excitatory or inhibitory pathways controlling neuropathic pain development show altered gene expression, caused by peripheral nerve injury.&amp;#xd;&amp;#xa;This study used several experimental pain models to demonstrate the occurrence of programmed cell death in the centers controlling pain induction and maintenance, such as spinal cord and pre-frontal cortex. We combined behavioural,...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/1549/version/1

Apotemnophilia - the Neurological Basis of a &amp;#x27;Psychological&amp;#x27; Disorder
Provedor de dados: 17
Autores: Paul D. McGeoch; David J. Brang; Tao Song; Roland R. Lee; Mingxiong Huang; Vilayanur S. Ramachandran.
The question of how the human brain combines disparate sensory inputs to construct a unified body image is of longstanding interest^1,2,3^ . We approached this subject by studying the unusual medical condition of apotemnophilia, in which otherwise mentally normal individuals express the strong and persistent desire for the amputation of a specific healthy limb^4,5,6^ . Here we show using functional brain imaging - magnetoencephalography (MEG) - that the condition is characterised by an absence of activity in the right superior parietal lobule (SPL) when the affected limb is touched. When this discovery is combined with our earlier finding of a simultaneous increase in skin conductance response (SCR) on touching the affected limb^7^ , which reflects...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2954/version/1

Apparent non-canonical trans-splicing is generated by reverse transcriptase in vitro
Provedor de dados: 17
Autores: David Tollervey; Jonathan Houseley.
Trans-splicing, the in vivo joining of two RNA molecules, is well characterized in several groups of simple organisms but was long thought absent from fungi, plants and mammals. However, recent bioinformatic analyses of expressed sequence tag (EST) databases suggested widespread trans-splicing in mammals^1-2^. Splicing, including the characterised trans-splicing systems, involves conserved sequences at the splice junctions. Our analysis of a yeast non-coding RNA revealed that around 30% of the products of reverse transcription lacked an internal region of 117 nt, suggesting that the RNA was spliced. The junction sequences lacked canonical splice-sites but were flanked by direct repeats, and further analyses indicated that the apparent splicing actually...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4203/version/1

Application of a periodic table for the genetic code of the influenza A/H3N2 virus
Provedor de dados: 17
Autores: Susumu Morimoto.
The progress of life sciences would be greatly enhanced if biological data were available in a manner similar to the periodic table of the elements. Currently, the mutation rules for influenza viruses remain ambiguous. In light of the threat of Avian Influenza there is an urgent need to understand the governing principles behind influenza virus mutations. Here, the applicability of a periodic table for the genetic code of influenza A/H3N2 virus is explored. In addition, two rules regarding single point mutations of the hemagglutinin gene are presented. The first rule states that non-synonymous single point mutations are intimately associated with the first or second base replacements between two congener codons of four groups (5, 6, 9, and 10) in the...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/428/version/2

Application of a periodic table for the genetic code to influenza A/H3N2 virus
Provedor de dados: 17
Autores: Susumu Morimoto.
If biologists can utilize a table to have access to biological phenomena in the manner analogous to the periodic table for chemical elements, they may get hold of a directing post in life science. Currently the mutational rule of influenza viruses have remained perplexed and to reveal it should be now desired when avian influenza virus has just then threatened human beings. Here I examine the applicability of a novel periodic table for the genetic code to influenza A/H3N2 virus, while presenting two rules regarding single point mutations of its virus hemagglutinin gene. One rule is that non-synonymous single point mutations are intimately associated with the first or second base replacements between four groups (5, 6, 9, and 10) in the periodic table....
Tipo: Manuscript
Palavras-chave: Chemistry; Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/428/version/1

Application of space technology to the design of sustainable settlements in hot deserts: Bioregenerative life support systems
Provedor de dados: 17
Autores: Yuriy Polyakov; Ibrahim Musaev; Sergey Polyakov.
Water scarcity in hot deserts, which cover about one-fifth of the Earth&amp;#x2019;s land area, along with rapid expansion of hot deserts into arable lands is one of the key global environmental problems. This paper proposes and substantiates an interdisciplinary approach to sustainable settlements in hot deserts using the accomplishments in the design of closed bioregenerative life support systems (CBLSS) for beyond-Earth (Lunar, Martian) settlements. Extensive space technology experience in the design of CBLSSes, which simultaneously produce food, water, nutrients, and fertilizers, process wastes, and revitalize air, has been analyzed and systematized with application to hot deserts, which represent extreme habitats with high input of solar energy, poor...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3926/version/1

Application of the Sensory Contact Model for Pharmacological Studies under Simulated Clinical Conditions
Provedor de dados: 17
Autores: Natalia N. Kudryavtseva; Damira F. Avgustinovich; Natalia P. Bondar; Michael V. Tenditnik; Irina L. Kovalenko.
The sensory contact model allows forming different psycho-pathological states (anxious depression, catalepsy, social withdrawal, pathological aggression, cognition disturbances, anhedonia, addictive states etc.) produced by repeated agonistic interactions in male mice and investigating the therapeutic and preventive properties of any drug as well as its efficiency under simulated clinical conditions. This approach can be useful for a better understanding of the drugs&amp;#x2019; action in different stages of disease development in individuals. It is suggested that this behavioral approach and pharmacological designs may be applied for the screening of novel psychotropic drugs. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/1439/version/1

Applications Of Microspectroscopy, Hyperspectral Chemical Imaging And Fluorescence Microscopy In Chemistry, Biochemistry, Biotechnology, Molecular And Cell Biology
Provedor de dados: 17
Autores: I. C. Baianu.
Chemical imaging is a technique for the simultaneous measurement of spectra (chemical information) and images or pictures (spatial information)^1,2^. The technique is most often applied to either solid or gel samples, and has applications in chemistry, biology^3-8^, medicine^9,10^, pharmacy^11^ (see also for example: Chemical Imaging Without Dyeing), food science, Food Physical Chemistry, Biotechnology^12,13^, Agriculture and industry. NIR, IR and Raman chemical imaging is also referred to as hyperspectral, spectroscopic, spectral or multi-spectral imaging (also see micro-spectroscopy). However, other ultra-sensitive and selective, chemical imaging techniques are also in use that involve either UV-visible or fluorescence microspectroscopy.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6593/version/1

Apply of Textmining Method to Study the Roles in Improving the Health by Lactoferrin, a Multi-Functional Milk Protein
Provedor de dados: 17
Autores: Kei-ichi K. Shimazaki; Tatsuya T. Kushida; Koji K. Yamauchi; Toshihisa T. Takagi.
Lactoferrin is a metal-binding glycoprotein found in milk, blood and other exocrine secretions.  This is a multi-functional protein that exhibits many activities such as: anti-microbial, anti-viral, immunomodulatory, anti-inflammatory, anti-tumor, anti-metastatic, cell growth-promoting, and anti-oxidant activities, as well as regulation of granulopoiesis and iron absorption, etc.  To date, a number of academic reports concerning the biological activities of lactoferrin have been published and are easily accessible through public databases.  In order to overcome the information overload associated with lactoferrin information, we have applied the text mining method to the accumulated lactoferrin literature.  To this end, we used the information extraction...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5100/version/1

Applying Biomedical Ontologies on Semantic Query Expansion
Provedor de dados: 17
Autores: Andre Bechara; Maria Luiza C. Machado; Vanessa Braganholo.
*1- Introduction*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The interpretation of a question (or information need) depends, among other things, of a series of lexicalsemantic relations that complement and help the cognitive process of answering that information need. Despite this fact, currently used information retrieval mechanisms take few advantages of the semantic interpretation of users&amp;#x2019; information needs (usually specified through keywords). In most of the cases, those mechanisms are based on keyword matching, and thus are excessively dependant on the query and document terms.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;There are several past results showing that, in general, information retrieval based on domain knowledge decreases the accuracy of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3550/version/1

Applying of novel subtracted method Genetically Directed Differential Subtraction Chain (GDDSC) in plant genomes
Provedor de dados: 17
Autores: Ewa Siedlecka; Aneta Hromada-Judycka; Magdalena Pawe&amp;#x142;kowicz; Rafa&amp;#x142; W&amp;#xf3;ycicki; Monika Rakoczy-Trojanowska; Zbigniew Przybecki.
We present a simple subtraction procedure of GDDSC as a modification of the original DSC and GDRDA methods. Genetically Directed Differential Subtraction Chain (GDDSC) is a process by which highly related genomes are compared in order to isolate tags carrying the polymorphisms. &amp;#xd;&amp;#xa;To detect specific DNA fragment (tag), we can then monitor offspring plants for efficient molecular breeding. The GDDSC protocol was applied to isolation of new sex related clones from cucumber plants (_Cucumis_ _sativus_ L.) and new tissue culture response clones from rye (_Secale_ _cereale_ L.). The newly identified tags, obtained by GDDSC represent pools of candidate genes and other sequences, which could serve as potential markers for requested traits.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5465/version/1

Applying of novel subtraction method Genetically Directed Differential Subtraction Chain (GDDSC) in plant genomes
Provedor de dados: 17
Autores: Ewa Siedlecka; Aneta Hromada-Judycka; Magdalena Pawe&amp;#x142;kowicz; Rafa&amp;#x142; W&amp;#xf3;ycicki; Monika Rakoczy-Trojanowska; Zbigniew Przybecki.
We present a simple subtraction procedure of GDDSC as a modification of the original DSC and GDRDA methods. Genetically Directed Differential Subtraction Chain (GDDSC) is a process by which highly related genomes are compared in order to isolate tags carrying the polymorphisms. &amp;#xd;&amp;#xa;To detect specific DNA fragment (tag), we can then monitor offspring plants for efficient molecular breeding. The GDDSC protocol was applied to isolation of new sex related clones from cucumber plants (_Cucumis_ _sativus_ L.) and new tissue culture response clones from rye (_Secale_ _cereale_ L.). The newly identified tags, obtained by GDDSC represent pools of candidate genes and other sequences, which could serve as potential markers for requested traits.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5465/version/2

Aptamer-based multiplexed proteomic technology for biomarker discovery
Provedor de dados: 17
Autores: Larry Gold; Deborah Ayers; Jennifer Bertino; Christopher Bock; Ashley Bock; Edward N. Brody; Jeff Carter; Virginia Cunningham; Andrew Dalby; Bruce E. Eaton; Tim Fitzwater; Dylan Flather; Ashley Forbes; Trudi Foreman; Cate Fowler; Bharat Gawande; Meredith Goss; Magda Gunn; Shashi Gupta; Dennis Halladay; Jim Heil; Joe Heilig; Brian Hicke; Gregory Husar; Nebojsa Janjic; Thale Jarvis; Susan Jennings; Evaldas Katilius; Tracy R. Keeney; Nancy Kim; Terese Kaske; Tad Koch; Stephan Kraemer; Luke Kroiss; Ngan Le; Daniel Levine; Wes Lindsey; Bridget Lollo; Wes Mayfield; Mike Mehan; Robert Mehler; Michele Nelson; Sally K. Nelson; Dan Nieuwlandt; Malti Nikrad; Urs Ochsner; Rachel M. Ostroff; Matt Otis; Thomas Parker; Steve  Pietrasiewicz; Dan Resnicow; John Rohloff; Glenn Sanders; Sarah Sattin; Dan Schneider; Britta Singer; Martin Stanton; Alana Sterkel; Alex Stewart; Suzanne Stratford; Jonathan D. Vaught; Mike Vrkljan; Jeffrey J. Walker; Mike Watrobka; Sheela Waugh; Allison Weiss; Sheri Wilcox; Alexey Wolfson; Steve Wolk; Chi Zhang; Dom Zichi.
Interrogation of the human proteome in a highly multiplexed and efficient manner remains a coveted and challenging goal in biology.  We present a new aptamer-based proteomic technology for biomarker discovery capable of simultaneously measuring thousands of proteins from small sample volumes (15 [mu]L of serum or plasma).  Our current assay allows us to measure ~800 proteins with very low limits of detection (1 pM average), 7 logs of overall dynamic range, and 5% average coefficient of variation.  This technology is enabled by a new generation of aptamers that contain chemically modified nucleotides, which greatly expand the physicochemical diversity of the large randomized nucleic acid libraries from which the aptamers are selected.  Proteins in complex...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4538/version/1

Aqueous Electrolyte Ionization over Extreme Ranges as Simple Fundamental Relation with Density and Believed Universal; Sodium Chloride Ionization from 0^o^ to 1000^o^C and to 1000 MPa (10000 Atm.)
Provedor de dados: 17
Autores: William L. Marshall.
The chemical nature of aqueous electrolyte ionization is illustrated by a simple relationship with water as a reactant believed to correlate ionization of aqueous sodium chloride approaching infinite dilution over the entire range of temperature and pressure [0 to 1000^o^C; 0.1 to 1000 MPa (10000 Atm)].  The derived equation accurately and smoothly describes the ionization constant of sodium chloride [_K_(NaCl)] in both water and water strongly diluted by inert solvent.  Effects of water density on ionization are quantitatively and simply described that oppose conventional theory that ionization is a function only of dielectric constant, and theorists should apply this simplicity with density in understanding aqueous electrolyte ionization.  There appears...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2476/version/1

Aqueous phase hydration and hydrate acidity of perfluoroalkyl and n:2 fluorotelomer aldehydes
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Perfluoroalkyl aldehydes (PFAlds) and n:2 fluorotelomer aldehydes (FTAlds) are degradation products of precursor compounds that include fluorotelomer alcohols, iodides, acrylates, phosphate esters, and other derivatives, as well as hydrofluorocarbons and hydrochlorofluorocarbons. The SPARC software program and comparative density functional theory (DFT) calculations were used to investigate the aqueous phase hydration equilibrium constants (K~hyd~) of PFAlds and FTAlds. DFT studies suggest that all PFAlds will be dominantly present as the hydrated form in aqueous solution. While SPARC correctly estimates the K~hyd~ for the C~1~ PFAld, it appears to incorrectly predict a large decline in K~hyd~ (particularly between C~1~ and C~2~) with increasing...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4520/version/1

Aqueous synthesis of CdTe quantum dot as biological fluorescent probe for monitoring methyl parathion by fluoro-immunosensor
Provedor de dados: 17
Autores: Raghuraj Chouhan; Aaydha Vinayaka; Munna Thakur.
Bioconjugation of quantum dots (QDs) provide high resolution in biological fluorescent labelling as a result of physical and optical properties of QDs. This intrinsic property of QDs can be made use of for sensitive detection of target analytes including food and environmental monitoring. In this investigation, we report the bioconjugation of thiol stabilized CdTe QD for the sensitive detection of methyl parathion (MP) at picogram level. The specificity in the analysis was attributed by highly specific competitive immunological reactions between free MP and CdTe QD bioconjugated MP (MP-BSA-CdTe) for immobilized anti-MP IgY antibodies in a simple flow injection system. We also report the possible resonance energy transfer phenomenon as a result of...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3451/version/1

Arbuscular mycorrhizal fungus spores host bacteria and their biofilm efficient in nutrient biodynamics and soil-borne plant pathogen suppression
Provedor de dados: 17
Autores: Andre Cruz; Takaaki Ishii.
The combination of bacteria and arbuscular mycorrhizal fungi (AMF) would be ideal for nutrient biodvnamics in soils and protection from soil-borne plant pathogens (SBPP). During the process of plant colonization AMF interact with bacteria where spores cytoplasm and hvphae provide specific niches for certain populations of bacteria. The clarification of the relationship AMF-bacteria has great potential for sustainable agriculture. The currently research aimed to isolate and characterize bacteria. Which we have designated most probable endobacteria (MPE) from an AMF spore. Three bacterial strains were taken from about 500 spores by using a 200 &amp;#xb5;m diameter hvpodermic needle. These bacteria were identified by DNA and morphological methods. Antagonism...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/5544/version/1

Archaebacterial Whole-Genome Duplication and Origin of Eukaryots
Provedor de dados: 17
Autores: Milanko Stupar.
Division of the ancestral prokaryotic pragenome into two circular double-stranded DNA molecules by genetic recombination, is a base for the future separate evolution of the nuclear and mitochondrial gene compartment. This suggests monophyletic origin of both mitochondrion and nucleus. Presumed organism which genome undergoes genetic recombination has to be searched among an aerobic, oxygen non-producing archaeon with no rigid cell wall, but a plasma membrane. Plastids evolve from an aerobic, oxygen producing proto-eukaryot, after mitoplastide genome duplication and subsequent functional segregation.In this proposal origin of eukaryots occur by a three-step mechanism. First, replication fork pauses and collapses generating a breakage in the genome of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2302/version/1

Archon Genomics X PRIZE Validation Protocol
Provedor de dados: 17
Autores: Larry Kedes; Granger Sutton; Edison  Liu; Victor Jongeneel.
This document is a collective assembly of techniques designed to test the quality and accuracy of 100 whole human genome sequences resulting from the $10 Million Archon Genomics X PRIZE (AGXP) competition. The purpose of this article is to enlist constructive criticism from the genomic and genetic community on the outlined approaches. The intent for the final version of this Validation Protocol is to become a useful standard by which to gauge the capabilities of whole genome sequencing technologies that emerge even after 2012.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5731/version/1

Are endocannabinoid type 1 receptor gene (CNR1) polymorphisms associated with obesity and metabolic syndrome in postmenopausal Polish women?
Provedor de dados: 17
Autores: Katarzyna Dunajska; Felicja Lwow; Diana Jedrzejuk; Andrzej Milewicz; Urszula Tworowska-Bardzinska; Lukasz Laczmanski.
Objective: The aim of this study was to determine whether genetic variation at the cannabinoid receptor-1 (CNR1) locus could have an effect on adiposity, fat distribution and obesity-related metabolic disorders in Polish postmenopausal women.Design and Subjects: The A3813G, G1422A and A4895G single nucleotide polymorphisms of CNR1 were genotyped in 348 randomly selected postmenopausal women aged 50-60 years recruited from the Wroclaw city population. Measurements: CNR1 genotypes, anthropometric measures (BMI, WC, body fat distribution by DEXA) and metabolic parameters (glucose, lipid profile, insulin FIRI) were determined.Results: The 3813G allele was not significantly associated with higher body mass, BMI, WC, total fat, or fat percentage, but was...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3946/version/1

Are men evolutionarily wired to love the &amp;#x22;Easy&amp;#x22; buttons?
Provedor de dados: 17
Autores: Irina Trofimova.
Men&amp;#x27;s drive for group control and power appears to be an evolutionary inheritance, but it is females, and not males, who developed better abilities for prolonged control and group interaction while males have higher rates of ADHD and autism. This contradictory allocation of sex-related abilities describes the observable behavior, but not the internal meaning attribution leading to the motivation of men and women. Our study in Canada, China and Russia shows that men estimate power- and status-related concepts in significantly more positive terms than women, but give significantly more negative estimations to work-related and reality-related concepts. Men also have a consistent tendency to estimate concepts as less real (even...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5562/version/1

Are plants with anti-cancer activity resistant to crown gall? : A test of hypothesis
Provedor de dados: 17
Autores: R Srirama; BT. Ramesha; G. Ravikanth; R. Uma Shaanker; KN Ganeshaiah.
The Crown gall tumour assay (CGTA) is one of several bench top bioassays recommended for the rapid screening of plants with anti-cancer activity. The rationale for the use of the bioassay is that the tumorogenic mechanism initiated in plant tissues by _Agrobacterium tumefaciens_ is in many ways similar to that of animals.  Several plant species with anti-cancer activity have already been discovered using this bioassay.  However till date no explicit test of an association between anti-cancer activity of plants and their resistance to crown gall formation has been demonstrated. Demonstration of an association could have exploratory potential when searching for plants with anti-cancer activity. In this paper, we determined whether or not a statistically...
Tipo: Manuscript
Palavras-chave: Cancer; Pharmacology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1456/version/1

Area Postrema
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Katie J. Glattfelder; Lydia L. Ng; John A. Morris.
This report contains a gene expression summary of the area postrema (AP), derived from the &amp;#x22;Allen Brain Atlas&amp;#x22;:http://www.brain-map.org/welcome.do;jsessionid=EDE40ADC940845D169DE378ADC9B71BD (ABA) in-situ hybridization (ISH) mouse data set.  The structure&amp;#x2019;s location and morphological characteristics in the mouse brain are described using the Nissl data found in the &amp;#x22;Allen Reference Atlas&amp;#x22;:http://www.brain-map.org/mouse/atlas/coronal/legend.html.  Using an established algorithm, the expression values of the AP were compared to the values of the macro/parent-structure, in this case the medulla, for the purpose of extracting regionally specific gene expression data. The highest ranking ratios were then manually...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2053/version/1

Argudas: arguing with gene expression information
Provedor de dados: 17
Autores: Kenneth McLeod.
In situ hybridization gene expression information helps biologists identify where a gene is expressed. However, the databases that republish the experimental information are often both incomplete and inconsistent. This presentation examines a system, Argudas, designed to help tackle these issues. Argudas is an evolution of an existing system, and so that system is reviewed as a means of both explaining and justifying the behavior of Argudas. Throughout the discussion of Argudas a number of issues will be raised including the appropriateness of argumentation in biology and the challenges faced when integrating apparently similar online biological databases.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5394/version/1

ARHI (DIRAS 3), an Imprinted Tumor Suppressor Gene, Binds to Importins, and Blocks Nuclear Translocation of Stat3
Provedor de dados: 17
Autores: Shaoyi Huang; In Soon Chang; Wenbo Lin; Robert Luo; Zhen Lu; Yiling Lu; Ke Zhang; Warren Liao; Tao Tao; Robert Bast, Jr.; Xiaomin Chen; Yinhua Yu.
ARHI (DIRAS3) is an imprinted tumor suppressor gene whose expression is lost in the majority of breast and ovarian cancers. Unlike its homologs Ras and Rap, ARHI functions as a tumor suppressor. Our previous study showed that ARHI can interact with transcription activator Stat3 and inhibit its nuclear translocation in human breast and ovarian cancer cells. To identify proteins that interact with ARHI in nuclear translocation, we have performed proteomic analysis and identified several importins that can associate with ARHI. To further explore this novel finding, we have purified 10 GST-importin fusion proteins (importin 7, 8, 13, b1, a1, a3, a5, a6, a7 as well as mutant a1). Using a GST-pull down assay, we found that ARHI can bind strongly to most...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2392/version/1

ArrayMining.net: a  web-server for integrative microarray and gene set analysis
Provedor de dados: 17
Autores: Enrico Glaab; Jonathan M. Garibaldi; Natalio Krasnogor.
DNA microarray experiments provide a means to understand cancer and genetic diseases on a molecular level, improve diagnosis and identify new drug targets. However, choosing appropriate data processing methods and parameters is a difficult and time-consuming task, particularly for researchers without prior experience in this field. &amp;#xd;&amp;#xa;We present *ArrayMining.net*, a free web-service for automatic microarray analysis to address these issues. ArrayMining.net covers several major areas in statistical microarray analysis - Feature Selection, Clustering, Prediction, Gene Set and Network Analysis - providing access to several algorithms for each of these tasks based on a single, easy-to-use interface.
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5552/version/1

Arrhenius&amp;#x27; theory of partial dissociation and hydration of electrolytes in solutions replaces existing activity concepts
Provedor de dados: 17
Autores: Raji Heyrovska.
The author shows that Arrhenius&amp;#x27;s theory of partial electrolytic dissociation was immaturely displaced about eight decades ago by the empirical concept of ionic activities and the assumption of complete dissociation of electrolytes at all concentrations. The latter brought the theory of electrolytes over the next decades into a complicated state without any physical significance. Therefore, the author started a systematic investigation of the available data and could completely restore the original theory of partial dissociation. Now solution properties can be easily understood and quantitatively explained in terms of absolute concentrations and volumes of ions and ion pairs and hydration.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6416/version/2

Artificial Antigen Presenting Cells With Preclustered anti-CD28/-CD3/-LFA-1 Monoclonal Antibodies Are Highly Effective To Induce The Ex-Vivo Expansion Of Functional Human Antitumor T Cells
Provedor de dados: 17
Autores: Roberta Zappasodi; Massimo Di Nicola; Carmelo Carlo-Stella; Roberta Mortarini; Alessandra Molla; Claudia Vegetti; Lorena Passoni; Salvatore Albani; Andrea Anichini; Alessandro M. Gianni.
Effective adoptive T cell therapy requires the _ex vivo_ generation of functional T lymphocytes with a long lifespan _in vivo_. We evaluated _in vitro_ T cell expansion by artificial antigen presenting cells (aAPC) generated with activating (human anti-CD3), co-stimulating (human anti-CD28) and adhesion (human anti-LFA-1) monoclonal antibodies pre-clustered in microdomains (MDs) held by a liposome scaffold. The co-localization of T cell ligands in MDs and the targeting of an adhesion protein, increasing the efficiency of immunological synapse formations, represent the novelties of our system. These aAPCs allowed increased expansion of polyclonal CD4^+^ and CD8^+^ T cells and of tumor antigen-specific CD8^+^ T cells compared to anti-CD28- and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Immunology.
Ano: 2007
URL: http://precedings.nature.com/documents/1250/version/1

Artificial Neural Network
Provedor de dados: 17
Autores: Smrita Singh.
In the postgenomic era, computational methods are being used in diverse areas like drug discovery, robotics, weather forecasting etc. Computational methods are incorporated with various programmes that are further instructed with complex algorithms based on different logistic approaches. Artificial neural network is one of them to be utilized in various molecular dynamics and simulation studies. Therefore, it is essential to understand the basic logic while programming in order to troubleshoot the computational methods.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6623/version/1

Artificial Photosynthesis Would Unify the Electricity-Carbohydrate-Hydrogen Cycle for Sustainability
Provedor de dados: 17
Autores: Yi-Heng Percival Zhang.
Sustainable development requires balanced integration of four basic human needs &amp;#x2013; air (O2/CO2), water, food, and energy.  To solve key challenges,  such as CO2 fixation, electricity storage, food production, transportation fuel production, water conservation or maintaining an ecosystem for space travel,  we wish to suggest the electricity-carbohydrate-hydrogen (ECHo) cycle, where electricity is a universal energy carrier, hydrogen is a clean electricity carrier, and carbohydrate is a high-energy density hydrogen (14.8 H2 mass% or 11-14 MJ electricity output/kg)carrier plus a food and feed source.  Each element of this cycle can be converted to the other reversibly &amp;#x26; efficiently depending on resource availability, needs, and costs.  In...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4167/version/1

Assemblage-structuring force of species interactions varies spatially and temporally: Co-occurrence analysis of canopy arthropod distributions
Provedor de dados: 17
Autores: Matthew K. Lau; Laura E. Hagenauer; Thomas G. Whitham.
*Background/Question/Methods* Understanding how interactions amongst species contribute to their distribution is central to community ecology. However, it is not understood how these processes may change under different environmental conditions. In this study, we present evidence that suggests interactions amongst canopy arthropods contribute to assemblage structure, depending on both the sampling time and location. We sampled canopy arthropod species abundances on individual trees in three adjacent, monospecific stands of Populus fremontii (Fremont cottonwood), which differ in planting year (2000, 2002, 2005). We then conducted null-model based co-occurrence analysis using the freely available software EcoSim (Kesey-Bear and Acquired Intelligence, Inc.)...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3600/version/1

Assembling the Tree of Life in Europe (AToLE)
Provedor de dados: 17
Autores: Olaf R. P. Bininda-Emonds; Wieslaw  Bogdanowicz; Thomas Borsch; Frederic Delsuc; Alexandre  Hassanin; Ulf Jondelius; Gitte Petersen; Susanne S. Renner; Vincent Savolainen; Ole Seberg; Erik Smets; Alfried Vogler.
A network of scientists under the umbrella of &amp;#x27;Assembling the Tree of Life in Europe (AToLE)&amp;#x27; seeks funding under the FP7-Theme: Cooperation - Environment (including Climate Change and Biodiversity Conservation) programme of the European Commission.&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2891/version/1

Assessing functional novelty of PSI structures via structure-function analysis of large and diverse superfamilies
Provedor de dados: 17
Autores: Benoit H. Dessailly; Oliver C. Redfern; Christine A. Orengo.
The structural genomics initiatives have had as one of their aims to improve our understanding of protein function by providing representative structures for many structurally uncharacterised protein families. As suggested by the recent assessment of the Protein Structure Initiative (Structural Genomics Initiative, funded by the NIH), doubts have arisen as to whether Structural Genomics as initially planned were really beneficial to our understanding of biological issues, and in particular of protein function.&amp;#xd;&amp;#xa;A few protein domain superfamilies have been shown to account for unexpectedly large numbers of proteins encoded in fully sequenced genomes.  These large superfamilies are generally very diverse, spanning a wide range of functions,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2214/version/1

Assessing performance of conservation-based Best Management Practices: Coarse vs. fine-scale analysis
Provedor de dados: 17
Autores: Denise A. Piechnik; Sarah C. Goslee; Tamie L. Veith.
Background/Questions/Methods&amp;#xd;&amp;#xa;Animal agriculture in the Spring Creek watershed of central Pennsylvania contributes sediment to the stream and ultimately to the Chesapeake Bay. Best Management Practices (BMPs) such as stream bank buffers are intended to intercept sediment moving from heavy-use areas toward the stream. The placement of BMPs on a farm is generally based on untested assumptions about flow paths. Most often, a straight-line distance from the heavy-use area to the stream is assumed to be correct. Our objective was to compare the straight-line path to hydrologic flow paths calculated from fine-, medium- and coarse-grained Digital Elevation Models (DEMs; 1m, 10m, 30m) for 471 mapped heavy-use points within 100m of the stream. The...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5248/version/1

Assessing the conservation value of farmland ponds: Use of predictive techniques to identify surrogare groups
Provedor de dados: 17
Autores: Margherita Gioria.
Background/Question/Methods. Ponds are among the most diverse and yet threatened components of freshwater biodiversity. The conservation of ponds would greatly benefit from the identification of surrogate taxa in preliminary assessments aimed at detecting ponds of potentially high biodiversity value. Vascular plants and water beetles have often been used in pond conservation assessments. To evaluate whether wetland plants are a suitable surrogate group to evaluate pond biodiversity, we used plant, beetle, and environmental data collected from 54 ponds located in two farmed regions in Ireland. Specifically, we aimed at assessing cross-taxon congruence between water beetles and plants; quantifying and comparing the capacity of vegetation data and...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5214/version/1

Assessing the Genotypic Differences for Seed Set and Seed Abortion in Tomato Genotypes
Provedor de dados: 17
Autores: Chalapathy  K. Reddy; Ganeshaiah Narayana; Uma  Shaanker.
Tomato (_Lycopersicon esculentum_ Mill.) is one of the most popular fruit vegetable around the world. Seed abortion where in only a small proportion of ovules in an ovary develops into matured seeds, is a wide spread phenomenon in multi-ovulated species. In agriculturally important crops such as chickpea, groundnut, Brassica, pigeon pea and field bean seed abortion substantially reduces their productivity. Tomato genotypes exhibited seed abortion where in only some proportion of ovules developed into matured seeds. Seed abortion in tomato cultivars would increase the cost of hybrid seed production. In this study, we have analyzed 19 genotypes for number of ovules, seed set and seed abortion. Tomato genotypes differed significantly for number of ovules per...
Tipo: Manuscript
Palavras-chave: Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3183/version/1

Assessment Of Response To Heart Failure Therapy: Ventricular Volume Changes Versus Shape Changes
Provedor de dados: 17
Autores: Srilakshmi Adhyapak; V.Rao Parachuri.
The prolate ellipsoid left ventricular geometry is crucial for its unique contraction and relaxation patterns. Perturbations in optimal cardiac function preceding overt heart failure ensue when this ellipsoid shape assumes a more spherical configuration. This stage of spherical configuration, prior to overt dilatation, is when therapy should be intensified. The dynamic shape changes during the cardiac cycle of systole and diastole in valvular regurgitations when ventricular volumes are within normal range have proved that shape changes are clearly dissociated from volume changes in the early stages. In the scenario of advanced heart failure, several therapeutic interventions have been tried with variable success. These therapies aim at decreasing the...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6707/version/1

Assisting natural forest regeneration in Northern Ethiopia: one intervention is not enough
Provedor de dados: 17
Autores: Raf Aerts; Eva November; Martin Hermy; Jozef Deckers; Mitiku Haile; Bart Muys.
Management strategies aimed at rehabilitating degraded and cleared forests often rely on temporary or permanent exclusion of herbivores (wild animals, livestock or both).  But in many cases, this simple management technique is not sufficient to induce ecosystem restoration: many negative effects keep the ecosystem in a suboptimal, low biomass state.  The presence of such stable states requires restoration measures to act on multiple stress factors simultaneously.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Compensating for all limiting factors is neither practically nor economically feasible.  But detailed knowledge about the autoecology of tree species &amp;#x2013; i.e. their site requirements, regeneration strategies and recruitment dynamics &amp;#x2013; may be...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/2437/version/2

Assisting natural forest regeneration in Northern Ethiopia: one measure is not enough
Provedor de dados: 17
Autores: Raf Aerts; Eva November; Martin Hermy; Jozef Deckers; Mitiku Haile; Bart Muys.
Management strategies aimed at rehabilitating degraded and cleared forests often rely on temporary or permanent exclusion of herbivores (wild animals, livestock or both).  But in many cases, this simple management technique is not sufficient to induce ecosystem restoration: many negative effects keep the ecosystem in a suboptimal, low biomass state.  The presence of such stable states requires restoration measures to act on multiple stress factors simultaneously.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Compensating for all limiting factors is neither practically nor economically feasible.  But detailed knowledge about the autoecology of tree species &amp;#x2013; i.e. their site requirements, regeneration strategies and recruitment dynamics &amp;#x2013; may be...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2437/version/1

Association Analysis Techniques for Discovering Functional Modules from Microarray Data
Provedor de dados: 17
Autores: Gaurav Pandey; Gowtham Atluri; Michael Steinbach; Vipin Kumar.
An application of great interest in microarray data analysis is the identification of a group of genes that show very similar patterns of expression in a data set, and are expected to represent groups of genes that perform common/similar functions, also known as functional modules. Although clustering offers a natural solution to this problem, it suffers from the limitation that it uses all the conditions to compare two genes, whereas only a subset of them may be relevant. Association analysis offers an alternative route for finding such groups of genes that may be co-expressed only over a subset of the experimental conditions used to prepare the data set. The techniques in this field attempt to find groups of data objects that contain coherent values...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2184/version/1

Association of autoimmune diseases to allele 2 of the 3&amp;#x27; immuno-globulines HS1.2 enhancer bearing an NF-&amp;#x3ba;B binding site.
Provedor de dados: 17
Autores: Domenico D. Frezza; Elisa Gremese; Vincenzo Giambra; Claudia Mattioli; Barbara Tolusso; Silvia Bosello; Maria DeSantis; Barbara Birshtein; Gianfranco Ferraccioli.
We identified allele *2 in the HS1.2 enhancer of the Igh 3&amp;#x27; regulatory region (3&amp;#x27;RR-1) as a risk factor for systemic lupus erythematosus (SLE), rheumatoid arthritis (RA) and systemic sclerosis (SSc) (scleroderma). An NF-&amp;#x3ba;B binding site specific to allele *2 may contribute to the association of this allele with chronic inflammatory autoimmune diseases.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/4102/version/1

Assortative human pair-bonding for partner ancestry and allelic variation of the dopamine receptor D4 (DRD4) gene
Provedor de dados: 17
Autores: Dan T. A. Eisenberg; Coren L. Apicella; Benjamin C. Campbell; Anna Dreber; Justin R. Garcia; J. Koji Lum.
The 7R allele of the dopamine receptor D4 gene has been associated with attention-deficit hyperactivity disorder and risk taking. On the cross-population scale, 7R allele frequencies have been shown to be higher in populations with more of a history of long-term migrations. It has also been shown that the 7R allele is associated with individuals having multiple-ancestries. Here we conduct a replication of this latter finding with two independent samples. Measures of subjects&amp;#x2019; ancestry are used to examine past reproductive bonds. The individuals&amp;#x2019; history of inter-racial/ancestral dating and their feelings about this are also assessed. Tentative support for an association between multiple ancestries and the 7R allele were found. These...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2660/version/1

Astrobiological Perspectives on Consciousness
Provedor de dados: 17
Autores: Rodrick Wallace.
The Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties are not likely to have followed the particular, highly contingent and path-dependent, trajectory found on Earth. Are many of these life forms likely to be conscious in ways that we would recognize? Almost certainly. Will many conscious entities develop high order technology? Less likely. If so, will we be able to communicate with them? Only on a basic level, and only with profound difficulty. The argument is straightforward.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5286/version/1

Asymmetric development of Cotyledons of Tomato Embryo:  Testing the prediction of Self-Organization
Provedor de dados: 17
Autores: Chalapathy  Reddy.
Developmental biologists have long strived to understand how organisms acquire shape and form. The architecture of the mature plant is established during embryogenesis. They have learned much about how gene expression controls the specification of cell type and about how cells interact with one another to coordinate such specific decisions. Far less is known about autocatalytic feedback flow of resource molecules regulating a plant and its parts, shape and form. Indeed, it has even been proposed that the development of shape is not under genetic control but rather is determined by physical forces. Asymmetric development of sinks that depend on common resource pool has been viewed as a consequence of autocatalytic feedback process of flow of resource units...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2989/version/1

Asynchronous Rhythm of Steroidogenic Factor 1 and Period Homolog 2 mRNA Expression in Mouse Y1 Adrenocorticol Tumor Cells
Provedor de dados: 17
Autores: Kenji Ohe; Kouichirou Sonoda; Makoto Akashi; Koichi Oba; Masatoshi Nomura; Taijiro Okabe; Koichi Node; Ryoichi Takayanagi; Hajime Nawata; Toshihiko Yanase.
The relationship between the expression of Steroidogenic factor 1 (Sf1) and the circadian-related gene, period homolog 2 (Per2), in the adrenal cortex is still unknown. We show here that in Y1 adrenocortical tumor cells, expression of steroidogenic-related genes such as P450scc mRNA and Sf1 mRNA were asynchronous with Per2 mRNA. SF1 promoter analyses showed that the E-box element functions in a rhythmic pattern. Rhythmic expression of Upstream factor 1 mRNA, correlated well with Sf1 mRNA expression. We propose that tumorigenesis of adrenocortical lesions cause disruption of synchronous expression of steroidogenic-related and circadian-related genes.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4523/version/1

Atlases of Minnesota Water Sustainability: Creation from Models, Analytical Methods, and Database of Watershed Characteristics
Provedor de dados: 17
Autores: John Nieber; Roman Kanivetsky; Heidi Peterson; Francisco Lahoud; David Mulla; Boris Shmagin.
Confident assessment of the numbers of regional water balance and water resources for Atlases of MN Water Sustainability (AMNWS) has to be based on the best science, advanced knowledge and modern technology. Creating a watershed characteristic database is the first and most significant step in the analysis of time spatial distributions of Minnesota&amp;#x2019;s water balance components. The database spatially associates hydrologic data (annual discharge, monthly proportion, and yield) with topographical, soil and vadoze zone, ecological and hydrogeological conditions and properties. USGS stream flow data for 129 gauging stations surrounding MN was manipulated within ArcGIS. Characteristics of the 129 watersheds (drainage areas 100-10000 square miles) were...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2378/version/1

Atmospheric hypoxia limits selection for large body size in insects
Provedor de dados: 17
Autores: C Jaco Klok; Jon Harrison.
Recent geological models indicate a marked increase in atmospheric oxygen partial pressure (aPO~2~) to 32 kPa in the Permo-Carboniferous (approx. 300 million years ago), subsequently falling to 13 kPa in the Triassic^1^.These aPO~2~ changes have been hypothesized to cause multiple major evolutionary events^2^ including the appearance and subsequent extinction of giant insects and other taxa^3, 4^. Patterns of increasing tracheal investment in larger insects support this hypothesis^5^, as do observations of positive relationships between aPO~2~ and body size in single- or multi-generational experiments with _Drosophila melanogaster_ and other insects^6^. Large species likely result from many generations of selection for large body size driven by predation,...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1831/version/1

Atomic and molecular structures of positronium, dipositronium and positronium hydride
Provedor de dados: 17
Autores: Raji Heyrovska.
The three positron based chemical entities, analogous to hydrogen atom, hydrogen molecule and hydride, are drawing increasing attention in the literature. While a lot is known about the binding energies, not much is known about the radii of the atoms and ions and bond lengths and structures of these exotic entities. This article brings for the first time exact values of these structural properties which are comparable with known data. It is hoped that the results will be of help for a better understanding and further development of the chemistry and physics of these exotic compounds and of their possible role as intermediates in chemical and interfacial processes.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6290/version/1

Atomic Structures of Molecules Based on Additivity of Atomic and/or Ionic Radii
Provedor de dados: 17
Autores: Raji Heyrovska; Sara Narayan.
The authors have shown in recent years that interatomic and interionic distances are sums of the radii of the adjacent atoms and/or ions. Many examples will be provided and it will be shown how the experimental bond lengths agree with the radii sums. The examples include inorganic compounds like alkali halides, metal hydrides, graphene, etc., organic like aliphatic and aromatic compounds and biochemical like nucleic acids, amino acids, caffeine-related compounds and vitamins.
Tipo: Poster
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3292/version/1

Attention induces dynamic changes in coherence between monkey area V1 and V4
Provedor de dados: 17
Autores: Iris Grothe; Simon D. Neitzel; Sunita Mandon; Andreas K. Kreiter.
Neurons receive a vast number of synaptic inputs at the same time. To successfully process a relevant piece of information, a neuron needs to select relevant, while suppressing irrelevant signals. In order to dynamically route a meaningful set of signals through processing pathways, neurons need to have a fast and flexible mechanism to change their effective connectivity. Here, we hypothesize that attention changes effective connectivity by modulating the synchrony between neuronal populations.&amp;#xd;&amp;#xa;We investigated whether attention dynamically changes effective connectivity between area V4 neurons and their V1 input. Single unit activity, multi unit activity and local field potentials (LFP) were recorded simultaneously from macaque...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5884/version/1

Attentional control and engagement with digital technology
Provedor de dados: 17
Autores: Tracy Alloway; Ross Alloway.
Multiple demands comprise the efficiency of attentional control. There is abundant evidence that when an individual attempts two or more attentionally demanding activities at the same time, the allocation of attention to the tasks is limited and performance suffers as a result. Yet, recent technological innovations require many individuals to manage multiple digital technologies simultaneously or to switch attentional control between tasks. The ability to multitask with various digital technologies involves dividing attention, switching between tasks, and keeping track of multiple strands of information in working memory.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5603/version/1

Auditory cortex mediates the perceptual effects of acoustic temporal expectation
Provedor de dados: 17
Autores: Santiago Jaramillo; Anthony M. Zador.
When events occur at predictable instants, anticipation improves performance. Knowledge of event timing modulates motor circuits, improving response speed. By contrast, the neuronal mechanisms underlying changes in sensory perception due to expectation are not well understood.  We have developed a novel behavioral paradigm for rats in which we manipulated expectations about sound timing.  Valid expectations improved both the speed and the accuracy of subjects&amp;#x27; performance, indicating not only improved motor preparedness but also enhanced perception.  Single neuron recordings in primary auditory cortex revealed enhanced representation of sounds during periods of heightened expectation. Furthermore, we found that activity in auditory cortex was...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5139/version/1

Autism-associated SNPs in the clock genes _npas2_, _per1_ and the homeobox gene _en2_ alter DNA sequences that show characteristics of microRNA genes.
Provedor de dados: 17
Autores: Brad Nicholas; Michael J. Owen; Dawn C. Wimpory; Thomas Caspari.
Intronic single nucleotide polymorphisms (SNPs) in the clock genes _npas2_ and _per1_ and the homeobox gene _en2_ are reported to be associated with autism. This bioinformatics analysis of the intronic regions which contain the autism-associated SNPs rs1861972 and rs1861973 in _en2_, rs1811399 in _npas2_, and rs885747 in _per1_, shows that these regions encode RNA transcripts with predicted structural characteristics of microRNAs. These microRNA-like structures are disrupted _in silico_ by the presence of the autism enriched alleles of rs1861972, rs1861973, rs1811399 and rs885747 specifically, as compared with the minor alleles of these SNPs. The predicted gene targets of these microRNA-like structures include genes reported to be implicated in autism...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2366/version/1

Automated Annotation-Based Bio-Ontology Alignment with Structural Validation
Provedor de dados: 17
Autores: Cliff Joslyn; Bob Baddeley; Judith Blake; Carol Bult; Mary Dolan; Rick Riensche; Karin Rodland; Antonio Sanfilippo; Amanda White.
We outline the structure of an automated process to both align multiple bio-ontologies in terms of their genomic co-annotations, and then to measure the structural quality of that alignment. We illustrate the method with a genomic analysis of 70 genes implicated in lung disease against the Gene Ontology.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3518/version/1

Automated ocular artifact removal: comparing regression and component-based methods
Provedor de dados: 17
Autores: Alois Schloegl; Andreas  Ziehe; Klaus-Robert M&amp;#xfc;ller.
Objective: The aim is to compare various fully automated methods for reducing ocular artifacts from EEG recordings.&amp;#xd;&amp;#xa;Methods: Seven automated methods including regression, six component-based methods for reducing ocular artifacts have been applied to 36 data sets from two different labs. The influence of various noise sources is analyzed and the ratio between corrected and uncorrected EEG spectra, has been used to quantify the distortion. &amp;#xd;&amp;#xa;Results: The results show that not only regression but also component-based methods are vulnerable to over- or under-compensation and can cause significant distortion of EEG. Despite common belief, component-based methods did not demonstrate an advantage over the simple regression method....
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3446/version/1

Automatic protein clustering as a basis of automatic annotation
Provedor de dados: 17
Autores: Naoki Sato.
Development of new generation sequencers enabled genome sequencing feasible for every organism in a laboratory. A typical data flow of de novo seuqencing includes (1) assembly of sequence reads, (2) estimation of open reading frames, (3) annotation of proteins, and (4) finding RNA genes. The annotation is normally performed by BLASTP searches against several different databases. However, it is usually hard to find a plausible annotation by just looking at the results of BLASTP searches.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Here I propose a potentially automatic method of annotation that exploits automatic protein clustering using the software GCLUST, which estimates proper similarity threshold for each list of homologs using &amp;#x2018;entropy-optimized...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5086/version/1

Automatisation in UniProtKB / Swiss-Prot Annotation: New Rules and Tools
Provedor de dados: 17
Autores: The HAPMAP Team; The PROSITE Team; Edouard de Castro; Alan Bridge; UniProt Consortium.
The development of next generation sequencing technologies promises a massive increase in the rate of submission of new protein sequences to sequence databases such as the Universal Protein Resource Knowledge Base, UniProtKB. At UniProtKB/Swiss-Prot we propose to meet this challenge by continuing to expand and develop systems for the automatic propagation of existing annotation to newly submitted protein sequences. These developments will promote the standardization of ortholog annotation both across and within kingdoms and significantly enhance our ability to accurately annotate new protein sequences which are being produced at an ever increasing rate.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3215/version/1

Autosegregation of enzyme loci Me1 and Gpi2 in agamospermous progenies of triploid sugarbeet plants
Provedor de dados: 17
Autores: Evgenii  Levites; Svetlana Kirikovich.
Ratios of malic-enzyme (ME1) and glucosephosphate isomerase (GPI2) phenotypic classes were studied in agamospermous progenies of triploid sugar beet plants. It was shown that the ratio of enzymes phenotypic classes quite well accords with the calculations based on the supposition about reduplication of chromosome sites carrying alleles of enzyme loci accompanied by a loss of excessive allelic copies in the first cell division under embryogenesis. Polyteny &amp;#x2013; conditioned allelic dose increase leads to the occurrence of alleles &amp;#x2013; absent in the initial parent &amp;#x2013; at a certain frequency in the developing progeny. The notions of &amp;#x201c;meiotic autosegregation&amp;#x201d; and &amp;#x201c;mitotic autosegregation&amp;#x201d;...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5464/version/1

Aven and Survivin Expression in Egyptian Acute Leukemia and Their Relation to Apoptosis
Provedor de dados: 17
Autores: Magda Assem; Thorraya Abedel- ALhameid; Gihan A-Basset; Amany M. Hilal; Mahmoud Kamel; Iman Khalil; Nahla Alsharkawey; Ayman Metwally.
Background: Several anti apoptotic signals have been recently identified. Aven and Survivin are broadly expressed and are conserved in mammalian species. Patients and Methods: 39 AML and 25 ALL were tested. Aven and Survivin expression were detected by RT-PCR. DNA fragmentation was carried out daily after treatment..Results: Survivin was expressed (P=0.06) more in AML (74%) than in ALL (52%). While, Aven was equally expressed in both leukemias. Patients were categorized into 3 groups based on DNA fragmentation. Absence of Aven significantly (p&amp;#x2039;0.001) contributed to DNA fragmentation,but Survivin did not contribute as much. None of the concordant both positive Survivin and Aven were in group III (the good 5 day fragmentation, (P&amp;#x3c; 0.001)....
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3771/version/1

Averaging Transformations of Synaptic Potentials on Networks
Provedor de dados: 17
Autores: Hamid Reza Noori.
The problem of the transformation of microscopic information to the macroscopic level is an intriguing challenge in computational neuroscience, but also of general mathematical importance. Here, a phenomenological mathematical model is introduced that simulates the internal information processing of brain compartments. Synaptic potentials are integrated over small number of realistically coupled neurons to obtain macroscopic quantities. The striatal complex, an important part of the basal ganglia circuit in the brain for regulating motor activity, has been investigated as an example for the validation of the model.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3348/version/1

Azadirachta indica induced suppression of Mycobacterium tuberculosis secreted proteins in human monocyte
Provedor de dados: 17
Autores: Jawed Iqbal; Ajay Kumar; Najmul Islam.
The H37Rv strain of MTB was grown in modified Sauton&amp;#x2019;s medium till mid-log phase. Peripheral blood mononuclear cells (PBMC) were isolated by density gradient sedimentation on Ficoll-Paque separation medium. Adherent monocytes obtained from PBMC&amp;#x2019;s were infected with H37Rv for 90 min. in the ratio of 1:1 (1 bug: 1 cell). Thereafter, after washing, infected cells were co-cultured with varying doses of neem extract for 24 hrs, and harvested subsequently. Modulation of secreted TNF-[alpha], iNOS and MTB Ag85 complex expressions in culture supernatants was estimated by ELISA.&amp;#xd;&amp;#xa;We report the high basal expression of secreted tumor necrosis factor-[alpha] (TNF-[alpha]), inducible nitric oxide synthase (iNOS) and MTB Ag85...
Tipo: Poster
Palavras-chave: Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1562/version/1

B6 deficient feeding or homocysteic acid induces the earlier Alzheimer&amp;#x27;s pathological change in normal C57BL male mice
Provedor de dados: 17
Autores: Tohru Hasegawa; Nobuyuki Mikoda; Masashi Kitazawa; Frank LaFerla.
It is the first report that the earlier Alzheimer&amp;#x27;s pathological changes can be induced in normal C57BL mice, by B6 deficient feeding for 3 month, and this pathological changes were completely inhibited by anti-homocysteic acid antibody. According to Koch&amp;#x27;s postulate, if a pathogen of Alzheimer&amp;#x27;s disease is administrated to the normal animal, we would observe the Alzheimer&amp;#x27;s pathology in the normal animal. We actually have observed this pathology in normal C57BL male mice.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2764/version/1

Backup machinery of yeast transcriptional regulatory network
Provedor de dados: 17
Autores: Dhriti Sengupta; Sudip Kundu.
Several studies have suggested the existence of backup machinery of transcriptional regulatory networks (TRNs). Here, we have quantified the backup machinery of yeast gene&amp;#x27;s TRNs under five different conditions in terms of alternate paths and have revealed that a statistically significant (p&amp;#x3c;0.0001) stronger backup is maintained for endogenous processes (ENPs) than exogenous processes (EXPs). A number of biologically important genes (SUC2, MF(ALPHA)2, CLN2 etc) are observed that maintain a higher backup. Hub and random transcription factor (TF) knockouts in TRNs have showed ENPs are more robust to deletion than EXPs. While higher average connectivity of TFs in EXPs than ENPs can&amp;#x27;t explain the higher robustness in ENPs, we have...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/1791/version/1

Bacteria have transient influences on marine corrosion of steel
Provedor de dados: 17
Autores: Robert E. Melchers; Robert Jeffrey.
The contribution of bacteria to the corrosion mass loss and to pitting of mild steel was observed over 2.5 years using parallel streams of unpolluted natural (biotic) and nominally sterilized (abiotic) Pacific Ocean coastal seawater. As also observed by others, in artificial laboratory exposures, corrosion mass loss within the first few days of exposure was much greater in the biotic stream. However, after only about 10 days the difference in mass losses were gradually reduced and were very similar up to about one year of exposure. Thereafter, the corrosion loss in the biotic stream again became more severe. Pitting corrosion in the biotic stream was more severe from the very first exposure throughout the 2.5 years. Corrosion in both seawater streams...
Tipo: Manuscript
Palavras-chave: Chemistry; Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/5767/version/1

Bacterial Capnine Blocks Transcription of Human Antimicrobial Peptides
Provedor de dados: 17
Autores: Trevor G. Marshall.
The US CDC believes that 65% of all infections in developed countries may be caused by pathogens in biofilms. Electron Microscopy has shown that these bacterial communities can evade phagocytosis, and persist in the cytoplasm of monocytes, macrophages, lymphocytes and neutrophils. Three decades ago, Wirostko _et al._ found such intraphagocytic communities in Crohn&amp;#x2019;s disease, Juvenile Rheumatoid Arthritis and Sarcoidosis. However, the mechanism(s) by which such persistent bacteria could evade the immune system have remained elusive. Recently, 16S RNA from species of gliding bacteria never thought to be able to survive _in vivo_, have been found in surgically removed biofilms. This study set out to identify whether the genomes of these gliding...
Tipo: Poster
Palavras-chave: Immunology; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/164/version/1

Bacteriophages as a model for studying carbon regulation in aquatic system
Provedor de dados: 17
Autores: Swapnil G. Sanmukh; Waman N. Paunikar; Sandhya Swaminathan; Satish K. Lokhande.
The interconversion of carbon in organic, inorganic and refractory carbon is still beyond the grasp of present environmentalists. The bacteria and their phages, being the most abundant constituents of the aquatic environment, represent an ideal model for studing carbon regulation in the aquatic system. The refractory dissolved organic carbon (DOC), a recently coined terminology from the microbe-driven conversion of bioavailable organic carbon into difficult-to-digest refractory DOC by microbial carbon pump (MCP), is suggested to have the potential to revolutionize our view of carbon sequestration. It is estimated that about 95% of organic carbon is in the form of refractory DOC, which is the largest pool of organic matter in the ocean. The refractory DOC...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/6770/version/1

Balancing noise and plasticity in gene expression
Provedor de dados: 17
Autores: Djordje Bajic; Juan F. Poyatos.
Coupling the control of expression stochasticity (noise) with the capacity to expression change (plasticity) can constrain gene function and limit adaptation. Which factors contribute then to modulate this coupling? Transcription re-initiation is generally associated with coupling and this is commonly related to strong chromatin regulation. We alternatively show how strong regulation can however lead to plasticity uncorrelated to noise. The character of the regulation is also relevant, with plastic but noiseless genes usually subjected to broad expression activation whereas plastic and noisy genes experience targeted repression. This differential action is similarly noticed in how histones influence these genes. In contrast, we find that translational...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6729/version/1

Ball Milling as a Tool Towards Solubility Problems in Synthesis &amp;#x2013; Simple and Solvent-free Preparation of K[B(CN)4]
Provedor de dados: 17
Autores: Roland Pawelke.
A simple ball milling route to the tetrayanoborate anion is presented: The K[B(CN)4] synthesis is one fine example, how a synthesis problem based on solubility may be solved by a ball milling approach. The solid state 13C- and 11B-MAS-NMR spectra have been recorded.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6258/version/1

Barlow-Hall in vitro Evolution Protocol
Provedor de dados: 17
Autores: Barry G. Hall; Miriam Barlow.
The Barlow-Hall method for in vitro evolution is a simple alternative to methods such as DNA shuffling and is particularly applicable to predicting the evolution of target genes in nature.  This detailed protocol includes the procedure itself and, as Appendices, describes particularly effective protocols for electroporation and for preparation of electrocompetent cells.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1772/version/1

Basic emotions: Differences in time sequence and functional imaging with low resolution brain electrical tomography (LORETA)
Provedor de dados: 17
Autores: Tommaso Costa; Manuella Crini.
The aim of the present study is to investigate the relationship between the time course of brain activation during the observation of pictures depicting scenes associated with the four basic emotion of happiness, sadness, fear and disgust. Twenty-nine right-handed volunteers (17 male, 12 female; mean age 24.6 years) took part in the study. To study the time course of the affective processing the low resolution brain electromagnetic tomography (LORETA) has been used. Each emotional condition has shown specific activation patterns in different brain regions, changing over time. Our findings are in good agreement with other brain-imaging studies (PET/fMRI) but with the advantage to investigate the temporal evolution of the emotional process in the millisecond...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5566/version/1

BBSRC Data Sharing Policy
Provedor de dados: 17
Autores: Amanda Collis; David McAllister; Michael Ball.
BBSRC recognizes the importance of contributing to the growing international efforts in data sharing. BBSRC is committed to getting the best value for the funds we invest and believes that making research data more readily available will reinforce open scientific inquiry and stimulate new investigations and analyses. BBSRC supports the view that data sharing should be led by the scientific community and driven by scientific need. It should also be cost effective and the data shared should be of the highest quality. Members of the community are expected and encouraged to practice and promote data sharing, determine standards and best practice, and create a scientific culture in which data sharing is embedded.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Immunology; Microbiology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Plant Biology; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6015/version/1

Beautifying Data in the Real World
Provedor de dados: 17
Autores: Jean-Claude Bradley; Rajarshi Guha; Andrew Lang; Pierre Lindenbaum; Cameron Neylon; Antony Williams; Egon Willighagen.
This chapter from the O&amp;#x27;Reilly book &amp;#x22;Beautiful Data&amp;#x22; describes the use of Open Notebook Science to crowdsource solubility data.  The use of GoogleDocs, wikis, ChemSpider, RDF, the Chemistry Development Kit and Second Life is described.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4918/version/1

Behavioral and Psychiatric Genetics: Learning from History
Provedor de dados: 17
Autores: Kenneth Schaffner.
Behavioral and Psychiatric Genetics (BPG) offers great promise for clarifying the causes of both normal behaviors as well as psychiatric disorders, and in the latter case serving as a more rational basis for treatments. But the field has also generated serious social concerns about individual and ethnic stereotyping of intelligence and violent behaviors. This short talk identifies some of these themes from the 1970s, 80s, and 90s, and reviews recent shifts about the directions BPG is taking in the first decade of the twenty-first century. I cover the collapse of simple molecular gene-behavior models in the 1990s, and the rise of gene-environment interaction paradigms, as well as the increasing role of neuroscience in BPG in the present decade. I close by...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2621/version/1

Behavioral Genetics and Equality
Provedor de dados: 17
Autores: Dan Brock.
I will explore the implications of findings in behavioral genetics for two conceptions of equality: equality of opportunity and the equal moral worth of persons. New findings in behavioral genetics showing that behavioral traits, and the variance in behavioral traits, have some genetic underpinnings would not seem in themselves to threaten either of these notions of equality--we have long known that there is significant variation in these traits across persons and have assumed that some significant portion of that variation has genetic sources. I believe it is the uncertain and probably distant prospect of genetic interventions to enhance some behavioral traits, which could greatly increase the range and inequality of those traits in humans, that may seem...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2566/version/1

Behavioral origins of metabolic syndrome disorders
Provedor de dados: 17
Autores: Milind Watve; Maithili Jog; Prajakta Belsare.
The metabolic syndrome disorders (MSD) including type 2 diabetes, hypertension, hypercholesterolemia, atherosclerosis and cardiovascular disease are known to be triggered by lifestyle change. We state and support a hypothesis here that changes in behavior rather than changes in diet and metabolism are central to MSD. We provide and discuss evidence in support of the following sequence of arguments. (i) Diet, thriftiness and obesity centered paradigm is inadequate to explain most of the physiological and immunological changes associated with metabolic syndrome disorders (MSD).  (ii) Comparative studies show that relative obesity rather than absolute obesity is strongly associated with various parameters of MSD and further perception of calories without...
Tipo: Presentation
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4833/version/1

Benchmarking the SPARC software program for estimating solubilities of naphthalene and anthracene in organic solvents
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
The SPARC software program was benchmarked for calculating the solubilities of two representative polyaromatic hydrocarbons (PAHs), naphthalene and anthracene, in a range of organic solvents at various temperatures. Although SPARC was able to reasonably approximate the solubilities of naphthalene in some organic solvents, gross errors were obtained for other solvents. For anthracene, poor prediction performance was observed in all solvents considered. Overall, the results suggest that SPARC is currently not suitable for accurately predicting the solubilities of representative PAHs relevant for the petroleum sector in various organic solvents.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6648/version/1

Benchmarking triple stores with biological data
Provedor de dados: 17
Autores: Vladimir Mironov.
We have compared the performance of five non-commercial triple stores, Virtuoso-open source, Jena SDB, Jena TDB, SWIFT-OWLIM and 4Store. We examined three performance aspects: the query execution time, scalability and run-to-run reproducibility. The queries we chose addressed different ontological or biological topics, and we obtained evidence that individual store performance was quite query specific. We identified three groups of queries displaying similar behavior across the different stores: 1) relatively short response time, 2) moderate response time and 3) relatively long response time. OWLIM proved to be a winner in the first group, 4Store in the second, and Virtuoso in the third. Our benchmarking showed Virtuoso to be a very balanced performer...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5417/version/1

Beneficial role of allicin from garlic in cervical cancer
Provedor de dados: 17
Autores: Irfan Ahmad Ansari; Najmul  Islam.
Introduction: Cervical cancer remains a global health concern for females. Thus, in order to control cervical cancer, attempts are being made by researchers globally to somehow induce programmed cell death in the said cancerous cells. Wide spectrums of molecules are being probed for its ability to induce apoptosis in cervical cancer cells. Focus has now shifted in exploring natural compounds having antioxidant and anti-inflammatory molecules that may induce apoptosis in cancerous cells. Thus, we have employed allicin from garlic- a natural antioxidant, to probe the above in the present study.&amp;#xd;&amp;#xa;Objective: To probe whether or not allicin from garlic, a natural antioxidant, induces apoptosis in monocytes from patients with cervical...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1561/version/1

Berberine induces caspase-independent cell death in colon tumor cells through activation of apoptosis-inducing factor
Provedor de dados: 17
Autores: Lihong Wang; Liping Liu; Yan Shi; Hamwei Cao; Rupesh Chaturvedi; Tianhui Hu; Keith Wilson; D. Brent Polk; Fang Yan.
Berberine, an isoquinoline alkaloid derived from plants, is a traditional medicine for treating bacterial diarrhea and intestinal parasite infections. Although berberine has recently been shown to suppress growth of several tumor cell lines, information regarding the effect of berberine on colon tumor growth is limited. Here, we investigated the mechanisms underlying the effects of berberine on regulating the fate of colon tumor cells, specifically the immorto Min mouse colonic epithelial (IMCE) cells carrying the Apcmin mutation, and of normal colon epithelial cells, namely young adult mouse colon (YAMC) epithelial cells. Berberine decreased colon tumor colony formation in agar, and induced cell death and LDH release in a time- and concentration-dependent...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2011
URL: http://precedings.nature.com/documents/6438/version/1

Best practices for building interoperable systems for translational research
Provedor de dados: 17
Autores: Warren Kibbe.
Research databases, clinical systems, and lab systems all have different standards, formats and drivers for data capture, operation, analysis and integration. For interdisciplinary nutritional researchers, however, there is a dependence on all of these areas and technologies. While building and integrating these systems can be difficult, using agile practices including short iterations, testing and continuous integration methods, and close engagement with all stakeholders to create useful systems for translational research. Interoperability also requires good data standards, including the use of structured data dictionaries and existing data standards such as HL7, UMLS, LOINC, ICD, and OBO foundry ontologies.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5197/version/1

Betaine aldehyde dehydrogenase (BADH) from Hordeum vulgare- an in-silico study
Provedor de dados: 17
Autores: Kaushal Kumar Bhati; Vijay  Kumar Singh.
Glycine Betaine is a quaternary amino compound that accumulates in stress conditions, mainly abiotic stresses like drought and salinity &amp;#x26; synthesized  by  the  two-step  oxidation  of  choline  via  the intermediate  betaine  aldehyde,  catalyzed  by  Choline  monooxygenase  and  Betaine  aldehyde dehydrogenase  (BADH).&amp;#xd;&amp;#xa;The sequence analysis of key enzymes of Glycine betaine biosynthesis i.e. BADH was carried out using various online proteomic tools available on Expasy and EBL, and then homologous modeling of this enzyme was performed using automated mode SWISS-MODEL &amp;#x26; GENO 3D and models were analyzed on QMEAN.  This was an attempt to find the possible model of BADH, because no physical model of BADH is yet available on...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6360/version/1

Better Analysis, Better Acceptance &amp;#x2010;Take up the Challenge of Publishing in Bioinformatics
Provedor de dados: 17
Autores: Malay Bhattacharyya.
This presentation teaches the novice in bioinformatics research to publish quality analysis in good venues.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7124/version/1

Bevacizumab-induced tumor calcifications can be elicited in glioblastoma microspheroid culture and represent massive calcium accumulation death (MCAD) of tumor endothelial cells
Provedor de dados: 17
Autores: Larry Weiseenthal; Summer Williamson; Cindy Brunschwiler; Constance Rueff-Weisenthal.
B&amp;#xe4;hr and colleagues reported that 22 of 36 glioblastoma patients treated with bevacizumab showed tumor calcifications on 8 week post therapy follow up with MRI. Early tumor calcification strongly predicted for response, time to progression, and overall survival. The authors didn&amp;#x2019;t understand the mechanism, but speculated that it was vascular in nature. At the 13th International Anti-Angiogenic Symposium (2011), we presented our discovery of the phenomenon of massive calcium accumulation death, wherein MCAD occurred in endothelial cells (tumor, circulating, and HUVEC), in response to VEGF depletion by bevacizumab and other putative anti-angiogenic agents, but not in response to non-specific cytotoxins. In subsequent work, we have...
Tipo: Poster
Palavras-chave: Cancer.
Ano: 2012
URL: http://precedings.nature.com/documents/7069/version/1

Beyond Spike Timing Theory &amp;#x2013; Thermodynamics of Neuronal Computation
Provedor de dados: 17
Autores: Dorian Aur; Mandar S. Jog.
This paper highlights ionic fluxes as information carriers in neurons. The theoretical framework regarding information transfer is presented as changes in the thermodynamic entropy that underlie specific computations determined by ionic flow. The removal or accumulation of information is analyzed in terms of ionic mass transfer related with changes in Shannon information entropy. Specifically, information transfer occurs during an action potential (AP) via the voltage gated ion channels in membranes and the same physical mechanism can be extended to various types of synapses. Since sequential APs from a selected neuron are not alike, then every spike may transfer slightly different amounts of information during their occurrence. The average efficiency in...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1254/version/1

Beyond Structure: KiSAO and TEDDY -- Two Ontologies Addressing Pragmatical and Dynamical Aspects of Computational Models in Systems Biology
Provedor de dados: 17
Autores: Dagmar K&amp;#xf6;hn; Nicolas Le Nov&amp;#xe8;re; Christian Kn&amp;#xfc;pfer.
Computational models are becoming more and more the central scientific paradigm for understanding the complexity of living systems. With the increasing number and size of these models there is a growing need for model reuse and exchange. Furthermore, detailed models are not manageable without computer support. There are efforts to formalise the mathematical structure of models (e.g. SBML) and to standardise the kinetic and biological meaning of model components (e.g. SBO, GO, UniProt). However, formalising only the structure of computational models is not sufficient to easily exchange and reuse models and to achieve full computer support for modelling. We also need to formalise the pragmatical and dynamical aspects of...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3137/version/1

Beyond the fuzzy lock-and-key: spontaneous symmetry shifts and glycan/lectin logic gates
Provedor de dados: 17
Autores: Rodrick Wallace.
Changes in the molecular topology of glycan/lectin interaction may explain observed reaction punctuation driven by experimental gradients in reactant concentration. Adoption of a &amp;#x27;biological renormalization&amp;#x27; perspective from statistical physics for the analysis of such phase transitions suggests, in marked contrast to conventional physical systems, a broad spectrum of possible universality class behaviors. This spectrum may, in typical perverse biological manner, be of central scientific interest. Generalization, via formalism abducted from coevolutionary theory, suggests that glycan/lectin molecular switches instantiate logic gates that may be as sophisticated as those characterizing basic neural process, if on a different scale.
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Microbiology; Molecular Cell Biology; Pharmacology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6849/version/1

BFO/DOLCE Primitive Relation Comparison
Provedor de dados: 17
Autores: A. Patrice Seyed.
This paper examines the primitive relations (dependence, quality, and constitution) of the BFO and DOLCE upper ontologies, employed in developing domain ontologies of the biomedical sciences. The strengths in both upper ontologies are examined, which sets a framework for developing a common upper ontology that utilizes the assets of both.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3481/version/1

BHL, The Biodiversity Heritage Library:  An Expanding International Collaboration
Provedor de dados: 17
Autores: Constance Rinaldo; Catherine  Norton.
*Background/Question/Methods*&amp;#xd;&amp;#xa;The Biodiversity Heritage Library (BHL; &amp;#x22;http://www.biodiversitylibrary.org/&amp;#x22;:http://www.biodiversitylibrary.org/), one of the cornerstones of the Encyclopedia of Life (eol.org), now contains nearly 13 million digitized pages of 12,000 titles comprised of 32,000 volumes of the published literature of biodiversity held in the collections of major natural history libraries. The BHL has made this literature available for open access and responsible use as a part of a global &amp;#x201c;biodiversity commons.&amp;#x201d; The BHL partnership is working with the global taxonomic community, publishers, organizations such as JSTOR and BIOONE, and the Internet Archive, to ensure that the biodiversity...
Tipo: Poster
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3620/version/1

Bias Correction in Logarithmic Regression and Comparison with Weighted Regression for Nonlinear Models
Provedor de dados: 17
Autores: Wei Sheng Zeng; Shou Zheng Tang.
Non-linear models with heteroscedasticity are commonly used in ecological and forestry modeling, and logarithmic regression and weighted regression are usually employed to estimate the parameters. Using the single-tree biomass data of three large samples, the bias correction in logarithmic regression for non-linear models was studied and comparison between logarithmic regression and weighted regression was discussed in this paper. Firstly, the imminent cause producing bias in logarithmic regression was analyzed, and a new correction factor was presented with which three commonly used bias correction factors were examined together, and the results showed that the correction factors presented here and derived by Baskerville (1972) should be recommended,...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6708/version/1

Bias in culture-independent assessments of microbial biodiversity in the global ocean
Provedor de dados: 17
Autores: Ben B. Temperton; Anna Oliver; Dawn Field; Bela Tiwari; Martin Muhling; Ian Joint; Jack Gilbert.
On the basis of 16S rRNA gene sequencing, the SAR11 clade of marine bacteria has almost universal distribution, being detected as abundant sequences in all marine provinces. Yet SAR11 sequences are rarely detected in fosmid libraries, suggesting that the widespread abundance may be an artefact of PCR cloning and that SAR 11 has a relatively low abundance. Here the relative abundance of SAR11 is explored in both a fosmid library and a metagenomic sequence data set from the same biological community taken from fjord surface water from Bergen, Norway. Pyrosequenced data and 16S clone data confirmed an 11-15% relative abundance of SAR11 within the community. In contrast not a single SAR11 fosmid was identified in a pooled shotgun sequenced data set of 100...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/2818/version/1

Biased amino acid composition in warm-blooded animals
Provedor de dados: 17
Autores: Guang-Zhong Wang; Martin  J. Lercher.
Among eubacteria and archeabacteria, amino acid composition is correlated with habitat temperatures. In particular, species living at high temperatures have proteins enriched in the amino acids E-R-K and depleted in D-N-Q-T-S-H-A. Here, we show that this bias is a proteome-wide effect in prokaryotes, and that the same trend is observed in fully sequenced mammals and chicken compared to cold-blooded vertebrates (Reptilia, Amphibia and fish). Thus, warm-blooded vertebrates likely experienced genome-wide weak positive selection on amino acid composition to increase protein thermostability.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2974/version/1

Binding Pattern Determination Of Class of Antifungal Drugs
Provedor de dados: 17
Autores: Arpit Tandon; A Naqvi; Nitin Chitranshi; Siddharth Sinha.
Crystal Structure of cytochrome p450 2B4 has 476 amino acids, through docking approach we have attempted to explain the specificity of CYP2B4, total 28 imidazole drug were used for the studies as antifungal drugs in which bound bifonazole (reference) shows the binding energy of -8.67 kcal/mol .Compound Miconazole shows the minimum binding energy of -10.45 kcal/mol. The 2B4-bifonazole structure identified 10 residues (ALA 298, GLY 299, GLU 301, THR 302, ILE 363, VAL 292) within 6.5 &amp;#xc5; of the active site of bifonazole. GLU 301, THR 302 are also located in 6.5 &amp;#xc5; of the bound ligand in 2B4 structure. Due to the presence of the multiple binding substrates in cytochrome p450, it acts as the major target of many drugs in xenobiotic...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4314/version/1

Binge and Emotional Eating in obese subjects seeking weight loss treatment
Provedor de dados: 17
Autores: Valdo Ricca; Giovanni Castellini; Carolina Lo Sauro; Claudia Ravaldi; Francesco Lapi; Edoardo Mannucci; Carlo Maria Rotella; Carlo Faravelli.
Objective: Binge Eating Disorder (BED) is highly prevalent among individuals seeking weight loss treatment. Considering the possible trigger factors for BED, different studies focused on the role of emotional eating. The present study compared threshold, subthreshold BED, and subjects without BED in a population of overweight/obese individuals seeking weight loss treatment, considering the anamnesis, the eating disorder specific and general psychopathology, the organic and psychiatric comorbidity, the emotional eating as a trigger factor for binge eating, and the quality of life. Design: cross-sectional survey.Subjects: Four hundred thirty eight overweight subjects seeking weight loss treatment have been enrolled in the study. Measurements: Subjects have...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2125/version/1

BiNoM Cytoscape Plugin for constructing, querying and analyzing biological networks, using systems biology standards
Provedor de dados: 17
Autores: Andrei Zinovyev.
BiNoM is a Cytoscape plugin which allows to read, analyze and convert biological networks represented in various systems biology standards.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5120/version/1

Bio2RDF: Convert, Provide And Reuse.
Provedor de dados: 17
Autores: Marc-Alexandre Nolin; Jacques Corbeil; Luc Lamontagne; Michel Dumontier.
The Bio2RDF project uses open-source Semantic Web technologies to provide interlinked life science data in order to maximize productivity and facilitate biological knowledge discovery. Using both syntactic and semantic data integration techniques, Bio2RDF puts into practice a simple methodology to generate and&amp;#xd;&amp;#xa;seamlessly integrate machine-interpretable data that can be powerfully interrogated with SPARQL-based queries to answer sophisticated questions.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;At its core, database records are converted into a set of statements or so-called triples that are captured together as a named graph annotated with provenance. The records and the entities they are about are provided with a Uniform Resource Identifier...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5060/version/1

BioBrick Promoter Measurement Kit Instruction Sheets
Provedor de dados: 17
Autores: Jason Kelly.
Instructions for inserting a test promoter into the measurement kit plasmid for characterization as well as instructions for measuring the activity of the test promoter in Standard Promoter Units (SPUs).  These instructions were distributed to the teams participating in the International Genetically Engineered Machines competition (iGEM).
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2028/version/1

BioCatalogue: A Curated Web Service Registry For The Life Science Community
Provedor de dados: 17
Autores: Carole A. Goble; Khalid Belhajjame; Franck  Tanoh; Jiten Bhagat; Katy Wolstencroft; Robert Stevens; Eric Nzuobontane; Hamish McWilliam; Thomas Laurent; Rodrigo Lopez.
Web Services have gained a momentum as a means for packaging existing data and computational resources in a form that is amenable for use and composition by third party applications. The life science community is certainly among the first adopters of Web Services. For example, &amp;#x22;Taverna&amp;#x22;:http://www.mygrid.org.uk, a workflow workbench that is popular within the life science community, provides access to over 3500 thousands web services that can be composed by scientists for constructing and enacting their _in silico_ experiments. However, one of the main issues that hinders the wide adoption and use of Web Services is the difficulty in locating the &amp;#x201c;appropriate&amp;#x201d; Web Service, i.e., the Web Service that performs the...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3132/version/1

Biochemical Composition of Normal Urine
Provedor de dados: 17
Autores: Atif  Baig.
The urine composition defines the quality of homeostasis of the body. Learning about the normal urine composition is very important to compare it with the suspended and non suspended particles in urine in different pathologies.
Tipo: Presentation
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6595/version/1

Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing Competences of Viruses
Provedor de dados: 17
Autores: Guenther Witzany.
Communicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral patterns even in which they organise themselves like multicellular organisms. They have existed for almost four billion years and still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that these bacterial competences derive from the aptitude of viruses for natural genome editing....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1738/version/2

Bio-Communication of Bacteria and its Evolutionary Interrelations to Natural Genome Editing Competences of Viruses
Provedor de dados: 17
Autores: Guenther Witzany.
Communicative competences enable bacteria to develop, organise and coordinate rich social life with a great variety of behavioral patterns even in which they organise themselves like multicellular organisms. They have existed for almost four billion years and still survive, being part of the most dramatic changes in evolutionary history such as DNA invention, cellular life, invention of nearly all protein types, partial constitution of eukaryotic cells, vertical colonisation of all eukaryotes, high adaptability through horizontal gene transfer and co-operative multispecies colonisation of all ecological niches. Recent research demonstrates that these bacterial competences derive from the aptitude of viruses for natural genome editing....
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1738/version/1

Biocommunication of Fungal Organisms
Provedor de dados: 17
Autores: Guenther Witzany.
The development and growth of fungal organisms depend on successful communication processes (a) within the organism and between organisms, (b) with the same or related species and (c) with non-related organisms. In order to generate an appropriate response behaviour, fungal organisms must also be able to (d) correctly interpret meaningful information from the abiotic environment. However, these communication and interpretation processes can also fail. In such cases the overall results can induce disease-causing and even lethal consequences for the organism. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;&amp;#x9;This review will not enrich the knowledge of specialists in fungal research, but will demonstrate to a broader readership the different levels of fungal...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/1883/version/1

Bio-communication of Plants
Provedor de dados: 17
Autores: Guenther Witzany.
Plants communicate with a great variety of symbiotic partners, above and below ground. Constant monitoring of signals of biotic origin as well as abiotic environmental influences allows plants to generate appropriate response behavior. These communication processes are primarily sign-mediated interactions and not simply an exchange of information. They involve active coordination and active organization of a great variety of different behavioural patterns &amp;#x2013; mediated by signs.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Molecular Cell Biology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1429/version/1

Bioconversion of eugenol into food flavouring agent vanillin
Provedor de dados: 17
Autores: Suaib  Luqman; Sudeep  Tandon; Alok  Somvanshi; Suchita  Srivastava; Mahendra  P. Darokar; Suman  P. S. Khanuja.
Microorganisms have the ability to chemically modify a wide variety of organic compounds by a process referred to as biological or microbial transformation, or in general, bioconversion. The microbial cells and their catalytic machinery (enzymes) accept a wide array of complex molecules as substrates, yielding products with unparallel chiral (enantio-), positional (region-) and chemical (chemo-) selectivity through various biochemical reactions. The present study was formulated on the objective of the conversion of abundantly available phytomolecules eugenol into vanillin, a compound of industrial importance, using microorganisms Aspergillus flavus, Aspergillus niger and Pseudomonas aeruginosa. These microbes were found to be capable of converting eugenol...
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6926/version/1

Biocuration Workflow Catalogue
Provedor de dados: 17
Autores: Gully Burns; Martin Krallinger; Kevin Cohen; Cathy Wu; Lynette Hirschman.
As the first phase of a knowledge engineering study of biocuration workflows, we performed a preliminary task-modeling exercise on seven separate bioinformatics systems. This involved constructing UML activity diagrams from detailed interviews with curators in order to understand the organization of the process the biocurators used to populate their system. The objective of this work was to identify common patterns within the workflows where we might apply text mining methods to accelerate curation. We compiled a number of workflows in a common format but were largely unable to consolidate these structures into a formal structure that facilitated comparison across workflows. We presented this work as a slideshow and publish this account of the catalog as...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3250/version/1

bioDBcore: overview of the checklist and steps towards implementation
Provedor de dados: 17
Autores: Pascale Gaudet (Pascale.Gaudet@isb-sib.ch); Philippe Rocca-Serra (proccaserra@googlemail.com).
Members of the International Society for Biocuration (ISB, biocurator.org) and the BioSharing (biosharing.org) initiative work together to develop and implement BioDBcore (biodbcore.org), a community-defined, uniform system for describing the core attributes of biological databases, in particular, indicating in a consistent manner which community-defined standards (minimal information checklists, terminologies and exchange formats) they implement. The BioSharing catalogue offers this &amp;#x201c;one-stop shop&amp;#x201d; for those seeking information about the standards and data sharing policies.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This presentation illustrates the rational for BioDBcore(P Gaudet) and the progresses for its implementation (P Rocca-Serra),...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6167/version/1

Biodegradable Luminescent Silicon Quantum Dots for Two Photon Imaging Applications
Provedor de dados: 17
Autores: Chen-An  Tien; Folarin Erogbogbo; Ching-Wen  Chang; Priscilla  Adjei-Baffour; Wing-Chueng Law; Mark T. Swihart.
Cadmium- and lead-based quantum dots are normally coated for biological applications, because their degradation may result in the release of toxic heavy metal ions. Here, we synthesize silicon quantum dots that are expected to biodegrade to non-toxic products. A chitosan coating is used to render the silicon quantum dots stable in storage conditions and biodegradable at physiological conditions. The applications of these particles are demonstrated in cellular imaging with single and two-photon excitation. These results open the door for a new generation of silicon quantum dots that may have a wide variety of applications derived from the flexibility of chitosan.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/7012/version/1

Biodiesel: Freedom from Dependence on Fossil Fuels?
Provedor de dados: 17
Autores: B. Anjan Kumar Prusty; Rachna Chandra; P. A.  Azeez.
In view of the depleting oil reserves and exponential rise in petroleum prices, the search for alternative sources of fuel is very timely and important. The present paper addresses the underlying issues in biodiesel production from biomaterials and sustainable production and supply of first-generation biofuels, especially the one from jatropha. The agencies and research institutions involved in the production of biofuels and the national and international efforts made in this regard are discussed here. There is also a dire need of a step towards large-scale production and supply of second-generation biofuels, although in infant stage, to strengthen the world economy in general and Indian economy in particular. However, the production of biofuels are likely...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2658/version/1

Biodiversity Conservation Of The Irtysh River
Provedor de dados: 17
Autores: Yevgeniy Kulikov; Olga Kirichenko.
One of the basic principles of environmental protection is the conservation of biological diversity of natural objects. In addressing this issue plays an important role the Red Book of Kazakh-stan, which is one of the main effective instruments for the preservation and restoration of rare and declining in numbers and endangered species. Red Books are the main weapon of environmental education tool for the inventory of rare and endangered species, scientifically sound foundation for their protection. Studies of fish that are listed and recommended for inclusion in the Red Book, is a priority and is evidenced not only on the state of study of the securities and small fish species, but also to demonstrate the quality of protection and conservation of...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5687/version/1

Biodiversity informatics: the challenge of linking data and the role of shared identifiers
Provedor de dados: 17
Autores: Roderic Page.
A major challenge facing biodiversity informatics is integrating data stored in widely distributed databases. Initial efforts have relied on taxonomic names as the shared identifier linking records in different databases. However, taxonomic names have limitations as identifiers, being neither stable nor globally unique, and the pace of molecular taxonomic and phylogenetic research means that a lot of information in public sequence databases is not linked to formal taxonomic names. This review explores the use of other identifiers, such as specimen codes and GenBank accession numbers, to link otherwise disconnected facts in different databases. The structure of these links can also be exploited using the PageRank algorithm to rank the results of searches on...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1760/version/1

Biodiversity is a cauliflower under the sunlight
Provedor de dados: 17
Autores: Roberto Gatti Cazzolla.
For a long time ecologists have questioned the variations of biodiversity across the latitudinal gradient. Recently it has emerged that the changes in [beta]-diversity are caused simply by changes in the sizes of species pools. I combined the species pool size and the fractal nature of ecosystems to clarify some general patterns of this gradient. Considering temperature, humidity and NPP as the main variables of an ecosystem niche and as the axis of the polygon in the Cartesian plane, it is possible to build fractal hypervolumes, whose the fractal dimension rises up to three, moving towards the equator. It follows that the best figure that graphically synthesizes the evolutionary forces that fit this ecosystem hypervolume is the fractal cauliflower.
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6917/version/1

Biodiversity Quality: a paradigm for biodiversity
Provedor de dados: 17
Autores: Alan Feest; Timothy Aldred; Katrin Jedamzik.
The internationally accepted definition of biodiversity creates difficulty in measuring difference and change. The authors suggest that well-sampled data can be used to generate a range of numerical indices reflecting species group characteristics/functionality (Species Richness, Simposons Index, Population Density, Biomass and Species Conservation Value) that can be viewed in combination to create a picture of biodiversity quality. This overall approach has considerable advantages over the currently accepted Convention on biological Diversity definition based on the &amp;#x22;variability&amp;#x22; of genes, species and ecosystems, since the numerical expression of the indices allows the probability of difference between biodiversity quality trends and...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3205/version/1

Biodiversity shapes tree species aggregations in tropical forests
Provedor de dados: 17
Autores: Shan-Huah Wu; Wei-Chun Chao; Chang-Fu Hsieh.
Spatial patterns of conspecific trees are considered as the consequences of biological interactions and environmental influences. They also reflect species interactions in plant communities. However, biological attributes are often neglected while deliberating the factors shaping species distributions. As rising attentions are paid to spatial patterns of tropical forest trees, we noticed that seven Center of Tropical Forest Sites and four Forest Dynamic Plots in Asia and America have presented analogously high proportions of species with aggregated conspecific individuals coincidently. This phenomenon is distinctive and repudiates fundamental ecology hypotheses which suggested dispersed distributions of conspecific tropical trees due to intensive density...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1670/version/1

BioenergyProduction From Plant Biomass: Bioethanol From Concept To Reality
Provedor de dados: 17
Autores: Israr  Khan; Muhammad Waheed Akhtar.
Natural energy reserves like petrol and diesel etc are depleting.  As such, it is of paramount importance to find alternative fuels. Solar energy is trapped as biomass in plants. Biomass provide an excellent reserve for trapping solar energy on field. Complex enzymatic machinery comprising of hydrolytic reactions  and consolidated bioprocessing is needed to make viable bioenergy, mostly biofuels like bioethanol for locomotives, industries and general use in the future.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6286/version/1

Biogeographic relationships among deep-sea hydrothermal vent faunas at global scale
Provedor de dados: 17
Autores: Charleyne Bachraty; Pierre Legendre; Daniel Desbruy&amp;#xe8;res.
The discovery of deep-sea hydrothermal vent fauna, kilometers deep in the oceans, is a great achievement of 20th-century marine biology. The deep-sea hydrothermal food web does not directly depend on the sun energy. Vent communities rely primarily on trophic associations between chemoautotrophic bacteria and consumers. A small number of endemic taxa are adapted to this highly toxic environment distributed along ridge crests. Where they appeared and how they dispersed is among the important questions ecologists must answer. Here, by statistical analysis of the most comprehensive data base ever assembled about deep-sea hydrothermal fauna, we delineate six major hydrothermal provinces in the World Ocean, then we identify five significant dispersal flows...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1823/version/1

bioGUID: resolving, discovering, and minting identifiers for biodiversity informatics
Provedor de dados: 17
Autores: Roderic Page.
Linking together the data of interest to biodiversity researchers (including specimen records, images, taxonomic names, and DNA sequences) requires services that can mint, resolve, and discover globally unique identifiers (including, but not limited to, DOIs, HTTP URIs, and LSIDs). bioGUID implements a range of services, the core ones being an OpenURL resolver for bibliographic resources, and a LSID resolver. The LSID resolver supports Linked Data-friendly resolution using  HTTP 303 redirects and content negotiation. Additional services include journal ISSN look-up, author name matching, and a tool to monitor the status of biodiversity data providers. bioGUID is available at &amp;#x22;http://bioguid.info/&amp;#x22;:http://bioguid.info/. Source code is...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3079/version/1

Bioinformatic approaches for the genetic and phenotypic characterization of a Saccharomyces cerevisiae wine yeast collection
Provedor de dados: 17
Autores: Ricardo Franco-Duarte; Lan Umek; Blaz Zupan; Dorit Schuller.
The objective of the present study was to compare genetic and phenotypic variation of 103 Saccharomyces cerevisiae strains isolated from winemaking environments. We used bioinformatics approaches to identify genetically similary strains with specific phenotypes and to estimate a strain&amp;#x27;s biotechnological potential.  &amp;#xd;&amp;#xa;A S. cerevisiae collection, comprising 440 strains that were obtained from winemaking environments in Portugal has been constituted during the last years. All strains were genetically characterized by a set of eleven highly polymorphic microsatellites and showed unique allelic combinations. Using neural networks, a subset of 103 genetically most diverse strains was chosen for phenotypic analysis, that included growth...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2288/version/1

Bioinformatics analysis of homologies between pathogen antigens, autoantigens and the CFTR cystic fibrosis protein: A role for immunoadsorption therapy?
Provedor de dados: 17
Autores: Christopher Carter.
The cystic fibrosis CFTR chloride channel is involved in pathogen entry into epithelial cells, and provides the glutathione and hypochlorous acid necessary for bactericidal and viricidal actions. CFTR mutations block these effects, diminishing pathogen defence and allowing pathogen accumulation in the extracellular space, where antibody encounter is likely. The pathogen antigens observed in cystic fibrosis (including P. Aeruginosa, S.Aureus and S.Maltophilia proteins) are homologous to the autoantigens reported in cystic fibrosis and all are homologous to the CFTR protein itself. Antibodies to pathogens and autoantigens may also target the CFTR protein, acting as antagonists, further compromising its function. The tripartite relationship between pathogen...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5352/version/1

Bioinformatics Approach for Functional Glycomics
Provedor de dados: 17
Autores: James C. Paulson.
Presentation in the Human Glycomics Proteomics Disease Initiative (HGPI) session.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/15/version/1

Bioinformatics for Human Proteomics: Current State and Future Status
Provedor de dados: 17
Autores: Amos Bairoch.
We are entering a new era in the exploration of the human proteome.&amp;#xd;&amp;#xa;Advances in technologies are allowing researchers to map with a much&amp;#xd;&amp;#xa;better resolution and improved accuracy this very complex universe. Such&amp;#xd;&amp;#xa;an exploration also requires a compendium of adequate bioinformatics&amp;#xd;&amp;#xa;tools, data repositories and knowledge resources. We are going to describe&amp;#xd;&amp;#xa;what are the state of the art in term of data and knowledge resources for&amp;#xd;&amp;#xa;human proteins: from repositories of proteomics data such as PRIDE,&amp;#xd;&amp;#xa;PeptideAtlas or Peptidome, databases such as SRMAtlas and HPA and&amp;#xd;&amp;#xa;knowledgebase such as UniProtKB/Swiss-Prot....
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5050/version/1

Biological Activities of Extracts from Sumac (Rhus spp.): A Review
Provedor de dados: 17
Autores: Sierra Rayne; Giuseppe Mazza.
Sumac is the common name for a genus (Rhus) that contains over 250 individual species of flowering plants in the family Anacardiaceae. These plants are found in temperate and tropical regions worldwide, often grow in areas of marginal agricultural capacity, and have a long history of use by indigenous peoples for medicinal and other uses. The research efforts on sumac extracts to date indicate a promising potential for this plant family to provide renewable bioproducts with the following reported desirable bioactivities: antifibrogenic, antifungal, antiinflammatory, antimalarial, antimicrobial, antimutagenic, antioxidant, antithrombin, antitumorigenic, antiviral, cytotoxic, hypoglycaemic, and leukopenic. As well, the bioactive components can be extracted...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/631/version/1

Biological networks and epistasis in genome-wide association studies
Provedor de dados: 17
Autores: Mathieu Emily; Leif  Schauser; Thomas Mailund; Mikkel H. Schierup.
Over the last few years, technological improvements have made possible the genotyping of hundreds of thousands of SNPs, enabling whole-genome association studies. The first genome-wide association studies have recently been completed to detect causal variant for complex traits. Although increasing evidence suggests that interaction between loci, such as epistasis between two loci, should be considered, most of these studies proceed by considering each SNP independently. One reason for this choice is that looking at all pairs of SNPs increases dramatically the number of tests (approximatively 50 billions of tests for a 300,000 SNPs data set) that faces with computational limitation and strong multiple testing correction.&amp;#xd;&amp;#xa;We proposed to...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/466/version/1

Biological resource catalog: NIF and NeuroLex
Provedor de dados: 17
Autores: Anita E. Bandrowski.
In the digital age one can find data and teaching materials on the web, however data and materials of a high quality are not always ranked very high on commercial search engines that look at the number of other sites that link to a page rather than the quality of the information. Additionally, many such materials are maintained within databases that are inaccessible to search technology. To solve these problems, the Neuroscience Information Framework (NIF: http://www.neuinfo.org) was created to aid the neuroscience community to discover useful digital resources, such as academic databases, and it has also developed a large digital catalog of resources that are related to neuroscience.&amp;#xd;&amp;#xa;NIF has developed a &amp;#x201c;resource...
Tipo: Presentation
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6238/version/1

Biological robotics and nanorobotred cells: Characterization and applications
Provedor de dados: 17
Autores: Rakesh Sharma; Soonjo Kwon; Ching J. Chen.
In human body, nanorobot-like red blood cells get exposed to human body fluids and many physico-chemical changes inside while these nanorobots (fullerene structure coated hemoglobin embedded iron inorganic elements) remain safe and perform killer action against bacteria or virus. We propose this killer action as &amp;#x2018;nanorobot driven nanomedical treatment&amp;#x2019; to combat a bacterial or viral infection. The red cells also act as imaging agent due to oxygen binding character. Our experiments were focused on the application of nanorobot (red cells) to make them immune resistant against viruses and making them as useful contrast agents in magnetic resonance imaging use based on their behavior in nanomagnetic fields. It consists of an injection of...
Tipo: Presentation
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4262/version/1

Biological taxonomy and ontology development: scope and limitations
Provedor de dados: 17
Autores: Nico M. Franz; David M. Thau.
The prospects of integrating full-blown biological taxonomies into an ontological reasoning framework are reviewed. We contrast the common usage of a static &amp;#x27;snapshot&amp;#x27; hierarchy in ontological representations of taxonomy with a more realistic situation that involves dynamic, piece-meal revisions of particular taxonomic groups and requires alignment with relevant preceding perspectives. Taxonomic practice is characterized by a range of phenomena that are orthogonal to the logical semantic background from which ontological entities and relationships originate, and therefore pose special challenges to ontological representation and reasoning. Among these phenomena are: (1) the notion that there is a single phylogenetic hierarchy in nature...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4593/version/1

Bioluminescence emission of the firefly
Provedor de dados: 17
Autores: Anurup Gohain Barua; Simanta Hazarika; Nayanmoni Saikia; Gaurangadhar Baruah.
We have recorded _in vivo_ emission and time-resolved spectra of the firefly species _Pyrophorus noctilucus_. The emission spectrum shows the FWHM value for this particular species to be 55 nm, which is significantly smaller than the half widths reported till now. The time-resolved spectrum reveals that a flash, of duration about a hundred milliseconds, is in fact composed of a number of microsecond pulses. This result suggests that the speed of the enzyme-catalyzed chemiluminescence reaction in the firefly for the emission of light is much greater than is believed to be.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/1351/version/1

Bioluminescence emissions of firefly _Luciola praeusta_ Kiesenwetter 1874 (Coleoptera : Lampyridae : Luciolinae)
Provedor de dados: 17
Autores: Anurup Gohain Barua; Simanta Hazarika; Nayanmoni Saikia; Gauranga Dhar Baruah.
_In vivo_ emission and time-resolved spectra of firefly _Luciola praeusta_ Kiesenwetter 1874 (Coleoptera : Lampyridae : Luciolinae) have been recorded. The emission spectrum shows the FWHM value for this particular species to be 55 nm, which is significantly narrower than the _in vivo_ half widths reported till now. The time-resolved spectrum reveals that a flash, of duration about a hundred milliseconds, is in fact composed of a number of microsecond pulses. This result suggests that the speed of the enzyme-catalysed chemiluminescence reaction in the firefly for the emission of light is much faster than is believed to be.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1351/version/2

BioMed Central - open data guidance for authors
Provedor de dados: 17
Autores: Naomi Attar.
All research articles published by BioMed Central are open access. In keeping with the spirit of open access publishing, we aim to maximize the availability of data associated with these articles.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6234/version/1

Biomedical Resource Ontology
Provedor de dados: 17
Autores: Trish  Whetzel.
none
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6354/version/1

Biomimetic assemblage of nucleobase 5-fluorouracil into nano-size three-dimensional particles
Provedor de dados: 17
Autores: Arun Chauhan; Swaleha Zubair; Qamar Zia; Saba Tufail; Asif Sherwani; Mohammad Sajid; Mohammad Owais.
Biomimetic nano-assembly formation offers a convenient and bio friendly approach to fabricate complex structures from simple components with sub-nanometer precision. Recently, extract from cells of microorganism/plant origin have emerged as a simple and viable route for the synthesis of metal and inorganic material nano-particles. In the present study, we have extended biological synthesis of nano-particles to organic molecules, namely the anticancer agent, 5-fluorouracil (5-FU) using Aloe vera leaf extract. The formation of 5-FU nano- particles was assessed by UV, FT-IR and fluorescence spectroscopic techniques. Transmission electron microscopy and atomic force microscopic techniques confirmed nano-size of the synthesized particles. Importantly, the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6182/version/1

BioModels Database: curation and annotation
Provedor de dados: 17
Autores: Michael Schubert; Ishan Ajmera; Vijayalakshmi Chelliah; Lukas Endler; Nicolas Rodriguez; Camille Laibe; Nicolas Le Nov&amp;#xe8;re.
The BioModels Database is a freely accessible online resource for storing, viewing, retrieving, and analyzing published, peer-reviewed quantitative models of biological processes.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In this poster we provide an overview of its capabilities, as well as the curation and annotation process with two use cases concerning blood coagulation and glucose homeostasis.
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6361/version/1

BioModels Database: Next generation model repository
Provedor de dados: 17
Autores: Camille Laibe; Michael Hoehl.
Public announce that the software system running BioModels Database (&amp;#x22;http://www.ebi.ac.uk/biomodels/&amp;#x22;:http://www.ebi.ac.uk/biomodels/) will evolve from open source to a community developed project.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5127/version/1

BioPax and SBML output from Reactome: where we are, where we are heading
Provedor de dados: 17
Autores: David Croft.
Reactome is a free, open-source, open access, pathway database. Currently, Reactome has over 5000 human proteins, involved in over 4000 manually curated reactions.  Additionally, it has nearly 30,000 reactions inferred by orthology projection from human to 20 other model organisms.  Facilities exist for exporting single pathways or the entire database to either BioPax or SBML.  SBML generation now uses libSBML, ensuring syntactic correctness, and has adopted MIRIAM URIs for references to external databases.  For the future, we anticipate that users will be able to submit a list of species to Reactome and obtain as an output customized BioPax or SBML, based on reactions extracted from Reactome.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6376/version/1

Biopax and Semantics
Provedor de dados: 17
Autores: Ismael Navas-Delgado; Maria Jes&amp;#xfa;s Garc&amp;#xed;a-Godoy; Maria del Mar Rold&amp;#xe1;n-Garc&amp;#xed;a; Jos&amp;#xe9; F. Aldana-Montes.
Biopax community is producing sets of data in RDF files, but most of them are not available through query interfaces. The publication of SPARQL endpoints is feasible with current sets of data, but the use of reasoning in these interfaces is unfeasible in many cases. The use of large scale reasoners is a need to take advantage of these data sets.
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6320/version/1

BioPAX: next steps for Semantic Web / CV workgroup
Provedor de dados: 17
Autores: Andrea Splendiani.
Outline of the next steps which will be proposed as actions in the Semantic Web/ Linking/ CV workgroup of BioPAX.&amp;#xd;&amp;#xa;One main focus will be to clean the RDF representation and adopt some basic relations, in order to address use cases in data-integration, pathway analysis and simple ontology/pathway integration.&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4968/version/1

BioPAX Support in CellDesigner
Provedor de dados: 17
Autores: Anushya Muruganujan; Huaiyu Mi.
BioPAX is a pathway data exchange language that is widely used by pathway database resources.  Here we describe a mechanism that allows users to curate pathway data in diagrams using CellDesigner, a pathway graphical editing tool, and save the pathway data in BioPAX format.  We used this mechanism to create BioPAX files for all 165 pathways from the PANTHER database.  In addition, we are also working on graphically visualizing BioPAX data by importing them into CellDesigner.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5679/version/1

Bio::Phylo - Phyloinformatic Analysis Using Perl
Provedor de dados: 17
Autores: Rutger Vos.
Recent years have seen the emergence of the field of phyloinformatics. In the course of a phyloinformatic analysis, data and metadata are generated, transformed, filtered, analyzed and summarized before they can be interpreted to answer meaningful biological questions. Based on first principles of good science such steps should be reproducible; and, in practice, analysis steps often need to be redone by the researcher multiple times anyway  and are too error-prone, tedious and time-consuming to do by hand. Hence, phyloinformatic analyses benefit from increased automation. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The Bio::Phylo toolkit promotes this by giving easy access to phylogenetic data objects (trees, taxa, character state matrices) read from a variety of...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4601/version/1

Biophysical Effects Of Ion Concenteration On The Affinity Between Nanopore, OmpF Lumen and Passing Nucleotide
Provedor de dados: 17
Autores: Saeid Hadi; Hamid Mobasheri.
OmpF an outer-membrane porin channel of _E. Coli_ posses beta-barrel structure, whose conductivity and gating phenomena are affected by changes in pH, salt concentration and so on. The distribution of amino acids in OmpF induces a non homologous electric potential in channel lumen. The intrinsic charge distribution caused be amino acid may be affected by lipid bilayer, extra and intra cellular ion concentration, and other physico-chemical condition of environment including, pH, temperature, polyelectrolytes etc. Nucleotides are considered as one of  most important metabolite in the cell that have pass through membrane whenever necessary. The experimental study of translocation of such a molecules through channels have provided invaluable information...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5101/version/1

Biophysical Mechanisms Supporting Conscious Perception: Prospects for an Artificial Astrocyte
Provedor de dados: 17
Autores: Alfredo Pereira Jr.
In perceptual processes, signals carrying information about a stimulus are transmitted through multiple processing lines to populations of receptive neurons and thalamocortical circuits, leading to the formation of a spatial ensemble of local field potentials. This paper addresses the problem of how the brain integrates patterns embodied in local fields to (re)construct the stimulus in a conscious episode. Four examples of human perception are given to illustrate the requirements of the integrative process. Considering the strategic position of astrocytes, mediating somatic signals carried by blood flow and information carried by the neuronal network, as well as their intrinsic information processing capabilities, these cells are in an adequate condition...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6484/version/1

Biophysical visual virtual reality in retinotopic visual areas
Provedor de dados: 17
Autores: Istv&amp;#xe1;n B&amp;#xf3;kkon; Jack Tuszynski; Vahid Salari.
Previously, we have pointed out that biophoton production can be a controlled process that originates from regulated redox/radical reactions. Our biophoton experiments support the notion that various visual related phenomena such as discrete retinal noise, retinal phosphenes as well as negative afterimages are due to biophotons. We have also suggested a new model, stating that the brain is able to create biophysical pictures in retinotopic visual areas via redox regulated biophotons of synchronized neurons. According to our interpretation, visualization (imagery) is a special kind of representation i.e., visual imagery requires peculiar inherent biophysical processes. Our idea of biophysical visual virtual reality in retinotopic areas may be a possible...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6051/version/1

BioPortal: Ontologies and Integrated Data Resources at the Click of a Mouse
Provedor de dados: 17
Autores: Patricia L. Whetzel; Nigam H. Shah; Natalya F. Noy; Benjamin Dai; Michael Dorf; Nicholas Griffith; Clement Jonquet; Cherie Youn; Adrien Coulet; Chris Callendar; Daniel L. Rubin; Barry Smith; Margaret-Anne Storey; Christopher G. Chute; Mark A. Musen.
BioPortal (&amp;#x22;http://bioportal.bioontology.org&amp;#x22;:http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides programmatic and web-based access to ontologies developed in OBO, OWL, Prot&amp;#xe9;g&amp;#xe9; frames, and RDF. Features include browsing, searching, and visualization of ontologies. Searching of integrated data resources is also possible through ontology-based indexing of biomedical resources with BioPortal ontologies. &amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3868/version/1

Bio-resources for sharing: which communities and what specific needs
Provedor de dados: 17
Autores: Andres Metspalu.
Biobanks are an important source to obtain samples and data for research purposes for a wide array of communities. In fact, sharing of bio-resources and data is an integral part of a biobank&amp;#x27;s role. For an effective partnership a list of requirements or needs have to be met, assuring quality of the resources shared as well as quality of the collaboration in general. Tracking and documenting bio-resource sharing and collaborations of a biobank can be seen as one indicator of the &amp;#x22;impact&amp;#x22; a biobank has to the field. As an example, the practice of the Estonian Genome Center of the University of Tartu is presented.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5659/version/1

BioSharing Overview
Provedor de dados: 17
Autores: Susanna-Assunta Sansone; Dawn Field; Annapaola Santarsiero; Eamonn  Maguire; Philippe Rocca-Serra; Chris Taylor; Lee Harland; The BioSharing  Communities.
Download this poster providing an overview of the BioSharing effort.
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5936/version/1

BioSharing: Standards, Policies and Communication in Bioscience
Provedor de dados: 17
Autores: Dawn Field; Susanna-Assunta Sansone; Philippe Rocca-Serra.
BioSharing works at the global level to build stable linkages between journals, funders, implementing data sharing policies, and well-constituted standardization efforts in the biosciences domain, to expedite the communication and the production of an integrated standards-based framework for the capture and sharing of high-throughput genomics and functional genomic bioscience data.
Tipo: Presentation
Palavras-chave: Biotechnology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6436/version/1

BioSharing - standards, policies and communication in bioscience
Provedor de dados: 17
Autores: Susanna-Assunta Sansone.
Research communities, funding agencies, and journals participate in the development of reporting standards for the bioscience domain to ensure that shared experiments are reported with enough information to be comprehensible and (in principle) reproducible, compared or integrated (Field, Sansone et al., Science, 2009). Similar trends exist in both the regulatory arena and commercial science.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Proliferation of standards is a positive sign of stakeholders&amp;#x2019; engagement, but how much do we know about these standards? Which ones are mature and stable enough to use or recommend? Which tools and databases implement which standard? Etc...&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The BioSharing catalogue (www.biosharing.org)...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6153/version/1

BioSilicoSystems - A Multipronged Approach Towards Analysis and Representation of Biological Data (PhD Thesis)
Provedor de dados: 17
Autores: Sridhar Hariharaputran.
The rising field of integrative bioinformatics provides the vital methods to integrate, manage and also to analyze the diverse data and allows gaining new and deeper insights and a clear understanding of the intricate biological systems. The difficulty is not only to facilitate the study of heterogeneous data within the biological context, but it also more fundamental, how to represent and make the available knowledge accessible. Moreover, adding valuable information and functions that persuade the user to discover the interesting relations hidden within the data is, in itself, a great challenge. Also, the cumulative information can provide greater biological insight than is possible with individual information sources. Furthermore, the rapidly growing...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5164/version/1

Biospheric context of Siberian development
Provedor de dados: 17
Autores: Georgii A. Alexandrov; Gen Inoue; Tsuneo Matsunaga.
Productivity of ecosystems surrounding a city is important for supporting its activities in a sustainable way. The total terrestrial net primary production (NPP) shows biosphere potential to supply primary food energy source for all non-autotrophic species including humans. Humans appropriate approximately 20% of NPP, in average. Even in the relatively well-populated regions of Siberia, NPP per capita exceeds the average level by several times suggesting the window of opportunity for achieving sustainable development. (3 pages, 1086 words, 2 maps)&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2478/version/1

Biospheric context of Siberian development
Provedor de dados: 17
Autores: Georgii A. Alexandrov; Gen Inoue; Tsuneo Matsunaga.
Recent publications on human appropriation of Net Primary Production (NPP) raise the question of how much of the biosphere&amp;#x2019;s productivity we can appropriate in a sustainable way.  This article brings the issue into the context of Siberian development.  In contrast to many other regions of the world, the population density in Siberia is still very low as compared to the NPP supplied by regional ecosystems. Hence, it is not too late to raise the question on how much of the NPP supplied by Siberian ecosystems we can appropriate in a sustainable way.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/2478/version/2

Biostratigraphic Study of the Gurpi Formation Based on Planktonic Foraminifera In Lar Area (Kuh-e-kurdeh Section)
Provedor de dados: 17
Autores: Meysam Shafiee Ardestani; Ebrahim Ghasemi-Nejad; Ali Mandanizadeh.
The study of planktonic foraminifera of the Gurpi formations at Lar area (Kuh-e-kurdeh section) enables me to find the most standard biozones defined in mediterranean regions, especially Tethysian domain. Five biozones were determined. Biozones I (Globotruncanita elevata zone) and II (Globotruncana ventricosa zone) and III (Radotruncana calcarata zone) indicate the Early Campanian and Middle and Late Campanian, respectively. Biozones IV (Globotruncanita stuarti zone) and V (Gansserina gansseri zone) suggest the Early and Middle Maastrichtian, respectively. In the Late Maastrichtian, due to decreasing in water depth at the study area, Abathomphalus mayaroensis zone defined in Tethysian domain was not recognised.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2947/version/1

Biostratigraphy and assigning the paleosalinity by using Echinocorys and Planktonic foraminifera at Upper Maastrichtian, in Jorband section, Central Alborz, Iran
Provedor de dados: 17
Autores: Masood Asgharian Rostami; Behnaz Balmaki; Meysam Shafiee Ardestani; Esmail Kohansal.
Jorband section is located in the north slope of central Alborz, and 28 Km south of Noor. It has been sampled and index fossilic groups of planktonic foraminifera and echinoids were studied in order to assign the paleosalinity and biozonation in central Alborz. The planktonic foraminiferal biozones identified within the Upper maastrichtian sequence of the Jorband section are three zones of Contustruncana contusa, Planoglobulina brazoensis, and Racemiguembelina fructicosa. The salinity changes were also searched in this section. In three layers in Jorband section examination echinocorys genus and is drawn as a diagram which in middle of the section, the salinity mounts is fewer than the beginning and top of the section.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3699/version/1

Biostratigraphy of the Danian/Selandian transition: A case study from Kamestan anticline section, northwest of Izeh city in Khuzestan province, Southern Iran
Provedor de dados: 17
Autores: Nasrin Hadavandkhani; Abbas Sadeghi.
The planktonic foraminifera turnover across the Danian-Selandian boundary (early to late Paleocene, ~60 Ma) has been studied in the Kamestan anticline section. The studied interval span planktonic foraminifera zones P2-P3. In this section Danian-Selandian boundary is located in Pabedeh &amp;#x2013; Gurpi Formations transition. Here, the boundary of Pabeh and Gurpi Formations is a transitional one and identified by with color change of from grey shale to purple shale of Gurpi Formation to Pabdeh Formation .&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4338/version/1

Biostratigraphy of the Ruteh Formation at Harijan section (Central Alborz) northern Iran using foraminifera and conodont
Provedor de dados: 17
Autores: Bahaoddin Hamdi; Abbas Sadeghi; Ebrahim Kohansa; Meysam  Shafiee Ardestani; Behnaz Balmak.
In order to study the fossil contents of the Ruteh Formation for biostratigraphical purposes, the 200 meters thick section was sampled at Harijan section, Central Alborz. The sequence is mainly made up of limestone and shale&amp;#x27;s. The lower contact of the formation with Dorud Formation is disconform while the upper contact with under learing Dorud Formation is disconformable with overling Nesen Formation is as well as disconformable. Fifty four species belonging to 27 genera (foraminifera and conodonts) were identified and three biozones were differentiated. These are formation: 1- _Schubertella giraudi_- _Codonofusiella distincta_ Assemblage Zone, 2- _Cribrigenerina sumatruna_- _Langella ocarina_ Assemblage Zone, 3- _Sweetognathus whitei_ Biozone....
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3376/version/1

Biotransformation of artemisinin mediated through fungal strains for obtaining derivatives with novel activities
Provedor de dados: 17
Autores: Suchita  Srivastava; Suaib  Luqman; Atiya  Fatima; Mahendra  P. Darokar; Arvind  S. Negi; J K. Kumar; Karuna  Shanker; Chandan  S. Chanotiya; Sudeep  Tandon; Suman  P. S. Khanuja.
Artemisinin, a sesquiterpene lactone, is the active antimalarial constituent of Artemisia annua. Several fungal strains Saccharomyces cerevisiae, Aspergillus flavus, Aspergillus niger and Picchia pastoris were used to biotransform artemisinin. Among these strains, A. flavus was the only microorganism capable of transforming artemisinin to deoxyartemisinin in higher yields than the previous reports. The structure of deoxyartemisinin was elucidated by spectroscopy. Deoxyartemisinin showed antibacterial activity against Staphylococcus aureus, S. epidermidis and S. mutans at a minimum inhibitory concentration (MIC) of 1 mg/mL compared to artemisinin whose MIC was &amp;#x3e;2 mg/mL.
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Microbiology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6925/version/1

Bird pollination of Canary Island endemic plants
Provedor de dados: 17
Autores: Jeff  Ollerton; Louise  Cranmer; Ralph Stelzer; Steve Sullivan; Lars Chittka.
The Canary Islands are home to a guild of endemic, threatened bird pollinated plants.  Previous work has suggested that these plants evolved floral traits as adaptations to pollination by flower specialist sunbirds, but subsequently they appear to be have co-opted passerine birds as sub-optimal pollinators. To test this idea we carried out a quantitative study of the pollination biology of three of the bird pollinated plants, Canarina canariensis (Campanulaceae), Isoplexis canariensis (Veronicaceae) and Lotus berthelotii (Fabaceae), on the island of Tenerife.  Using colour vision models, we predicted the detectability of flowers to bird and bee pollinators. We measured pollinator visitation rates, nectar standing crops, as well as seed set and pollen...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1977/version/1

Bird surveys for REDD+: avian communities indicate forest degradation in a Peruvian coffee landscape
Provedor de dados: 17
Autores: Raf Aerts; Sarah Spranghers; Bruno Verbist; Luc Lens; Cagan Sekercioglu.
Shade coffee cultivation in the Peruvian Andes assists in reducing emissions from deforestation because it avoids conversion to non-forest land uses such as coca and sun grown coffee farming.  REDD+ is a potential finance mechanism which may provide incentives for local coffee cooperatives to maintain high shade tree cover.  REDD+ has potential multiple benefits other than carbon sequestration, including the conservation of biodiversity.  When monitoring for REDD+, surveys of bird biodiversity may prove to be particularly valuable: apart from their high intrinsic value and their value as essential ecosystem service providers, birds inhabiting forest habitats are extremely sensitive to forest loss and forest degradation and are therefore potential useful...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6589/version/1

Birth Control Does Not Significantly Alter Women&amp;#x2019;s Preferences for Variants of Men&amp;#x2019;s Voices
Provedor de dados: 17
Autores: Jason W. J. W. W. Whitaker; Ryan R. S. Setten; Ulv U. A. Ankerstjerne.
Research shows that women&amp;#x2018;s preferences for masculine voices (low pitch) vary as a function of the menstrual cycle, becoming positively augmented around ovulation. The proximate cause catalyzing this effect is attributed to fluctuating estrogen levels. Thus, the introduction of hormonally based birth control has been to shown to have a dampening effect in experiments researching women&amp;#x2018;s preference of dimorphic secondary sexual characteristics. However, this dampening effect has not yet been explored in respect to women&amp;#x2018;s preferences for masculine voice types. This experiment sought, first, to investigate the effect of birth control on subjects off and on birth control; and, second, to replicate past findings:...
Tipo: Poster
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5895/version/1

Body Fat is Associated with Decreased Endocrine and Cognitive Resilience to Acute Emotional Stress
Provedor de dados: 17
Autores: Lilianne R. Mujica-Parodi; Rudolph Renelique; Marcus K. Taylor.
*Objective:* Cortisol is elevated both in individuals with increased emotional stress as well as with higher percentages of body fat. Cortisol is also known to affect cognitive performance, particularly spatial processing, selective attention, and working memory. We hypothesized that increased body fat might therefore be associated with decreased performance on a spatial processing task, in response to an acute real-world stressor. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Design:* We tested two separate samples of subjects undergoing their first (tandem) skydive. In the first sample (N=78), subjects were tested for salivary cortisol and state-anxiety (Spielberger State Anxiety Scale) during the plane&amp;#x27;s fifteen-minute ascent to altitude in immediate...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2072/version/1

Body-specific representations of action word meanings in right and left handers
Provedor de dados: 17
Autores: Daniel Casasanto.
If understanding action words involves mentally simulating our own actions, then the neurocognitive representation of word meanings must differ for people with different kinds of bodies, who perform actions in systematically different ways. In a test of the _Body-Specificity Hypothesis_, right- and left-handers were compared on two motor-meaning congruity tasks. Double dissociations in both action execution and recognition memory results showed that right and left handers form body-specific representations of words for manual actions.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1321/version/1

Bogoch Replikins Pandemic Prevention: Increase of Strain-Specific Influenza Genomic Replikin Counts, Having Predicted Outbreaks and their Location Seven Times Consecutively, Up to Two Years in Advance, Provides Time for Prevention of Pandemics
Provedor de dados: 17
Autores: Samuel     Bogoch; Elenore S. Bogoch.
Earlier studies have shown that the increased concentration of a new class of virus genomic peptides, Replikins, precedes and predicts virus outbreaks. We now find that the area in the genome of the highest concentration of Replikins, and the country in which this peak exists in scout viruses, have permitted in the past five years seven consecutive accurate predictions of the geographic localization of coming outbreaks, including those now realized in Mexico for H1N1, and in Cambodia for H5N1. Real-time Replikin analysis of the evolution of the virus genome identified both mutations and structural reorganization of the hemagglutinin and p B1 genes over several years before each outbreak. This information, together with the specific Replikin sequences so...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6952/version/1

Bottom-up and top-down effects on algal community dynamics in an aridland river:  the Middle Rio Grande, New Mexico&amp;#xb;
Provedor de dados: 17
Autores: Ayesha S. Burdett; Rebecca J. Bixby.
Background/Question/Methods&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In this study, we examined interactive effects of nutrient availability, river flow and food web structure on algal growth and species composition in the Middle Rio Grande, New Mexico. Algal community dynamics can be affected by both bottom-up and top-down factors. Algal production may be limited by low levels of nutrients or low light availability. Conversely, production is expected to increase when nutrient levels are high and light availability is not limited.  Top-down factors such as grazing by invertebrates can also alter periphyton growth and community composition. Generally, a reduction in grazers results in periphyton biomass increases and shifts in growth forms (to more upright...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3664/version/1

BRAGOMAP - a new Perl script for high throughoutput blast results analysis including GO and MapMan automatic annotations
Provedor de dados: 17
Autores: Rafal Woycicki; Wojciech Gutman; Zbigniew Przybecki.
Analyzing of sequences similarities is the first and most important method used to find out the function of unknown nucleotides. Searching of homologs should be done carefully not to loose any important ones. Having thousands of results from various long-read sequencing projects (ie. differentially expressed tags, genomic polymorphons or BAC ends), the by-hand ability to retrieve interesting (to our goal) similarities in hundreds of Blast results decreases rapidly. Decreasing the number of retrieved sequences by giving more stringency in e-value threshold or displaying less results could lead to false deductions. Functional genomics, proteomics and metabolomics could give us answers to the role of nucleotide sequences. It makes the need to annotate as much...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3900/version/1

Brain, language, and handedness: a family affair
Provedor de dados: 17
Autores: Bernard Mazoyer; Gregory Simon; Fabrice Crivello; Laure Zago; Laurent Petit; Emmanuel Mellet; Nathalie Tzourio-Mazoyer.
The left planum temporale is a marker of left hemisphere language specialization. We investigated the effect of individual handedness and familial sinistrality on left planum temporale surface area and found the size is reduced in proportion with the number of left-handed immediate family members and is lowest when one&amp;#x27;s mother is left-handed. This reduction is independent of an individual&amp;#x27;s handedness or sex and has no counterpart in the right hemisphere.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2982/version/1

BrainGrab: Capturing Curator Expertise as Reusable Annotation Rules
Provedor de dados: 17
Autores: Daniel H. Haft; Malay K. Basu; Roland A. Richter.
Experienced biocurators can outperform automated systems on specific genes once they determine which pieces of evidence should drive annotation, and which annotations should be spread. The annotation logic may weigh both homology evidence (BLAST matches or HMM hits) and non-homology evidence (neighboring genes, metabolic context, taxonomic group). Unfortunately, the expertise developed to annotate each gene is short-lived, and is mostly lost if the logic driving the annotation is not captured. We report the development of BrainGrab, an interface added to the MANATEE manual annotation tool for prokaryotic genomes. The curator can specify evidence scenarios that should always lead to equivalent annotation for similar genes in similar contexts, and thus...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3313/version/1

Breast Cancer Associated Metastasis is Significantly Increased in a Model of Autoimmune Arthritis
Provedor de dados: 17
Autores: Lopamudra  Das Roy; Latha Pathangey; Teresa Tinder; Pinku Mukherjee.
Chronic inflammation is known to play a role in cancer initiation, promotion,and metastasis. However, the mechanism by which inflammation promotes metastasis is still unclear. We evaluated if chronic inflammation induced by autoimmune arthritis may contribute to increased breast cancer-associated metastasis. We report a three-fold increase in lung metastasis and a significant increase in the incidence of bone metastasis in the pro-arthritic mice compared to control mice. The metastatic breast tumors in turn augment the severity of arthritis resulting in a vicious cycle that increases both bone destruction and metastasis. Enhanced neutrophilic and granulocytic infiltration in lungs and bone of the pro-arthritic mice and subsequent increase in circulating...
Tipo: Manuscript
Palavras-chave: Cancer; Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/2632/version/1

Breeding biology of pond heron in Kerala, South India
Provedor de dados: 17
Autores: K Seedikkoya; PA Azeez; EA  Abdul Shukkur.
Regular intensive investigations to locate nesting colonies were carried out early monsoon of 1999 up to 2002. For detailed study a few breeding colonies were selected. The nesting trees, nest characteristics, eggs characteristics, incubation, hatching and hatchlings were investigated.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Altogether 17 plant species were used for nesting. Nest materials were collected from 24 plant species for building nest. The mean maximum size of the nest material used was 29.05 cm and the mean minimum size was 13.46 cm. The clutch size varied from 2-5 and clutches of three were very common. The maximum and minimum length and breadth of eggs were 48.0 x 32.0 and 33.3 x 24.1 respectively. The weight of eggs varied between 17.8 and 11.2 gm....
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2558/version/1

Breeding ecology and conservation of Brown booby in Gorgona Island, eastern tropical Pacific Ocean
Provedor de dados: 17
Autores: Andres Ospina-Alvarez.
Breeding ecology and reproductive traits of Brown Booby _Sula leucogaster_ etesiaca in Gorgona Natural National Park, Colombia, were studied. Adults morphometrics, eggs dimensions, chicks growth and nesting site characteristics, were examined at three different locations in the park. As with other subspecies, Brown Booby in Gorgona presents inverted sexual dimorphism, with adult females being lengthier, wider and heavier than adult males. Breeding of S. l. etesiaca results in eggs from the first deposition bigger in weight and dimensions than eggs from the second or third deposition. Growth of brown boobies chicks fit to a natural log equation: bodymass(g) = 0.8773 ln(days) + 3.3895. A variety of spawning aggregations was found, and their relationship with...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5620/version/1

BridgeDb: standardized access to gene, protein and metabolite identifier mapping services
Provedor de dados: 17
Autores: Martijn P. van Iersel; Alexander R. Pico; Thomas Kelder; Jianjiong Gao; Isaac Ho; Kristina Hanspers; Bruce R. Conklin; Chris T. A. Evelo.
Many interesting problems in bioinformatics require integration of data from various sources. For example when combining microarray data with a pathway database, or merging co-citation networks with protein-protein interaction networks. Invariably this leads to an identifier mapping problem, where different datasets are annotated with identifiers that are related, but originate from different databases.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Solutions for the identifier mapping problem exist, such as Biomart, Synergizer, Cronos, PICR, HMS and many more. This creates an opportunity for bioinformatics tool developers. Tools can be made to flexibly support multiple mapping services or mapping services could be combined to get broader coverage. This approach...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5023/version/1

Bridging the gap between social tagging and semantic annotation: E.D. the Entity Describer
Provedor de dados: 17
Autores: Benjamin M. Good; Edward A. Kawas; Mark D. Wilkinson.
Semantic annotation enables the development of efficient computational methods for analyzing and interacting with information, thus maximizing its value.   With the already substantial and constantly expanding data generation capacity of the life sciences as well as the concomitant increase in the knowledge distributed in scientific articles, new ways to produce semantic annotations of this information are crucial.  While automated techniques certainly facilitate the process, manual annotation remains the gold standard in most domains.  In this manuscript, we describe a prototype mass-collaborative semantic annotation system that, by distributing the annotation workload across the broad community of biomedical researchers, may help to produce the volume of...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/945/version/1

Bridging the gap between social tagging and semantic annotation: E.D. the Entity Describer
Provedor de dados: 17
Autores: Benjamin M. Good; Edward A. Kawas; Mark D. Wilkinson.
Semantic annotation enables the development of efficient computational methods for analyzing and interacting with information, thus maximizing its value.   With the already substantial and constantly expanding data generation capacity of the life sciences as well as the concomitant increase in the knowledge distributed in scientific articles, new ways to produce semantic annotations of this information are crucial.  While automated techniques certainly facilitate the process, manual annotation remains the gold standard in most domains.  In this manuscript, we describe a prototype mass-collaborative semantic annotation system that, by distributing the annotation workload across the broad community of biomedical researchers, may help to produce the volume of...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/945/version/2

Bridging the Gaps between Fundamental, Preclinical and Clinical Research: Report from a Global HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: Lawrence  Corey; Brigitte  Autran; Louis  Picker; the Working Group convened by the Global HIV Vaccine Enterprise.
The Global HIV Vaccine Enterprise (the Enterprise) convened a two-day workshop on 17-18 September 2009, at the Enterprise offices in New York; to discuss approaches to bridging the gaps between fundamental,preclinical and clinical HIV vaccine research. The topic of this Working Group originated from discussions of the Enterprise Science Committee,which proposed that more effective collaboration between these three areas of HIV vaccine research is needed in order to accelerate the pace of scientific progress in the field. Because the meeting took place before the release of the RV144 trial results held in Thailand, the conclusions reached during the meeting were further discussed during consultations at scientific conferences and at a joint meeting of the...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4799/version/1

Bridging the Gaps between Fundamental, Preclinical and Clinical Research: Report from a Global HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: Lawrence  Corey; Brigitte  Autran; Louis  Picker; the Working Group convened by the Global HIV Vaccine Enterprise.
The Global HIV Vaccine Enterprise (the Enterprise) convened a two-day workshop on 17-18 September 2009, at the Enterprise offices in New York; to discuss approaches to bridging the gaps between fundamental,preclinical and clinical HIV vaccine research. The topic of this Working Group originated from discussions of the Enterprise Science Committee,which proposed that more effective collaboration between these three areas of HIV vaccine research is needed in order to accelerate the pace of scientific progress in the field. Because the meeting took place before the release of the RV144 trial results held in Thailand, the conclusions reached during the meeting were further discussed during consultations at scientific conferences and at a joint meeting of the...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4799/version/2

BRIF and Variant Databases
Provedor de dados: 17
Autores: Raymond Dalgleish.
Databases of sequence variation in human genes (LSDBs) are an important resource for biology and medicine. Currently, the measurement of importance is not as objective as it might be and the establishment of impact factors would be of benefit to those who curate LSDBs. Specific issues relating to such databases are discussed.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5586/version/1

BRIF Workshop Introduction
Provedor de dados: 17
Autores: Anne Cambon-Thomsen.
This presentation aims at introducing the place of BRIF in the landscape of data sharing, the BRIF concept, a presentation of the working group, the ongoing debates and the workshop objectives.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5658/version/1

BRIF Workshop Minutes
Provedor de dados: 17
Autores: Laurence Mabile.
This document is a detailed summary of the presentations and discussions from the BRIF (Bioresource Impact Factor) workshop, held in Toulouse on 17-18 january 2011.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5879/version/1

BRIF workshop working group.
Provedor de dados: 17
Autores: Laurence Mabile.
Number of attendees, geographical origin of the group, skills and areas represented, tools developed to help the BRIF progress.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5582/version/1

Bringing Text Miners and Biologists Closer Together
Provedor de dados: 17
Autores: An&amp;#xe1;lia Louren&amp;#xe7;o; S&amp;#xf3;nia Carneiro; Rafael Carreira; Miguel Rocha; Isabel Rocha; Eug&amp;#xe9;nio C. Ferreira.
The boosting of Biomedical Text Mining (BioTM) research in the last few years has led the way for finally bridging out the gap between text miners and biologists. Beyond the development of enhanced entity recognisers and the construction of relationship extraction systems, now, more than ever, it is the time for applying available tools to real-world scenarios. Moreover, it is crucial to develop end-user tools that can assist biologists in their research activities. Such tools should be able to emulate biologist conventional curation, recurring to the same knowledge bases and making the same assumptions that biologists usually do, whereas delivering automated capabilities. The search and selection of PubMed articles, the construction of dictionaries from...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3188/version/1

Broadening Pfam Protein Sequence Annotations
Provedor de dados: 17
Autores: Jaina Mistry; Penny Cogghill; Sean Eddy; Rob Finn; John  Tate; Alex Bateman.
Pfam is a database of conserved protein families or domains commonly used for genome annotation and sequence classification. It comprises two parts: (1) Pfam-A families, which are fully annotated and consist of a representative seed alignment, HMMs, and a full alignment comprising all sequences that score above the curated threshold; (2) Pfam-B families, which are automatically generated clusters of domains not matched by Pfam-A but that often indicate conserved sequence regions. Pfam release 23.0 predicts at least one Pfam-A domain on 74% of the sequences in UniProtKB, and predicts either a Pfam-A or Pfam-B domain on 93% of the sequences in UniProtKB.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;With the ever increasing rate of deposition of new proteins of all...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3194/version/1

Building and Using Geospatial Ontology in the BioCaster Surveillance System
Provedor de dados: 17
Autores: Son Doan; Quoc-Hung Ngo; Ai Kawazoe; Nigel Collier.
This abstract presents an approach to building a geospatial ontology from Wikipedia and using it in BioCaster, a system for detecting and tracking infectious disease outbreaks from online news. Motivated by the need to interpret the geospatial dynamics of events we built a database containing the names of countries and major cities from Wikipedia. We started by automatically extracting country and dependent territory names and sub-country (subdivision and dependent area) names in the form of ISO 3166-1 and ISO 3166-2, respectively. Then, we re-created the part-whole relation between countries and sub-countries by verifying links from countries to their sub-countries. Verification was done by manual checking. The building process is semi-automatically...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2110/version/1

Building Block and Building Rule: Dual Descriptor Method for Biological Sequence Analysis
Provedor de dados: 17
Autores: Bin-Guang Ma.
The emergence of &amp;#x201c;Systems Biology&amp;#x201d; in recent years highlights the systematic viewpoint of bio-system modeling. Building on such a background, Dual Descriptor Method, a generic methodology for biological sequence analysis is proposed. From a systematic perspective, Dual Descriptor is defined as a two element set of Composition Weight Map and Position Weight Function which aim at reflecting the composition and permutation information of a sequence. An alternate training algorithm is provided to get an optimum description of the building patterns of the sequences. In this paper, dual descriptor method has been applied to the analysis of two typical problems of molecular biology: gene identification and the prediction of protein function....
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2223/version/1

Building conceptual spaces for exploring and linking biomedical resources
Provedor de dados: 17
Autores: Rafael Berlanga; Voctoria Nebot; Ernesto Jimenez-Ruiz.
The establishment of links between data (e.g., patient records) and Web resources (e.g., literature) and the proper visualization of such discovered knowledge is still a challenge in most Life Science domains (e.g., biomedicine). In this paper we present our contribution to the community in the form of an infrastructure to annotate information resources, to discover relationships among them, and to represent and visualize the new discovered knowledge. Furthermore, we have also implemented a Web-based prototype tool which integrates the proposed infrastructure.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5381/version/1

Bumblebees gain fitness through learning
Provedor de dados: 17
Autores: Nigel E. Raine; Lars Chittka.
Despite the widespread assumption that the learning abilities of animals are adapted to the particular environments in which they operate, the quantitative effects of learning performance on fitness remain virtually unknown. Here we evaluate the learning performance of bumblebees (_Bombus terrestris_) from multiple colonies in an ecologically relevant associative learning task under laboratory conditions, before testing the foraging performance of the same colonies under the field conditions. We demonstrate that variation in learning speed among bumblebee colonies is directly correlated with foraging performance, a robust fitness measure, under natural conditions. Colonies vary in learning speed by a factor of nearly 5, with the slowest learning colonies...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/1298/version/1

Bumblebees under the midnight sun - Monitoring circadian rhythms of bumblebees under continuous daylight, using radio frequency identification (RFID)
Provedor de dados: 17
Autores: Ralph J. Stelzer; Lars Chittka.
Circadian rhythms enable organisms to anticipate and to prepare for predictable changes in their environment. Most previous studies on circadian rhythms focused on solitary animals. However, in social insects, the colony as a superorganism has a foraging rhythm aligned to the patterns of resource availability. Within this colony rhythm, the activity patterns of individuals are embedded. In temperate regions bumblebee foragers show strong circadian rhythms that adjust their foraging activity to the changing light conditions in the course of the day. But what about circadian foraging patterns under continuous daylight? One would assume that the colony as a whole extends its foraging activity over the whole 24 hours of a day under such light conditions to...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1719/version/1

Bystander B cells rapidly acquire antigen receptors from activated B cells by membrane transfer: a novel mechanism for enhancing specific antigen presentation
Provedor de dados: 17
Autores: Ben J. C. Quah; Vaughan  P. Barlow; Virginia McPhun; Klaus   I. Matthaei; Mark  D. Hulett; Christopher   R. Parish.
The B cell antigen receptor (BCR) efficiently facilitates the capture and processing of a specific antigen for presentation on MHC class II molecules to antigen specific CD4+ T cells (1). Despite this, the majority of B cells are only thought to play a limited role in CD4+ T cell activation since BCRs are clonotypically expressed. Here we show, however, that activated B cells can, both in vitro and in vivo, rapidly donate their BCR to bystander B cells, a process that is mediated by direct membrane transfer between adjacent B cells and is amplified by the interaction of the BCR with specific antigen. This results in a dramatic expansion in the number of antigen-binding B cells in vivo, with the transferred BCR endowing recipient B cells with the ability to...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2007
URL: http://precedings.nature.com/documents/1207/version/1

CA2 Pyramidal Layer
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Rachel A. Dalley; Lydia L. Ng; Angela L. Guillozet-Bongaarts.
This report contains a gene expression summary of the CA2 pyramidal cell layer (CA2sp), derived from the Allen Brain Atlas (ABA) in situ hybridization mouse data set. The structure&amp;#x27;s location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the CA2sp were compared to the values of the macro/parent-structure, in this case the pyramidal layer of Ammon&amp;#x2019;s Horn, for the purpose of extracting regionally selective gene expression data. The genes with the highest ranking selectivity ratios were manually curated and verified. 50 genes were then selected and compiled for expression characterization. The experimental...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2096/version/1

Calming down the seas: the near collapse of an Atlantic coastal fishery
Provedor de dados: 17
Autores: Pablo Pita; Juan Freire.
For years now the estimates of the consequences of overfishing for marine ecosystems have differed greatly within the scientific community^1^. The use of commercial catch statistics to estimate tendencies has been much criticised^2^, but alternative information sources with long time series are rare. Here we employ the historic archive (1953-2007) of the recreational spearfishery in Galicia (NW Spain), which does not have the problems common to other fishery registers, to estimate long-term changes in coastal ecosystems. Using generalized additive regression models (GAM) we estimated decreases of around 83% in the abundances of coastal fish over the last 50 years. In the same period the average body size decreased by 36%. In addition, the relative catch...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4529/version/1

Caloric restriction causes symmetric cell division and delays aging in Escherichia coli
Provedor de dados: 17
Autores: Milind G. Watve; Samit Watve; Prajakta Belsare; Uttara Lele; Snehal Bari; Sarika Karande.
Aging is one of the most intriguing processes of biology and despite decades of research, many aspects of aging are poorly understood. Aging is known to occur in bacteria and yeast that divide with morphological asymmetry. Morphologically symmetrically dividing bacteria such as _Escherichia coli_ were assumed not to age until they were shown to divide with functional asymmetry leading to aging and death of some of the cells even in exponentially growing cultures. In asymmetrically dividing _E. coli_ the newly synthesized components are presumed to occupy one pole so that after division one of the daughter cells receives newly synthesized components whereas the other retains the older components. Mathematical models predicted that at the population level,...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2071/version/1

Calorific values and ash contents of different organs of Masson pine (Pinus massoniana) in southern China
Provedor de dados: 17
Autores: Wei Sheng Zeng; Shou Zheng Tang; Qian Hui Xiao.
Calorific values of plants are important indices for evaluating and reflecting material cycle and energy conversion in forest ecosystems. Based on the data of Masson Pine (Pinus massoniana) in southern China, the calorific values (CVs) and ash contents (ACs) of different plant organs were analyzed systematically using hypothesis test and regression analysis in this paper. The results show: (i) the CVs and ACs of different plant organs are almost significantly different, and the order by AFCV (ash-free calorific value) from the largest to the smallest is foliage (23.55 kJ/g), branches (22.25 kJ/g), stem bark (21.71 kJ/g), root (21.52 kJ/g) and stem wood (21.35 kJ/g); and the order by AC is foliage (2.35%), stem bark (1.44%), root (1.42%), branches (1.08%)...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2012
URL: http://precedings.nature.com/documents/6750/version/1

Can ABC be Used for Model Selection?
Provedor de dados: 17
Autores: Xavier  Didelot; Rich  Everitt; Adam  Johansen; Dan  Lawson.
Over the past ten years, Approximate Bayesian Computation (ABC) has become hugely popular to estimate the parameters of a model when the likelihood function cannot be computed in a reasonable amount of time. ABC can in principle be used also to perform Bayesian model comparison, but this raises the  question of which summary statistic should be used for such applications. Here we present a general method for constructing a summary statistic that is sufficient for the model choice problem. We apply this construction to models from the exponential family. Unfortunately, in more complex models, our construct often results in statistics with too high dimensionality to use in ABC. We therefore discuss the possibility of applying ABC with non-sufficient...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5955/version/1

Can bacteria adapt to starvation-free environment?
Provedor de dados: 17
Autores: Kei Kitahara.
Bacteria will experience starvation-free environment if infinite nutrition is supplied continuously for a long period. In this study, an evolutionary experiment was performed for 118 days where bacteria adapted to starvation-free environment and reduced their doubling time. It is anticipated that this finding will help to select bacterial strains that can grow more rapidly in rich media.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7017/version/1

Can global models reproduce the current increase in Western United States Wildfires and project a reliable future trend?
Provedor de dados: 17
Autores: Dominique  Bachelet; Dave Conklin; Brendan Rogers; Maureen McGlinchy; Jim Lenihan; Ron Neilson; Ray Drapek.
Background/Question/Methods:&amp;#xd;&amp;#xa;Wildfires in the western U.S. are generally thought to have increased since the 1980s. Many factors have contributed to this increase such as fire suppression, livestock grazing, and urban sprawl. Fires have also been associated with variations in sea surface temperatures and described by indices such as El Ni&amp;#xf1;o Southern Oscillation (ENSO), the Pacific Decadal Oscillation (PDO), and the Atlantic Multidecadal Oscillation (AMO). Recent analyses have also shown that we may have entered a new fire regime starting with a climate shift in 1998 and are currently entering years of combined long-term warm AMO phase with cool ENSO and PDO phases usually associated with increased drought-induced fires in the...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3618/version/1

Can Hawaiian carnivorous caterpillars attack invasive ants or vice versa?
Provedor de dados: 17
Autores: Shinji Sugiura.
The Hawaiian Islands have allowed insects to evolve unique habits, because the islands are isolated and originally lacked predators, such as ants and wasps. Ambush carnivorous caterpillars (_Eupithecia_ spp.; Lepidoptera: Geometridae) provide a remarkable example of a feeding behaviour unique to the Hawaiian Islands. Their prey includes various arthropods species. _Eupithecia_ larvae even attack predatory arthropods such as parasitoids. However, it is unclear whether _Eupithecia_ can attack ants. Here, I examined whether _Eupithecia orichloris_ can attack the invasive ant _Pheidole megacephala_ under laboratory conditions. _Eupithecia orichloris_ could successfully attack the minor worker of _P. megacephala_. However, the major worker of _P. megacephala_...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5374/version/1

Can one invasion lead to another? Niche space and the future of Southwestern U.S. riparian zones
Provedor de dados: 17
Autores: Lindsay Reynolds; David Cooper.
Background/Question/Methods: Invasive species are increasingly problematic world-wide. Scientists working to understand why invasive species are successful must first understand the processes of invasion. Invasion facilitation and empty niche exploitation are key processes that have not been well-studied in species rich ecosystems such as riparian areas. In the southwestern United States (U.S.) two prominent invaders of riparian habitats are the exotic woody plant species tamarisk (Tamarix ramosissima, T. chinensis, and their hybrids) and Russian olive (Eleagnus angustifolia). These plants were introduced by humans throughout the southwest around 1900. Both tamarisk and Russian olive have invaded the ephemeral stream system in Canyon de Chelly National...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3842/version/1

Can Plant-Made Copper Chaperones Heal Early Alzheimer&amp;#x2019;s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; J&amp;#xfc;rgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However, medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids. Therapeutic recombinant proteins, plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves, may establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of younger Alzheimer patients (&amp;#x3e; 50 years). Medications developed from plant-made copper chaperone proteins may delay progression...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/6

Can Plant-Made Copper Chaperones Heal Early Alzheimer&amp;#x2019;s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; J&amp;#xfc;rgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However, medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids. Therapeutic recombinant plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves may establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of younger Alzheimer patients (&amp;#x3e; 50 years). Medications developed from plant-made copper chaperone proteins may delay progression during early...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/4

Can Plant-Made Copper Chaperones Heal Early Alzheimer&amp;#x2019;s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; J&amp;#xfc;rgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However, medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids. Therapeutic recombinant plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves may establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of younger Alzheimer patients (&amp;#x3e; 50 years). Medications developed from plant-made copper chaperone proteins may delay progression during early...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/3

Can Plant-Made Copper Chaperones Heal Early Alzheimer&amp;#x2019;s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; J&amp;#xfc;rgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However, medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids. Therapeutic recombinant plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves may establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of younger Alzheimer patients (&amp;#x3e; 50 years). Medications developed from plant-made copper chaperone proteins may delay progression during early...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/5

Can Plant-Made Copper Chaperones Heal Early Alzheimer&amp;#x2019;s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; J&amp;#xfc;rgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However, medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids. Therapeutic recombinant proteins, plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves, may establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of younger Alzheimer patients (&amp;#x3e; 50 years). Medications developed from plant-made copper chaperone proteins may delay progression...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/8

Can Plant-Made Copper Chaperones Heal Early Alzheimer&amp;#x2019;s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; J&amp;#xfc;rgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However, medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids. Therapeutic recombinant proteins, plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves, may establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of younger Alzheimer patients (&amp;#x3e; 50 years). Medications developed from plant-made copper chaperone proteins may delay progression...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/7

Can Plant-Made Copper Chaperones Heal Early Alzheimer&amp;#x2019;s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; J&amp;#xfc;rgen Horst.
Therapeutic recombinant plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves may establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of younger Alzheimer patients (&amp;#x3e; 50 years). Medications developed from plant-made copper chaperone proteins may delay progression during early disease stages or even be a basis for a possible causal treatment of preclinical stages of Alzheimer&amp;#x2019;s disease by restoring cellular function of the CCS-SOD-1 mechanism and by preventing formation of A&amp;#x3b2; plaques, a major putative factor involved in Alzheimer&amp;#x2019;s disease pathogenesis.
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/1

Can Plant-Made Copper Chaperones Heal Early Alzheimer&amp;#x2019;s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; J&amp;#xfc;rgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However, medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids. Therapeutic recombinant proteins, plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves, may establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of younger Alzheimer patients (&amp;#x3e; 50 years). Medications developed from plant-made copper chaperone proteins may delay progression...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/9

Can Plant-Made Copper Chaperones Heal Early Alzheimer&amp;#x2019;s Disease?
Provedor de dados: 17
Autores: Bernd Kastenholz; Basil Horst; J&amp;#xfc;rgen Horst.
Commercially available medicinal plant extracts such as Ginkgo biloba leaf extract show no consistent pattern of clinical benefit for people with dementia or cognitive impairment, and have been suggested to be toxic to cells at higher doses. However, medicinal plants may contain other more efficient bioactive molecules apart from the well-known flavonoids and terpenoids. Therapeutic recombinant plant-made copper chaperone for superoxide dismutase (CCS) derived from Ginkgo biloba leaves may establish and maintain physiologic Cu levels through restoration and modulation of biometal metabolism in organ systems of younger Alzheimer patients (&amp;#x3e; 50 years). Medications developed from plant-made copper chaperone proteins may delay progression during early...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5907/version/2

Can the nutrient dynamics of a northern hardwood forest explain variation in its trophic structure?
Provedor de dados: 17
Autores: Erik E. Stange; Matthew P. Ayres.
Background/Question/Methods: A time series of Lepidoptera larvae (caterpillar) abundance and biomass in the northern hardwood forests of central New Hampshire, USA, shows large interannual fluctuations in aggregated caterpillar biomass (52-fold variation in mg caterpillars/ 8000 leaves) that were spatially correlated across a regional landscape. Primary production of these mature forests has not varied over this period, and many hundreds of Lepidoptera species share comparatively few host plants. Therefore, interannual changes in nutritional quality of even one host plant species may be capable of generating correlated population dynamics for many species in the Lepidoptera community. We tested the hypothesis that variation in soil nutrient availability...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3859/version/1

Can Vision Exist Without Somatosensation?
Provedor de dados: 17
Autores: Manivannan Muniyandi; Pawan Kumar Suresh.
The interconnection between vision and somatosensation is already well-established and is further supplemented by the evolutionary link between eyes and photoreceptors, and the functional connection between photosensation and thermoreception. However, our analysis hypothesizes a possibility that vision is not just linked to somatosensation, but may not exist without somatosensation. Surprisingly, our photoreceptor itself needs somatosensory proteins for its functioning, and our entire visual pathway depends on somatosensory cues for its functioning.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3436/version/1

Can we detect changes in high-latitude soil respiration over decadal time scales?
Provedor de dados: 17
Autores: Ben Bond-Lamberty; Allison Thomson.
Soil respiration (RS), the soil surface CO~2~ flux, is the second-largest terrestrial carbon flux, but because of its high variability and the inaccessibility of the soil medium it remains one of the least well-constrained parts of the terrestrial carbon cycle. If the carbon stored in high-latitude ecosystems is being mobilized by climate changes (whether by increasing temperature, changing precipitation, altered disturbance regimes, etc.) we may be able to detect RS changes in the now forty-year record of RS chamber measurements. We searched the published literature and found 194 RS observations from 1964 to 2008 at high latitudes, and paired their known measurement locations with a global climate data set spanning the time period. Linear regression was...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/4093/version/1

caNanoLab &amp;#x2013; A Tool To Benefit Biomedical Nanomaterials Research
Provedor de dados: 17
Autores: Michal Lijowski.
The cancer Nanotechnology Laboratory Web portal (&amp;#x22;http://cananolab.nci.nih.gov/caNanoLab/welcome.do&amp;#x22;:http://cananolab.nci.nih.gov/caNanoLab/welcome.do) is designed to promote sharing of nanomedicine data and to provide support for the annotation of nanoparticles with information about their composition, function, and characterization. The project is a part of NCI cancer Biomedical Informatics Grid (caBIG&amp;#xae;), and includes a collaboration among the NCI Center for Biomedical Informatics and Information Technology (CBIIT), the NCI Nanotechnology Characterization Laboratory (NCL), and the NCI Alliance for Nanotechnology.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Currently, caNanolab contains nanomaterial data of 765 &amp;#x22;public&amp;#x22;...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5175/version/1

Cancer and the social induction of aging
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
Age has long been known as the primary population &amp;#x27;risk factor&amp;#x27; for cancer. We suggest that the observed disparities in hormonal cancers by ethnicity, gender, and other indices of social structure and power relationships, imply a differential aging by psychosocial and environmental exposures, in the context of cross-generational epigenetic heritage. A relatively simple model of malignancy regulation illuminates the cellular root of induced aging, and explains the decline in cancer rate with extreme old age via telomere shortening. We find that the multifactorial determinants of the disorder cannot be effectively addressed by &amp;#x27;small molecule&amp;#x27; interventions at the individual level, but must involve comprehensive prevention...
Tipo: Manuscript
Palavras-chave: Cancer; Immunology; Pharmacology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6146/version/1

Cancer Biology Data Curation at the Mouse Tumor Biology Database (MTB)
Provedor de dados: 17
Autores: Debra M. Krupke; Dale A. Begley; Steven B. Neuhauser; Joel E. Richardson; John P. Sundberg; Carol J. Bult; Janan T. Eppig.
Many advances in the field of cancer biology have been made using mouse models of human cancer. The Mouse Tumor Biology (MTB, &amp;#x22;http://tumor.informatics.jax.org&amp;#x22;:http://tumor.informatics.jax.org) database provides web-based access to data on spontaneous and induced tumors from genetically defined mice (inbred, hybrid, mutant, and genetically engineered strains of mice). These data include standardized tumor names and classifications, pathology reports and images, mouse genetics, genomic and cytogenetic changes occurring in the tumor, strain names, tumor frequency and latency, and literature citations.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Although primary source for the data represented in MTB is peer-reviewed scientific literature an...
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3245/version/1

Cancer chemopreventive action of &amp;#x3b1;-(-)-bisabolol, a sesquiterpene alcohol involves inhibition of cathepsin D and ornithine decarboxylase via tramping nitric oxide
Provedor de dados: 17
Autores: Suchita  Srivastava; Suaib Luqman.
Terpenoids, traditionally used for cosmetic and medicinal purposes, are currently being explored as cancer chemopreventive as well as chemotherapeutic agent in clinical trials. &amp;#x3b1;-(-)-bisabolol, a naturally occurring monocyclic sesquiterpene alcohol is a major component of essential oil of chamomile (Matricaria recutita L., Chamomilla recutita L., Matricaria chamomilla; Family Asteraceae). As substantiated previously, &amp;#x3b1;-(-)-bisabolol is known to have antimicrobial, anti-irritant, anti-inflammatory and anti-allergic properties. It also affects cell viability and growth of various human and murine cell lines by either inducing apoptosis or suppressing Akt activation or down regulating expression of some genes implicated in carcinogenesis....
Tipo: Poster
Palavras-chave: Cancer; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6902/version/1

Cancer Clinical Trials Optimization and Pharmacogenomics
Provedor de dados: 17
Autores: I. C. Baianu.
A critical overview of recent clinical trials in cancer is presented focused on signaling pathways blockers or inhibitors with a view to developing successful clinical trials employing personalized cancer therapies. Rational, pharmacogenomic strategies in cancer trials should be adopted that include specific molecular targeting based on adequate data for, and detailed modeling of, cancer cell genomes, modifications of cancer signaling pathways and epigenetic mechanisms. Novel translational oncogenomics research is rapidly expanding through the application of highly sensitive and specific advanced technology, research findings and computational tools and complex models to both pharmaceutical and clinical problems. Multiple sample analyses from several...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7046/version/1

Cancer invasion associated gene expression signature is present in differentially expressed genes in the reprogramming of fibroblasts into stem cells
Provedor de dados: 17
Autores: Wei-yi Cheng; Hoon Kim; Jessica Kandel; Dimitris Anastassiou.
Tumors become invasive by penetrating adjacent connective tissue, but the underlying biological mechanisms remain obscure. We recently identified a precise gene expression signature of fibroblastic origin associated with cancer invasion, the first step of the metastatic cascade. The signature contains many coordinately overexpressed genes, prominent among which are COL11A1, THBS2 and INHBA. Here we show that there is a striking similarity between the set of expressed genes in this metastasis-associated fibroblastic (MAF) signature and the set of genes that are downregulated when fibroblasts are reprogrammed to induced pluripotent stem cells (iPSCs). Because it is known that fibroblast reprogramming involves a mesenchymal epithelial transition (MET), the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5924/version/1

Cancer is a side effect of evolution of viruses and bacteria
Provedor de dados: 17
Autores: Valentin Mitin.
Any human organism is home to viruses and bacteria. However, viruses (as well as other intracellular parasites) are interested in continuous division of the host cells.  Unlimited division of the host cells means unlimited expansion of the living space and possibility for unlimited multiplication of viral particles. For this, human Cell Cycle Regulation System has to be affected in such a way to induce unlimited division of host cells. The present work describes oncogenome`s model of cancer development, according to which, in order to stimulate cell division, viruses affect a gene (or several genes) during transduction of a signal for cell division from growth factor to cyclin/CDK system. At the same time, controlling gene (p53, RB etc.) function and a...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2011
URL: http://precedings.nature.com/documents/6322/version/1

Capsaicin protects neuromuscular junctions from the inhibitory effects of botulinum neurotoxin A
Provedor de dados: 17
Autores: Baskaran Thyagarajan; Carmen Garcia; Joseph Potian; Natalia Krivitskaya; Kormakur Hognason; Joseph McArdle.
Within 24 hrs after injecting botulinum neurotoxin A (BoNT/A) into the hindlimb, mice lost the toe spread reflex and developed progressive muscle weakness. At the same time, the compound muscle action potential amplitude decreased. Injection of capsaicin before BoNT/A significantly reduced these affects and protected the muscle twitch tension of the Extensor digitorum longus (EDL) nerve muscle preparation. Acute in vitro exposure of isolated nerve muscle preparations, as well as Neuro 2a cells, to capsaicin prevented uptake of Alexa 647 BoNT/A. Motor nerve endings as well as Neuro 2a cells express the capsaicin receptor, a transient receptor potential channel of the vanilloid family (TRPV1). Capsaicin as well as disruption of clathrin coated pits (CCPs)...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2717/version/1

Capturing lost research
Provedor de dados: 17
Autores: Rebecca Lawrence.
A very significant proportion of valuable research conducted is lost, either after presentation at a meeting or even at the stage of the creation of the initial dataset; _F1000 Posters_ and _F1000 Research_ aim to capture this valuable information.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6175/version/1

Capturing Protein Sequence Data: UniProt Knowledgebase (UniProtKB) submissions and Journal Scanning
Provedor de dados: 17
Autores: Paul Browne; Ruth Eberhardt.
Most sequences in UniprotKB are derived from the translation of nucleotide sequence, but we also add sequences obtained through direct sequencing of peptides by Edman degradation and tandem mass spectrometry. This allows us to capture protein sequences for which no nucleotide sequence is available, and can also confirm that a predicted protein exists and elucidate the post-translational processing it undergoes. Scientists submit protein sequences to UniProtKB via the web-based submission tool &amp;#x22;SPIN&amp;#x22;:http://www.ebi.ac.uk/swissprot/Submissions/spin. Curators use a range of sequence analysis tools to check the submission and frequently discuss the sequence and supporting evidence with the submitter. Submitted entries can be kept confidential...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3120/version/1

Carbon Dioxide Splitting: A Summary of the Peer-Reviewed Scientific Literature
Provedor de dados: 17
Autores: Sierra Rayne.
Increasing concentrations of carbon dioxide (CO2) in the atmosphere have stimulated significant global research and development efforts regarding the reduction in CO2 emissions from all point and non-point sources. In addition to technologies that do not use carbon feedstocks or which capture and &amp;#x22;permanently&amp;#x22; store CO2 (i.e., sequestration), there is considerable worldwide interest among the academic, industrial, and government communities regarding methods for dissociating waste stream carbon dioxide molecules into their constituent carbon and oxygen (&amp;#x22;CO2 splitting&amp;#x22;) atoms as a final &amp;#x22;end-of-pipe&amp;#x22; treatment option. The splitting of carbon dioxide has also been actively discussed and researched in the...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1741/version/1

Carbon Finance Schemes - Incentives for Forest and Agroforestry Systems
Provedor de dados: 17
Autores: Christina Seeberg-Elverfeldt; Stefan Schwarze; Manfred Zeller.
Deforestation contributes a quarter of all anthropogenic greenhouse gas emissions. On the island of Sulawesi in the vicinity of the Lore Lindu National Park, smallholders contribute to deforestation processes with their agricultural practices, specifically with cocoa plantations. This study assesses the impact of carbon sequestration payments for forest management systems on the prevailing land use systems. Additionally, the level of incentives which induces farmers to adopt sustainable agroforestry practices is determined. We show that low carbon credit prices have a small impact on household income. However, with rising prices, the poorest households can realise an increase of 18 percent. The majority of the households have an incentive to adopt the more...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2504/version/1

Carbon Storage: Integrating Experiments &amp;#x26; Modelling to Quantify Trapping Capacity &amp;#x26; Efficiency in the Subsurface
Provedor de dados: 17
Autores: Christopher H. Pentland; Saleh Al-Mansoori; Stefan Iglauer; Ran Qi; Branko Bijeljic; Tara LaForce; Martin J. Blunt.
This is a fundamental study of trapping of non-wetting fluids in porous media. When injecting CO~2~ into an aquifer for carbon storage, the non-wetting phase (CO~2~) is trapped due to capillary forces. This process is investigated in the laboratory for analogue fluids. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We then design an injection strategy to maximise CO~2~ storage capacity and efficiency on the field scale - incorporating experimental and pore scale modelling results. A streamline based simulator is modified for this purpose.
Tipo: Poster
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2626/version/1

Carbon-driven Chemical Interactions between Alumina and Iron: A possible reaction pathway in Earth&amp;#x27;s interior
Provedor de dados: 17
Autores: Rita Khanna; Mohammad Ikram-ul Haq; Veena Sahajwalla.
Seismological and geochemical observations have revealed a complex structure for the earth&amp;#x27;s core-mantle boundary (CMB) region, with lateral and chemical heterogeneities. The presence of higher than expected concentrations of siderophile elements (Ni, Co, Pt etc) in the earth&amp;#x27;s mantle, iron enrichment of the lower mantle relative to the upper mantle, and a possible carbon flux from the core suggest the possibility of continual long-term exchange of materials between the core and the mantle. The chemical interactions of molten iron with complex mantle oxides and diffusion have been postulated as key mechanisms. A number of studies have been carried out on the reduction reactions taking into account the extreme conditions of...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2336/version/1

Cardiovascular Gene Ontology Annotation Initiative
Provedor de dados: 17
Autores: Varsha K. Khodiyar; Daniel G. Barrell; Peter Scambler; Mike Hubank; Rolf Apweiler; Philippa J. Talmud; Ruth C. Lovering.
Gene Ontology (GO) provides a controlled vocabulary, which is used by several groups around the world to provide functional annotation to proteins across a wide range of species (&amp;#x22;www.geneontology.org&amp;#x22;:http://www.geneontology.org).  The BHF-UCL team is funded by the British Heath Foundation to supply GO annotation specifically for human proteins involved in cardiovascular (CV) processes.  This is the first time that a physiological process-centered approach has been used for human protein GO annotation.  Experienced GO curators from the BHF-UCL team work alongside the bench scientists from the CV genetics group at University College London. By working in a CV dedicated environment the GO curators are able to build up their expertise in...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3135/version/1

CARE1, a TY3-gypsy long terminal repeat retrotransposon in the food legume chickpea (Cicer arietinum L)
Provedor de dados: 17
Autores: Manoj D. R. Rajput; Kailash C. Upadhyaya.
We report a novel Ty3-gypsy long terminal repeat retrotransposon CARE1 (_Cicer arietinum_ retro-element 1) in chickpea. This 5920-bp AT-rich (63%) element carries 723-bp 5&amp;#x27; and 897-bp 3&amp;#x27; LTRs respectively flanking an internal region of 4300-bp. The LTRs of CARE1 show 93.9% nucleotide identity to each other and have 4-bp (ACTA) terminal inverted repeats. A 17-bp potential tRNAmet primer binding site downstream to 5&amp;#x27; LTR and a 13-bp polypurine tract upstream to 3&amp;#x27; LTR have been identified. The order of domains (Gag-proteinase-reverse transcriptase-RNaseH-integrase) in the deduced amino acid sequence and phylogenetic tree constructed using reverse transcriptase sequences places CARE1 in the gypsy group of retrotransposons....
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/819/version/1

Carrier cell-mediated cell lysis of squamous cell carcinoma by squamous cell carcinoma antigen 1 promoter-driven oncolytic adenovirus
Provedor de dados: 17
Autores: Katsuyuki Hamada; Ting Zhang; Junzo Desaki; Koh-ichi Nakashiro; Hiroshi Ito; Kenzaburo Tani; Yoshiyuki Koyama; Hiroyuki Hamakawa.
The squamous cell carcinoma antigen (SCCA) serves as a serological marker for squamous cell carcinomas. Molecular cloning of the SCCA genomic region has revealed the presence of two tandemly arrayed genes, SCCA1 and SCCA2. We examined the promoter activity of the 5&amp;#x27;-flanking proximal region of the SCCA1 gene. Deletion analysis of SCCA1 promoter identified a 175-bp core promoter region and an enhancer region at -525 to -475 bp upstream of the transcription start site. The transcriptional activity of the SCCA1 promoter was up-regulated in squamous cell carcinoma cells, compared with normal keratinocyte, normal non-keratinocyte and adenocarcinoma cells. Five tandem repeats of enhancer increased SCCA1 promoter activity by 4-fold. Oncolytic adenovirus...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3213/version/1

Cartographic scale effect on channel slopes and stream power calculations
Provedor de dados: 17
Autores: Adalto Gon&amp;#xe7;alves Lima.
The channel slope is important in determining the stream power. In some research situations the slope is measured by topographical maps that, depending on the scale, can provide differentiated values. The objective of the research here reported was to delineate the implications of the inter-scales differences of channel slopes on the stream power calculation. Slopes of a small river, with a mixed bedrock&amp;#x2013;alluvial bed, located in a basaltic plateau in south Brazil, were examined. The measured slopes were compared at 1:50,000 and 1:10,000 scales. In the field, the bankfull geometry was surveyed in ten cross sections, for discharge calculation. The slopes measured by maps were used to determine the discharge, using the Gauckler&amp;#x2013;Manning...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1359/version/1

CASIMIR &amp;#x26; ENFIN
Provedor de dados: 17
Autores: John Hancock.
I review the development of draft database registries in the CASIMIR and ENFIN projects and the development of the CASIMIR Database Description Framework.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6158/version/1

Category of Metabolic-Replication Systems in Biology and Medicine
Provedor de dados: 17
Autores: I. C. Baianu.
Metabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life&amp;#x27;s origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important question of the minimal living organism by defining the functional relations that would have made life possible in such a minimal system- a grandad and grandma of all living organisms on Earth.
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Neuroscience; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7045/version/1

Cationic State Distributions over Chlorophyll Pairs in Photosystem I and II
Provedor de dados: 17
Autores: Keisuke Saito; Hiroshi Ishikita.
Photosystem I (PSI) and II (PSII) possess chlorophyll pairs P~A~/P~B~ and P~D1~/P~D2~, respectively. These chlorophylls are the primary electron donors in the light-induced electron transfer. After the electron transfer, the radical cation remains on these chlorophyll pairs, forming [P~A~/P~B~]^&amp;#xb7;+^ and [P~D1~/P~D2~]^&amp;#xb7;+^. The positive charge distributions over the two chlorophylls were reported to be 10/90-50/50 for P~A~^&amp;#xb7;+^/P~B~^&amp;#xb7;+^ [1,2] and 70/30-80/20 for P~D1~^&amp;#xb7;+^/P~D2~^&amp;#xb7;+^ [3,4]. To clarify the origin of the distributions, we calculated ratios of P~A~^&amp;#xb7;+^/P~B~^&amp;#xb7;+^ and P~D1~^&amp;#xb7;+^/P~D2~^&amp;#xb7;+^ with a quantum mechanical/molecular mechanical (QM/MM) approach and the...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6486/version/1

Cattle Egrets and dry fish business in coastal areas
Provedor de dados: 17
Autores: Kotta Seedikkoya; PA Azeez.
Cattle Egret is one of the common wetland birds in India known for its efficiency to make use of human interfered habitats. The present study is an attempt to document maggots of houseflies and calliphorids in the coastal sun drying fish yards and the role of the species in containing the vector species. The number of flies and maggots were found related with the visit of cattle egrets, demonstrating the importance of the species in controlling the vectors.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/2752/version/2

Cattle Egrets and dry fish business in coastal areas
Provedor de dados: 17
Autores: Kotta Seedikkoya; PA Azeezpa.
Cattle Egret is one of the common wetland birds in India known for its efficiency to make use of human interfered habitats. The present study is an attempt to document maggots of houseflies and calliphorids in the coastal sun drying fish yards and the role of the species in containing the vector species. The number of flies and maggots were found related with the visit of cattle egrets, demonstrating the importance of the species in controlling the vectors.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/2752/version/1

Causal Stability Ranking
Provedor de dados: 17
Autores: Daniel J. Stekhoven; Lars Hennig; Gardar Sveinbj&amp;#xf6;rnsson; Izabel Moraes; Marloes H. Maathuis; Peter B&amp;#xfc;hlmann.
Genotypic causes of a phenotypic trait are typically determined via randomized controlled intervention experiments. Such experiments are often prohibitive with respect to durations and costs. We therefore consider inferring stable rankings of genes, according to their causal effects on a phenotype, from observational data only. Our method allows for efficient design and prioritization of future experiments, and due to its generality it is useable for a broad spectrum of applications.
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/6716/version/1

Caveat Emptor: The Meaning of Perception and Integration in Speech Perception
Provedor de dados: 17
Autores: Dominic Massaro.
A recent letter^1^ claimed integration of auditory and tactile information in speech perception. Although I have been an advocate of multisensory integration, neither perception nor integration was sufficiently formalized, operationalized, and tested to support this claim.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/4016/version/1

_Cavernularia malabarica_ Fowler, 1894 from the Bay coast of Visakhapatnam, Andhra Pradesh
Provedor de dados: 17
Autores: Veena Shettigar; Kaladharan P.
Many initiatives have come up to investigate the fauna around India. Due to accidental sighting and dislocation caused due to fishing and forming a part of the trash brought ashore is how the organisms are located. During regular sampling carried out from Mangamaripeta fish landing centre of Visakhapatnam, delicate shallow-water sea pens were collected and investigated. No previous records are available pertaining to the presence of these animals from this area and the species have not been identified from these waters. This report identifies and describes the species as _Cavernularia malabarica_ Fowler, 1894 for the first time from these waters.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4952/version/1

CD14 Modulates PI3K/AKT/p38-MAPK Licensing of Negative Regulators of TLR Signaling to Restrain Chronic Inflammation
Provedor de dados: 17
Autores: Bikash Sahay; Rebeca L. Patsey; Nicole Whatley; Sasmita Nayak; Christian H. Eggers; Justin D. Radolf; Timothy J. Sellati.
Current thinking emphasizes the primacy of CD14 in facilitating TLR recognition of microbes to initiate proinflammatory signaling events and the importance of p38-MAPK in augmenting such responses. Herein, this paradigm is challenged by demonstrating that recognition of _Borrelia burgdorferi_ not only triggers an inflammatory response in the absence of CD14, but one that is uncontrolled as a consequence of impaired PI3K/AKT/p38-MAPK signaling and negative regulation of TLR2. CD14 deficiency results in hyperphosphorylation of AKT and reduced activation of p38. Such aberrant signaling leads to decreased negative regulation by SOCS1, SOCS3, and CIS thereby engendering a more severe and persistent inflammatory response to _B. burgdorferi_. Perturbation of this...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2005/version/1

CDAO-Store: A New Vision in Data Integration
Provedor de dados: 17
Autores: Brandon Chisham; Trung Le; Enrico Pontelli; Tran Son; Ben Wright.
The Comparative Data Analysis Ontology (CDAO) 1 is an ontology developed, as part of the EvoInfo2 and EvoIO3 groups supported by NESCent4, to provide semantics to the descriptions of data and transformations commonly found in the domain of phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic &amp;#xd;&amp;#xa;trees and associated character data matrices. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4585/version/2

CDAO-Store: A New Vision in Data Integration
Provedor de dados: 17
Autores: Brandon Chisham; Trung Le; Enrico Pontelli; Tran Son; Ben Wright.
The Comparative Data Analysis Ontology (CDAO)  is an ontology developed, as part of the EvoInfo and EvoIO groups supported by NESCent, to provide semantics to the descriptions of data and transformations commonly found in the domain of phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic trees and associated character data matrices. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;CDAO-store is a repository providing a rich set of API&amp;#x2019;s for querying and visualizing phyloinformatics data. It is a triple-store encoding data as RDF triples constructed according to the CDAO concept vocabulary. CDAO-store provides three classes of services: a service for importing data in CDAO format, a PhyloWS interface supporting an...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4586/version/1

CDAO-Store: A New Vision in Data Integration
Provedor de dados: 17
Autores: Brandon Chisham; Trung Le; Enrico Pontelli; Tran Son; Ben Wright.
The Comparative Data Analysis Ontology (CDAO) 1 is an ontology developed, as part of the EvoInfo2 and EvoIO3 groups supported by NESCent4, to provide semantics to the descriptions of data and transformations commonly found in the domain of phylogenetic inference. The core concepts of the ontology enables the description of phylogenetic &amp;#xd;&amp;#xa;trees and associated character data matrices. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4585/version/1

CDK2 and CKI targeting can significantly lower the cellular senescence bar - reveals a mathematical model of G1/S checkpoint pathway
Provedor de dados: 17
Autores: Hong  Ling; Sandhya Samarasinghe; Don  Kulasiri.
Cellular senescence, a mechanism employed by cells for thwarting proliferation, has shown to play an important role in protecting cells against cancer development in recent experimental observations, indicating that a deeper understanding of the cellular senescence pathway can help exploit its capacity for more effective cancer treatment. Furthermore, some experimental evidence points out that inhibition of CDK2 or Skp2 can be the critical trigger for cellular senescence. However, no mathematical model has been developed to highlight cellular senescence until now. In this study, we first implement a mathematical model of G1/S transition involving the DNA-damage pathway to highlight cellular senescence by lowering the critical trigger- CDK2. For this, we...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4950/version/1

Cell Adhesion: A surprising cohesive force
Provedor de dados: 17
Autores: Hugues H. Vasseur.
When an experimentalist or a biological mechanism applies an external force onto a cell chemically sticking to its substrate, a reacting &amp;#x22;suction&amp;#x22; force, due to the slow penetration of the surrounding fluid between the cell and the substrate, opposes to the dissociation. This force can overcome other known adhesive forces when the process is sufficiently violent (typically 10^5^ pN). Its maximal contribution to the total adhesive energy of the cell can then be estimated to 2 10^-3^ J/m2. The physical origin of this effect is quite simple, and it may be compared with that leaning a &amp;#x22;suction-cup&amp;#x22; against a bathroom wall. We address the consequences of this effect on (i) the separation energy, (ii) the motion of the fluid...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1416/version/1

Cell Proteomic Footprint
Provedor de dados: 17
Autores: Petr Lokhov; Elena Balashova; Maxim Dashtiev.
The authentication of mammalian cell cultures and their subpopulations are of tremendous demand in biotechnology and cell therapy. However, current techniques are either not efficient or can be very complex and expensive. Here we report a simple and straightforward approach for authentication of biological cells and their subpopulations with high speed, high throughput, low sample cost, and high sensitivity. We discovered that cell cultures treated with protease at soft, &amp;#x201c;non-killing&amp;#x201d; conditions release fragments of cell surface proteins, which composition is a strong characteristic of the cells. Mass spectrometric analysis of the released fragments allows a direct comparison of the produced mass spectrum with the mass spectrum of...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2091/version/1

Cell-free Embryonic Stem Cell Extract-mediated Derivation of Multi-potent Stem Cells from NIH3T3 Fibroblasts for Functional and Anatomical Ischemic Tissue Repair
Provedor de dados: 17
Autores: Johnson Rajasingh; Hiromichi Hamada; Evelyn Bord; Tina Thorne; Ilona  Goukassian; Erin  Lambers; Prasanna Krishnamurthy; Gangjian  Qin; Karen Schlauch; Kenneth M. Rosen; Deepali Ahluwalia; Yan  Zhu; Douglas W. Losordo; Raj Kishore.
The oocyte-independent generation of multipotent stem cells is one of the goals in regenerative medicine. We report that upon exposure to mouse ES cell (ESC) extracts, reversibly permeabilized NIH3T3 cells undergo de-differentiation followed by stimulus-induced re-differentiation into multiple lineage cell types. Genome-wide expression profiling revealed significant differences between NIH3T3 and ESC-extract treated NIH3T3 cells including re-activation of ESC specific transcripts. Epigenetically, ESC extracts induced CpG de-methylation of Oct4 promoter, hyper-acetylation of histones 3 and 4 and decreased lysine 9 (K-9) dimethylation of histone 3. In mouse models of surgically-induced hind limb ischemia (HLI) or acute myocardial infarction (AMI)...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2007
URL: http://precedings.nature.com/documents/1208/version/1

CellML 1.1 modularity
Provedor de dados: 17
Autores: Poul Nielsen.
CellML 1.1 is an open XML-based language designed  to store and exchange computer-based mathematical models. It has a simple facility to import existing models in order to create new models. The import facility encourages the development of hierarchical models and model reuse through the creation of well-curated model components in public model repositories. This presentation describes some of the features of CellML 1.1 and best practices for taking advantage of these features.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5005/version/1

CellML + [CMISS | OpenCMISS]
Provedor de dados: 17
Autores: David P. Nickerson.
A brief introduction and comparison to the usage of CellML models in CMISS and OpenCMISS.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5896/version/1

CellML: current status and future directions
Provedor de dados: 17
Autores: David Nickerson.
An overview of the current status of the CellML project and some ideas on where things are heading.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6417/version/1

Cellular delivery of antibodies: effective targeted subcellular imaging and new therapeutic tool
Provedor de dados: 17
Autores: Marzia  Massignani; Irene Canton; Nisa Patikarnmonthon; Nicholas J. Warren; Steven P. Armes; Andrew L. Lewis; Giuseppe Battaglia.
It is already more than a century since the pioneering work of the Nobel Laureate Ehrlich gave birth to the side chain theory1, which helped to define antibodies and their ability to target specific biological sites. However, the use of antibodies is still restricted to the extracellular space due to the lack of a suitable delivery vehicle for the efficient transport of antibodies into live cells without inducing toxicity. In this work, we report the efficient encapsulation and delivery of antibodies into live cells with no significant loss of cell viability or any deleterious affect on the cell metabolic activity. This delivery system is based on poly(2-(methacryloyloxy)ethyl phosphorylcholine)-block-(2-(diisopropylamino)ethyl methacrylate), (PMPC-PDPA),...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Immunology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4427/version/1

Cerebellar Cortex, Purkinje Cell Layer
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Emily M. Wright; Lydia  L. Ng; Angela L. Guillozet-Bongaarts.
This report contains a summary of expression patterns for genes that are enriched in the Purkinje cell layer (CBXpu) of the cerebellum.  All data is derived from the Allen Brain Atlas (ABA) in situ hybridization mouse project. The structure&amp;#x27;s location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the CBXpu were compared to the values of its larger parent structure, in this case the cerebellar cortex, for the purpose of extracting regionally selective gene expression data. The highest ranking genes were manually curated and verified. 50 genes were then selected and compiled for expression analysis. The experimental...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2200/version/1

Cerebral and Spinal Modulation of Pain by Emotions
Provedor de dados: 17
Autores: Mathieu Roy; Mathieu Piche; Jen-I Chen; Isabelle Peretz; Pierre Rainville.
Emotions have powerful effects on pain perception. However, the brain mechanisms underlying these effects remain largely unknown. In this study, we combined functional cerebral imaging with psychophysiological methods to explore the neural mechanisms implicated in the emotional modulation of spinal nociceptive responses (RIII-reflex) and pain perception in healthy participants. Emotions induced by pleasant or unpleasant pictures modulated the responses to painful electrical stimulations in the right insula, paracentral lobule, parahippocampal gyrii, thalamus and amygdala. Right insula activation covaried with the modulation of pain perception, consistent with a role of this structure in the integration of pain signals with the ongoing emotion. In contrast,...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2885/version/1

Cerebral malaria admissions in Papua New Guinea may show inter-annual cyclicity: An example of about a 1.5-year cycle for malaria incidence in Burundi
Provedor de dados: 17
Autores: Borislav D. Dimitrov; Penka A. Atanassova.
Best available descriptions of malaria incidence and mortality dynamics are important to better plan and evaluate the implementation of programs to monitor (e.g., remote sensing) and control the disease, especially in endemic zones. This was stressed recently by Cibulskis et al (2007) in the view of completeness of monthly reporting for cerebral malaria admissions in Papua New Guinea (latitude 6 degree S, 1987-1996). Notably, regardless of the rate of its completeness, the temporal dynamics of admissions was preserved over the years, however, neither raw data nor results on further analyses about eventual inter-annual cyclic components (periods T&amp;#x3e;1 year) were provided despite obvious graphical patterns for such a specific time structure...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/1769/version/1

Cervical Cancer-Associated Human Papillomavirus 16 E7 Oncoprotein Inhibits Induction of Anti-Cancer Immunity by a CD4+ T Cell Dependent Mechanism
Provedor de dados: 17
Autores: Marion E. G. Brunck; Xiao Song Liu; Jie Zhong; Germain J. Fernando.
Attempts to develop therapeutic vaccines against cervical cancer have been proven difficult. One of the major causes of the failure is due to the use of the wrong mouse models based on transplantable tumours in testing the efficacy of vaccines. Now that a transgenic epithelial mouse model has been developed to closely mimic cervical cancer, the mechanisms needed to eliminate this type of cancer could be studied. The E7 oncoprotein of Human Papillomavirus (HPV) is the most expressed HPV protein in cervical cancers and its continuous production is essential to maintain the cancerous state and therefore the obvious target in the development of vaccines. Skin grafts expressing the HPV 16 E7 protein (E7 autografts) are not spontaneously rejected from an MHC...
Tipo: Manuscript
Palavras-chave: Cancer; Immunology.
Ano: 2009
URL: http://precedings.nature.com/documents/3405/version/1

CFP and YFP photostabilities are differentially affected by common mounting fluids
Provedor de dados: 17
Autores: Johannes A. Schmid.
The use of spectrally distinct variants of green fluorescent protein (GFP) such as cyan or yellow mutants (CFP and YFP, respectively) is very common in all different fields of life sciences, e.g. for marking and tracing of specific proteins or cells or to determine protein interactions. In the later case, the quantum physical phenomenon of fluorescence resonance energy transfer (FRET) is visualized by specific microscopy techniques. When we applied a commonly used FRET microscopy technique - the increase in CFP-fluorescence after bleaching of YFP, we noticed that it worked well for live cells, but that most of the FRET-signal was lost in fixed cells mounted in commercial microscopy mounting fluids. Subsequently, we could show that CFP bleached much faster...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4517/version/1

Challenges in modeling disturbances&amp;#x27; effects on terrestrial carbon cycling
Provedor de dados: 17
Autores: Ben Bond-Lamberty.
Ecosystem disturbance presents modelers with a number of problems, of which the disturbance event itself may be the least problematic. First, most ecosystem models depend on reaching a steady state before the main computation begins; this already-tricky initial value problem is complicated by disturbances during spinup, which may prevent steady state from being reached. Second, vegetation dynamics becomes more important in disturbed ecosystems, with nutrient cycling, albedo, and evapotranspiration all changing markedly. Succession is handled crudely (or not at all) by many large-scale models, however. Third, disturbances tend to export the carbon--and its climate forcing potential--from the system under study, complicating and expanding the scope of the...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/4095/version/1

Challenges in Whole-Genome Annotation of Pyrosequenced Fungal Genomes
Provedor de dados: 17
Autores: Alan Kuo; Igor Grigoriev.
Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454 sequenced fungal genome that is larger than a yeast (&amp;#x3e;30 Mbp). The pezizomycotine (filamentous ascomycote) _Aspergillus carbonarius_ belongs to the _Aspergillus_...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3191/version/1

Challenging or Reinforcing Social Prejudice?
Provedor de dados: 17
Autores: Helen Longino.
Behavior genetics holds out the hope of unbiased study of the biological bases of human behavior. Without more rigorous reflection on behavioral concepts, however, behavior genetics will succeed only in reinforcing social biases. This point is illustrated with reference to studies on aggression, sexual orientation, and gender differences.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To watch Professor Longino&amp;#x27;s presentation, please see the &amp;#x22;Google Video posting&amp;#x22;:http://video.google.com/videoplay?docid=-3926548921438712173&amp;#x26;hl=en.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2567/version/1

Changes in Antioxidant Enzymes Activity and Oxidative Damage in Four Argania spinosa Ecotypes Under Water Stress Conditions
Provedor de dados: 17
Autores: Abdelghani Chakhchar; Abderrahim  Ferradous; Mouna   Lamaoui; Said Wahbi; Cherkaoui  El Modafar.
_Argania spinosa_ L. Skell, a tree endemic of Morocco, grows in semiarid and arid areas. Biochemical response to drought in four ecotypes of the _A. spinosa_ was compared. Choice of ecotypes was based on evident differences in geographical features in south-west Morocco: two coastal ecotypes (Essaouira and Agadir) and two paralittorale ecotypes (Aoulouz and Lakhssas). Lipid peroxidation (malonyldialdehyde (MDA)), content of endogenous hydrogen peroxide (H2O2) and antioxidant enzyme system (Catalase (CAT), Ascorbate peroxidase (APX), Total peroxidase (POD) and Polyphenoloxidase (PPO) were measured in control (100% relative humidity (RH) at field capacity (FC)) and water-stressed plants (50 and 25% RH at FC). For all ecotypes, drought stress significantly...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6189/version/1

Changes in Cholesterol Metabolism in Peripheral Cells of Alzheimer Disease Patients and Their Relatives
Provedor de dados: 17
Autores: Alessandra Pani; Paolo La Colla; Claudia Abete; Claudia Mulas; Marirosa Putzolu; Claudia Norfo; Sergio Laconi; Anna Borgia; Christina Zaru; Manuela Palmas; Paolo  F. Putzu; Alessandra Mocali; Francesco Paoletti; Sandra Dessi.
Background. Previous epidemiological and experimental studies indicated cholesterol as a central player  in Alzheimer disease (AD). Here, we utilized skin fibroblasts and PBMC as possible ex vivo models for the study of dysfunctions of cholesterol homeostasis which may be related to AD development. &amp;#xd;&amp;#xa;Methods. We analyzed cholesterol homeostasis using colorimetric, thin layer chromatography (TLC), and histologic technique in ex vivo cultures of skin fibroblasts and PBMCs from patients with probable AD and their first-degree relatives. Additionally, healthy age-matched individuals served as controls. &amp;#xd;&amp;#xa;Findings. As compared to controls, skin fibroblasts and PBMCs from AD patients, displayed an evident alteration of cholesterol...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1246/version/1

Changes in enzyme activities and in the functional diversity of actinomycetes due to long term agricultural management
Provedor de dados: 17
Autores: Jessica L. M. Gutknecht; Elke Schulz; Venukumar Vemula; Jana Schmidt; Gabi Henning; Jackie Rose; Yvonne Eckstein; Mika Tarkka.
Long-term agricultural management alters soil organic matter, nutrient status, and potentially the decomposer community. We measured the abundance and activity of cellulose, chitin, and protease degrading bacteria, and total soil extra-cellular enzyme activity for cellulose (&amp;#x3b2;-glucosidase), chitinase (N-acetyl-glucosaminidase), xylosidase, and phosphatase activity. By combining these methods, we could determine how bacterial decomposer abundance and function were altered by long-term management, and how the bacterial decomposer community relates to overall soil enzyme activity. We also measured microbial total fungal and bacterial biomass, soil organic carbon pools, and extractable nitrogen for supplementary comparisons. Soil samples were taken...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/6792/version/1

Changes in Fitness, physical activity, fatness, and screen time: A longitudinal study in children and adolescents
Provedor de dados: 17
Autores: Luisa Aires; Lars Bo Andersen; Denisa Mendon&amp;#xe7;a; Clarice Martins; Gustavo Silva; Maria Paula Santos; Jose  Ribeiro; Jorge Mota.
*_Objective:_* To analyze whether changes in Physical Activity Index (PAI), sedentary time (ST; TV and PC use), and Body Mass Index (BMI) made a significant contribution to longitudinal changes in Physical Fitness (PF) of children and adolescents. Additionally, we analyzed interaction between baseline fitness level and changes in fitness. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*_Methods:_* This is a three years longitudinal study of 345 high school students aged 11-19 years. Students were invited to perform tests from Fitnessgram battery for strength (curl-ups, push-up), and Cardiorespiratory fitness (20m-shuttle run). PAI and ST were evaluated using a standard questionnaire. Standardized scores of physical fitness tests were summed (ZPF). Changes over time,...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3004/version/1

Changes in Scholarly Communication and the Potential Impact on Biocuration
Provedor de dados: 17
Autores: Philip Bourne.
Open access in particular and changes in on-line scholarship have the potential to impact biocuration which often involves translating information currently read in papers to knowledge that is found in a variety of biological resources. The implication of these changes in scholarly communication to the biocuration process will be discussed with references to our work and that of others.&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3229/version/1

Changes in Simpson&amp;#x2019;s Diversity Index in Microcosms Impacted with Monosodium Methane Arsenate
Provedor de dados: 17
Autores: Peter A. Kish; Nelson W. Daniel.
The objective of our studies is to analyze environmental impacts of Monosodium Methane Arsenate, MSMA, on aquatic habitats using the Aqua-Terra microcosm system. MSMA was applied at environmentally relevant(recommended) doses to microcosms to determine the change in biodiversity and the bio-concentration of arsenic in the aquatic plants (_Elodea Sp._) used in the microcosms as an oxygen source.  The microcosms are filled with unfiltered pond water and the diversity of each microcosm was determined before application of the herbicide.  After population stabilization, the herbicide is applied to the terrestrial portion of the microcosm.  The herbicide is watered into the microcosm by allowing the herbicide to be filtered by soil into the aquatic portion of...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3663/version/1

Changes in temperature-moisture covariance could increase soil carbon loss
Provedor de dados: 17
Autores: Asko S. Noormets; Michael Gavazzi; Sara Strickland; Ge Sun; Jiquan Chen; John King; Steve G. McNulty.
Soils store about 1.5x10^16 g of carbon (C), about as much as terrestrial vegetation and atmosphere combined 1. The complex interplay between factors that regulate C release from soil through respiration is not completely understood, but could potentially exert strong influence on global radiation balance and climate change2. Respiration exerts strong effect on the spatial heterogeneity of terrestrial C cycle 3 and its temporal variation remains more poorly understood compared to gross ecosystem production (GEP) 4. This variation can analytically be attributed to changes in environmental factors, but forecasting individual deviations remains a challenge 4. Here we propose that deviations of the typical covariance pattern of primary environmental drivers...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/290/version/1

Changing the Culture of &amp;#x201c;Ding&amp;#x201d;: Education, Legislation and Research on Concussive Brain Injury in Youth Athletics
Provedor de dados: 17
Autores: Claire D. Overturf; Donald C. Cooper.
The number of emergency department visits concerning sport related TBI in youth increased 57% from 2001 to 2009 and while a fraction of that increase may be attributed to injuries that were once missed now being identified due to greater general awareness, the fact remains that there are nearly 200,000 children every year who suffer sport related concussion or other TBI serious enough to prompt a visit to the ED. 40% of sports related concussions involve children between the ages of 8 and 13, and in this group the rate of concussion doubled between 1997 and 2007. The risk of concussion is highest in football and there are nearly 67,000 diagnosed concussions in high school football every year. In other sports that males and females play, such as basketball,...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/7076/version/1

Characteristics of oligonucleotide frequencies across genomes: Conservation versus variation, strand symmetry, and evolutionary implications
Provedor de dados: 17
Autores: Shang-Hong Zhang; Ya-Zhi Huang.
One of the objectives of evolutionary genomics is to reveal the genetic information contained in the primordial genome (called the primary genetic information in this paper, with the primordial genome defined here as the most primitive nucleic acid genome for earth&amp;#x2019;s life) by searching for primitive traits or relics remained in modern genomes. As the shorter a sequence is, the less probable it would be modified during genome evolution. For that reason, some characteristics of very short nucleotide sequences would have considerable chances to persist during billions of years of evolution. Consequently, conservation of certain genomic features of mononucleotides, dinucleotides, and higher-order oligonucleotides across various genomes may exist;...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2146/version/1

Characteristics of Staphylococcus aureus infections to consider in designing an effective vaccine.
Provedor de dados: 17
Autores: Francisco Romero-Pastrana; Pablo Hern&amp;#xe1;ndez-J&amp;#xe1;uregui; Beatriz E. Baca.
_Staphylococcus aureus_ is a very versatile and adaptable microorganism. It can potentially infect virtually any host tissue. Given the appropriate conditions it can become a life-threatening pathogen, or a commensal colonizer of the nose. Extensive antibiotic use for infection control facilitated the rise of antibiotic resistance, stressing the need for alternate forms of control. Vaccine efforts in other pathogens have proved successful, but so far _S. aureus_ candidate vaccines have not been as effective. Here we review _S. aureus_ factors involved in pathogenesis that could help develop a successful vaccine, like host nasal colonization and immune evasion factors. An effective multicomponent vaccine could incorporate antigenic fragments from several...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4598/version/1

Characteristics of Uremic Cardiomyopathy with Reversible Systolic Dysfunction
Provedor de dados: 17
Autores: Srilakshmi Adhyapak; Shamanna Iyengar.
Background: There exists a sub group of patients with uremic cardiomyopathy who experience resolution of heart failure following hemodialysis. It has been hypothesized that these patients are fluid overloaded, and following hemodialysis, show improvements in cardiac geometry and function. We wanted to study their clinical, biochemical and echocardiographic features to define any other additional characteristics.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Aim: To define characteristics of reversible systolic dysfunction.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: We studied 72 patients with chronic kidney disease on hemodialysis of whom 52 presented with congestive heart failure, over a period of 190 days. We studied their echocardiographic profile and blood...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3199/version/1

Characterization And Rejuvenation Of Local Ecorace Sukinda In Odhisa State
Provedor de dados: 17
Autores: Alok Sahay; Subrat Satpathy; Shashikant Sharan.
An experiment of outdoor rearing was conducted with the available Sukinda (TV) stock of BSM&amp;#x26;TC, Sundargarh (SG), CTSSS, Lakha (CTS) and CTR&amp;#x26;TI, Ranchi. The objective of this activity is to utilize economic wild life, conserving the associated environment for sustainable rural and tribal development (Raffi and Ramanujam, 2001; Gill and Lal, 2002; Mahapatra, 2009).&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The crop performance of SG showed highest cocoon yield i.e., 83 cocoons / dfl in 1st crop followed by 80 cocoons / dfl in 3rd crop and 42 cocoons / dfl during 2nd crop. Yellow coloured cocoons dominated (94-96%) the population in all the three crops. The cocoon weight, Shell weight and Silk Ratio were (9.72g, 1.07g&amp;#x26;11 %) in 1st...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6210/version/1

Characterization of a pig skeletal muscle microarray to study pork quality: the GenmascqChip 15K
Provedor de dados: 17
Autores: Marie Damon; Fr&amp;#xe9;d&amp;#xe9;ric Herault; Annie Vincent; Pascale Le Roy; Pierre Cherel.
Pork quality is highly variable and availability of relevant predictors of fresh meat quality at slaughter is critical to optimize carcass use and improve its valuation. High throughput gene expression studies have been widely used to describe biological mechanisms underlying variation of several traits but data are scarce regarding their use as tools for development of biomarkers. The GENMASCQ (GENomics enabled Marker Assisted Selection and Certification of Quality in Pork products ) research program was set up to select, using high-throughput gene expression screening, markers of the biological variation mostly appropriate to describe, and ultimately forecast, the sensory quality of an important meat product, accounting for nearly 40 % of meat protein...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5730/version/1

Characterization of Fut10 and Fut11, Putative Alpha-1-3/4 Fucosyltransferase Genes Important for Vertebrate Development
Provedor de dados: 17
Autores: Santosh K. Patnaik.
Two new, putative alpha-1-3/4 fucosyltransferases ([alpha]1-3/4 Fuc-Ts), Fuc-TX and Fuc-TXI, were identified in the vertebrate genome and transcriptome sequence databases through sequence homology-based queries. These proteins have a significant sequence similarity to only [alpha]1-3/4 Fuc-Ts, and possess peptide motifs that are evolutionarily conserved among the known vertebrate [alpha]1-3/4 Fuc-Ts. However, Fuc-TX and Fuc-TXI lack the HH[R/W][D/E] sequence that determines the specificity for type 1 or 2 substrates among the known vertebrate enzymes, and Fuc-TXI proteins do not possess a transmembrane domain. The Fut10 and Fut11 genes that encode these proteins are expressed ubiquitously in the adult mouse and in the mouse embryo throughout development....
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/141/version/1

Characterizing genetic diversity and creating novel gene pools in rice for trait dissection and gene function discovery
Provedor de dados: 17
Autores: Ramil Mauleon; Kenneth McNally; Hei Leung; Richard Bruskiewich; Ruaraidh Sackville-Hamilton.
Rice diversity is the foundation for rice improvement programs. At IRRI, over 100,000 rice accessions are deposited, and intelligent use of this diversity can not only help solve current production problems but also create future production opportunities and tackle climate change challenges. To fully explore and utilize rice diversity, two ingredients are needed: 1 - the genetic blueprints of diverse rice accessions in use, 2 - plant populations with recombined genotypes allowing expression of phenotypic variation and discovery of new genes/QTLs  for use in breeding programs. Sequencing of the genomes &amp;#x26; obtaining SNP genotypes of many rice accessions is feasible due to decreasing cost of advanced DNA sequencing technologies. Coupled with the...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5114/version/1

Charting the NF-kB pathway interactome map
Provedor de dados: 17
Autores: Paolo Tieri; Alberto Termanini; Elena Bellavista; Stefano Salvioli; Claudio Franceschi.
One of the phenomena observed in human aging is the progressive increase of a systemic inflammatory state, a condition referred to as &amp;#x201c;inflammaging&amp;#x201d;, negatively correlated with longevity. The five components of the Nuclear Factor kB (NF-kB) family are prominent mediators of inflammation. Several different signaling pathways activated by very diverse stimuli converge on NF-kB, resulting in a regulatory system characterized by high complexity. It is increasingly recognized that the number of components that impinges upon phenotypic outcomes of signal transduction pathways may be higher than those taken into consideration from canonical pathway representations. Scope of this analysis is to provide a wider, systemic picture of such...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5266/version/1

ChEBI &amp;#x2013; an Open-access Chemistry Resource for the Life Sciences:&amp;#xb;Facilities for On-line Submission and Curation
Provedor de dados: 17
Autores: Marcus Ennis; Nico Adams; Adriano Dekker; Paula de Matos; Janna Hastings; Kenneth Haug; Duncan Hull; Zara Josephs; Gareth Owen; Steve Turner; Christoph Steinbeck.
ChEBI (Chemical Entities of Biological Interest) is a database of &amp;#x2018;small&amp;#x2019; molecular entities structured around a chemical ontology. It contains almost 600,000 entries, of which approximately 20,000 have been manually curated, as well as entries for groups (parts of molecular entities) and classes of entities. It provides a wide range of information such as chemical nomenclature, structures and related chemical values, and establishes interrelationships between entities in the ontology, in terms of both structure and role. ChEBI places a strong focus on quality, with exceptional efforts being applied to upholding IUPAC nomenclature recommendations and best IUPAC practices when drawing chemical structures....
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5089/version/1

ChEBI, an Open-access Chemistry Resource for the Life Sciences:  Facilities for On-line Submission and Curation
Provedor de dados: 17
Autores: Marcus Ennis.
ChEBI (Chemical Entities of Biological Interest) is a database of &amp;#x2018;small&amp;#x2019; molecular entities structured around a chemical ontology. It contains almost 600,000 entries, of which approximately 20,000 have been manually curated, as well as entries for groups (parts of molecular entities) and classes of entities. It provides a wide range of information such as chemical nomenclature, structures and related chemical values, and establishes interrelationships between entities in the ontology, in terms of both structure and role. ChEBI places a strong focus on quality, with exceptional efforts being applied to upholding IUPAC nomenclature recommendations and best IUPAC practices when drawing chemical structures....
Tipo: Presentation
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5091/version/1

Check Your Data Freedom: A Taxonomy to Assess Life Science Database Openness
Provedor de dados: 17
Autores: Melanie Dulong de Rosnay.
Molecular biology data are subject to terms of use that vary widely between databases and curating institutions. This research presents a taxonomy of contractual and technical restrictions applicable to databases in life science. It builds upon research led by Science Commons demonstrating why open data and the freedom to integrate facilitates innovation and how this openness can be achieved. The taxonomy describes technical and legal restrictions applicable to life science databases, and its metadata have been used to assess terms of use of databases hosted by Life Science Resource Name (LSRN) Schema. While a few public domain policies are standardized, most terms of use are not harmonized, difficult to understand and impose controls that prevent others...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/2083/version/1

ChemAxiom &amp;#x2013; An Ontological Framework for Chemistry in Science
Provedor de dados: 17
Autores: Nico Adams; Edward O. Cannon; Peter Murray-Rust.
We present ChemAxiom as the first ontological framework for chemistry in science. ChemAxiom enables discourse about chemical objects in a computable language and is useful for the management of chemical concepts and data, the retrospective typing of resources, the identification of ambiguity and supports chemical text mining.
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3714/version/1

ChemCloud: Chemical e-Science Information Cloud
Provedor de dados: 17
Autores: Alexandru Todor; Adrian Paschke; Stephan Heineke.
Our Chemical e-Science Information Cloud (ChemCloud) &amp;#x2013; a Semantic Web based eScience infrastructure &amp;#x2013; integrates and automates a multitude of databases, tools and services in the domain of chemistry, pharmacy and bio-chemistry available at the Fachinformationszentrum Chemie (FIZ Chemie), at the Freie Universitaet Berlin (FUB), and on the public Web. Based on the approach of the W3C Linked Open Data initiative and the W3C Semantic Web technologies for ontologies and rules it semantically links and integrates knowledge from our W3C HCLS knowledge base hosted at the FUB, our multi-domain knowledge base DBpedia (Deutschland) implemented at FUB, which is extracted from Wikipedia (De) providing a public semantic resource for chemistry, and...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5642/version/1

Chemical Physics of Phonons &amp;#x26; Superconductivity: A Heuristic Approach
Provedor de dados: 17
Autores: Michael  J. Bucknum.
Several lines of thought are pursued in an attempt to further clarify the role played by phonons in the theory of superconductivity. The central results of BCS theory are examined in the context of anharmonicity in the phonon motion and the role that Badger&amp;#x27;s rule of spectroscopy can play in simplifying and making more chemically intuitive the nature of the mechanism of superconductivity.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1586/version/1

Chemical Physics of Phonons &amp;#x26; Superconductivity: A Heuristic Approach
Provedor de dados: 17
Autores: Michael  J. Bucknum.
Several lines of thought are pursued in an attempt to further clarify the role played by phonons in the theory of superconductivity. The central results of BCS theory are examined in the context of anharmonicity in the phonon motion and the role that Badger&amp;#x27;s rule of spectroscopy can play in simplifying and making more chemically intuitive the nature of the mechanism of superconductivity.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1586/version/2

Chemical Profiles of Essential Oils and Non-Polar Extractables from Sumac (Rhus spp.)
Provedor de dados: 17
Autores: Sierra Rayne.
Sumac is the common name for a genus (Rhus) with &amp;#x3e;250 individual species of flowering plants in the family Anacardiaceae. These plants are globally distributed in temperate and tropical regions and can grow on marginal lands, making them strong candidates for renewable bioproduct sources. Despite the extensive historical use of some members of Rhus spp. for tannins and other commercial phenolics, little is known about the non-phenolic components of extracts and essentials oils. The current review highlights opportunities available to extend these limited prior studies to other sumac species, and for obtaining value-added compounds to complement already established phenolic extractions in these commercial plant species. To date, a number of...
Tipo: Manuscript
Palavras-chave: Chemistry; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5926/version/1

Chemical Topology of Crystalline Matter
Provedor de dados: 17
Autores: Michael J. Bucknum.
This work is intended as a review and extension of the seminal work in chemical topology developed by the crystallographer A.F. Wells in the 20th century.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1587/version/1

Chemical Topology of Crystalline Matter and the Transcendental Numbers &amp;#x3d5;  , e  and &amp;#x3c0;
Provedor de dados: 17
Autores: Michael J. Bucknum; Eduardo A. Castro.
This work is intended as a review and extension of the seminal work in chemical topology developed by the crystallographer A.F. Wells in the 20th century.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1587/version/2

Chemical Topology of Crystalline Matter and the Transcendental Numbers &amp;#x3d5;  , e  and &amp;#x3c0;
Provedor de dados: 17
Autores: Michael J. Bucknum; Eduardo A. Castro.
This work is intended as a review and extension of the seminal work in chemical topology developed by the crystallographer A.F. Wells in the 20th century.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/1587/version/3

Chemistry Crowdsourcing and Open Notebook Science
Provedor de dados: 17
Autores: Jean-Claude Bradley; Kevin Owens; Antony Williams.
This is a pre-proposal written for the NSF program  CDI (Cyber-Enabled Discovery and Innovation) in Jan 2008.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The current system of dissemination of scientific data and knowledge is far less efficient than it needs to be to facilitate improved collaborative science, especially considering current publication vehicles and infrastructure.  There is a growing movement promoting more Open Science with the belief that a more transparent scientific process can perform far more effectively.  The logical extension of this concept is full transparency - exposing a researcher&amp;#x27;s complete record of progress to the public in near real time. Not only will such a process enable ongoing data sharing it also provides an...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1505/version/1

Chemopreventive potential of natural products isolated from a alchornea glandulosa, pterogyne nitens and its semisynthetic analogs
Provedor de dados: 17
Autores: Mauro  C. C. Morais; Laura  E. Marler; Suaib  Luqman; Tamara  P. Kondratyuk; Maicon  S. Petronio; Luis  O. Regasini; Dulce  H. S. Silva; Vanderlan  S. Bolzani; Christiane  P. Soares; John  M. Pezzuto.
INTRODUCTION: Chemoprevention involves the use of natural or synthetic substances to reduce the risk of developing cancer. Gallic acid was found to possess several pharmacological activities, such as anti-oxidant and anti-inflammatory. Guanidine alkaloids display a broad spectrum of biological activities and its cytotoxic effect were well investigated.&amp;#xd;&amp;#xa;OBJECTIVES: The present study evaluated the chemopreventive potential of natural products and its semi-synthetic analogs using quinone reductase (QR) induction, aromatase inhibition and the suppression of NF&amp;#x3ba;B activity, which are well established strategies for screening compounds to cancer chemoprevention. &amp;#xd;&amp;#xa;METHODS: Gallic acid was isolated from Alchornea...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6923/version/1

Chemotherapy effects on brain glucose metabolism at rest
Provedor de dados: 17
Autores: Bruno Baudino; Federico D&amp;#x27;Agata; Giancarlo Castellano; Paola Caroppo; Simona Cauda; Antonella Parente; Matteo  Manfredi; Elisabetta Geda; Laura Orsi; Franco Cauda; Lorys Castelli; Katiuscia Sacco; Rita Ardito; Riccardo Torta; Gianni Bisi.
Background: A growing number of studies reports that chemotherapy may impair brain functions inducing cognitive changes which can persist in a subset of cancer survivors. &amp;#xd;&amp;#xa;Aims: To investigate the neural basis of the chemotherapy-induced neurobehavioral changes by means of metabolic imaging and voxel-based statistical parametric mapping analyses.&amp;#xd;&amp;#xa;Methods: We studied the resting brain [18]FDG-PET/CT images of 43 adult cancer patients with solid (n=12, 28%) or hematologic malignancies (n=31, 72%); 12 patients were studied prior to chemotherapy (No chemotherapy) while treated patients were divided into two matched subgroups: Early High (&amp;#x3c;9 months after chemotherapy, &amp;#x3e;6 chemotherapy cycles, n=10), and Late...
Tipo: Manuscript
Palavras-chave: Cancer; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5637/version/1

ChemTextMiner: An open source tool kit for mining  medical literature abstracts
Provedor de dados: 17
Autores: Muthukumarasamy  Karthikeyan; Yogesh  Pandit; Deepak  Pandit; Ganesh Nainaru; Sunil  Nalwade; Renu  Vyas; Esha  Jain.
Text mining involves recognizing patterns from a wealth of information hidden latent in unstructured text and deducing explicit relationships among data entities by using data mining tools. Text mining of Biomedical literature is essential for building biological network connecting genes, proteins, drugs, therapeutic categories, side effects etc. related to diseases of interest. We present an approach for textmining biomedical literature mostly in terms of not so obvious hidden relationships and build biological network applied for the textmining of important human diseases like MTB, Malaria, Alzheimer and Diabetes. The methods, tools and data used for building biological networks using a distributed computing environment previously used for ChemXtreme[1]...
Tipo: Poster
Palavras-chave: Chemistry; Developmental Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6435/version/1

China is on the track tackling Enteromorpha spp forming green tide
Provedor de dados: 17
Autores: Naihao  Ye; Zhimeng Zhuang; Xianshi Jin; Qingyin Wang; Xiaowen Zhang; Demao Li; Hongxia Wang; Yuze Mao; Zengjie Jiang; Bin Li; Zhixin Xue.
Green tide management is supposed to be a long term fight rather than an episode during the 29th Olympic Games for China, since it has been gaining in scale and frequency during the past 3 decades in both marine and estuary environment all over the world. A number of rapid-responding studies including oceanographic comprehensive surveys along the coastline have been conducted during the bloom and post-bloom periods in 2008 by Chinese marine scientists. The preliminary results are as below: (1) phylogenetic analysis indicates that the bloom forming alga forms a clade with representatives of the green seaweed Enteromorpha linza, though, the alga has been identified as E. proliera by means of morphological; (2) the present data suggest that the bloom was...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2352/version/1

ChIP-on-chip significance analysis reveals large-scale binding and regulation by human transcription factor oncogenes
Provedor de dados: 17
Autores: Adam A. Margolin; Teresa Palomero; Pavel Sumazin; Andrea Califano; Adolfo Ferrando; Gustavo A. Stolovitzky.
ChIP-on-chip has emerged as a powerful tool to dissect the complex network of regulatory interactions between transcription factors and their targets. However, most ChIP-on-chip analysis methods use conservative approaches aimed to minimize false-positive transcription factor targets. We present a model with improved sensitivity in detecting binding events from ChIP-on-chip data. Biochemically validated analysis in human T-cells reveals that three transcription factor oncogenes, NOTCH1, MYC, and HES1, bind one order of magnitude more promoters than previously thought. Gene expression profiling upon NOTCH1 inhibition shows broad-scale functional regulation across the entire range of predicted target genes, establishing a closer link between occupancy and...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1364/version/1

ChlamyCyc - a comprehensive database and web-portal centered on _Chlamydomonas reinhardtii_
Provedor de dados: 17
Autores: Jan-Ole  Christian; Patrick May; Stefan Kempa; Dirk Walther.
*Background* - The unicellular green alga _Chlamydomonas reinhardtii_ is an important eukaryotic model organism for the study of photosynthesis and growth, as well as flagella development and other cellular processes. In the era of high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the whole cellular system of a single organism.&amp;#xd;&amp;#xa;*Results* - In the framework of the German Systems Biology initiative GoFORSYS a pathway/genome database and web-portal for _Chlamydomonas reinhardtii_ (ChlamyCyc) was established, which currently features about 270 metabolic pathways...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3108/version/1

Chlorinated Diphenyl Ethers in Sediments, Biota, and the Water Column from Coastal British Columbia, Canada
Provedor de dados: 17
Autores: Sierra Rayne; Ikonomou G. Michael; Chris Garrett.
Polychlorinated diphenyl ethers (PCDEs) are impurities in technical chlorophenol mixtures, are used as dielectric fluids in capacitors and as herbicides, antiseptics, food preservatives, and papers and textiles, and can be formed through the chlorination of organics in water and wastewater streams. Samples from semipermeable membrane devices (SPMDs), sediments, English sole, mussels, and Dungeness crab were collected from urban/industrial and remote sites along the marine coast of British Columbia and analyzed by congener-specific GC-MS analysis for mono- through deca-substituted PCDEs. Higher concentrations in biota and sediments were observed near urban/industrial areas, with evidence for food-chain biomagnification within major harbours. Correlations...
Tipo: Presentation
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/690/version/1

Chloroplast and Cell Imaging at Submicron Resolution by Two-Photon Excitation
Provedor de dados: 17
Autores: I C. Baianu.
Novel, two-photon NIR excitation fluorescence correlation microspectroscopy tests and preliminary results were presented in this article with submicron resolution for concentrated suspensions of functional cells and chloroplast membranes. Related developments of these technique involve applications of Fluorescence Cross-Correlation Spectroscopy (FCCS) detection to monitoring: &amp;#xd;&amp;#xa;DNA- telomerase interactions, DNA hybridization kinetics, ligand-receptor interactions, and HIV-HBV testing. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Plant Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7116/version/1

Choice reveals that rats are majoritarily resilient to cocaine addiction
Provedor de dados: 17
Autores: Lauriane Cantin; Magalie Lenoir; Sarah Dubreucq; Fushia Serre; Caroline Vouillac; Serge H. Ahmed.
Assessing the relative reward value of cocaine and how it changes with repeated use represents a long-standing goal in addiction research. Surprisingly, recent experimental research in rats &amp;#x2013; the most frequently used animal model in the field &amp;#x2013; suggests that the reward value of cocaine may in fact be relatively weak at least in the majority of individuals. Here, we provide strong additional evidence that confirms and extends the validity and generality of this research. Specifically, we demonstrate that no matter how heavy is past cocaine self-administration, most rats value cocaine poorly and readily decide to quit when offered the opportunity of making a different choice (i.e., drinking water sweetened with saccharin, an otherwise...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3738/version/1

Cholesterol Esterification During Differentiation by Hexamethylene Bisacetamide of Friend Virus-Induced Erythrokeukemia
Provedor de dados: 17
Autores: Maria  F. Mulas; Antonella Mandas; Claudia Abete; Sandra Dessi; Mario Pani; Rosa Manconi; Alessandra Mocali; Francesco Paoletti.
Cholesterol is an essential constituent of all mammalian cell membranes, and its availability is therefore a prerequisite for cellular growth and other functions. Several lines of evidence are now indicating an association between alterations of cholesterol homeostasis and cell cycle progression in cancer cells. However, the role of cholesterol in cell differentiation is still largely unknown. To begin to address this issue, in this study we examined changes in cholesterol metabolism and in the mRNA levels of proteins involved in cholesterol import and esterification (multi-drug resistance, MDR-3) and acylCoA:cholesterol acyltransferase (ACAT) and cholesterol export (caveolin-1) in Friend virus-induced erythroleukemia cells (MELC), in the absence or in the...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5155/version/1

Cholinergic innervation is necessary to shift reward timing activity in rodent visual cortex
Provedor de dados: 17
Autores: Emma Roach; Marshall Hussain Shuler.
While the biological analogue of prediction error has been well characterized in the midbrain dopaminergic system, the possibility of other neuromodulatory systems acting as global reinforcers is a topic of much debate. Reward timing, the phenomenon by which single unit responses in primary visual cortex (V1)&amp;#xd;&amp;#xa;reflect an operantly learned stimulus&amp;#x2010;reward interval, offers a tractable preparation to investigate reinforcement learning in vivo: theoretical work suggests that reward timing results from the interaction of stimulus&amp;#x2010;evoked recurrent network activity and a global reinforcement signal that indicates the time of&amp;#xd;&amp;#xa;received reward. We hypothesized that this signal is conveyed by cholinergic neurons...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5813/version/1

Chopped Arms &amp;#x26; Big Macs: ERP Correlates of Viewing and Imagining Aversive and Food Photos
Provedor de dados: 17
Autores: Amy Comeau; Wei-Hsien Yeh; Alfonso Abizaid; Kim Hellemans; Amedeo D&amp;#x27;Angiulli.
OBJECTIVES&amp;#xd;&amp;#xa;We investigated the Event-Related Potential (ERP) correlates of perceived and imagined food photos and their relation to the perception and imagery of unpleasant emotional photos. Our aim was to determine whether similar or different patterns of neural activity were associated with viewing and imagining food photos versus emotional photos. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;METHODS &amp;#xd;&amp;#xa;Nine volunteers with prescreened normal mood and anxiety levels wore a 32 channel Cap with embedded electrodes (10/20 international system) connected to a high-density low-noise Neuroscan EEG system. Participants were tested during two different blocks: a hunger block (containing 25 neutral and food photos) and an emotional block...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4576/version/1

Chorionic Structures in Maternal Blood
Provedor de dados: 17
Autores: Nilo Pereira Luz.
Chorionic villi are the exchange structures of the placenta where human fetuses receive oxygen and nutrients from maternal blood, this article reports an improvement of a published method to recover them from the blood of pregnant, women, quotes their number and illustrates their size and trypsin impregnation. The reasons to explain the presence of chorionic structures and villi in the circulating maternal blood, the possible significance of their existence in maternal blood and the mechanisms to remove them are discussed. Their size and trypsin impregnation are illustrated. This paper discusses the significance of the presence of such allogeneic structures in the circulating blood of pregnant women and presents a brief discussion on the role of trypsin...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1393/version/1

Chromium uptake by Fenugreek
Provedor de dados: 17
Autores: Xanthate D S; Murthy  Ch V R; Rajan  S C S; Sekhar D M R.
Fenugreek (Trigonella foenum- graecum) is both herb (leaves) and a spice (seed) belonging to the family Fabaceae. Fenugreek leaves and seeds are used in the cuisine of India. Fenugreek also has medicinal value. Fenugreek seeds are known to reduce serum glucose and improve glucose tolerance and hence are prescribed to diabetic patients. In the recent past supplemental Chromium is being prescribed to diabetic patients to activate (increased- insulin binding, insulin receptor number, insulin receptor phosphorylation) insulin. Plants can uptake substantial quantities of toxic metals from contaminated soils if these soils are well ameliorated. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;It is then probable that the medicinal efficacy of Fenugreek in the case of...
Tipo: Manuscript
Palavras-chave: Pharmacology; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6762/version/1

Chromobacterium violaceum ATCC12472: Multi-drug and ethidium bromide resistant
Provedor de dados: 17
Autores: Cristiana G. O. Dal&amp;#x27;Molin; Regina V. Ant&amp;#xf4;nio; Luismar M. Porto.
_Chromobacterium violaceum_ is an opportunistic human pathogen causing a range of gastric infections and occasionally septicemia. This Gram-negative bacillus is a common inhabitant of soil and water in tropical and subtropical areas of the world. Infection occurs after contamination of damaged skin exposed to soil or environmental water. Alternatively, systemic infection can follow the aspiration or ingestion of contaminated water. The major features of infections by _C. violaceum_ are, in generally, rapid clinical course, multiple visceral abscesses, and high mortality. Genomic data on the type strain ATCC 12472 has provided a comprehensive basis for detailed studies of pathogenicity, virulence and drug resistance genes. In this study, the susceptibility...
Tipo: Manuscript
Palavras-chave: Microbiology; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3366/version/1

Chromosomal mutational algebra: a new algebra to manipulate chromosomal mutation
Provedor de dados: 17
Autores: Dipankar Mazumdar.
This study leads to a new algebra. An algebra is defined on the common mechanisms of chromosomal mutation. The algebra (_S^[PSI](C)_^, ~*~, &amp;#x27;, [DELTA], _D_) is constructed for a given _C_ and [PSI]. This algebra represents the most common chromosomal mutational mechanisms. This can lead to a new way to manipulate chromosomal mutation with higher structures of abstract mathematics. The first proposal of the algebra was reported in Mazumdar _et al._, 2007.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3874/version/1

Chronic cocaine enhances release of neuroprotective amino acid taurine: a microdialysis study
Provedor de dados: 17
Autores: Elena Yablonski-Alter; Mervan Agovic; Eleonora Gashi; Theodore Lidsky; Eitan Freedman; Shailesh Banerjee.
Cocaine inhibits high-affinity neurotransmitter uptake at the presynaptic nerve terminals to increase synaptic levels of dopamine, norepinephrine and serotonin^1^. This increase of synaptic dopamine may cause neurotoxicity^2,3^. At least two different mechanisms have been proposed for the development of dopamine-related neurotoxicity: 1) dopamine produces a free radical that may induce cell toxicity^2,3^ and 2) dopamine reduces glutamate transport at its presynaptic sites to increase synaptic levels of this amino acid^4^ and augments glutamate transmission by activating dopamine D1 receptors in different areas of the brain^5-7^. Increase in glutamatergic transmission mediated by the activation on N-methyl dextro-aspartate (NMDA) receptors has been shown to...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2319/version/1

Chronic hyperplastic anemia as an independent risk factor for atherosclerotic lesions: a lesson from thalassemia intermedia
Provedor de dados: 17
Autores: Maria Eliana  Lai; Stefania  Vacquer; Maria Paola  Carta; Alessandra   Spiga; Pier Luigi   Cocco; Fabrizio   Angius; Antonella   Mandas; Sandra  Dessi.
Introduction. Cardiovascular involvement represents a well-known complication and the primary cause of mortality, both in transfusion-dependent beta thalassemia major (&amp;#x3b2;-TM) and in transfusion-independent beta thalassemia intermedia (&amp;#x3b2;-TI). In &amp;#x3b2;-TM, heart iron overload is considered the main cause of this complication. This is likely due to poor adherence to iron-chelating therapy, resulting in the inability of the body to efficiently remove iron excess derived from transfused red blood cell breakdown. Different clinical pictures may instead be evoked in cardiovascular involvement occurring in &amp;#x3b2;-TI; however, until now, no factor has emerged as the major one responsible for these complications....
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4169/version/1

Chronic Morbilliviral Encephalitis in a Young Striped Dolphin from Italy
Provedor de dados: 17
Autores: Giovanni Di Guardo; Cristiano Cocumelli; Francesco  Scholl; Cristina Esmeralda Di Francesco; Roberto  Speranza; Massimiliano Pennelli; Claudia Eleni.
A young male striped dolphin (Stenella coeruleoalba) found stranded in November 2009 was affected by a chronic non-suppurative encephalitis, with prominent mononuclear cell perivascular cuffs, neuronal degeneration, microgliosis, neuronophagia and occasional presence of multinucleate syncytia. Immunohistochemical and biomolecular investigations for Morbillivirus were positive exclusively from the brain, but not from the cerebellum nor from any other tissue, with morbilliviral antigen being detected in neurons and astrocytes. A low neutralizing antibody titer (1:10) against Morbillivirus (CDV) was also found, with no simultaneous presence of anti-Brucella antibodies.&amp;#xd;&amp;#xa;The main reason why the present case appears to be of interest is provided...
Tipo: Manuscript
Palavras-chave: Microbiology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4912/version/1

Chronic thoracic hemisection spinal cord injury in adult rats induces a progressive decline in transmission from uninjured fibers to lumbar motoneurons
Provedor de dados: 17
Autores: Victor L. Arvanian; Lisa  Schnell; Li Lou; Roobeh Golshani; Arsen Hunanyan; Arko Ghosh; Damien D. Pearse; John K. Robinson; Martin E. Schwab; James W. Fawcett; Lorne M. Mendell.
Although most spinal cord injuries are anatomically incomplete, only limited functional recovery has been observed in people and rats with partial lesions. To address why surviving fibers cannot mediate more complete recovery, we evaluated the physiological and anatomical status of spared fibers after unilateral hemisection (HX) of thoracic spinal cord in adult rats. We made intracellular and extracellular recordings at L5 (below HX) in response to electrical stimulation of contralateral white matter above (T6) and below (L1) HX. Responses from T6 displayed reduced amplitude, increased latency and elevated stimulus threshold in the fibers across from HX, beginning 1-2 weeks after HX. Ultrastructural analysis revealed demyelination of intact axons...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2165/version/1

Chronobiology of Epilepsy
Provedor de dados: 17
Autores: Sachin S. Talathi; Dong-Uk Hwang; William Ditto; Mark Spano; Hector Sepulveda; Tom Mareci; Paul Carney.
A fine balance between neuronal excitation and inhibition governs the physiological state of the brain. It has been hypothesized that when this balance is lost as a result of excessive excitation or reduced inhibition, pathological states such as epilepsy emerge. Decades of investigation have shown this to be true in vitro. However, in vivo evidence of the emerging imbalance during the &amp;#x22;latent period&amp;#x22; between the initiation of injury and the expression of the first spontaneous behavioral seizure has not been demonstrated. Here, we provide the first demonstration of this emerging imbalance between excitation and inhibition in vivo by employing long term, high temporal resolution, and continuous local field recordings from microelectrode...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1679/version/1

CIPRO 2.5: Ciona intestinalis Protein integrated database with large-scale omics data, bioinformatic analyses and curated annotation, with ability for user rating and comments
Provedor de dados: 17
Autores: Toshinori Endo; Keisuke Ueno; Kouki Yonezawa; Katsuhiko Mineta; Kohji Hotta; Yutaka Satou; Lixy Yamada; Michio Ogasawara; Hiroki Takahashi; Ayako Nakajima; Mia Nakachi; Mamoru Nomura; Junko Yaguchi; Alu Konno; Sasakura Yasunori; Akiyasu C. Yoshizawa; Hisaaki Taniguchi; Chisato Yamasaki; Miho Sera; Tadashi Imanishi; Kazuo Inaba.
CIPRO database is an integrated protein database for a tunicate species Ciona intestinalis that belongs to the Urochordata.  Although the CIPRO database deals with proteomic and transcriptomic data of a single species, the animal is considered unique in the evolutionary tree, representing a possible origin of the vertebrates and is a good model for understanding chordate evolution, including that of humans.  Furthermore, C. intestinalis has been one of the favorites of developmental biologists; there exists a huge amount of accumulated knowledge on its development and morphology, in addition to the recent genome sequence and gene expression data.  The CIPRO database is aimed at not only collecting published data, but also presenting unique information,...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5435/version/1

Ciproxifan, an H~3~ Receptor Antagonist, Improves Learning and Memory in the APP Mouse Model of Alzheimer&amp;#x27;s Disease
Provedor de dados: 17
Autores: Mark E. Bardgett; Natasha N. Davis; Molly S. Griffith.
Mice that express the mutant form of the human amyloid precursor gene associated with early-onset familial Alzheimer&amp;#x27;s disease demonstrate memory deficits and amyloid plaques. We show here that ciproxifan, a prototypical antagonist of H~3~-type histamine receptors, alleviates two types of learning and memory impairments in such mice. These data support the idea that modulation of H~3~ receptors represents a viable therapeutic strategy in the treatment of Alzheimer&amp;#x27;s disease.
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/4041/version/1

Circadian Preference and Sexual Selection: A Novel Evolutionary Approach
Provedor de dados: 17
Autores: Davide Piffer.
Human sleep patterns differ across age groups and between males and females, and their association with age and gender suggest that they might have been the target of sexual selection during human evolutionary history. In this study, I will test the hypothesis that a phase-delayed circadian phase is a sexually selected trait in humans. A short version of the Horne and Ostberg questionnaire and a questionnaire on sexual behaviour were administered to 134 males and 140 females. A significant negative relationship was found between the MEQ score and the number of sexual partners among males, with evening types reporting more sexual partners than morning types. No significant relationship between females MEQ and number of sexual partners was found. Findings...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2964/version/1

Circadian Preference and Sexual Selection: A Novel Evolutionary Approach
Provedor de dados: 17
Autores: Davide Piffer.
Human sleep patterns differ across age groups and between males and females, and their association with age and gender suggest that they might have been the target of sexual selection during human evolutionary history. In this study, I will test the hypothesis that a phase-delayed circadian phase is a sexually selected trait in humans. A short version of the Horne and Ostberg questionnaire and a questionnaire on sexual behaviour were administered to 134 males and 140 females. A significant negative relationship was found between the MEQ score and the number of sexual partners among males, with evening types reporting more sexual partners than morning types. No significant relationship between females MEQ and number of sexual partners was found. Findings...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/2964/version/2

Circadian rhythmic kinase CK2&amp;#x3b1; phosphorylates BMAL1 to regulate the mammalian clock
Provedor de dados: 17
Autores: Teruya Tamaru; Jun Hirayama; Yasushi Isojima; Katsuya Nagai; Shigemi Norioka; Ken Takamatsu; Paolo Sassone-Corsi.
Clock proteins govern circadian physiology and their function is regulated by a variety of signaling pathways. Here, we show that p45^PFK^, a previously reported circadian rhythmic kinase, corresponds to CK2[alpha]. Rhythmic phosphorylation of the core clock protein BMAL1 by CK2[alpha] occurs in the suprachiasmatic nuclei (SCN), the mammalian central pacemaker. Circadian BMAL1 phosphorylation controls its nucleocytoplasmic localization. Gene silencing for CK2[alpha] and BMAL1 mutagenesis of a highly conserved CK2 phosphorylation site (Ser 90) result in impaired BMAL1 accumulation in the nucleus and subsequent disruption of clock function. These findings reveal that circadian rhythmic kinase CK2 is an essential regulator of the mammalian circadian system.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1702/version/1

Circulating Neutrophils from Trauma Patients Induce Apoptosis Through Dephosphorylation of Epithelial Cell Caspase-8
Provedor de dados: 17
Autores: Songhui Jia; Jean Parodo; Emmanuel Battisti-Charbonney; Jennifer Tsang; Sangyang Jia; Ori D. Rotstein; Andras Kapus; John C. Marshall.
Activated neutrophils can cause oxidant-mediated bystander injury to host cells. This injury has previously been ascribed to the direct effects of oxidants on membrane phospholipids. We show here that oxidants released by neutrophils activated in vivo in survivors of multiple trauma or in vitro by exposure to bacterial lipopolysaccharide (LPS) can also promote the apoptotic death of epithelial cells, through the SHP-1-mediated dephosphorylation of epithelial cell caspase-8. Neutrophils from a cohort of patients who sustained serious injury induced the apoptotic death of cultured epithelial cells in a manner that was dependent on the activity of the NADPH oxidase and the generation of neutrophil-derived reactive oxygen intermediates. Caspase-8 is...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2011
URL: http://precedings.nature.com/documents/6393/version/1

Citizen Science in Disaster and Conflict Resilience
Provedor de dados: 17
Autores: Keith G Tidball; Marianne Krasny.
*Background/Question/Methods*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Within the disaster and conflict response communities, concern about lack of effectiveness of outside responses has led to a debate about the role of local people in developing the capacity to prepare for a crisis and to respond after calamity has struck.  Pelling (2007) points out the potential for participatory disaster risk assessment to build local capacity and for generating knowledge that, along with more expert-driven data collection, is used to identify and reduce the risk of disaster. Similarly, Weinstein and Tidball (2007) and Tidball et al. (2008) present an alternative model for post-crisis intervention based on local assets, including ongoing attempts of communities to manage...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5200/version/1

City rats: From rat behaviour to human spatial cognition in urban environments
Provedor de dados: 17
Autores: David Eilam; Juval Portugali; Osnat Yaski.
The structure and shape of an urban environment influence our ability to find our way about in the city^1-2^. Indeed, urban designers who face the challenge of planning environments that facilitate wayfinding^3^, have a consequent need to understand the relations between the urban environment and spatial cognition^4^. Previous studies have suggested that certain qualities of city elements, such as a distinct contrast with the background (e.g. The Eiffel Tower in Paris), or a clear morphology (e.g. the grid layout of Manhattan&amp;#x27;s streets) affect spatial behaviour and cognition^1,5-7^. However, only a few empirical studies have examined the relations between the urban environment and spatial cognition. Here we suggest that testing rats in...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4759/version/1

ClassTAL
Provedor de dados: 17
Autores: Federico D&amp;#x27;Agata.
This is the description of a Matlab script (classTAL.m) that automatically classifies BrainVoyager .voi maps with afni, MRIStudio white matter and fcon1000 Intrinsic Connectivity Networks brain atlas. The script saves many useful output files (tables, figures and .voi).
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6142/version/2

ClassTAL
Provedor de dados: 17
Autores: Federico D&amp;#x27;Agata.
This is the description of a Matlab script (classTAL.m) that automatically classifies BrainVoyager .voi maps with afni brain atlas. The script saves many useful output files.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6142/version/1

Clays: Colloidal Properties in Nanodomain
Provedor de dados: 17
Autores: Siddhartha S. Mukhopadhyay.
The ever-growing application of clays in nanotechnology rests on fundamental principles of colloid chemistry. They make soils as nature&amp;#x2019;s great electrostatic chemical reactor. Highly anisotropic and often irregular particle shape, broad particle size distribution, different types of charges within the unit cells, heterogeneity of layer charges, pronounced CEC, dis-articulation and flexibility of layers, and different modes of aggregation make clays different from other colloidal materials. Their inseparable association with the genesis of life on Earth and evolutionary diversification of Neoproterozoic life is a safety-belt of nanotechnology. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Nanotechnology promises to be the greatest technological...
Tipo: Presentation
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5807/version/1

Clean Coal and Spirulina maxima (Cyanobacteria) Production through Alkaline-Seawater
Provedor de dados: 17
Autores: Md. Abu Affan; Dae-Won  Lee; Heung-Sik Park; Jae-Hoon Noh; Soo-Jin Heo; Chulhong Oh; Seon-Mi Jeon; Joo-Won Son; Seung-Gyu Son; Hyi-Seung Lee; Hyeon Yong Lee; Do-Hyung Kang.
Carbon capture and storage have involved high cost and an earthquake threat. Coal in NaOH-natural seawater (NSW) can produce clean coal, and organic carbon enriched pretreated sweater (PSWS) can be used to grow Spirulina maxima. However, with freshwater shortage, high cost CO2 feedstock incurs S. maxima biomass production, and using PSWS should be considered as an alternative. NaHCO3 and Na2CO3 were used to sediment Mg2+ and Ca2+ of NSW to resolve turbidity and decreasing phosphate solubility. Here, we show that pre-combustion coal and NaOH concentration calculated by our devised formulae for any salinity could dilute volatile matter 19.8 Kg plus CO2 116.50 to 168.89 Kg Ton^-1^ coal in NaOH-NSW by sedimentation Mg2+ and Ca2+ of 99.91% and 32.52%,...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2012
URL: http://precedings.nature.com/documents/6930/version/1

Climate Change and Disease Simulation
Provedor de dados: 17
Autores: Somnath Jha.
Climate change has manifested differential impacts on various components of the earth system. The impact of climate change is not merely limited to the climatic variable. Climate change has resulted in complex, unforeseen consequences in the biosphere of earth. The silent but gradual changes arise out of varied responses of disease-causing organism to the combination of the disease-conducive environmental variables. The change is the same for both the target hosts plant as well as the animal kingdom. There is an urgent need to look into the changing disease dynamics and the disease pathogen genome sensitivity to the changes in climatic variables. The long memory of genetic makeup of disease pathogen to capture, inherit and evolve or mutate the changed or...
Tipo: Presentation
Palavras-chave: Ecology; Genetics &amp; Genomics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6949/version/1

Clinical Study and Molecular Genetic Analyses of Malaysian GEFS+ Patients
Provedor de dados: 17
Autores: Emmilia Tan; Salmi Abdul Razak; Abdul Aziz Mohamed Yusoff; Jafri Malin Abdullah.
Generalized epilepsy with febrile seizure plus (GEFS+) is a familial epilepsy syndrome characterized by phenotypic and genetic heterogeneity. Neuronal voltage gated sodium channel &amp;#x3b1;-1 subunit gene, SCN1A is the most clinically relevant and associated with GEFS+. The objective was to study the clinical presentations of GEFS+ and analyze the SCN1A gene associated with Malaysian GEFS+ patients. Blood samples were collected from 30 unrelated GEFS+ patients and genomic DNA was obtained using the Qiagen DNA Blood Mini Kit following the manufacturer&amp;#x2019;s instructions. The 26 exons of SCN1A genes were analyzed by polymerase chain reaction (PCR) and denaturing high performance liquid chromatography (DHPLC). The aberrant profile peak from DHPLC...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5393/version/1

Clinical validity assessment of a breast cancer risk model combining genetic and clinical information
Provedor de dados: 17
Autores: Matthew E. Mealiffe; Renee P. Stokowski; Brian K. Rhees; Ross L. Prentice; Mary Pettinger; David A. Hinds.
_Background:_ The extent to which common genetic variation can assist in breast cancer (BCa) risk assessment is unclear.  We assessed the addition of risk information from a panel of BCa-associated single nucleotide polymorphisms (SNPs) on risk stratification offered by the Gail Model.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;_Methods:_ We selected 7 validated SNPs from the literature and genotyped them among white women in a nested case-control study within the Women&amp;#x2019;s Health Initiative Clinical Trial.  To model SNP risk, previously published odds ratios were combined multiplicatively.  To produce a combined clinical/genetic risk, Gail Model risk estimates were multiplied by combined SNP odds ratios.  We assessed classification performance using...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/4295/version/1

Clonal Complexes in Biomedical Ontologies
Provedor de dados: 17
Autores: Albert Goldfain; Lindsay G. Cowell; Barry Smith.
An accurate classification of bacteria is essential for the proper identification of patient infections and subsequent treatment decisions. Multi-Locus Se-quence Typing (MLST) is a genetic technique for bacterial classification. MLST classifications are used to cluster bacteria into clonal complexes. Importantly, clonal complexes can serve as a biological species concept for bacteria, facilitating an otherwise difficult taxonomic classification. In this paper, we argue for the inclusion of terms relating to clonal complexes in biomedical ontologies.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3476/version/1

Clonal origin of Epstein-Barr virus-infected T/NK-cell subpopulations in chronic active Epstein-Barr virus infection
Provedor de dados: 17
Autores: Shouichi Ohga; Masataka Ishimura; Goichi Toshimoto; Toshihiro Miyamoto; Hidetoshi Takada; Tamami Tanaka; Koichi  Ohshima; Ken-Ichi Imadome; Yasunobu Abe; Koichi Akashi; Toshiro Hara.
Clonal expansion of Epstein-Barr virus (EBV) infected B-cells occasionally occurs in immunocompromized subjects. EBV-infected T/natural killer (NK)-cells proliferate in patients with chronic active EBV infection (CAEBV) that is a rare mononucleosis syndrome. It is classified into either T-cell type or NK-cell type according to the primary target of infection, while the pathogenesis remains unclear. To search the clonal origin of EBV-infected T/NK-cells, virus distribution and clonotype were assessed by using highly purified cell fractions obtained from 6 patients. Patient 1 had a monoclonal proliferation of EBV-infected T-cell receptor V&amp;#x3b4;2/V&amp;#x3b3;9-expressing cells, and carried lower copy number of EBV in &amp;#x3b1;&amp;#x3b2;T-cells....
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4238/version/1

Cloning and expression of first gene for biodegrading microcystins by Sphingopyxis sp. USTB-05
Provedor de dados: 17
Autores: Hai Yan; Junfeng Wang; Jian Chen; Wei Wei; Hui Wang.
Harmful cyanobacterial blooms (HCBs) in natural waters are a growing environmental problem worldwide because microcystins (MCs) produced by cyanobacteria are potent hepatotoxins and tumor promoters. MCs are resistant against physical and chemical factors. Thus, biodegradation is the most efficient method for removing MCs, and a number of bacterial strains, especially genus _Sphingomonas_, have been isolated for biodegrading MCs. Although the pathway, enzyme, and gene for biodegrading MCs by _Sphingomonas sp._ have been widely identified recently, no gene concerned with the biodegradation of MCs has been successfully cloned and expressed. In this study, we show that the first and most important gene of mlrA, containing 1,008 bp nucleotides in length, in the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4846/version/1

Closed bioregenerative life support systems: Applicability to hot deserts
Provedor de dados: 17
Autores: Yuriy Polyakov; Ibrahim Musaev; Sergey Polyakov.
Water scarcity in hot deserts, which cover about one-fifth of the Earth&amp;#x2019;s land area, along with rapid expansion of hot deserts into arable lands is one of the key global environmental problems. As hot deserts are extreme habitats characterized by the availability of solar energy with a nearly complete absence of organic life and water, space technology achievements in designing closed ecological systems may be applicable to the design of sustainable settlements in the deserts. This review discusses the key space technology findings for closed biogenerative life support systems (CBLSS), which can simultaneously produce food, water, nutrients, fertilizers, process wastes, and revitalize air, that can be applied to hot deserts. Among them are the...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/3926/version/2

CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) Mothur &amp;#x2013; a C++-based software package used for clustering 16S rRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha diversity);&amp;#xd;&amp;#xa;B) The Ribosomal Database (RDP) nai&amp;#x308;ve Bayesian classifier assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;&amp;#xd;&amp;#xa;C) Qiime &amp;#x2013; a python-based workflow package,...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5888/version/3

CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) Mothur &amp;#x2013; a C++-based software package used for clustering 16S rRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha diversity);&amp;#xd;&amp;#xa;B) The Ribosomal Database (RDP) nai&amp;#x308;ve Bayesian classifier assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;&amp;#xd;&amp;#xa;C) Qiime &amp;#x2013; a python-based workflow package,...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5888/version/2

CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing &amp;#x2013; standard operating procedure, version 1.1
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets: &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) Qiime &amp;#x2013; a Python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including the phylogenetic distance metric UniFrac, UCLUST, PyNAST and the RDP Bayesian classifier;  &amp;#xd;&amp;#xa;B) UCHIME &amp;#x2013; a tool for rapid identification of chimeric 16S sequence fragments; &amp;#xd;&amp;#xa;C) Mothur &amp;#x2013; a C++-based software package for 16S analysis;&amp;#xd;&amp;#xa;D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;CloVR-16S...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6287/version/2

CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing &amp;#x2013; standard operating procedure, version 1.1
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets: &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) Qiime &amp;#x2013; a Python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including the phylogenetic distance metric UniFrac, UCLUST, PyNAST and the RDP Bayesian classifier;  &amp;#xd;&amp;#xa;B) UCHIME &amp;#x2013; a tool for rapid identification of chimeric 16S sequence fragments; &amp;#xd;&amp;#xa;C) Mothur &amp;#x2013; a C++-based software package for 16S analysis;&amp;#xd;&amp;#xa;D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;CloVR-16S...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6287/version/1

CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing &amp;#x2013; standard operating procedure, version1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) Mothur [1] &amp;#x2013; a C++ - based software package used for clustering 16SrRNA sequences into operational taxonomic units (OTUs). Mothur creates OTUs using a matrix that describes pairwise distances between representative aligned sequences and subsequently estimates within-sample diversity (alpha diversity);&amp;#xd;&amp;#xa;B)The Ribosomal Database (RDP) naive Bayesian classifier [2] assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies;&amp;#xd;&amp;#xa;C) Qiime [3] &amp;#x2013; a python-based workflow package,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5888/version/1

CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic whole-genome shotgun (WGS) sequence datasets:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) UCLUST [1] &amp;#x2013; a C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates [1]; &amp;#xd;&amp;#xa;B) BLASTX and BLASTN [2] for functional and taxonomic assignment of sequences, respectively;&amp;#xd;&amp;#xa;C) Metastats [3] and custom R scripts to generate additional statistical and graphical evaluation.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The CloVR-Metagenomics pipeline accepts as input multiple fasta files (1 sample per file) and a corresponding tab-delimited metadata file that specifies features associated...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5886/version/1

CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcom Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic whole-genome shotgun (WGS) sequence datasets:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) UCLUST &amp;#x2013; a C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates;&amp;#xd;&amp;#xa;B) BLASTX and BLASTN for functional and taxonomic assignment of sequences, respectively;&amp;#xd;&amp;#xa;C) Metastats and custom R scripts to generate additional statistical and graphical evaluation.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The CloVR-Metagenomics pipeline accepts as input multiple fasta files (1 sample per file) and a corresponding tab-delimited metadata file that specifies features associated with the samples,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5886/version/2

CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: James R. White; Cesar Arze; Malcom Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic whole-genome shotgun (WGS) sequence datasets:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A) UCLUST &amp;#x2013; a C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates;&amp;#xd;&amp;#xa;B) BLASTX and BLASTN for functional and taxonomic assignment of sequences, respectively;&amp;#xd;&amp;#xa;C) Metastats and custom R scripts to generate additional statistical and graphical evaluation.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The CloVR-Metagenomics pipeline accepts as input multiple fasta files (1 sample per file) and a corresponding tab-delimited metadata file that specifies features associated with the samples,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5886/version/3

CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: Kevin Galens; James R. White; Cesar Arze; Malcolm Matalka; Michelle Gwinn Giglio; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C) Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described elsewhere (K Galens et al. submitted). The assembly component of CloVR- Microbe can be executed independently from the gene identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454 GS FLX or Illumina GAII or...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5887/version/2

CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: Kevin Galens; James R. White; Cesar Arze; Malcolm Matalka; Michelle Gwinn Giglio; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke.
The CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C) Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described elsewhere (K Galens et al. submitted). The assembly component of CloVR- Microbe can be executed independently from the gene identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454 GS FLX or Illumina GAII or...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5887/version/3

CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects &amp;#x2013; standard operating procedure, version 1.0
Provedor de dados: 17
Autores: Kevin Galens; James R. White; Cesar Arze; Malcolm Matalka; Michelle Gwinn Giglio; The CloVR Team; Samuel V. Angiuoli; W. Florian  Fricke.
The CloVR-Microbe pipeline performs the basic processing and analysis steps required for standard microbial single-genome sequencing projects: A) Whole-genome shotgun sequence assembly; B) Identification of protein and RNA-coding genes; and C) Functional gene annotation. B) and C) are based on the IGS Annotation Engine (http://ae.igs.umaryland.edu/), which is described elsewhere (K Galens et al. submitted). The assembly component of CloVR-Microbe can be executed independently from the gene identification and annotation components. Alternatively, pre-assembled sequence contigs can be used to perform gene identifications and annotations. The pipeline input may consist of unassembled raw sequence reads from the Sanger, Roche/454 GS FLX or Illumina GAII or...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5887/version/1

Cluster Analysis of Breast Cancer Microarray Data
Provedor de dados: 17
Autores: Kirtan  P. Dave.
High-throughput genomic technology has rapidly become a major tool for the study of breast cancer. The recent development gene expression microarray and related technology provide to an opportunity to perform more detail profiling of the disease However, whole-genome approaches are still relatively new and critics have been quick to highlight, non-overlapping results from groups testing similar hypotheses. In this canopy, cluster analysis helps to reduce complex multivariate data and may be used to devise in the development of classification systems or taxonomies by gene ontology.
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4936/version/1

c-Myc induced changes in higher order rDNA structure accompany growth factor stimulation of quiescent cells
Provedor de dados: 17
Autores: Chiou-Nan Shiue; Rachel G. Berkson; Anthony P. H. Wright.
Human c-Myc is believed to be a high level coordinator of protein synthesis capacity and cell growth rate, capable of activating transcription by all three nuclear RNA Polymerases. Direct activation of rDNA transcription by c-Myc is functionally conserved in rat cells, despite high divergence in non-coding rDNA sequences, suggesting that this coordinating role is likely to be a general within mammals. Upon re-feeding of starved cells, c-Myc activity enhances the efficiency of RNA Polymerase I and SL1/TIF-1B recruitment to the rDNA and rapidly induces higher order gene loop structures in rDNA chromatin that juxtapose upstream and downstream rDNA sequences. Furthermore c-Myc induced gene-loop formation in rDNA genes occurs independently of rDNA...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2007
URL: http://precedings.nature.com/documents/1448/version/1

cn.FARMS: a probabilistic model to detect DNA copy numbers
Provedor de dados: 17
Autores: Djork-Arn&amp;#xe9;  Clevert; Andreas Mitterecker; Andreas Mayr; Robert Burger; An  De Bondt; Marianne Tuefferd; Willem Talloen; Hinrich G&amp;#xf6;hlmann; Sepp Hochreiter.
Motivation: Existing pre-processing methods for DNA microarrays designed to detect copy number variations (CNVs) lead to high false discovery rates (FDRs). High FDRs misguide researchers especially in the medical context where CNVs are wrongly associated with diseases. We propose a probabilistic latent variable model, cn.FARMS, for array-based CNV analysis which controls the FDR without loss of sensitivity. At a DNA region, cn.FARMS constructs a model by a Bayesian maximum a posteriori estimation where the unobserved, latent variable represents the copy number that is measured by observed genetic markers (probes). The latent variable&amp;#x2019;s prior prefers parameters which represent the null hypothesis, (same copy number for all samples), from which...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4712/version/1

CO2 Enhancement of Forest Productivity Constrained by Limited Nitrogen Availability
Provedor de dados: 17
Autores: Richard J. Norby; Jeffrey M. Warren; Colleen M. Iversen; Charles T. Garten; Belinda E. Medlyn; Ross E. McMurtrie.
Stimulation of terrestrial productivity by rising CO~2~ concentration is projected to reduce the airborne fraction of anthropogenic CO~2~ emissions; coupled climate-carbon (C) cycle models, including those used in the IPCC Fourth Assessment Report (AR4), are sensitive to this negative feedback on atmospheric CO~2~^1^. The representation of the so-called CO~2~ fertilization effect in the 11 models used in AR4 and subsequent models^2,3^ was broadly consistent with experimental evidence from four free-air CO~2~ enrichment (FACE) experiments, which indicated that net primary productivity (NPP) of forests was increased by 23 +/- 2% in response to atmospheric CO~2~ enrichment to 550 ppm^4^. Substantial uncertainty remains, however, because of the expectation...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3747/version/1

Cocaine self-administration in the mouse: A low-cost, chronic catheter preparation
Provedor de dados: 17
Autores: Matthew B. Pomrenze; Michael  V. Baratta; Brian A. Cadle; Donald C. Cooper.
Intravenous drug self-administration is the most valid animal model of human addiction because it allows volitional titration of the drug in the blood based on an individual&amp;#x2019;s motivational state together with the pharmacokinetic properties of the drug. Here we describe a reliable low-cost mouse self-administration catheter assembly and protocol that that can be used to assess a variety of drugs of abuse with a variety of protocols. We describe a method for intravenous catheter fabrication that allows for efficient and long-lasting intravenous drug delivery. The intravenous catheters remained intact and patent for several weeks allowing us to establish stable maintenance of cocaine acquisition. This was followed by a dose response study in the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7040/version/1

Co-detection: Ultra-reliable Nanoparticle-Based Electrical Detection of Biomolecules in the Presence of Large Background Interference
Provedor de dados: 17
Autores: Yang Liu; Evangelyn Alocilja; Shantanu Chakrabartty.
Contrary to popular belief, we report that background interference in conductimetric biochips can be exploited using a novel &amp;#x22;co-detection&amp;#x22; principle to significantly improve the reliability of detecting trace quantities of biomolecules. The technique called &amp;#x22;co-detection&amp;#x22; exploits the non-linear redundancy amongst synthetically patterned biomolecular logic circuits for deciphering the presence or absence of target biomolecules in a sample. In this paper, we demonstrate the &amp;#x22;co-detection&amp;#x22; principle on gold-nanoparticle based conductimetric soft-logic circuits which uses a silver-enhancement technique for signal amplification. Using co-detection, we have been able to measure a 1000 times improvement in...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4389/version/1

Codonopsis pilosula twines either to the left or to the right
Provedor de dados: 17
Autores: Gonghua Lin; Fang Zhao; Eviatar Nevo; Tongzuo Zhang; Jianping Su.
We report the twining handedness of Codonopsis pilosula, which has either a left- or right-handed helix among different plants, among different tillers within a single plant, and among different branches within a single tiller. The handedness was randomly distributed among different plants, among the tillers within the same plants, but not among the branches within the same tillers. Moreover, the handedness of the stems can be strongly influenced by external forces, i.e. the compulsory left and right forming inclined to produce more left- and right-handed twining stems, respectively, and the reversing could make a left-handed stem to be right-handed and vice versa. We also discuss the probable mechanisms these curious cases happen.
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7026/version/1

Coexistence by recruitment variation: How large is the contribution of relative nonlinearity?
Provedor de dados: 17
Autores: Chi Yuan; Peter Chesson.
*Background/Question/Methods*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Recruitment variation is believed to be an important mechanism of species coexistence in variable environments. This mechanism, however, is a composite of two other mechanisms: the storage effect, and relative nonlinearity. The storage effect is a formalization of the concept of temporal environmental niche differentiation.  It is well-understood theoretically and has been tested in natural systems such as forests and annual plant communities. Relative nonlinearity results from species differences in nonlinear responses to fluctuations in competition. Such differences arise whenever species differ in life-history traits such as mean longevity. While the storage effect is assumed to be the...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3595/version/1

Coexistence of grazed and grazing excluded patches increases plant and invertebrate diversity in a Mediterranean oak woodland
Provedor de dados: 17
Autores: Miguel M. N. Bugalho; Lecomte Xavier; Maria Caldeira; Mer&amp;#xed;cia Gon&amp;#xe7;alves; Manuela Branco.
Grazing is a global, dominant land use affecting biodiversity and ecosystem processes. In Mediterranean ecosystems grazing is a major ecological and evolutionary driver but, surprisingly, there is little information on the use of grazing as a tool to manage biodiversity in these ecosystems. We conducted an experiment to assess if the coexistence of grazing and grazing-excluded patches would increase plant and invertebrate diversity in a Mediterranean evergreen oak woodland. Plant community traits were different between treatments. Plant and litter biomass was higher, and the proportion of bare ground was lower, in grazing-excluded plots. Grazing affected functional diversity with legumes, invertebrate detritivores and sup sucking insects being more...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5194/version/1

Co-expression Toggling of MicroRNAs in Alzheimer&amp;#x2019;s Brain
Provedor de dados: 17
Autores: Malay Bhattacharyya.
We present the findings on how microRNA expression profiles changes in Alzheimer&amp;#x27;s brain.
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7123/version/1

Cognitive deficits of schizophrenia: the flower workshop initiative
Provedor de dados: 17
Autores: Maria Alice Ornellas Pereira; Alfredo Pereira Jr.
Advancement of research on the neurobiology of the schizophrenic brain has revealed a complex of factors, from genetic tendencies affecting the development of brain structure to functional impairment caused by defective molecular signaling. Recently, the attention of psychiatrists and mental health professionals has been directed to the presence of cognitive deficits, responsible for most of the obstacles to the social insertion of patients.The schizophrenic person has a difficulty to manage the flux of consciousness in social interactions. We address this difficulty with the Flower Arrangement Workshop, a methodology of Psycho-Social Rehabilitation that reduces the vulnerability of the schizophrenic in the social environment. The workshop was offered...
Tipo: Presentation
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1497/version/1

Cognitive dimensions of predator responses to imperfect mimicry?
Provedor de dados: 17
Autores: Lars Chittka; Daniel Osorio.
Many palatable insects, for example hoverflies, deter predators by mimicking well-defended insects such as wasps. However, for human observers, these flies often seem to be little better than caricatures of wasps &amp;#x2013; their visual appearance and behaviour are easily distinguishable. This imperfect mimicry baffles evolutionary biologists, because one might expect natural selection to do a more thorough job. Here we discuss two types of cognitive processes that might explain why mimics distinguishable mimics might enjoy increased protection from predation. Speed accuracy tradeoffs in predator decision making might give imperfect mimics sufficient time to escape, and predators under time constraint might avoid time-consuming discriminations between...
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1258/version/1

Cognitive epidemiology of ethnic health and the CHRM2 vagal vigour hypothesis
Provedor de dados: 17
Autores: Roy A. Frye.
Ethnic populations representing areas throughout California were compared regarding cognitive ability, socioeconomic position, and mortality. Cognition and socioeconomic position were inversely correlated with mortality. The single nucleotide polymorphism rs8191992 in the M2 muscarinic receptor gene (CHRM2) was previously linked to IQ and modulation of vagal tone. The CHRM2 vagal vigour hypothesis posits that variation at rs8191992 alters the binding site for a brain-expressed microRNA (hsa-mir-383) thereby changing expression of brain M2 muscarinic receptors to cause pleiotropic effects on cognition and vagus nerve signalling which then affects health via the vagal cholinergic anti-inflammatory pathway. This may help explain ethnic health differences,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2862/version/1

Cognitive Sciences and Child Poverty: Facts and Challenges
Provedor de dados: 17
Autores: Amedeo D&amp;#x27;Angiulli; Sebastian Lipina.
In the context of cognitive neuroscience, the study of poverty and social gradients is a very young area of research where a core consensus of basic results is quickly emerging. However, as any emerging scientific discipline, the approaches used are influenced by epistemological stances inherited from other disciplines, and potentially implicit ideological systems as well. Explicitly or inadvertently, such influences can lead this critically important new area of research to methodological and ethical foundational challenges and to issues that are in need of debate (e.g., poverty definition criteria, lack of specificity when considering child poverty in terms of how children experience different type of deprivations, or lack of critics regarding social...
Tipo: Presentation
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4679/version/1

Coincidence between transcriptome analyses on different microarray platforms using a parametric framework
Provedor de dados: 17
Autores: Tomokazu Konishi; Fumikazu Konishi; Shigeru Takasaki; Kohei Inoue; Kouji Nakayama; Akihiko Konagaya.
A parametric framework for the analysis of transcriptome data is demonstrated to yield coincident results when applied to data acquired using two different microarray platforms. Discrepancies among transcriptome studies are frequently reported, casting doubt on the reliability of collected data. The inconsistency among observations can be largely attributed to differences among the analytical frameworks employed for data analysis. The existing frameworks normalizes data against a standard determined from the data to be analyzed. In the present study, a parametric framework based on a strict model for normalization is applied to data acquired using an in-house printed chip and GeneChip. The framework is based on a common statistical characteristic of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1746/version/1

Collaborate in conservation: A method for volunteer-scientist teams to monitor plant community composition long-term in a private old-growth forest
Provedor de dados: 17
Autores: Erin J. Fleming; Nelson F. Galvis; Bette A. Loiselle; Julia  F. Nerbonne.
To date, most studies on the management of invasive species have been done in nature reserves or national parks. Few published studies demonstrate how scientists and local communities might collaborate to develop science-based management programs in private forests. We present an example of such collaboration. The Congregational Summer Assembly (CSA) is a mixture of common and privately owned lots within old-growth beech-maple forest in Lower Michigan. The community is trying to conserve the forest and, thus, is interested in ecological variables that should be considered when designing a long-term ecosystem based management plan. &amp;#xd;&amp;#xa; In this base-line study we developed methods for volunteer-scientist teams to monitor 1) the abundance of...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/5527/version/1

Collaborative platforms for streamlining workflows in Open Science
Provedor de dados: 17
Autores: Konrad U. F&amp;#xf6;rstner; Gregor  Hagedorn; Claudia  Koltzenburg; M. Fabiana   Kubke; Daniel  Mietchen.
Despite the internet&amp;#x2019;s dynamic and collaborative nature, scientists continue to produce grant proposals, lab notebooks, data files, conclusions etc. that stay in static formats or are not published online and therefore not always easily accessible to the interested public. Because of limited adoption of tools that seamlessly integrate all aspects of a research project (conception, data generation, data evaluation, peer-reviewing and publishing of conclusions), much effort is later spent on reproducing or reformatting individual entities before they can be repurposed independently or as parts of articles.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We propose that workflows - performed both individually and collaboratively - could potentially become more...
Tipo: Manuscript
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6066/version/1

Collagen-bound low density lipoprotein modifies endothelial cell adhesion to type V collagen: Implications for atherosclerosis
Provedor de dados: 17
Autores: Stefan Lorkowski; J&amp;#xfc;rgen Rauterberg; B&amp;#xe4;rbel Harrach-Ruprecht; David Troyer.
Low density lipoprotein (LDL) is retained in the extracellular matrix of the arterial wall where it is considered to be atherogenic, but little is known about how cell adhesion to the matrix is affected by collagen-bound LDL. We tested the effect of native, oxidized and acetylated LDL reacted with adsorbed monomeric type I, III and V collagen on endothelial cell adhesion to collagen using a colorimetric adhesion assay. We found that none of the LDL species affected adhesion to type I and III collagen, but that collagen-bound native and acetylated LDL enhanced attachment to type V collagen, whereas bound oxidized LDL inhibited adhesion to this collagen. We suggest that oxidized LDL associated with type V collagen in the arterial wall would favor...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1238/version/1

Collective Animal Behavior from Bayesian Estimation and Probability Matching
Provedor de dados: 17
Autores: Alfonso Perez-Escudero; Gonzalo de Polavieja.
Animals living in groups make movement decisions that depend, among other factors, on social interactions with other group members. Our present understanding of social rules in animal collectives is based on empirical fits to observations and we lack first-principles approaches that allow their derivation. Here we show that patterns of collective decisions can be derived from the basic ability of animals to make probabilistic estimations in the presence of uncertainty. We build a decision-making model with two stages: Bayesian estimation and probabilistic matching.&amp;#xd;&amp;#xa;In the first stage, each animal makes a Bayesian estimation of which behavior is best to perform taking into account personal information about the environment and social...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/5939/version/1

Collective Animal Behavior from Bayesian Estimation and Probability Matching
Provedor de dados: 17
Autores: Alfonso Perez-Escudero; Gonzalo G. de Polavieja.
Animals living in groups make movement decisions that depend, among other factors, on social interactions with other group members. Our present understanding of social rules in animal collectives is mainly based on empirical fits to observations, with less emphasis in obtaining first-principles approaches that allow their derivation. Here we show that patterns of collective decisions can be derived from the basic ability of animals to make probabilistic estimations in the presence of uncertainty. We build a decision-making model with two stages: Bayesian estimation and probabilistic matching.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In the first stage, each animal makes a Bayesian estimation of which behavior is best to perform taking into account personal...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/5939/version/2

Collective cell guidance by cooperative intercellular forces
Provedor de dados: 17
Autores: Dhananjay T. Tambe; Charles C. Hardin; Jeffrey J. Fredberg; Xavier Trepat.
Cells comprising a tissue migrate as part of a collective. In order to coordinate collective multi- cellular migration, each constituent cell integrates local information including chemical signals and mechanical stresses.&amp;#x9;The boundary between a constituent cell and its immediate neighbors comprises cell-cell junctions and cryptic lamellipodia, but the state of local mechanical stress exerted at that boundary has not been accessible experimentally. As such it is not clear how collective mechanical processes could be coordinated over length scales spanning large multi-cellular assemblies. We report here maps of the stresses exerted within and between cells comprising a monolayer. Within the cell sheet there arise unanticipated fluctuations of...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5405/version/1

Colored filters improve exclusion of perceptual noise in visually symptomatic dyslexics
Provedor de dados: 17
Autores: Nadia Northway; Velitchko Manahilov; William A. Simpson.
Dyslexic individuals have deficits in detecting visual stimuli embedded in high levels of perceptual noise. Here we show that visually symptomatic dyslexics, who otherwise had elevated contrast thresholds for discriminating symbols in visual noise, had thresholds similar to non-dyslexics when wearing colored filters. These findings provide evidence that colored filters, which minimize the visual distortions and discomfort of dyslexics when reading, improve dyslexics&amp;#x27; noise exclusion to normal levels.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1729/version/1

Colour reverse learning and animal personalities: the advantage of behavioural diversity assessed with agent-based simulations
Provedor de dados: 17
Autores: Adrian G. Dyer; Alan Dorin; Verena Reinhardt; Marcello G. P. Rosa.
Foraging bees use colour cues to help identify rewarding from unrewarding flowers, but as conditions change, bees may require behavioural flexibility to reverse their learnt preferences. Perceptually similar colours are learnt slowly by honeybees and thus potentially pose a difficult task to reverse-learn. Free-flying honeybees (N = 32) were trained to learn a fine colour discrimination task that could be resolved at ca. 70% accuracy following extended differential conditioning, and were then tested for their ability to reverse-learn this visual problem multiple times. Subsequent analyses identified three different strategies: &amp;#x2018;Deliberative-decisive&amp;#x2019; bees that could, after several flower visits, decisively make a large change to...
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/7037/version/1

COMBINE - a vision
Provedor de dados: 17
Autores: Nicolas Le Novere.
A decade ago, the creation of the Systems Biology Markup Language (SBML) changed the way people exchanged, verified and re-used models in systems biology. The robustness and versatility of this format, coupled to a wide software support, fostered the emergence of an entire area of research centered on model processing such as encoding, annotation, merging, comparison and integration with other datasets. Recently, new languages appeared that complement the model description, such as SED-ML to describe the simulation experiments or SBRML to encode the numerical results. In neuroscience, other fledgling efforts cover for instance multi-compartment neurons with NeuroML, and neuronal networks with NineML. More are needed to cover the wide spectrum of...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5992/version/1

COMBINE and MIRIAM Registry
Provedor de dados: 17
Autores: Nicolas Le Novere.
N/A
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6152/version/1

COMBINE - What it is, what it could be
Provedor de dados: 17
Autores: Nicolas Le Novere.
The &amp;#x27;COmputational Modeling in BIology&amp;#x27; NEtwork (COMBINE) is an initiative to coordinate the development of the various community standards and formats for computational models, initially in Systems Biology and related fields. By doing so, it is expected that the federated projects will develop a set of interoperable and non-overlapping standards covering all the aspects of modeling in biology.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Building on the experience of mature projects, which already have stable specifications, software support, user-base and community governance, COMBINE will help foster or support fledging efforts aimed at filling gaps or new needs. As those efforts mature, they may become part of the core set of COMBINE...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6332/version/1

Combining systems biology and pharmacokinetics - drug cardiotoxicity assessment
Provedor de dados: 17
Autores: Sebastian Polak.
Cardiotoxicity assessment is a compulsory element of the drug development process required by drug agencies including the FDA and EMA. The risk of fatal ventricular arrhythmia triggered by drugs is the rationale for such requirements. Over the last two decades prolongation of QT interval has been responsible for the withdrawal of several drugs from the market and extensive black box labeling restrictions. Although there are a number of mechanisms by which drugs may lead to QT prolongation, inhibition of the potassium channels encoded by the hERG gene has been a cause in many cases. Thus, it is not surprising that interaction with the hERG channel has become a major pharmacological safety concern. It can be reliably assessed with use of in silico realized...
Tipo: Presentation
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5900/version/1

Combining Transfer of TTF-1 and Pax-8 Gene: a Potential Strategy to Promote Radioiodine Therapy of Thyroid Carcinoma
Provedor de dados: 17
Autores: Da Mu; Rui Huang; Xiaojuan Ma; Suping Li; Anren Kuang.
Cotransfer of TTF-1 and Pax-8 gene to tumor cells, resulting in the reexpression of iodide metabolism-associated proteins, such as sodium iodide symporter (NIS), thyroglobulin (Tg), thyroperoxidase (TPO), offers the possibility of radioiodine therapy to non-iodide-concentrating tumor because the expression of iodide metabolism-associated proteins in thyroid are mediated by the thyroid transcription factors TTF-1 and Pax-8. The human TTF-1 and Pax-8 gene were transducted into the human thyroid carcinoma (K1 and F133) cells by the recombinant adenovirus, AdTTF-1 and AdPax-8. Reexpression of NIS mRNA and protein, but not TPO and Tg mRNA and protein, was detected in AdTTF-1-infected F133 cells, following with increasing radioiodine uptake (6.1~7.4 times),...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2011
URL: http://precedings.nature.com/documents/6546/version/1

Combustion Analysis of a Meteorite Debris
Provedor de dados: 17
Autores: Saheeb Ahmed Kayani.
In this research paper, nature and origins of a meteorite debris identified near village Lehri in district Jhelum, Pakistan have been determined. Total carbon content of a specimen of the meteorite debris is determined using combustion analysis and this abundance has been compared with values reported in literature to establish likely origins of the debris.
Tipo: Poster
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5066/version/1

Combustion Analysis of a Meteorite Debris
Provedor de dados: 17
Autores: Saheeb Ahmed Kayani.
In this research paper, nature and origins of a meteorite debris identified near village Lehri in district Jhelum, Pakistan have been determined. Total carbon content of a specimen of the meteorite debris is determined using combustion analysis and this abundance has been compared with values reported in literature to establish likely origins of the debris.
Tipo: Poster
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5066/version/2

Comment on &amp;#x201c;On the Doubly Hydrogen Bonded Dimer of 7-Azaindole (0.1 M) as a Model for DNA Base Pairs in Acetonitrile Solutions at Rt&amp;#x201d;
Provedor de dados: 17
Autores: Oh-Hoon Kwon; Omar F. Mohammed.
In continuation of comments by Catal&amp;#xe1;n, the latest here questions the steady-state emission spectra of 7-azaindole, and hence the validity of non-concerted proton transfer. In this comment, we show that his results are at fault and not supportive of his claims. We provide possible causes of the misleading claims, including the contamination of the solvent with water moisture. We conclude by calling for an end to such practice, which is counter productive, as it does not follow the scholarly approach of science.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/2522/version/1

Comment on &amp;#x22;Embryological evidence identifies wing digits in birds as digits 1, 2, and 3.&amp;#x22;
Provedor de dados: 17
Autores: Xing Xu; Jonah  Choiniere; Corwin Sullivan; Fenglu Han.
Tamura et al. (Science, 11 Febuary 2011, p. 753) claim that the three avian wing digits should be identified as digits I-III based on new embryological data and suggest that these identifications help to remove the conflict between the paleontological data and developmental data concerning the homology of the avian digits. However, their results are not novel, and the authors fail to address the critical problems relating to this interesting issue.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6433/version/1

Comment on Lobell et al &amp;#x22;Climate Trends and Global Crop Production Since 1980&amp;#x22;
Provedor de dados: 17
Autores: Mikhail A. Semenov; Peter R. Shewry.
Lobel et al (ScienceXpress) analysed changes in global yields which can be attributed to climate change trend, and reported a 5.5% decline in global wheat production since 1980. We have failed to confirm these results using a process-based crop model, which showed no decline in wheat yield since the 1950s at two European sites. The Lobel et al conclusions are not valid due to the limitations of the regression analysis used.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6289/version/1

Comment to &amp;#x22;Endogenous Viral Etiology of Prion Diseases&amp;#x22;
Provedor de dados: 17
Autores: Claudiu Bandea.
This note is intended as a comment to a paper in Nature Precedings entitled &amp;#x22;Endogenous viral etiology of prion diseases&amp;#x22;:http://precedings.nature.com/documents/3887/version/1 . Because it contains illustrations that could not be displayed in the comments section of that paper, I&amp;#x2019;m posting this comment here as a PDF document.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Neuroscience; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4101/version/1

Comments and Suggestions for Improvement of the  Archon Genomics X PRIZE Validation Protocol
Provedor de dados: 17
Autores: Alexander Wait Zaranek; Tom Clegg; Ward  Vandewege; Joseph V. Thakuria.
This document is a comment on the X PRIZE validation protocol written by Kedes et al. (2011).  We propose several modifications which we think will improve the fairness and transparency of the contest while keeping the cost of the validation process under control.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5766/version/1

Comments on &amp;#x201c;Assessing future risk: quantifying the effects of sea level rise on storm surge risk for the southern shores of Long Island, New York&amp;#x201d;
Provedor de dados: 17
Autores: David A. Burton.
Tide gauge and satellite data indicate that the rate of sea level rise has not increased significantly in response to the last 3/4 century of CO2 emissions, so there is no reason to expect that it will do so in response to the next 3/4 century of CO2 emissions. The best prediction for sea level in the future is simply a linear projection of the history of sea level at the same location in the past. For Long Island, that is about 7-8 inches by 2080.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/7067/version/1

Common Transactivation Motif 9aaTAD recruits multiple general co-activators TAF9, MED15, CBP and p300
Provedor de dados: 17
Autores: Martin Piskacek.
More than 2000 transcription factors are involved in the human gene regulation to provide cellular function and development. Transactivation domain, TAD, mediates the interaction of transcription factors with general transcriptional co-activators such as TAF9, MED15, CBP and p300. Recently reported NMR-data for interactions of these co-activators with transcription factors reveal tightly binding of KIX and TAZ domains to common 9aaTAD motif. Nine-amino-acid Trans-Activation Domain, 9aaTAD, defines a transactivation domain common to a large super-family of eukaryotic transcription factors represented in yeast by Gal4, Oaf1, Pdr1, Rtg3, Pho4, Gln3, Gcn4 and in mammals by p53, E2A, NFAT, NFkB, HSF1, NF-IL6, MLL, EBNA2, VP16. The 9aaTAD family was derived from...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3488/version/2

Common Transactivation Motif 9aaTAD recruits multiple general co-activatorsTAF9, MED15, CBP and p300
Provedor de dados: 17
Autores: Martin Piskacek.
More than 2000 transcription factors are involved in the human gene regulation to provide cellular function and development. Transactivation domain, TAD, mediates the interaction of transcription factors with general transcriptional co-activators such as TAF9, MED15, CBP and p300. Recently reported NMR-data for interactions of these co-activators with transcription factors reveal tightly binding of KIX and TAZ domains to common 9aaTAD motif. Nine-amino-acid Trans-Activation Domain, 9aaTAD, defines a transactivation domain common to a large super-family of eukaryotic transcription factors represented in yeast by Gal4, Oaf1, Pdr1, Rtg3, Pho4, Gln3, Gcn4 and in mammals by p53, E2A, NFAT, NFkB, HSF1, NF-IL6, MLL, EBNA2, VP16. The 9aaTAD family was derived from...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3488/version/1

Commonness and rarity of species: Does species&amp;#x27; rank influence contribution to ecosystem function?
Provedor de dados: 17
Autores: Meha Jain; Case Prager; Dan Flynn; Caroline Devan; Georgia Hart; Farshid Ahrestani; Dan Bunker; Matt Palmer; Sean Smukler; Jason Sircely; Shahid Naeem.
Across the globe, biodiversity loss is occurring at an unprecedented rate. Rare species are especially susceptible to extinction, given that they typically have small population sizes and restricted geographic ranges, are less adaptable to disturbances, and are greater habitat specialists. However, while rare species may be prone to extinction, it remains unclear whether the loss of rare species is important to ecosystem function. In addition, it is important to consider the way in which rarity is defined, given that there are multiple definitions of rarity based on a species&amp;#x27; geographic range, habitat specificity, and abundance in a community. Therefore, to better understand the contribution of rare species to community function, our study has...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5243/version/1

Community content building for evolutionary biology: Lessons learned from LepTree and Encyclopedia of Life
Provedor de dados: 17
Autores: Cynthia Parr; Dana Campbell; John Park.
Online resources to aid large-scale ecological and evolutionary biology are beginning to take root, only a decade behind fields such as genomics and molecular biology. One barrier has been a long tradition, in evolutionary biology at least, of work by individuals on the order of a few hundred of species rather than the thousands or hundreds of thousands necessary to understand the general evolutionary or ecological processes that explain species characteristics and distributions. Advances in collaborative and semantic software offer promise &amp;#x2013; it should be possible to develop high quality online species-level datasets for comparative analyses and even to integrate, via machine reasoning, across highly customized datasets. In this talk we will...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4603/version/1

Community curation on WikiPathways: How we assist knowledge collection
Provedor de dados: 17
Autores: Chris Evelo.
Biologists typically use knowledge represented as pathways to better understand the results of genomics experiments. Through integration of data from different omics techniques with what we already know, statistical evaluation and subsequent data visualization the results often start to make sense. An important problem is that we often do not have the relevant pathways, or they may be incomplete or not suitable for usage by analytical tools. Wikipathways is meant to be an answer to the problems described above. It uses mediawiki technology and dedicated open source java code to allow biologists to edit pathway content on the web. We assist this process through the development of helpful software like a Diff tool, Go and KEGG converters, portal mechanism,...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3115/version/1

Community dynamics generates complex epidemiology through self-induced amplification and suppression
Provedor de dados: 17
Autores: Zhenyuan Zhao; Juan Pablo Calderon; Chen Xu; Pak Ming Hui; Neil Johnson.
The development of quantitative models of outbreaks is key to their eventual control, from human and computer viruses through to social (and antisocial) activities. Standard epidemiological models can reproduce many general features of outbreaks. Unfortunately, the large temporal fluctuations which often dominate real-world data are thought to require more complicated, system-specific models involving super-spreaders, specific social network topologies and rewirings, and birth-death processes. However we show here that these large fluctuations have a generic explanation in terms of underlying community dynamics. Communities increasing (or decreasing) in size, act as instantaneous amplifiers (or suppressors) yielding a complex temporal evolution whose...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2030/version/1

Community Outreach through Genomics Education Partnership
Provedor de dados: 17
Autores: Ramana Madupu; Anne G. Rosenwald; A. Malcolm Campbell; Satish C. Bhalla; Granger Sutton.
The J Craig Venter Institute (JCVI) has recently partnered with undergraduate university faculty to expand the scope of education and outreach program as part of the NIAID&amp;#x2019;s BRC initiative, by joining forces with faculty members participating in the Genomics Education Partnership (GEP). The goal of the GEP is to provide opportunities for undergraduate students to participate in genomics research and gain hands on experience.  Faculty members trained on annotation methodologies and tools during the Prokaryotic Annotation Workshop conducted at JCVI, impart their knowledge in the classroom as part of the semester course. As a pilot project, we are currently collaborating with 3 groups lead by a faculty member, spread across 3 universities in the...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3149/version/1

Community-level analysis of anthropogenic impacts on rocky shore communities in Sri Lanka
Provedor de dados: 17
Autores: Ashoka D. K. H. Manage.
Human activities threat seashore communities in many areas of the world and their impacts on coastal ecosystem are a matter of increasing concern. Present study describes the anthropogenic disturbances on the rocky shore community structure by comparing the benthic communities of disturbed and non-disturbed areas in Sri Lanka where rocky shores remain virtually untouched so far by experimental studies. Impacts of human disturbances; trampling, handling and exploitation on the community structure of rocky macro benthic assemblages were tested in high-, mid- and low-intertidal area by stratified sampling method at Rumassala marine sanctuary and adjacent two localities at either side of the marine sanctuary, Galle and Unawatuna. Univariate measures, log...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2317/version/1

Comparative density functional theory study on the relative gas phase enthalpies and free energies of formation for the mono- through hepta-halogenated (X=F, Cl, Br) anthraquinones
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase standard state (298.15 K, 1 atmosphere) relative enthalpies and free energies of formation were calculated for all mono- through hepta-halogenated (X=F, Cl, Br) anthraquinone congeners using the B3LYP, BHandHLYP, M062X, PBE0, and B97D density functionals with the 6-311++G(d,p) basis set. All levels of theory yielded similar results with strong intra- and inter-method correlations for both the relative enthalpy and free energy values and the corresponding thermodynamic stability rank. Within each homolog group, the most thermodynamically stable isomers are those which maximize substitution at the lateral positions (2, 3, 7, and 8) versus the less stabilizing peri positions (1, 4, 6, and 9), while also minimizing destabilizing adjacent substitution...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5153/version/1

Comparative Enumeration Gene Expression
Provedor de dados: 17
Autores: Leonardo Varuzza; Carlos A. D. E. B. Pereira.
This paper is about differential gene expression measured by transcript counting methods such as SAGE or MPSS.  It introduces two significance tests for detection of differential expressed tags: frequentist and Bayesian. Under the frequentist view, it is proposed a test that computes the critical level as a function of each tag total frequency. Under the Bayesian view the Full Bayesian Significance Test is used considering the logistic normal distribution. The two proposed significance levels, the frequentist and the Bayesian, are compared for a data set with four libraries. The linking function between them is a Beta distribution function with mean 0.39 and standard deviation 0.30.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2002/version/1

Comparative functional genomics approach for the annotation of proteins in Unclassified Halophilic archaeon DL31
Provedor de dados: 17
Autores: N S. Sardeshmukh; S G. Sanmukh; E Nakkeeran.
The structure, function and sub-cellular location prediction for the unknown proteins from Unclassified Halophilic archaeon DL31 were carried out for characterization of the proteins in their respective families. The 991 genes for hypothetical proteins in Halophilic archaeon DL31 chromosome were predicted by the application of computational methods and Bioinformatics web tools. The structure predictions for 206 unknown proteins were possible whereas functions were predicted in 825 protein sequences. The function prediction for the proteins were done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN and PFAM by searching protein databases for the presence of conserved domains. The Sub-cellular location predictions were done for all the unknown...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6784/version/1

Comparative genomics and disorder prediction identify biologically relevant SH3 protein interactions
Provedor de dados: 17
Autores: Pedro Beltrao; Luis Serrano.
Protein interaction networks are an important part of the post-genomic effort to integrate a part-list view of the cell into system-level understanding. Using a set of 11 yeast genomes we show that combining comparative genomics and secondary structure information greatly increases consensus-based prediction of SH3 targets. Benchmarking of our method against positive and negative standards gave 83% accuracy with 26% coverage. The concept of an optimal divergence time for effective comparative genomics studies was analyzed, demonstrating that genomes of species that diverged very recently from _Saccharomyces cerevisiae_ (_S. mikatae_, _S. bayanus_, and _S. paradoxus_), or a long time ago (_Neurospora crassa_ and _Schizosaccharomyces pombe_), contain less...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/16/version/1

Comparative Litter Quality and Recalcitrance Among Native Grasses and the Invasive, Non-indigenous KR Bluestem (_Bothriochloa ischaemum_)
Provedor de dados: 17
Autores: Amanda Benbow; Kelly G. Lyons.
KR Bluestem (_Bothriochloa ischaemum_) is a non-indigenous, invasive, C4 grass that was introduced throughout the Midwestern and Southwestern U.S. short- to midgrass prairies with the aim of improving degraded rangelands.  The aggressive nature of KR bluestem has led to dramatic alterations of natural and managed ecosystems. Comparative studies of decomposition often show that non-indigenous, invasive plant species have higher rates of nutrient cycling than indigenous species; however, KR bluestem appears to deviate from this trend.  Large amounts of litter are observed in KR-dominated grasslands as compared to intact native grasslands, suggesting that the species has a relatively lower decomposition rate and may slow nutrient cycling in these systems....
Tipo: Presentation
Palavras-chave: Ecology; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3614/version/1

Comparative methods in R hackathon
Provedor de dados: 17
Autores: Brian O&amp;#x27;Meara; Michael Alfaro; Charles Bell; Benjamin Bolker; Marguerite Butler; Peter Cowan; Damien de Vienne; Richard Desper; Joseph Felsenstein; Luke Harmon; Christoph Heibl; Andrew Hipp; Gene Hunt; Thibaut Jombart; Steve Kembel; Hilmar Lapp; Scott Loarie; Wayne Maddison; Peter Midford; David Orme; Emmanuel Paradis; Sam Price; Dan Rabosky; Brian Sidlauskas; Stacey Smith; Dave Swofford; Todd Vision; Peter Waddell; Amy Zanne; Derrick Zwickl.
The R statistical analysis package has emerged as a popular platform for implementation of powerful comparative methods to understand the evolution of organismal traits and diversification. A hackathon was organized to bring together active R developers as well as end-users working on the integration of comparative phylogenetic methods within R to actively address issues of data exchange standards, code interoperability, usability, documentation quality, and the breadth of functionality for comparative methods available within R. Outcomes included a new base package for phylogenetic trees and data, a public wiki with tutorials and overviews of existing packages, code to allow Mesquite and R to interact, improvement of existing packages, and increased...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2126/version/1

Comparative semiempirical, ab initio, and DFT study on the thermodynamic properties of linear and branched PFSA/Fs, PFCA/Fs, and perhydroalkyl sulfonic acids, alkanes, and alcohols
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
A systematic and comprehensive semiempirical, Hartree-Fock (HF) ab initio, and B3LYP density functional theory (DFT) study was conducted on the relative thermodynamic properties of various linear and branched perfluorinated and perhydrogenated alkyl compounds. The semiempirical AM1, PM3, and PM6 methods all consistently and accurately predict that branched alkyl compounds will generally be more thermodynamically stable than their linear counterparts. In contrast, HF and B3LYP calculations with the 6-31G(d,p), 6-31++G(d,p), and 6-311++G(d,p) basis sets predict that linear isomers will be more stable than branched analogs. These different linear versus branched perfluoroalkyl/perhydroalkyl thermodynamic property trends between semiempirical and ab initio/DFT...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3928/version/1

Comparative study on the gas to solution phase solvation free energies of model combustion flue gas compounds (N~2~, O~2~, CO~2~, H~2~O, SO~2~, and CO) in 178 organic solvents using the IEFPCM-UFF, CPCM, and SMD implicit solvent models at the Gaussian-4 (G4) level of theory
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas to solution phase Gibbs free energies of solvation at 298.15 K for transfer of six representative combustion flue gas compounds (N~2~, O~2~, CO~2~, H~2~O, SO~2~, and CO) were calculated at the Gaussian-4 (G4) level of theory using the IEFPCM-UFF, CPCM, and SMD implicit solvent models for 178 organic solvents. The IEFPCM-UFF and CPCM models yield similar free energies of solvation for all six compounds in each of the solvents considered, having maximum absolute intra-solvent deviations &amp;#x3c;1.6 kJ mol^-1^. Substantial free energy of solvation differences were observed between the IEFPCM-UFF/CPCM and SMD models, with maximum absolute intra-solvent deviations up to 45.5 kJ mol^-1^. The IEFPCM-UFF and CPCM models displayed strong free energy of...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5227/version/1

Comparative theoretical investigation on the isomerization energies of long-chain perfluoroalkanes: A case study with perfluorooctane sulfonic acid congeners
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
The gas and solution phase relative thermodynamic stabilities of the 89 perfluorooctane sulfonic acid (PFOS) congeners play an important role in assessing whether synthetic conditions for commercial mixtures are under thermodynamic or kinetic control, and in calculating various physico-chemical properties for these important industrial compounds and environmental contaminants. In the present study, 4,272 gas and solvent phase (water and n-octanol) calculations were conducted at various levels of semiempirical (PM6), density functional (B3LYP, B97D, PBE1PBE [PBE0], and M062X functionals with the 6-311++G(d,p) basis set), and second order Moller-Plesset perturbation (MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p)) theory and the SMD, IEFPCM-UFF, and CPCM implicit...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5353/version/1

Comparative theoretical investigation on the isomerization energies of long-chain perfluoroalkanes: A case study with perfluorooctanoic acid congeners
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
The gas and solution phase relative thermodynamic stabilities of the 39 linear and branched perfluorooctanoic acid (PFOA) congeners in both their acid and anionic forms were calculated at various levels of density functional (B3LYP, wB97XD, and M062X functionals with the 6-311++G(d,p) basis set) and second order Moller-Plesset perturbation (MP2/6-311++G(d,p)//B3LYP/6-311++G(d,p)) theory using the SMD implicit solvation model. The B3LYP functional does not accurately model the expected trends in thermodynamic stability of PFOA isomers with linear versus branched perfluoroalkyl chains. Calculations obtained with the M062X and MP2 model chemistries suggest these theoretical methods may be more appropriate for relative thermodynamic stability studies on...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/5528/version/1

Comparing and Explaining Public Acceptance Of Ecological Forestry in Tasmania and the U.S. Pacific Northwest
Provedor de dados: 17
Autores: Robert Ribe; Rebecca Ford; Kath Williams.
Major controversies have erupted in recent years about extensive and intensive timber harvesting programs in Tasmania and the U.S. Pacific Northwest.  These conflicts have centered on ecological impacts and both regions have responded by adopting similar programs of &amp;#x201c;ecological forestry.&amp;#x201d;  Both programs emphasize the retention of varying amounts of trees in aggregated or dispersed patterns within harvests, and seek to &amp;#x201c;life boat&amp;#x201d; mature-forest habitat functions across some harvest prescriptions.  Are these programs garnering similar public acceptance?  Do people with similar ideologies judge the acceptability of forests similarly in both regions?  Do perceptions differ between regions due to differences in...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3744/version/1

Comparison of Cholesterol Lowering Diets: Apple, Casein Cytochrom P450 protein and Cholesterol 7&amp;#x3b1; Hydroxylase Activities in Hamsters
Provedor de dados: 17
Autores: Rakesh  Sharma; Rakesh K. Tandon.
Lithogenic diet, casein and apple fiber diets were fed to hamsters for 3-5 weeks. For control group, animals were fed on normal Purina chow without any supplement. The cholesterol lowering effect of lithogenic diet, casein and apple diets were compared. After dietary regimen, animals were screened for any gall stone formation. The isolated liver microsomes were separated from animals and tested for the cholesterol-7&amp;#x3b1; Hydroxylase (CH) enzyme activity measurement in all three groups. The control animals did not show any gall stone formation and their CH enzyme activities were normal. The lithogenic diet showed significantly enhanced CH enzyme activities while animals fed on casein and apple diet regimen showed moderate increase in microsomal CH...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4205/version/1

Comparison of computationally- and manually-assigned Gene Ontology annotations to improve functional characterization of gene products.
Provedor de dados: 17
Autores: Maria Costanzo; Rama Balakrishnan; Karen Christie; Eurie Hog; Julie Park; J. Michael Cherry.
The Gene Ontology (GO) describes molecular functions, biological processes, and cellular components of gene products using controlled-vocabulary terms that are related to each other in a structure that facilitates computing on GO annotations within and across species. Experimentally-based GO annotations that are manually curated from the literature are often used to predict the functions of related uncharacterized proteins. The accuracy of such annotations is thus critically important, particularly for a well-studied model organism such as _Saccharomyces cerevisiae_ which is frequently used as the source of the experimental data. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Comparison of experimentally-based annotations with those predicted by computational methods...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5095/version/1

Comparison of Efficiency of Photodynamic Diagnostics with Topical Use of the 3% and 15% Aminolevulinic Acid in the Detection of Vulvar Lesions
Provedor de dados: 17
Autores: Agnieszka Mazdziarz; Habib Alkhalayla; Aleksandra Zielinska; Beata Spiewankiewicz.
The objective of the study was evaluating the efficiency of the photodynamic method PDD (photodynamic diagnosis) in the detection of vulvar lesions when two concentrations of the photosensitizer were used ( 3%- and 15%-aminolevulinic acid ), as well as evaluating the efficiency of this method when compared to the efficiency of vulvoscopy, against the result of histological examination. Two concentrations of the 5-ALA cream ( aminolevulinic acid ) - 3% and 15% - were used in the PDD testing. The study group was divided into two subgroups A and B. In subgroup A the 15% eucerine - based cream was used. In subgroup B the 3% ALA gel with addition of 2% DMSO was used. The photosensitizer was applied to the vulva four to six hours before the examination. In order...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2011
URL: http://precedings.nature.com/documents/6272/version/1

Comparison of histopathological&amp;#xb;features of Vibrio cholerae O1 El Tor and&amp;#xb;O139 Bengal infections in rabbit intestinal mucosa
Provedor de dados: 17
Autores: Atif  A. Baig.
Vibrio cholerae is the causative agent of the infectious disease, cholera. The bacteria adhere to the mucosal membrane and release cholera toxin, leading to watery diarrhea. There are &amp;#x3e;100 serovars of V. cholerae, but the O1 and O139 serovars are the main causative agents of cholera. The present study aimed to compare the severity of intestinal mucosal infection caused by O1 El Tor and O139 V. cholerae in a rabbit ileal loop model.&amp;#xd;&amp;#xa;The results showed that although the fluid accumulation was similar in the loops inoculated with O1 and O139 V. cholerae, the presence of blood was detected only in the loops inoculated with the O139 serovar. Serosal hemorrhage was confirmed by histopathological examination and the loops inoculated with...
Tipo: Presentation
Palavras-chave: Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/6418/version/1

Comparison of Plasmid yield between L.B. and using Molasses as a medium
Provedor de dados: 17
Autores: Nitin Sharma; Purshottum Kaushik.
During the initial studies I have found that the molasses may be a good alternative to costly L.B media where one can manipulate the C/N ratio as per requirement of cell. Molasses is one of the best alternatives as it is cheap and can be easily manipulated. Escherichia coli is a bacterium that is commonly found in the lower intestine of warm-blooded animals. it is possible to produce vaccine by molasses medium. The paper is opening a new face of study.
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3897/version/1

Competent intermediate hosts and genetic re-assortment: what does the ferret and raccoon model tell us about influenza pandemic risk?
Provedor de dados: 17
Autores: Paul Alexander.
Avian influenza virus (AI) strains such as H5N1 and H9N2 are endemic among birds and poultry globally and mainly within Eurasia. Human cases have been reported yet the transmission among humans has been inefficient. While swine and pigs have functioned as the primary intermediate host and genetic re-assorter of AI virus, other intermediate and competent hosts may be emerging. This could be potentially disastrous for humans should this lead to the generation of a pandemic strain. This letter to the editor highlights recent findings of AI spread among ferrets and raccoons and the real prospect of genetic re-assortment and evolution among these intermediate non-avian species that could lead to a pandemic strain. These hosts revealed efficient transmission to...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/2506/version/1

Competition between spiders and pitcher plants?  Prey availability and trophic interactions in bogs
Provedor de dados: 17
Autores: Clarisse Hart; Jonathan Mejia; Nicholas J. Gotelli; Aaron M. Ellison.
Web-building spiders (e.g. _Frontinella communis_ and _Neriene radiata_) and northern pitcher plants (_Sarracenia purpurea_) are co-occurring sit-and-wait predators that may compete for shared arthropod prey. We evaluated prey availability and capture rates by web-weaving spiders and pitcher plants in a headwater stream box complex (Harvard Pond) in central Massachusetts. We established 40 plots with spider and pitcher plant removal treatments, and collected arthropod prey captured by open pitcher plants, pitfall traps, and sticky traps in those plots. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The removal of web-building spiders significantly changed the distribution of prey captured by the pitcher plants (Chi-square test: P = 2.2 &amp;#xd7; 10-16 at Harvard...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3662/version/1

Complex Systems Analysis of Arrested Neural Cell Differentiation during Development and Analogous Cell Cycling Models in Carcinogenesis
Provedor de dados: 17
Autores: V. I. Prisecaru; I C. Baianu.
A new approach to the modular, complex systems analysis of nonlinear dynamics of arrested neural cell Differentiation--induced cell proliferation during organismic development and the analogous cell cycling network transformations involved in carcinogenesis is proposed. Neural tissue arrested differentiation that induces cell proliferation during perturbed development and Carcinogenesis are complex processes that involve dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments. Such &amp;#x27;dynamically inter-connected&amp;#x27; biomolecules form numerous inter-related pathways referred to as &amp;#x27;molecular networks&amp;#x27;. One such family of signaling pathways contains the cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7101/version/2

Complex Systems Analysis of Arrested Neural Cell Differentiation during Development and Analogous Cell Cycling Models in Carcinogenesis
Provedor de dados: 17
Autores: I C. Baianu; V. I. Prisecaru.
A new approach to the modular, complex systems analysis of nonlinear dynamics of arrested neural cell Differentiation--induced cell proliferation during organismic development and the analogous cell cycling network transformations involved in carcinogenesis is proposed. Neural tissue arrested differentiation that induces cell proliferation during perturbed development and Carcinogenesis are complex processes that involve dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments. Such &amp;#x27;dynamically inter-connected&amp;#x27; biomolecules form numerous inter-related pathways referred to as &amp;#x27;molecular networks&amp;#x27;. One such family of signaling pathways contains the cell...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7101/version/1

Complex Systems Analysis of Cell Cycling Models in Carcinogenesis
Provedor de dados: 17
Autores: I. C. Baianu.
A new approach to the modular, complex systems analysis of nonlinear dynamics in cell cycling network transformations involved in carcinogenesis is proposed. Carcinogenesis is a complex process that involves dynamically inter-connected biomolecules in the intercellular, membrane, cytosolic, nuclear and nucleolar compartments that form numerous inter-related pathways referred to as networks.&amp;#xd;&amp;#xa;The variable biotopology of such dynamic networks is highly complex, and has a number of interesting properties that can be formally characterized at one level of organization by mathematical structures called &amp;#x27;biogroupoids&amp;#x27;. &amp;#xd;&amp;#xa;One such family of pathways contains the cell cyclins. Cyclins are proteins that link several...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6205/version/1

Complex Systems Biology of Organisms
Provedor de dados: 17
Autores: I. C. Baianu.
Complex Systems Biology models and theories are axiomatically defined in terms of concrete categories and organismic supercategories (OS) to include both complete self-reproduction of logically defined pi-entities founded in Quine&amp;#x27;s logic and dynamic system diagrams subject to both algebraic and topological transformations. Mathematical models of complex organisms are expressed in terms of category theory and organismic supercategories (OS). OS theories have applications in: Bioinformatics, Developmental Biology, Genomics and Molecular Cell Biology
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7044/version/1

Composition of Biochemical Networks using Domain Knowledge
Provedor de dados: 17
Autores: Martin Goodfellow; John Wilson; Ela  Hunt.
Graph composition has applications in a variety of practical applications. In drug development, for instance, in order to understand possible drug interactions, one has to merge known networks and examine topological variants arising from such composition. Similarly, the design of sensor nets may use existing network infrastructures, and the superposition of one network on another can help with network design and optimisation. The problem of network composition has not received much attention in algorithm and database research. Here, we work with biological networks encoded in Systems Biology Markup Language (SBML), based on XML syntax. We focus on XML merging and examine the algorithmic and performance challenges we encountered in our work and the...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4966/version/1

Compressibility of Calcium Nitride to 137 Kb
Provedor de dados: 17
Autores: Michael  J. Bucknum.
A compressibility study was carried out of calcium nitride using a powdered sample in a diamond anvil cell with a Debeye-Scherrer camera at Cornell High Energy Synchrotron Source (CHESS) in 1992. This is the first such high pressure study of the equation of state of calcium nitride reported in the literature.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1771/version/3

Compressibility of Calcium Nitride to 137 Kb
Provedor de dados: 17
Autores: Michael  J. Bucknum.
A compressibility study was carried out of calcium nitride using a powdered sample in a diamond anvil cell with a Debeye-Scherrer camera at Cornell High Energy Synchrotron Source (CHESS) in 1992. This is the first such high pressure study of the equation of state of calcium nitride reported in the literature.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1771/version/1

Compressibility of Calcium Nitride to 137 Kb
Provedor de dados: 17
Autores: Michael  J. Bucknum.
A compressibility study was carried out of calcium nitride using a powdered sample in a diamond anvil cell with a Debeye-Scherrer camera at Cornell High Energy Synchrotron Source (CHESS) in 1992. This is the first such high pressure study of the equation of state of calcium nitride reported in the literature.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1771/version/2

Compressibility of Calcium Nitride to 137 Kb
Provedor de dados: 17
Autores: Michael  J. Bucknum.
[alpha]-Ca3N2 as an opaque, red-brown crystalline powder lying in the cubic Ia-3 space group, was placed into a specially designed glove box under nitrogen atmosphere, along with powdered f.c.c. Au, and carefully loaded within the [beta]-brass gasket of a conventional high pressure diamond anvil cell (DAC). The powdered samples were then sealed under nitrogen atmosphere to a pressure of 8.40 Kb and taken to Cornell High Energy Synchrotron Source where conventional&amp;#xd;&amp;#xa;Debeye-Scherrer diffraction photographs were recorded at 8.40, 91.0 and 137 Kb. The pressure of the sample was monitored by using the equation of state of Au, and no phase change from the Ia-3 structure was observed in the sample of powdered [alpha]-Ca3N2 up to a pressure of 137...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1771/version/4

Computational binding mechanism of Mycobacterium tuberculosis UDP-NAG enolpyruvyl transferase (MurA) with inhibitors fosfomycin, cyclic disulfide analog RWJ-3981, pyrazolopyrimidine analog RWJ-110192, purine analog  RWJ-140998, 5-sulfonoxy-anthranilic aci
Provedor de dados: 17
Autores: C. M. Anuradha; B. Babajan; M. Chaitanaya; C. Rajasekhar; Suresh Kumar Chitta.
Worldwide, tuberculosis (TB) remains the most frequent and important infectious disease causing morbidity and death. One-third of the world&amp;#x27;s population is infected with Mycobacterium tuberculosis (Mtb), the etiologic agent of TB. In this context, TB is in the top three, with malaria and HIV being the leading causes of death from a single infectious agent, and about two million deaths are attributable to TB annually. The bacterial enzyme MurA catalyzes the transfer of enolpyruvate from phosphoenolpyruvate (PEP) to uridine diphospho-N-acetylglucosamine (UNAG), which is the first committed step of bacterial cell wall biosynthesis.  In this work, 3D structural model of Mtb-MurA enzyme has been developed, for the first time, by homology modeling and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3731/version/1

Computational methods in cancer gene networking
Provedor de dados: 17
Autores: Edwin Wang.
In the past few years, many high-throughput techniques have been developed and applied to biological studies. These techniques such as &amp;#x201c;next generation&amp;#x201d; genome sequencing, chip-on-chip, microarray and so on can be used to measure gene expression and gene regulatory elements in a genome-wide scale. Moreover, as these technologies become more affordable and accessible, they have become a driving force in modern biology. As a result, huge amount biological data have been produced, with the expectation of increasing number of such datasets to be generated in the future. High-throughput data are more comprehensive and unbiased, but &amp;#x2018;real signals&amp;#x2019; or biological insights, molecular mechanisms and biological principles...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2737/version/1

Computational Prediction and Analysis of the NAPP - DR6 Interaction: Implications for Alzheimer&amp;#x27;s Research
Provedor de dados: 17
Autores: Josheph Audie; Sergei Ponomarev.
Alzheimer&amp;#x27;s disease (AD) is a progressive neurodegenerative disorder that involves a devastating clinical course and lacks an effective treatment. A biochemical model for neuronal development that might have implications for AD, recently proposed by Nikolaev and co-workers, hinges on a novel protein-protein interaction between the death cell receptor six (DR6) ectodomain and an N-terminal fragment of amyloid precursor protein (NAPP). The model provides a coherent and satisfying framework for better understanding AD pathophysiology. Moreover, the DR6-NAPP interaction offers a tempting target for novel pharmacological intervention. Given all of this, we constructed a structural model of the DR6-NAPP interaction using the neurotrophin p75 receptor as...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4545/version/1

Computational Studies Of Huntington Protein: Classification &amp;#x26; Binding Pattern Determination
Provedor de dados: 17
Autores: Nitin M. R. Chitranshi; Shipra M. S. Gupta.
Huntington&amp;#x27;s disease (HD) is a dominantly inherited neurodegenerative disorder characterized by progressive motor deficits, psychiatric deterioration, worsening chorea, cognitive impairment due to neuronal cell loss in the basal ganglia, cerebral cortex, and its fragments interactions with themselves and other biomolecules that results in aggregates , transcriptional repression , oxidative injury  and mitochondrial dysfunction . The repeat domain of Huntingtin interacting protein (HIP) 14 (PDB id 3eu9) is used to study the structure based drug design. We made the selection of 50 different small molecules which were screened out through various fixed parameters and applied descriptors to generate the model for molecules that shows the drug likeness...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5581/version/1

Computational system biology
Provedor de dados: 17
Autores: Ankit Geete.
Systems biology is a multi-disciplinary &amp;#xfb01;eld that deals with mechanisms involved in complex biological processes by considering them as integrated systems of multiple interacting components. The huge amount of data involved in this study necessitates the use of computational tools.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7104/version/1

Computer aided drug design studies to explore novel antagonist of human myotrophin
Provedor de dados: 17
Autores: Sandeep Swargam; K Mahesh; Amineni Umamaheswari.
Human myotrophin is the smallest ankyrin repeat protein implicated as a factor to induce cardiac hypertrophy.  Activation of myotrophin was observed during acute myocardial infarction (MI). In acute coronary syndrome (ACS) patients, myotrophin acts as a self-governing predictor of major adverse cardiac events (MACE). Therefore, human myotrophin serves as an effective drug target for discovery of new potential drugs. Recent human myotropin inhibitors have poor pharmalogical properties leading to intolerable side effects. Hence, ligand based virtual screening protocol of CADD method was persuaded in the present study to propose new class potential myotrophin inhibitors. Docking was done by using Schr&amp;#xf6;dinger software suite 2010 (maestro v9.1), docked...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6562/version/1

Computer simulations on the sympatric speciation modes for the Midas cichlid species complex
Provedor de dados: 17
Autores: Karen Luz-Burgoa; Suzana Moss de Oliveira; Jorge de S&amp;#xe1; Martins.
Cichlid fishes are one of the best model system for the study of evolution of the species. Inspired by them, in this paper we simulated the splitting of a single species into two separate ones via random mutations, with both populations living together in sympatry, sharing the same habitat.  We study the ecological, mating and genetic conditions needed to reproduce the polychromatism and polymorphism of three species of the Midas Cichlid species complex. Our results show two scenarios for the A. Citrinellus speciation process, one with and the other without disruptive natural selection. &amp;#xd;&amp;#xa;In the first scenario, the ecological and genetic conditions are sufficient to create two new species, while in the second the mating and genetic...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/798/version/1

Computerized Protein Modeling and Molecular Docking Analysis of Human Proto Oncogene Tyrosine Protein Kinase YES for Discovery of Novel Lead Molecules
Provedor de dados: 17
Autores: Karuna  J. Jaya Sai; Dibyabhaba  Pradhan; Amineni  Umamaheswari.
Human proto-oncogene tyrosine-protein kinase YES (YES) is a non receptor kinase belongs to Src family. This gene lies in close proximity to thymidylate synthase gene on chromosome 18, and a corresponding pseudogene has been found on chromosome 22. In hepatocellular carcinoma and colorectal carcinoma elevated human YES activity was observed. Inhibitors of human YES reported till date are in clinical trials and associated with several side effects. The present study was mainly aimed in homology modeling of human YES and discovery of novel lead molecules that inhibit YES kinase more efficiently with fewer side effects. Virtual screening and docking techniques were applied to identify novel lead molecule of YES kinase. As there was no reported human YES...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4902/version/1

Computing the inverse of the neurophysiological spike-response transform
Provedor de dados: 17
Autores: Vladimir Brezina; Estee Stern; Keyla Garcia-Crescioni; Mark W. Miller; Charles S. Peskin.
Consider the transform from a discrete neuronal spike train to a continuous neurophysiological response such as postsynaptic membrane voltage or muscle contraction.  Often, we can record only the response.  Here we therefore ask about the inverse of this transform: given the response, how can we estimate from it the spike train that produced it?  In previous work, we have developed a kernel-based &amp;#x22;decoding&amp;#x22; method for system identification of the forward transform.  Using several variant approaches based on this method, here we demonstrate how to identify the spike train, in the minimal case from just the response, with synthetic as well as real synaptic and neuromuscular data.
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3472/version/1

Concentration-dependent free radical scavenging and ferric reducing ability of Vetiveria zizanioides (L.) Nash: Protective effect of vetiver root extract during oxidative stress
Provedor de dados: 17
Autores: Suaib  Luqman; Ritesh  Kumar; Shubhangi  Kaushik; Suchita  Srivastava; Mahendra  P. Darokar; Suman  P. S. Khanuja.
Vetiveria zizanioides, popularly known as &amp;#x2018;KHUS&amp;#x2019; grass, has been known to India since ancient times. It is the major source of well-known oil of vetiver, which is used in medicine and in perfumery. A concentration-dependent ferric reducing, free radical scavenging and antioxidant activity of two genotypes, namely KS 1 and gulabi of vetiver (Vetiveria zizanioides L. Nash) root, were evaluated by using in vitro assays: the ferric reducing antioxidant power (FRAP), 1, 1-Diphenyl-2-picrylhydrazyl (DPPH), total phenolic content (TPC), total antioxidant capacity (TAC) and reducing power (RP) assay. A positive co-relation was observed between FRAP, DPPH and TPC of cv KS 1, whereas TAC and RP showed a negative co-relation. A significant...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6920/version/1

Concentrations and profiles of melatonin and serotonin in fruits and vegetables during ripening: A mini-review
Provedor de dados: 17
Autores: Sierra Rayne.
Melatonin and serotonin are important phytochemicals with hormonal, antioxidant, immunoactive, and neuroactive biological properties, and have been identified and quantitated in a broad range of fruits, vegetables, and derivative products. Relatively little is known about the temporal profiles of these compounds during fruit and vegetable development. Improved knowledge in this area would help guide our understanding of fundamental plant physiology, as well as potentially facilitate better control of melatonin and serotonin concentrations and relative abundances in functional foods. The current work synthesizes the current state-of-the-art regarding the presence and trends of these compounds during fruit and vegetable development. The literature reflects...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4722/version/1

Concentrations of Polychlorinated Biphenyls (PCBs), Polychlorinated Dibenzo-p-dioxins and Furans (PCDD/Fs), and Polybrominated Diphenyl Ethers (PBDEs) as Functions of Sample Depth in Killer Whale (Orcinus orca) Blubber
Provedor de dados: 17
Autores: Michael G. Ikonomou; Sierra Rayne; Norman F. Crewe.
Concentrations of polychlorinated biphenyls (PCBs), polychlorinated dibenzo-p-dioxins and dibenzofurans (PCDD/Fs), and polybrominated diphenyl ethers (PBDEs) were examined as a function of depth in killer whale (Orcinus orca) blubber samples. Lipid-normalized concentrations of PCBs, PCDD/Fs, and PBDEs did not display significant variation with depth in three distinct blubber layers (outer, central, and inner). Significantly more variation in contaminant concentrations were observed with depth on a wet weight basis for the killer whale sample. The current study indicates that non-invasive microdart biopsy sampling methods commonly used for monitoring contaminants in marine mammals yield representative details on contaminant burdens for chlorinated and...
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/638/version/1

Conceptual model of E. coli transcriptional machinery
Provedor de dados: 17
Autores: Anatoly Sorokin; Timur Dzhelyadin; Svetlana G. Kamzolova.
At the moment one type of analysis of transcription regulatory networks (TRNs) in prokaryotes is topological analysis of graph structure of possible regulatory interaction links (see for example [1]). That type of analysis takes into account possibility links that designate the fact that one gene product in some conditions can modulate transcription of the other. The benefit of such approach is that it is allow analyzing TRN at the whole cell level. At the same type it is known that at least some responses are regulated by abundance of elements of transcription machinery [2-3]. We have developed conceptual model of whole cell E. coli TRN with SBGN ER, SBGN PD and SBGN AF languages [4]. That model is the first step towards incorporation of some quantitative...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6341/version/1

Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
Provedor de dados: 17
Autores: Henry L. Niman; Magdi D. Saad; Mona M. Aly; Jeffery  Tjaden; Kenneth C. Earhart; Marshall R. Monteville; Moustafa M. Mansour; Nasr El-Sayed; Ahmed E. Nayel; Ahmed S. Abdelghani; Hala M. Esmat; Emad M. Labib; Ehab A. Ayoub; Abdelattar  Arafa; Gregory A. Raczniak; Mensah Agyen-Frempong; William K. Ampofo; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60%. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the current...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Ecology; Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/459/version/3

Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
Provedor de dados: 17
Autores: Henry L. Niman; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60%. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the current...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/459/version/2

Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
Provedor de dados: 17
Autores: Henry L. Niman; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997 1,2. The number of confirmed human cases now exceeds 300, and the associated Case Fatality Rate exceeds 60% 3. The genetic diversity of the serotype continues to increase. Four distinct clades or sub-clades have been linked to human cases 4-7. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift 8. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, and Ghana. These changes are not easily explained by the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/459/version/1

Concurrent Acquisition of a Single Nucleotide Polymorphism in Diverse Influenza H5N1 Clade 2.2 Sub-clades
Provedor de dados: 17
Autores: Henry Niman; Mona M. Aly; Abdel-Satar  Arafa; Nasr El-Sayed; Ahmed  E. Nayel; Ahmed  S. Abdelghani; Hala  M. Esmat; Gregory  A. Raczniak; Mensah  Agyen-Frempong; William  K. Ampofo; Bruce R. Boynton.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997 1,2. The number of confirmed human cases now exceeds 300 and the associated Case Fatality Rate exceeds 60% 3. The genetic diversity of the serotype continues to increase.  Four distinct clades or sub-clades have been linked to human cases 4-7. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift 8. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, clade 2.2 sub-clades in Egypt, Russia, Kuwait, and Ghana. These changes are not easily...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/459/version/4

Concurrent, Collaborative &amp;#xb;Ontology Building&amp;#xb; with Collaborative Prot&amp;#xe9;g&amp;#xe9; (CP)
Provedor de dados: 17
Autores: Daniel Schober.
Creation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by the distribution of the ontology&amp;#x2019;s developers. An obvious solution therefore is to build collaboration into ontology development tools. Such support necessarily includes both the technical means to perform editing operations upon an ontology, but also support for the communication that makes collaboration such a vital part of much ontology development. To investigate the distributed, collaborative ontology engineering process and the corresponding capabilities of the Collaborative Protege 3 (CP) tool, members of the OntoGenesis network came together and enriched the Ontology of Biomedical Investigations (OBI) with new...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3516/version/1

Congener specific organic carbon normalized soil and sediment-water partitioning coefficients for the C1 through C8 perfluorinated alkylsulfonic and alkylcarboxylic acids
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Organic carbon normalized soil and sediment-water partitioning (Koc) coefficients were estimated for all C1 through C8 perfluorinated alkylsulfonic acid (PFSA) and alkylcarboxylic acids (PFCA) congeners. The limited experimental Koc dataset for the straight chain C7 through C10 PFCAs and C8 and C10 PFSAs was correlated to SPARC and ALOGPS computationally estimated octanol-water partitioning constants and used to predict Koc values for both branched and linear C1 through C8 isomers. All branched and linear congeners in this homologue range are expected to have Koc values&amp;#x3e;1, leading to their accumulation in organic matter on sediments and soils, retardation during ground and pore water flow, and the preferential association with dissolved organic...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3011/version/1

Congener specific organic carbon normalized soil and sediment-water partitioning coefficients for the C~1~ through C~8~ perfluoroalkyl carboxylic and sulfonic acids
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Organic carbon normalized soil and sediment-water partitioning coefficients (K~oc~) were estimated for all C~1~ through C~8~ perfluoroalkyl carboxylic (PFCA) and sulfonic (PFSA) acid congeners. The limited experimental K~oc~ dataset for the straight chain C~7~ through C~10~ PFCAs and C~8~ and C~10~ PFSAs was correlated to SPARC and ALOGPS computationally estimated octanol-water partitioning / distribution constants and used to predict K~oc~ values for both branched and linear C~1~ through C~8~ isomers. Branched and linear congeners in this homologue range are generally expected to have K~oc~ values &amp;#x3e;1, leading to their accumulation in organic matter on sediments and soils, retardation during ground and pore water flow, and the preferential...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3011/version/2

Congener-Specific Numbering Systems for the Environmentally Relevant C4 through C8 Perfluorinated Homologue Groups of Alkyl Sulfonates, Carboxylates, Telomer Alcohols and Acids, and Their Derivatives
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest; Ken J. Friesen.
We introduce a congener-specific numbering system for the C4 through C8 perfluorinated homologue groups of alkyl sulfonates, carboxylates, telomer alcohols and acids, and their derivatives. Increasing length of the carbon chain beyond C3 leads to a corresponding rapid increase in the number of potential isomers (C4 =4, C5 =8, C6 =17, C7 =39, and C8 =89 congeners). There is a need for clear and unambiguous chemical shorthand to ensure accuracy and consistency in the future perfluorinated alkyl substance (PFA) literature, and to correct previous misconceptions that may have restricted research efforts into developing full-congener PFA analysis. If adopted by the research community, introduction of a numbering system at this relatively early stage of...
Tipo: Poster
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1957/version/2

Congener-Specific Numbering Systems for the Environmentally Relevant C4 through C8 Perfluorinated Homologue Groups of Alkyl Sulfonates, Carboxylates, Telomer Alcohols and Acids, and Their Derivatives
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest; Ken J. Friesen.
We introduce a congener-specific numbering system for the C4 through C8 perfluorinated homologue groups of alkyl sulfonates, carboxylates, telomer alcohols and acids, and their derivatives. Increasing length of the carbon chain beyond C3 leads to a corresponding rapid increase in the number of potential isomers (C4 =4, C5 =8, C6 =17, C7 =39, and C8 =89 congeners). There is a need for clear and unambiguous chemical shorthand to ensure accuracy and consistency in the future perfluorinated alkyl substance (PFA) literature, and to correct previous misconceptions that may have restricted research efforts into developing full-congener PFA analysis. If adopted by the research community, introduction of a numbering system at this relatively early stage of...
Tipo: Poster
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1957/version/1

Connecting Carbon Capture with Oceanic Biomass Production
Provedor de dados: 17
Autores: Chen Wang.
The climate change believed by anthropogenic emission is not isolated but tightly coupled with other issues including biodiversity loss and ocean acidification etc., and in order to prevent the potential serious impacts, both political and technological methods are being tried for greenhouse mitigation. Dimming the income sunlight by some &amp;#x201c;geoengineering&amp;#x201d; approaches currently seem ruinously expensive and technically difficult, and would not prevent the increase of greenhouse gases (GHGs) in atmosphere and ocean acidification, so capturing carbon to reduce the environmental concentration of carbon dioxide (CO2) and promoting renewable energy development for the reduction of using fossil fuels are very necessary. Biofuels derived from...
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5161/version/1

Connecting Seed Lists of Mammalian Proteins Using Steiner Trees
Provedor de dados: 17
Autores: Amelia G. White; Avi Ma&amp;#x27;ayan.
Multivariate experiments and genomics studies applied to mammalian cells often produce lists of genes or proteins altered under treatment/disease vs. control/normal conditions. Such lists can be identified in known protein-protein interaction networks to produce subnetworks that &amp;#x201c;connect&amp;#x201d; the genes or proteins from the lists. Such subnetworks are valuable for biologists since they can suggest regulatory mechanisms that are altered under different conditions. Often such subnetworks are overloaded with links and nodes resulting in connectivity diagrams that are illegible due to edge overlap. In this study, we attempt to address this problem by implementing an approximation to the Steiner Tree problem to connect seed lists of mammalian...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1768/version/1

Connectivity reflects coding: A model of voltage-based spike-timing-dependent-plasticity with homeostasis
Provedor de dados: 17
Autores: Claudia Clopath; Lars B&amp;#xfc;sing; Eleni Vasilaki; Wulfram Gerstner.
Electrophysiological connectivity patterns in cortex often show a few strong connections in a sea of weak connections. In some brain areas a large fraction of strong connections are bidirectional, in others they are mainly unidirectional. In order to explain these connectivity patterns, we use a model of Spike-Timing-Dependent Plasticity where synaptic changes depend on presynaptic spike arrival and the postsynaptic membrane potential. The model describes several nonlinear effects in STDP experiments, as well as the voltage dependence of plasticity under voltage clamp and classical paradigms of LTP/LTD induction. We show that in a simulated recurrent network of spiking neurons our plasticity rule leads not only to receptive field development, but also to...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3362/version/1

Consciousness and subjective time: a plausible auditory approach
Provedor de dados: 17
Autores: Sepehr Ehsani.
The perception of time is an indispensable facet of human consciousness, and may in fact be dynamically present in primates and other species, albeit with different manifestations. Moreover, contrary to the physical measures of time, cognitive temporal perception may be subjectively affected by both internal and environmental cues. Here we review the evidence for the potential role of the auditory system in shaping the cortical measures of time, and propose possible auditory methods for studying this aspect of consciousness.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5941/version/1

Consciousness as Recursive, Spatiotemporal Self-Location
Provedor de dados: 17
Autores: Frederic Peters.
At the phenomenal level, consciousness can be described as a singular, unified field of recursive self-awareness, consistently coherent in a particular way; that of a subject located both spatially and temporally in an egocentrically-extended domain, such that conscious self-awareness is explicitly characterized by I-ness, now-ness and here-ness. The psychological mechanism underwriting this spatiotemporal self-locatedness and its recursive processing style involves an evolutionary elaboration of the  basic orientative reference frame which consistently structures ongoing spatiotemporal self-location computations as i-here-now. Cognition computes action-output in the midst of ongoing movement, and consequently requires a constant self-locating...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2444/version/1

Consciousness as Recursive, Spatiotemporal Self-Location
Provedor de dados: 17
Autores: Frederic Peters.
At the phenomenal level, consciousness can be described as a singular, unified field of recursive self-awareness, consistently coherent in a particular way; that of a subject located both spatially and temporally in an egocentrically-extended domain, such that conscious self-awareness is explicitly characterized by I-ness, now-ness and here-ness. The psychological mechanism underwriting this spatiotemporal self-locatedness and its recursive processing style involves an evolutionary elaboration of the  basic orientative reference frame which consistently structures ongoing spatiotemporal self-location computations as i-here-now. Cognition computes action-output in the midst of ongoing movement, and consequently requires a constant self-locating...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2444/version/2

Consensus virtual screening approaches to predict protein ligands
Provedor de dados: 17
Autores: Andreas Kukol.
In order to exploit the advantages of receptor-based virtual screening, namely time/cost saving and specificity, it is important to rely on algorithms that predict a high number of active ligands at the top ranks of a small molecule database. Towards that goal consensus methods combining the results of several docking algorithms were developed and compared against the individual algorithms. Furthermore, a recently proposed rescoring method based on drug efficiency indices was evaluated. Among AutoDock Vina 1.0, AutoDock 4.2 and GemDock, AutoDock Vina was the best performing single method in predicting high affinity ligands from a database of known ligands and decoys. The rescoring of predicted binding energies with the water/butanol partition coeffcient...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5979/version/1

Conservation Pakage for Modal Ecorace
Provedor de dados: 17
Autores: Ajit Kumar Sinha.
Conserving biodiversity is about genetic variety, species, habitats and ecosystems. All are important, but it is often most appropriate, practical and effective to focus on species. With modern conservation awareness, there is a welcome and popular commitment to maintaining the diversity of species in India. Nevertheless, over the last 50 years, we have witnessed the severe decline of many once widespread and familiar species, such as tropical Tasar silkworm Antherea mylitta D. Conservation is not just about avoiding extinctions, but about restoring or recovering species populations to secure levels and preventing other species from reaching such a perilous situation in the first place. Species, by their very nature, have specific ecological requirements....
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6162/version/1

Considerate Approaches to Achieving Sufficiency for ABC Model Selection
Provedor de dados: 17
Autores: Chris Barnes; Sarah Filippi; Michael  Stumpf; Tom  Thorne.
ABC methods have gained popularity in situations where traditional methods which involve explicit evaluation of likelihoods are either too cumbersome or fail outright. This, almost by definition means that for any interesting real-world scenario we have no or little recourse to sufficient statistics, which had previously been central to ABC approaches and their derivation. In the context of model selection this can have particularly undesirable consequences if we have to compress the data through the use of summary statistics. In this talk we discuss complementary approaches that allow us to address this problem in a principled manner, and outline the scenarios where ABC model selection is unproblematic. We will argue that many of the most interesting...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5952/version/1

Consortium Building For PEM MFC Using Synthetic Media As Substrate
Provedor de dados: 17
Autores: Muralidharan Ayyappan; Dimpal Parida; Arti Yadav; Ramya Mohandass.
Microbial production of electricity is an important form of bioenergy since Microbial Fuel cells (MFC) offer the possibility of extracting electric current from a wide range of organic wastes and renewable biomass. Factors affecting the MFC operational effectiveness are the MFC design and the bacterial metabolism and electron transfer. The purpose of this study is to identify species which are responsible for electricity generation so as to build a suitable consortium and to investigate the relative efficiencies between the microbial consortiums. Enrichment by repeated transfer of a bacterial consortium harvested from the anode compartment of a MFC with synthetic media as a substrate increased the output from an initial level of 34 mA to a maximal level of...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/6632/version/1

Consortium for Functional Glycomics Overview
Provedor de dados: 17
Autores: James C. Paulson.
This presentation provides an overview of the Consortium for Functional Glycomics.
Tipo: Presentation
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/11/version/1

Constraint-Guided Workflow Composition Based on the EDAM Ontology
Provedor de dados: 17
Autores: Anna-Lena Lamprecht; Stefan Naujokat; Bernhard Steffen; Tiziana Margaria.
Methods for the automatic composition of services into executable workflows need detailed knowledge about the application domain, in particular about the available services and their behavior in terms of input/output data descriptions. In this paper we discuss how the EMBRACE data and methods ontology (EDAM) can be used as background knowledge for the composition of bioinformatics workflows. We show by means of a small example domain that the EDAM knowledge facilitates finding possible workflows, but that additional knowledge is required to guide the search towards actually adequate solutions. We illustrate how the ability to flexibly formulate domain-specific and problem-specific constraints supports the workflow development process.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5397/version/1

Constraints of FL Motif on the Targeting and Function of Sodium-Bicarbonate Cotransporter 1
Provedor de dados: 17
Autores: Hong C. Li; Ali Shawki; YoonKyung Park; Emily Y Li; Kyung-Soo Hahm; Joel H.  Collier; Bryan  Mackenzie; Manoocher  Soleimani.
A C-terminal dihydrophobic FL motif plays a vital role in the basolateral targeting of sodium bicarbonate cotransporter 1. To further characterize the role of dihydrophobic FL motif, 1). the FL motif in wild type (PFLS) was reversed to LF (PLFS), 2). the FL motif (PFLS) was shifted upstream (FLPS), and 3). the FL motif (PFLS) was shifted downstream (PSFL). The wild type (PFLS) and its mutant (PLFS) were exclusively expressed on the basolateral membrane by con-focal microscopy, however, the mutant (FLPS) and (PSFL) were predominantly mistargeted to the apical membrane and the cytoplasm, respectively. Functional studies showed that the mutant (PSFL) displayed a remarkably reduced current (p value&amp;#x3c;0.05 vs wild type). The mutant (PSFL) displayed a...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1638/version/1

Constructing ABC summary statistics: semi-automatic ABC
Provedor de dados: 17
Autores: Paul Fearnhead; Dennis  Prangle.
To analyze complex datasets efficiently, ABC algorithms require well-chosen low dimensional summary statistics of the data. We present a method to construct appropriate summary statistics for ABC in a semi-automatic manner. Previous attempts at this have been based around constructing statistics that are sufficient (or approximately sufficient). However, in most real applications it is difficult to know if low-dimensional sufficient statistics exist, or how to approximate them if they do. We take an alternative approach of aiming for summary statistics which will enable inference about certain parameters of interest to be as accurate as possible. &amp;#xa0;This talk describes our method, the underpinning theory, and promising empirical results on a range...
Tipo: Presentation
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5959/version/1

Construction of direction selectivity in V1: from simple to complex cells
Provedor de dados: 17
Autores: Timm Lochmann; Tim Blanche; Daniel A. Butts.
Despite detailed knowledge about the anatomy and physiology of the primary visual cortex (V1), the immense number of feed-forward and recurrent connections onto a given V1 neuron make it difficult to understand how the physiological details relate to a given neuron&amp;#x2019;s functional properties. Here, we focus on a well-known functional property of many V1 complex cells: phase-invariant direction selectivity (DS). While the energy model explains its construction at the conceptual level, it remains unclear how the mathematical operations described in this model are implemented by cortical circuits. To understand how DS of complex cells is constructed in cortex, we apply a nonlinear modeling framework to extracellular data from macaque V1. We use a...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5861/version/1

Contaminant Trapping Behind Large Dams: A Mini-Review
Provedor de dados: 17
Autores: Sierra Rayne; Ken J. Friesen.
It appears likely that the installation of many large dams on major rivers worldwide over the past century has led to large and complex contaminant loadings becoming trapped in the sediments behind these dams. Future planned large dam removal efforts or unintentional breaches may result in substantial contaminant releases downstream. We review the current state of the art regarding knowledge of contaminant loadings behind large dams and potential downstream impacts following dam breaches.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2965/version/1

Context-based generation of kinetic equations with SBMLsqueezer 1.3
Provedor de dados: 17
Autores: Andreas Dr&amp;#xe4;ger; Sandra Nitschmann; Alexander D&amp;#xf6;rr; Johannes Eichner; Michael J. Ziller; Andreas Zell.
The development of predictive, quantitative models constitutes a common task in today&amp;#x2018;s systems biology. To obtain a mathematical model description for the simulation of gene-regulatory, signaling, and metabolic networks, kinetic equations are required for each reaction within the network. Deriving and assembling these formulas is a complicated, time-consuming, and error-prone process that requires knowledge about the structure of interactions, consistently choosing a rate law for each type of reaction, and assignment of appropriate units to all parameters. In many cases, thermodynamic dependencies between the parameters have to be taken into account. For multi compartment models, the concentration units of reacting species have to be converted...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4983/version/1

Control in technological systems and physical intelligence: an emerging theory
Provedor de dados: 17
Autores: Bradly Alicea.
The transduction and processing of physical information is becoming important in a range of research fields, from the design of materials and virtual environments to the dynamics of cellular microenvironments. Previous approaches such as morphological computation/soft robotics, neuromechanics, and embodiment have provided valuable insight. This work approaches haptic, proprioception, and physical sensing as all part of the same subject. In this presentation, three design criteria for applying physical intelligence to engineering applications will be presented. These criteria have several properties in common, which inspires two types of end-effector model: stochastic (based on a spring) and deterministic (based on a piezomechanical array). The generalized...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5910/version/1

Control of cell division in the adult brain by heparan sulfates in fractones and vascular basement membranes
Provedor de dados: 17
Autores: Frederic Mercier; Vanessa Douet.
Regulation of cell division in adult tissues and organs requires the coordination of growth factors at the surface of potentially-dividing cells in specific anatomic loci named germinal niches. However, the biological components and physiological system that control growth factors in the germinal niches are unknown. In the adult brain, no function has been attributed to fractones, the fractal-shaped extracellular matrix structures located in the subventricular zone (SVZ) next to neural stem and progenitor cells. Here, we show that BMP-7 (bone morphogenetic protein-7) and FGF-2 (fibroblast growth factor-2) modulate cell division in the SVZ only if the growth factors bind to heparan sulfates localized in fractones and adjoined vascular basement membranes....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5444/version/1

Control of konzo in the Democratic Republic of Congo
Provedor de dados: 17
Autores: J. Howard Bradbury; Chretienne Mandombi; D Nahimana; J. P. Banea; Ian C. Denton; N Kuwa.
Konzo is an upper motor neuron disease that causes irreversible paralysis of the legs mainly in children and young women^1,2^, due to consumption of large amounts of cyanogens from poorly processed cassava, the staple food of tropical Africa^3^. Konzo occurs in the Democratic Republic of Congo (DRC),Mozambique, Tanzania, Cameroon, Central African Republic and Angola. In March 2010 the wetting method, which removes cyanogens from cassava flour^4,5,6^, was taught to and used by the mothers of Kay Kalenge village. This reduced the total cyanide content of cassava flour to the FAO/WHO limit of 10ppm^7^. Cyanogen intake of school children, monitored by urinary thiocyanate analyses, decreased from mean values of 332 to 130 &amp;#x3bc;mole/L. The percentage of...
Tipo: Manuscript
Palavras-chave: Chemistry; Neuroscience; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6520/version/1

Control over stress induces plasticity of individual prefrontal cortical neurons: A conductance-based neural simulation
Provedor de dados: 17
Autores: Juan  A. Varela; Jungang  Wang; Andrew L. Varnell; Donald  C. Cooper.
Behavioral control over stressful stimuli induces resilience to future conditions when control is lacking. The medial prefrontal cortex(mPFC) is a critically important brain region required for plasticity of stress resilience. We found that control over stress induces plasticity of the intrinsic voltage-gated conductances of pyramidal neurons in the PFC. To gain insight into the underlying biophysical mechanisms of this plasticity we used the conductance- based neural simulation software tool, NEURON, to model the increase in membrane excitability associated with resilience to stress. A ball and stick multicompartment conductance-based model was used to realistically fit passive and active data traces from prototypical pyramidal neurons in neurons in rats...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6267/version/1

Controlling sap-sucking insect pests with recombinant endophytes expressing plant lectin
Provedor de dados: 17
Autores: Xiuyun Zhao; Gaofu Qi; Xianfang Zhang; Nan Lan; Xinrong Ma.
We developed a novel pest management strategy, which uses endophytes to express anti-pest plant lectins. Fungal endophyte of Chaetomium globosum YY-11 with anti-fungi activities was isolated from rape seedlings, and bacterial endophytes of SJ-10 (Enterobacter sp.) and WB (Bacillus subtilis) were isolated from rice seedlings. Pinellia ternate agglutinin gene was cloned into SJ-10 and WB for expression by a shuttle vector, and YY-11 was mediated by Agrobacterium tumefaciens. Positive transformants were evaluated using PCR and Western blot assay. Recombinant endophytes colonized most of crops, and resistance of rice seedlings, which were inoculated with the recombinant endophytic bacteria, to white backed planthoppers was dramatically enhanced by decreasing...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4862/version/1

Convergence of atmospheric and North Atlantic CO2 trends on multidecadal timescales
Provedor de dados: 17
Autores: Galen  McKinley; Amanda Fay; Taro Takahashi; Nicolas Metzl.
The oceans&amp;#x2019; carbon uptake substantially reduces the rate of anthropogenic carbon accumulation in the atmosphere1, and thus slows global climate change. Some diagnoses of trends in ocean carbon uptake have suggested a significant weakening in recent years2-8, while others conclude that decadal variability confounds detection of long-term trends9-11.  Here, we study trends in observed surface ocean partial pressure of CO2 (pCO2) in three gyre-scale biomes of the North Atlantic, considering decadal to multidecadal timescales between 1981 and 2009.  Trends on decadal timescales are of variable magnitudes and depend sensitively on the precise choice of years. As more years are considered, oceanic pCO2 trends begin to converge to the trend in...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5993/version/1

Cooperative effect of ribosomal protein s19 and Pim-1 kinase on murine c-Myc expression and myeloid/erythroid cellularity
Provedor de dados: 17
Autores: Anne-Sophie Frojmark; Jitendra Badhai; Joakim  Klar; Maria  Thuveson; Jens Schuster; Niklas Dahl.
Diamond Blackfan anemia (DBA) is a bone marrow failure syndrome associated with heterozygous mutations in the ribosomal protein S19 (RPS19) gene in a subgroup of patients. One of the interacting partners with RPS19 is the oncoprotein PIM-1 kinase. We intercrossed Rps19+/- and Pim-1-/- mice strains to study the effect from the disruption of both genes. The double mutant (Rps19+/-Pim-1-/-) mice display normal growth with increased peripheral white- and red blood cell counts when compared to the w.t. mice (Rps19+/+Pim-1+/+). Molecular analysis of bone marrow cells in Rps19+/-Pim-1-/- mice revealed up-regulated levels of c-Myc and the anti-apoptotic factors Bcl2, BclXL and Mcl-1. This is associated with a reduction of the apoptotic factors Bak and Caspase 3 as...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2882/version/1

Copper and other heavy metals in specialized crops and their effects on soil coenosis
Provedor de dados: 17
Autores: Anna Steindl; Thomas Strumpf; Frank Riepert.
The background of the project are claims of the EU regulation to generate reliable data considering the extent of copper contamination in soils of specialized crops in order to decide about copper restrictions in organic farming.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;2522 single soil samples were collected on 85 vineyard and 13 hop areas with different management histories. Samples were taken from sites presently under cultivation, formerly cultivated, and sites without anthropogenic copper contamination as control, indicating natural background values. In addition to Aqua Regia extraction for determining total copper contents, available plant copper content was analyzed in NH~4~NO~3~ extraction. Soil parameters such as pH-value, C/N ratio, soil type etc....
Tipo: Presentation
Palavras-chave: Chemistry; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5737/version/1

Copper induced peroxidase, CCPP form Caribbean copper plant
Provedor de dados: 17
Autores: Reetesh Kumar.
Plant peroxidase exhibit broad substrate specificity and is active in a wide range of pH and temperature, and in the presence of organic compounds as well as other additives. The peroxidase is known to be involved in many physiological and regulatory processes in plants. This ppt presents an introduction on plant peroxidase and their applications. A purification protocol has been developed and the purified protein, named as CCPP is biochemically and physiologically characterized. The physiochemical properties such as molecular weight, isoelectric point have been experimentally determined. The enzymatic efficiency has been evaluated through temperature optimum, pH optimum, Km and other enzymatic properties along with spectroscopic parameters like circular...
Tipo: Presentation
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6410/version/1

Copyrights and digitizing the systematic literature: the horror... the horror...
Provedor de dados: 17
Autores: N. Dean Pentcheff.
It is time for us to take full advantage of the investment that our societies have made in documenting the biodiversity of the world. It is time for us to fully, and legally, make systematic literature available worldwide. Using U.S. &amp;#x22;Fair Use&amp;#x22; guidelines, we can.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4644/version/1

(Corrected) Osmotic stress and water isotope effects in kinesin-1 gliding motility assays
Provedor de dados: 17
Autores: Steven J. Koch; Andy Maloney; Lawrence J. Herskowitz.
The osmotic pressure and kinetic properties of water play important roles in biomolecular interactions.  As pointed out by Parsegian, Rand, and Rau, these crucial roles are often overlooked[1].  In some fields, osmotic stress and isotope effects have been exploited for probing the role water plays in binding interactions of biomolecules.  To our knowledge, there have been no studies of osmotic stress and water isotope effects for kinesin, and only a handful for myosin.  We&amp;#x27;re currently using the gliding motility assay to see whether we can extract new information about kinesin-1 / microtubule interactions by changing osmotic stress and water isotopes.  We will describe our open-source, automated analysis platform for extracting microtubule gliding...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4479/version/2

(Corrected) Osmotic stress and water isotope effects in kinesin-1 gliding motility assays
Provedor de dados: 17
Autores: Steven J. Koch; Andy Maloney; Lawrence J. Herskowitz.
The osmotic pressure and kinetic properties of water play important roles in biomolecular interactions.  As pointed out by Parsegian, Rand, and Rau, these crucial roles are often overlooked[1].  In some fields, osmotic stress and isotope effects have been exploited for probing the role water plays in binding interactions of biomolecules.  To our knowledge, there have been no studies of osmotic stress and water isotope effects for kinesin, and only a handful for myosin.  We&amp;#x27;re currently using the gliding motility assay to see whether we can extract new information about kinesin-1 / microtubule interactions by changing osmotic stress and water isotopes.  We will describe our open-source, automated analysis platform for extracting microtubule gliding...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4479/version/3

(Corrected) Speed effects in gliding motility assays due to surface passivation, water isotope, and osmotic stress.
Provedor de dados: 17
Autores: Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
The molecular motor kinesin-1, an ATPase, and the substrate it walks along, microtubules, are vital components of eukaryotic cells. Kinesin converts chemical energy to linear motion as its two motor domains step along microtubules in a process similar to how we walk. Cells create systems of microtubules that direct the motion of kinesin. This directed motion allows kinesin to transport various cargoes inside cells.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;During the stepping process, the kinesin motor domains bind and unbind from their binding sites on the microtubules.  Binding and unbinding rates of biomolecules are highly dependent on hydration and exclusion of water from the binding interface. Osmotic stress will likely strongly affect the binding and...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4469/version/3

(Corrected) Speed effects in gliding motility assays due to surface passivation, water isotope, and osmotic stress.
Provedor de dados: 17
Autores: Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
The molecular motor kinesin-1, an ATPase, and the substrate it walks along, microtubules, are vital components of eukaryotic cells. Kinesin converts chemical energy to linear motion as its two motor domains step along microtubules in a process similar to how we walk. Cells create systems of microtubules that direct the motion of kinesin. This directed motion allows kinesin to transport various cargos inside cells.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;During the stepping process, the kinesin motor domains bind and unbind from their binding sites on the microtubules.  Binding and unbinding rates of biomolecules are highly dependent on hydration and exclusion of water from the binding interface. Osmotic stress will likely strongly affect the binding and...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4469/version/2

Correlation between Ground Level Ultra-Violet Radiation &amp;#x26; Lower Atmospheric Aerosol Load
Provedor de dados: 17
Autores: Shweta Yadav; Ankit Tandon.
UV radiation is known to affect many biological and chemical processes, and is largely detrimental to individual organisms. Specific concerns include increase in the incidence of skin cancer, ocular damage, and other health effects in humans and other animals; damage to terrestrial and oceanic vegetation; changes in the chemistry of the lower atmosphere e.g. photochemical smog formation. Present study was undertaken to monitor lower atmospheric aerosol load with Respirable Dust Sampler and ultraviolet radiation with UV-radiometer in the ambient environment of Delhi. PM10 (&amp;#x3c; 10 &amp;#xb5;m) and SPM (&amp;#x3e; 10 &amp;#xb5;m) samples collected for the period of the study (8 weeks, 2 samples per week, total 16 samples). Hourly UV Fluxes (UV-B...
Tipo: Poster
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2677/version/1

Correlation between Pineal Activation and Religious Meditation Observed by Functional Magnetic Resonance Imaging
Provedor de dados: 17
Autores: Chien-Hui Liou; Chang-Wei Hsieh; Chao-Hsien Hsieh; Si-Chen Lee; Jyh-Horng Chen; Chi-Hong Wang.
The human brain possesses plenty of functions but little is known about its scientific relationship with mind and spirit. Conferences^1,2^ focused on the connection between science and religion were held very recently in which neuroscientists, Buddhist scholars and Dalai Lama discussed attention, mental imagery, emotion, mind, brain functions and meditation, suggesting religious meditation offers an effective means to investigate the mystery of mind and spirit. In the past decade, scientists struggled to obtain brain mappings for various meditation styles using different brain imaging techniques and stimulating results have been observed^3-17^. In this letter we report that, together with other brain regions, pineal body exhibit significant activation...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1328/version/1

Correlations between experimental and theoretical adiabatic ionization energies for organic compounds and rate constants for atmospheric reactions with hydroxyl radicals
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Adiabatic ionization energy (AIE) calculations were performed at the AM1, PM3, PM6, PDDG, HF/QZVP, and B3LYP/QZVP levels of theory on 722 atmospherically relevant organic compounds with available experimental rate constants for atmospheric reactions with hydroxyl radicals (k~OH~). From the starting set of molecules, a final suite of 114 mono- and polyfunctionalized compounds provided converged neutral and cationic geometries without imaginary frequencies for all six levels of theory. NIST evaluated AIEs were available for 54 compounds, providing mean absolute AIE prediction errors of 0.31 (AM1), 0.28 (PM3), 0.50 (PM6), 0.36 (PDDG), 1.22 (HF/QZVP), and 0.20 eV (B3LYP/QZVP). Modest correlations were found between the experimental (r=-0.68, SE=0.81) and...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5447/version/1

Cortical activity modulation of language processing by dynamic optimization of task complexity and functional restrictions
Provedor de dados: 17
Autores: Shantanu Ghosh; Amrita Basu; Subash Khushu; Senthil S. Kumaran.
Language, regarded as a hierarchical cognitive code activated by functional operational modes of the brain by most neuropsychologists, is characterized by increased cognitive load in successively higher levels of processing. Language comprehension is posited to be executed through symbolic-iconic information being encoded neurally as modulated phenomena, and can be studied _in vivo_ by functional brain imaging. Using a lexical decision-making task in conjunction with syntactic error correction that effectively isolated the regulatory neural substrate of processing structural-functional information, and minimizing the possible confounds of gender and proficiency, functional magnetic resonance imaging (fMRI) was performed on bilingual volunteers to ascertain...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3941/version/1

Cortical Bone Ontogeny: Activity, Nutritional Stress and Archaeology
Provedor de dados: 17
Autores: Gwen Robbins.
This poster introduces the idea that femoral compact bone growth and development demonstrates a very different pattern among infants and children in a contemporary sample of well-nourished active children versus archaeological samples of stressed, malnourished children.
Tipo: Poster
Palavras-chave: Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2470/version/1

Cortical responses reflecting inhibition of return (IOR): a magnetoencephalographic study
Provedor de dados: 17
Autores: Akiko Hashimoto; Yasuyuki Takeshima; Koji Inui; Ryusuke Kakigi.
Inhibition of return (IOR) is a phenomenon whereby the reaction time (RT) to detect a second stimulus (target) presented at the same location as the first stimulus (cue) is longer than when the target is presented at an un-cued location. In the present study, we investigated cortical activities under a standard IOR paradigm by recording visual evoked magnetic fields (VEFs). In Experiment 1, subjects directed their attention to the target at the periphery of the screen and the RT was measured. In Experiment 2, they paid attention to the center of the screen and the RT was not measured. In both experiments, the peak latency of the major deflection of VEFs in the occipito-temporal area was greater for the cued target than un-cued target. This is the first...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2063/version/1

Corticofugal projections from the anterior olfactory nucleus target olfactory bulb principal cells
Provedor de dados: 17
Autores: Kurt R. Illig.
The anterior olfactory nucleus (AON) is a cortical structure reciprocally connected with the olfactory bulb (OB) and the piriform cortex. Here, using small extracellular and intracellular injections to trace the terminal projections in the OB from individual cells in the rat AON, and examining the morphology and distribution of these projections, I report that these projections appear to preferentially target and directly synapses with mitral cells. These findings suggests that the AON acts to modulate incoming olfactory information based on ongoing processing, perhaps in a way that tunes the OB to signal the presence of particular odors.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6641/version/1

Cosmetic Use of Botulinum Toxin-A Affects Processing of Emotional Language
Provedor de dados: 17
Autores: David Havas; Arthur Glenberg; Karol Gutowski; Mark Lucarelli; Richard Davidson.
Language can evoke powerful emotions and influence consequent actions in readers, but the mechanisms underlying interactions of language and emotion are largely unknown. Since Darwin, emotional expressions have been implicated in emotional cognition, experience and understanding, but the functional role of the affective periphery is difficult to test. In a first experiment, facial electromyography revealed that silent reading of emotional (angry, sad, and happy) sentences automatically elicits differential patterns of activity in facial muscles used in expression of corresponding emotions (smiling and frowning). In a second experiment, temporary paralysis of the facial muscle corrugator supercilli (responsible for producing a frown) hindered processing,...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3683/version/1

Cost effective mass multiplication of Gymnema sylvestre in hydroponic system
Provedor de dados: 17
Autores: Raju Karthic; Sundaram Seshadri.
Present experiment was designed with an objective to develop a cost efficient mass multiplication method for Gymnema sylvestre using hydroponic system. A plastic tub, with polyethylene cover, containing 1/10 strength of MS salts supplemented with Indole butyric acid (IBA) at different concentrations (0.5, 1.0, 2.5 mg/L) was studied. Medium containing 0.5mg/L of IBA produced highest rooting (66%) with 96 % survival. This protocol will serve as an alternative to the existing in vitro and clonal multiplication protocols.
Tipo: Manuscript
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3770/version/1

Co-transformation of Oil Palm Using Agrobacterium-Mediated Transformation
Provedor de dados: 17
Autores: Vu Le.
Agrobacterium-mediated transformation is being used as an alternative method for improving the conventional breeding. In this study, immature embryos (IEs) of oil palm are chosen as explants for transformation. &amp;#x3b2;-glucuronidase (gus) and green fluorescence protein (GFP) were harbored by the two plasmids pCAMBIA 1304 and pCAMBIA 1302 respectively. The results were obtained at least four days after transformation. The IEs placing in the N6O medium for 7 days were then co-cultivated with A.tumefaciens suspension within 30 mins and then incubated in the dark for 1 day. In single transformation, GUS assay revealed that about 64% transient transformation frequency was obtained for IEs two weeks after co-cultivation, GFP activity was recorded as 41.67%...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/5441/version/1

Counting absolute number of molecules using unique molecular identifiers
Provedor de dados: 17
Autores: Teemu Kivioja; Anna V&amp;#xe4;h&amp;#xe4;rautio; Kasper Karlsson; Martin Bonke; Sten Linnarsson; Jussi Taipale.
Advances in molecular biology have made it easy to identify different DNA or RNA species and to copy them. Identification of nucleic acid species can be accomplished by reading the DNA sequence; currently millions of molecules can be sequenced in a single day using massively parallel sequencing. Efficient copying of DNA-molecules of arbitrary sequence was made possible by molecular cloning, and the polymerase chain reaction. Differences in the relative abundance of a large number of different sequences between two or more samples can in turn be measured using microarray hybridization and/or tag sequencing. However, determining the relative abundance of two different species and/or the absolute number of molecules present in a single sample has proven much...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5903/version/1

Coupling of capillary RBC flow failure with neuronal depolarization
Provedor de dados: 17
Autores: Minoru Tomita; Yutaka Tomita; Haruki Toriumi; Miyuki Unekawa; Norihiro Suzuki.
RBC (oxygen-carrier) behaviour in the cerebrocortical microvasculature during K^+^-induced cortical spreading depression (CSD) was examined in urethane-anesthetized male Wistar rats (n=10). The movements of FITC-labeled RBCs in single capillaries in the cortical region were traced with a high-speed camera laser scanning confocal fluorescence microscope and analyzed with Matlab domain software, KEIO-IS2, to obtain the velocities of all labeled RBCs appearing in local capillaries during CSD wave propagation. We found that CSD induced periodic decreases in both RBC number and velocity until RBCs halted or disappeared for 3.3 +/- 2.3 s, and then RBC flow was restored. The RBC flow stall was statistically significant (P &amp;#x3c; 0.05). During capillary flow...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3220/version/1

Coupling perception and action using probabilistic control
Provedor de dados: 17
Autores: Constantin A. Rothkopf; Paul Schrater.
Although there is a long tradition of separating perception, decision making and action, the theoretical conditions for such a separation are very restrictive and not applicable even to the most basic every day tasks in humans. Instead, all uncertainties relating states of the world to observations, actions to future states and rewards, and actions to observations need to be considered in order to act optimally. In the most general formulation this can be formalized as a partially observable Markov decision process (POMDP).&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We consider the task of intercepting a moving ball for which a multitude of previous studies has shown that humans use a constant bearing angle strategy. Here we manipulated the observation function in...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6566/version/1

Courtship plasticity reveals the evolution of dialects in allopatric fish populations
Provedor de dados: 17
Autores: Cesar Gonzalez Zuarth; Adriana Vallarino; Constantino Macias Garcia.
Traditionally, reproductive isolation between disjoint populations has been thought to emerge as a result of the accumulation of different mutations, genetic drift, or through the effects of natural and sexual selection^1^. Alternatively, the ability of an organism to express different phenotypes depending on the environment (i.e. phenotypic plasticity) could produce reproductive isolation^2,3^. Sexually selected traits are expected to be phenotypically plastic and can result in modifications of the species recognition system and thus originate new species^4^. Here we show that the population-characteristic male courtship behaviour of a fish (Girardinichthys multiradiatus) is modified in the presence of females from other populations, that this is due to...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2155/version/1

Covalently bound substrate at the regulatory site triggers allosteric enzyme activation
Provedor de dados: 17
Autores: Steffen Kutter; Manfred Weiss; Georg Wille; Ralph Golbik; Michael Spinka; Stephan K&amp;#xf6;nig.
The mechanism by which the enzyme pyruvate decarboxylase from yeast is activated allosterically has been elucidated. A total of seven three-dimensional structures of the enzyme, of enzyme variants or of enzyme complexes form two yeast species (three of them reported here for the first time) provide detailed atomic resolution snapshots along the activation coordinate. The prime event is the covalent binding of the substrate pyruvate to the side chain of cysteine 221, thus forming a thiohemiketal. This reaction causes the shift of a neighbouring amino acid, which eventually leads to the rigidification of two otherwise flexible loops, where one of the loops provides two histidine residues necessary to complete the enzymatically competent active site...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1639/version/1

COX inhibition: Catalepsy and Striatum Dopaminergic-GABAergic-Glutamatergic Neurotransmission
Provedor de dados: 17
Autores: Hadi Fathi-Moghaddam; Mehdi Shafiee Ardestani; Meysam Shafiee Ardestani; Davood Barzegar-Pourshuraki; Amin Gravand; Latifeh Navidpour; Hojat Ebrahiminik; Abbas Shafiee.
Selective COX-2 and COX-1 inhibitors were administered (i.p. acutely) to normal and parkinsonian rats, followed by the analysis of the striatal dopamine, GABA and glutamate concentrations using the microdialysis technique, simultaneously, the catalepsy of animals was evaluated. Selective COX-2 inhibition showed improving effects on the catalepsy followed by decreasing the striatum glutamatergic-GABAergic and enhancing the dopaminergic neurotransmission. Nonetheless COX inhibition had no significant improving effects on damaged Substantia Nigra Pars Compacta (SNc) neurons.
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/1481/version/1

Creatine kinase in energy metabolic signaling in muscle
Provedor de dados: 17
Autores: Olav Kongas; Johannes H. G. M. van Beek.
There has been much debate on the mechanism of regulation of mitochondrial ATP synthesis to balance ATP consumption during changing cardiac workloads. A key role of creatine kinase (CK) isoenzymes in this regulation of oxidative phosphorylation and in intracellular energy transport had been proposed, but has in the mean time been disputed for many years. It was hypothesized that high-energy phosphoryl groups are obligatorily transferred via CK; this is termed the phosphocreatine shuttle. The other important role ascribed to the CK system is its ability to buffer ADP concentration in cytosol near sites of ATP hydrolysis. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Almost all of the experiments to determine the role of CK had been done in the steady state, but...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1317/version/1

Creating a Translational Medicine Ontology
Provedor de dados: 17
Autores: Christine Denney; Colin Batchelor; Olivier Bodenreider; Sam Cheng; John Hart; John Hill; John Madden; Mark Musen; Elgar Pichler; Matthias Samwald; Sa&amp;#x301;ndor Szalma; Lynn Schriml; David Sedlock; Larisa Soldatova; Koji Sonoda; David Statham; Holger Stenzhorn; Patricia L. Whetzel; Elizabeth Wu; Susie Stephens.
*Abstract*&amp;#xd;&amp;#xa;We, participants in the Translational Medicine Ontology activity of the World Wide Web Consortium&amp;#x2019;s Health Care and Life Sciences Interest Group (&amp;#x22;http://esw.w3.org/topic/HCLSIG&amp;#x22;:http://esw.w3.org/topic/HCLSIG) and members of the National Center for Biomedical Ontology (&amp;#x22;http://bioontology.org/&amp;#x22;:http://bioontology.org/), are developing a high-level, patient-centric ontology for translational medicine which will draw on existing domain ontologies and allow the integration of data throughout the drug development process.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Introduction*&amp;#xd;&amp;#xa;The pharmaceutical industry has historically focused on the development of novel blockbuster drugs....
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3686/version/1

Creating &amp;#x201c;fire-smart&amp;#x201d; forest stands and landscapes
Provedor de dados: 17
Autores: Paulo Fernandes.
Wildland fire is an important feature of the Mediterranean Basin. Past fire incidence has been limited by landscape diversity and the intensity of biomass use. Fire activity and the meteorological component of fire danger have increased during the last decades, but the fire regime modification was primarily fuel-driven, i.e. caused by changes in land cover and land use. Fire-smart forests and landscapes are resistant to fire spread and resilient to its occurrence. In cultural landscapes where fires are seldom allowed to spread &amp;#x22;fire smartness&amp;#x22; is attained through proactive management by either treating fuels in fire-prone vegetation types or decreasing the importance of those vegetation types in the landscape. The presentation overviews...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6245/version/1

Creating and improving detoxification pathways for interpretation of toxicogenomics data
Provedor de dados: 17
Autores: Pieter Giesbertz; Jonas Hummel; Stan Gaj; Danyel Jennen; Thomas Kelder; Chris Evelo; Joost van Delft; Jos Kleinjans.
Current high-throughput technology in genomics creates a large amount of biological data. Bioinformatics approaches are directed towards understanding such data on a systems biology level. Advanced mathematical methods like principal component analysis, clustering, neural networks, support vector machine (SVM) approaches and neural networks can help to find patterns in the data. However, to really understand the data the patterns must be combined with existing knowledge. One of the approaches to do so is to associate these data to functional classifications such as can be found in the Gene Ontology. Other methods focus on using biological pathways coming from both public and private pathway databases like KEGG, WikiPathways, Reactome, and MetaCore. Some of...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4575/version/1

Crinumin, a novel substitute of chymotrypsin, may control pancreatic insufficiency and inflammation: Purification and characterization
Provedor de dados: 17
Autores: Kunwar Awaneesh Singh; Chandan  Singh; G.R.K. Rao; M.V. Jagannatham.
Crinumin, a glycosylated serine protease with chymotrypsin like catalytic specificity was purified from a medicinally important plant _Crinum asiaticum_ of family _Amaryllidaceae_. Ethno-botanical information and Pharmacological studies confirming about the presence of active bio- molecules in the _Crinum_ played crucial role in injury, inflamed joint, local pain and arthritis. Biomedical research suggests chymotrypsin was not only used as digestive aid but also helpful in the above disease. These findings support towards the crinumin may be the active bio-molecule. Crinumin shows activity over a wide range of pH (4.5-11.5 and optimum at 8.5), temperature (75 &amp;#xb0;C and optimum at 70 &amp;#xb0;C) and is also functional against chaotrophs, organic...
Tipo: Poster
Palavras-chave: Pharmacology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4339/version/1

Critical Concentration Gradient Model of Bacterial Cell Division
Provedor de dados: 17
Autores: Aijaz A. Rashid; Perminder P. Sing.
Critical concentration gradient model is helpful in understanding the mechanism of Z-ring formation. The distribution of positive and negative regulators of Z-ring formation in cell is not random but well programmed. The positive and negative regulators in cell lead to a critical concentration gradient from mid cell to the poles. The critical concentration of FtsZ required for Z-ring assembly at the centre of cell is less than that at the poles. So FtsZ starts polymerizing at cell centre and afterwards by cooperative association of more and more monomers leads to the Z-ring formation. Simultaneously during Z-ring formation the recruitment of other accessory proteins takes place, leading to the formation of a stable divisome complex.
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4659/version/1

Critical dynamics in homeostatic memory networks
Provedor de dados: 17
Autores: Sakyasingha Dasgupta; J. Michael Herrmann.
Critical behavior in neural networks characterized by scale-free event distributions and brought about by self-regulatory mechanisms such as short-term synaptic dynamics or homeostatic plasticity, is believed to optimize sensitivity to input and information transfer in the system. Although theoretical predictions of the spike distributions have been confirmed by in-vitro experiments, in-vivo data yield a more complex picture which might be due to the in-homogeneity of the network structure, leakage in currents or massive driving inputs which has so far not been comprehensively covered by analytical or numerical studies.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We address these questions by the study of a neural model of memory that allows for storage and...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5829/version/1

Critical nutritional stress among adult tribal populations of West Bengal and Orissa, India.
Provedor de dados: 17
Autores: Samiran Bisai; Kaushik  Bose.
This paper deals with cross-sectional studies carried out during the period 2004-2007. It is based on eight data sets of tribals of Paschim Medinipur and Bankura Districts of West Bengal and Keonjhar District of Orissa.  The tribes include Bhumijs, Kora Mudis, Lodhas, Santals, Bathudis and Savars.  Height and weight were measured following standard techniques.  The body mass index (BMI) was computed following standard equation.  Nutritional status (chronic energy deficiency, CED) was evaluated using internationally accepted cut-off values of BMI.  We followed the World Health Organization&amp;#x27;s classification (1995) of the public health problem of low BMI, based on adult populations worldwide.  Our results show that, in general, among the tribes...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth &amp; Environment; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7068/version/2

Critical nutritional stress among adult tribal populations of West Bengal and Orissa, India.
Provedor de dados: 17
Autores: Samiran Bisai; Kaushik  Bose.
This paper deals with cross-sectional studies carried out during the period 2004-2007. It is based on eight data sets of tribals of Paschim Medinipur and Bankura Districts of West Bengal and Keonjhar District of Orissa.  The tribes include Bhumijs, Kora Mudis, Lodhas, Santals, Bathudis and Savars.  Height and weight were measured following standard techniques.  The body mass index (BMI) was computed following standard equation.  Nutritional status (chronic energy deficiency, CED) was evaluated using internationally accepted cut-off values of BMI.  We followed the World Health Organization&amp;#x27;s classification (1995) of the public health problem of low BMI, based on adult populations worldwide.  Our results show that, in general, among the tribes...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth &amp; Environment; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7068/version/1

Critical studies on systematics of Murdannia lanuginosa (Wall. EX C. B. Cl) Brueck. (Commelinaceae)
Provedor de dados: 17
Autores: M D. Nandikar; R V. Gurav.
_Murdannia lanuginosa_ (C. B. Cl.) Brucek. (Commelinaceae), an endemic plant to Western Ghats of Peninsular India. It is categorized as regionally endangered taxon owing to its restricted habitat and low population status in ateritic plateaus of Maharashtra and Karnataka. It is observed in higher abundance in lateritic plateaus  and hilly slopes at an altitude range of 900 to 1600 m. _M. lanuginosa_ found on open grassy plateaus along with herbs like _M. simplex_, _M. versicolor_, _Ischaemum impressum_, _Glyphochloa forficulata_, _Paspalum canarae_, _Smithia bigemina_, _S. purpurea_, _Rotala densiflora_, _Pogostemon deccanensis_, etc. Extent of occurrence of _M. lanuginosa_ estimated to be 4,000 sq. km and found only at few locations. This paper presents...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4619/version/2

Critical studies on systematics of Murdannia lanuginosa (Wall. EX C. B. Cl) Brueck. (Commelinaceae)
Provedor de dados: 17
Autores: M D. Nandikar; R V. Gurav.
_Murdannia lanuginosa_ (C. B. Cl.) Brucek. (Commelinaceae), an endemic plant to Western Ghats of Peninsular India. It is categorized as regionally endangered taxon owing to its restricted habitat and low population status in ateritic plateaus of Maharashtra and Karnataka. It is observed in higher abundance in lateritic plateaus  and hilly slopes at an altitude range of 900 to 1600 m. _M. lanuginosa_ found on open grassy plateaus along with herbs like _M. simplex_, _M. versicolor_, _Ischaemum impressum_, _Glyphochloa forficulata_, _Paspalum canarae_, _Smithia bigemina_, _S. purpurea_, _Rotala densiflora_, _Pogostemon deccanensis_, etc. Extent of occurrence of _M. lanuginosa_ estimated to be 4,000 sq. km and found only at few locations. This paper presents...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4619/version/1

Crossing Disciplinary Boundaries to Understand Human Drivers of Environmental Threats
Provedor de dados: 17
Autores: Eugene A. Rosa; Thomas Dietz.
A wide range of ecological studies affirms the cumulative damage to ecosystem capital and services around the globe.  They also point to the overwhelming role that anthropogenic or human drivers play in global ecological damage.  The MAHB is intended to combine what we know about human drivers of environmental threats with what the social sciences know about changing human behavior and institutions.  A variety of social sciences have taken up the first task of identifying the key human activities&amp;#x2014;at both the local, cumulative level and at the systemic level&amp;#x2014;most responsible for global environmental change.  Considerable progress has been made in our understanding of land use and land cover change, of vulnerability, resilience, and...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5251/version/1

Crossing Lilium Orientals of different ploidy creates Fusarium-resistant hybrid
Provedor de dados: 17
Autores: Zheng Sixiang; Wu Hongzhi; Zhao Yan; Liu Feihu.
Oriental hybrid lily is of great commercial value, but it is susceptible to Fusarium disease that causes a significant loss to the production. A diploid Oriental hybrid resistant to Fusarium, Cai-74, was diploidized from triploid obtained from the offspring of tetraploid (from &amp;#x2018;Star Fighter&amp;#x2019;) and diploid (&amp;#x2018;Con Amore&amp;#x2019;, &amp;#x2018;Acapulco&amp;#x2019;) by screening the hybrids of different cross combinations following inoculating Fusarium oxysporum to the tissue cultured plantlets in a greenhouse. By analyzing saponins content in bulbs of a number of lily genotypes with a known Fusarium resistance, it was found that the mutant Cai-74 had a much higher content of saponin than its parents.  Highly resistant wild _L....
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4830/version/1

Cross-modal facilitation of visual and tactile motion
Provedor de dados: 17
Autores: David Burr; Giulio Sandini; Monica Gori.
Robust and versatile perception of the world is augmented considerably when information from our five separate sensory systems is combined. Much recent evidence has demonstrated near-optimal integration across senses, but it remains unclear at what level the integration occurs, at a &amp;#x22;sensory&amp;#x22; or &amp;#x22;decisional&amp;#x22; level. Here we show that non-informative &amp;#x22;pedestal&amp;#x22; motion stimuli in one sensory modality (vision or touch) selectively lowers thresholds in the other, to the same degree as pedestals in the same modality: strong evidence for functionally important cross-sensory integration at early levels of sensory processing.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2675/version/1

Cross-Product Extensions of the Gene Ontology
Provedor de dados: 17
Autores: Christopher J. Mungall; Michael Bada; Tanya Z. Berardini; Jennifer Deegan; Amelia Ireland; Midori A. Harris; David P. Hill; Jane Lomax.
The Gene Ontology is being normalized and extended to include computable logical definitions. These definitions are partitioned into mutually exclusive cross-product sets, many of which reference other OBO Foundry ontologies. The results can be used to reason over the ontology, and to make cross-ontology queries.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3496/version/1

Crosstalk and the spectrum of biological global broadcasts: Toward generalization of the Baars consciousness model across physiological subsystems
Provedor de dados: 17
Autores: Rodrick Wallace.
Once cognitive biological phenomena are recognized as necessarily having &amp;#x27;dual&amp;#x27; information sources, it is easy to show that the information theory chain rule implies isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to dynamic global broadcasts of interacting cognitive biological processes analogous to, but slower than, consciousness, itself included within the paradigm. The argument is closely analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Immunology; Molecular Cell Biology; Neuroscience; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6898/version/1

Cryopreservation of a whole liver
Provedor de dados: 17
Autores: Zohar Gavish; Amir Arav; Menahem Ben-Haim.
Preservation of vascularized organs such as the liver is limited to 24hrs. before destructive processes disqualify it for transplantation. This narrow time window prevents surgeons from performing optimal pathogen screening and matching tests which often lead to re-transplantation. Numerous problems are associated with viably freezing and thawing a whole liver: complicated geometry, poor heat transfer, release of latent heat and the difficulty of generating a uniform cooling rate. Our past success led us to apply our novel freezing technique to a larger solid organ, the liver. Whole livers were frozen/thawed using a directional solidification apparatuses; viability was tested by means of integrity and functionality in vitro and in auxiliary liver...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2007
URL: http://precedings.nature.com/documents/1352/version/1

Cryopreservation of cell/hydrogel constructs based on a new cell-assembling technique
Provedor de dados: 17
Autores: Xiaohong  Wang; Huirong  Xu; Yongnian  Yan; Renji  Zhang.
Organ manufacturing products hold the promise to be used widely in the future for complex organ failings. The cryopreservation of the product is a very important step in the commercialization activities. In this article, a new cell cryopreservation technique, whereby, cryoprotectants were directly incorporated into the cell/hydrogel constructs, prototyped according to the predesigned structure and then subjected to a special freezing/thawing process. The rheological and hydration properties of the cryopreservation systems indicated that the hydratabilities of the gelatin/alginate hydrogels were greatly increased while the eutectic temperatures were greatly decreased by the addition of glycerol. Dextran-40 was found to be effective to improve the cell...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3722/version/1

Cu2+ uptake by Chlorococcum hemicolum - A Xeric Chlorophycean Alga
Provedor de dados: 17
Autores: Mr. Harish; S. Sundaramoorthy; Devendra Kumar; S.G. Vaijapurkar.
Bioremediation of copper by xeric chlorophycean bioremediator, Chlorococcum hemicolum was investigated. The growth rates at various concentrations of Cu2+ were assessed in terms of protein level and 8 mg L-1 (37.67 % level in growth kinetics) is the tolerance limit. Absorption/adsorption kinetics was estimated after 240 hrs of Cu2+ treatments. Absorptions were higher than adsorption with maximum accumulation factor (AF) of 1.40. The Cu2+ concentration and absorption were linearly related (r = 0.99; p&amp;#x3e;0.01). Other biochemical parameters like total sugar, chlorophyll and carotenoids were also quantified to correlate the state of metabolism and these exhibited reduction due to heavy metal stress.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5657/version/1

Cueing in a perceptual task causes long-lasting interference that generalizes across context to affect only late perceptual learning and is remediated by the passage of time
Provedor de dados: 17
Autores: Ramesh Rajan.
Perceptual learning, the improvement in sensory discriminations with practise, is also subject to stimulus-specific interference from temporal jitter in a learning session or manipulations applied between or immediately after sessions. We demonstrate a novel form of perceptual interference where even a brief cueing exposure to a complex speech-in-noise task produces a forward interference on subsequent speech-in-noise learning. This potent interference generalizes across cueing context but specifically affects only late learning in the subsequent task, is resistant to the remediating effects of sleep and persists across an overnight delay involving sleep, and can be evoked by a single exposure 1 day before the learning. Learning in the speech-in-noise task...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2387/version/1

Cunningham: a BLAST Runtime Estimator
Provedor de dados: 17
Autores: James R. White; Malcolm Matalka; W. Florian Fricke; Samuel V. Angiuoli.
BLAST is arguably the single most important piece of software ever written for the biological sciences. It is the core of most bioinformatics workflows, being a critical component of genome homology searches and annotation. It has influenced the landscape of biology by aiding in everything from functional characterization of genes to pathogen detection to the development of novel vaccines. While BLAST is very popular, it is also often one of the most computationally intensive parts of bioinformatics analysis. In our workflows, BLAST typically takes the majority of cpu time, and we need to parallelize to finish in a reasonable time frame. Waiting for BLAST to finish without having any clue of how long it&amp;#x2019;s going to take is kind of depressing, and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5593/version/1

Cunningham: a BLAST Runtime Estimator
Provedor de dados: 17
Autores: James R. White; Malcolm Matalka; W. Florian Fricke; Samuel V. Angiuoli.
BLAST is arguably the single most important piece of software ever written for the biological sciences. It is the core of most bioinformatics workflows, being a critical component of genome homology searches and annotation. It has influenced the landscape of biology by aiding in everything from functional characterization of genes to pathogen detection to the development of novel vaccines. While BLAST is very popular, it is also often one of the most computationally intensive parts of bioinformatics analysis. In our workflows, BLAST typically takes the majority of cpu time, and we need to parallelize to finish in a reasonable time frame. Waiting for BLAST to finish without having any clue of how long it&amp;#x2019;s going to take is kind of depressing, and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5593/version/2

Curating Genetic Association Literature for Common Diseases
Provedor de dados: 17
Autores: Elana Silver; Eran Halperin; Kord M. Kober; Badri Padhukasahasram; Nila Patil; Michelle Sommargren; Dietrich A. Stephan; Daryl J. Thomas; Heather Trumbower; Michele Cargill.
Papers describing genetic associations with common diseases are currently being published at a rapid rate. These new papers add to an already large body of literature which includes candidate gene studies, genome wide association studies, review papers, and meta-analyses. Related papers describe the basic epidemiology of these common diseases, as well as interactions between genes and environment, other genes, and drugs (pharmacogenomics), all of which may affect disease predisposition and management. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As the field of personalized genomics continues to grow and mature, this body of literature is being synthesized in various ways. One aspect of utmost importance is to track gene-disease associations over time to see if...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3174/version/1

Curation and annotation for BioModels Database, a resource of published quantitative kinetic models
Provedor de dados: 17
Autores: Chelliah Vijayalakshmi; Lukas Endler; Camille Laibe; Chen Li; Nicolas Le Nov&amp;#xe8;re.
BioModels Database (&amp;#x22;http://www.ebi.ac.uk/biomodels/&amp;#x22;:http://www.ebi.ac.uk/biomodels/) is a free resource for storing, viewing and retrieving published, peer-reviewed, quantitative models of biochemical and cellular systems. As a storage format, BioModels Database uses the Systems Biology Markup Language (SBML), but also allows submission and export of models in various other commonly used formats.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To offer scientists reliable information, models are curated to comply with the MIRIAM (Minimal Information Requested In the Annotation of biochemical Models) standard. This curation process involves verification of the model structure, the parameter and variable values and its mathematical relations....
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3124/version/1

Curation at the NCBI: Genomes, Genes, &amp;#x26; Sequence Standards
Provedor de dados: 17
Autores: Garth Brown; Catherine Farrell; Jennifer Hart; Melissa Landrum; Donna Maglott; Bonnie Maidak; Michael Murphy; Terence Murphy; Bhanu Rajput; Kim D. Pruitt; Lillian Riddick; David Webb; Janet Weber; Wendy Wu.
The National Center for Biotechnology Information (NCBI) provides curation support for many genomes, and  disseminates information in several resources including Entrez Gene, reference sequences (RefSeq), the Consensus CDS (CCDS) database, and the Genome Reference Consortium (GRC).  These projects are supported by several collaborations to provide:1) support to the international consortium maintaining the assemblies for human and mouse (GRC); 2) sequence standards for chromosomes, genes, transcripts and proteins (RefSeq); 3) reports of integrated information including nomenclature, publications, phenotypes and diseases, sequences, ontologies, interactions (Gene); and 4) identification of proteins that are consistently annotated on the human and mouse...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3287/version/1

Curation of NISEED, an integrative framework for the digital representation of embryonic development
Provedor de dados: 17
Autores: Delphine Dauga; Olivier Tassy; Fabrice Daian; Daniel Sobral; Patrick Lemaire.
NISEED (Network for In situ Expression and Embryological Data) is a generic infrastructure for the creation, maintenance and integration of molecular and anatomical information on model organisms. We applied it to ascidians which are marine invertebrate chordates. These animals constitute model organisms of choice for developmental biology because their embryos develop with a small number of cells and an invariant lineage, allowing their study with a cellular level of resolution.  In ANISEED (Ascidian NISEED), embryogenesis of ascidian is represented at the level of the genome via functional gene annotations, cis-regulatory elements or gene expression data, at the level of the cell by representing its morphology, fates, lineage, and relations with its...
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3168/version/1

Curcumin Functions as a Positive Regulator of miRNA Processing &amp;#x26; a Negative Regulator of Cancer Stem Cell Proliferation
Provedor de dados: 17
Autores: Lakshmanane P. Boominathan.
Identifying agents that inhibit the proliferation of cancer stem cells is of great importance in cancer biology.  Curcumin has been shown to function as an anti-cancer agent.  One of the tumor suppressors that appear to be induced in response to curcumin treatment is p53.  A recent study suggests that curcumin increases the expression of miRNAs, such as miR-22, miR-181a, b, c, miR-34, miR-103, and miR-21.  Intriguingly, miR-34, 181b, c, miR-103, miR-21, and miR-24 have been identified as transcriptional targets of the tumor suppressor p53.  This data suggests a possibility that curcumin, by inducing the expression of p53, it could increase the expression of these microRNAs.  A number of groups have shown that c-Myc, Sox-2, Klf-4, Oct-4, Sox-2, Nanog, and...
Tipo: Poster
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/4110/version/1

Current State of JUMMP
Provedor de dados: 17
Autores: Martin Gr&amp;#xe4;&amp;#xdf;lin.
In computational biology there is a strong need to exchange quantitative models of biological processes in a standardized way. For storing and retrieving peer-reviewed models the BioModels Database has been available for several years. But at the moment there is no tool available to bring a model from development in the lab directly to the peer-reviewed online resource.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The JUMMP (JUst a Model Management Platform) project aims at providing a generic model management platform for any standardized model file. Through a well-elaborated security layer models can be developed and shared privately and later on be made available to the curation process and the broader community. Each change to a model is recorded in a version...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6371/version/1

Current status of herbal and their future perspectives
Provedor de dados: 17
Autores: Ramar Perumal  R. Samy; Ponnampalam Gopalakrishnakone.
Traditional medicine is the synthesis of therapeutic experience of generations of practicing physicians of indigenous systems of medicine. Throughout the history of mankind, many infectious diseases have been treated with herbals. The traditional medicine is increasingly solicited through the tradipractitioners and herbalists in the treatment of infectious diseases. Among the remedies used, plant drugs constitute an important part. A number of scientific investigations have highlighted the importance and the contribution of many plant families i.e. Asteraceae, Liliaceae, Apocynaceae, Solanaceae, Caesalpinaceae, Rutaceae, Piperaceae, Sapotaceae used as medicinal plants. Medicinal plants play a vital role for the development of new drugs (export and import...
Tipo: Manuscript
Palavras-chave: Pharmacology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1176/version/1

Cutting the trees to save the forest: The Finch Pruyn working forest
Provedor de dados: 17
Autores: Rachel Neugarten; Steven Wolf; Rich Stedman.
The past two decades have seen sales of millions of acres of commercial forest land in the United States. Changed ownership often results in altered forest management, parcelization or development. Such changes have profound implications for forest species and ecosystems, as well as the timber industry, recreational opportunities, and local and regional economies. An emerging strategy seeks to protect lands through complex public-private partnerships involving state agencies, conservation organizations, and commercial investors. By definition, these partnerships have both environmental and socioeconomic goals; as such, they represent contemporary experiments in sustainable development applied to forested landscapes. As this approach is a recent innovation,...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3690/version/1

Cyclin kinase inhibitor p21: a mediator of immune tolerance: direct and indirect evidence
Provedor de dados: 17
Autores: Ashwani Khanna.
*Background:* Uncontrolled proliferation of T-cells is considered a barrier to the induction of transplantation tolerance by T regulatory cells. Therefore, cyclin kinase inhibitor p21, one of the most potent inhibitors of cell proliferation, may exert an important role in the induction/generation of T regulatory cells.&amp;#xd;&amp;#xa;*Methods:* CD4^+^CD25^+^ and CD4^+^CD25^-^ cells were isolated from normal healthy blood donors (n=6), p21^-/-^ mice (n=9) and wild type mice (n=9). Proliferation with and without cyclosporine was quantified by ^3^H-thymidine uptake assay (expressed as counts per minute) and FoxP3 mRNA was studied by real-time quantitative RT-PCR. &amp;#xd;&amp;#xa;*Results:* The difference in proliferation (p&amp;#x3c;0.003) among...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2009
URL: http://precedings.nature.com/documents/3378/version/1

D2RQ Platform &amp;#x2013; Treating Non-RDF Databases as Virtual RDF Graphs
Provedor de dados: 17
Autores: Radoslaw Oldakowski.
D2RQ is a complete solution to map and expose relational databases as RDF.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5660/version/1

DARPP-32 is a robust integrator of dopamine and glutamate signals
Provedor de dados: 17
Autores: Nicolas Le Novere; Eric Fernandez; Renaud Schiappa; Jean-Antoine Girault.
Integration of neurotransmitter and neuromodulator signals in the striatum plays a central role in the functions and dysfunctions of the basal ganglia. DARPP-32 is a key actor of this integration in the GABAergic medium-size spiny neurons, in particular in response to dopamine and glutamate. When phosphorylated by cAMP-dependent protein kinase (PKA) DARPP-32 inhibits protein phosphatase-1 (PP1), whereas when phosphorylated by cyclin-dependent kinase 5 (CDK5) it inhibits PKA. DARPP-32 is also regulated by casein kinases and by several protein phosphatases. These complex and intricate regulations make simple predictions of DARPP-32 dynamic behaviour virtually impossible. We used detailed quantitative modelling of the regulation of DARPP-32 phosphorylation to...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2006
URL: http://precedings.nature.com/documents/9/version/1

D-aspartate exerts an opposing role upon age-dependent NMDAR-related synaptic plasticity and memory decay
Provedor de dados: 17
Autores: Francesco Errico; Robert Nistico&amp;#x27;; Antimo D&amp;#x27;Aniello; Sandra Sivilia; Michela Giustizieri; Francesco Napolitano; Enza Topo; Giorgio Bernardi; Laura Calza; Nicola Mercuri; Alessandro Usiello.
In the present study, we demonstrated that D-aspartate acts as an _in vitro_ and _in vivo_ neuromodulatory molecule upon hippocampal NMDAR transmission. Accordingly, we showed that this D-amino acid, widely expressed during embryonic phase, was able to strongly influence hippocampus-related functions at adulthood. Thus, while up-regulated levels of D-aspartate increased LTP and spatial memory in four-month old adult mice, the prolonged deregulation of this molecule in thirteen-month old animals induced a substantial acceleration of age-dependent decay of synaptic plasticity and cognitive functions. Moreover, we highlighted a role for D-aspartate in enhancing NMDAR-dependent synaptic plasticity through an inducible &amp;#x22;turn-on/turn-off-like...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1891/version/1

Data Basin Climate Center: sharing and manipulating spatial information on the web
Provedor de dados: 17
Autores: Dominique Bachelet; James Strittholt; Tosha Comendant.
Monitoring datasets is essential to detect changes that are occurring and identify thresholds that cause them, but scientists around the world are now generating large volumes of data that vary in quality, format, supporting documentation, and accessibility. Moreover, diverse models are being run at various spatial and temporal scales to try and understand past climate variability and its impacts, generate future climate and land use scenarios, and project potential future impacts to the planet. Conservation practitioners and land managers are struggling to synthesize this wealth of information, identify relevant and usable datasets, and translate evolving science results into on-the-ground climate-aware strategies.&amp;#xd;&amp;#xa;In partnership with...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5256/version/1

Data Basin Climate Center: sharing and manipulating spatial information on the web
Provedor de dados: 17
Autores: Dominique Bachelet; James Strittholt; Tosha Comendant.
Monitoring datasets is essential to detect changes that are occurring and identify thresholds that cause them, but scientists around the world are now generating large volumes of data that vary in quality, format, supporting documentation, and accessibility. Moreover, diverse models are being run at various spatial and temporal scales to try and understand past climate variability and its impacts, generate future climate and land use scenarios, and project potential future impacts to the planet. Conservation practitioners and land managers are struggling to synthesize this wealth of information, identify relevant and usable datasets, and translate evolving science results into on-the-ground climate-aware strategies.&amp;#xd;&amp;#xa;In partnership with...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5256/version/2

Data citation in the wild
Provedor de dados: 17
Autores: Valerie Enriquez; Sarah Walker Judson; Nicholas M. Walker; Suzie Allard; Robert B. Cook; Heather A. Piwowar; Robert J. Sandusky; Todd J. Vision; Bruce E. Wilson.
Consistent attribution of research data upon reuse is necessary to reward the original data-producing investigators, reconstruct provenance, and inform data sharing policies, tool requirements, and funding decisions.  Unfortunately, norms for data attribution are varied and often weak.  As part of the DataONE 2010 summer internship program, three interns studied the policies, practice, and implications of current data attribution behavior in the environmental sciences.  We found that few policies recommend robust data citation practices: in our preliminary evaluation, only one-third of repositories (n=26), 6% of journals (n=307), and 1 of 53 funders suggested a best practice for data citation.  We manually reviewed 500 papers published between 2000 and...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5452/version/1

Data Curation in Biology - Past, Present and Future
Provedor de dados: 17
Autores: Janet Thornton.
Data curation has been critical in the development of biology from Darwin and Linnaeus to UniProt, the careful collection and organisation of data has been the spring from which new hypotheses and understanding have emerged. In this presentation, I will describe how we have used data curation in my own research group - and also present an overview of curation at the EBI. With new technical developments and the move towards the semantic web, the role of curation in the future needs to develop to take advantage of these new opportunities. This will be discussed.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3225/version/1

Data, Databases, and Communities
Provedor de dados: 17
Autores: Matthew Day.
Overview&amp;#xd;&amp;#xa;* Publishing landscape and challenges&amp;#xd;&amp;#xa;* Nature gateways and databases&amp;#xd;&amp;#xa;* NCI-Nature Pathway Interaction Database&amp;#xd;&amp;#xa;* A few other communication tools
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2884/version/1

Data integration in myGrid with Taverna
Provedor de dados: 17
Autores: Duncan Hull.
Many areas of life sciences research involve integrating terabytes of heterogeneous, &amp;#xd;&amp;#xa;distributed and autonomous data available on the Web. The myGrid project has addressed &amp;#xd;&amp;#xa;these challenging problems by developing and applying novel grid and semantic web &amp;#xd;&amp;#xa;services technology to life science data integration, particularly genome annotation and &amp;#xd;&amp;#xa;microarray analysis. This presentation outlines the past, present and future of the Taverna workflow system.&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/331/version/1

Data Management Plan for Monogram BioSciences
Provedor de dados: 17
Autores: Christos J. Petropoulos.
This is the data plan for access to data underlying published reports by Monogram BioSciences.
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Pharmacology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5668/version/1

Data Mining for Simple Sequence Repeats in Oil Palm Expressed Sequence Tags
Provedor de dados: 17
Autores: Aikkal Riju; Vadivel Arunachalam.
Expressed Sequence Tags or ESTs are small pieces of DNA sequence that are generated by sequencing either one or both ends of an expressed gene. ESTs provide researchers with a quick and inexpensive route for discovering new genes, for obtaining data on gene expression and regulation, and for constructing genome maps. Oil palm EST sequences as available in public domain are downloaded. They were grouped and made contigs using CAP3 and Phrap. Microsatellite repeats are located using 5 softwares (MISA, TRA, TROLL, SSRIT, SSR primer). Among the 5 methods MISA is found to be the best. It can elucidate the compound repeat also. Frequency and total number (202) of SSR were detected. Mononucleotide repeat is more abundant especially &amp;#x2018;A/T&amp;#x2019;...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3581/version/1

Data mining of protein families using common peptides
Provedor de dados: 17
Autores: Assaf Gottlieb; Uri Weingart; David Horn.
Predicting the function of a protein from its sequence is typically addressed using sequence-similarity. Here we propose a motif-based approach, using supervised motif extraction from protein sequences belonging to one functional family. The resulting deterministic motifs form Common Peptides (CPs) that characterize this family, allow for data mining of its proteins and facilitate further partition of the family into clusters
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2189/version/1

Data Mining of the Coffee Rust Genome
Provedor de dados: 17
Autores: David Octavio  Botero-Rozo; William Giraldo; Alvaro Gaitan; Marco Cristancho; Diego M. Ria&amp;#xf1;o-Pachon; Silvia Restrepo.
The genomes of nine isolates of _Hemileia vastatrix_, the causal agent of coffee leaf rust were sequenced by Illumina and 454. Quality control, cleaning and _de novo_ assemblies of data were performed. Since isolates were obtained from the field and it is not possible to produce axenic cultures of _H. vastatrix_, MEGAN software was used to evaluate contamination levels and to select contigs with fungal similarities. Mitochondrial contigs were identified and annotated by comparing this assembly against the _Puccinia_ genome. Furthermore, two transcriptomes from isolates of _H. vastatrix_ were assembled to complement the genomic data.
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7034/version/1

Data sharing: What about epidemiological cohorts?
Provedor de dados: 17
Autores: Marcel Goldberg; Marie Zins.
General-purpose population-based cohorts can be powerful scientific platforms. The Gazel Cohort Study, a French cohort of 20,000 adults followed-up since more than 20 years, was designed as an open epidemiologic laboratory, hosting more than 40 nested research projects from French and international teams.&amp;#xd;&amp;#xa;Formal rules were elaborated to define the way that the Gazel database can be accessed.&amp;#xd;&amp;#xa;One of the main problems faced by the Gazel team members is scientific recognition of their work, as the large majority of the publications come from external research groups.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Earth &amp; Environment; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5575/version/1

Data submission and curation for caArray, a standard based microarray data repository system
Provedor de dados: 17
Autores: X Bian; J Klemm; A Basu; J Hadfield; R Srinivasa; T Parnell; S Miller; W Mason; D Kokotov; M Duncan; P Duvall; L Gurses; T Boal; L Misquitta; D Swan; R Wysong; A Klink; A Johnson; G Fontenay; J Liu; M Colbert; G Komatsoulis.
caArray is an open-source, open development, web and programmatically accessible array data management system developed at National Cancer Institute. It was developed to support the exchange of array data across the Cancer Biomedical Informatics Grid (caBIG&amp;#x2122;), a collaborative information network that connect scientists and practitioners through a shareable and interoperable infrastructure to share data and knowledge.  caArray adopts a federated model of local installations, in which data deposited are shareable across caBIG&amp;#x2122;.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Comprehensive in annotation yet easy to use has always been a challenge to any data repository system. To alleviate this difficulty, caArray accepts data upload using the...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3138/version/1

Dating the cyanobacterial ancestor of the chloroplast
Provedor de dados: 17
Autores: Luisa Falcon; Susana Magallon; Amanda Castillo.
Cyanobacteria have played a pivotal role in the history of life on Earth being the first organism to carry out oxygenic photosynthesis, which changed atmospheric chemistry and allowed the evolution of Eukarya. Chloroplasts are the cellular organelles of photoautotrophic eukaryotes in which photosynthesis is conducted. Although the initial suggestion from Mereschkowsky (1905) that cyanobacteria are the ancestors of chloroplasts was greeted with skepticism, the idea is now widely accepted. Here we attempt to resolve and date the cyanobacterial ancestry of the chloroplast using phylogenetic analysis and molecular clocks, because until now, the long-standing question of, from which, among the vast diversity of cyanobacteria, did chloroplasts evolve, has not...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3696/version/1

Day-length is central to maintaining consistent seasonal diversity in marine bacterioplankton
Provedor de dados: 17
Autores: Jack A. Gilbert; Paul Somerfield; Ben Temperton; Susan Huse; Ian Joint; Dawn Field.
Marine bacterial diversity is vast, but seasonal variation in diversity is poorly understood. Here we present the longest bacterial diversity time series consisting of monthly (72) samples from the western English Channel over a 6 year period (2003-2008) using 747,494 16SrDNA-V6 amplicon-pyrosequences. Although there were characteristic cycles for each phylum, the overall community cycle was remarkably stable year after year. The majority of taxa were not abundant, although on occasion these rare bacteria could dominate the assemblage. Bacterial diversity peaked at the winter solstice and showed remarkable synchronicity with day-length, which had the best explanatory power compared to a combination of other variables (including temperature and nutrient...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4406/version/1

DDBJ Activities: Contribution to the Research in Information Biology
Provedor de dados: 17
Autores: Jun Mashima; Takehide Kosuge; Toshihisa Okido; Yuichi Kodama; Kazuho Ikeo; Hideaki Sugawara; Yoshio Tateno; Takashi Gojobori.
DDBJ (DNA Data Bank of Japan; &amp;#x22;http://www.ddbj.nig.ac.jp/&amp;#x22;:http://www.ddbj.nig.ac.jp/)started its database activities in 1986. From the beginning, DDBJ has been one of INSDC (International Nucleotide Sequence Database Collaboration; &amp;#x22;http://www.insdc.org/&amp;#x22;:http://www.insdc.org/) that is a tripartite collaboration with EMBL-Bank/EBI and GenBank/NCBI.The total base number of the primary nucleotide sequence data collected and distributed by INSDC exceeded 100 Gbases in August 2005. Since then it took only three years for the total base number to be doubled (200 Gbases). Now, the collaboration is being expanded to Traces (DNA sequence chromatograms) and Short Reads (raw reads data from 454, Solexa, SOLiD etc). DDBJ is also...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3211/version/1

DDBJ Sequence Read Archive / DDBJ Omics Archive
Provedor de dados: 17
Autores: Yuichi Kodama; Satoshi Saruhashi; Eli Kaminuma; Hideaki Sugawara; Toshihisa Takagi; Kousaku Okubo; Yasukazu Nakamura.
Massively parallel sequencers become widespread and produce unprecedented amounts of sequence reads in many biological fields.  DNA Data Bank of Japan (DDBJ) has constructed the international sequence database collaboration (INSDC) together with EBI and NCBI.  In 2008, DDBJ has established the DDBJ Read Archive (DRA) to archive raw output data from the new sequencing platforms.  DRA archives and provides the raw data sets together with the other two INSDC partners the Sequence Read Archive (SRA) at NCBI and the European Sequence Read Archive (ERA) at EBI. These new sequencing platforms are also used to count DNA/RNA molecules instead of microarray experiment because of their higher accuracy.  Since 2004, DDBJ has operated CIBEX as a repository database for...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5085/version/1

Death of human tumor endothelial cells in vitro through a probable calcium-associated mechanism induced by bevacizumab and detected via a novel method
Provedor de dados: 17
Autores: Larry Weisenthal; Haddy Liu; Constance Rueff-Weisenthal.
We isolated three dimensional cell clusters from fresh human solid tumors and also isolated human neoplastic and normal lymphatic cells. Cells were cultured for 96 hours with and without bevacizumab and other agents. At concentrations of bevacizumab which completely removed VEGF from the culture medium, dead microvascular cells were detected through Fast Green/H&amp;#x26;E staining as previously described. These peculiar staining characteristics suggested the involvement of calcium, and this was confirmed through staining with Alizarin red S. Using Alizarin staining as a marker for endothelial cell death permitted the use of public domain image analysis software which resulted in a sensitive and specific system for identifying active pharmaceuticals which...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2010
URL: http://precedings.nature.com/documents/4499/version/1

Debugging Mappings between Biomedical Ontologies: Preliminary Results from the NCBO BioPortal Mapping Repository
Provedor de dados: 17
Autores: Jyotishman Pathak; Christopher Chute.
The ability to provide semantic mappings between multiple large biomedical ontologies is considered as a very important, albeit labor-intensive and error-prone task. To facilitate such a process, several approaches for collaborative ontology mapping building and sharing have been proposed in the recent past. However, despite the improvements in community-wide mappings development, more often the mapping rules are redundant, incoherent, and at times, incorrect. In this paper, we present an approach for identifying such &amp;#x201c;erroneous mappings&amp;#x201d; using Distributed Description Logics. Specifically, we illustrate how logical reasoning can be used to discover semantic inconsistencies caused by erroneous mappings, and provide preliminary results...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3455/version/1

Debugging Mappings between Biomedical Ontologies: Preliminary Results from the NCBO BioPortal Mapping Repository
Provedor de dados: 17
Autores: Jyotishman Pathak; Christopher Chute.
The ability to provide semantic mappings between multiple large biomedical ontologies is considered as a very important, albeit labor-intensive and error-prone task. To facilitate such a process, several approaches for collaborative ontology mapping building and sharing have been proposed in the recent past. However, despite the improvements in community-wide mappings development, more often the mapping rules are redundant, incoherent, and at times, incorrect. In this paper, we present an approach for identifying such &amp;#x201c;erroneous mappings&amp;#x201d; using Distributed Description Logics. Specifically, we illustrate how logical reasoning can be used to discover semantic inconsistencies caused by erroneous mappings, and provide preliminary results...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3456/version/1

Decadal-scale changes in seagrass coverage on the Mississippi barrier islands, northern Gulf of Mexico
Provedor de dados: 17
Autores: Gregory A. Carter; G. Alan Criss; Gabriel A. Blossom; Patrick D. Biber.
Seagrasses provide habitat for a wide variety of aquatic species, and reduce coastal erosion via sediment stabilization. The areal coverage of seagrass beds on the Mississippi barrier islands appears to have declined substantially since the 1960s. However, difficulties in sampling benthic vegetation, differences among previous studies in survey methods, and a lack of data on year-to-year variation in coverage have impeded quantitative study of this decline. Thus, the goal of the present study was to utilize historical remote sensing data to quantitatively determine changes in seagrass (predominantly Halodule wrightii Ascherson) coverage on the Mississippi barrier islands. Analyses were limited to imagery acquired during late summer through autumn, when...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3669/version/1

Deciphering the genome structure and paleohistory of _Theobroma cacao_
Provedor de dados: 17
Autores: Xavier Argout; Jerome Salse; Jean Marc Aury; Gaetan Droc; Jerome Gouzy; Mathilde Allegre; Cristian Chaparro; Thierry Legavre; Mark Guiltinan; Siela Maximova; Michael Abrouk; Florent Murat; Olivier Fouet; Julie Poulain; Manuel Ruiz; Yolande Roguet; Maguy Rodier-Goud; Jose Fernandes Barbosa-Neto; Francois Sabot; Dave Kudrna; Jetty Siva S. Ammiraju; Stephan C. Schuster; John E. Carlson; Erika Sallet; Schiex T.; Anne Dievart; Melissa Kramer; Laura Gelley; Zi Sh; Aur&amp;#xe9;lie B&amp;#xe9;rard; Christopher Viot; Michel Boccara; Ange Marie Risterucci; Valentin Guignon; Xavier Sabau; Michael Axtell; Zhaorong Ma; Yufan Zhang; Spencer Brown; Mickael Bourge; Wolfgang Golser; Xiang Song; Didier Clement; Ronan Rivalan; Mathias Tahi; Joseph Moroh Akaza; Bertrand Pitollat; Karina Gramacho; Ang&amp;#xe9;lique D&amp;#x2019;Hont; Dominique Brunel; Diogenes Infante; Ismael Kebe; Pierre Costet; Rod Wing; W.  Richard McCombie; Emmanuel Guiderdoni; Francis Quetier; Olivier Panaud; Patrick Wincker; Stephanie Sidibe-Bocs; Claire Lanaud.
We sequenced and assembled the genome of _Theobroma cacao_, an economically important tropical fruit tree crop that is the source of chocolate. The assembly corresponds to 76% of the estimated genome size and contains almost all previously described genes, with 82% of them anchored on the 10 _T. cacao_ chromosomes. Analysis of this sequence information highlighted specific expansion of some gene families during evolution, for example flavonoid-related genes. It also provides a major source of candidate genes for _T. cacao_ disease resistance and quality improvement. Based on the inferred paleohistory of the T. cacao genome, we propose an evolutionary scenario whereby the ten _T. cacao_ chromosomes were shaped from an ancestor through eleven chromosome...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Plant Biology; Evolutionary Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4908/version/1

Deciphering the phylogenetic history of neuroserpin orthologs  across metazoans by analysis of synteny and rare genomic characters
Provedor de dados: 17
Autores: Abhishek Kumar; Hermann Ragg.
The superfamily of serine proteinase inhibitors (serpins) is involved in wide arrays of fundamental biological processes such as blood coagulation, complement activation, fibrinolysis, angiogenesis, inflammation and tumor suppression. The average protein size of a serpin family member is 350-400 amino acids, but gene structure varies in terms of number and position of exons and introns. All known serpins can be grouped into 16 clades and 10 orphan sequences. Vertebrate serpins can be conveniently classified into six sub-groups, based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels.&amp;#xd;&amp;#xa;The objective of this study was to elucidate the phylogenetic kinships of serpins involved in...
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2496/version/1

Declarative modelling in the ecological and environmental sciences
Provedor de dados: 17
Autores: Robert Muetzelfeldt.
Most simulation models in ecological and environmental research are implemented as computer programs in a conventional programming language.   This brief paper argues for a radically different approach, based on the representation of the model structure, relationships and equations in a declarative format (e.g. XML).   Simulation code can then be generated from this, but in addition the model can be displayed and processed in a wide range of useful ways, greatly increasing the efficiency and effectiveness of the modelling process.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/17/version/1

Decoding Sequence Classification Models for Acquiring  New Biological Insights
Provedor de dados: 17
Autores: Ulrich Bodenhofer; Andreas Kothmeier; Ingrid G. Abfalter; Carsten C. Mahrenholz; Sepp Hochreiter.
Classifying biological sequences is one of the most important tasks in computational biology. In the last decade, support vector machines (SVMs) in combination with sequence kernels have emerged as a de-facto standard. These methods are theoretically well-founded, reliable, and provide high-accuracy solutions at low computational cost. However, obtaining a highly accurate classifier is rarely the end of the story in many practical situations. Instead, one often aims to acquire biological knowledge about the principles underlying a given classification task. SVMs with traditional sequence kernels do not offer a straightforward way of accessing this knowledge.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In this contribution, we propose a new approach to analyzing...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4708/version/1

Decoding the Design Principles of Amino Acids and the Chemical Logic of Protein Sequences
Provedor de dados: 17
Autores: B. Jayaram.
That only 20 amino acids occur naturally accounting for the structural and functional diversity of proteins remains a mystery. We show here that this is a consequence of the action of a symmetry group, identify the presence of hydrogen bond donor groups, presence of sp3 hybridized [gamma] carbons, absence of [delta] carbons and linearity as properties central to side chain design and quantify the chemical logic of protein sequences.
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2135/version/1

Decomposing CO2 emissions data into a pair of logistic growth pulses
Provedor de dados: 17
Autores: Gleb G. Alexandrov.
Numerous scenarios of emissions growth presume that it can not grow infinitely: there are certain limits that may not or must not be exceeded. Applying the theory of pulsing logistic growth, I detected two pulses of logistic growth. This led me to the conclusion that constructing a scenario of emissions growth one should pay attention to the fact that limits to their growth do not remain constant.
Tipo: Poster
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4306/version/1

Decrease in gyrase A protein expression in _E. coli_ cells inhibited by antisense ribozymes
Provedor de dados: 17
Autores: Shilpakala Sainath Rao; Malathi Raghunathan.
RNase P complexed with external guide sequence (EGS) represents a novel nucleic-acid-based gene interference approach to modulate gene expression. Nucleic acid-based gene interference technologies represent promising strategies for specific inhibition of mRNA sequences of choice. Recently, small interfering RNAs have been implicated in inducing endogenous RNase of the RNA-induced silencing complex in the RNA interference pathway to inhibit gene expression and growth of several human viruses. We report down regulation of protein expression of _E. coli_ gyrase A, an essential gene for DNA supercoiling and antibiotic susceptibility in BL21 (DE3) strain of _E. coli_, using Ribonuclease P based external guide sequence (EGS) technique. EGS directed against...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2408/version/1

Decrease of vanillin sucrose intake by victorious and defeated mice: development of anhedonia?
Provedor de dados: 17
Autores: Natalia N. Kudryavtseva; Natalia P. Bondar; Irina L. Kovalenko; Damira F. Avgustinovich.
Hedonic reactions to various rewards play a key role in various forms of motivated behavior. The influence of repeated experience of social victories or defeats in daily agonistic interactions between male mice on voluntary consumption of vanillin sucrose solution used as hedonic reinforcer was studied. Intake of vanillin sucrose solution was shown to decrease in the winners and losers exposed to social confrontations as compared with the controls. Three days of deprivation failed to restore the intake of vanillin sucrose solution to the control level in the losers and did so in the winners. The results obtained imply that similar reaction of animals to a hedonic non-drug reinforcer may have different motivational origin depending on positive or negative...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/988/version/1

Defective FoxP3+ Treg cell differentiation in the gut of Type 1 Diabetic patients
Provedor de dados: 17
Autores: Ester Badami; Chiara Sorini; Margherita Coccia; Laura Molteni; Andrea Mario Bolla; Marina Scavini; Alberto Mariani; Emanuele Bosi; Marika Falcone.
Environmental factors that act at the intestinal level such as diet, drugs, and microflora have a high impact on the pathogenesis of autoimmune Type 1 Diabetes (T1D), but it is still unclear how the gut milieu affects autoimmunity outside the intestine. Here we show that peripheral FoxP3+ Treg cell differentiation, a mechanism that takes place in the gut and is crucial to maintain systemic immune tolerance, is impaired in T1D patients. These results provide the first evidence that gut mucosa alteration could predispose to autoimmune T1D by affecting systemic immune regulation.
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4417/version/1

Deficiency of interleukin-1 receptor antagonist causes spontaneous femoral artery aneurysms
Provedor de dados: 17
Autores: Kikuo Isoda; Tomiharu Niida; Harumi Kondo; Fumikaka Ohsuzu.
Interleukin (IL) -1, a proinflammatory cytokine, increases in aneurysm, and the IL-1 receptor antagonist (IL-1Ra) modulates IL-1 activity endogenously. We show here that IL-1Ra-deficiency in hematopoietic cells disrupts immune system homeostasis and causes spontaneous femoral artery aneurysms in mice lacking interventions such as drugs or surgery. Thus, IL-1Ra-deficient mice provide easy observations with age and diminish mortality that typically follows surgical procedures. Furthermore, since IL-1Ra-deficient mice contain the entire spectrum of lesions observed during inflammatory aneurysm, this mouse model likely will provide numerous opportunities to study the pathogenesis and therapy of inflammatory aneurysm.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2826/version/1

Delayed-Type hypersensitivity to latex: Computational prediction of MHC class II epitopes on latex allergens
Provedor de dados: 17
Autores: Bell R. Eapen.
Delayed type hypersensitivity to natural rubber latex is rare compared to IgE mediated immediate reactions. Binding of allergens to MHC Class II is a crucial step in the presentation of antigens to CD4+ T Cells responsible for delayed reactions. Computational prediction of MHC class II epitopes on thirteen known latex allergens using SMM-align method revealed strong binding with several alleles. This shows that latex allergens are capable of initiating delayed type hypersensitivity in susceptible individuals.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2931/version/1

Deletion of the rat trpc4 gene and its influence on motivated responding for natural reward
Provedor de dados: 17
Autores: William D. Klipec; Bridget Deeney; Claire  Williamson; Kami  Wenzel; Phuong Nguyen; Eric Ostertag; Donald C. Cooper.
TRPC4 ion channels are expressed extensively in corticolimbic brain regions and a subpopulation of midbrain dopamine neurons. TRPC4 knockout (KO) rats show reduced sociability and social exploration, but show no differences in simple and complex strategic learning compared to normal wild type (WT) rats. Using water reward, we found no differences between TRPC4-KO and WT rats in the break point on a progressive ratio schedule of reinforcement. Although deletion of the trpc4 gene alters social interaction/anxiety it does not appear to affect motivation for natural rewards. Current experiments are underway testing the role of trpc4 gene deletion on cocaine reward (see www.neuro-cloud.net/nature-precedings/klipec3 for updates and collaborations).
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/7109/version/1

Deletion of the trpc4 gene and its role in simple and complex strategic learning
Provedor de dados: 17
Autores: William  D. Klipec; Phuong  Nguyen; Bridget  Deeney; Claire  Williamson; Kami  Wenzel; Jessica  Stumme; Marissa  Collins; Abby  Drish; Laura  Swenson; Eric  Ostertag; Donald C. Cooper.
The TRPC4 ion channel is expressed extensively in corticolimbic and a subpopulation of midbrain dopamine neurons. While TRPC4 knockout (KO) rats exhibit reduced sociability and social exploration, little is known about the role of TRPC4 in motivation and learning. To identify a function for TRPC4 channels in learning processes &amp;#xa0;we tested TRPC4 KO and normal&amp;#xa0;wild type (WT) rats. TRPC4 KO and WT rats exhibited no differences in Y-&amp;#xad;maze&amp;#xa0;learning or simple discrimination learning. Furthermore, on a more complex serial reversal shift task designed &amp;#xa0;to assess strategic learning where the reward and non-&amp;#xad;reward cues were repeatedly reversed between training sessions both TRPC4 KO and WT rats &amp;#xa0;...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6929/version/1

Delving into Vertebrate Serpins for Understanding their Evolution
Provedor de dados: 17
Autores: Abhishek Kumar.
The superfamily of serine proteinase inhibitors (serpins) is involved in an array of fundamental biological processes such as blood coagulation, cell differentiation, cell migration, complement activation, embryo implantation, fibrinolysis, angiogenesis, and inflammation, and tumor suppression. Vertebrate serpins can be conveniently classified into six sub-groups, based on three independent biological features - genomic organization, diagnostic amino acid sites and rare indels. The present vertebrate serpins are derived from an original serpin most probably by intron insertion and we are trying to reconstruct the phylogeny of vertebrate serpin and looking for the reconstruction of original vertebrate gene(s). We started with fish genomes and characterized...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3050/version/1

Demographic vital rates and population growth:  rethinking the relationship in a harvested elk population
Provedor de dados: 17
Autores: Jonathan M. Conard; Philip S. Gipson.
Understanding the nature of the relationship between demographic vital rates and the rate of population change (&amp;#x3bb;) is important for determining effective strategies for population management and conservation. We examined the relative impacts of various demographic vital rates on &amp;#x3bb; within the range of temporal vital rate variability observed in a harvested population to test the hypotheses that adult survival rates in ungulates are relatively invariant when compared to other vital rates and that variability in calf survival has a greater influence on rates of population change than adult survival. Vital rates were estimated for an elk (_Cervus elaphus_) population at Fort Riley, Kansas from October 2003 &amp;#x2013; February 2007. The...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3609/version/1

Dendritic spike induction of postsynaptic cerebellar LTP
Provedor de dados: 17
Autores: Marco Canepari; Kaspar E. Vogt.
The architecture of parallel fiber (PF) axons contacting cerebellar Purkinje neurons (PNs) retains spatial information over long distances. PF synapses can trigger local dendritic calcium spikes, but whether and how this calcium signal leads to plastic changes that decode the PF input organization is unknown. By combining voltage and calcium imaging, we show that PF-elicited calcium signals, mediated by voltage-gated calcium channels, increase non-linearly during high-frequency bursts of electrically constant calcium spikes because they locally and transiently saturate the endogenous buffer. We demonstrate that these non-linear calcium signals, independently of NMDA or metabotropic glutamate receptor activation, can induce PF long-term potentiation (LTP)....
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2020/version/1

Denitrification Hotspots and N20 Flux in Fluvial Systems
Provedor de dados: 17
Autores: Julia Hyman; Arthur Gold; Kelly Addy; Ken Forshay; Paul Mayer; Peter Groffman.
a)&amp;#x9;Background/Question/Methods&amp;#xd;&amp;#xa;Watersheds have a profound capacity to retain and remove nitrogen (N) inputs before entering coastal waters thereby minimizing eutrophication and hypoxia in estuarine waters. Research suggests that much of this N cycling occurs within aquatic ecosystems, e.g., lakes, streams and wetlands, which may become &amp;#x201c;hotspots&amp;#x201d; of nitrous oxide (N2O) production. We examined the effects of woody debris on nitrate removal and denitrification rates in streams of different N enrichment levels. Three different standardized substrates (fresh wood blocks, bundles of naturally occurring streambed wood, and clay&amp;#x2010;fired blocks) that were expected to vary in their pool of labile carbon were...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5284/version/1

Density alteration in non-physiological cells
Provedor de dados: 17
Autores: Yu Liu; Yuan-Chang Zhu; Bin-Bin Wu; Xiao-Hua Wu; Fei-Fei Lan; Jian-Ge Wei; Ming Wang; Hai-Cheng Li; Lin-Na Li; Ju-Xiang Li; Jia Fei.
In the present study an important phenomenon of cells was discovered: the change of intracellular density in cell&amp;#x27;s response to drug and environmental factors. For convenience, this phenomenon is named as &amp;#x22;density alteration in non-physiological cells&amp;#x22; ( DANCE). DANCE was determined by discontinuous sucrose gradient centrifugation (DSGC), in which cells were separated into several bands. The number and position of the bands in DSGC varied with the change of cell culture conditions, drugs, and physical process, indicating that cell&amp;#x27;s response to these factors was associated with alteration of intracellular density. Our results showed that the bands of cells were molecularly different from each other, such as the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6541/version/1

Density Functional Study on the Stability and Reactivity of Pt(100) and Pt(111) Surfaces Modified by Ni Atoms
Provedor de dados: 17
Autores: Mar&amp;#xed;a L&amp;#xf3;pez; Eduardo Castro.
DFT study on the the stability and reactivity  of  Pt(100) and Pt(111) surfaces modified by nickel UPD monolayer deposition  have been carried out. We used the binding energy calculation of bimetallic structures  versus the cohesion energy of  the bulk  adsorbate  to quantify the underpotential shift (&amp;#x394;Eupd) to determine the stability of the bimetallic systems. The reactivity of the clean and modified surface was analized by energy levels of the highest occupied molecular orbital (HOMO), softness and local softness. We concluded that the stability of  Pt(100)25Ni9 and Pt(111)25Ni10 bimetallic structures cannot be explained by excess of the metal- substrate binding energy but  the instability can be explained by structural effects.  We found that...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3909/version/1

Density functional theory calculation of interaction between bisphosphate and farnesyl pyrophosphate synthase
Provedor de dados: 17
Autores: Kazuki Ohno; Kenichi Mori; Yohsuke Hagiwara; Masaya Orita; Makoto Takeuchi.
Bisphosphonates (BPs) are the most widely used and effective treatment for osteoporosis and Pagets disease of the bone. To date, a number of BPs-namely alendronate, risedronate, and minodronate-have been launched to market. Nitrogen-BPs (N-BPs) act by inhibiting the enzyme farnesyl pyrophosphate synthase (FPPS), and several crystal structures of complexes between FPPS and N-BPs have been identified. Understanding the physical basis of the binding between proteins and small molecules is an important goal in both medicinal chemistry and structural biology. Here, we conducted density functional theory calculations for BPs and their surrounding residues and were able to successfully reproduce experimental results qualitatively. In addition, we found that both...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4867/version/1

Dentate Gyrus
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Rachel A. Dalley; Lydia L. Ng; Angela L. Guillozet-Bongaarts.
This report contains a gene expression summary of the dentate gyrus (DG), derived from the Allen Brain Atlas (ABA) _in situ_ hybridization mouse data set. The structure&amp;#x27;s location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the dentate gyrus were compared to the values of the macro/parent-structure, in this case the hippocampal region, for the purpose of extracting regionally selective gene expression data. The genes with the highest ranking selectivity ratios were manually curated and verified. 50 genes were then selected and compiled for expression characterization. The experimental data for each gene may be...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2095/version/1

Depolarization increases cellular light transmission
Provedor de dados: 17
Autores: Minoru Tomita; Norihiro  Suzuki; Yutaka Tomita; Haruki Toriumi; Takashi Osada; Miyuki Unekawa; Jemal Tatarishvili.
Application of optical methods to human brain tissue in vivo, e.g., measuring oxyhemoglobin and deoxyhemoglobin concentration changes with near-infrared spectroscopy (NIRS), requires the a priori assumption that background optical properties remain unchanged during measurements1,2. However, fundamental knowledge about light scattering by brain cells per se remains sparse; many factors influence light transmission changes through living brain tissue, bringing into question what is being measured. We have observed slow wave-ring spreads of light transmission changes on the rat cerebral cortex during potassium-induced cortical spreading depression (CSD) and ascribed them to squeezing-out of blood from capillaries by swollen brain cells3,4. However, in rat...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2001/version/1

Description of a method for localizing swarming mosquitoes and other insects in 3D space with visualizations
Provedor de dados: 17
Autores: Nicholas C. Manoukis.
Male mosquitoes swarm to find mates, but the characteristics of these swarms have not yet been quantitatively analyzed in the field. This paper describes a simple method used recently to localize individual Anopheles gambiae in a swarm via stereoscopic image analysis of video footage swarms recorded in Doneguebougou, Mali. The methods described here represent a streamlining of simple triangulation for insect localization in the hope that other researchers will be able to apply the method for studying fundamental questions about flying insects or other taxa.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2599/version/1

Description of variation of genlculate&amp;#x27;s features of _Phyllodiaptomustunguidus_ shen et Tai and sex-linked inheritance of Calanoida in freshwater
Provedor de dados: 17
Autores: Sheng-Xing Long; Xiao-Ming Gou; Pin-Hua Xia; Qi-Fei Ren; San Wan; Chuan Chen.
In the present paper, variation of genlculate&amp;#x27;s features of _Phyllodiaptomustunguidus_ shen et Tai of Calanoida are described.The authors find that the right first antenna of female species has changed into genlculate and first antenna of male species changed into genlculate, which can be explained by X-sex-linked inheritance. This isn&amp;#x27;t a disease but a genetic characteristic that is better for the living of the species.
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/3003/version/1

Desiderata for an ontology of diseases for the annotation of biological datasets.
Provedor de dados: 17
Autores: Olivier Bodenreider; Anita Burgun.
There is a plethora of disease ontologies available, all potentially useful for the annotation of biological datasets. We define seven desirable features for such ontologies and examine whether or not these features are supported by eleven disease ontologies. The four ontologies most closely aligned with our desiderata are Disease Ontology, SNOMED CT, NCI thesaurus and UMLS.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3531/version/1

Design and construction of a new Drosophila species, D.synthetica, by synthetic regulatory evolution
Provedor de dados: 17
Autores: Eduardo Moreno.
Here, I merge the principles of synthetic biology^1,2^ and regulatory evolution^3-11^ to create a new species^12-15^ with a minimal set of known elements. Using preexisting transgenes and recessive mutations of Drosophila melanogaster, a transgenic population arises with small eyes and a different venation pattern that fulfills the criteria of a new species according to Mayr&amp;#x27;s &amp;#x22;Biological Species Concept&amp;#x22;^7,10^. The genetic circuit entails the loss of a non-essential transcription factor and the introduction of cryptic enhancers. Subsequent activation of those enhancers causes hybrid lethality. The transition from &amp;#x22;transgenic organisms&amp;#x22; towards &amp;#x22;synthetic species&amp;#x22;, such as Drosophila...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6511/version/1

Design and development of a Europe-wide case specific monitoring method
Provedor de dados: 17
Autores: Angelika  Ziegler; Wenke  M&amp;#xf6;nkemeyer; Ralf  Wilhelm; Kerstin Schmidt.
Directive 2001/18 EC demands the cultivation of genetically modified organisms (GMO) to be accompanied by post-market environmental monitoring (PMEM). It is composed of a general surveillance for unanticipated adverse effects and case specific monitoring (CSM), which is set up to reduce substantial uncertainties in relevant risk scenarios identified in the environmental risk assessment. PMEM should also allow early identification of potential long-term effects of cultivating GMOs. It should facilitate decisions in risk management.&amp;#xd;&amp;#xa;In this project, a method for a Europe-wide CSM was to be developed. Starting with critical questions from ERA, exposure scenarios (first for non target organisms, later for all other partitions of the ERA) were...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4472/version/1

Design and Implementation of the UniProt Website
Provedor de dados: 17
Autores: Eric Jain; Isabelle Phan; Severine Duvaud; Elisabeth Gasteiger; Nicole Redaschi; Maria J. Martin; Peter McGarvey; Amos Bairoch.
The UniProt consortium is the main provider of protein sequence and annotation data for much of the life sciences community. The &amp;#x22;www.uniprot.org&amp;#x22;:http://www.uniprot.org website is the primary access point to this data and to documentation and basic tools for the data. This paper discusses the design and implementation of the new website, which was released in July 2008, and shows how it improves data access for users with different levels of experience, as well as to machines for programmatic access.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2611/version/1

Design of a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico
Provedor de dados: 17
Autores: Alexander V. Spirov; David M. Holloway.
A new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, with new crossover operators especially designed for these purposes. The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. The effectiveness of the approach is demonstrated on a series of benchmark tests.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3913/version/1

Design of a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico
Provedor de dados: 17
Autores: Alexander V. Spirov; David M. Holloway.
A new approach to design a dynamic model of genes with multiple autonomous regulatory modules by evolution in silico is proposed. The approach is based on Genetic Algorithms, with new crossover operators especially designed for these purposes. The approach exploits the subbasin-portal architecture of the fitness functions suitable for this kind of evolutionary modeling. The effectiveness of the approach is demonstrated on a series of benchmark tests.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/3913/version/2

Design of carbon dioxide storage
Provedor de dados: 17
Autores: Martin J. Blunt.
Carbon capture and storage (CCS) &amp;#x2013; the collection of carbon dioxide (CO~2~) from industrial sources and its injection underground &amp;#x2013; is an important technology to reduce CO~2~ emissions to the atmosphere, mitigating climate change.  The North Sea, with mature hydrocarbon fields and saline aquifers offers an attractive storage location for CO~2~ produced by the UK&amp;#x2019;s gas and coal-fired power plants.  The principal concern with CCS is to ensure that the CO~2~ does not leak into the oceans or atmosphere over hundreds or thousands of years.  We propose a storage strategy where CO~2~ and brine are injected together followed by brine injection alone.  We predict that using this technique around 95% of the CO~2~ can be rendered...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2628/version/1

Design of RNAi reagents for invertebrate model organisms and human disease vectors
Provedor de dados: 17
Autores: Thomas Horn; Michael Boutros.
RNAi has become an important tool to silence gene expression in a variety of organisms, in particular when classical genetic methods are missing. However, application of this method in functional studies has raised new challenges in the design of RNAi reagents in order to minimize false positive and false negative results. Since the performance of reagents can be rarely validated on a genome-wide scale, improved computational methods are required that consider experimentally derived design parameters. Here, we describe computational methods for the design of RNAi reagents for invertebrate model organisms and human disease vectors, such as Anopheles. We describe procedures on how to design short and long double-stranded RNAs for single genes, and evaluate...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6665/version/1

Design of selective peptide antibiotics by using the sequence moment concept
Provedor de dados: 17
Autores: Davor Juretic; Nada Ilic; Damir Vukicevic; Nikolinka Antcheva; Alessandro Tossi.
New antibiotics against multidrug-resistant bacteria are urgently needed, but rapid acquisition of resistance limits their usefulness. Endogenous antimicrobial peptides (AMPs) with moderate selectivity, but multimodal mechanism of action, have remained effective against bacteria for millions of years. Their therapeutic application, however, requires optimizing the balance between antibacterial activity and selectivity, so that rational design methods for increasing selectivity are highly desirable. We have created training (n=36) and testing (n=37) sets from frog-derived AMPs with determined therapeutic index (TI). The &amp;#x27;sequence moments&amp;#x27; concept then enabled us to find a one-parameter linear model resulting in a good correlation between...
Tipo: Manuscript
Palavras-chave: Biotechnology; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3068/version/1

Design of selective peptide antibiotics by using the sequence moment concept
Provedor de dados: 17
Autores: Davor Juretic; Nada Ilic; Damir Vukicevic; Nikolinka Antcheva; Alessandro Tossi.
Withdrawn&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Incomplete data
Tipo: Manuscript
Palavras-chave: Biotechnology; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3068/version/2

Designing L-Systems for making three and six open reading frames from the leading strand of a single DNA molecule
Provedor de dados: 17
Autores: Arunava Goswami; Rajneesh Singh; Pabitra Choudhury; Sk. Sarif Hassan Hassan.
Current molecular biology dogma (except alternative splicing) suggests that leading strand of DNA produces mRNA and usually the leading strand gives one ORF (ORF) among the available six ORFs. We attempted to break this rule where three and six ORFs from the leading strand will be formed by designing L-Systems, originally proposed to study symmetry of biological world. We thought this would revolutionize the world of synthetic biology. While doing so, we found L-System containing A&amp;#x2192;T, T&amp;#x2192;G, C&amp;#x2192;A, and G&amp;#x2192;C, i.e., single nucleotide production rule will stop growing after one nucleotide. L-System containing either (a) A&amp;#x2192;TG, T&amp;#x2192;GC, C&amp;#x2192;GA, G&amp;#x2192;TC or (b) A&amp;#x2192;CTG,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4844/version/1

Designing nature reserves in the face of uncertainty
Provedor de dados: 17
Autores: Michael McCarthy; Colin Thompson; Hugh Possingham.
Conservation reserves are one of the most important tools for managing biodiversity. Ever since Diamond, based on theory of island biogeography, proposed that a single large reserve was preferable to several small reserves of the same total area, there has been an enduring debate about the veracity of his assertion. The so-called SLOSS debate - should we have a Single Large reserve Or Several Small reserves - features in every conservation text book and is central to conservation theory. Population dynamic models suggest that the design that minimizes the risk of extinction of species is case-specific, with the optimal number of reserves ranging between one and very many. Uncertainty is pervasive in ecology, but, the previous analyses of the SLOSS debate...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3387/version/1

Designing Novel Lead Molecules For Human Ribosomal Protein S6 Kinase Beta-1 Involved In Cancers: Ligand Based Virtual Screening Approach
Provedor de dados: 17
Autores: Nainaru Ganesh; Dibyabhaba Pradhan; Amineni Umamaheswari.
Protein kinases are clinically relevant and attractive drug targets for most of the cancerous diseases. Ribosomal protein s6 kinase (P70s6 kinase) is a mitogen activated Ser/Thr protein kinase, essential for cell growth, G1 cell cycle progression and cell survival. Human P70s6 kinase is involved in different signaling pathways and phosphorylates the downstream S6 protein of the 40S ribosomal subunit there by controlling the translational activity. Over expression of human P70s6 or rapid amplification of gene (RPS6KB1) leads to rapid cell proliferation causing cancer in various organs of humans like colon, breast, ovary, etc. The over expression is principally due to activation of some phosphorylating sites or ATP binding sites in the domain regions. In the...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4906/version/1

Designing Potent Inhibitors Of Human p38&amp;#x3b3; For Effective Breast Cancer Therapy
Provedor de dados: 17
Autores: Natarajan  Pradeep; Dibyabhaba  Pradhan; Amineni Umamaheswari.
Oncogenic constitutive enzyme human p38&amp;#x3b3; is a serine/threonine protein kinase, activated through phosphorylation by environmental stress and pro-inflammatory cytokines responses. Breast cancer, hepatoma, colon cancer, atherosclerotic lesion (coronary artery lesion / hardening of artery), hypertension and inflammations are some of the diseases caused by human p38&amp;#x3b3; due to over expression. Over expression of the protein in turn induces anti-apoptosis and inflammatory responses, increased malignant transformation and cell differentiation. Thus, designing potent inhibitors against p38&amp;#x3b3; would be highly practicable for development of novel means of breast cancer therapeutics.  Extensive preclinical data and proteomic analysis support...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4904/version/1

Desynchronization of pathological low-frequency brain activity by the hypnotic drug zolpidem.
Provedor de dados: 17
Autores: Stephen D. Hall; Naoki Yamawaki; Alison E. Fisher; Ralf P. Clauss; Gavin L. Woodhall; Ian M. Stanford.
Reports of the beneficial effects of the hypnotic imidazopyridine, zolpidem, described in persistent vegetative state^1, 2^ have been replicated recently in brain-injured and cognitively impaired patients^3-7^. Previous single photon emission computed tomography (SPECT) studies have suggested that sub-sedative doses of zolpidem increased regional cerebral perfusion in affected areas^5, 8^, implying enhanced neuronal metabolic activity; which has led to speculation that zolpidem &amp;#x27;reawakens&amp;#x27; functionally dormant cortex. However, a neuronal mechanism by which this hypnotic drug affords benefits to brain injured patients has yet to be demonstrated. Here, we report the action of sub-sedative doses of zolpidem on neuronal network oscillatory...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/1966/version/1

Detecting differential usage of exons from RNA-Seq data
Provedor de dados: 17
Autores: Simon Anders; Alejandro Reyes; Wolfgang Huber.
RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires sensitive and specific detection of differential isoform abundance in comparisons between conditions, cell types or tissues. We present DEXSeq, a statistical method to test for differential exon usage in RNA-Seq data. DEXSeq employs generalized linear models and offers reliable control of false discoveries by taking biological variation into account. DEXSeq detects genes, and in many cases specific exons, that are subject to differential exon usage with high sensitivity. We demonstrate the versatility of DEXSeq by applying it to several data sets. The method facilitates the study of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6837/version/2

Detecting differential usage of exons from RNA-Seq data
Provedor de dados: 17
Autores: Simon Anders; Alejandro Reyes; Wolfgang Huber.
RNA-Seq is a powerful tool for the study of alternative splicing and other forms of alternative isoform expression. Understanding the regulation of these processes requires comparisons between treatments, tissues or conditions. For the analysis of such experiments, we present _DEXSeq_, a statistical method to test for differential exon usage in RNA-Seq data. _DEXSeq_ employs generalized linear models and offers good detection power and reliable control of false discoveries by taking biological variation into account. An implementation is available as an R/Bioconductor package.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6837/version/1

Detection of BCR-ABL kinase domain mutations in CD34+ cells from newly diagnosed chronic phase CML patients and their association with imatinib resistance
Provedor de dados: 17
Autores: Zafar Iqbal; Ijaz Shah; Aamer Aleem; Mubashar Naqvi; Ammara Tahir; Tariq Gill; Abid Taj; Abdul Qayyum; Najeeb ur-Rehman; Muhammad Ferhan; Mudassar Iqbal; Muhammad Khalid; Weng Qin; Ahmad Khalid; Mahwish Khan; Shahid Baig; Abid Jamil; Tanveer Akhtar; Muhammad Abbad; Riaz ul-Haq.
BCR-ABL kinase domain (KD) mutations, the most common cause of imatinib resistance, are infrequently detected in newly diagnosed chronic-phase chronic myeloid leukemia (CP-CML) patients. Recent studies indicate pre-existing mutations (PEMs) can be detected in a higher percentage of CML patients using CD34+ stem/progenitor cells, and these mutations may correlate with imatinib resistance. We investigated KD mutations in CD34+ stem cells from 100 CP-CML patients by multiplex ASO-PCR and sequencing ASO-PCR products at the time of diagnosis. PEMs were detected in 32/100 patients and included F311L, M351T, and T315I. After a median follow-up of 30 months (range 8-48), all patients with PEMs exhibited imatinib resistance. Of 68 patients without PEMs, 24...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6645/version/1

Detection of genetic diversity among Indian strains of _Xanthomonas campestris_ pv. _mangiferaeindicae_ using PCR-RAPD
Provedor de dados: 17
Autores: Ram Kishun; Vijai Kumar Gupta.
The randomly amplified polymorphic DNA (RAPD) technique was used to investigate the genetic diversity in 6 strains of _Xanthomonas campestris_ pv. _mangiferaeindicae_ (_Xcmi_), the causal pathogen of mango bacterial canker disease (MBCD). The RAPD analysis was also intended to identify molecular markers, specific to the species to develop PCR-based markers for detection of _Xcmi_ in mango field and planting materials. Twenty RAPD primers (CP 1-CP 20) were evaluated to establish molecular characters and genetic variability in the genome of _Xcmi_. Among these, only 4 were found efficient for development of reproducible banding pattern. It has been observed that the largest and smallest amplified RAPD products were of 2.036 and 0.201 kbp. A total of 136...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2403/version/1

Detection of Metabolites by Proton Ex Vivo NMR, in Vivo MR Spectroscopy Peaks and Tissue Content Analysis: Biochemical-Magnetic Resonance Correlation: Preliminary Results
Provedor de dados: 17
Autores: Rakesh Sharma; Madan Rehani; Arun Agrawala.
*Aim*: Metabolite concentrations by in vivo magnetic resonance spectroscopy and ex vivo NMR spectroscopy were compared with excised normal human tissue relaxation times and tissue homogenate contents.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Hypothesis*: Biochemical analysis combined with NMR and MR spectroscopy defines better tissue analysis.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Materials and Methods*: Metabolites were measured using peak area, amplitude and molecular weights of metabolites in the reference solutions. In normal brain and heart autopsy, muscle and liver biopsy tissue ex vivo NMR peaks and spin-lattice (T1) and spin-spin (T2) relaxation times, were compared with diseased tissue NMR data in meningioma brain, myocardial infarct heart,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4121/version/1

Detection of MicroRNAs in Dried Serum Blots
Provedor de dados: 17
Autores: Santosh K. Patnaik; Reema Mallick; Sai Yendamuri.
MicroRNAs are short RNAs which can be utilized as biomarkers for a variety of conditions. They are detectable in serum, and changes in the levels of circulating microRNAs have been associated with different diseases. We tested for the presence of microRNAs in serum that is dried on paper and stored unrefrigerated instead of being kept frozen. MicroRNAs were readily detectable in such blots, and their detectability was improved by using paper made of cellulose instead of glass fiber, and by re-hydrating dried blots with Trizol&amp;#x2122; instead of water, phosphate-buffered saline, or guanidine hydrochloride before RNA extraction. MicroRNA preservation was not diminished by drying of blots at 37, 45 or 60 &amp;#xba;C instead of room temperature or by...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4785/version/1

Detection of Nonlinear Effects in Gene Expression Pathways
Provedor de dados: 17
Autores: Andreas Mayr; Djork-Arne Clevert; Sepp Hochreiter.
One of the main topics in systems biology is to model genetic pathways. Genes of a pathway, which show linear dependencies of their expression values, are easy to identify to belong to the pathway. However, if feedback loops or signal cascades are present, gene expression values of pathway genes can be nonlinearly dependent on the expression values of other genes in the pathway. In this situation such genes are hard to detect as belonging to the pathway because nonlinearity and noise must be distinguished.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We propose an algorithm to infer nonlinear network elements in pathways from microarray data. Our model assumes, that gene expression values, belonging to one pathway, are mainly driven by one single latent factor. We...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4715/version/1

Detection of Stomach Cancer by TV-Endoscope Colour Enhancement Image Processing
Provedor de dados: 17
Autores: Masaki Miyamoto.
Using modern TV-endoscope equipment, we have experimented image processing in several ways. This time, we designed new image processing unit called &amp;#x201c;Color Subtracted Enhancement  image processing unit&amp;#x201d;. This unit&amp;#x3000;was made by combining the RGB-Subtraction&amp;#x3000;image processing device with the color enhancement image processing device. The&amp;#x3000;RGB-subtraction device is an analogue unit  that&amp;#x3000;enables us to remove the visible red, green and blue peaks from the image. We can subtract the images R-G, R-B, G-R, B-R, B-G simply by changing the switches. The color enhancement device (developed  by Olympus optical corporation inc.) is a digital processing unit that lets us reinforce any of these colors. This...
Tipo: Poster
Palavras-chave: Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/2255/version/1

Detection of substrate binding motifs for morphine biosynthetic pathway intermediates in novel wound inducible (R,S)-reticuline 7-O-methyltransferase of Papaver somniferum
Provedor de dados: 17
Autores: Sonal Mishra; Abha Meena; Sema Singh; Dharmendra Kumar Yadav; Feroz  Khan; Rakesh K. Shukla.
The benzylisoquinoline alkaloids (BIA) comprise a large and diverse group of nitrogen-containing secondary metabolites with about 2500 compounds identified in plants. BIA biosynthesis begins with the condensation of the tyrosine derived precursors dopamine and p-hydroxyphenylacetaldehyde to (S)-norcoclaurine. Subsequent regiospecific O- and N-methylations and aromatic ring hydroxylation lead to (S)-reticuline, which is the central intermediate for almost all BIAs. For morphinan alkaloid biosynthesis, (S)-reticuline undergoes an inversion of stereochemistry to (R)-reticuline, followed by C-C phenol coupling catalyzed by a unique cytochrome P450-dependent monooxygenase to yield salutaridine. The cDNA sequence of enzymes leading to (S)-reticuline, as well as...
Tipo: Poster
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5790/version/1

Detection of Sugarcane Yellow Leaf Luteovirus of India
Provedor de dados: 17
Autores: Rajarshi K. Gaur; G.P Rao; Axel  Lehrer.
A luteovirus was found associated with midrib yellowing symptoms of sugarcane in India. The virus was earlier identified as sugarcane yellow leaf virus (SCYLV) on the basis of particle morphology and serological relationships. In this study, we attempted molecular characterization of an Indian isolate of SCYLV through reverse trascriptase-polymerase chain reaction (RT-PCR). Comparison showed that the deduced amino acid sequence share 98% homology with an isolate from Texas (cultivar CC85-964) and 100% homology with corresponding sequences of an Australian isolate of SCYLV (found in cultivar CP 65-357). Phylogenetic analysis also suggests that the coat protein of the SCYLV genome possesses different taxonomic affinities with other members of the family...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3388/version/1

Detection strategies for non-authorized GMO products on the European market
Provedor de dados: 17
Autores: Patrick G&amp;#xfc;rtler; Esther  Meissner; Ulrich  Busch.
Import and planting of biotech crops is strictly regulated in Europe. In order to observe these strict regulations, an efficient surveillance of the European market is required. In Europe, data on authorised biotech crops from foreign countries are on hand, however, only scarce information on non-authorised biotech crops is available. Experience of the last years has shown that non-authorized biotech crops (e.g. biotech-papaya, Bt10-maize, LL601-rice and Bt63-rice) were detected on the European market. The Bavarian Health and Food Safety Authority is responsible for the detection of illegal imports and for labelling control of Food and Feed in Bavaria (Germany). The quantitative real-time PCR is the method of choice for the detection of genetic...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4444/version/1

Detection systems cross reacting with peptides - Analysis at the amino acid level
Provedor de dados: 17
Autores: Carsten C. Mahrenholz; Victor  Tapia; Rolf Stigler; Rudolf Volkmer.
There are several methods commonly used to measure protein-protein interactions and binding affinities. Quite contrary to most of these methods, protein- and peptide arrays on cellulose membranes or glass slides are suitable for high-throughput measurement, as they provide a higher density of probes and a multitude of peptide-protein interactions can be measured in parallel [1]. The most important application of the SPOT synthesis technique is to simultaneously detect a high number of peptides that have a strong binding affinity to defined targets. The validity of the results, however, depends on the ability of the detection system to indicate binding events whilst not interfering with the experiment itself through cross reaction. We tested three common...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4448/version/1

Determination of adsorptive and diffusive properties of carbon dioxide - methane - water in coal-like structures using molecular simulations
Provedor de dados: 17
Autores: Alaaeldin Salih; Erich A. M&amp;#xfc;ller.
This work employs molecular modeling to simulate both the equilibrium and kinetic behavior pertaining adsorption/desorption and permeation of carbon dioxide within the enhanced coal bed methane (ECBM) process and the corresponding CO~2~ sequestration processes in deep coal mines. The coal structure is modeled on the basis of a carbon, nanotubes, slit pores and more realistic &amp;#x201c;virtual&amp;#x201d; carbons. (from bottom up in the figure) The grand canonical Monte Carlo method is used to simulate the adsorption isotherms and isosteric heats of adsorption of the methane-carbon dioxide-water ternary mixture into the carbon structure, while Molecular Dynamics is applied to the same systems to study the competitive diffusion properties of these fluids...
Tipo: Presentation
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2625/version/1

Determination of Isoflavone Contents for Selected Soybean Lines and Soy Foods by  Fourier Transform Near Infrared Reflectance Spectroscopy
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng You; Randall L. Nelson.
Soybean isoflavones are of considerable interest in relation to their possible health effects in human diets. Rapid and economical determination of soybean isoflavone contents is essential for breeding and selection of soybean seeds with optimal isoflavone levels for food applications. Fourier Transform Near Infrared Spectroscopy (FT-NIR) calibrations were developed for rapid and reliable analysis of soybean isoflavone content. Our isoflavone calibrations are characterized by low standard errors (&amp;#x3c;0.02%) and high degrees of correlation (&amp;#x3e;99%).
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Immunology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6194/version/1

Determination of linkage disequilibrium region suggests association of the ancient haplotype, hX with neural function
Provedor de dados: 17
Autores: Makoto Shimada; Tsutomu Kanasashi.
Modern human populations are known to contain &amp;#x22;ancient haplotypes&amp;#x22; that originated from archaic humans by hybridization.  Some of them had been reported before the development of human genomic diversity databases, such as HapMap.  Consequently, some of them have no information about linkage disequilibrium (LD) regions.  Because genetic information within LD is tightly linked, to know LD region containing ancient haplotypes will be useful to estimate basic parameters of admixture events, and to infer biological functions that linked with the ancient haplotypes.  One of these ancient haplotypes, haplotype X (_hX_) was found in a 10.1 kb-region located on Xp11.22, which diverged at 1.4 M years ago, with low diversity within the cluster in...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6737/version/1

Determination of Mineralogical Contents of a Bangle Shard from an Indus Valley Settlement through X-ray Diffraction Analysis
Provedor de dados: 17
Autores: Saheeb Ahmed Kayani; Rehan ul Haq Siddiqi.
Some initial results of XRD testing of a bangle shard collected from Harrappa, an Indus Valley settlement located in Pakistan are presented. The mineralogical structure of the bangle shard includes montmorillonite, gypsum, and quartz.
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6127/version/1

Determination of Mineralogical Contents of a Bangle Shard from an Indus Valley Settlement through X-ray Diffraction Analysis
Provedor de dados: 17
Autores: Saheeb Ahmed Kayani; Rehan ul Haq Siddiqui.
Some initial results of XRD testing of a bangle shard collected from Harrappa, an Indus Valley settlement located in Pakistan, are presented. The mineralogical structure of the bangle shard includes montmorillonite, gypsum, and quartz.
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6127/version/2

Determination of Soybean Oil, Protein and Amino Acid Residues in Soybean Seeds by High Resolution Nuclear Magnetic Resonance (NMRS) and Near Infrared (NIRS)
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng  You; Doina Costescu; P R. Lozano; Valentin Prisecaru; Randall   L. Nelson.
A detailed account is presented of our high resolution nuclear magnetic resonance (HR-NMR) and near infrared (NIR) calibration models, methodologies and validation procedures, together with a large number of composition analyses for soybean seeds. NIR calibrations were developed based on both HR-NMR and analytical chemistry reference data for oil and twelve amino acid residues in mature soybeans and soybean embryos. This is our first report of HR-NMR determinations of amino acid profiles of proteins from whole soybean seeds, without protein extraction from the seed.  It was found that the best results for both oil and protein calibrations were obtained with a Partial Least Squares Regression (PLS-1) analysis of our extensive NIR spectral data, acquired...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7053/version/1

Determinative atom model and the nature of chemical bond
Provedor de dados: 17
Autores: Wanchung Hu.
Quantum mechanics including Schrodinger and Dirac&amp;#x2019;s equations are used to describe the atom model. However, the basic assumption assuming electron energy can be described by E=h&amp;#x2019;w is wrong. If E=h&amp;#x2019;w, then the total energy of the electron will be E=rmv^2 in contrary to E=rmc^2 from special relativity. Here, I propose a new atom model integrating frame-dragging force, centrifugal force, electrostatic force, and magnetic force. In this new model, the proton group and neutron group in atomic nucleus are rotating in different direction. Thus, they provide equal and opposite frame-dragging force for orbiting electrons. The electrons are orbiting in the equator plane of nucleus. There is no net force or net acceleration for...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6719/version/1

Deterministic individual-based cellular automata modelling of single species population dynamics
Provedor de dados: 17
Autores: Lev Kalmykov; Vyacheslav Kalmykov.
This presentation was created to characterise foundations of cellular automata modelling of single species population dynamics. We show models of single species population growth based on deterministic birth-death-regeneration process and demonstrate a relationship between fecundity rate and population growth rate. Our models provide mechanistic simulation of logistic-like and double logistic-like curves of population growth that is not possible in the classical Verhulst model (logistic growth model). This method is deterministic individual-based and is based on logical &amp;#x201c;if-then&amp;#x201d; statements only. As this method is bottom-up mechanistic and provides a direct visual insight into dynamics of complex systems, we used it to study...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6661/version/1

Deterministic Separation of Cancer Cells from Blood at 10 mL/min
Provedor de dados: 17
Autores: Kevin Loutherback; Joseph D&amp;#x27;Silva; Liyu Liu; Amy Wu; Robert Austin; James Sturm.
Circulating tumor cells (CTCs) and circulating clusters of cancer and stromal cells have been identified in the blood of patients with malignant cancer and can be used as a diagnostic for disease severity, assess the efficacy of different treatment strategies and possibly determine the eventual location of metastatic invasions for possible treatment. There is thus a critical need to isolate, propagate and characterize viable CTCs and clusters. Here, we present a microfluidic device for mL/min flow rate, continuous-flow capture of viable CTCs from blood using deterministic lateral displacement arrays. We show here that a deterministic bump array can be designed such that it will isolate with efficiency greater than 85% CTCs over a large range in sizes from...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2012
URL: http://precedings.nature.com/documents/6861/version/1

Developing a Mammalian Behaviour Ontology
Provedor de dados: 17
Autores: Tim Beck; John M. Hancock; Ann-Marie Mallon.
The use of the Entity + Quality (EQ) model in phenotypic descriptions is dependent on the use of specialised domain ontologies to define the entity under observation.  A domain currently lacking a specialised ontology is mammalian behaviour, and so the Mammalian Behaviour Ontology is being constructed to address this.  Top-level class distinctions are made between behavioural activities and behavioural functions of individuals, and those between two or more individuals.  The ontology is manually developed and encourages contributions from domain experts.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3565/version/1

Developing a Text Mining Prototype for the Comparative Toxicogenomics Database Biocuration Process
Provedor de dados: 17
Autores: Thomas C. Wiegers.
Understanding interactions between environmental chemicals and genes provides insights into the mechanisms of chemical action, disease susceptibility, therapeutic drug interactions, and toxicity. The Comparative Toxicogenomics Database (CTD; http://ctd.mdibl.org) is a web-based resource that integrates diverse information for the cross-species analysis of chemical, gene, and disease relationships.  Much of the data contained in CTD is manually gathered by biocurators; CTD integrates data curated manually from over 10,000 scientific documents.  CTD biocurators manually curate chemical-gene and chemical/gene-disease interactions from the scientific literature using controlled vocabularies.  Unfortunately, there are many more scientific documents available...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3142/version/1

Developing an application ontology for annotation of experimental variables &amp;#x2013; Experimental Factor Ontology
Provedor de dados: 17
Autores: James Malone; Tomasz Adamusiak; Ele Holloway; Helen Parkinson.
The Experimental Factor Ontology (&amp;#x22;www.ebi.ac.uk/efo&amp;#x22;:http://www.ebi.ac.uk/efo) is an application focused ontology modelling the experimental factors in ArrayExpress. The ontology has been developed to increase the richness of the annotations that are currently made in the ArrayExpress repository, to promote consistent annotation, to facilitate automatic annotation and to integrate external data. The methodology employed in the development of EFO involves construction of mappings to multiple existing domain specific ontologies, such as the Disease Ontology and Cell Type Ontology.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3806/version/1

Developing Language Abilities by a Non-verbal Training : A fMRI Study
Provedor de dados: 17
Autores: Laurent Lefebvre; Danielle Bal&amp;#xe9;riaux; Philippe Paquier; Francis Lowenthal.
The language ability is a critical aspect of experimental design in functional imaging studies. Today, it is commonly accepted that the brain structures underlying the language are more distributed than the traditional Broca&amp;#x2019;s and Wernicke&amp;#x2019;s areas. Currently, some other areas as the premotor cortex, the supplementary motor area, the cerebellum or subcortical structures, notably, are recognised. However, a lesser studied question is to define if it is possible to observe a reorganisation of the activation observed during language tasks when the subjects have been trained to develop non-verbal abilities. Particularly, Bates and Ellman (1996) claim that probabilistic regularities are the basis of the language acquisition processing.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1904/version/1

Developing ontologies in decentralised settings
Provedor de dados: 17
Autores: Alexander  Garcia; Kieran O&amp;#x2019;Neill; Leyla J. Garcia; Phillip Lord; Robert Stevens; Oscar Corcho; Frank Gibson.
This paper addresses two research questions: &amp;#x201c;How should a well-engineered methodology facilitate the development of ontologies within communities of practice?&amp;#x201d; and &amp;#x201c;What methodology should be used?&amp;#x201d; If ontologies are to be developed by communities then the ontology development life cycle should be better understood within this context. This paper presents the Melting Point (MP), a proposed new methodology for developing ontologies within decentralized settings. It describes how MP was developed by taking best practices from other methodologies, provides details on recommended steps and recommended processes, and compares MP with alternatives. The methodology presented here is the product of direct first-hand...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3231/version/1

Developing Ontology Support for Human Malaria Control Initiatives
Provedor de dados: 17
Autores: Daramola Olawande; Fatumo Segun.
Malaria is one of the most common infectious diseases and an enormous public health problem in Sub-Sahara Africa, Asia and parts of America. In this paper, we discuss the development of the Human Malaria Control Ontology (HMCO) which contains general information on Malaria and epidemiological information that can help in the formulation of effective malaria control policies. The HMCO is aimed at providing interoperability support for the knowledge management of malaria control initiatives, and serve as an open semantic web infrastructure for malaria research and treatment.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3591/version/1

Developing Predictive Molecular Maps of Human Disease through Community-based Modeling
Provedor de dados: 17
Autores: Jonathan M. J. Derry; Lara M. Mangravite; Christine Suver; Matt Furia; David  Henderson; Xavier  Schildwachter; Jonathan Izant; Solveig K. Sieberts; Michael R. Kellen; Stephen H. Friend.
The failure of biology to identify the molecular causes of disease has led to disappointment in the rate of development of new medicines. By combining the power of community-based modeling with broad access to large datasets on a platform that promotes reproducible analyses we can work towards more predictive molecular maps that can deliver better therapeutics.
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5883/version/1

Development and application of molecular and bioinformatic tools for the genetic monitoring of wild beets
Provedor de dados: 17
Autores: Matthias Enders; Lothar  Frese; Marion Nachtigall.
Crop Wild Relatives (CWR) are an economically important plant genetic resource (PGR) for plant breeding. One strategy to conserve PGR in the natural habitat (in situ) is the genetic reserve technique. This approach protects the existing intraspecific diversity and allows, in contrast to the ex situ approaches, the emergence of new diversity. &amp;#xd;&amp;#xa;The genetic reserve conservation technique will be tested in practice with the Genus _Beta_ within the framework of the EU Project &amp;#x201c;AEGRO&amp;#x201d;. _Beta patula_ (Ait.) (BP) and _Beta vulgaris_ (L.) _maritima_ (Arcang.) (BVM) are used as models. Both species are important resources for sugar beet breeding. BP is a rare and endangered species with a very limited habitat. In contrast BVM...
Tipo: Presentation
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5742/version/1

Development and Characterization of Eudragit RS 100 Loaded Microsponges and its Colonic Delivery Using Natural Polysaccharides
Provedor de dados: 17
Autores: Vikas Jain; Ranjit Singh.
In the present work, paracetamol loaded eudragit based microsponges were prepared using quasi-emulsion solvent diffusion method. The compatibility of the drug with various formulation components was established. Process parameters were analyzed in order to optimize the formulation. Shape and surface morphology of the microsponges were examined using scanning electron microscopy. The colon specific formulations were prepared by compression coating of microsponges with pectin:hydroxypropylmethylcellulose (HPMC) mixture followed by tabletting. The in vitro dissolution studies were done on all formulations and the results were evaluated kinetically and statically. The kinetics of release study showed that the release data followed Higuchi matrix and the main...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3676/version/2

Development and Characterization of Eudragit RS 100 Loaded Microsponges and its Colonic Delivery Using Natural Polysaccharides
Provedor de dados: 17
Autores: Vikas Jain; Ranjit Singh.
In the present work, paracetamol loaded eudragit based microsponges were prepared using quasi-emulsion solvent diffusion method. The compatibility of the drug with various formulation components was established. Process parameters were analyzed in order to optimize the formulation. Shape and surface morphology of the microsponges were examined using scanning electron microscopy. The colon specific formulations were prepared by compression coating of microsponges with pectin:hydroxypropylmethylcellulose (HPMC) mixture followed by tabletting. The in vitro dissolution studies were done on all formulations and the results were evaluated kinetically and statically. The kinetics of release study showed that the release data followed Higuchi matrix and the main...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3676/version/1

Development and comparison of ECC-rtPCR with in vivo method to determine the viability and infectivity of Giardial cysts
Provedor de dados: 17
Autores: M. Khalid Ijaz; Absar Alum; Basel  Sbai; Hamas  Asaad; Joseph Rubino.
Globally, Giardia is one of the major cause of diarrheal illnesses and rapid diagnostic methods differentiating infectious cysts are critical for developing intervention strategies through contaminated surfaces, food and water. This is currently hampered by lack of an in vitro model.  We evaluated mRNA expression in trophozoites and their attachment to a CaCo2 (C2bb) cell monolayer and changes in trans-cellular resistance as an indicator of Giardia viability and infectivity.  Heat shock mRNA in Giardia cysts and variant specific protein (VSP) mRNA in trophozoites were quantified by RT-PCR. When compared with neonatal mice infectivity, the attachment of trophozoites to cell monolayers, expression of VSP, and changes in the trans-cellular resistance, the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Microbiology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5501/version/1

Development and Evaluation of an Efficient Process for the Detoxification of Jatropha Oil and Meal
Provedor de dados: 17
Autores: Sarthak Gaur; Balaji Viswanathan; Rachadaporn  Seemamahannop; Shubhender Kapila; Neil L. Book.
The poster deals with an often mentioned bioenergy plant - Jatopha curcas. The potential of the plant as a sustainable energy source has been hampered by toxicity of its oil and protein rich seeds. The research done by our group describes a simple process for detoxification of the protein rich Jatropha meal thereby making it suitable for animal feed. The process will accelerate use of Jatropha as an energy and feed source thereby enhancing its economic viability. &amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6118/version/1

Development and validation of a method for the detection of altered resistance in transgenic plants against herbivore-pathogen-complexes
Provedor de dados: 17
Autores: Nadine  Drechsler; Antje Habeku&amp;#xdf;; Thomas  Thieme; J&amp;#xf6;rg  Schubert.
Enhanced or reduced uptake of viruses by vectors and changes in resistance level can be sensitive indicators for metabolic changes in transgenic plants caused by the new trait and not observed by conventional methods. In addition, the plant transformation process itself can lead to such changes. To be able to investigate this hypothesis in cereals we decided to use two highly important insect-transmitted viruses infecting them - _Barley yellow dwarf virus_ (BYDV) and _Wheat dwarf virus_ (WDV). Corresponding molecular tools for their quantification in plants as well as virus vectors had to be developed. &amp;#xd;&amp;#xa;Both viruses cause similar symptoms: dwarfing, stunting, leaf discoloration leading to yield losses or death of plant. BYDV...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4493/version/1

Development and validation of an analysis method for the detection of altered resistance in transgenic plants to herbivore-pathogen-complexes
Provedor de dados: 17
Autores: Anja  H&amp;#xfc;hnlein; J&amp;#xf6;rg  Schubert; Thomas  Thieme.
Genetically modified plants (GMPs) have to pass several safety evaluations before they can be approved but identification of undesired changes in metabolism is hard to achieve due to its complexity. Such unexpected changes could be reflected by changes in virus resistance and feeding behaviour of herbivores such as aphids. Altered behaviour can be determined by so- called life table statistics where e. g. the lifetime and the reproduction rate are analysed. Such experiments are time consuming and costly. The behaviour alterations should also be detectable by changes in virus uptake und transmission. Thus, quantitative detection methods are needed in order to measure the absolute virus content in plants and in aphids. _Potato leafroll virus_ (PLRV) and...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4473/version/1

Development of a Decision Support System (DSS) for an integrated test system towards the effective and competitive risk assessment on transgenic plants
Provedor de dados: 17
Autores: Christine  H&amp;#xf6;flich; Andreas  M&amp;#xfc;ller; J&amp;#xf6;rg  Schmidtke; Kerstin  Schmidt; Inge  Broer.
Transgenic plants need specific approaches to analyse their potential impact on environment and consumer. The procedures used to date are often too extensive and time-consuming and associated with high costs. The BioOK network was established to develop an effective and competitive risk assessment on transgenic plants based on interdisciplinary research. New and effective methods for the risk assessment were established which focus on transgene-specific effects measured in in vitro systems in the laboratory or greenhouse whenever possible. Nevertheless event-specific field experiments have to be carried out in addition to implement environmental effects e.g. on non-targets or the variability of transgene expression.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4438/version/2

Development of a Decision Support System (DSS) for an integrated test system towards the effective and competitive risk assessment on transgenic plants
Provedor de dados: 17
Autores: Christine  H&amp;#xf6;flich; Andreas  M&amp;#xfc;ller; J&amp;#xf6;rg  Schmidtke; Kerstin  Schmidt; Inge  Broer.
Transgenic plants need specific approaches to analyse their potential impact on environment and consumer. The procedures used to date are often too extensive and time-consuming and associated with high costs. The BioOK network was established to develop an effective and competitive risk assessment on transgenic plants based on interdisciplinary research. New and effective methods for the risk assessment were established which focus on transgene-specific effects measured in in vitro systems in the laboratory or greenhouse whenever possible. Nevertheless event-specific field experiments have to be carried out in addition to implement environmental effects e.g. on non-targets or the variability of transgene expression.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4438/version/1

Development of a method for phenotyping Black Rot (_Guignardia bidwellii_) resistance on grapevine (_Vitis_ spp.)
Provedor de dados: 17
Autores: Friederike Rex; Iris Fechter; Ludger Hausmann; Reinhard T&amp;#xf6;pfer.
Black Rot of grapevine is caused by the Ascomycet _Guignardia bidwellii_. The pathogen was introduced from North America to Europe in the 19th century. Since 2002, increased effects of the disease have been noticed, causing significant yield losses in the region of Mosel and infections in all German wine-growing regions. For that reason, it is important to breed Black Rot-resistant grapevine cultivars. A method has been developed to characterize lots of vines in a fast and reliable way concerning their susceptibility. Initial data has been collected and can be used for genetic analysis (here QTL). The aim of the project is to develop a molecular marker correlating with Black Rot resistance which can be used to select juvenile plants and therefore support...
Tipo: Presentation
Palavras-chave: Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5743/version/1

Development of a new method to preserve caprine cauda epididymal spermatozoa in-situ at -10 degrees Centigrade
Provedor de dados: 17
Autores: Uttam Datta; M Chandrasekar; Manik Lal Hembram; Raju Dasgupta.
Electrolyte free mediums prepared with soybean lecithin-glycerol,Coenzyme Q10&amp;#x2013;glycerol and soybean lecithin-Coenzyme Q10-glycerol were inoculated separately into ligated cauda epididymides, equilibrated 2 h at 5 degree centigrade, wrapped with aluminium foils along with testis and freezed at -10 degree centigrade.Spermatozoan characters were evaluated  7 and 21 days after thawing at 38.5 degree centigrade in a water bath for 5 min. Spermatozoan characters were diminished gradually and significantly (P&amp;#x3c;0.001, P&amp;#x3c;0.05) between the mediums and observation days. Soybean lecithin-CoenzymeQ10-glycerol effectively protected spermatozoa against cold shock where spermatozoan progressive motility, livability, hypo-osmotic swelling...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3377/version/1

Development of a sampling regime for research with environmental relevance based on variability of transgene expression in plants
Provedor de dados: 17
Autores: Carla  Struzyna-Schulze; Heike  Mikschofsky; Wenke  M&amp;#xf6;nkemeyer; J&amp;#xf6;rg  Schmidtke; Kerstin  Schmidt; Inge  Broer.
Transgenic plants often produce proteins that are unknown in conventional crops. Therefore, it requires a fundamental analysis before approval of a new genetically modified plant is given. Since the EFSA-guidelines for risk assessment on transgenic plants provide only recommendations but no detailed instructions, we wanted to develop a valid test scheme that defines sample size and sampling organ to enable a statically valid and efficient analysis of transgene expression and its variability. The scheme will be based on data obtained for the variability in expression i. of different recombinant proteins in one variety; ii. of different integration sites of one transgene in one variety; iii. of the same recombinant protein between different varieties and...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4443/version/1

Development of an Ontology of Microbial Phenotypes (OMP)
Provedor de dados: 17
Autores: Michelle Giglio; Chris Mungall; Peter Uetz; Lanlan Yin; Johannes Goll; Deborah Siegele; Marcus Chibucos; James Hu.
*Abstract*&amp;#xd;&amp;#xa;Phenotypic data are routinely used to elucidate gene and protein function in most organisms amenable to experimental manipulation. However, although phenotype ontologies exist for many eukaryotic model organisms, no standardized system exists for the capture of phenotypic information in bacteria. We propose to build an Ontology of Microbial Phenotypes and use it to annotate the prokaryotic model organism _Escherichia coli_.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Introduction*&amp;#xd;&amp;#xa;Phenotypes are the observable characteristics of an organism that result from the combination of a particular genotype and a particular environment, and thus are a basic and fundamental aspect of the biology of all organisms. The awesome power...
Tipo: Poster
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3639/version/1

Development of Future Habitat Suitability Models for the Swift fox (Vulpes velox) in the American Southwest
Provedor de dados: 17
Autores: Jennifer Redman; Michael  T. Calkins; Mark C. Andersen; Kenneth  G. Boykin.
The Swift fox (Vupes velox) is a habitat specialist species of short or mixed grass prairie. We used bioclimatic envelope models and habitat suitability models under three future climate scenarios (based on CO2 emission rates) from &amp;#x22;www.climatewizard.org&amp;#x22;:http://www.climatewizard.org to fit species distribution models, using the maximum entropy method. Current suitable habitat for the swift fox covers an area of 161,984 km2. Under the future climate scenarios the habitat decreases by 27% in the low emission scenario, 63% for medium emissions, and 53% in the high emissions scenario. This decrease in suitable habitat corresponded to an overall decrease in total grassland landcover. The current total area of grassland is 423,440 km2. Under...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3717/version/1

Development of GCP Ontology for Sharing Crop Information
Provedor de dados: 17
Autores: Rosemary Shrestha; Ramil Mauleon; Reinhard Simon; Jayashree  Balaji; Stephanie  Channeli&amp;#xe8;re; Adriana  Alercia; Martin Senger; Kevin Manansala; Thomas Metz; Guy  Davenport; Richard Bruskiewich; Graham McLaren; Elizabeth Arnaud.
The Generation Challenge Programme (GCP &amp;#x2013; &amp;#x22;http://www.generationcp.org&amp;#x22;:http://www.generationcp.org) is a globally distributed crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. GCP adopted the development paradigm of a &amp;#x2018;model-driven architecture&amp;#x2019; to achieve the interoperability and integration of diverse GCP data types that are available through distributed data sources and consumed by end-user data analysis tools. Its objective is to ensure semantic compatibility across the Consortium that will lead to the creation of robust global public goods from GCP research results....
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3087/version/1

Development of human limbs.
Provedor de dados: 17
Autores: Alexander Ermolenko.
This work offers a new view on the developmental history of tetrapods. It proposes an original evolution model of human limbs based on metameric formation of osteogenic buds in accordance to primary segmentation and biplanar symmetry. While going through evolution, osteogenic buds initially identical to each other were changing their sizes, realigning, regressing, uniting while keeping the direction of the formation in accordance to the following formula (taking into account sesamoid bones):&amp;#xd;&amp;#xa;2; 1; 2; 3; 2; 3; 5; 5; 8; 8 (in the upper limb together with the upper limb girdle); 3; 2; 3; 2; 1; 2; 8; 8; 5; 5 (in the lower limb together with the pelvic bones).
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5539/version/1

Development of Incentives for Data Sharing in Ecology, Evolution, and Organismal Biology
Provedor de dados: 17
Autores: Clifford S. Duke.
Ready access to data is a key concern in both basic research and problem-solving in the biological sciences, as the scale and scope of the questions that researchers ask expand, and as global problems demand data collected from around the world. With a grant from the National Science Foundation, from 2004 through 2009, the Ecological Society of America (ESA) has led a series of five workshops on data sharing, to help the ecology, evolution, and organismal biology communities find common ground on how to make data more readily discoverable and accessible in their own disciplines. The most recent of these focused in the development of incentives for data sharing, both at the individual and organizational level. This presentation will summarize the workshop...
Tipo: Presentation
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3647/version/1

Development of Integrative Bioinformatics Applications using Cloud Computing resources and Knowledge Organization Systems (KOS).
Provedor de dados: 17
Autores: Jonas Almeida; Helena Deus; Wolfgang Maass.
Use of semantic web abstractions, in particular of domain neural Knowledge Organization Systems (KOS), to manage distributed, cloud based, integrative bioinformatics infrastructure. This presentation derives from recent publication:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Almeida JS, Deus HF, Maass W. (2010) S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics. 2010 Jul 20;11(1):387. [PMID 20646315].&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;These PowerPoint slides were presented at Semantic Web Applications and Tools for Life Sciences December 10th, 2010, Berlin, Germany (http://www.swat4ls.org/2010/progr.php), keynote 9-10 am.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5537/version/1

Development of Java based graphical user interface for Diagnosis of Hepatitis UsingI Mixture of Expert
Provedor de dados: 17
Autores: M Shankaracharya; Suchitra Kumari; Ambarish S. Vidyarthi.
Hepatitis is deadly, and the fifth leading cause of death after heart disease, stroke, chest disease and cancer. Worldwide, 1.5 million deaths per year have been estimated. Detection of hepatitis is a big problem for general practitioners. An expert doctor commonly makes decisions by evaluating the current test results of a patient or by comparing the patient with others with the same condition with reference to the previous decisions. Many machine learning and data mining techniques have been designed for the automatic diagnosis of hepatitis. However, no one tool is available to the general population for the diagnosis of Hepatitis. Hence, a graphical user interface-enabled tool needs to be developed, through which medical practitioners can feed patient...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7093/version/1

Development of Neural Electromagnetic Ontologies (NEMO): Ontology-based Tools for Representation and Integration of Event-related Brain Potentials
Provedor de dados: 17
Autores: Gwen A. Frishkoff; Paea LePendu; Robert M. Frank; Haishan Liu; Dejing Dou.
We describe a first-generation ontology for&amp;#xd;&amp;#xa;representation and integration of event-related brain potentials (ERPs). The ontology is designed following OBO &amp;#x201c;best practices&amp;#x201d; and is augmented with tools to perform ontology-based labeling and annotation of ERP data, and a database that enables semantically based reasoning over these data. Because certain high-level concepts in the ERP domain are illdefined, we have developed methods to support coordinated updates to each of these three components. This approach consists of &amp;#x201c;top-down&amp;#x201d; (knowledge-driven) design and implementation, followed by &amp;#x201c;bottom-up&amp;#x201d; (data-driven) validation and refinement. Our goal is to build an ERP...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3458/version/1

Development of Novel Calibrations for FT-NIR Analysis of Protein, Oil, Carbohydrates and Isoflavones in Foods
Provedor de dados: 17
Autores: I Baianu; Jun Guo.
The development of calibration methodology for novel FT-NIRS analysis of soybean-based foods is presented together with high-precision NIRS spectra and composition measurements in terms of proteins, oil and carbohydrates in soybean-based foods/soy foods.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Pharmacology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6317/version/1

Developments in CFG glycan and pathogen polysaccharide arrays
Provedor de dados: 17
Autores: Ola Blixt.
This presentation summarizes developments in glycan and pathogen polysaccharide arrays at the Consortium for Functional Glycomics (CFG).
Tipo: Presentation
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/12/version/1

Diabetes and kidney cancer: A direct or indirect association?
Provedor de dados: 17
Autores: Rohit P. Ojha; Eva L. Evans; Tabatha N. Powell; Bahij S. Nuwayhid; Zuber D. Mulla.
A positive association between diabetes and kidney cancer has been reported in several investigations, but it is unclear whether diabetes or its complications account for this association. Recent advances in estimating direct associations may be useful for elucidating the association between diabetes and kidney cancer.  Therefore, we performed a case-control analysis to evaluate whether the direct association between diabetes and kidney cancer is the primary concern in this exposure-outcome relation.  Discharge data (with International Classification of Diseases &amp;#x2013; 9 codes) from 2001 for hospitals throughout Florida were used to construct a case-control population of inpatients aged &amp;#x2265;45 years. Cases (n=1,909) were inpatients with...
Tipo: Poster
Palavras-chave: Cancer.
Ano: 2010
URL: http://precedings.nature.com/documents/4922/version/1

Diagnostic robustness of DNA microarrays in the classification of acute leukemia
Provedor de dados: 17
Autores: Marie Loh; Adrian Mondry.
Countless statistical methods have been described for the analysis of DNA microarrays, and each yields distinct results. This raises the question whether DNA microarrays are robust diagnostic tools.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In order to address this issue, we compared five formally similar statistical tests for gene selection on a single data set derived from acute leukemia patients. Inter-test agreement of gene selection, of sample classification and with standard clinical diagnosis was calculated using Cohen&amp;#x27;s &amp;#x3ba;-score.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The inter-test agreement scores were 0.15 &amp;#x3c; &amp;#x3ba; &amp;#x3c; 0.68 for gene selection, and 0.60 &amp;#x3c; &amp;#x3ba; &amp;#x3c; 0.89 for sample classification....
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1056/version/1

Diamagnetic levitation enhances growth of liquid bacterial cultures by increasing oxygen availability
Provedor de dados: 17
Autores: Camelia E. Dijkstra; Oliver J. Larkin; Paul Anthony; Michael R. Davey; Laurence Eaves; Catherine E. D. Rees; Richard J. A. Hill.
Diamagnetic levitation is a technique that uses a strong, spatially-varying magnetic field to reproduce aspects of weightlessness, on the Earth. We used a superconducting magnet to levitate growing bacterial cultures for up to 18 hours, to determine the effect of diamagnetic levitation on all phases of the bacterial growth cycle. We find that diamagnetic levitation increases the rate of population growth in a liquid culture and reduces the sedimentation rate of the cells. Further experiments and microarray gene analysis show that the increase in growth rate is due to enhanced oxygen availability. We also demonstrate that the magnetic field that levitates the cells also induces convective stirring in the liquid. We present a simple theoretical model,...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4216/version/2

Diamond nanowires, a new approach towards next generation electrochemical gene sensor platforms
Provedor de dados: 17
Autores: Nianjun Yang; Hiroshi Uetsuka; Jiuhong Yu; Eiji Osawa; Norio Tokuda; Christoph Nebel.
A novel bio-sensing platform is introduced by combination of a) geometrically controlled DNA bonding using vertically aligned diamond nano-wires and b) the superior electrochemical sensing properties of diamond as transducer material. Ultra-hard vertically aligned diamond nanowires are electrochemically modified to bond phenyl linker-molecules to their tips which provide mesospacing for DNA molecules on the transducer. The nano-wires are generated by reactive ion etching of metallically boron doped atomically smooth single crystalline CVD diamond. Surface properties are characterized by atomic force, scanning electron and scanning tunneling microcopy. Electro- and biochemical sensor properties are investigated using cyclic and differential pulse...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/1714/version/1

Dibutyltin Disrupts Glucocorticoid Receptor Function and Impairs Glucocorticoid-induced Suppression of Cytokine Production
Provedor de dados: 17
Autores: Christel Gumy; Charlie Chandsawangbhuwana; Anna A. Dzyakanchuk; Denise V. Kratschmar; Michael E. Baker; Alex Odermatt.
_Background_. Organotins are highly toxic and widely distributed environmental chemicals. Dibutyltin (DBT) is used as stabilizer in the production of polyvinyl chloride plastics, and it is also the major metabolite formed from tributyltin (TBT) _in vivo_. DBT is immunotoxic, however, the responsible targets remain to be defined. Due to the importance of glucocorticoids in immune-modulation, we investigated whether DBT could interfere with glucocorticoid receptor (GR) function.&amp;#xd;&amp;#xa;_Methodology_. We used HEK-293 cells transiently transfected with human GR as well as rat H4IIE hepatoma cells and native human macrophages and human THP-1 macrophages expressing endogenous receptor to study organotin effects on GR function. Docking of organotins was...
Tipo: Manuscript
Palavras-chave: Immunology; Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2312/version/1

Dicroidium: no more a Triassic Gondwana index fossil
Provedor de dados: 17
Autores: Ashwini Srivastava; Rashmi Srivastava; Deepa Agnihotri.
A large number of _Dicroidium_-frond, considered as the marker of Early Triassic Gondwana flora, are discovered for the first time with well preserved cuticle from Early Permian (Lower Gondwana) sequence of Barakar Formation, Satpura Gondwana Basin, India. The presence of _Dicroidium_ in Late Permian mixed floral zone of Jordan has been viewed as its possible origin in paleotropics but the evidence in hand exhibits its Gondwanic derivation and threatens the recognition of _Dicroidium_ flora for Middle Gondwana in association with Lower Gondwana Glossopteris and Upper Gondwana Ptilophyllun flora.
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4777/version/1

Did nature also choose arsenic?
Provedor de dados: 17
Autores: Felisa Wolfe-Simon; Paul C. W. Davies; Ariel Anbar.
All known life requires phosphorus (P) in the form of inorganic phosphate (PO&amp;#x3c;sub&amp;#x3e;4&amp;#x3c;/sub&amp;#x3e;&amp;#x3c;sup&amp;#x3e;-&amp;#x3c;/sup&amp;#x3e; or P&amp;#x3c;sub&amp;#x3e;i&amp;#x3c;/sub&amp;#x3e;) and phosphate-containing organic molecules. P&amp;#x3c;sub&amp;#x3e;i&amp;#x3c;/sub&amp;#x3e; serves as the backbone of the nucleic acids that constitute genetic material and as the major repository of chemical energy for metabolism in polyphosphate bonds. Arsenic (As) lies directly below P on the periodic table and so the two elements share many chemical properties, although their chemistries are sufficiently dissimilar that As cannot directly replace P in modern biochemistry. Arsenic is toxic precisely because As and P are similar...
Tipo: Manuscript
Palavras-chave: Chemistry; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1482/version/1

Dielectric Constant of Liquids (Fluids) Shown to be Simple Fundamental Relation of Density over Extreme Ranges from - 50^o^ to + 600^o^C, Believed Universal
Provedor de dados: 17
Autores: William L. Marshall.
Examinations of past complex theoretical equations describing isothermal dielectric constants (_[epsilon]_) of liquids show that none describe experiments throughout and that only a two-constant equation of density is required.  The dielectric susceptibility (_[epsilon]_ &amp;#x2013; 1) as a simple exponential function of density is shown here to describe _[epsilon]_ for both polar and non-polar organic liquids over all available experimental ranges from 0.50 to 1.2 g cm^-3^ and temperatures to 400^o^C.  For water above 0.25 g cm^-3^, the equation describes the excellent dielectric-constant formulation of Fern&amp;#xe1;ndez, et al., (1997) throughout its experimental range [-35 to +600^o^C; to 1000 MPa (10000 Atm)] and even when diluted by...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2474/version/1

Dielectric Constant of Water Discovered to be Simple Function of Density over Extreme Ranges from &amp;#x2013; 35 to + 600^o^C and to 1200 MPa (12000 Atm.), Believed Universal
Provedor de dados: 17
Autores: William L.  Marshall.
The experimental static dielectric constants (_[epsilon]_) of water formulated by Fern&amp;#xe1;ndez, et al., (1997-International Association for the Properties of Water and Steam, IAPWS), &amp;#x2013;35 to 600^o^C; 0.1 to 1200 MPa, are discovered to be closely described throughout by a simple equation of density (_[rho]_), presented here, and agreeing with their reported calculated (extrapolated) values to 923^o^C.  Eight limiting boundary conditions are observed.  Values of _[epsilon]_ follow isothermal straight-line slopes of log (_[epsilon]_ &amp;#x2013; 1) vs log _[rho]_ down to densities of 0.25 g cm^-3^ water, even in dioxane-water solutions.   At lower densities, all slopes curve asymptotically in approaching unity, while becoming unity throughout...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2472/version/1

Diet, Genetic Factors, and the Gut Microbiome in Crohn&amp;#x27;s Disease
Provedor de dados: 17
Autores: Gary D. Wu; James D. Lewis; Frederic D. Bushman.
This manuscript is part of a pilot effort on the part of NIH staff and the Nature publishing group to provide a more convenient archive for &amp;#x22;marker papers&amp;#x22; to be published.  These &amp;#x22;marker papers&amp;#x22; are designed to provide the users of community resource data sets with information regarding the status and scope of individual community resource projects.  For further information see editorial in September 2010 edition of Nature Genetics (Nature Genetics, 42, 729 (2010)), and the Nature Precedings HMP summary page.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Project IDs: 46313, 46879&amp;#xd;&amp;#xa;Publication moratorium: 1 year&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;     We propose to investigate the hypothesis that consistent changes...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5006/version/1

Diet of Northern Map Turtles (_Graptemys geographica_): Relationship to Sexual Dimorphism and Potential Impacts of an Altered River System in Maryland
Provedor de dados: 17
Autores: Teal Richards-Dimitrie; Richard Seigel.
Last recorded in Maryland in the early 1990&amp;#x2019;s, the Northern Map Turtle (_Graptemys geographica_) is listed as state endangered and is currently only known in the lower Susquehanna River drainage. This river is divided by a hydroelectric dam, used for recreation, and has increasing shoreline development, all of which may negatively impact this population. Knowing this population&amp;#x2019;s diet and if alterations to the river affect their prey base is important to understanding the species&amp;#x2019; current status. Northern Map Turtles are mostly molluscivorous but will also consume other invertebrates. Studies have shown that map turtle species will subsidize their diet with invasive mussels, potentially decreasing dietary diversity. The...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4840/version/1

Diet transition to a high-fat diet for 3 weeks reduces brain omega-3-fatty acid levels, alters BDNF signaling and induces anxiety &amp;#x26; depression-like behavior in adult rats
Provedor de dados: 17
Autores: Sandeep Sharma; Yumei Zhuang; Fernando Gomez-Pinilla.
Background: The consumption of diets high in calories and low in nutrient value is becoming increasingly common in modern society, which can lead to metabolic disorders like diabetes and obesity, and potentially to psychiatric disorders. We have performed studies to assess how the shift from a healthy diet rich in omega-3 fatty acids to a diet rich in saturated fatty acid affects the substrates for brain plasticity and function, and anxiety and depression-like behavior. Methods: Pregnant rats were fed with omega-3 supplemented diet from their 2nd day of gestation period as well as their male pups for 12 weeks. Afterwards, the animals were randomly assigned to either a group fed on the same diet or a group fed on a high-fat diet (HFD) rich in saturated fats...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Neuroscience; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6950/version/1

Difference in response reliability predicted by STRFs in the cochlear nuclei of barn owls
Provedor de dados: 17
Autores: Louisa J. Steinberg; Jose L. Pena.
The brainstem auditory pathway is obligatory for all aural information. Brainstem auditory neurons must encode the level and timing of sounds, as well as their time-dependent spectral properties, the fine structure and envelope, which are essential for sound discrimination. This study focused on envelope coding in the two cochlear nuclei of the barn owl, nucleus angularis (NA) and nucleus magnocellularis (NM). NA and NM receive input from bifurcating auditory nerve fibers and initiate processing pathways specialized in encoding interaural time (ITD) and level (ILD) differences, respectively. We found that NA neurons, though unable to accurately encode stimulus phase, lock more strongly to the stimulus envelope than NM units. The spectrotemporal receptive...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5798/version/2

Difference in response reliability predicted by STRFs in the cochlear nuclei of barn owls
Provedor de dados: 17
Autores: Louisa J. Steinberg; Jose L. Pena.
The brainstem auditory pathway is obligatory for all aural information. Brainstem auditory neurons must encode the level and timing of sounds, as well as their time-dependent spectral properties, the fine structure and envelope, which are essential for sound discrimination. This study focused on envelope coding in the two cochlear nuclei of the barn owl, nucleus angularis (NA) and nucleus magnocellularis (NM). NA and NM receive input from bifurcating auditory nerve fibers and initiate processing pathways specialized in encoding interaural time (ITD) and level (ILD) differences, respectively. We found that NA neurons, though unable to accurately encode stimulus phase, lock more strongly to the stimulus envelope than NM units. The spectrotemporal receptive...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5798/version/1

Differences in the gene expression profile of human monocytic cells activated by high and low affinity Fc-gamma-receptors.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Renji Reghunathan; Alirio Jose Melendez; Peter Natesan Pushparaj.
Receptors for the constant (Fc) region of immunoglobulin G, play an important role in linking the humoral and cellular arms of immune response. Three different classes of receptors have been defined, Fc&amp;#x3b3;RI (CD64), Fc&amp;#x3b3;RII (CD 32), and Fc&amp;#x3b3;RIII (CD16). We have previously shown that in a human monocyte model (IFN&amp;#x3b3;-primed U937 cells), Fc&amp;#x3b3;RI and Fc&amp;#x3b3;RII stimulation trigger two very distinct intracellular signalling pathways. Here we show for the first time, the use of oligonucleotide microarrays to investigate the overall gene-expression profile of human monocytes triggered with Fc&amp;#x3b3;RI or Fc&amp;#x3b3;RII. Our data indicate that several interesting genes are differentially expressed in response...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1149/version/1

Differences of morphological and ecological characters among lineages of Chilean Rhinocryptidae in relation an sister lineage of  Furnariidae.
Provedor de dados: 17
Autores: Alejandro Correa Rueda; Jorge Mpodozis; Michel Sallaberry.
Eight species of Rhinocryptidae are recognized from Chile. Moreover, morphological, ecological and behavioral differences  among two lineages of  _Scytalopus_ and two species of _Pteroptochos_ are  unclear. According to our results, there are no decisive criteria differentiating among subspecific sister taxa of _Scelorchilus albicollis_, _S. rubecula_ and _Pteroptochos megapodius_. Here we discuss the speciation of the chilean Rhinocryptidae based in their behaviour. We propose  a new methodology  based on ecological and behavioural patterns in order to understand the concept of speciation in this group of birds.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1606/version/1

Differences of morphological and ecological characters among lineages of Chilean Rhinocryptidae in relation an sister lineage of  Furnariidae.
Provedor de dados: 17
Autores: Alejandro Correa Rueda; Jorge Mpodozis; Michel Sallaberry.
Eight species of Rhinocryptidae are recognized from Chile. Moreover, morphological, ecological and behavioral differences  among two lineages of  Scytalopus  and two species of Pteroptochos are  unclear. According to our results, there are no decisive criteria differentiating among subspecific sister taxa of Scelorchilus  albicollis, S.rubecula and Pteroptochos megapodius. Here we discuss the speciation of the chilean Rhinocryptidae based in their behaviour and we carried out an integrated analysis with specie outgroup Cinclodes oustaleti (Furnariidae). We propose  a new methodology  based on ecological and behavioural patterns in order to understand the concept of speciation in this group of birds.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1606/version/3

Differences of morphological and ecological characters among lineages of Chilean Rhinocryptidae in relation an sister lineage of  Furnariidae.
Provedor de dados: 17
Autores: Alejandro Correa Rueda; Jorge Mpodozis; Michel Sallaberry.
Eight species of Rhinocryptidae are recognized from Chile. Moreover, morphological, ecological and behavioral differences  among two lineages of  _Scytalopus_ and two species of _Pteroptochos_ are  unclear. According to our results, there are no decisive criteria differentiating among subspecific sister taxa of _Scelorchilus albicollis_, _S. rubecula_ and _Pteroptochos megapodius_. Here we discuss the speciation of the chilean Rhinocryptidae based in their behaviour. We propose  a new methodology  based on ecological and behavioural patterns in order to understand the concept of speciation in this group of birds.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1606/version/2

Different Approaches For Protein Engineering In Industrial Biotechnology
Provedor de dados: 17
Autores: Israr  Khan; Muhammad  Waheed Akhtar.
Protein engineering is the novel field which has wide applications from pharmaceutics, industry, commercial, laundry and research. It may apply rational design or non rational design or both. Site directed mutagenesis is a classical approach involving the protein folding principles and as such different techniques involving multidisciplinary research and broad knowledge is required involving biocomputing of complex data obtained from various sequencing projects and prediction of the future protein structure either chemically or genetically modified. Non rational mutagenesis or directed evolution involves random mutations in the gene encoding protein or shuffling the genes encoding different domains producing a random set of numerous large libraries of...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/5601/version/1

Differential expression analysis for sequence count data
Provedor de dados: 17
Autores: Simon Anders; Wolfgang Huber.
*Motivation:* High-throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq) or cell counting (barcode sequencing). Statistical inference of differential signal in such data requires estimation of their variability throughout the dynamic range. When the number of replicates is small, error modelling is needed to achieve statistical power.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Results:* We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Availability:* A free...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4282/version/2

Differential expression analysis for sequence count data
Provedor de dados: 17
Autores: Simon Anders; Wolfgang Huber.
Motivation: High throughput nucleotide sequencing provides quantitative readouts in assays for RNA expression (RNA-Seq), protein-DNA binding (ChIP-Seq), cell counting. Statistical inference of differential signal in these data needs to take into account their natural variability throughout the dynamic range. When the number of replicates is small, error  modeling is needed to achieve statistical power. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: We propose an error model that uses the negative binomial distribution, with variance and mean linked by local regression, to model the null distribution of the count data. The method controls type-I error and provides good detection power.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Availability: A free open-source...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4282/version/1

Differential Gene Expression of Human Mast cell Activation Reveals Gene profiles of Innate and Adaptive Immunity.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Reghunathan Renji; Peter Natesan Pushparaj; Alirio Jose Melendez.
High-density oligonucleotide microarray is a promising approach for high throughput analysis. It has been extensively used in many areas of biomedical research. Immunoglobulin E (IgE) mediated allergic response (type-1 hypersensitivity) is one of the most powerful reactions of the immune system. Tissue Mast Cells (MCs) and circulating basophils are the major effector cells in these reactions. By dissecting the regulatory circuitry of mast cells by analyzing the genome wide effects of antigen stimulation triggered by Fc&amp;#x3b5;RI, offers a potential for finding novel genes as &amp;#x2018;targets&amp;#x2019; for therapeutic intervention. In this work, we tried to study the gene expression pattern in IgE sensitized and Fc&amp;#x3b5;RI cross linked cord...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1148/version/1

Differential photosynthetic adaptation between size-classes of Spruce  and Fir juveniles help to explain the co-existence of the two species.
Provedor de dados: 17
Autores: Edgard Bontempo e Silva; Toshihiko Hara; Akihiro Sumida; Kiyomi Ono.
Background/Question/Methods &amp;#xd;&amp;#xa;_Abies sachalinensis_ (Sakhalin Fir) and _Picea glehnii_ (Glehn&amp;#x2019;s Spruce) are major components of the sub-boreal forests of Hokkaido, Japan. Similar Spruce-Fir forests can be found in many other places in the northern hemisphere and will probably be impacted by global warming. Therefore, detailed knowledge of these species&amp;#x2019; physiology and life-history strategies at different growth stages is important to understand present communities and to support reliable prediction of possible consequences of global climate change. &amp;#xd;&amp;#xa;Accordingly, the objective of this study was to establish relations between community dynamics, life-history strategies and photosynthetic adaptation of...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5298/version/1

Diffusion Approximations for Demographic Inference: DaDi
Provedor de dados: 17
Autores: Ryan N. Gutenkunst; Ryan D. Hernandez; Scott H. Williamson; Carlos D. Bustamante.
Models of demographic history (population sizes, migration rates, and divergence times) inferred from genetic data complement archeology and serve as null models in genome scans for selection. Most current inference methods are computationally limited to considering simple models or non-recombining data. We introduce a method based on a diffusion approximation to the joint frequency spectrum of genetic variation between populations. Our implementation, DaDi, can model up to three interacting populations and scales well to genome-wide data. We have applied DaDi to human data from Africa, Europe, and East Asia, building the most complex statistically well-characterized model of human migration out of Africa to date.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4594/version/1

Digital BioCuration: A Question of Balance
Provedor de dados: 17
Autores: James Ostell.
Curation of biomedical data has come to encompass a broad range of activities and considerations, which include the building of digital archives, making decisions on the relative value and longevity of one dataset vs another, editing data records manually, performing or assessing computational processes over very large sets of data, and grappling with issues of web usability and data standards. People who consider themselves biological curators may range from a single domain expert, who develops a collection which reflects their personal judgments and priorities, to groups of people supporting large, long term public resources such as GenBank, RefSeq, or PubMed, and everything in between. Finding the right balance between objective measures of quality and...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3257/version/1

Digital Image Analysis of Actinomycetes Colonies as a Potential Aid for Rapid Taxonomic Identification
Provedor de dados: 17
Autores: Sonashia Velho-Pereira; Nandkumar M. Kamat.
High frequency isolation of actinomycetes poses a challenge for the taxonomists hence simple and rapid identification methods are required. Our work to catalogue biodiversity of actinomycetes of Goa yielded several distinct morphotypes. After their tentative identification, the feasibility to distinguish these using digital image analyses (DIA) was explored. Digital images of wild colony morphotypes were processed using public domain SCION image analysis software. DIA revealed some intricate digital characters. A combination of these with standard morphological and microscopic characters could be potentially useful for preparing a digital identification key of the actinomycetes strains with potential application in rapid taxonomic identification.
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4209/version/1

Dimension-based attention in the recognition of facial identity and facial expression
Provedor de dados: 17
Autores: Zhicheng Lin.
Although the human visual system is constantly flooded with sensory information, the brain is remarkable in inferring structures from the massive inputs and selectively attending to behaviorally relevant information. However, how the two processes interact remains largely unknown. Can top-down attention efficiently select the task-relevant dimension (e.g. gender) during face recognition to override interference in the task-irrelevant dimension (e.g. expression)? To address this issue, participants were asked to classify real face images according to gender or expression, which were preceded by other faces (masked priming task) or words (face-word Stroop task). Results show that face classification was 1) affected by the task-relevant but not the...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2222/version/1

Direct fluorophore conjugation to genomic DNA for microarray-based epigenomic profiling
Provedor de dados: 17
Autores: Vineet Gupta.
A methodology for microarray based epigenomic profiling is presented. The method relies on platinum-based fluorescence labeling reagents for direct (non-enzymatic) labeling of DNA and RNA. This is a work in progress and only preliminary data is presented here.
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Chemistry; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/444/version/1

Direct submission system and literature annotation of rice genes in Oryzabase
Provedor de dados: 17
Autores: Yukiko Yamazaki; Rie Tsuchiya; Takao Asanuma; Yo Shidahara; Shingo Sakaniwa.
Oryzabase (&amp;#x22;http://www.shigen.nig.ac.jp/rice/oryzabase/&amp;#x22;:http://www.shigen.nig.ac.jp/rice/oryzabase/) is a comprehensive rice science database ^1^. It houses a variety of genetic resources, relevant literatures, gene dictionary, DNA sequences, and basic information such as developmental biology and anatomy. In order to keep the gene dictionary up-to-date, literature annotation has been conducted manually since 1995. However as the publication of journal articles increases year by year after genomic sequences were released, it became more difficult to update the dictionary timely and in high quality without sufficient annotators. To overcome this difficulty, we applied machine learning and text-mining to extract known and unknown genes...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3164/version/1

Discovery of multiple lead compounds as M2 inhibitors through the focused screening of a small primary amine library.
Provedor de dados: 17
Autores: Wenhui Hu; Shaogao Zeng; Chufang Li; Yanling Jie; Zhiyuan Li; Ling Chen.
The discovery of new anti-influenza drugs is urgent, particularly considering the recent threat of swine flu. In this study, the influenza virus M2 protein was expressed in HEK293 cells and shown to have selective ion channel activity for monovalent ions. The anti-influenza virus drug amantadine hydrochloride significantly attenuated the inward current induced by hyperpolarization of HEK293 cell membranes. Although adamantine derivatives are the only M2 drugs for influenza virus A, their use is limited in the US due to drug resistance. Here we report the discovery of multiple M2 inhibitor lead compounds that were rapidly generated through focused screening of a small primary amine library. The screen was designed using a scaffold-hopping strategy based on...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3688/version/1

Discovery of the Principal Cystic Fibrosis Mutation (F508del) in Ancient DNA from Iron Age Europeans
Provedor de dados: 17
Autores: Philip Farrell; Cedric  Le Marechal; Claude Ferec; Malika  Siker; Maria Teschler-Nicola.
The most common, life-threatening autosomal recessive disease of Europeans and Euro-Americans, cystic fibrosis (CF), occurs predominately in patients with the F508del mutation.1 Although F508del is currently detectable as a single allele in 1/30-1/40 Europeans2-4 and Euro-Americans,5 it has not been determined what heterozygote selective advantage(s) might account for its relatively high prevalence. Indirect evidence6 suggests that this mutation was present in Brittany at least 3000 years ago, but no direct analyses of ancient DNA have been reported to identify F508del and clarify its frequency in prehistoric inhabitants of Europe. Here we show that F508del was present in 3 of 32 Iron Age inhabitants of Austria from whom DNA could be recovered from molar...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1276/version/1

Discovery of transcription factor binding sites through integration of generic motif finders
Provedor de dados: 17
Autores: Edward Wijaya; Siu-Ming Yiu; Thanh Son Ngo; Rajaraman Kanagasabai; Wing-Kin Sung.
Locating transcription factor binding sites is a key step in understanding gene regulation. Due to its importance, many _de novo_ motif-finding methods have been proposed. Individually, these motif finders perform unimpressively overall based on Tompa&amp;#x27;s benchmark datasets. Moreover, these motif finders vary in their definitions of what constitute a motif, and in their methods for finding statistically overrepresented motifs. There is no clear way for biologists to choose the motif finder that is most suitable for their task. The purpose of this work is to describe a method called MotifVoter to identify transcription factor binding sites by integrating the results found by motif finders of different models. Validation of our method on...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1251/version/1

Discriminatory power of MicroResp^TM^ analyses across variable spatial scales in semiarid ecological zones
Provedor de dados: 17
Autores: Mohammad E. W. Tahtamouni; Adrian Unc; Mary Lucero; Sa&amp;#x27;eb Khresat.
Indirect assessment of enzymatic activity potential via substrate induced respiration is a common tool used to evaluate variability in soil microbial activity induced by environmental or management variables. The MicroResp&amp;#x2122; method for total soil sample catabolic profiling has been employed to estimate divergence in microbial activities under contrasting conditions. Here we evaluate the potential for the method to discriminate across samples exposed to similar ecological conditions at distinct geographical locations, and across samples exposed to distinct soil management conditions. Samples used in this report came from four spatially distinct arid or semi arid locations in New Mexico, USA and Jordan. For all scales of comparison, similar...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6204/version/1

Discussion on preservation mechanism of Yersinia pestis by Citellus undulatus
Provedor de dados: 17
Autores: Cunning Qian; Jichun Lin; Yuming Feng; Xiaoxue Zhang; Cheng Wang; Gang Lei.
Studies prove that plague in _Citellus undulatus_ exists in the nature with the pattern of successive prevalence every year. _Citellophilus tesquorum altaicus_ is not only the main transmission vector, but also the reservoir of _C. undulatus_ plague. And the latter can spread _Yersinia pestis_. The fact challenges to the traditional theory of natural focus and carries out a theory breakthrough.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3260/version/1

Disordered proteins and network disorder in network descriptions of protein structure, dynamics and function. Hypotheses and a comprehensive review
Provedor de dados: 17
Autores: Peter Csermely; Kuljeet Singh Sandhu; Eszter Hazai; Zsolt Hoksza; Huba J. M. Kiss; Federico Miozzo; Daniel V. Veres; Francesco Piazza; Ruth Nussinov.
During the last decade, network approaches became a powerful tool to describe protein structure and dynamics. Here we review the links between disordered proteins and the associated networks, and describe the consequences of local, mesoscopic and global network disorder on changes in protein structure and dynamics. We introduce a new classification of protein networks into &amp;#x2018;cumulus-type&amp;#x2019;, i.e., those similar to puffy (white) clouds, and &amp;#x2018;stratus-type&amp;#x2019;, i.e., those similar to flat, dense (dark) low-lying clouds, and relate these network types to protein disorder dynamics and to differences in energy transmission processes. In the first class, there is limited overlap between the modules, which implies higher...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5608/version/1

Dispersal of _Aedes aegypti_: field study in temperate areas and statistical approach
Provedor de dados: 17
Autores: Paula Bergero; Carlos A. Ruggerio; Rub&amp;#xe9;n Lombardo; Nicol&amp;#xe1;s Schweigmann; Hern&amp;#xe1;n Solari.
We studied the dispersion of _Aedes aegypti_ during egg laying in natural conditions. Two independent experiments involving mosquitoes dispersing from urbanization towards adjacent un-urbanized areas were carried out and analyzed in statistical terms. We find relations between stochastic variables related to the egg laying mosquito activity (ELMA), useful to assess dispersion probabilities, despite the lack of knowledge of the total number of ovipositions in the zone. We propose to evaluate the activity as minus the logarithm of the fraction of negative ovitraps at different distances from buildings. We also estimate the average number of eggs laid per oviposition using a regression between the ELMA and the number of eggs found. Three zones with different...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2012
URL: http://precedings.nature.com/documents/6960/version/1

Disruptive Strategies for Removing Drug Discovery Bottlenecks
Provedor de dados: 17
Autores: Sean Ekins; Chris L. Waller; Mary  P. Bradley; Antony J. Williams.
Drug Discovery is shifting focus from the industry to outside partners and in the process creating new bottlenecks, suggesting the need for a more disruptive overhaul. Technologies like high throughput screening (HTS) have moved to a larger number of academic and institutional laboratories in the US, with little apparent coordination or consideration of the outputs and creating a translational gap. While there have been collaborative public private partnerships in Europe to share pharmaceutical data, the USA has lagged behind. Sharing precompetitive computational models may be the next frontier to provide more confidence in the quality of the leads produced and attract investment. We suggest there needs to be an awareness of what research is going on in...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/6961/version/1

Dissecting the Biological Motherboard (Systems Biology and Beyond)
Provedor de dados: 17
Autores: Abhay Krishna; Ajit Narayanan.
Genome-scale molecular networks, including gene pathways, gene regulatory networks and protein interactions, are central to the investigation of the nascent disciplines of systems biology and bio-complexity. Dissecting these genome-scale molecular networks in its all-possible manifestations is paramount in our quest for a genotype-input phenotype-output application which will also take environment-genome interactions into account.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Machine learning approaches are now increasingly being used for reverse engineering such networks. Our work stresses the importance of a system approach in biological research and how artificial neural networks are at the forefront of Artificial Intelligence techniques that are increasingly...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2003/version/1

Dissecting the mechanisms of learning-by-doing in Drosophila
Provedor de dados: 17
Autores: Bj&amp;#xf6;rn Brembs; Wolfgang Plendl.
At the heart of learning-by-doing lies a well-known psychological phenomenon: information will be remembered better if it is actively generated rather than passively read or heard. First described in humans, this generation effect can also be observed in various animal models. However, the neurobiological mechanisms underlying the generation effect are unknown. Here we show that two reciprocal interactions between its active and passive components contribute to the generation effect in flies. One interaction consists of the active (skill-learning) component facilitating the passive (fact-learning) component. Fact-learning, on the other hand, inhibits skill-learning. Experiments with adenylyl cyclase I deficient _rutabaga_ mutant flies revealed that the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1354/version/1

Dissociation of Alzheimer&amp;#x27;s morphological pathology from cognitive impairment
Provedor de dados: 17
Autores: Tohru Hasegawa; Nobuyuki Mikoda.
We observed the Alzheimer&amp;#x27;s morphological pathology, amyloid production induces Alzheimer&amp;#x27;s cognitive impairment, was dissociated from the cognitive impairment. The earlier Alzheimer&amp;#x27;s pathological changes can be induced in normal C57BL mice, by B6 deficient feeding 4 months with no amyloid, and this cognitive and memory impairments were completely inhibited by anti-homocysteic acid antibody. According to Koch&amp;#x27;s postulate, if a pathogen of Alzheimer&amp;#x27;s disease is administrated to the normal animal, we would observe the Alzheimer&amp;#x27;s cognitive impairment in the normal animal. We actually have observed this cognitive impairment in normal C57BL male mice with no amyloid. From our observations, it is suggested...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2949/version/1

Distinct cytokine patterns in Occult Hepatitis C and Chronic Hepatitis C Virus Infection
Provedor de dados: 17
Autores: Nasser Mousa; Nashwa Abousamra; Azza Azza Abdel-Aziz; Yahia Gad; Mona Elhadidy; Mohamed Abd-elmaksoud.
Background &amp;#x26; Aim: &amp;#xd;&amp;#xa;The immunopathogenesis of chronic hepatitis C virus (HCV) infection is a matter of great controversy. The imbalance of T-helper lymphocyte cell cytokine production was believed to play an important pathogenic role in chronic viral hepatitis. Occult hepatitis C infection is regarded as a new entity that should be considered when diagnosing patients with a liver disease of unknown origin. The aim of this study was to determine serum T-helper 1 and T-helper 2 cytokine production in patients with occult HCV infection and its role in pathogenesis versus chronic viral hepatitis C infection.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: &amp;#xd;&amp;#xa;Serum levels of cytokines of T-helper 1 (IL-2, IFN-[gamma]) and...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2011
URL: http://precedings.nature.com/documents/6654/version/1

Distribution of ABO blood groups and Rh(D) factor among the Brahmin and Kushwaha populations of Jhansi District(U.P)
Provedor de dados: 17
Autores: Nawab John Dar; Ankit Srivastava; Farooq A. Dar.
The distribution of ABO blood groups and Rh(D) factor has been studied among the Brahmin and Kushwaha populations of Jhansi Uttar Pradesh. The A,B,O and AB blood group percentage in Brahmins was recorded as 20.88%, 36.64%, 37.02% and 10.44% .The Rh(D) positive percentage was 96.20% and Rh(d) negative 3.79%. In Kushwaha population the percentage of A,B,O and AB  was recorded as 25.65%, 30.26%, 31.25% and 12.82% respectively. The Rh (D)  positive was recorded as 97.36% and Rh(d) negative as 2.63%. The allele frequency of ABO among Brahmins was 0.198, 0.266, 0.536 and in Kushwaha the allele frequency of ABO was recorded as 0.251, 0.278, and 0.471 respectively. So the prevalence of the ABO from the area under study can be shown with a general formula as...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6362/version/1

DNA expression microarrays may be the wrong tool to identify biological pathways
Provedor de dados: 17
Autores: Adrian Mondry; Marie Loh; Alessandro Giuliani.
DNA microarray expression signatures are expected to provide new insights into patho- physiological pathways. Numerous variant statistical methods have been described for each step of the signal analysis. We employed five similar statistical tests on the same data set at the level of gene selection. Inter-test agreement for the identification of biological pathways in BioCarta, KEGG and Reactome was calculated using Cohen&amp;#x2019;s k- score. The identification of specific biological pathways showed only moderate agreement (0.30 &amp;#x3c; k &amp;#x3c; 0.79) between the analysis methods used.  Pathways identified by microarrays must be treated cautiously as they vary according to the statistical method used.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1036/version/1

DNA Genealogy, Mutation Rates, and Some Historical Evidences Written in Y-Chromosome
Provedor de dados: 17
Autores: Anatole Klyosov.
Origin of peoples in a context of DNA genealogy is an assignment of them to a particular tribe (all members of which belong to a certain haplogroup) or its branch (a lineage), initiated in a genealogical sense by a common ancestor and an estimation of a time span between the common ancestor and its current descendants. We have developed an approach to kinetics of haplotype mutations in non-recombinant segments of the Y-chromosome and illustrated it with a number of haplotype series related to various populations (timespans to common ancestors shown as years before the present): Basques R1b1b2 (4,050), near thirty of European countries R1a1 (between 4,100 and 4,825), India R1a1 (3,675), the Arabian Peninsula R1a1 (3,750), South India Chenchu R1a1 (3,200 and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2733/version/1

DNA Sequence Evolution through Integral Value Transformations
Provedor de dados: 17
Autores: Sk Sarif Hassan; Pabitra Pal Choudhury; Ranita Guha; Shantanav Chakraborty; Arunava Goswami.
In deciphering the DNA structures, evolutions and functions, Cellular Automata (CA) do have a significant role. DNA can be thought of as a one-dimensional multi-state CA, more precisely four states of CA namely A, T, C, and G which can be taken as  numerals 0, 1, 2 and 3. Earlier, G.Ch. Sirakoulis et al reported the DNA structure, evolution and function through quaternary logic one dimensional CA and the authors have found the simulation results of DNA evolutions with the help of only four linear CA rules. The DNA sequences which are produced through the CA evolutions, however, are seen by our research team not to exist in the established databases of various genomes although the initial seed (initial global state of CA) was taken from the database. This...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5729/version/1

DNA SEQUENCE PATTERNS
Provedor de dados: 17
Autores: Sriram Kannan.
There is significance in the molecular weight derived sequence patterns of adenosine, guanosine, cytosine, thymine, methyl cytosine and hydroxyl methyl cytosine if one has to consider the molecular events holistically by including single nucleotide polymorphisms, tumor suppressor gene activity like that of ten eleven translocation gene, CpG methylation, miRNA SNP patterns and SNPs neighboring CpGs. This research article focuses on observing simulation results of validated SNPs in a sequence using substitution patterns of molecular weight of A, G, C, T, 5OHC, 5MC.  The outcome helped to bring out positions in a DNA sequence where in validated bi allelic SNPs were never found to occur and SNPs neighboring methylated CpGs do show disconcordance and a...
Tipo: Presentation
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4933/version/1

DNA sequences classification and computation scheme based on the symmetry principle
Provedor de dados: 17
Autores: Xiao-Gang Song; Wen-Yuan Qiu.
The DNA sequences containing multifarious novel symmetrical structure frequently play crucial role in how genomes work. Here we present a new scheme for understanding the structural features and potential mathematical rules of symmetrical DNA sequences using a method containing stepwise classification and recursive computation. By defining the symmetry of DNA sequences, we classify all sequences and conclude a series of recursive equations for computing the quantity of all classes of sequences existing theoretically; moreover, the symmetries of the typical sequences at different levels are analyzed. The classification and quantitative relation demonstrate that DNA sequences have recursive and nested properties. The scheme may help us better discuss the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3116/version/1

DNALinux Virtual Desktop Edition
Provedor de dados: 17
Autores: Sebastian Bassi; Virginia V. C. Gonzalez.
The new version of DNALinux (VDE) is presented. DNALinux VDE is a departure from traditional distributions since it uses a virtual machine to bundle together the operating system and bioinformatics applications. The main advantage of this approach is that a virtualized environment doesn&amp;#x27;t affect a installed system. With a virtual machine a Linux system can be run under a Windows system, provided that the virtual machine player is installed. The included programs are listed and specifications to add more programs are explained. We believe that DNALinux could be used as a standardized virtual machine for learning, using, developing and testing bioinformatics applications.
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/670/version/1

DNA^+Pro^: an Improved Progressive Multiple Sequence Alignment Algorithm for Evolutionary Analysis Using Combined DNA-Protein Sequences
Provedor de dados: 17
Autores: Xiaolong Wang; Shuang-yong  Xu; Deming  Gou.
Alignment of DNA and protein sequences is a basic tool in the study of evolutionary, structural and functional relationship among macromolecules. Present sequence alignment methods are somewhat error-prone, often producing systematic bias. Errors in sequence alignments sometimes lead to subsequent misinterpretation of evolutionary, structural and functional information in genes, proteins and genomes. In traditional sequence alignment algorithms, alignments of DNA and protein sequences are conducted separately. It has been long believed that the phylogenetic signal disappears more rapidly from DNA sequences than from encoded proteins. It is therefore generally preferable to align sequences at the amino acid level. Here we present a new...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4898/version/1

Do enzyme activities during decomposition follow predicted patterns? A test of the conceptual model of litter decay.
Provedor de dados: 17
Autores: Zachary L. Rinkes; Michael N. Weintraub; Jared L. DeForest; Daryl L. Moorhead.
Surprisingly, there remains a paucity of research examining specific interactions between the relationship between microbial community behavior and plant litter chemistry during decomposition. A more mechanistic understanding of the relationship between these drivers will ultimately help determine the trajectory of litter decomposition and the conditions in which soils serve as either a source or sink for atmospheric C. In order to examine these relationships, a laboratory incubation was established using _Acer saccharum_ litter and a sandy soil (&amp;#x3c; 1.5% organic matter). Extracellular enzyme activities ([BETA]-glucosidase, N-acetyl glucosaminidase, leucine-amino peptidase, acid phosphatase, phenol oxidase, and peroxidase) were monitored on a...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6226/version/1

Do not log-transform count data
Provedor de dados: 17
Autores: Robert B. O&amp;#x27;Hara; Johan Kotze.
1. Ecological count data (e.g., number of individuals or species) are often log-transformed to satisfy parametric test assumptions.&amp;#xd;&amp;#xa;2. Apart from the fact that generalized linear models are better suited in dealing with count data, a log-transformation of counts has the additional quandary in how to deal with zero observations. With just one zero observation (if this observation represents a sampling unit), the whole dataset needs to be fudged by adding a value (usually 1) before transformation. &amp;#xd;&amp;#xa;3. Simulating data from a negative binomial distribution, we compared the outcome of fitting models that were transformed in various ways (log, square-root) with results from fitting models using Poisson and negative binomial...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4136/version/1

Do they or don&amp;#x27;t they? A synthesis of microbial response to environmental change
Provedor de dados: 17
Autores: Teri C. Balser.
Background/Question/Methods&amp;#xd;&amp;#xa;Microbial communities have long been thought to possess infinite plasticity, yet evidence in recent years increasingly indicates compositional resistance to change.&amp;#xd;&amp;#xa;While this discovery may largely be due to the changing nature of soil biological research &amp;#x2013; with its move beyond single-season and single-factor experiments, it nevertheless highlights a critical area in current ecosystem studies and soil microbial ecology. Do they or don&amp;#x27;t they change? When? Under what circumstances? And does it matter?&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results/Conclusions&amp;#xd;&amp;#xa;In this talk I review microbial community compositional shifts. First I address general microbial response...
Tipo: Presentation
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5504/version/1

Docking and QSAR Studies of Camptothecin Derivatives as Inhibitor of DNA Topoisomerase-I
Provedor de dados: 17
Autores: Dharmendra  K. Yadav; Feroz  Khan; Santosh K. Srivastava.
Camptothecin (CPT) is a cytotoxic quinoline alkaloid which inhibits the DNA enzyme Topoisomerase-I (Topo-I) and has shown remarkable anticancer activity in preliminary clinical trials. The major limitation is its low solubility and high adverse reaction. In the studied work, we performed molecular docking of CPT derivatives against Topo-I and developed the quantitative structure activity relationship (QSAR) model for anticancer activity screening. For QSAR, we used CPT and other anticancer drugs with its IC50 values. We used a total of forty seven anticancer drugs as training set and eight compounds as test set and thirty derivatives of CPT as query set. Total of fifty two chemical descriptors were used for the quantitative data calculation. Only four...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5773/version/1

Docking studies to explore novel inhibitors against human beta-site APP cleaving enzyme (BACE-1) involved in Alzheimer&amp;#x2019;s disease
Provedor de dados: 17
Autores: S Anjum Mobeen; Manne  Munikumar; Amineni Umamaheswari.
Alzheimer&amp;#x2019;s disease (AD) is one of the most prominent neurodegenerative disorders, particularly in elder persons over 65 age. It is characterized by progressive cognitive deterioration together with declining activities. Amyloid precursor protein (APP) cleaves at A-beta (A&amp;#x3b2;) peptide by rate limiting factor of Beta-site APP cleaving enzyme (BACE-1) in amyloidogenic pathway. Elevated level of BACE-1 leads to the accumulation of an insoluble form of A&amp;#x3b2; peptides (Senile Plaques), an important hallmark in the pathogenesis of Alzheimer disease. Five published inhibitors of BACE-1, thiazolidinediones, rosiglitazone, pioglitazone, Sc7 and tartaric acid are available with poor pharmacological properties and intolerable side effects....
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6964/version/1

Docking studies to explore novel lead molecules for human Spleen tyrosine kinase involved in chronic lymphocytic leukemia
Provedor de dados: 17
Autores: Naveen  Kadaari; Dibyabhaba  Pradhan; Manne  Munikumar; Amineni  Umamaheswari.
B-cell chronic lymphocytic leukemia (CLL) is the most prevalent B-cell malignancy in adults. Despite advances in treatment, the disease remains incurable, warranting further efforts to identify novel molecular targets and inhibitors. Spleen tyrosine kinase (SYK) plays a pivotal role for B-lymphocyte development and maturation in the B-cell receptor (BCR) signaling pathway and hence represents a potential therapeutic target for CLL. The present study is directed towards finding novel inhibitors of SYK through ligand based virtual screening. The co-crystal structure of SYK was investigated to locate active site residues (Glu-449, Ala-451 Arg-498, Asn-499, Ser-511, and Asp-512). Five SYK specific published inhibitors (Gleevec, staurosporine, Bay61-3606, R-406...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5460/version/1

Docking-based virtual screening for the exploration of potential antagonists for human IGFBP6
Provedor de dados: 17
Autores: Bhuvanagiri Sravani; Dibyabhaba Pradhan; Amineni  Umamaheswari.
Design of potential drug-like candidates for cardiovascular therapy is of interest in recent years. Elevated level of IGFBP-6 leads to perilous diseases like atherosclerosis, high output cardiac failure and myocardial infarction. The current IGFBP-6 inhibitors available in clinical practice are not having satisfactory anti-cardiovascular effects, leaving room for further improvement. Therefore, with an aim to propose a potent inhibitor to arrest the cardiovascular disease caused by IGFBP-6, tools of computer-aided drug designing were used for virtual screening from small molecule databases. Accordingly, IGFBP-6 tertiary structure was solved through nuclear magnetic resonance techniques retrieved from the protein data bank. Fifteen IGFBP-6 inhibitors were...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6525/version/1

Does accounting for imperfect detection improve species distribution models?
Provedor de dados: 17
Autores: Christopher T. Rota; Robert J. Fletcher; Jason M. Evans; Richard L. Hutto.
Background/Question/Methods&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Models of species distributions are increasingly being used to address a variety of problems in ecology and conservation biology. In many applications, perfect detectability of species, given presence, is assumed. While this problem has been acknowledged and addressed through the development of occupancy models, we still know little regarding whether or not addressing the potential for imperfect detection improves the predictive performance of species distribution models in nature. Here, we ask if explicitly accounting for imperfect detection improves predictive performance of species distribution models relative to approaches that assume perfect detection.  We contrast logistic regression...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5201/version/1

Does human imitate successful behaviors immediately?
Provedor de dados: 17
Autores: Zhao-Jin Xu; Lian-Zhong Zhang.
The emergence and abundance of cooperation in animal and human societies is a challenging puzzle to evolutionary biology. Over the past decades, various mechanisms have been suggested which are capable of supporting cooperation. Imitation dynamics, however, are the most representative microscopic rules of human behaviors on studying these mechanisms. Their standard procedure is to choose the agent to imitate at random from the population. In the spatial version this means a random agent from the neighborhood. Hence, imitation rules do not include the possibility to explore the available strategies, and then they have the possibility to reach a homogeneous state rapidly when the population size is small. To prevent evolution stopping, theorists allow for...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4480/version/1

Does Optic Flow Explain the Firing of Grid Cells?
Provedor de dados: 17
Autores: Florian Raudies; Ennio Mingolla; Michael Hasselmo.
*Problem.* Various cues such as vestibular, sensorimotor, or visual information can lead to the firing of grid cells recorded in entorhinal cortex of rats. A recent model uses boundary vector cells to provide information about the 2D spatial position (Barry et al., Review Neuroscience, 17, 2006). However, boundary vector cells need to know the angle and distance of the boundary wall. In contrast we study the estimation of 2D velocity and change of heading of the rat from optic flow and if this information can lead to grid cell firing.&amp;#xd;&amp;#xa;*Approach.* A simple circular cage is modeled as a 3D world and trajectories of a rat&amp;#x2019;s movement are simulated. Optic flow for a spherical camera model is calculated for regularly sampled locations...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5839/version/1

Does the Density of Invasive Rusty Crayfish Affect Stream Macroinvertebrates?
Provedor de dados: 17
Autores: Mark Kuhlmann; Anthony Prisciondaro; Megan Irland; Greg Hamilton; Sara Caldwell; Ryan Oliver.
Rusty crayfish (_Orconectes rusticus_) have invaded streams of the upper Susquehanna River catchment (New York, USA), replacing native crayfish and probably increasing overall crayfish density. Crayfish are important consumers and agents of disturbance in aquatic communities, so the introduction and expansion of rusty crayfish could affect the invaded community through the change in crayfish species composition, the increase in crayfish density, or some combination of the two. Other macroinvertebrates are prey of, competitors with, or subject to disturbance by crayfish and so are likely to be affected by changes in the crayfish assemblage. We conducted correlative field sampling and an enclosure experiment to investigate the effects of invading _O....
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3701/version/1

Dogs Never Gets Prion Diseases. The Entropic Landscape Analysis of Prion Proteins Answers Why.
Provedor de dados: 17
Autores: Kentaro Onizuka.
The Entropic Landscape Analysis was applied to the prion protein sequences of various mammals in order to detect potential sites of variants that would be responsible for the susceptibility of prion disease infection. Among familiar mammals, canines including dogs have been demonstrating strong resistance to prion diseases. Among the canine specifc substitutions the entropic landscape analysis pinpoints the substitutions Asn104Gly and Ser107Asn having the biggest impact to the conformational transition and stability. Although they must be further corroborated by experiments in vivo et vitro, the results are demonstrating that the entropic landscape analysis is useful enough to screen substitutions and polymorphisms potentially relevant to conformational...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3043/version/1

Donor mesenchymal stem cells trigger chronic graft-versus-host disease following minor antigen-mismatched bone marrow transplantation
Provedor de dados: 17
Autores: Yoko Ogawa; Satoru Morikawa; Hideyuki Okano; Yo Mabuchi; Sadafumi Suzuki; Tomonori Yaguchi; Saori Yaguchi; Takaaki Inaba; Shinichiro Okamoto; Yutaka Kawakami; Kazuo Tsubota; Shigeto Shimmura; Yumi Matsuzaki.
Chronic graft-versus-host disease (cGVHD) is a complication after minor antigen mismatched bone marrow transplantation (BMT) characterized by an autoimmune-type reaction in various organs. Aberration in T cell regulation is involved, with donor mesenchymal stem cells (MSCs) playing a possible role in immunomodulation. In a minor-antigen mismatched mouse BMT model, transplantation of mismatched, but not syngeneic MSCs triggered the onset of cGVHD, and was associated with fibrosis, increased IL-6 secretion, decreased Foxp3+ regulatory T cells and increased Th17 in the peripheral blood. Mismatched MSCs alone were sufficient to induce cGVHD, while removal of donor MSCs rescued mice from cGVHD. RAG2 knockout recipient mice did not suffer cGVHD, indicating that...
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology.
Ano: 2012
URL: http://precedings.nature.com/documents/6843/version/1

Dorsal Nucleus Raph&amp;#xe9;
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Josh J. Royall; Lydia L. Ng; John A. Morris.
This report contains a gene expression summary of the dorsal nucleus raph&amp;#xe9; (DR), derived from the Allen Brain Atlas (ABA) in-situ hybridization (ISH) mouse data set.  &amp;#xd;&amp;#xa;The structure&amp;#x2019;s location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the DR were compared to the values of the macro/parent-structure, in this case the midbrain, for the purpose of extracting regionally specific gene expression data.  The highest ranking ratios were then manually curated and verified.  The 50 Select Genes were compiled for expression characterization.  The experimental data for each gene may be accessed...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2054/version/1

Double burden of malnutrition among urban Bengalee adolescent boys in Midnapore, West Bengal, India
Provedor de dados: 17
Autores: S Bisai; R Khongsdier; K Bose; D Mahalanabis.
Malnutrition is an important public health problem worldwide. Therefore a study was undertaken to assess the prevalence of adolescent thinness, overweight and obesity in Midnapore town, West Bengal, India. A total of 974 adolescent boys aged 10-18 years were selected following multistage cluster sampling method from three higher secondary schools. Data was collected using pretested questionnaire following standard technique. Presence of thinness was evaluated using the cut-off values of international survey as suggested by Cole et al (2007). While overweight and obesity was determine by using international cut-off values develop by Cole et al (2000) based on international surveys as recommended by IOTF.   Overall the prevalence of thinness, overweight and...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth &amp; Environment; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7106/version/1

Double burden of malnutrition among urban Bengalee adolescent boys in Midnapore, West Bengal, India
Provedor de dados: 17
Autores: S Bisai; R Khongsdier; K Bose; D Mahalanabis.
Malnutrition is an important public health problem worldwide. Therefore a study was undertaken to assess the prevalence of adolescent thinness, overweight and obesity in Midnapore town, West Bengal, India. A total of 974 adolescent boys aged 10-18 years were selected following multistage cluster sampling method from three higher secondary schools. Data was collected using pretested questionnaire following standard technique. Presence of thinness was evaluated using the cut-off values of international survey as suggested by Cole et al (2007). While overweight and obesity was determine by using international cut-off values develop by Cole et al (2000) based on international surveys as recommended by IOTF.   Overall the prevalence of thinness, overweight and...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth &amp; Environment; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7106/version/2

Down-regulation of serotonergic genes expression in the raphe nuclei of midbrain under chronic social defeat stress in male mice
Provedor de dados: 17
Autores: Ul&amp;#x2019;yana A.  Boyarskikh; Natalya P. Bondar; Maxim L. Filipenko; Natalia N. Kudryavtseva.
Background: &amp;#xd;&amp;#xa;There is ample experimental evidence supporting the hypothesis that the brain serotonergic system is involved in the control of chronic social defeat stress (CSDS), depression and anxiety. The study aimed to analyze mRNA levels of the serotonergic genes in the raphe nuclei of the midbrain that may be associated with chronic social defeats consistently shown by male mice in special experimental settings. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methodology/Principal Findings: &amp;#xd;&amp;#xa;The serotonergic genes were the Tph2, Sert, Maoa and Htr1a. The Bdnf, Creb, Cphn, Gapdh, Hprt, B2M, 18S and Actb genes were also studied. The experimental groups were composed of male mice with experience of defeats in 21 daily encounters and...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6543/version/1

Down-regulation of Survivin enhances sensitivity to BPR0L075 in human cancer cells via caspase-independent mechanisms
Provedor de dados: 17
Autores: Chun Hei Antonio Cheung; Ching-Chuan Kuo; Chi-Yen  Chang; Mohane Selvaraj Coumar; Hsing-Pang Hsieh; Jang-Yang Chang.
Background: BPR0L075 [6-methoxy-3-(3&amp;#x27;,4&amp;#x27;,5&amp;#x27;-trimethoxy-benzoyl)-1H-indole] is a novel anti-cancer compound. It inhibits tubulin polymerization and induces mitochondrial-dependent apoptosis in various human cancer cells with different multi-drug resistance (MDR) status. Over-expression of an anti-apoptotic molecule, survivin, causes drug-resistance in various cancers. Survivin inhibits apoptosis by interfering caspase-3 and promotes cell growth by stabilizing microtubule networks. Here, we determined the effects of down-regulation of survivin in BPR0L075 (L075) treatment. Methods: Western blot analysis was used to determine the expression level of survivin in L075-untreated/-treated human oral carcinoma KB and nasopharyngeal...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/2729/version/1

Drone congregation areas of red dwarf honeybee, Apis florea
Provedor de dados: 17
Autores: Narayanappa Nagaraja; Axel Brockmann.
The drones of dwarf honeybees assemble at the drone congregation areas close to small trees with dense leafage at the heights between 2 to 4 meters.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3955/version/1

_Drosophila_ and human transcriptomic data mining provides evidence for therapeutic mechanism of pentylenetetrazole in Down syndrome
Provedor de dados: 17
Autores: Abhay Sharma.
Pentylenetetrazole (PTZ) has recently been found to ameliorate cognitive impairment in rodent models of Down syndrome (DS). The mechanism underlying PTZ&amp;#x2019;s therapeutic effect is however not clear. Microarray profiling has previously reported differential expression of genes in DS. No mammalian transcriptomic data on PTZ treatment however exists. Nevertheless, a _Drosophila_ model inspired by rodent models of PTZ induced kindling plasticity has recently been described. Microarray profiling has shown PTZ&amp;#x2019;s downregulatory effect on gene expression in fly heads. In a comparative transcriptomics approach, I have analyzed the available microarray data in order to identify potential mechanism of PTZ action in DS. I find that transcriptomic...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4330/version/1

Drug Use During Antenatal Period at a Tertiary Care Hospital
Provedor de dados: 17
Autores: Nargis Kureshee; Priti Dhande; Vijaya Pandit.
Objective- To assess current treatment practices and awareness of drug intake, in pregnant women, at a tertiary care hospital.&amp;#xd;&amp;#xa;Methodology- Observational, cross-sectional study, involving interview with 60 pregnant women, in outpatient clinic and ward of Obstetrics-Gynaecology department. Data from prescriptions &amp;#x26; case-files also collected. Drugs were classified according to pharmacological class and teratogenic potential using U.S. FDA classification.&amp;#xd;&amp;#xa;Results- Most commonly prescribed drugs were iron, folic acid and calcium supplements. Out of the total 215 drugs prescribed, majority were from Category A(70.2%) followed by Category B(18.6%),Category C(8.8%),Category-X(1.3%) and Category-D(0.9%). 26.6% women...
Tipo: Presentation
Palavras-chave: Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/5424/version/1

Dual Diode Array and Fourier Transform Near Infrared Reflectance Spectrometer Calibrations for Composition Analysis of Single Soybean Seeds for Genetic Selection, Cross-Breeding Experiments
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng You; Randall  L. Nelson.
Experimental results of extensive evaluations of Diode-Array and FT-NIRS instruments are presented that aim at developing reliable and robust NIR calibrations for single soybean seed composition analysis on both Dual Diode Array and Fourier Transform NIR reflectance instruments. Single soybean seed, bulk, and powder calibrations were developed on four different NIRS spectrometer models that are commercially available.
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6195/version/1

Dual expression recombinase based (DERB) single vector system for high throughput screening and verification of protein interactions in living cells
Provedor de dados: 17
Autores: Jian-Ping Lu; Laura Beatty; Jehonathan  Pinthus.
Identification of novel protein interactions and their mediators is fundamental in understanding cellular processes and is necessary for protein-targeted therapy. Evidently high throughput formatting of these applications in living cells would be beneficial, however no adequate system exists. We present a novel platform technology for the high throughput screening and verification of protein interactions in living cells. The platform&amp;#x2019;s series of Dual Expression Recombinase Based (DERB) destiny vectors individually encode two sets of recombinase recognizable sequences for inserting the protein open reading frame (ORF) of interest, two sets of promoters and reporter tags in frame with the ORFs for detecting interactions. Introduction into living...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1550/version/2

Dual expression recombinase based (DERB) single vector system for high throughput screening and verification of protein interactions in living cells
Provedor de dados: 17
Autores: JianPing Lu; Laura Beatty; Jehonathan Pinthus.
Identification of novel protein interactions and their mediators is fundamental in understanding cellular processes and is necessary for protein-targeted therapy. Evidently high throughput formatting of these applications in living cells would be beneficial, however no adequate system exists. We present a novel platform technology for the high throughput screening and verification of protein interactions in living cells. The platform&amp;#x27;s series of Dual Expression Recombinase Based (DERB) destiny vectors individually encode two sets of recombinase recognizable sequences for inserting the protein open reading frame (ORF) of interest, two sets of promoters and reporter tags in frame with the ORFs for detecting interactions. Introduction into living...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/1550/version/1

Dung beetles can eat acorns to increase their fitness
Provedor de dados: 17
Autores: Jose R. Verdu; Jose L. Casas; Jorge Lobo; Catherine Numa.
Animals eat different foods in proportions that yield a more favourable balance of nutrients. In spite of known examples of these behaviours across different taxa, the ecological and physiological benefits remain unknown. We identified a surprising dietary shift that confers ecophysiological advantages in a dung beetle species. _Thorectes lusitanicus_, a Mediterranean ecosystem species adapted to eat dung, is also actively attracted to oak acorns - consuming and burying them. Acorn consumption appears to confer advantages over beetles that do not eat acorns: acorn-fed beetles showed important improvements in fat body mass, haemolymph composition, and ovary development. Beetles incorporating acorns into their diets should have greatly improved resistance to...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3263/version/1

Dust in the wind &amp;#x2013; drift of dust containing insecticides &amp;#x2013; a risk for honey bees (_Apis mellifera_ L.)?
Provedor de dados: 17
Autores: Pablo T. Georgiadis; Jens Pistorius; Udo Heimbach.
In late April 2008, dust drift containing insecticide resulted in the largest bee poisoning in Germany for 30 years. The reason for these incidents was the contamination of flowering bee forage plants with dust particles abraded from maize seeds treated with Clothianidin recorded in the Upper Rhine Valley, Baden-Wuerttemberg and in parts of Bavaria during sowing of maize.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Clothianidin, an insecticidal active substance from the group of neonicotinoids, works as agonist at the nicotinic acetylcholine receptors with broad spectrum of efficacy. Clothianidin is also used as a seed dressing of maize (agent for seed treatment &amp;#x201c;Poncho Pro&amp;#xae;&amp;#x201d;; 1,.25 mg a.i. Clothianidin./kernel) for the control of the...
Tipo: Presentation
Palavras-chave: Chemistry; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5738/version/1

Dynamic gating in the nucleus accumbens: Behavioral state-dependent synchrony with the prefrontal cortex and hippocampus
Provedor de dados: 17
Autores: Rifat J. Hussain; Aaron J. Gruber; Patricio O&amp;#x27;Donnell.
Contextual and sensory information, goals, and the motor plan to achieve them are integrated in the nucleus accumbens (NA). Although this integration needs flexibility to operate in a variety of environments, models of NA function rarely consider changing behavioral states. Here, intracellular recordings in anesthetized rats revealed rapid changes in the synchronization between NA up states and prefrontal cortical (PFC) local field potentials (LFPs). The synchronization of the NA with the PFC and ventral hippocampus also varied over time in awake rats, depending on the behavioral state of the animal: NA LFPs followed hippocampal theta rhythms during spatial exploration, but not during an operant task when they were instead synchronized with slower PFC...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1629/version/1

Dynamic hydration valve controlled ion permeability and stability of NaK channel
Provedor de dados: 17
Autores: Rong Shen; Wanlin Guo; Wenyu Zhong.
The K^+^, Na^+^, Ca^2+^ channels are essential to neural signalling, but our current knowledge at atomic level is mainly limited to that of K^+^ channels. Unlike a K^+^ channel having four equivalent K^+^-binding sites in its selectivity filter, a NaK channel conducting both Na^+^ and K^+^ ions has a vestibule in the middle part of its selectivity filter, in which ions can diffuse but not bind specifically. However, how the NaK channel conducts ions remains elusive. Here we find four water grottos connecting with the vestibule of the NaK selectivity filter. Molecular dynamics and free energy calculations show that water molecules moving in the vestibule-grotto complex hydrate and stabilize ions in the filter and serve as a valve in conveying ions through...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2045/version/1

Dynamic is-a Hierarchy Generation from a Clinical Medical Ontology
Provedor de dados: 17
Autores: Hiroko Kou; Jun Zhou; Mamoru Ohta; Kouji Kozaki; Ken Imai; Kazuhiko Ohe; Riichiro Mizoguchi.
This article discusses an ontology-handling technology to provide on-demand reorganization of is-a hierarchy of diseases instead of one fixed hierarchy to cope with various viewpoints which physicians might have. It is one of the important benefits of our medical ontology which is developed as a Japanese national project. This technology tackles with the multi-perspective issues of medical knowledge.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3501/version/1

Dynamic is-a Hierarchy Generation from a Clinical Medical Ontology
Provedor de dados: 17
Autores: Hiroko Kou; Jun Zhou; Mamoru Ohta; Kouji Kozaki; Ken Imai; Riichiro Mizoguchi; Kazuhiko Ohe.
This article discusses an ontology-handling technology to provide on-demand reorganization of is-a hierarchy of diseases instead of one fixed hierarchy to cope with various viewpoints which physicians might have. It is one of the important benefits of our medical ontology which is developed as a Japanese national project. This technology tackles with the multi-perspective issues of medical knowledge.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3502/version/1

Dynamic Modeling of Vaccinating Behavior as a Function of Individual Beliefs
Provedor de dados: 17
Autores: Fl&amp;#xe1;vio C. Coelho; Cl&amp;#xe1;udia T. Code&amp;#xe7;o.
Individual perception of vaccine safety is an important factor in determining a person&amp;#x27;s adherence to a vaccination program and its consequences for disease control. This perception, or belief, about the safety of a given vaccine, is not a static parameter but a variable subject to environmental influence. To complicate matters, perception of risk (or safety) does not correspond to actual risk. In this paper we propose a way to model the dynamics of such beliefs in the context of a realistic epidemiological scenario. The methodology proposed is based on Bayesian inference, and can be extended to model more complex belief systems associated with decision models.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2447/version/1

Dynamic reorganization of the middle fusiform gyrus: long-term bird expertise predicts decreased face selectivity
Provedor de dados: 17
Autores: Chun-Chia Kung; Colin Ellis; Michael J. Tarr.
What is the functional relationship between face-selective and expertise-predicated object-selective regions in the human middle fusiform gyrus? In two separate fMRI experiments, superior behaviorally-measured bird expertise predicts both higher middle fusiform gyrus selectivity for birds and, concomitantly, lower selectivity for faces. This finding suggests a long-term dynamic reorganization of the neural mechanisms underlying the visual recognition of faces and non-face.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2467/version/1

Dynamic Structures in SBML
Provedor de dados: 17
Autores: Chris Myers.
This talk describes ideas on how to integrate dynamic structures in SBML.
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6342/version/1

Dynamic Topology of Biological Networks
Provedor de dados: 17
Autores: Ravi Iyengar.
The mammalian cell can be represented as a large modular network that consists of a central signal network that interacts with and regulates multiple cellular machines that are responsible for phenotypic behavior.  We have used graph-theory approaches to analyze signal flow through a network representing the hippocampal neuron and find that signal-induced connectivity results in the formation of many regulatory motifs. Information flow through the central signaling network is initiated by extra-cellular signals such as hormones binding to their receptors. The flow of information through the signaling network results in the appearance of regulatory motifs such as feedback loops, feedforward and bifan motifs. Within the large cellular networks, these...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/24/version/1

Dynamical Mean Field approximation of a canonical cortical model for studying inter-population synchrony
Provedor de dados: 17
Autores: Ram&amp;#xf3;n  Mart&amp;#xed;nez-Cancino; Roberto Carlos Sotero Diaz.
The goal of this paper is twofold.  We propose and explore a model to study the synchronization among populations in the canonical model of the neocortex proposed previously by (R.J. Douglas, K.A.C. Martin, A functional microcircuit for cat visual cortex. J.Physiol. 440(1991) 735&amp;#x2013;769). For this, a model describing N synapses of each m-population (m = 1, 2,3) is proposed. Each synapse is described by a system of 2 stochastic differential equations (SDEs). Then, by using the dynamical mean field approximation (DMA) (H. Hasegawa, Dynamical mean-field theory of spiking neuron ensembles: Response to a single spike with independent noises, Phys. Rev. E. (2003)1-19.) the system of several SDEs is reduced to 12 ordinary differential equations for the...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5583/version/1

Dynamical patterns of human postural responses to emotional stimuli
Provedor de dados: 17
Autores: Pandelis Perakakis; Jaime Vila; Sofia Idrissi; Plamen Ivanov.
Erotic scenes and images of mutilated bodies are emotional stimuli that have repeatedly shown to evoke specific neurophysiological responses associated with enhanced attention and perceptual processing. Remarkably however, only a handful of studies have investigated human motor reactions to emotional activation as a direct index of physical approximation or withdrawal. Given the inconclusive results of these studies, the approach-avoidance distinction, one of the most salient concepts in human motivational research, remains a broadly exploited hypothesis that has never been empirically demonstrated. Here, we investigate postural responses elicited by discrete emotional stimuli in healthy young adults. We discover that both positive and negative affective...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6428/version/1

Dynamics of proteins and DNA in a Paul trap
Provedor de dados: 17
Autores: Kushal Shah.
Paul traps are increasingly being used in a wide variety of applications in biology including study of protein dynamics and DNA sequencing. In this paper, statistical properties of a macromolecule chain in a Paul trap are theoretically analyzed using a simple model of charged particles connected by rigid rods. It is found that the mean displacement of chain varies linearly with the chain length, showing properties of enhanced diffusion, compared to the normal diffusion relation which exists for the case of a macromolecule chain in a force-free region. The dependence of the mean displacement on the chain length and trap parameters is also found to be very different for the case of pure dc operation and pure ac operation of the Paul trap.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6297/version/1

Dysbindin-1 in dorsolateral prefrontal cortex of schizophrenia cases is reduced in an isoform-specific manner unrelated to altered dysbindin-1 gene expression
Provedor de dados: 17
Autores: Junxia Tang; Robert P. LeGros; Natalia Louneva; Lilly Yeh; Julia W. Cohen; Chang-Gyu Hahn; Derek J. Blake; Steven E. Arnold; Konrad Talbot.
DTNBP1 (dystrobrevin binding protein 1) remains one of the top candidate genes in schizophrenia. Reduced expression of this gene and the protein it encodes, dysbindin-1, has been reported in the dorsolateral prefrontal cortex (DLPFC) of schizophrenia cases. It has not been established, however, if all dysbindin-1 isoforms are reduced in the DLPFC or if the reduction is associated with reduced DTNBP1 gene expression. Using Western blotting of whole-tissue lysates of the DLPFC with antibodies differentially sensitive to the three major isoforms of this protein (dysbindin-1A, -1B, and -1C), we found no significant differences between our schizophrenia cases and matched controls in dysbindin-1A or -1B, but did find a mean 46% reduction in dysbindin-1C in 71%...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2779/version/1

Dyslexia and the assessment of visual attention
Provedor de dados: 17
Autores: John Skoyles; Bernt C. Skottun.
Visual stream segregation has been proposed as a method to measure visual attention in dyslexia. Another task proposed to do this is the line-motion illusion. Both tasks, it is observed, can be carried out with spatially distributed stimuli. This, however, appears inconsistent with these tasks being linked speci?cally to attentional processes since this would require them to spatially focus cognitive resources. Also, both line-motion and visual stream segregation involve the perception of movement raising the possibility that what is actually measured by these tasks is not attention but some aspect of motion perception.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5529/version/1

Dyslexia, magnocellular integrity and rapidly presented stimuli
Provedor de dados: 17
Autores: Bernt C. Skottun; John R. Skoyles.
Conlon at al. (2011, Brain and Cognition, 76, 197-205) studied the responses of dyslexic readers and controls to rapidly presented stimuli. They found that the dyslexic readers showed poorer performance than the controls but only when the interstimulus interval (ISI) was short (150 ms), not when it was long (350 ms). This difference they attributed to a magnocellular or dorsal stream deficiency. However, they did not compute the temporal frequency spectra of the two stimuli. This is done here. It is found that it is very difficult to draw any conclusions with regard to the magnocellular system or the dorsal stream using these stimuli.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6050/version/1

Dys-regulated Gene Expression Networks by Meta-Analysis of Microarray Data on Oral Squamous Cell Carcinoma
Provedor de dados: 17
Autores: Zhongyu Liu; Yulong Niu; Chao Li; Yang Zhou; Yi Yang; Chunfang Gao.
Background: Oral squamous cell carcinoma (OSCC) is the sixth most common type of carcinoma worldwide. Development of OSCC is a multi-step process involving genes related to cell cycle, growth control, apoptosis, DNA damage response and other cellular regulators. The pathogenic pathways involved in this tumor are mostly unknown and therefore a better characterization of OSCC gene expression profile would represent a considerable advance. The availability of publicly available gene expression datasets has opened up new challenges especially for the integration of data generated by different research groups and different array platforms with the purpose of obtaining new insights on the biological process...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4269/version/1

EAG K+ channel joins the p53&amp;#x2212;miR-34&amp;#x2212;E2F1 signaling pathway as a terminal effecter component for its oncogenic overexpression and action
Provedor de dados: 17
Autores: Zhiguo Wang; Chang Chen; Zhe Li; Xiaobin Luo; Jiening Xiao; Huixian Lin; Jianchun Zhang; Deli Dong; Yanjie Lu; Baofeng Yang.
The human ether-&amp;#xe0;-go-go-1 (h-eag1) voltage-dependent K+ channel is necessary for cell cycle progression and its overexpression stimulates tumorigenesis; specific inhibition of h-eag1 expression leads to a reduction in tumor cell proliferation in vitro and in vivo. On the other hand, the tumor-suppressor gene p53 and its downstream genes consist of a complex molecular signaling network and p53 is at the center of this network regulating diverse physiological responses to cancer-related stresses. We report here that h-eag1 expression is controlled by the p53&amp;#x2212;miR-34&amp;#x2212;E2F1 pathway through a negative feed-forward mechanism. We first established E2F1 as a transactivator of h-eag1 gene. We then revealed that miR-34, a known...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4507/version/1

eagle-i: An Ontology-Driven Framework For Biomedical Resource Curation And Discovery
Provedor de dados: 17
Autores: Erik  Segerdell; Melanie L. Wilson; Ted Bashor; Daniela Bourges-Waldegg; Karen Corday; H. Robert Frost; Tenille Johnson; Christopher J. Shaffer; Larry Stone; Carlo Torniai; Melissa A. Haendel.
The eagle-i Consortium (&amp;#x22;http://www.eagle-i.org/home&amp;#x22;:www.eagle-i.org/home) comprises nine geographically and ethnically diverse universities across America working to build a federated network of research resources. Biomedical research generates many resources that are rarely shared or published, including: reagents, protocols, instruments, expertise, organisms, training opportunities, software, human studies, and biological specimens. The goal of eagle-i is to improve biomedical research by helping researchers more easily find scientific resources that are difficult to discover, reducing time-consuming and expensive duplication of resources. Now in early development, the system will ultimately expand to include research resources at...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5176/version/1

Early Diagnosis of Alzheimer&amp;#x27;s disease by NIRF Spectroscopy  and Nuclear Medicine
Provedor de dados: 17
Autores: I. C. Baianu.
There is an urgent need for the early detection of diseases such as Alzheimer&amp;#x2019;s (AD) and Cancers in order to enable their successful treatment. Cancer is the second major cause of death after Heart Disease, and AD is the third major cause of death with major, human and financial/economics trillion dollar consequences for the society. Nuclear Medicine is concerned with applications in Medicine of Nuclear Science and Engineering techniques and knowledge. Three major Nuclear Medicine techniques that are established for diagnostic and research purposes are: Positron Emission Tomography (PET) and CAT/CT, Nuclear Magnetic Resonance Imaging (NMRI/MRI). However, these three techniques have also major limitations in terms of either cost or image...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6271/version/1

Early Diagnosis of Alzheimer&amp;#x27;s disease by NIRF Spectroscopy  and Nuclear Medicine-v.4.0
Provedor de dados: 17
Autores: I Baianu.
There is an urgent need for the early detection of diseases such as Alzheimer&amp;#x2019;s (AD) and Cancers in order to enable their successful treatment. Cancer is the second major cause of death after Heart Disease, and AD is the third major cause of death with major, human and financial/economics trillion dollar consequences for the society. Nuclear Medicine is concerned with applications in Medicine of Nuclear Science and Engineering techniques and knowledge. Three major Nuclear Medicine techniques that are established for diagnostic and research purposes are: Positron Emission Tomography (PET) and CAT/CT, Nuclear Magnetic Resonance Imaging (NMRI/MRI). However, these three techniques have also major limitations in terms of either cost or image...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6273/version/1

Early exposure to environmental toxin contributes to neuronal vulnerability and axonal pathology in a model of familial ALS
Provedor de dados: 17
Autores: Grace Lee; Christopher A. Shaw.
Adult onset amyotrophic lateral sclerosis (ALS) arises due to progressive and irreversible functional deficits to the central nervous system, specifically the loss of motor neurons. Sporadic ALS causality is not well understood, but is almost certainly of multifactorial origin involving a combination of genetic and environmental factors. The discovery of endemic ALS in the native Chamorro population of Guam during the 1950s and the co-occurrence of parkinsonism and dementia in some patients led to searches for an environmental toxins that could be responsible. In the present paper, we report that an environmental neurotoxin enhances mutant superoxide dismutase (SOD)-induced spinal motor neuron death and pathology and induces motor axon abnormalities. These...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6559/version/1

Early Life Relict Feature in Peptide Mass Distribution
Provedor de dados: 17
Autores: Roman A. Zubarev; Konstantin Artemenko; Alexander  R. Zubarev; Corina Mayrhofer; Eva Y. M. Fung.
Molecular mass of a biomolecule is characterized in mass spectroscopy by the monoisitopic mass M~mono~ and the average isotopic mass M~av~. We found that peptide masses mapped on a plane made by two parameters derived from M~mono~ and M~av~ form a peculiar global feature in form of a band-gap 5-7 ppm wide stretching across the whole peptide galaxy, with a narrow (FWHM 0.2 ppm) line in the centre. The a priori probability of such a feature to emerge by chance is less than 1:100. Peptides contributing to the central line have elemental compositions following the rules S=0; Z = (2C - N - H)/2 =0, which nine out of 20 amino acid residues satisfy. The relative abundances of amino acids in the peptides contributing to the central line correlate with the...
Tipo: Manuscript
Palavras-chave: Chemistry; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2402/version/1

Early onset preeclampsia is characterized by altered placental lipid metabolism and a premature increase in circulating FABP4
Provedor de dados: 17
Autores: Victor  H. Han; Gilles Lajoie; Jennifer Ballard; Aaron Booy; Nicholas Carruthers; Delfina  Siroen.
Preeclampsia is a pregnancy-associated disorder that manifests as a sudden increase in maternal blood pressure accompanied by proteinuria. Because the placenta is a key organ in preeclampsia, we used proteomic and lipidomic analyses to compare placentae from preeclamptic and gestational age matched control pregnancies. Fatty acid binding protein 4 (FABP4), enoyl-CoA dehydrogenase and delta-3,5-delta-2,4-dienoyl-CoA isomerase had altered abundance in preeclamptic placentae compared to controls. FABP4 placental protein and RNA and plasma levels were all increased in early-onset preeclampsia (prior to 28 weeks gestation) compared to controls (6-fold, 3.3-fold and 3.5-fold respectively). After 28 weeks, FABP4 protein in control placenta and plasma increased to...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/4885/version/1

Earth History and the Evolution of Caribbean Bats
Provedor de dados: 17
Autores: Liliana D&amp;#xe1;valos.
Although the natural history of the Caribbean is better understood now than ever before, a general biogeographic explanation for the peculiar faunal composition of the islands remains elusive. New molecular phylogenetic and divergence analyses presented here show that dispersal and diversification in Caribbean bats are synchronous with sea level drops during inter-stage transitions in the Miocene. The phylogenies indicate that several continental bat species descended from West Indian ancestors, as the exceptionally low sea level of the Miocene transitions allowed for two-way biotic exchange between the islands and the continent. These results suggest a common mechanism underlies colonization and subsequent speciation in the Caribbean, and underscore the...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3901/version/1

Eco-evolutionary consequences of road adjacency and road salt on the wood frog, Rana sylvatica
Provedor de dados: 17
Autores: Steven P. Brady.
The network of roads on the landscape is vast, and has wide-reaching ecological influence. Recent investigations have focused on understanding impacts of contaminants from road runoff, especially deicing agents such as road salt. Despite growing research concerning ecological impacts of roads, our understanding of long-term consequences remains nascent. This stems in part from a dearth of investigations, and in part because ecological research typically ignores evolution on contemporary timescales. Yet reports of evolution influencing ecological outcomes are growing, suggesting this influence may be the rule rather than the exception. This may be especially true for species with spatially structured populations. For amphibians, such structuring coupled...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3674/version/1

Eco-evolutionary consequences of road adjacency and road salt on the wood frog, Rana sylvatica
Provedor de dados: 17
Autores: Steven P. Brady.
The network of roads on the landscape is vast, and has wide-reaching ecological influence. Recent investigations have focused on understanding impacts of contaminants from road runoff, especially deicing agents such as road salt. Despite growing research concerning ecological impacts of roads, our understanding of long-term consequences remains nascent. This stems in part from a dearth of investigations, and in part because ecological research typically ignores evolution on contemporary timescales. Yet reports of evolution influencing ecological outcomes are growing, suggesting this influence may be the rule rather than the exception. This may be especially true for species with spatially structured populations. For amphibians, such structuring coupled...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3674/version/2

ECoG-based short-range recurrent stimulation techniques to stabilize tissue at risk of progressive damage:  Theory based on clinical observations
Provedor de dados: 17
Autores: Markus A. Dahlem; Felix M. Schneider; Jens P. Dreier; Anthony J. Strong; Eckehard Schoell.
We introduce theoretical concepts based on chaos control to stabilize in acute stroke the tissue at risk of progressive damage by preventing adverse effects of waves of mass neuronal depolarization.  Moreover, we present clinical electrocorticography (ECoG) recordings of relevant signals suggested for the feedback control. The recordings are performed in combination with novel subdural opto-electrode technology for simultaneous laser-Doppler flowmetry in patients with aneurysmal subarachnoid haemorrhage (aSAH). In aSAH patients waves of spreading depolarization (SD) have a high incidence and cause hypoxia in tissue at risk, and, importantly, the haemodynamic response is the inverse of that seen in healthy tissue. In previous clinical studies, clusters of...
Tipo: Poster
Palavras-chave: Biotechnology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3408/version/1

Ecoinformatics: where are we, where do we want to go, and how to reach there.
Provedor de dados: 17
Autores: Abhay Krishna.
Compared to other natural sciences ecological sciences has always been about seeing the bigger picture. The realization that local actions can have global impact has been the hallmark of ecological research. This integrative view is getting more and more accepted now with the recognition that whole is definitely more then sum of its parts. Advancement in computer sciences has now made it possible to comprehend the complexity arising from an integrative approach. This has given rise to a field interfacing computer science and ecological sciences called Ecoinformatics. The other popular parallel and more mature field is bioinformatics or computational biology. The presentation will take the audience on an Ecoinformatics tour touching on present status of...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2018/version/1

Ecological connection between fish preference in the diet of Siberian cranes and their incubation period in tundra zone
Provedor de dados: 17
Autores: Maria Vladimirtseva; Inga Bysykatova; Sergey Sleptsov.
We researched the ecology of the third rarest crane species, Siberian crane, which breeds in northern-eastern Siberian tundra. Nesting in places near great lakes, this crane appears to be an indicator of the global warming processes that affect lake growth as a result of the permafrost situation close to the surface in tundra. Research has shown that these birds are presumably fish-eating during their incubation period, coinciding with the flooding season when fish come to areas around great lakes. Such a diet may be explained by the necessity of high-energy food during the incubating period as well as the particularity of this species for leaving plant resources around the nest point for the period of the first days after chick hatching. This situation...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2012
URL: http://precedings.nature.com/documents/6997/version/1

Ecological control on micro-ornamentation of conodont elements
Provedor de dados: 17
Autores: Andrey V. Zhuravlev.
Conodonts are considered now as specific group of early Chordata or even Vertebrata. Fifteen tooth-like conodont elements of seven morphological types compose the oral apparatus of conodonts. The elements demonstrate complex morphology. All the elements bear polygonal micro-ornamentation. The ornamentation is considered as representing imprints of the epithelium cells. Ecological dependencies of the cell sizes are known for some recent organisms.&amp;#xd;&amp;#xa;The maximum cell sizes are characteristic of optimal environmental conditions. Thus, one can supposes that decreasing in cell imprint size in the conodonts marks disturbance in water temperature or/and oxygen content.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/659/version/1

Ecological correlates of wildlife diseases
Provedor de dados: 17
Autores: Milind Watve; Maithili Jog.
The parasite loads appear to differ widely within and between species of free ranging wild mammals. Using data on fecal propagule densities of 29 species of wild mammals from 20 wild life parks in India we tried to identify the ecological factors that are best predictors of parasite loads. Parasite loads were consistently negatively correlated with predatory pressures at both interspecific and intraspecific levels. Carnivores had higher mean parasite loads and the effect of diet and that of predatory pressure appeared to be independent of each other. No other ecological factors were significantly and consistently associated with fecal parasite loads.
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4834/version/1

Ecological dynamics and the basis of sympatric phenotypic diversification
Provedor de dados: 17
Autores: Mario  Pineda-Krch; Richard Svanb&amp;#xe4;ck; Michael Doebeli.
Theoretical and empirical studies are showing evidence in support of evolutionary branching and sympatric speciation due to frequency&amp;#x2010;dependent competition. However, phenotypic diversification due to underlying genetic diversification is only one possible evolutionary response to disruptive selection. Another potentially general response is phenotypic diversification in the form of phenotypic plasticity. It has been suggested that genetic variation is favored in stable environments, whereas phenotypic plasticity is favored in unstable and fluctuating environments. We investigate the &amp;#x201c;competition&amp;#x201d; between the processes of evolutionary branching and the evolution of phenotypic plasticity in a predator&amp;#x2010;prey model...
Tipo: Presentation
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3672/version/1

Ecological optimum of ectothermic organisms: static-dynamical approach
Provedor de dados: 17
Autores: Vladimir V. B. Verbitsky; Tamara T. I. Verbitskaya.
During 20th century the majority of researchers interpreted ecological optimum as a certain combination of ambient factors which is optimal for growth, existence and reproduction of an organism. However, it was revealed in many species, that the maximum rates of various processes in an organism are achieved at various combinations of values of different factors, and under variable regimes as opposite to constant regimes. One may state that there is no well defined general concept which takes into account a bulk of data that do not conform the traditional definition of ecological optimum. Here, we show that it is necessary to make distinction between concepts of &amp;#x22;static&amp;#x22; and &amp;#x22;dynamic&amp;#x22; optima. It is needed for definition...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/1324/version/1

Ecological, phenological and biochemical significance of bimodal fruiting of Boletus alutaceus morgan
Provedor de dados: 17
Autores: Nandkumar Kamat.
Boletus alutaceus Morgan an ectomycorrhizal species was extensively studied from an ecologically fragmented microhabitt colonized by its&amp;#x27; host plant Ficus benghalensis L. in the Goa University campus, Taleigao, Goa, India. Qualitatively the fruiting cycles were monitored for three years and thereafter detail ecological and morphological investigations were carried out in May and November 2004. A bimodal temporal fruting pattern emerged which may have significant ecological, phenological and biochemical role in EM dynamics.
Tipo: Presentation
Palavras-chave: Biotechnology; Developmental Biology; Ecology; Genetics &amp; Genomics; Microbiology; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2835/version/1

Ecologists and the development of sustainability curricula for majors vs. non-majors
Provedor de dados: 17
Autores: Carmen R. Cid.
*Background/Question/Methods*&amp;#xd;&amp;#xa;Ecologists usually study interactions among living and non-living things at a particular spatial scale. Ecological curricula often have a biological focus except in ecosystem or applied ecology courses. At the undergraduate level, the impact of human activity on ecology class discussions is often relegated to urban ecology classes. The discussion of sustainability is a side line in introductory or upper level ecology courses, except in applied research courses, and more intensely addressed in non-science general education courses. To develop a global sustainable society will require that different disciplines understand the many factors that affect &amp;#x22;sustainability&amp;#x22; and work with a common...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3611/version/1

Ecology of Environmental Education: Feedbacks, Education, and Resilience
Provedor de dados: 17
Autores: Keith G Tidball; Marianne  Krasny.
The ecology education community has focused on the suite of knowledge and competencies that constitute environmental literacy, including self-knowledge, evidence-based habits of mind, and ecological concepts and connections (Jordan et al., 2009). Whereas the environmental education (EE) community also is concerned with knowledge, it further embraces goals related to changing attitudes and behavior. In both of these sub-disciplines, educational researchers most often focus on outcomes of specific interventions. Less attention has been paid to the interrelations among the ecological or environmental education activities themselves and the larger social-ecological system. This poster will explore the notion of an ecology of EE, and will attempt to situate EE...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5199/version/1

Ecophysiological traits of grasses: resolving the effects of photosynthetic pathway and phylogeny
Provedor de dados: 17
Autores: Samuel H. Taylor; Mark Rees; Stephen P. Hulme; Rob Freckleton; Brad S. Ripley; F. I. Woodward; Colin P. Osborne.
C4 photosynthesis is an important example of convergent evolution in plants, having arisen in eudicots, monocots and diatoms. Comparisons between such diverse groups are confounded by phylogenetic and ecological differences, so that only broad generalisations can be made about the role of C4 photosynthesis in&amp;#xd;&amp;#xa;determining ecophysiological traits. However, 60% of C4 species occur in the grasses (Poaceae) and molecular phylogenetic techniques confirm that there are between 8 and 17 independent origins of C4 photosynthesis in the Poaceae. In a screening experiment, we compared leaf physiology and growth traits across several major&amp;#xd;&amp;#xa;independent C3 &amp;#x26; C4 groups within the Poaceae, asking 1) which traits differ...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3937/version/1

Ecotoxicological risk assessment of agriculture intensification in Argentinean cropping lands using a fuzzy-logic based model
Provedor de dados: 17
Autores: Diego Ferraro.
Current agricultural models have an increasing dependence on non-renewable resources that have significant implications for the ecosystem health. Pesticides are considered one main impact force that affects both the structure and functions of agroecosystems. In this work we presented results from the application of an environmental pesticide risk assessment of a large database of cropping systems in the Inland Pampa (Argentina) where, since 1990, the traditional mixed grazing&amp;#x2013;cropping systems were being replaced by permanent agriculture and the intensification of pesticide use has increased significantly. However, there is no clear awareness of the ecotoxicological risk associated with these land use changes. The ecotoxicological risk on both...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5215/version/1

Edge states and possible magnetic states in nanographene and open-shell conjugated systems
Provedor de dados: 17
Autores: Kikuo Harigaya.
Nanocarbon materials are investigated intensively. In this paper, the edge-state in nanographene materials with zigzag edges is studied theoretically. In particular, while the inter-layer interactions are considered, we prove that edge states exist at the energy of the Dirac point in the doubly stacked nanographene, and in the case of the infinitely-wide lower layer case. This property applies both for the A-B and A-C stackings. We also study possible magnetic properties in fullerenes with defects and buckybowl molecules. When the number of lattice defects in C60 is even, we obtain magnetic and nonmagnetic solutions. The total energy of the nonmagnetic solution is lower than that of the magnetic solution. The occurrence of the localized spin is reduced for...
Tipo: Presentation
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3880/version/1

Ediacaran Macro Body Fossils
Provedor de dados: 17
Autores: Timothy D. Huang; Jei-Fu Shaw; Liang Zheng; Chun-Lan Huang; YiLung Chang; ChuanWei Yang.
This paper, Ediacaran Macro Body Fossils, reports a new discovery of well preserved three dimensional macro body fossils of the Ediacaran Period in central YunNan province in the People&amp;#x27;s Republic of China. These body fossils will enable more detailed and in-depth exploration of the evolution of multi-cellular macro organisms on this planet, whereas in the past, researches could only rely on cast or imprint fossils.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4423/version/1

Edinger-Westphal Nucleus
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Josh J. Burnell; Lydia  L. Ng; Angela L. Guillozet-Bongaarts.
This report contains a summary of expression patterns for genes that are enriched in the Edinger-Westphal nucleus (EW) of the midbrain.  All data are derived from the Allen Brain Atlas (ABA) in situ hybridization mouse project. The structure&amp;#x27;s location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the Edinger-Westphal nucleus were compared to the values of its larger parent structure, in this case the midbrain, for the purpose of extracting regionally selective gene expression data. The highest ranking genes were manually curated and verified. 50 genes were then selected and compiled for expression analysis. The...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2198/version/1

Effect of 2-H and 18-O water isotopes in kinesin-1 gliding assay
Provedor de dados: 17
Autores: Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
We show here the effects of heavy-hydrogen water (^2^H~2~O) and heavy-oxygen water (H~2~^18^O) on the gliding speed of microtubules on kinesin-1 coated surfaces. Increased fractions of isotopic waters used in the motility solution decreased the gliding speed of microtubules by a maximum of 21% for heavy-hydrogen and 5% for heavy-oxygen water. We discuss possible interpretations of these results and the importance for future studies of water effects on kinesin and microtubules. We also discuss the implication for biomolecular devices incorporating molecular motors.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7004/version/1

Effect Of A Dialysis Session On Plasma Branched Chain Aminio Acids In Hemodialysis Patients
Provedor de dados: 17
Autores: Varikasuvu Seshadri Reddy; PVLN Srinivasa Rao; Aparna R. Bitla; Siva V. Kumar; MM Suchitra; Prabhakar E. Reddy.
Protein and amino acid (AA) metabolism is abnormal in End stage renal disease (ESRD). Hemodialysis (HD) procedure is a strong catabolic stimulus. Branched chain amino acids (BCAAs) can affect other AA levels by reducing AA efflux from muscle due to inhibition of muscle protein degradation. Essential amino acids and keto acid supplements including BCAA and branched-chain keto acid (BCKA) are proposed to decrease protein intake while maintaining protein status. This study was taken up to evaluate the effect of a dialysis session on plasma BCAA&amp;#x2019;s for which fifteen patients of ESRD on Maintenance HD, thrice a week were recruited into the study. Analysis was done on samples drawn at the beginning (pre-HD) and after the end of each dialysis session...
Tipo: Presentation
Palavras-chave: Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6475/version/1

Effect of a single Dialysis session on plasma Lp(a) levels in patients on Maintenance haemodialysis
Provedor de dados: 17
Autores: Varikasuvu Seshadri Reddy; MM Suchitra; Prabhakar E. Reddy; Aparna R. Bitla; Siva V. Kumar; PVLN Srinivasa Rao.
Background: &amp;#xd;&amp;#xa;Cardiovascular disease (CVD) is a major cause of mortality in End stage renal disease (ESRD) patients on Maintenance haemodialysis (MHD). Lp (a), is a specialized form of glycoprotein-LDL-cholesterol complex and is an independent risk factor for myocardial infarction. The risk is related to its atherogenic and thrombogenic properties. The present study was taken up to evaluate changes in Lp(a) and Lipid profile in patients undergoing hemodialysis session. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methodology: &amp;#xd;&amp;#xa;Twenty seven patients with end stage renal disease who were on maintenance hemodialysis were included. Plasma samples were collected hourly during a dialysis session with polysulfone membrane using bicarbonate...
Tipo: Poster
Palavras-chave: Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6473/version/1

Effect of antisense oligodeoxynudeotide targeted against NF-&amp;#x3ba;B/P65 on cell proliferation and tumorgenesis of gastric cancer
Provedor de dados: 17
Autores: Qi Li; Yingyan  Yu; Yong   Gao; Hong jiang; Zhenggang   Zhu.
Gastric cancer is still a major health problem worldwide due to its frequency, poor prognosis and limited treatment options. To study the inhibitory effect of nuclear transcription factor kappa B(NF-&amp;#x3ba;B) antisense oligodeoxynucleotide(ASODN) on the growth and tumorgenesis of human gastric cancer, we synthesis and transfect ASODN of NF-&amp;#x3ba;B/P65 to gastric cancer cell line. The effect of ASODN of NF-&amp;#x3ba;B/P65 on the proliferation of gastric cancer cells was measured by MTT method. The subcutaneous xenograft model of human gastric cancer was established in nude mice and the tumor growth curve was observed. The cell proliferation was significantly inhibited in P65 ASODN transfected group in vitro (P&amp;#x3c;0.05). In vivo, tumor...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2010
URL: http://precedings.nature.com/documents/5262/version/1

Effect of Baicalin on inflammatory mediator levels and microcirculation disturbance in rats with severe acute pancreatitis
Provedor de dados: 17
Autores: Xiping Zhang; Hua Tian; Chen-Jun Wu; Xin-Ge Jiang; Qian  Ye; Li Chen; Yang Cai; Ru-Jun Xu; Qi Xie; Wenqin Yuan.
Objective: To investigate the effect of Bacailin on inflammatory mediator levels and microcirculation disturbance in severe acute pancreatitis (SAP) rats and explore its therapeutic mechanism on this disease. Methods: SAP model rats were randomly divided into model control group and Baicalin treated group, 45 rats in each group. The same number of normal rats were included in sham-operated group. These groups were further subdivided into 3 h, 6 h and 12 h subgroups, respectively (15 rats in each subgroup). At 3, 6 and 12 hours after operation, rats were killed to conduct the following experiments: (1) to examine the mortality rates of rats, the ascites volume and pancreatic pathological changes in each group; (2) to determine the contents of amylase,...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/1968/version/1

Effect of Crohn&amp;#x27;s Disease Risk Alleles on Enteric Microbiota Marker Paper
Provedor de dados: 17
Autores: Ellen Li; Erica Sodergren; George Weinstock; Thaddeus Stappenbeck; Daniel Frank; Charles Robertson; Norman Pace; Wei Zhu; Edgar Boedeker; R. Balfour Sartor; Phillip Tarr; Lloyd Mayer; David Dietz.
This UH2/UH3 demonstration project entitled &amp;#x201c;Effects of Crohn&amp;#x2019;s disease risk alleles on enteric microbiota&amp;#x201d; is focused on characterizing intestinal associated microbiota in patients with ileal Crohn&amp;#x2019;s disease (ileal CD), ulcerative colitis (UC) and control patients without inflammatory bowel diseases (non-IBD).  We hypothesize that genetic factors that affect Paneth cell function, contribute to compositional changes in intestinal microbiota.  These changes in microbiota may lead to reduction of protective commensal organisms and increased numbers of aggressive organisms that incite intestinal inflammation. This hypothesis is being tested by high throughput 16S rRNA sequence analysis of de-identified ileal and...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Microbiology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4975/version/1

Effect of Different Dates of Dry Seeding and Staggered Nursery Sowing on Growth and Yield of Kharif Rice
Provedor de dados: 17
Autores: Sivapuram Venkata Rama Krishna Prabhakar; S Narsa Reddy.
A field experiment was conducted to study the effect of different dates of dry seeding and staggered nursery sowing on growth and yield of Kharif rice. The experiment was based on the difficulties faced by the farmers in the coastal areas of Andhra Pradesh and those who depend on canal irrigation and are located at the tail end areas. The experimental results have showed no difference among the methods of stand establishment in terms of yield. However, among the dates of sowing the delay in sowing beyond 30th July significantly reduced the grain yield and returns per rupee invested. It has been concluded that the rice crop may be established either by direct seeding or by transplanting nurseries but the sowing of the respective cultures should be done by...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5399/version/1

Effect of Different Dates of Dry Seeding and Staggered Nursery Sowing on Growth and Yield of Kharif Rice
Provedor de dados: 17
Autores: Sivapuram Venkata Rama Krishna Prabhakar; S Narsa Reddy.
A field experiment was conducted to study the effect of different dates of dry seeding and staggered nursery sowing on growth and yield of Kharif rice. The experiment was based on the difficulties faced by the farmers in the coastal areas of Andhra Pradesh and those who depend on canal irrigation and are located at the tail end areas. The experimental results have showed no difference among the methods of stand establishment in terms of yield. However, among the dates of sowing the delay in sowing beyond 30th July significantly reduced the grain yield and returns per rupee invested. It has been concluded that the rice crop may be established either by direct seeding or by transplanting nurseries but the sowing of the respective cultures should be done by...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5399/version/2

Effect of Escherichia coli endotoxin on Archachatina marginata haemolymph coagulation system
Provedor de dados: 17
Autores: Musa Salawu; Oyelola Oloyede; Adenike Oladiji; Nasiru Muhammad; Musa Yakubu.
The effect of _E. coli_ endotoxin on the heamolymph coagulation response of _Archachatina marginata_ was studied. Heamocyte Lysate(HL), Haemocyte Lysate Supernatant(HLS) and Haemocyte Lysate Debris (HLD) were exposed to _Escherichia coli_ endotoxin. Controls were prepared with endotoxin-free water(&amp;#x3c;0.025 EU/ml). The differential protein coagulation was estimated in each mixture. Fractions of the haemolymph exposed to endotoxin produced higher protein coagulates than endotoxin-free fractions when incubated at 37 &amp;#xb0;C for 1 h (p&amp;#x3c;0.05). The results showed significantly higher (p&amp;#x3c;0.05) concentrations of protein coagulated when HL/plasma mixture were used than when either fraction was used. At a ratio 1:1 of HL:Plasma, highest...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4552/version/1

Effect of hyperglycemia on inflammatory markers in patients with Type 2 Diabetes
Provedor de dados: 17
Autores: Rajeev Goyal; Abul F. Faizy; Najmul  Islam.
The role of inflammation in causation of both Diabetes and its complications has gained acceptance. Initially, hyperglycemia was thought to be the factor causing inflammation, but recently, obesity has gained attraction as probable cause of inflammation. We have studied the levels of markers of inflammation in Diabetic patients, with uncontrolled hyperglycemia, before and after treatment. The results indicate that hyperglycemia significantly causes increase in inflammatory markers like TNF-&amp;#x3b1; and IL-6, which further contribute to pathogenesis of Diabetes mellitus type 2 as well as its complications such as atherosclerosis and neuropathy.
Tipo: Poster
Palavras-chave: Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/1567/version/1

Effect of Non-Coding RNA on Post-Transcriptional Gene Silencing of Alzheimer Disease
Provedor de dados: 17
Autores: Krishnan Namboori; Arun Mohan; Radhagayathri K.U.; Varun Gopal; Vasavi C.S.; Premkumar P; Deepa  Gopakumar; Ramachandran K.I.
A large amount of hidden biological information is contained in the human genome, which is not expressed or revealed in the form of proteins; the usual end product form of gene expression. Instead, most of such information is in the form of non-coding RNAs (ncRNAs). ncRNAs correspond to genes that are transcribed, but do not get translated into proteins. This part of the genome was, till recently, considered as &amp;#x2018;junk&amp;#x2019;. The term &amp;#x2018;junk&amp;#x2019; implied lack of any discernible function of these RNA. More than 98% of the human genomic size encompasses these non-coding RNAs. But, recent research has evidently brought out the indispensible contribution of non-coding RNA in controlling and regulating gene expression. ncRNA such...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4467/version/1

Effect of p21Waf1 and p27Kip1 on centrosome replication and proliferation of breast cancer cell
Provedor de dados: 17
Autores: Fu-Nian Li; Dan-Dan  Jiang; Xiang-Ping Liu; Yin-Lin Ge; Ming-Zhi Cao; Xin-Gang Wang.
Aberrant centrosome numbers are detected in virtually all cancers&amp;#xff0c;increasing the risk for cell division errors and chromosomal instability. Deregulation of the centrosome duplication cycle is considered as the major contributing factor for abnormal ampli&amp;#xfb01;cation of centrosomes. p21Waf1 and p27Kip1, general CDK inhibitors by inhibiting cyclin-dependent kinase 2 (CDK2)/cyclin E and cyclin A complexes, controlled the initiation and progress of centrosome duplication . We transfected p21 Waf1, p27 Kip1 or p21 Waf1- p27 Kip1 genes into MCF-7 cells by lipofection to explore the effect of the genes on centrosome duplication and proliferation of breast cancer cell. The result shows that the cell growth was obviously inhibited after being...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/4426/version/1

Effect Of Pre-freeze Addition Of Cysteine Hydrochloride And Reduced Glutathione On Post-thaw Sperm Parameters And Field Fertility In Jersey Crossbred Bull Semen
Provedor de dados: 17
Autores: P Perumal; S Selvaraju; A.K. Barik; D. N.  Mohanty; Srinibas Das; P.C. Mishra.
The present study was aimed to assess the effect of pre-freeze addition of cysteine hydrochloride and glutathione (GSH) on post-thaw sperm functional parameters and field fertility. The experimental bulls aged 4 to 6 years were used for the present study. A total of 36 ejaculates, 6 ejaculates from each bull (n=6) were collected and divided in to three groups, group I (control), group II (5mM cysteine hydrochloride) and group III (5mM GSH). The extended semen samples were added with @5mM additives, filled in mini straw using automatic filling and sealing machine (IMV, France) and cryopreserved in liquid nitrogen. Post-freeze seminal traits were also recorded after thawing at 37oC for 30 seconds. Post thaw livability was significantly (p&amp;#x3c; 0.01)...
Tipo: Presentation
Palavras-chave: Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/7009/version/1

Effect of Stimulating Magenetic Field on Plants
Provedor de dados: 17
Autores: R. V. K.  Charan.
A plant&amp;#x27;s metabolism contains 90-95 percent of diamagnetic water and rest contains several apra, ferro and dia metals and non-metals.The present work is to study stimulating magnetic effect on plants. In result I find abrupt rising of the pulse rate which may enhance the growth of the plant resulting in removing of necessity of using fertilizers and chemicals for plant growth if it is for human consumption. A relation can also be established in between plant pulsation and the applied field.
Tipo: Manuscript
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3300/version/1

Effect of Stimulators upon Human Hepatic Adenylate Cyclase Activity: A Tool of Nitroimidazole Cytotoxicity Assessment
Provedor de dados: 17
Autores: Rakesh Sharma; Soonjo Kwon.
Nitroimidazole is an antibiotic and radiosensitizer chemical with great potentials in imaging. The hepato-cytoxicity evaluation of nitroimidazole and possible energy status changes in liver cells due to its anti-inflammatory characteristics are crucial in tumor imaging and chemotherapy. Adenylate cyclase is key enzyme to cause energy imbalance leading to cytotoxicity. To evaluate energy status in hepatocytes and Kupffer cells, adenylate cyclase activities in isolated liver cells were compared in presence of stimulators. To evaluate the effect of effectors on adenylate cyclase in cultured hepatocyte cells, adenylate cyclase enzyme was stimulated by different GITP, GTP, progesterone and nitroimidazole effectors. In cultured Kupffer cells, prostaglandin E~2~...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2850/version/1

Effect of temperature on waterflea Daphnia magna (Crustacea:Cladocera)
Provedor de dados: 17
Autores: Quddus Khan; Munawer Khan.
Acclimation of the waterflea Daphnia magna Straus (Crustacea: Cladocera) at 2 o to 12 o C above their habitat temperature (16 o C) for 6 months increased the rate of their metabolic activity (respiration and heartbeat rates). Temperature-enhanced activity appeared to be supported by cellular ATP synthesis (increased cytochrome c oxidase and succinic dehydrogenase activities) and hydrolysis (increased ATPases activities), indicating high rate of intermediary metabolism, the substrates for which may come from the stored glycogen and fat in addition to ingested food. Temperature-enhanced activity was associated with loss of body mass and decrease in body size, both of which may result from hyperactivity (causing lack of replenishment of consumed stored...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1909/version/1

Effective denitrification scales predictably with water residence time across diverse systems
Provedor de dados: 17
Autores: Mark B. Green; Wilfred M. Wollheim; Nandita B. Basu; Gretchen Gettel; P. Suresh Rao; Nathaniel Morse; Robert Stewart.
Nitrogen provides a fundamental building block for life. However, some nitrogen species (e.g., NO~3~) cause water quality degradation and contribute to climatic warming as a greenhouse gas (e.g., N~2~O).  Denitrification is a central process in the nitrogen cycle, transforming water-soluble nitrogen to gaseous nitrogen, thereby removing nitrogen from the system. The factors controlling denitrification are known, yet the general quantitative comparison of controls on denitrification remains a rich area of study. Understanding the relative importance of various controls over denitrification is critical given its biological importance, role in the Earth system, and the current perturbation of the global nitrogen cycle by human activity. We demonstrate that...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3520/version/1

Effective Phylogenetic Compression with TreeZip
Provedor de dados: 17
Autores: Suzanne J. Matthews; SeungJin Sul; Tiffani L. Williams.
Phylogenetic trees are family trees that represent the relationships between a group of organisms, or taxa. The most popular techniques for reconstructing phylogenetic trees intelligently navigate an exponentially-sized tree space by solving NP-hard optimization problems that that best hypothesize the evolutionary history for a given set of taxa. Instead of reconstructing a single tree, these heuristics often return tens to hundreds of thousands of trees that represent equally-plausible hypotheses for how the taxa of interest evolved from a common ancestor. As biologists attempt to reconstruct increasingly larger phylogenies, these tree collections only continue to grow in size. To combat the cost of storage and to facilitate the transfer of these large...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4613/version/1

Effective Sample Size: Quick Estimation of the Effect of Related Samples in Genetic Case-Control Association Analyses
Provedor de dados: 17
Autores: Yaning B. Yang; Elaine L. Remmers; Chukwuma Ogunwole; Daniel Kastner; Peter K. Gregersen; Wentian F. Li.
Correlated samples have been frequently avoided in case-control&amp;#xd;&amp;#xa;genetic association&amp;#xd;&amp;#xa; studies in part  because the methods for handling them are either not&amp;#xd;&amp;#xa;easily implemented or not widely known. We&amp;#xd;&amp;#xa;advocate one method for case-control association analysis of correlated&amp;#xd;&amp;#xa;samples -- the effective sample size method -- as a simple and&amp;#xd;&amp;#xa;accessible approach that does not require specialized computer programs.&amp;#xd;&amp;#xa;The effective sample size method captures the variance inflation&amp;#xd;&amp;#xa;of allele frequency estimation exactly, and can be used to modify the&amp;#xd;&amp;#xa;chi-square test statistic, p-value, and 95% confidence interval...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology.
Ano: 2007
URL: http://precedings.nature.com/documents/400/version/1

Effects of Cations and PH on Antimicrobial Activity of Thanatin and s-Thanatin against _Escherichia coli_ ATCC25922 and _B. subtilis_ ATCC 21332
Provedor de dados: 17
Autores: Guoqiu Wu; Jiaxuan Ding; Hui Li; Linxian Li; Rui Zhao; Xiaobo Fan; Zilong Shen.
Thanatin and s-thanatin were insect antimicrobial peptides which have shown potent antimicrobial activities on a variety of microbes. In order to investigate the effect of cations and pH on the activity of these peptides against Gram-negative bacteria and Gram-positive bacteria, the antimicrobial activities of both peptides were studied in increasing concentrations of monovalent cations (K^+^ and Na^+^), divalent cations (Ca^2+^ and Mg^2+^) and H^+^. The NCCLS broth microdilution method showed that both peptides were sensitive to the presence of cations. The divalent cations showed more antagonized effect on the activity against Gram-negative bacteria than the monovalent cations, since the two peptides lost the ability to inhibit bacterial growth at a very...
Tipo: Manuscript
Palavras-chave: Microbiology; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2006/version/1

Effects of diamagnetic levitation on bacterial growth in liquid
Provedor de dados: 17
Autores: Richard J. A. Hill; Oliver J. Larkin; Paul Anthony; Michael R. Davey; Laurence Eaves; Catherine E. D. Rees; Camelia E. Dijkstra.
Diamagnetic levitation is a technique that uses a strong, spatially-varying magnetic field to levitate diamagnetic materials, such as water and biological cells. This technique has the potential to simulate aspects of weightlessness, on the Earth.  In common with all ground-based techniques to simulate weightlessness, however, there are effects introduced by diamagnetic levitation that are not present in space. Since there have been few studies that systematically investigate these differences, diamagnetic levitation is not yet being fully exploited. For the first time, we critically assess the effect of diamagnetic levitation on a bacterial culture in liquid. We used a superconducting magnet to levitate growing bacterial cultures for up to 18 hours, in a...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4216/version/1

Effects of habitat, microsite and seed density on recruitment limitation in native scrubland and scrub undergoing restoration
Provedor de dados: 17
Autores: Elizabeth L. Stephens; Pedro F. Quintana-Ascencio; Maliha Beg.
*Background/Questions/Methods*&amp;#xd;&amp;#xa;Recruitment influences population and community dynamics by determining the replacement of older individuals, decreasing population expansion and reducing/excluding a species from a community. There is insufficient information on the relative importance of mechanisms affecting seed availability and how interactions between recruitment limitation, other life history stages and environmental variables affect plant demography. Seed availability is pertinent to restoration projects, in which the establishment of native plant populations is a priority. We hypothesize that seed and seedling dynamics are affected by seed production, predation, and microsite characteristics, which may differ among habitats with...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3629/version/1

Effects of Pre- and Post-natal smoke exposure on airway neural responses
Provedor de dados: 17
Autores: Zhong.-Xin Wu; Vincent Kish; Thomas Batchelor; Richard Dey.
Abundant epidemiological data shows that maternal smoking during pregnancy or second-hand smoke exposure during neonatal life and infancy increases the incidence of respiratory illnesses later in life. However, underlying mechanisms initiated in early life but affecting adult disease remain undefined. Neurotrophins, including nerve growth factor (NGF) and brain-derived neurotrophic factor (BDNF), are neurotrophic factors essential in promoting and maintaining differentiation, growth, and survival of central and peripheral nervous system. The goal of this proposal is to examine the potential role of neurotrophin release in mediating long-term effects of prenatal and early postnatal smoke exposure. Our studies showed that an initial exposure to smoke during...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1432/version/1

Effects of processes at the population and community level on carbon dynamics of an ecosystem model
Provedor de dados: 17
Autores: Carlos A. Sierra; Mark E. Harmon.
Ecological processes at the population and community level are often ignored in biogeochemical models, however, the effects of excluding these processes at the ecosystem level is uncertain. In this study we analyzed the set of behaviors that emerge after introducing population and community processes into an ecosystem carbon model. We used STANDCARB, a hybrid model that incorporates population, community, and ecosystem processes to predict carbon dynamics over time. Our simulations showed that at the population level, colonization and mortality rates can limit the maximum biomass achieved during a successional sequence. Specifically, colonization rates control temporal lags in the initiation of carbon accumulation, and mortality rates can have important...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1918/version/1

Effects of surface passivation on gliding motility assays
Provedor de dados: 17
Autores: Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
In this study, we report differences in the observed gliding speed of microtubules dependent on the choice of bovine casein used as a surface passivator. We observed differences in both speed and support of microtubules in each of the assays. Whole casein, comprised of [alpha]~s1~, [alpha]~s2~, [beta], and [kappa] casein, supported motility and averaged speeds of 966 &amp;#xb1; 7 nm/s. Alpha casein can be purchased as a combination of s1 and s2 and supported gliding motility and average speeds of 949 &amp;#xb1; 4 nm/s. Beta casein did not support motility very well and averaged speeds of 870 &amp;#xb1; 30 nm/s. Kappa casein supported motility very poorly and we were unable to obtain an average speed. Finally, we observed that mixing alpha, beta, and kappa...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5278/version/2

Effects of surface passivation on gliding motility assays
Provedor de dados: 17
Autores: Andy Maloney; Lawrence J. Herskowitz; Steven J. Koch.
In this study, we report differences in the observed gliding speed of microtubules&amp;#xd;&amp;#xa;dependent on the choice of bovine casein used as a surface passivator. We observed&amp;#xd;&amp;#xa;differences in both speed and support of microtubules in each of the assays. Whole&amp;#xd;&amp;#xa;casein, comprised of [alpha]~s1~, [alpha]~s2~, [beta], and [kappa] casein, supported motility and averaged speeds of&amp;#xd;&amp;#xa;966 &amp;#xb1; 7 nm/s. Alpha casein can be purchased as a combination of s1 and s2 and&amp;#xd;&amp;#xa;supported gliding motility and average speeds of 949 &amp;#xb1; 4 nm/s. Beta casein did not&amp;#xd;&amp;#xa;support motility very well and averaged speeds of 870 &amp;#xb1; 30 nm/s. Kappa casein&amp;#xd;&amp;#xa;supported...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5278/version/1

Efficient learning in Approximate Bayesian Computation
Provedor de dados: 17
Autores: Mohammed  Sedki; Pierre  Pudlo.
Efficient learning in Approximate Bayesian Computation
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5962/version/1

Efficient polyethylenimine-mediated gene delivery proceeds via a caveolar pathway in HeLa cells.
Provedor de dados: 17
Autores: Nathan P. Gabrielson; Daniel W. Pack.
Most in vivo gene therapies will require cell-specific targeting. Although vector targeting through ligand attachment has met with success in generating gene delivery particles that are capable of specific cellular interactions, little attention has been given to the possible effects of such ligands on subsequent intracellular processing. In this study, we examine the impact of targeting two distinct endocytic routes-the caveolar and clathrin pathways-on polyethylenimine-mediated gene delivery in HeLa cells. Targeting complexes to the caveolar pathway with folic acid and the clathrin pathway with transferrin yields enhanced gene delivery relative to unmodified polyethylenimine. Colocalization studies with caveolin-1 and clathrin heavy chain indicate that...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/2262/version/1

Efficient Replication of Over 180 Genetic Associations with Self&amp;#x2010;Reported Medical Data
Provedor de dados: 17
Autores: Joyce Y. Tung; Chuong B. Do; David A. Hinds; Amy K. Kiefer; J. Michael Macpherson; Arnab B. Chowdry; Uta Francke; Brian T. Naughton; Joanna L. Naughton; Anne Wojcicki; Nicholas Eriksson.
While the cost and speed of generating genomic data have come down dramatically in recent years, the slow pace of collecting medical data for large cohorts continues to hamper genetic research. Here we evaluate a novel online framework for amassing large amounts of medical information in a recontactable cohort by assessing our ability to replicate genetic associations using these data. Using web&amp;#x2010;based questionnaires, we gathered self-reported data on 50 medical phenotypes from a generally unselected cohort of over 20,000 genotyped individuals. Of a list of genetic associations curated by NHGRI, we successfully replicated about 75% of the associations that we expected to (based on the number of cases in our cohort and reported odds ratios, and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6014/version/1

Efficient Replication of Over 180 Genetic Associations with Self-Reported Medical Data
Provedor de dados: 17
Autores: Joyce Y. Tung; Chuong B. Do; David A. Hinds; Amy K. Kiefer; J. Michael Macpherson; Arnab B. Chowdry; Uta Francke; Brian T. Naughton; Joanna L. Mountain; Anne Wojcicki; Nicholas Eriksson.
While the cost and speed of generating genomic data have come down dramatically in recent years, the slow pace of collecting medical data for large cohorts continues to hamper genetic research. Here we evaluate a novel online framework for amassing large amounts of medical information in a recontactable cohort by assessing our ability to replicate genetic associations using these data.  Using web-based questionnaires, we gathered self-reported data on 50 medical phenotypes from a generally unselected cohort of over 20,000 genotyped individuals.  Of a list of genetic associations curated by NHGRI, we successfully replicated about 75% of the associations that we expected to (based on the number of cases in our cohort and reported odds ratios, and excluding a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6014/version/2

EGFP-FMRP Granules Are Proto-Granules That Can Be Shunted to Stress Granules During a Stress Response
Provedor de dados: 17
Autores: Robert Denman.
Overexpressed EGFP-FMRP has been used as a substitute for endogenous fragile X mental retardation protein (FMRP) in protein-protein interaction studies, and in studies concerning the composition, the formation and the localization of neuronal granules. However, the question of whether this tool truly recapitulates the properties of the endogenous protein has not been addressed. Here we demonstrate that overexpressed EGFP-FMRP forms three distinct granule types based on colocalization with various marker proteins. The majority of EGFP-FMRP-containing granules are larger and more amorphous than known granule types. Consistent with this, there is only partial colocalization with stress granule or P-body markers and no colocalization with a putative Drosophila...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5442/version/1

Electrocortical activity can predict pianist&amp;#x27;s proficiency
Provedor de dados: 17
Autores: Malcolm M. H. Mills.
Electro-cortical changes associated with learning and performing were investigated in eighteen pianists over three closely-spaced performances of sight-reading a novel music score. Six musical criteria were assessed: right hand errors, left hand errors, rhythmic errors, speed accuracy, fluency, and musical expression. These skills correlated specifically to electrical rhythms of 8.5-10.5 cycles per second near the sensory-motor cortex and the supplementary area. The correlations progressively reduced with each performance as it improved and learning occurred. Further, these electro-cortical potentials can predict the quality of performer and performance at the same or later occasion based on the same or different skill. Understanding this physiology will...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2477/version/1

Electron Microprobe Chemical Dating of Uraninite as a Reconnaissance Tool for Leucogranite Geochronology
Provedor de dados: 17
Autores: Jose M. Hurtado; Nilanjan Chatterjee; Jahandar Ramezani; Kip V. Hodges; Samuel A. Bowring.
We suggest that electron microprobe techniques may be employed to date Tertiary samples of uraninite (UO~2~), which can contain very high concentrations of radiogenic Pb after only a few million of years of U and Th decay.  Although uraninite is regarded as a rare accessory mineral, it is relatively abundant in leucogranitic rocks such as those found in the Himalayan orogen.  We apply the U-Th-total Pb electron microprobe chemical dating method to a uraninite crystal from a ca. 18.3 Ma dike of the Mugu granite from the Upper Mustang region of central Nepal.  With this technique, we calculate a mean chemical date that is consistent with isotope-dilution thermal ionization mass spectrometry (ID-TIMS) U-Pb dates obtained from seven other uraninite grains and...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/655/version/1

Electron microscopy analysis of FcR&amp;#x3b3; localization after its capture by T cells by trogocytosis
Provedor de dados: 17
Autores: Stephanie Balor; Marc Da&amp;#xeb;ron; Pierre Bruhns; Denis Hudrisier.
T cells acquire various proteins from their cellular partners by the process of trogocytosis. We recently demonstrated that the Fc&amp;#x3b3;RIIIA receptor and its associated FcR&amp;#x3b3; are captured by T cells during their co-culture with Fc&amp;#x3b3;R-expressing target cells upon both antigen- or antibody-mediated stimulation. Interestingly, we found that FcR captured by T cells could bind ligands but did not transmit detectable intracellular signals or signaling-depending functions upon ligand binding suggesting their improper integration in the recipient T cell membrane. In this study, we provide morphological data in support of this hypothesis. Indeed, we show that the FcR&amp;#x3b3;-subunit, which we used as a fusion to GFP, was clearly present...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2009
URL: http://precedings.nature.com/documents/3824/version/1

Electron Transfer Pathways in Cell
Provedor de dados: 17
Autores: Yan Liu.
Analysis of the electron salvation process data indicates that the electron transfer between the electron donor and acceptor is hindered by the electron salvation process. It is proposed that the electron transfer in the cell environment must be assisted by intermediate messenger called the &amp;#x201c;transport protein&amp;#x201d;.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7149/version/1

Electronic Nose Technology to Measure Soil Microbial Activity and Classify Soil Metabolic Status
Provedor de dados: 17
Autores: Fabrizio De Cesare; Elena Di Mattia; Simone Pantalei; Emiliano Zampetti; Vittorio Vinciguerra; Antonella Macagnano.
The electronic nose (E-nose) is a sensing technology that has been widely used to monitor environments in the last decade. In the present study, the capability of an E-nose, in combination with biochemical and microbiological techniques, of both detecting the microbial activity and estimating the metabolic status of soil ecosystems, was tested by measuring on one side respiration, enzyme activities and growth of bacteria in natural but simplified soil ecosystems over 23 days of incubation through traditional methodologies, and on the other side VOCs and/or gases evolution in their headspace during the same period through the E-nose. Both kinds of measurements, i.e. biochemical-microbiological and sensorial, succeeded in discriminating between inoculated...
Tipo: Presentation
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6364/version/1

Elevated central serotonin levels inhibit emotional crying
Provedor de dados: 17
Autores: Frederik van der Veen; Joyce Jorritsma; Carola Krijger; Ad Vingerhoets.
Previous research has suggested a possible role of serotonin in emotional expressions, such as crying. We have found that a transient increase of central serotonin levels by means of oral administration of paroxetine reduces crying in response to emotional movies in healthy female volunteers. This is the first direct evidence of an important role of serotonin in this uniquely human emotional response.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5136/version/1

Elevated CO2 and O3 Effects on Fine-Root Life Span in Ponderosa Pine
Provedor de dados: 17
Autores: Donald L. Phillips; Mark G. Johnson; David T. Tingey; Marjorie J. Storm.
Atmospheric carbon dioxide (CO2) and ozone (O3) concentrations are rising, which may have opposing effects on tree C balance and allocation to fine roots.  More information is needed on interactive CO2 and O3 effects on roots, particularly fine-root life span, a critical demographic parameter and determinant of soil C and N pools and cycling rates.  We conducted a study in which ponderosa pine (Pinus ponderosa) seedlings were exposed to two levels of CO2 and O3 in sun-lit controlled-environment terracosms for three years.  Minirhizotrons were used to monitor individual fine roots in three soil horizons every 28 days.  Proportional hazards regression was used to analyze effects of CO2, O3, diameter, depth, and season of root initiation on fine-root...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3703/version/1

Elucidating Signal Transduction Modulatory Drug Target Network of Colon Cancer: A Network Biology Approach
Provedor de dados: 17
Autores: Deepak Ranjan Sethi; Sanjay Kundu; Ibnul Hassan; Biplab  Bhattacharjee; Jayadeepa R.M; Sushil Kumar  Middha.
Latest evaluation and validation of cancer drugs and their targets has demonstrated the lack and inadequate development of new and better drugs, based on available protocols. Even though the specificity of drug targets is a great challenge in the pharmaco-proteomics field of cancer biology, for eradicating such hurdles and paving the way for the drugs of future, a novel step has been envisaged here to study the relation between drug target network and the corresponding drug network using the advanced concepts of proteomics and network biology. The literature mining was done for the collection of receptors and the ligands. About 1000 natural compounds were collected and out of those 300 molecules showed anti-cancer activity against colon cancer. Ligand Vs...
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4709/version/1

Embedding machine-readable proteins interactions data in scientific articles for easy access and retrieval
Provedor de dados: 17
Autores: Paolo Tieri; Alberto Termanini; Piero Fariselli; Claudio Franceschi.
Extraction of protein-protein interactions data from scientific literature remains a hard, time- and resource-consuming task. This task would be greatly simplified by embedding in the source, i.e. research articles, a standardized, synthetic, machine-readable codification for protein-protein interactions data description, to make the identification and the retrieval of such very valuable information easier, faster, and more reliable than now.&amp;#xd;&amp;#xa;We shortly discuss how this information can be easily encoded and embedded in research papers with the collaboration of authors and scientific publishers, and propose an online demonstrative tool that shows how to help and allow authors for the easy and fast conversion of such valuable biological data...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2337/version/1

Emergence and Fixing of Antiviral Resistance in Influenza A Via Recombination and Hitch Hiking
Provedor de dados: 17
Autores: Henry L. Niman.
The dramatic rise of oseltamivir resistance in the H1N1 serotype in the 2007/2008 season and the fixing of H274Y in the 2008/2009 season has raised concerns regarding individuals at risk for seasonal influenza, as well as development of similar resistance in the H5N1 serotype.  Previously, oseltamivir resistance produced changes in H1N1 and H3N2 at multiple positions in treated patients.  In contrast, the recently reported resistance involved patients who had not recently taken oseltamivir.  Moreover, the resistance was limited to the H1N1 which had acquired H274Y.  Using phylogenetic analysis I show that the fixing of H274Y was due to hitch hiking on a genetic background that acquired key changes from another circulating sub-clade.  H274Y jumped from...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Immunology.
Ano: 2009
URL: http://precedings.nature.com/documents/2832/version/1

Emergence of macroscopic simplicity from the Tumor Necrosis Factor-alpha signaling dynamics
Provedor de dados: 17
Autores: Kentaro Hayashi; Vincent  Piras; Masaru  Tomita; Masa  Tsuchiya; Kumar Selvarajoo.
The Tumor Necrosis Factor-&amp;#x3b1; (TNF-&amp;#x3b1;), a cytokine produced during the innate immune response to invading pathogens, is involved in numerous fundamental cellular processes. Here, to understand the temporal activation profiles of the TNF-&amp;#x3b1; regulated signaling network, we developed a dynamic computational model based on the perturbation-response approach and the law of information (signaling flux) conservation. Our simulations show that the temporal average population response of the TNF-&amp;#x3b1; stimulated transcription factors NF-&amp;#x3ba;B and AP-1, and 3 groups of 180 downstream gene expressions follow first-order equations. Using the model, in contrast to a well-known previous study, our model suggests that the continuous...
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6495/version/1

Emerging challenges: Massive green algae blooms in the Yellow Sea
Provedor de dados: 17
Autores: Song Sun; Fan Wang; Chaolun Li; Song Qin; Mingjiang Zhou; Lanping Ding; Shaojun Pang; Delin Duan; Guangce Wang; Baoshu Yin; Rencheng Yu; Peng Jiang; Zhiliang Liu; Guang-Tao Zhang; Xiugen Fei; Meng Zhou.
The massive green algae (Enteromorpha prolifera) bloom in a coastal area of Qingdao between May and July 2008 prior to the sailing competition of the 29th Olympic Games has raised great concerns in local and regional communities and governmental agencies on environmental deterioration, causes and mitigation of such massive algal blooms. Results from field and laboratory studies during the bloom and post-bloom periods revealed that the bloom was originated from an offshore area 150 km south of Qingdao, and caused by complex coupled land-ocean and natural-human processes associated with increases in nutrient and organic matter loadings to the coastal ocean due to rapid expansions of agriculture, aquaculture and urbanization, behavior of algae, seasonal wind...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2266/version/1

Emerging Trends of Nanotechnology towards Picotechnology: Energy and Biomolecules
Provedor de dados: 17
Autores: Rakesh Sharma; Avdhesh Sharma; Ching J. Chen.
In nature, metal oxide particles display their existence at the level of picomolecules in solution state and bioactive states in the body. We present evidence of picomolar behavior of molecules different than nanomolar behavior of particles. These particles can be encapsulated in polymers and can be functionalized with protein, nucleotides, and drugs to develop as smart intracellular targeting pico-devices. The preparation technique and physiological conditions decide the size and functionality of these pico-carrier devices. Their usable success rate, feasibility and potentials are yet to be proven or we do not know. The major difference between nanodevices and pico-devices is their intermolecular and intramolecular thermodynamics in medium and their...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4525/version/1

Empirical predictions of an intrinsically disordered protein theory approach to glycan/lectin reaction kinetics
Provedor de dados: 17
Autores: Rodrick Wallace.
Newly-developed methods from the theory of intrinsically disordered proteins can be applied to the flexible glycan structures that coat cellular surfaces and provide rich channels for biological information transmission. Extension of a mechanistic &amp;#x27;arm-in-sleeve&amp;#x27; model via a nonrigid molecule symmetry analysis leads to expectation of empirical observation of punctuated &amp;#x27;spectral&amp;#x27; classifications in glycan/lectin interaction, parameterized by an appropriate index of glycan frond length or other index of topological complexity, possibly requiring groupoid classifications analogous to quasicrystals.
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6752/version/1

ENA as an Information Hub
Provedor de dados: 17
Autores: Petra ten Hoopen; Ruth Akhtar; Richard Gibson; Bob Vaughan; Nadeem Faruque; Guy Cochrane.
The European Nucleotide Archive (ENA; &amp;#x22;http://www.ebi.ac.uk/ena/&amp;#x22;:http://www.ebi.ac.uk/ena/) is a comprehensive repository for public nucleotide sequence data from nearly four hundred thousand taxonomic nodes. Together with partners in the International Nucleotide Sequence Database Collaboration (INSDC; EBI, NCBI and DDBJ) we provide a broad spectrum of sequences, from raw reads (Sequence Read Archive data class), assembled contigs (Whole Genome Shotgun data class), assemblies of EST transcripts (Transcriptome Shotgun Assembly data set), to partial or complete assembled nucleic acid molecules with functional annotation derived from direct and third party experimental evidence (Standard and TPA data classes, respectively). Resources beyond...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5108/version/1

Endogenous human brain dynamics recover slowly following cognitive effort
Provedor de dados: 17
Autores: John Suckling; Anna Barnes; Ed Bullmore.
In functional magnetic resonance imaging, the brain&amp;#x27;s response to experimental cognitive tasks is usually assumed to be independent of endogenous oscillations. To test this assumption, we measured fractal scaling of fMRI time-series before and after a working memory task. Prolonged and task difficulty-related changes in post-task &amp;#x27;resting&amp;#x27; data suggest that brain dynamics recover slowly from cognitive effort, contrary to the reflexive model that background oscillations are independent of task performance.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2665/version/1

Endogenous Viral Etiology of Prion Diseases
Provedor de dados: 17
Autores: Claudiu I. Bandea.
Transmissible spongiform encephalopathies (TSEs), or prion diseases, are a group of incurable neurodegenerative disorders, including Kuru and Creutzfeldt-Jakob disease in humans, &amp;#x201c;mad cow&amp;#x201d; disease in cattle, and scrapie in sheep. This paper presents structural, genetic, and evolutionary evidence supporting an endogenous TSE virus model that integrates the three major traditional views on the nature of TSE pathogens, the conventional virus view, the prion hypothesis, and the virino concept, into a novel conceptual and evolutionary framework. According to this model, the TSE pathogens are symbiotic endogenous viruses that inadvertently produce transmissible viral particles that lack the viral genome and are composed primarily of the...
Tipo: Manuscript
Palavras-chave: Microbiology; Neuroscience; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3887/version/1

Endoscopy
Provedor de dados: 17
Autores: Perumal P.
Endoscopy is a minimally invasive diagnostic medical procedure that is used to assess the interior surfaces of an organ by inserting a tube into the body. The instrument may have a rigid or flexible tube and not only provide an image for visual inspection and photography, but also enable taking biopsies and retrieval of foreign objects. Endoscopy is the vehicle for minimally invasive surgery and patients may receive conscious sedation so they do not have to be consciously aware of the discomfort. Many endoscopic procedures are considered to be relatively painless and, at worst, associated with moderate discomfort.
Tipo: Presentation
Palavras-chave: Developmental Biology; Microbiology.
Ano: 2012
URL: http://precedings.nature.com/documents/7064/version/1

Endothelial Massive Calcium Accumulation Death (MCAD): Mechanism, Target, and Predictive Biomarker for Anti-Angiogenic Therapy
Provedor de dados: 17
Autores: Larry  Weisenthal.
We cultured human umbilical vein endothelial cells with bevacizumab, with tyrosine kinase inhibitors known to be AA, and with traditional cytotoxic drugs. The images below show that, in the presence of physiological saline and non-favorable culture conditions, the vast majority of the endothelial cells undergo a &amp;#x22;non-specific&amp;#x22; type of cell death (NSCD), not associated with calcium accumulation, but with loss of cell membrane integrity, allowing uptake of the Fast Green dye, staining these dead dells a pale blue green. In the presence of known AA agents (e.g. bevacizumab, some TK inhibitors) a large percentage of the endothelial cells undergo death associated with massive calcium accumulation (MCAD), with these cells staining...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6647/version/1

Endothelin-Induced Sarcoplasmic Reticulum Calcium Depletion Waves in Vascular Smooth Muscle Cells
Provedor de dados: 17
Autores: Mitra Esfandiarei; Yohan Choi; Arash Y. Tehrani; Jeremy G. Hoskins; Nicola Fameli; Cornelis van Breemen.
Agonist-stimulated waves of elevated cytoplasmic Ca2+ concentration ([Ca2+]i ) regulate blood vessel tone and vasomotion in vascular smooth muscle. Previous studies employing cytoplasmic Ca2+ indicators revealed that these Ca2+ waves were generated by a combination of inositol 1,4,5-trisphosphate (IP3) and Ca2+ induced Ca2+ release (CICR) from the sarcoplasmic reticulum (SR); although, some of the mechanistic details remain uncertain. However, these findings were derived indirectly from observing agonist-induced [Ca2+]i fluctuations in the cytoplasm.&amp;#xd;&amp;#xa;Here, for the first time, we have recorded Endothelin-1 (ET-1) induced waves of Ca2+ depletion from the SR lumen in vascular smooth muscle cells (VSMCs) using a calsequestrin-targeted Ca2+...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6280/version/1

Endothelin-Induced Sarcoplasmic Reticulum Calcium Depletion Waves in Vascular Smooth Muscle Cells
Provedor de dados: 17
Autores: Mitra Esfandiarei; Yohan Choi; Arash Y. Tehrani; Jeremy G. Hoskins; Nicola Fameli; Cornelis van Breemen.
Agonist-stimulated waves of elevated cytoplasmic Ca2+ concentration ([Ca2+]i ) regulate blood vessel tone and vasomotion in vascular smooth muscle. Previous studies employing cytoplasmic Ca2+ indicators revealed that these Ca2+ waves were generated by a combination of inositol 1,4,5-trisphosphate (IP3) and Ca2+ induced Ca2+ release (CICR) from the sarcoplasmic reticulum (SR); although, some of the mechanistic details remain uncertain. However, these findings were derived indirectly from observing agonist-induced [Ca2+]i fluctuations in the cytoplasm.&amp;#xd;&amp;#xa;Here, for the first time, we have recorded Endothelin-1 (ET-1) induced waves of Ca2+ depletion from the SR lumen in vascular smooth muscle cells (VSMCs) using a calsequestrin-targeted Ca2+...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6280/version/2

Energy or chow, that&amp;#x2019;s a question: &amp;#x201c;two-bottle&amp;#x201d; may be more suitable than &amp;#x201c;one-bottle&amp;#x201d; in modeling nutritional obesity
Provedor de dados: 17
Autores: JG Zhang; XW Sun; P Gao; L Xie; WQ Liu; HT Xiao; H Ai.
*Objective:* To model nutritional obesity in rats with two-bottle-feeding method according to human eating feature. &amp;#xd;&amp;#xa;*Design:* Animals were grouped into control and model randomly according to their initial body weight. The control rats fed with standard chow singly and the model rats fed with the standard chow and a high fat (HF) diet simultaneously for 20 weeks. Lee&amp;#x2019;s index of control was used as the reference of obesity identification. The inducing effect of this method and animals&amp;#x2019; eating features were studied. &amp;#xd;&amp;#xa;*Subjects:* 142 weaned male Sprague-Dawley (SD) rats (body weight: 43.95&amp;#xb1;4.0g). &amp;#xd;&amp;#xa;*Measurements:* Body weight (BW), body length (BL), and food accumulation were...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2572/version/1

Enforced expression of PPP1R13L increases tumorigenesis and invasion through p53-dependent and p53-independent mechanisms.
Provedor de dados: 17
Autores: Magdalena J. Laska; Scott Lowe; Lars Zender; Stephen Hearn; Ulla Vogel; Uffe Birk Jensen; Anka Bric; Bj&amp;#xf8;rn A. Nex&amp;#xf8;.
PPP1R13L was initially identified as a protein that binds to the NF-[kappa]B subunit p65/RelA and inhibits its transcriptional activity. It also binds p53 and inhibits its action. One set of experimental findings based on over-expression of PPP1R13L indicates that PPP1R13L blocks apoptosis. Another set of experiments, based on endogenous production of PPP1R13L, suggests that the protein may sometimes be pro-apoptotic. We have used primary mouse embryonic fibroblasts (MEFs), dually transformed by H-ras and Adenovirus E1A and differing in their p53 status, to explore the effects of PPP1R13L over-expression, thus examining the ability of PPP1R13L to act as an oncoprotein. We found that over-expression of PPP1R13L strongly accelerated tumor formation by...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/2004/version/1

Enhanced anti-cancer activity of microglia by AAV2-mediated IL-12 in the therapy of glioblastoma multiforme
Provedor de dados: 17
Autores: Tsung-Lang Chiu; Mei-Jen Wang; Chin-Cheng Su.
Microglia has been found to diversify its function by cancerous cells or in a cancerous environment, thereby contributing to cancer growth and metastasis. Its immuno-activity, however, can be modulated by interleukin-12. So a strategy was designed using AAV2 carrying IL-12 to activate microglia then to eliminate cancerous cells. The transduction efficacy of AAV was evaluated with AAV2 encoding GFP and IL-12 on cancerous and CNS cells. The bioactivity of microglia modulated by IL-12 was examined and death receptors 4 and 5 were detected on cancerous cells. The effects of IL-12 and AAV2/IL-12 on microglial cytoxoxicity were evaluated too. The results demonstrated human cell line DBTRG, surgical specimen of GBM, and rat astrocyte expressed GFP quite well....
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3101/version/1

Enhanced anti-tumor effects of combined MDR1 RNA interference and human sodium/iodide symporter (NIS) radioiodine gene therapy using an adenoviral system in a colon cancer model
Provedor de dados: 17
Autores: Sohn Joo Ahn; Yong Hyun Jeon; Yong Jin Lee; You La Lee; Sang-Woo Lee; Byeong-Cheol Ahn; Jeoung-Hee Ha; Jaetae Lee.
Using an adenoviral system as a delivery mediator of therapeutic gene, we investigated the therapeutic effects of the use of combined _MDR1_ shRNA and human _NIS_ (hNIS) radioiodine gene therapy in a mouse colon xenograft model. _In vitro_ uptake of Tc-99m sestamibi was increased approximately two-fold in cells infected with an adenovirus vector that expressed _MDR1_ shRNA (Ad-shMDR) and I-125 uptake was 25-fold higher in cells infected with an adenovirus vector that expressed human _NIS_ (Ad-hNIS) as compared to control cells. As compared with doxorubicin or I-131 treatment alone, the combination of doxorubicin and I-131 resulted in enhanced cytotoxicity for both Ad-shMDR and Ad-hNIS infected cells but not for control cells. In vivo uptake of Tc-99m...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3307/version/1

Enhanced display of scienti&amp;#xfb01;c articles using extended metadata
Provedor de dados: 17
Autores: Roderic D. M. Page.
Although the Web has transformed science publishing, scientific papers themselves are still essentially &amp;#x22;black boxes&amp;#x22;, with much of their content intended for human readers only.  Typically, computer-readable metadata associated with an article is limited to bibliographic details. By expanding article  metadata to include taxonomic names, identifiers for cited material (e.g., publications, sequences, specimens, and other data), and geographical  coordinates,  publishers could greatly  increase the scientific value of their digital content. At the same time this will provide  novel ways for users to discover and navigate through this content, beyond the relatively limited linkage provided by bibliographic...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3173/version/1

Enhancing Jatropha Productivity by Canopy Management
Provedor de dados: 17
Autores: Chalapathy  K. Reddy; Vishal V. Naole.
Jatropha seed and oil yield is function of planting material used, growing conditions, plant architecture development and maintenance. Jatropha is hardy plant; thrives well in arid and semi arid regions with an average rainfall ranging from 500 to 1200 mm. It has been planted in varied soil types, marginal and waste lands; where in utilization of in situ resources by agronomic practices and development and management of canopy by pruning are very crucial for harvesting higher seed for biodiesel production. Building ideal canopy by pruning during first growing season is very important. Pruning is done during winter season when plants are in dormant condition.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Earth &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3700/version/1

Enhancing me - hope or hype?
Provedor de dados: 17
Autores: Pete Moore.
Many people talk about human enhancement as if it is about to happen. Some suggest that it already has. To join in the debate you need to distinguish between social, personal and species enhancement. Social and personal are certianly with us - but talk of species enhancement leans more to hype than hope.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2139/version/1

Enhancing RNAi efficiency by inserting Nuclear factor-&amp;#x3ba;B binding sequence into SiRNA expression cassette
Provedor de dados: 17
Autores: Jianzhong Yi; Chenqian Liu.
RNAi based applications have been widely used to manipulate cellular phenotypes, analyze gene function and as a promising molecular therapy, however, there are rare reports in how to target the SiRNA expression constructs from the cytoplasm to nucleus. In this study, we inserted NF-&amp;#x3ba;B binding sequence into the SiRNA expression cassette to enhance RNAi efficiency, tested this propose by use of tRNAval and human H1 promoters, and eGFP and luciferase as reporter protein. The results showed that inserting NF-&amp;#x3ba;B binding sequence at the 3&amp;#x2019;-terminal of the SiRNA expression construct could enhance RNAi efficiency.
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4283/version/1

Entropic Landscape: the method to predict folding patterns and regional stability of proteins
Provedor de dados: 17
Autores: Kentaro Onizuka.
I propose a new method to calculate the entropy of a given protein sequence fragment. The set of fragment entropies over all possible fragments of the given sequence shows which region of the sequence is statistically stable and which region has a strong desire to fold into particular conformations. Here are three methods to calculate fragment entropy, the results from each of which represent entropies of different stage of protein folding.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2972/version/1

Envelope protein as molecular target for YFV (Yellow fever virus) drug discovery
Provedor de dados: 17
Autores: Manne  Munikumar; Dibyabhaba Pradhan; I. Vani Priyadarshini; Amineni Umamaheswari.
Yellow fever (YF), a mosquito-borne viral haemorrhagic fever, is one of the most lethal viral diseases. Despite the availability of vaccines, yellow fever virus (YFV) strikes an estimated 2, 00,000 persons world-wide each year and causes 30,000 deaths approximately. There are no approved antiviral therapies for the treatment of YFV disease in humans. YFV 17D strain RNA genome is of 10,862 nucleotides, which encodes three structural proteins (C, PrM, and E) and seven nonstructural proteins (NS1, NS2A, NS2B, NS3, NS4A, NS4B, and NS5). Identification of different protein functions facilitates a mechanistic understanding of YFV infection and opens novel means for drug development. Functional assignment of complete YFV proteome was done through support Vector...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5151/version/1

Environmental modelling and Web 2.0 - using Connotea to share XML-represented information
Provedor de dados: 17
Autores: Robert Muetzelfeldt.
Much academic information can be represented in a structured way and published on the web as XML documents.   Such information can then be displayed in a wide variety of ways, using different XSLT stylesheets.   &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This presentation presents MultiGuise, a Web application which allows any of several XML documents to be displayed using any of several stylesheets.   Both the documents and the stylesheets are bookmarked in Connotea, from where MultiGuise retrieves them using a special tag.   This approach means that anyone can add documents and stylesheets, simply by bookmarking them in Connotea.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The approach is illustrated primarily with environmental models represented in XML, but also with...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/18/version/1

Environmental Pursuits In Nanomaterial Systems Science With Indian Exemplars
Provedor de dados: 17
Autores: Ranen  Sen; Dipankar Seth; Indrani Roy; Debmalya Dasgupta; Arunava  Goswami.
The behavior and pattern of NPs of minerals in the evolutionary history of the earth vis &amp;#x2013; a &amp;#x2013;vis the environmental context are inquired into, with a riverine system as a model. The study of fractal dimensions of NPs of interest serves as an aid to obtain a comprehensive view of natural NPs in the model system. The present study combines inputs from work done on nanoparticles, derived from the Subanarekha River System and products of base metal mine effluents that are rich in NPs of minerals. The authors believe this study would help to establish certain universalities about NPs and provide an updated framework for understanding the current state of nanomineral science.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6166/version/2

Environmental Pursuits In Nanomaterial Systems Science With Indian Exemplars
Provedor de dados: 17
Autores: Ranen  Sen; Dipankar Seth; Indrani Roy; Debmalya Dasgupta; Arunava  Goswami.
The behavior and pattern of NPs of minerals in the evolutionary history of the earth vis &amp;#x2013; a &amp;#x2013;vis the environmental context are inquired into, with a riverine system as a model. The study of fractal dimensions of NPs of interest serves as an aid to obtain a comprehensive view of natural NPs in the model system. The present study combines inputs from work done on nanoparticles, derived from the Subanarekha River System and products of base metal mine effluents that are rich in NPs of minerals. The authors believe this study would help to establish certain universalities about NPs and provide an updated framework for understanding the current state of nanomineral science.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6166/version/1

Envisioning a data reuse registry
Provedor de dados: 17
Autores: Heather A. Piwowar; Wendy W. Chapman.
Repurposing research data holds many benefits for the advancement of biomedicine, yet is very difficult to measure and evaluate. We propose a data reuse registry to maintain links between primary research datasets and studies that reuse this data. Such a resource could help recognize investigators whose work is reused, illuminate aspects of reusability, and evaluate policies designed to encourage data sharing and reuse.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2152/version/1

Enzyme activities and glyphosate biodegradation in a riparian soil affected by  simulated saltwater incursion
Provedor de dados: 17
Autores: Changming Yang; Mengmeng Wang.
Soil salinization due to saltwater incursion, is a major threat to biochemical activities and thus strongly alters biogeochemical processes in a freshwater riparian of coastal estuary region. A pot incubation experiment was conducted to investigate the effects of simulated saltwater incursion on some key enzymatic activities and biodegradation dynamics of herbicide glyphosate in a riparian soil in Chongming Island located in the Yangtze River estuary, China. The results showed that saltwater addition with 10% artificial seawater significantly increased the biodegradation efficiency of glyphosate with the lowest residual concentration among all the treatments. However, glyphosate degradation was markedly decreased in the riparian soil with high levels of...
Tipo: Poster
Palavras-chave: Microbiology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6187/version/1

Enzyme activities in brown forest soils after introduction of Bacillus thuringiensis-based bioinsecticides
Provedor de dados: 17
Autores: Hasmik  S. Movsesyan; Arevik  M. Sargsyan; Naira  P. Ghazaryan.
Much attention in the complex of forest pest control methods nowadays is devoted to the application of biological preparations, especially to bacterial formulations produced on the base of Bacillus thuringiensis (BT) that in addition to their high biological effectiveness against injurious insects are safe for man, homoi&amp;#x43e;therms, beneficial insects and fish. As is known only 20-40% of sprayed preparation influences directly on pests while its 60-80% by different ways eventually penetrates into the soil. Taking into account also the fact that usage norm of commercial bacterial preparations makes up to 1-3 kg ha^-1^ and that preparation powder contains 45-100 billion viable spores g^-1^ it becomes evident that as a result of spraying huge quantity...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6426/version/1

Enzyme activity and dynamics in near-anhydrous conditions
Provedor de dados: 17
Autores: Murielle Lopez; Vandana Kurkal-Siebert; Rachel Dunn; Moeava Tehei; John Finney; Jeremy Smith; Roy Daniel.
Water is widely assumed to be essential for life 1, although the exact molecular basis of this requirement is unclear 2-4. Water facilitates protein motions 5-9 and although enzyme activity has been demonstrated at low hydrations in organic solvents 10-13, such non-aqueous solvents may allow the necessary motions for catalysis. To examine enzyme function in the absence of solvation and bypass diffusional constraints we have tested the ability of an esterase to catalyse alcoholysis as an anhydrous powder, using a closed reaction system in which the substrates and products of the enzyme reaction are gaseous 14-15, and where the water content can be well defined 16. At hydrations equivalent to 3 (&amp;#xb1;2) molecules of water per molecule of enzyme,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3884/version/1

Epidemiological Baseline of Influenza Virus in Wild Aquatic Birds in Hong Kong during the Pre-H5N1 Endemic Era
Provedor de dados: 17
Autores: Mario P. S. Chin; Kennedy F. Shortridge.
Influenza virus surveillance was conducted on wild ducks and shorebirds in Hong Kong at the Mai Po Nature Reserve to determine whether East Asian wild aquatic birds passing through or overwintering in Hong Kong are reservoirs of H5N1 influenza viruses and to establish an epidemiological baseline of influenza virus in wild aquatic birds during the pre-H5N1 endemic era. Three influenza viruses were isolated from 3178 faecal samples collected over three sampling periods from 1988 to 2001 during the southern and northern migration periods. The isolation rates and viruses were, respectively 0.08% (H10N5) in 1988 &amp;#x2013; 1990, 0.12% (H11N1) in 1998 and 0.09% (H3N8) in 1999 &amp;#x2013; 2001. Whereas tracheal and intestinal colon explants from representative...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/5110/version/1

Epigrass: a tool to study disease spread in complex networks.
Provedor de dados: 17
Autores: Fl&amp;#xe1;vio Code&amp;#xe7;o Coelho; Claudia Codeco; Oswaldo Cruz.
The construction of complex statial simulation models such as those used in network epidemiology, is a daunting task due to the large amount of data involved in their parameterization. Such data, which frequently resides on large geo-referenced databases, has to be processed and assigned to the various components of the model. All this just to construct the model, then it still has to be simulated and analyzed under different epidemiological scenarios. This workflow can only be achieved efficiently by computational tools that can automate most if not all these time-consuming tasks. In this paper, we present a simulation software, Epigrass, aimed to help designing and simulating network-epidemic models with any kind of node behavior.&amp;#xd;&amp;#xa;...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/378/version/1

Epitopes in ChEBI - A Collaboration with the IEDB
Provedor de dados: 17
Autores: Zara Josephs; Marcus Ennis; Steve Turner; Gareth Owen; Bjoern Peters; Randi Vita; Christoph Steinbeck.
*ChEBI background:* Chemical Entities of Biological Interest (ChEBI) is a curated database of small chemical entities important in biosystems. As well as a description of entities, it provides a semantically rich knowledge base; and an internal hierarchy that organises the entities by their molecular structure types and potential r&amp;#xf4;les.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*The ChEBI-IEDB collaboration:* The Immune Epitope and Analysis Resource (IEDB) is a project supported by contract from the National Institute of Allergy and Infectious Diseases (NIAID). Its goal is to make epitope-related data on infectious diseases and immune disorders freely available to researchers worldwide. In June 2009, ChEBI began working with the IEDB on a project aimed...
Tipo: Poster
Palavras-chave: Chemistry; Immunology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5094/version/1

ER localized bestrophin1 activates Ca2+ dependent ion channels TMEM16A and SK4
Provedor de dados: 17
Autores: Ren&amp;#xe9; Barro-Soria; Fadi AlDehni; Joana Alma&amp;#xe7;a; Jiraporn Ousingsawat; Ralph Witzgall; Rainer Schreiber; Karl Kunzelmann.
Bestrophins form Ca2+ activated Cl- channels and regulate intercellular Ca2+ signaling1. We demonstrate that bestrophin 1 is localized in the endoplasmic reticulum (ER), where it physically interacts with stromal interacting molecule 1 (Stim1), the ER-Ca2+ sensor2,3. Intracellular Ca2+ transients in HEK293 cells elicited by stimulation of purinergic P2Y2-receptors were augmented but more transient after expression of hBest1, in contrast to dominant negative hBest1-R218C, which attenuated Ca2+ increase. The p21-activated protein kinase Pak2 was found to phosphorylate hBest1, thereby enhancing Ca2+ signaling and activation of Ca2+ dependent Cl- (TMEM16A)4 and K+ (SK4)5 channels. Lack of bestrophin 1 expression in respiratory epithelial cells of mBest1...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2881/version/1

Errors in Length-weight Parameters at FishBase.org
Provedor de dados: 17
Autores: Michael Courtney; Simeon Cole-Fletcher; Lucas  Marin-Salcedo; Ajaya Rana.
Background:  FishBase.org is an on-line database of fish related data that has been cited over 1500 times in the fisheries literature.  Length-weight relationships in fish traditionally employ the model, W(L) = aL^b^, where L is length and W is weight.  Parameters a and b are catalogued by FishBase for a large number of sources and species.  FishBase.org detects outliers in a plot of log(a) vs. b to identify dubious length-weight parameters.&amp;#xd;&amp;#xa;Materials and Methods: To investigate possible errors, length-weight parameters from FishBase.org were used to graph length-weight curves for six different species: channel catfish (Ictalurus punctatus), black crappie (Pomoxis nigromacalatus), largemouth bass (Micropterus salmoides), rainbow trout...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/5927/version/1

Escherichia coli EHEC Germany outbreak preliminary functional annotation using BG7 system
Provedor de dados: 17
Autores: Marina Manrique; Pablo Pareja-Tobes; Eduardo Pareja-Tobes; Eduardo Pareja; Raquel Tobes.
We have annotated the  European outbreak E. coli EHEC genome sequenced by BGI (6-2-2011) and assembled with MIRA by Nick Loman (6-2-2011 ). Our system BG7, Bacterial Genome annotation of Era7 Bioinformatics, predicts ORFs and annotates them based on fragments of similarity with Uniprot proteins. We have predicted 6327 genes, 6156 encoding proteins y 171 corresponding to ribosomal and tRNA. Based on the preliminary results of our semi-automated method of annotation we have selected some predicted proteins with potential implications in pathogenicity and virulence.&amp;#xd;&amp;#xa;There are 33 predicted genes annotated as toxins and we have found three putative hemolysins: Hemolysin E, a putative hemolysin expression modulating protein and a channel...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6001/version/1

ESG: Extended Similarity Group method for automated protein function prediction
Provedor de dados: 17
Autores: Meghana Chitale; Troy Hawkins; Changsoon Park; Daisuke Kihara.
We present here the Extended Similarity Group (ESG) method, which annotates query sequences with Gene Ontology (GO) terms by assigning probability to each annotation computed based on iterative PSI-BLAST searches. Conventionally sequence homology based function annotation methods, such as BLAST, retrieve function information from top hits with a significant score (E-values). In contrast, the PFP method, which we have presented previously, goes one step ahead in utilizing a PSI-BLAST result by considering very weak hits even an E-value of up to 100 and also by incorporating the functional association between GO terms (FAM matrix) computed using term co-occurrence frequencies in the UniProt database. PFP is very successful which is evidenced by the top rank...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2193/version/1

Essay: On the close relationship between speciation, inbreeding and recessive mutations.
Provedor de dados: 17
Autores: Etienne Joly.
Whilst the principle of adaptive evolution is unanimously recognised as being caused by the process of natural selection favouring the survival and/or reproduction of individuals having acquired new advantageous traits, a consensus has proven much harder to find regarding the actual origin of species. Indeed, since speciation corresponds to the establishment of reproductive barriers, it is difficult to see how it could bring a selective advantage because it amounts to a restriction in the opportunities to breed with as many and/or as diverse partners as possible. In this regard, Darwin himself did not believe that reproductive barriers could be selected for, and today most evolutionary biologists still believe that speciation can only occur through a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5003/version/1

Essay: On the close relationship between speciation, inbreeding and recessive mutations.
Provedor de dados: 17
Autores: Etienne Joly.
Whilst the principle of adaptive evolution is unanimously recognised as being caused by the process of natural selection favouring the survival and/or reproduction of individuals having acquired new advantageous traits, a consensus has proven much harder to find regarding the actual origin of species. Indeed, since speciation corresponds to the establishment of reproductive barriers, it is difficult to see how it could bring a selective advantage because it amounts to a restriction in the opportunities to breed with as many and/or as diverse partners as possible. In this regard, Darwin himself did not believe that reproductive barriers could be selected for, and today most evolutionary biologists still believe that speciation can only occur through a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5003/version/2

Establishing a multicellular model by three-dimensional cell-assembly technique for metabolic syndrome
Provedor de dados: 17
Autores: Mingen Xu; Yongnian Yan; Renjie Zhang; Ri Yao; Haixia Liu; Xiaohong Wang.
One of the major obstacles in developing multifunctional drugs for the metabolic syndrome (MS) is lack of in vitro models that capture more complex features of the disease. Here we give the first report that establishes an energy metabolic system model using cell-assembly technique which can assemble cells into designated places to form complex three-dimensional structures. Adipose-derived stromal cells were assembled and induced differentiation into adipocytes and endothelial cells; pancreatic islets were then deposited at designated locations and constituted adipoinsular axis with adipocytes. Analysis of the factors involved in energy metabolism showed our system could capture more physiological and pathophysiological features of the in vivo energy...
Tipo: Manuscript
Palavras-chave: Biotechnology; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/1496/version/1

Estimated carboxylic acid ester hydrolysis rate constants for food and beverage aroma compounds
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Aroma compounds in the Flavornet database were screened for potentially hydrolyzable carboxylic acid ester functionalities. Of the 738 aroma compounds listed in this database, 140 molecules contain carboxylic acid ester groups that may be amenable to hydrolysis in various food and beverage products.  Acid- (k~A~) and base- (k~B~) catalyzed and neutral (k~N~) hydrolysis rate constants in pure water at 25&amp;#xb0;C were estimated for these aroma compounds. Where available, good agreement between theoretical and experimental hydrolytic half-lives was obtained at various pH values. Wide ranges and broad frequency distributions for k~A~, k~B~, and k~N~ are expected among the various hydrolyzable aroma compounds, with estimated k~A~ ranging from...
Tipo: Manuscript
Palavras-chave: Chemistry; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6471/version/1

Estimating body Mass and Nutritional Status from Subadult Hominin Skeletons
Provedor de dados: 17
Autores: Gwendolyn Robbins.
Hominin body size and shape are key components to reconstructing phylogeny, life history, adaptation, and behavior in ancestral populations^1^. For adults, geometric properties of the femoral midshaft cross-section are used to infer locomotor behavior^2-5^, subsistence practices^6-7^, and functional adaptations^8-10^. Recently research has focused on patterns of compact bone ontogeny, particularly in regard to changes in bone strength with the acquisition of bipedal locomotion^11-13^ and examining population differences in ontogenetic trajectories for subadult humans^14-16^ and Neandertals^16^. Because femoral midshaft geometry is primarily shaped by biomechanical strains-weight bearing, locomotion, and muscle action-ontogenetic research requires estimates...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2468/version/1

Estimation of DNA Sequence Context-dependent Mutation Rates Using Primate Genomic Sequences: Application to Estimation of Selection Bias in Protein (Human TP53) Evolution
Provedor de dados: 17
Autores: Wei Zhang.
Understanding of the mechanism of DNA mutation process is critical for studying the functional consequences of genetic variation in clinical medicine (eg. drug response) as well as other complex traits (eg. gene expression and cause of common diseases). During the last several decades, many probabilistic models of DNA nucleotide substitution have been proposed for studying this process. A common feature of these mutation models is that they assume the nucleotides evolve independently at each site. In other words, they are sequence context-independent models. However, based on various biochemical studies, it is now recognized that the DNA mutation process resulting in substitutions in both coding and non-coding regions may depend on sequence context. We...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1243/version/1

Estimation of extracellular lipase enzyme produced by thermophilic bacillus sp. isolated from arid and semi-arid region of Rajasthan, India
Provedor de dados: 17
Autores: Deeksha   Gaur; Pankaj Kumar   Jain; Yamini Singh  Sisodia; Vivek  Bajpai.
Thermophilic organisms can be defined as microorganisms which are adapted to live at high temperatures. The enzymes produce by thermophilic bacteria are capable of catalyzing biochemical reactions at high temperatures. Thermophilic bacteria are able to produce thermostable lipase enzymes capable of degradation of lipid at temperatures higher than those of mesophilic bacteria. Therefore, the isolation of thermophilic bacteria from natural sources and their identification are quite useful in terms of discovering thermophilic lipase enzymes. Due to great temperature fluctuation in hot arid and semi-arid regions of Rajasthan, this area could serve as a good source for new thermophilic lipase producing bacteria with novel industrially important properties. The...
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology.
Ano: 2012
URL: http://precedings.nature.com/documents/7072/version/1

Estimation of oxidative status in lymphocytes of type2 diabetes mellitus patients
Provedor de dados: 17
Autores: Awadhesh K Arya; Kamlakar Tripathi.
Introduction: Diabetes mellitus (DM) is a group of metabolic disorders which opens the door for many diseases leading to various complications like neuropathy, nephropathy and retinopathy. Type 2 diabetes mellitus (T2DM) is associated with elevated level of oxidative stress, which is one of the most important factors responsible for the development of chronic complications of this disease. Antioxidants like reduced glutathione (GSH), superoxide dismutase (SOD) and catalase protects cells against oxidative damage.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Purpose: Our present study suggests that hyperglycemia induced oxidative stress leads to various complications in T2DM patients. Here we investigated oxidative stress markers in lymphocytes of healthy control and...
Tipo: Poster
Palavras-chave: Immunology.
Ano: 2011
URL: http://precedings.nature.com/documents/5975/version/1

Estimation of the Multiple Testing Burden for Genomewide Association Studies of Common Variants
Provedor de dados: 17
Autores: Itsik Pe&amp;#x27;er; Roman Yelensky; David Altshuler; Mark J. Daly.
Genomewide association studies are an exciting strategy in genetics, recently becoming feasible. While pioneering studies are being underway, it is already clear that the analytic issue of determining the significance of results presents a challenge to the wide community of researchers. Rather than each study engaging in independent evaluation, there is need in the community to have standards set for whole-genome significance. &amp;#xd;&amp;#xa;We have therefore undertaken the task of developing such standards, based on data collected with collaborators in the International Haplotype Map Consortium. We report an estimated burden of a million independent tests genomewide in Europeans, and twice that number in Africans. We further identify the sensitivity of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/359/version/1

Eukaryotic translation initiation machinery can operate in a prokaryotic-like mode without eIF2
Provedor de dados: 17
Autores: Ivan N. Shatsky; Ilya Terenin; Sergey Dmitriev; Dmitri Andreev.
Unlike prokaryotes, a specialized eukaryotic initiation factor 2 (eIF2), in the form of the ternary complex eIF2*GTP*Met-tRNAiMet is utilized to deliver the initiator tRNA to the ribosome within all eukaryotic cells1. Phosphorylation of eIF2 is known to be central to the global regulation of protein synthesis under stress conditions and infection2. Another distinctive feature of eukaryotic translation is scanning of mRNA 5&amp;#x27;-leaders, whose origin in evolution may be relevant to the appearance of eIF2 in eukaryotes. Translation initiation on the hepatitis C virus (HCV) internal ribosome entry site (IRES) occurs without scanning3,4. Whether these unique features of the HCV IRES account for the formation of the final 80S initiation complex is unknown....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1518/version/1

Eutrophication: Can nanophosphorous control this menace?
Provedor de dados: 17
Autores: Deepika  Bhalla; Siddhartha  S. Mukhopadhyay.
Eutrophication is a threat to quality of surface and ground water bodies (SWB) and to bio-diversity of the aquatic eco-system. One of the causes of P accumulation in SWB is its excess application as a fertilizer on agricultural lands. Phosphorus buffering also contributes to eutrophication and remains a major problem years after the release of P is brought under control. It could be discerned from many experiments conducted world over that addition of small amount of P can remove excess P from soils, provided the solution P is maintained in such a manner that productivity is sustained, and nano-P could possibly play a role in it. In such endeavours, P must be applied to soils in amount exact to the requirement of crop. Of course ecological cautions of use...
Tipo: Presentation
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3763/version/1

Evaluating experiential education through an intertidal ecology field trip.
Provedor de dados: 17
Autores: Kate E. Lowry; Cynthia Wilber; Rodolfo Dirzo.
*Background/Question/Methods*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Stanford SEEDS and the Jasper Ridge Biological Preserve have worked together with Redwood High School to implement an experiential ecology education program. The Redwood Environmental Academy of Leadership(REAL) is designed to bring underserved high school students out of the classroom and into the outdoors to create a unique and effective learning experience. Though the program focuses on riparian ecosystem restoration, the course curriculum is interdisciplinary and designed to inspire continuation high school students to attend college or pursue environmental careers. Through a SEEDS special grant, REAL students were taken to Fitzgerald Marine Reserve in Half Moon Bay, California, to learn...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3875/version/1

Evaluating Modelling  Approaches for Medical  Image Annotations
Provedor de dados: 17
Autores: Jasmin Opitz; Bijan Parsia; Ulrike Sattler.
Information system designers face many challenges with regards to selecting appropriate semantic technologies and deciding on a modeling approach for their system. However, there is no clear methodology yet to evaluate &amp;#x201c;semantically enriched&amp;#x201d; information systems. In this paper we present a case study on different modeling approaches for annotating medical images and introduce a conceptual framework that can be used to analyze the fitness of information systems and help designers to spot the strengths and weaknesses of various modeling approaches as well as managing trade-o&amp;#xfb00;s between modeling e&amp;#xfb00;ort and their potential benefits.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5609/version/1

Evaluating restoration success and applying adapative management in the Middle Rio Grande Bosque
Provedor de dados: 17
Autores: Ondrea Hummel; Todd Caplan.
The U.S. Army Corps of Engineers Albuquerque District, in collaboration with various local partners, has been implementing restoration projects in the Albuquerque Reach of the Middle Rio Grande.  These projects have included the removal of the metal jetty jacks, debris, and dense thickets of non-native vegetation (salt cedar, Russian olive, and Siberian elm) that occur in the bosque (riparian forest), creation of wet habitats (such as willow swales and high-flow channels), and revegetation schemes focused on increasing the diversity and quality of wildlife habitat.  The goal of many of these projects is to develop a framework to restore the bosque into a more functional and sustainable ecosystem.  Projects implemented on the ground are being monitored for...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3649/version/1

Evaluation and Validation of clinical 4.23 T sodium MRI in animals and human: Application of oblique multi-slice spin-echo pulse sequence
Provedor de dados: 17
Autores: Rakesh Sharma; Jose Katz.
Objective: Application of high-field 4.23 T MRI clinical imager was demonstrated for sodium-magnetic resonance imaging (MRI) data acquisition. Primary hypothesis: Sodium [Na] in brain is MR visible. Secondary hypothesis was, if, application of multislice spin echo (MSSE) pulse sequence at selected scan parameters can sufficiently visualize the total sodium signal as indicator of sub-clinical activity. Material and Methods: MSSE pulse sequence technique was used to simulate sodium images of human brain. For validation purpose, inversion recovery pulse sequence was validated by optimization of scan inversion time (TI). Phantom of sodium and rat brain were imaged. Sodium images were validated and compared with proton MRI images. Results: MSSE pulse technique...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2856/version/1

Evaluation of Antimicrobial Studies of Traditional Medicine
Provedor de dados: 17
Autores: Ramar Perumal Samy; S. Ignacimuthu; Vincent  TK Chow.
Synthetic drugs, which are having serious side effects, are cytotoxic to human beings. Moreover, bacteria slowly become resistant against antibiotics. In order to overcome these problems, scientists are continuing to search for antibacterial and novel principles from plants. Zanthoxylum limonella has been popularly used in traditional systems of medicine for the treatment of dental caries, cardiac, respiratory diseases and stomach problems. The present study was therefore focused on finding out the medicinal properties of the bark of Z. limonella tested against some selected bacteria using disc-diffusion method at the concentration of 100, 200 and 300 mg/ml. The methanol and water extracts of the bark exhibited effective antibacterial activity against S....
Tipo: Manuscript
Palavras-chave: Microbiology; Pharmacology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6027/version/1

Evaluation of CD4+ T Cells in HIV Patients Presenting with Malaria at the University of Ilorin Teaching Hospital Nigeria
Provedor de dados: 17
Autores: Olajide O. Agbede; Temitope O. Ajiboye; Olatunji M. Kolawole; Samuel A. Babatunde; Louis  O. Odeigha.
CD4 count is an important immunological marker of disease progression in HIV seropositive patients. This study was carried out to determine the effect of malaria or fever of unknown origin on the population of CD4+ T lymphocytes of HIV seropositive patients attending the highly active antiretroviral therapy (HAART) clinic of the University of Ilorin Teaching Hospital, Ilorin, Nigeria. 36 subjects were selected for this study. Ongoing history of fever was used as a case definition for malaria and malaria was confirmed from microscopic examination of thick and thin film of blood sample obtained from the patients during presentation with fever. The CD4 count was evaluated during presentation of fever and post-fever using flow cytometry. There was significant...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/3974/version/1

Evaluation of diversity, specialization, and gene specificity in transcriptomes
Provedor de dados: 17
Autores: Octavio Martinez; Humberto Reyes-Vald&amp;#xe9;s.
The transcriptome is a set of genes transcribed in a given tissue under specific conditions and can be characterized by a list of genes with their corresponding frequencies of transcription. Transcriptome changes can be measured by counting gene tags from mRNA libraries or by measuring light signals in DNA microarrays. Recently we proposed an approach to define and estimate the diversity and specialization of transcriptomes and gene specificity. This approach can be useful for the determination and measure of transcriptional networks. We defined transcriptome diversity as the Shannon entropy of its frequency distribution. Gene specificity is defined as the mutual information between the tissues and the corresponding transcript, allowing detection of either...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3012/version/1

Evaluation of effective parameters on fabrication of BSA nanoparticles
Provedor de dados: 17
Autores: Mostafa Rahimnejad; Ghasem Najafpour; Mohsen Jahanshahi.
Coacervation technique was implemented in fabrication of BSA nanoparticle for the purpose of drug delivery system. Nanoparticle was purified with 48,800 g centrifuge, and then followed by dialysis, micro and ultra filtration. The fabricated nanoparticles were subjected to physical, morphological and biochemical characterization. The analyzed samples by SEM and AFM proved the semi-spherically shape of the particles whilst the size distribution was measured by photon correlation spectroscopy. Fourier transforms infra-red spectroscopy (FTIR) spectrum indicated that the fabricated nanoparticles were pure. The impact of various parameters upon the particle size was extensively investigated. The concentration of glutaraldehyde at fixed temperature had absolutely...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2966/version/1

Evaluation of HIV infected Cells
Provedor de dados: 17
Autores: Kumaresan Nallasamy.
In this paper, Human Immunodeficiency Virus (HIV) infected cells is found out using a Simulink model. The Simulink solution is equivalent or very close to the exact solution of the problem. Accuracy of the Simulink solution to this problem is better than the existing numerical methods. The main advantage of Simulink model is that solution of any dynamicalproblem can be obtained by anybody without writing any codes. Anillustrative numerical example is presented for the proposed method.
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4961/version/1

Evaluation of protein surface roughness index using its heat denatured aggregates
Provedor de dados: 17
Autores: Hrishikesh Mishra; Tapobrata Lahiri.
Recent research works on potential of different protein surface describing parameters to predict protein surface properties gained significance for its possible implication in extracting clues on protein&amp;#x27;s functional site. In this direction, Surface Roughness Index, a surface topological parameter, showed its potential to predict SCOP-family of protein. The present work stands on the foundation of these works where a semi-empirical method for evaluation of Surface Roughness Index directly from its heat denatured protein aggregates (HDPA) was designed and demonstrated successfully. The steps followed consist, the extraction of a feature, Intensity Level Multifractal Dimension (ILMFD) from the microscopic images of HDPA, followed by the mapping of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3693/version/1

Evaluation of resistance in wheat against Rhopalosiphumpadi (L.) (Homoptera:Aphididae) Under laboratory Conditions
Provedor de dados: 17
Autores: Naheed Akhtar; Noreen Moin; Ghulam Jilani; Ata  U. Mohsin; Shaheena  Yasmin; Afzala Afzala; Munir Goraya; Atif A. Baig.
Aims and introduction&amp;#xd;&amp;#xa;All over the world aphids are pests of economic importance, affecting all varieties of plants like cereal crops, vegetables, ornamental plants and fruits. Aphids damage plants either directly or indirectly. Aphids are one of the major agricultural pests. There are only a few plants that are not susceptible to infestation by this destructive pest. They cause direct damage by sucking the sap of leaves, blocking photosynthesis which results in leaf distortion, gall production, discoloration, stunting, leaf curling, wilting, twisting and premature leaf falls. They are directly involved in transmission of plant viruses and indirectly by depositing honey dew that reduces photosynthetic activity and induces sooty mold...
Tipo: Presentation
Palavras-chave: Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5947/version/1

Evaluation of some cellular immune index in HIV infected participants
Provedor de dados: 17
Autores: Martin Ifeanyichukwu; Sam Meludu; Prince Ele; Nkiru Ukibe; Charles Onyenekwe; Michael Ezeani; Clement Ezechukwu; Grace Amilo; Pauline Umeanaeto.
The study was designed to evaluate some cellular immune index of HIV infected participants. For the study, 80 HIV infected participants were recruited for the study. They were aged 15 - 55 years. 45 of these participants were classified as Symptomatic HIV (Stage 11), while the remaining 35 were Asymptomatic HIV (Stage 1). Similarly, 40 HIV seronegative participants served as Control. Blood samples collected from the participants were used HIV screening and confirmation, CD4+ T cell count, absolute lymphocyte count and percent lymphocyte transformation. The CD4+T cell count and percent Lymphocyte Transformation count were significantly lowered in HIV infected participants compared with the HIV Seronegative participants (p&amp;#x3c;0.05 in each case)....
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4299/version/1

Evaluation of the Cell Ontology (CL)
Provedor de dados: 17
Autores: Lindsay G. Cowell.
An ontological representation of the entities relevant to biological research is urgently needed.  The cell ontology developed by Bard and colleagues (CL) (Bard et al. 2005) makes a significant contribution towards fulfilling this need by providing an ontology of cell types.  The CL has already proven useful for data annotation (e.g. Grumbling et al. 2006), although the ontology&amp;#x2019;s potential utility goes well beyond that specific application.  For example, using the number of distinct cell types in an organism as a measure of biological complexity, Vogel and Chothia (2006) compared the proteomes of 38 organisms of varying complexity and identified patterns in the evolution and expansion of protein domain superfamilies.  This work has implications...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3971/version/1

Evaluation of the cutaneous microbiome in psoriasis
Provedor de dados: 17
Autores: Martin  J. Blaser; Barbara Methe; Bruce  Strober; Guillermo I. Perez Perez; Stuart Brown; Alexander  Alekseyenko.
Psoriasis, a highly prevalent disease of humans of unknown cause, is a chronic inflammatory disorder primarily involving skin, with distinctive clinical characteristics. With the newly developed tools that facilitate microbiome research, it now is possible to assess whether the cutaneous microbiome plays a role in the pathogenesis of this disorder. Preliminary data from our studies suggest that the cutaneous microbiome in psoriasis is complex and possibly different from normal. To deal with this complexity, we propose to examine the cutaneous microbiome in relation to psoriasis with explorations at several taxonomic and informatic levels. Our overall objective is to examine how changes in the normal cutaneous microbiome contributes to the pathogenesis of...
Tipo: Marker Paper / Data Plan
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5276/version/1

Events of reclaiming marshes for rice fields between 7000BP and 4500 BP in east China
Provedor de dados: 17
Autores: Yunfei Zheng; Guoping  Sun; Ling Qin; Chunhai Li; Xiaohong  Wu; Xugao Chen.
Discovery of the oldest rice fields at the Tianluoshan site in east China has provided data of recovering reclaimation, cultivation, and the ecological system of rice fields between 7000BP and 4500 BP. People opened up marshes of dense reeds with fire and wooden or bone spades, in order to create rice fields. In the rice fields, there was not only rice, but a lot of weeds as well. The excavations proved that little or even no weeding or irrigation was adopted. However, tilling soil by wooden and bone tools was evidenced. The yields are estimated to have been about 8.3 kg for the early period and 9.5 kg per acre for the later period. The cultivation system was low-level. Although the Tianluoshan people cultivated rice, they still obtained a great deal of...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2853/version/1

Evidence attribution in the UniProt Knowledgebase
Provedor de dados: 17
Autores: Michele Magrane; UniProt Consortium.
UniProtKB provides the scientific community with a comprehensive collection of protein sequence records containing extensive curated information including functional and sequence annotation. This information is derived from a variety of sources such as scientific literature and sequence analysis programs as well as data imported from automatic annotation systems and external databases. To allow users to ascertain the origin of each data item in a UniProtKB record, an evidence attribution system is being introduced which links each piece of information to its original source. This system allows users to trace the origin of all information, to differentiate easily between experimental and computational data, and to assess data reliability. The current system...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3129/version/1

Evidence for gliadin antibodies as causative agents in schizophrenia.
Provedor de dados: 17
Autores: Chris J. Carter.
Antibodies to gliadin, a component of gluten, have frequently been reported in schizophrenia. Highly immunogenic B cell epitopes along its length are homologous to numerous proteins relevant to schizophrenia, including members of the DISC1 interactome, glutamate, dopamine and neuregulin signaling networks, and plasticity or myelination pathways. Antibodies to gliadin may cross react with these key proteins, as has already been observed with synapsin 1 and calreticulin. Gliadin may thus be a causative agent in schizophrenia, under certain genetic and immunological conditions, producing its effects via antibody mediated knockdown of multiple proteins relevant to the disease process. Because of such homology, an autoimmune response may be sustained by the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5351/version/1

Evidence of existence of totally different types of ribosomes in intermediate animals
Provedor de dados: 17
Autores: Haoran H. Wang; Mary X. Gao; Sato Kenzo; Kazumitsu Hirai.
In all organisms, messenger-directed protein synthesis is catalyzed by ribonucleoprotein particles called ribosomes. A ribosome is typically composed of one small and one large subunit which contain one short (18S) and one long (28S) rRNAs, respectively. Surprisingly, in this study, three similar size rRNAs (18-21S) were revealed in the electrophoresis profile of the total RNAs of tapeworm _Spirometra erinaceiuropaei_. Northern blot analysis shows that one of the three bands belongs to 18S rRNA, and the other two bands are of 28S rRNAs, implying structurally distinct ribosomes in this intermediate animal. Furthermore, similar, but not identical profiles were observed in two other tapeworms _Diphyllobothrium hottai_ and _Diphyllobothrium Nipponkaiizeme_....
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2608/version/2

Evidence of Massive Horizontal Gene Transfer Between Humans and Plasmodium vivax
Provedor de dados: 17
Autores: Daniel Z. Bar.
The horizontal transfer of DNA between different organisms is a major force shaping the genomes of prokaryotes, but is considered to have a minor role in eukaryotes, with only a handful of known examples, mostly of limited size. The nucleotide databases of Plasmodium genomes were divided into small fragments and compared to human, as well as to other Plasmodium genomes.  This computational approach revealed that the Plasmodium vivax genome is interlaced with multiple DNA fragments that were likely acquired via horizontal transfer from humans. Contamination is a major concern in such studies; moreover, it must be determined if the identified homologies might be due to chance. These reservations are supported by the fact that the identified homologous...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5690/version/1

Evidence of mature adipocyte proliferation regulated by proliferin
Provedor de dados: 17
Autores: Kazuo Kajita; Ichiro Mori; Takayuki Hanamoto; Wu Zhiliang; Takahide Ikeda; Kei Fujioka; Masahiro Yamauchi; Hideyuki Okada; Aki Minami; Toshiko Kajita; Yoshihiro Uno; Hiroyuki Morita; Isao Nagano; Masao Takemura; Mitsuru Seishima; Yuzo Takahashi; Tatsuo Ishizuka.
Despite much research, whether mature adipocytes proliferate remains controversial. Here, we examined 5-bromo-2&amp;#x2032;-deoxyuridine (BrdU)-labelling of mature adipocytes. Although BrdU incorporation into subcutaneous adipocytes was less than that in visceral adipocytes, pioglitazone (Pio) treatment increased BrdU incorporation in subcutaneous, but not visceral, adipocytes in rats. Fully differentiated 3T3-L1 adipocytes exhibited an increase in cell number and BrdU incorporation with time, with this increase enhanced by Pio treatment. We therefore screened for genes that encode growth factors regulated by Pio, and selected proliferin (PLF). Both gene silencing of PLF by small interfering RNA and treatment with anti-PLF antibody suppressed proliferation...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4714/version/1

Evidence of novel type of ribosome in eukaryotic intermediate flatworm
Provedor de dados: 17
Autores: Haoran  H. Wang; Mary X. Gao; Sato Kenzo; Kazumitsu Hirai.
In all organisms, messenger-directed protein synthesis is catalyzed by ribonucleoprotein particles called ribosomes. A ribosome is typically composed of one small and one large subunit which contain one short (18S) and one long (28S) rRNAs, respectively. Surprisingly, in this study, three similar size rRNAs (18-21S) were revealed in the electrophoresis profile of the total RNAs of tapeworm _Spirometra erinaceiuropaei_. Northern blot analysis shows that one of the three bands belongs to 18S rRNA, and the other two bands are of 28S rRNAs, implying structurally distinct ribosomes in this intermediate animal. Furthermore, similar, but not identical profiles were observed in two other tapeworms _Diphyllobothrium hottai_ and _Diphyllobothrium Nipponkaiizeme_....
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2608/version/1

Evidence of salt secretion at the stem of _Melaleuca cuticularis_ Labill.
Provedor de dados: 17
Autores: Amanda J. Twomey; Bodapati P. Naidu; Shu Fukai.
It has been observed that _Melaleuca cuticularis_ Labill. has the ability to secrete salt solution to the surface of its stem. No literature has been found to illustrate other species&amp;#x27; capacity to secrete salts at the stem and with what little literature there is on _M. cuticularis_ under saline conditions ^1, 2^, there was no evidence documented by those authors to have witnessed salt secreting at the stem. Most recorded observations of salt secretion by plants has usually been on leaf salt secretion through specialized glands or bladders often in mangroves, salt bushes and grass species, among others ^3-8^. This observation is the first known record of a plant species capable of secreting salts mostly at the stem.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Earth &amp; Environment; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2450/version/1

EvoIO: Community-driven standards for sustainable interoperability
Provedor de dados: 17
Autores: Arlin Stoltzfus; Karen Cranston; Hilmar Lapp; Sheldon McKay; Enrico Pontelli; Rutger Vos; Nico Cellinese.
Interoperability is the property that allows systems to work together independent of who created them, or how or for what purpose they were implemented. It is crucial for aggregating data from different online resources and for integrating different kinds of data. Interoperability is based on effective standards that become and remain broadly adopted. We argue that to develop and apply such standards for evolutionary and biodiversity data sustainably, we need a community-driven, open, and participatory approach. With the goal to build such an approach, the EvoIO collaboration emerged in 2009 from several NESCent-sponsored activities.  EvoIO aims to be a nucleating center for developing, applying and disseminating interoperability technology that connects...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4588/version/1

Evolution as a language that speaks itself
Provedor de dados: 17
Autores: Rodrick Wallace.
The &amp;#x27;self-referential&amp;#x27; character of evolutionary process noted by Goldenfeld and Woese (2010) can be restated through a &amp;#x27;language&amp;#x27; model in which genes, gene expression, and environment are represented as interacting information sources. The larger, composite, source that characterizes the high probability evolutionary paths then becomes, in a real sense, a language that speaks itself. The approach represents a significant extension of nonequilibrium condensed matter formalism in which the asymptotic limit theorems of information theory beat back the mathematical thicket a full step, providing necessary, but not sufficient, conditions for punctuated evolutionary transitions that can themselves be expressed as highly...
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5339/version/1

Evolution is Viral: The Theory  of Collective Discontinuous Evolution
Provedor de dados: 17
Autores: Mikhail L.  Gershteyn; Iosif M. Gershteyn.
Herein will be discussed the problems associated with the origin of species according to Darwinist processes of individual mutations. We will argue that individual mutations cannot be the driving force of species origination. A far more probable explanation is a process of collective mutation that affects numerous individuals near simultaneously akin to an infectious disease. These types of mutations might be precipitated by viruses which would create a discontinuous leap into another species. Such a mechanism also sheds light on the increased rate of evolution observed currently.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5203/version/1

Evolution of 11[beta]-Hydroxysteroid Dehydrogenase-Type 1 and 11[beta]-Hydroxysteroid Dehydrogenase-type 3
Provedor de dados: 17
Autores: Michael E. Baker.
A key regulator of glucocorticoid action is 11[beta]-hydroxysteroid dehydrogenase type-1 (11[beta]-HSD1), which catalyzes the conversion of cortisone to cortisol, the biologically active glucocorticoid.  11[beta]-HSD1 is a paralog of 11[beta]-HSD3, whose physiological function remains unclear.  As reported here, 11[beta]-HSD3 has orthologs in sea urchin, amphioxus and Ciona, while 11[beta]-HSD1 first appears in sharks.  Thus, 11[beta]HSD3 arose before the evolution of glucocorticoid signaling, suggesting different ancestral function(s) for 11[beta]-HSD3.  Four perplexing findings arise from this evolutionary analysis: 1) 11[beta]-HSD1 is not present in a ray-finned fish genome, 2) zebrafish and fathead minnow contain two isoforms of 11[beta]-HSD3; 3)...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Genetics &amp; Genomics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4296/version/1

Evolution of Cooperation on Playing Prisoner&amp;#x27;s Dilemma Game in the Finite-Capacity Spot
Provedor de dados: 17
Autores: Hiroshi Toyoizumi.
Explaining the evolution of cooperative behavior has been one of main challenges in evo- lutionary theory^1-6^. Cooperation may collapse a surge of defectors who enjoy the benefit without cooperation in situation called prisoner&amp;#x27;s dilemma. In the concept of evolutionary game theory, there are many proposals to explain the evolution of cooperation by adding further mechanism such as, kin selection^1^, reciprocity^7^, punishment^8,9^  and the finiteness of the population^6^. In evolutionary game theory, a pair is randomly picked from population, and play a prisoner&amp;#x27;s dilemma game. Here we also show the finiteness encourages cooperation but use different approach: in spite of random-pick, individuals join and leave a spot or territory with a...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3071/version/1

Evolution of Co-operation When the Strategies are Hidden: The Human Mating Game
Provedor de dados: 17
Autores: Milind Watve; Anuja Damle; Bratati Ganguly; Anagha Kale.
Defection is frequently seen in co-operative systems [1-3]. Game theoretical solutions to stabilize cooperation rely on reciprocity and reputation in iterated games[4-5]. One of the basic requirements for reciprocity or reputation building is that the strategies of players and the resulting payoffs should be open at the end of every interaction. For games in which the strategies and payoffs remain hidden, these stabilizing factors are unlikely to work. We examine the evolution of cooperation for hidden-strategy games using human mating game as an example.  Here faithful parenting can be considered as cooperation and extra-pair mating (EPM) or cuckoldry as defection. Cuckoldry may get exposed only occasionally and the genetic benefits of cuckoldry also...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/740/version/1

Evolution of malaria virulence in cross-generation transmission through selective immune pressure
Provedor de dados: 17
Autores: David E. Gurarie.
Theoretical arguments and some mathematical models of host-parasite coevolution (e.g. [1- 6]) suggest host immunity as the driving source for the evolution of parasite virulence. Imperfect vaccines in particular, can play the role and recent work [7] sets to test these ideas experimentally, using the mouse malaria model, Plasmodium chabaudi. To this end the authors evolve parasite lines in immunized and nonimmunized (&amp;#x201c;na&amp;#xef;ve&amp;#x201d;) mice using serial passage of infected blood samples. They find parasite lines evolved in immunized mice become more virulent than those evolved in naive mice. Furthermore, this feature persisted even when the evolved strains were transmitted through mosquitoes. &amp;#xd;&amp;#xa;Here we develop a...
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/203/version/1

Evolution of social behaviour
Provedor de dados: 17
Autores: Vidyanand Nanjundiah.
Nowak et al.1 wish to explain why the version of kin selection theory that is summarised by the formula R&amp;#x3e;c/b (c=cost of performing &amp;#x27;altruistic&amp;#x27; act, b=benefit derived by recipient of act, R=relatedness between the two) is of little utility for understanding the evolution of eusociality. But in trying to do so they omit much that is relevant and risk misrepresenting the issue to anyone who is not familiar with the literature. A fairer account would include the following facts.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4941/version/1

Evolution of the Protein Universe. Time Scales and Selection
Provedor de dados: 17
Autores: Marco Cosentino Lagomarsino; Alessandro Sellerio; Philip Heijning; Bruno Bassetti.
The availability of many genome sequences gives us abundant information, which is, however, very difficult to decode. As a consequence, in order to advance our understanding of biological processes at the whole-cell scale, it becomes very important to develop higher-level, synthetic descriptions of the contents of a genome. At the protein level, an effective scale of description is provided by protein domains. Domains are independent unit-shapes (or &amp;#x22;folds&amp;#x22;) forming proteins. They are structurally stable and have thermodynamic origin. A domain determines a set of potential functions and interactions for the protein that carries it, for example DNA- or protein-binding capability or catalytic sites. Protein domains are found on genomes with...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1376/version/1

Evolution of the Sequence Ontology terms and relationships
Provedor de dados: 17
Autores: Karen Eilbeck; Christopher J. Mungall.
The Sequence Ontology is undergoing reform to meet the standards of the OBO Foundry. Here we report some of the incremental changes and improvements made to SO. We also propose new relationships to better define the mereological, spatial and temporal aspects of biological sequence.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3495/version/1

Evolution of Thriftiness: An analytical viewpoint
Provedor de dados: 17
Autores: Prajakta Belsare; Milind Watve.
We examine here, using a simple mathematical model, the conditions under which thrifty genes or fetal programming could evolve. Obesity and related disorders are thought to have their roots in metabolic thirftiness that evolved to combat periodic starvation. The failure to detect any thrifty genes and the association of low birth weight with type 2 diabetes, caused a shift in the concept from thrifty gene to thrifty phenotype and fetal programming. This hypothesis assumes that intra-uterine undernutrition programs the body to be thrifty, predicting and preparing for starvation in later life. However, there are reproductive costs associated with thriftiness. Results of the model suggest that under no condition thrifty and non-thrifty genes would co-exist...
Tipo: Poster
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2709/version/1

Evolution signatures in genome network properties
Provedor de dados: 17
Autores: Rita de Almeida; Leonardo Brunnet; Jos&amp;#xe9; Luiz Rybarczyk-Filho; Ricardo Ferreira; Jose Claudio Moreira; Mauro Castro; Rodrigo Dalmolin.
Genomes maybe organized as networks where protein-protein association plays the role of network links. The resulting networks are far from being random and their topological properties are a consequence of the underlying mechanisms for genome evolution. Considering data on protein-protein association networks from STRING database, we present experimental evidence that degree distribution is not scale free, presenting an increased probability for high degree nodes. We also show that the degree distribution approaches a scale invariant state as the number of genes in the network increases, although real genomes still present finite size effects. Based on the experimental evidence unveiled by these data analyses, we propose a simulation model for genome...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6653/version/1

Evolutionary descent of prion genes from a ZIP metal ion transport ancestor
Provedor de dados: 17
Autores: Gerold Schmitt-Ulms; Sepehr Ehsani; Joel C. Watts; David Westaway; Holger Wille.
In the more than 20 years since its discovery, both the phylogenetic origin and cellular function of the prion protein (PrP) have remained enigmatic. Insights into the function of PrP may be obtained through a characterization of its molecular neighborhood. Quantitative interactome data revealed the spatial proximity of a subset of metal ion transporters of the ZIP family to mammalian prion proteins. A subsequent bioinformatic analysis revealed the presence of a prion-like protein sequence within the N-terminal, extracellular domain of a phylogenetic branch of ZIPs. Additional structural threading and ortholog sequence alignment analyses consolidated the conclusion that the prion protein gene family is phylogenetically derived from a ZIP-like ancestor...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2867/version/1

Evolutionary game theory and the evolution of neuron populations, ring rates, and decisionmaking
Provedor de dados: 17
Autores: Yosef Cohen; Jeremiah Cohen.
Ours, is the first application of dynamical evolutionary games to decision making in neuroscience. Firing neurons are the players. The strategy is their firing rate. Neurons with equal firing rates define a population. The neurons do not know the rules of the game, they do not know what the reward is, they are not required to be rational and they do not even know they are playing the game. Interactions are inhibitory. The theory confirms experimental data about decision making in vision: (i ) A parameter of the game model determines how many populations of neurons participate in the decision; (ii ) the solution of the game dictates how many loci in the brain participate in the decision; (iii ) the theory clarifies the difference between ultimate and...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3373/version/1

Evolutionary trade-offs among decomposers may constrain responses to nitrogen
Provedor de dados: 17
Autores: Kathleen Treseder; Stephanie Kivlin; Christine Hawkes.
We tested the extent to which evolutionary trade-offs among species traits might constrain the responses of different functional groups of decomposers to global change. Specifically, we hypothesized that bacteria targeting large recalcitrant compounds require relatively high levels of nitrogen (N) availability to support the construction costs of requisite extracellular and carrier enzymes. Conversely, bacteria adapted to N-poor environments may invest scarce resources in enzymes targeting organic N instead of recalcitrant carbon. We cross-referenced carbon substrate use profiles (from Biolog plates), functional genes from published bacterial genomes, the global ocean sampling (GOS) expedition, and a global synthesis of environmental DNA sequences of...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5205/version/1

Evolvability of Chaperonin Substrate Proteins
Provedor de dados: 17
Autores: Emanuele Raineri; Paolo Ribeca; Luis Serrano; Tobias Maier.
Molecular chaperones ensure that their substrate proteins reach the functional native state, and prevent their aggregation. Recently, an additional function was proposed for molecular chaperones: they serve as buffers (_capacitors_) for evolution by permitting their substrate proteins to mutate and at the same time still allowing them to fold productively.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Using pairwise alignments of _E. coli_ genes with genes from other gamma-proteobacteria, we showed that the described buffering effect cannot be observed among substrate proteins of GroEL, an essential chaperone in _E. coli_. Instead, we find that GroEL substrate proteins evolve less than other soluble _E. coli_ proteins. We analyzed several specific structural and...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2968/version/1

EvolveAGene 3: A DNA coding sequence evolution simulation program
Provedor de dados: 17
Autores: Barry G. Hall.
EvolveAGene 3 is a realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions, including variable regions of selection intensity within the sequence and variation in intensity of selection over branches.  Variation includes base substitutions, insertions and deletions.  Output includes a log file,  the true tree and both unaligned coding sequence and protein sequences and the true DNA and protein alignments.
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1230/version/1

Evolving standards and infrastructure for systems biology: SBML, SBGN, and BioModels.net
Provedor de dados: 17
Autores: Michael Hucka.
Systems biology has arisen through the convergence of theoretical, computational, and mathematical modeling of systems and the need to understand the wealth of information being rapidly generated in biology.  Systems biology by its nature requires collaborations between scientists with expertise in biology, chemistry, computer sciences, engineering, mathematics, and physics.  Successful integration of these disciplines depends on bringing to bear both social and technological tools: namely, consortia that help forge collaborations and common understanding, software tools that permit analysis of vast and complex data, and agreed-upon standards that enable researchers to communicate and reuse each other&amp;#x27;s results in practical and unambiguous ways....
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2007
URL: http://precedings.nature.com/documents/20/version/1

Examining methanogens in northern peatlands: Potential role of ecological and latitudinal trends
Provedor de dados: 17
Autores: Hinsby Cadillo-Quiroz.
Background/Question/Methods&amp;#xd;&amp;#xa;Peatlands are a type of wetlands where accumulation of organic matter exceeds its decomposition. They are primarily distributed in northern latitudes and store more carbon than any other terrestrial ecosystem (~455 Pg). Methane (CH4) production is one of the most important microbially-driven processes relevant to the global influence of peatlands in carbon cycling and atmospheric change. Multiple factors have been found to affect CH4 production in peatlands. However, little is known about the Archaea performing this process. Geochemical, molecular, culturing and genomics techniques have allowed us to pursue questions about the diversity, abundance, distribution, and adaptations of methanoarchaea inhabiting...
Tipo: Presentation
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5507/version/1

Examining the PM6 semiempirical method for pKa prediction across a wide range of oxyacids
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest; Ken J. Friesen.
The pK~a~ estimation ability of the semiempirical PM6 method was evaluated across a broad range of oxyacids and compared to results obtained using the SPARC software program. Compound classes under consideration included acetic acids, alicyclic and aromatic heterocyclic acids, benzoic acids, boronic acids, hydroxamic acids, oximes, peroxides, peroxyacids, phenols, &amp;#x3b1;-saturated acids, &amp;#x3b1;-saturated alcohols, sulfinic acids, &amp;#x3b1;-unsaturated acids, and &amp;#x3b1;-unsaturated alcohols. PM6 accurately predicts the acidity of acetic and benzoic acids and their derivatives, but is less reliable for alicyclic and aromatic heterocyclic acids and phenols. &amp;#x3b1;-Saturated acids are reliably modeled by PM6 except for polyacid...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2981/version/1

Examining the uses of shared data
Provedor de dados: 17
Autores: Heather A. Piwowar; Douglas B. Fridsma.
Background&amp;#xd;&amp;#xa;    Many initiatives and repositories exist to encourage the sharing of research data, and thousands of microarray gene expression datasets are publicly available. Many studies reuse this data, but it is not well understood which datasets are reused and for what purpose.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;    Materials and Methods&amp;#xd;&amp;#xa;    We trained a machine-learning algorithm to automatically classify full-text gene expression microarray studies into two classes: those that generated original microarray data (n=900) and those which only reused data (n=250). We then compared the Medical Subject Heading (MeSH) terms of two classes to identify MeSH topics which were over- or under-represented by publications with...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/425/version/2

Examining the uses of shared data
Provedor de dados: 17
Autores: Heather A. Piwowar; Douglas B. Fridsma.
Background&amp;#xd;&amp;#xa;    Many initiatives and repositories exist to encourage the sharing of research data, and thousands of microarray gene expression datasets are publicly available. Many studies reuse this data, but it is not well understood which datasets are reused and for what purpose.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;    Materials and Methods&amp;#xd;&amp;#xa;    We trained a machine-learning algorithm to automatically classify full-text gene expression microarray studies into two classes: those that generated original microarray data (n=900) and those which only reused data (n=250). We then compared the Medical Subject Heading (MeSH) terms of two classes to identify MeSH topics which were over- or under-represented by publications with...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/425/version/1

Examining the uses of shared data
Provedor de dados: 17
Autores: Heather A. Piwowar; Douglas B. Fridsma.
Does your research area re-use shared datasets?&amp;#xd;&amp;#xa;*   Re-using data has many benefits, including research synergy and efficient resource use&amp;#xd;&amp;#xa;*   Some research areas have tools, communities, and practices which facilitate re-use&amp;#xd;&amp;#xa;*   Identifying these areas will allow us to learn from them, and apply the lessons to areas which underutilize the sharing and re-purposing of scientific data between investigators&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;    Which datasets?&amp;#xd;&amp;#xa;This preliminary analysis examines the re-use of microarray gene expression datasets. Thousands of microarray gene expression datasets have been deposited in publicly available databases. &amp;#xd;&amp;#xa;Many studies reuse this data,...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/425/version/3

Exaptation and emergence as mechanisms to cross fitness valleys during evolution: an example using simulated homing behaviour
Provedor de dados: 17
Autores: Richard Stafford.
Evolution is often considered a gradual hill climbing process, slowly increasing the fitness of organisms. I investigate the evolution of homing behaviour in simulated intertidal limpets. In order to evolve path integration as a homing mechanism, a temporary reduction in an organism&amp;#x2019;s fitness is required &amp;#x2013; since high developmental costs occur before a successful homing strategy evolves. Simple hill-climbing algorithms, therefore, only rarely result in the evolution of a functional homing behaviour. The inclusion of a second behaviour (trail-following) greatly increases the frequency of success of evolution of a path integration strategy. Initially an emergent homing behaviour is formed combining path integration with trail following....
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2172/version/1

Exchanging Experimental Kinetic Data via SabioML
Provedor de dados: 17
Autores: Martin Golebiewski.
The simulation of quantitative biochemical models not only requires qualitative information about the stoichiometry of the described networks, but also kinetic data describing their dynamics. Such kinetic data have to be experimentally measured, collected, systematically structured and stored to finally make them accessible. However, the dataflow from the experiment to the model is still a bottleneck, calling for systems that capture the data directly from the instrument, process and normalize it to agreed standards and finally transfer the data to publicly available databases.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;SABIO-RK (http://sabio.h-its.org) is a curated database system which we have developed for bundling data referring to biochemical reactions and...
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5030/version/1

Exciton Effects in Optical Absorption Spectra of Boron-Nitride Nanotubes
Provedor de dados: 17
Autores: Kikuo Harigaya.
Exciton effects are studied in single-wall boron-nitride (BN) nanotubes. Linear absorption spectra are calculated with changing&amp;#xd;&amp;#xa;the chiral index of the zigzag nanotubes. We consider the extended Hubbard model with atomic energies at the boron and nitrogen sites.&amp;#xd;&amp;#xa;Exciton effects are calculated using the configuration interaction technique. The Coulomb interaction dependence of the band gap,&amp;#xd;&amp;#xa;the lowest exciton energy, and the binding energy of the exciton are discussed. The optical gap of the (5,0) nanotube is about 6 eV&amp;#xd;&amp;#xa;at the onsite interaction U=2t with the hopping integral t=1.1 eV. The binding energy of the exciton is 0.50 eV for these parameters.&amp;#xd;&amp;#xa;This energy agrees...
Tipo: Presentation
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3879/version/1

ExO: An Ontology for Exposure Science
Provedor de dados: 17
Autores: Carolyn J. Mattingly; Thomas  E. McKone; Michael Callahan; Judith  Blake; Elaine A. Cohen Hubal.
An ontology is a formal representation of knowledge within a domain and typically consists of classes, the properties of those classes, and the relationships between them.  Ontologies are critically important for specifying data of interest in a consistent manner, thereby enabling data aggregation, analysis and exchange.  An exposure ontology, consistent with those being used in toxicology and other health sciences, is required to formally represent exposure concepts, the relationships between these concepts and most important, the relationships between exposure, susceptibility, and toxicology information.  A successful exposure ontology must facilitate the semantic retrieval of exposure data in the context of environmental health science, medical...
Tipo: Presentation
Palavras-chave: Chemistry; Ecology; Genetics &amp; Genomics; Bioinformatics; Earth &amp; Environment; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6321/version/1

Expanding the modern synthesis II: Formal perspectives on the inherent role of niche construction in fitness
Provedor de dados: 17
Autores: Rodrick Wallace.
Expanding the modern synthesis requires elevating the role of interaction within and across various biological scales to the status of an evolutionary principle. One way to do this is to characterize genes, gene expression, and embedding environment as information sources linked by crosstalk, constrained by the asymptotic limit theorems of information theory (Wallace, 2010a). This produces an inherently interactive structure that escapes the straightjacket of mathematical population genetics or other replicator dynamics. Here, we examine fitness from that larger perspective, finding it intimately intertwined with niche construction. Two complementary models are explored: niche construction as mediating the connection between environmental signals and gene...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5059/version/1

Expanding the modern synthesis II: Formal perspectives on the inherent role of niche construction in fitness
Provedor de dados: 17
Autores: Rodrick Wallace.
Expanding the modern synthesis requires elevating the role of interaction within and across various biological scales to the status of an evolutionary principle. One way to do this is to characterize genes, gene expression, and embedding environment as information sources linked by crosstalk, constrained by the asymptotic limit theorems of information theory (Wallace, 2010a). This produces an inherently interactive structure that escapes the straightjacket of mathematical population genetics or other replicator dynamics. Here, we examine fitness from that larger perspective, finding it intimately intertwined with niche construction. Two complementary models are explored: niche construction as mediating the connection between environmental signals and gene...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5059/version/2

Experiment study on Ma-Xing-Shi-Gan-Tang (MXSGT) and its decomposed recipes on anti-influenza virus A
Provedor de dados: 17
Autores: Wen Gao; Jiyang Li; Ying Tang; Changlong Zhuang; Bo Li; Shuguang Wang; Hai Huang.
Ancient China was an East Asian country with large population. As we review the history of China, large scale epidemic like Black Death in Europe rarely occurs. It can be seen that the Traditional Chinese Medicine (TCM) make great effort to antivirus and anti-infection treatment. When the SARS broke out in China in 2003, all medical drugs cannot to prevent or treat it. Preventive with TCM and strict disinfection help control the extension of SARS in short time.The using of TCM in clinical must abide by a most important principle that called principal, assistant, complement and guide. We investigate a famous complex recipe Ma Xing Shi Gan Tang (MXSGT) which is record by well-known clinical textbook &amp;#x22;Treatise on Cold-induced Febride...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/2260/version/1

Experimental and theoretical study of DNA oxidation
Provedor de dados: 17
Autores: Yuanzhi Song.
The electrochemical oxidation of DNA and bases at a glassy carbon electrode were investigated using cyclic and square-wave voltammetry analysis. The predicted oxidative potentials for DNA and bases using DFT method (B3LYP) are in agreement with the experimental ones.The DNA oxidation ascribes to N-protonated guanine and adenine. The calculated oxidative peaks indicate that the initial potential of DNA oxidation is around 0.432V for N-protonated guanine and 0.368V (vs.hydrogen standard electrode) at pH 7.00, and DNA as well as bases in acidity solution are more stable than those in alkalescent solution.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1797/version/1

Experimental demonstration of associative memory with memristive neural networks
Provedor de dados: 17
Autores: Yuriy Pershin; Massimiliano Di Ventra.
When someone mentions the name of a known person we immediately recall her face and possibly many other traits. This is because we possess the so-called associative memory - the ability to correlate different memories to the same fact or event. Associative memory is such a fundamental and encompassing human ability (and not just human) that the network of neurons in our brain must perform it quite easily. The question is then whether electronic neural networks - electronic schemes that act somewhat similarly to human brains - can be built to perform this type of function. Although the field of neural networks has developed for many years, a key element, namely the synapses between adjacent neurons, has been lacking a satisfactory electronic representation....
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3258/version/1

Expert Assertions Through Community Annotation Jamborees
Provedor de dados: 17
Autores: Lauren Brinkac; Ramana Madupu; Elisabet Caler; Derek Harkins; Hernan Lorenzi; Mathangi Thiagarajan; Granger Sutton.
Although there is significant optimism that community involvement can drive genome curation, results to date are disappointing. The Human Genome and Saccharomyces Genome Databases both tried community annotation experiments and few community contributions were obtained. JCVI&amp;#x2019;s own early experiences with community curation were also largely unsuccessful. Although community curation tools were publicly available on JCVI web resources and much effort was made by JCVI personnel to advertise these resources, little curation was actually submitted. Starting in late 2007, JCVI&amp;#x2019;s model for community curation changed. Instead of simply providing curation tools on websites and advertising their utility at meetings and conferences, JCVI...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3170/version/1

Explaining microbial population genomics through phage predation
Provedor de dados: 17
Autores: Francisco Rodriguez-Valera; Ana-Bel&amp;#xe9;n Mart&amp;#xed;n-Cuadrado; Beltr&amp;#xe1;n Rodriguez-Brito; Lejla Pasic; T. Frede Thingstad; Forest Rohwer; Alex Mira.
The remarkable diversity of genes within the pool of prokaryotic genomes belonging to the same species or pan-genome is difficult to reconcile with the widely accepted paradigm which asserts that periodic selection within bacterial populations would regularly purge genomic diversity by clonal replacement. Recent evidence from metagenomics indicates that even within a single sample a large diversity of genomes can be present for a single species. We have found that much of the differential gene content affects regions that are potential phage recognition targets. We therefore propose the operation of Constant-Diversity dynamics in which the diversity of prokaryotic populations is preserved by phage predation. We provide supporting evidence for this model...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/3489/version/1

Exploitation, secondary extinction and the altered trophic structure of Jamaican coral reefs
Provedor de dados: 17
Autores: Peter D. Roopnarine; Rachel A. Hertog.
Coral reef communities of the Greater Antilles in the Caribbean have a long history of anthropogenic disturbance, driven by the exploitation for food of both vertebrate and invertebrate species. Exploitation, coupled with region wide declines of coral environments has resulted in local and regional vertebrate extinctions. The impact of those extinctions on reef communities, however, remains largely unexplored. Here we show, using a highly resolved model coral reef-seagrass food web, that at least 40 of 188 expected vertebrate species are absent from Jamaican coral reefs. Twenty one of the absent species are of high trophic level and are exploited by humans. The remainder of the absent species are unexploited, and comprises a significantly high proportion...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4186/version/1

Exploiting evolution to treat drug resistance: Combination therapy and the double bind
Provedor de dados: 17
Autores: David Basanta; Robert Gatenby; Alexander R. A. Anderson.
Although many anti cancer therapies are successful in killing a large percentage of tumour cells when initially administered, the evolutionary dynamics underpinning tumour progression mean that often resistance is an inevitable outcome, allowing for new tumour phenotypes to emerge that are unhindered by the therapy. Research in the field of ecology suggests that an evolutionary double bind could  be an effective way to treat tumours. In an evolutionary double bind two therapies are used in combination such that evolving resistance to one leaves individuals more susceptible to the other. In this paper we present a general evolutionary game theory model of a double bind to study the effect that such approach would have in cancer. Furthermore we use this...
Tipo: Manuscript
Palavras-chave: Cancer; Ecology; Pharmacology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6380/version/1

Exploiting Nonlinear Recurrence and Fractal Scaling Properties for Voice Disorder Detection
Provedor de dados: 17
Autores: Max A. Little; Patrick E. McSharry; Stephen A. Roberts; Declan A. E. Costello; Irene  M. Moroz.
Background: Voice disorders affect patients profoundly, and acoustic tools can potentially measure voice function objectively. Disordered sustained vowels exhibit wide-ranging phenomena, from nearly periodic to highly complex, aperiodic vibrations, and increased &amp;#x22;breathiness&amp;#x22;. Modelling and surrogate data studies have shown significant nonlinear and non-Gaussian random properties in these sounds. Nonetheless, existing tools are limited to analysing voices displaying near periodicity, and do not account for this inherent biophysical nonlinearity and non-Gaussian randomness, often using linear signal processing methods insensitive to these properties. They do not directly measure the two main biophysical symptoms of disorder: complex...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2007
URL: http://precedings.nature.com/documents/326/version/1

Exploring binding site of human RBP4 towards discovery of novel inhibitor for treatment of cardiovascular diseases
Provedor de dados: 17
Autores: C Lakshmi Narayana Rao; LA  Raziya Beevi; Amineni Umamaheswari.
Retinol binding proteins (RBPs) are transport proteins that act by solubilizing and protecting their labile ligands in aqueous spaces. In addition, RBPs have diverse and specific functions in regulating the disposition, metabolism and activities of retinoids. Elevated levels of retinol-binding protein 4 (RBP4) are observed in cardiovascular disease conditions, which prompts it as a potential drug target. Therefore, computational approach methods were implemented herein to design a novel inhibitor for RBP4. Crystal structure (2wq9) of RBP4 was retrieved and investigated to locate retinol binding site residues (Lys29, Pro32, Leu35, Phe36, Leu37, Phe45, Ala55, Ala57, Met73, Val74, Gly75, Met88, Try90, His104, Gln117, Arg121, Try133, Phe135, Phe137). Five...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6587/version/1

Exploring hidden dimensions of soil fungal biodiversity: A simple technique to detect soil fungi resistant to antifungal compounds
Provedor de dados: 17
Autores: Sonashia Velho-Pereira; Nandkumar M. Kamat.
Soils are known to be ultimate and complex reservoirs of microbial diversity. The complex dimensions of bacterial and fungal diversity in tropical soils and microbial community dynamics are underexplored. Isolation techniques aimed at Actinomycetes generally employ highly selective media, powerful antibiotics and antifungal compounds to suppress undesirable bacteria and fungi. However some soil fungi may show their resistance towards these antifungal compounds. During our work to explore soil actinomycetes diversity, slides coated with Arginine Vitamin agar  (AVA) incorporating a cocktail of antibiotics and antifungal compounds such as Nystatin, Cycloheximide, Terbinafin, Griseofulvin, and Fluconazole were exposed to soil environment and were retrieved  at...
Tipo: Poster
Palavras-chave: Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4208/version/1

Exploring NAG active site of human CD59 towards discovery of novel activators for treatment of atherosclerosis
Provedor de dados: 17
Autores: Challa Lakshmi Narayana Rao; Dibyabhaba Pradhan; Amineni Umamaheswari.
CD59 is a potent inhibitor of the complement membrane attack complex (MAC) action that acts by binding to the C8 and C9 complements of the assembling MAC, thereby preventing incorporation of the multiple copies of C9 required for complete formation of the osmolytic pore. Human CD59 low expression leads to atherosclerosis. Therefore, computational approach methods were implemented herein to design novel activators for CD59. Crystal structure (PDB ID: 1CDR) of CD59 was investigated to locate N-acetyl glucosamine (NAG) active site residues (Leu1, Gln2, Val17, Asn18, Ser20, Ser21, Asp22 and Asp67). CD59 is known for its binding affinity towards NAG and Alpha-L-Fucose, hence, were explored against more than one million entries of Ligand.Info metadatabase to...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6531/version/1

Exploring The Hidden Realms Of Global Biodiversity: Interesting Endophytic Yeast Flora From Floral Ovaries
Provedor de dados: 17
Autores: Nandkumar Kamat; Shweta S. Saudagar.
Soil is considered the ultimate reservoir of all the microbiota  and specifically the yeasts. However their association with different plant organs and at different developmental stages is not fully explored. Although about 1000 yeast species have been identified, exploration of various microhabitats such as plant storage organs, flowers, nectar, and tree sap is expected to yield a large number of novel species, including interesting endophytic yeasts(Carlos &amp;#x26; Gabor, 2006). Angiosperms are considered the most diverse group of the plant kingdom comprising of about 250,000 species (Kenrick, 1999). As part of an exhaustive exploration of yeasts associated with angiosperm flowers, specific attention was paid to floral ovaries to detect the presence of...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Ecology; Genetics &amp; Genomics; Microbiology; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6268/version/1

Exposing The Cancer Genome Atlas (TCGA) as a SPARQL endpoint
Provedor de dados: 17
Autores: Helena Deus.
Automated discovery of candidate biomarkers from multiple databases has been the central challenge in the Life Sciences in general and in the study of systemic processes such as those documented by The Cancer Genome Atlas (TCGA) in particular. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The maturation of Semantic Web technologies offers solutions to those problems by allowing the query to be defined by navigating a normally represented domains of discourse instantiated by the data. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We address the systems challenge of The Cancer &amp;#xd;&amp;#xa;Genome Atlas initiative (http://cancergenome.nih.gov/), which generates a large scale repository of high throughput molecular biology data generated and processed at 5 academic...
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6303/version/1

Exposing WikiPathways as Linked Open Data
Provedor de dados: 17
Autores: Andra Waagmeester; Helena Deus; Chris T. Evelo.
Biology has become a data intensive science. Discovery of new biological facts increasingly relies on the ability to find and match appropriate biological data. For instance for functional annotation of genes of interest or for identification of pathways affected by over-expressed genes. Functional and pathway information about genes and proteins is typically distributed over a variety of databases and the literature.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Pathways are a convenient, easy to interpret way to describe known biological interactions. WikiPathways  provides community curated pathways. WikiPathways users integrate their knowledge with facts from the literature and biological databases. The curated pathway is then reviewed and possibly corrected or...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6679/version/1

Expression cartography of human tissues using self organizing maps
Provedor de dados: 17
Autores: Henry Wirth; Hans Binder.
Background: The availability of parallel, high-throughput microarray and sequencing experiments poses a challenge how to best arrange and to analyze the obtained heap of multidimensional data in a concerted way. Self organizing maps (SOM), a machine learning method, enables the parallel sample- and gene-centered view on the data combined with strong visualization and second-level analysis capabilities. The paper addresses aspects of the method with practical impact in the context of expression analysis of complex data sets.&amp;#xd;&amp;#xa;Results: The method was applied to generate a SOM characterizing the whole genome expression profiles of 67 healthy human tissues selected from ten tissue categories (adipose, endocrine, homeostasis, digestion,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5825/version/1

Expression cartography of human tissues using self organizing maps
Provedor de dados: 17
Autores: Henry Wirth; Markus L&amp;#xf6;ffler; Martin von Bergen; Hans Binder.
Background: The availability of parallel, high-throughput microarray and sequencing experiments poses a challenge how to best arrange and to analyze the obtained heap of multidimensional data in a concerted way. Self organizing maps (SOM), a machine learning method, enables the parallel sample- and gene-centered view on the data combined with strong visualization and second-level analysis capabilities. The paper addresses aspects of the method with practical impact in the context of expression analysis of complex data sets.&amp;#xd;&amp;#xa;Results: The method was applied to generate a SOM characterizing the whole genome expression profiles of 67 healthy human tissues selected from ten tissue categories (adipose, endocrine, homeostasis, digestion,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5825/version/2

Expression of Green Fluorescence Protein (GFP) in Zebrafish Muscle through Injection: A Gene Therapy Model
Provedor de dados: 17
Autores: C. S.  Lin; Jhen Ru  Shih; C. H.  Hsu; Z.H.  Wen; Chiranjib  Chakraborty.
Expression of the target gene is important for gene therapy. Presently, localized transgenesis is used for gene therapy which can be achieved by a target gene expression. Here, we have reported the plasmid mediated gene therapy to zebrafish model. For this purpose, we have chosen green fluorescent protein (GFP) as a target gene because the expression can be detected easily.  GFP was inserted in a plasmid vector, pQE30 to develop the vector pQE30GFP.  The plasmid pQE30GFP was constructed form plasmid, pQE30 and pEGFPC2. pQE30GFP injected directly in one group of fish into the muscle where luciferase expression was noted. In another group, after injection electroporation was performed where we have also noted luciferase expression; but, electroporation cause...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2718/version/1

Expression profile of genes involved in hydrogen sulphide liberation by _Saccharomyces cerevisiae_ grown under different nitrogen concentrations
Provedor de dados: 17
Autores: Ana  Mendes-Ferreira; Catarina Barbosa; Marcel.l&amp;#xed; del Olmo; Arlete Mendes-Faia; Cec&amp;#xed;lia Le&amp;#xe3;o.
The present work aims to elucidate molecular mechanisms underlying hydrogen sulphide production in _S. cerevisiae_ associated to nitrogen deficiency. To assess, at a genome-wide level, how the yeast strain adapted to the progressive nitrogen depletion and to nitrogen re-feeding, gene expression profiles were evaluated during fermentation at different nitrogen concentrations, using the DNA array technology. The results showed that most MET genes displayed higher expression values at the beginning of both control and N-limiting fermentation, just before the time at which the release of sulphide was observed. MET genes were downregulated when yeast stopped growing which could associate MET gene expression levels with cell growth. The over expression of MET...
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2736/version/1

Extending Astrobiology: Consciousness and Culture
Provedor de dados: 17
Autores: Rodrick Wallace.
The Stanley Miller experiment suggests that amino acid-based life is ubiquitous in our universe, although its varieties are not likely to have followed the particular, highly contingent and path-dependent, evolutionary trajectory found on Earth. Are many alien organisms likely to be conscious in ways that we would recognize? Almost certainly. Will some develop high order technology? Less likely, but still fairly probable. If so, will we be able to communicate with them? Only on a basic level, and only with profound difficulty. The argument is fairly direct.
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5286/version/2

Extending libSedML to support CellML models
Provedor de dados: 17
Autores: David Nickerson; Dongxue Amy You.
libSedML is a collection of libraries and tools developed in support of the Simulation Experiment Markup Language (&amp;#x22;SED-ML&amp;#x22;:http://sed-ml.org/). &amp;#x22;libSedML&amp;#x22;:http://libsedml.sourceforge.net/ is implemented in C# and provides libraries for processing SED-ML documents and for running the numerical simulations required for the encoded simulation experiment(s). SED-ML supports models encoded in any encoding format, although predominantly expected to be an XML based encoding. To date, however, libSedML has only supported performing simulations using models encoded in the Systems Biology Markup Language (&amp;#x22;SBML&amp;#x22;:http://sbml.org/). The presented project looked at using the &amp;#x22;CellML...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5897/version/1

Extending the Foundational Model of Anatomy with Automatically Acquired Spatial Relations
Provedor de dados: 17
Autores: Manuel M&amp;#xf6;ller; Christian  Folz; Michael Sintek; Sascha Seifert; Pinar Wennerberg.
Formal ontologies have made significant impact in bioscience over the last ten years. Among them, the Foundational Model of Anatomy Ontology (FMA) is the most comprehensive model for the spatio-structural representation of human anatomy. In the research project MEDICO we use the FMA as our main source of background knowledge about human anatomy. Our ultimate goals are to use spatial knowledge from the FMA (1) to improve automatic parsing algorithms for 3D volume data sets generated by Computed Tomography and Magnetic Resonance Imaging and (2) to generate semantic annotations using the concepts from the FMA to allow semantic search on medical image repositories. We argue that in this context more spatial relation instances are needed than those currently...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3471/version/1

Extending the Modern Synthesis: The evolution of ecosystems
Provedor de dados: 17
Autores: Rodrick Wallace.
The Modern Evolutionary Synthesis formalizes the role of variation, heredity, differential reproduction, and mutation in population genetics. Here we explore a mathematical structure, based on the asymptotic limit theorems of communication theory, that instantiates the punctuated dynamic relations of organisms with their embedding environments, including the possibility of the transfer of heritage information between different classes of organisms. In essence, we provide something of a formal roadmap for the modernization of the Modern Synthesis, making application to both relatively rapid evolutionary punctuated equilibrium and to the conservation of ecological interactions across deep evolutionary time.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4496/version/2

Extending the Modern Synthesis: The evolution of ecosystems
Provedor de dados: 17
Autores: Rodrick Wallace.
The Modern Evolutionary Synthesis formalizes the role of variation, heredity, differential reproduction and mutation in population genetics. Here we explore a mathematical structure, based on the asymptotic limit theorems of information theory, that instantiates the punctuated dynamic relations of organisms and their embedding environments. The mathematical overhead is considerable, and we conclude that the model must itself be extended even further to allow the possibility of the transfer of heritage information between different classes of organisms. In essence, we provide something of a formal roadmap for the modernization of the Modern Synthesis.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4496/version/1

Extending the semi-empirical PM6 method for carbon oxyacid pKa prediction to sulfonic acids: Application towards congener-specific estimates for the environmentally and toxicologically relevant C1 through C8 perfluoroalkyl derivatives
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest; Ken J. Friesen.
A positive bias in the semi-empirical PM6 method for estimating pKa values of sulfonic acids was corrected by a correlation developed between non-adjusted PM6 pKa values and the corresponding experimentally obtained/estimated acidity constants for a range of representative alkyl, aryl, and halogen substituted sulfonic acids. Application of this correction to PM6 values allows for extension of this computational method to a new acid functional group.
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2922/version/1

Extending Tlusty&amp;#x27;s method to the glycome: Tuning the repertoire of glycan determinants
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
We apply Tlusty&amp;#x27;s information-theoretic analysis of the genetic code to the glycome, using a cognitive paradigm in which external information sources constrain and tune the glycan code error network, in the context of available metabolic energy. The resulting dynamic model suggests the possibility of observing spontaneous symmetry breaking of the glycan code as a function of metabolic energy intensity. These effects may be currently present, or embedded in evolutionary trajectory, recording large-scale ecosystem resilience shifts in energy availability such as the aerobic transition.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology; Pharmacology; Bioinformatics; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5932/version/1

Extensive Viral mimicry of human proteins in AIDS, autoimmune disorders, late-onset and familial Alzheimer&amp;#x27;s disease and other genetic diseases
Provedor de dados: 17
Autores: Christopher J. Carter.
Peptide stretches within HIV-1 proteins display homology to over 50 components from all compartments of the human immune defence network. The homologous peptides are in most cases immunogenic, suggesting that antibodies to HIV-1 proteins could mount an autoimmune attack against multiple components of the immune system itself. HIV-1 proteins are also homologous to autoantigens in Alzheimer&amp;#x27;s disease, chronic obstructive pulmonary disorder, multiple sclerosis, Myasthenia Gravis, Pemphigus Vulgaris, Sjogrens syndrome and systemic Lupus Erythematosus, all of which have been associated with HIV-1 infection. This mimicry suggests that HIV-1/AIDS has a major autoimmune component and that HIV-1 antibodies could selectively target the immune system and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4582/version/1

Extracting conclusion sections from PubMed abstracts for rapid key assertion integration in biomedical research
Provedor de dados: 17
Autores: Matthias Samwald.
Key assertions are extracted from &amp;#x201c;conclusions&amp;#x201d; sections of PubMed abstracts and&amp;#xd;&amp;#xa;converted into Semantic Web / Linked Data format. The results are made accessible via&amp;#xd;&amp;#xa;files, a SPARQL endpoint, and a faceted search interface. Conclusion sections are&amp;#xd;&amp;#xa;identified as valuable resources for machine-augmented key assertion identification and&amp;#xd;&amp;#xa;integration in the biomedical domain. Results are discussed and opportunities for future&amp;#xd;&amp;#xa;work and cooperation are highlighted.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3775/version/1

Extracting Functional Modules from Biological Pathways
Provedor de dados: 17
Autores: Sihai D. Zhao; Yong Li.
It has been proposed that functional modules are the fundamental units of cellular function. Methods to identify these modules have thus far relied on gene expression data or protein-protein interaction (PPI) data, but have a few limitations. We propose a new method, using biological pathway data to identify functional modules, that can potentially overcome these limitations. We also construct a network of these modules using functionally relevant PPI data. This network displays the flow and integration of information between modules and can be used to map cellular function.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1457/version/1

Extragenic Suppression analysis of TS mutations using Sec61p
Provedor de dados: 17
Autores: Sterling Smith.
During synthesis, secretory and membrane proteins are cotranslationally translocated into the lumen of the endoplasmic reticulum through an aqueous gated channel. Proper folding, degradation, and transport of many polypeptides depend on a diverse set of helper proteins termed chaperone. I hypothesize that&amp;#xd;&amp;#xa;Sec 61p is a membrane chaperone, which actively directs membrane protein folding.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/651/version/1

Extreme energy lability in human children: An overlooked and central aspect of human biology
Provedor de dados: 17
Autores: John Skoyles.
A four year old child devotes half their total energy expenditure (TEE) to their brains. Even by 10 years-of-age it is still 30% (compared to an adult&amp;#x2019;s &amp;#x2248;12%). This extreme energy use results from a high brain/body size ratio &amp;#x2013; combined with a doubling of cerebral gray matter energy utilization (due to synaptic exuberance during cognitive neuromaturation). &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;With extreme energy expenditure goes extreme vulnerability to hypoglycemia: (1) children become hypoglycemic after 24-36 hours of fast (compared to 60-72 hours in adults), and (2) their brains suffer neurological impairment (shown in disrupted P300 potentials) at a lower decrease in plasma glucose: 3.6 - 4.2 mmol L-1 in children rather...
Tipo: Presentation
Palavras-chave: Developmental Biology; Neuroscience; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7097/version/1

F1000 and data publishing
Provedor de dados: 17
Autores: Rebecca Lawrence.
Utility of the BioSharing standards and the BioDBCore registry in F1000 journal publishing.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6172/version/1

Face Cognition: A Set of Distinct Mental Abilities
Provedor de dados: 17
Autores: Oliver Wilhelm; Grit Herzmann; Olga Kunina; Werner Sommer.
Perceiving, learning, and recognizing faces swiftly and accurately is of paramount importance to humans as a social species. Though established functional models of face cognition&amp;#x3c;sup&amp;#x3e;1,2&amp;#x3c;/sup&amp;#x3e; suggest the existence of multiple abilities in face cognition, the number of such abilities and the relationships among them and to other cognitive abilities can only be determined by studying individual differences. Here we investigated individual differences in a broad variety of indicators of face cognition and identified for the first time three component abilities: face perception, face memory, and the speed of face cognition. These component abilities were replicated in an independent study and were found to be robustly...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1385/version/1

Facial Expression Processing Varies with Political Affiliation
Provedor de dados: 17
Autores: Jacob Vigil.
Conservative political beliefs have been linked to heightened stress reactivity and protective cognitive biases. Using a facial discrimination task designed to measure perceptions of threat (vs. non threat) and dominance (vs. submissiveness), I show that Republicans demonstrate a greater tendency to interpret ambiguous facial stimuli as expressing more threatening and more dominant emotions than do Democrats. The findings suggest the political ideology may be associated with basic social perceptual sensitivities.
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2414/version/1

Facial Motor Nucleus
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Rachel A. Dalley; Lydia  L. Ng; Angela L. Guillozet-Bongaarts.
This report contains a summary of expression patterns for genes that are enriched in the facial motor nucleus (VII) of the medulla. All data is derived from the Allen Brain Atlas (ABA) in situ hybridization mouse project. The structure&amp;#x27;s location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the facial motor nucleus were compared to the values of its larger parent structure, in this case the medulla, for the purpose of extracting regionally selective gene expression data. The highest ranking genes were manually curated and verified. 50 genes were then selected and compiled for expression analysis. The experimental...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2201/version/1

Facile Synthesis and Versatilities of Polyanthraquinoylamine Nanofibril Bundles with Self Stability and High Carbon Yield
Provedor de dados: 17
Autores: Xin-Gui Li; Mei-Rong Huang; Hu Li; Mark G. Moloney.
A facile synthesis for nanosized conducting polymers with inherent self-stability and multi-functionalities is a main challenge. Here we simply synthesize intrinsically self-stabilized nanofibril bundles of poly(1-anthraquinoylamine) (PAQ) by a template-free method. The critical polymerization parameters were studied to significantly optimize the synthesis, size, properties, and functionalities of the resulted fine nanofibrils with a diameter of ca. 30 nm and length of ~6 &amp;#x3bc;m. The PAQ obtained with ammonium persulfate possesses higher polymerization yield, purer composition, higher conductivity, better melting behaviour, higher thermostability, lower burning enthalpy, and slower degradation than that with other oxidants. Furthermore, the polymer...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/2396/version/1

Factors influencing immature Dermacentor variabilis burdens on white-footed mice (Peromyscus leucopus)
Provedor de dados: 17
Autores: Tad Dallas; Stephanie  Fore; Hyun-Joo Kim; Mary Peng; Jake Henderson; Georgia Mueller; Laura Fielden.
The host-parasite relationship is an important and complex ecological interaction.&amp;#xd;&amp;#xa;Parasite load affects pathogen transfer and can influence host fitness. Mice were&amp;#xd;&amp;#xa;live trapped in three night trapping sessions conducted on two permanent grids&amp;#xd;&amp;#xa;every other month from June 2006 to December 2008. Grids were established in&amp;#xd;&amp;#xa;an old field and an early successional forest each with 104 sampling points. Data&amp;#xd;&amp;#xa;were analyzed with negative binomial regression. Gender and body size both had&amp;#xd;&amp;#xa;significant effects on tick load (P =0.012 and P =0.029, respectively), with males and&amp;#xd;&amp;#xa;larger hosts harboring more immature ticks. However, body size and gender...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3713/version/1

Factors influencing impala distribution patterns in Nairobi National Park, Kenya
Provedor de dados: 17
Autores: Vincent Obade; Eva Clercq.
Monitoring the distribution of wild animals using appropriate methods and survey techniques is essential not only for sustainable management but also to avoid wastage of resources. This study applied remote sensing to investigate the factors influencing the distribution of herbivores in Nairobi National Park, Kenya. Impala was selected as indicator specie for the herbivores within the park, because the population of impala had drastically reduced over time. The influence of food availability, water and disturbance on herbivore presence was investigated. A positive significant statistical relationship between impala population density and feed availability was observed. However, the correlation between impala population density and water distance was...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3799/version/1

Failure of Abeta(1-40) amyloid fibrils under tensile loading
Provedor de dados: 17
Autores: Raffaella Paparcone; Markus J. Buehler.
Amyloid fibrils and plaques are detected in the brain tissue of patients affected by Alzheimer&amp;#x2019;s disease, but have also been found as part of normal physiological processes such as bacterial adhesion. Due to their highly organized structures, amyloid proteins have also been used for the development of novel nanomaterials, for a variety of applications including biomaterials for tissue engineering, nanolectronics, or optical devices. Past research on amyloid fibrils resulted in advances in identifying their mechanical properties, revealing a remarkable stiffness. However, the failure mechanism under tensile loading has not been elucidated yet, despite its importance for the understanding of key mechanical properties of amyloid fibrils and plaques...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5174/version/1

FAIRE-seq data analysis of Chlamydomonas reinhardtii under carbon deprivation
Provedor de dados: 17
Autores: David Urbina-G&amp;#xf3;mez; Flavia  Vischi Winck; Bernd M&amp;#xfc;ller-R&amp;#xf6;ber; Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n.
For the genome-wide identification of nucleosome depleted regions under carbon deprivation, we analyze an available set of data from an assay of formaldehyde-assisted isolation of regulatory elements followed by sequencing (FAIRE-seq). Mapping to the sequenced nuclear genome of C.reinhardtii, followed by the identification of the enrichment-sequenced fragments was performed. We examined the location of these fragments relative to annotated genes. The related genes were associated to the corresponding Gene-Ontology (GO), for an evaluation of over-representate GO categories. Some genes, link with functions or locations, that have been previous described, indicating the success of the method finding carbon-metabolism related fragments.
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7035/version/1

Familial and late-onset Alzheimer&amp;#x27;s disease: Autoimmune disorders triggered by viral, microbial and allergen mimics of beta-amyloid and APP mutants ?
Provedor de dados: 17
Autores: Christopher Carter.
Beta-amyloid (A[beta]) autoantibodies are common in Alzheimer&amp;#x27;s disease. Some may be derived from Herpes simplex and 68 other virus proteins matching an immunogenic and fibrillogenic VGGVV A[beta] sequence.Many other viral, microbial and allergenic proteins (particularly from dust mites) align with A[beta] as do proteins from _C.Neoformans_ which has been associated with a rare but curable form of the disorder. Immune-related proteins are present in amyloid plaques and the complement membrane attack complex in neurones in Alzheimer&amp;#x27;s disease brains. Alzheimer&amp;#x27;s disease may thus be an autoimmune disorder triggered by pathogenic antigens homologous to A[beta], whose antibodies target and kill A[beta] containing neurones, via immune...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4662/version/1

Family values: Maternal care in rattlesnakes is more than mere attendance
Provedor de dados: 17
Autores: Melissa Amarello; Jeffrey J. Smith; John Slone.
Parental care is important in many diverse taxa because of its positive impact on the parent&amp;#x27;s fitness.  Relatively simple forms of parental care, such as female attendance and defense, which is present in many squamate reptiles, will likely provide insight into the evolution of more complex forms observed in crocodilians, birds, and mammals. Historically, observations of adult and newborn rattlesnakes in close proximity were dismissed as mere coincidence of live-birth, and only recently acknowledged as examples of parental care. In 2010, we monitored 11 pregnant Arizona black rattlesnakes (_Crotalus cerberus_): 4 solitary individuals and 2 aggregations composed of three and four individuals.  We documented various forms of parental care,...
Tipo: Poster
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6671/version/1

Far-infrared rays control prostate cancer cells _in vitro_ and _in vivo_
Provedor de dados: 17
Autores: Hiroki Shima; Shingo Yamamoto; Jun Qiu; Mayumi Shincho; Seiichi Hirota; Yoshie Yoshikawa; Reigetsu Yoshikawa; Tomoko Hashimoto-Tamaoki.
We introduce a new effective method to control hormone refractory prostate cancer cells by using an activated rubber/resin form (RB), far-infrared ray emitter, with or without sodium butyrate (SB). The growth of three human prostate cancer cell lines (Du145, PC-3 and LNCaP) was suppressed _in vitro_ and _in vivo_ by using RB, and the cells were eradicated with RB + 3 mM SB. G1 arrest and apoptotic pathway proteins were induced by RB with intensified expressions of apoptosis - related mRNA on cDNA microarray. RB radiates far-infrared rays of the 4 to 25 [mu]m wavelengths to an object which exert a favorable influence on a cancer control. These results may render us a new therapeutic modality in hormone refractory prostate cancer.
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/1980/version/2

Far-infrared rays control prostate cancer cells _in vitro_ and _in vivo_
Provedor de dados: 17
Autores: Hiroki Shima; Shingo Yamamoto; Jun Qiu; Mayumi Shincho; Seiichi Hirota; Yoshie Yoshikawa; Reigetsu Yoshikawa; Tomoko Hashimoto-Tamaoki.
We introduce a new effective method to control hormone refractory prostate cancer cells by using an activated rubber/resin form (RB), far-infrared ray emitter, with or without sodium butyrate (SB). The growth of three human prostate cancer cell lines (Du145, PC-3 and LNCaP) was suppressed _in vitro_ and _in vivo_ by using RB, and the cells were eradicated with RB + 3 mM SB. G1 arrest and apoptotic pathway proteins were induced by RB with intensified expressions of apoptosis - related mRNA on cDNA microarray. RB radiates the infra-red rays of the 4 to 25 [mu]m wavelengths to an object which exert a favorable influence on a cancer control. These results may render us a new therapeutic modality in hormone refractory prostate cancer.
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/1980/version/1

Fast and Scriptable Molecular Graphics in Web Browsers without Java3D
Provedor de dados: 17
Autores: Egon Willighagen; Miguel Howard.
Jmol is a free, open source molecule viewer for chemistry and biochemistry. It is cross-platform, running on Windows, Mac OS X, and Linux/Unix systems. The software consists of three parts: the JmolApplet is a web browser applet that can be integrated into web pages; the Jmol application is a standalone Java application that runs on the desktop; and the JmolViewer is a development tool kit that can be integrated into other Java applications.
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/50/version/1

Fatty acids composition of some freshwater fish
Provedor de dados: 17
Autores: Chukwuemeka  Ugoala; George Ndukwe; Tokunbo Audu.
The aims of this paper were to investigate the component fatty acids of some freshwater fish species by comparing the levels of essential fatty acids present. The FAME were determined by GC-MS and were identified using retention time locked methods and retention time databases. The fatty acids profiles include minor amounts of odd-number, branched-chain, and even-number fatty acids as well as saturated components, the MUFA and PUFA. The major SFA were C14:0 and C16:0. The C18:1 was the prominent MUFA.  The dominant PUFA are of the omega-6 series and are found chiefly in C18:2 fatty acids. The essential fatty acids compositions showed prominence in C18:3n-3 and C18:2n-6. The branched chain fatty acids identified C15:0, C16:0, C17:0, C18:2 and C20:0. The...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3239/version/1

FDserver: A web service for protein folding research
Provedor de dados: 17
Autores: Bin-Guang Ma; Ling-Ling Chen; Hong-Yu Zhang.
*Summary:* To facilitate the study of protein folding, we have developed a web service for protein folding rate and folding type prediction as well as for the calculation of a variety of topological parameters of protein structure, which is freely available to the community.&amp;#xd;&amp;#xa;*Availability:* http://sdbi.sdut.edu.cn/FDserver
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2349/version/1

Feeding preferences of _Microcerotermes championi_ (snyder) on different timbers dried at different temperatures under choice and no choice trials
Provedor de dados: 17
Autores: Khalid Zamir Rasib.
Ten species of wood were tested for their natural resistance and to reveal feeding preferences of _M. championi_. In &amp;#x22;no choice&amp;#x22; laboratory experiments, _Abies pindrow_ was found highly resistant and _Populus euramericana_ highly palatable. The impact of drying temperature (60&amp;#xb0;C, 70&amp;#xb0;C, 80&amp;#xb0;C, 90&amp;#xb0;C and 100&amp;#xb0;C) was studied. The amount of wood consumed in general, increased with increase in drying temperature indicating that heat contributed to the loss of natural resistance components of the woods. When _M. championi_ was given a choice and the woods were offered in combination of two, this termite species repeated its instinct, easily identified the more preferred wood and consumed more of it....
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2048/version/1

Female Scent Signals Enhances Male Resistance to Influenza
Provedor de dados: 17
Autores: Ekaterina A. Litvinova; Elena P. Goncharova; Alla M. Zaidman; Marina A. Zenkova; Mikhail P. Moshkin.
Scent of receptive females as signal to reproduction stimulate male mice to olfactory search of a potential breeding partner^1, 2^. This searching behavior is coupled with infection risk due to bacterial contamination of the fecal and urine scent marks^4^. The theoretical consideration of host evolution under inevitable parasitic pressures, including helminthes, bacteria, virus etc., predicts adaptations that help protect against parasites associated with breeding^7^. In this study, we propose that acceptation of female signals by male mice leads to adaptive redistribution of immune defense directed to protection against respiratory infection risks. Our results reveal migration of macrophages and neutrophils to upper airways upon exposure to female odor...
Tipo: Manuscript
Palavras-chave: Ecology; Immunology.
Ano: 2009
URL: http://precedings.nature.com/documents/3311/version/1

Ferric reducing antioxidant power and free radical scavenging activity of  Moringa oleifera: Relevance in oxidative stress
Provedor de dados: 17
Autores: Suaib  Luqman.
Moringa oleifera of family Moringaceae, commonly known as Horseradish-tree or the Ben-oil tree is an exceptionally nutritious vegetable tree with a variety of medicinal uses, distributed in tropical and subtropical regions of the world. The tree&amp;#x27;s bark, roots, fruit (pod), flowers, leaves, seeds and gum are used as an antiseptic, anticancer, anti-inflammatory, hepatoprotective and in treating rheumatism, venomous bites and other conditions. The immature green pods, called &amp;#x2018;drumsticks&amp;#x2019; are probably the most valued and widely used part of the tree for water purification (e.g. desalination of ocean salt water). The leaves are highly nutritious, being a significant source of beta-carotene, vitamin C, protein, iron and potassium...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6924/version/1

Fibromyalgia: A Unifying Neuroendocrinologic Model for Understanding Its Pathophysiology
Provedor de dados: 17
Autores: Peter Dorsher.
Fibromyalgia is believed to affect at least 2% of the population. Despite advances in the scientific understanding of the derangements of central and peripheral pain processing mechanisms in fibromyalgia, no current models of its pathophysiology account for the other clinical conditions associated with it such as fatigue, migraine headache, irritable bowel syndrome, and sleep cycle abnormalities. A neuroendocrinologic model of fibromyalgia is presented that accommodates both its known central and peripheral pain mechanisms as well as the myriad of hormonal, visceral, and psychological symptoms associated with that disorder. This model also provides a unifying pathophysiologic basis of fibromyalgia and chronic muscle pain, and offers the potential for...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2595/version/1

Field Trial Experiment Of Artificial Diet On Tasar Silkworm, Anthereaea myltta D.
Provedor de dados: 17
Autores: Alok Sahay; Subrat Satpathy; Shashi Sharan.
An indoor and outdoor experiment was conducted at Shyamsunderpur, Mayurbhanj, Odhisa to test the efficacy of the artificial diet, Tasar Amrit on the young aged Antheraea mylitta silkworm larvae. The results of the experiment reveal that survival and effective rate of rearing (ERR) was higher when larvae were brushed on Tasar Amrit (75 and 42.45%) in contrast to complete outdoor rearing (44 and 33.56 %). Uniform moulting was also observed in the larvae fed with Tasar Amrit.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6701/version/1

FieldML
Provedor de dados: 17
Autores: Poul M. F. Nielsen; Christopher Bradley; Randall Britten; Richard Christie; Peter Hunter; Caton Little; Andrew Miller.
FieldML is an open format for storing and exchanging models containing field information. It is able to represent a wide variety of field value types, including scalar, vector, tensor, logical, and strings. Fields are defined over domains explicitly in terms of functions. Domains may be nested to form embedding hierarchies.
Tipo: Manuscript
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6386/version/1

FieldML &amp;#x2013; a meta-language for field interchange
Provedor de dados: 17
Autores: Richard Christie; Poul M. F. Nielsen; Chris P. Bradley; Caton Little; Randall Britten; Peter J. Hunter.
FieldML is being developed as an XML standard for communicating computational field descriptions and data. Important principles in its design include building models from as few and as fundamental a set of concepts as necessary, supporting maximum reuse, and allowing the functional derivation of fields to be of unlimited complexity.&amp;#xd;&amp;#xa;This talk introduces concepts from the FieldML data model (at version 0.3), and demonstrates how they combine to describe rich field representations.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5901/version/1

Fighting Risky Population Synchronization: Desynchronization and Stabilization in Spatially Structured Ecological Systems
Provedor de dados: 17
Autores: Ming Luo.
Population synchronization exists ubiquitously in ecological systems, of which the underlying causes and the roles in species extinction remain a perplexing puzzle. It is generally believed that the coherence of population dynamics is detrimental and regarded as a major cause of global extinction. A central but unsolved question in ecology of great importance for conservation and biological control is how to destroy the pernicious coherent structures. Here, a top-down approach is adopted to tackle the challenge. A feedback strategy accordingly is applied to stabilize the metacommunity, i.e., to reduce excessive metapopulation fluctuations by means of introducing or removing a planned number of individuals. As a result, the feedback desynchronizes...
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6673/version/1

Finding Bicliques in Digraphs: Application into Viral-host Protein Interactome
Provedor de dados: 17
Autores: Malay Bhattacharyya; Sanghamitra Bandyopadhyay; Ujjwal Maulik.
We provide the first formalization true to the best of our knowledge to the problem of finding bicliques in a directed graph. The problem is addressed employing a two-stage approach based on an existing biclustering algorithm. This novel problem is useful in several biological applications of which we focus only on analyzing the viral-host protein interaction graphs. Strong and significant bicliques of HIV-1 and human proteins are derived using the proposed methodology, which provides insights into some novel regulatory functionalities in case of the acute immunodeficiency syndrome in human.
Tipo: Presentation
Palavras-chave: Immunology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7148/version/1

Finding scientific articles in a large digital archive: BioStor and the Biodiversity Heritage Library
Provedor de dados: 17
Autores: Roderic Page.
The Biodiversity Heritage Library (BHL) is a large digital archive of legacy biological literature, comprising over 31 million pages scanned from books, monographs, and journals. During the digitisation process basic metadata about the scanned items is recorded, but not article-level metadata. Given that the article is the standard unit of citation, this makes it difficult to locate cited literature in BHL. Adding the ability to easily find articles in BHL would greatly enhance the value of the archive. A service was developed to locate articles in BHL based on matching article metadata to BHL metadata using approximate string matching, regular expressions, and string alignment. This article finding service is exposed as a standard OpenURL resolver on the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4928/version/1

Finding the key transition states and intermediates controlling net reaction rates and selectivity
Provedor de dados: 17
Autores: Carsten  Stegelmann; Anders Andreasen.
In this paper Campbell&amp;#x27;s degree of rate control is extended to introduce the concepts of degree of kinetic rate control, degree of kinetic selectivity control, degree of thermodynamic rate control and degree of thermodynamic selectivity control. It is demonstrated by applying hypothetical but realistic kinetic models of varying complexity that the new methods offers a rigorous framework to analyze the importance of kinetic and thermodynamic parameters i.e. establishing the critical parameters of the kinetic model. The methods are general and can be applied to complex reaction networks with multiple overall reactions not only in heterogeneous catalysis but for all sorts of chemical kinetic models.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6076/version/1

Finding the key transition states and intermediates controlling net reaction rates and selectivity
Provedor de dados: 17
Autores: Carsten  Stegelmann; Anders Andreasen.
In this paper Campbell&amp;#x27;s degree of rate control is extended to introduce the concepts of degree of kinetic rate control, degree of kinetic selectivity control, degree of thermodynamic rate control and degree of thermodynamic selectivity control. It is demonstrated by applying hypothetical but realistic kinetic models of varying complexity that the new methods offers a rigorous framework to analyze the importance of kinetic and thermodynamic parameters i.e. establishing the critical parameters of the kinetic model. The methods are general and can be applied to complex reaction networks with multiple overall reactions not only in heterogeneous catalysis but for all sorts of chemical kinetic models.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6076/version/2

Findings From an Accelerated _In Vivo_ Corrosion Model of Magnesium
Provedor de dados: 17
Autores: Chi Keung Yuen; Wing Yuk Ip.
In this article, we are presenting some findings of magnesium corrosion in an _in vivo_ model. While there is consensus that subcutaneous bubbles will occur, it was found in our corrosion-accelerated model that magnesium corrosion is more severe in areas under the gas bubbles. This finding may bring insights to novel methods in reducing the uneven corrosion.
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1833/version/1

Finite Predation Rate: a Novel Parameter for the Quantitative Measurement of Predation Potential of Predator at Population Level
Provedor de dados: 17
Autores: Hsin Chi; De-Fen Mou; Hossein Allahyari; Jih-Zu Yu; Yu-Bing Huang; Ta-Chi Yang; Roya Farhadi; Majid Gholizadeh.
Demography and population growth are the most important subjects of population ecology and economics. Finite and intrinsic growth rates have been used as standard parameters for describing and comparing growth potentials of populations. The predation potentials of predator populations or consumption potentials of consumer populations cannot be properly described using these growth rates alone. A standard parameter is needed for the description of the predation or consumption potential, as well as for the quantitative evaluation of a predator population in an ecosystem or biological control program. We show that the finite predation rate can be the standard parameter by linking the finite rate, the stable age-stage distribution, and the age-stage specific...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6651/version/1

Fire history, fire regimes, and climate change &amp;#x2013; integrating information for management and planning
Provedor de dados: 17
Autores: William T. Sommers.
Background/Question/Methods   &amp;#xd;&amp;#xa;Federal and other natural resource managers in the United States are now required to consider climate change in their planning. Wildland fire is a major component included in many of these planning efforts. Fire is a widespread ecosystem disturbance process that is global in scope with local to regional, event driven, resource and societal impacts.  The frequency, severity and extent of Wildland fires are largely a function of interactions between vegetation and atmospheric processes. Fire activity and management costs have increased significantly over the last few decades. There is growing evidence that these increases relate to measured changes in climate variables. Our understanding of fire history, fire...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5238/version/1

Firing statistics and correlations in spiking neurons: a level-crossing approach
Provedor de dados: 17
Autores: Laurent Badel.
We present a time-dependent level-crossing theory for linear dynamical systems perturbed by colored Gaussian noise. We apply these results to approximate the firing statistics of conductance-based integrate-and-fire neurons receiving excitatory and inhibitory Poissonian inputs. Analytical expressions are obtained for three key quantities characterizing the neuronal response to time-varying inputs: the mean firing rate, the linear response to sinusoidally-modulated inputs, and the pairwise spike-correlation for neurons receiving correlated inputs. The theory yields tractable results that are shown to accurately match numerical simulations, and provides useful tools for the analysis of interconnected neuronal populations.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6454/version/1

First Hematological Signals of Latent Anemia to Aging Population
Provedor de dados: 17
Autores: Aurelian Udristioiu.
Anemia is an independent risk factor for morbidity and mortality in an array of disorders common to seniors including cancer, renal diseases and heart diseases.  The aim of this study was to identify the first hematological signals of latent anemia to aging population using as screening the hematological aspects of cells from peripheral blood and additional tests, establishing the etiology of anemia in the elderly.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;_Method_: Additional to level of hemoglobin(HGB) and hematocrit (HCT) have been included Hematological Indexes( MCV, HCV,  MCHC ), red cell distribution width,(RDW), reticulocyte count (RET),  serum iron (SI), total  iron binding capacity,(TIBC), transferrin saturation index, (TSI), serum ferritin( SF), on an...
Tipo: Presentation
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3285/version/1

First Report of 1 Micron Spatial Resolution Chemical Imaging of a Zirconium Single Crystal by FT-NIR Microspectroscopy
Provedor de dados: 17
Autores: I. C. Baianu.
This is the first report of 1 micron resolution chemical images of a Zirconium single crystal by FT-NIR Microspectroscopy. The FT-NIR spectra were obtained with a PerkinElmer SpectrumONE NTS spectrometer. The chemical images were obtained with a PerkinElmer Autoimage model FT-NIR microscope equipped with a very high sensitivity In /GaAs detector capable of precise measurements at ~10 ng, that was coupled to the SpectrumONE NTS FT-NIR spectrometer.
Tipo: Manuscript
Palavras-chave: Chemistry; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6599/version/1

First reports of computed tomographic colonography for the screening of colorectal polyps in acromegalic patients
Provedor de dados: 17
Autores: Odery Ramos Jr; C&amp;#xe9;sar Luiz Boguszewski; Sandra Teixeira; Anke Boeving; Ricardo De Bem; Benito Parolim; J&amp;#xfa;lio C&amp;#xe9;sar Pisani; Jo&amp;#xe3;o Carlos Prolla.
*Aim:* To analyze the CTC performance for the screening of colorectal polyps in acromegalic patients.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Materials and Methods:* A prospective study of 21 acromegalic patients, 12 male and 9 female, average age 49, who underwent CTC and CC. CTC was performed with a GE Helical Multislice Computed Tomography Apparatus. The colonoscopy was performed, in the same day, without previous knowledge of the CTC diagnostics. The study evaluated the capacity of CTC to detect patients with colorectal polyps and identify each colorectal lesion described by CC.   &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Results:* In two patients (2/21), CC was incomplete. However, in all patients CTC was complete. In Phase I (&amp;#x201c;Per...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/2323/version/1

First steps towards WikiPathways RDF
Provedor de dados: 17
Autores: Andra Waagmeester.
This presentation presents the first steps in modeling WikiPathways content in RDF. WikiPathways is stored in a proprietary GPML format. By modeling this data in RDF, semantic web features become available to WikiPathways content.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6300/version/1

Fish play Minority Game as humans do
Provedor de dados: 17
Autores: Sy-Sang Liaw; Ruey-Tarng Liu; Fei Fang Chung.
Previous computer simulations of the Minority Game (MG) have shown that the average agent number in the winning group (i.e., the minority group) had a maximal value such that the global gain was also maximal when an optimal amount of information was available to all agents . This property was further examined and its connection to financial markets has also been discussed . Here we report the results of an unprecedented real MG played by university staff members who clicked one of two identical buttons (A and B) on a computer screen while clocking in or out of work. We recorded the number of people who clicked button A for 1288 games, beginning on April 21, 2008 and ending on October 31, 2010, and calculated the variance among the people who clicked A as a...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5440/version/1

Five years of winter climate change-related research in the Canadian low Arctic: What have we learned?
Provedor de dados: 17
Autores: Paul Grogan; Kate Buckeridge.
The importance of the fall, winter and spring periods to ecosystem functioning and biogeochemical cycling in tundra has only become apparent in the past two decades.  Our research group has been conducting winter climate change-related studies at a low arctic tundra site near Daring Lake, north of Yellowknife in northern Canada for the past five years.  Most of these studies have focused on the biogeochemical interactions between plants, soils, and soil microbes during fall, winter and spring, and on their responses to experimentally deepened snow.  In addition, we have measured trace gas production and isotopic nitrogen tracer distributions among plant and soil components in several vegetation-types.  The central goal has been to understand the potential...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3665/version/1

Flaw-tolerance in silk fibrils explains strength, extensibility and toughness of spider silk
Provedor de dados: 17
Autores: Melis Arslan; Markus  J. Buehler.
Silk is an ancient but remarkably strong, extensible and tough material made from simple protein building blocks. Earlier work has shown that the particular molecular geometry of silk with a composite of semi-amorphous and nanocrystalline beta-sheet protein domains provides the structural basis for its characteristic softening-stiffening behavior and remarkable strength at the nanoscale. Yet, an open question remains as to how these nanoscale properties are upscaled so effectively to create strong, extensible and tough silk fibers. Here we discover that the geometric confinement of fibrils to &amp;#x2248;50-100 nm width and arranged in bundles to form larger-scale silk fibers, is the key to explaining the upscaling of the mechanical properties of silk from...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5916/version/1

Fluctuating population dynamics promotes the evolution of phenotypic plasticity
Provedor de dados: 17
Autores: Mario Pineda-Krch; Richard Svanb&amp;#xe4;ck; Michael Doebeli.
An increasing number of studies are showing evidence in support of sympatric speciation. One basic question remains, however. When a population has undergone a branching in its phenotype, is this due to an evolutionary branching in the underlying genotype or due to phenotypic plasticity modifying a single genotype? Thus, phenotypic plasticity has come to be viewed as a trait subject to selection, just like any other phenotypic character1,2. Here we present a model addressing the conditions under which a predator phenotype experiencing selection for two alternative optimal phenotypes gives rise to genetically based phenotypic branching or to phenotypic plasticity, allowing the corresponding genotype to give rise to two alternative, well-adapted...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/56/version/1

Fluorescence Correlation Spectroscopy as a Quantitative Tool Applied to Drug Delivery Model Systems
Provedor de dados: 17
Autores: Christoph Jung; Sigrun Polier; Markus Schoeffel; M Drechsler; Valerie Jerome; Ruth Freitag.
The delivery of drugs to cells is a very active area of research. Drugs are commonly believed to ameliorate illnesses. The targeted, controlled and/or enhanced uptake of the drug into cells is facilitated by loading the drug into carrier vehicles (nanoparticles, e.g.. micelles).The distribution of a drug over the nanoparticles used to deliver the drug to the targeted cells is of vital importance. It makes a difference, whether all nanoparticles carry the same amount of drug or whether a little amount of the nanoparticles carries a high proportion of the drug material and most nanoparticles carry no material. This depends on the method used to load the drugs into the carriers. Furthermore, the absolute amount of drug present in the nanoparticles and the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4140/version/1

Folding pathway of the B1 domain of protein G explored by a multiscale modeling
Provedor de dados: 17
Autores: Andrzej Kolinski; Sebastian Kmiecik.
The understanding of the folding mechanisms of single domain proteins is an essential step in the understanding of protein folding in general. Recently, we developed a mesoscopic CABS protein model which was successfully applied in protein structure prediction, studies of protein thermodynamics and modeling of protein complexes. In the present research this model is employed in a detailed characterization of the folding process of a simple globular protein, the B1 domain of IgG-binding protein G (GB1). There is a vast body of experimental facts and theoretical findings for this protein. Performing unbiased, _ab initio_ simulations, we demonstrated that the GB1 folding proceeds via the successive formation of an extended folding nucleus, followed by slow...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/129/version/1

Food Physical Chemistry and Biophysical Chemistry
Provedor de dados: 17
Autores: I.C. Baianu.
Food Physical Chemistry is considered to be a branch of Food Chemistry^1,2^ concerned with the study of both physical and chemical interactions in foods in terms of physical and chemical principles applied to food systems, as well as the applications of physical/chemical techniques and instrumentation for the study of foods^3,4,5,6^.  This field encompasses the &amp;#x22;physiochemical principles of the reactions and conversions that occur during the manufacture, handling, and storage of foods&amp;#x22;^7^. Two rapidly growing, related areas are Food Biotechnology and Food Biophysical Chemistry.  &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6573/version/1

Food Physical Chemistry and Biophysical Chemistry (v2)
Provedor de dados: 17
Autores: I. C. Baianu.
Food Physical Chemistry is considered to be a branch of Food Chemistry^1,2^ concerned with the study of both physical and chemical interactions in foods in terms of physical and chemical principles applied to food systems, as well as the applications of physical/chemical techniques and instrumentation for the study of foods^3,4,5,6^.  This field encompasses the &amp;#x22;physiochemical principles of the reactions and conversions that occur during the manufacture, handling, and storage of foods&amp;#x22;^7^. Two rapidly growing, related areas are Food Biotechnology and Food Biophysical Chemistry.  &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6573/version/2

Foregut microbiome in development of esophageal adenocarcinoma
Provedor de dados: 17
Autores: Liying Yang; William  E. Oberdorf; Erika Gerz; Tamasha  Parsons; Pinak  Shah; Sukhleen Bedi; Carlos W. Nossa; Stuart  M. Brown; Yu Chen; Mengling Liu; Michael Poles; Fritz Francois; Morris Traube; Navjeet  Singh; Todd Z. DeSantis; Gary L. Andersen; Monika  Bihan; Les Foster; Aaron  Tenney; Daniel  Brami; Mathangi  Thiagarajan; Indresh K. Singh; Manolito   Torralba; Shibu  Yooseph; Yu-Hui  Rogers; Eoin L. Brodie; Karen E. Nelson; Zhiheng Pei.
Esophageal adenocarcinoma (EA), the type of cancer linked to heartburn due to gastroesophageal reflux diseases (GERD), has increased six fold in the past 30 years.  This cannot currently be explained by the usual environmental or by host genetic factors. EA is the end result of a sequence of GERD-related diseases, preceded by reflux esophagitis (RE) and Barrett&amp;#x2019;s esophagus (BE). Preliminary studies by Pei and colleagues at NYU on elderly male veterans identified two types of microbiotas in the esophagus. Patients who carry the type II microbiota are &amp;#x3e;15 fold likely to have esophagitis and BE than those harboring the type I microbiota. In a small scale study, we also found that 3 of 3 cases of EA harbored the type II biota. The findings...
Tipo: Marker Paper / Data Plan
Palavras-chave: Cancer; Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5026/version/1

Formal Systems Architectures for Biology
Provedor de dados: 17
Autores: Bradly Alicea.
When the word &amp;#x22;systems&amp;#x22; is used in systems biology, it invokes a variety of assumptions about what defines the subject under investigation, which in turn can lead to divergent research outcomes. We will take the position that systems are defined by their potential organizing and &amp;#x22;control&amp;#x22; mechanisms, which distinguishes complex, living systems from a primordial soup. This will be accomplished by defining and investigating three interesting control motifs in biological systems: dominoes and clocks, futile cycles, and complex feedforward regulation. Additional mechanisms that combine feedback and feedforward mechanisms will also be briefly elaborated upon. Throughout these examples, our focus will be on the connection...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6369/version/2

Formal Systems Architectures for Biology
Provedor de dados: 17
Autores: Bradly Alicea.
When the word &amp;#x22;systems&amp;#x22; is used in systems biology, it invokes a variety of assumptions about what defines the subject under investigation, which in turn can lead to divergent research outcomes. We will take the position that systems are defined by their potential organizing and &amp;#x22;control&amp;#x22; mechanisms, &amp;#xd;&amp;#xa;which distinguishes complex, living systems from a primordial soup. This will be accomplished by defining and investigating three interesting control motifs in biological systems: dominoes and clocks, futile cycles, and complex feedforward regulation. Additional mechanisms that combine feedback and feedforward mechanisms will also be briefly elaborated upon. Throughout these examples, our focus will be on...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6369/version/1

Formation of an SIR-Nucleosome Filament in vitro and Its Modulation by O-Acetyl-ADP-Ribose
Provedor de dados: 17
Autores: Yu-Yi Wu; Jia-Yang Hong; Sue-Ping Lee; Hsiao-Hsuian  Shen; Shu-Ping Tsai; Gunn-Guang Liou.
It is not possible to clearly visualize how chromatin condenses to heterochromatin in vivo. However, in an in vitro system for Saccharomyces cerevisiae, the requirements for heterochromatin filament formation mirror those found in vivo. Here we report that the nucleosomes and the Sir2, Sir3 and Sir4 proteins, which are required for in vitro filament assembly, are also components of these filaments, confirming that the filaments are SIR-nucleosome filaments. We show the individual localization patterns of the Sir proteins on this SIR-nucleosome filament, and demonstrate that the metabolite, AAR, plays a specific and essential role in promoting the formation of this SIR-nucleosome filament.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6063/version/1

Formation of Plant Battery from Xerophytic Plants
Provedor de dados: 17
Autores: R.V.K. Charan.
Nature has supplied abundant energy to plants in form of electricity and among them the xerophytics and specially the Opuntias have got the maximum due to adaptness of dry condition. Several researchers have already found voltage across their cells but the present endeavour to harness the total electrical energy conserved in plants in form of a Plant Battery, however of low potential, but is a step forward towards non-conventional energy.
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4390/version/1

Formulating MEDLINE queries for article retrieval based on PubMed exemplars
Provedor de dados: 17
Autores: Alexander Garnett; Heather A. Piwowar; Edie M. Rasmussen; Judy Illes.
Bibliographic search engines allow endless possibilities for building queries based on specific words or phrases in article titles and abstracts, indexing terms, and other attributes. Unfortunately, deciding which attributes to use in a methodologically sound query is a non-trivial process.  In this paper, we describe a system to help with this task, given an example set of  PubMed articles to retrieve and a corresponding set of articles to exclude.  The system provides the users with unigram and bigram features from the title, abstract, MeSH terms, and MeSH qualifier terms in decreasing order of precision, given a recall threshold.  From this information and their knowledge of the domain, users can formulate a query and evaluate its performance.  We apply...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4270/version/1

Formulating MEDLINE queries for article retrieval based on PubMed exemplars
Provedor de dados: 17
Autores: Alexander Garnett; Heather A. Piwowar; Edie M. Rasmussen; Judy Illes.
Bibliographic search engines allow endless possibilities for building queries based on specific words or phrases in article titles and abstracts, indexing terms, and other attributes. Unfortunately, deciding which attributes to use in a methodologically sound query is a non-trivial process.  In this paper, we describe a system to help with this task, given an example set of  PubMed articles to retrieve and a corresponding set of articles to exclude.  The system provides the users with unigram and bigram features from the title, abstract, MeSH terms, and MeSH qualifier terms in decreasing order of precision, given a recall threshold.  From this information and their knowledge of the domain, users can formulate a query and evaluate its performance.  We apply...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4270/version/2

Formulation and in vitro Evaluation of Eudragit L100 piroxicam
Provedor de dados: 17
Autores: Mostafa Saffari; Malihe Shahbazi; Mehdi Shafiee Ardestani.
The aim of this study was to formulate and evaluate controlled release preparations of a water-insoluble drug using Copolymers synthesized from acrylic and methacrylic acid&amp;#xd;&amp;#xa;esters (Eudragit L 100) as the retardant material. Microspheres were prepared by solvent evaporation method using an alcohol / liquid paraffin system. Span60 was used as the droplet stabilizer. The prepared microspheres were characterized for their micromeritic properties and drug loading, as well as by differential scanning calorimetry. The in vitro release studies were performed first in pH1.2 and then pH 6.8, phosphate buffer. The prepared microspheres were yellow, and spherical in shape. The drugloaded microspheres showed 71-85% of entrapment and release was...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/1544/version/1

Fossil evidence for the origin of spider spinnerets
Provedor de dados: 17
Autores: Paul A. Selden; William A. Shear.
Silk production from opisthosomal glands is a defining characteristic of spiders (Araneae). Silk emerges from spigots (modified setae) borne on spinnerets (modified appendages). Spigots from _Attercopus fimbriunguis_ (Shear, Selden &amp;#x26; Rolfe, 1987^1^), from Middle Devonian (386 Ma) strata of Gilboa, New York were described in 1989^2^ as evidence for the oldest spider and the first use of silk by animals. Slightly younger (374 Ma) material from South Mountain, New York, conspecific with _A. fimbriunguis_, includes spigots and other evidence which elucidate the evolution of early Araneae and the origin of spider silk. No known _Attercopus_ spigots, including the original specimen^2^, occur on true spinnerets but are arranged along the edges of plates....
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2088/version/1

Fractal geometry of nature (bone) may inspire medical devices shape
Provedor de dados: 17
Autores: Salvatore Longoni; Matteo Sartori.
Medical devices, as orthopaedics prostheses and dental implants, have been designed over years on the strength of mechanical, clinical and biological indications. This sequence is the commonly accepted cognitive and research process: adapting the device to the surrounding environment (host tissue). Inverting this traditional logical approach, we started from bone microarchitecture analysis. Here we show that a unique geometric rule seems to underlie different morphologic and functional aspects of human jaw bone tissue: fractal properties of white trabeculae in low quality bone are similar to fractal properties of black spaces in high quality bone and vice versa. These data inspired the fractal bone quality classification and they were the starting point...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4512/version/1

Fractal-like Distributions over the Rational Numbers in High-throughput Biological and Clinical Data
Provedor de dados: 17
Autores: Vladimir Trifonov; Laura Pasqualucci; Riccardo Dalla-Favera; Raul Rabadan.
Recent developments in extracting and processing biological and clinical data are allowing quantitative approaches to studying living systems. High-throughput sequencing, expression profiles, proteomics, and electronic health records are some examples of such technologies. Extracting meaningful information from those technologies requires careful analysis of the large volumes of data they produce. In this note, we present a set of distributions that commonly appear in the analysis of such data. These distributions present some interesting features: they are discontinuous in the rational numbers, but continuous in the irrational numbers, and possess a certain self-similar (fractal-like) structure. The first set of examples which we present here are drawn...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5037/version/1

Fracture Toughness of Human Solid Cancers
Provedor de dados: 17
Autores: Nagesh Ragavendra; William Klug; J Woody  Ju.
Human solid cancers typically are harder and firmer than surrounding normal tissue upon clinical palpation. This characteristic has been linked to the presence of abundant collagen in the tumor stroma, referred to as the desmoplastic reaction. Recent evidence indicates that tumor-associated desmoplastic stroma is critical to cancer&amp;#x2019;s growth and progression. However, how best to measure, interpret, and/or model the mechanical attributes of tumor microenvironment in vivo remain unclear. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;During routine sonographically-guided fine needle biopsy of solid tumors of the human thyroid gland, it was serendipitously observed by the lead author that the nature and strength of the haptic force feedback cues varied among...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/2461/version/1

FReD: The floral reflectance spectra database
Provedor de dados: 17
Autores: Sarah E. J. Arnold; Vincent Savolainen; Lars Chittka.
Floral reflectance measurements are of great value to researchers who need consider the real colour of flowers, for example in the context of how the flowers appear to their pollinators. We have thus developed the Floral Reflectance Database (FReD) to assist these researchers, gathering together floral reflectance data in a publicly available, searchable online database. The first version of the database is now available online at &amp;#x22;http://www.reflectance.co.uk&amp;#x22;:http://www.reflectance.co.uk. We anticipate that this resource will be of interest to researchers working on flower colour and animal vision.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1846/version/1

Free Will or Not: Causality Preserved but Access to Motor Decisions Obscured
Provedor de dados: 17
Autores: Andrei Gorea; Lukasz Grzeczkowski; Delphine Rider.
Empirical studies having addressed the free-will issue suffer from controversial methodologies and interpretations. We present a new paradigm involving a synchronization task where the time interval to synchronize with is randomly within and without subject&amp;#x27;s synchronization capabilities and ask subjects to retrospectively evaluate (Q1) which of the two occurred or (Q2) whether their motor response had had been reactive/speeded or delayed. Contrary to the non-FW view, Q1-judgments correlate with the actual duration of the synchronization interval rather than with subjects&amp;#x27;s motor response latencies. Instead of postidictively reshuffling their judgment to make it match the outcome of their actions, subjects preserve the causal chain of...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4633/version/1

FreePub: Collecting and Organizing Scienti&amp;#xc;c Material Using Mindmaps
Provedor de dados: 17
Autores: Theodore Dalamagas; Tryfon Farmakakis; Manolis Maragkakis; Artemis Hatzigeorgiou G. Hatzigeorgiou.
This paper presents a creativity support tool, called FreePub,to collect and organize scientifi&amp;#xc;c material using mindmaps. Mindmaps are visual, graph-based representations of concepts, ideas, notes, tasks, etc. They generally take a hierarchical or tree branch format, with ideas branching into their subsections. FreePub supports creativity cycles. A user starts such a cycle by setting up her domain of interest using mindmaps. Then, she can browse mindmaps and launch search tasks to gather relevant publications from several data sources. FreePub, besides publications, identifies helpful supporting material (e.g., blog posts, presentations). All retrieved information from FreePub can be imported and organized in mindmaps. FreePub has been fully...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5432/version/1

French birds lag behind climate warming
Provedor de dados: 17
Autores: Vincent Devictor; Romain Julliard; Denis Couvet; Fr&amp;#xe9;d&amp;#xe9;ric Jiguet.
Biodiversity responses to climate warming have been documented through the study of changes in distributions, abundances or phenologies of individual species or in more integrated measures such as species community richness and composition. However, whether these observed population and community changes are occurring fast enough to cope with new climatic conditions remain uncertain and hardly quantifiable. Here, using spatial and temporal trends from the French breeding bird survey, we show that although bird assemblages are strongly responding to climate warming, this response is slower than expected for catching up with the current temperature increase. During the last two decades, French birds have only achieved 54% of the response required to follow...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1275/version/1

Frequency and accuracy of weight comments by others, and the association with weight misperception among Hong Kong adolescents
Provedor de dados: 17
Autores: Wing-Sze Lo; Sai-Yin Ho; Kwok-Kei Mak; Yuen-Kwan Lai; Tai-Hing Lam.
*Purpose:* To assess the frequency and accuracy of weight comments received from different sources among Chinese adolescents and the relation of weight comments to weight misperception.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Methods:* In the Hong Kong Student Obesity Surveillance (HKSOS) project 2006-07, 22612 form 1 to 7 students (41.5% boys) completed a questionnaire on obesity. Students were asked if they had received serious &amp;#x22;too fat&amp;#x22; or &amp;#x22;too thin&amp;#x22; comments over the past 30 days from family members, peers and professionals, and the accuracy of the comments was assessed against the actual weight status. Weight misperception was defined as discordance between the actual and perceived weight status. Logistic regression was...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2742/version/1

Frequency-dependent selection predicts patterns of radiations and biodiversity
Provedor de dados: 17
Autores: Carlos Melian; David Alonso; Diego Vazquez; James Regetz; Stefano Allesina.
Most empirical studies support a decline in speciation rates through time, although evidence for constant speciation rates also exists. Declining rates have been explained by invoking niche-filling processes, whereas constant rates have been attributed to non-adaptive processes such as sexual selection, mutation, and dispersal. Trends in speciation rate and the processes underlying it remain unclear, representing a critical information gap in understanding patterns of global diversity. Here we show that the speciation rate is driven by frequency dependent selection. We used a frequency-dependent and DNA sequence-based model of populations and genetic-distance-based speciation, in the absence of adaptation to ecological niches. We tested the...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3752/version/1

Frizzled Proteins are bona fide G Protein-Coupled Receptors
Provedor de dados: 17
Autores: Vladimir L. Katanaev; Silke Buestorf.
Receptors of the Frizzled family initiate Wnt ligand-dependent signaling controlling&amp;#xd;&amp;#xa;multiple steps in organism development and highly conserved in evolution.&amp;#xd;&amp;#xa;Misactivation of the Wnt/Frizzled signaling is cancerogenic. Frizzled receptors&amp;#xd;&amp;#xa;launch several signaling cascades: the canonical pathway regulating beta-catenin-dependent transcription; the planar cell polarity pathway polarizing the&amp;#xd;&amp;#xa;cytoskeleton within the epithelial plane; and the calcium pathway. Frizzled&amp;#xd;&amp;#xa;receptors possess seven transmembrane domains and their signaling depends on&amp;#xd;&amp;#xa;trimeric G proteins in various organisms. However, Frizzleds constitute a&amp;#xd;&amp;#xa;distinct group within the G...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Molecular Cell Biology; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2765/version/1

From antenna to antenna: Lateral shift of olfactory memory in bees
Provedor de dados: 17
Autores: Lesley J. Rogers; Giorgio Vallortigara.
Honeybees, _Apis mellifera_, readily learn to associate odours with sugar rewards and we show here that recall of the olfactory memory, as demonstrated by the bee extending its proboscis when presented with the trained odour, involves first the right and then the left antenna. At 1-2 hour after training using both antennae, recall is possible only when the bee uses its right antenna but by 6 hours after training the memory has made a lateral shift and can now be recalled only when the left antenna is in use. Long-term memory one day after training is also accessed only via the left antenna. This time-dependent shift from right to left antenna is seen as side biases in responding to odour presented to the bee&amp;#x27;s left or right side and hence may be...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1466/version/1

From aptamer-based biomarker discovery to  diagnostic and clinical applications: an aptamer-based, streamlined multiplex proteomic assay
Provedor de dados: 17
Autores: Stephan Kraemer; Jonathon  D. Vaught; Christopher Bock; Larry Gold; Evaldas Katilius; Tracy R. Keeney; Nancy Kim; Nicholas A. Saccomano; Sheri K. Wilcox; Dom Zichi; Glenn M. Sanders.
Recently, we reported an aptamer-based, highly multiplexed assay for the purpose of biomarker identification. To enable seamless transition from highly multiplexed biomarker discovery assays to a format suitable and convenient for diagnostic and life-science applications, we developed a streamlined, plate-based version of the assay. The plate-based version of the assay is robust, sensitive (sub-picomolar), rapid, can be highly multiplexed (upwards of 60 analytes), and fully automated.  We demonstrate that quantification by microarray-based hybridization, Luminex bead-based methods, and qPCR are each compatible with our platform, further expanding the breadth of proteomic applications for a wide user community.
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4642/version/1

From Blood Oxygenation Level Dependent (BOLD) signals to brain temperature maps
Provedor de dados: 17
Autores: Roberto C Sotero; Yasser Iturria-Medina.
A theoretical framework is presented for converting Blood Oxygenation Level Dependent (BOLD) images to temperature maps, based on the idea that disproportional local changes in cerebral blood flow (CBF) as compared with cerebral metabolic rate of oxygen consumption (CMRO2) during functional brain activity, lead to both brain temperature changes and the BOLD effect. Using an oxygen limitation model and a BOLD signal model we obtain a transcendental equation relating CBF and CMRO2 changes with the corresponding BOLD signal, which is solved in terms of the Lambert W function. Inserting this result in the dynamic bio-heat equation describing the rate of temperature changes in the brain, we obtain a non autonomous ordinary differential equation that depends on...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4772/version/1

From Machine Learning to Learning Machines - A Perspective toward Personalized Medicine
Provedor de dados: 17
Autores: Malay Bhattacharyya.
We describe how to learn a network using a bottom-up approach by building networks from expression profiles. Then we can analyze these networks with different graph mining approaches and by studying topological behaviors. Finally, how we can achieve personalized medicine from the network biology.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7118/version/1

Frost and flowers: Predicting the effects of climate change on spring frost damage using a large pollen count dataset
Provedor de dados: 17
Autores: Daniel Katz.
Background/Question/Methods &amp;#xd;&amp;#xa;Climate change is resulting in warmer average temperatures in much of North America, leading to earlier flowering dates for most tree genera.  However, earlier flowering dates can increase the chance of frost damage which may in turn reduce or eliminate seed and fruit production.  This has important implications for both forest regeneration and the organisms which depend on these resources.&amp;#xd;&amp;#xa;Although specific examples, such as the &amp;#x201c;Easter frost&amp;#x201d; of 2007, show that frost damage can have extreme short term impacts on tree reproduction, we lack a general understanding of the frequency and importance of these events in non-agricultural contexts.  Moreover, the magnitude by...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5365/version/1

Function, Role, and Disposition in Basic Formal Ontology
Provedor de dados: 17
Autores: Robert Arp; Barry Smith.
Numerous research groups are now utilizing Basic Formal Ontology (BFO) as an upper-level framework to assist in the organization and integration of biomedical information. This paper provides elucidation of the three BFO categories of function, role, and disposition, and considers two proposed sub-categories of artifactual function and bio-logical function. The motivation is to help advance the coherent treatment of functions, roles, and dispositions, to help provide the potential for more detailed classification, and to shed light on BFO&amp;#x2019;s general structure and use.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1941/version/1

Functional analysis of &amp;#x3b2;C1 protein encoded by Tomato leaf curl Java virus, a monopartite begomovirus
Provedor de dados: 17
Autores: Pradeep Sharma; Tatsuya Kon; Masato Ikegami.
Tomato leaf curl disease is among the most important limiting factors that affect tomato production in world wide including south East Asia. Recently, we have isolated tomato leaf curl Java virus, a whitefly-transmitted monopartite begomovirus, which belongs to the family Geminiviridae. ToLCJAV have been shown to be associated with a novel signal stranded DNA satellite, known as [beta]DNA. Post transcriptional gene silencing (PTGS) in plants is a natural defense response against virus infections, and as a counter defense strategy, viruses have evolved to encode silencing suppressor proteins. The present work we have identified the suppressor activities encoded by [beta]C1 protein encoded by ToLCJAV DNA[beta] satellite, which poses a serious threat to...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3317/version/1

Functional annotation of bacterial sugars
Provedor de dados: 17
Autores: Frederique Lisacek.
Glyco-bioinformatics means different things to different people. It ranges, for example, from the mining of the genome for glycosylation pathway enzymes, through to analysis of microarray expression of glycosyltransferases, to glycoprotein identification data, to the development of tools that facilitate the interpretation of mass spectra and to the construction of structural glycan databases. Lastly, these data need to be mined so that the function of the glycan structures attached to the range of glycoconjugates in nature can be determined. The quality of the data in these databases needs to be maintained for this work to be meaningful.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;For easier analysis, glycan structures are often characterised independent of the...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5107/version/1

Functional annotation of human parvovirus b19 proteome and Molecular docking of VP1 protein with Teniposide
Provedor de dados: 17
Autores: Amburu Praneetha; Dibyabhaba Pradhan; Vani Priyadarshini; Amineni Umamaheswari.
Parvovirus B19 is a common source of infection with a seroprevalence of 60-70% in the adult population. Human parvovirus causes several distinct clinical syndromes such as erythema, polyarthritis resembling rheumatoid arthritis, vasculitis, hydrops fetalis, myocarditis etc. Recent years have witnessed manifest increase in clinical knowledge of parvovirus B19-associated complications, diagnosis and treatment. Traditional immunosuppressive therapy being unsuccessful, anti-viral therapy might be worthy of consideration. Functional annotation of human parvoviral proteome may provide insights into role of viral proteome in its survival and pathogenic mechanisms. Availability of whole proteome in the open source aided functional annotation of protein using...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5170/version/1

Functional aspects of titanosaur osteoderms
Provedor de dados: 17
Autores: Thiago S. Marinho.
Though titanosaur osteoderms are not common findings, these elements are recorded widely in Gondwana and part of Laurasia. This assembly known by the date offers few resources for studies on the ecology of this group of dinosaurs. Recently, some eggs bearing titanosaur embryos with preserved skin, from Patagonia, Argentina, may shed some light on the function and disposition pattern of these dermic bones. Some of the skin patches associated with the titanosaur embryos show two distinct patterns of tuberosities: a longitudinal row and rosettes, both composed of closely attached tuberosities. These tuberosities do not seem to be ossified, but this might be due to the ontogenetic stage of the titanosaurs. Here we propose that these tuberosities might have...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/508/version/1

Functional Curation: Potential Future Directions for SED-ML
Provedor de dados: 17
Autores: Jonathan Cooper; Gary Mirams.
&amp;#x22;Functional curation&amp;#x22;:http://dx.doi.org/10.1016/j.pbiomolbio.2011.06.003 of models is essentially about enabling a set of models to be tested for reproduction of a particular behaviour under some protocol. The idea is to examine which of the models are capable of replicating experimentally observed results, and evaluate their suitability for &amp;#xd;&amp;#xa;reuse in particular modelling studies. This requires a description of the protocol being performed on the models, and ideally a community agreed standard for these. Clearly SED-ML is the obvious candidate here, however, in its current form it has a few limitations that preclude this application.  This talk discusses the requirements posed by functional curation, and introduces our...
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6327/version/1

Functional differentiation within the monkey cortex as revealed by near-infrared spectroscopy
Provedor de dados: 17
Autores: Allen Ardestani; Felix Darvas; Jens Steinbrink; Arthur Toga; Joaquin M. Fuster.
The role of prefrontal cortex in working memory (WM) is well established.  However, questions remain regarding the topography and &amp;#x201c;domain-specific differentiation&amp;#x201d; of different types of information processing in the cortex.  While it has been theorized that dorsolateral (DPFC) and ventrolateral (VPFC) prefrontal cortex preferentially process spatial and object WM, respectively, both electrophysiological evidence in the monkey and neuroimaging in the human have largely failed to demonstrate such regional differentiation.  In this study we use near-infrared spectroscopy (NIRS) to detect functional changes, across relatively large cortical cell populations, simultaneously from prefrontal and posterior parietal cortices.  Imaging data...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1673/version/1

Functional presynaptic [alpha]6-containing nicotinic acetylcholine receptors participate in nicotine reward in the VTA: where and how
Provedor de dados: 17
Autores: Kechun Yang; Lori Buhlman; Ming Gao; Ghous M. Khan; Robert A. Nichols; Jamie DeChon; Guozhang Jin; Paul Whiteaker; Ronald J. Lukas; Jie Wu.
In the ventral tegmental area (VTA), [alpha]6-nAChRs express abundantly, but their location, function, pharmacology, and roles in cholinergic modulation of dopaminergic (DA) neurons remain elusive. Using a VTA neuron-adherent bouton preparation, we report that functional [alpha]6-nAChRs are located on GABAergic presynaptic boutons, where they mediate cholinergic modulation of GABA release onto DA neurons. Smoking-relevant concentrations of nicotine desensitize [alpha]6-nAChRs, cause a disinhibition in DA neurons and consequently mediate nicotine reward.
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2875/version/1

Fundamental Principles of Neural Organization of Cognition
Provedor de dados: 17
Autores: Leonid I. Perlovsky.
The manuscript advances a hypothesis that there are few fundamental principles of neural organization of cognition, which explain several wide areas of the cognitive functioning. We summarize the fundamental principles, experimental, theoretical, and modeling evidence for these principles, relate them to hypothetical neural mechanisms, and made a number of predictions. We consider cognitive functioning including concepts, emotions, drives-instincts, learning, &amp;#x201c;higher&amp;#x201d; cognitive functions of language, interaction of language and cognition, role of emotions in this interaction, the beautiful, sublime, and music. Among mechanisms of behavior we concentrate on internal actions in the brain, learning and decision making. A number of...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/7098/version/1

Fundamentally different strategies for transcriptional regulation are revealed by analysis of binding motifs
Provedor de dados: 17
Autores: Zeba Wunderlich; Leonid Mirny.
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6^-10^9^ decoy sites? Our analysis of 319 known TF binding motifs clearly demonstrates that prokaryotes and eukaryotes use strikingly different strategies to target TFs to specific genome locations; eukaryotic TFs exhibit widespread nonfunctional binding and require clustering of sites in regulatory regions for specificity.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2688/version/2

Fundamentally different strategies for transcriptional regulation are revealed by analysis of binding motifs
Provedor de dados: 17
Autores: Leonid Mirny; Zeba Wunderlich.
To regulate a particular gene, a transcription factor (TF) needs to bind a specific genome location. How is this genome address specified amid the presence of ~10^6-10^9 decoy sites? Our analysis of 319 known TF binding motifs clearly demonstrates that prokaryotes and eukaryotes use strikingly different strategies to target TFs to specific genome locations; eukaryotic TFs exhibit widespread nonfunctional binding and require clustering of sites in regulatory regions for specificity.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2688/version/1

Fundamentals of Molecular Biology
Provedor de dados: 17
Autores: Malay Bhattacharyya.
We present some basic concepts of molecular biology and the related open problems.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7121/version/1

Future Outlook for Databases from the Perspective of Bioresources Databases
Provedor de dados: 17
Autores: Yukiko Yamazaki.
Databases, like journals, are now an essential component of our research activities. However, the maintenance of databases and the timely, accurate, and complete incorporation into them of the wealth of data being created daily through scientific activities represent a difficult problem.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;I have been working on bioresources databases and come to appreciate the need for closer links between journals and databases to improve the scientific value of databases. For example, it is frequently difficult to identify experimental materials from articles in journals. In experimental science, it is vital that one scientist&amp;#x2019;s experiments are readily reproducible by others; this requires an environment that provides other...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5068/version/1

Future Predictions of _Cyclamen_ Distribution in the Mediterranean Region
Provedor de dados: 17
Autores: Claudia Ciotir; Chris Yesson; Alastair Culham.
_Cyclamen_ (Myrsinaceae) occupy the Mediterranean region, with highest diversity in Greece and Turkey, with a few species endemic to islands. _Cyclamen_ species have a phenological preference for dry summers and wet winters. A recent study developed models of the climatic niches of _Cyclamen_. These models were projected into future climate scenarios for 2050. The area of climatic suitability for every _Cyclamen_ species is predicted to decrease. A limited dispersal capacity places them at high risk of extinction. Half of the species are threat ened with extinction due to their potential area loss, indicating that conservation and protection for these species has to be implemented by adding them to the red list.
Tipo: Poster
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3066/version/1

Fuzzy logic as a decision-making support system for the indication of bariatric surgery based on an index (MAFOI) generated by the association between body fat and body mass index.
Provedor de dados: 17
Autores: Susana A. Miyahira; Joao L. M. C. Azevedo; Jos&amp;#xe9;  E. Araujo Filho.
Background: A fuzzy obesity index (MAFOI) for use as an alternative to bariatric surgery indication (BSI) is presented. The search for a more accurate method to evaluate obesity and to indicate a better treatment is important in the world health context. BMI (body mass index) is considered the main criteria for obesity treatment and BSI. Nevertheless, the fat excess related to the percentage of Body Fat (%BF) is actually the principal harmful factor in obesity disease that is usually neglected. This paper presents a new fuzzy mechanism for evaluating obesity by associating BMI with %BF that yields a fuzzy obesity index for obesity evaluation and treatment and allows building up a Fuzzy Decision Support System (FDSS) for BSI. Methods: Seventy-two patients...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5516/version/2

Fuzzy logic as a decision-making support system for the indication of bariatric surgery based on an index (OBESINDEX) generated by the association between body fat and body mass index
Provedor de dados: 17
Autores: Joao L. M. C. Azevedo; Susana A. Miyahira; Lucas P. F. F. Leal; Glicia C. Azevedo; Otavio C. Azevedo; Joao L. C. Azevedo; Gustavo P. S. Miguel.
Background: A Fuzzy Obesity Index (OBESINDEX) for use as an alternative in bariatric surgery indication (BSI) is presented. The search for a more accurate method to evaluate obesity and to indicate a better treatment is important in the world health context. BMI (body mass index) is considered the main criteria for obesity treatment and BSI. Nevertheless, the fat excess related to the percentage of Body Fat (%BF) is actually the principal harmful factor in obesity disease that is usually neglected. This paper presents a new fuzzy mechanism for evaluating obesity by associating BMI with %BF that yields a fuzzy obesity index for obesity evaluation and treatment and allows building up a Fuzzy Decision Support System (FDSS) for...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5516/version/1

GabiPD: Gabi Primary Database - a plant integrative &amp;#x2018;omics&amp;#x2019; database in GABI-FUTURE
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n; Axel Nagel; Robert Wagner; Elke Weber; Birgit Kersten.
GabiPD (&amp;#x22;http://gabi.rzpd.de&amp;#x22;:http://gabi.rzpd.de) was established within GABI-I and further developed in GABI-II and constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high throughput experiments developed by members of the GABI/WPG community. Currently, data from different fronts (genomics, transcriptomics, proteomics, metabolomics) are incorporated in GabiPD, representing 14 different biological species.  Last year GabiPD moved to the Max Planck Institute of Molecular Plant Physiology. In the progressing GABI-FUTURE phase, the GabiPD team has been creating a more integrative data view, expanding the tools and information provided by our well-known GreenCards. Links to different...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1684/version/1

GabiPD: GABI primary database - a plant integrative &amp;#x27;omics&amp;#x27; database
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n; Axel Nagel; Robert Wagner; Jost Neigenfind; Elke Weber; Svenja Diehl; Birgit Kersten.
The GABI Primary Database, GabiPD, was established eight years ago in the frame of the German initiative for Genome Analysis of the Plant Biological System (Genomanalyse im biologischen System Pflanze, GABI), funded by the German Federal Ministry of Education, Research and Technology (BMBF) as well as a number of private enterprise companies. The main goal of GabiPD is to collect, integrate, visualize and link primary information from GABI projects. GabiPD, in contrast to other plant databases constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high-throughput experiments in several plant species. Currently, data from different &amp;#x27;omics&amp;#x27; fronts are incorporated in GabiPD (i.e., genomics,...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2221/version/1

GabiPD: The GABI Primary Database - a plant integrative &amp;#x2018;omics&amp;#x2019; database
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n; Axel Nagel; Jost Neigenfind; Robert Wagner; Rico Basekow; Elke Weber; Bernd  Mueller-Roeber; Svenja Diehl; Birgit Kersten.
The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyse and visualise primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different &amp;#x2018;omics&amp;#x2019; fronts are incorporated (i.e., genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text based retrieval of all data types in GabiPD (e.g., clones, genes, mutant lines). All data...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2210/version/1

Gain-of-function oncogenic mutations in TP53 enhance defined factor-mediated cellular reprogramming
Provedor de dados: 17
Autores: Jeong Ho Moon; Hideshi Ishii; Dyah Laksmi Dewi; Yoshihiro Kano; Kazuyoshi Yamamoto; Shinpei Nishikawa; Yoshiyuki Fujiwara; Yuichiro Doki; Masaki Mori.
Cancer is a disorder with various genetic and epigenetic alterations. Genetic alterations such as mutations, i.e., substitutions, amplifications, and deletions of nucleotide sequences, are largely irreversible, whereas epigenetic alterations can be modified by pharmacological agents that target components of the epigenetic machinery. Recent studies have showed that introduction of defined factors such as those encoded by c-MYC, SOX2, OCT3/4, and KLF4 in normal somatic cells results in their dedifferentiation into induced pluripotent stem (iPS) cells. In addition, we have reported that these iPS factors induce the development of induced multipotent cancer (iPC) cells from gastrointestinal cancer cells by reducing tumor aggressiveness. The efficiency of iPS...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5681/version/1

Gas phase bond dissociation enthalpies and enthalpies of isomerization/reaction for small hydrocarbon combustion related compounds between 300 and 1500 K: A comparison of Gaussian-4 (G4) theoretical values against experimental data
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase calculations at 1 atmosphere pressure between 300 and 1500 K at 200 K intervals were conducted using the Gaussian-4 (G4) composite method level of theory on a representative set of reactions having broad relevance in hydrocarbon combustion chemistry. Reasonable agreement between the experimental and theoretical data was obtained across the temperature range under consideration for all bond dissociation enthalpies, isomerization enthalpies, and enthalpies of reaction. For some reaction schemes, chemical accuracy for the theoretical method was maintained over the complete temperature range, whereas other systems displayed up to several kcal mol^-1^ deviations from experimental data. The direction of signed errors generally increased as the...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5021/version/1

Gas phase bond dissociation enthalpies and enthalpies of isomerization/reaction for small hydrocarbon combustion related compounds between 300 and 1500 K: A comparison of Gaussian-4 (G4) theoretical values against experimental data
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase calculations at 1 atmosphere pressure between 300 and 1500 K at 200 K intervals were conducted using the Gaussian-4 (G4) composite method level of theory on a representative set of reactions having broad relevance in hydrocarbon combustion chemistry. Reasonable agreement between the experimental and theoretical data was obtained across the temperature range under consideration for all bond dissociation enthalpies, isomerization enthalpies, and enthalpies of reaction. For some reaction schemes, chemical accuracy for the theoretical method was maintained over the complete temperature range, whereas other systems displayed up to several kcal mol^-1^ deviations from experimental data. The direction of signed errors generally increased as the...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5021/version/2

Gas phase carbon acidity and correlations with aqueous pK~a~ values: A comparison of B3LYP/6-311++G(d,p), Gaussian-4 (G4), and experimental approaches
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase standard state (298.15 K, 1 atm) calculations were conducted at the B3LYP/6-311++G(d,p) density functional and the Gaussian-4 (G4) composite method levels of theory to estimate the acidity of various carbon acids. Excellent agreement was found between the G4 gas phase enthalpies and free energies of carbon acid dissociation and corresponding experimental values. The B3LYP/6-311++G(d,p) level of theory displayed a significantly lower accuracy for gas phase acidity prediction, but with similar qualitative trends as the G4 calculations. Good correlations using both theoretical methods were found with corresponding carbon acid aqueous pK~a~ values. However, the pK~a~ prediction accuracy of carbon acids based on correlations with theoretical gas phase...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4381/version/1

Gas phase constant pressure heat capacities (C~p,gas~) for the C~1~ through C~10~ straight chain alkanes, isobutane, hydrogen atom, hydroxyl and methyl radicals, and water between 298.15 and 1500 K: A comparison of theoretical values against experimental data
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase constant pressure heat capacities (C~p,gas~) for the C~1~ through C~10~ straight chain alkanes, isobutane, hydrogen atom, hydroxyl and methyl radicals, and water were calculated between 298.15 and 1500 K using various low (semiempirical PM6) through high level (CBS-Q//B3 and G4 composite) theoretical methods. All levels of theory provided good agreement with experimental C~p,gas~ data (&amp;#x3c;+/-10% deviation) regardless of molecular size. A modest but progressive loss of C~p,gas~ predictive accuracy occurs with increasing molecular size among the n-alkanes. For most compounds at all levels of theory, the highest C~p,gas~ estimation accuracy occurs at elevated temperatures, with decreasing accuracy as the temperature is lowered or raised about...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5024/version/1

Gas phase enthalpies of formation for aminonitroacetylene, aminonitromethane, and diaminodinitromethane: A Gaussian-4 (G4) theoretical study
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase (298.15 K, 1 atm) enthalpies of formation were calculated at the Gaussian-4 (G4) level of theory using the atomization energy approach for the proposed high energy materials aminonitroacetylene (284.0 to 285.7 kJ/mol), aminonitromethane (-66.4 to -65.0 kJ/mol), and diaminodinitromethane (-84.0 to -81.6 kJ/mol). The results are in good agreement with prior G2 and G3 level estimates, and should help constrain the actual enthalpies of formation for these potential HEMs.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5467/version/1

Gas phase enthalpies of formation for potential nitro-substituted borazine high energy materials: A G4MP2 and G4 theoretical study
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase (298.15 K, 1 atm) enthalpies of formation ([DELTA]~f~H~(g)~) were calculated at the G4MP2 and G4 levels of theory using the atomization energy approach for various nitro-substituted borazines proposed as high energy materials (HEMs). Modest general agreement was obtained between the G4MP2/G4 atomization energy [DELTA]~f~H~(g)~ estimates and those previously reported using density functional theory methods and homodesmic reaction approaches, with deviations ranging between +9.7 to -56.5 kJ/mol. The results should help constrain the actual enthalpies of formation for these potential HEMs, and suggest the nitroborazines are a particularly challenging case for [DELTA]~f~H~(g)~ calculations using theoretical approaches, requiring high-level composite...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/5580/version/1

Gas phase enthalpies of formation, isomerization, and disproportionation of mono- through tetra-substituted tetrahedranes: A G4MP2/G4 theoretical study
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase (298.15 K, 1 atm) enthalpies of formation (&amp;#x394;~f~H&amp;#xb0;~(g)~), enthalpies of disproportionation to two corresponding acetylene molecules (&amp;#x394;~rxn~H&amp;#xb0;~(g),Td&amp;#x2192;acet~), and enthalpies of isomerization from a tetrahedrane geometry to a 1,3-cyclobutadiene structure (&amp;#x394;~isom~H&amp;#xb0;~(g),Td&amp;#x2192;CBD~) were calculated for the mono- through tetra-substituted hydro, fluoro, chloro, bromo, methyl, ethynyl, and cyano carbon tetrahedrane derivatives at the G4MP2 and G4 levels of theory. All derivatives have endothermic &amp;#x394;~f~H&amp;#xb0;~(g)~ indicative of the cage strain in these systems. In all cases, &amp;#x394;~rxn~H&amp;#xb0;~(g),Td&amp;#x2192;acet~ and...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6421/version/1

Gas phase homolytic bond dissociation enthalpies of common laboratory solvents: A G4 theoretical study
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase standard state (298.15 K, 1 atm) calculations were conducted at the Gaussian-4 (G4) composite method level of theory to estimate the bond dissociation enthalpies (BDEs) of various common laboratory solvents. Excellent agreement was obtained between experimental and G4 estimated BDEs. The current study demonstrates the BDE prediction accuracy of the G4 method, and is also intended to function as a potentially useful resource in any reevaluations of the preferred BDEs for these common laboratory solvents.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4425/version/1

Gas phase hydration, bond dissociation enthalpies, and acidity of aldehydes: A CBS-Q//B3, G4MP2, and G4 theoretical study of substituent effects
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
CBS-Q//B3, G4MP2, and G4 composite method calculations were used to estimate gas phase standard state (298.15 K, 1 atm) free energies of hydration (&amp;#x394;~hydr~G&amp;#xb0;~(g)~), hydration equilibrium constants (log K~hydr,(g)~), bond dissociation enthalpies (BDEs), and enthalpies (&amp;#x394;~d~H&amp;#xb0;~(g)~) and free energies (&amp;#x394;~d~G&amp;#xb0;~(g)~) of aldehydic proton acid dissociation for various substituted aldehydes with electron withdrawing and electron releasing groups. Good quality log K~hydr,(g)~ correlations with the Swain-Lupton resonance effect parameters R and R^+^ were found, allowing extension of the model to predict log K~hydr,(g)~ values for 487 substituted aldehydes having available R-values and 108 substituted aldehydes...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5084/version/1

GENCODE: Creating a Validated Manually Annotated Geneset for the Whole Human Genome
Provedor de dados: 17
Autores: A. Bignell; A. Frankish; B. Aken; M. Diekhans; F. Kokocinski; M. Lin; M. Tress; J. Van Baren; I. Barnes; T. Hunt; D. Carvalho-Silva; C. Davidson; S. Donaldson; J. Gilbert; E. Hart; M. Kay; R. Kinsella; D. Lloyd; J. Loveland; J. E. Mudge; C. Snow; J. Vamathevan; L. Wilming; M. Brent; M. Gerstein; R. Guig&amp;#xf3;; R. Harte; M. Kellis; S. Searle; J. Harrow; T. Hubbard.
The Human and Vertebrate Analysis and Annotation (HAVANA) group at the Wellcome Trust Sanger Institute produced the manually annotated geneset for the Encyclopedia of DNA Elements (ENCODE) pilot project and, as part of the Gencode subgroup, are reprising this role in the scale up to cover the whole human genome. Our manual annotation is checked computationally and validated experimentally. Loci and transcripts predicted to be absent from the initial annotation are identified by comparison with a number of state-of-the-art algorithms for identifying exons, splice sites, transcripts and pseudogenes. Where novel features are confirmed the annotation is updated. Annotated coding transcripts are analysed to assess their coding potential by investigating...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3155/version/1

GenColors: Annotation and comparative genomics made easy
Provedor de dados: 17
Autores: Marius Felder; Alessandro Romualdi; Gernot Gloeckner; Matthias Platzer; Juergen Suehnel.
GenColors is a web-based software/database system initially aimed at an improved and accelerated annotation of prokaryotic genomes making extensive use of genome comparison (Romualdi et al., _Bioinformatics_ 2005; Romualdi et al., _Methods Mol. Biol._ 2007). It offers a seamless integration of data from ongoing sequencing projects and annotated genomic sequences obtained from GenBank. With GenColors dedicated genome browsers containing a group of related genomes can be easily set up and maintained. The tool has been efficiently used for sequenceing and annotating the Borrelia garinii genome and is currently applied to a number of other ongoing genome projects on _Legionella_, _Pseudomonas_ and _E. coli_ genomes. Examples for freely accessible...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3111/version/1

Gender differences in a Drosophila transcriptomic model of chronic pentylenetetrazole induced behavioral deficit
Provedor de dados: 17
Autores: Abhay Sharma; Farhan Mohammad; Priyanka Singh.
A male Drosophila model of locomotor deficit induced by chronic pentylenetetrazole (PTZ), a proconvulsant used to model epileptogenesis in rodents, has recently been described. Antiepileptic drugs (AEDs) ameliorate development of this behavioral abnormality. Time-series of microarray profiling of heads of male flies treated with PTZ has shown epileptogenesis-like transcriptomic perturbation in the fly model. Gender differences are known to exist in neurological and psychiatric conditions including epileptogenesis. We describe here the effects of chronic PTZ in Drosophila females, and compare the results with the male model. As in males, chronic PTZ was found found to cause a decreased climbing speed in females. In males, overrepresentation of Wnt, MAPK,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3460/version/1

Gender Differential in the Association of Body Mass Index and Abdominal Obesity with Prehypertension and Hypertension in Iranian Adults
Provedor de dados: 17
Autores: Mohsen  Janghorbani; Masoud  Amini; Mohammad Mehdi Gouya; Alireza Delavari; Siamak Alikhani; Alireza Mahdavi.
*Objective:* The aim of this study was to determine the gender differential in the relationship of body mass index (BMI) and abdominal obesity with blood pressure (BP) and prevalence of hypertension (HTN) and prehypertension (Pre-HTN) among the adult population of Iran.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Design:* A nationwide cross-sectional survey was conducted from December 2004 to February 2005. The selection was conducted by stratified probability cluster sampling through household family members in Iran.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Subjects and Measurements:* Weight, height, waist circumference (WC), and systolic and diastolic BP of 45,082 men and 44,322 women aged 15-65 (mean 39.2) were measured....
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1829/version/1

Gender effects on cytidine analogue metabolism and myelodysplastic syndrome treatment outcomes
Provedor de dados: 17
Autores: Reda Mahfouz; Ania Jankowska; Quteba Ebrahem; Zhenbo Hu; Pramod Terse; Joseph Covey; Kenneth Chan; Yonghua Ling; Kory Engelke; Mikkael Sekeres; Ramon Tiu; Jaroslaw Maciejewski; Tomas Radivoyevitch; Yogen Saunthararajah.
In vivo, half-lives of cytidine analogues such as 5-azacytidine and decitabine, used to treat myelodysplastic syndromes (MDS), are determined largely by cytidine deaminase (CDA), an enzyme that rapidly metabolizes these drugs into inactive uridine counterparts. Genetic factors influence CDA activity, and hence, could impact 5-azacytidine/decitabine levels and efficacy, a possibility requiring evaluation. Using an HPLC assay, plasma CDA activity was confirmed to be decreased in individuals with the CDA SNP A79C. More interestingly, there was an even larger decrease in females. Explaining the decrease in enzyme activity, liver CDA expression was significantly lower in female versus male mice. As expected, decitabine plasma levels, measured by...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6971/version/1

Gene and Pathway-Based Analysis: Second Wave of Genome-wide Association Studies
Provedor de dados: 17
Autores: Gang Peng; Li Luo; H1oicheong Siu; Yun Zhu; Pengfei Hu; Shengjun Hong; Jinying Zhao; Xiaodong Zhou; John D. Reveille; Li Jin; Christopher I. Amos; Momiao Xiong.
Despite great success of GWAS in identification of common genetic variants associated with complex diseases, the current GWAS have focused on single SNP analysis. However, single SNP analysis often identifies a number of the most significant SNPs that account for only a small proportion of the genetic variants and offers limited understanding of complex diseases. To overcome these limitations, we propose gene and pathway-based association analysis as a new paradigm for GWAS. As a proof of concept, we performed a comprehensive gene and pathway-based association analysis for thirteen published GWAS. Our results showed that the proposed new paradigm for GWAS not only identified the genes that include significant SNPs found by single SNP analysis, but also...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2068/version/1

Gene Curation Software at the Rat Genome Database (RGD)
Provedor de dados: 17
Autores: Stanley J. F. Laulederkind; Mary  Shimoyama; Brad Taylor; Victoria  Petri; Timothy F. Lowry; G. Thomas Hayman; Shur-Jen Wang; Jennifer R. Smith; Rajni Nigam; Jeff De Pons; Weisong Liu; George Kowalski; Melinda R. Dwinell; Diane H. Munzenmaier; Howard J. Jacob.
At model organism databases data is curated for numerous biological categories using various ontologies and vocabularies.  The Rat Genome Database (RGD) uses four different ontologies to standardize annotation information for genes and their associations with disease, phenotypes, and pathways. For manual gene curation this is all done in a single user interface of a web-based annotation tool developed at RGD.  The same interface can be used for the curation of QTLs and strains. The development of the tool has been achieved through a collaboration of curators and software developers.  Features have been tailored to the needs of the curators to allow optimum efficiency of the data entry portion of the curation process.  Annotations using the Gene Ontology,...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5058/version/1

Gene diversity among some endogamous population of Amravati District, Maharashtra, India.
Provedor de dados: 17
Autores: Rupali P. Tekade; Nandkishor E. Warghat; M. M. Baig.
The present work deals with the distribution of ABO, Rh and sickling alleles as markers to study the genetic structure and micro-demarcation among castes and tribal populations from the Amravati district of Maharashtra. Three loci namely, ABO, Rh and sickling were selected to measure the relative frequency of respective alleles in ten (10) endogamous populations inhabiting the Amravati District. The ABO locus was found to be less polymorphic when compared with other loci. On the other hand, Rh and sickling loci were found to be more polymorphic. Construction of a dendrogram using allele frequency data reveals an interesting relationship among the caste and tribe. An analysis shows three major clades comprising A, B and C. Clade A comprises Islamic Dawoodi...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5379/version/1

Gene Expression Profiling of the Hepatic Transcriptome in Presence of TNF-alpha
Provedor de dados: 17
Autores: Amit Kumar Pandey; Neha Munjal; Malabika  Datta.
Diabetes mellitus, often simply termed Diabetes, is a syndrome characterized by disordered metabolism and high blood sugar. It is caused due to low levels of insulin hormone or from abnormal resistance to insulin in its target tissues. World Health Organization estimates that India will alone have 79.4 million diabetic patients in 2030. One of its major form Type 2 diabetes, is often associated with obesity, hypertension, elevated cholesterol and metabolic syndrome. Changes in life style, such as consumption of high-calorie diet and lack of exercise, have increased the global prevalence not only of diabetes but also of obesity. Type 2 diabetes is characterized by insulin resistance in target tissue, occurs due to several reasons and one of them being the...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2527/version/1

Gene therapy of hypoparathyroidism with TheraCyte-encapsulated stem cells
Provedor de dados: 17
Autores: Fong Choulu; Shun-Chen Huang; Kun-Chou Hsieh; Shun-Yu Chi; Pei-Hua Hung; Feng-Sheng Wang.
The parathyroid hormone (PTH) (1-34) gene was inserted into a pcDNA3 promoter and E. coli competent cells were used to amplify the cDNA. C3H/10T1/2 stem cells were transfected with PTH (1-34) cDNA using Lipofectamine reagents. After G418 treatment live cells at a density of 4x107 were loaded onto a TheraCyte unit. After parathyroidectomy, rats were either the implanted with 4x107 TheraCyte-encapsulated cells (group A), subcutaneously injected with 4x107 live cells containing PTH (1-34) cDNA (group B) or injected with nothing (group C).Serum levels of calcium, phosphorus and PTH (1-34) were measured at baseline, 1 month, 2 months, 3 months and 4 months after therapy. Immunohistochemical staining and RT-PCR were performed to find PTH (1-34)-positive cells...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/4534/version/1

Gene Transfer of Calcitonin Gene-Related Peptide Inhibits Macrophages and Inflammatory Mediators in Vein Graft Disease
Provedor de dados: 17
Autores: Xiaoning Zhang; Jian Zhuang; Hongsui Wu; Zhihong Chen; Jian Su; Shiliang Chen; Jianguang Chen; Yuhui Zheng; Huanxin Yang.
Vein graft disease is a chronic inflammatory disease and limits the late results of coronary revascularization. Calcitonin gene-related peptide (CGRP) inhibits macrophages infiltrated and inflammatory mediators, we hypothesized that transfected CGRP gene inhibits macrophages infiltrated and inflammatory mediators in vein graft disease. Autologous rabbit jugular vein grafts were incubated ex vivo in a solution of mosaic adeno-associated virus vectors containing CGRP gene (AAV2/1.CGRP) &amp;#x3001;escherichia coli lac Z gene (AAV2/1.LacZ) or saline and then interposed in the carotid artery. Intima/media ratio were evaluated at postoperative 4 weeks, Macrophages were marked with CD68 antibody by immunocytochemistry. Inflammatory mediators were mensurated with...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2456/version/1

Gene tree reconciliation: new developments in Bayesian concordance analysis with BUCKy
Provedor de dados: 17
Autores: C&amp;#xe9;cile An&amp;#xe9;; Colin N. Dewey; Satish K. Kotha; Bret R. Larget.
When phylogenetic trees inferred from different genes are incongruent, several methods are available to reconcile gene trees and extract the shared phylogenetic information from the sequence data. Bayesian Concordance Analysis, implemented in BUCKy, aims to extract the vertical signal and to infer clusters of genes that share the same tree topology. The new version of BUCKy includes a quartet-based estimate of the species tree with branch lengths in coalescent units.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4625/version/1

Gene-Environment Interaction: Definitions and Study Designs
Provedor de dados: 17
Autores: Ruth Ottman.
Dr. Ruth Ottman first discussed different models of gene-environment interactions and then delved into designs of studies attempting to elucidate such interactions.  She stressed the importance of using the correct measurement scale, whether additive or multiplicative, noting that the additive measurement scale is more consistent with biological models.  Dr. Ottman concluded by reminding the audience of the need for very large sample sizes, and thus collaboration, in gene-environment interaction studies. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To watch Dr. Ottman&amp;#x2019;s presentation, please see the Panel 2 &amp;#x22;Google Video posting.&amp;#x22;:http://video.google.com/videoplay?docid=-8804321603731619003&amp;#x26;hl=en &amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2653/version/1

General updates about SBML and SBML Team activities
Provedor de dados: 17
Autores: Michael Hucka.
In this presentation, I summarize very briefly some recent updates to SBML.org, SBML development, and software from the SBML Team.
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6345/version/1

Generalised and abdominal adiposity are important risk factors for chronic disease in older people: results from a nationally representative survey
Provedor de dados: 17
Autores: Vasant Hirani.
Objective: To look at the trends in prevalence of generalised (body mass index (BMI)&amp;#x2265; 25 kg/m2) and abdominal obesity (waist circumference (WC) &amp;#x3e;102cm, men; &amp;#x3e;88cm, women) among older people from 1993 to 2008, prevalence of chronic disease by overweight/obesity and waist circumference categories in England 2005 and evaluate the association of these measures with chronic diseases. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: Analyses of nationally representative cross-sectional population surveys, the Health Survey for England (HSE), including non-institutionalised men and women aged &amp;#x2265;65years.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: Generalised obesity and abdominal obesity increased among men and women from 1993...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4515/version/1

Generalized Theory of Life
Provedor de dados: 17
Autores: Vyacheslav L. Kalmykov.
The paper is mathematically, physically and biologically inspired - it is a deductive attempt of the biologist to find the most appropriate language for modelling of life. Applications of mathematical structures - groupoids, groups, categories, functors and monads, which are the most effective for the description of the complex objects, are discussed. Some new conceptions and interpretations were introduced: unified classification of complex systems; the generalized conception about stationary states of any autonomous agent (&amp;#x22;Statology&amp;#x22;); the total quantitative criterions of evolutionary direction; the generalized group of symmetry. The definitions of information, entropy, organization, behavior, evolution, creation, life, culture,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7108/version/1

Generalized time-frequency coherency for assessing neural interactions in electrophysiological recordings
Provedor de dados: 17
Autores: Saeid Mehrkanoon; Michael  Breakspear; Andreas Daffertshofer; Tjeerd W. Boonstra.
Time-frequency coherence has been widely used to quantify statistical dependencies in bivariate data and has proven to be vital for the study of neural interactions in electrophysiological recordings. Conventional methods establish time-frequency coherence by smoothing the cross and power spectra using identical smoothing procedures. Smoothing entails a trade-off between time-frequency resolution and statistical consistency and is critical for detecting instantaneous coherence in single-trial data. Here, we propose a generalized method to estimate time-frequency coherency by using different smoothing procedures for the cross spectra versus power spectra. This novel method has an improved trade-off between time resolution and statistical consistency...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6615/version/1

Generating descriptive text from functional brain images
Provedor de dados: 17
Autores: Francisco Pereira; Greg Detre; Matthew Botvinick.
Recent work has shown that it is possible to take brain images of a subject acquired while they saw a scene and reconstruct an approximation of that scene from the images. Here we show that it is also possible to generate _text_ from brain images. We began with images collected as participants read names of objects (e.g., ``Apartment&amp;#x27;). Without accessing information about the object viewed for an individual image, we were able to generate from it a collection of semantically pertinent words (e.g., &amp;#x22;door,&amp;#x22; &amp;#x22;window&amp;#x22;). Across images, the sets of words generated overlapped consistently with those contained in articles about the relevant concepts from the online encyclopedia Wikipedia. The technique described, if...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5666/version/1

Generating Homology Relationships by Alignment of Anatomical Ontologies
Provedor de dados: 17
Autores: Frederic B. Bastian; Gilles Parmentier; Marc Robinson-Rechavi.
The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we aim to establish homology relations between ontologies describing different species. We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. These relationships and the Homolonto software are available at &amp;#x22;http://bgee.unil.ch/.&amp;#x22;:http://bgee.unil.ch/
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3547/version/1

Generating Homology Relationships by Alignment of Anatomical Ontologies
Provedor de dados: 17
Autores: Frederic Bastian; Gilles Parmentier; Marc Robinson-Rechavi.
The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we aim to establish homology relations between ontologies describing different species. We present a new algorithm, and its implementation in the software Homolonto, to create new relationships between anatomical ontologies, based on the homology concept. These relationships and the Homolonto software are available at &amp;#x22;http://bgee.unil.ch/&amp;#x22;:http://bgee.unil.ch/
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3546/version/1

Generation of &amp;#x22;backbone&amp;#x22; free, low transgene copy plants by launching T-DNA from the _Agrobacterium_ chromosome
Provedor de dados: 17
Autores: Heiko Oltmanns; Bronwyn Frame; Lan-Ying Lee; Susan Johnson; Bo Li; Kan Wang; Stanton Gelvin.
In both applied and basic research, _Agrobacterium_-mediated transformation is commonly used to introduce genes into plants. We investigated the effect of three _Agrobacterium tumefaciens_ strains and five T-DNA origins of replication on transformation frequency, transgene copy number, and the frequency of integration of non-T-DNA portions of the T-DNA-containing vector (&amp;#x22;backbone&amp;#x22;) into the genome of _Arabidopsis thaliana_ and _Zea mays_. Launching T-DNA from the _picA_ locus of the _Agrobacterium_ chromosome increases the frequency of single transgene integration events and almost eliminates the presence of vector backbone sequences in transgenic plants. Along with novel _Agrobacterium_ strains we have developed, our findings are useful...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3497/version/1

Generation of directional selectivity by individual thin dendrites in neocortical pyramidal neurons
Provedor de dados: 17
Autores: Guy Major.
Patterned 2-photon glutamate uncaging and local GABA iontophoresis were used to test, in brain slices, whether basal and oblique dendrites possess the biophysical machinery to contribute to the directional selectivity exhibited by many sensory neocortical neurons. On average, Distal-to-Proximal (DP) sequences of glutamate stimuli along individual dendrites produced ~1.5-fold larger responses than the same stimuli in reverse order (PD). Proximal inhibition consistent with spatially-offset receptive subfields, preceding PD but following DP sequences, enhanced directionality to ~2.1-fold.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4654/version/1

Generation of Human Epidermis-Derived Mesenchymal Stem Cell-like Pluripotent Cells and their reprogramming in mouse chimeras
Provedor de dados: 17
Autores: Bing Huang; KaiJing Li; Jie Yu; Min Zhang; YongPing Li; XiaoPing Xu; Ting Luo; JianFa Huang; LiPing Guan; WeiHua Li; WenXin Zhang; ShaoChun Lin; XinTao Huang; LiPing Lin; YongLiang Lin; YiChi Zhang; WenCong Wang; ZhiChong Wang; QianYing Gao; XiGu Chen; XinMing Song; Jian Ge.
Stem cells can be derived from the embryo (embryonic stem cells, ESCs), from adult tissues (adult stem cells, ASCs), and by induction of fibroblasts (induced pluripotent stem cells, iPSs). Ethical problems, immunological rejection, and difficulties in obtaining human tissues limit the use of ESCs in clinical medicine. Induced pluripotent stem cells are difficult to maintain in vitro and carry a greater risk of tumor formation. Furthermore, the complexity of maintenance and propagation is especially difficult in the clinic. Adult stem cells can be isolated from several adult tissues and present the possibility of self-transplantation for the clinical treatment of a variety of human diseases. Recently, several ASCs have been successfully isolated and...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/6016/version/1

Genes of the serotonergic and dopaminergic pathways and their interaction affect the expression of Behavioural and Psychological Symptoms in Dementia (BPSD).
Provedor de dados: 17
Autores: Petroula Proitsi; Michelle Lupton; Suzanne Reeves; Gillian Hamilton; Nicola Archer; Belinda Martin; Paul hollingworth; Brian Lawlord; Michael Gill; Michael J. Owen; Julie Williams; Simon Lovestone; John Powell.
Although there is evidence for the involvement of genes of serotonergic and dopaminergic systems in the manifestation of the Behavioural and Psychological Symptoms in Dementia (BPSD), genetic association studies are contradictory. We used 1008 probable AD patients from the UK and applied a Multiple Indicators Multiple Causes (MIMIC) approach to investigate the effect of 11 polymorphisms in the serotonergic and dopaminergic systems, on four behavioural sub-phenotypes, namely &amp;#x22;psychosis&amp;#x22;,&amp;#x22; moods&amp;#x22;, &amp;#x22;agitation&amp;#x22; and &amp;#x22;behavioural dyscontrol&amp;#x22;, as well as on 12 NPI items. Significant findings included the association of DRD1 A48G with &amp;#x22;psychosis&amp;#x22; (p=0.037), the association of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3896/version/1

Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks
Provedor de dados: 17
Autores: Avi Ma&amp;#x27;ayan.
In recent years, in-silico literature-based mammalian protein-protein interaction network datasets have been developed. These datasets contain binary interactions extracted manually from legacy experimental biomedical research literature. Placing lists of genes or proteins identified as significantly changing in multivariate experiments, in the context of background knowledge about binary interactions, can be used to place these genes or proteins in the context of pathways and protein complexes.&amp;#xd;&amp;#xa;Genes2Networks is a software system that integrates the content of ten mammalian literature-based interaction network datasets. Filtering to prune low-confidence interactions was implemented. Genes2Networks is delivered as a web-based service using...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/35/version/1

Genes2Networks: Connecting Lists of Proteins by Using Background Literature-based Mammalian Networks
Provedor de dados: 17
Autores: Jeremy I. Posner; Seth Berger; Avi M. Ma&amp;#x27;ayan.
In recent years, in-silico literature-based mammalian protein-protein interaction network datasets have been developed. These datasets contain binary interactions extracted manually from legacy experimental biomedical research literature. Placing lists of genes or proteins identified as significantly changing in multivariate experiments, in the context of background knowledge about binary interactions, can be used to place these genes or proteins in the context of pathways and protein complexes.&amp;#xd;&amp;#xa;Genes2Networks is a software system that integrates the content of ten mammalian literature-based interaction network datasets. Filtering to prune low-confidence interactions was implemented. Genes2Networks is delivered as a web-based service using...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/35/version/2

Genetic Analysis of ABO and Rh Blood Groups in Brahmin Population of Uttar Pradesh, India&amp;#x201d;
Provedor de dados: 17
Autores: Vandana V. Rai.
A series of glycoprotein and glycolipids on the red blood cell surface constitute blood group antigens. These are A, B, AB and O in ABO blood group system and Rh in rhesus blood group system. These antigens are genetically controlled. Certain diseases have been shown to be associated with certain blood groups. In the present study an attempt is made to study the distribution of ABO and Rh. (D) blood group systems among the Brahmin caste population of Uttar Pradesh State. A total of 200 unrelated Brahmin individuals from Uttar Pradesh were studied for the phenotype and allele frequency distribution of ABO and Rh (D) blood groups. The order of occurrence of ABO phenotypes is B&amp;#x3e;O&amp;#x3e;A&amp;#x3e;AB. The corresponding allele frequencies of O, A,...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/5931/version/1

Genetic and Immune Predictors for Hypersensitivity Syndrome to Antiepileptic Drugs
Provedor de dados: 17
Autores: Manuela G. Neuman; Radu M. Nanau; Lawrence Cohen; Paul A. Hwang.
Hypersensitivity syndrome reactions (HSR) to antiepileptic drugs (AED) are associated with severe clinical cutaneous adverse reactions (SCAR).Our aims are: to assess HSRs to AEDs using the in vitro lymphocyte toxicity assay (LTA) in patients who manifested HSRs clinically, to correlate LTA results with the clinical syndrome, to correlate LTA results with the human leukocyte antigen (HLA) allele B*1502 (HLA-B*1502) positivity in a Han Chinese-Canadian population, and to determine the cytokine network in this population. HSR patients developed fever and cutaneous eruptions in the presence or absence of organ involvement within 8 weeks of exposure to carbamazepine (CBZ), phenytoin (PHY) or lamotrigine (LTG). Control patients received AEDs without presenting...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Immunology; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6477/version/1

Genetic differentiation of wild and managed _Coffea arabica_ populations in Afromontane rainforest fragments in SW Ethiopia
Provedor de dados: 17
Autores: Raf Aerts; Gezahegn Berecha; Pieter Gijbels; Sabine Van Glabeke; Katrien Vandepitte; Bart Muys; Isabel Rold&amp;#xe1;n-Ruiz; Olivier Honnay.
*1.*  _Coffea arabica_ L. has its origin and centre of diversity in the Afromontane rainforests of southwestern Ethiopia.  Deforestation, habitat fragmentation and forest degradation threaten this wild coffee gene pool, which is vital to global coffee cultivation.&amp;#xd;&amp;#xa;*2.*  We investigated genetic variation and diversity within and between eleven coffee stands across a gradient of increasing forest management intensity (&amp;#x2018;forest coffee&amp;#x2019;, unmanaged large continuous forest vs. &amp;#x2018;semi-forest coffee&amp;#x2019;, managed, small fragments) using two multiplex panels of five microsatellite markers each.  We used analysis of molecular variance (AMOVA) to partition total genetic diversity and applied a Bayesian...
Tipo: Presentation
Palavras-chave: Ecology; Genetics &amp; Genomics; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5870/version/1

Genetic incorporation of D-Lysine into diketoreductase in Escherichia coli cells
Provedor de dados: 17
Autores: Zhi Zhi Liu; Xin Yang; Denghuan Yi; Shuzhen Wang; Yijun Chen.
D-Lysine has been genetically introduced into diketoreductase in E. coli cells by utilization of an orthogonal Ph tRNA /Lysyl-tRNA synthetase pair. This is the first report on the genetic incoporation of D-amino acids into proteins, which may be generally applicable to a wide variety of applications.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Microbiology; Molecular Cell Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6777/version/1

Genetic Normalization of Differentiating Aneuploid Human Embryos
Provedor de dados: 17
Autores: Paul Brezina; Andrew Barker; Andrew Benner; Ric Ross; Khanh-Ha Nguyen; Raymond Anchan; Kevin Richter; Garry Cutting; William Kearns.
Early embryogenesis involves a series of dynamic processes, many of which are currently not well described or understood. Aneuploidy and aneuploid mosaicism, a mixture of aneuploid and euploid cells within one embryo, in early embryonic development are principal causes of developmental failure.^1,2^ Here we show that human embryos demonstrate a significant rate of genetic correction of aneuploidy, or &amp;#x22;genetic normalization&amp;#x22; when cultured from the cleavage stage on day 3 (Cleavage) to the blastocyst stage on day 5 (Blastocyst) using routine in vitro fertilization (IVF) laboratory conditions. One hundred and twenty-six human Cleavage stage embryos were evaluated for clinically indicated preimplantation genetic screening (PGS). Sixty-four of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6045/version/1

Genetic similarity promotes evolution of cooperation under lethal intergroup competition
Provedor de dados: 17
Autores: Oleg Smirnov; John Orbell.
Altruism (helping others at a cost to oneself) may evolve via group selection if the cost of altruism to the individual is compensated for by growth differences among groups when (1) there is high genetic variation among members of different groups; (2) more altruistic groups grow faster and (3) between-group migration is low. Nevertheless, group selection may not fully explain the actual evolution of helping behaviour if between-group migration was sufficiently common to have reduced between-group genetic variance. Lethal intergroup competition, which amplifies such growth differences between groups, appears to have been frequent in humans&amp;#x27;; ancestral environments and could bear importantly on the evolution of altruism. Here we show that...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1710/version/1

Genetic variability among _Coleus sp_ studied by RAPD banding pattern analysis
Provedor de dados: 17
Autores: Muthusamy Govarthanan; Arunapriya S; Guruchandar A; Selvankumar T; Gnanasekaran N; Manoharan Koildhasan.
Genetic improvement of the medicinal plants depends upon the existence, nature and extent of the genetic variability available for manipulation. Genetic analysis with RAPD markers has been extensively used to determine genetic diversity among _Coleus sp_ and to identify the best quality for human consumption for its medicinal purpose. The objectives of the present study were to assess molecular variation among _C.amboinicus_, _C.aromaticus_ and _C.forskohlii_. and to determine the level of genetic similarity among them. We performed random amplification of polymorphic DNA (RAPD) analysis on three strains of _Coleus sp_. Random primers were used for the PCR. Electrophoresis on denaturing acrylamide gels improved RAPD reproducibility and increased the band...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/5631/version/1

Genetic vehicle comprising majority of lowly expressed genes guides cell fate decision
Provedor de dados: 17
Autores: Masa Tsuchiya; Vincent Piras; Masaru Tomita; Alessandro Giuliani; Kumar Selvarajoo.
Cells remarkably take a specific differentiation path among the multiple possibilities that can arise through the multi-dimensional regulation of genome activities. Such deterministic processes suggest the existence of cellular attractors.  However, the origins and drivers of the attractors still remain elusive. Here we analyzed the temporal neutrophil differentiation microarray data for two different stimuli, dimethyl sulfoxide (DMSO) and all-trans-retinoic acid (atRA), and expressed their collective dynamics by temporal Pearson correlation and mutual information coordinates. We constructed ensemble of the genes which showed reduction of correlation fluctuations following the inverse square root law. Evaluating their temporal probability density...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4401/version/1

Genetically modified Cotton species detection by LISS-III satellite data
Provedor de dados: 17
Autores: Saumitra Mukherjee; Satyanarayan  Shashtri; Chander  Kumar Singh; Bindu  Kumari; Reena  Kumari; Ram  Avatar; Anita  Mukherjee; Bhoop  Singh.
It is possible to infer the genetically modified species by using remotely sensed data. Using ERDAS software the algorithm of BT (Bacillus thuringiensis) Cotton in Punjab, India was developed successfully. GPS enabled space technology has the potential to identify the exact location of Bt Cotton by generating Normalized Difference Vegetation Index (NDVI) for the calculation of total area covered by this species. It was possible to develop a correlation in between genetically modified Cotton crop and NDVI value. In parts of Bhatinda district of Punjab the yield of Bt Cotton and NDVI showing R2 value of more than 4.5 in regression analysis. A correlation matrix was also generated which shows that NDVI values of BT cotton has reasonably acceptable correlation...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2659/version/1

Genetically modified Cotton species detection by LISS-III satellite data
Provedor de dados: 17
Autores: Saumitra Mukherjee; Satyanarayan Shashtri; Chander Kumar  Singh; Bindu  Kumari; Reena Kumari; Ram  Avatar; Amit  Singh; Anita  Mukherjee; Bhoop  Singh.
It is possible to infer the genetically modified species by using remotely sensed data. Using ERDAS software the algorithm of BT (Bacillus thuringiensis) Cotton in Punjab, India was developed successfully. GPS enabled space technology has the potential to identify the exact location of Bt Cotton by generating Normalized Difference Vegetation Index (NDVI) for the calculation of total area covered by this species. It was possible to develop a correlation in between genetically modified Cotton crop and NDVI value. In parts of Bhatinda district of Punjab the yield of Bt Cotton and NDVI showing R2 value of more than 4.5 in regression analysis. A correlation matrix was also generated which shows that NDVI values of BT cotton has reasonably acceptable correlation...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2659/version/2

Genetically modified Cotton species detection by LISS-III satellite data
Provedor de dados: 17
Autores: Saumitra Mukherjee; Satyanarayan Shashtri; Chander Kumar  Singh; Bindu  Kumari; Reena Kumari; Ram  Avatar; Amit  Singh; Anita  Mukherjee; Bhoop  Singh.
It is possible to infer the genetically modified species by using remotely sensed data. Using ERDAS software the algorithm of BT (Bacillus thuringiensis) Cotton in Punjab, India was developed successfully. GPS enabled space technology has the potential to identify the exact location of Bt Cotton by generating Normalized Difference Vegetation Index (NDVI) for the calculation of total area covered by this species. It was possible to develop a correlation in between genetically modified Cotton crop and NDVI value. In parts of Bhatinda district of Punjab the yield of Bt Cotton and NDVI showed R2 value of more than 4.5 in regression analysis. A correlation matrix was also generated which shows that NDVI values of BT cotton also has reasonably acceptable...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/2659/version/3

Genome activity profiling of monomeric-IgE and Fc-epsilon-RI-aggregation on human mast cells reveals a complex network of genes involved in inflammatory responses.
Provedor de dados: 17
Autores: Jayapal J. Manikandan; Alirio Jose P. N. Melendez; Peter Natesan A. J. Pushparaj.
Mast cell activation, mediates type-1 allergic responses, one of the most powerful reactions of the immune system. However, mast cells activation is becoming increasingly linked to inflammatory, autoimmunity, and to adaptive immunity by regulating T-cell activation.&amp;#xd;&amp;#xa;Here we analyzed the gene expression pattern in IgE-sensitized and Fc&amp;#x3b5;RI aggregation on human mast cells. Our data revealed coordinated changes in gene expression. We observed increased expression of gene-transcripts involved in allergic, innate and adaptive&amp;#xd;&amp;#xa;immune responses. Among the most prominent findings is the increased expression of transcripts encoding for MIP3a, SPARCL1, AREG, IL18, CCL1, TNFRSF9, IL1b, CX3CR1, PTGER3, MIF, MMP12, ADORA3,...
Tipo: Poster
Palavras-chave: Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1150/version/1

Genome Network Project: An Integrated Genomic Platform
Provedor de dados: 17
Autores: Jose C. Clemente; So Nakagawa; Kazuho Ikeo; Takashi Gojobori.
With the objective of elucidating the structure of gene interactions in the human genome, the Genome Network Project has generated a vast quantity of experimental data, mainly focusing on transcriptional control and transcription-factor related protein-protein interactions (PPI). This data has been collected and organized into the Genome Network Platform (&amp;#x22;http://genomenetwork.nig.ac.jp/&amp;#x22;:http://genomenetwork.nig.ac.jp/) at the National Institute of Genetics. Expression data was obtained through CAGE (Cap Analysis Gene Expression), qRT-PCR, tiling array, microarray and short RNA analysis, while PPI information was gathered through yeast two hybrid (Y2H), mammalian two hybrid (M2H) and _in vitro_ virus (IVV) methods. The Genome Network...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3180/version/1

Genome Replikin Count Predicts Increased Infectivity/Lethality of Viruses
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
The genomes of all groups of viruses whose sequences are listed on Pubmed, specimens since 1918, analyzed by a software from Bioradar UK Ltd., contain Replikins which range in concentration from a Replikin Count (number of Replikins per 100 amino acids) of less than 1 to 30 (see accompanying communications for higher Counts in tuberculosis, malaria, and cancer, associated with higher lethality). Counts of less than 4.0 were found in &amp;#x2018;resting&amp;#x2019; virus states; Counts greater than 4.0, found to be associated with rapid replication, were found invariably to accompany or to predict virus outbreaks, by as much as two years, in viral hosts examined from salmon, to birds, to livestock, to humans. X-ray diffraction showed Replikins to be on the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7144/version/1

Genome Replikin Count Predicts Increased Lethality of Cancer
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
Those cancers, like thyroid and pancreatic cancer, with the lowest 5-year mortality rates, have Replikin Counts of about 20; lung and brain cancers, with the highest 5-year mortality rates, have Replikin Counts of 275 and 325 respectively; the others fall in between with approximate linearity. This is the first quantitative relationship of a genomic structure, Replikins, to 5-year mortality rates.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7143/version/1

Genome Replikin Count Predicts Increased Lethality of Resistant Tuberculosis
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
The genomic Replikin Count of all the sequences  on Pubmed of different strains of tuberculosis were analyzed. The lowest Counts occurred with species within the lowest drug resistance, the highest Counts with sequences of the highest drug resistance and lethality.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7141/version/1

Genome sequence and genetic linkage analysis of Shiitake mushroom _Lentinula edodes_
Provedor de dados: 17
Autores: Hoi Shan Kwan; Chun Hang Au; Man Chun Wong; Jing Qin; Iris Sze Wai Kwok; Winnie Wing Yan Chum; Pui Ying Yip; Kin Sing Wong; Lei Li; Qian Li Huang; Wen Yan Nong.
_Lentinula edodes_ (Shiitake/Xianggu) is an important cultivated mushroom. Understanding the genomics and functional genomics of _L. edodes_ allows us to improve its cultivation and quality. Genome sequence is a key to develop molecular genetic markers for breeding and genetic manipulation. We sequenced the genome of _L. edodes_ monokaryon L54A using Roche 454 and ABI SOLiD genome sequencing. Sequencing reads of about 1400Mb were de novo assembled into a 40.2 Mb genome sequence. We compiled the genome sequence into a searchable database with which we have been annotating the genes and analyzing the metabolic pathways. In addition, we have been using many molecular techniques to analyze genes differentially expressed during development. Gene ortholog groups...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics.
Ano: 2012
URL: http://precedings.nature.com/documents/6855/version/1

Genome Structural-Functional Peculiarities Affecting Plant Epigenetic Variability and Evolution
Provedor de dados: 17
Autores: Evgenii  Levites.
There is an attempt to explain some evolutionary processes in plants such as saltatory changes on the base of multidimensionality of plant inherited information coding. According to the suggested hypothesis, inherited information is coded by not only a nucleotide sequence but also by chromosome differential endoreduplication. It is supposed that chromosomes compete among each other for the contact with the nuclear membrane, but a change in the endoreduplication degree of various chromosome sites can result in a change of  a competition ability for the contact with a nuclear membrane. A simultaneous increase of chromosome endoreduplication degree of many sites can lead to an increase of nuclear membrane surface and to a change in chromosome competitive...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Plant Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4405/version/1

Genome-scale approach proves that the lungfish-coelacanth sister group is the closest living relative of tetrapods with the BEST program
Provedor de dados: 17
Autores: Yunfeng Y. S. Shan; Robin Gras.
The origin of tetrapods has not been resolved for decades. Three principal hypotheses (lungfish-tetrapod, coelacanth-tetrapod, or lungfish-coelacanth sister group) have been proposed. We used the Bayesian method under the coalescence model with the latest program (BEST) to perform a phylogenetic analysis for seven relevant taxa and 43 nuclear genes encoding amino acid residues with the jackknife method for taxon sub-sampling. The results, combined with those of other three genome-scale approaches, successfully prove the hypothesis that lungfishes and coelacanths form a monophyletic sister group and are equally related to tetrapods supported by high Bayesian posterior probabilities of the branch (a lungfish-coelacanth clade) and high taxon jackknife supports.
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3865/version/1

Genome-wide analysis to predict protein sequence variations that change phosphorylation sites or their corresponding kinases
Provedor de dados: 17
Autores: Gil-Mi Ryu; Pamela Song; Kyu-Won Kim; Kyung-Soo Oh; Jong Hun Kim.
We define phosphovariants as genetic variations that change phosphorylation sites or their interacting kinases. Considering the essential role of phosphorylation in protein functions, it is highly likely that phosphovariants change protein functions and may constitute a proportion of the mechanisms by which genetic variations cause individual differences or diseases. We categorized phosphovariants into three subtypes and developed a system that predicts them. Our method can be used to screen important polymorphisms and help to identify the mechanisms of genetic diseases.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2079/version/1

Genome-wide association study identifies _FUT8_ and _ESR2_ as co-regulators of a bi-antennary N-linked glycan A2 (GlcNAc~2~Man~3~GlcNAc~2~) in human plasma proteins
Provedor de dados: 17
Autores: Gordan Lauc; Jennifer Huffman; Caroline Hayward; Ana Knezevic; Ozren Polasek; Olga Gornik; Veronique Vitart; Ivana Kolcic; Zrinka Biloglav; Lina Zgaga; Nicholas D. Hastie; Alan F. Wright; Harry Campbell; Pauline M. Rudd; Igor Rudan.
HPLC analysis of N-glycans quantified levels of the biantennary glycan (A2) in plasma proteins of 924 individuals. Subsequent genome-wide association study (GWAS) using 317,503 single nucleotide polymorphysms (SNP) identified two genetic loci influencing variation in A2: FUT 8 and ESR2. We demonstrate that human glycans are amenable to GWAS and their genetic regulation shows sex-specific effects with _FUT 8_ variants explaining 17.3% of the variance in pre-menopausal women, while _ESR2_ variants explained 6.0% of the variance in post-menopausal women.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2864/version/1

Genome-wide comparison of cyanobacterial transposable elements, potential genetic diversity indicators
Provedor de dados: 17
Autores: Shen Lin; Stefan Haas; Tomasz Zemojtel; Peng Xiao; Martin Vingron; Renhui Li.
Background:&amp;#xd;&amp;#xa;Transposable elements are widely distributed in archaea, bacteria and eukarya domains. Considerable discrepancies of transposable elements in eukaryotes have been reported; however, the studies focusing on the diversity of transposable systems in prokaryotes were scarce. Understanding the transposable element system in cyanobacteria by the genome-wide analysis will greatly improve the knowledge of cyanobacterial diversity.&amp;#xd;&amp;#xa;Results:&amp;#xd;&amp;#xa;In this study, the transposable elements of seventeen cyanobacterial genomes were analyzed. The abundance of insertion sequence (IS) elements differs significantly among the cyanobacterial genomes examined. In particular, water bloom forming Microcystis aeruginosa...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4923/version/1

Genome-wide scanning versus candidate gene approach in the genetic architecture of common diseases.
Provedor de dados: 17
Autores: Carlos J. Pirola; Silvia  Sookoian.
In the Nature 7 June issue, researchers from the Welcome Trust Case Control Consortium (WTCCC) reported the findings of a large genome-wide association (GWA) study of 14,000 cases of common diseases and 3000 controls studies revealing the role of several loci in the genetic risk of common diseases. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We wish to emphasize that by making public the access to databases, consortia allow other investigators to search for association between candidate genes and T2D-related phenotypes. As an example we found, in a pilot study enrolling 1100 individuals that SNPs in the CLOCK (i.e. rs1554483 and rs6843722) were associated with hypertension (p value &amp;#x3c; 0.01, and 0.01, respectively). Interestingly, the same association was...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2007
URL: http://precedings.nature.com/documents/1438/version/1

Genome-wide transcription analysis of interaction between the human macrophage and Mycobacterium tuberculosis during concurrent drug administration by conventional and novel methods
Provedor de dados: 17
Autores: Awadh Bihari Yadav; Amit K. Singh; Amit Misra.
Targeted drug delivery to alveolar macrophages harboring Mycobacterium tuberculosis (Mtb) holds promise of high efficacy against pulmonary tuberculosis (TB). It was investigated whether inhalable microparticles (MP) can rescue macrophages from &amp;#x2018;alternative&amp;#x2019; activation induced by pathogenic Mtb in addition to achieving targeted drug delivery. A genome-wide transcription analysis (Affymetrix HG-U133 Plus 2.0 DNA microarray) of THP-1 cell line derived macrophages was undertaken after exposing them to infection with 10 MOI of MTB H37Rv at 0, 12 and 24 hours post infection. The Molecular markers of macrophage bactericidal activity were assayed in THP-1- and primary human peripheral blood mononuclear cell (PBMC)-derived macrophages, in the...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2453/version/1

Genomic Replikin Count Predicts Increased Lethality of Malaria
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
Genomic Replikin Counts predict both the increase and the decrease of lethality of malaria
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Immunology; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7142/version/1

Genomic Replikin Counts of Infectious Salmon Anemia Virus (ISAV) in Canada Exceed the Counts in Lethal Outbreaks in Norway, Chile, and Scotland. Real-Time Tracking of the Evolution of the ISAV Genome and the Resultant Replikins Solid Phase ISAV Vaccine Make ISAV Pandemic Prevention Possible.
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
Genomic Replikin CountsTM  of Infectious Salmon Anemia Virus (ISAV) in Canada Exceed the Counts in Lethal Outbreaks in Norway, Chile, and Scotland. Real-Time Tracking of the Evolution of the ISAV Genome and the Resultant Replikins Solid Phase ISAV Vaccine Make ISAV Pandemic Prevention Possible.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6991/version/1

Genomics and synthetic biology as a viable option to intensify sustainable use of biodiversity
Provedor de dados: 17
Autores: Elibio L. Rech.
The Amazon basin is an area of mega-biodiversity. Different models have been proposed^1-8^ for the establishment of an effective conservation policy, increasing sustainability and adding value for biodiversity. Currently, a broad spectrum of technologies from genomics to synthetic biology is available, and these permit the collection, manipulation and effective evaluation of countless organisms, metabolic pathways and molecules that exist as potential products of a large, biodiverse ecosystem. The use of Genomics and synthetic biology may constitute an important tool and be a viable option for the prospection, evaluation and manipulation of biodiversity as advocated as well as be useful for developing methods for sustainable use and the production of novel...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5759/version/1

Geographical and chronological origin and evolution of Hepatitis C Virus.
Provedor de dados: 17
Autores: amjesh revikumar; Achuthsankar  S. Nair; Sugunan V.S.
Hepatitis C Virus (HCV) infection is a major health problem that leads to cirrhosis and hepatocellular carcinoma. World over, more than 270-300 million people are estimated to be infected with the virus. HCV is a positive sense single stranded RNA virus and replicates within the cytoplasm of the hepatocyte using its own RNA dependent RNA polymerase (RdRp). RdRp does not have proof reading capacity, and hence generates mutants of the virus, resulting in a chronic infection, which ultimately ends in hepatocellular carcinoma.  Such mutations have given rise to several genotypes, subtypes, strains and variants with significant difference in disease outcomes.  The mutation rate varies among genotypes, subtypes, strains or even in different sites of the genome....
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6710/version/1

Geological Controls on Water Resource Variability in Minnesota, USA
Provedor de dados: 17
Autores: Howard  Mooers; Roman Kanivetsky; John  Nieber; Heidi  Peterson; Carol Johnston; Boris Shmagin.
Sustainable management of water resources requires quantitative description of spatio-temporal variability, and the map is a universal medium to reflect the spatio-temporal distribution of water resources. The long history of cartography and the recent digital revolution have culminated in the Google Earth web portal with unprecedented frequency of daily use. System analysis with combination of a cyber model of landscapes, multidimensional methods of data analysis, and GIS cartography of water resources in Minnesota started in 1996 with support from faculty of Department of Geology University of Minnesota-Duluth and has continued ever since. The &amp;#x201c;Water Resource Sustainability&amp;#x201d; project, funded by the Legislative Citizens Commission on...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3957/version/1

Geometric bionics: Lotus effect helps polystyrene nanotube films get good blood compatibility
Provedor de dados: 17
Autores: Chun Mao; Wen-Bo Zhao; Wen-Ping Luo; Cun-Xia Liang; Xiao-Mei Hou; Xiao-Hua Huang; Hong-Ke Liu; Ying-Hong Xiao; Jian-Chun Bao; Jian Shen.
Various biomaterials have been widely used for manufacturing biomedical applications including artificial organs, medical devices and disposable clinical apparatus, such as vascular prostheses, blood pumps, artificial kidney, artificial hearts, dialyzers and plasma separators, which could be used in contact with blood^1^. However, the research tasks of improving hemocompatibility of biomaterials have been carrying out with the development of biomedical requirements^2^. Since the interactions that lead to surface-induced thrombosis occurring at the blood-biomaterial interface become a reason of familiar current complications with grafts therapy, improvement of the blood compatibility of artificial polymer surfaces is, therefore a major issue in biomaterials...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3002/version/1

Geometric Representations of Language Taxonomies
Provedor de dados: 17
Autores: Philippe Blanchard; Filippo Petroni; Maurizio Serva; Dimitri Volchenkov.
Complex relationships between different languages in a language family encoded in the lexicostatistic data can be subjected to a component analysis and represented geometrically, in terms of distances and angles. The fully automated method for construction of language taxonomy is tested on a sample of fifty languages of the Indo-European language group and applied to a sample of fifty languages of the Austronesian language group. The Anatolian and Kurgan hypotheses of the Indo-European origin and the &amp;#x27;express train&amp;#x27; model of the Polynesian origin are thoroughly discussed.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3156/version/3

Geometrical-topological correlation in structures
Provedor de dados: 17
Autores: Michael J. Bucknum; Eduardo A. Castro.
The topology of polyhedra, tessellations and networks is described as to their mapping in Schlaefli space. A description of the topological form index is given and it is applied to these structural classes in terms of their geometries.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1651/version/1

Geometries of the perchlorinated and perbrominated C~3~ through C~6~ n-alkanes: A comparative density functional theory study
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase standard state (298.15 K, 1 atm) geometries of the perchlorinated and perbrominated C~3~ through C~6~ n-alkanes were calculated using the B3LYP, B97D, M062X, and PBE0 density functionals with the 6-311++G(d,p) basis set. For both halogen classes and at all levels of theory, the C~3~ compounds adopt a trans conformation analogous to that of perfluoropropane. Similar to their perfluorinated counterparts, the perchlorinated and perbrominated C~4~ through C~6~ n-alkanes are predicted to have helical geometries. In contrast to perfluoroalkyl chains, the central CCCC dihedral angles of the perchlorinated and perbrominated derivatives are expected to decline with increasing chain length.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5157/version/1

GESTATION LENGTH OF KARI SHEEP
Provedor de dados: 17
Autores: Sohail Ahmad.
Previously, the concept of a gestation period of sheep shorter than 121 days was unheard of in the field of sheep biology. Our findings during a farmers&amp;#x2019; survey in the Lotkho area of Chitral, Pakistan, revealed that the sheep native to the region, locally called &amp;#x201c;Kari&amp;#x201d;, gestates for a period of only three months. This duration is 25-40% short of the usual gestation length and is shorter than ever recorded for the species. The mean and mode gestation length (GL) was 110 and 92 days respectively and was concentrated in three distinct clusters: day 87-95, 120-123 and 151-153, accounting for 52% of all observations. GL was influenced by location, season of conception and lambing and the interaction of location with season; had...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1620/version/1

Getting The Most Out of Your Research
Provedor de dados: 17
Autores: Folarin A. Erogbogbo.
Research is the cornerstone of invention, facilitator of innovation, and mother of discovery. Even though many students are competent in advancing through the class room and getting good grades, excellent research requires a different set of attitudinal and academic skills. This workshop, &amp;#x22;Get the most out of your research&amp;#x22; is an outstanding program developed from extensive time spent with brilliant scientists and a wide variety of mentored students.  Familiarize yourself with the fine points of this workshop and arm yourself for a successful research career.
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/5702/version/1

Ghost hand: My hand is not mine
Provedor de dados: 17
Autores: Yuta Nishiyama; Shinpei Tatsumi; Shusaku Nomura; Yukio Gunji.
Synchronous visuo-tactile stimulation of the type in the rubber hand illusion (RHI)^1-3^ and in out of body experience (OBE)^4,5^ can induce the brain to incorporate external objects or images into a part or whole of body image. Whether in the context of RHI or OBE, since the participant passively receives visuo-tactile stimulations, body image appears only with the sense of ownership (SoO), not with the sense of agency (the registration that we are the initiators of our actions; SoA)^6,7^. Insofar as self-consciousness as a body image is a unity acting in its environments, body image has to be investigated in the relationship between SoO and SoA^8,9^. It requires an experimental condition in which SoO and SoA can be independently separated in an active...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3019/version/1

GillespieSSA: A user-friendly stochastic simulation package for R
Provedor de dados: 17
Autores: Mario Pineda-Krch.
GillespieSSA is a package for the statistical computing and graphics language and environment R. GillespieSSA provides a simple to use and extensible interface to several stochastic simulation algorithms for generating simulated trajectories of finite population continuous-time model. Currently it implements Gillespie&amp;#x2019;s exact stochastic simulation algorithm (Direct method) and several approximate methods (Explicit tau-leap, Binomial tau-leap, and Optimized tau-leap). The package also contains a library of template models that can be run as demo models and can easily be customized and extended. Currently the following models are included, decaying-dimerization reaction set, linear chain system, logistic growth model, Lotka predator-prey model,...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3673/version/1

Glacial cycles promote greater dispersal, which can help explain larger clutch sizes, in north temperate birds
Provedor de dados: 17
Autores: David W. Winkler; Russell Greenberg; Thomas E. Martin; Frederick R. Adler; Samuel  M. Flaxman.
Earth&amp;#x2019;s glacial history and patterns in the life history traits of the planet&amp;#x2019;s avifauna suggest the following interpretations of how recent geological history has affected these key characteristics of the biota: 1) Increased colonizing ability has been an important advantage of increased dispersal, and life history strategies are better categorized by dispersive colonizing ability than by their intrinsic growth rates; 2) Birds of the North Temperate Zone show a greater tendency to disperse, and they disperse farther, than tropical or south temperate birds; 3) Habitat changes associated with glacial advance and retreat selected for high dispersal ability, particularly in the North; and 4) Selection for greater dispersal throughout the...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/2911/version/1

Global Awakening in Genetic Counseling
Provedor de dados: 17
Autores: Janice Edwards; Jacquie Greenberg; Margaret Sahhar.
The article by Ricki Lewis, Nature, Volume 449,October 18, 2007, correctly points out that the genetic counseling profession is on the &amp;#x22;verge of being discovered by the rest of the world&amp;#x22;. The rapid recognition of genes associated with single-gene disorders and complex conditions has deepened our understanding of the role of genetics in health and illness. The impact of genetic conditions on individuals and families, particularly in ethical, legal and psychosocial arenas, requires specially trained professionals to work in this unique and growing dimension of healthcare. The Transnational Alliance for Genetic Counseling (TAGC) represents fifteen countries currently providing genetic counselor education across five continents.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/1574/version/1

Global Eradication of Lymphatic Filariasis: The Value Of Chronic Disease Control in Parasite Elimination Programs
Provedor de dados: 17
Autores: Edwin Michael; Mwele N. Malecela; Mihail Zervos; James W. Kazura.
The ultimate goal of the global programme against lymphatic filariasis is eradication through irrevocable cessation of transmission using 4 to 6 years of annual single dose mass drug administration. The costs of eradication, and logistical and managerial impediments to executing national and regional control programmes, and scientific uncertainty about transmission endpoints, are challenges to the success of this effort, especially in areas of high endemicity where financial resources are limited. We used a combined analysis of empirical community data describing the association between infection and chronic disease prevalence, mathematical modelling, and economic analyses to identify and evaluate the feasibility of setting an infection target level at...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1564/version/1

Global Network Alignment
Provedor de dados: 17
Autores: Oleksii Kuchaiev; Natasa Przulj.
Motivation: High-throughput methods for detecting molecular interactions have lead to a plethora of biological network data with much more yet to come, stimulating the development of techniques for biological network alignment. Analogous to sequence alignment, efficient and reliable network alignment methods will improve our understanding of biological systems. Network alignment is computationally hard. Hence, devising efficient network alignment heuristics is currently one of the foremost challenges in computational biology. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: We present a superior heuristic network alignment algorithm, called Matching-based GRAph ALigner (M-GRAAL), which can process and integrate any number and type of similarity measures...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4505/version/1

Global warming affected some morphological characters of Pistachio trees (_Pistacia vera_ L.)
Provedor de dados: 17
Autores: Amanollah A. Javanshah.
Pistachio is one of the main horticulture crops in Iran where have the first cultivation and exportation position in the world. Climate change has already affected species distribution shifts in many parts of the world and more impacts are expected for the future, yet few studies have aimed for a general understanding of the regional basis for species vulnerability. In this research meteorology data of four months (December, January, February and March) from 1991 to 2008 and Phenology data of six pistachio cultivars that ranked in 3 groups: early flowering (Kalehghoochi and Ahmadaghaei), mid flowering (Momtaz and Amiri) and late flowering (Akbari and Shahpasand) during summer of 1997, 2001-5, and 2007 were studied in Kerman province. The evaluated factors...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2574/version/1

Global warming is reducing thermal stability and mitigating the effects of eutrophication in Lake Victoria (East Africa)
Provedor de dados: 17
Autores: Brian Marshall; Charles Ezekiel; John Gichuki; Oliva Mkumbo; Lewis Sitoki; Fred Wanda.
The impacts of global warming have been reported from several deep lakes in the African Rift Valley and in each thermal gradients within the water column have increased thus strengthening already existing oxyclines, below which the water is permanently anoxic^1,2,3,4^. The temperature of Lake Victoria rose by 0.9&amp;#xb0;C between 1960 and 1990 raising fears that thermal stability would increase resulting in more extensive and severe anoxia in the deeper waters^5^. This is of concern because of the eutrophication of the lake, which began in the 1960s,^6,7^ and led to dense blooms of sometimes toxic cyanobacteria, increased deoxygenation of the bottom waters, and fish kills in some parts of the lake^8,9,10^. Here we show that thermal gradients in the water...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3726/version/1

Glucocorticoids Inhibit Sodium Depletion-induced Salt Appetite in Rat
Provedor de dados: 17
Autores: Chao Liu; Jing Guan; Ying Chen; Kunshen Liu.
Glucocorticoids, produced in adrenal cortex, exert potent natriuretic and diuretic actions in the kidney. Recently, it has been found that glucocorticoids could upregulate the expression of natriuretic peptide receptor A (NPR-A), the primary receptor of atrial natriuretic peptide, in the hypothalamus of the rat. Consequently, systemic administration of glucocorticoid could block dehydration-induced water intake by activation hypothalamic NPR-A. We describe here glucocorticoids could inhibit sodium intake when administrated systemically in conscious, salt-depleted rats; an effect which was strong and long-lasting. The study provided further evidence for the actions of glucocorticoids on central nervous system, which together with their established renal...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/5376/version/1

Glucose-6-phosphate-dehydrogenase deficiency as a risk factor in proliferative disorder development
Provedor de dados: 17
Autores: Antonella Mandas; Enrico Peiretti; Pierluigi Cocco; Claudia Norfo; Claudia Abete; Fabrizio Angius; Alessandra Pani; Giacomo Diaz; Sandra Dess&amp;#xec;; Maurizio Fossarello.
Glucose-6-phosphate dehydrogenase (G6PD) is an important site of metabolic control in the pentose phosphate pathway (PPP) which provides reducing power (NADPH) and pentose phosphates. The former is mainly involved in the detoxification of chemical reactive species; the latter in the regulation of cell proliferation. G6PD deficiency is the most common enzymopathy in the human population, characterized by decreased G6PD activity, mainly in red blood cells, but actually also in nucleated cells. This decreased activity is not due to enzyme synthesis impairment, but rather to reduced enzyme stability, which leads to a shortening of its half-life. Therefore, a major problem is to understand the underlying mechanisms linking G6PD deficiency to oxidative stress...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3001/version/1

Glutathione (GSH) conjugates with dopamine (DA)-derived quinones to form reactive or non-reactive GSH-conjugates
Provedor de dados: 17
Autores: Zhidong Zhou; Tit Meng Lim.
In this study we demonstrate for the first time that GSH could rapidly conjugate with dopamine (DA)-derived DA-o-quinones without enzymatic catalysis to form short-lived intermediate GSH-conjugates (2-S-GSH-DA-o-quinone and 5-S-GSH-DA-o-quinone). These intermediate GSH-conjugates are unstable and would finally form reactive or non-reactive GSH-conjugates dependent on ambient reductive forces. Under insufficient reductive forces, the intermediate GSH-conjugates could cyclize spontaneously to form reactive 7-S-GSH-aminochrome (7-S-GSH-AM). The 7-S-GSH-AM is so reactive that it could further react with another GSH to form 4,7-bi-GSH-5,6-dihydroindole. Its reactivity could also abrogate tyrosinase activity in solutions. In addition, the 7-S-GSH-AM could...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Neuroscience; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2963/version/1

GMOD for Evolutionary Biology
Provedor de dados: 17
Autores: Robert Buels; Dave Clements.
The Generic Model Organism Database (GMOD, &amp;#x22;http://gmod.org&amp;#x22;:http://gmod.org) project provides interoperable, open source software tools for managing, visualizing and annotating biological data.  GMOD is also a community of people addressing common challenges with biological data.  Some well known software in GMOD includes GBrowse and JBrowse for genome browsing, Apollo for genome annotation, Chado for managing data, CMap for comparative map viewing, Galaxy for workflow creation and persistence, and BioMart for warehousing biological data.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This talk will focus on three areas of particular interest to iEvoBio participants.  &amp;#xd;&amp;#xa;1) GBrowse_syn comparative genomics viewer&amp;#xd;&amp;#xa;2)...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4611/version/1

GO faster ChEBI with Reasonable Biochemistry
Provedor de dados: 17
Autores: Duncan Hull.
Chemical Entities of Biological Interest (ChEBI) [1] is a database and ontology that represents knowledge about more than 15,000 small molecules and their biochemistry. The database does not currently use description logic reasoning or OWL, but is investigating this possibility for better, cheaper and faster ontology development in the future. This poster describes four specific problems and solutions to reasoning in ChEBI: 1. Using necessary and sufficient conditions 2. identifying inconsistencies 3. Improving alignment with the the Gene Ontology (GO) 4. Reasoning with chemical structures.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2435/version/1

GO faster ChEBI with Reasonable Biochemistry
Provedor de dados: 17
Autores: Duncan Hull.
Chemical Entities of Biological Interest (ChEBI) is a database and ontology that represents biochemical knowledge about small molecules. Recent changes to the ontology have created new opportunities for automated reasoning with description logic, that have not previously been fully exploited in Chemistry. These changes open up the possibility of building an improved chemical semantic web, by making more use of necessary and sufficient conditions, allowing reasoning about chemical structure, highlighting ambiguous inconsistencies and improving alignment with the Gene Ontology (GO). This paper briefly discusses some of the problems with reasoning over the current version of ChEBI, to tackle these issues, and their potential solutions.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2329/version/1

GOAssay: from Gene Ontology to Assays IDentifiers - Towards Automatic Functional Annotation of PubChem BioAssays
Provedor de dados: 17
Autores: Rajarshi Guha; Julien Gobeill; Patrick Ruch.
OBJECTIVES: We report on a experiment to functionally annotate PubChem assays using the Gene Ontology Categorizer (GOCat). &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;METHODS and MATERIALS: The assays are processed to filter out non functional information, then the textual content is sent to the categorizer, which provide a ranked list of GO descriptors based on a GOA-learned association model. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;RESULTS: The GO descriptors are regarded as irrelevant for only 18% of the assays. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;CONCLUSION: Semantic enrichment of PubChem assays with functional genomics categories seems effective at least to navigate PubChem assays. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;AVAILABILITIES: the database is hosted by the...
Tipo: Poster
Palavras-chave: Chemistry; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3176/version/1

Golden sections of inter-atomic distances as exact ionic radii of atoms
Provedor de dados: 17
Autores: Raji Heyrovska.
The Golden ratio which appears in the geometry of a variety of creations in Nature is found to arise right in the Bohr radius of the hydrogen atom due to the opposite charges of the electron and proton. The bond length of the hydrogen molecule is the diagonal of a square on the Bohr radius and hence also has two Golden sections, which form the cationic and anionic radii of hydrogen. It is shown here that these radii account quantitatively for the bond lengths of many hydrides when added to the atomic and Golden ratio based ionic radii of many other atoms.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/2929/version/1

GO-WORDS: An Entropic Approach to Semantic Decomposition of Gene Ontology Terms
Provedor de dados: 17
Autores: Tuanjie Tong; Yugyung Lee; Deendayal Dinakarpandian.
The Gene Ontology (GO) has a large and growing number of terms that constitute its vocabulary. An entropy-based approach is presented to automate the characterization of the compositional semantics of GO terms. The motivation is to extend the machine-readability of GO and to offer insights for the continued maintenance and growth of GO. A proto-type implementation illustrates the benefits of the approach.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1933/version/1

Grapevines (Vitis spp.) as Components of the &amp;#xb;North American Prairie Biomass Economy:&amp;#xb;&amp;#xb; High-Value Phytochemicals, Platform Chemicals, and Bioenergy
Provedor de dados: 17
Autores: Sierra Rayne.
Grapevines (Vitis spp.) offer the potential for contributing to the North American prairie biomass based economy. While these regions are too cold for the traditional V. vinifera wine grape species, they are well-suited for more cold hardy varietals. The grapevines provide opportunities for high-value phytochemicals and platform chemicals (primarily stilbene based) as well as bioenergy production from resulting lignocellulosic residues. In a biorefinery concept, the &amp;#x27;front-end&amp;#x27; high-value phytochemicals could help subsidize the lower-value bioenergy production.
Tipo: Presentation
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2145/version/1

Graphs, Networks, Extinction and Paleocommunity Food Webs
Provedor de dados: 17
Autores: Peter Roopnarine.
Food webs represent the trophic interactions among species in communities. Those interactions both structure and are structured by species richness, ecological diversity, and evolutionary processes. Geological and macroevolutionary timescales are therefore important to the understanding of food web dynamics, and there is a need for proper reconstruction and analysis of paleocommunity food webs. The fossil record presents many challenges, but the problem may be approached with combinatoric analysis, and graph and network theories. This paper is a brief introduction to the aspects of those disciplines relevant to the study of paleo-food webs, and explores several probabilistic and numerical approaches.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4433/version/1

Green Fluorescent Protein (GFP) in Vector Systems Played Sense Role of Epigenetic in Plants
Provedor de dados: 17
Autores: Hany A. El-Shemy; Mutasim M. Khalafalla; Masao Ishimoto.
The green fluorescent protein (GFP) of jellyfish (_Aequorea victoria_) has significant advantages over other reporter genes, because expression can be detected in living cells without any substrates. Recently, epigenetic phenomena are important to consider in plant biotechnology experiments for elucidate unknown mechanism. Therefore, soybean immature cotyledons were generated embryogenesis cells and engineered with two different gene constructs (pHV and pHVS) using gene gun method. Both constructs contain a gene conferring resistance to hygromycin (_hpt_) as a selective marker and a modified glycinin (11S globulin) gene (_V3-1_) as a target. However, sGFP(_S65T_) as a reporter gene was used only in pHVS as a reporter gene for study the relation between...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1845/version/1

GreenPhylDB: A Gene Family Database for plant functional Genomics
Provedor de dados: 17
Autores: Matthieu G. Conte; Marie-Ang&amp;#xe9;lique Laporte; Christophe P&amp;#xe9;rin; Mathieu  Rouard.
With the increasing number of genomes being sequenced, a major objective is to transfer accurate annotation from characterised proteins to uncharacterised sequences. Consequently, comparative genomics has become a usual and efficient strategy in functional genomics. The release of various annotated genomes of plants, such as _O. sativa_ and _A. thaliana_, has allowed setting up comprehensive lists of gene families defined by automated methods. However, like for gene sequence, manual curation of gene families is an important requirement that has to be undertaken. GreenPhylDB comprises protein sequences of 12 plant species fully sequenced that were grouped into homeomorphic families using similarity-based methods. Clusters are finally processed by...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3136/version/1

Grid Potential Analysis and Docking Studies on a Dataset of  N-Arylsulfonyl-3-AcetylIndoles as Anti-HIV Agent
Provedor de dados: 17
Autores: Surendra Kumar; Meena Tiwari.
A grid potential analysis employing the AutoGPA module in MOE2009.10 was performed on a dataset of 42 molecules of N-arylsulfonyl-3-acetylindoles as anti-HIV agent. The molecular docking simulations were also employed to position the inhibitors to their binding site to determine the most appropriate binding mode for different conformations of molecule. The uniqueness of AutoGPA module is that it automatically builds the 3D-QSAR model on the pharmacophore based molecular alignment. The best AutoGPA 3D-QSAR model obtained in the present study gives the cross-validated q2 value of 0.588 and r2pred value of 0.701 among the fifty six 3D-QSAR model developed. Furthermore, the steric and electrostatic contour maps for AutoGPA model along with the 3D structure of...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6932/version/1

Grid technology for collaborative ontology development
Provedor de dados: 17
Autores: Stuart Aitken; Kemian Dang; Jonathan Bard.
In contrast with the centrally-organised curation of the Gene Ontology, many biological ontologies are developed by loosely-organised groups who develop their ontology remotely. These groups tend to be formed from scientists and bio-informaticians from research groups with a common interest, who want to create a resource that will be useful to the community, rather than being formally mandated. Until recently, technological support for bio-ontology development relied on stand-alone editors running on users&amp;#x2019; desk- tops for creating new ontology versions (e.g. OBO-Edit, COBrA and Prot&amp;#xe9;g&amp;#xe9;) and on private email, email lists and perhaps Wikis for the distribution of ontology files and discussions. Clearly, much better use could be...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3186/version/1

Grofit: Fitting biological growth curves
Provedor de dados: 17
Autores: Matthias Kahm; Guido Hasenbrink; Hella Lichtenberg-Frate; Jost Ludwig; Maik Kschischo.
Growth experiments are routinely used to analyze basic properties of a given organism or cellular model. Similarly, within the TRANSLUCENT project the characterization of cellular growth and particularly under conditions of high extra cellular potassium or sodium is an important task. Any growth analysis should ideally reveal a relationship between the concentration of a compound/substrate and its effect on a particular growth parameter. In view of the quite labor intensive analysis of hundreds of growth curves - sometimes not revealing ideal relationships - the Grofit-software was developed to support biologists and such approaches. Within the software package, specifically tailored regression and bootstrapping techniques are utilized to statistically...
Tipo: Poster
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4508/version/1

GUDMAP - An Online GenitoUrinary Resource
Provedor de dados: 17
Autores: Chris Armit; Simon Harding; Jamie A. Davies; Jane Armstrong; Jane Brennan; Sue Lloyd-MacGilp; Derek Houghton; Mehran Sharghi; Xingjun Pi; Y. Cheng; Bruce Aronow; Kevin Gaido; Sean Grimmond; Peter Koopman; Jim Lessard; Melissa Little; Andy McMahon; Cathy Mendelsohn; Steve Potter; Michelle Southard-Smith; Duncan Davidson.
The GenitoUrinary Development Molecular Anatomy Project (GUDMAP) is a consortium of laboratories working to provide the scientific and medical community with gene expression data and tools to facilitate research (see &amp;#x22;www.gudmap.org&amp;#x22;:http://www.gudmap.org). The data provided by GUDMAP includes large _in situ_ hybridization screens (wholemount and section) and expression microarray analysis of components of the developing mouse urogenital system (including laser-captured material and FACS-isolated cells from transgenic reporter mice). In addition, a high-resolution anatomy ontology has been developed by members of the GUDMAP consortium to describe the subcompartments of the developing murine genitourinary tract....
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3297/version/1

Guided Tissue Remineralization of Resin-Bonded Acid-Etched Dentin
Provedor de dados: 17
Autores: Franklin R. Tay; David H. Pashley.
Contemporary biomineralization strategies incorporate non-classical crystallization pathways of fluidic amorphous nanoprecursors and mesoscopic transformation. Using two functional biomimetic molecules, we previously regenerated mineralized dentin from acid-etched dentin using the Guided Tissue Remineralization (GTR) approach, with definitive intrafibrillar remineralization of type-I collagen. Degradation of denuded collagen within dentin adhesive resin-infiltrated dentin is a pertinent problem in dentin bonding. Here, we show that GTR provides a means of salvaging these degrading bonds by remineralizing resin-dentin interfaces. The GTR medium consists of a Portland cement/simulated body fluid that includes polyacrylic acid and polyvinylphosphonic acid...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2022/version/1

Gulf War Syndrome: A role for organophosphate induced plasticity of locus coeruleus neurons
Provedor de dados: 17
Autores: Jun-li  Cao; Andrew L. Varnell; Donald C. Cooper.
Gulf War syndrome is a chronic multi-symptom illness that has affected about a quarter of the deployed veterans of the 1991 Gulf War. Exposure to prolonged low-level organophosphate insecticides and other toxic chemicals is now thought to be responsible. Chlorpyrifos was one commonly used insecticide. The metabolite of chlorpyrifos, chlorpyrifos oxon, is a potent irreversible inhibitor of acetylcholinesterase, much like the nerve agent Sarin. To date, the target brain region(s) most susceptible to the neuroactive effects of chlorpyrifos oxon have yet to be identified. To address this we tested ability of chlorpyrifos oxon to influence neuronal excitability and induce lasting changes in the locus coeruleus, a brain region implicated in anxiety, substance...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6057/version/2

Gulf War Syndrome: A role for organophosphate induced plasticity of locus coeruleus neurons
Provedor de dados: 17
Autores: Jun-li  Cao; Andrew L. Varnell; Donald C. Cooper.
Gulf War syndrome is a chronic multi-symptom illness that has affected about a quarter of the deployed veterans of the 1991 Gulf War. Exposure to prolonged low-level organophosphate insecticides and other toxic chemicals is now thought to be responsible. Chlorpyrifos was one commonly used insecticide. The metabolite of chlorpyrifos, chlorpyrifos oxon, is a potent irreversible inhibitor of acetylcholinesterase, much like the nerve agent Sarin. To date, the target brain region(s) most susceptible to the neuroactive effects of chlorpyrifos oxon have yet to be identified. To address this we tested ability of chlorpyrifos oxon to influence neuronal excitability and induce lasting changes in the locus coeruleus, a brain region implicated in anxiety, substance...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6057/version/1

H5N1 Clade 2.2 Polymorphism Tracing Identifies Influenza Recombination and Potential Vaccine Targets
Provedor de dados: 17
Autores: Henry L. Niman; Magdi D. Saad; Elassai M. Labib; E Ayoub; Mona M. Aly; A-SA Arafa; Marshall R. Monteville; Bruce R. Boynton; Jeffery Tjaden; Kenneth C. Earhart; Moustafa M. Mansour; Nasr M. ElSayed; A I. Nayei; A A. Abdelghani; Hala M. Essmat.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997 1. The number of confirmed human cases now exceeds 300 and the associated Case Fatality Rate exceeds 60% 2. The genetic diversity of the serotype continues to increase.  Four distinct clades or sub-clades have been linked to human cases 3.4. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift 5. We traced polymorphism acquisition in Clade 2.2 sequences. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, Clade 2.2 sub-clades in Egypt, Russia...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/553/version/2

H5N1 Clade 2.2 Polymorphism Tracing Identifies Influenza Recombination and Potential Vaccine Targets
Provedor de dados: 17
Autores: Henry L. Niman; Magdi D. Saad; Bruce R. Boynton; Jeffery Tjaden; Kenneth C. Earhart; Moustafa M. Mansour; Nasr M. ElSayed; A I. Nayei; A A. Abdelghani; Hala M. Essmat; Elassai M. Labib; E Ayoub; Mona M. Aly; A-SA Arafa; Marshall R. Monteville.
Highly pathogenic Influenza A H5N1 was first identified in Guangdong Province in 1996, followed by human cases in Hong Kong in 1997 1. The number of confirmed human cases now exceeds 300 and the associated Case Fatality Rate exceeds 60% 2. The genetic diversity of the serotype continues to increase.  Four distinct clades or sub-clades have been linked to human cases 3.4. The gradual genetic changes identified in the sub-clades have been attributed to copy errors by viral encoded polymerases that lack an editing function, thereby resulting in antigenic drift 5. We traced polymorphism acquisition in Clade 2.2 sequences. We report here the concurrent acquisition of the same polymorphism by multiple, genetically distinct, Clade 2.2 sub-clades in Egypt, Russia...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/553/version/1

Habitat use of Northern Map Turtles (Graptemys geographica) in an  altered system, the Susquehanna River, Maryland (USA)
Provedor de dados: 17
Autores: Teal M. Richards; Richard A. Seigel.
*_Background/Question/Methods_*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Riverine turtle populations are declining worldwide and many of these species have been extirpated from large areas of their range. In Maryland, the northern map turtle (Graptemys geographica) occurs only in the lower Susquehanna River, which is the eastern edge of its range. The northern map turtle is a Maryland state endangered species and had not been seen in Maryland since the early 1990&amp;#x2019;s. The Susquehanna River is divided by a hydroelectric dam and is heavily used for recreational activities, both of which may negatively impact turtles. To determine the status of map turtles in Maryland, we performed visual encounter surveys for basking turtles at 12 sites from April to...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3680/version/1

Hacking the JPEG/PDF tree format
Provedor de dados: 17
Autores: Joseph Hughes.
We have been illustrating the relationships between species and genes as trees for over a century. Whilst in the early years of morphological and molecular phylogenetics, embedding illustrations into manuscripts might have been the most appropriate way to disseminate knowledge, this has resulted in the locking up of phylogenetic hypotheses into the pages of journals and books without an easy way to access this information. As a result, most phylogenetic knowledge is lost upon publication. I will explain the reasons for re-using published trees, discuss ways to liberate this information and avoid these problems in the future.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6556/version/1

Harnessing Aquatic Yeasts For Developing A New Generation of Sunscreens
Provedor de dados: 17
Autores: Hycienth Braganca; Nandkumar Kamat.
Around 100 yeast genera and 800 species have been isolated and characterized. Nagahama (2006) has reviewed yeast biodiversity in freshwater, marine and deep-Sea Environments. Our work aims at systematic biodiversity assessment of freshwater aquatic yeasts from Goa with major focus on carotenogenic basidiomycetes yeasts which on exposure to potentially damaging levels of solar ultraviolet radiation (UVR) accumulate photoprotective compounds (PPC) such as mycosporine-glutaminol-glucoside (myc-glu-glu, peak absorption at 309-310nm) that server as sunscreens and /or antioxidant. These yeasts are a potential source of a particularly diverse family of such substances, collectively referred to as mycosporine- like amino-acids (MAAs). This paper presents the...
Tipo: Poster
Palavras-chave: Biotechnology; Ecology; Microbiology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4249/version/1

HBsAg-vectored DNA vaccines elicit concomitant protective responses to multiple CTL epitopes relevant in human disease.
Provedor de dados: 17
Autores: Dekun Chen; Allan Gould; Michael Mather; Oscar Haigh; Melanie Barnes; Jacqueline Kattenbelt; Scott Thomson; Robert R. Tindle.
Vaccines capable of controlling neoplastic and infectious diseases which depend on the cellular immune response for their resolution, have proven difficult to develop. We, and others, have previously demonstrated that the potent immunogenicity of hepatitis B surface antigen (HBsAg), the already- licensed human vaccine for hepatitis B infection, may be exploited to deliver foreign antigens for cytotoxic T-lymphocyte (CTL) induction. In this study we demonstrate that recombinant (r) HBsAg DNA delivering a CTL polyepitope appended at the C&amp;#x27; terminus elicits concomitant responses to multiple epitopes restricted through a diversity of MHC class I haplotypes, which are relevant in a number of human diseases. We show that the rHBsAg DNA vaccine elicits...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/1910/version/1

HEAT: a New Tool for Gene Set Enrichment Analysis Using Comprehensive Annotation of Human Genes in H-InvDB
Provedor de dados: 17
Autores: Tadashi Imanishi; Akiko O. Noda; Miho Sera.
H-InvDB Enrichment Analysis Tool (HEAT) is a new data-mining tool for gene set enrichment analysis based on comprehensive annotations of human genes in H-InvDB.  HEAT searches for H-InvDB annotations that are significantly enriched in a user-defined gene set, as compared with the entire H-InvDB representative transcripts.  The advantage of HEAT is the wide variety of annotation items used for its analysis: chromosomal bands, InterPro functional domains, Gene Ontology terms, KEGG pathways, H-InvDB gene families/groups, SCOP structural domains, subcellular localization predicted by using the Wolf-PSORT program, tissue-specific gene expression as defined in the H-ANGEL database, and transcription factor binding sites in promoter regions based on JASPAR.  HEAT...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5185/version/1

Heat shock transcription factor 1 preserves cardiac angiogenesis and adaptation during pressure overload
Provedor de dados: 17
Autores: Jiming Li; Junbo Ge; Jie Yuan; Hong Jiang; Hong Ma; Yanyan Liang; Yuhong Niu; Hui Gong; Ning Zhou; Aili Guan; Zhen Ma; Lingyan Yuan; Aijun Sun; Yuqi Wang; Akira Nakai; Issei Komuro; Yunzeng Zou.
To examine how heat shock transcription factor 1 (HSF1) protects against maladaptive hypertrophy during pressure overload, we subjected HSF1 transgenic (TG), knockout (KO) and wild type (WT) mice to a constriction of transverse aorta (TAC), and found that cardiac hypertrophy, functions and angiogenesis were well preserved in TG mice but were decreased in KO mice compared to WT ones at 4 weeks, which was related to HIF-1 and p53 expression. Inhibition of angiogenesis suppressed cardiac adaptation in TG mice while overexpression of angiogenesis factors improved maladaptive hypertrophy in KO mice. In vitro formation of vasculatures by microvascular endothelial cells was higher in TG mice but lower in KO mice than in WT ones. A siRNA of p53 but not a HIF-1...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2716/version/1

Hematopoietic Cell Types:  Prototype for a Revised Cell Ontology
Provedor de dados: 17
Autores: Alexander D. Diehl; Alison D. Augustine; Judith A. Blake; Lindsay G. Cowell; Elizabeth S. Gold; Timothy A. Gondr&amp;#xe9;-Lewis; Anna Maria Masci; Terrence F. Meehan; Penelope A. Morel; Anastasia Nijnik; Bjoern Peters; Bali Pulendran; Richard H. Scheuermann; Q. Alison Yao; Martin S. Zand; Christopher J. Mungall.
The Cell Ontology (CL) aims for the representation of in vivo and in vitro cell types from all of biology.  Although the CL is a reference ontology of the OBO Foundry, it requires extensive revision to bring it up to current standards for biomedical ontologies, both in its structure and its coverage of various subfields of biology.  A recent workshop sponsored by NIAID on hematopoietic cell types in the CL addressed both issues.  The section of the ontology dealing with hematopoietic cells was extensively revised, and plans were set for structuring these cell type terms as cross-products with logical definitions built from relationships to external ontologies, such as the Protein Ontology and the Gene Ontology.  The methods and improvement to the CL in...
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3635/version/1

Hematopoietic Cell Types:  Prototype for a Revised Cell Ontology
Provedor de dados: 17
Autores: Alexander D. Diehl.
The Cell Ontology (CL) is an OBO Foundry candidate ontology intended for the representation of cell types from all of biology.  A recent workshop sponsored by NIAID on hematopoietic cell types in the CL addressed issues of both the content and structure of the CL.  The section of the ontology dealing with hematopoietic cells was extensively revised, and plans were made for restructuring these cell type terms as cross-products with logical definitions based on relationships to external ontologies, such as the Protein Ontology and the Gene Ontology.  The improvements to the CL in this area represent a paradigm for the future revision of the whole of the CL.
Tipo: Presentation
Palavras-chave: Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3543/version/1

Hematopoietic Cell Types:  Prototype for a Revised Cell Ontology
Provedor de dados: 17
Autores: Alexander D. Diehl; Alison D. Augustine; Judith A. Blake; Lindsay G. Cowell; Elizabeth S. Gold; Timothy A. Gondr&amp;#xe9;-Lewis; Anna Maria Masci; Terrence F. Meehan; Penelope A. Morel; Anastasia Nijnik; Bjoern Peters; Bali Pulendran; Richard H. Scheuermann; Q. Alison Yao; Martin S. Zand; Christopher J. Mungall.
The Cell Ontology (CL) is an OBO Foundry candidate ontology intended for the representation of cell types from all of biology.  A recent workshop sponsored by NIAID on hematopoietic cell types in the CL addressed issues of both the content and structure of the CL.  The section of the ontology dealing with hematopoietic cells was extensively revised, and plans were made for restructuring these cell type terms as cross-products with logical definitions based on relationships to external ontologies, such as the Protein Ontology and the Gene Ontology.  The improvements to the CL in this area represent a paradigm for the future revision of the whole of the CL.
Tipo: Presentation
Palavras-chave: Immunology; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3543/version/2

Hematopoietic Stem Cell Transcription Factor PU.1 with Mutated &amp;#x3b2;3/&amp;#x3b2;4 Domain Selectively Elicits Myeloid Differentiation
Provedor de dados: 17
Autores: Pallavi Gupta; Gurudutta U. Gangenahalli; Daman Saluja; Yogesh K. Verma; Jyoti Zack; Vimal K. Singh; Neeraj K. Satija; Rajendra P. Tripathi.
In many hematopoietic malignancies such as lymphomas &amp;#x26; leukemias, aberrant differentiation is the major feature of malignant phenotype that often results from a single genetic alteration and provides a site-specific target for therapy. Therefore, targeting of protein-protein interactions that have been identified as mediators of transcriptional repression that blocks normal hematopoietic differentiation holds great promise for therapeutic applications. An example is GATA-1, a critical erythroid transcription factor that is capable of suppressing the myeloid phenotype by down-regulating PU.1 in a dose-dependent manner. PU.1 is the most crucial transcription factor known to be required for myeloid differentiation of hematopoietic stem cells or...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5453/version/1

Hemodynamic and electrophysiological evidence of resting-state network activity in the primate
Provedor de dados: 17
Autores: Allen Ardestani; Wei Shen; Felix Darvas; Arthur Toga; Joaquin Fuster.
An expanding body of literature describes the existence of concerted brain activations in the absence of any external stimuli.  Resting-state networks have been identified and demonstrated to be modulated during the performance of specific cognitive operations.  However, despite mounting evidence the possibility still remains that those correlated signal fluctuations reflect non-neural phenomena.  In order to isolate functionally relevant spontaneous coactivations, we utilized a multi-level sampling approach to obtain co-registered brain signals across a range of sampling resolution and sensitivity.  Surface and local field potentials, hemodynamic signals (near-infrared spectroscopy, NIRS), and cell spiking were recorded from dorsolateral prefrontal and...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2562/version/1

Herbal Drugs in Mirror of Alzheimer&amp;#x2019;s Disease
Provedor de dados: 17
Autores: Bernd Kastenholz; Kerstin Nagel; David E. Garfin; J&amp;#xfc;rgen Horst.
Commercially available Ginkgo biloba leaf extracts may lack specificity as to the binding of copper and zinc ions in human cells. This might be the reason why Ginkgo extracts have no predictable and clinically significant benefit for people with dementia or cognitive impairment. A novel generation of herbal drugs is proposed as antioxidant and metal chelator in the treatment of Alzheimer&amp;#x27;s disease.
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience; Pharmacology; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3334/version/1

Herd Immunity/Herd Infection: Cultural Artifacts of Marginalization and the Dynamics of AIDS
Provedor de dados: 17
Autores: Rodrick Wallace.
We examine conditions under which high prevalence of infectious disease can become endemic within a community, in effect constituting a state of &amp;#x27;herd infection&amp;#x27; inverse to epidemiological herd immunity. For something like AIDS, under such circumstances, a single behavioral lapse or adverse accident will probably be a death sentence.
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Pharmacology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5864/version/1

Heterogeneity in Ty1-copia group of retroelements in chickpea (Cicer arietinum) genome
Provedor de dados: 17
Autores: Manoj K. Rajput; Kailash C. Upadhyaya.
Retrotransposons constitute a major fraction of plant genomes and these elements may have played a significant role in evolution and sequence organization of genomes. In order to access the diversity of Ty1-copia group of retroelements, reverse transcriptase (RT) sequences were amplified from chickpea genome, using the primers derived from two conserved domains of RT region. Thirty-six RT regions from independent amplicons were cloned and sequenced. On the basis of homology of deduced amino acids, the RT sequences could be grouped into three major families. The intra-family divergence at amino acid level ranges from 2 to 19%. Though intra-family RT sequences were conserved but no two sequences were identical. The results indicate a high degree of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/697/version/1

Hexose-6-phosphate dehydrogenase modulates the effect of inhibitors and alternative substrates of 11[beta]-hydroxysteroid dehydrogenase 1
Provedor de dados: 17
Autores: Zolt&amp;#xe1;n Bal&amp;#xe1;zs; Lyubomir G. Nashev; Charlie Chandsawangbhuwana; Michael E. Baker; Alex Odermatt.
Intracellular glucocorticoid reactivation is catalyzed by 11[beta]-hydroxysteroid dehydrogenase 1 (11[beta]-HSD1), which functions predominantly as a reductase in cells expressing hexose-6-phosphate dehydrogenase (H6PDH). We recently showed that the ratios of cortisone to cortisol and 7-keto- to 7-hydroxy-neurosteroids are regulated by 11[beta]-HSD1 and very much depend on co-expression with H6PDH, providing cosubstrate NADPH. Here, we investigated the impact of H6PDH on the modulation of 11[beta]-HSD1-dependent inter-conversion of cortisone and cortisol by inhibitors and alternative substrates. Using HEK-293 cells expressing 11[beta]-HSD1 or co-expressing 11[beta]-HSD1 and H6PDH, we observed significant differences of 11[beta]-HSD1 inhibition by natural...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2430/version/1

HGNC: The Why and How of Standardised Gene Nomenclature
Provedor de dados: 17
Autores: Ruth Seal; Susan Gordon; Michael Lush; Mathew Wright; Elspeth Bruford.
The HUGO Gene Nomenclature Committee (HGNC) aims to approve a unique gene symbol and gene name for every human gene.  Standardisation of gene symbols is necessary to allow researchers and curators to refer to the same gene without ambiguity.  Consistent use of gene symbols in publications and across different websites makes it easy for researchers to find all relevant information for a particular gene and facilitates data mining and retrieval.  For each gene that we name we curate relevant information including symbol aliases, chromosomal location, locus type, sequence accessions and links to relevant databases.  Therefore, our website is a central resource for human genetics. &amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;We endeavour to approve gene symbols that...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3182/version/1

Hierarchical coexistence of universality and diversity controls robustness and multi-functionality in intermediate filament protein networks
Provedor de dados: 17
Autores: Theodor Ackbarow; Markus  J. Buehler.
Proteins constitute the elementary building blocks of a vast variety of biological materials such as cellular protein networks, spider silk or bone, where they create extremely robust, multi-functional materials by self-organization of structures over many length- and time scales, from nano to macro.  Some of the structural features are commonly found in a many different tissues, that is, they are highly conserved.  Examples of such universal building blocks include alpha-helices, beta-sheets or tropocollagen molecules.  In contrast, other features are highly specific to tissue types, such as particular filament assemblies, beta-sheet nanocrystals in spider silk or tendon fascicles. These examples illustrate that the coexistence of universality and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Ecology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/826/version/1

Hierarchical inference of disparity
Provedor de dados: 17
Autores: Ivana Tosic; Bruno A. Olshausen.
Disparity selective cells in V1 respond to the correlated receptive fields of the left and right retinae, which do not necessarily correspond to the same object in the 3D scene, i.e., these cells respond equally to both false and correct stereo matches. On the other hand, neurons in the extrastriate visual area V2 show much stronger responses to correct visual matches [Bakin et al, 2000]. This indicates that a part of the stereo correspondence problem is solved during disparity processing in these two areas. However, the mechanisms employed by the brain to accomplish this task are not yet understood. Existing computational models are mostly based on cooperative computations in V1 [Marr and Poggio 1976, Read and Cumming 2007], without exploiting the...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5824/version/1

Hierarchical Model Composition updates
Provedor de dados: 17
Autores: Lucian Smith.
A summary of the status of the hierarchical model composition package for SBML Level 3, and of its current implementation.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6402/version/1

Hierarchical nanomechanics of collagen microfibrils
Provedor de dados: 17
Autores: Alfonso Gautieri; Simone  Vesentini; Alberto Redaelli; Markus J. Buehler.
Collagen constitutes one third of the human proteome, providing mechanical stability, elasticity and strength to connective tissues. Collagen is also the dominating material in the extracellular matrix (ECM) and is thus crucial for cell differentiation, growth and pathology. However, fundamental questions remain with respect to the origin of the unique mechanical properties of collagenous tissues, and in particular its stiffness, extensibility and nonlinear mechanical response. By using x-ray diffraction data of a collagen fibril reported by Orgel et al. (Proceedings of the National Academy of Sciences USA, 2006) in combination with protein structure identification methods, here we present an experimentally validated model of the nanomechanics of a...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4995/version/1

Hierarchical nanomechanics of collagen microfibrils
Provedor de dados: 17
Autores: Alfonso Gautieri; Simone  Vesentini; Alberto Redaelli; Markus J. Buehler.
Collagen constitutes one third of the human proteome, providing mechanical stability, elasticity and strength to organisms and is thus the prime construction materials in biology. Collagen is also the dominating material in the extracellular matrix and its stiffness controls cell differentiation, growth and pathology. However, the origin of the unique mechanical properties of collagenous tissues, and in particular its stiffness, extensibility and nonlinear mechanical response remains unknown. By using x-ray diffraction data of a collagen fibril (Orgel et al., PNAS, 2006) here we present an experimentally validated model of the nanomechanics of a collagen microfibril that incorporates the full biochemical details of the amino acid sequence of constituting...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4995/version/2

High efficiency transfection of thymic epithelial cell lines and primary thymic epithelial cells by Nucleofection
Provedor de dados: 17
Autores: Richard T. O&amp;#x27;Neil; Qiaozhi Wei; Brian G. Condie.
Thymic epithelial cells (TECs) are required for the development and differentiation of T cells and are sufficient for the positive and negative selection of developing T cells. Although TECs play a critical role in T cell biology, simple, efficient and readily scalable methods for the transfection of TEC lines and primary TECs have not been described. We tested the efficiency of Nucleofection for the transfection of 4 different mouse thymic epithelial cell lines that had been derived from cortical or medullary epithelium. We also tested primary mouse thymic epithelial cells isolated from fetal and postnatal stages. We found that Nucleofection was highly efficient for the transfection of thymic epithelial cells, with transfection efficiencies of 30-70% for...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6283/version/1

High energy-charged cell factory for heterologous protein synthesis
Provedor de dados: 17
Autores: Pil Kim; Hye Jung Kim; Yeong Deok Kwon; Sang Yup Lee.
Overexpression of gluconeogenic phosphoenolpyruvate carboxykinase (PCK) under glycolytic conditions enables Escherichia coli to maintain a greater intracellular ATP concentration and, consequently, to up-regulate genes for amino acid and nucleotide biosynthesis. To investigate the effect of a high intracellular ATP concentration on heterologous protein synthesis, we studied the expression of a foreign gene product, enhanced green fluorescence protein (eGFP), under control of the T7 promoter in E. coli BL21(DE3) strain overexpressing PCK. This strain was able to maintain twice as much intracellular ATP and to express two times more foreign protein than the control strain. These results indicate that a high energy-charged cell can be beneficial as a...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3953/version/1

High Perceptual Load Makes Monocular Attention Different
Provedor de dados: 17
Autores: Dingyuan Tan.
Attention is a fundamental function of the human which is important in our daily life. Perceptual load is thought to play an important role in selective attention^1,2^. When perceptual load is high, the distracting information will be kept out of perception and will not affect us. When perceptual load is low, the distracting information will be processed deeply by us and will influence us^3^. However, most of the past research was concerned with binocular attention instead of monocular attention. In spite of the differences such as visual acuity^4^, stereopsis^5,6^ between binocular and monocular vision, there were few reports of their difference regarding to perceptual load which means more items and features in our research. Here we show their difference...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5166/version/1

High Resolution Imaging of the Fusiform Face Area (FFA) Using Nonlinear Classifiers Shows Diagnosticity for Nonface Categories
Provedor de dados: 17
Autores: Stephen Hanson; Arielle Schmidt.
How are objects represented in the human visual pathway? This question continues to elude the neuroimaging field due to at least two kinds of problems: first, the relatively low spatial resolution of fMRI and second, the bias inherent in prevailing statistical methods for analyzing the actual diagnosticity of cortical tissue. We collected high-resolution (1mm x 1mm) imaging data of the fusiform face area (FFA) from 4 subjects while they categorized images as &amp;#x27;animal&amp;#x27;, &amp;#x27;car&amp;#x27;, &amp;#x27;face&amp;#x27;, or &amp;#x27;sculpture.&amp;#x27; We performed exploratory analysis to determine the nature of the distributions over classes and the similarity structure between classes. The FFA was visualized using nonmetric...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2235/version/1

Higher accuracy protein Multiple Sequence Alignment by Stochastic Algorithm
Provedor de dados: 17
Autores: M. S. Jeevitesh; Narayan Behera; Justin Jose; Krishna Kant; Alpana Dey.
Multiple Sequence Alignment gives insight into evolutionary, structural and functional relationships among the proteins. Here, a novel Protein Alignment by Stochastic Algorithm (PASA) is developed. Evolutionary operators of a genetic algorithm, namely, mutation and selection are utilized in combining the output of two most important sequence alignment programs and then developing an optimized new algorithm. Efficiency of protein alignments is evaluated in terms of Total Column score which is equal to the number of correctly aligned columns between a test alignment and the reference alignment divided by the total number of columns in the reference alignment. The PASA optimizer achieves, on an average, significant better alignment over the well known...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4258/version/1

Higher Efficiency In Prediction Of TIBO Activity By Evolutionary Neural Network
Provedor de dados: 17
Autores: Abhik Seal.
The treatment of acquired immunodeficiency syndrome (AIDS) is a challenging medical problem. TIBO is a nonnucleoside reverse transcriptase inhibitor, which binds non-competitively to the hydrophobic pocket on the p66 subunit of RT enzyme. We used a dataset consisting of physicochemical properties and reverse transcriptase inhibitor activities of 88 set of 4,5,6,7-tetrahydro-y-imidazo-[4,5,1-jk][1,4]-x-benzodiazepin-2-(1h)one derivatives that are variously substituted by halogens, alkyl groups. The dataset was taken from the BIOBYTE database at (www.davidhoekman.com). The concentration of the compound leading to 50% effect has been measured and expressed as IC50. The logarithm of the inverse of this parameter has been used as biological end points (log 1/C)...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5585/version/1

Highly Efficient Gene Expression in B Lymphocytes Mediating by Lentivirus Vector
Provedor de dados: 17
Autores: Akira Tempaku.
Gene transduction and expression efficiencies among several type cell lines were compared by using vesicular stomatitis virus-glycoprotein (VSV-G) pseudotyped human immunodeficiency virus type-1 (HIV-1) based lentivirus vector. Large discrepancies of the efficiencies were shown among them. B lymphocytes showed high susceptibility of gene transduction and expression, while other cell lines marked lower potential. Variable gene transduction strategies have been assessed to apply immunological therapies. This study showed that B lymphocytes had facilities enough to support the gene transduction and expression by lentivirus vector. Our result suggested that the lentivirus vector would be a powerful tool to express exogenous genes in B lymphocytes.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology.
Ano: 2012
URL: http://precedings.nature.com/documents/7030/version/1

High-order chromatin architecture determines the landscape of chromosomal  alterations in cancer
Provedor de dados: 17
Autores: Geoffrey  Fudenberg; Gad Getz; Matthew Meyerson; Leonid Mirny.
The rapid growth of cancer genome structural information provides an opportunity for a better understanding of the mutational mechanisms of genomic alterations in cancer and the forces of selection that act upon them. Here we test the evidence for two major forces, spatial chromosome structure and purifying (or negative) selection, that shape the landscape of somatic copy-number alterations (SCNAs) in cancer. Using a maximum likelihood framework we compare SCNA maps and three-dimensional genome architecture as determined by genome-wide chromosome conformation capture (HiC) and described by the proposed fractal-globule (FG) model. This analysis provides evidence that the distribution of chromosomal alterations in cancer is spatially related to...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6356/version/1

High-Throughput Transcriptome Profiling Of Human Mesenchymal Stem  Cells Reveals A Role For Wnt/GSK-3 Signaling In Their Hypoimmunomodulation
Provedor de dados: 17
Autores: Gurudutta Gangenahalli; Neeraj Satija; Farhat Afrin; Rajender Prasad Tripathi.
Mesenchymal stem cells (MSCs) are gaining importance among clinicians following recent demonstration of safe allogeneic transplantation due to their ability to modulate the immune response. However,the molecular machinery regulating the expression of immunomodulatory factors in MSCs is unknown. We, therefore, inhibited glycogen synthase kinase-3 (GSK-3),a Wnt signaling inhibitor, to elucidate the role of Wnt signaling in mediating immunoregulatory effects of human MSCs using gene expression profiling. Our results highlight enhanced ability of GSK-3 inhibitor (lithium) treated MSCs to evade immune response as a result of decreased expression of immune stimulatory cytokines and chemokines.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Immunology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5512/version/1

High-Value Phytochemicals from Grape Cane Waste: Potential Value-Added Viticultural Sources of Trans-Resveratrol and Trans-e-Viniferin with Medicinal and Anti-Phytopathogenic Applications
Provedor de dados: 17
Autores: Sierra Rayne.
Grape canes as agricultural waste from commercial viticultural activities represent a potentially important source of the well-known medicinal and anti-phytopathogenic stilbene compounds trans-resveratrol and trans-e-viniferin. Reports in the literature suggest that concentrations of these compounds range up to 5 mg/g dw and 2 mg/g dw, respectively, and can be quantitatively extracted from the cane residue using low-cost, environmental benign, and non-toxic aqueous alcoholic solvent systems such as ethanol:water mixtures. With current commercial values of  these compounds between US$2,000 to US$3,000 per kg, established stilbene yields from cane waste could represent an agricultural coproduct valued at US$2,000 to US$3,000 per hectare of production. At the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Pharmacology; Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/636/version/1

H-InvDB: A Comprehensive Annotation Resource For Human Transcriptome
Provedor de dados: 17
Autores: Chisato Yamasaki; Jun-ichi Takeda; Takuya Habara; Makoto Ogawa; Akiko Noda; Ryuichi Sakate; Katsuhiko Murakami; Tadashi Imanishi; Takashi Gojobori.
H-Invitational Database (H-InvDB: &amp;#x22;http://www.h-invitational.jp/&amp;#x22;:http://www.h-invitational.jp/) is a comprehensive annotation resource for human transcriptome. By extensive analyses of all human transcripts, we provide curated annotations of human genes, transcripts and proteins that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups.  The latest release of H-InvDB (release 7.0) provides annotation for 296,912 human transcripts in...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5272/version/1

H-InvDB: A Comprehensive Annotation Resource For Human Transcriptome
Provedor de dados: 17
Autores: Chisato Yamasaki; Jun-ichi Takeda; Takuya Habara; Makoto Ogawa; Akiko Noda; Ryuichi Sakate; Katsuhiko Murakami; Tadashi Imanishi; Takashi Gojobori.
H-Invitational Database (H-InvDB: &amp;#x22;http://www.h-invitational.jp/&amp;#x22;:http://www.h-invitational.jp/) is a comprehensive annotation resource for human transcriptome. By extensive analyses of all human transcripts, we provide curated annotations of human genes, transcripts and proteins that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups.  The latest release of H-InvDB (release 7.0) provides annotation for 296,912 human transcripts in...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5271/version/1

H-InvDB release 6, a comprehensive annotation resource for human genes and transcripts
Provedor de dados: 17
Autores: Chisato Yamasaki; Katsuhiko Murakami; Jun-ichi Takeda; Yoshiharu Sato; Akiko Noda; Ryuichi Sakate; Takuya Habara; Hajime Nakaoka; Fusano Todokoro; Akihiro Matsuya; Tadashi Imanishi; Takashi Gojobori.
H-Invitational Database (H-InvDB; &amp;#x22;http://www.h-invitational.jp/&amp;#x22;:http://www.h-invitational.jp/) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing isoforms, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms, relation with diseases, gene expression profiling, molecular evolutionary features, protein-protein interactions (PPIs) and gene families/groups.  The latest release of H-InvDB (release 6.0) provide annotation for 219,765 human transcripts in 43,159 human gene...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3251/version/1

Historical deforestation patterns and the conservation value of church forests in the northern Ethiopian highlands
Provedor de dados: 17
Autores: Raf Aerts; Richard Pankhurst; Koen Van Overtveld; Eva J. J. November; Martin Hermy; Bart Muys.
Mountain forest plants have a limited capacity for migration because altitudinal gradients usually set strict limits to plant species&amp;#x2019; ranges and often present physical barriers against dispersal.  Innate &amp;#x2018;islands&amp;#x2019; of biodiversity, mountain forests are therefore particularly vulnerable to the effects of climatic change and habitat fragmentation, both key drivers of global species loss.  Conservation of these ecosystems must for that reason rely on protecting not only large fragments but also small habitat patches and relictual vegetation along a wide altitudinal range.&amp;#xd;&amp;#xa;When large fragments in such ecosystems are no longer available, small fragments become an environmental priority.  Striking examples of...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1786/version/1

Historical temporal trends in groundwater levels from British Columbia, Canada
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
A time trend study of groundwater monitoring well levels was conducted in British Columbia, Canada. Trend data was available for a total of 210 groundwater monitoring well stations throughout the province with end-of-month water levels over the period of record. Significant temporal trends in groundwater levels were found at 67 stations (40.4% of all stations amenable to statistical examination, and 31.9% of all available stations). Of these 67 stations, 10 had increasing groundwater level trends and the remaining 57 had declining groundwater level trends. Thus, 34.3% of stations with a sufficiently long time series for analysis displayed declining groundwater level trends, while 6.0% have increasing trends, and 59.6% of these stations appear to have no...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/6844/version/1

Historical temporal trends in monthly, seasonal, and annual mean, minimum, and maximum streamflows from the Okanagan River watershed in south-central British Columbia, Canada
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Historical trends in monthly, seasonal, and annual mean streamflows, as well as minimum and maximum monthly streamflows, were investigated at nine hydrometric stations in the Okanagan River watershed from south-central British Columbia, Canada. Overall, mean annual streamflows in the Okanagan River watershed are not exhibiting any significant time trends. No consistent declines in monthly minimum streamflows are evident at any point during the hydrologic year. Mean monthly and monthly maximum streamflows in tributary streams to the mainstem system appear to be significantly increasing over time during the spring snowmelt period of March and April. Any temporal changes in flow patterns at the mainstem Okanagan River stations likely reflect alterations in...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6662/version/1

Historical temporal trends in overwinter and spring snowpack for the Okanagan and Similkameen River watersheds in south-central British Columbia, Canada
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Potential historical temporal trends in the overwinter and spring snowpack were investigated for the Canadian portions of the Okanagan and Similkameen Valleys in south-central British Columbia. Significant evidence is available that the Okanagan and Similkameen River watersheds are exhibiting both spatially and temporally heterogeneous declines in snowpacks over the past several decades, but whether the causes are part of a natural cycle or result from longer term climatic changes is not clear. The variability in the magnitude, timing, and location of any significant time trends in snowpack decline also precludes efforts towards developing reliable hydrologic models that reflect a response to potential future changes in snowpack patterns for these regions...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6590/version/1

Historical Trends in Annual Water Yields for the Okanagan Basin, British Columbia, Canada
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
The Okanagan Basin in south-central British Columbia, Canada, includes the Okanagan River watershed upstream from the outlet of Osoyoos Lake, with a total area of 8,046 km^2^. Over the past century, the population of the Basin has grown rapidly, and this trend is expected to continue. Water management issues attract significant attention in the region, given projected declines in supply and increases in demand. Historical streamflow data was obtained for three hydrometric stations on the Okanagan River between the outlet of Okanagan Lake at Penticton and near the U.S. border at Oliver. Collectively, the historical data series indicate no temporal changes in regional annual water yields for the Okanagan Basin over the past century, despite large increases...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4946/version/1

History and Philosophy of Gene Environment Interaction
Provedor de dados: 17
Autores: Kenneth  Schaffner.
Dr. Kenneth Schaffner gave a brief introduction to the symposium topics.  He began with a history of the thinking on gene-environment interactions and described the ensuing controversies.  He cited the lack of a consensus theory of the environment and then described some methodological and technological advances in the studies of gene-environment interactions.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To watch Dr. Schaffner&amp;#x2019;s presentation, please see the Panel 1 &amp;#x22;Google Video posting.&amp;#x22;:http://video.google.com/videoplay?docid=-3097337289947323438&amp;#x26;hl=en
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2656/version/1

HMGA1a induces aberrant splicing of estrogen receptor &amp;#x3b1; in MCF-7 breast cancer cells
Provedor de dados: 17
Autores: Kenji Ohe; Toshiaki Utsumi; Akila Mayeda.
The well known transcription factor, HMGA1a, also known as an oncogene, causes aberrant splicing of Presenilin-2 found in sporadic Alzheimer&amp;#x27;s disease, through sequence specific RNA binding. Since HMGA1 protein levels correlate with tumorigenic malignancy, we are interested in the potential of HMGA1a as an aberrant splicing factor in cancer. The N-terminal truncated isoform of Estrogen Receptor alpha, ER&amp;#x3b1;46, is known to increase expression when breast cancer cells (MCF-7) become hyperconfluent. Transiently expressed HMGA1a induced ER&amp;#x3b1;46 mRNA expression. Plasmid driven micro RNA containing the presenilin-2 HMGA1a RNA binding site and a micro RNA nuclear localization signal (miR_HMGBS_NLS), inhibited ER&amp;#x3b1;46 mRNA...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4104/version/2

HMGB1 release by C5a anaphylatoxin is an effective target for sepsis treatment
Provedor de dados: 17
Autores: Hidechika Okada; Noriko Okada; Masaki Imai; Alan Okada; Fumiko Ono.
Antibodies to C5a have proven to be effective in treating experimental septic primate models. A 17 amino acid peptide (ASGAPAPGPAGPLRPMF) named PepA binds to C5a and prevents complement-mediated lethal shock in rats. AcPepA harboring an acetyl group at the N-terminal alanine showed increased inhibitory activity against C5a. Cynomolgus monkeys destined to expire from a lethal dose of bacterial endotoxin (4mg/kg) were rescued by intravenous administration of AcPepA. AcPepA could have interfered with the ability of C5a to stimulate C5L2 which is responsible for HMGB1 release and stimulation of TLR4 as an endogeneous ligand with LPS behavior. The suppression of HMGB1 release by AcPepA administration to LPS-shock monkeys is likely responsible for rescuing the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5727/version/1

Homeoprotein Hbx4 represses adhesion molecule governing cytokinesis and development
Provedor de dados: 17
Autores: Ji-Sun Kim; Ji-Hui Seo; Hyung-Soon Yim; Sa-Ouk Kang.
Homeobox genes encode proteins with a highly conserved DNA-binding motif and provoke morphological diversification of body segments by differentially controlling the expression of downstream targets. Here, we have identified _hbx4_, one of many homeobox genes in _Dictyostelium discoideum_ and investigated its role during growth and development. In suspension, Hbx4-overexpressing cells, Hbx4^OE^, showed defects in cytokinesis and growth rate. During development, Hbx4^OE^ and _hbx4_-disrupting cells, _hbx4&amp;#xaf;_ made differences in shape of mound and slug, cell-type proportioning from wild type KAx3 cells. These phenotypes were similar to those of mutant defective in _cadA_ encoding Ca^2+^-dependent cell adhesion molecule so that we investigated the...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4194/version/1

Homochirality through Photon-Induced Melting of RNA/DNA: the Thermodynamic Dissipation Theory of the Origin of Life
Provedor de dados: 17
Autores: Karo Michaelian.
The homochirality of the molecules of life has been a vexing problem with no generally accepted solution to date. Since a racemic mixture of chiral nucleotides frustrates the extension and replication of RNA and DNA, understanding the origin of homochirality has important implications to the investigation of the origin of life. Theories on the origin of life have generally elected to presume an abiotic mechanism giving rise to a large prebiotic enantiomer enrichment. Although a number of such mechanism have been suggested, none has enjoyed sufficient plausibility or relevance to be generally accepted. Here we suggest a novel solution to the homochirality problem based on a recently proposed thermodynamic dissipation theory for the origin of life. The...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5177/version/1

Homocysteic acid as a pathogen for Alzheimer&amp;#x27;s disease
Provedor de dados: 17
Autores: Tohru Hasegawa.
It has been considered that Alzheimer&amp;#x2019;s disease may be induced by multi-pathogenic factors.  However recent Nature Genetics has reported that sporadic Alzheimer&amp;#x2019;s disease is also genetically determined by such as ApoE4, Clusterin, so on. We already understand familiar Alzheimer&amp;#x2019;s disease is determined by such APP, Presenilin genes. These reports should allow us to consider that these genes stimulate the biological process and consequently Alzheimer&amp;#x2019;s disease would be determined by certain pathogen. Then what is the pathogen? First this pathogen should be stimulated by certain biological process by these genetic activation, which I mean that these genes separately work to induce this pathogen. I really propose...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3739/version/1

Homologous self-organising scale-invariant properties characterise long range species spread and cancer invasion
Provedor de dados: 17
Autores: Diana D. E. Marco; Sergio S. A. Cannas; Marcelo M. A. Montemurro; Bo Hu; Shiyuan Cheng.
The invariance of some system properties over a range of temporal and/or spatial scales is an attribute of many processes in nature1, often characterised by power law functions and fractal geometry2. In particular, there is growing consensus in that fat-tailed functions like the power law adequately describe long-distance dispersal (LDD) spread of organisms 3,4. Here we show that the spatial spread of individuals governed by a power law dispersal function is represented by a clear and unique signature, characterised by two properties: A fractal geometry of the boundaries of patches generated by dispersal with a fractal dimension D displaying universal features, and a disrupted patch size distribution characterised by two different power laws. Analysing...
Tipo: Manuscript
Palavras-chave: Cancer; Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/907/version/1

Homologous self-organising scale-invariant properties characterise long range species spread and cancer invasion
Provedor de dados: 17
Autores: Diana E. Marco; Sergio A. Cannas; Marcelo A. Montemurro; Bo Hu; Shi-Yuan Cheng.
Occupancy of new habitats through dispersion is a central process in nature. In particular, long distance dispersal is involved in the spread of species and epidemics, although it has not been previously related with cancer invasion, a process that involves cell spreading to tissues far away from the primary tumor.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Using simulations and real data we show that the early spread of cancer cells is similar to the species individuals spread and that both processes are represented by a common spatio-temporal signature of long-distance dispersal and subsequent local proliferation. This signature is characterized by a particular fractal geometry of the boundaries of patches generated, and a power law-scaled, disrupted patch size...
Tipo: Manuscript
Palavras-chave: Cancer; Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/907/version/2

Homology modeling and docking studies to explore the novel drug for monocyte differentiation antigen CD14
Provedor de dados: 17
Autores: Bhimisetty Reshma; Sandeep Swaragam; Amineni Umamaheswari.
Monocyte differentiation antigen CD14 belongs to the leucine rich family. Elevated levels of monocyte differentiation antigen CD14 and toll-like receptor 4 (TLR4) play a major role in inflammatory response and cause ischemic heart diseases, neuropathic pain and LPS (endotoxin) induced septic shock. IAXO compounds (IAXO-101, IAXO-102 and IAXO-103) inhibit the CD14-dependent and TLR4-independent signaling pathways but they have severe side effects.  Due to unavailability of human monocyte differentiation antigen CD14 crystal structure, 3D structure was constructed based on template structure (1WWL) using Modeler 9v9. The modeled structure was refined, energy minimized and validated. Binding site residues of human monocyte differentiation antigen CD14 were...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6580/version/1

Homology modeling and in silico screening of inhibitors for human CD5 antigen-like protein involved in cardiovascular disease
Provedor de dados: 17
Autores: Varala Sravani; S Rajitha Reddy; Amineni Umamaheswari.
CD5L (CD5 antigen -like) is a secreted glycoprotein that belongs to the SRCR (scavenger receptor cysteine rich) group B family of proteins that regulate leukocyte function. Over expression of human CD5L leads to Kawasaki disease and atherosclerosis. In the quest of designing novel inhibitors against CD5L, homology models for the protein were predicted based on crystal structures of 1BY2, 2OYA and 2OY3 as multiple templates using Modeller 9v9. The CD5L homology models were selected using GA341 score, DOPE score, PROCHECK and ProSA to select the best model. The selected CD5L model was analyzed using CASTp to locate the largest ligand binding pocket. Five known inhibitors of human CD5L were searched for structural analogs from Ligand.Info Meta database. The...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6586/version/1

Homology Modeling of Human &amp;#x3b1;~2A~-Adrenoceptor
Provedor de dados: 17
Autores: Jignesh Patel; Gourja G; Vivek Kumar; Yogesh Narkhede; Shikhar Gupta; C. Gopi Mohan.
&amp;#x3b1;~2A~-adrenoceptor (ADA2A) is a membrane bound receptor which has been classified as the member of larger superfamily G-protein coupled receptors (GPCRs); also known as seven transmembrane (7-TM) domains receptor. Around 50% drugs currently available in the market exert their effects through GPCRs. Membrane proteins are difficult to crystallize as compared to soluble proteins. There is a need of 3D-structure of ADA2A to understand   binding modes of various agonists and antagonists and hence homology model of ADA2A was developed. Homology model of ADA2A constructed based on crystal structure of &amp;#x3b2;~2~-adrenoceptor. The crystal structure of &amp;#x3b2;~2~-adrenoceptor (PDB ID: 2RH1) was used as template, which has good sequence identity...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4106/version/1

Host factors affecting abomasal parasites in Alpine Ibex
Provedor de dados: 17
Autores: Roberta  Ceccarelli; Valentina Valenti; Paolo Lanfranchi; Nicola Ferrari.
Alpine ibex is characterized by strong sexual differences, both morphological and in population dynamics. Host sex has been shown to strongly affect parasite load with males usually more infected than females. Moreover ibex exhibit a peculiar pattern of survival with subadult males having a slow growing rate coupled with high survival which rapidly decline in old individual. This peculiar life history has been suggested to have been developed as adaptation to an harsh environment. In this way by investing fewer resources in growing the ibex can direct more energy in survival. At the same time the investment in immunodefence can change over the age. To verify the hypothesis that sex and age affect parasite infection, we analysed the abomasal parasite...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3805/version/1

Host Genetics and Viral Diversity: Report from a Global HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: Andrew McMichael; Francine  McCutchan; the Working Group convened by the Global HIV Vaccine Enterprise.
The Global HIV Vaccine Enterprise convened a workshop in September 2009 to discuss human and viral genetic variation and its impact on future directions for HIV vaccine research and development. The formidable challenges presented by virus and host genetic variability are interrelated and complicate vaccine development. HIV vaccine researchers need to develop innovative approaches that will facilitate addressing these questions in novel ways.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4797/version/1

Host Genetics and Viral Diversity: Report from a Global HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: Andrew McMichael; Francine  McCutchan; the Working Group convened by the Global HIV Vaccine Enterprise.
The Global HIV Vaccine Enterprise convened a workshop in September 2009 to discuss human and viral genetic variation and its impact on future directions for HIV vaccine research and development. The formidable challenges presented by virus and host genetic variability are interrelated and complicate vaccine development. HIV vaccine researchers need to develop innovative approaches that will facilitate addressing these questions in novel ways.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4797/version/2

Hot Cradle of El Ni&amp;#xf1;o
Provedor de dados: 17
Autores: Liguang Sun; Zhouqing Xie.
Here we propose that the El Ni&amp;#xf1;o is originated in the region of west-east oriented Galapagas ocean ridge and hydrothermal plumes. This region has a distinct tectonic structure: the subductions of ocean ridges go under continental volcanic activity zones; a special geographic location: equatorial ocean currents almost coincide with ocean ridge; and a unique south-north oriented convergent epi-continent ocean currents. The striking correlation between El Ni&amp;#xf1;o, seismic and submarine volcanic activities in this area and earth rotation speed changes strongly suggests that the sea floor near Peru coast sounds the &amp;#x22;Hot Cradle&amp;#x22; of El Ni&amp;#xf1;o.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1764/version/1

How and why physicists and chemists use blogs
Provedor de dados: 17
Autores: Christina K. Pikas.
This study examined how and why chemists and physicists blog. Two qualitative methods were used: content analysis of blog and &amp;#x201c;about&amp;#x201d; pages and in-depth responsive interviews with chemists and physicists who maintain blogs. Analysis of the data yielded several cross-cutting themes that provide a window into how physicists and chemists use their blogs and what value they receive from maintaining a blog and participating in a blogging community. The article concludes with a discussion of implications for supporting scientists&amp;#x2019; work.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4429/version/1

How Britain became an island
Provedor de dados: 17
Autores: Philip Gibbard.
Island Britain is separated from the European continent by the English Channel and the North Sea. But it was not always so. The floor of the Channel provides evidence for two catastrophic floods arising from the drainage of huge glacial lakes in the area of the southern North Sea. These megafloods carved the Dover Strait to make Britain the island it is today.
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1205/version/1

How can cells in the anterior medial face patch be viewpoint invariant?
Provedor de dados: 17
Autores: Joel Z. Leibo; Jim Mutch; Tomaso Poggio.
In a recent paper, Freiwald and Tsao (2010) found evidence that the responses of cells in the macaque anterior medial (AM) face patch are invariant to significant changes in viewpoint. The monkey subjects had no prior experience with the individuals depicted in the stimuli and were never given an opportunity to view the same individual from different viewpoints sequentially. These results cannot be explained by a mechanism based on temporal association of experienced views. Employing a biologically plausible model of object recognition (software available at cbcl.mit.edu), we show two mechanisms which could account for these results. First, we show that hair style and skin color provide sufficient information to enable viewpoint recognition without...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5845/version/1

How could a natural catastrophe impact the ecology of a species? The Nicobar megapode and tsunami
Provedor de dados: 17
Autores: Sivakumar Kuppusamy.
This study on the impact of the 2004 tsunami on the Nicobar megapode Megapodius nicobariensis, endemic coastal living bird species in the Nicobar group of islands showed a significant decline (nearly 70%) in the number of individuals when compared to before tsunami populations (Paired sample test, t=2.061, df=14, p&amp;#x3c;0.05). The tsunami has also adversely influenced the nest-site selection of the megapodes. The post tsunami impact on this species is also expected to be severe, pushing the species into the category of &amp;#x22;critically endangered&amp;#x22;.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1627/version/1

How do we quantify biodiversity? All the evidence in one place.
Provedor de dados: 17
Autores: Olga Lyashevska.
Biodiversity is a multi-dimensional concept that is represented by a large variety of measures. This complexity and lack of consistency limits the development of a coherent scientific understanding of biodiversity and how properties, such as ecosystem services, may depend on it. Here, I demonstrate that the formal discipline of creating a relational database (RDB) for information about biodiversity and its measures,  is a useful tool in organising such knowledge into coherent sense. Following steps of the logical database design and data normalization to build a RDB, results in a formal definition of biodiversity within a well defined concept structure; mapping rules between the concepts of biodiversity and entities of RDB and a consistent information...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3327/version/1

How do you choose your literature search tool(s)?
Provedor de dados: 17
Autores: Kshitish  K. Acharya; Greta Kasliwal; Haritha Haridas.
With increasing number of bio-literature search engines, scientists and health professionals either make a subjective choice of tool(s) or face a challenge of analyzing multiple features of a plethora of bibliographic software. There is an urgent need for a thorough comparative analysis of the available literature scanning tools, from the user&amp;#x2019;s perspective. We report results of the first time semi-quantitative comparison of 21 search programs, which can search published (partial or full text) documents in life science areas. The observations can assist life science researchers and medical professionals to make an informed selection among the programs, depending on their search objectives. &amp;#xd;&amp;#xa;Some of the important findings are:...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2101/version/2

How gut sampling and microbial invasiveness/noninvasiveness provides mucosal immunity with a nonmolecular pattern means to distinguish commensals from pathogens: A review
Provedor de dados: 17
Autores: John R. Skoyles.
Mucosal immunity distinguishes not only different microbial antigens but also separates those of pathogens from those of commensals. How this is done is unknown. The present view is that the pathogen/commensal determination of antigens depends upon as yet to be discovered molecular patterns. Here I review the biological feasibility that it also involves the detection of the invasive differences in their motility towards the gut wall when they are sampled by differently biased methods. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;By their nature, pathogens and commensals have different motility &amp;#x2013; invasive and noninvasive &amp;#x2013; in regard to the epithelium. The immune system is in a position to detect such motility differences. This biological...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/1895/version/1

How Predictable are Temperature-series Undergoing Noise-controlled Dynamics in the Mediterranean
Provedor de dados: 17
Autores: Nazzareno Diodato; Gianni Bellocchi.
Mediterranean is thought to be sensitive to global climate change, but its future interdecadal variability is uncertain for many climate models. A study was made of the variability of the winter temperature over the Mediterranean Sub-regional Area (MSA), employing a reconstructed temperature series covering the period 1698 to 2010. This paper describes the transformed winter temperature data performed via Empirical Mode Decomposition for the purposes of noise reduction and statistical modeling. This emerging approach is discussed to account for the internal dependence structure of natural climate variability.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5786/version/1

How the Discovery of Brain Correlates of Consciousness Supports Non-Reductive Physicalism
Provedor de dados: 17
Autores: Alfredo Pereira Jr.
In this work I attempt to justify the claim that the discovery of statistically relevant brain correlates of consciousness supports Non-Reductive Physicalism. First I distinguish the main varieties of Reductive and Non-Reductive Physicalism, selecting the right one that is benefited by progress in brain sciences. Second, I discuss epistemological problems in the search of brain correlates of consciousness, focusing on the simultaneous occurrence of conscious activity, known by means of subjective report, and the corresponding brain activity, registered with the help of technology. Finally, I argue &amp;#x2013; using Salmon&amp;#xb4;s concept of Statistical Explanation - that statistics affords a distinction of causal (physical) from casual (illusory)...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/6969/version/1

HP-23: Co-ordinated Regulation of Gene Expression in H. Pylori in Response to Low pH and Iron Limiting Growth Conditions
Provedor de dados: 17
Autores: Ananya Gupta; Sergey Ustinov; Kaveh Mashayekhi; Anthony P. Moran.
Establishing a successful infection within the gastric environment and its varied and changing niches requires adaptation achieved through regulation of bacterial gene expression. In the gastric environment in addition to the low pH Helicobacter pylori is required to adapt to conditions of iron limitation. In this study, we used cDNA microarrays to identify genes whose expression was altered when the bacterium was grown under differing conditions of pH (5 versus 7) and iron limitation. cDNA microarray analyses following exposure to different growth conditions were carried out for three H. pylori strains 26695 (gastritis-associated), J99 (ulcer-associated) and AG-1 (atrophic gastritis-associated). Genes were identified whose expression was acid pH-dependent...
Tipo: Poster
Palavras-chave: Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/5842/version/1

HTRIdb: an open-access database for experimentally verified human transcriptional regulation interactions
Provedor de dados: 17
Autores: Luiz A. Bovolenta; Marcio L. Acencio; Ney Lemke.
Background: The modeling of interactions among transcription factors (TFs) and their respective target genes (TGs) into transcriptional regulatory networks is important for the complete understanding of regulation of biological processes. In the case of human TF-TG interactions, there is no database at present that explicitly provides such information even though many databases containing human TF-TG interaction data have been available. In an effort to provide researchers with a repository of TF-TG interactions from which such interactions can be directly extracted, we present here the Human Transcriptional Regulation Interactions database (HTRIdb).&amp;#xd;&amp;#xa;Description: The HTRIdb is an open-access database of experimentally validated...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6995/version/1

HTself2: Combining p-values to Improve Classification of Differential Gene Expression in HTself
Provedor de dados: 17
Autores: Daniel A. Cortez; Angela P. Tonon; Pio Colepicolo; Ricardo Z. N. V&amp;#xea;ncio.
HTself is a web-based bioinformatics tool designed to deal with the classification of differential gene expression for low replication microarray studies. It is based on a statistical test that uses self-self experiments to derive intensity-dependent cutoffs. The method was previously described in V&amp;#xea;ncio et al, (DNA Res. 12: 211- e 214, 2005). In this work we consider an extension of HTself by calculating p-values instead of using a fixed credibility level &amp;#x3b1;. As before, the statistic used to compute single spots p-values is obtained from the gaussian Kernel Density Estimator method applied to self-self data. Different spots corresponding to the same biological gene (replicas) give rise to a set of independent p-values which can be...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4855/version/1

Human Cancer Cells Express Slug-based Epithelial-Mesenchymal Transition Gene Signature Obtained in Vivo
Provedor de dados: 17
Autores: Dimitris Anastassiou; Viktoria Rumjantseva; Wei-yi Cheng; Jianzhong Huang; Peter D. Canoll; Darrell J. Yamashiro; Jessica J. Kandel.
The biological mechanisms underlying cancer cell motility and invasiveness remain unclear, although it has been hypothesized that they involve some type of epithelial-mesenchymal transition (EMT). Here we show that human cancer cells express in vivo a precise multi-cancer invasion-associated gene expression signature characterized by the prominent presence of collagen COL11A1 and thrombospondin THBS2. The signature is present in the expression of all solid tumor datasets that we analyzed and includes numerous EMT markers, among them the transcription factor Slug, fibronectin, and &amp;#x3b1; SMA. Using xenograft models of human cancer cells in immunocompromised mice and profiling the harvested tumors separately with species specific probes, we found that...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6243/version/1

Human Heart Development Pathways
Provedor de dados: 17
Autores: Samuel Sklar; Alexander Pico.
This pathway has been largely adapted from an article by Deepak Srivastava, Cell. 2006 Sep 22;126(6):1037-48. In this pathway are known transcription factors, miRNAs and regulatory proteins that impact the regional specificity of the human heart. Activating signals are indicated by arrows while inhibitory signals are indicated by T-bars. Special thanks to Kim Cordes for her assistance in revising this pathway, based on recent heart development research. A live version of the pathway can be found at http://www.wikipathways.org/index.php/Pathway:WP1591
Tipo: Poster
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6500/version/1

Human Immune Responses to Plasmodium falciparum infection: Molecular Evidence for a Suboptimal TH&amp;#x3b1;&amp;#x3b2;(TH9) and TH17 Bias over Ideal and Effective Traditional TH1 Immunity
Provedor de dados: 17
Autores: Wan-Chung(Wan-Jiung) Hu; August Louis Bourgeois; Nathan Wolfe; Sher Singh; Anne Jedlicka; Alan Scott.
Using microarray analysis, we showed up-regulation of  Toll-like receptors 1,2,4,7,8, NF-[kappa][BETA], TNF-[alpha], p38-MAPK and MHC molecules in human peripheral blood mononuclear cells following infection with Plasmodium falciparum. We report herein further studies based on time-course microarray analysis with a focus on malaria-induced host immunity.  Results show that in early malaria; selected immunity-related genes were up-regulated including alpha, beta, and gamma interferon related genes, as well as genes of IL-15, CD36, chemokines (CXCL10, CCL2, S100A8/9, CXCL9, and CXCL11), TRAIL and IgG Fc receptors.  During acute febrile malaria, up-regulated genes included alpha, beta, and gamma interferon related genes, IL-8, IL-1[beta], IL-10 downstream...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5930/version/1

Human metabolic adaptations and prolonged expensive neurodevelopment: A review
Provedor de dados: 17
Autores: John R. Skoyles.
1.&amp;#x9;After weaning, human hunter-gatherer juveniles receive substantial (&amp;#x2248;3.5-7 MJ day^-1^), extended (&amp;#x2248;15 years) and reliable (kin and nonkin food pooling) energy provision.&amp;#xd;&amp;#xa;2.&amp;#x9;The childhood (pediatric) and the adult human brain takes a very high share of both basal metabolic rate (BMR) (child: 50-70%; adult: &amp;#x2248;20%) and total energy expenditure (TEE) (child: 30-50%; adult: &amp;#x2248;10%).&amp;#xd;&amp;#xa;3.&amp;#x9;The pediatric brain for an extended period (&amp;#x2248;4-9 years-of-age) consumes roughly 50% more energy than the adult one, and after this, continues during adolescence, at a high but declining rate. Within the brain, childhood cerebral gray matter has an even higher 1.9 to...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Neuroscience; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1856/version/2

Human metabolic adaptations and prolonged expensive neurodevelopment: A review
Provedor de dados: 17
Autores: John R. Skoyles.
1.&amp;#x9;After weaning, human hunter-gatherer juveniles receive substantial (&amp;#x2248;3.5-7 MJ day^-1^), extended (&amp;#x2248;15 years) and reliable (kin and nonkin food pooling) energy provision.&amp;#xd;&amp;#xa;2.&amp;#x9;The childhood (pediatric) and the adult human brain takes a very high share of both basal metabolic rate (BMR) (child: 50-70%; adult: &amp;#x2248;20%) and total energy expenditure (TEE) (child: 30-50%; adult: &amp;#x2248;10%).&amp;#xd;&amp;#xa;3.&amp;#x9;The pediatric brain for an extended period (&amp;#x2248;4-9 years-of-age) consumes roughly 50% more energy than the adult one, and after this, continues during adolescence, at a high but declining rate. Within the brain, childhood cerebral gray matter has an even higher 1.9 to...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1856/version/1

Human microglial cells synthesize albumin in brain
Provedor de dados: 17
Autores: Sung-Min Ahn; Kyunghee Byun; Kun Cho; Jin Young Kim; Jong Shin Yoo; Deokhoon Kim; Sun Ha Paek; Seung U. Kim; Richard J. Simpson; Bonghee Lee.
Albumin has been implicated in Alzheimer&amp;#x27;s disease since it can bind to and transport amyloid beta, the causative agent; albumin is also a potent inhibitor of amyloid beta polymerization. In a pilot phase study of Human Brain Proteome Project, we found evidence that albumin may be synthesized in immortalized human microglial cells, human primary microglial cells, and human fetal and adult brain tissues. We also found the synthesis and secretion is enhanced upon microglial activation by Amyloid [beta]~1-42~, lipopolysaccharide treatment or human Alzheimer&amp;#x27;s brain.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1652/version/1

Human neuromaturation, juvenile extreme energy liability, and adult cognition/cooperation
Provedor de dados: 17
Autores: John Skoyles.
Human childhood and adolescence is the period in which adult cognitive competences (including those that create the unique cooperativeness of humans) are acquired. It is also a period when neural development puts a juvenile&amp;#x2019;s survival at risk due to the high vulnerability of their brain to energy shortage. The brain of a 4 year-old human uses &amp;#x2248;50% of its total energy expenditure (TEE) (cf. adult &amp;#x2248;12%). This brain expensiveness is due to (1) the brain making up &amp;#x2248;6% of a 4 year-old body compared to 2% in an adult, and (2) increased energy metabolism that is &amp;#x2248;100% greater in the gray matter of a child than in an adult (a result of the extra costs of synaptic neuromaturation). The high absolute number of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Neuroscience; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7096/version/1

Human ovarian reserve from conception to the menopause
Provedor de dados: 17
Autores: William H. B. Wallace; Thomas W. Kelsey.
Current understanding is that the human ovary contains a fixed number of several million non-growing follicles (NGF), established by five months of gestational age, that declines with increasing age to the menopause when approximately 1,000 NGF remain at an average age of 50-51 years. With approximately 450 ovulatory monthly cycles in the normal human reproductive lifespan, this progressive decline in NGF numbers is attributed to follicle death by apoptosis. Individual histological studies have quantified NGF numbers over limited age ranges. However, no model describing the rate of establishment and decline of the NGF population from conception to menopause has been previously reported. Here we describe the best fitting model of the age-related NGF...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3179/version/1

Human Transcript Database Search Showed Existence Of Extremely Short Introns
Provedor de dados: 17
Autores: Makoto Shimada; Noriko Haraguchi; Akila Mayeda.
Since pre-mRNA splicing is processed by a spliceosome that is a huge complex consists of RNAs and as many as 200 proteins, it is considered that minimum intron size is limited by molecular size of the spliceosome.  To understand splicing mechanism, we investigate human intron size distribution using annotated transcriptome database, H-InvDB.  Distribution of obtained intron length shows that there is a mode at 83 nt in length with 4049 transcripts and number of introns decreases drastically in shorter than 65 nt, where numbers of transcripts in each locus also decrease.  However, some introns less than 65 nt are observed, both shows high Codon Adaptation Index (CAI) and also observed orthologous transcripts in other mammals.  These suggests that there is a...
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5115/version/1

Human-triggered earthquakes and their impacts on human security
Provedor de dados: 17
Autores: Christian D. Klose.
A comprehensive understanding of earthquake risks in urbanized regions requires an accurate assessment of both urban vulnerabilities and earthquake hazards. Socioeconomic risks associated with human-triggered earthquakes are often misconstrued and receive little scientific, legal, and public attention. However, more than 200 damaging earthquakes, associated with industrialization and urbanization, were documented since the 20th century. This type of geohazard has impacts on human security on a regional and national level. For example, the 1989 Newcastle earthquake caused 13 deaths and US$3.5 billion damage (in 1989). The monetary loss was equivalent to 3.4 percent of Australia&amp;#x2019;s national income (GDI) or 80 percent of Australia&amp;#x2019;s GDI...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4745/version/3

Human-triggered earthquakes and their impacts on human security
Provedor de dados: 17
Autores: Christian Klose.
A comprehensive understanding of earthquake risks in urbanized regions requires an accurate assessment of both urban vulnerabilities and earthquake hazards. Socioeconomic risks associated with human-triggered earthquakes are often misconstrued and receive little scientific, legal, and public attention. However, more than 200 damaging earthquakes, associated with industrialization and urbanization, were documented since the 20th century. This type of geohazard has impacts on human security on a regional and national level. For example, the 1989 Newcastle earthquake caused 13 deaths and US$3.5 billion damage (in 1989). The monetary loss was equivalent to 3.4 percent of Australia&amp;#x2019;s national income (GDI) or 80 percent of Australia&amp;#x2019;s GDI...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4745/version/1

Human-triggered earthquakes and their impacts on human security
Provedor de dados: 17
Autores: Christian Klose.
A comprehensive understanding of earthquake risks in urbanized regions requires an accurate assessment of both urban vulnerabilities and earthquake hazards. Socioeconomic risks associated with human-triggered earthquakes are often misconstrued and receive little scientific, legal, and public attention. However, more than 200 damaging earthquakes, associated with industrialization and urbanization, were documented since the 20th century. This type of geohazard has impacts on human security on a regional and national level. For example, the 1989 Newcastle earthquake caused 13 deaths and US$3.5 billion damage (in 1989). The monetary loss was equivalent to 3.4 percent of Australia&amp;#x2019;s national income (GDI) or 80 percent of Australia&amp;#x2019;s GDI...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4745/version/2

Hunter-Gatherers in a Howling Wilderness: Farming economic systems for human needs
Provedor de dados: 17
Autores: Rodrick Wallace.
Recent advances in evolutionary theory applied to economic structure and process may permit construction of both new economic theory and new tools for data analysis that can help in the design of more robust economic policies and practices, resulting in less frequent and less disruptive Knightian transitions, and enabling as well the design of institutions that are, in turn, less disrupted by those that do occur.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5650/version/2

Hunter-gatherers in a howling wilderness: Neoliberal capitalism as a language that speaks itself
Provedor de dados: 17
Autores: Rodrick Wallace.
The &amp;#x27;self-referential&amp;#x27; character of evolutionary process noted by Goldenfeld and Woese (2010) can be restated in the context of a generalized Darwinian theory applied to economic process through a &amp;#x27;language&amp;#x27; model: The underlying inherited and learned culture of the firm, the short-time cognitive response of the firm to patterns of threat and opportunity that is sculpted by that culture, and the embedding socioeconomic environment, are represented as interacting information sources constrained by the asymptotic limit theorems of information theory. If unregulated, the larger, compound, source that characterizes high probability evolutionary paths of this composite then becomes, literally, a self-dynamic language that...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5650/version/1

Huntington&amp;#x2019;s disease is a TH17 related autoimmune disorder against mutant Huntingtin coded by multiple CAG triplets
Provedor de dados: 17
Autores: Wanchung(Wanjiung) Hu.
Huntington&amp;#x2019;s disease is an inherited neurodegenerative disorder. It belongs to the polyQ accumulation disease with mutant Huntington protein. The mutant Huntington has expanded CAG triplet repeats which make it easy to accumulate. However, the exact mechanism causing Huntington&amp;#x2019;s disease pathophysiology is unknown. Here, I propose that Huntington&amp;#x2019;s disease is an autoimmune disease. During childhood, there are Treg cells from the thymus to prevent autoimmune reaction against mutant Huntington. When the patient grows older with thymus atrophy, the accumulated mutant Huntington triggers TH17 related inflammatory reaction via heat shock proteins and toll-like receptor activation. Then, TH17 related cytokines such as...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6129/version/1

Hybrid Extraction Method; Innovative Method to Produce Non Oxidative Tuna Oil
Provedor de dados: 17
Autores: Yoshinori Ito.
Summary: The function of Polyunsaturated Fatty Acid such as DHA, EPA are now well known world widely through strong scientific evidences and the importance of nutritional value and popularity are increasing every day all over the world with the name of omega 3 fatty acids.^1,2,3^ However, the fish oil, the source of omega 3 fatty acid had been considered as very vulnerable to oxidation. Many papers say the reason why is because its very easy to oxidize fish oil. The greater the Polyunsaturated Fatty Acid contents in the fish oil is, the faster oxidation takes place.^4,5^ Here I show that tuna oil extracted from Albacore Tuna Head in closed circuit under low temperature, at first decompressing then pressurizing and heating in a container, is very stable...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3110/version/1

Hydro tropes as promoters in soap flotation
Provedor de dados: 17
Autores: Abubakar  Khadri; Vijay Kumar P; Yasser  Dassin; Prabhulingaiah Gowda; Sekhar  DMR.
Soaps, the salts of fatty acids are generally used as collectors in the flotation process to separate salt type minerals. Some times light diesel oil is mixed with soaps and the emulsion is used as collector. Addition of detergents to soaps not only enhances the collector efficiency but also reduces the consumption of soap. Urea a known hydro trope is found to improve the flotation efficiency of soaps. Our current testing is indicating that other hydro tropes such as tri sodium citrate and sodium salicylate are also effective in improving the flotation efficiency of soap and also the soap-LDO emulsion.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6571/version/1

Hydrogen sulfide: a neurotransmitter or just a cofactor of the nitrite in the NO production?
Provedor de dados: 17
Autores: Loris Grossi.
The hydrogen sulfide has been recently claimed to have an important role in the cardiovascular system, as well in the central nervous system, but its action seems directly connected to the presence of NO/NO-derivatives. We want to report here chemical evidences that suggest for the H2S a role as a cofactor, able to induce NO release from NO-donors, more than a direct neurotransmitter.
Tipo: Manuscript
Palavras-chave: Chemistry; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2026/version/1

Hydrologic and climate trends for the Coldwater River watershed in south-central British Columbia, Canada
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Historical trends in streamflow and climate were investigated for the Coldwater River watershed in south-central British Columbia, Canada. Temporal increases in rainfall and total precipitation during the spring, summer, and autumn periods, as well as on an annual basis, at the city of Merritt near the mouth of the watershed, and year-round temperature increases at this site, compare with declining summertime and annual streamflows at the nearby Merritt hydrometric station on the Coldwater River. Declining summer flows at this site could reflect the dominance of temporally increasing evaporation that is offsetting increased precipitation over the same periods of the hydrologic year. Alternatively, increased water abstractions, altered regulation regimes,...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/6785/version/1

Hypercytokinemia: Increased or decreased innate immunity?
Provedor de dados: 17
Autores: Milind Watve; Sonam  Mandani; Prajakta Belsare.
The adipose tissue is an active endocrine organ which secretes proinflammatory cytokines and chemokines resulting into raised serum levels. Hypercytokinemia has been interpreted as raised level of innate immunity and its evolution is interpreted as a response to increased chances of infection under starvation conditions in which the thrifty phenotype evolved. If starvation and infection challenges co-occurred during hunter gatherer life, thrifty genotype and infection resistant genotype may have co-evolved. An inherent weakness of this explanation is that in obesity or insulin resistance there is no evidence of increased resistance to infections. The raised levels of inflammatory cytokines have not been demonstrated to combat infections or enhance wound...
Tipo: Poster
Palavras-chave: Ecology; Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/2710/version/1

Hyperinsulinemia and insulin resistance : What comes first ?
Provedor de dados: 17
Autores: Pramod  P. Patil; Milind M. Watve.
Background&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;1)&amp;#x9;Classical explanation :&amp;#xd;&amp;#xa;Classical explanation of diabetic pathophysiology states that obesity induced insulin resistance develops first and is followed by compensatory hyperinsulinnemia. Further  insulin resistance leads to prolonged, increased secretary demand on  beta cells  leading to subsequent secondary beta cell failure, giving rise  to hyperglycaemia and diabetes^2^.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;2)&amp;#x9; Neurobehavioral origin hypothesis :&amp;#xd;&amp;#xa;The  Neurobehavioral origin hypothesis suggests that insulin resistance mediates a shift from muscle dependent (soldier) to brain dependent (diplomat) strategies of making a livelihood.  If nutrient limitation...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5416/version/1

Hypothesis: Is the Omega-3 PUFA Content of Milk Related to Type 1 Diabetes?
Provedor de dados: 17
Autores: Harvey Arbesman; Marian C. Arbesman.
The incidence of Type 1 Diabetes (T1D) has been increasing over the past 50 years. The geographical variation in the incidence of T1D varies 400 fold from a low rate in China to a very high incidence in Finland, Sardinia and Yemenite Jews in Israel. The reason behind these epidemiologic findings is unclear at this time and further elucidating the factors related to this intriguing epidemiology of T1D can help us better understand certain risk factors, the pathogenesis of the disease, and help reduce the incidence of T1D. We hypothesize that the _variation_ of the omega-3 polyunsaturated fatty acid (PUFA) content of cow&amp;#x2019;s milk and human breast milk may play a very important role in the development of Type 1 Diabetes in genetically predisposed...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2011
URL: http://precedings.nature.com/documents/5876/version/1

Hypothesis: Klotho can decouple insulin resistance from the associated pathophysiology
Provedor de dados: 17
Autores: Milind Watve; Ulfat Baig.
A very fundamental paradox of insulin resistance is that in a wide variety of animal models impairment of insulin signaling increases life span. But in humans it increases the risk of a range of fatal disorders. The Klotho protein appears to resolve this paradox. Overexpression of the Klotho gene increases longevity in mammals by inducing insulin resistance. But the Klotho protein is simultaneously anti-inflammatory, antioxidant and pro-angiogenesis. A number of other studies have indicated that systemic inflammation, angiogenesis dysfunction and oxidative stress are the main causes of pathological complications of diabetes. The Klotho protein has demonstrated that insulin resistance can be decoupled from these pathogenic mechanisms and if decoupled it...
Tipo: Poster
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5420/version/1

Hypothetical Allotropes of Carbon Built from 1,4-Cyclohexadiene Rings
Provedor de dados: 17
Autores: Michael J. Bucknum.
Disclosure Document #337,466 filed with the U.S. Patent &amp;#x26; Trademark Office on August 23, 1993 describes, for the first time in the published literature, certain hypothetical constructions known as 3-,4-connected networks built from 1,4-cyclohexadiene rings, as allotropes of carbon and binaries. These hypothetical structures include an allotrope of carbon of tetragonal symmetry (space group P4(2)/mmc) built entirely from 1,4-cyclohexadiene rings and called glitter, and an allotrope of carbon of orthorhombic symmetry (space group Pmmm) built entirely from 1,4-cyclohexadiene rings, as well, and given another name.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1530/version/1

Icebergs boost phytoplankton growth in the Southern Ocean
Provedor de dados: 17
Autores: Jill N. Schwarz; Michael P. Schodlok.
Icebergs which calve from the Antarctic ice shelves and drift in the Southern Ocean deliver fresh water, dust and minerogenic particles to the surface ocean along the iceberg&amp;#x27;s path. Each of these components may have an effect on growth conditions for phytoplankton, as might the mechanical effects of the iceberg keel disturbing the water. Although anecdotal evidence and small-scale surveys suggest that drifting icebergs increase local primary production, no large-scale studies have reported on this possibility in detail. A combination of satellite and automated iceberg tracking data presented here shows that the probability of increased surface phytoplankton biomass was two-fold higher in the wake of a tracked iceberg compared to background...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1706/version/1

Identification and correction of systematic error in high-throughput sequence data
Provedor de dados: 17
Autores: Frazer Meacham; Dario Boffelli; Joseph Dhahbi; David I. K. Martin; Meromit Singer; Lior Pachter.
A feature common to all DNA sequencing technologies is the presence of base-call errors in the sequenced reads. The implications of such errors are application specific, ranging from minor informatics nuisances to major problems affecting biological inferences. Recently developed &amp;#x201c;next-gen&amp;#x201d; sequencing technologies have greatly reduced the cost of sequencing, but have been shown to be more error prone than previous technologies. Both position specific (depending on the location in the read) and sequence specific (depending on the sequence in the read) errors have been identified in Illumina and Life Technology sequencing platforms. We describe a new type of _systematic_ error that manifests as statistically unlikely accumulations of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5989/version/1

Identification and Evolution of Transcription Factors in Stramenopiles
Provedor de dados: 17
Autores: Francisco Buitrago; Silvia Restrepo; Diego Ria&amp;#xf1;o-Pach&amp;#xf3;n.
Background. &amp;#xd;&amp;#xa;Many transcriptional regulatory proteins have been identified and classified into several families on the basis of sequence similarity (Fukami, 2003), these families usually regulate important biological processes, such as development and responses to external stimuli. Transcription factors (TFs) regulate spatial and temporal gene expression by binding to DNA and either activating or repressing the action of RNA polymerases (Latchman, 2004); in addition to TFs, other Transcriptional regulators (TRs) participate in transcriptional modulation by e.g., chromatin remodeling. With the availability of genome sequences for several organisms and computational strategies for gene functional annotation, the entire set of Transcription...
Tipo: Presentation
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6400/version/1

Identification and Evolution of Transcription Factors in Stramenopiles
Provedor de dados: 17
Autores: Francisco Buitrago; Silvia Restrepo; Diego Ria&amp;#xf1;o-Pach&amp;#xf3;n.
Transcription factors (TFs) regulate spatial and temporal gene expression by binding to DNA and either activating or repressing the action of RNA polymerases; in addition to TFs, other transcriptional regulators (TRs) participate in transcriptional modulation. With the availability of genome sequences for several organisms and computational strategies for gene functional annotation, the entire set of TFs and TRs can be identified, described, and compared between species and lineages. The diversity among Stramenopiles is striking; they range from large multicellular seaweeds to tiny unicellular species, they are present in freshwater, marine and terrestrial habitats and embrace many ecologically important algal (e.g. diatoms, brown algae, chrysophytes), and...
Tipo: Poster
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6672/version/1

Identification of 22 novel mutations in patients with Glanzmann&amp;#x27;s thrombasthenia
Provedor de dados: 17
Autores: Meganathan Kannan; Firdos Ahmad; Birendra Yadav; Abdul Ethayathulla; Rajive Kumar; Ved Choudhry; Renu Saxena.
Glanzmann&amp;#x27;s thrombasthenia (GT) is an autosomal recessive inherited platelet function defect that characterized by reduction in, or absence of, platelet aggregation in response to multiple physiologic agonists. GT is characterized by normal platelet count, prolonged bleeding time, and abnormal clot retraction. The defect is caused by mutations in the genes encoding GPIIb or GPIIIa that result in qualitative or quantitative abnormalities of the platelet membrane GPIIb/IIIa. GT occurs in high frequency in certain ethnic populations with an increased incidence of consanguinity, such as Indians, Iranians, Iraqi Jews, Palastinian and Jordanian Arabs and French gypsies. Forty-five unrelated patients of GT were enrolled in the study to identify the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2398/version/1

Identification of a highly polymorphic tetranucleotide repeat locus (DXpS) at Xp and development of a DXpS/HUMARA biplex methylation-based PCR assay that enhances detection of X-chromosome inactivation
Provedor de dados: 17
Autores: Filipe B. Machado; Ester S. Ramos; Pamela C.  Radic; Carlos D. de Brasi; Enrique Medina-Acosta.
The methylation-based PCR assay at the polymorphic (CAG)n repeat in exon 1 of the human androgen receptor _AR_ gene (HUMARA) is a standard method for determination of the methylation state of alleles in active X (Xa) and inactive X (Xi) chromosomes. HUMARA assay is endowed with heterozygosity rates ~85% worldwide. This means that in a proportion of females it is uninformative. The HUMARA genotype is not neutral, being linked to Kennedy&amp;#xb4;s disease. Moreover, allele designation and quantification from trinucleotide repeats demand normalizing for minor (stutter) products differing from the original template by multiples of the repeat unit. Here, we report on the identification of a highly polymorphic tetranucleotide repeat (named DXpS) mapping to...
Tipo: Poster
Palavras-chave: Biotechnology; Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6633/version/1

Identification of Common Genetic Variants Predisposing to Neurobehavioral Disease by way of Genome-Wide SNP Association Studies
Provedor de dados: 17
Autores: David Craig.
Dr. David Craig began by explaining expression and linkage studies.  He then focused on genome-wide association studies (GWAS), giving examples from Diabetes Type 2 and Alzheimer&amp;#x2019;s research.  Dr. Craig concluded with the recognition that GWAS cannot at the present adequately account for environmental influences on disease.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To watch Dr. Craig&amp;#x2019;s presentation, please see the Panel 3 &amp;#x22;Google Video posting.&amp;#x22;:http://video.google.com/videoplay?docid=-7775076897136846879&amp;#x26;hl=en&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2652/version/1

Identification of MHC Class II Binders/ Non-binders using Negative Selection Algorithm
Provedor de dados: 17
Autores: S.S.  Soam; Feroz  Khan; Bharat  Bhasker; B. N.  Mishra.
The identification of major histocompatibility complex (MHC) class-II restricted peptides is an important goal in human immunological research leading to peptide based vaccine design. These MHC class&amp;#x2013;II peptides are predominantly recognized by CD4+ T-helper cells, which when turned on, have profound immune regulatory effects. Thus, prediction of such MHC class-II binding peptides is very helpful towards epitope-based vaccine design. HLA-DR proteins were found to be associated with autoimmune diseases e.g. HLA-DRB1*0401 with rheumatoid arthritis. It is important for the treatment of autoimmune diseases to determine which peptides bind to MHC class II molecules. The experimental methods for identification of these peptides are both time consuming...
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6608/version/1

Identification Of Mitotically Competent SOX2+ Cells In White Matter Of Normal  Human Adult Brain
Provedor de dados: 17
Autores: Jorge Oliver-De la Cruz; Josefa Carrion-Navarro; Antonio Gutierrez-Martin; Carmen Escobedo-Lucea; Jose Manuel Garcia-Verdugo; Angel Ayuso-Sacido.
SOX2 expression is linked to the undifferentiated state of stem cells in mammalian neurogenic niches. While its expression has been reported in the adult human subventricular zone (SVZ), to date it has not been detected in adult human white matter. Here we describe a population of SOX2+ cells from the white matter of the adult human temporal lobe, which proliferate and express glial markers in vitro.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6259/version/1

Identification of new leads for human IGFBP-2: a therapeutic target for cardiovascular diseases
Provedor de dados: 17
Autores: Kanipakam Hema; I Vani Priyadarshini; Amineni Umamaheswari.
IGFBP-2, the largest member of insulin-like growth factor binding proteins family, is under-expressed in hazardous cardiovascular diseases like obesity and type II diabetes mellitus, which upon aging leads to heart stroke. Therefore, IGFBP-2 has been proposed as a possible target for the development of novel leads for cardiovascular disease therapy. High-throughput virtual screening, one of the most common methods used to identify lead compounds was implemented here to identify potential IGFBP-2 activators. The NMR (nuclear magnetic resonance) structure of human IGFBP-2 was retrieved from the protein data bank. A 2D similarity search was performed for known IGFBP-2 activator TPA to acquire 383 structural analogs. The 3D structural conversion and multiple...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6570/version/1

Identification of potent inhibitors for p38&amp;#x3b4; MAPkinase of human through in silico analysis
Provedor de dados: 17
Autores: Naga Lakshmi M; Manne Munikumar; Dibyabhaba  Pradhan; Amineni  Umamaheswari.
P38&amp;#x3b4; Mitogen activated protein kinase is a serine/threonine protein kinase that participates in signaling cascades, mediating cellular responses to cytokinines, UV radiation, hyperosmotic stress, inducing keratinocyte differentiation and regulating apoptosis. Over expression of p38&amp;#x3b4; leads to tumor development by impairing the ERK1/2 &amp;#x2013;AP1 pathway that is critically linked to the control of cell proliferation and tumorigenesis on skin which was experimentally proven in knockout mice. Therefore, herein, a computational approach was undertaken to design novel inhibitors against p38delta for effective cancer therapy. The tertiary structure of p38&amp;#x3b4; was retrieved from a protein databank and active sites were predicted from...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5459/version/1

Identification of Potent Leads for Human cAMP Dependent Protein Kinase Catalytic Subunit Alpha: A Strategic Application of Virtual Screening for Cancer Therapeutics
Provedor de dados: 17
Autores: Sandeep Swargam; Dibyabhaba Pradhan; Amineni  Umamaheswari.
The advancement in therapeutic applications focused on specific macromolecular compounds of deregulated cell signaling pathways bestowed novel approach to design the ligands as drug molecules against several life threatening diseases such as Cancer. In humans, protein kinase A is one of the important kinases those were involved in cell signaling mechanism. cAMP, G-proteins and ATP molecules were required for activation of protein kinase A (PKA), upon activation, PKA catalytic subunits (PRKACA,PRKACB and PRKACG) undergoes many cellular functions like cell proliferations, cell cycle regulation, and survival of cells through acting on many substrates. Overexpression of extracellular cAMP dependent protein kinase A catalytic subunits (PRKACA) causes severe...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4903/version/1

Identification of small molecule inhibitor of cyclophilin-A using high throughput virtual screening and molecular docking Studies
Provedor de dados: 17
Autores: Pallapotu Navya; I Vani Priyadarshini; Amineni Umamaheswari.
The inhibitors of cyclophilin A (CyPA) have drawn a great deal of attention due to their promising potential as small-molecule therapeutics for the treatment of cardiovascular diseases. This ultimately prompts to explore structural geometries of these inhibitors to obtain insights on next generation CyPA inhibitors through rational drug designing. Herein, 2D similarity search for the seven CyPA inhibitors was performed using Ligand.Info database. Small subsets of 2800 molecules from one million compounds were predicted to have activity against cardiovascular drug target CyPA. The binding strength of 2800 ligands with CyPA was assessed through molecular docking analysis using Schr&amp;#xf6;dinger software 2011. The CyPA co-crystal structure and ligand...
Tipo: Presentation
Palavras-chave: Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6529/version/1

Identification of the prebiotic translation apparatus within the contemporary ribosome
Provedor de dados: 17
Autores: Ilana Agmon; Chen Davidovich; Anat Bashan; Ada Yonath.
A structural element that could have existed independently in the prebiotic era was identified at the active site of the contemporary ribosome. It is suggested to have functioned as a proto-ribosome catalyzing peptide bond formation and non-coded elongation in the same manner that contemporary ribosomes exert positional catalysis, namely by accommodating the reactants in stereochemistry favourable for inline nucleophilic attack. This simple apparatus is a dimer of self-folding RNA units that could have assembled spontaneously into a symmetrical pocket-like structure, sufficiently efficient to be preserved throughout evolution as the active site of modern ribosomes, thus presenting a conceivable starting point for translation.Here we discuss the...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2921/version/1

Identification of transcription factor genes and their correlation with the high diversity of Stramenopiles
Provedor de dados: 17
Autores: Francisco Buitrago; Silvia Restrepo; Diego Ria&amp;#xf1;o-Pach&amp;#xf3;n.
In this study we identify, and classify into families, transcription factors (TFs) and other transcriptional regulators (TRs) in genome sequences available from the Stramenopile group. For this we exploit the presence of protein domains and their combinations to build rules in the form of boolean rules, that are specific for each family of TFs and TRs. We found a correlation between the family size and some traits that has been described to be involved in the complexity of organisms. Furthermore, we found specific gains, losses and families that shows higher abundance in different lineages, which may be involved in the regulation of specific traits for some Stramenopile species.
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7002/version/1

Identification of transcription regulation associated proteins in plants and stramenopiles
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o Pach&amp;#xf3;n; Silvia Restrepo; Bernd Mueller-Roeber; Francisco Buitrago Florez.
The generation of biodiversity is tied to the evolution and re-wiring of gene regulatory networks (GRNs). One component of these GRN are transcription factors and other transcriptional regulators. We have devised a pipeline for the identification of TFs and TRs, exploiting the domain architecture of these proteins. Currently we have a set of rules, representing 138 proteins families, that we have applied to the identification of ~20 different plant species and several species of Stramenopiles, where important plant pathogens are found. Results for plant species are available at http://plntfdb.uniandes.edu.co/; we are now developing a newer interface for Stramenopiles.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7000/version/1

Identification of Unique proteins of Candida albicans as Antifungal Drug Targets
Provedor de dados: 17
Autores: Himanshu Tripathi; Abha  Meena; Feroz  Khan; Suaib  Luqman.
There are growing examples of drug resistance in the fungal pathogens to evade antifungal drugs by developing mutation in the key targeted enzymes and high expression of drug transporter genes including ABC transporters and MFS transporters. This led to the urgent need to identify novel (unique or essential to fungus) targets that can be used in development of potential antifungal drugs. We have used a comparative genomics approach to find out novel targets in opportunistic fungus, Candida albicans responsible for severe infection in immunocompromised humans. To identify novel targets we have analyzed available total 14,633 protein sequences (proteome) of C. albicans [SC5314] retrieved through RefSeq, an experimentally curated reference sequence database...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6619/version/1

Identifiers.org and MIRIAM Registry: perennial identifiers for crossreferencing purposes
Provedor de dados: 17
Autores: Camille Laibe.
The MIRIAM Registry provides unique, perennial and location independent identifiers for data used in the biomedical domain. At its core is a shared catalogue of data collections, for each of which a unique namespace is created, and extensive metadata recorded. This namespace allows the generation of Uniform Resource Identifiers (URIs) to uniquely identify any record in a collection. We present here the new Identifiers.org service which is built upon the information stored in the Registry and which provides directly resolvable identifiers, in the form of Uniform Resource Locators (URLs). The flexibility of the identification scheme and resolving system allows its use in many different fields, where unambiguous and perennial identification of data entities...
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6479/version/1

Identifiers.org/MIRIAM Registry annotation and cross-referencing framework
Provedor de dados: 17
Autores: Nick  Juty; Camille Laibe; Nicolas Le Novere.
We describe the MIRIAM Registry, which forms a foundation layer database upon which persistent, unambiguous and perennial identifiers of data can be built. We describe the existing MIRIAM URI identifiers, and the newly minted resolvable, parallel forms of these identifiers which use Identifiers.org URLs.
Tipo: Poster
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6396/version/1

Identifying Copy Number Variations based on Next Generation Sequencing Data by a Mixture of Poisson Model
Provedor de dados: 17
Autores: Karin Schwarzbauer; G&amp;#xfc;nter  Klambauer; Andreas Mayr; Sepp Hochreiter.
Next generation sequencing (NGS) technologies have profoundly impacted biological research and are becoming more and more popular due to cost effectiveness and their speed. NGS can be utilized to identify DNA structural variants, namely copy number variations (CNVs) which showed association with diseases like HIV, diabetes II, or cancer.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;There have been first approaches to detect CNVs in NGS data, where most of them detect a CNV by a  significant difference of read counts within neighboring windows at the chromosome. However these methods suffer from systematical variations of the underlying read count distributions along the chromosome due to biological and technical noise. In contrast to these global methods, we locally...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4716/version/1

Identifying Data Sharing in Biomedical Literature
Provedor de dados: 17
Autores: Heather Piwowar; Wendy W. Chapman.
Many policies and projects now encourage investigators to share their raw research data with other scientists. Unfortunately, it is difficult to measure the effectiveness of these initiatives because data can be shared in such a variety of mechanisms and locations. We propose a novel approach to find shared datasets: using NLP techniques to identify declarations of dataset sharing within the full text of primary research articles. Using regular expression patterns and machine learning algorithms on open access biomedical literature, our system was able to identify 61% of articles with shared datasets with 80% precision. A simpler version of our classifier achieved higher recall (86%), though lower precision (49%). We believe our results demonstrate the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1721/version/2

Identifying Data Sharing in Biomedical Literature
Provedor de dados: 17
Autores: Heather Piwowar; Wendy W. Chapman.
Many policies and projects now encourage investigators to share their raw research data with other scientists. Unfortunately, it is difficult to measure the effectiveness of these initiatives because data can be shared in such a variety of mechanisms and locations. We propose a novel approach to finding shared datasets: using NLP techniques to identify declarations of dataset sharing within the full text of primary research articles. Using regular expression patterns and machine learning algorithms on open access biomedical literature, our system was able to identify 61% of articles with shared datasets with 80% precision. A simpler version of our classifier achieved higher recall (86%), though lower precision (49%). We believe our results demonstrate the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1721/version/1

Identifying reliable traits across laboratory mouse exploration arenas: A meta-analysis
Provedor de dados: 17
Autores: Michael J. Galsworthy; Rime Madani; Hans-Peter Lipp.
This study is a meta-analysis of 367 mice from a collection of behaviour neuroscience and behaviour genetic studies run in the same lab in Zurich, Switzerland. We employed correlation-based statistics to confirm and quantify consistencies in behaviour across the testing environments. All 367 mice ran exactly the same behavioural arenas: the light/dark box, the null maze, the open field arena, an emergence task and finally an object exploration task. We analysed consistency of three movement types across those arenas (resting, scanning, progressing), and their relative preference for three zones of the arenas (home, transition, exploration). Results were that 5/6 measures showed strong individual-differences consistency across the tests. Mean inter-arena...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/6981/version/1

Identity in research infrastructure and scientific communication: Report from the 1st IRISC workshop, Helsinki Sep 12-13, 2011
Provedor de dados: 17
Autores: Gudmundur A. Thorisson; Mikael  Linden; Anthony J. Brookes; Myles Byrne; Juha Muilu; Tommi Nyronen.
Motivation for the IRISC workshop came from the observation that identity and digital identification are increasingly important factors in modern scientific research, especially with the now near-ubiquitous use of the Internet as a global medium for dissemination and debate of scientific knowledge and data, and as a platform for scientific collaborations and large-scale e-science activities.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The 1 1/2 day IRISC2011 workshop sought to explore a series of interrelated topics under two main themes: i) unambiguously identifying authors/creators &amp;#x26; attributing their scholarly works, and ii) individual identification and access management in the context of identity federations. Specific aims of the workshop...
Tipo: Manuscript
Palavras-chave: Biotechnology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6609/version/1

Idiosyncratic evolution of conserved eukaryote proteins that are similar in sequence to archaeal or bacterial proteins
Provedor de dados: 17
Autores: Roy J. Britten.
&amp;#x9;Sequence comparisons have been made between the proteins of 571 prokaryote species including 46 archaea and 525 bacteria and the set of  human proteins. Highly conserved eukaryotic proteins are often strikingly similar in sequence to archaeal and bacterial proteins. Yet in many cases similarity to archaeal proteins is not correlated to the similarity to bacterial proteins. In these comparisons there are hundreds of eukaryote proteins that match well archeal proteins, but do not match recognizably to bacterial proteins, while thousands of proteins match well to bacterial proteins but not recognizably to archeal proteins. Forty percent of the 21,440 human proteins that significantly match prokaryote proteins are in this extreme idiosyncratic...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1752/version/1

IL-1 regulates the IL-23 response to wheat gliadin, the etiologic agent of Celiac Disease
Provedor de dados: 17
Autores: Kristina M. Harris; Alessio Fasano; Dean L. Mann.
Celiac disease (CD) is an autoimmune disease prevalent in ~1% of the general population. CD is unique because both the major genetic (Human Leukocyte Antigen-DQ2/DQ8 alleles) and etiologic factors (dietary glutens) for susceptibility are known. While these alleles are responsible for the inappropriate T cell response that characterizes CD, they are not sufficient since most HLA-DQ2+/DQ8+ individuals exposed to glutens never develop disease. The reasons for this have not been explained; however our novel findings strongly advocate a role for interleukin-23 (IL-23) in the immunopathogenesis of CD. We demonstrate that wheat gliadin stimulates monocytes to produce significantly higher amounts of inflammatory cytokines IL-1b, IL-23, and tumor necrosis factor-a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/1882/version/1

IMGT/Automat: the strategy for the annotation of human and mouse cDNA nucleotide sequences of IG and TR
Provedor de dados: 17
Autores: G&amp;#xe9;raldine Folch; Joumana Jabado-Michaloud; Fatena Bellahcene; Laetitia Regnier; V&amp;#xe9;ronique Giudicelli; Marie-Paule Lefranc.
The cDNA sequences of immunoglobulins (IG) and T cell receptors (TR) represent more than one half of the sequences in the IMGT^&amp;#xae;^ nucleotide database IMGT/LIGM-DB^1^ and 75% of them are from human and mouse. A few cDNA are germline but the great majority results from a V-D-J or V-J gene rearrangement, spliced to a C gene. The IG and TR genes have been studied extensively in IMGT^&amp;#xae;^ (&amp;#x22;http://www.imgt.org&amp;#x22;:http://www.imgt.org) ^2^, which allowed to set up their nomenclature and the corresponding germline reference sequences. These standardized reference directory sets (one for each group of each locus) and the IMGT-ONTOLOGY axioms and derived concepts^3^ are the key elements indispensable to perform the annotation of IG...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3159/version/1

IMGT/GENE-DB: genomic reference sequences for human and mouse IG and TR genes and alleles
Provedor de dados: 17
Autores: Fatena Bellahcene; Ge&amp;#x301;raldine Folch; Joumana Jabado-Michaloud; Chantal Ginestoux; Patrice Duroux; Ve&amp;#x301;ronique Giudicelli; Marie-Paule Lefranc.
The immunoglobulin (IG) and T cell receptor (TR) major loci span about 6 Megabases (Mb) of the human genome on chromosomes 2, 7, 14 and 22, and 9 Mb in mouse on chromosomes 6, 12, 13, 14 and 16. There are seven major loci: three IG loci (IGH, IGK, IGL) and four TR loci (TRA, TRB, TRG, TRD), with a distinct repartition of the variable (V), diversity (D), joining (J) and constant (C) genes. The human genome comprises a total number of 608-665 IG and TR genes (371-422 IG and 237-243 TR), depending on the haplotypes, per haploid genome ^1, 2^ of which 531-588 genes are located in the major loci (distributed in 369-418 V, 32 D, 105-109 J and 25-29 C genes). There are also 77 orphons (68 IG and 9 TR) including two processed IG genes, outside the major loci. The...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3158/version/1

Immunity to self co-generates regulatory T cells
Provedor de dados: 17
Autores: James A. Dromey; Bo Han Lee; Helen E. Young; Stuart I. Mannering; Kent P. Jensen; Daniel J. Thearle; Spiros Fourlanos; Larissa Belov; Leonard C. Harrison.
Immune responses to self are kept in check by tolerance mechanisms, including suppression by regulatory T cells (Tregs). The defective generation of Tregs specific for self-antigens may lead to autoimmune disease. We identified a novel population of human CD4^+^ Tregs, characterized by high surface expression of CD52, which is co-generated in response to autoantigen. Blood CD4^+^CD52^hi^ T cells were generated preferentially in response to low-dose autoantigen and suppressed proliferation and interferon-[gamma] production by other T cells. Depletion of resting CD4^+^CD52^hi^ T cells enhanced the T-cell response to autoantigen. CD4^+^CD52^hi^ Tregs were neither derived from nor distinguished by markers of conventional resting CD4^+^CD25^+^ Tregs. In...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/1774/version/1

Immunogenetic sequence annotation based on IMGT-ONTOLOGY
Provedor de dados: 17
Autores: Joumana  Jabado-Michaloud; G&amp;#xe9;raldine Folch; Fatena Bellahcene; Fran&amp;#xe7;ois Ehrenmann; Patrice Duroux; V&amp;#xe9;ronique Giudicelli; Marie-Paule Lefranc.
IMGT/LIGM-DB^1^ is the first and the largest IMGT^&amp;#xae;^ database^2^ in which are managed, analysed and annotated more than 136,000 immunoglobulin (IG) and T cell receptor (TR) nucleotide sequences from human and 235 other vertebrate species (April 2009). The expert annotation of these sequences and the added standardized knowledge are based on IMGT-ONTOLOGY, the first ontology developed in the field of immunogenetics and immunoinformatics.^3^ The annotation of immunogenetic sequences requires important expertise, owing to the unusual structure (non-classical exon/intron structure) of the IG and TR genes and characteristic chain synthesis owing to DNA V-J and V-D-J rearrangements. The way to annotate these sequences depends on the molecular type...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3165/version/1

Immunogenic Modulations Induced by Prospective Anti-Malarial Herbal Extracts in Murine Model
Provedor de dados: 17
Autores: Sudipta Chakraborty; Swapna Chhetri; Sajal Ray; Shyamal Das Gupta; Suman Mukherjee; Niladri Sekhar Bhunia; Manoj Das; Sanat Biswas; Sreemayee Sarkar; Guruprasad Mandal; Dipankar Singha; Chinmoy Karjee.
Keeping in view the ever increasing problem of drug resistance and affordability of the antimalarial drugs by the poor mass, herbal medicines can become an important and alternative sustainable strategy for malaria treatment. Aqueous extracts of three Himalayan herbs&amp;#x2015; _Equisetum ravense_, _Artemisia vulgaris_ and _Centella asiatica_, with reported antimalarial property were screened for clinical efficacy against a local strain of _Plasmodium vivax_ antigen in murine model. _E. arvense_ extract was consistent in boosting phagocytic activity, nitric oxide generation, acid phosphatase and alkaline phosphatase activities in the peritoneal macrophages. The effectiveness of the rest herbals was discrete. A need for further detailed investigation to...
Tipo: Manuscript
Palavras-chave: Immunology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4157/version/1

Immunogenicity of human spermatozoa
Provedor de dados: 17
Autores: Jhinuk Chatterjee.
Investigation and experimental design of the study was basically aimed at developing insight into the antigenicity of spermatozoa-associated proteins. Apart from studying the natural antigenicity of washed whole spermatozoa, their immunogenicity was also demonstrated _in vitro_. The whole live spermatozoa were immobilized and agglutinated _in vitro_ by the antibodies they induced in the laboratory model - a female rabbit. A regular immunization routine induced a high titre of antisperm polyclonal antibodies. To prepare a spermatozoa specific antigen which will not produce a cross-reacting antibody against other human tissues, only the motile and live spermatozoa were selected for antigen preparation. In investigation the laboratory-bred female rabbits were...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/1855/version/1

Immunogenicity of human spermatozoa
Provedor de dados: 17
Autores: Jhinuk Chatterjee; Sukumar Chattopadhyay.
Investigation and experimental design of the study was basically aimed at developing insight into the antigenicity of spermatozoa-associated proteins. Apart from studying the natural antigenicity of washed whole spermatozoa, their immunogenicity was also demonstrated _in vitro_. The whole live spermatozoa were immobilized and agglutinated _in vitro_ by the antibodies they induced in the laboratory model - a female rabbit. A regular immunization routine induced a high titre of antisperm polyclonal antibodies. To prepare a spermatozoa specific antigen which will not produce a cross-reacting antibody against other human tissues, only the motile and live spermatozoa were selected for antigen preparation. In investigation the laboratory-bred female rabbits were...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/1855/version/2

Immunogens and Antigen Processing: Report from a Global HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: John Mascola; Richter C. King; Ralph  Steinman; the Working Group convened by the Global HIV Vaccine Enterprise.
The Global HIV Vaccine Enterprise convened a meeting of a Working Group in July 2009 to discuss recent progress in rational design of the components of an HIV vaccine, such as inserts, vectors and adjuvants,and in understanding antigen processing and presentation to T and B cells. This Report summarizes the key points of that discussion, and subsequent discussions with the Chairs of the other Enterprise Working Groups, the Enterprise Science Committee, the Enterprise Council and the broader scientific community during open sessions at scientific conferences.
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4796/version/1

Immunogens and Antigen Processing: Report from a Global HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: John Mascola; Richter C. King; Ralph  Steinman; the Working Group convened by the Global HIV Vaccine Enterprise.
The Global HIV Vaccine Enterprise convened a meeting of a Working Group in July 2009 to discuss recent progress in rational design of the components of an HIV vaccine, such as inserts, vectors and adjuvants,and in understanding antigen processing and presentation to T and B cells. This Report summarizes the key points of that discussion, and subsequent discussions with the Chairs of the other Enterprise Working Groups, the Enterprise Science Committee, the Enterprise Council and the broader scientific community during open sessions at scientific conferences.
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4796/version/2

Impact of Behavior Genetics on Medicine and Society
Provedor de dados: 17
Autores: Dean Hamer.
Understanding the role of genes in human behavior will impact both medicine and society, but not always in the manner expected. Knowledge about behavioral genes can be used for the good, for example by improving psychiatric diagnoses, developing new drugs to treat mental illnesses, and dispelling harmful myths about certain types of human variation. However, the same sort of information could be used to discriminate against people, to provide quick fixes for social problems, or to support eugenics. How we use the new knowledge about molecular behavior genetics will depend on the legal, ethical and social policies that we develop.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To watch Dr. Hamer&amp;#x27;s presentation, please see the &amp;#x22;Google Video...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2564/version/1

Impact of Climate Change on Northeast Monsoon System of India - Role of Siberian Teleconnection
Provedor de dados: 17
Autores: Somnath Jha; Vinay Kumar Sehgal; Ramesh Raghava.
The Northeast monsoon (NEM) precipitation has undergone a significant change in pattern over the last half century. The changing pattern of climatic variables over the moisture source (i.e. west Pacific High) and the heat sink (Siberian High) of the winter monsoon dynamics over time has caused a shift in the pattern of NEM precipitation over the southern peninsular region of India. There is no significant trend in NEM precipitation in the Indian region whereas the surface temperature has a significantly increasing trend over India during the NEM season. There is no significant trend in outgoing long wave radiation (OLR) of Siberian High (SH) while the west Pacific High (WPH) has a significantly increasing trend in OLR. Surface pressure of both the SH...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5899/version/1

Impact of ocean stratification on submarine melting of a major Greenland outlet glacier
Provedor de dados: 17
Autores: Fiammetta Straneo; Ruth Curry; David  Sutherland; Gordon Hamilton; Claudia Cenedese; Kjetil  Vaage; Leigh Stearns.
Submarine melting is an important balance term for tidewater glaciers1,2 and recent observations point to a change in the submarine melt rate as a potential trigger for the widespread acceleration of outlet glaciers in Greenland3-5. Our understanding of the dynamics involved, and hence our ability to interpret past and predict future variability of the Greenland Ice Sheet, however, is severely impeded by the lack of measurements at the ice/ocean interface. To fill this gap, attempts to quantify the submarine melt rate and its variability have relied on a paradigm developed for tidewater glaciers terminating in fjords with shallow sills. In this case, the fjords&amp;#x2019; waters are mostly homogeneous and the heat transport to the terminus, and hence the...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5670/version/1

Impact of polyplex micelles installed with cyclic RGD peptide as ligand on gene delivery to vascular lesions
Provedor de dados: 17
Autores: Hiroyuki Koyama; Hideo Kagaya; Makoto Oba; Yutaka Miura; Takehiko Ishii; Tsuyoshi Takato; Kazunori Kataoka; Tetsuro Miyata.
Gene therapy is expected to open a new strategy for the treatment of refractory vascular diseases, so the development of appropriate gene vectors for vascular lesions is needed. To realize this requirement with a non-viral approach, cyclo(RGDfK) peptide (cRGD) was introduced to block copolymer, poly(ethylene glycol)-block-polycation carrying ethylenediamine units (PEG-PAsp(DET)). cRGD recognizes &amp;#x3b1;v&amp;#x3b2;3 and &amp;#x3b1;v&amp;#x3b2;5 integrins, which are abundantly expressed in vascular lesions. cRGD-conjugated PEG-PAsp(DET) (cRGD-PEG-PAsp(DET)) formed polyplex micelles through complexation with plasmid DNA (pDNA), and the cRGD-PEG-PAsp(DET) micelles achieved significantly more efficient gene expression and cellular uptake as compared with...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5020/version/1

Impact of sea surface height anomalies on cyclone track
Provedor de dados: 17
Autores: M.M Ali; Palash Sinha; Sarika Jain; U.C Mohanty.
Predicting accurate cyclone tracks is crucial for disaster management practices.   The unusual westward movement of the 6-11 May 2002 Arabian Sea cyclone has been investigated through community mesoscale National Centre for Atmospheric Research  model  by giving different sea surface temperatures (SST) in different experiments keeping all  other conditions same. In one experiment, we converted sea surface height anomalies (SSHAs) to SST.    Oceanic eddies and SSHAs, representing the subsurface thermal structure, played a prominent role in the unusual westward movement of this cyclone.  This is the first time that the effect of eddies and SSHAs on cyclone track has been reported.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1001/version/1

Impact of tissue microstructure on a model of cardiac electromechanics based on MRI data
Provedor de dados: 17
Autores: Valentina Carapella; Vicente Grau; Pras Pathmanathan; Kevin Burrage.
Cardiac motion is a vital process as it sustains the pumping of blood in the body. For this reason motion abnormalities are often associated with severe cardiac pathologies. Clinical imaging techniques, such as MRI, are powerful in assessing motion abnormalities but their connection with pathology often remains unknown.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Computational models of cardiac motion, integrating imaging data, would thus be of great help in linking tissue structure (i.e. cells organisation into fibres and sheets) to motion abnormalities and to pathology. Current models, though, are not able yet to correctly predict realistic cardiac motion in the healthy or diseased heart.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Our hypothesis is that a more realistic...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6594/version/1

Impacts &amp;#x2013; The Key to Understand Earth
Provedor de dados: 17
Autores: Hua Huang.
A significant factor, where are the major elements e.g. Mg, Fe, Si, Al, Ca, P, Ni that make up the asteroid or comet after the impact, has been ignored since the proposal of the impact events. In a striking contrast, there are many remaining unanswered or poorly answered questions regarding the formation and nature of banded iron formation (BIF), iron stone, phosphorite, bedded manganese ore, dolomite and carbonaceous black shales. The appearance of Lake Superior type banded ion formation  associated with dolomite, quartzite, and black shale, the deposition of manganese ore and the occurrence of large phosphate repository during the Plaeoproterozoic; the onset of BIF with phosphate deposition and sedimentary manganese deposits and cap dolomite during the...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4678/version/1

Implementation Methods for Estimating Haplotypes with Grid Computing Technology
Provedor de dados: 17
Autores: Zafri Muhammad; Sanjaya KC; Phua Kia Kien.
Introduction: PHASE is a software for haplotype reconstruction and recombination rate estimation from population data and implements the methods for estimating haplotypes from population genotype data. This software require enormous computing power due to the complexity algorithms used. Recent advancement in grid computing and multi-core processing technology has resulted in the creating of virtual supercomputers (that are capable of massive parallel computations).&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Method: PHASE version 2.0 was downloaded from PHASE&amp;#x2019;s homepage (http://stephenslab.uchicago.edu/software.html), and installed on 10 Apple iMac computers (20 CPUs) running Mac OS 10.5 using Apple&amp;#x2122; Xserve as a controller. A PHP web-based...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4168/version/1

Implementation of computational methods for designing potential inhibitors against human p38&amp;#x3b1; protein
Provedor de dados: 17
Autores: Durga Devi M; Dibyabhaba  Pradhan; Manne Munikumar; Amineni Umamaheswari.
p38&amp;#x3b1;, a non-receptor serine/threonine kinase, plays an essential role in cell proliferation, cell differentiation, apoptosis, production of cytokines such as IL1&amp;#x3b2; and TNF&amp;#x3b1;, senescence and tumorigenesis. Over expression of p38&amp;#x3b1; enhances the production of cytokines, leading to inflammation causing cancers. Therefore, the protein p38&amp;#x3b1; is selected as a target for the inhibition of progression of inflammatory cancers. SB203580, BIRB796, 2H-quinolizine-2-one, 7-alkyl-1,5-bis&amp;#x2013;aryl-pyrazolo pyridinones, aML3403, N-pyrimidyl amides, Fused pyrazoles, SD0006, 4-3-(4-fluoro phenyl )-1H-pyrazol-4-yl)pyridine are the nine published inhibitors for the p38&amp;#x3b1;, but they show side effects like liver...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5456/version/1

Implementation of SBML Level 3 Support within iBioSim
Provedor de dados: 17
Autores: Chris J. Myers.
This presentation gives details about our experiences when adding SBML Level 3 support to our iBioSim tool.&amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4988/version/1

Implications of single-neuron gain scaling for information transmission in networks
Provedor de dados: 17
Autores: Julijana Gjorgjieva; Michael  Famulare; Rebecca  Mease; William J. Moody; Adrienne L. Fairhall.
Summary: &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Many neural systems are equipped with mechanisms to efficiently encode sensory information. To represent natural stimuli with time-varying statistical properties, neural systems should adjust their gain to the inputs&amp;#x27; statistical distribution. Such matching of dynamic range to input statistics has been shown to maximize the information transmitted by the output spike trains (Brenner et al., 2000, Fairhall et al., 2001). Gain scaling has not only been observed as a system response property, but also in single neurons in developing somatosensory cortex stimulated with currents of different amplitude (Mease et al., 2010). While gain scaling holds for cortical neurons at the end of the first post-natal...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5860/version/1

Implications of uncertainty for Canada&amp;#x2019;s commercial hunt of harp seals (Pagophilus groenlandicus)
Provedor de dados: 17
Autores: Russell Leaper; Justin Matthews.
The Canadian government&amp;#x27;s current management procedure for harp seals is described by Fisheries and Oceans Canada as using the Precautionary Approach.  Employing a similar underlying population model, we simulated the effects of uncertainty involving bias in estimates of human induced mortality, natural mortality, and pup production estimates as a set of robustness trials.  Our results indicated that for the range of annual total allowable catches (TAC) considered and set for Canada&amp;#x2019;s commercial harp seal hunt (250,000 &amp;#x2013; 350,000), there were plausible circumstances under which the government&amp;#x27;s management procedures failed to meet their own conservation objectives.   By contrast, a precautionary management regime...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1798/version/1

Improved Imputation of Common and Uncommon Single Nucleotide Polymorphisms (SNPs) with a New Reference Set
Provedor de dados: 17
Autores: Zhaoming Wang; Kevin Jacobs; Meredith Yeager; Amy  Hutchinson; Joshua Sampson; Nilanjan Chatterjee; Demetrius Albanes; Sonja I. Berndt; Charles C. Chung; W. Ryan Diver; Susan M. Gabstur; Lauren R. Teras; Christopher M. Haiman; Brian E. Henderson; Daniel Stram; Xiang Deng; Ann W. Hsing; Jarmo Virtamo; Michael A. Eberle; Jennifer L. Stone; Mark P. Purdue; Phil Taylor; Margaret Tucker; Stephen Chanock.
Statistical imputation of genotype data is an important technique for analysis of genome-wide association studies (GWAS). We have built a reference dataset to improve imputation accuracy for studies of individuals of primarily European descent using genotype data from the Hap1, Omni1, and Omni2.5 human SNP arrays (Illumina). Our dataset contains 2.5-3.1 million variants for 930 European, 157 Asian, and 162 African/African-American individuals.  Imputation accuracy of European data from Hap660 or OmniExpress array content, measured by the proportion of variants imputed with R^2^&amp;#x3e;0.8, improved by 34%, 23% and 12% for variants with MAF of 3%, 5% and 10%, respectively, compared to imputation using publicly available data from 1,000 Genomes and...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6576/version/1

Improved prediction of protein interaction from microarray data using asymmetric correlation
Provedor de dados: 17
Autores: Kojiro Yano.
Background:Detection of correlated gene expression is a fundamental process in the characterization of gene functions using microarray data. Commonly used methods such as the Pearson correlation can detect only a fraction of interactions between genes or their products. However, the performance of correlation analysis can be significantly improved either by providing additional biological information or by combining correlation with other techniques that can extract various mathematical or statistical properties of gene expression from microarray data. In this article, I will test the performance of three correlation methods-the Pearson correlation, the rank (Spearman) correlation, and the Mutual Information approach-in detection of protein-protein...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4430/version/1

Improvement of PubMed Literature Searching using Biomedical Ontology
Provedor de dados: 17
Autores: Zuoshuang Xiang; Yongqun He.
PubMed articles are annotated using the Medical Subject Headings (MeSH) to increase search efficiency. However, MeSH contains limited information on many biomedical domains (e.g., vaccine). Biomedical ontologies may be used to improve PubMed searching capability. This study demonstrates that Vaccine Ontology (VO) can be used to significantly improve PubMed searching efficacy in the vaccine domain. The recall and precision of the ontology-based literature mining approach are analyzed and discussed.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3491/version/1

Improving cellular cancer vaccines
Provedor de dados: 17
Autores: Petr Lokhov.
Immunization with cancer cells is of great demand in anti-cancer therapy. However, current cellular vaccines are inefficient and there are questions regarding their overall safety. We report a simple and straightforward approach for improving of cellular cancer vaccines. Through treatment of cancer cell cultures with purified protease, it is possible to make preparations of cell-surface antigens that are free of intracellular content and contain two orders-of-magnitude less protein than the whole lysate of an equivalent number of cancer cells. Despite this difference in total protein content, protease-generated preparations stimulate anti-cancer responses from immune cells better those stimulated with cancer cells themselves. The composition of collected...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4356/version/1

Improving metabolite evaluation in integrated pathway analysis
Provedor de dados: 17
Autores: Rasanpreet Kaur; Anwesha  Dutta; Martina Kutmon; Martijn Iersel; Chris Evelo.
Biological molecules such as proteins and metabolites interact to accomplish a biological function and to respond to environmental stimuli. Pathways capture this information derived through scientific experimentation and data analysis. They contain information about genes that appear in complexes, the interacting genes, the directionality of the interactions (e.g. inhibitors versus activators), the cellular locations where the reactions occur, and the metabolites that are affected by the processes. Using our open-source pathway analysis platform, PathVisio, we will connect pathway analysis to different quantitative approaches already in development for metabolic network modeling, such as flux balance analysis and dynamic simulation. In order to use...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6970/version/1

Improving the worthiness of the Elder problem as a benchmark for buoyancy driven convection models
Provedor de dados: 17
Autores: Maarten van Reeuwijk; Simon A. Mathias; Craig T. Simmons; James D. Ward.
An important trapping mechanism associated with the geosequestration of CO~2~ is that of dissolution into the formation water. Although supercritical CO~2~ is significantly less dense than water, experimental data reported in the literature show that the density of an aqueous solution of CO~2~ could be slightly greater. Under normal situations, the transfer of gas to solution is largely controlled by the relatively slow process of molecular diffusion. However, the presence of variable densities can trigger off gravity instabilities leading to much larger-scale convection processes. Such processes can potentially enhance rates of dissolution by an order of magnitude. Consequently there is a need for future performance assessment models to incorporate...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2633/version/1

In Principle Method for Noninvasive Determination of the Fetal Genome
Provedor de dados: 17
Autores: Christina Fan; Stephen Quake.
We illustrate the concept of noninvasive determination of the fetal genome by shotgun sequencing maternal plasma. The approach is based on molecular counting of alleles in maternal cell-free DNA: the inheritance of paternal haplotypes can be determined by counting paternal specific alleles present on each of the paternal haplotypes; the inheritance of maternal haplotypes can be revealed by counting the alleles on each maternal haplotype and determining the relative representation of the two maternal haplotypes. The concept was experimentally proven by sequencing a synthetic mixture of genomic DNA samples from a child and her mother, whose whole-genome haplotypes (defined by ~800,000 SNPs), together with those of the father, were previously determined....
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5373/version/1

In search of the right literature search engine(s)
Provedor de dados: 17
Autores: Akhilesh K. Bajpai; Sravanthi Davuluri; Haritha Haridas; Greta Kasliwal; Deepti H; Sreelakshmi KS; Darshan S. Chandrashekar; Pranami Bora; Mohammed Farouk; Neelima Chitturi; Samudyata V; ArunNehru KP; Kshitish K. Acharya.
*Background*&amp;#xd;&amp;#xa;Collecting scientific publications related to a specific topic is crucial for different phases of research, health care and &amp;#x2018;effective text mining&amp;#x2019;. Available bio-literature search engines vary in their ability to scan different sections of articles, for the user-provided search terms and/or phrases. Since a thorough scientific analysis of all major bibliographic tools has not been done, their selection has often remained subjective. We have considered most of the existing bio-literature search engines (http://www.shodhaka.com/startbioinfo/LitSearch.html) and performed an extensive analysis of 18 literature search engines, over a period of about 3 years. Eight different topics were taken and about 50...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/2101/version/3

In Silico Analysis and Identification of Potent Inhibitors for Human Serine/Threonine Protein Kinase PIM-3 Involved in Hepatic Cancer
Provedor de dados: 17
Autores: Prasanna Kumar Guttala; Dibyabhaba  Pradhan; Amineni Umamaheswari.
PIM3 belongs to a family of proto oncogenes that encode serine/threonine protein kinases in human. Pim-3 is involved in cell cycle progression, suppression of apoptosis and proliferation of human hepatoma cell lines. During normal cell cycle progression, Bcl-2 associated death promoter (BAD protein) inactivates Bcl-2 and Bcl-xL there by promoting apoptosis. However, phosphorylation of BAD protein by Pim-3 leaves Bcl-2 free to inhibit Bax-triggered apoptosis. Thus, designing inhibitors against Pim-3 would stop BAD phosphorylation, hence would be highly useful for development of novel means of cancer therapeutics. Computer aided drug designing approach was followed here to explore lead molecules targeting human Pim-3. For this, proteomic nature and phylogeny...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4899/version/1

In silico analysis for the presence of HARDY an Arabidopsis drought tolerance DNA binding transcription factor product in chromosome 6 of Sorghum bicolor genome
Provedor de dados: 17
Autores: Arun K. Shanker; M Maheswari; S K. Yadav; B Ventateswarlu.
Expression of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2) has been shown to increase WUE in rice by Karaba et al 2007 (PNAS, 104:15270&amp;#x2013;15275). We conducted a detail analysis of the complete sorghum genome for the similarity/presence of either DNA, mRNA or protein product of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2). Chromosome 6 showed a sequence match of 61.5 percent positive between 61 and 255 mRNA residues of the query region. Further confirmation was obtained by TBLASTN which showed that chromosome 6 of the sorghum genome has a region between 54948120 and 54948668 which has 80 amino acid similarities out of the 185 residues. A homology...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3432/version/1

In silico analysis for the presence of HARDY an Arabidopsis drought tolerance DNA binding transcription factor product in chromosome 6 of Sorghum bicolor genome
Provedor de dados: 17
Autores: Arun K. Shanker; M Maheswari; S K. Yadav; B Ventateswarlu.
Expression of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2) has been shown to increase WUE in rice by Karaba et al 2007 (PNAS, 104:15270&amp;#x2013;15275). We conducted a detail analysis of the complete sorghum genome for the similarity/presence of either DNA, mRNA or protein product of the Arabidopsis HARDY (hrd) DNA binding transcription factor (555 bp present on chromosome 2). Chromosome 6 showed a sequence match of 61.5 percent positive between 61 and 255 mRNA residues of the query region. Further confirmation was obtained by TBLASTN which showed that chromosome 6 of the sorghum genome has a region between 54948120 and 54948668 which has 80 amino acid similarities out of the 185 residues. A homology...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3432/version/2

In Silico Analysis To Explore Novel Inhibitors For Human Proto-oncogene Tyrosine Protein Kinase Src
Provedor de dados: 17
Autores: Nagapriya Mahanandi; Dibyabhaba  Pradhan; Amineni  Umamaheswari.
The first oncogene and the first non receptor tyrosine kinase, Src, plays a key role in cell morphology, motility, proliferation and survival. Over expression of Src kinase activity disrupts the RAS pathway in signaling pathway, where it loses its ability to hydrolyse GTP and thus, leads to cancer. A wide range of evidences indicated that Src-signaling was important in the oncogenesis of prostate cancer and other tumours. Src-signaling is involved in androgen-induced proliferation of prostate cancer in cancer tissue of patients having castration-refractory prostate cancer. Once prostate cancer becomes castration-resistant, bone metastases become significant problem for which treatment options are limited. As Src is involved in multiple signaling pathways,...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4905/version/1

In Silico Characterization of Tomato leaf curl Joydebpur virus (ToLCJV) DNA-A Proteins
Provedor de dados: 17
Autores: Rajneesh  Prajapat; Avinash  Marwal; Anurag  Sahu; Rajarshi Kumar  Gaur.
We retrieved six protein sequences of Tomato leaf curl Joydebpur virus (ToLCJV) DNA-A [FJ345402] from GenBank-NCBI (ACJ03821, ACJ03822, ACJ03823, ACJ03824, ACJ03825 and ACJ03826) which were used for computational modeling structure prediction. Ramachandran plot of ACJ03826-AC4 had maximum 73.3% and ACJ03822-AV1 had 71% residues in core region therefore these models cannot be placed in a good quality category. ACJ03824-AC2 had only 18.6% residues in core and 13.6% residues in disallowed regions and therefore it was the least stable protein. Verify-3D graph profile scores for selected ToLCJV proteins were greater than zero. Therefore all the verify-3D graph corresponds to an acceptable environment for the model. Findings of the present study provide a base...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6658/version/1

In silico comparative analysis of conserved genes expressed in solanaceous plants under abiotic stresses
Provedor de dados: 17
Autores: sanchita gupta; sunita singh dhawan; ashok  sharma.
The gene expression data was studied in order to analyze genes involved in different abiotic stresses in solanaceous plants.  Salt, temperature (heat &amp;#x26; cold) and drought are the main abiotic stresses to the plants. Abiotic stress responses are important for sessile organisms like plants because they have to cope with environmental changes to survive. The idea was to analyze those differentially expressed genes, which show common expression in response to different abiotic stress conditions in each plant.  Mitogen activated protein kinases (MAPK) are important mediators in signal transmission, connecting the perception of external stimuli to cellular responses. In plants, MAPKs plays a major role in the signaling of abiotic stresses. The expression...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6717/version/1

In silico comparative study of epitopes predicted from different strains of genus parvovirus.
Provedor de dados: 17
Autores: Rahul  B. Chamute; Mahadev A. Jadhav; Anant Patil.
Parvoviruses are typically linear, non-segmented single-stranded DNA viruses, with an average genome size of 5000 nucleotides. Parvoviruses are some of the smallest viruses found in nature. Some have been found as small as 23 nm. Many types of mammalian species have a strain of parvovirus associated with them. Parvoviruses tend to be specific about the taxon of animal they will infect, but this is a somewhat flexible characteristic. Thus, all strains of parvovirus will affect dogs, wolves, and foxes, but only some of them will infect human. Parvovirus is treated with the help of vaccines but the traditional vaccine development process is very expensive and unsafe, with the help of insilico software tools and databases we can predict the epitopes of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5574/version/1

In silico design of novel leads for inhibition of human beta-2-microglobulin
Provedor de dados: 17
Autores: Pallapotu Navya; Dibyabhaba Pradhan; Amineni Umamaheswari.
Human myotrophin is the smallest ankyrin repeat protein implicated as a factor to induce cardiac hypertrophy.  Activation of myotrophin was observed during acute myocardial infarction (MI). In acute coronary syndrome (ACS) patients, myotrophin acts as a self-governing predictor of major adverse cardiac events (MACE). Therefore, human myotrophin serves as an effective drug target for discovery of new potential drugs. Recent human myotropin inhibitors have poor pharmacological properties leading to intolerable side effects. Hence, ligand based virtual screening protocol of CADD method was pursued in the present study to propose new class potential myotrophin inhibitors. Docking was done by using Schr&amp;#xf6;dinger software suite 2010 (maestro v9.1), docked...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6569/version/1

In silico design of potent agonists for human PPAR &amp;#x3b3;
Provedor de dados: 17
Autores: Navya Pallapotu; Divya M; Kanipakam Hema; Amineni Umamaheswari.
Peroxisome proliferator-activated receptor (PPAR &amp;#x3b3;) acts as a key regulator on adipocyte differentiation and glucose homeostasis. PPAR &amp;#x3b3; has been implicated in the pathology of type 2 diabetes. As human PPAR &amp;#x3b3; activity is considered important in improving insulin sensitivity, in silico screening was carried out to find potent agonists for human PPAR &amp;#x3b3; protein. The co-crystal structure of PPAR &amp;#x3b3;, solved through X-Ray diffraction method was retrieved from the protein data bank. Four PPAR &amp;#x3b3; agonists selected from literature were submitted to subsequent 2D searching protocol using Ligand.Info, which yielded 1699 structural analogs. The PPAR &amp;#x3b3; co-crystal structure and ligand dataset were...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6957/version/1

In silico designing of activator for human IGF2 protein for effective cardiovascular disease therapeutics
Provedor de dados: 17
Autores: M Sandhya rani; Manne  Munikumar; Amineni  Umamaheswari.
Insulin like growth factor-II (IGF2) is a member of IGF family, the main role of IGF2 is as a growth hormone during gestation or fetal development. Ischematic stroke, atherosclerosis and pathological cardiac hypertrophy are associated with low circulating levels of IGF2. 5-aza-2&amp;#x2019;-deoxycytidine increases the activity of IGF2, due to high toxicity of 5aza2&amp;#x2019;deoxycytidine, some silenced genes are also expressed that cause various cancer diseases. In the present study an in silico approach was used to design the potential activator for IGF2 without side effects to treat cardiovascular diseases. Ligand binding sites were predicted using CASTp for drug target. 361 ligand analogs for 5-aza-2&amp;#x2019;-deoxycytidine were identified through...
Tipo: Presentation
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6558/version/1

In Silico Docking Analysis of Peptide Deformylase (PDF) - A Novel Target for Prophylaxis of Leptospirosis
Provedor de dados: 17
Autores: Virupaksha A. Bastikar; Shweta R. Fulsundar; Jagdish S. Nair.
Peptide deformylase (PDF) is a metalloproteinase and executes an essential step in the maturation of proteins in eubacteria, by removing the formyl group from the N-terminal methionine residue of ribosome-synthesized polypeptides. This process is crucial for bacterial survival because mature proteins do not retain N-formyl-methionine, and all known N-terminal peptidases cannot utilize formylated peptides as substrate. Thus, inhibition of PDF is essential to obstruct the bacterial protein maturation process. Antibiotics based on PDF inhibition have the potential to provide the much needed antibacterial activity against most of the major drug-resistant pathogens. This study comprises an implementation of _in-silico_ techniques to validate and map the...
Tipo: Manuscript
Palavras-chave: Microbiology; Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1520/version/1

In silico Gene Characterization and biological annotation of Aspergillus niger CBS 513.88
Provedor de dados: 17
Autores: Anuraj  Nayarisseri; Mukesh Yadav; Vini Lokhande; Rajesh  Patidar; Mayura  Maynal.
Genome annotation is the process of estimation of biological features from genomic data. The target of a genome annotation is to identify the key features of the genome sequence particularly, the genes and gene products. The characteristics of a gene, its products, and gene prediction programs of Aspergillus niger are discussed. Although the number of genomes in genomic databases are increasing day by day, genome-wide analyses are affected by the quality of the genome annotations. This study illustrates the importance of integrative approaches for automatic annotations of genomes of Aspergillus niger by computational methods. However, the annotation process is more complicated in Eukaryotes; we used a comparative study for gene prediction using the FgenesH...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5806/version/1

In silico Genetic Network Models for &amp;#xb;Pre-clinical Drug Prioritization
Provedor de dados: 17
Autores: Jianghui Xiong; Juan Liu; Simon Rayner; Ze Tian; Yinghui Li; Shanguang Chen.
The high rates of failure in oncology drug clinical trials highlight the problems of using pre-clinical data to predict the clinical effects of drugs. Patient population heterogeneity and unpredictable physiology complicate pre-clinical cancer modeling efforts. We hypothesize that gene networks associated with cancer outcome in heterogeneous patient populations could serve as a reference for identifying drug effects. Here we propose a novel in vivo genetic interaction which we call &amp;#x2018;synergistic outcome determination&amp;#x2019; (SOD), a concept similar to &amp;#x2018;Synthetic Lethality&amp;#x2019;. SOD is defined as the synergy of a gene pair with respect to cancer patients&amp;#x27; outcome, whose correlation with outcome is due to...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5343/version/1

In silico identification of potential inhibitors for human aurora kinase b
Provedor de dados: 17
Autores: Mahesh Babu G; Pradeep N.; Dibyabhaba  Pradhan; Manne  MuniKumar; Amineni  Umamaheswari.
Cell cycle progression through mitosis and meiosis involves regulation by serine/threonine kinases from the aurora family. Aurora kinase b (Aurkb) is mainly involved in the proper segregation of chromosomes during mitosis as well as meiosis. However, over expression of Aurkb leads to the unequal distribution of genetic information creating aneuploid cells, a hallmark of cancer. Thus, Aurkb can be used as an effective molecular target for computer-aided drug discovery against cancer. Existing Aurkb inhibitors are less efficient, hence an in silico work was carried out to identify novel potent inhibitors. Three published inhibitors azd1152, zm447439 and  N-(4-{[6-methoxy-7-(3-morpholin-4-ylpropoxy) quinazolin- 4-yl] amino} phenyl) benzamide were subjected to...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5458/version/1

_In silico_ microRNA identification from  paprika (_Capsicum annuum_) ESTs
Provedor de dados: 17
Autores: T. M. Manila; A. Riju; K. Lakshmi Priya Darshini; A. Chandrasekar; S. J. Eapen.
A total of 33,311 Expressed Sequence Tags (EST) of paprika were mined from the GenBank EST database. The redundancy of the EST sequences was removed using CAP3 and it resulted 4,541 contigs 8,539 singletons as nonredundant data sets. The microRNAs were predicted using the program miRNAfinder. This program predicted a total of 85 miRNAs miRNAs. Another study was carried out to find the homologes miRNA using blast based tool named &amp;#x201c;miRseeK&amp;#x2019; A total of 13 miRNAs with significant similarity with the plant miRNAs were obtained from paprika ESTs. The targets of the predicted miRNAs were found using the program miRU2. Findings suggest that most miRNAs play an important role in plant development, signal transduction, protein degradation and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3737/version/1

In silico Protein Structural Modeling and Active binding site Evaluation of Streptococcus pneumoniae
Provedor de dados: 17
Autores: M. Balakrishnan; R.C. Srivastava; M. Ramachandran.
Structure function relation of glucose kinese in Streptococcus pneumoniae. However, a solved structure for _Streptococcus pneumoniae_ glucose kinese is not available at the protein data bank. Glucose kinase is a regulatory enzyme capable of adding phosphate group to glucose in the first step of streptomycin biosynthesis. The activity of glucose kinase was regulated by the Carbon Catabolite Repression system. So, we created a model of glucose kinese from _Streptococcus pnemoniae_ using the X-ray crystallography structure of glucose kinese enzymes from _Enterobacteria faecalis_ as template with Molsoft ICM v3.5 software. The model was validated using protein structure checking tools such as PROCHECK, WHAT IF: for reliability. The active site amino acid...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3207/version/1

In Vitro Bactericidal Activities of Extracts From Ripe and Unripe Fruit of &amp;#x27;Noni&amp;#x27;
Provedor de dados: 17
Autores: Rajarajan Swaminathan; Shanthi Sabari; Nisha K John.
In an era of nutraceuticular research, &amp;#x2018;Noni&amp;#x2019; fruit is considered as a panacea because of the profound claim on its medicinal uses in treating many diseases inclusive of infections of microbial origin. Hence, the present study was done to know the antibacterial activity of aqueous extracts from ripe and unripe fruits of &amp;#x2018;Noni&amp;#x2019; Morinda citrifolia L on gastroenteritic and pyogenic bacteria. The study was done for eight gastroenteritic bacteria and six pyogenic bacteria.  The estimation of antibacterial activity of the ripe fruit &amp;#x26; unripe fruit extract were carried out by serial two fold tube dilution techniques.  Minimum Bactericidal Concentration of the ripe as well as unripe fruit extracts for the...
Tipo: Manuscript
Palavras-chave: Microbiology; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3954/version/1

In vitro Evolution and Engineering for Improved Ribozyme Polymerase Production
Provedor de dados: 17
Autores: Israr  Khan; Muhammad Waheed Akktar; Ayaz Ali Khan.
According to the &amp;#x22;RNA World Hypothesis&amp;#x22; the first self replicating molecule formed from the prebiotic chemicals is the ribozyme. A model compartmentalized self replicating system for ribozyme polymerases is designed and used to improve activity, fidelity and generality of the enzyme.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6064/version/1

In vitro shoot regeneration from cotyledon of redgram
Provedor de dados: 17
Autores: Telugu Raghavendra; Palagiri Sudhakar; K Balakrishna Reddy; Keerthi Venkaiah; Putta Latha; Tollamadugu NVKV Prasad; Lakkireddi Prasanthi.
Pigeonpea is one of the most popular legume grains in the world, especially in the Indian sub-continent. Keeping in view the importance of the crop, an efficient protocol for rapid in vitro plant regeneration from cotyledon of redgram has been reported in this paper. The concentraion of the hormones played an important role in shoot and root regeneration.
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7041/version/1

In vitro synergistic anti-prion effect of cholesterol ester modulators
Provedor de dados: 17
Autores: Christina Doriana Orr&amp;#xf9;; Maria Dolores  Cannas; Sarah Vascellari; Fabrizio Angius; Pier Luigi  Cocco; Claudia Norfo; Antonella Mandas; Paolo La Colla; Sandra Dess&amp;#xec;; Alessandra Pani.
Background. Our studies on the role of cholesterol in prion infection/replication showed that brains and peripheral cells of sheep susceptible to or suffering from Scrapie were characterized by an altered cholesterol homeostasis compared to animals with a scrapie-resistant genotype, and that drugs influencing cholesterol esterification were endowed with selective anti-prion activity in N2a cell lines infected with the 22L and RML prion strains. &amp;#xd;&amp;#xa;Results. In prion-infected N2a cell lines we now report increased anti-prion activity of dual-drug combinations consisting of cholesterol ester modulators associated with prion inhibitors Synergism was obtained with the cholesterol ester modulators everolimus, pioglitazone, progesterone, and...
Tipo: Manuscript
Palavras-chave: Microbiology; Neuroscience; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3883/version/1

In vivo evidence for NMDA receptor mediated excitotoxicity in a murine genetic model of Huntington Disease
Provedor de dados: 17
Autores: Mary Heng; Peter Detloff; Phillip Wang; Joe Tsien; Roger Albin.
N-methyl-D-aspartate receptor (NMDAR) mediated excitotoxicity is implicated as a proximate cause of neurodegeneration in Huntington Disease (HD). However, this hypothesis has not been tested rigorously in vivo. NMDAR NR2B-subunits are the predominant NR2 subunit expressed by the striatal medium spiny neurons that degenerate in HD. To test this hypothesis, we crossed a well validated murine genetic model of HD (Hdh(CAG)150) with a transgenic line overexpressing NMDAR NR2B-subunits. In the resulting double mutant line, we show exacerbation of selective striatal neuron degeneration. These results provide the first direct in vivo evidence of NR2B-NMDAR mediated excitotoxicity in the context of HD. Our results are consistent with prior suggestions that direct...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1996/version/1

_In vivo_ photoacoustic molecular imaging with simultaneous multiple selective targeting using antibody-conjugated gold nanorods
Provedor de dados: 17
Autores: Pai-Chi Li; Dar-Bin Shieh; Churng-Ren Wang; Chen-Wei Wei; Chao-Kang Liao; Ann-Ann Ding; Ya-Na Wu; Carolina Poe; Suwen Jhan.
The use of gold nanorods for photoacoustic molecular imaging in vivo with simultaneous multiple selective targeting is reported. The extravasation of multiple molecular probes is demonstrated, and used to probe molecular information of cancer cells. This technique allows molecular profiles representing tumor characteristics to be obtained and a heterogeneous population of cancer cells in a lesion to be determined. The results also show that the image contrast can be enhanced by using a mixture of different molecular probes. In this study, HER2, EGFR, and CXCR4 were chosen as the primary target molecules for examining two types of cancer cells, OECM1 and Cal27. OECM1 cells overexpressed HER2 but exhibited a low expression of EGFR, while Cal27 cells showed...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/1687/version/1

Inactivation of the Retinoblastoma Protein by Mutant B-Raf in Malignant Melanoma
Provedor de dados: 17
Autores: Yusuke Furukawa; Yukiko Kobayashi; Takahisa Kobayashi; Jiro Kikuchi; Taeko Wada; Ken Futaki; Eiji Kusano; Satoru Murata; Mamitaro Ohtsuki.
Although activating mutations of B-Raf are the most common genetic abnormalities in human melanomas, the mechanism by which mutant B-Raf transforms melanocytes is poorly understood. Here we show that the retinoblastoma tumor suppressor protein (pRB) is a direct target of B-Raf and is inactivated by phosphorylation in melanomas carrying B-Raf mutations. In contrast, pRB is undetectable in melanomas with wild-type B-Raf. Mutant B-Raf directly interacts with pRB and induces its phosphorylation at serine-249 and threonine-252 (S249/T252). Inhibition of B-Raf activity results in dephosphorylation of pRB at S249/T252 along with other sites in melanoma cells. S249/T252 are phosphorylated earlier than other sites during cell cycle entry of normal melanocytes....
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4857/version/1

INCF Lithuanian Workshop on Neuroscience and Information Technology
Provedor de dados: 17
Autores: Au&amp;#x161;ra Saudargiene.
The aim of this workshop was to give a current overview of neuroscience and informatics research in Lithuania, and to discuss the strategies for forming the Lithuanian Neuroinformatics Node and becoming a member of INCF. The workshop was organized by Dr. Au&amp;#x161;ra Saudargiene (Department of Informatics, Vytautas Magnus University, Kaunas, and Faculty of Natural Sciences, Vilnius University, Lithuania) and INCF.&amp;#xd;&amp;#xa;The workshop was attended by 15 invited speakers, among them 4 guests and 11 Lithuanian neuroscientists, and over 20 participants. The workshop was organized into three main sessions: overview of the INCF activities including the Swedish and UK nodes of INCF; presentations on Neuroscience research carried out in Lithuania;...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6931/version/1

INCF  --   new capability for global coordination in neuroinformatics
Provedor de dados: 17
Autores: Jan G. Bjaalie.
The Global Science Forum (GSF) of the OECD has initiated a new international organization, INCF, to further the development of Neuroinformatics as a global effort with the support of all ministers of research within OECD. This presentation explains the background for the establishment of the INCF, outlines some of the goals, and defines the operations of the INCF Secretariat in relation the INCF National nodes and the general neuroscience community.
Tipo: Presentation
Palavras-chave: Neuroscience.
Ano: 2006
URL: http://precedings.nature.com/documents/7/version/1

INCF Workshops on Needs for Training in Neuroinformatics: Extended and Short Course Provision
Provedor de dados: 17
Autores: David Willshaw.
The second and third _INCF Workshops on Training in Neuroinformatics_ were organized by the INCF National Node of the UK. In these workshops, the issues arising in providing extended courses, such as a full time Masters, or short courses, of a few days or a few weeks, were discussed. There was a focus on how the INCF could facilitate training in these types of courses. In this report, the recommendations from all three Training workshops are brought together.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5599/version/1

Incidence response to a suddenly increased cancer risk
Provedor de dados: 17
Autores: &amp;#xd6;rjan Hallberg.
Incidence rates of several cancers, including melanoma of the skin and breast cancer, have increased since the middle of the 20th century in Western countries. Here, we developed a model for cancer incidence over time, when considering a suddenly increased cancer risk from an environmental change. A two parameter exponential function was used to simulate cancer risk over calendar time since birth, taking into account the time lapse since the environmental change took place. The calculated incidence for all age cohorts over calendar time was used to calculate the age-standardized rates. The best fit between calculated and reported age-standardized rates was sought by parameter variation. The model was tested using reported rates for melanoma and breast...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2012
URL: http://precedings.nature.com/documents/6779/version/1

Incident light orientation lets C4 monocotyledonous leaves make light work differently
Provedor de dados: 17
Autores: Ana S. Soares; Simon P. Driscoll; Till K. Pellny; Enrique Olmos; Maria Arraba&amp;#xe7;a; Christine Foyer.
Photosynthesis is an important driver of ecosystem sustainability in the face of climate change. Monocotyledonous crop species with C4 photosynthesis such as maize (Zea mays L; corn) and sugar cane are crucial for future food security and biofuel crop requirements, while C4 pasture grasses such as Paspalum are central to natural ecosystems. The global demand for corn will exceed that for wheat and rice by 2020, making it the world&amp;#x27;s most important crop. Light-driven photosynthesis supports plant biomass production, but plants have also evolved safety valve mechanisms that attenuate the absorption of potentially lethal levels of excess light. The array of survival responses that enables leaves to evade photoinhibition is complex and involves...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Earth &amp; Environment; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1672/version/1

Incorporating Community Annotation Interfaces into the CIPRO2.5 Database with Comprehensible Sketches to Support Quick Annotations of Proteome Data.
Provedor de dados: 17
Autores: Keisuke Ueno; Kouki Yonezawa; Katsuhiko Mineta; Toshinori Endo.
User annotation or comment interfaces are now widely used in several web sites such as journals, news, weblogs and Wikipedia. However, there are only a few biological databases with annotation interfaces. The _Ciona_ _intestinalis_ protein database (CIPRO) was created in order to provide integrated proteome data especially for experimental biologists. The current database contains 89,673 unique sequences covering all the known and predicted gene models. Typical tasks include which gene models are reliable and which function is plausible. The human-curated annotation is most important for the meaningful database.&amp;#xd;&amp;#xa;Here we incorporate three new functions into the CIPRO2.5 database (http://cipro.ibio.jp/2.5/), providing enriched resources for...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5064/version/1

Increased flood frequency and magnitude decreases density of a stream-breeding salamander in urbanized watersheds
Provedor de dados: 17
Autores: Kyle Barrett; Craig Guyer.
Background/Question/Methods&amp;#xd;&amp;#xa;As urbanization increases across the globe, more ecologists have taken note of its consequences to stream systems. Sufficient data have been collected to document repeated patterns in urbanized streams for many abiotic parameters, aquatic insects, and fish. For example, we now know that urbanized streams experience more frequent and intense spates as a result of increased runoff form impervious surfaces in the urban watershed. The spates eventually lead to a more incised and wider stream bed. Such abiotic shifts consistently result in decreased aquatic invertebrate and fish diversity. More recently, stream-breeding salamanders have been observed to decrease in density in urban areas. We monitored the density of...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3972/version/1

Increased regeneration efficiency of _Brassica napus_ L. cultivars Star, Westar and Cyclone from hypocotyle and cotyledonary explants
Provedor de dados: 17
Autores: Israr Khan; Waqar  Ali; Zahir Ali Takar; Arfa Farooqi; Sikandar Khan; Muhammadwaheed Akhtar.
The comparative organogenesis of _Brassica napus_ L cultivars Cyclone, Star and Westar was studied. The cotyledonary explants gave a higher response to all the combinations of 0.5 mg/L 2,4-D and BAP (0.5, 1.0,1.5 and 2.0 mg/L} used for optimizing the conditions for callus induction. The best mean weight and mean length of callus was obtained at 0.5 mg/L 2,4-D and 1.5mg/L BAP for Star cotyledonary explants. For the complete plant regeneration the new method of exposing the explants culture to Growth regulator free medium was performed. The method was applicable to both hypocotyl and cotyledonary explants. The Shoot Induction Frequency for hypocotyl (6-34%) in the three cultivars is higher than the cotyledonary explants (3-23%). The method is speedy and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4781/version/1

Increased risk and benefit simultaneously alter the outcome of territorial fights
Provedor de dados: 17
Autores: Tsunenori Koga; Satoshi Ikeda.
Competition for resource, including territories is seen in a broad range of taxa. There has been much research on factors that determine the intensity and outcome of competitions (e.g. resource holding potentials: RHP, and resource value: RV). No research, however, has shown how different factors can simultaneously alter the intensity and outcome of contests. We investigated the effects of RV on fighting behavior and success in inter-tidal, territorial male crabs. Under natural conditions the larger rival won contests irrespective of whether he was the resident or intruder (i.e. there was no residency effect). We then motivated intruders to fight hard by subjecting them to the threat of predation, and found that they were more likely to win contests. When...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1619/version/1

Increasing Access To Bioinformatics Resources: Increase Community Curation by Increasing Your Community
Provedor de dados: 17
Autores: Jennifer M. Williams.
The amount of biological data has risen exponentially over the last decade. Along with this rise, the number and types of bioinformatics resources has risen such that the sheer number of bioinformatics resources is overwhelming. For these resources to attain their full potential, they must be efficiently and extensively utilized. But in such a plethora of resources, how does a researcher new to a field find the resources that will meet their needs. Once a resource is found, how does the researcher quickly learn to utilize that resource fully? There are resource lists such as those provided by the journal Nucleic Acid Research (NAR), BioMed Central and the Univ. of Pittsburgh Health Sciences Library, and most resources include their own documentation. But...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3163/version/1

Increasing incidence of thyroid cancer in shanghai, China, 1983-2007
Provedor de dados: 17
Autores: Youxin Wang; Wei Wang.
Increasing incidences of thyroid cancer were observed in some countries, like USA, UK, France, etc. Jointpoint regression was used to analyze the incidence of thyroid cancer in Shanghai, China, from 1983 to 2007. The results showed there were both two distinct slopes, in males representing a significant APC of 2.6% from 1983 to 2000 (P&amp;#x3c;0.001), followed by a sharply increased APC of 14.4% (P &amp;#x3c;0 .001), and in females representing a significant APC of 4.9% from 1983 to 2003 (P&amp;#x3c;0.001), followed by a sharply increased APC of 19.9% (P =0 .001). Incidence of thyroid cancer increased 5 to 8 years after the supplement of iodine, for males and females respectively, suggesting that either the developed screening techniques or supplement of...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2011
URL: http://precedings.nature.com/documents/5994/version/1

Increasing Insect Reactions in Alaska: Is this Related to Changing Climate?
Provedor de dados: 17
Autores: Jeffrey Demain; Bradford Gessner; Joseph McLaughlin; Derek Sikes; Timothy Foote.
During the summer of 2006, Fairbanks Alaska experienced its first two known cases of fatal anaphylaxis as a result of Hymenoptera stings, presumably from yellowjackets. An increase in insect bites and stings has been observed throughout the state.Has there been an increased incidence of medical visits due to insect bites and stings in Alaska in recent years? We conducted a retrospective review of three independent patient databases in Alaska to identify trends of patients seeking medical care for adverse reactions following insect bites and stings. For each database, an insect bite or sting episode warranting medical care was defined as a claim for the Clinical Modification of the International Classification of Diseases, Ninth Revision (ICD-9-CM), codes...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2481/version/1

Independent elaboration of steroid hormone signaling pathways in Metazoans
Provedor de dados: 17
Autores: Gabriel V. Markov; Raquel Tavares; Chantal Dauphin-Villemant; Barbara A. Demeneix; Michael E. Baker; Vincent Laudet.
Steroid hormones regulate many physiological processes in vertebrates, nematodes and arthropods through binding to nuclear receptors (NR), a metazoan-specific family of ligand-activated transcription factors.  The main steps controlling the diversification of this family are now well understood.  In contrast, the origin and evolution of steroid ligands remain mysterious although this is crucial for understanding the emergence of modern endocrine systems.  Using a comparative genomic approach, we analyzed complete metazoan genomes to provide a comprehensive view of the evolution of major enzymatic players implicated in steroidogenesis at the whole Metazoan scale.  Our analysis reveals that steroidogenesis has been independently elaborated in the three main...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3374/version/1

Indigenous ecological knowledge as social capital: How citizen science can help us replenish the bank
Provedor de dados: 17
Autores: Kaberi  Kar Gupta; Madhusudan V. Katti.
*Background/Question/Methods* &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In our increasingly urban world, indigenous knowledge of local ecology is declining rapidly, because survival in industrialized urban environments does not depend on knowing the details of local flora, fauna, or phenologies. While traditional ecological knowledge has been documented since 1980s, this is has been largely descriptive, e.g., ethnobotany of sacred groves, cultivation practices, or use of medicinal plants. Until recently, conservation biologists and managers of protected areas have followed western models of conservation that exclude local people and often abandon local ecological knowledge. However, many scientific studies of local ecosystems would not have been possible without...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3601/version/1

Individual and seasonal variation in the diet of the endangered Barton Springs Salamander (Eurycea sosorum): An application of stable isotope analysis to the conservation of an endangered species
Provedor de dados: 17
Autores: J. Hayley Gillespie.
It is well known that many species show strong temporal variation in diet. Long-term dietary trends may be important in assessing the effects of ecological change such as global warming, land use change, or introductions of invasive species. Short-term variation in food sources or prey selection may be crucial for understanding population dynamics in poorly understood species. The Barton Springs Salamander (_Eurycea sosorum_) is an endangered species endemic to four small spring outflows in downtown Austin, Texas. This species remains aquatic throughout life and inhabits benthic rocky substrate. While little is known about its foraging ecology, _E. sosorum_ is assumed to be a generalist predator with the abundant amphipod _Hyalella azteca_ as its primary...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3598/version/1

Induced fit, conformational selection and independent dynamic segments: an extended view of binding events
Provedor de dados: 17
Autores: Peter Csermely; Robin Palotai; Ruth Nussinov.
Single molecule and NMR measurements of protein dynamics increasingly uncover the complexity of binding scenarios. Here we describe an extended conformational selection model which embraces a repertoire of selection and adjustment processes. Induced fit can be viewed as a subset of this repertoire, whose contribution is affected by the bond-types stabilizing the interaction and the differences between the interacting partners. We argue that protein segments whose dynamics are distinct from the rest of the protein (&amp;#x2018;discrete breathers&amp;#x2019;) can govern conformational transitions and allosteric propagation that accompany binding processes, and as such may be more sensitive to mutational events. Additionally, we highlight the dynamic...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4422/version/1

Induction of Stress Granule Assembly is Essential for the Orchestration of DNA Damage Response
Provedor de dados: 17
Autores: Nicole S. Verkaik; Stephan Persengiev.
DNA damage provokes several responses including DNA repair, cell cycle regulation and apoptosis that collectively represent the DNA damage response (DDR). Here, we demonstrate that the DDR incorporates the activation of stress granule (SG) formation pathway as a mechanism to process destabilized RNAs. UV irradiation induced the assembly of SGs during the G2 phase and newly formed SGs appeared exclusively in the early G1 phase. SG assembly pathway was activated within the first hours after DNA damage, suggesting that the processing of destabilized RNAs is activated at an early stage. The induction of SGs and RNAi effector protein Argonaute 2 recruitment after UV exposure was independent of ATM and ATR signaling cascades. Apoptosis occurred only in...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1591/version/1

Inference of population splits and mixtures from genome-wide allele frequency data
Provedor de dados: 17
Autores: Joseph K. Pickrell; Jonathan K. Pritchard.
Many aspects of the historical relationships between populations in a species are reflected in genetic data. Inferring these relationships from genetic data, however, remains a challenging task. In this paper, we present a statistical model for inferring the patterns of population splits and mixtures in multiple populations. In this model, the sampled populations in a species are related to their common ancestor through a graph of ancestral populations. Using genome-wide allele frequency data and a Gaussian approximation to genetic drift, we infer the structure of this graph. We applied this method to a set of 55 human populations and a set of 82 dog breeds and wild canids. In both species, we show that a simple bifurcating tree does not fully describe the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6956/version/1

Inferior Colliculus
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Beth M. Solan; Lydia  L. Ng; John A. Morris.
This report contains a gene expression summary of the inferior colliculus (IC), derived from the Allen Brain Atlas (ABA) in-situ hybridization (ISH) mouse data set.  The structure&amp;#x2019;s location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas.  Using an established algorithm, the expression values of the IC were compared to the values of the macro/parent-structure, in this case the midbrain, for the purpose of extracting regionally specific gene expression data. The highest ranking ratios were then manually curated and verified.  The 50 Select Genes were compiled for expression characterization.  The experimental data for each gene may be accessed via the links provided;...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2033/version/1

Inferring a Transcriptional Regulatory Network from Gene Expression Data Using Nonlinear Manifold Embedding
Provedor de dados: 17
Autores: Hossein Zare; Mostafa  Kaveh; Arkady  Khodursky.
Transcriptional networks consist of multiple regulatory layers corresponding to the activity of global regulators, specialized repressors and activators of transcription as well as proteins and enzymes shaping the DNA template. Such intrinsic multi-dimensionality makes uncovering connectivity patterns difficult and unreliable and it calls for adoption of methodologies commensurate with the underlying organization of the data source. Here we present a new computational method that predicts interactions between transcription factors and target genes using a compendium of microarray gene expression data and the knowledge of known interactions between genes and transcription factors. The proposed method called Kernel Embedding of REgulatory Networks (KEREN) is...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5008/version/1

Inferring decoding strategy from choice probabilities in the presence of noise correlations
Provedor de dados: 17
Autores: Ralf M. Haefner; Sebastian Gerwinn; Jakob H. Macke; Matthias Bethge.
The activity of cortical neurons in sensory areas covaries with perceptual decisions, a relationship often quantified by choice probabilities. While choice probabilities have been measured extensively, their interpretation has remained fraught with difficulty. Here, we derive the mathematical relationship between choice probabilities, read-out weights and noise correlations within the standard neural decision making model. Our solution allows us to prove and generalize earlier observations based on numerical simulations, and to derive novel predictions. Importantly, we show how the read-out weight profile, or decoding strategy, can be inferred from experimentally measurable quantities. Furthermore, we present a test to decide whether the decoding weights...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/7014/version/1

Inflammation, DNA-centered radicals, and oxidative genotoxicity: The role of HOCl produced by myeloperoxidase in carcinogenesis
Provedor de dados: 17
Autores: Sandra E. Gomez-Mejiba; Zili Zhai; Dario C. Ramirez.
Myeloid cells (macrophages and neutrophils) infiltrate and synthesize myeloperoxidase (MPO) in sites of inflammation, producing gentotoxicity. In RAW 264.7 macrophages, bacterial lipopolysaccharide (LPS) induces superoxide radical anion, nuclear deformation (nuclear protuberances), MPO synthesis, biomolecule oxidation and cell death. &amp;#x201c;Freezing&amp;#x201d; LPS-triggered macrophage activation with the nitrone spin trap 5,5-dimethyl-1-pyrroline N-oxide (DMPO) prevented cell activation and death. Oxidation of proteins and genomic DNA was also blocked, with formation of protein- and DNA-DMPO nitrone adducts, as analyzed by immuno-spin trapping with a polyclonal anti-DMPO serum. Interestingly, confocal microscopy analysis of these cells showed that...
Tipo: Poster
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/4047/version/1

Inflammation targets specific organs for cancer in carriers of BRCA1/2 pathway mutations
Provedor de dados: 17
Autores: Bernard Friedenson.
Women who inherit a defective BRCA1 or BRCA2 gene have risks for breast/ovarian cancer that are so high and apparently so selective that many mutation carriers choose to have the most likely targets for cancer surgically removed.  Recent research has focused on better methods of treating such seemingly unavoidable hereditary cancers.  Prevention has received much less attention so a positive test result for a cancer gene leaves carriers with very limited options.  &amp;#xd;&amp;#xa;In order to prevent BRCA1/2 related cancers, it may be important to understand why they seem to occur only in certain characteristic organs.   Results here show that mutations in a pathway depending on BRCA1/2 gene products magnify cancer risks from chronic infection and...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4225/version/1

Influence of different iron availability on phosphoenolpiruvate carboxilase and malate dehydrogenase in roots of maize (Zea Mays L.) plants grown under iron deficiency
Provedor de dados: 17
Autores: Marco Antonio Russo; Adalgisa Belligno.
The effect of the different nitrate availability on some enzymatic activities has been evaluated in iron deficient and iron sufficient maize plants (Zea mays L.). In order to evaluate if the induction of sensitive to pH enzymatic activities is affected by the variation of the apoplast reaction due to the different nitrate availability, two experimental tests were done on maize plants grown in nutrient solution with different NO3- availability and with Fe-sufficiency (+Fe) (added with 80 uM Fe(III)-EDTA) and Fe-deficiency (-Fe) (added with 0.1 uM Fe(III)-EDTA).&amp;#xd;&amp;#xa;As regards 0.4 mM NO3- (NS2), independently of iron availability, phosphoenolpiruvate carboxilase and malate dehydrogenase inductions are higher than those recorded for the...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4175/version/1

Information and Data Sharing Policy, Genomic Science Program, DOE
Provedor de dados: 17
Autores: Susan Gregurick.
The Office of Biological and Environmental Research (OBER) will require that all publishable information resulting from GTL funded research must conform to community recognized standard formats when they exist, be clearly attributable, and be deposited within a community recognized public database(s) appropriate for the research conducted. Furthermore, all experimental data obtained as a result of GTL funded research must be kept in an archive maintained by the Principal Investigator (PI) for the duration of the funded project. Any publications resulting from the use of shared experimental data must accurately acknowledge the original source or provider of the attributable data. The publication of information resulting from GTL funded research must be...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5973/version/1

Information homeostasis as a fundamental principle governing the cell division and death
Provedor de dados: 17
Autores: Arvind Kumar; Harinder P. Singh.
To express genetic information with minimal error is one of the key functions of a cell. Here we propose an information theory based phenomenological model for the expression of genetic information. Based on the model we propose, the concept of &amp;#x22;information homeostasis&amp;#x22; ensures that genetic information is expressed with minimal error. We suggest that together with energy homeostasis, information homeostasis is a fundamental working principle of a biological cell.  This model proposes a novel explanation of why a cell divides and why it stops to divide and thus provides novel insight into oncogenesis and various neuro-degenerative diseases. Moreover, the model suggests a theoretical framework to understand cell division and death, beyond...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/5940/version/1

Information on Transcriptional Regulation and Signal Transduction of _Escherichia coli_ K-12 Integrated in the Database RegulonDB.
Provedor de dados: 17
Autores: Socorro Gama-Castro; Alberto Santos-Zavaleta; Martin Peralta-Gil; Verena Weiss; Heladia  Salgado; Hilda Solano; Julio Collado-Vides.
Since its inception, RegulonDB (&amp;#x22;http://regulondb.ccg.unam.mx/&amp;#x22;:http://regulondb.ccg.unam.mx/) has been a database that compiles information about the regulation of transcription initiation of _Escherichia coli_ K-12. However, we are aware that transcriptional regulation is not an isolated process; instead, it is the response to the different environmental conditions that trigger a series of concatenated reactions that end in transcriptional regulation, and it implies an adequate response in terms of induced and repressed gene products. We are working now to include all these new data in RegulonDB. As a consequence, transcriptional regulation in RegulonDB will be part of a unit that initiates with the signal, continues with the signal...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5270/version/1

Information on Transcriptional Regulation and Signal Transduction of _Escherichia coli_ K-12 Integrated in the Database RegulonDB.
Provedor de dados: 17
Autores: Socorro Gama-Castro; Alberto Santos-Zavaleta; Martin Peralta-Gil; Verena Weiss; Heladia  Salgado; Hilda Solano; Julio Collado-Vides.
Since its inception, RegulonDB (&amp;#x22;http://regulondb.ccg.unam.mx/&amp;#x22;:http://regulondb.ccg.unam.mx/) has been a database that compiles information about the regulation of transcription initiation of _Escherichia coli_ K-12. However, we are aware that transcriptional regulation is not an isolated process; instead, it is the response to the different environmental conditions that trigger a series of concatenated reactions that end in transcriptional regulation, and it implies an adequate response in terms of induced and repressed gene products. We are working now to include all these new data in RegulonDB. As a consequence, transcriptional regulation in RegulonDB will be part of a unit that initiates with the signal, continues with the signal...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5270/version/2

Informativeness of St14 VNTR Polymorphic Marker in the Carrier Detection of Hemophilia A
Provedor de dados: 17
Autores: Beenish Arif; Atif A. Baig; Saqib Mahmood; Mohammad Naeem.
Hemophilia A is the most common hereditary severe disorder of blood clotting. In families affected with hemophilia, genetic analysis provides opportunities to prevent recurrence of the disease. This study establishes a diagnostic strategy for carrier-ship determination in Pakistani population using an extragenic polymorphic marker for the first time. The analysis of St14 VNTR (DXS52) was carried out by polymerase chain reaction (PCR), in order to determine its informativeness in terms of heterozygosity in Pakistani population. This may be a milestone for further analysis of other polymorphic markers for carrier detection and prenatal diagnosis of hemophilia. Seventy eight blood samples (Hemophiliac = 23, Normal = 55) from 15 families were analyzed for...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/4272/version/1

In-group/out-group bias in contagious yawning
Provedor de dados: 17
Autores: J. Ryan  Porter; Steven M. Platek.
Bias for an in-group is a social phenomenon characterized by an affinity for one&amp;#x2019;s in-group over a perceived out-group. Activation in the amygdala, which is implicated in social and emotional processes, is increased when humans view other-race faces. This increase in activation is associated with implicit racial bias as indicated by scores on an implicit attitude test. Contagious yawning is a social process that appears to subserve empathic processes enabling the inferential modeling of the mental states of others and is exhibited in few species other than humans, including chimpanzees (Pan troglodytes), stumptail macaques (Macaca arctoides), dogs (Canis familiaris), and budgerigars (Melopsittacus undulatus). Despite these comparative data,...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6875/version/1

Inhaled Insulin: Intrapulmonary or Intranasal?
Provedor de dados: 17
Autores: Danish Ahmed; Sweta Kumari; Shruti Mishra; Shivangi Jaiswal.
Initial attempts delivered the insulin hormone intramuscularly, intravenously, and eventually subcutaneously. Other routes of administration of the drug were explored. These included oral, rectal, sublingual, buccal, transdermal, vaginal, intramuscular, intrapulmonary, and intranasal delivery systems. The purpose of these latter studies was to determine a noninjectable method to deliver insulin to patients with type 1 and 2 diabetes that would effectively lower blood sugar, control hemoglobin A1c (in much later studies), and allow patients a simpler, less invasive, and more direct control oftheir underlying disease process. &amp;#xb; In January 2006 the United States Food and Drug Administration approved Exubera (Pfizer Pharmaceuticals, New York, NY) as...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7115/version/1

Inherited mutations impair responses to environmental carcinogens:  Cancer prevention in mutation carriers
Provedor de dados: 17
Autores: Bernard Friedenson.
Some environmental carcinogens may be responsible for a modest increase in the numbers of cancers after years of exposure.  Economic or political factors weigh against widespread bans of carcinogens.  However, lists of chemicals and agents that cause cancer assume that everyone is equally susceptible to their carcinogenic effects. &amp;#xd;&amp;#xa;Hereditary cancer gene mutations can target specific tissues if they are exposed to a carcinogen and the hereditary deficit impairs normal protective responses.  Mutation carriers should then have higher risks for specific cancers caused by specific carcinogens.&amp;#xd;&amp;#xa;  &amp;#xd;&amp;#xa;For example, it can be predicted that BRCA1 or BRCA2 mutation carriers should be highly susceptible to the...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6024/version/1

Inherited mutations impair responses to environmental carcinogens:  Cancer prevention in mutation carriers
Provedor de dados: 17
Autores: Bernard  Friedenson.
Some environmental carcinogens may be responsible for an increase in the numbers of cancers but economic or political factors weigh against widespread bans.  However, lists of chemicals and agents that cause cancer assume that everyone is equally susceptible to their carcinogenic effects. &amp;#xd;&amp;#xa;In carriers of cancer gene mutations, carcinogens can target specific tissues especially during periods of stem cell activity if the hereditary deficit impairs normal protective responses.  Mutation carriers should then have higher risks for specific cancers caused by specific environmental carcinogens.  &amp;#xd;&amp;#xa;For example, it can be predicted that BRCA1 or BRCA2 mutation carriers should be highly susceptible to the carcinogen formaldehyde....
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6024/version/2

Inhibition of Acid Phosphatase Enzyme Activity in the Presence of Noncrystalline Calcium Phosphate and Nanocrystalline Calcium Apatite: a Preliminary Study
Provedor de dados: 17
Autores: Yassen Pekounov.
_Background_&amp;#xd;&amp;#xa;Our bones are remodelled repeatedly throughout life. New and &amp;#x201c;healthy&amp;#x201d; bone tissue replaces the old one. It has been shown that the bone degrading cells, the osteoclasts, prefer old and fatigued bone. The young bone mineral, i.e. calcium apatite, is less crystalline than the mature one. Is it possible that the osteoclasts distinguish between relatively old and new bone via its mineral crystallinity?&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;_Methodology/Principal Findings_&amp;#xd;&amp;#xa;Acid phosphatase is an enzyme abundantly expressed by the osteoclasts during resorption and therefore used as a marker of the cells&amp;#x2019; activity. This study explores whether its enzymatic activity would be decreased in...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/3658/version/2

Inhibition of Acid Phosphatase Enzyme Activity in the Presence of Noncrystalline Calcium Phosphate and Nanocrystalline Calcium Apatite: a Preliminary Study
Provedor de dados: 17
Autores: Yassen Pekounov.
*Background*&amp;#xd;&amp;#xa;Our bones are remodelled repeatedly during life. A new and &amp;#x201c;healthy&amp;#x201d; bone tissue replaces the old one. Accordingly, the bone degrading cells, the osteoclasts, prefer old and fatigued bone. The young bone mineral, i.e. calcium apatite, is less crystalline than the mature one. Is it possible that the osteoclasts distinguish between relatively old and new bone via its crystallinity?&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Methodology/Principal Findings*&amp;#xd;&amp;#xa;Acid phosphatase is an enzyme largely expressed by the osteoclasts during resorption and therefore used as a marker of the cells activity. This study explores whether its enzymatic activity would be decreased in the presence of biomimitetically...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3658/version/1

Inhibition of central insulin-receptor signaling by S961 causes hyperglycemia and glucose intolerance in rats
Provedor de dados: 17
Autores: Ajit Vikram; Gopabandhu Jena.
Genetic ablation studies confirmed the role of central insulin-receptor signaling (CIRS) in fuel metabolism. However, the need to examine the role of CIRS in glucose homeostasis under normal physiological condition is indispensable, as insulin affects the neuronal growth, differentiation and synaptic plasticity. Intracerebral administration of S961 induced hyperglycemia and glucose intolerance in normal rats, and provided direct evidence for the involvement of CIRS in the regulation of glucose homeostasis.
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5701/version/1

Inhibition of pteridine reductase 1 (PTR1) expression in Leishmania promastigotes using a full-length antisense construct
Provedor de dados: 17
Autores: Farnaz Kheirandish; Mojgan Bandehpour; Nushin Davoudi; Nariman Mosaffa; Fereydoun Mahboudi; Bahram Kazemi; Ali Haghighi; Mehdi Mohebali.
Leishmania exhibit many unusual features, one of which is the pteridine metabolic pathway essential for the growth for these parasites. Leishmania have evolved a complex and versatile pteridine salvage network capable of scavenging a wide array of conjugated and unconjugated pteridines. The L. major PTR1 gene was cloned into pcDNA3 digested with KpnI and BamHI. The gene was cloned antiparallel to the promoter and named pcDNA-Rptr. L. major promastigotes were divided into two groups. One group was transfected with 50 &amp;#x3bc;g of pcDNA-Rptr, whereas the other group was electroporated with pcDNA3. Mentioned cells were cultured and plated onto semi-solid media.Western blotting was performed on extracts from transfected promastigotes of L. major using an...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/2807/version/1

Inhibiton of NF&amp;#x3ba;B activation and aromatase activity by vanilloids: An in vitro and in silico study
Provedor de dados: 17
Autores: Suaib  Luqman; Abha  Meena; Laura  E. Marler; Tamara  P. Kondratyuk; John  M. Pezzuto.
Target-specific drugs, including natural products, offer promise for the amelioration of cancer and other human ailments with reduced side-effects. Capsaicin, the pungent ingredient present in chillies (Capsicum annuum L.), and capsazepine, a synthetic analogue of capsaicin (collectively referred to as vanilloids), are known to possess a variety of pharmacological and physiological properties. In our continuous effort to discover cancer chemopreventive agents from natural products, we investigated the effect of vanilloids on NF&amp;#x3ba;B activation with stably transfected 293/NF&amp;#x3ba;B-Luc human embryonic kidney cells induced by treatment with tumor necrosis factor (TNF&amp;#x3b1;), and aromatase activity. Capsaicin and capsazepine blocked...
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6913/version/1

Innovation in cardiology. A new diagnostic standard establishing criteria of quantitative &amp;#x26; qualitative evaluation of main parameters of the cardiac &amp;#x26; cardiovascular system according to ECG and Rheo based on cardiac cycle phase analysis
Provedor de dados: 17
Autores: M Rudenko; S Kolmakov; Konstantine Weber; O Voronova; V Zernov; S Rudenko; K Mamberger; D Makedonsky.
Over more than 50 years the theory of functioning of the cardiac &amp;#x26; cardiovascular system remained unchanged. As a rule, all conventional diagnostics methods are based on statistics data on changes in shapes of cardiac signals only, so that it is impossible to determine the relevant cause-effect relations with respect to their formation [1,2]. But a theory of elevated fluidity of liquid offered twenty five years ago makes it possible to develop an innovative method of the phase analysis of the cardiac cycle [3]. The successful application of the said method in researches for the last 5 years has enabled a practical implementation of an indirect measuring concept with respect to volumetric hemodynamic parameters [4]. By evaluating hemodynamic...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3667/version/1

Inositol-Related Gene Knockouts Mimic Lithium&amp;#x27;s Effect on Mitochondrial Function
Provedor de dados: 17
Autores: Galila Agam; RH Belmaker; Dieder  Moechars; Vered Chalifa-Caspi; Yuly Bersudsky; Inbar Plaschkes; Lilach Toker; Gerard Berry.
Bipolar-disorder, characterized by switches between depressive and manic mood, is treated by mood-stabilizers, lithium being one of them. Among hypotheses suggested, the inositol-depletion hypothesis proposes that lithium attenuates hyperactivation of phosphatidylinositol signaling linked to neurotransmission-related receptors.Available for us are knockout-mice of two genes (IMPA1 or Slc5a3) each encoding for a protein related to inositol metabolism. We previously characterized these mice as exhibiting lithium-like neurochemical and behavioral phenotype. We performed a DNA-microarray study searching for pathways commonly affected by chronic lithium treatment and by the knockout of each of the genes. Here we show up-regulation of mitochondrial function in...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6318/version/1

Insights from the Structure of Estrogen Receptor into the Evolution of Estrogens: Implications for Endocrine Disruption
Provedor de dados: 17
Autores: Michael E. Baker.
In the last decade, there has been important progress in understanding the origins and evolution of receptors for adrenal steroids (aldosterone, cortisol) and sex steroids (estradiol, progesterone, testosterone) due to the sequencing of genomes from animals that are at key sites in vertebrate evolution.  Although the estrogen receptor [ER] appears to be the ancestral vertebrate steroid receptor and estradiol [E2] is the physiological ligand for vertebrate ERs, the identity of the ancestral ligand(s) for the ER remains unknown.  Here, using an analysis of crystal structures of human ER[alpha] with E2 and other chemicals and 3D models of human ER[alpha] with 27-hydroxycholesterol and 5-androsten-3[beta],17[beta]-diol, we propose that one or more [DELTA]5...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Ecology; Genetics &amp; Genomics; Pharmacology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5777/version/1

In-silico analysis and identification of novel lead molecule for human IGFBP-4 involved in cardiovascular diseases
Provedor de dados: 17
Autores: Kavali  Roopesh; Manne Munikumar; Amineni Umamaheswari.
Cardiovascular disease is the major cause of disability and premature death throughout the world and contributes substantially to the escalating costs of health care. Insulin like growth factor binding protein 4 (IGFBP-4) mainly belongs to the family of IGFB protein. Over expression of IGFBP-4 leads to cardiovascular diseases namely stroke, acute myocardial infarction and heart failure. IGFBP-4 serves as an effective drug target against cardiovascular disease. Hence, ligand based virtual screening was persuaded in the present study to propose potential inhibitors of IGFBP-4. Two inhibitors (mainly from literature search) were selected to initiate high throughput virtual screening from small molecule databases namely, NCI, ChemBank, ChemPDB, AKos GmbH,...
Tipo: Presentation
Palavras-chave: Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6530/version/1

In-silico analysis of human IGFBP-4 involved in cardiovascular diseases
Provedor de dados: 17
Autores: Manne MuniKumar; Kavali Roopesh; Amineni  Umamaheswari.
Cardiovascular disease is the major cause of disability and premature death throughout the world and contributes substantially to the escalating costs of health care. Insulin like growth factor binding protein 4 (IGFBP-4) mainly belongs to the family of IGFB protein. Over expression of IGFBP-4 leads to cardiovascular diseases namely stroke, acute myocardial infarction and heart failure. IGFBP-4 serves as an effective drug target against cardiovascular disease. Hence, ligand based virtual screening was pursued in the present study to propose potential inhibitors of IGFBP-4. Two published inhibitors were selected to initiate high throughput virtual screening from small molecule databases namely, NCI, ChemBank, ChemPDB, AKos GmbH, Asinex Ltd and KEGG ligand....
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6567/version/1

Insilico based designing of short peptide and ligands for calcineurin receptor
Provedor de dados: 17
Autores: Vishwamhabr V. Bhandare; T. G. Jagtap; M. M. Pillai; P. S. Patil.
Calcineurin is a target protein for Cyclosporin A (CsA) an immunosuppressive drug which prevents transplant rejection. CsA has complex structure of 11 amino acids, a cyclic structure with uncommon amino acids, and can&amp;#x2019;t be chemically synthesized. CsA can be synthesized commercially by using fermentation. One report shows chemical synthesis of CsA with partial success (Jason and Diver, 2002). In view of this it is proposed to model a peptide and ligand as an alternate for CsA with the same function and can be chemically synthesized. The target for Cyclosporin is Cyclophilin which forms a ternary complex with calcineurin (CN). An in silico study concludes that all four peptides (1 wild + 3 mutant) were found to bind in the catalytic site of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6072/version/1

In-silico identification of potential antagonists for human Casein kinase II subunit alpha&amp;#x27; (CK2&amp;#x3b1;2)
Provedor de dados: 17
Autores: Kanipakam Hema; Harika  Meduru; Navya Pallapotu; Amineni Umamaheswari.
Human CK2&amp;#x3b1;2 is an enzyme that belongs to the Serine/Threonine protein kinase family which is involved in signal transduction. Over expression of CK2&amp;#x3b1;2 causes kidney cancer therefore, human CK2&amp;#x3b1;2 has been identified as a drug target for the development of potential antagonists against cancer therapy. The existing human CK2&amp;#x3b1;2 inhibitors in clinical practice are having side effects like fatigue, diarrhea, nausea, anorexia and vomiting. High-throughput virtual screening is one of the most common method used to identify lead compounds was implemented in the present study to identify potential inhibitors of human CK2&amp;#x3b1;2. The co-crystal structure of human CK2&amp;#x3b1;2 was retrieved from the protein data bank. A...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6958/version/1

In-silico Predictive Mutagenicity Model Generation Using Supervised Learning Approaches
Provedor de dados: 17
Autores: Anurag  Passi; Abhik Seal; OSDD  Consortium; UC Abdul  Jaleel.
With the advent of High Throughput Screening techniques, it is feasible to filter possible leads from a mammoth chemical space that can act against a particular target and inhibit its action. Virtual screening complements the in-vitro assays which are costly and time consuming. This process is used to sort biologically active molecules by utilizing the structural and chemical information of the compounds and the target proteins in order to screen potential hits. Various data mining and machine learning tools utilize Molecular Descriptors through the knowledge discovery process using classifier algorithms that classify the potentially active hits for the drug development process.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6116/version/1

Instantaneous Capture and Mineralization of Flue Gas Carbon Dioxide: Pilot Scale Study
Provedor de dados: 17
Autores: KJ Reddy; Hollis Weber; Pradip Bhattacharyya; Argyle Morris; David Taylor; Mikol Christensen; Thomas Foulke; Paul Fahlsing.
Multiple CO2 capture and storage (CCS) processes are required to address anthropogenic CO2 problems. However, a method which can directly capture and mineralize CO2 at a point source, under actual field conditions, has advantages and could help offset the cost associated with the conventional CCS technologies. The mineral carbonation (MC), a process of converting CO2 into stable minerals (mineralization), has been studied extensively to store CO2. However, most of the MC studies have been largely investigated at laboratory scale. Objectives of this research were to develop a pilot scale AMC (accelerated mineral carbonation) process and test the effects of flue gas moisture content on carbonation of fly ash particles. A pilot scale AMC process consisting of...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5404/version/1

Insular gigantism and dwarfism in a snake, adaptive response or spandrel to selection on gape size?
Provedor de dados: 17
Autores: Shawn Vincent; Matthew Brandley; Takeo Kuriyama; Akira Mori; Anthony Herrel; Masami Hasegawa.
In biology, spandrels are phenotypic traits that evolve through their underlying developmental, genetic, and/or structural links to another trait under selection^1, 2, 3^. Despite the importance of the concept of spandrels in biology, empirical examples of spandrels are exceedingly rare at the organismal level^2, 3^. Here we test whether body size evolution in insular populations of a snake (_Elaphe quadrivirgata_) is the result of an adaptive response to differences in available prey, or the result of a non-adaptive spandrel resulting from selection on gape size. In contrast to previous hypotheses, Mantel tests show that body size does not coevolve with diet. However, gape size tightly matches diet (birds vs. lizards) across populations, even after...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3360/version/1

Intact mitochondria migrate in membrane tubular network connections formed between human stem cells
Provedor de dados: 17
Autores: Attila Csordas; Attila Cseleny&amp;#xe1;k; Ferenc Uher; Marianna Mur&amp;#xe1;nyi; Simone Hennerbichler; Heinz Redl; M&amp;#xe1;rk Kollai; Zsombor Lacza.
The hypothesis of mitochondrial transfer between eukaryotic animal cells is intriguing, although its route of action and physiological role is unknown. Our goal was to examine intercellular connections among several types of stem cells and to observe whether intact functional mitochondria may travel via these connections. Time-lapse laser scanning confocal microscopy has shown that human amnion-derived stem cells as well as bone marrow derived mouse and human mesenchymal stem cells form cell-to-cell connections via a tubular membrane network. The maximal length of these micrometer-thick tubes is around 180 ?m. Interestingly, freshly isolated amniotic epithelial stem cells did not form these connections, only after several passages when the morphology of...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/44/version/1

Integral presentation of Experimental Results and Bioinformatic Analyses on _Ciona_ _intestinalis_ Proteins
Provedor de dados: 17
Autores: Kouki Yonezawa; Keisuke Ueno; Katsuhiko Mineta; Toshinori Endo.
For the aim of facilitating biologists to find new knowledge through the comprehensive proteomic and transcriptomic data of _Ciona intestinalis_, we have been developing an intuitive and integral view of experimental and bioinformatic results for each protein, which, unlike on human proteins, was incomplete for _Ciona_ proteins.  In the presentation, we integrated in a view the experimental results of 2D-PAGE analyses done at Shimoda Marine Research Center, University of Tsukuba, 3D-view of expressions (3DPL) done by Hotta _et al_., and cross-references with JGI version 1 and ENSEMBL.  A total of 1,673 entries of 2D-PAGE and 57 of 3DPL are currently contained in CIPRO database.  The information is summarized in a single page for a protein.  Together with...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5088/version/1

Integrated disease management using environmental control in tea fields
Provedor de dados: 17
Autores: Tsuyoshi Tomihama; Nonaka Toshiyuki; Nishi Yatsuka; Arai Kei.
The occurrence of plant disease depends on interactions between the host plant, a pathogen, and the environment in a dynamic called &amp;#x22;the disease triangle&amp;#x22;. Bacterial shoot blight (BSB) disease, caused by _Pseudomonas syringae_ pv. _theae_ (_Pst_), is a major bacterial disease of tea plants in Japan and substantially reduces tea productivity. BSB mainly occurs in the low-temperature season, and lesion formation by _Pst_ is enhanced by both low temperature and the presence of ice nucleation-active _Xanthomonas campestris_ (INAX), which catalyses ice formation at -2 to -4^o^C and is frequently co-isolated with _Pst_ from tea plants^5^. Low temperature is thus the most important environmental factor to influence the incident; however, the...
Tipo: Manuscript
Palavras-chave: Microbiology; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1836/version/1

Integrating &amp;#xa0;text-&amp;#xad;mining&amp;#xa0;effort requires&amp;#x9;output standards
Provedor de dados: 17
Autores: Andra Waagmeester.
We recently released a plugin to Pathvisio to assist the curator with automatic integration of heterogeneous pathway knowledge. Pathway curation involves gathering this knowledge not only through discussions with peers, but also from biological databases and the scientific literature. Integrating this all into one pathway is challenging and to date still mainly a laborious manual process. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;More and more biological databases provide webservices (ie. REST or SOAP). The main objective of webservices is to provide an interface for other computer applications. Our plug-in uses these interfaces to gather binary relationships of a given pathway entity and present the relation in star shaped figures to the curator. The plug-in...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5850/version/1

Integrating genomics, transcriptomics, proteomics, and metabolomics into environmental enzymology:  the next frontier or fool&amp;#x27;s gold?
Provedor de dados: 17
Autores: Matthew D. Wallenstein.
Extracellular enzymes are widely measured as indices of microbial activity, resource allocation, and substrate availability.  However, interpretation of enzyme activities is hampered by a limited understanding of controls on enzyme production, turnover, and in-situ activity.  In part, this is the consequence of methodological limitations, which require artificial substrates and are conducted under conditions that differ from in situ conditions.  Recently, new tools have emerged that have potential to provide new insights into microbial enzymology. Will these methods open a new frontier in enzymology research, or will they only result in the discovery of fool&amp;#x2019;s gold? I will highlight how genomic, transcriptomic, proteomic, and metabolomic tools...
Tipo: Presentation
Palavras-chave: Ecology; Microbiology; Bioinformatics; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6159/version/1

Integrating microbial community data with ecological theory
Provedor de dados: 17
Autores: Steven D. Allison.
Background/Question/Methods&amp;#xd;&amp;#xa;Molecular and bioinformatics techniques are revealing the rich diversity of microbial communities. These approaches generate valuable data that ecologists could use to develop and test theories that apply to a large fraction of living organisms. However, the complexity of microbial community data is a challenge to achieving this integration. A fundamental question in microbial ecology is how to aggregate microbial communities so that their taxa may be represented in theoretical models. Recently, models based on microbial traits have been developed to tackle this question. Such models may represent microbial taxa as functional groups or stochastic assemblages with a distribution of trait values. Here, I define...
Tipo: Presentation
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5511/version/1

Integrating Open Lab Notebooks with Online Databases
Provedor de dados: 17
Autores: Carl Boettiger.
My slides from a presentation and panel discussion on integrating open lab notebooks with online databases.  A video archive of the presentation is available here: http://vimeo.com/20100632
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/6853/version/1

Integrating Text Mining into the MGI Biocuration Workflow
Provedor de dados: 17
Autores: Karen G. Dowell; Monica S. McAndrews-Hill; David P. Hill; Harold J. Drabkin; Judith A. Blake.
A major challenge for the development of resources for functional and comparative genomics is the extraction of data from the biomedical literature.  Although text retrieval and extraction for biological data is an active research field, few applications have been integrated into production literature curation systems such as those of the model organism databases.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In September 2008, Mouse Genome Informatics (MGI) at The Jackson Lab initiated a search for dictionary-based text mining tools that we could integrate into our curation workflow.  MGI has rigorous document triage and annotation procedures designed to identify articles about mouse genome biology and determine whether those articles should be curated.  We...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3262/version/1

Integration of Co-expression Networks for Gene Clustering
Provedor de dados: 17
Autores: Malay Bhattacharyya; Sanghamitra Bandyopadhyay.
Simultaneous overexpression or underexpression of multiple genes, used in various forms as probes in the high-throughput microarray experiments, facilitates the identification of their underlying functional proximity. This kind of functional associativity (or conversely the separability) between the genes can be represented proficiently using co-expression networks. The extensive repository of diversified microarray data encounters a recent problem of multi-experimental data integration for the aforesaid purpose. This paper highlights a novel integration method of  gene co-expression networks, based on the search for their consensus network, derived from diverse microarray experimental data for the purpose of clustering. The proposed methodology avoids the...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7126/version/1

Integration of microbial communities into large-scale ecosystem models
Provedor de dados: 17
Autores: Steven D. Allison.
*Background/Question/Methods*&amp;#xd;&amp;#xa;Micro-organisms, including Bacteria, Archaea, and Fungi, control major processes throughout the Earth system. Recent advances in microbial ecology and microbiology have revealed an astounding level of genetic and metabolic diversity in microbial communities. However, a framework for interpreting the meaning of this diversity has lagged behind the initial discoveries. Microbial communities have yet to be included explicitly in any major biogeochemical models in terrestrial ecosystems, and have only recently broken into ocean models. Although simplification of microbial communities is essential in complex systems, omission of community parameters may seriously compromise model predictions of biogeochemical...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3633/version/1

Integration of the scientific literature into the Semantic Web: Facts from biomedical data resources
Provedor de dados: 17
Autores: Dietrich Rebholz; Samuel Croset; Christoph Grabmueller.
Scientific literature is the primary resource for relevant and innovative information. The integration of the literature with other data resources in the biomedical research community generates overhead that can be avoided through the used of Semantic Web Technology generating openly accessible data. Projects such as SESL and CALBC have producted significant amount of data that that are ready for exploitation.&amp;#xd;&amp;#xa;The tutorial will teach different approaches on how to integrate the scientific literature with the content from biomedical databases, and will discuss the inferences that can be achieved. Furthermore, the tutorial will point to the resources that are ready for use and enable integration of the literature at your discretion. A good...
Tipo: Presentation
Palavras-chave: Biotechnology; Immunology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7011/version/1

Integrative analysis of large-scale  biological data sets
Provedor de dados: 17
Autores: Enrico Glaab; Jonathan M. Garibaldi; Natalio Krasnogor.
We present two novel web-applications for microarray and gene/protein set analysis, ArrayMining.net and TopoGSA. These bioinformatics tools use integrative analysis methods, including ensemble and consensus machine learning techniques, as well as modular combinations of different analysis types, to extract new biological insights from experimental transcriptomics and proteomics data. They enable researchers to combine related algorithms and datasets to increase the robustness and accuracy of statistical analyses and exploit synergies of different computational methods, ranging from statistical learning to optimization and topological network analysis.
Tipo: Presentation
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5598/version/1

Integrative Approach - New Level Knowledge of Functions: Opportunities and Prospects
Provedor de dados: 17
Autores: Vladimir M. Pokrovskii.
In this article, the example of the mechanisms of heart rhythmogenesis in the intact organism is used to demonstrate the new capabilities provided by an integrative approach. It is shown that the rhythm is formed in the brain, transmitted to the heart in the form of signals along the vagus nerves and reproduces the heart. Evidence: the heart rhythm reproduces the natural efferent signals in the vagus nerves in the cardio-respiratory synchronism and in the intact organism sino-atrial node performs the functions of the latent pacemaker. Integration of the two hierarchical levels of rhythmogenesis (brain and intracardiac) provides the reliability and functional perfection of cardiac rhythm generation in the body. It is expedient to extend the presented...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6938/version/1

Integrative concept of homeostasis: translating physiology into medicine
Provedor de dados: 17
Autores: Ivan Spasojevic.
To truly understand living systems they must be viewed as a whole. In order to achieve this and to come to some law to which living systems obey, data obtained on cells, tissues and organs should be integrated. Because there are no such laws yet, there is usually a long path for physiological findings obtained by reductionist approaches to be translated into medical practice. The concept and accompanying equations of homeostasis presented here are aimed to develop biological laws and to bridge this gap between physiology and medicine. The concept of homeostasis takes into account energy input and output, enlisting all relevant contributors. In homeostasis, input should equal the output. What I suggest here is that if the system is out of homeostasis, the...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6741/version/1

Integrative concept of homeostasis: translating physiology into medicine
Provedor de dados: 17
Autores: Ivan Spasojevic.
To truly understand living systems they must be viewed as a whole. In order to achieve this and to come to some law to which living systems obey, data obtained on cells, tissues and organs should be integrated. Because there are no such laws yet, there is usually a long path for physiological findings obtained by reductionist approaches to be translated into medical practice. The concept and accompanying equations of homeostasis presented here are aimed to develop biological laws and to bridge this gap between physiology and medicine. The concept of homeostasis takes into account energy input and output, enlisting all relevant contributors. In homeostasis, changes in the input should equal changes in the output within any specific period of time. What I...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6741/version/2

Integrative Network-based Association Studies: Leveraging cell regulatory models in the post-GWAS era
Provedor de dados: 17
Autores: Andrea Califano; Atul Butte; Stephen Friend; Trey Ideker; Eric E. Schadt.
After completion of a number of large scale Genome-Wide Association Studies (GWAS), there is still a significant amount of trait and disease variance that cannot be explained by existing genetic variability. This review introduces new, Integrative Network-based Association Study (INAS) approaches that aim to minimize the impact from multiple hypothesis testing statistics, thus allowing the identification of rare variants/alterations and epistatic interactions. In particular we discuss methods that rely on the de novo computational, experimental, and integrative dissection of context specific molecular interaction networks (or interactomes, for short). We provide several examples of how these approaches may be used to tackle discovery of genetic variants...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5732/version/1

Integrin-mediated membrane blebbing is dependent on the NHE1 and NCX1 activities.
Provedor de dados: 17
Autores: Yung-Hsiang Yi; Yu-Sun Chang; Chi-Hung Lin; Tien-Shen Lew; Chih-Yung Tang; Tsung-Yu Chen; Wei-Lien Tseng; Ching-Ping Tseng; Szecheng J. Lo.
Integrin-mediated signal transduction and membrane blebbing have been well studied to modulate cell adhesion, spreading and migration^1-6^. However, the relationship between membrane blebbing and integrin signaling has not been explored. Here we show that integrin-ligand interaction induces membrane blebbing and membrane permeability change. We found that sodium-proton exchanger 1 (NHE1) and sodium-calcium exchanger 1 (NCX1) are located in the membrane blebbing sites and inhibition of NHE1 disrupts membrane blebbing and decreases membrane permeability change. However, inhibition of NCX1 enhances cell blebbing to cause cell swelling which is correlated with an intracellular sodium accumulation induced by NHE17. These data suggest that sodium influx induced...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5723/version/1

Intelligence-based medicine
Provedor de dados: 17
Autores: Pierre Squara; Didier Journois.
Despite seven hundred thousand new medical references last year, the relationship between a given set of medical features and specific pathophysiology, treatment, and criteria of improvement is often weak. Moreover, the generalization of evidences obtained in specific settings may lead to under-treat or to over-treat a significant proportion of patients. We expose an application of the cybernetic loop, based on traditional medical steps: nosology, semeiology, pathophysiology, therapy and on the four transitions between these steps. This approach leads to formulate eight basic questions evaluating the steps in terms of reproducibility and the transitions in terms of predictivity. We detail two practical applications: 1) the evaluation of a medical decision...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3196/version/1

Interaction ammonium-nitrate: Response to oxidative stress in chicory plants
Provedor de dados: 17
Autores: Marco Antonio M. A. Russo; Sonja Veljovic-Jovanovic; Adalgisa Belligno.
The aim of this work was to study, as a function of the different availability of nitrogen in the reduced form, mineral and organic, the induction of the synthesis of some ROS-scavenging molecules and the evolution of some enzymatic activities such as ascorbate peroxidase (APX) and polyphenoloxidase (PPO). &amp;#xd;&amp;#xa;Chicory seedlings were grown in nutritive solution for 35 days in controlled conditions. On the 14th day, one third of the plants was transferred into a nutritive solution containing (NH4)2SO4  60 mM, one third was transferred into a medium containing Urea 60 mM, and the remaining was let grow into the nutrition solution, as a control. Three samplings of leaves were performed, respectively after 21, 28 and 35 days of...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4173/version/1

Interaction of the TNFR-receptor associated factor TRAF1 with I-kappa B kinase 2 (IKK2, IKK-beta, IKBKB) and TRAF2 indicating a dose dependent regulatory function of TRAF1 for NF-kappa B signaling
Provedor de dados: 17
Autores: Johannes A. Schmid; Andreas Birbach.
IKK2 is one of the most crucial signaling kinases for activation of the transcription factor NF-kappa B. Since many NF-kappa B activating pathways converge at the level of IKK2, we searched for interaction partners of this kinase using the C-terminal part (aa 466-756) as bait in a yeast two-hybrid system. We identified the N-terminal part (aa 1-228) of the TNF-receptor associated factor TRAF1 as putative interaction partner, which was subsequently confirmed in mammalian cells by coimmunoprecipitation experiments. However, this interaction seemed weaker than the interaction between TRAF1 and TRAF2, an important activating adapter molecule of NF-kappa B signaling indicating that relative levels of IKK2, TRAF1 and TRAF2 might be important for the final...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4153/version/1

Interaction of the TNFR-Receptor Associated Factor TRAF1 with I-kappa B Kinase-2 and TRAF2 Indicates a Regulatory Function for NF-kappa B Signaling
Provedor de dados: 17
Autores: Kalsoom A. Sughra; Andreas Birbach; Rainer de Martin; Johannes A. Schmid.
*Background*&amp;#xd;&amp;#xa;I-kappa B kinase 2 (IKK2 or IKK-beta) is one of the most crucial signaling kinases for activation of NF-kappa B, a transcription factor that is important for inflammation, cell survival and differentiation. Since many NF-kappa B activating pathways converge at the level of IKK2, molecular interactions of this kinase are pivotal for regulation of NF-kappa B signaling.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Methodology/Principal Findings*&amp;#xd;&amp;#xa;We searched for proteins interacting with IKK2 using the C-terminal part (amino acids 466-756) as bait in a yeast two-hybrid system and identified the N-terminal part (amino acids 1-228) of the TNF-receptor associated factor TRAF1 as putative interaction partner. The interaction...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4153/version/2

Interactions between short-term and long-term plasticity: shooting for a moving target
Provedor de dados: 17
Autores: Jean-Pascal Pfister; M&amp;#xe1;t&amp;#xe9; Lengyel.
Far from being static transmission units, synapses are highly dynamical elements that change over multiple time scales depending on the history of the neural activity of both the pre- and postsynaptic neuron. Moreover, synaptic changes on different time scales interact: long-term plasticity (LTP) can modify the properties of short-term plasticity (STP) in the same synapse. Most existing theories of synaptic plasticity focus on only one of these time scales (either STP or LTP or late-LTP) and the theoretical principles underlying their interactions are thus largely unknown. Here we develop a normative model of synaptic plasticity that combines both STP and LTP and predicts specific patterns for their interactions. Recently, it has been proposed that STP...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5857/version/1

Interactions between urban water policy, residential irrigation, and plant &amp;#x26; bird diversity in the Fresno-Clovis Metro Area
Provedor de dados: 17
Autores: Madhusudan Katti; Seth T. Reid; Bradley W. Schleder; John T. Bushoven; Andrew R. Jones; Henry D. Delcore; Derya &amp;#xd6;zg&amp;#xf6;c-&amp;#xc7;a&amp;#x11f;lar.
*Background/Question/Methods:*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Ecological theory has begun to incorporate humans as part of coupled socio-ecological systems. Modern urban development provides an excellent laboratory to examine the interplay among socio-ecological relationships. Urban land and water management decisions result from dynamic interactions between institutional, individual and ecological factors. Landscaping and irrigation at any particular residence, for example, is a product of geography, hydrology, soil, and other local environmental conditions, the homeowners&amp;#x2019; cultural preferences, socioeconomic status, identity construction, neighborhood dynamics, as well as zoning laws, market conditions, city policies, and...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6228/version/1

Interleukin-10 containing normal human serum inhibits granzyme B release but not perforin release from alloreactive and EBV-specific T cell clones
Provedor de dados: 17
Autores: Motoko Nishimura; Hideya Sato; Hitoshi Okazaki; Masahiro Satake; Kenji Tadokoro.
Interleukin-10 (IL-10), also known as cytokine synthesis inhibitory factor, has pleiotropic effects in immunoregulation and inflammation. It is capable of inhibiting synthesis of pro-inflammatory cytokines like interferon &amp;#x3b3; (IFN&amp;#x3b3;), IL-2, IL-3, tumor necrosis factor &amp;#x3b1;(TNF&amp;#x3b1;) and granulocyte macrophage colony stimulating factor (GM-CSF) made by cells such as macrophages and T helper Type 1 cells. We observed that normal human serum, derived from a healthy individual but containing large amounts of IL-10 (arbitrarily designated as &amp;#x22;IL-10 serum&amp;#x22;), inhibited cytotoxic activity and interfered with granzyme B release from alloreactive cytotoxic T cell (CTL) clones _in vitro_, but did not affect perforin...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2007
URL: http://precedings.nature.com/documents/1464/version/1

Interleukin-10 containing normal human serum inhibits granzyme B release but not perforin release from alloreactive and EBV-specific T cell clones
Provedor de dados: 17
Autores: Motoko Nishimura; Hideya Sato; Hitoshi Okazaki; Masahiro Satake; Kenji Tadokoro.
Interleukin-10 (IL-10), also known as cytokine synthesis inhibitory factor, has pleiotropic effects in immunoregulation and inflammation. It is capable of inhibiting synthesis of pro-inflammatory cytokines like interferon [gamma] (IFN[gamma]), IL-2, IL-3, tumor necrosis factor [alpha] (TNF[alpha]) and granulocyte macrophage colony stimulating factor (GM-CSF) made by cells such as macrophages and T helper Type 1 cells. We observed that normal human serum, derived from a healthy individual but containing large amounts of IL-10 (arbitrarily designated as &amp;#x22;IL-10 serum&amp;#x22;), inhibited cytotoxic activity and interfered with granzyme B release from alloreactive cytotoxic T cell clones in vitro, but did not affect perforin release. The addition of...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2007
URL: http://precedings.nature.com/documents/1390/version/1

Internal conformation of the &amp;#x27;protein folding code&amp;#x27; inferred from empirical tertiary structural classifications using Tlusty&amp;#x27;s topological approach
Provedor de dados: 17
Autores: Rodrick Wallace.
Tlusty&amp;#x27;s topological arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. The underlying &amp;#x27;protein folding code network&amp;#x27; is found to have one major, highly dominant &amp;#x27;spherical&amp;#x27; component, a minor attachment handle in the Morse Theory sense, and as many as two or three additional subminor handles.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4640/version/1

Internal ribosomal entry site lacks secondary structure
Provedor de dados: 17
Autores: Xuhua Xia.
The search for mechanisms of translational regulation has yielded many experimentally identified internal ribosome entry sites (IRES). Because of the lack of sequence similarity among the experimentally IRESs, it is widely assumed that IRESs posses stable secondary structure allowing them to interact with the components of the translation machinery. Contrary to this view, here we show that IRES activity in nine yeast IRESs, mapped to 60 nt immediately upstream of the initiation AUG, is strongly associated with the lack of secondary structure of IRESs. Furthermore, the reverse complements of these IRESs, with their secondary structure more stable than those of the IRESs, exhibit little IRES activity. The generality of this association is exemplified by the...
Tipo: Manuscript
Palavras-chave: Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1248/version/1

Interoperability With Moby 1.0 - It&amp;#x27;s Better Than Sharing Your Toothbrush!
Provedor de dados: 17
Autores: Mark Wilkinson.
The BioMoby project was initiated in 2001 from within the model organism database community.  It aimed to standardize methodologies to facilitate information exchange and access to analytical resources, using a consensus driven approach.  Six years later, the BioMoby development community is pleased to announce the release of the 1.0 version of the interoperability framework, registry API, and supporting Perl and Java code-bases.  Together, these provide interoperable access to over 1400 bioinformatics resources worldwide through the BioMoby platform, and this number continues to grow.  Here we highlight and discuss the features of BioMoby that make it distinct from other Semantic Web Service and interoperability initiatives, and that have been...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1486/version/1

Interoperable Semantic Web services (Tutorials)
Provedor de dados: 17
Autores: Mat&amp;#xfa;&amp;#x161; Kala&amp;#x161;; Jon Ison.
Life-scientific Web services are increasingly available and diverse. Their semantic interoperability is crucial to enable automated workflow construction and efficient searching for the right service. At the same time, smooth programmatic access must be possible with all the main programming, scripting, or workflow languages.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This tutorial gave an introduction to the &amp;#x22;SAWSDL&amp;#x22;:http://www.w3.org/standards/techs/sawsdl#w3c_all standard for semantic annotation of Web services and XML Schemas; the &amp;#x22;EDAM&amp;#x22;:http://edamontology.sourceforge.net ontology for describing bioinformatics tools; and &amp;#x22;BioXSD&amp;#x22;:http://bioxsd.org as a canonical data model for bioinformatics Web services....
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5565/version/1

InterPro Curation: Integrating Predictive Protein Signatures Into Biological Hierarchies
Provedor de dados: 17
Autores: Sarah Burge.
InterPro is an integrated database of predictive protein signatures used for the classification and automatic annotation of proteins and genomes. As InterPro curators, we are responsible for assimilating information from our member databases and communicating it to our end users in a way that adds value to each individual signature. We categorise signatures according to their type (for example, Family, Domain or Repeat) and annotate entries with links to other databases, abstracts and protein matches.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The InterPro database also identifies relationships between entries. For example, signatures at a general Family level are related to more specific subfamilies through a Parent/Child relationship. Families may also Contain...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5330/version/1

Interruption of [beta]-Catenin Signaling Reduces Neurogenesis in Alzheimer&amp;#x27;s Disease Brains
Provedor de dados: 17
Autores: Ping He; Matthias Staufenbiel; Yong Shen.
Although studies show new neurons generated from progenitor cells in a healthy adult neocortex, neurogenic potential derived from stem/progenitor cells in the cortex of Alzheimer&amp;#x27;s patients still remains unsolved. In this study, we isolated the glial progenitor cells (GPCs) from the cortex of healthy (HC) and Alzheimer&amp;#x27;s disease (AD). The AD-GPCs displayed reduced capability to renew and decreased production of new neurons. Interestingly, we found significant reduction of [beta]-catenin in AD-GPCs compared to HC while glycogen synthase kinase 3[beta] (GSK-3[beta]) was promoted. Moreover, we found both increased phosphorylation of [beta]-catenin in AD-GPCs and their progeny cells. Amyloid [beta] peptide (A[beta]) treatment results in...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2257/version/1

Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm _Elaeis guineensis_ and _E. oleifera_
Provedor de dados: 17
Autores: Aikkal Riju; Vadivel Arunachalam.
Oil palm is the second largest source of edible oil, which meets one-fifth of global demands of oils and fats. Expressed sequence tag (EST) sequencing programs have provided a wealth of information, identifying novel genes from a broad range of organisms and providing an indication of gene expression level in particular tissues. It also provides the richest source of biologically useful SNPs due to the relatively high redundancy of gene sequence, the diversity of genotypes represented within databases. EST based SNPs are potential molecular markers and aid in genetic improvement. A total of 21062 and 2053 polymorphic (SNP and Indel) sites in _E. guineensis_ species and in _E. oleifera_, 4955 SNPs and 1172 Indels were detected. SNP(17.5/kbp) and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3593/version/2

Interspecific differences in single nucleotide polymorphisms (SNPs) and indels in expressed sequence tag libraries of oil palm _Elaeis guineensis_ and _E. oleifera_
Provedor de dados: 17
Autores: Aikkal Riju; Vadivel Arunachalam.
Oil palm is the second largest source of edible oil, which meets one-fifth of global demands of oils and fats. Expressed sequence tag (EST) sequencing programs have provided a wealth of information, identifying novel genes from a broad range of organisms and providing an indication of gene expression level in particular tissues. It also provides the richest source of biologically useful SNPs due to the relatively high redundancy of gene sequence, the diversity of genotypes represented within databases. EST based SNPs are potential molecular markers and aid in genetic improvement. A total of 21062 and 2053 polymorphic (SNP and Indel) sites in _E. guineensis_ species and in _E. oleifera_, 4955 SNPs and 1172 Indels were detected. SNP(17.5/kbp) and...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3593/version/1

Inter-Tunneling Mechanism of Colliding Population Waves
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
Here we show a new interaction mechanism of colliding population waves. It provides a stable coexistence of two similar but different species competing for the same limiting resource during their asexual propagation in a limited homogeneous environment under constant conditions. The revealed mechanism opens new opportunities in conservation biology.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6990/version/1

Interventions to Promote Cancer Awareness and Early Presentation: Systematic Review
Provedor de dados: 17
Autores: J Austoker; C Bankhead; Lindsay J. L. Forbes; L Atkins; F Martin; K Robb; J Wardle; A J. Ramirez.
Low cancer awareness contributes to delay in presentation for cancer symptoms and may lead to delay in cancer diagnosis. The aim of this study was to review the evidence for the effectiveness of interventions to raise cancer awareness and promote early presentation in cancer to inform policy and future research. We searched bibliographic databases and reference lists for randomised controlled trials of interventions delivered to individuals, and controlled or uncontrolled studies of interventions delivered to communities. We found some evidence that interventions delivered to individuals modestly increase cancer awareness in the short term and insufficient evidence that they promote early presentation. We found limited evidence that public education...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3815/version/1

Intestinal Electric Stimulation Accelerates Whole Gut Transit and Promotes Fat Excrement in Conscious Rats
Provedor de dados: 17
Autores: Ying Sun; Jiande Chen.
*_Introduction:_* Intestinal electric stimulation (IES) is proposed as a potential tool for the treatment of morbid obesity. Our previous study showed that IES with one pair of electrodes accelerated intestinal transit and decreased fat absorption in a segment of the jejunum in the anesthetized rats. The aims of this study were to assess the effects of IES on the whole gut transit and fat absorption in conscious rats, to examine the effects of multi-channel IES, and to explore the cholinergic mechanism behind the effects of IES. &amp;#xd;&amp;#xa;*_Methods:_* Thirty-eight male rats implanted with serosal electrodes were randomized into five groups: control without IES, 2/3 channel IES with short pulses, atropine and atropine plus IES. The whole gut transit...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/2854/version/1

Intra- and inter-individual genetic differences in gene expression
Provedor de dados: 17
Autores: Mark J. Cowley; Chris J. Cotsapas; Rohan B. H. Williams; Eva K. F. Chan; Jeremy N. Pulvers; Michael Y. Liu; Oscar J. Luo; David J. Nott; Peter F. R. Little.
Genetic variation is known to influence the amount of mRNA produced by a gene. Given that the molecular machines control mRNA levels of multiple genes, we expect genetic variation in the components of these machines would influence multiple genes in a similar fashion. In this study we show that this assumption is correct by using correlation of mRNA levels measured independently in the brain, kidney or liver of multiple, genetically typed, mice strains to detect shared genetic influences. These correlating groups of genes (CGG) have collective properties that account for 40-90% of the variability of their constituent genes and in some cases, but not all, contain genes encoding functionally related proteins. Critically, we show that the genetic influences...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1799/version/1

Intracellular Regulatory Networks are close to Monotone Systems
Provedor de dados: 17
Autores: Avi Ma&amp;#x27;ayan; Ravi Iyengar; Eduardo D. Sontag.
Several meso-scale biological intracellular regulatory networks that have specified directionality of interactions have been recently assembled from experimental literature. Directed networks where links are characterized as positive or negative can be converted to systems of differential equations and analyzed as dynamical systems. Such analyses have shown that networks containing only sign-consistent loops, such as positive feed-forward and feedback loops function as monotone systems that display well-ordered behavior. Perturbations to monotone systems have unambiguous global effects and a predictability characteristic that confers advantages for robustness and adaptability. We find that three intracellular regulatory networks: bacterial and yeast...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/25/version/1

Intra-mammary single infusion of casein hydrolyzate in dairy cows as alternative dry period treatment: Curing bacterial infection and increasing milk yield in the subsequent lactations
Provedor de dados: 17
Autores: Nissim Silanikove; Shamay Yacoby; Gabriel Leitner.
Conclusions: This study sustain previous results that treatment with CNH is a powerful mean to eradicated bacterial infection, and strongly highlight the potential of this method to serve as a viable non-antibiotic dry cow therapy treatment. The increase in milk yield is a valuable bonus and its effectiveness is comparable with that achieved with growth hormone treatment, albeit in much simple mode of treatment and without the problematic of hormonal treatment.
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2130/version/1

Intrarectal administration of hCG (Human Choriogonadotropin) and fat loss as assessed by Dual energy X-ray absorptiometry (DXA) in experimental animals.
Provedor de dados: 17
Autores: Daniel Belluscio; Ezequiel Klimovsky; Alejandro Kaniuk; Sergio Vaney.
Our studies suggest that in experimental animals, submitted to a hypocaloric diet, the intrarectal administration of hCG (Human Chorionic Gonadotropin) decreases body fat and increases lean mass content in relative values to a greater extent that control animals who did not receive hCG.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7074/version/2

Intraspecific variability drives diversity in food webs
Provedor de dados: 17
Autores: Carlos J. Melian; Cesar Vilas; Francisco Baldo; Enrique Gonzalez-Ortegon; Pilar Drake; Richard Williams.
Biodiversity theories neglect individual-level variability in ecological interactions even though empirical work has revealed considerable genetic and phenotypic variation among individuals in natural populations. This impedes assessing the impact of individual-level variability on biodiversity in multi-trophic ecosystems. Here we use a density-dependent and individual-based food web model, tested against the largest individual-based food web to date, to show that non-random intraspecific variation in prey selection alters species diversity in food webs. Predators consuming many prey increase diversity by preferentially selecting common prey; predators consuming few prey inhibit diversity by preferentially selecting rare prey, putting them at risk of...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6251/version/1

Intra-specific variation in plant hydraulic sectoriality along a latitudinal gradient
Provedor de dados: 17
Autores: Angela Zeng; Roberto Salguero-Gomez; Agustin Santos-Alvarez; Amy Zanne; Brenda Casper.
High temperatures and nutrient limitations in deserts challenge plant survival. Large temperature oscillations and droughts typical of cold deserts can result in cavitation, the precipitation of dissolved air within a xylem vessel. If xylem vessels are closely packed, then a cavitation event may expand to neighboring vessels, resulting in runaway embolism, and potentially paralyze the vital functions of the plant.&amp;#xd;&amp;#xa;      Hydraulic sectoriality, where the plant  is functionally composed of independent hydraulic units, has been suggested as a strategy to decrease the risk associated with cavitation. This can occur by increasing xylem vessel isolation and/or increasing the physical modularity of the plant. Furthermore, hydraulic sectoriality...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5277/version/1

Intrinsic Activity in the Fly Brain Gates Visual Information during Behavioral Choices
Provedor de dados: 17
Autores: Shiming Tang; Mikko Juusola.
The small insect brain is often described as an input/output system that executes reflex-like behaviours. It can also initiate neural activity and behaviours intrinsically, seen as spontaneous behaviours, different arousal states and sleep. However, little is known about how intrinsic activity in neural circuits affects sensory information processing in the insect brain and variability in behaviour. Here, by simultaneously monitoring Drosophila&amp;#x2019;s behavioural choices and brain activity in a flight simulator system, we identify intrinsic activity that is associated with the act of selecting between visual stimuli. We recorded neural output (multi-unit action potentials and local field potentials) in the left and right optic lobes of a tethered...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4325/version/1

Introduction of Transmembrane Inner Ear (tmie) Gene Can Recover the Hearing Impairment and Abnormal Behavior in the Circling Mouse
Provedor de dados: 17
Autores: Mi Jung Shin; Jeong-Han Lee; Dong Hoon Yu; Bong Soo Kim; Hei Jung Kim; Sung Hyun Kim; Myoung Ok Kim; Channy Park; Byung-Hwa Hyun; Sanggyu Lee; Jun-Gyo Suh; Hong-Seob So; Raekil Park; Zae Young Ryoo.
The spontaneous mutant circling mouse (cir/cir) shows a circling behavior and hearing loss. We produced transgenic mice overexpressing the causative gene, transmembrane inner ear (tmie), for the phenotypic rescue of the circling mouse. Through the continuous breeding with circling mice, the cir/cir homozygous mice carrying the transgene (cir/cir-tg) were produced. The rescued cir/cir -tg mice were able to swim in the water with proper orientation and did not show any circling behavior like wild type mice. Western blot and immunohistochemical analysis exhibited that the transgenic tmie was expressed in the inner ear. Inner and outer hair cells were recovered in the cochlea and spiral ganglion neurons were also recovered in the rescued mice. Auditory...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2106/version/1

Introduction to Medical Genetics
Provedor de dados: 17
Autores: Atif A. Baig.
Medical genetics is the key to modern biochemistry and underlying mechanisms of many diseases.
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6596/version/1

Introduction to the Baltimore Ecosystem Study, Long-Term Ecological Research Project, Phase III
Provedor de dados: 17
Autores: Steward T. A. Pickett.
The Baltimore Ecosystem Study (BES) is one of two urban Long-Term Ecological Research (LTER) projects in the United States.  It began its third funding cycle in 2011.  Although the project continues key measurements that were started in 1997 at the inception of the research, the third phase is characterized by a new conceptual framework.  Phase III of BES focuses on metropolitan Baltimore, Maryland, as a system poised for transition from a &amp;#x22;sanitary city&amp;#x22; -- characterized by engineered environmental solutions, management via discrete disciplines, and government control to a &amp;#x22;sustainable city&amp;#x22; -- which would be characterized by additional biological solutions, collaborative management, and polycentric and multi-level...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6499/version/1

Invariant mRNA content and mitotic protein breakdown as a solution to the Russian Doll problem of the mammalian cell cycle
Provedor de dados: 17
Autores: Stephen Cooper; Kerby Shedden; Dang Vu-Phan.
It is widely accepted that numerous genes are expressed in a cell-cycle dependent manner, with cycle-specific variations in mRNA content or peaks of protein content during the cell cycle. These proposed variations raise the problem of how varying cell cycle gene expression is regulated. This is the &amp;#x22;infinite regression&amp;#x22; problem or Russian Doll problem where postulating a cell-cycle specific control element merely pushes the explanation of cell-cycle variation back one step to the problem of how that control element itself appears and disappears at particular times during the cell cycle. We present evidence that cyclin mRNA content is invariant during the cell cycle and calculations reveal that mRNA variation does not account for observed...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1218/version/1

Invasional conflict: Do invasive insect herbivores mediate the effects of enemy release for their invasive plant hosts?
Provedor de dados: 17
Autores: Kerry R. Bohl; Peter Stiling.
Although many factors have been proposed that potentially contribute to invasion success in plants, it remains unclear why some species successfully establish and become dominant while others do not.  The most often cited explanation for the success of invasive plants worldwide is the enemy release hypothesis (ERH), which maintains that populations are kept in check by their co-evolved natural enemies in their native range, but are released from this regulation in the new range. Although there is evidence that introduced plant species often experience a decrease in damage by herbivores in the novel range, it is uncertain if this decrease affects plant productivity.  The purpose of this study was 1) to determine if the invasive plant _Eugenia uniflora_...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3716/version/1

Invasive monitoring of the clinical effects of high intra-abdominal pressure for insertion of the first trocar.
Provedor de dados: 17
Autores: Octavio H. M. Hypolito; Joao-Luiz Azevedo; Fernanda   A. B. Gama; Otavio  C. Azevedo; Otavio M. Becker Junior; Afonso C. C. G. Machado; Susana A. Miyahira; Glicia   C. Azevedo; Bianca Marigliani; Jos&amp;#xe9;  F. Borborema; Linda  Bernardes; Gustavo P. S. Miguel.
Background: To analyze the effects of transitory, high intra-abdominal pressure on clinical, hemodynamic, blood gas and metabolic parameters.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: Sixty-seven laparoscopic patients were divided into groups P12 (n = 30, maximum intra-abdominal pressure of 12 mmHg) and P20 (n = 37, maximum intra-abdominal pressure of 20 mmHg). Through radial artery cannulation, mean arterial pressure (MAP) was assessed and blood gas analysis &amp;#x2013; pH, arterial oxygen tension (PaO2), arterial carbon dioxide tension (PaCO2), bicarbonate (HCO3) and base excess (BE) &amp;#x2013; was performed. These parameters were evaluated in both groups at time point zero, before CO2 insufflation; at time point one (TP1), when intra-abdominal...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/6536/version/1

Invasive Plant (_Microstegium vimineum_) Reduces Abundance and Richness of Insect Communities
Provedor de dados: 17
Autores: Maria Carolina Simao; Jennifer Rudgers; S. Luke Flory.
Plant invasions are known to have negative impacts on native plant communities, yet their effects on higher trophic levels have not been well documented. Past studies investigating the effects of invasive plants on herbivores and carnivores have been largely observational in nature and thus lack the ability to tease apart whether differences are a cause or consequence of the invasion. In addition, understanding how plant traits and plant species compositions change in invaded habitats may increase our ability to predict when and where invasive plants will have effects that cascade to animals. We experimentally introduced a non-native plant (_Microstegium vimineum_, Japanese stiltgrass) to evaluate impacts on arthropods. We also investigated possible...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3651/version/1

Inverse relationship between genetic diversity and epigenetic complexity
Provedor de dados: 17
Autores: Shi Huang.
Early studies of molecular evolution revealed a correlation between genetic distance and time of species divergence.  This observation provoked the molecular clock hypothesis and in turn the &amp;#x2018;Neutral Theory&amp;#x2019;, which however remains an incomplete explanation since it predicts a constant mutation rate per generation whereas empirical evidence suggests a constant rate per year.  Data inconsistent with the molecular clock hypothesis have steadily accumulated in recent years that show no correlation between genetic distance and time of divergence.  It has therefore become a challenge to find a testable idea that can reconcile the seemingly conflicting data sets.  Here, an inverse relationship between genetic diversity and epigenetic...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1751/version/1

Inverse relationship between genetic diversity and epigenetic complexity
Provedor de dados: 17
Autores: Shi Huang.
Early studies of molecular evolution revealed a correlation between genetic distance and time of species divergence.  This observation provoked the molecular clock hypothesis and in turn the &amp;#x2018;Neutral Theory&amp;#x2019;, which however remains an incomplete explanation since it predicts a constant mutation rate per generation whereas empirical evidence suggests a constant rate per year.  Data inconsistent with the molecular clock hypothesis have steadily accumulated in recent years that show no correlation between genetic distance and time of divergence.  It has therefore become a challenge to find a testable idea that can reconcile the seemingly conflicting data sets.  Here, an inverse relationship between genetic diversity and epigenetic...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/1751/version/2

Investigating prostate cancer tumour-stroma interactions - clinical and biological insights from an evolutionary game
Provedor de dados: 17
Autores: David Basanta; Jacob G. Scott; Mayer N. Fishman; Gustavo E. Ayala; Simon W. Hayward; Alexander R. A. Anderson.
BACKGROUND: Tumours are made up of a mixed population of different types of cells that include normal structures as well as ones associated with the malignancy, and there are multiple interactions between the malignant cells and the local microenvironment. These intercellular interactions, modulated by the microenvironment, effect tumour progression and represent a largely under appreciated therapeutic target. We use observations of primary tumor biology from prostate cancer to extrapolate a mathematical model: specifically; it has been observed that in prostate cancer three disparate cellular outcomes predominate: (i) the tumour remains well differentiated and clinically indolent - in this case the local stromal cells may act to restrain the growth of the...
Tipo: Manuscript
Palavras-chave: Cancer; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6385/version/1

Investigating the frontoparietal network in mental calculation in primary school children - An fMRI study
Provedor de dados: 17
Autores: Katrien Mondt; Danielle Bal&amp;#xe9;riaux; Thierry Metens; Philippe Paquier; Piet Van de Craen; Vincent Denolin.
The frontoparietal network activated during calculation processing is investigated in a pediatric population. Subjects assessed correctness of two and three operand equations. Besides traditional frontoparietal activation, clear activation of sites associated with error processing was observed.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1694/version/1

Investigation of the Adsorption Characteristics of Antimony, Cadmium, and Lead by Nano- and Microparticle Titania
Provedor de dados: 17
Autores: Jared Zia; Dula Amarasiriwardena; Baoshan Xing.
The utilization of nanotechnology is expected to rise greatly within the next decade. The increasing ubiquity of nanotechnology, coupled with the fact that the toxicity of a nanomaterial is partially dependent on its adsorbed components, emphasizes the general importance, and environmental significance, of nanomaterial adsorption studies. Using nanoparticle titania (and microparticle titania for comparison), a series of adsorption experiments were performed. The antimony, lead, and cadmium adsorption capacity of nanoparticle titania was compared to that of microparticle titania. During a typical adsorption experiment, a known amount of nanomaterial was shaken with a solution containing a known concentration of antimony, lead, and cadmium. Following an...
Tipo: Poster
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3698/version/1

Investigations on biological activity of Vetiveria zizanioides L. Nash, a palingenesis of some important findings in miracle grass
Provedor de dados: 17
Autores: Suaib Luqman.
Vetiveria zizanioides L. Nash synonymously known as Chrysopogon zizanioides L. Roberty (Family: Poaceae/Graminae), widely cultivated in the tropical regions of the world, is a miraculous grass native to India first developed for soil and water conservation by the World Bank during mid 1980s. Popularly known as &amp;#x2018;KHUS&amp;#x2019;, it is the major source of the well-known oil of vetiver, which is used in medicine, cosmetics and in perfumery making agarbattis, soaps, soft drinks, pan masala. Being a major constituent of &amp;#x2018;Rasayana&amp;#x2019; in Ayurveda, different parts of the vetiver plant have traditionally been used by the Indian tribes for treating various ailments, diseases and disorders including boils, burns, epilepsy, fever,...
Tipo: Poster
Palavras-chave: Cancer; Microbiology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6904/version/1

In-vitro Antifungal Activity of Some 1,3,5-triazine Derivatives
Provedor de dados: 17
Autores: Udaya Pratap Singh; Prashant Gahtori; Ramendra K. Singh.
A series of substituted phenylthiazolyl 1,3,5-triazine derivatives were screened for their _in-vitro_ antifungal activity (MIC and MFC) against four fungi viz. _Candida_ species (_C. albicans_ NCIM-3102, _C. glabrata_ NCIM-3266), _Cryptococcus neoformans_ NCIM-3542, and _Aspergillus niger_ NCIM-620 using modified broth microdilution method recommended by CLSI, with reference to  fluconazole and amphotericin B.
Tipo: Manuscript
Palavras-chave: Chemistry; Microbiology; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5751/version/1

In-Vivo Lipidomics using Single-Cell Raman Spectroscopy
Provedor de dados: 17
Autores: Huawen Wu; Joanne Volponi; Ann Oliver; Atul Parikh; Blake Simmons; Seema Singh.
We describe a method for direct, quantitative, in vivo lipid profiling of oil producing microalgae using single-cell laser-trapping Raman spectroscopy (LTRS). This approach is demonstrated in the quantitative determination of the degree of unsaturation and transition temperatures of constituent lipids within microalgae. These properties are important markers for determining engine compatibility and performance metrics of algal biodiesel. We show that these factors can be directly measured from a single living microalgal cell held in place with an optical trap while simultaneously collecting Raman data. Cellular response to different growth conditions is monitored in real time. Our approach circumvents the need for lipid extraction and analysis that is both...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4428/version/1

Involvement of proteasome b1i subunit, LMP2, on uterine leiomyosarcma tumorigenesis
Provedor de dados: 17
Autores: Takuma Hayashi; Akiko Horiuchi; Ikuo Konishi.
Although the majority of smooth muscle neoplasms found in the uterus are benign, uterine leiomyosarcoma (LMS) is extremely malignant, with high rates of recurrence and metastasis. The development of gynecologic tumors is often correlated with secretion of female hormone; however, the development of human uterine LMS is not substantially correlated with hormonal conditions, and the risk factors are unclearly understood. Importantly, a diagnostic-biomarker, which distinguishes malignant human uterine LMS from benign tumor leiomyoma (LMA) is yet to be established. Accordingly, it is necessary to analyze risk factors associated with human uterine LMS, in order to establish a clinical treatment method. Homozygous deficient mice for a proteasome...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2011
URL: http://precedings.nature.com/documents/6478/version/1

Ionic Liquid Mediated Dye Recovery from Aqueous Solution
Provedor de dados: 17
Autores: Shahnaz Qadri; Ashley Ganoe; Yousef Haik.
We describe a method to retrieve hazardous dye from aqueous solution that employs magnetic nanoparticles with strong affinity to dyes. Ionic liquids with stronger affinity to the magnetic particles promote up to 99% dye recovery.
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2111/version/1

Ionization effects on the partitioning behavior of food and beverage aroma compounds between aqueous phases and air and organic matrices
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Aroma compounds in the Flavornet database were screened for ionizable functional groups such as carboxylic acids, aliphatic and aromatic amines, phenols, alcohols, and thiols. Of the 738 aroma compounds listed in this database, 101 molecules have ionizable moieties with estimated monomeric aqueous pK~a~ values ranging between 1.75 and 10.97. pH dependent effective air/water partitioning coefficients (K~aw,eff~) and n-octanol/water partitioning coefficients (D~ow~) were estimated for all ionizable aroma compounds over the pH range from 0 to 14. The ionizable aroma compounds display a broad range of K~aw,eff~ (1.8&amp;#xd7;10^-23^ to 6.1 atm M^-1^) and log D~ow~ (-6.2 to +7.2 units) values. For many aroma compounds, pH dependent ionization will have a...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6269/version/1

IQ variations across time and race are explained by literacy differences
Provedor de dados: 17
Autores: David F. Marks.
Intelligence quotient (IQ) scores are intended to assess the cognitive competences of individuals, groups and populations. A body of data collected during the last 50 years has revealed that IQ average population scores vary significantly over time, nationality, and race. The causes of these variations remain a mystery. Theories focusing on nutrition, brain size, dysgenic factors, social class and education have proved inexact or unsatisfactory. Here I describe a new explanation based on the fact that intelligence test performance requires a level of literacy not present in all people to the same degree. I show that literacy variations across time, place and race are highly associated with changes in IQ scores. These findings have widespread implications....
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/1293/version/2

IQ variations across time and race are explained by literacy differences
Provedor de dados: 17
Autores: David Marks.
Intelligence quotient (IQ) scores are intended to assess the cognitive competences of individuals, groups and populations. A body of data collected during the last 50 years has revealed that IQ average population scores vary significantly over time, nationality, and race. The causes of these variations remain a mystery. Theories focusing on nutrition, brain size, dysgenic factors, social class and education have proved inexact or unsatisfactory. Here I describe a new explanation based on the fact that intelligence test performance requires a level of literacy not present in all people to the same degree. I show that literacy variations across time, place and race are highly associated with changes in IQ scores. These findings have widespread implications....
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/1293/version/1

Iridium complex, a phosphorescent light-emitting diode material, serves as a novel chemical probe for imaging hypoxic tumor tissues
Provedor de dados: 17
Autores: Shaojuan Zhang; Masahiro Hosaka; Toshitada Yoshihara; Yasuhiko Iida; Keigo Endo; Seiji Tobita; Toshiyuki Takeuchi.
Iridium complex, a promising organic light-emitting diode for next generation television displays, emits phosphorescence. Phosphorescence is quenched by oxygen. We used this oxygen-quenching feature for imaging tumor hypoxia. Red light-emitting iridium complex Ir(btp)~2~(acac) (BTP) presented hypoxia-dependent light emission in culture cell lines, whose intensity was in parallel with HIF-1[alpha] expression. BTP was further applied to imaging five tumors (four from human origin and one from mouse origin) transplanted in athymic mice. All tumors presented a bright BTP-emitting image even 5 min after the injection. The BTP-dependent tumor image peaked at 1 to 2 h after the injection, and was then cleared from tumors within 24 h. The minimal BTP image...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry.
Ano: 2007
URL: http://precedings.nature.com/documents/1443/version/1

Iron (FeSO4) Bioavailability in Obese Subjects Submitted to Bariatric Surgery
Provedor de dados: 17
Autores: Luciana Bueno; Juliana  Pizzo; Jos&amp;#xe9; Ernesto dos Santos; Julio S&amp;#xe9;rgio Marchini; Jos&amp;#xe9; Eduardo Dutra de Oliveira.
Objective: To determine iron bioavailability in obese subjects after the ingestion of a nutritional supplement containing multiple nutrients. Methods: Fourteen persons were studied before and after bariatric surgery after the ingestion of a nutritional formulation containing 25 mg iron, 25 g fiber and 800 mg calcium. Serum iron levels were measured basally and every hour after the ingestion of 200 mL of the formulation, and serum ferritin, unsaturated iron binding capacity (UIBC), hemoglobin, albumin, total proteins, total triglycerides, total cholesterol and fractions (LDL-cholesterol and HDL-cholesterol) sere determined at the same time points.Results: The following ferremia values (median/minimum - maximum) were obtained before and after bariatric...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3787/version/1

Is it Prostate Cancer ?
Provedor de dados: 17
Autores: Hans-Heinrich Gl&amp;#xe4;ttli; Juergen Durner; Hans-J&amp;#xfc;rg Gerber.
Given a set of PSA values, we answer the question: &amp;#x201c;Is its information content typical for the existence of a prostate cancer, or not?&amp;#x201d; Our findings support PSA screening.
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4556/version/1

Is severity of clinical manifestations following _H. lepturus_ envenomation related to serum TNF-&amp;#x3b1; level?
Provedor de dados: 17
Autores: Amir A. Jalali; Mohammad H. Pipelzadeh; Mohammad M. Taraz; Ali A. Khodadadi; Manoochr M. Makvandi.
Thirty six patients, with varying degrees of severity of envenomation, because of envenomation by _Hemiscorpius lepturus_ scorpion, were systematically investigated. The serum levels (by double-ligand ELIZA kit) of interlukin-1 (IL-1), interlukin-6 (IL-6), interlukin-8 (IL-8) and tumor necrosis factor-&amp;#x3b1; (TNF- &amp;#x3b1;) were compared with 30 healthy controls and 10 age-matched patients envenomed by _Mesobuthus eupeus_ scorpion. Blood samples from _M. eupeus_ and _H. lepturus_ victims were taken on admission and once more after 6 hr after serotherapy with multivalent antivenom from _H. lepturus_ envenomed subjects. The results suggest that, unlike _M. eupeus_, the toxic manifestations observed following H lepturus may be associated with increase...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4382/version/1

Is Sustainable Development of Deserts Feasible?
Provedor de dados: 17
Autores: Yuriy S. Polyakov; William B. Eimicke; Ibrahim M. Musaev; Sergey V. Polyakov.
Hot deserts that presently cover about one-fifth of the land area of our planet are rapidly devouring more and more arable lands mostly due to anthropogenic causes. We propose an interdisciplinary approach to revitalizing and commercializing hot deserts, which is based on systems thinking and Russian and NASA space technology experience in designing life-support systems for long-duration flights. We formulate ten principles for the design of sustainable life support systems in deserts, which can make the development of the deserts feasible. It is discussed how the principles can be employed to design and operate desert&amp;#x2019;s eco-industrial parks with greenhouses in which the transpired and evaporated moisture is collected and condensed. The...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2569/version/1

Is the infection/latency/reactivation cycle of viruses an oncogenic engine?
Provedor de dados: 17
Autores: Alessandro Ripalti.
Human oncogenic viruses are defined as necessary but not sufficient to initiate cancer. Experimental evidence suggests that the oncogenic potential of a virus is effective only in cells that have already accumulated a number of genetic mutations leading to cell cycle deregulation. Current models for viral driven oncogenesis cannot explain why tumor development in carriers of tumorigenic viruses is a very rare event, occurring decades after virus infection. Considering that viruses are mutagenic agents _per se_ and human oncogenic viruses additionally establish latent and persistent infections, I attempt here to provide a mechanism of tumor initiation both for RNA and DNA viruses, suggesting viruses could be both necessary and sufficient in human...
Tipo: Manuscript
Palavras-chave: Cancer; Microbiology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1285/version/1

Is the innate bio-protection power against human virus the same between males and females? A conclusion based on blood donor data of HTLV-I infection
Provedor de dados: 17
Autores: Nobuoki Eshima; Minoru Tabata; Yasunori Higuchi; Shigeru Karukaya.
Human T-cell leukemia virus type I (HTLV-I) is a retrovirus that causes adult T-cell leukemia. The male-to-female transmission is stronger than the reverse, so the carrier proportion of women is greater than that of men. On the other hand, since the mother-to-child transmission route via the breast-feeding is common for baby boys and girls, it has been thought the HTLV-I proportions of boys and girls are the same until now. A question arises as to whether the &amp;#x22;innate protection powers against human virus&amp;#x22; are the same between baby boys and girls. We utilize Blood donors in 1995-1998, which were provided by Japan Red Cross Society of Oita, Japan. The data are summarized into the frequency table with respect to gender and age. The age...
Tipo: Manuscript
Palavras-chave: Cancer; Immunology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/1987/version/1

Is the innate bio-protection power against human virus the same between males and females? A conclusion based on blood donor data of HTLV-I infection and case data of infectious diseases
Provedor de dados: 17
Autores: Nobuoki Eshima; Minoru Tabata; Yasunori Higuchi; Shigeru Karukaya.
Human T-cell leukemia virus type I (HTLV-I) is a retrovirus that causes adult T-cell leukemia. The male-to-female transmission is stronger than the reverse, so the carrier proportion of women is greater than that of men. On the other hand, since the mother-to-child transmission route via the breast-feeding is common for baby boys and girls, it has been thought the HTLV-I proportions of boys and girls are the same until now. A question arises as to whether the &amp;#x2018;innate protection powers against human virus&amp;#x2019; are the same between males and females. We utilize HTLV-I infection blood donor data in 1995-1998 and case data of main infectious diseases such as influenza, mumps, herpangina, hand-hoot-and-mouse disease, chicken pox, etc. Blood...
Tipo: Manuscript
Palavras-chave: Cancer; Immunology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/1987/version/2

Is the new cognitive neuroscience of social inequality equal?  Deconstructing the current neurocognitive research on children&amp;#x2019;s attention
Provedor de dados: 17
Autores: Amedeo D&amp;#x27;Angiulli; Pavel Grebenkov.
The relation between socioeconomic status (SES) and various outcomes, such as cognitive ability, behavior, social skills and health, has been studied for over half a century. The general consensus in interpreting the results as been that low SES is necessarily associated with cognitive and/or behavioral pathologies or deficits. Contrary to this deficit hypothesis new evidence suggests that the differences between low- and high-SES populations may be due to cognitive preferences associated with the social context where children develop.  Much of this evidence has come from developmental neuroimaging studies on attention and executive control generally showing that despite differences between low- and high-SES children in neural correlates, there are no...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4470/version/1

Is there a Weed Shift in Roundup Ready Maize?
Provedor de dados: 17
Autores: Arnd Verschwele.
The cultivation of transgenic glyphosate-resistant crop varieties can simplify weed control in crops such as maize and others. On the other hand, the repeated use of broadly effective herbicides like glyphosate, especially in the same crop, can have a negative effect on biodiversity. Additionally there is a risk for a spread of more tolerant or even resistant weed species.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;It was the aim of a 6-years field study (2003-2008) to investigate weed effects of use of glyphosate in a continuous transgenic herbicide-resistant maize rotation at three sites in Germany. These sites differed significantly in terms of soil, climate and initial weed spectrum. The studies focussed on the comparison between local herbicide standards and...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4527/version/1

Is your phylogeny informative? Measuring the power of comparative methods
Provedor de dados: 17
Autores: Peter Ralph; Graham Coop; Carl Boettiger.
Phylogenetic comparative methods have become all but ubiquitous in only a few decades, forcing us to reconsider if information from a phylogenetic tree can justify the results. Existing approaches to this question have been inadequate and do not scale with tree size or the ability to resolve branches. For instance, selection between phylogenetic models typically based on information criteria fails to adequately reflect this uncertainty, and can lead to preference for arbitrarily complicated models. Common measures of phylogenetic signal tend to characterize the goodness-of-fit of a Brownian motion model to the data, rather than indicate whether the data is sufficient to confidently distinguish between different hypotheses. We present a Monte Carlo based...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6453/version/1

Isoglitter
Provedor de dados: 17
Autores: Michael J. Bucknum; Eduardo A. Castro; Bin Wen.
Described herein is a novel crystalline pattern in space group Ammm, that is a model of a C allotrope. This so-called isoglitter structure-type is a model of a graphite-diamond hybrid. A DFT geometry optimization and band structure calculation indicates that the lattice is metallic in a C realization.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6483/version/2

Isoglitter
Provedor de dados: 17
Autores: Michael J. Bucknum; Eduardo A. Castro; Bin Wen.
Described herein is a novel crystalline pattern in space group Ammm, that is a model of a C allotrope. This so-called isoglitter structure-type is an analogue to the graphite-diamond hybrids. A DFT geometry optimization and band structure calculation indicates that the lattice is metallic in a C realization.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/6483/version/3

Isoglitter
Provedor de dados: 17
Autores: Michael J. Bucknum; Eduardo A. Castro; Bin Wen.
Described herein is a novel crystalline pattern in space group Ammm, that is a model of a C allotrope. This so-called isoglitter structure-type is a model of a graphite-diamond hybrid. A DFT geometry optimization and band structure calculation indicates that the lattice is metallic in a C realization.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6483/version/1

Isolated ileal interposition in enteroendocrine L cells differentiation
Provedor de dados: 17
Autores: Bianca Marigliani; Joao-Luiz  M. C. Azevedo; Lucas P. F. F. Leal; Ismael D. C. G. Silva; Valderez B. V. Lapchick; Sang W. Han; Karina F. Neves; Linda O. A. Bernardes; Gilmara S. A. Yamaguchi; Wellington Cardia; Jose F. Borborema; Joao L. C. Azevedo; Otavio C. Azevedo; Gustavo P. S. Miguel.
INTRODUCTION: &amp;#xd;&amp;#xa;Due to the progressive nature of type 2 diabetes, its complexity and drug treatment perpetuity, there is currently a search for surgical procedures that can promote euglycemia also in non-obese patients. Diabetic patients glycemic control can be achieved by increasing the blood concentration of GLP-1, a hormone produced by L cells that are more densely concentrated in the terminal ileum. Early and extended improvement of diabetes in patients submitted to bariatric surgeries awakened the necessity of investigating the isolated ileal interposition as surgical alternative for the treatment of diabetes. The interposition of this ileal segment to a more anterior region (proximal jejunum) can promote a greater stimulation of the L...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6614/version/2

Isolated ileal interposition in enteroendocrine L cells differentiation
Provedor de dados: 17
Autores: Bianca Marigliani; Joao-Luiz M. C. Azevedo; Lucas P. F. F. Leal; Karina F. Neves; Linda O. A. Bernardes; Gilmara S. Aguiar-Yamaguchi; Wellington  Cardia; Jo&amp;#xe3;o  L. C. Azevedo; Otavio  C. Azevedo; Jose F. Borborema; Gustavo P. S. Miguel.
INTRODUCTION: &amp;#xd;&amp;#xa;Due to the progressive nature of type 2 diabetes, its complexity and drug treatment perpetuity, there is currently a search for surgical procedures that can promote euglycemia also in non-obese patients. Diabetic patients glycemic control can be achieved by increasing the blood concentration of GLP-1, a hormone produced by L cells that are more densely concentrated in the terminal ileum. Early and extended improvement of diabetes in patients submitted to bariatric surgeries awakened the necessity of investigating the isolated ileal interposition as a surgical alternative for the treatment of diabetes. The interposition of this ileal segment to a more anterior region (proximal jejunum) can promote a greater stimulation of the...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6614/version/1

Isolation of Acidic, Basic and Neutral Metalloproteins by QPNC-PAGE
Provedor de dados: 17
Autores: Bernd Kastenholz; David E. Garfin.
A standard protocol for isolating metalloproteins in complex biological samples is presented using quantitative preparative native continuous polyacrylamide gel electrophoresis (QPNC-PAGE)
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Pharmacology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4617/version/1

Isolation of new racemic sugar (D/L galacturonic acid) from leaves of Paederia foetida Linn.
Provedor de dados: 17
Autores: Vikas Kumar; Yadav Pankajkumar S; Udaya Pratap Singh; Hans Raj Bhatt; Kamaruz Zaman; Md. Ali.
New racemic sugars (D/L galacturonic acid) were isolate from the leaves of Paederia foetida Linn by the column chromatography. Identification of these isolated compound achieved by TLC, 1H-NMR, 13C-NMR, FTIR and Mass spectral data.
Tipo: Manuscript
Palavras-chave: Chemistry; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5752/version/1

Isoprene Emission and Carbon Dioxide Protect Aspen Leaves from Heat Stress
Provedor de dados: 17
Autores: Joseph N. T. Darbah; Thomas D. Sharkey; David F. Karnosky.
High temperature, especially above 35oC, is known to reduce leaf photosynthetic rate in many tree species. This study investigated the effect of high temperature on isoprene-emitting (aspen) and non- emitting (birch) trees under ambient and elevated CO2 under open field conditions. Aspen trees tolerate heat better than birch trees and elevated CO2 protects both species against moderate heat stress. The increased thermotolerance in aspen trees compared to the birch trees may result from the aspen&amp;#x27;s ability to produce isoprene. Elevated CO2 increased carboxylation capacity, photosynthetic electron transport capacity and triose phosphate use in both birch and aspen trees. High temperature decreased all of these parameters in birch regardless of CO2...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1533/version/1

Isotope fractionation during impacts
Provedor de dados: 17
Autores: Hua Huang.
Evaporation-condensation, a significant process, happens during impact events. Of special interest, this process can lead to significant isotope fractionations e.g. C, O, Mg, Si, S, Fe,and Cr.The nature of  mass-independent fractionation of sulphur of the sulfur isotopes is that the fractionation of isotope is still mass dependent during impacts, which means the measured nonzero &amp;#xd;&amp;#xa;&amp;#x22bf;33S values of Archean sulfide- and sulfate-bearing minerals indicate that their different condensation sequences.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4622/version/2

Isotope fractionation during impacts
Provedor de dados: 17
Autores: Hua Huang.
Evaporation-condensation, a significant process, happens during impact events^1^. Of special interest, this process can lead to significant isotope fractionations e.g. C, O, Mg, Si, S, Fe, and Cr.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4622/version/1

It is better than you think: fluid intelligence across the lifespan
Provedor de dados: 17
Autores: Tracy Packiam Alloway; Ross Alloway.
The growth and decline of fluid intelligence is associated with brain structural changes. For example, development of fluid IQ is associated with cortex thickness during the critical period between 6 to 12 years old. On the other end of the lifespan, poor performance in cognitive functioning is attributed to a decrease of frontal gray matter density in elderly populations. In particular, there is a sharp decline in fluid IQ scores after 65 years of age. There is substantial evidence that working memory and fluid intelligence (Gf) share neural substrates, such as the prefrontal and parietal cortices. However, very little research has examined whether the pattern of growth and decline in working memory mirrors that of fluid intelligence. For example, does...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4655/version/1

It was (not) me: Causal Inference of Agency in goal-directed actions
Provedor de dados: 17
Autores: Tobias Beck; Carlo Wilke; Barbara Wirxel; Dominik Endres; Axel Lindner; Martin A. Giese.
Summary: &amp;#xd;&amp;#xa;The perception of one&amp;#x2019;s own actions depends on both sensory information and predictions derived from internal forward models [1]. The integration of these information sources depends critically on whether perceptual consequences are associated with one&amp;#x2019;s own action (sense of agency) or with changes in the external world that are not related to the action. The perceived effects of actions should thus critically depend on the consistency between the predicted and the actual sensory consequences of actions. To test this idea, we used a virtual-reality setup to manipulate the consistency between pointing movements and their visual consequences and investigated the influence of this manipulation on self-action...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5858/version/2

It was (not) me: Causal Inference of Agency in goal-directed actions
Provedor de dados: 17
Autores: Tobias F. Beck; Carlo Wilke; Barbara Wirxel; Dominik Endres*; Axel Lindner; Martin A. Giese*.
Summary: &amp;#xd;&amp;#xa;The perception of one&amp;#x27;s own actions depends on both sensory information and predictions derived from internal forward models [1]. The integration of these information sources depends critically on whether perceptual consequences are associated with one&amp;#x2019;s own action (sense of agency) or with changes in the external world that are not related to the action. The perceived effects of actions should thus critically depend on the consistency between the predicted and the actual sensory consequences of actions. To test this idea, we used a virtual-reality setup to manipulate the consistency between pointing movements and their visual consequences and investigated the influence of this manipulation on self-action...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5858/version/1

Items on the Left Are Better Remembered
Provedor de dados: 17
Autores: Sergio Della Sala; Stephen Darling; Robert Logie.
We report evidence of a new phenomenon from three experiments: a leftward bias when people try to remember visually presented information. Experiments 1 and 2 showed lateral leftward biases in memory in a large (total N&amp;#x3e;60000) sample of participants, with data collected via the British Broadcasting Corporation (BBC) web site. Experiment 3 replicated the findings of a leftwards bias in short-term memory with a more intensive data collection.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2540/version/1

IUPHAR-DB: An Expert-Curated, Peer-Reviewed Database of Receptors and Ion Channels
Provedor de dados: 17
Autores: Joanna L. Sharman; Valerie A. Hale; Rebecca Hills; Edward M. Rosser; Martin Jones; Stuart D. Greenhill; Anthony J. Harmar; NC - IUPHAR.
The International Union of Basic and Clinical Pharmacology database (IUPHAR-DB) integrates peer-reviewed pharmacological, chemical, genetic, functional and anatomical information on the 354 non-sensory G protein-coupled receptors (GPCRs), 71 ligand-gated ion channel subunits and 141 voltage-gated ion channel subunits encoded by the human, rat and mouse genomes. These genes represent the targets of about a third of currently approved drugs and are a major focus of drug discovery and development programs in the pharmaceutical industry.  Individual gene pages provide a comprehensive description of the genes and their functions, with information on protein structure, ligands, expression patterns, signaling mechanisms, functional assays and biologically...
Tipo: Poster
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3230/version/1

Java support for SED-ML
Provedor de dados: 17
Autores: Richard R. Adams.
This presentation describes Java support for the SED-ML simulation experiment description language. Firstly, a Java API library for low-level manipulations of the SED-ML object model, and secondly a SED-ML editor, SED-ED, for visualizing and editing SED-ML workflows
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6334/version/1

Jellyfish as vectors of bacterial disease for farmed fish.
Provedor de dados: 17
Autores: Hugh W. Ferguson; Christian M. J. Delannoy; James Nicolson; David Sutherland; Margaret Crumlish; Steven Hay.
Gill diseases are common, especially in intensively reared fish; they result in respiratory distress, as well as impaired osmoregulation and excretion (1). Bacteria and parasites are common causes of gill disease, as is poor water quality, including planktonic blooms. Swarms or blooms of jellyfish are increasingly and especially problematical (2), and can result in high mortality of farmed fish. Small species of jellyfish such as Philalella quadrata (13 mm diameter) are capable of passing through the mesh of sea-cages and of being sucked into the mouth of fish during respiration. Here we show that the initial damage to gills of farmed Atlantic salmon, likely produced by nematocyst-derived toxins from the jellyfish, was compounded by secondary bacterial...
Tipo: Manuscript
Palavras-chave: Microbiology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3631/version/1

Jhamarkotra phosphate ore processing plant
Provedor de dados: 17
Autores: Sekhar Dmr; C.L Jain.
ABSTRACT: Low grade phosphate ore of Jhamarkotra that analyzes 16.5% P~2~O~5~ is upgraded to 34% P~2~O~5~ by a two stage flotation process after size reducing the ore to 90% passing through 200mesh using conventional equipment such as jaw and cone crushers followed by ball mills. Re-engineering the flotation circuit reduced the power consumption from 55 kWh per metric ton of ore treated to 50 kWh. Incorporation of roller press in the grinding circuit resulted into further reduction of power consumption to 32 kWh per metric ton of ore treated.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2770/version/1

jlibSEDML - a Java library for working with SED-ML
Provedor de dados: 17
Autores: Richard Adams; Ion Moraru; Anuradha Lakshminaryana.
jlibSEDML is an open-source  Java library to support the emerging SED-ML standard to record the operations needed to run simulations and other operations on biochemical models. It is compatible with level 1 version 1 of the specification and is available from http://sourceforge.net/projects/jlibsedml
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4965/version/1

JSBML
Provedor de dados: 17
Autores: Nicolas Rodriguez; Andreas Dr&amp;#xe4;ger.
The XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to SBML&amp;#x27;s clearly defined specifications and the availability of libSBML, a portable, robust and easy-to-use&amp;#xd;&amp;#xa;library.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;LibSBML provides many methods for manipulating and validating SBML files through its Application Programming Interface (API). Originally written in C and C++, libSBML also provides automatically-generated language bindings for Java, MATLAB, Perl, Python, and many more. However, the platform independence of Java is compromised in libSBML due to...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4986/version/1

JSBML: a flexible and entirely Java-based library for working with SBML
Provedor de dados: 17
Autores: Andreas Dr&amp;#xe4;ger; Nicolas Rodriguez; Marine Dumousseau; Alexander D&amp;#xf6;rr; Clemens Wrzodek; Roland Keller; Sebastian Fr&amp;#xf6;hlich; Nicolas Le Nov&amp;#xe8;re; Andreas Zell; Michael Hucka.
The specifications of the Systems Biology Markup Language (SBML) define standards for storing and exchanging computer models of biological processes in text files. In order to perform model simulations, graphical visualizations and other software manipulations, an in-memory representation of SBML is required. We developed JSBML for this purpose. In contrast to prior implementations of SBML APIs, JSBML has been designed from the ground up for the Java&amp;#x2122; programming language, and can therefore be used on all platforms supported by a Java Runtime Environment. This offers important benefits for Java users, including the ability to distribute software as Java Web Start applications. JSBML supports all SBML Levels and Versions through Level 3 Version...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6372/version/1

JSBML:  a flexible and entirely Java-based library for working with SBML
Provedor de dados: 17
Autores: Nicolas Rodriguez; Marine Dumousseau; Andreas Dr&amp;#xe4;ger; Clemens Wrzodek; Alexander D&amp;#xf6;rr; Sarah M. Keating; Akiya Jouraku; Nicolas Le Nov&amp;#xe8;re; Andreas Zell; Michael Hucka.
The XML-based Systems Biology Markup Language (SBML) is the de facto standard file format for the storage and exchange of biochemical network models, and is supported by more than 180 software packages to date. Much of this success is due to its clearly defined specifications and the availability of libSBML, a portable, robust, and easy-to-use library.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;LibSBML provides many methods for manipulating and validating SBML files through its Application Programming Interface (API).  Originally written in C and C++, libSBML also provides automatically-generated language bindings for Java, MATLAB, Perl, and many more. However, the platform independence of Java is compromised in libSBML due to the fact that the language binding is...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6718/version/1

JSBML update
Provedor de dados: 17
Autores: Andreas Dr&amp;#xe4;ger; Nicolas Rodriguez.
This presentation gives an overview about the major changes in JSBML since the release of version 0.8-b1, which will become part of the first release candidate.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6358/version/1

Just-in-time assembly of cell-cycle protein complexes
Provedor de dados: 17
Autores: Lars J. Jensen; Ulrik de Lichtenberg; Thomas S. Jensen; S&amp;#xf8;ren Brunak; Peer Bork.
Our comparative analysis of eukaryotic cell-cycle complexes reveals that the identity of the periodically expressed subunits differs significantly between organisms and is often mirrored by changes in cell-cycle-dependent phosphorylation of the protein products. This indicates that many different solutions have evolved for just-in-time assembly of the same molecular machines.
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2273/version/1

KaPPA-View4: A Pathway Database for Gene Co-expression and Metabolite Co-accumulation Analysis
Provedor de dados: 17
Autores: Nozomu Sakurai.
Correlations of gene-to-gene co-expression and metabolite-to-metabolite co-accumulation are considered to be useful for uncovering unknown functions of genes and regulatory systems of the metabolic pathways. Although many databases and tools are available to interpret quantitative data of transcriptome and metabolome, there are only limited ones that connect correlation data to biological knowledge and can be utilized to find biological significance of it. We developed a new metabolic pathway database, KaPPA-View4 (&amp;#x22;http://kpv.kazusa.or.jp/kpv4/&amp;#x22;:http://kpv.kazusa.or.jp/kpv4/), that enables to overlay gene-to-gene and/or metabolite-to-metabolite relationships as quadratic Bez&amp;#xed;er curves on metabolic pathway maps. For up to 4 maps...
Tipo: Presentation
Palavras-chave: Microbiology; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5065/version/1

Keratinocytes from human skin respond as typical immune cells after the stimulation with _Trichophyton rubrum_
Provedor de dados: 17
Autores: Alfonso E. Islas-Rodr&amp;#xed;guez; Luz A. Garc&amp;#xed;a-Madrid.
_Trichophyton rubrum_ is the main agent causing dermatophytosis (1). Keratinocytes are&amp;#xd;&amp;#xa;considered to be the first physical barrier of defense against pathogens (2). But not&amp;#xd;&amp;#xa;only a physical barrier. They recognize antigens through Toll like receptors (TLR) (3).&amp;#xd;&amp;#xa;The activation of this TLR, present on the surface of the keratinocytes, induce the&amp;#xd;&amp;#xa;expression of different pro-inflammatory cytokines, co-stimulatory molecules and&amp;#xd;&amp;#xa;antimicrobial peptides such as [beta]-defensins (4).&amp;#xd;&amp;#xa;The main objective of this work is to determine if lipopolysaccharides of G &amp;#x2013; bacteria&amp;#xd;&amp;#xa;(LPS), lipotheichoic acid from G+ bacteria (LTA), and conidias,...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/930/version/1

Keynote: A renaissance for the point mutation: from legacy data to semantic web service
Provedor de dados: 17
Autores: Christopher J. O. Baker.
Experiments that construct or discover protein point-mutations and investigate their functional consequences represent one of the cornerstones of biomedical investigation. And yet, despite the importance of these annotations, the interpretation and reuse of knowledge about their impacts remains a formidable task. This is due to a number of reasons including (i) the publishing of salient mutation impact descriptions in unstructured text, (ii) the existence of numerous boutique databases of mutation information which can have many years of latency, and (iii) errors within manually populated mutation databases. In recent years the mining of mutations from scientific documents has emerged as a promising research theme resulting in automated methods for...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5443/version/1

Kinase independent inhibition of NF&amp;#x3ba;B transcriptional activity by GRK5 through I&amp;#x3ba;B&amp;#x3b1; stabilization.
Provedor de dados: 17
Autores: Daniela  Sorriento; Michele  Ciccarelli; Gaetano  Santulli; Alfonso  Campanile; Giovanna Giuseppina  Altobelli; Vincenzo  Cimini; Gennaro Galasso; Dalila  Astone; Federico Piscione; Lucio Pastore; Bruno Trimarco; Guido  Iaccarino.
Members of the G protein receptor kinase (GRK) family that regulates receptor desensitization and members of the nuclear transcription factors family NF[kappa]B have been recently and convincingly demonstrated to interact, although the effects on transcription and gene expression have not yet been described. Using overexpression, knockdown (small interfering RNA) and mutagenesis experiments, we demonstrate that GRK5 couples to and stabilizes the NF[kappa]B inhibitor I[kappa]B[alpha], and inhibits NF[kappa]B activity. Studies with minigenes suggest that the N-terminal Regulation of G protein Signaling (RGS) homology (RH) domain confers GRK5 such ability. GRK5-RH domain overexpression affects NF[kappa]B dependent phenotypes, such as apoptosis protection,...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1196/version/1

Kinetic control of eukaryotic chromatin structure by recursive topological restraints
Provedor de dados: 17
Autores: Dominika Borek; Zbyszek Otwinowski.
Chromatin structure undergoes many changes during the cell cycle and in response to regulatory events. A basic unit of chromatin organization is the nucleosome core particle. However, very little is known about how nucleosomes are arranged into higher-order structures in vivo, even though the efficiency and precision of cell division imply high levels of structural organization. We propose abandoning the current paradigm of chromatin organization based on thermodynamics of the lowest energy state and replace it with the idea of a topologically restrained, high-energy structure. We propose that DNA is subject to a recursive topological restraint, and is anchored by hemicatenates that are part of the chromosomal scaffold. Long-distance _cis_-regulation of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2672/version/1

Kinetic model based on molecular mechanism for action potential
Provedor de dados: 17
Autores: Lizhong Xu.
The Hodgkin-Huxley model for action potentials has been widely used but was not built on a microscopic description of the neuronal membrane. Through molecular dynamics simulations, the molecular mechanism of the channel currents is becoming clear. However, the quantitative link between molecular mechanism and action potential remains to be elucidated. Here, a kinetic model for action potential based on the molecular mechanism of the channel currents is proposed. Using it, the experimental observations about action potential are reproduced quantitatively and explained based on molecular mechanism. We find that the accumulation of Na+ ions near exit of the electivity filter is the dominant event to cause the refractory period of the Na+ channel and the types...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5697/version/1

Kinetic resolution of racemates under chiral catalysis: connecting the dots
Provedor de dados: 17
Autores: Sosale Chandrasekhar.
The current theory of the titled phenomenon is apparently based on an inconsistent use of concentration units, as employed in the derivation of the fundamental equations. Thus, manifestly, whilst the relation between extent of conversion and e.e. is derived with mole fractions, the succeeding kinetic equations employ units of molarity. This invalidates the derivation in the general case. Fortuitously, however, it is applicable in the majority of simple cases, wherein the total number of moles involved in the reaction remains constant. Herein is presented a rigorous approach which is generally valid.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/7127/version/1

Kinetic Simulation Algorithm Ontology
Provedor de dados: 17
Autores: Anna Zhukova; Dagmar Waltemath; Nick Juty; Camille Laibe; Nicolas Le Nov&amp;#xe8;re.
To enable the accurate and repeatable execution of a computational simulation task, it is important to identify both the algorithm used and the initial setup. These minimum information requirements are described by the MIASE guidelines. Since the details of some algorithms are not always publicly available, and many are implemented only in a limited number of simulation tools, it is crucial to identify alternative algorithms with similar characteristics that may be used to provide comparable results in an equivalent simulation experiment. The Kinetic Simulation Algorithm Ontology (KiSAO) was developed to address this issue by describing existing algorithms and their inter-relationships through their characteristics and parameters. The use of KiSAO in...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6330/version/1

Koffka&amp;#x27;s Ring Effect Depends on Thickness, Not Continuity
Provedor de dados: 17
Autores: Abigail E. Huang; Alice J. Hon; Eric L. Altschuler.
More than 70 years ago Gestalt psychologist Kurt Koffka described a fascinating effect1,2: When a contiguous grey ring is placed on a background half of one shade of grey (different from the ring) and half of another shade of grey, the ring appears to be a homogenous. However, if the ring is slightly divided, now the two halves of the ring appear different shades of grey with the half of the ring on the darker background appearing lighter than the half of the ring on the darker background. The Gestalt principle of continuity in visual perception is invoked to explain this effect. Here we show that in fact when the ring is made thinner it appears heterogeneous even when contiguous. Furthermore, when viewing a thick ring after first viewing a thin ring, the...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1433/version/1

LabelHash: A Flexible and Extensible Method for Matching Structural Motifs
Provedor de dados: 17
Autores: Mark Moll; Lydia E. Kavraki.
There is an increasing number of proteins with known structure but unknown function. Determining their function would have a significant impact on understanding diseases and designing new therapeutics. Computational methods can facilitate function determination by identifying proteins that have high structural and chemical similarity. Below, we will briefly describe LabelHash, a new method for partial structure comparison. In partial structure comparison, the goal is to find the best geometric and chemical similarity between a set of 3D points called a _motif_ and a subset of a set of 3D points called the _target_. Both the motif and targets are represented as sets of labeled 3D points. A motif is ideally composed of the functionally most-relevant residues...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2199/version/1

Laboratory and field evaluation for the resistance of commonly used woods against _Coptotermes heimi_ (Wasmann).
Provedor de dados: 17
Autores: Farkhanda  Manzoor; Nadeem Sheikh; Asma  Zawar.
The current study was conducted to evaluate the resistance of four wood species (_Azadirachta indica_, _Pinus roxberghii_, _Dalbergia sissoo_ and _Populus deltoides_) against subterranean termite species _Coptotermes heimi_ by choice and no choice field and laboratory trials. Of these four wood species  _P. roxberghii_ and  _D. sissoo_ proved to be most resistant to termite attack. Taken together these results we can conclude that _D. sissoo_ is the least preferred and _P. deltoides_ is the most preferred wood by the _C. heimi_. The data obtained from the field choice and no-choice the woods are arranged in order of preference DS&amp;#x3e;PR&amp;#x3e;AI&amp;#x3e;PD whereas in laboratory choice and no-choice trials the order of preference was...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4485/version/1

Laboratory culture of stem borer, _Aeolesthes holosericea_ F., method developed
Provedor de dados: 17
Autores: Ravi Bhushan Sinha; Anil Kumar Debnath; Bishwa Mohan Kumar Singh; Bhagwan Chandra Prasad.
_Aeolesthes holosericea_, a polyphagous stem borer has been reported to damage up to 40% of tropical tasar silkworm host-plants wherever infestation is high. Known control measures are not very effective as information on its life cycle and susceptible stages against insecticides and bio-agents are insufficient. Laboratory culture of the insect is inevitable for developing control measures as the insect passes most of its life within stem tissues. Culture method of other borer species was not applied to it due to sophistication of process. A convenient laboratory culture method has been developed for the insect. The culture includes complete larval rearing; preservation of pupa; rearing and mating of adults followed by oviposition, incubation and hatching....
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5640/version/1

Laparoscopy Pneumoperitoneum Fuzzy Modeling
Provedor de dados: 17
Autores: Otavio M. Becker Jr.; Jose E. Araujo Jr.; Joao L. M. C. Azevedo.
Abstract: Gas volume to intra-peritoneal pressure fuzzy modeling for evaluating pneumoperitoneum in videolaparoscopic surgery is proposed in this paper. The proposed approach innovates in using fuzzy logic and fuzzy set theory for evaluating the accuracy of the prognosis value in order to minimize or avoid iatrogenic injuries due to the blind needle puncture. In so doing, it demonstrates the feasibility of fuzzy analysis to contribute to medicine and health care. Fuzzy systems is employed here in synergy with artificial neural network based on backpropaga tion, multilayer perceptron architecture for building up numerical functions. Experimental data employed for analysis were collected in the accomplishment of the pneumoperitoneum in a random population of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6060/version/1

Large scale expansion of mobile elements in specific hotspot regions of the German outbreak _Escherichia coli_ O104:H4
Provedor de dados: 17
Autores: Lisa C. Crossman.
The outbreak strain of _E. coli_ O104:H4 has been sequenced by several groups and made available publicly for CrowdSourcing purposes.  Genome comparisons of the complete finished sequence of TY2482 (BGI), have been made with the draft assemblies of c22711 (PacBio) and an historical outbreak strain from 2001 (U. M&amp;#xfc;nster &amp;#x26; Life Technologies).  A plasmid, pTY2, carrying the _agg_ operon specifying the genes for aggregative adherence fimbriae reveals a frameshift in a gene, _aggB_, that may result in altered binding _in vivo_ compared to the unframeshifted state.  Comparisons additionally reveal the presence of genomic islands specific to the outbreak strain relative to other sequenced _E. coli_ strains.  These regions, and islands shared...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6466/version/1

Large sets of edit-metric sequence identification tags to facilitate large-scale multiplexing of reads from massively parallel sequencing
Provedor de dados: 17
Autores: Brant C. Faircloth; Travis C. Glenn.
*Background*&amp;#xd;&amp;#xa;Massively parallel DNA sequencing technologies provide exponential increases in the amount of data returned from the sequencing process, relative to traditional (Sanger-based) techniques.  Use of unique, synthetic oligonucleotides (identifying sequence tags) on each sample enables the deconvolution of samples pooled prior to massively parallel sequencing.  To counteract oligonucleotide synthesis and sequencing errors, sequence tags should be drawn from combinations with sufficient differences and with an appropriate error-correcting code over the alphabet [A,C,G,T].  This method ensures that errors within the tags do not cause sequences to be assigned to the wrong sample while also enabling correction and recovery of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5672/version/1

Large-scale imaging of brain network activity from &amp;#x3e;10,000 neocortical cells
Provedor de dados: 17
Autores: Shigehiro Namiki; Norio Matsuki; Yuji  Ikegaya.
Large-scale recording from populations of neurons is a promising strategy in the study of complex brain function. Here we introduce a simple optical technique that simultaneously probes the calcium activity of ~10,000 cells at the single cell resolution _in vitro_. We employed a combination of a low-magnification objective lens and an electron-multiplying charge-coupled device megapixel camera to achieve large-view-field and high-resolution imaging.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2893/version/1

Lattice Parameters of Calcite in the PT-Plane to 7.62 Kb and 800 K
Provedor de dados: 17
Autores: Michael J. Bucknum.
Lattice parameters (a &amp;#x26; c) of powdered, polycrystalline calcite in the trigonal-hexagonal system have been determined as a function of pressure and temperature using a hydrothermal diamond anvil cell (DAC), that has been separately described, and a synchrotron x-ray source. Diffraction data was collected using white synchrotron radiation in an energy dispersive technique (EDXRD). Temperature in the resistance heated hydrothermal DAC was measured by thermocouples to a maximum temperature of 800 K, and pressure was measured by the equation of state (EOS) of water, in which powdered calcite was immersed, to a maximum pressure of 7.62 Kb. The resulting study is an attempt to explore the potential of calcite as a double (P &amp;#x26; T) internal x-ray...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1514/version/1

LBFO: toward an artificial language for ontology development
Provedor de dados: 17
Autores: Leonard  F. Jacuzzo.
The syntax of LBFO represents the initial step toward the creation of a rigorously characterized, recursively defined, artificial language for the sole purpose of ontology development. The underlying idea is that maximally fruitful application of ontology requires accurate representation of reality in accordance with current textbook science. Hence, creating a robust, accurate representation of reality is a fundamental concern. &amp;#xd;&amp;#xa;An ontology represents general types of entities and relations between them. A domain ontology represents the general types and relations for a given domain of research. A top-level ontology represents the general types of entities in any domain of research. Ontologies serve many purposes in computerized...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4001/version/1

Lead identification and docking studies of metastatic protein human mitogen activated protein kinase kinase4
Provedor de dados: 17
Autores: Harika  Meduru; Dibyabhaba Pradhan; Manne  Munikumar; Amineni Umamaheswari.
Human dual specificity mitogen-activated protein kinase kinase 4 (MAP2K4) is a direct activator of MAP kinases in response to various environmental stresses or mitogenic stimuli. Upon phosphorylation, MAP2K4 has been shown to activate MAPK8, MAPK9 and MAPK14/p38 but not MAPK1/ERK2 or MAPK3/ERK1. Over expression of MAP2K4 causes carcinogenic effects, such as ovarian cancer, colorectal cancer, prostate cancer and pancreatic cancer. Our present study was carried out to design a potent drug molecule against MAP2K4 to control over expression. As there is no experimentally determined structure for MAP2K4, the homology modeling technique of Modeller9v7 was implemented to generate a MAP2K4 3D model based on the co-crystal structure of MAP2K6 (PDB ID: 3FME) with...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5457/version/1

Leaping and Accelerometry: A Theoretical Approach
Provedor de dados: 17
Autores: William I. Sellers.
Accelerometry has always been a popular method of monitoring locomotor activity but its use is becoming more widespread due to the easy availability of low cost, low power sensors. However one of the major problems with interpreting accelerometer data is that rotation of the sensor alters the output and obtaining independent orientation information is currently difficult. For the specific case of leaping locomotion full orientation information is unecessary as long as an independent measure of height change is available such as can be obtained from a sensitive pressure sensor. Therefore a 4 channel logging system recording 3 accelerometry axes combined with a channel measuring pressure could be used to accurately assess leaping locomotion. This approach...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2515/version/1

Learning a Bayesian prior in interval timing
Provedor de dados: 17
Autores: Hansem Sohn; Sang-Hun Lee.
Behavioral studies on perceptual learning (PL) often attributed an improvement in task performance to an enhancement in sensory processing of stimuli. However, the framework of Bayesian inference suggests that perceptual improvements can arise from learning-induced changes either in a likelihood function or in a prior expectation for sensory input. We developed and adapted Bayesian observer models to long-term changes in interval timing (IT) performance by human subjects to assess relative contributions of the prior and likelihood to PL of IT.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;While subjects were viewing a small bar that drifted for a while and disappeared, we estimated subjective time intervals ([DELTA]Ts) from subjects&amp;#x2019; natural reactions to...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5804/version/1

Learning alters theta-nested gamma oscillations in inferotemporal cortex
Provedor de dados: 17
Autores: Keith M. Kendrick; Yang Zhan; Hanno Fischer; Alister U. Nicol; Xuejuan Zhang; Jianfeng Feng.
How coupled brain rhythms influence cortical information processing to support learning is unresolved. Local field potential and neuronal activity recordings from 64- electrode arrays in sheep inferotemporal cortex showed that visual discrimination learning increased the amplitude of theta oscillations during stimulus presentation. Coupling between theta and gamma oscillations, the theta/gamma ratio and the regularity of theta phase were also increased, but not neuronal firing rates. A neural network model with fast and slow inhibitory interneurons was developed which generated theta nested gamma. By increasing N-methyl-D-aspartate receptor sensitivity similar learning-evoked changes could be produced. The model revealed that altered theta nested gamma...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3151/version/2

Learning alters theta-nested gamma oscillations in inferotemporal cortex
Provedor de dados: 17
Autores: Keith M. Kendrick; Yang Zhan; Hanno Fischer; Alister U. Nicol; Xuejuan Zhang; Jianfeng Feng.
How coupled brain rhythms influence cortical information processing to support learning is unresolved. Local field potential and neuronal activity recordings from 64- electrode arrays in sheep inferotemporal cortex showed that visual discrimination learning increased the amplitude of theta oscillations during stimulus presentation. Coupling between theta and gamma oscillations, the theta/gamma ratio and the regularity of theta phase were also increased, but not neuronal firing rates. A neural network model with fast and slow inhibitory interneurons was developed which generated theta nested gamma. By increasing N-methyl-D-aspartate receptor sensitivity similar learning-evoked changes could be produced. The model revealed that altered theta nested gamma...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3151/version/1

Learning complex tasks with probabilistic population codes
Provedor de dados: 17
Autores: Richard  E. Turner; Pietro Berkes; Jozsef Fiser.
Recent psychophysical experiments imply that the brain employs a neural representation of the uncertainty in sensory stimuli and that probabilistic computations are supported by the cortex.  Several candidate neural codes for uncertainty have been posited including Probabilistic Population Codes (PPCs).  PPCs support various versions of probabilistic inference and marginalisation in a neurally plausible manner. However, in order to establish whether PPCs can be of general use, three important limitations must be addressed. First, it is critical that PPCs support learning. For example, during cue combination, subjects are able to learn the uncertainties associated with the sensory cues as well as the prior distribution over the stimulus. However, previous...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5838/version/1

Learning Features of Simple and Complex Cells: A Generative Approach via Multiplicative Interactions
Provedor de dados: 17
Autores: Wentao Huang; Zhengping Ji; Garrett  Kenyon.
We develop a hierarchical generative model to learn features of simple and complex cells in the primary visual cortex via multiplicative interactions and address the problem of learning invariant visual representation from natural image sequences. Generally, the overall objective of a generative sparse coding model (Olshausen and Field, Nature, 1996) is to reconstruct the input *x* via a linear combination of feature bases  *A = [A~1~,A~2~,...,A~M~]*, such that *x = As*, where s is the latent representation with a sparse constraint. &amp;#xd;&amp;#xa;In the proposed model, we added another hidden layer with complex cells to modulate the latent representation *s*, such that *s* is generated via an element-wise product of bottom-up representation   *y =...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5943/version/1

Learning to discount transformations as the computational goal of visual cortex
Provedor de dados: 17
Autores: Joel Z. Leibo; Jim Mutch; Tomaso Poggio.
It has been long recognized that a key obstacle to achieving human-level object recognition performance is the problem of invariance.  The human visual system excels at factoring out the image transformations that distort object appearance under natural conditions.  Models with a cortex-inspired architecture such as HMAX as well as nonbiological convolutional neural networks are invariant to translation (and in some cases scaling) by virtue of their wiring.  The transformations to which this approach has been applied so far are _generic_; a single example image of any object contains all the information needed to synthesize a new image of the transformed object.  In contrast, viewpoint and illumination transformations depend on the object&amp;#x27;s 3D...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6078/version/1

Learning to Leap: Nanotechnology&amp;#x27;s Root in Soil Science
Provedor de dados: 17
Autores: Siddhartha Sankar Mukhopadhyay.
Dr. Nil Ratan Dhar Memorial Lecture&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Soil could be perceived as a four dimensional system where a broad three dimensional structural fabric is filled by dynamic and reactive colloidal constituents. There are interconnected relationships between authegenic, neogenic and stable-phase crystallite constituents, most of which are in nano-phase, and the system seldom reaches  equilibrium. Also, variations in composition, pH, and other properties make soil unique at each place. Therefore, understanding of soil system helps to develop insight into mobility and reactivity of nano-materials. The origin of nanoscience can be traced to the discovery that clay minerals were crystalline and of micrometer size. The unit cell dimensions...
Tipo: Presentation
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6656/version/1

Learning with the Amerindians: the evaluation of pelvic floor disorders among indigenous women who live in the Xingu Indian Park,Brazil
Provedor de dados: 17
Autores: Maita M. Araujo; Manoel Jo&amp;#xe3;o Batista Castello Gir&amp;#xe3;o; Claudia Cristina Takano; Marair Gracio Ferreira Sartori.
Objective: to evaluate the pelvic floor muscles and the incidence of pelvic organ prolapse among indigenous women who live in Xingu Indian Park, Mato Grosso, Brazil. &amp;#xd;&amp;#xa;Methods: observational study with 377 indigenous women, mean age 31+/-15 years, mean gravity 5+/-4, mean parity 4+/-3 and mean body mass index 23,3+/-4 Kg/m2. The Pelvic Organ Prolapse Quantification (POP-Q) was the system used to quantification the staging of pelvic support and the pelvic floor muscle strength was assessed by a perineometer. Logistic regression was used to determine odds ratios and 95% CI for factors that were associated with prolapse. &amp;#xd;&amp;#xa;Results: The overall distribution of POP-Q stage system was the following: 15,6% stage 0, 19,4% stage I,...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1958/version/1

Left Anterior Negativity reflects distinct neural substrate for linguistic rule application
Provedor de dados: 17
Autores: Riadh Lebib; Andrea Krott.
A critical issue for understanding language processing in the brain is whether linguistic rule application is subserved by a distinct neural substrate. Previous evidence based on electroencephalographic measurements is indirect because studies focus on neural changes after rule violation, which may reflect processes caused by the violation such as error handling. Here we show that correct rule-governed formations are associated with left frontal negative-going activity, providing direct evidence for rule application in the brain.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2090/version/1

Lego DNA assembling, a simple in vitro method for constructing DNA molecule
Provedor de dados: 17
Autores: Mo Xian; Xinglin Jiang; Jianming Yang; Haibo Zhang; Huaiwei Liu; Yanning Zheng; Cong Wang; Sizheng Su.
Digestion-ligation based and recombination based methods for constructing recombinant DNA are the basic techniques in molecular biology and thus built one of the foundations for the modern life sciences. Here we describe a new strategy that can radically simplify some of the same task. The lego DNA assembling, based on strand annealing, allows in vitro assembly of multi DNA fragments in one step with precise junctions and excludes the need for any enzyme. As a proof of concept, we rapidly constructed plasmids from 4, 6 and 8 fragments with very high efficiencies (100%). And we found this method a powerful tool for synthetic biology, constructing a partial isoprene biosynthesis pathway (consisting of four genes) in 2 days. We also assembled a customized...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5147/version/1

Length, Weight, and Yield in Channel Catfish, Lake Diane, MI
Provedor de dados: 17
Autores: Elizabeth Keenan; Sarah Warner; Ashley Crowe; Michael Courtney.
Background:  Channel catfish (Ictalurus punctatus) are important to both commercial aquaculture and recreational fisheries.  Little published data is available on length-weight relationships of channel catfish in Michigan.  Though there is no record of public or private stocking, channel catfish appeared in Lake Diane between 1984 and 1995 and it has developed into an excellent fishery. &amp;#xd;&amp;#xa;Materials and Methods: Sport angling provided 38 samples which were weighed and measured (fork length).  Fillets were also weighed.  The best fit estimates of parameters a and b in the model, W(L) = aLb, were obtained by both linear least-squares (LLS) regression (log(W) = log(a) + b log(L)) and non-linear least-squares (NLLS) regression.  Best-fit...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/5706/version/1

Lengthening of 3&amp;#x27;UTR Increases Morphological Complexity in Animal Evolution
Provedor de dados: 17
Autores: Cho-Yi Chen; Shui-Tein Chen; Hsueh-Fen Juan; Hsuan-Cheng Huang.
By analyzing the structure of mRNA transcripts in multiple metazoan species, we observed a striking exponential correlation between the length of 3&amp;#x27; untranslated regions (3&amp;#x27;UTR) and morphological complexity as measured by the number of cell types in each organism. Cellular diversity was similarly associated with the accumulation of microRNA genes and their putative targets. We propose that the lengthening of 3&amp;#x27;UTRs together with a commensurate expansion in post-transcriptional regulation can contribute to the emergence of new cell types during animal evolution.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4915/version/1

Less is more: rarity trumps quality in luxury markets
Provedor de dados: 17
Autores: Agnes Gault; Yves Meinard; Franck Courchamp.
The international market for luxury goods has almost doubled since 1990, with a worldwide increase of 10% annually. This trade is fuelled by a great deal of legally and illegally exploited wildlife species, putting enormous pressure on many of them, with potentially irreversible consequences. The dramatic decline of sturgeon populations exploited for their caviar, is a good example: all 27 species are threatened and the most coveted are on the verge of extinction. We aim to identify the mechanism responsible for the continued overexploitation of sturgeon species, despite caviar&amp;#x27;s ever-increasing price and the imminent loss of these species. Here, we demonstrate consumer preference for rarity over intrinsic quality: customers tasting two caviar...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1690/version/1

Lethal and sublethal effects of polybrominated diphenyl ethers (PBDEs) for turbot (_Psetta maxima_) early life stage (ELS)
Provedor de dados: 17
Autores: Lazhar Mhadhbi; Jose  Fumega; Moncef Boumaiza; Ricardo Beiras.
A new toxic menace, polybrominated diphenyl ethers (PBDEs), is being detected in the aquatic environment all over the world. The environmental presence of PBDEs and its entry into the environment as BDE-47 and -99 make quality aquatic toxicity data necessary to assess the aquatic hazard risk of PBDs. This study examines the effects of three PBDE-47 and -99 on embryo and larval stages of the marine flatfish turbot (_Psetta maxima_). The acute toxicity of the three PBDEs was examined and NOEC, LOEC, LC10 and LC50 were calculated. All tested compounds caused lethal as well as nonlethal malformations during embryo development. The effects of PBDEs in the different life stages of turbot were analysed. PBDEs seemed to be teratogenic at concentrations higher than...
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4656/version/2

Lethal and sublethal effects of polybrominated diphenyl ethers (PBDEs) for turbot (_Psetta maxima_) early life stage (ELS)
Provedor de dados: 17
Autores: Lazhar Mhadhbi; Jose  Fumega; Moncef Boumaiza; Ricardo Beiras.
A new toxic menace, polybrominated diphenyl ethers (PBDEs), is being detected in the aquatic environment all over the world. The environmental presence of PBDEs and its entry into the environment as BDE-47 and -99 make quality aquatic toxicity data necessary to assess the aquatic hazard risk of PBDs. This study examines the effects of three PBDE-47 and -99 on embryo and larval stages of the marine flatfish turbot (_Psetta maxima_). The acute toxicity of the three PBDEs was examined and NOEC, LOEC, LC10 and LC50 were calculated. All tested compounds caused lethal as well as nonlethal malformations during embryo development. The effects of PBDEs in the different life stages of turbot were analysed. PBDEs seemed to be teratogenic at concentrations higher than...
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4656/version/1

Letting the Cat Out of the Bag: &amp;#xb;OBO and the Semantic Web
Provedor de dados: 17
Autores: John E. Rose.
The tools developed to work with an expanding number of biomedical ontologies are all directed &amp;#x201c;inward,&amp;#x201d; back toward the scientists. The Semantic Web is an effort to assign meaning to data available on the internet resulting in a universal platform of knowledge exchange. For the Open Biomedical Ontologies to become a part of the Semantic Web, a more &amp;#x201c;outward-looking&amp;#x201d; tool is required. A prototype, AmiGA, based on 21 ontologies with over 600,000 terms,&amp;#xd;&amp;#xa;has been constructed.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3527/version/1

Levy flights are not evolved behavior
Provedor de dados: 17
Autores: Jay Willis; Lucas Merckelbach.
Tracks of moving animals have many short moves interspersed with longer moves, and frequencies of all moves together often indicate Levy flights (a type of power law)^1^. The Levy flight foraging hypothesis suggests that, &amp;#x27;since Levy flights and walks can optimize search efficiencies, therefore natural selection should have led to adaptations for Levy flight foraging^1^ and it has been apparently supported by several studies of large numbers of tracks of marine animals^234^. We show that Levy flights are caused by marine animals attempting to move in simple ways and they are unlikely to be evolved behavior. We do this by analyzing the tracks of autonomous underwater gliders which conform to Levy flights while they were programmed to perform simple...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6564/version/1

LexOWL: A Bridge from LexGrid to OWL
Provedor de dados: 17
Autores: Cui Tao; Jyotishman Pathak; Harold Solbrig; Christopher Chute.
The Lexical Grid project is an on-going community driven initiative that provides a common terminology model to represent multiple vocabulary and ontology sources as well as a scalable and robust API for accessing such information. In order to add more powerful functionalities to the existing infrastructure and align LexGrid more closely with various Semantic Web technologies, we introduce the LexOWL project for representing the ontologies modeled within the LexGrid environment in OWL (Web Ontology Language). The crux of this effort is to create a &amp;#x201c;bridge&amp;#x201d; that functionally connects the LexBIG (a LexGrid API) and the OWL API (an interface that implements OWL) seamlessly. In this paper, we discuss the key aspects of designing and...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3468/version/1

LexOWL: A Bridge from LexGrid to OWL
Provedor de dados: 17
Autores: Cui Tao; Jyotishman Pathak; Harold Solbrig; Christopher  Chute.
The Lexical Grid project is an on-going community driven initiative that provides a common terminology model to represent multiple vocabulary and ontology sources as well as a scalable and robust API for accessing such information. In order to add more powerful functionalities to the existing infrastructure and align LexGrid more closely with various Semantic Web technologies, we introduce the LexOWL project for representing the ontologies modeled within the LexGrid environment in OWL (Web Ontology Language). The crux of this effort is to create a &amp;#x201c;bridge&amp;#x201d; that functionally connects the LexBIG (a LexGrid API) and the OWL API (an interface that implements OWL) seamlessly. In this paper, we discuss the key aspects of designing and...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3469/version/1

LibSBGN: current status and future plans
Provedor de dados: 17
Autores: Alice C. Villeger.
LibSBGN is a community project started in 2009: it aims at facilitating the development of SBGN-compliant tools, and improving interoperability between these tools.&amp;#xd;&amp;#xa;These goals will be achieved by defining a standardized electronic implementation of the Systems Biology Graphical Notation: an XML-based file format (SBGN-ML), complemented by a software library (LibSBGN).&amp;#xd;&amp;#xa;The project is organized around a number of online tools, which allow the community to discuss problems, share ideas, and formalize solutions.&amp;#xd;&amp;#xa;Current versions of SBGN-ML and LibSBGN have already been adopted by three different SBGN-compliant tools. The first official release of SBGN-ML is imminent.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;For...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5304/version/1

LibSBGN: Electronic Processing of SBGN maps
Provedor de dados: 17
Autores: Martijn P. van Iersel; Sarah E. Boyd; Frank Bergmann; Stuart Moodie; Falk Schreiber; Tobias Czauderna; Emek Demir; Nicolas Le Nov&amp;#xe8;re; Anatoly Sorokin; Huaiyu Mi; Augustin Luna; Ugur Dogrusoz; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano; Mirit I. Aladjem; Michael L. Blinov; Alice C. Vill&amp;#xe9;ger.
Introduction&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4967/version/1

LibSBGN: Electronic Processing of SBGN maps
Provedor de dados: 17
Autores: Martijn P. van Iersel; Sarah E. Boyd; Frank Bergmann; Stuart Moodie; Falk Schreiber; Tobias Czauderna; Emek Demir; Nicolas Le Nov&amp;#xe8;re; Anatoly Sorokin; Huaiyu Mi; Augustin Luna; Ugur Dogrusoz; Yukiko Matsuoka; Akira Funahashi; Hiroaki Kitano; Mirit I. Aladjem; Michael L. Blinov; Alice C. Vill&amp;#xe9;ger.
Introduction&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Graphical representations of participants and their relationships are essential for exchanging knowledge about complex biological processes. To convey this information clearly and unambiguously, it is necessary to assign standard meanings to symbols and their connectivity. For this purpose, the System Biology Graphical Notation (SBGN) has been developed.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As SBGN is becoming more widely adopted, and used in various software tools, there is an increasing need for a standard file format able to capture the SBGN maps. Exchange using graphics-only file formats (such as SVG) is insufficient, because the biological meaning of elements is lost. There is a need for a toolset that...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/4967/version/2

LibSBGN Status Update
Provedor de dados: 17
Autores: Martijn van Iersel; Tobias Czauderna; Alice C. Villeger.
LibSBGN is a library for reading, writing and validating maps that use the Systems Biology Graphical Notation (SBGN). The goals of LibSBGN are to 1) increase interoperability between pathway visualization tools, 2) increase the amount of code re-used, and 3) make it easier for tool developers to adopt the SBGN standard. This presentation is a status update of the project, presented at the COMBINE 2011 meeting.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6373/version/1

libSBML New conversion API
Provedor de dados: 17
Autores: Sarah M. Keating; Frank T. Bergmann.
Description of the new API for including converters within libSBML.
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6395/version/1

libSBML Status update
Provedor de dados: 17
Autores: Sarah M. Keating.
Overview of current status of libSBML development.
Tipo: Presentation
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6394/version/1

Life fingerprints of nuclear reactions in the body of animals
Provedor de dados: 17
Autores: Jun Zeng; Ji-hui Han; Tao Sun; Ji-hui Su; Qi-yin Sun; Quan-shi Zhang; Wen-hui Xie; Ci-yi Liu; Xiao-jia Cai.
Nuclear reactions are a very important natural phenomenon in the universe. On the earth, cosmic rays constantly cause nuclear reactions. High energy beams created by medical devices also induce nuclear reactions in the human body. The biological role of these nuclear reactions is unknown. Here we show that the in vivo biological systems are exquisite and sophisticated by nature in influence on nuclear reactions and in resistance to radical damage in the body of live animals. In this study, photonuclear reactions in the body of live or dead animals were induced with 50-MeV irradiation. Tissue nuclear reactions were detected by positron emission tomography (PET) imaging of the induced beta+ activity. We found the unique tissue...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4897/version/1

Life Tables of Bactrocera cucurbitae (Coquillett) (Diptera: Tephritidae): with a Mathematical Invalidation for Applying the Jackknife Technique to the Net Reproductive Rate
Provedor de dados: 17
Autores: Hsin Chi; Yu-Bing J. O. Y. C. E. Huang.
Life table data for the melon fly, Bactrocera cucurbitae (Coquillett), reared on cucumber (Cucumis sativus L.) were collected under laboratory and simulated field conditions. Means and standard errors of life table parameters were estimated for two replicates using the jackknife technique. At 25&amp;#xba;C, the intrinsic rates of increase (_r_) found for the two replicates were 0.1354 and 0.1002 day-1, and the net reproductive rates (_R_~0~) were 206.3 and 66.0 offspring, respectively. When the cucumbers kept under simulated field conditions were covered with leaves, the _r_ and _R_~0~ for the two replicates were 0.0935 and 0.0909 day-1, 17.5 and 11.4 offspring, respectively.  However, when similar cucumbers were left uncovered, the _r_ and _R_~0~ for the...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2012
URL: http://precedings.nature.com/documents/7070/version/1

LifeWatch &amp;#x2013; A European e-Science and observatory infrastructure supporting access and use of biodiversity and ecosystem data
Provedor de dados: 17
Autores: Mark Frenzel; Stefan Klotz; Alex Hardisty; Olaf Banki.
There are many promising earth and biodiversity-monitoring projects underway across the globe, but they often operate in information islands, unable easily to share data with others. This is not convenient: It is a barrier to scientists collaborating on complex, cross-disciplinary projects which is an essential nature of biodiversity research. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;LifeWatch (www.lifewatch.eu) is an ESFRI (European Strategy Forum on Research Infrastructures) initiative which has just entered its construction phase. It is aiming at new ways of collaboration, in an open-access research environment to solve complex societal and scientific questions on biodiversity and ecosystems. It installs a range of new services and tools to help the...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5843/version/1

Ligand based virtual screening studies to design drug molecules for human PIN1 causing cardiovascular disease
Provedor de dados: 17
Autores: C Ramana; Manne  Munikumar; Amineni Umamaheswari.
PIN1 is a member of the cis/trans peptidyl-prolyl isomerase family which plays critical roles in cell-cycle regulation. Over expression of PIN1 in endothelial cells causes cardiovascular disease. The present study has focused on computational analysis to identify the potential inhibitors for PIN1. The human PIN1 crystal structure was retrieved from the protein data bank and prepared using protein preparation wizard of Maestro v9.2.  Fourteen PIN1 inhibitors reported in recent literature were acquired and searched for structural analogs using Ligand.Info tool. 5675 PIN1 inhibitor analogs yielded were converted to 3D structures using LigPrep with constraints of ADME evaluation and toxicity assessments.  The 3D ligand dataset was docked to PIN1 through...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6604/version/1

Ligand Based Virtual Screening to Design Novel Human MEK1 Protein Inhibitors for Potential Development of Drugs Against Melanoma
Provedor de dados: 17
Autores: Vijayasree Potluri; Dibyabhaba  Pradhan; Amineni Umamaheswari.
The Ras-dependent Raf/MEK/ERK signaling pathway is a major regulator of cell proliferation and survival. Hyper activation of the pathway is frequently observed in human malignancies as a result of aberrant activation of receptor tyrosine kinases or mutations in RAF (V600E).  MEK1 is dual-specificity tyrosine/threonine protein kinases found in the pathway. The RAF  mutation (present in 50% of melanomas) have been shown to be highly dependent on MEK1 activity and also MEK1 is the only acknowledged activator of ERK, making them attractive targets for therapeutic intervention. In view of its importance, identification of potent inhibitor against MEK1 may be valuable to design effective drugs against melanoma. Inhibitors for human MEK1 reported till dates have...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4901/version/1

Ligand induced cleavage and nuclear localization of the rice XA21 immune receptor
Provedor de dados: 17
Autores: Chang-Jin Park; Pamela C. Ronald.
The rice XA21 receptor confers immunity to the Gram-negative bacterial pathogen, _Xanthomonas oryzae_ pv. _oryzae_ (_Xoo_) upon recognition of the conserved microbial signature AxY^S^22. Here, we demonstrate that the intracellular kinase domain of XA21 translocates to the nucleus upon AxY^S^22-mediated perception and that this translocation event is required for XA21-mediated immunity.
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6776/version/1

Light converts endosymbiotic fungus to pathogen, influencing seedling survival and host tree recruitment
Provedor de dados: 17
Autores: Patricia Alvarez; James White Jr; Nataly Gil; Jens-Christian Svenning; Henrik Balslev; Thea Kristiansen.
Endophytic fungi that asymptomatically colonize plants^1^ are diverse and abundant in tropical ecosystems^2^. These organisms can be weakly pathogenic^3^ and/or mutualistic, frequently enabling plants to adapt to extreme environments, alter competitive abilities of host individuals and improve host fitness under abiotic or biotic stresses^4,5,6^. _Diplodia mutila_ is a symbiotic endophyte/plant pathogenic fungus infecting the palm _Iriartea deltoidea_^7^, which dominates many wet lowland Neotropical forests. The fungus is an asymptomatic endophyte in mature plants, and disease and mortality are expressed in some seedlings, while others remain disease free. Here we show that seedlings bearing the endophyte show enhanced resistance to insect herbivory....
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1908/version/1

Lightning Talk: Biopython (bio) Geography Module
Provedor de dados: 17
Autores: Nicholas J. Matzke.
For Google Summer of Code 2009/NESCENT Phyloinformatics Summer of Code 2009, I built a Geography module for Biopython.  The purpose of the module is to search, download, and process biogeographical data from GBIF, much as Biopython currently accesses Genbank.  Application of the tool to a historical biogeography study on bivalves will be illustrated.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As required by Google Summer of Code and Biopython, the code is open access and is released under the Biopython License:&amp;#xd;&amp;#xa;&amp;#x22;http://www.biopython.org/DIST/LICENSE&amp;#x22;:http://www.biopython.org/DIST/LICENSE&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The module is described, and a tutorial is presented, on the Biopython...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4676/version/1

Lightning talk: PyPop - a software pipeline for large-scale multilocus population genomics
Provedor de dados: 17
Autores: Alex K. Lancaster; Richard M. Single; Owen D. Solberg; Mark P. Nelson; Glenys Thomson.
PyPop (Python for Population Genomics) is an open-source framework for performing large-scale population genetic analyses on multilocus genotype and allele frequency data. It computes tests and measures of Hardy-Weinberg equilibrium (locus-level and individual genotype-level), linkage disequilibrum, and selection, and estimates multi-locus haplotypes. PyPop supplements and extends existing population genetic software incorporating them as modules, modified to accommodate highly polymorphic data, rather than reimplementing them from scratch. It facilitates evolutionary analyses by integrating population genetic statistics within and across populations.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Originally developed to analyze the highly polymorphic genetic data of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4700/version/1

Limitation of F1 hybrids uniformity law
Provedor de dados: 17
Autores: Evgenii Levites.
Using isozymes as markers, data indicative of polymorphisms in the progeny produced from crossing two beet plants, homozygous on contrastive alleles of enzyme loci, were obtained.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6734/version/1

Limiting effect of diazepam on Lewis lung carcinoma metastasis in anxious male mice
Provedor de dados: 17
Autores: Vasily N. Kaledin; Svetlana I. Ilnitskaya; Valery P. Nikolin; Nelly A. Popova; Dmitry A. Smagin; Natalia N. Kudryavtseva.
_Aim:_ It has been shown previously that chronic social defeat stress produces development of strong anxiety and increases intensity of experimental metastasis in the losers in comparison with the control mice. The question was: is it possible to decrease the number of metastases in the losers by chronic or acute diazepam treatment. _Materials and Methods._ Sensory contact model was used for generating male mice with repeated experience of social defeats or victories in daily agonistic interactions. Lewis Lung Carcinoma cells (LLC) were injected into the tail vein of animals after 10 days of agonistic interactions. Then mice were treated acutely or chronically (7 days) with diazepam (1 mg/kg, i.p). Number of metastases in the lung was calculated in 16 days...
Tipo: Manuscript
Palavras-chave: Cancer; Neuroscience; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2748/version/1

Limits to the detection of early warning signals of population collapse
Provedor de dados: 17
Autores: Carl Boettiger; Alan Hastings.
Background/Question/Methods&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The recog&amp;#xad;ni&amp;#xad;tion that ecosys&amp;#xad;tems can undergo sud&amp;#xad;den shifts to alter&amp;#xad;nate, less desir&amp;#xad;able sta&amp;#xad;ble states has led to the desire to iden&amp;#xad;tify early warn&amp;#xad;ing signs of these impend&amp;#xad;ing col&amp;#xad;lapses.  This search has been moti&amp;#xad;vated by the math&amp;#xad;e&amp;#xad;mat&amp;#xad;ics of bifur&amp;#xad;ca&amp;#xad;tions, in which sud&amp;#xad;den shifts result not from direct per&amp;#xad;tur&amp;#xad;ba&amp;#xad;tions to the state (i.e. the pop&amp;#xad;u&amp;#xad;la&amp;#xad;tion abun&amp;#xad;dance, through mech&amp;#xad;a&amp;#xad;nisms such as over-harvesting)  but to a slowly...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/6857/version/1

_Limusaurus_ and bird digit identity
Provedor de dados: 17
Autores: Alexander O. Vargas; G&amp;#xfc;nter P. Wagner; Jacques A. Gauthier.
_Limusaurus_ is a remarkable herbivorous ceratosaur unique among theropods in having digits II, III and IV, with only a small metacarpal vestige of digit I. This raises interesting questions regarding the controversial identity of avian wing digits. The early tetanuran ancestors of birds had tridactyl hands with digital morphologies corresponding to digits I, II &amp;#x26; III of other dinosaurs. In bird embryos, however, the pattern of cartilage formation indicates that their digits develop from positions that become digits II, III, &amp;#x26; IV in other amniotes. _Limusaurus_ has been argued to provide evidence that the digits of tetanurans, currently considered to be I, II and III, may actually be digits II, III, &amp;#x26; IV, thus explaining the...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3828/version/1

Linking stoichiometric homeostasis with ecosystem structure, functioning, and stability
Provedor de dados: 17
Autores: Qiang Yu; Quansheng Chen; James Elser; Arianne  Cease; Nianpeng He; Honghui Wu; Guangming Zhang; Jianguo Wu; Yongfei Bai; Xingguo Han.
Ecosystem structure, functioning, and stability have been a focus of ecological and environmental sciences during the past two decades.  The mechanisms underlying their relationship, however, are not well understood.  Based on comprehensive studies in Inner Mongolia grassland, here we show that species-level stoichiometric homeostasis was consistently positively correlated with dominance and stability on both 2-year and 27-year temporal scales and across a 1200-km spatial transect.  At the community level, stoichiometric homeostasis was also positively correlated with ecosystem function and stability in most cases.  Thus, homeostatic species tend to have high and stable biomass; and ecosystems dominated by more homeostatic species have higher productivity...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5255/version/1

Lipid models for united-atom molecular dynamics simulations of protein
Provedor de dados: 17
Autores: Andreas Kukol.
Molecular dynamics (MD) simulations of biomolecules are performed at various levels of atomic detail from all-atom models to coarse grained models. United-atom models are at an intermediate level, in which non-polar hydrogen atoms are subsumed into their adjacent carbon-atom reducing the number of particles for a DPPC lipid molecule by 60%. United-atom models of the lipids DPPC, DMPC, POPC and POPG in the GROMOS96 53a6 force field were developed, that reproduced experimental properties of lipid bilayers without assumption of a constant surface area or inclusion of surface pressure. In the absence of experimental data a&amp;#x9;surface&amp;#x9;per lipid area for the negatively charged POPG of 0.700&amp;#xb1;0.007 nm2 was obtained&amp;#x9;that is higher than...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5977/version/1

LipidMaps Core Update
Provedor de dados: 17
Autores: Shankar Subramaniam; Eoin Fahy.
LipidMaps (http://www.lipidmaps.org) is a multidisciplinary project involving multiple institutions. The goal of this project is to identify lipid metabolites and reconstruct pathways associated with lipids in mammalian cells using quantitative measurements of lipids in macrophage cells.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/23/version/1

Literature Triage and Indexing in the Mouse Genome Informatics (MGI) Group
Provedor de dados: 17
Autores: Randal P. Babiuk; Dale A. Begley; Susan M. Bello; Dirck W. Bradt; Donna L. Burkart; Howard Dene; Alexander D. Diehl; Harold J. Drabkin; Jacqueline H. Finger; Terry F. Hayamizu; David P. Hill; Michelle Knowlton; Debra M. Krupke; Ira Lu; Lois J. Maltais; Monica McAndrews-Hill; Terrence F. Meehan; Li Ni; Hiroaki Onda; Dmitry Sitnikov; Constance M. Smith; Cynthia L. Smith; Monika Tomczuk.
The Mouse Genome Informatics (MGI; &amp;#x22;http://www.informatics.jax.org&amp;#x22;:http://www.informatics.jax.org) group is comprised of several collaborating projects including the Mouse Genome Database (MGD) Project, the Gene Expression Database (GXD) Project, the Mouse Tumor Biology (MTB) Database Project, and the Gene Ontology (GO) Project. Literature identification and collection is performed cooperatively amongst the groups.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In recent years many institutional libraries have transitioned from a focus largely on print holdings to one of electronic access to journals. This change has necessitated adaptation on the part of the MGI curatorial group. Whereas the majority of journals covered by the group used to be...
Tipo: Poster
Palavras-chave: Cancer; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3246/version/1

Lithostratigraphy and study of planktonic foraminifera of the Abderaz Formation at type section, Kopet-Dagh basin, IRAN
Provedor de dados: 17
Autores: Meysam Shafiee Ardestani; Mohsen  allameh; Esmail Kohansal.
In order to study the fossil contents of the Abderaz Formation for biostratigraphical purposes the 300 meters thick section was sampled at type section. The sequence is mainly made up of grey shales and marls with two units of chalky limestone in upper part. The lower contact of the formation with Aitamir Formation is disconform while the upper contact with Abtalkh is continuous. There are huge amounts of inoceramids and ammonite. In the chalk limestone bonds of this formation which is belong to Santonian time planktonic, would exist some foraminifera with a less diversity because during the Santonian, the members of morphotype group three (M3) shows a regression in the above-mentioned section, with association of tegilla shapes decreases in the area and...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3944/version/1

Little cost of injury to growth and development of damselflies
Provedor de dados: 17
Autores: Timothy M. Sesterhenn; Philip H. Crowley.
*_Background:_*&amp;#xd;&amp;#xa;Damaged or missing appendages are a common problem in numerous vertebrate and invertebrate taxa and can negatively affect many aspects of life: mobility, foraging, predator avoidance, growth, and development have all been shown to suffer.  Many animals use autotomy to survive a predation attempt but suffer diminished performance until the missing appendage heals or regenerates.  Animals that regenerate face an extra problem, as they must re-allocate resources away from growth and development in order to regrow their missing parts.  We examined the effect of appendage loss on the growth and development of the damselfly Ischnura posita.  Damselfly larvae have three caudal lamellae, external gills that can be autotomized and...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3612/version/1

Living dangerously: an orb-weaving spider potentially exploits an ant-acacia mutualism for enemy-free space
Provedor de dados: 17
Autores: John D. Styrsky.
Exploitation of commodities exchanged in mutualistic interactions has been broadly documented, but typically involve the exploitation of a reward rather than a service.  Further, examples of exploiter species are extremely rare in certain groups of animals, such as spiders.  In 2008 and 2009, we investigated the potential exploitation by an orb-weaving spider (Eustala oblonga) of the plant protection services of ants on an ant-defended acacia (Acacia melanocerus) in lowland rainforest in central Panama.  Despite vigorous patrolling of the acacias by the very pugnacious ants (Pseudomyrmex satanicus), we observed the spiders constructing orb webs among the branches at night and resting quietly during the day on the leaves or at the bases of the thorns in...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5196/version/1

Living unicellular eukaryote Tetrahymena pyriformis as a model for study
Provedor de dados: 17
Autores: Elena Mokhova.
Some animals are able to survive for a long time under conditions of drastically reduced oxidative metabolism, called metabolic depression. The most investigated type of metabolic depression is hibernation. Research into the basic properties of liver mitochondria energetics during hibernation is essential for fundamental biology and medicine. However, the absence of the suitable hepatocyte culture makes it impossible to study the characteristic features of mitochondrial metabolic states in living cells during hibernation. We proposed that under selected conditions, the unicellular eukaryote Tetrahymena pyriformis resembles hepatocytes under hibernation, as (i) both cell types survive under condition of restricted food supply, hypoxia, and accumulation of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4521/version/3

Living unicellular eukaryote Tetrahymena pyriformis as a model for study
Provedor de dados: 17
Autores: Elena N. Mokhova.
Some animals are able to survive for a long time under conditions of drastically reduced oxidative metabolism, called metabolic depression. The most investigated type of metabolic depression is hibernation. Research into the basic properties of liver mitochondria energetics during hibernation is essential for fundamental biology and medicine. However, the absence of a suitable hepatocyte culture makes it impossible to study the characteristic features of mitochondrial metabolic states in living cells during hibernation. We proposed that under selected conditions, the unicellular eukaryote Tetrahymena pyriformis resembles hepatocytes under hibernation, as (i) both cell types survive under condition of restricted food supply, hypoxia, and accumulation of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4521/version/4

Living unicellular eukaryote Tetrahymena pyriformis as a model for study of mitochondrial energetics in mammalian cells under conditions of reduced oxidative metabolism.
Provedor de dados: 17
Autores: Elena Mokhova.
Some &amp;#x201c;animal-like&amp;#x201d; protozoa are used instead of mammalian cells in diverse investigations.  _Tetrahymena pyriformis_ cells in stationary phase of growth and washed from oxidative substrates (_T.pyriformis_) function under conditions of reduced oxidative metabolism. To elucidate if _T.pyriformis_ can be applied as a model for mitochondrial energetics study in   mammalian cells during hibernation, the features of _T.pyriformis_ mitochondria were compared with that of liver mitochondria isolated from hibernating animals; the published earlier data were used. Based on the respiration recording and observation of Mito Tracker Red fluorescence in living _T.pyriformis_ we tentatively concluded that the mitochondrial electrical membrane...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4521/version/2

Living unicellular eukaryote Tetrahymena pyriformis as a model for study of mitochondrial energetics in mammalian cells under conditions of reduced oxidative metabolism.
Provedor de dados: 17
Autores: Elena Mokhova.
Some &amp;#x201c;animal-like&amp;#x201d; protozoa are used instead of mammalian cells in diverse investigations.  _Tetrahymena pyriformis_ cells in stationary phase of growth and washed from oxidative substrates (_T.pyriformis_) function under conditions of reduced oxidative metabolism. To elucidate if _T.pyriformis_ can be applied as a model for mitochondrial energetics study in   mammalian cells during hibernation, the features of _T.pyriformis_ mitochondria were compared with that of liver mitochondria isolated from hibernating animals; the published earlier data were used. Based on the respiration recording and observation of Mito Tracker Red fluorescence in living _T.pyriformis_ we tentatively concluded that the mitochondrial electrical membrane...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4521/version/1

Local and global modes of drug action in biochemical networks
Provedor de dados: 17
Autores: Jean-Marc Schwartz; Jose C. Nacher.
It becomes increasingly accepted that a shift is needed from the traditional target-based approach of drug development to an integrated perspective of drug action in biochemical systems. We here present an integrative analysis of the interactions between drugs and metabolism based on the concept of drug scope. The drug scope represents the set of metabolic compounds and reactions that are potentially affected by a drug. We constructed and analyzed the scopes of all US approved drugs having metabolic targets. Our analysis shows that the distribution of drug scopes is highly uneven, and that drugs can be classified into several categories based on their scopes. Some of them have small scopes corresponding to localized action, while others have large scopes...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2516/version/1

Local environment and valence state of iron in microinclusions in fibrous diamonds: X-ray Absorption and M&amp;#xf6;ssbauer data
Provedor de dados: 17
Autores: Andrei Shiryaev.
Iron valence state and local environment in a set of fibrous diamonds from Brazilian and Zairean placers were investigated using X-ray Absorption and M&amp;#xf6;ssbauer spectroscopies. It is shown that the diamonds could be divided into two main groups, differing in the type of dominant Fe-bearing inclusions. In the first group Fe is mostly trivalent and is present in octahedral coordination; diamonds from the second group contain a mixture of Fe^2+^ and Fe^3+^, most likely with Fe^2+^ in dodecahedral coordination. A few other diamonds contain iron in a more reduced state: the presence of metallic Fe and Fe~3~O~4~ is inferred from XAS measurements. Spatially resolved XANES and M&amp;#xf6;ssbauer measurements on polished diamond plates show that in some...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4452/version/1

Local field potentials, BOLD and spiking activity &amp;#x2013; relationships and physiological mechanisms
Provedor de dados: 17
Autores: Philipp Berens; Nikos K. Logothetis; Andreas S. Tolias.
Extracellular voltage fluctuations (local field potentials, LFPs) reflecting neural mass action are ubiquitous across species and brain regions. Numerous studies have characterized the properties of LFP signals in the cortex to study sensory and motor computations as well as cognitive processes like attention, perception and memory. In addition, its extracranial counterpart &amp;#x2013; the electroencephalogram &amp;#x2013; is widely used in clinical applications. However, the link between LFP signals and the underlying activity of local populations of neurons is still largely elusive. For the LFP to aid our understanding of cortical computation, however, we need to know as precisely as possible what aspects of neural mass action it reflects. In this...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5216/version/1

Local statistics in natural scenes predict the saliency of synthetic textures
Provedor de dados: 17
Autores: Gasper Tkacik; Jason S. Prentice; Jonathan D. Victor; Vijay Balasubramanian.
To represent behaviorally relevant information efficiently, neural circuits in sensory periphery are matched to the first and second-order statistical structure of natural inputs. The retina, for example, removes stimulus components that are predictable (and therefore uninformative), and transmits what is unpredictable (and therefore informative). Here we show that this efficient coding principle applies to complex aspects of natural scenes, and to central visual processing (Tka&amp;#x10d;ik et al, PNAS 2010). &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The aspect of natural scenes that we examine in detail is texture in image patches. Texture is determined partly by the distribution of light intensities and partly by the spatial organization of light across...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6009/version/1

Local winter deer density: Effects of forest structure and snow in a managed forest landscape
Provedor de dados: 17
Autores: James D. A. Millington; Michael B. Walters; Megan S. Matonis; Jianguo Liu.
*Background/Questions/Methods*&amp;#xd;&amp;#xa;White-tailed deer (_Odocoileus virginianus_) are a &amp;#x2018;keystone herbivore&amp;#x2019; with the potential to cause tree regeneration failure and greatly affect vegetation dynamics, stand structure and ecological function of forests across eastern North America. In northern mixed conifer-hardwood forests, local winter-time deer populations are dependent on habitat characterized by patterns of forest cover that provide shelter from snow and cold temperatures (lowland conifer stands) in close proximity to winter food (deciduous hardwood stands). Stand structure may also influence winter spatial deer distribution. Consequently, modification of forest cover patterns and stand structure by timber harvesting...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3666/version/1

Logarithmic laws of echoic memory and auditory change detection in humans
Provedor de dados: 17
Autores: Koji Inui; Tomokazu Urakawa; Koya Yamashiro; Naofumi Otsuru; Yasuyuki Takeshima; Ryusuke Kakigi.
The cortical mechanisms underlying echoic memory and change detection were investigated using an auditory change-related component (N100c) of event-related brain potentials. N100c was elicited by paired sound stimuli, a standard followed by a deviant, while subjects watched a silent movie. The amplitude of N100c elicited by a fixed sound pressure deviance (70 dB vs. 75 dB) was negatively correlated with the logarithm of the interval between the standard sound and deviant sound (1 ~ 1000 ms), while positively correlated with the logarithm of the duration of the standard sound (25 ~ 1000 ms), indicating that the temporal representation of echoic memory is logarithmic. The amplitude of N100c elicited by a deviance in sound pressure, sound frequency and sound...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3652/version/1

Logic motif of combinatorial control in transcriptional networks
Provedor de dados: 17
Autores: Xuebing Wu; Zhirong Sun; Rui Jiang.
Combinatorial control is prevalent in transcriptional regulatory networks. However, whether there are specific logic patterns over- or under-represented in real networks remains uninvestigated. Using a theoretic model and _in-silico_ simulations, we systematically study how the relative abundance of distinct regulatory logic patterns influences the network&amp;#x2019;s global dynamics. We find that global dynamic characteristics are sensitive to several specific logic patterns regardless of the detailed network topology. We show it is possible to infer logic motifs based on the sensitivity profile and the biological interpretations of these global characteristics.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2227/version/1

Logical implications for regulatory relations represented by verbs in biomedical texts
Provedor de dados: 17
Autores: Sine Zambach.
Relations used in biomedical ontologies can be very general or very specific in respect to the domain. However some relations are used widely in for example regulatory networks. This work focuses on positive and negative regulatory relations, in particular their usage expressed as verbs in different biomedical genres and the properties of the relations.
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3560/version/1

Logical Operation Based Literature Association with Genes and its application, PosMed.
Provedor de dados: 17
Autores: Yuko Makita; Rinki Bhatia; Mrinalini Deshpande; Akihiro Matsushima; Manabu Ishii; Yoshiki Mochizuki; Yuko Yoshida; Norio Kobayashi; Testuro Toyoda.
PosMed prioritizes candidate genes for positional cloning by employing our original database search engine GRASE, which uses an inferential process similar to an artificial neural network comprising documental neurons (or &amp;#x27;documentrons&amp;#x27;) that represent each document contained in databases such as MEDLINE and OMIM (Yoshida, _et al_. 2009, Makita, _et al_. 2009). PosMed immediately ranks the candidate genes by connecting phenotypic keywords to the genes through connections representing gene&amp;#x2013;gene interactions other biological relationships, such as metabolite&amp;#x2013;gene, mutant mouse&amp;#x2013;gene, drug&amp;#x2013;gene, disease&amp;#x2013;gene, and protein&amp;#x2013;protein interactions, ortholog data, and...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5071/version/1

LogMap 2.0: towards logic-based, scalable and interactive ontology matching
Provedor de dados: 17
Autores: Ernesto Jimenez-Ruiz; Bernardo Cuenca Grau; Yujiao Zhou.
In this paper we present a much improved version of LogMap, a highly scalable ontology matching system with &amp;#x2018;built-in&amp;#x2019; reasoning and diagnosis capabilities. LogMap 2.0 is not only more scalable and robust than its predecessor, but it also provides the necessary infrastructure for domain experts to interactively contribute to the matching process.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6670/version/1

Long double stranded RNA is present in scrapie infected cells and tissues
Provedor de dados: 17
Autores: Yervand E. Karapetyan.
The nature of the infectious agent causing scrapie and other Transmissible Spongiform Encephalopathies remains an enigma despite decades of research efforts. The protein-only prion hypothesis posits that abnormal conformer of a host protein is the infectious agent. Virus and virino theories include host-independent nucleic acid as the genome of the infectious agent in addition to protein component (in case of virino a host protein and in case of virus a viral protein).  Viral or sub-viral nucleic acids have long been sought in scrapie to explain the existence of multiple agent strains.  Many different approaches were undertaken to find such nucleic acid. Despite that no scrapie specific nucleic acid sequences have been found in infected cells or tissues....
Tipo: Manuscript
Palavras-chave: Microbiology; Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/6759/version/1

Long term trend of chemical oxygen demand in Saroma-ko Lagoon, Japan; possible effects of climatic warming
Provedor de dados: 17
Autores: Akihiro Shiomoto.
A trend of shortening duration of ice coverage has been reported in many rivers, ponds and lakes around the world due to climatic warming. The shortening will have much influence on organic production due to the greater supply of light intensity and hence on water quality. Chemical Oxygen Demand (COD), a useful measure of water quality, has been monitored over the past thirty years in Saroma-ko Lagoon, a boreal lake in Japan characterized by wintertime ice coverage. Here the data set of water quality in the lagoon is analyzed to reveal long-term trends in COD and the influence of climatic warming on such trends. There has been a significant increasing trend, caused primarily by an abrupt increase in the early 1990s. However, the increase could not be...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1857/version/1

Longitudinal Metagenomic Analysis of the Water and Soil from Gulf of Mexico Beaches Affected by the Deep Water Horizon Oil Spill
Provedor de dados: 17
Autores: William  R. Widger; Georgiy Golovko; Antonio F. Martinez; Efren V. Ballesteros; Jesse J. Howard; Zhenkang Xu; Utpal Pandya; Viacheslav Y. Fofanov; Mark Rojas; Christopher Bradburne; Ted Hadfield; Nels A. Olson; Joshua L. Santarpia; Yuriy Fofanov.
Estimates of 7x105 cubic meters of crude oil were released into the Gulf of Mexico as a consequence of the April 20th, 2010 Deep Water Horizon drilling rig explosion, leaving thousands of square miles of earth&amp;#x27;s surface covered in crude oil. Dispersants were used on large slicks and injected at the well head, resulting in oil being suspended throughout the water column. Starting in June 2010, oil reached hundreds of miles of Louisiana, Alabama, Mississippi, and Florida shoreline disturbing the ecological balance and economic stability of the region. While visible damages are evident in the wildlife populations and marine estuaries, the most significant affect may be on the most basic level of the ecosystems: the bacterial and plankton...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5733/version/1

Long-Lasting Context Dependence Constrains Neural Encoding Models in Rodent Auditory Cortex
Provedor de dados: 17
Autores: Hiroki Asari; Anthony M. Zador.
Acoustic processing requires integration over time.  However classical linear encoding models, which typically integrate over a few hundred milliseconds, have failed to account fully for neural responses in the auditory cortex.  We have used in vivo intracellular recording to measure neuronal integration times in anesthetized rats.  Probing with natural sounds and other stimuli, we found that context-dependent effects in the primary auditory cortex could last for surprisingly long, up to four seconds or longer in some neurons.  Thalamic neurons showed only a much faster form of adaptation, indicating that the long-lasting form originated in the cortex.  Restricting knowledge of the stimulus history to only a few hundred milliseconds reduced the predictable...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2282/version/1

Long-term Benefits of GM crops: Potential for Diabrotica Suppression in Europe using Bt Maize
Provedor de dados: 17
Autores: Nicholas P. Storer; Peter Schlotter; Kevin L. Steffey.
Transgenic crops producing insecticidal proteins from _Bacillus thuringiensis_ (Bt) have been widely adopted since 1996 in the United States of America to combat important pests of maize and cotton. There is growing evidence that several target pest populations have been dramatically reduced in areas where the Bt crops have been most intensively adopted over multiple years. The evidence is most dramatic for nonmigratory monophagous and oligophagous species that show high mortality on Bt crops, such as European corn borer (_Ostrinia nubilalis_), and tobacco budworm (_Heliothis virescens_). Bt cotton is currently being used in the southwestern USA as part of an area-wide eradication program for pink bollworm (_Pectinophora gossypiella_). Single, stacked, and...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4447/version/1

Long-term impacts of tropical storms and earthquakes on human population growth in Haiti and Dominican Republic
Provedor de dados: 17
Autores: Christian D. Klose; Christian Webersik.
The two Caribbean states, Haiti and the Dominican Republic, have experienced similar natural forces since the 18th century, including hurricanes and earthquakes. Although, both countries seem to be two of the most prone of all Latin American and Caribbean countries to natural hazard events, historically, Haiti tends to be more vulnerable to natural forces. The purpose of this article is to understand to what extent geohazards shape demographic changes. Research findings of this study show that neither atmospheric nor seismic hazards that directly hit the territory of Haiti have significant impacts on population densities and growth rates. Quantitative evidence is provided, that between 1850 to 2009 urbanization processes have exposed more people to natural...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4737/version/1

Long-term impacts of tropical storms and earthquakes on human population growth in Haiti and the Dominican Republic
Provedor de dados: 17
Autores: Christian D. Klose; Christian Webersik.
Since the 18th century, Haiti and the Dominican Republic have experienced similar natural forces, including earthquakes and tropical storms. These countries are two of the most prone of all Latin American and Caribbean countries to natural hazards events, while Haiti seems to be more vulnerable to natural forces. This article discusses to what extent geohazards have shaped both nation&amp;#x27;s demographic developments. The data show that neither atmospheric nor seismic forces that directly hit the territory of Haiti have significantly affected the country&amp;#x27;s population growth rates and spatial population densities. Conversely, since the 1950s more people were exposed to atmospheric hazards, in particular, in regions which historically experienced...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5981/version/1

Looking at the Beginnings: Enquiries about Emergence of Cognition in Evolution
Provedor de dados: 17
Autores: Walter Riofrio.
Trying to understand when and how the cognitive phenomena arise in evolution continues being a hard problem of confronting. &amp;#xd;&amp;#xa;One important task is to find the ways in which we will be able to arrive at those explanations that will enable us to understand how living beings put together perceived sensory information as well as how they represent it. &amp;#xd;&amp;#xa;In this presentation, we address some conceptual questions involved in the relationships between sensorial information perceived by brains and its representational capacities. &amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Ecology; Molecular Cell Biology; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/413/version/1

Lost in information. On the processing of irrelevant signals in normal ageing
Provedor de dados: 17
Autores: Edmund Wascher; Nele Wild-Wall; Michael Falkenstein.
Healthy older adults often have problems to ignore irrelevant information. A lack of executive control upon irrelevant signals might be a core deficit affecting also higher level cognitive functions such as working memory. Here we show the origin of that deficit in a cuing task and demonstrate that older adults are not only unable to ignore irrelevant stimuli, but process them like relevant ones. Ample processing time can help to overcome this deficit.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2489/version/1

Lost in translation: Toward a formal model of multilevel, multiscale medicine
Provedor de dados: 17
Autores: Rodrick Wallace.
For a broad spectrum of low level cognitive regulatory and other biological phenomena, isolation from signal crosstalk between them requires more metabolic free energy than permitting correlation. This allows an evolutionary exaptation leading to dynamic global broadcasts of interacting physiological processes at multiple scales. The argument is similar to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological subsystems. Not only is the living state characterized by cognition at every scale and level of organization, but by multiple, shifting, tunable, cooperative larger scale broadcasts that link selected subsets of functional modules to address problems. This multilevel dynamical viewpoint has implications...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Immunology; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6973/version/1

Low Cardiorespiratory Fitness is an Independent Predictor of Metabolic Syndrome in Young Korean Adults
Provedor de dados: 17
Autores: Hyun-Sik Kang; Soo-Hyun Park; Shinuk Kim.
Objective: To investigate the relationship between cardio/respiratory fitness (CRF) and metabolic syndrome (MS) in young Korean men. Design: In a cross-sectional study, we examined 909 young Korean men (mean&amp;#xb1;SD age, 24.0&amp;#xb1;2 years) who were healthy and not taking any medications affecting blood pressure, glucose, or lipids concentrations. Body fatness, resting blood pressures, and fasting blood levels of lipids, glucose, and insulin were measured with our standardized laboratory protocols. CRF was quantified as the maximum volume of minute oxygen consumption measured during a graded treadmill test. Metabolic syndrome was defined with the National Cholesterol Education Program Adult Treatment Panel III criteria and a modified cut-off value...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2236/version/1

Low dose IR-induced IGF-1-sCLU expression: a p53-repressed expression cascade that interferes with TGF&amp;#xdf;1 signaling to confer survival
Provedor de dados: 17
Autores: Dmitry Klokov; Konstantin Leskov; Shinako Araki; Yonglong Zou; Eva Goetz; Xiuquan Luo; David Willson; David Boothman.
To better understand tissue responses after low IR doses, we generated a reporter system using human clusterin promoter fused to firefly luciferase (hCLUp-Luc). Secretory clusterin (sCLU), an extra-cellular molecular chaperone, induced by low doses of cytotoxic agents, clears cell debris promoting survival. Low dose IR (&amp;#x3e;2 cGy) exposure induced hCLUp-Luc activity with peak levels at 96 h, consistent with endogenous sCLU levels. As doses increased (&amp;#x3e;1 Gy), sCLU induction amplitudes increased and time to peak response decreased. sCLU expression was stimulated by IGF-1, but suppressed by p53. Responses in transgenic hCLUp-Luc reporter mice after low IR doses showed that specific tissues (i.e., colon, spleen, mammary, thymus, bone marrow) of...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2011
URL: http://precedings.nature.com/documents/6451/version/1

Low Protein Diet Consumption Antagonize the Age-associated Change in Hypothalamic GABA Receptor activity
Provedor de dados: 17
Autores: Bidhan C. Bandyopadhyay; Lina Chakrabarti; Mrinal K. Poddar.
Amounts of dietary protein as well as the duration of its supplementation are critical&amp;#xd;&amp;#xa;factors that correlate with the hypothalamic GABAergic activity and immune function&amp;#xd;&amp;#xa;during aging. Here we evaluate the effect of low (5%) and high (40%) protein diet on the&amp;#xd;&amp;#xa;functional state of hypothalamic GABA receptor in the aging brain in albino rats. Longterm&amp;#xd;&amp;#xa;(LT; for 30 consecutive days) supplementation of low protein diet (LDP) retarded&amp;#xd;&amp;#xa;the age-associated (3 to 18 months) (a) loss of both low and high affinity hypothalamic&amp;#xd;&amp;#xa;GABA receptor sensitivity and (b) increase of high affinity GABA receptor density.&amp;#xd;&amp;#xa;Short-term (ST; for 7 consecutive days)...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2284/version/1

Lyme Borreliosis During Pregnancy
Provedor de dados: 17
Autores: Andr&amp;#xe1;s Lakos; Norbert Solymosi.
One of the authors (AL) presented a poster on 34 pregnancies of maternal Lyme borreliosis (Lb) in 1995. It was striking that untreated Lb associated with higher probability of adverse outcome but the number of patients were small and the statistical power was low. We have recently published a paper on 95 maternal Lb and the outcome of their pregnancies. Since the closure of the database for that manuscript the number of the pregnant women with Borrelia infection observed in our Centre increased to 124, and the statistical analysis strengthened our previous doubtful observations and reached significant results in important aspects by now. This series is the largest study to date on this topic. Treatment was administered parenterally to 87 (70%) women and...
Tipo: Poster
Palavras-chave: Microbiology.
Ano: 2012
URL: http://precedings.nature.com/documents/7027/version/1

_M. tuberculosis_ interactome analysis unravels potential pathways to drug resistance
Provedor de dados: 17
Autores: Karthik Raman; Nagasuma Chandra.
Drug resistance is a major problem for combating tuberculosis. Lack of understanding of how resistance emerges in bacteria upon drug treatment limits our ability to counter resistance. By analysis of the _Mycobacterium tuberculosis_ interactome network, along with drug-induced expression data from literature, we show possible pathways for the emergence of drug resistance. To a curated set of resistance related proteins, we have identified sets of high propensity paths from different drug targets. Many top paths were upregulated upon exposure to anti-tubercular drugs. Different targets appear to have different propensities for the four resistance mechanisms. Knowledge of important proteins in such pathways enables identification of appropriate...
Tipo: Manuscript
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1674/version/1

Magnetic Resonance imaging (MRI) in detection of _Bifidobacterium longum_ and _Clostridium novyi-NT_ labeled with superparamagnetic iron oxide (SPIO) nanoparticle
Provedor de dados: 17
Autores: Jianhua Wang; Xuebin Zhang; Dayong Zhou; Qingguo Wang; Dan Li.
*Purpose:* To investigate the MR imaging of _Bifidobacterium longum_ and _Clostridium novyi-NT_ labeling with superparamagnetic iron oxide (SPIO) nanoparticles.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Materials and methods:* Tubes containing _B. longum_-SPIO, Free-SPIO, _B. longum_ and PYG Medium were incubated under anaerobic condition in _in vitro_ experiment. Transmission electron microscope and Prussian blue staining were used to demonstrate intra-bacteria nanoparticles. R~2~^*^ mapping and R~2~ mapping were reconstructed after MR scanning. _B. longum_-SPIO and _C. novyi_-NT-SPIO were injected respectively _in vivo_ to show whether it might be traced by MR imaging.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Results:* Magnetosomes in bacteria were observed by...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/3435/version/1

Magnetoencephalography May Allow the Electromagnetic &amp;#x27;Biopsy&amp;#x27; of Central Nervous System Neoplastic Tissue
Provedor de dados: 17
Autores: Michael Pearlman; Eduardo Castillo; Andrew Papanicolaou; Ian Butler; John Slopis; Richard Frye.
Developing a non-invasive method for definitively diagnosing intracranial neoplasms would reduce the risks involved with diagnosis and improve the treatment of such tumors. We used magnetoencephalography to measure the power spectral densities of malignant brain tumor cells in vitro and found that meningioma and medulloblastoma cells produce unique electromagnetic signatures. Our results suggest that non-invasive identification of neoplastic tissue is possible through the use of magnetoencephalography.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3973/version/1

Maize gene review - A new on-line journal promotes community curation of phenotypes
Provedor de dados: 17
Autores: Mary L. Schaeffer.
The first formal phenotype summaries for maize can be found in early editions of the&amp;#xd;&amp;#xa;Maize Genetics Cooperation Newsletter (MNL). Prior to on-line databases, the MNL&amp;#xd;&amp;#xa;served to systematize available mutant stocks, genetic maps, and addresses for maize&amp;#xd;&amp;#xa;geneticists. In fact, the first phenotypic data entered into MaizeGDB, in 1991, was from&amp;#xd;&amp;#xa;the MNL stock center report. To support renewed, community submission of similar&amp;#xd;&amp;#xa;data, the MNL has initiated a new on-line journal, called the &amp;#x2018;maize gene review&amp;#x2019; (MGR,&amp;#xd;&amp;#xa;www.maizegenereview.org). It represents an extension of the Mutants of Maize (1997),&amp;#xd;&amp;#xa;eds MG Neuffer, EH Coe, SR...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3221/version/1

MaizeGDB , maize genetics cooperation and the ~2500MB B73 genome generated tsunami
Provedor de dados: 17
Autores: Mary Schaeffer; Jack Gardiner; Elisabeth Harper; Carson Andorf; Darwin Campbell; Ethalinda Cannon; Taner Z. Sen; Carolyn Lawrence.
Advances in sequencing technology have made it possible to sequence the 2500 MB B73 maize genome, both cheaply and in a relatively short time. Nearly simultaneously, other sequencing-based data are on the leading edge of a data tsunami: sequenced differences (currently &amp;#x3e;300,000 SNP for  &amp;#x3e;1000 inbred lines and related species) and gene expression data.  The MaizeGDB team integrates access to these datasets after considerable cooperation among both data users and suppliers, and typically while the data are being generated. In this way, data suppliers have resources in place to format data ready for integration with MaizeGDB.  And, we learn what details, including links to other resources, are needed to support our user community and what...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5258/version/1

Malaria Diagnosis and the Plasmodium Life Cycle: the BFO Perspective
Provedor de dados: 17
Autores: Werner Ceusters; Barry Smith.
Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed clarifications will be derived from a careful representation of the entities on the side of the patient which form the ultimate truthmakers for clinical statements. We address a challenge to this realist approach relating to the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3960/version/1

Malaria Diagnosis and the Plasmodium Life Cycle: the BFO Perspective
Provedor de dados: 17
Autores: Werner Ceusters; Barry Smith.
Definitive diagnosis of malaria requires the demonstration through laboratory tests of the presence within the patient of malaria parasites or their components. Since malaria parasites can be present even in the absence of malaria manifestations, and since symptoms of malaria can be manifested even in the absence of malaria parasites, malaria diagnosis raises important issues for the adequate understanding of disease, etiology and diagnosis. One approach to the resolution of these issues adopts a realist view, according to which the needed clarifications will be derived from a careful representation of the entities on the side of the patient which form the ultimate truthmakers for clinical statements. We here address a challenge to this realist approach...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/3960/version/2

Mammalian cells in culture actively export specific microRNAs
Provedor de dados: 17
Autores: Kai Wang; Shile Zhang; Jessica Weber; David Baxter; David J. Galas.
The discovery of microRNAs (miRNAs) as a new class of regulators of gene expression has triggered an explosion of research, but has left many unanswered questions about how this regulation works and how it is integrated with other regulatory mechanisms. A number of miRNAs have been found to be present in blood plasma and other body fluids of humans and mice in surprisingly high concentrations. This observation was unexpected in two respects: first, the fact that these molecules are present at all outside the cell at significant concentrations; and second, that these molecules appear to be stable outside of the cell. In light of this it has been suggested that the biological function of miRNAs may also extend outside of the cell and mediate cell-cell...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3718/version/1

Management and provision of computational models
Provedor de dados: 17
Autores: Camille Laibe.
Quantitative models of biological systems provide an understanding of chemical and biological phenomena based on their underlying mechanisms. Moreover, they can be used for example, to predict the behaviour of a system under given conditions or direct future experiments. This has made quantitative models the perfect tools to answer a variety of questions in the biological sciences and has lead to a steady growth of the number of published models.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To maximise the benefits of this growing body of models, the field needs centralised model repositories that will encourage, facilitate and promote model dissemination and reuse. BioModels Database(http://www.ebi.ac.uk/biomodels/) has been developed to exactly fulfil those needs....
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7013/version/1

Managing Bio-Models: &amp;#xb;Model Storage, Retrieval, Ranking and Versioning
Provedor de dados: 17
Autores: Ron Henkel; Dagmar Waltemath; Olaf Wolkenhauer.
In this poster, we present our experience with techniques for the management of bio-models (i.e. XML-encoded computational models of biological systems) in repositories. These techniques support users to find, access, adapt and then re-submit models - tasks which are essential for the reuse of models in systems biology. Here, we focus on model retrieval, the ranking of search results and concepts to track the history of a model through version control. These concepts have so far not been sufficiently  addressed in existing systems.&amp;#xd;&amp;#xa;To validate our techniques, we have been implemented a framework called Sombi. The underlying database called mDB is tailored towards a fine-grained storage of the model and its annotations. The design is...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6325/version/1

Managing Multiple Parameter Sets in SBML
Provedor de dados: 17
Autores: Frank Bergmann.
This document describes the elements of a SBML annotation, for storing multiple parameter sets in an SBML model. A user might wish to store different parameter sets that exhibit interesting behavior of computational models. One common example would be to store parameter values for steady states, or even oscillating regimes.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4233/version/1

Manual annotation of the mouse genome: HAVANA and EUCOMM
Provedor de dados: 17
Autores: Mark Thomas.
The European Conditional Mouse Mutagenesis (EUCOMM) project aims to establish a mutant resource containing up to 13,000 conditional mouse mutations in C57BL/6N embryonic stem cells. As part of this resource, up to 8,000 targeted conditional mutations will be generated for genes that can not be readily trapped by random gene trapping methods. Non-symmetrical critical exons are identified as part of the targeting approach, which when deleted produce a knockout (KO) transcript that is susceptible to nonsensemediated decay (NMD). The success of this approach is dependent on detailed and accurate genome annotation, which is provided by the Human and Vertebrate Analysis and Annotation (HAVANA) group at the Wellcome Trust Sanger Institute. Based on a combination...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3181/version/1

Manual Curation of Vertebrate Proteins  in the UniProt Knowledgebase.
Provedor de dados: 17
Autores: Michael  J. Gardner; Lionel  Breuza; The UniProt  Consortium.
The UniProt Knowledgebase (UniProtKB) aims to provide the scientific community with a comprehensive, consistent and authoritative resource for protein sequence and functional information. Given the importance of human and vertebrate model data in biomedical research, a major focus is the high-quality manual curation of human proteins and their vertebrate orthologues. Manual curation involves (1) the extraction of experimental results from scientific literature to enrich protein records with a wide range of information including function, structure, interactions and subcellular location, (2) the manual verification of each sequence and clarification of discrepancies between sequence reports, and (3) the assessment of the output of a range of analysis...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5165/version/1

Many in vivo  &amp;#x27;protein folding codes&amp;#x27; can be inferred from empirical classifications using Tlusty&amp;#x27;s topological approach
Provedor de dados: 17
Autores: Rodrick Wallace.
Tlusty&amp;#x27;s topological rate distortion approach to the genetic code is applied to the problem of protein symmetries and to the analysis of protein folding rates. Unlike the genetic case, numerous &amp;#x27;protein folding codes&amp;#x27; can be identified from empirical classifications. Protein folding rates follow from a topologically-driven rate distortion argument. These results imply markedly different evolutionary trajectories for the genetic and protein folding codes, and suggest that the &amp;#x27;protein folding code&amp;#x27; is, in fact, a complicated composite, distributed across protein production and a cellular, or higher, regulatory apparatus acting as a canalizing catalyst that drives the system to converge on particular transitive...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4665/version/2

MAP7D2 is a brain expressing X-linked maternal imprinted gene in humans
Provedor de dados: 17
Autores: Yo Niida; Akihiro Yachie.
Increasing evidence suggests imprinted genes influence mouse and human behaviors and cognitive functions. Unlike autosomal imprinted genes, X-linked imprinted genes are expressed in a sex-dependent manner because of male hemizygosity. Therefore, these genes could directly affect sex-specific brain functions and sex-biased vulnerability to psychiatric disorders such as autism1. Comparing lymphoblastoid cell lines (LCL) and peripheral blood mononuclear cells (PBMC) from healthy adult male and females, we identified MAP7 domain containing 2 (MAP7D2) as the first human X-linked imprinted gene. Both in LCL and PBMC, MAP7D2 expression was significantly suppressed in males by maternal imprinting. In each female LCL clone, MAP7D2 was expressed higher in paternally...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6684/version/1

Mapping from Statistical to Biological Proximity
Provedor de dados: 17
Autores: Malay Bhattacharyya.
We verify whether the proximity claimed by state-of-the-art statistical similarity measures are indeed biologically appropriate or not. We present some analytical results on it.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7122/version/1

Margarine products quality monitoring using reflectance UV-VIS-SWNIR spectroscopy
Provedor de dados: 17
Autores: Rui C. Martins; Vitor V. Lopes; Ant&amp;#xf3;nio A. Vicente.
Margarine is a term that can indicate any of a wide range of butter substitutes. Due to the great diversity of the raw material, margarine end-product quality characteristics are expected to be highly diversified. This article proposes the use of reflectance UV-VIS-SWNIR spectroscopy to monitor the margarine end-product quality properties. The main effort in this work was the development of a fast monitoring procedure to assess the quality of the manufactured margarines. &amp;#xd;&amp;#xa;The study was performed on two margarine products: regular margarine (less than 80% fat) and reduced-fat margarine (less than 60% fat). The nine product samples were collected during the production line normal operating conditions on different days. The samples had the...
Tipo: Poster
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2293/version/1

Marked Rise in Replikin Counts in H5N1 Influenza Virus Localized to Lethality Gene p B1.
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
Abstract: Virus outbreaks have been found to be related to the concentration of a new class of genomic peptides, Replikins^1^. The eight genes of H5N1 influenza virus were analyzed for the distribution of Replikin Counts (number Replikins /100 amino acids) in 2,441 sequences from birds and humans. An increase (p&amp;#x3c;0.001) occurred from 2004 to August 2011 in one gene, pB1.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Immunology; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6420/version/1

Markedly enhanced intratumoral spread and antitumor effect of oncolytic adenovirus expressing decorin
Provedor de dados: 17
Autores: Chae-Ok Yun; Joo-Hang Kim; Il-Kyu Choi; Young-Sook Lee; Ji Young Yoo; A-Rum Yoon; Hoguen Kim; Daniela G. Seidler.
With the aim of improving viral distribution and tumor penetration, we have engineered decorin expressing replication-incompetent (dl-LacZ-DCNG) and -competent (Ad-[DELTA]E1B-DCNG) adenoviruses. In both tumor spheroids and established solid tumors in vivo, administration of dl-LacZ-DCNG resulted in greater transduction efficiency and viral spread throughout the tumor mass. Ad-[DELTA]E1B-DCNG also enhanced viral distribution and tumor spread, leading to an increased anti-tumor effect and survival advantage. Upon histological analysis, Ad-[DELTA]E1B-DCNG also elicited greater percentage of apoptotic cells and extensive necrosis compared to those from untreated or control virus-treated tumors. Furthermore, Ad-[DELTA]E1B-DCNG substantially decreased...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/1485/version/1

Marker Paper: The Urethral Microbiome of Adolescent Males
Provedor de dados: 17
Autores: J. Dennis Fortenberry; David E. Nelson; Qunfeng Dong.
Project ID: 46317 &amp;#x2013; No publication moratorium.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The microflora of the anterior male urethra during adolescence is poorly described and no data address the range of &amp;#x201c;typical&amp;#x201d; urethral organisms during adolescence as functions of pubertal development or onset of various types of partnered sexual activity. This means that current understanding of the urethral microbiome in adolescent men rests entirely on limited data inferred from adults, and from epidemiologic and behavioral explanations. Marked ethnic group variation in adolescent sexual behaviors and disparity in conditions such as sexually transmitted infections (STI) justifies exploration of potential ethnic group differences in the...
Tipo: Marker Paper / Data Plan
Palavras-chave: Microbiology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5221/version/1

Mass Cultivation of _Chroococcus turgidus_ and _Oscillatoria sp._ and Effective Harvesting of Biomass by Low-cost methods
Provedor de dados: 17
Autores: Mohan N; Hanumantha Rao P; Ranjith Kumar R; Sivasubramanian V.
The potential of microalgal biomasses for the production of biochemicals such as pigments, vitamins, antibiotics, polysaccharides, proteins, essential fatty acids, bio-flocculants, enzymes, etc. is well known. The purpose of this study was to cultivate two cyanobacterial species namely _Chroococcus turgidus_ and _Oscillatoria sp._, isolated from industrial effluents, using a suitable growth medium in a large-scale High Rate Algal (HRA) pond. The biomolecules such as total protein, total carbohydrate and total lipid, and the pigments chlorophyll, phycobilins, &amp;#x3b2;-carotene, were analysed at regular intervals during cultivation. In addition, the total bacterial cell numbers were enumerated during the study and their influence on algal growth was...
Tipo: Manuscript
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4331/version/1

Mathematical Modeling of the Neuronal Processes in Sugar Addiction
Provedor de dados: 17
Autores: Andre Almeida; Hamed  Celaymanian; Natalie Seel; Boris Zak; Hamid R. Noori.
It has already been demonstrated that the body responds to enhanced intake of sugar and is conducive to a natural form of addiction. There are substantial neurochemical changes in the brain (especially dopamine and acetylcholine systems) similar to other addictive drugs. A mathematical model comprised by a system of delayed leaky integrate-and-&amp;#xc;re equations is established to simulate the eff&amp;#xb;ects of sugar on a reward-circuitry. Simulations with Neuron suggest agreement with the neurobiological hypotheses of hyperactivity of neural systems due to binge sugar intake.
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5546/version/2

Mathematical Modeling of the Neuronal Processes in Sugar Addiction
Provedor de dados: 17
Autores: Andre Almeida; Hamed  Celaymanian; Natalie Seel; Boris Zak; Hamid R. Noori.
It has already been demonstrated that the body responds to enhanced intake of sugar and is conducive to a natural form of addiction. There are substantial neurochemical changes in the brain (especially dopamine and acetylcholine&amp;#xd;&amp;#xa;systems) similar to other addictive drugs. A mathematical model comprised by a system of delayed leaky integrate-and-&amp;#xc;re equations is established to simulate the eff&amp;#xb;ects of sugar on a reward-circuitry. Simulations with Neuron suggest agreement with the neurobiological hypotheses of hyperactivity of neural systems due to binge sugar intake.
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5546/version/1

Maximization of learning speed in motor cortex due to neuron redundancy
Provedor de dados: 17
Autores: Ken Takiyama; Masato Okada.
Many kinds of redundancies play important roles in the motor system. Many combinations of muscle activity can generate an identical movement. One of the functional and computational roles of this muscle redundancy is to control joint impedance for stabilizing movements against applied external perturbation. Many combinations of joint angles can yield an identical fingertip position. A functional and computational role of this kinematic redundancy is to ensure motor accuracy, if a joint angle is perturbed, by adjusting redundant ones. Neurons are overwhelmingly more numerous than muscles in our motor system. However, an open question remains as to what the functional and computational roles of this neuron redundancy are. To generate desired motor commands,...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5867/version/1

Maximizing decision rate in multisensory integration
Provedor de dados: 17
Autores: Jan Drugowitsch; Alexandre Pouget; Gregory C. DeAngelis; Dora E. Angelaki.
Effective decision-making in an uncertain world requires making use of all available information, even if distributed across different sensory modalities, as well as trading off the speed of a decision with its accuracy. In tasks with a fixed stimulus presentation time, animal and human subjects have previously been shown to combine information from several modalities in a statistically optimal manner. Furthermore, for easily discriminable stimuli and under the assumption that reaction times result from a race-to-threshold mechanism, multimodal reaction times are typically faster than predicted from unimodal conditions when assuming independent (parallel) races for each modality. However, due to a lack of adequate ideal observer models, it has remained...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5822/version/1

Measurement &amp;#x26; Prediction of Phase Behaviour of Carbon Dioxide Mixtures
Provedor de dados: 17
Autores: Esther Forte; Amparo Galindo; Livio  G. Ruffine; J.P. Martin Trusler.
Acquiring a comprehensive understanding of the behaviour of carbon dioxide under reservoir conditions is essential for optimizing its usage in enhanced oil recovery (EOR) and for developing sequestration schemes. In order to obtain this understanding, it is necessary to study the physical properties and phase behaviour of mixtures of carbon dioxide with hydrocarbons and brines under conditions of high pressure. In this work we are addressing both the experimental and the theoretical aspects of this problem. A new apparatus, based on the static-analytical method, has been developed to measure phase equilibrium. The equipment comprises a high-pressure cell with sapphire windows for visual observation and phase sampling, with on-line gas chromatography...
Tipo: Poster
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2649/version/1

Measuring impact in online resources with the CI&amp;#xad;number (the CitedIn Number for online impact)
Provedor de dados: 17
Autores: Andra Waagmeester; Chris Evelo.
CitedIn is a webservice that can be found at www.citedin.org. It tracks online citations in databases, blogs, wikis, and community sites to the literature covered in Pubmed. For biomedical scientific literature Pubmed is by far the most interesting resource. Pubmed is the interface to the Medline repository which covers over 1 century of publications and contains almost all relevant publications in the field. Pubmed uses very simple unique numeric identifiers. This makes it easy to cite publications using these Pubmed Identifiers (PMIDs) or to link to Pubmed itself based on those. This ease of use results in PMIDs often being used for online citations, this is often the standard in biomedical databases and for instance in Wikipedia. CitedIn uses a federate...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6037/version/1

Mechanism and circuitry underlying retinal sensitization
Provedor de dados: 17
Autores: David B. Kastner; Yusuf Ozuysal; Stephen A. Baccus.
Recently we have described a population of retinal ganglion cells that increase their sensitivity after the presentation of a high contrast stimulus. This process, termed contrast sensitization is a form of short-term information storage that enables ganglion cells to store the location of a previously moving object for several seconds. Effectively, sensitizing ganglion cells make a prediction that the location of a strong stimulus at one point in time will continue to be important in the near future, even after the strong stimulus ceases. To understand how the retina can paradoxically increase its sensitivity in the face of a strong stimulus, we recorded intracellularly from sensitizing ganglion cells, and found that a depolarization of the baseline...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5881/version/1

Mechanisms linking plant diversity to large herbivore performance
Provedor de dados: 17
Autores: Ling Wang; Deli Wang; Zhengbiao He; Guofang Liu; Ken Hodgkinson.
There is established concern that loss of biodiversity will affect ecosystem productivity, nutrient cycling, carbon storage, stability and other properties^1,2^. Interactions between trophic levels are thought to link changes to biodiversity and ecosystem processes^3-6^. However, there is a lack of empirical studies linking plant diversity with altered trophic levels^7,8^, especially for large herbivores, the important but often neglected, controlling trophic level in terrestrial systems. Here we examine responses in performance of the large generalist herbivore to changes in plant diversity, using an indoor cafeteria trial and a field experiment. Our results show that increased plant diversity improves herbivore performance but it is depressed at highest...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2058/version/1

Mechanisms of cadmium toxicity and tolerance in Populus
Provedor de dados: 17
Autores: Brahma Reddy Induri; Stephen DiFazio; Danielle  Ellis; Gancho  Slavov; Tong-Ming Yin; Gerald  Tuskan.
Abstract ID#: 26642&amp;#xd;&amp;#xa;Background and Methods:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Cadmium (Cd), ranked the 7th most hazardous substance, is one of the most widespread pollutants of soil and water in industrialized nations. Its increased movement in soil-plant systems is posing a serious threat to human health. Cd, without any known functions in plants, was found to be toxic even at minute concentrations, leading to the development of symptoms such as leaf roll, chlorosis and root and shoot growth reduction. Phytoremediation is an emerging cost-effective and environment friendly technology that utilizes high biomass producing plants including Populus plants to remove, transform or stabilize contaminants in soils. The objectives of our study...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5410/version/1

Mechanisms Of Inhibition Of Cigarette Smoke Genotoxicity And Carcinogenicity
Provedor de dados: 17
Autores: Roumen Balansky; Francesco D&amp;#x27;Agostini; Alberto  Izzotti; P Kalpakam; Vernon E. Steele; Silvio De Flora.
Epidemiological studies have demonstrated that it is possible to prevent lung cancer and other smoke-related diseases by avoiding exposures to tobacco smoke. A complementary strategy is chemoprevention, which is based on the administration of dietary and pharmacological agents, which is addressed to (a) addicted active smokers, who are unable to quit smoking, (b) ex-smokers, who are still at risk for several years, and (c) involuntary smokers, including passively exposed individuals as well as transplacentally exposed individuals. The biological effects of cigarette smoke (CS) as a complex mixture, either mainstream (MCS) or sidestream (SCS) or environmental (ECS), have been poorly explored. We showed that MCS and ECS induce a broad variety of alterations...
Tipo: Presentation
Palavras-chave: Cancer.
Ano: 2010
URL: http://precedings.nature.com/documents/5328/version/1

Mechanisms to overcome ecosystem nitrogen and phosphorus limitation
Provedor de dados: 17
Autores: Rebecca Ostertag.
Nutrients limit plant growth in many ecosystems, and many species develop adaptations to either obtain more nutrients or to avoid losses. Much past ecological work has focused either on temperate nitrogen-limited systems or has addressed infertile soils as a single entity, rather than addressing the nature of the limitation. Although low nitrogen (N) and phosphorus (P) soils are found worldwide, the consequences of N and P limitation for plants may vary due to fundamental differences in the soil mobility, availability, uptake, and cellular uses of N and P. Using a well-studied chronosequence in the Hawaiian Islands, which contains both low N and P soils but which is dominated by similar plant communities, foliar N and P plant responses to fertilization...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1993/version/1

Mechanistic Approaches To The Prevention Of Mutation And Cancer
Provedor de dados: 17
Autores: Silvio S. De Flora.
Cancer and other mutation-related diseases can be prevented at three levels: primary prevention, which is addressed to healthy individuals in order to prevent occurrence of the disease; secondary prevention, which is addressed to early stage patients in order to prevent progression of the disease; and tertiary prevention, which is addressed to patients after therapy in order to prevent relapses of the disease. Although the most obvious approach to prevention is to minimize exposures to recognized risk factors, a complementary strategy is represented by chemoprevention, using dietary and pharmacological agents that reinforce the host defence machinery. Since 1988, I proposed detailed classifications of mechanisms of inhibitors of mutagenesis and...
Tipo: Presentation
Palavras-chave: Cancer; Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5317/version/1

Mechanistic mechanisms of competition and biodiversity
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The nature of competition and biodiversity are open basic questions since Darwin. To investigate mechanisms of interspecific competition and their contribution in biodiversity as closely as possible we offer a white-box modelling method based on physically interpreted ecological axioms. These models are implemented as deterministic individual-based cellular automata and able to give a direct physico-mechanistic insight into studied phenomena. Competition of two trophically identical but fitness different species, competing for one limiting resource in one stable uniform habitat (which is closed for immigration, emigration, predation, herbivory and parasitism) has been investigated in conditions, which are the most unfavourable for their coexistence. The...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7105/version/1

Medicine beyond magic bullets: a formal case for multilevel interventions
Provedor de dados: 17
Autores: Rodrick Wallace.
Western medicine&amp;#x27;s paradigmatic search for &amp;#x27;magic bullet&amp;#x27; interventions is facing increasing difficulty: Between 1950 and 2010 the inflation-adjusted cost per USFDA-approved drug has increased exponentially in time, a draconian inverse of the famous Moore&amp;#x27;s Law of computing. A sequence of empirically-oriented statistical models suggests that carefully designed synergistic multifactorial and multiscale strategies might evade this relationship.
Tipo: Manuscript
Palavras-chave: Biotechnology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6780/version/1

Mega- change gene copies are produced by reverse transcription of precursor RNA with replaced introns.
Provedor de dados: 17
Autores: Drew Schwartz.
This report describes the presence of copy genes in plants where the sequence similarity to their parental genes is almost completely limited to limited to the exons. Evidence is presented that indicates that they arose via a novel processing of transcribed precursor RNA during which the introns are replaced rather than excised, followed by reverse transcription and incorporation into the chromosomes. Intron replacement may play an important role in evolution as it results in megagene changes.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3834/version/1

Membrane repair against H. pylori promotes cancer cell proliferation
Provedor de dados: 17
Autores: Li-Ling  Lin; Hsuan-Cheng Huang; Satoshi  Ogihara; Jin-Town Wang; Chiung-Nien Chen; Hsueh-Fen Juan.
Membrane repair is a universal response against physical and biological insults and enables cell survival. Helicobacter pylori is one of the most common human pathogens and the first formally recognized bacterial carcinogen associated with gastric cancer. However, little is known about host membrane repair in the context of H. pylori infection. Here we show that H. pylori disrupts the host plasma membrane and induces Ca2+ influx, which triggers the translocation of annexin family members A1 and A4 to the plasma membrane. This in turn activates a membrane repair response through the recruitment of lysosomal membranes and the induction of downstream signaling transduction pathways that promote cell survival and proliferation. Based on our data, we propose a...
Tipo: Manuscript
Palavras-chave: Cancer; Microbiology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4887/version/1

MEMOFinder: combining _de_ _novo_ motif prediction methods with a database of known motifs
Provedor de dados: 17
Autores: Bartek Wilczynski; Milosz  Darzynkiewicz; Jerzy  Tiuryn.
*Background:* Methods for finding overrepresented sequence motifs are useful in several key areas of computational biology. They aim at detecting very weak signals responsible for biological processes requiring robust sequence identification like transcription-factor binding to DNA or docking sites in proteins. Currently, general performance of the model-based motif-finding methods is unsatisfactory; however, different methods are successful in different cases. This leads to the practical problem of combining results of different motif-finding tools, taking into account current knowledge collected in motif databases.&amp;#xd;&amp;#xa;*Results:* We propose a new complete service allowing researchers to submit their sequences for analysis by four different...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2289/version/2

MEMOFinder: combining _de_ _novo_ motif prediction methods with a database of known motifs
Provedor de dados: 17
Autores: Bartek Wilczynski; Milosz  Darzynkiewicz; Jerzy  Tiuryn.
*Background:* Methods for finding overrepresented sequence motifs are useful in several key areas of computational biology. They aim at detecting very weak signals responsible for biological processes requiring robust sequence identification like transcription-factor binding to DNA or docking sites in proteins. Currently, general performance of the model-based motif-finding methods is unsatisfactory; however, different methods are successful in different cases. This leads to the practical problem of combining results of different motif-finding tools, taking into account current knowledge collected in motif databases.&amp;#xd;&amp;#xa;*Results:* We propose a new complete service allowing researchers to submit their sequences for analysis by four different...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2289/version/1

Memristance can explain Spike-Time-Dependent-Plasticity in Neural Synapses
Provedor de dados: 17
Autores: Bernab&amp;#xe9; Linares-Barranco; Teresa Serrano-Gotarredona.
Interdisciplinary research broadens the view of particular problems yielding fresh and possibly unexpected insights. This is the case of neuromorphic engineering where technology and neuroscience cross-fertilize each other. For example, consider on one side the recently discovered memristor, postulated in 1974, thanks to research in nanotechnology electronics. On the other side, consider the mechanism known as Spike-Time-Dependent-Plasticity (STDP) which describes a neuronal synaptic learning mechanism that outperforms the traditional Hebbian synaptic plasticity proposed in 1949. STDP was originally postulated as a computer learning algorithm, and is being used by the machine intelligence and computational neuroscience community. At the same time its...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3010/version/1

Memristive model of amoeba&amp;#x27;s learning
Provedor de dados: 17
Autores: Yuriy V. Pershin; Steven La Fontaine; Massimiliano  Di Ventra.
Recently, behavioural intelligence of the plasmodia of the true slime mold has been demonstrated. It was shown that a large amoeba-like cell Physarum polycephalum subject to a pattern of periodic environmental changes learns and changes its behaviour in anticipation of the next stimulus to come. Currently, it is not known what specific mechanisms are responsible for such behaviour. Here, we show that such behaviour can be mapped into the response of a simple electronic circuit consisting of an LC contour and a memory-resistor (a memristor) to a train of voltage pulses that mimic environment changes. We identify a possible microscopic origin of the memristive behaviour in the Physarum polycephalum, which together with the naturally occurring biological...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2431/version/1

Men fear other men most: Gender specific brain activations in perceiving threat from dynamic faces and bodies. An fMRI study.
Provedor de dados: 17
Autores: Beatrice de Gelder; Swann Pichon; Mariska Kret; Julie Grezes.
We report a functional magnetic resonance imaging experiment showing different activation patterns as a function of threatening signals from facial or bodily expressions and these differed between male and female participants as a function of male and female actors. Male observers showed a clear motor preparation response to threatening male body language.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4801/version/1

Metabolic Activity of Human Chorionic Gonadotropin (hCG) on Glycemia and Leptinemia in Experimental Animals Fed a Cafeteria Diet
Provedor de dados: 17
Autores: Daniel Belluscio; Nestor Lago; Ezequiel Klimovsky; Maria Berdeal; Andrea Federico.
Objectives: To elucidate the relationship of hCG administration to glycemia, Non Esterified Fatty Acids (NEFA), leptin and adiponectin levels on experimental animals previously submitted to a cafeteria diet, and then to a Low Calorie Diet (LCD). Design: Forty-one rats were selected (21 females, 20 males) and divided into seven (0-6) groups. Animals from groups 1 to 6 were fed a &amp;#x22;cafeteria diet&amp;#x22; with a mean energy content of 10% protein, 30% carbohydrate and 60% fat. Animals from group 0 were fed the standard laboratory diet. After the fattening period, animals from groups 1 to 6 were submitted to a restricted diet consisting of one-third the average daily intake for rats. hCG was administered for five weeks according to a specific...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5781/version/1

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects?
Provedor de dados: 17
Autores: Rodrick Wallace.
A mathematical model based on Tlusty&amp;#x27;s topological deconstruction suggests that multiple punctuated ecosystem shifts in available metabolic free energy, broadly akin to the &amp;#x27;aerobic&amp;#x27; transition, enabled a punctuated sequence of increasingly complex genetic codes. These evolved until the ancestor to the present narrow spectrum of nearly maximal codes became locked-in by path dependence.
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4120/version/1

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Provedor de dados: 17
Autores: Rodrick Wallace.
A mathematical model based on Tlusty&amp;#x27;s topological deconstruction suggests that multiple punctuated ecosystem shifts in available metabolic free energy, broadly akin to the &amp;#x27;aerobic&amp;#x27; transition, enabled a punctuated sequence of increasingly complex genetic codes and protein translators under mechanisms similar to the Serial Endosymbiosis effecting the Eukaryotic transition. These evolved until the ancestor to the present narrow spectrum of nearly maximally robust codes became locked-in by path dependence.
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4120/version/2

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry lifting model based on Tlusty&amp;#x27;s elegant topological deconstruction suggests that multiple punctuated ecosystem resilience regime changes in metabolic free energy that were broadly similar to the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. In a manner similar to the Serial Endosymbiosis effecting the Eukaryotic transition, codes and translators coevolved until the ancestor of the present narrow spectrum of protein machineries became locked-in by evolutionary path dependence at a relatively modest level of fitness reflecting a modest embedding metabolic free energy ecology. The simplest coevolutionary model of code-translator interaction has high and low...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4120/version/4

Metabolic constraints on the evolution of genetic codes: Did multiple &amp;#x27;preaerobic&amp;#x27; ecosystem transitions entrain richer dialects via Serial Endosymbiosis?
Provedor de dados: 17
Autores: Rodrick Wallace.
A spontaneous symmetry lifting model based on Tlusty&amp;#x27;s elegant topological deconstruction suggests that multiple punctuated ecosystem resilience regime changes in metabolic free energy that were broadly similar to the aerobic transition enabled a punctuated sequence of increasingly complex genetic codes and protein translators. In a manner similar to the Serial Endosymbiosis effecting the Eukaryotic transition, codes and translators coevolved until the ancestor of the present narrow spectrum of protein machineries became locked-in by evolutionary path dependence at a relatively modest level of fitness reflecting a modest embedding metabolic free energy ecology. The simplest coevolutionary model of code-translator interaction has high and low...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4120/version/3

Metabolic Network Representation in SBGN PD: EC and Identity Gate
Provedor de dados: 17
Autores: Alexander Mazein.
This presentations describes proposed changes in SBGN PD that would allow this language to be better adopted for representing metabolic network.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4974/version/1

Metabolic, Replication and Genomic  Category of Systems in Biology,  Bioinformatics and Medicine
Provedor de dados: 17
Autores: I. C. Baianu.
Metabolic-repair models, or (M,R)-systems were introduced in Relational Biology by Robert Rosen. Subsequently, Rosen represented such (M,R)-systems (or simply MRs)in terms of categories of sets, deliberately selected without any structure other than the discrete topology of sets. Theoreticians of life&amp;#x2019;s origins postulated that Life on Earth has begun with the simplest possible organism, called the primordial. Mathematicians interested in biology attempted to answer this important question of the minimal living organism by defining the functional relations that would have made life possible in such a minimal system- a grandad and grandma of all living organisms on Earth. Genomic systems are also considered as molecular realizations of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7051/version/1

Metacuration Standards and Minimum Information about a Bioinformatics Investigation
Provedor de dados: 17
Autores: Tin Wee Tan; Asif M. Khan; Shen Jean Lim; Yong Li Hu; Mark de Silva; Kuan Siong Lim.
Many bioinformatics databases published in journals are here this year and gone the next. There is generally (i) no requirement, mandatory or otherwise, by reviewers, editors or publishers for full disclosure of how databases are built and how they are maintained; (ii) no standardized requirement for data in public access databases to be kept as backup for release and access when a project ends, when funds expire and website terminates; (iii) the case of proprietary resources, there is no requirement for data to be kept in escrow for release under stated conditions such as when a published database disappears due to company closure. Consequently, much of the biological databases published in the past twenty years are easily lost, even though the...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5078/version/1

Metagenomic Analysis of the Structure and Function of the Human Gut Microbiota in Crohn&amp;#x27;s Disease
Provedor de dados: 17
Autores: Claire  M. Fraser-Liggett.
Inflammatory bowel diseases (IBD), such as Crohn&amp;#x2019;s disease, are chronic, immunologically mediated disorders that have severe medical consequences. The current hypothesis is that these diseases are due to an overly aggressive immune response to a subset of commensal enteric bacteria. Studies to date on IBD have suggested that the disorder may be caused by a combination of bacteria and host susceptibility; however the etiologies of these diseases remain an enigma. In this application, we propose to develop and demonstrate the ability to profile Crohn&amp;#x2019;s disease at an unprecedented molecular level by elucidation of specific biomarkers (bacterial strains, genes, or proteins) that correlate to disease symptoms. To achieve this goal, we will...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4958/version/1

Metagenomic study of the human skin microbiome associated with acne
Provedor de dados: 17
Autores: Huiying Li.
The human microbiota contributes to our normal postnatal development and plays a significant role in defining our physiology. To understand the role of microbiota in human health and disease, we study the skin microbiome in pilosebaceous units (hair follicles) and its association with acne.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Acne is one of the most common skin diseases. Although its etiology still needs to be defined, a bacterial factor has been suggested in the development of the disease. In fact, antibiotic therapy targeting _Propionibacterium acnes_ has been a mainstay treatment for more than 30 years.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Our preliminary study shows that the microcomedone, a specialized skin compartment where acne arises, has a tractable...
Tipo: Marker Paper / Data Plan
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5305/version/1

Metapopulation capacity with self-colonization: Finding the best patches in fragmented habitats
Provedor de dados: 17
Autores: Jessica K. Schnell; Gareth J. Russell; Grant M. Harris; Stuart L. Pimm.
Habitat fragmentation continues to be a leading threat for our global future. Methods to quantify fragmentation of habitat landscapes, particularly for endangered species, would be especially useful in conservation planning. Using the principles of metapopulation theory, we updated and devised two methods for analyzing fragmented landscapes: metapopulation capacity and abandonment rate. Our version of metapopulation capacity includes a self-colonization component to counteract the issue metapopulation theory experiences with single large patches. We then tested these methods on satellite image range maps of endemic birds in the highland forests of northern Central America.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The metapopulation capacity method proved to be a...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5356/version/1

Meta-Potentiation: Neuro-Astroglial Interactions Supporting Perceptual Consciousness
Provedor de dados: 17
Autores: Alfredo Pereira Jr; F&amp;#xe1;bio Augusto Furlan.
Conscious perceptual processing involves the sequential activation of cortical networks at several brain locations, and the onset of oscillatory synchrony affecting the same neuronal population. How do the earlier activated circuits sustain their excitation to synchronize with the later ones? We call such a sustaining process &amp;#x22;meta-potentiation&amp;#x22;, and propose that it depends on neuro-astroglial interactions. In our proposed model, attentional cholinergic and stimulus-related glutamatergic inputs to astroglia elicit the release of astroglial glutamate to bind with neuronal NMDA receptors containing the NR2B subunit. Once calcium channels are open, slow inward currents activate the CaM/CaMKII complex to phosphorylate AMPA receptors in a...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/760/version/1

Metarel: an Ontology to support the inferencing of Semantic Web relations within Biomedical Ontologies
Provedor de dados: 17
Autores: Ward Blond&amp;#xe9;; Erick Antezana; Bernard De Baets; Vladimir Mironov; Martin Kuiper.
While OWL, the Web Ontology Language, is often regarded as the preferred language for Knowledge Representation in the world of the Semantic Web, the potential of direct representation in RDF, the Resource Description Framework, is underestimated. Here we show how ontologies adequately represented in RDF could be semantically enriched with SPARUL. To deal with the semantics of relations we created Metarel, a meta-ontology for relations. The utility of the approach is demonstrated by an application on Gene Ontology Annotation (GOA) RDF graphs in the RDF Knowledge Base BioGateway. We show that Metarel can facilitate inferencing in BioGateway, which allows for queries that are otherwise not possible. Metarel is available on http://www.metarel.org.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3562/version/1

Metarel: An Ontology to Support the Inferencing of Semantic Web Relations within Biomedical Ontologies
Provedor de dados: 17
Autores: Ward Blond&amp;#xe9;.
Metarel allows the creation of millions of relational inferences in the RDF Knowledge Base BioGateway, by using five types of SPARUL closure queries. Metarel can be found at &amp;#x22;http://www.metarel.org&amp;#x22;:http://www.metarel.org.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3463/version/1

Metastable Nanosized Diamond Formation from Fluid Systems
Provedor de dados: 17
Autores: Sergei Simakov.
The model of nanosized diamond particles formation at metastable P-T parameters from fluid is presented. It explains the specific of CVD diamond synthesis gases mixtures and hydrothermal growth of diamond at low P-T parameters as well as it explains the geneses of metamorphic and magmatic nano- and microdiamond in the shallow depth Earth rocks and the genesis of interstellar nanodiamond formations in the space.
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4195/version/1

Metastasis as a faulty recapitulation of ontogeny
Provedor de dados: 17
Autores: Ulf R. Rapp.
RAF oncogenes are involved in a variety of phenotypic switch phenomena. If for example oncogenic RAF is expressed together with Myc in B lineage cells, a lineage switch to macrophages occurs at low frequency in vitro and in vivo. In addition, if RAF is expressed in type II alveolar epithelial cells slow growing lung adenomas are formed and a switch from columnar to cuboidal cells is detected in these mice upon p53 deletion. A similar switch is also seen, if ectopic Myc is present in our lung tumor mouse model. Moreover, in the liver of these mice with both oncogenes metastases are found. If E-cadherin function is impaired in our RAF-dependent lung tumor model, a switch from adenoma to adenocarcinoma occurs and genes characteristic for the early endodermal...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Genetics &amp; Genomics.
Ano: 2007
URL: http://precedings.nature.com/documents/805/version/1

Methanogen consortium metabolism characteristic analysis of Illinois basin by real time monitor method
Provedor de dados: 17
Autores: Dong Xiao; Enyuan Wang.
Microbially Enhance Coalbed Methane technology is used to improve methane content in coalbeds. The methanogen consortium metabolism process is the basic avenue for MECoM to yield methane with some organic compounds in coal. Detailed information about the metabolism process is needed in studying the microbial consortium mechanism. Traditional gas analysis is limited by gas source and test complexity. The real time monitor with Infrared gas sensor breaks the gas analysis limitation. It shows much more detailed information than the traditional analysis method including information about microbial growth factor changes, reaction speeds for environmental changes, the detailed relationship between CH4 and CO2, methane yield and the consumption factor by real...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/5426/version/1

Method of Detecting and Targeting Mutations in Cancer
Provedor de dados: 17
Autores: Byard Edwards.
While there are many differences between tumor and non-tumor cells, the basic underlying distinction is in the DNA.  Tumor cells harbor mutations, at least some of which are not present in non-tumor cells.  Thus, a method of directly targeting cells containing specific mutations has potential for detection or treatment of cancer without the toxicity associated with more indirect approaches.  Also, as mutations are a necessary component of malignancy, such a method is potentially applicable to all tumors.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;I propose a method by which several recently developed techniques can be utilized in a novel way to accomplish the goal of directly targeting mutations for cancer detection and therapy.  The model can be summarized as...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2007
URL: http://precedings.nature.com/documents/1314/version/1

mGluR5 knockout mice exhibit normal conditioned place-preference to cocaine
Provedor de dados: 17
Autores: Melissa  A. Fowler; Andrew L. Varnell; Donald C. Cooper.
Metabotropic glutamate receptor 5 (mGluR5) null mutant (-/-) mice have been reported to totally lack the reinforcing or locomotor stimulating effects of cocaine. We tested mGluR5 -/- and +/+ mice for their locomotor and conditioned place- preference response to cocaine. Unlike the previous finding, here we show that compared to mGluR5 +/+ mice, -/- mice exhibit no difference in the locomotor response to low to moderate doses of cocaine (10 or 20 mg/kg). A high dose of cocaine (40 mg/kg) resulted in a blunted rather than absent locomotor response. We tested mGluR5 -/- and +/+ mice for conditioned place-preference to cocaine and found no group differences at a conditioning dose of 10 mg/kg, suggesting normal conditioned rewarding properties of cocaine. These...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6180/version/1

mGluR5 knockout mice exhibit normal conditioned place-preference to cocaine
Provedor de dados: 17
Autores: Melissa  A. Fowler; Andrew L. Varnell; Donald C. Cooper.
Metabotropic glutamate receptor 5 (mGluR5) null mutant (-/-) mice have been reported to totally lack the reinforcing or locomotor stimulating effects of cocaine. We tested mGluR5 -/- and +/+ mice for their locomotor and conditioned place- preference response to cocaine. Unlike the previous finding, here we show that compared to mGluR5 +/+ mice, -/- mice exhibit no difference in the locomotor response to low to moderate doses of cocaine (10 or 20 mg/kg). A high dose of cocaine (40 mg/kg) resulted in a blunted rather than absent locomotor response. We tested mGluR5 -/- and +/+ mice for conditioned place-preference to cocaine and found no group differences at a conditioning dose of 10 mg/kg, suggesting normal conditioned rewarding properties of cocaine. These...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6180/version/2

MHC Restriction of V-V Interactions in Serum IgG
Provedor de dados: 17
Autores: Earnest Leung; Geoffrey W. Hoffmann.
According to Jerne&amp;#x2019;s idiotypic network hypothesis, the adaptive immune system is regulated by interactions between the variable regions of antibodies, B cells, and T cells. The symmetrical immune network theory is based on Jerne&amp;#x2019;s hypothesis, and provides a basis for understanding many of the phenomena of adaptive immunity. The theory includes the postulate that the repertoire of serum IgG molecules is regulated by T cells, with the result that IgG molecules express V region determinants that mimic V region determinants present on suppressor T cells. In this paper we describe rapid binding between purified murine serum IgG of H-2b and H-2d mice and serum IgG from the same strain and from MHC-matched mice, but not between serum IgG...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4240/version/1

Microarray Analysis of PBMC after Plasmodium falciparum Infection: Molecular Insights into Disease Pathogenesis
Provedor de dados: 17
Autores: Wan-Chung(Wan-Jiung) Hu; Alan Scott; Nathan Wolfe; Sher Singh; Anne Jedlicka; August Louis Bourgeois.
Our laboratory&amp;#x2019;s previous microarray analysis of subjects with  Plasmodium falciparum revealed up-regulation of Toll-like receptor, NF-kB, TNF-&amp;#x3b1;, IFN-&amp;#x3b3;, IL-1&amp;#x3b2;, p38 MAPK, and MHC  molecules. We performed further time-course microarray analysis focusing on malaria pathogenesis by using peripheral leukocytes as a cellular model. We found up-regulation of coagulation-related genes (SERPINB2, thrombomodulin, thrombospondin), heat shock proteins, glycolytic enzymes, glucose transporters, and vacuolar H+-ATPases in acute febrile malaria. In early malaria, prior to detectable parasitemia, CD36 and ICAM1 were up-regulated. During acute malaria, a correlation was observed between IL-1&amp;#xdf; and  heat shock proteins,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5929/version/1

Microbial adaptations to envrionmental change: a moving target for global change ecology
Provedor de dados: 17
Autores: Matthew D. Wallenstein; Sarah Evans.
Background/Question/Methods &amp;#xd;&amp;#xa;As the abiotic conditions that structure biological communities and elicit physiological responses continue to change at an unprecedented rate, we need to understand how biological responses to global change will affect ecosystem functioning. A number of studies have detected shifts in the structure of microbial communities in response to experimental warming, elevated CO2 altered&amp;#xd;&amp;#xa;precipitation, and increased N deposition. However, since the links between microbial phylogeny and function are poorly understood, it can be challenging to predict how these changes in community structure will affect the rates of specific processes. It is often assumed that the high diversity of microbial communities...
Tipo: Presentation
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5510/version/1

Microbial ecosystem constructed in water for successful organic hydroponics
Provedor de dados: 17
Autores: Makoto Shinohara; Hiromi Ohmori; Yoichi Uehara.
Conventional hydroponics systems generally use only chemical fertilisers, not organic ones, since there are no microbial ecosystems present in such systems to mineralise organic compounds to inorganic nutrients. Addition of organic compounds to the hydroponic solution generally has phytotoxic effects and causes poor plant growth. We developed a novel hydroponic culture method using organic fertiliser. A microbial ecosystem was constructed in hydroponic solution by regulating the amounts of organic fertiliser and soil, with moderate aeration. The microbial ecosystem mineralised organic nitrogen to nitrate-nitrogen via ammonification and nitrification. A 97.6% efficiency of nitrate-nitrogen generation from the organic nitrogen in the organic fertiliser was...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2494/version/1

Microbial responses to changes in land use
Provedor de dados: 17
Autores: Rebecca C. Mueller; Klaus N&amp;#xfc;sslein; Jorge Rodrigues; James Tiedje; Vivian Pellizari; Brigitte Feigl; Brendan Bohannan.
Background/Question/Methods&amp;#xd;&amp;#xa;Land use change is one of the greatest threats to biodiversity worldwide. This is especially true for land use change that results in the destruction of intact forest, or &amp;#x22;deforestation&amp;#x201d;. Deforestation is causing a loss of biological diversity on an unprecedented scale, especially in the Tropics. It is unclear how the majority of the biodiversity on Earth &amp;#x2013; microbial biodiversity &amp;#x2013; is responding to these extraordinary rates of deforestation. I will provide an overview of our current understanding of microbial responses to deforestation. I will focus, as an example, on our current research regarding the effects of deforestation on the diversity of arbuscular mycorrhizal...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5505/version/1

Microbiological Aspects and Immunity Response of Bacteria Causing Pulpitis
Provedor de dados: 17
Autores: Deepak Dwivedi; Sapna  Kushwah; Dr. Vinod Singh.
The oral cavity is a very widely distributed ecosystem in which several hundred microbial species normally cohabit harmoniously. Under special conditions some microorganisms with  potential are promoted, leading to inflammation &amp;#x26; infection by induced de-mineralization of dental enamel that normally constitutes an impermeable barrier that protects the underlying dentin and the connective tissue situated in the center of the tooth &amp;#x26; dental pulp such as pulpitis, dental caries, and periodontal infection. In inflammation of the dental pulpitis the immunity response against oral infection leads to infection and results in a high level of morbidity and economic burden to society.
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/5889/version/1

MicroDNAs and Transcriptional Regulation
Provedor de dados: 17
Autores: Reza sheikhnejad.
Synthetic &amp;#x22;microDNAs (MIDs)&amp;#x22;is a new class of ~ 20-25 nucleotide-long DNAs capable of repressing the activity of the target gene at the level of transcription by mechanisms that have not been clarified yet. However they are designed to target non-coding regions of the cancer causing genes, thus interfering with transcription. The inhibition might be possible through the direct binding of MIDs to cis-regulatory sites and/or to some Transcription Factors (TF) that normally activate transcription. Synthetic MIDs in some ways are similar to the newly discovered microRNAs a mechanism by which cell regulates its genetic activities at post-transcriptional level. Synthetic MIDs can provide a powerful tool to prevent massive production of mRNA by...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3931/version/1

Microfouling of Manganese-oxidizing microorganisms in Rameswaram Coastal Waters.
Provedor de dados: 17
Autores: Hari Muraleedharan; V Kalaigandhi; E Kannapiran.
Manganese oxidizing marine microorganisms was studied from the coupons of PVC, Titanium, Brass, Copper and Stainless Steel were immersed one meter below water surface, using wooden rafts. The metal coupons, Brass, Titanium and Brass were exposed for a period of six months (October 2005 to March 2006). The PVC and SS were suspended in the sea for two months (February and March 2006). Sea water samples were also collected from the study area using water sampler to estimate the physiochemical and nutrients were analyzed. The population of HB and MHB on PVC was registered as 3.62 x 107 CFU/cm2 and 2.87 x 107 CFU/cm2, respectively while on Stainless Steel the population density of HB and MHB was recorded as 3.79 x 105 CFU/cm2 and 1.34 x 105 CFU/cm2. The PVC and...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/3777/version/1

Micro-magnetic resonance imaging (micro-MRI) study on the sepsis effected eyeball of zebrafish
Provedor de dados: 17
Autores: Bimal Kumar  Sarkar; Wu  Zen; Shangwu  Ding; C. H.  Hsu; Z.H.  Wen; C. S.  Lin; Chiranjib  Chakraborty.
We have studied the normal and sepsis effected zebrafish eyeball with micro-magnetic resonance imaging (micro-MRI). T2 weighted image was studied and pixel-wise T2 maps were co registered among the normal and sepsis effected eye. From the micro-image the sepsis effect in the eye has been demonstrated. The pixel-wise brightness distribution is not so scattered in the normal eyeball image, whereas it is very scattered in case of sepsis affected eyeball image. Also the T2 mapping on the eye has given valuable information that would be a potential tool for the study of diseased organ in the micro level. From T2 mapping, it has shown that the T2 in normal eyeball have low values in comparison to the sepsis affected eyeball.
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2694/version/1

Microparticles specific for lung delivery: in-vivo drug distribution in monkeys
Provedor de dados: 17
Autores: Rahul Verma; Amit Misra.
In spite of extensive research in tuberculosis (TB), it is still one of the major infectious diseases and cause of high mortality worldwide. To enhance efficacy with lower dosing, newer drug delivery systems has been developed which provide targeted drug delivery and controlled release at the primary site of infection, i.e., the lung macrophage. Our lab has previously reported poly(D, L-lactic acid) (PLA) microparticles containing rifabutin (RFB) and isoniazid (INH) for pulmonary delivery and explored various facets of treatment with microparticle DPI. We have utilized this dry powder aerosol drug delivery system to deposit drugs directly at the site of infection in lungs and have been investigating such DPI as a novel approach to increase therapeutic...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7061/version/1

Microstructural Correlates of Resilience against Major Depressive Disorder: Epigenetic Mechanisms?
Provedor de dados: 17
Autores: Thomas Frodl; Yolande Ferguson; Andrew Fagan; Danusia Lisiecka; Angela Carballedo; Ian Daly; James Meaney; Dermot Kelleher.
Mental disorders are a major cause of long-term disability and are a direct cause of mortality, with approximately 800.000 individuals dying from suicide every year worldwide - a high proportion of them related to major depressive disorder (MDD)^1^. Healthy relatives of patients with major depressive disorder (MDD) are at risk to develop the disease. This higher vulnerability is associated with structural^2-4^ and functional brain changes^5^. However, we found using high angular resolution diffusion imaging (HARDI) with 61 diffusion directions that neuron tracts between frontal cortices and limbic as well as temporal and parietal brain regions are characterized by better diffusion coefficients in unaffected relatives (UHR), who managed to stay healthy,...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4793/version/2

Microstructural Correlates of Resilience against Major Depressive Disorder: Epigenetic Mechanisms?
Provedor de dados: 17
Autores: Thomas Frodl; Yolande Ferguson; Andrew Fagan; Danusia Lisiecka; Angela Carballedo; Ian Daly; James Meaney; Dermot Kelleher.
Mental disorders are a major cause of long-term disability and are a direct cause of mortality, with approximately 800.000 individuals dying from suicide every year worldwide - a high proportion of them related to major depressive disorder (MDD)^1^. Healthy relatives of patients with major depressive disorder (MDD) are at risk to develop the disease. This higher vulnerability is associated with structural^2-4^ and functional brain changes^5^. However, we found using high angular resolution diffusion imaging (HARDI) with 61 diffusion directions that neuron tracts between frontal cortices and limbic as well as temporal and parietal brain regions are characterized by better diffusion coefficients in unaffected relatives (UHR), who managed to stay healthy,...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4793/version/1

MIF-AMPK cascades
Provedor de dados: 17
Autores: Heng Ma; Jingying Wang; Erin Lane; Lin Leng; Wenkui Wang; Jun Ren; Richard Bucala; Ji Li.
Withdrawn for publication
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2466/version/2

Migraine aura: retracting particle-like waves in weakly susceptible cortex
Provedor de dados: 17
Autores: Markus A. Dahlem; Nouchine Hadjikhani.
Cortical spreading depression (SD) has been suggested to underlie migraine aura. Despite a precise match in speed, the spatio-temporal patterns of SD and aura symptoms on the cortical surface ordinarily differ in aspects of size and shape. We show that this mismatch is reconciled by utilizing that both pattern types bifurcate from an instability point of generic reaction-diffusion models. To classify these spatio-temporal pattern we suggest a susceptibility scale having the value [sigma]=1 at the instability point. We predict that human cortex is only weakly susceptible to SD ([sigma]&amp;#x3c;1), and support this prediction by directly matching visual aura symptoms with anatomical landmarks using fMRI retinotopic mapping. We discuss the increased...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2070/version/1

Migration potential as a new predictor of long-distance dispersal rate for plants
Provedor de dados: 17
Autores: Tianhua He; Byron B. Lamont; Neal Enright; Siegy Krauss; Laura Merwin.
How biotic and abiotic factors interact to shape the overall pattern of dispersal of propagules is critical in understanding the evolution of dispersal mechanisms as well as predicting dispersal rates between patchily-distributed habitats. But which plant traits, demographic and/or habitat factors best predict the capacity for dispersal? We introduce the concept of migration potential (v), a readily interpretable parameter that combines recruitment efficiency (recruits per adult / seeds per adult per dispersal cycle) with level of habitat occupancy for predicting effective long-distance dispersal (LDD) of seeds. Using our empirical (genotype assignment) estimates of LDD and statistics on life-history traits and demographic features for contrasting...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5890/version/1

Milk is for Children, Colostrum silage is for calves.
Provedor de dados: 17
Autores: Mara Helena Saalfeld; Daniela  Brayer Pereira; Kathleen Kr&amp;#xfc;guer Silveira; Marcia Gularte; Julia Valente; Renata Schramm; F&amp;#xe1;bio Leivas Leite.
One sixth of the world population is starving. In the meantime, producers from all over the world daily disdain billions of liters of bovine colostrum, which is seen as rich in nutrients, immunoglobulin and bioactive substances. The milk is the most expensive component in the final costs of calves breeding. Considering the impossibility of substituting the milk to feed the calf, different ways to use the colostrum have been studied however with controversial results. We have developed colostrum silage. This product is economical and possible to store in the environment for up to eighteen months. Being efficient for calf breeding, yielding income and profit to the dairy business. The colostrum silage keeps the necessary physicochemical characteristics for...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/6553/version/1

Millisecond-scale differences in neural activity in auditory cortex can drive decisions
Provedor de dados: 17
Autores: Yang Yang; Michael R. DeWeese; Gonzalo Otazu; Anthony M. Zador.
Neurons in the auditory cortex can lock with millisecond precision to the fine timing&amp;#xd;&amp;#xa;of acoustic stimuli, but it is not known whether this precise spike timing can be used&amp;#xd;&amp;#xa;to guide decisions. We used chronically implanted microelectrode pairs to stimulate&amp;#xd;&amp;#xa;neurons in the rat auditory cortex directly. Here we demonstrate that rats can&amp;#xd;&amp;#xa;exploit differences in the timing of cortical activity as short as three milliseconds to&amp;#xd;&amp;#xa;guide decisions.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2280/version/1

Mind over chatter: plastic up-regulation of the fMRI alertness network by EEG neurofeedback
Provedor de dados: 17
Autores: Tomas Ros; Jean Theberge; Paul A. Frewen; Rosemarie  Kluetsch; Maria Densmore; Vince D. Calhoun; Ruth A. Lanius.
EEG neurofeedback (NFB) is a brain-computer interface (BCI) approach used to shape brain oscillations by means of real-time feedback from the electroencephalogram (EEG), which is known to reflect neural activity across cortical networks. Although NFB is being evaluated as a novel tool for treating brain disorders, evidence is scarce on the mechanism of its impact on brain function. In this study with 34 healthy participants, we examined whether, during the performance of an attentional auditory oddball task, the functional connectivity strength of distinct fMRI networks would be plastically altered after a 30-min NFB session of alpha-band reduction (n=17) versus a sham-feedback condition (n=17). Our results reveal that compared to sham, NFB induced a...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/7060/version/1

Minimal Information About Sample Preparation for Phosphoproteomics
Provedor de dados: 17
Autores: Montserrat Carrascal; David Ovelleiro; Marina Gay; Joaquin Abian.
This guideline describes parameters and conditions involved in phosphopeptide sample preparation. It covers from the description and preparation of the cells and tissues to the fractionation and specific enrichment of phosphopeptides for MS analysis. The guideline is prepared in order to easily cope with many of the experimental designs used in phosphoproteomic studies. &amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;The document is subdivided as follows:&amp;#xd;&amp;#xa;1. General features&amp;#xd;&amp;#xa;2. Sample processing&amp;#xd;&amp;#xa;3. Protein Purification/Fractionation&amp;#xd;&amp;#xa;4. Peptide Purification/Fractionation&amp;#xd;&amp;#xa;5. Phosphopeptide enrichment&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3131/version/1

Minimum Information about a Neuroscience Investigation (MINI): Electrophysiology
Provedor de dados: 17
Autores: Frank Gibson; Paul G. Overton; Tom V. Smulders; Simon R. Schultz; Stephen J. Eglen; Colin D. Ingram; Stefano Panzeri; Phil Bream; Miles Whittington; Evelyne Sernagor; Mark Cunningham; Christopher Adams; Christoph Echtermeyer; Jennifer Simonotto; Marcus Kaiser; Daniel C. Swan; Martyn Fletcher; Phillip Lord.
This module represents the formalised opinion of the authors and the CARMEN consortium, which identifies the minimum information required to report the use of electrophysiology in a neuroscience study, for submission&amp;#xd;&amp;#xa;to the CARMEN system (&amp;#x22;http://www.carmen.org.uk&amp;#x22;:www.carmen.org.uk).
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/1720/version/2

Minimum Information about a Neuroscience Investigation (MINI) Electrophysiology
Provedor de dados: 17
Autores: Frank Gibson; Paul  G. Overton; Tom V. Smulders; Simon R. Schultz; Stephen  J. Eglen; Colin D. Ingram; Stefano  Panzeri; Phil Bream; Evelyne  Sernagor; Mark Cunningham; Christopher Adams; Christoph Echtermeyer; Jennifer Simonotto; Marcus Kaiser; Daniel C. Swan; Marty Fletcher; Phillip Lord.
This module represents the formalized opinion of the authors and the CARMEN consortium, which identifies the minimum information required to report the use of electrophysiology in a neuroscience study, for submission to the CARMEN system (www.carmen.org.uk).&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1720/version/1

Mining Co-expression Graphs: Applications to MicroRNA Regulation and Disease Analysis
Provedor de dados: 17
Autores: Malay Bhattacharyya.
MicroRNAs (miRNAs) are known to translationally repress or post-transcriptionally regulate mRNAs and are responsible for many diseases. We are preparing a comprehensive framework of co-expression analysis to figure out co-expression, differential co-expression and co-expression dynamics within multiple phenotypes in expression profiles. The purpose is to elucidate the disease association of miRNAs via co-regulatory pattern analysis.
Tipo: Presentation
Palavras-chave: Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7119/version/1

Mining PubMed for Biomarker-Disease Associations to Guide Discovery
Provedor de dados: 17
Autores: Walter J. Jessen; Katherine T. Landschulz; Thomas G. Turi; Rachel Y. Reams.
Biomedical knowledge is growing exponentially; however, meta-knowledge around the data is often lacking. PubMed is a database comprising more than 21 million citations for biomedical literature from MEDLINE and additional life science journals dating back to the 1950s. To explore the use and frequency of biomarkers across human disease, we mined PubMed for biomarker-disease associations. We then ranked the top 100 linked diseases by relevance and mapped them to medical subject headings (MeSH) and, subsequently, to the Disease Ontology. To identify biomarkers for each disease, we queried Covance BioPathways, an online data resource that maps commercial biomarker assays to biological and disease pathways. We then integrated pathways-based information to...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6941/version/1

Mining SOM expression portraits: Feature selection and integrating concepts of molecular function
Provedor de dados: 17
Autores: Henry Wirth; Martin von Bergen; Hans Binder.
Background: &amp;#xd;&amp;#xa;Self organizing maps (SOM) enable the straightforward portraying of high-dimensional data of large sample collections in terms of sample-specific images. The analysis of their texture provides so-called spot-clusters of co-expressed genes which require subsequent significance filtering and functional interpretation. We address feature selection in terms of the gene ranking problem and the interpretation of the obtained spot-related lists using concepts of molecular function.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: &amp;#xd;&amp;#xa;Different expression scores based either on simple fold change-measures or on regularized Students t-statistics are applied to spot-related gene lists and compared with special emphasis on the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6666/version/1

Mining the Largest Quasi-clique in Human Protein Interactome
Provedor de dados: 17
Autores: Sanghamitra Bandyopadhyay; Malay Bhattacharyya.
A clique is a complete subgraph of a graph. Often, a clique is interpreted as a dense module of vertices within a graph. However, in many real-world situations, the classical problem of finding a clique is required to be relaxed. This motivates the problem of finding quasicliques that are almost complete subgraphs of a graph. In sparse and very large scale-free networks, the problem of finding the largest quasi-clique becomes hard to manage with the existing approaches. Here, we propose a heuristic algorithm in this paper for locating the largest quasi-clique from the human protein-protein interaction networks. The results show promise in computational biology research by the exploration of significant protein modules.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7125/version/1

Miraculous Survival of Three Trapping Miners by Drinking High Mineral Mine Water for 25
Provedor de dados: 17
Autores: Cheng C. Liang; Deng Sheng; Wang Lin; Mu Mao.
Little is known that how long a human been can survive a complete starvation. There were dozens of miners who lost their lives in a coal mine disaster at Qinglong,Guizhou,China in June 2009, only three of them were rescued 25 days later after they had been trapped in a coal mine 600 meters underground. They maintained their lives only by drinking mineral water in the mine, which created a miracle of life. We reported here on this life miracle in relation to high mineral mine water.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5438/version/1

MIREOT: the Minimum Information to Reference an External Ontology Term
Provedor de dados: 17
Autores: Melanie Courtot; Frank Gibson; Allyson L. Lister; James Malone; Daniel Schober; Ryan R. Brinkman; Alan Ruttenberg.
While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct OWL imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be under active development and not aligned with the chosen design principles. Importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of application, and outline...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/3574/version/1

MIREOT: the Minimum Information to Reference an External Ontology Term
Provedor de dados: 17
Autores: M&amp;#xe9;lanie Courtot; Frank Gibson; Allyson L. Lister; James Malone; Daniel Schober; Ryan R. Brinkman; Alan Ruttenberg.
While the Web Ontology Language (OWL) provides a mechanism to import ontologies, this mechanism is not always suitable. First, given the current state of editing tools and the issues they have working with large ontologies, direct OWL imports have sometimes proven impractical for day-to-day development. Second, ontologies chosen for integration may be under active development and not aligned with the chosen design principles. Importing heterogeneous ontologies in their entirety may lead to inconsistencies or unintended inferences. In this paper we propose a set of guidelines for importing required terms from an external resource into a target ontology. We describe the guidelines, their implementation, present some examples of application, and outline...
Tipo: Presentation
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3576/version/1

MIRIAM Resources: a robust annotation and cross referencing framework
Provedor de dados: 17
Autores: Camille Laibe; Nick Juty; Nicolas Le Nov&amp;#xe8;re.
_Background_&amp;#xd;&amp;#xa;More than ever, the era of data integration has highlighted the key requirement to reference specific data in an unambiguous and perennial way, in order to enable community-level sharing, development, exchange and reuse of information. In the field of Systems Biology, which is concerned with creating quantitative models of biological processes, these requirements have directly led to the creation of the Minimal Information Required In the Annotation of Models (MIRIAM, &amp;#x22;http://biomodels.net/miriam/&amp;#x22;:http://biomodels.net/miriam/). MIRIAM provides a specific set of guidelines that can be implemented within any structured modelling format.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;_Objectives_&amp;#xd;&amp;#xa;To...
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5128/version/1

MIRIAM Resources: next steps
Provedor de dados: 17
Autores: Camille Laibe.
This presentation gives a short introduction of MIRIAM Resources (&amp;#x22;http://www.ebi.ac.uk/miriam/&amp;#x22;:http://www.ebi.ac.uk/miriam/), a robust annotation and cross referencing framework, based on URNs.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The presentation also explains some potential issues with the current system and presents a possible solution.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Finally, the presentation introduces some forthcoming and suggested updates and extensions to the current infrastructure.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5130/version/1

Missouri River Watershed: the Object for Hydrological Study and Uncertainty of Models
Provedor de dados: 17
Autores: Boris Shmagin.
The longest river (2540 mi) and the second drainage area (529 346 mi2) in the North America the Missouri River is one from the most interesting hydrological objects to study. The issue of uncertainty is the basis for any application of knowledge (&amp;#x201c;Uncertainty is an attribute of information.&amp;#x201d; From Zadeh, 2005) and has to be one of the main tasks in Earth&amp;#x2019;s systems study. Knowledge about natural systems (watershed in our case) may be only obtained by the analysis of the empirical (instrumental) data (observations). Principle of Uncertainty is the basic low in Physic. In Hydrology, the Uncertainty starts from the unveiling of the research task by the researcher. The main source of the uncertainty comes from the natural system...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6537/version/1

Mitigation of GHGs Emission From Soils by a Catalyzed In-Situ Photo-Oxidative Polymerization of Soil Organic Matter
Provedor de dados: 17
Autores: Alessandro Piccolo; Riccardo Spaccini.
Agricultural lands under food and bio-energy crops, managed grass and permanent crops including agro-forestry, occupy about 40-50% of the Earth&amp;#x27;s land surface^1^. In 2005, agriculture accounted for an estimated emission of 5.1 to 6.1 GtCO2-eq/yr (10-12% of total global anthropogenic emissions of greenhouse gases (GHGs))^1^. However, measures to mitigate GHGs emission from agricultural soils are limited to improved cropland practices such as crop rotation, nutrient management, tillage/residue management, agroforestry, and return to natural vegetation^2^. These practices are not only far from substantially reducing GHGs emissions from soils or permanentlystabilizing soil organic matter^1-4^, but are also predicted to hardly match more than amaximum...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4129/version/1

Mitochondrial Molecular Adaptations and Life History Strategies Coevolve in Plants
Provedor de dados: 17
Autores: Neeraja M. Krishnan; Basuthkar J. Rao.
Messenger RNA secondary structure prevents mutations at functionally important sites. Mutations at exposed sites would cause micro-adaptations, niche-specialization, and therefore, can be thought to promote K-strategists. Exposing, rather than protecting, conserved sites, is also potentially adaptive because they probably promote macro-adaptive changes. This presumably fits r-strategists: their population dynamics tolerate decreased survival. We found that helix-forming tendencies are greater at evolutionary conserved sites of plant mitochondrial mRNAs than at evolutionary variable sites in a majority (73%) of species&amp;#x2013;gene combinations. K-strategists preferentially protect conserved sites in short genes, r-strategists protect them most in larger...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1922/version/1

MitoWheel, visualizing the  human mitochondrial genome
Provedor de dados: 17
Autores: G&amp;#xe1;bor  Zsurka; Attila Csord&amp;#xe1;s.
So far researchers, web users were restricted to non-intuitive and visually poor text based databases every time they wanted to take a look on the mitochondrial DNA and find a region of interest. But with MitoWheel the situation is about to change. MitoWheel is a graphical representation of the circular human mitochondrial genome available on the web at &amp;#x22;http://mitowheel.org&amp;#x22;:http://mitowheel.org.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The human mitochondrial DNA is a 16569 basepair long, circular molecule and this very circularity is the basic idea behind MitoWheel. The mitochondrial genome can be represented with a wheel and by spinning this wheel users can quickly scan through, browse and identify the particular regions. The spinning is...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3167/version/1

Mizoribin as a inhibitor for leukocyte immunoglobulin receptor sub family A member3
Provedor de dados: 17
Autores: Varala Sravani; I Vani Priyadarshini; Amineni Umamaheswari.
The Leukocyte Immunoglobulin-like Receptors (LILRs) are a family of receptors that was broadly expressed on all leukocytes and have the ability to regulate their function. The increased levels of human LILRA3 in rheumatoid arthritis patients leads to stroke. In quest of designing novel inhibitors against LILRA3 an accurate homology model for the protein was based on crystal structures of 1GOX and 3P2T using Modeller 9V9. The use of multiple templates for structure prediction led us to propose a structure comprising all 439 amino acids of human LILRA3 for the first time.  The best model was selected based on GA341 and DOPE score and further assessed through ProSA and PROCHECK. The validated structure was subjected to CASTp analysis ligand binding site...
Tipo: Presentation
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6532/version/1

MMsPred: a bioactivity and toxicology predictive system
Provedor de dados: 17
Autores: Joel Masciocchi; Luca Pireddu; Ricardo Medda; Piergiorgio Palla; Matteo Floris; Luca Pani; Patricia Rodriguez-Tome.
In the last decade, the development and use of new methods in combinatorial chemistry and high-throughput screening has dramatically increased the number of known biologically active compounds. Paradoxically, the number of drugs reaching the market has not followed the same trend, often because many of the candidate drugs present poor qualities in absorption, distribution, metabolism, excretion, and toxicological properties (ADME-Tox). The ability to recognize and discard bad candidates early in the drug discovery steps would save lost investments in time and money. Machine learning techniques could provide solutions to this problem.&amp;#xd;&amp;#xa;The goal of my research is to develop classifiers that accurately discriminate between active and inactive...
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4188/version/1

Mobile Image Ratiometry: A New Method for Instantaneous Analysis of Rapid Test Strips
Provedor de dados: 17
Autores: Donald  C. Cooper; Bryan Callahan; Phil  Callahan; Lee  Burnett.
Here we describe Mobile Image Ratiometry (MIR), a new method for the automated quantification of standardized rapid immunoassay strips using consumer-based mobile smartphone and tablet cameras. To demonstrate MIR we developed a standardized method using rapid immunotest strips directed against cocaine (COC) and its major metabolite, benzoylecgonine (BE). We performed image analysis of three brands of commercially available dye-conjugated anti-COC/BE antibody test strips in response to three different series of cocaine concentrations ranging from 0.1 to 300 ng/ml and BE concentrations ranging from 0.003 to 0.1 ng/ml. These data were then used to create standard curves to allow quantification of COC/BE in biological samples. MIR quantification of COC and BE...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6827/version/1

Mobile Image Ratiometry for the Detection of Botrytis cinerea (Gray Mold)
Provedor de dados: 17
Autores: Donald  C. Cooper.
Mobile Platform Informatics (MPI) and Smartphone Informatics (SPI) methods like Mobile Image Ratiometry (MIR) are potentially transformative point-of-use instantaneous analysis tools that are useful across a variety of industries. In agriculture, MIR-compatible immuno test strips allow early detection of a number of biotic stressors before devastating crop losses occur. Here we describe a low-cost and easy-to-use Smartphone and/or tablet-based protocol (Mobile Assay Inc., www.mobileassay.com) for the detection and on-sight instantaneous analysis of B. cinerea, a fungus that causes significant damage to a variety of plants and flowers. Early detection and tracking of the B. cinerea fungus before the visible gray mold appears has the potential to increase...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Earth &amp; Environment; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6989/version/1

Modeling Animal Movements in Response to Human Disturbances
Provedor de dados: 17
Autores: Haiganoush K. Preisler; Alan A. Ager; David R. Brillinger; Michael J. Wisdom.
1) Background/Question/Methods&amp;#xd;&amp;#xa;The advent of GPS technology has made it possible to study human - wildlife interactions on large landscapes and quantify behavioral responses to recreation and other anthropogenic disturbances at increasingly fine scales.  Of particular interest are the potential impacts on habitat use patterns, energetics, and cascading impacts on fecundity and other life history traits for key wildlife species that are increasingly exposed to human activities.  However, the dynamics of free-ranging animal movements are complex, even without disturbances, and quantifying reactions to disturbance on heterogeneous landscapes is difficult.  A modeling framework is required that can sort out diel and random movements that mask...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5312/version/1

Modeling cardiac rhythm and heart rate using BFO and DOLCE
Provedor de dados: 17
Autores: Lynda Temal; Arnaud Rosier; Olivier Dameron; Anita Burgun.
This paper presents an application ontology for modeling cardiac rhythm and its anomalies such as tachycardia and bradycardia. We use BFO and DOLCE as ontological reference framework in order to compare their impact on ontology design. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3558/version/1

Modeling Compatible Single-Tree Aboveground Biomass Equations of Masson Pine (Pinus massoniana) in South China
Provedor de dados: 17
Autores: Wei Sheng Zeng; Shou Zheng Tang.
In the background of facing up to the global climate change, it is becoming the inevitable demand to add forest biomass estimation to national forest resource monitoring. The biomass equations to be developed for forest biomass estimation should be compatible with volume equations. Based on the tree volume and aboveground biomass data of Masson pine (Pinus Massoniana Lamb.) in south China, the one, two and three-variable aboveground biomass equations and biomass conversion functions compatible with tree volume equations were constructed using the error-in-variable simultaneous equations in this paper. The results showed: (i) the prediction precision of aboveground biomass estimates from one variable equation was more than 95%; (ii) the regressions of...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2012
URL: http://precedings.nature.com/documents/6754/version/1

Modeling forest insect population dynamics
Provedor de dados: 17
Autores: Mario Pineda-Krch.
Overview of the Special Interdisciplinary Minisymposium at the 2009 meeting of the Society for Mathematical Biology on modeling of forest insect population dynamics.
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3638/version/1

Modeling long-range interactions across the visual field in stereo correspondence
Provedor de dados: 17
Autores: Jenny C. A. Read.
When the eyes are converged, most objects in the visual scene will have a significant vertical disparity as measured at the retina. The pattern of vertical disparity across the retina is largely independent of object depth, depending mainly on the particular eye position adopted. Recently, Phillipson and Read (2010, European Journal of Neuroscience, doi:10.1111/j.1460-9568.2010.07454.x) showed that humans are better at achieving stereo correspondence when the vertical disparity field indicated infinite viewing distance, even when the physical viewing distance was just 30cm. They interpreted this as indicating that disparity encoding is optimized for long viewing distances, and is not updated to reflect changes in eye posture. Their results also indicated a...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5840/version/1

Modeling miRNA regulation in signaling networks: miR-34a regulation of the p53/Sirt1 module
Provedor de dados: 17
Autores: Xin Lai.
Micro RNAs are a family of small regulatory RNAs whose function is to regulate the activity and stability of specific messenger RNA targets through post-translational regulatory mechanisms. We studied a signaling module composed by p53, Sirt1 and the small regulatory miRNA, miR-34a, based on the integration of experimental evidence and quantitative data, with mathematical modeling. We further used the model to investigate different possible designs of the silencing mechanisms exerted by miR-34a on Sirt1, and to simulate the dynamics of the system under pathological conditions of deregulation of its components. &amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5123/version/1

Modeling of ARS-interacting multifunctional proteins p18 and p38.
Provedor de dados: 17
Autores: Viktor V. Deineko.
ARS-interacting multifunctional proteins (auxiliary components) &amp;#x2013; are nonezymatic proteins, associated with aminoacyl-tRNA synthetases &amp;#x2013; enzymes that catalyse the joining of amino acids with their corresponding tRNAs. All these proteins are complexed into large macromolecular multisynthetase complex in eukaryotes. It includes nine different ARSs and three auxiliary components. Their spatial structures precisely defined by X-ray analysis are still not known. Nevertheless, it very useful to have this structure while making biochemical studies. Bioinformatical tools were used to create structural models of two auxiliary components of multisynthetase complex &amp;#x2013; p18 and p38.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1047/version/1

Modeling Pinus edulis growth in a changing climate: Carbon dioxide, growing season length, and precipitation
Provedor de dados: 17
Autores: Susannah Tysor; George  Koch; Amy Whipple.
Background/Question/Methods&amp;#xd;&amp;#xa;Pinus edulis (pinyon pine) is a foundation tree species in the southwestern United States that has experienced high levels of mortality in a drought extending from the mid-1990s to the present.  Despite high mortality levels, radial growth of pinyon pine in northern Arizona over the past century shows an increasing trend not found in four centuries of preindustrial growth.  Atmospheric carbon dioxide concentration ([CO2]) shows a strong correlation with recent radial growth, and a simple linear AR(1) model with only [CO2] as a covariate explains average yearly growth well.  No climate variable except [CO2] has a consistent long-term trend that accounts for increasing radial growth, but growing season and...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5193/version/1

Modeling reaction-diffusion of molecules on surface and in volume spaces with the E-Cell System
Provedor de dados: 17
Autores: Satya N. V. Arjunan; Masaru Tomita.
The-Cell System is an advanced open-source simulation platform to model and analyze biochemical reaction networks. The present algorithm modules of the system assume that the reacting molecules are all homogeneously distributed in the reaction compartments, which is not the case in some cellular processes. The MinCDE system in Escherichia coli, for example, relies on intricately controlled reaction, diffusion and localization of Min proteins on the membrane and in the cytoplasm compartments to inhibit cell division at the poles of the rod-shaped cell. To model such processes, we have extended the E-Cell System to support reaction-diffusion and dynamic localization of molecules in volume and surface compartments. We evaluated our method by modeling the in...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3526/version/1

Modeling Resting-State Brain Functional Integration
Provedor de dados: 17
Autores: Xi-Nian Zuo.
During the past 15 years, resting state fMRI has rapidly emerged as a powerful and reliable approach to explore the human brain architecture. There are two concepts of human brain working mechanism: functional segregation and integration. In this report, I mainly focused on functional integration. Relevant mathematics and statistics in this &amp;#xfb01;eld are reviewed including both seed-based and independent component analysis (ICA) resting state functional connectivity. Moreover, ICA was applied to study the abnormalities of a fronto-striatal-insular network in ADHD. First, mathematical methods to investigate the functional integration by using rs-fMRI were reviewed as well as more details on ICA. Two topics have been addressed: ranking components and...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4380/version/1

Modeling, Simulation and Application of Bacterial Transduction in Genetic Algorithms
Provedor de dados: 17
Autores: Carlos Perales-Gravan; Javier de Vicente Buendia; Rafael Lahoz-Beltra.
At present, all methods in Evolutionary Computation are bioinspired in the fundamental principles of neo-Darwinism as well as on a vertical gene transfer. Thus, on a mechanism in which an organism receives genetic material from its ancestor. Horizontal, lateral or cross-population gene transfer is any process in which an organism transfers a genetic segment to another one that is not its offspring. Virus transduction is one of the key mechanisms of horizontal gene propagation in microorganism (e.g. bacteria). In the present paper, we model and simulate a transduction operator, exploring a possible role and usefulness of transduction in a genetic algorithm. The genetic algorithm including transduction has been named PETRI (abbreviation of Promoting...
Tipo: Manuscript
Palavras-chave: Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3732/version/1

Modeling the hydrolysis of perfluorinated compounds containing carboxylic and phosphoric acid ester functions, alkyl iodides, and sulfonamide groups
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Temperature dependent rate constants were estimated for the acid- and base-catalyzed and neutral hydrolysis reactions of perfluorinated telomer acrylates (FTAcrs) and phosphate esters (FTPEs), and the SN1 and SN2 hydrolysis reactions of fluorotelomer iodides (FTIs). Under some environmental conditions, hydrolysis of monomeric FTAcrs could be rapid (half-lives of several years in marine systems and as low as several days in some landfills) and represent a dominant portion of their overall degradation. Abiotic hydrolysis of monomeric FTAcrs may be a significant contributor to current environmental loadings of fluorotelomer alcohols (FTOHs) and perfluoroalkyl carboxylic acids (PFCAs). Polymeric FTAcrs are expected to be hydrolyzed more slowly, with estimated...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3728/version/1

Modeling the hydrolysis of the polymeric brominated flame retardants BC-58 and FR-1025
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
The SPARC software program was used to estimate the acid-catalyzed, neutral, and base-catalyzed hydrolysis rate constants for the polymeric brominated flame retardants BC-58 and FR-1025, as well as the hydrolyzable daughter products of BC-58. Relatively rapid hydrolysis of BC-58, producing 2,4,6-tribromophenol and tetrabromobisphenol A as the hydrolytically stable end products from all potential hydrolysis reactions, is expected in both environmental and biological systems with starting material hydrolytic half lives (t~1/2,hydr~) ranging from less than one hour in marine systems, several hours in cellular environments, and up to several weeks in slightly acid fresh waters. Hydrolysis of FR-1025 to give 2,3,4,5,6-pentabromobenzyl alcohol is expected to be...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4160/version/1

Modeling Three-Dimensional Spatial Regulation of Bacterial Cell Division (Dissertation)
Provedor de dados: 17
Autores: Satya N. V. Arjunan.
Many important cellular processes are regulated by reaction-diffusion (RD) of molecules that takes place both in the cytoplasm and on the membrane. To model and analyze such multicompartmental processes, we developed a lattice-based Monte Carlo method, Spatiocyte that supports RD in volume and surface compartments at single molecule resolution. Stochasticity in RD and the excluded volume effect brought by intracellular molecular crowding, both of which can significantly affect RD and thus, cellular processes, are also supported. We verified the method by comparing simulation results of diffusion, irreversible and reversible reactions with the predicted analytical and best available numerical solutions. Moreover, to directly compare the localization...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4201/version/1

Modelling Hepatic Endoderm Development: Highly Efficient Differentiation of Human Embryonic Stem Cells to Functional Hepatic Endoderm Requires ActivinA and Wnt3a Signalling.
Provedor de dados: 17
Autores: David Hay; Judy Fletcher; Catherine Payne; John D. Terrace; Ronald C. J. Gallagher; Jan Snoeys; Jim Black; Davina Wojtacha; Kay Samuel; Zara Hannoun; Anne Pryde; Celine Filippi; Ian S. Currie; Stuart J. Forbes; James A. Ross; Philip Newsome; John Iredale.
Human embryonic stem cells (hESCs) are a valuable source of pluripotential primary cells. However, their homogeneous cellular differentiation to specific cell types _in vitro_ has proven difficult thus far. Wnt signalling has been shown to play important roles in coordinating development and we demonstrate that Wnt3a is differentially expressed at critical stages of human liver development _in vivo_. The essential role of Wnt3a in hepatocyte differentiation from hESCs is paralleled by our _in vitro_ model, demonstrating the importance of a physiological approach to cellular differentiation. Our studies provide compelling evidence that Wnt3a signaling is important for coordinated hepato-cellular function _in vitro_ and _in vivo_. In addition, we demonstrate...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1454/version/1

Modelling Hepatic Endoderm Development: Highly Efficient Differentiation of Human Embryonic Stem Cells to Functional Hepatic Endoderm Requires ActivinA and Wnt3a Signalling.
Provedor de dados: 17
Autores: David C. Hay; Judy Fletcher; Catherine Payne; John D. Terrace; Ronald C. J. Gallagher; Jan Snoeys; Jim Black; Davina Wojtacha; Kay Samuel; Zara Hannoun; Anne Pryde; Celine Filippi; Ian S. Currie; Stuart J. Forbes; James A. Ross; Philip Newsome; John P. Iredale.
Human embryonic stem cells (hESCs) are a valuable source of pluripotential primary cells. However, their homogeneous cellular differentiation to specific cell types _in vitro_ has proven difficult thus far. Wnt signalling has been shown to play important roles in coordinating development and we demonstrate that Wnt3a is differentially expressed at critical stages of human liver development _in vivo_. The essential role of Wnt3a in hepatocyte differentiation from hESCs is paralleled by our _in vitro_ model, demonstrating the importance of a physiological approach to cellular differentiation. Our studies provide compelling evidence that Wnt3a signaling is important for coordinated hepato-cellular function _in vitro_ and _in vivo_. In addition, we demonstrate...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1454/version/2

Modelling predicts that heat stress and not drought will limit wheat yield in Europe
Provedor de dados: 17
Autores: Mikhail A. Semenov; Peter R. Shewry.
Global warming is characterised by shifts in weather patterns and increases in extreme weather events. New crop cultivars with specific physiological traits will therefore be required if climate change is not to result in losses of yield and food shortages. However, the intrinsic uncertainty of climate change predictions poses a challenge to plant breeders and crop scientists who have limited time and resources and must select the most appropriate traits for improvement. Modelling is, therefore, a powerful tool to identify future threats to crop production and hence targets for improvement. Wheat is the most important crop in temperate zones, including Europe, and is the staple food crop for many millions of humans and their livestock. However, its...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4335/version/1

Models of Multifunctional Central Pattern Generators: Polyrhythmic Bursting
Provedor de dados: 17
Autores: Andrey Shilnikov.
We demonstrate a motif of three reciprocally inhibitory cells that is able to produce multiple patterns of bursting rhythms. Through the examination of the qualitative geometric structure of two-dimensional maps for phase lag between the cells we reveal the organizing centers of emergent polyrhythmic patterns and their bifurcations, as the asymmetry of the synaptic coupling is varied. The presence of multistability and the types of attractors in the network are shown to be determined by the duty cycle of bursting. This analysis does not require knowledge of the equations that model the system, and so provides a powerful new approach to studying regulatory networks. Thus, the approach is applicable to a variety of biological phenomena beyond motor control.
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5800/version/1

Modularity maps reveal community structure in the resting human brain
Provedor de dados: 17
Autores: Paul Laurienti; Christina Hugenschmidt; Satoru Hayasaka.
The brain is a complex network of interconnecting neurons that combines regional specificity with distributed processing. Recent advances in the field of network theory have facilitated ground-breaking analyses demonstrating that brain connectivity exhibits small-world properties similar to other self-organized networks such as the internet, the genome, or even social organizations. Brain connectivity supports local and global processing through high clustering and short connectivity paths, respectively. While these comprehensive network indices highlight the global organization of the network, the regional specificity is related to the interconnectivity of local neighborhoods within the global system. The work presented here evaluated the community...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3069/version/1

Modularization for the Cell Ontology
Provedor de dados: 17
Autores: Christopher J. Mungall; Melissa A. Haendel; Amelia Ireland; Shahid Manzoor; Terry Meehan; David Osumi-Sutherland; Carlo Torniai; Alexander D. Diehl.
One of the premises of the OBO Foundry is that development of an orthogonal set of ontologies will increase domain expert contributions and logical interoperability, and decrease maintenance workload. For these reasons, the Cell Ontology (CL) is being re-engineered. This process requires the extraction of sub-modules from existing OBO ontologies, which presents a number of practical engineering challenges. These extracted modules may be intended to cover a narrow or a broad set of species. In addition, applications and resources that make use of the Cell Ontology have particular modularization requirements, such as the ability to extract custom subsets or unions of the Cell Ontology with other OBO ontologies. These extracted modules may be intended to...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6685/version/1

Modulation of auditory responses by modality-specific attention in rat primary auditory cortex
Provedor de dados: 17
Autores: Lung-Hao Tai; Anthony M. Zador.
How does attention modulate sensory representations? In order to probe the underlying neural mechanisms, we established a simple rodent model of modality-specific attention. Here we describe results of experiments in freely moving rats in which we have used tetrodes to record neural responses in primary auditory cortex (area A1) while subjects performed this behavior.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Subjects were first trained to perform distinct auditory and olfactory two alternative forced-choice (2AFC) tasks.  Training and testing were conducted in a custom three-poke computer-controlled behavioral apparatus. Subjects initiated trials with a center-poke, which triggered presentation of a tone (either 5 or 15 Hz), an odor (either R(-)-2-Octanol or...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2354/version/1

Modulation of interferon-[alpha] secretion by activated platelets in systemic lupus erythematosus.
Provedor de dados: 17
Autores: Pierre Duffau; Julien Seneschal; Carole Nicco; Jean-Fran&amp;#xe7;ois Viallard; Jean-Luc Pellegrin; Bernard Weill; Jean-Fran&amp;#xe7;ois Moreau; Fr&amp;#xe9;d&amp;#xe9;ric Batteux; Patrick Blanco.
Type I interferons play a key role in systemic lupus erythematosus (SLE) pathogenesis as an &amp;#x22;IFN signature&amp;#x22; is found in the majority of patients with active SLE. Immune complexes are internalized by plasmacytoid dendritic cells (DC) via Fc-[gamma] ReceptorIIA, reach the endosomal compartment and activate IFN-[alpha] secretion through TLR7/9-dependent pathways. Naturally occurring differences in expression of the TLR7/9 gene as well as factors that modulate TLR7/9 expression, including CD154 could therefore contribute to SLE pathogenesis. Although its origin is not elucidated CD154 is hyperexpressed in SLE patients, and is important for the differentiation of autoantibody-secreting cells. We hypothesized that platelets which are an...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/1528/version/1

Modulation of iron responsive gene expression and enzymatic activities in response to changes of the iron nutritional status in _Cucumis sativus_ L.
Provedor de dados: 17
Autores: Patrizia De Nisi; Gianpiero Vigani; Graziano Zocchi.
Regulation exerted by the iron status of the plant on the iron deficiency responses was investigated in cucumber roots (_Cucumis sativus_ L.) both at the biochemical and molecular level. Absence of iron induced the expression of the CsFRO1, CsIRT1, CsHA1 and the Cspepc1 transcripts that was followed by an increase in the corresponding enzymatic activities. Supply of iron repressed gene expression, in particular those of the Fe(III)-chelate reductase and for the high affinity iron transporter and reduce the enzymatic activities. Our results confirm and extend the hypothesis of a coordinate regulation of these responses. Besides  these two activities strictly correlated with iron deficiency adaptation, we considered also the H+-ATPase and the...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4658/version/1

Modulation of the Nuclear Transcription Factor of Activated T Cells by Duck Hepatitis B Virus
Provedor de dados: 17
Autores: Christine Loscher; Urte Matschl; Alicja Iwanski; Schau-Feng Chang; Michael Bruns.
During infection with hepadnaviruses besides the infectious agent a high number of subviral particles without nucleocapsids are produced, which are able to change the infection dramatically. In addition, it was observed that the activation of the nuclear factor of activated T cells, regulated usually in cells of the immune system, was strongly influenced after infection. When primary duck liver cells were infected with purified virions of duck hepatitis B virus the activation of this factor was reduced in a similar way as it was achieved by inhibition of calcineurin, a cellular phosphatase necessary to control the factor, whereas the addition of subviral particles inhibited this reduction. It was found that the large surface protein of the virus was...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/3519/version/1

Moisture availability influences the effect of ultraviolet-B radiation on leaf litter decomposition
Provedor de dados: 17
Autores: William K. Smith; Wei Gao; Heidi Steltzer; Matthew D. Wallenstein; Roger  Tree.
Altered surface ultraviolet-B (UV-B) radiation resulting from a combination of factors that include changes in stratospheric ozone concentrations, cloud cover, and aerosol conditions may affect litter decomposition and, thus, terrestrial nutrient cycling on a global scale.  Although litter decomposition rates vary across biomes, patterns of decomposition suggest that UV-B radiation accelerates litter decay in xeric environments where precipitation is infrequent.  However, under more frequent precipitation regimes where litter decay rates are characteristically high, the effect of UV-B radiation on litter decomposition has not been fully elucidated.  To evaluate this association between moisture regime and UV-B exposure, a litter decomposition experiment...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3634/version/1

Molecular analysis of promoter region of the SMN2 gene in the patients of spinal musculatr atrophy.
Provedor de dados: 17
Autores: Atif A. Baig; Watihayati M. Shamsudin; Marini  Marzuki; Fatemeh Hayati; Teguh H. Suriano; Chan Y. Yean; Ravichandran Manicam; Zilfalil B. Alwi.
Spinal muscular atrophy (SMA) is a neurodegenerative disorder caused by the absence of the full length SMN protein (FL-SMN) as a result of mutation or deletion of SMN1 gene. The isoform to this gene, SMN2 gene, with mutation in 1 base pair, encodes for 10% of FL-SMN protein and is reported to decrease the severity of the disease when there is an increase gene dosage. There are 3 clinical types of SMA; type I, type II and type III. Type I SMA is the most severe type and only a small amount of FL-SMN protein is present in these individuals. We postulated that the difference in the promoter region of SMN2 gene produces the different level of FL-SMN protein. To verify this hypothesis, the DNA samples of 69 SMA patients who were referred to the Human Genome...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5329/version/1

Molecular and nanostructural mechanisms of deformation, strength and toughness of spider silk fibrils
Provedor de dados: 17
Autores: Andrea Nova; Sinan Keten; Nicola Pugno; Alberto Redaelli; Markus  J. Buehler.
Spider silk is one of the strongest, most extensible and toughest biological materials known, exceeding the properties of many engineered materials including steel.  Silks feature a hierarchical architecture where highly organized, densely H-bonded beta-sheet nanocrystals are arranged within a semi-amorphous protein matrix consisting of 31-helices and beta-turn protein structures. By using a bottom-up molecular-based mesoscale model that bridges the scales from Angstroms to hundreds of nanometers, here we show that the specific combination of a crystalline phase and a semi-amorphous matrix is crucial for the unique properties of silks. Specifically, our results reveal that the superior mechanical properties of spider silk can be explained solely by...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4336/version/1

Molecular Bio-imprinting of Biocatalysts
Provedor de dados: 17
Autores: Israr  Khan; Muhammad Waheed Akhtar.
Energy conservation is the cry of the day. Attempts are made all over the world to occupy and use energy reserves. Increased industrialization and mechanization has led to the  depletion of natural energy reserves. Its unavoidable to search for renewable sources of energy, which may be not used now but can be used by future generations. We are using the expertise of our ancestors. Thus exploiting the nature and newer techniques in this area would yield the best results. Bio-imprinting is one of those techniques whereby chemical modification is done in order to achieve highly expressed protein which can be stored in its highly active form in the specific solvent.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Earth &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5665/version/1

Molecular crowding defines a common origin for the Warburg effect in proliferating cells and the lactate threshold in muscle physiology
Provedor de dados: 17
Autores: Alexei Vazquez.
Aerobic glycolysis is a seemingly wasteful mode of ATP production that is seen both in rapidly proliferating mammalian cells and highly active contracting muscles, but whether there is a common origin for its presence in these widely different systems is unknown. To study this issue, here we develop a model of human central metabolism that incorporates a solvent capacity constraint of metabolic enzymes and mitochondria, accounting for their occupied volume densities, while assuming glucose and/or fatty acid utilization. The model demonstrates that activation of aerobic glycolysis is favored above a threshold metabolic rate in both rapidly proliferating cells and heavily contracting muscles, because it provides higher ATP yield per volume density than...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5784/version/1

Molecular Evaluation of exons 8 and 22 of the SHANK3 gene in Autism Spectrum Disorders
Provedor de dados: 17
Autores: A L. Bossolani-Martins; F C. Rodrigues-Lisoni; M L. Nogueira; A Barbosa-Gonc&amp;#x327;alves; E H. Tajara; A C. Fett-Conte.
Autism spectrum disorders are a group of neurodevelopmental disorders with a complex and heterogeneous etiology. Studies have shown that genetic factors play an important role in the aetiology of these diseases. Recently, de novo mutations, frameshifts and deletions have been described in the SHANK3 gene, also known as ProSAP2 gene, which encodes a synaptic scaffolding protein. All the participants of this study had normal karyotypes and underwent screening for Fragile-X syndrome. Subsequently, they were analyzed by direct sequencing of different points of exons 8 and 22 of the SHANK3 gene. None of the study participants presented with changes in these regions. These findings may be due to the fact that mutations, deletions and duplications of the SHANK3...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/4200/version/1

Molecular evidence for the hadrosaur B. canadensis as an outgroup to a clade containing the dinosaur T. rex and birds
Provedor de dados: 17
Autores: Shi Huang.
Molecular analysis of collagen sequences from an 80 million year old hadrosaur _B. canadensis_ and a 68 million year old dinosaur _T. rex_ suggest strongly that _B. canadensis_ is an outgroup to a clade containing _T. rex_ and birds, fully consistent with the well-established phylogeny based on morphological analyses of fossils.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3255/version/1

Molecular evidence for Toxoplasma gondii in the brain of striped dolphins (Stenella coeruleoalba) stranded along the Ligurian Sea coast of Italy
Provedor de dados: 17
Autores: Donato  Traversa; Angela Di Cesare; Cristina Casalone; Barbara Iulini; Walter Mignone; Cristiana Tittarelli; Umberto Proietto; Silvana Meloni; Giulia Buffatello; Fiona Forster; Seamus Kennedy; Giovanni Di Guardo.
Toxoplasma gondii is a protozoan agent of increasing concern for both free-ranging and captive cetaceans. Nonetheless, information on epidemiology, biology, genetics and pathogenic potential of T. gondii for aquatic mammals is incomplete. This work provides molecular evidence for T. gondii in the brain tissue from five striped dolphins (Stenella coeruleoalba) found stranded in 2007-2008 along the Ligurian Sea coast of Italy. These animals showed a more or less severe, subacute to chronic, non purulent, multifocal meningo-encephalitis. Additionally, the cerebral parenchyma of 3 animals harboured protozoan cysts and zoites which were immunohistochemically linked to T. gondii. Consequently, a preliminary molecular investigation was undertaken to confirm the...
Tipo: Poster
Palavras-chave: Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4930/version/1

Molecular evolution of RRM-containing proteins and glycine-rich RNA-binding proteins in plants
Provedor de dados: 17
Autores: Judith L. Gomez-Porras; Martin Lewinski; Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n; Dorothee Staiger.
*Abstract*&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Background:*&amp;#xd;&amp;#xa;In angiosperms, RNA-binding proteins with an RNA recognition motif (RRM)-type RNA interaction domain play an important role in developmental and environmental responses. Despite their pivotal role, a comprehensive analysis of their number and diversity has only been performed in _Arabidopsis_ so far.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Results:*&amp;#xd;&amp;#xa;Here we present a detailed phylogenetic analysis of RRM-containing proteins in plants, the red algae _Cyanidioschyzon merolae_ and cyanobacteria. We identified two major events during the diversification of the RRM in plants, one at the emergence of green plants, and the other at the water-to-land transition. We focused on...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5970/version/1

Molecular implications of prolonged aggression experience: Th, Dat1, Snca and Bdnf gene expression in the ventral tegmental area of the victorious male mice
Provedor de dados: 17
Autores: Natalia P. Bondar; Ul&amp;#x27;yana A.  Boyarskikh; Irina L. Kovalenko; Maxim L. Filipenko; Natalia  N. Kudryavtseva.
Th, Dat1, Snca and Bdnf were the genes whose mRNA levels in the ventral tegmental area of the midbrain were measured in male mice that were victorious in 20 daily agonistic interactions and in a group of such victorious mice that had later not been allowed to fight for 14 days. This experiment demonstrated increased Th, Dat1 and Snca but not Bdnf mRNA levels in the former group as compared to the controls. In the latter group, the expression of the Th and Dat1 genes was still enhanced, while the level of Snca mRNA did not differ from that in the controls. These findings suggest that positive fighting experience enhances the expression of the genes concerned with dopaminergic systems and this enhanced expression is preserved for a long time afterwards....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2042/version/1

Molecular implications of prolonged aggression experience: Th, Dat1, Snca and Bdnf gene expression in the ventral tegmental area of the victorious male mice
Provedor de dados: 17
Autores: N.  P. Bondar; U.  A. Boyarskikh; I. L. Kovalenko; M. L. Filipenko; N.  N. Kudryavtseva.
Th, Dat1, Snca and Bdnf were the genes whose mRNA levels in the ventral tegmental area of the midbrain were measured in male mice that were victorious in 20 daily agonistic interactions and in a group of such victorious mice that had later not been allowed to fight for 14 days. This experiment demonstrated increased Th, Dat1 and Snca but not Bdnf mRNA levels in the former group as compared to the controls. In the latter group, the expression of the Th and Dat1 genes was still enhanced, while the level of Snca mRNA did not differ from that in the controls. These findings suggest that positive fighting experience enhances the expression of the genes concerned with dopaminergic systems and this enhanced expression is preserved for a long time afterwards....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2043/version/1

Molecular mechanisms of the regulation of ATPase cycle in striated muscle
Provedor de dados: 17
Autores: Yuri S. Borovikov; Olga E. Karpicheva; Charles S. Redwood.
New data on the molecular mechanism of the regulation of ATPase cycle by troponin-tropomyosin system have been obtained in reconstructed muscle fibers by using the polarized fluorescence technique, which allowed us following the azimuthal movements of tropomyosin, actin subdomain-1 and myosin SH1 helix motor domain during the sequential steps of ATPase cycle. We found that tropomyosin strands &amp;#x22;rolling&amp;#x22; on thin filament surface from periphery to center at ATPase cycle increases the amplitudes of multistep changes in special arrangement of SH1 helix and subdomain-1 at force generation states. These changes seem to convey to actin monomers and to myosin &amp;#x22;lever arm&amp;#x22;, resulting in enhance of the effectiveness of each...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1391/version/1

Molecular Modeling study of Protein Kinase PKnB from Mycobacterium Tuberculosis with derivatives of 1, 3, 4- Thiadiazoles
Provedor de dados: 17
Autores: Vivek Gupta; Asif Naqvi; Jayendra Tanwar; Kaushlesh Mishra.
Tuberculosis causes more than two million deaths per year. Faced with this global threat it is crucial to better understand the physiology of the causative organism, Mycobacterium Tuberculosis, in order to develop efficient therapeutic strategies. PKnB from Mycobacterium tuberculosis is a crucial receptor-like protein kinase involved in signal transduction. M. tuberculosis PKnB is a trans-membrane Ser/Thr protein kinase (STPK) highly conserved in Gram-positive bacteria and apparently essential for Mycobacterial viability. We have attempted with the help of virtual screening and docking approaches to expound the extent of specificity of protein kinase B towards different classes of Thiadiazoles (an anti-tubercular agent).  The selected Thiadiazoles were...
Tipo: Manuscript
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6136/version/1

Molecular modelling and Function Prediction of hABH7, human homologue  of _E. coli_ ALKB7
Provedor de dados: 17
Autores: Mr. Shankaracharya; Saibal Das; Ambarish Sharan Vidyarthi.
Human homologues of ALKB protein have shown the prime role in DNA damaging drugs, used for cancer therapy. Little is known about structure and function of hABH7, one of the members of this superfamily. Therefore, in the present study we intend to predict its structure and function using various bioinformatics tools. Modeling was done with modeller 9v7 to predict the 3D structure of the hABH7 protein. The tertiary structure model of hABH7, ALKBH7.B99990002.pdb was predicted and evaluated. Validation results showed 97.8% residues in favored and additional allowed regions of Ramachandran plots. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, presence of a Phe120-Gly121-Gly122 conserved pattern in...
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5841/version/1

Molecular Models of DNA Structures and Dynamics: Principles, Techniques and Applications
Provedor de dados: 17
Autores: I. C. Baianu.
Molecular models of DNA structures are representations of the molecular geometry and topology of Deoxyribonucleic acid (DNA) molecules using one of several means, such as: closely packed spheres (CPK models) made of plastic, metal wires for &amp;#x27;skeletal models&amp;#x27;, graphic computations and animations by computers, artistic rendering, and so on, with the aim of simplifying and presenting the essential, physical and chemical, properties of DNA molecular structures either in vivo or in vitro. Computer molecular models also allow animations and molecular dynamics simulations that are very important for understanding how DNA functions in vivo.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7075/version/1

Molecular phylogenies and evolutionary behavior of AhR (aryl hydrocarbon receptor) pathway genes in aquatic animals
Provedor de dados: 17
Autores: Hailong Zhou; Ying Qu; Qinzhao Xue.
Phylogenetic analysis of AhR pathway genes and their evolutionary rate variations were studied on aquatic animals. The gene sequences for the proteins involved in this pathway were obtained from major phylogenetic groups of mollusc, amphibian, fish and aquatic mammal. These genes were distributed under four major steps of toxicology regulation: formation of cytosolic complex, translocation of AhR, heterodimerization of AhR and induction of CYP1A. The NJ, MP and ML algorithm were used on protein coding DNA sequences to deduce the evolutionary relationship for the respective AhR pathway gene among different aquatic animals. The rate of nonsynonymous nucleotide substitutions per nonsynonymous site (d~N~) and synonymous nucleotide substitutions per synonymous...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2928/version/1

Molecular simulations to study the effect of pore geometry and structure on the adsorption of CH4/H2 mixtures in carbon pores
Provedor de dados: 17
Autores: Vasanth K. Kumar; Erich A. M&amp;#xfc;ller; Francisco  Rodriguez-Reinoso.
We used molecular simulations to study the effect of pore structure and geometry on the selectivity of carbon materials for the adsorption of methane from a mixture of methane and hydrogen at 50 bar and 298 K. We modeled hydrogen as a more realistic dumb-bell shaped fluid and methane as spherical Lennard-Jones sphere. The pore geometry studied includes the slit, nanotube, random carbon structure and carbon pores that mimic a foam structure. Our results confirm that both the pore size and pore structure have a significant effect on the selectivity for methane molecules. An array of nanotubes that have a closed structure has the highest selectivity for methane molecules, followed by carbon foam, slit and random pore structures. Energetic and packing effects...
Tipo: Poster
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6132/version/1

Molecular Static and Dynamic Analyses reveal Flaw in Murine Model used by US FDA to Detect Drug Carcinogenicity
Provedor de dados: 17
Autores: Trevor Marshall.
The US FDA currently accepts carcinogenicity studies of pharmaceutical drugs based on murine models. In addition to 6 month studies with p53(+/-) and ras.H2 transgenic mice, lifetime studies (typically 2 years) in WT mice or rats are also considered as evidence that a drug lacks carcinogenic activity. This model is not always exhaustive. For example, during the acceptance testing of the ARB Olmesartan[1], possible carcinogenicity observed in hamsters was not able to be duplicated in rats, or in transgenic mice. We have previously used the static molecular modeling of AutoDock to demonstrate that Olmesartan has agonostic activity in the PDB:1DB1 model of the human VDR Nuclear Receptor[2], while it has antagonistic activity in the PDB:1RK3 model of the rat...
Tipo: Poster
Palavras-chave: Biotechnology; Cancer; Immunology; Pharmacology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/52/version/1

Molecular-genetic analysis of Mycobacterium tuberculosis strains spread in different patient groups in St.Petersburg (Russia)
Provedor de dados: 17
Autores: Ekaterina Chernyaeva; Pavel Dobrynin; Natalia Pestova; Natalia Matveeva; Vladimir Zhemkov; Andrei Kozlov.
Molecular epidemiological features of M.tuberculosis strains spread among different patient groups in Russia is not studied well. The aim of our study was to compare genotypes of M.tuberculosis strains circulating among TB patients from different groups: homeless, HIV-infected, prisoners and general population of St.Petersburg citizens. &amp;#xd;&amp;#xa;One hundred fifty M.tuberculosis complex isolates from different TB patient groups were studied using spoligotyping method. &amp;#xd;&amp;#xa;The majority of studied M.tuberculosis isolates in all groups belonged to Beijing family (56% among homeless; 77% among HIV-infected; 60% among general population; 83% among prisoners). There were no significant difference in Beijing family prevalence among homeless...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/6073/version/1

Molecular-genetic analysis of Mycobacterium tuberculosis strains spread in different patient groups in St.Petersburg (Russia)
Provedor de dados: 17
Autores: Ekaterina Chernyaeva; Pavel Dobrynin; Natalia Pestova; Natalia Matveeva; Vladimir Zhemkov; Andrei Kozlov.
Molecular epidemiological features of Mycobacterium tuberculosis strains spread among different patient groups in Russia is not studied well. The aim of our study was to compare genotypes of M.tuberculosis strains circulating among TB patients from different groups: homeless, HIV-infected, prisoners and general population of St.Petersburg citizens. &amp;#xd;&amp;#xa;One hundred fifty M.tuberculosis complex isolates from different TB patient groups were studied using spoligotyping method. &amp;#xd;&amp;#xa;The majority of studied M.tuberculosis isolates in all groups belonged to Beijing family (56% among homeless; 77% among HIV-infected; 60% among general population; 83% among prisoners). There were no significant difference in Beijing family prevalence...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/6073/version/2

Money handling influences BMI: a survey of cashiers
Provedor de dados: 17
Autores: Shraddha Karve; Ketaki Shurpali; Neelesh Dahanukar; Maithili Jog; Milind Watve.
Money is a recent phenomenon in the evolutionary history of man and therefore no separate brain centre to handle money is likely to have evolved. The brain areas activated by food reward and money reward are extensively overlapping. In an experimental set-up, hunger was demonstrated to influence money related decisions and money related thoughts to influence hunger. This suggests that the brain areas evolved for handling food related emotions are exapted to handle money and therefore there could be a neuronal cross-talk between food and money. If this is true then attitude and behavior related to money and wealth could influence obesity. We conducted a survey of 211 individuals working as full time cashiers in order to test whether ownership over the cash,...
Tipo: Poster
Palavras-chave: Developmental Biology; Ecology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2708/version/1

More damn lies about data access
Provedor de dados: 17
Autores: Myles Axton.
More data than we can handle is no excuse to give up our efforts to promote data access, but it may make us think about new ways to make it sustainable.&amp;#xd;&amp;#xa;[This draft was written in the hope that participants of the Sage Congress will write an Nature Genetics Editorial in the manner of Tom Sawyer&amp;#x2019;s white fence (Twain M. 1876). All contributions received by April 10th 2011 will be attributed.]&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5873/version/1

Motif analysis of amphioxus, lamprey and invertebrate estrogen receptors and amphioxus and human estrogen-related receptors: Towards a better understanding of estrogen receptor evolution
Provedor de dados: 17
Autores: Michael E. Baker; Charlie Chandsawangbhuwana.
*Background.*  The origins of steroid-dependent regulation of the vertebrate estrogen receptor (ER) are poorly understood.  Genes with statistically significant sequence similarity to vertebrate ERs have been found in lamprey, a basal vertebrate, and amphioxus, a basal chordate.  Motif analysis of these sequences provides an opportunity to investigate early events in the evolution of the ER.&amp;#xd;&amp;#xa;*Results.*  We used artificial intelligence-based software to construct twelve motifs specific to the estrogen-binding domain of ER[alpha] and ER[beta] in land vertebrates and teleosts.  We mapped these ER-specific motifs onto the sequences of lamprey, amphioxus, invertebrate and selected vertebrate ERs and amphioxus, Ciona and human estrogen-related...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1542/version/2

Motif analysis of amphioxus, lamprey and invertebrate estrogen receptors and amphioxus and human estrogen-related receptors: Towards a better understanding of estrogen receptor evolution
Provedor de dados: 17
Autores: Michael E. Baker; Charlie Chandsawangbhuwana.
*Background.*  The origins of steroid-dependent regulation of the vertebrate estrogen receptor (ER) are poorly understood.  Genes with statistically significant sequence similarity to vertebrate ERs have been found in lamprey, a basal vertebrate, and amphioxus, a basal chordate.  Motif analysis of these sequences provides an opportunity to investigate early events in the evolution of the ER.&amp;#xd;&amp;#xa;*Results.*  We used artificial intelligence-based software to construct twelve motifs specific to the estrogen-binding domain of ER[alpha] and ER[beta] in land vertebrates and teleosts.  We mapped these ER-specific motifs onto the sequences of lamprey, amphioxus, invertebrate and selected vertebrate ERs and amphioxus and human estrogen-related receptor...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1542/version/1

Motor fluency shapes abstract concepts
Provedor de dados: 17
Autores: Daniel Casasanto; Evangelia Chrysikou.
People with different types of bodies tend to think differently in predictable ways, even about abstract ideas that seem far removed from bodily experience. Right- and left-handers implicitly associate positive ideas like goodness and honesty more strongly with their dominant side of space, the side on which they can interact with their environment more fluently, and negative ideas with their non-dominant side. This suggests a role for motor experience in shaping abstract thoughts. Yet, previous evidence is also consistent with an experience-independent account. Here we show that right-handers&amp;#x27; tendency to associate &amp;#x27;good&amp;#x27; with right and &amp;#x27;bad&amp;#x27; with left can be reversed due to both long- and short-term changes in...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4802/version/1

Motor Nucleus of the Trigeminal Nerve
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Nicholas A. Kostakis; Lydia  L. Ng; Angela L. Guillozet-Bongaarts.
This report contains a summary of expression patterns for genes that are enriched in the motor nucleus of the trigeminal nerve (V) of the pons. All data is derived from the Allen Brain Atlas (ABA) in situ hybridization mouse project. The structure&amp;#x27;s location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the motor nucleus of the trigeminal nerve were compared to the values of its larger parent structure, in this case the pons, for the purpose of extracting regionally selective gene expression data. The highest ranking genes were manually curated and verified. 50 genes were then selected and compiled for expression...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2202/version/1

MR Neurography and Diffusion Tensor Imaging: Origin, History and Impact
Provedor de dados: 17
Autores: Aaron G. Filler.
*Objective:* Methods were invented that made it possible to image peripheral nerves in the body and to image neural tracts in the brain. Over a 15 year period, these techniques &amp;#x2013; MR Neurography and Diffusion Tensor Imaging &amp;#x2013; were then deployed in the clinical and research community and applied to about 50,000 patients. Within this group, about 5,000 patients having MR Neurography were carefully tracked on a prospective basis.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Method:* In the study group a uniform imaging methodology was applied and all images were reviewed and registered by referral source, clinical indication, efficacy of imaging and quality. Various classes of image findings were identified and subjected to a variety of small...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1932/version/2

MR Neurography and Diffusion Tensor Imaging: Origin, History and Impact
Provedor de dados: 17
Autores: Aaron G. Filler.
Objective &amp;#x2013; Methods were invented that made it possible to image peripheral nerves in the body and to image neural tracts in the brain. Over a 15 year period, these techniques &amp;#x2013; MR Neurography and Diffusion Tensor Imaging &amp;#x2013; were then deployed in the clinical and research community and applied to about 50,000 patients. Within this group, about 5,000 patients having MR Neurography were carefully tracked on a prospective basis.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Method &amp;#x2013; In the study group a uniform imaging methodology was applied and all images were reviewed and registered by referral source, clinical indication, efficacy of imaging and quality. Various classes of image findings were identified and subjected to a...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1932/version/1

MR Neurography and Diffusion Tensor Imaging:  Origins, History &amp;#x26; Clinical Impact
Provedor de dados: 17
Autores: Aaron G. Filler.
Objective &amp;#x2013; Methods were invented that made it possible to image peripheral nerves in the body and to image neural tracts in the brain. Over a 15 year period, these techniques &amp;#x2013; MR Neurography and Diffusion Tensor Imaging &amp;#x2013; were then deployed in the clinical and research community and applied to about 50,000 patients. Within this group, about 5,000 patients having MR Neurography were carefully tracked on a prospective basis.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Method &amp;#x2013; In the study group a uniform imaging methodology was applied and all images were reviewed and registered by referral source, clinical indication, efficacy of imaging and quality. Various classes of image findings were identified and subjected to a...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2877/version/1

MR Neurography and Diffusion Tensor Imaging:  Origins, History &amp;#x26; Clinical Impact
Provedor de dados: 17
Autores: Aaron G. Filler.
Objective &amp;#x2013; Methods were invented that made it possible to image peripheral nerves in the body and to image neural tracts in the brain. Over a 15 year period, these techniques &amp;#x2013; MR Neurography and Diffusion Tensor Imaging &amp;#x2013; were then deployed in the clinical and research community and applied to about 50,000 patients. Within this group, about 5,000 patients having MR Neurography were carefully tracked on a prospective basis.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Method &amp;#x2013; In the study group a uniform imaging methodology was applied and all images were reviewed and registered by referral source, clinical indication, efficacy of imaging and quality. Various classes of image findings were identified and subjected to a...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2877/version/2

MRI and MRSI Application in Neurodegeneration
Provedor de dados: 17
Autores: Rakesh Sharma.
MRI combined with MR spectroscopy generates better information of both brain tissue composition and mesurement of metabolites or neurochemicals in multiple sclerosis(MS), Alzheimer&amp;#x27;s disease and epilepsy. New fast imaging techniques are technical advance in visualizing accurate anatomy and measurement of absolute neurochemicals in brain. Gray metter seated MS lesions is a new form of disease and lesion may appear normal on MRI but show spectroscopy peaks. High magnetic field scanners are available for fast imaging.
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4317/version/1

mRNA diffusion explains protein gradients in Drosophila early development
Provedor de dados: 17
Autores: Rui Dilao; Daniele Murro.
We propose a new model describing the production and the establishment of the stable gradient of the Bicoid protein along the antero-posterior axis of the embryo of _Drosophila_. In this model, we consider that _bicoid_ mRNA diffuses along the antero-posterior axis of the embryo and the protein is produced in the ribosomes localized near the syncytial nuclei. Bicoid protein stays localized near the syncytial nuclei as observed in experiments.We calibrate the parameters of the mathematical model with experimental data taken during the cleavage stages 11 to 14 of the developing embryo of _Drosophila_. We obtain good agreement between the experimental and the model gradients, with relative errors in the range 5-8%. The inferred diffusion coefficient of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3402/version/1

MSTd Neurons Encode Nonlinear Combinations of Retinal and Extra-retinal Signals
Provedor de dados: 17
Autores: Lukas Brostek.
Neuronal activity in the dorsal Medial Superior Temporal area (MSTd) is assumed to depend on both retinal and extra-retinal input. Most of the neurons show activity when presented with a moving large-field visual stimulus. In addition, many MSTd neurons are activated during smooth pursuit eye movements even in the absence of retinal input. However, the interaction between the retinal and extra-retinal input is not yet fully understood.&amp;#xd;&amp;#xa;Here we present novel insights regarding the tuning of MSTd neurons for combinations of different input variables using an information-theoretic approach. Neuronal tuning functions can be expressed by the conditional probability of observing a spike given any combination of input variables. However,...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5938/version/1

MUEGANO: A divide and conquer algorithm to overcome memory limitations when assembling shotgun projects
Provedor de dados: 17
Autores: Octavio Martinez; Araceli Fernandez-Cortes.
When assembling a large quantity of reads in a genomic shotgun project a serious limitation is the amount of random access memory (RAM) of the computers used in the project. This arises because all assembling programs must look at all the overlaps between reads at the same time, using RAM in order to construct contigs, and the memory of the computer can be filled up during this step, causing the abortion of the assembling process.&amp;#xd;&amp;#xa;Here we propose an algorithm that is capable of overcoming any memory limitation by using redundancy of processing and thus producing an increase in computing time but overcoming the memory limitation.&amp;#xd;&amp;#xa;The proposed algorithm consists in dividing the reads in a set of groups which size is half the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3712/version/1

Multi-Cancer Computational Analysis Reveals Metastasis-Associated Variant of Desmoplastic Reaction Involving INHBA and THBS2
Provedor de dados: 17
Autores: Hoon Kim; John Watkinson; Vinay Varadan; Dimitris Anastassiou.
Despite extensive research, the details of the metastasis-associated biological mechanisms are largely unknown. Here, we analyze data from multiple cancers using a novel computational method identifying sets of genes whose coordinated overexpression indicates the presence of a particular phenotype. We conclude that there is one shared &amp;#x201c;core&amp;#x201d; metastasis-associated gene expression signature corresponding to a specific variant of desmoplastic reaction, present in a large subset of samples that have exceeded a threshold of invasive transition specific to each cancer, indicating that the biological mechanism is triggered at that point. For example this threshold is reached at stage IIIc in ovarian cancer and at stage II in colorectal...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4503/version/1

Multidimensional Analysis of Snow Cover Data in South Dakota Diversity of Landscapes
Provedor de dados: 17
Autores: Boris Shmagin; Carol Johnston.
Snow distribution in SD was studied with Factor Analysis (FA) of monthly total snowfall [in]. The long-term data obtained from the High Plains Regional Climate Center were used for the territory of South Dakota. The perspective for creating an Atlas of Climate and Water Resources for SD directed this study of total monthly snowfall with connection to landscape diversity.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The initial matrix {Xn*p} where n is number of stations and p is number of variables of monthly average for period of observations. The maximum number of stations n with mutual interval of observations for SD is equal 93 (n=93). These stations have mutual time interval of 18 years observations (1952-53 &amp;#x2013; 1969-70). Total monthly snowfall has...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2445/version/1

Multidimensional structure of stream flow regime in a hierarchy of landscapes within the U.S. Great Lakes basin
Provedor de dados: 17
Autores: Boris Shmagin; Carol  Johnston; Scott Bridgham.
Stream flow data were used to evaluate a landscape hierarchy ranging from the Ontonagon River watershed (OW) to the upper peninsula of Michigan (MUP) to the entire Great Lakes basin (GLB). Flow records (1926-1988) were obtained for 45 USGS gauging stations within the GLB with drainage areas of 100-1450 sq. mi. Data were arranged in five initial matrixes with number of time series from 14 to 45. Factor analysis of average annual flow revealed from three to six patterns of stream runoff within distinct regions of the GLB. A typical watershed was selected to represent each of the five distinct regions identified for the period 1956-88, and its data were used to analyze monthly average flow values. This analysis identified two to five groupings of months with...
Tipo: Poster
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1371/version/1

Multidrug resistance of non-adherent cancer cells
Provedor de dados: 17
Autores: Navneet  Singh; Subhas Chakrabarty; Guangming Liu.
Metastases are the cause of 90% of human cancer deaths. Cancer in _situ_ can usually be effectively removed by surgery. Once cancer cells disseminate from the original site and start to circulate in blood, lymph, or other body fluids, the disease becomes almost incurable. Here we show that cancer cells in a non-adherent, 3-dimentional growth pattern are highly drug resistant compared to their adherent counterparts that grow in monolayer, attaching to the wall of tissue culture plates. The non-adherent cancer cells retain the adhering potential and can attach to an appropriate surface to reacquire adherent phenotype. Once the non-adherent cancer cells become attached, they regain drug response, similar to the original adherent cells. A significant increase...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4488/version/1

Multifunction moonlighting and intrinsically disordered proteins: Information catalysis, nonrigid molecule symmetries, and the &amp;#x27;logic gate&amp;#x27; spectrum
Provedor de dados: 17
Autores: Rodrick Wallace.
Intrinsically disordered proteins (IDP) appear far more likely to engage in functional moonlighting than well-structured proteins. The recent use of nonrigid molecule theory to address IDP structure and dynamics produces this result directly: Mirror image subgroup or subgroupoid tiling matching of the molecular fuzzy lock-and-key can be much richer for IDPs since the number of possible group or groupoid symmetries can grow exponentially with molecule length, while tiling matching for 3D structured proteins is relatively limited. A simple information catalysis model suggests how this mechanism can produce a vast spectrum of biological &amp;#x27;logic gates&amp;#x27; having subtle properties far beyond familiar AND, OR, XOR, etc. behaviors. Inferring the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Molecular Cell Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6413/version/1

Multifunctional Hybrid Silica Particles for Multicolor Imaging and Multiplex Tasking
Provedor de dados: 17
Autores: Sang Man koo; Hae Sung Kim; Chan Yoon Jung; Ha Young Kim; Hoe Jin Hah.
Multifunctional submicron particles have recently emerged as great promises for biological applications such as bio-labeling, medical diagnostics, and drug delivery. These particles are non-toxic and have size comparable to biomolecules, becoming very suitable for biomedical applications. The particle structures can be engineered to perform multicolor imaging, as well as multiplex tasking such as site-selective binding, detection, and separation. In addition, these particles can load a large amount of fluorescent dye for signal amplification. Several synthetic techniques have been developed for a variety of submicron particles, including core-shell synthesis, layer-by-layer techniques, multi-block polymer emulsifications, and surface modifications. Silica...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1621/version/1

Multifunctional Nanoparticles for Imaging Guided Interventions
Provedor de dados: 17
Autores: Yousef Haik; Basel al-Ramadi; Bashar Issa; Shahnaz Qadri; Saleh Hayek; Hassan Hijaze.
We describe multifunctional magnetic nanoparticles (MNPs) encapsulated in thermosensitive, drug-bearing shells and delivered to the tumor site by genetically modified and non-pathogenic strains of bacteria with known affinity to tumors for an effective and minimally invasive protocol for tumor management. The magnetic nanoparticles also serve as a non-invasive imaging contrast agent, heating agent as well as thermometry monitoring agents. We have shown an efficient tumor management on a mouse model utilizing the MNPs. Our studies showed that these novel MNPs significantly reduce the progress of tumor and prolong the animal life and function as an imaging contrast to visually monitor the tumor treatment and evolution.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/2190/version/1

Multiple Ontologies for Integrating Complex Phenotype Datasets
Provedor de dados: 17
Autores: Mary Shimoyama; Melinda Dwinell; Howard Jacob.
There has been an emergence of multiple large scale phenotyping projects in the rat model organism community as well as renewed interest in the ongoing phenotype data generated by thousands of researchers using hundreds of rat strains worldwide.  Unfortunately, this data is scattered and is neither described nor formatted in a standardized manner.  A system to integrate complex phenotype data from multiple sources and facilitate data mining and analysis is being developed using multiple ontologies.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Introduction*&amp;#xd;&amp;#xa;The potential value of integrating phenotype data from multiple sources (different laboratories, varying techniques to measure similar phenotypes, multiple strains) is enormous. Presented here is...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3554/version/2

Multiple Ontologies for Integrating Complex Phenotype Datasets
Provedor de dados: 17
Autores: Mary Shimoyama; Melinda Dwinell; Howard Jacob.
There has been an emergence of multiple large scale phenotyping projects in the rat model organism community as well as renewed interest in the ongoing phenotype data generated by thousands of researchers using hundreds of rat strains worldwide.  Unfortunately, this data is scattered and is neither described nor formatted in a standardized manner.  A system to integrate complex phenotype data from multiple sources and facilitate data mining and analysis is being developed using multiple ontologies.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Introduction*&amp;#xd;&amp;#xa;The potential value of integrating phenotype data from multiple sources (different laboratories, varying techniques to measure similar phenotypes, multiple strains) is enormous. Presented here is...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3554/version/1

Multi-scale network biology model &amp;#x26; the model library
Provedor de dados: 17
Autores: Jianghui Xiong.
Multi-scale network biology model &amp;#x26; the model library
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5778/version/1

Multi-site precipitation downscaling via an expanded conditional density network
Provedor de dados: 17
Autores: Alex J. Cannon.
Statistical downscaling models are used to estimate weather data at a station or stations based on atmospheric circulation data defined at a coarser resolution, for example gridded outputs from a Global Climate Model (GCM). Downscaled data can be used as inputs to environmental models that require finer-scale climate fields than are currently available from GCMs. Maintaining realistic downscaling relationships between sites and variables is particularly important in hydrological models, as streamflow depends strongly on the spatial distribution of precipitation in a watershed and on interactions with temperature that determine whether precipitation falls as rain or snow. More generally, precipitation is a difficult variable to downscale because of its...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/446/version/1

Multivalent ligands of CD22 for targeting of B cells
Provedor de dados: 17
Autores: James C. Paulson.
Multivalent ligands of CD22 for active targeting of B cells. Mary O&amp;#x2019;Reilly, Wei Hsu Chen, Gladys Completo, Ying Zeng, Satoshi Futakawa and Cory Rillahan and James C. Paulson, Departments of Chemical Physiology and Molecular Biology, The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The siglecs comprise 13 members of the immunoglobulin superfamily that recognize sialic acid containing glycans, and are differentially expressed on leukocytes and glial cells.   The natural ligands of siglecs typically occur on the same cell (in cis) and/or on adjacent cells (in trans).  Cis ligands mask the binding of multivalent synthetic sialoside ligands and are thought to regulate the activity of...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Chemistry; Immunology; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3549/version/1

Mummification in a Bitch: A case report
Provedor de dados: 17
Autores: Perumal P; Venkateswaralu B; D.N. Mohanty; Srinibas  Das; Ashok Kumar Barik; P.C. Mishra.
A pug aged 5 years was admitted in the Lyka pet clinic with difficulty in parturition. Breeding history of the dog was collected from the owner. X-ray was conducted which confirmed the presence of foetus. The bitch was manually handled to relieve the Dystocia following intravenous drip of N.S.S. and oxytocin. In the vent of unsuccessful attempt the bitch was surgically operated for C.S. and six fetuses of which four normal and two mummified were relieved. Routine post operative care were undertaken and the bitch recovered normally with out any complication. Photographic recording was also made during the recovery of mummified foetus.
Tipo: Presentation
Palavras-chave: Microbiology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7063/version/1

Mushroom-bodies mediate hierarchical interactions between fact- and skill-learning in _Drosophila_
Provedor de dados: 17
Autores: Bj&amp;#xf6;rn Brembs; Wolfgang Plendl.
Different brain circuits mediate the acquisition of skills and habits (via operant/instrumental learning) and the acquisition of facts (via classical/Pavlovian learning). Realistic learning situations always comprise interactions of skill- and fact-learning components (composite learning). So far, these interactions have escaped thorough scrutiny. Fixed flying _Drosophila melanogaster_ at the torque meter provide one of the very few systems where the relationship of operant and classical predictors in composite learning can be studied with sufficient rigor. Experiments with wildtype, mutant and transgenic flies show that there is an interaction between predictive stimuli (classical component) and goal-directed actions (operant component) which makes...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/905/version/1

Mushroom-bodies regulate habit formation in _Drosophila_
Provedor de dados: 17
Autores: Bj&amp;#xf6;rn Brembs.
Our past experience is one of the primary sources of information when faced with a choice. We ask ourselves: &amp;#x22;what will happen if I do this?&amp;#x22;&amp;#xd;&amp;#xa;Accurately predicting the consequences of our actions is usually modeled by operant (instrumental) learning experiments. These types of experiments are often contrasted with classical (Pavlovian) conditioning experiments in a dichotomy. And indeed, different brain circuits mediate the acquisition of skills and habits (via operant/instrumental learning) and the acquisition of facts (via classical/Pavlovian learning). However, realistic learning situations always comprise interactions of skill- and fact-learning components (composite learning). Fixed flying Drosophila melanogaster at...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2171/version/1

Music can reduce cognitive dissonance
Provedor de dados: 17
Autores: Nobuo  Masataka; Leonid Perlovsky.
The fundamental cognitive functions of music in the brain have not been known and evolutionary reasons for musical abilities seem mysterious. A recent hypothesis suggested that a fundamental function of music has been to help mitigating cognitive dissonances. A cognitive dissonance is &amp;#x22;a discomfort caused by holding conflicting cognitions&amp;#x22; simultaneously; it usually leads to devaluation of conflicting knowledge. Since every concept implies some degree of contradictions to other knowledge, unmitigated cognitive dissonances could prevent evolution of cognition. Thus music might be fundamental for the evolution of cognition. Here we provide experimental confirmation of this hypothesis using a classical paradigm known to induce a cognitive...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7080/version/1

Music in the first days of life
Provedor de dados: 17
Autores: Daniela Perani; Maria Cristina Saccuman; Paola Scifo; Danilo Spada; Guido Andreolli; Rosanna Rovelli; Cristina Baldoli; Stefan Koelsch.
In adults, specific neural systems with right-hemispheric weighting are necessary to process pitch, melody and harmony, as well as structure and meaning emerging from musical sequences. To which extent does this neural specialization result from exposure to music or from neurobiological predispositions? We used fMRI to measure brain activity in 1 to 3 days old newborns while listening to Western tonal music, and to the same excerpts altered, so as to include tonal violations or dissonance. Music caused predominant right hemisphere activations in primary and higher-order auditory cortex. For altered music, activations were seen in the left inferior frontal cortex and limbic structures. Thus, the newborn&amp;#x27;s brain is able to plenty receive music and...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2114/version/1

MUSIC - Multisimulation Coordinator: Request For Comments
Provedor de dados: 17
Autores: &amp;#xd6;rjan Ekeberg; Mikael Djurfeldt.
MUSIC is an API allowing large scale neuron simulators using MPI internally to exchange data during runtime. MUSIC provides mechanisms to transfer massive amounts of event information and continuous values from one parallel application to another. Special care has been taken to ensure that existing simulators can be adapted to MUSIC. In particular, MUSIC handles data transfer between applications that use different time steps and different data allocation strategies. This RFC - Request For Comments - document invites comments on the proposed design and prototype specifications. &amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1830/version/1

Mutations in pathways depending on BRCA1 and BRCA2 may increase cancer risks from an environmental carcinogen
Provedor de dados: 17
Autores: Bernard Friedenson.
Recently, the President&amp;#x2019;s Cancer Panel [2008-2009] protested that preventive action is not taken when uncertainty exists about potential harm from a chemical, because the US regulatory approach demands that a hazard be incontrovertibly demonstrated.  It is now incontrovertible that formaldehyde increases risks for leukemias.  Evidence is also strong that formaldehyde causes some types of DNA damage in humans that are known to require repairs mediated by BRCA1/2 containing pathways.  Homologous recombination repairs require BRCA1/2, Fanconi and ATM proteins in these pathways.  Biallelic BRCA2 mutations interfere with these repairs and are clearly associated with leukemias, especially myeloid leukemias.  Fanconi anemia homozygotes have very high...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/5669/version/1

Mutations in the _SC4MOL_ gene encoding a novel methyl sterol oxidase cause autosomal recessive psoriasisiform dermatitis, microcephaly and developmental delay
Provedor de dados: 17
Autores: Miao He; Lisa Kratz; Jushua Michel; Abbe Vallejo; Laura Ferris; Richard Kelley; Jacqueline Hoover; Michael Gibson; Gerard Vockley.
Disorders of cholesterol biosynthesis have clinical manifestations involving skeleton, eyes, neurologic development, and skin. We describe a patient with congenital cataracts, developmental delay, microcephaly, and low serum cholesterol who developed severe psoriasiform dermatitis and arthralgias beginning at age 3. Her brain MRI indicatedminor gliosis. Quantitative sterol analysis of patient plasma and skin showed marked elevation of 4alpha-methyl- and 4, 4&amp;#x27;-dimethylsterols, indicating a deficiency in the first step of sterol C4 demethylation in cholesterol biosynthesis. Molecular studies showed mutations in _SC4MOL_, a gene predicted to encode a sterol C4 methyl oxidase. Thus, our patient has a previously undescribed inborn error of cholesterol...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/2163/version/1

My experiment with open science: Why the benefits of sharing go beyond source code
Provedor de dados: 17
Autores: Carl Boettiger.
I briefly describe three themes that help maximize the benefits of an open science approach towards code, literature, discussions, and lab notebooks.
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4602/version/1

Myosin II isoforms with separate but linked functions determine the fate of lamellipodia extension during cell spreading
Provedor de dados: 17
Autores: Venkaiah Betapudi.
Non-muscle myosin II role has been implicated in the extension of lamellipodia, a critical step in the initiation of directed cell migration, invasion and other cellular processes, but the mechanistic details are limited to driving retrograde actin filaments. The present study reveals distinct localization of myosin IIA and IIB with an unexpected opposite mechanical roles in mediating lamellipodia extension during spreading. Attachment of cells to matrix is impaired in the absence of either isoforms, but differential regulation of focal contacts formation occurs in myosin IIA^-^; and IIB^-^; cells. Spreading cells expressing both isoforms display an organized actin network consisting of retrograde filaments, arcs and central filaments. Loss of actin arcs...
Tipo: Manuscript
Palavras-chave: Cancer; Microbiology; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2868/version/1

Myosin VI Lever Arm Rotation: Fixed or Variable?
Provedor de dados: 17
Autores: Yujie Sun; Harry  W. Schroeder III; John  F. Beausang; Kazuaki Homma; Mitsuo Ikebe; Yale  E. Goldman.
Two recent articles addressed the power-stroke of myosin VI molecules during stepping. Although both groups measured the angles of fluorescent probes attached on the myosin VI molecule lever arm using polarized fluorescence techniques, they differ about whether the myosin VI lever arm rotation is fixed1 or variable2. Here we discuss the causes of the discrepancy between the two studies and the implications for myosin VI processive motility.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4182/version/1

Myth about neuronal nitric oxide synthase in the sarcolemma of skeletal muscles
Provedor de dados: 17
Autores: Igor Buchwalow; Werner Boecker.
In skeletal muscles, neuronal NO synthase (nNOS, designated also as NOS1) was reported to be restricted to the sarcolemma. With the advent of modern powerful immunocytochemical techniques this commonly accepted view appears to be a delusion and has to be re-evaluated.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1718/version/1

Names on Nodes: Automating the Application of Taxonomic Names within a Phylogenetic Context
Provedor de dados: 17
Autores: T. Michael Keesey.
_Names on Nodes_^1^ is an open&amp;#x2011;source^2^ Flex application which utilizes a mathematical approach to automate the application of phylogenetically&amp;#x2011;defined names to phylogenetic hypotheses. Phylogenetic hypotheses are modeled as directed, acyclic graphs, and may be read from bioinformatics or graph files (NEXUS, NexML, Newick, and GraphML) or created de novo. Hypotheses may also be merged from multiple sources. _Names on Nodes_ stores hypotheses as MathML, an XML&amp;#x2011;based language for representing mathematical content and presentation. Phylogenetic definitions may be constructed using a visual editor and exported in MathML. Thus, it is possible to create a dictionary of defined names and automatically apply them to phylogenetic...
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4653/version/1

NamesforLife Semantic Resolution Services for the Life Sciences
Provedor de dados: 17
Autores: Charles T. Parker; Dorothea K. Taylor; Kara Mannor; Sarah Wigley; Nicole Osier; Catherine Lyons; George M. Garrity.
A major challenge in bioinformatics, life sciences, and medicine is using correct and informative names. While this sounds simple enough, many different naming conventions exist in the life sciences and medicine that may be either complementary or competitive with other naming conventions. For a variety of reasons, proper names are not always used, leading to an accumulated semantic ambiguity that readers of the literature and end users of databases are left to resolve on their own. This ambiguity is a growing problem and the biocuration community is aware of its consequences. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To assist those confronted with ambiguous names (which not only includes researchers but clinicians, manufacturers, patent attorneys, and others...
Tipo: Poster
Palavras-chave: Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5137/version/1

Nanoconfinement of spider silk fibrils begets superior strength, extensibility and toughness
Provedor de dados: 17
Autores: Tristan Giesa; Melis Arslan; Nicola Pugno; Markus J. Buehler.
Silk is an exceptionally strong, extensible and tough material made from simple protein building blocks. The molecular structure of dragline spider silk repeat units consists of semi-amorphous and nanocrystalline beta-sheet protein domains. Here we show by a series of computational experiments how the nanoscale properties of silk repeat units are scaled up to create macroscopic silk fibers with outstanding mechanical properties despite the presence of cavities, tears and cracks. We demonstrate that the geometric confinement of silk fibrils to diameters of 50&amp;#xb1;30 nm width is critical to facilitate a powerful mechanism by which hundreds of thousands of protein domains synergistically resist deformation and failure to provide enhanced strength,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5916/version/2

Nano-enabled Biological Materials
Provedor de dados: 17
Autores: Bradly J. Alicea.
This talk is an attempt to define a new field called &amp;#x201c;Nano-enabled Biological Tissues&amp;#x201d;. As such, this talk serves as a review of both the theoretical underpinnings and relevant recent results. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The presentation is divided into several parts: &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;* in the first section (slides 3-4), the concept of nano-enabled tissues are introduced as a complex system that can be engineered at multiple scales.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;* the second section (slides 5-12) contains three essential ingredients to achieve the technological vision. Current examples of each ingredient are introduced separately.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;* in the third section (slides 13-17),...
Tipo: Presentation
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5448/version/1

Nanofiber fabrication in a temperature and humidity controlled environment for improved fibre consistency
Provedor de dados: 17
Autores: Oliver Hardick; Bob Stevens; Daniel G.  Bracewell.
To fabricate nanofibers with reproducible characteristics, an important demand for many applications, the effect of controlled atmospheric conditions on resulting electrospun cellulose acetate (CA) nanofibers was evaluated for temperature ranging 17.5 - 35&amp;#xb0;C and relative humidity ranging 20% - 70%. With the potential application of nanofibers in many industries, especially membrane and filter fabrication, their reproducible production must be established to ensure commercially viability.&amp;#xd;&amp;#xa;Cellulose acetate (CA) solution (0.2 g/ml) in a solvent mixture of acetone/DMF/ethanol (2:2:1) was electrospun into nonwoven fibre mesh with the fibre diameter ranging from 150nm to 1&amp;#xb5;m.&amp;#xd;&amp;#xa;The resulting nanofibers were...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4524/version/1

Nanomaterials: Look at the Earth
Provedor de dados: 17
Autores: Siddhartha S. Mukhopadhyay.
Nanotechnology promises to be the greatest technological breakthrough in history, doing for our control of matter what computers did for our control of information. The origins of nanoscience can be traced to clay mineralogy and crystallography when it was discovered that clay minerals were crystalline and of micrometer size. The unit cell dimensions of clay minerals are in nanometer scale in all three axes (x, y, and z). The advantages of clays are: (i) their ordered arrangements, (ii) their large adsorption capacity, (iii) their shielding against sunlight (ultraviolet radiation), (iv) their ability to concentrate organic chemicals, and (v) their ability to serve as polymerization templates. Clay minerals in nanoforms played a catalytic role in the...
Tipo: Presentation
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5809/version/1

Nanoscience and Nano-Technology: Cracking Prodigal Farming
Provedor de dados: 17
Autores: Siddhartha S. Mukhopadhyay; Vir Rajinder  Parshad; Inderpreet S. Gill.
Nano-science coupled with nano-technology has emerged as possible cost-cutting measure to prodigal farming and environmental clean-up operations. It has ushered as a new interdisciplinary field by converging various science disciplines, and is highly relevant to agricultural and food systems.  Environmental Protection Agency of USA defined nanotechnology as the understanding and control of matter at dimensions of roughly 1-100 nm, where unique physical properties make novel applications possible. By this definition all soil-clays, many chemicals derived from soil organic matter (SOM), several soil microorganisms fall into this category. Apart from native soil-materials, many new nanotech products are entering into soil system, some of which are used for...
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3203/version/1

Nanotechnology: Giga game for soils
Provedor de dados: 17
Autores: Siddhartha Mukhopadhyay.
Research on colloidal properties of soils, especially of its clay and decayed organic matter components are pillars of edifice of soil science. The colloids control almost all soil reactions, but their behavior is controlled by dilution, change in pH, ion exchange, accretion of bases and many other processes, some of which are natural, while many others are anthropogenic. The anthropogenic manipulation of soils is the foundation of agrarian civilization, but spread into managed-forest, and urban ecosystems with time. In the twentieth century, great breakthroughs have been achieved in order to make soils more productive and responsive to environmental challenges. Historically, soil science as a discipline showed enormous capacity to absorb scientific...
Tipo: Presentation
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5791/version/1

Nanotechnology in Agriculture: Propagating, Perpetuating, and Protecting Life
Provedor de dados: 17
Autores: Siddhartha S. Mukhopadhyay.
Natural agricultural production is an open system, both energy and matters are exchanged freely in this system involving interactions of geosphere (especially pedosphere), biosphere, and atmosphere. Agriculture provides crops for food and industry, fiber, fuel, auto-fuel and drugs. On one hand it faces ever escalating food prices and farmer&amp;#x2019;s suicides, and on the other hand input use efficiency is low. Present agricultural practices have made harvests toxic, mother&amp;#x2019;s milk a poison, and breathing-air venom. In this background, nanotechnology brings new hope. Nanotechnology is an interdisciplinary venture-field that converge science, engineering, and agriculture and food systems into one. The Environmental Protection Agency of the US...
Tipo: Presentation
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5808/version/1

Nanotoxicity Assessment toward the Applications of Carbon Nanotubes as a Small Biomolecule Carrier in Drug Delivery Systems
Provedor de dados: 17
Autores: Rakesh  Sharma; Soonjo  Kwon; R Baktur; Avdhesh Sharma.
Carbon Nanotube (CNT) materials have superior properties in electric current carrying capacity, thermal conductivity, and thermal stability. Due to their structure with high aspect ratio, they have structural unusual toxicity and complicate safety issue in a target tissue.  In optimized quantities with limited functionality, special type of CNT assembly such as &amp;#x201c;buckyball&amp;#x201d; can be used as a potential drug carrier of bioactive molecules and display with increased circulating time and acceptable functionality.  We analyzed cytoxicity and inflammatory response following exposure of different size, mass, shape, and functionality of CNTs. We monitored the transport across skin, physiological perturbation of transepithelial electrical...
Tipo: Presentation
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3948/version/1

Narrow genetic and apparent phenetic diversity in Jatropha curcas: initial success with generating low phorbol ester interspecific hybrids
Provedor de dados: 17
Autores: Siam  Popluechai; Diego Breviario; Sujatha Mulpuri; Harinder P. S. Makkar; Manish Raorane; Attipalli R. Reddy; Enrico Palchetti; Angharad M. R. Gatehouse; Keith J. Syers; Anthony G. O&amp;#x27;Donnell; Ajay Kohli.
Due to the increasing popularity of Jatropha curcas as a feedstock for biodiesel, generating non-toxic and high yielding varieties of the plant requires genotypic characterization towards identifying breeding lines. There is little information on the phylogenetic relationships between its global accessions and species. Assessing genetic variation by RAPD, AFLP and combinatorial tubulin based polymorphism (cTBP) in 38 J. curcas accessions from 13 countries on 3 continents revealed narrow genetic diversity. However, 6 different species of Jatropha from India exhibited pronounced genetic diversity indicating possibilities of improving J. curcas by interspecific breeding. The relatively unexplored cTBP approach we used was a highly efficient and cost effective...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Earth &amp; Environment; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2782/version/1

Nasal Bacterial Microbiome: Probing a Healthy Porcine Family
Provedor de dados: 17
Autores: Min Yue; Weicheng Bei; Huanchun Chen.
Upper respiratory tract (URT) infection caused the leading and devastating diseases in pigs. It was believed that the normal microbiome of URT plays a vital role in health and disease development. As the entry point of the URT, little knowledge of bacterial microbiome in porcine nasal was known. A cultivation-independent approach directly to 16s ribosomal RNA genes enabled us to reveal the nasal bacterial community, structure and diversity. Here, we found that an unprecedented 207 phylotypes were characterized from 933 qualified clones, indicating the variable, species richness but particularly dominant bacterial microbiome. The dominant species were from genus Comamonas and Acinetobacter, which constitute core normal bacterial microbiome in porcine nasal....
Tipo: Manuscript
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6699/version/1

Nationwide Study of Breast Cancer Risk Factors in Latinas
Provedor de dados: 17
Autores: Michael Dean; Latoya Silverton; Julie Sawitzke.
Breast cancer is the most common cancer among American women. Any woman can be affected by breast cancer, with risk for the disease increasing with age.  Risk for breast cancer is also exacerbated in women who have certain genetic alterations. Mutations in the BRCA1 and BRCA2 genes predispose women to breast and ovarian cancer, and are increasingly recognized in prostate and pancreatic cancers (1-3).  In Caucasian and Asian ethnicities BRCA mutations are associated with basal-type/triple-negative disease. However this association between BRCA gene mutations and basal/triple-negative disease has been understudied in other ethnicities (4-6). The incidence and mortality of breast cancer of Hispanics and Native Americans are lower than other ethnicities;...
Tipo: Marker Paper / Data Plan
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5691/version/2

Nationwide Study of Breast Cancer Risk Factors in Latinas
Provedor de dados: 17
Autores: Michael Dean; Latoya Silverton; Julie Sawitzke.
Breast cancer is the most common cancer among American women. Any woman can be affected by breast cancer, with risk for the disease increasing with age.  Risk for breast cancer is also exacerbated in women who have certain genetic alterations. Mutations in the BRCA1 and BRCA2 genes predispose women to breast and ovarian cancer, and are increasingly recognized in prostate and pancreatic cancers (1-3).  In Caucasian and Asian ethnicities BRCA mutations are associated with basal-type/triple-negative disease. However this association between BRCA gene mutations and basal/triple-negative disease has been understudied in other ethnicities (4-6). The incidence and mortality of breast cancer of Hispanics and Native Americans are lower than other ethnicities;...
Tipo: Marker Paper / Data Plan
Palavras-chave: Cancer; Genetics &amp; Genomics; Immunology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5691/version/1

Natural Biomolecules from Marine Snail Telescopium telescopium and structure of its sperm: A Phylogenetic Study
Provedor de dados: 17
Autores: Uttam Datta; Manik Lal Hembram; Subhasis Roy; Prasenjit Mukherjee.
Abstract:&amp;#xd;&amp;#xa;Biochemical analysis of the cytosol fraction isolated from the ovotestis / spermatheca glands of marine mollusc Telescopium telescopium and it&amp;#x2019;s sperm microtubular structure revealed that relatively similar biomolecules like different enzymes,  hormones, minerals and structures of the sperm  are also exist in humans. Moreover, antiserum of the cytosol fraction was found to cross-react with the human sperm antigen indicated presence of a common sperm surface antigenicity between these two diversified species. These findings might support and / or hypothesize about the origin and diversification of the vertebrate molecules from its ancestral form (s) from the invertebrates, and basic physiological functions of these...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3386/version/1

Natural Diet of an Australian Freshwater Pipefish
Provedor de dados: 17
Autores: Andrew W. Jones; Lars  G. Rudstam; Thomas S. Rayner.
Globally, the family Syngnathidae (seahorses and pipefish) is recognized as being both under threat from anthropogenic pressures and poorly studied. Of the 47 species that are listed on the IUCN Red List, 33 are currently listed as &amp;#x2018;data deficient&amp;#x2019;, with inadequate information available to make an assessment of their risk of extinction. Within Australia, this has prompted environmental assessments of specific fisheries, as well as a number of recent ecological studies of marine syngnathids. However, no work has been published on the continent&amp;#x2019;s four freshwater species. To begin to remedy this, a thorough analysis of the feeding habits of one such species was conducted. Twenty-two specimens of _Hippichthys heptagonus_...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/329/version/1

Natural Environment Research Council - Data Policy
Provedor de dados: 17
Autores: Mark Thorley.
The Natural Environment Research Council (NERC) has a policy on data in order to:&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;(a) Ensure the continuing availability of environmental data of long-term value for research, teaching, and for wider exploitation for the public good, by individuals, government, business and other organisations;&amp;#xd;&amp;#xa;(b) Support the integrity, transparency and openness of the research it supports;&amp;#xd;&amp;#xa;(c) Help in the formal publication of data sets, as well as enabling the tracking of their usage through citation and data licences;&amp;#xd;&amp;#xa;(d) Meet relevant legislation and Government guidance on the management and distribution of environmental information.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Earth &amp; Environment; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6017/version/1

Natural evidence for garnet-spinel transition (GST) in the Earth&amp;#x27;s mantle
Provedor de dados: 17
Autores: BenXun Su.
This study based on compiled world-wide garnet peridotite data confirms the GST in high P and T conditions, which was obtained from Al-free experimental system (MgO-Cr~2~O~3~-SiO~2~) by Klemme (2004). A new spinel-phase peridotite zone, garnet peridotite discontinuous zone, is defined, and another GST, although no experimental data, is principally and presumably proposed to exist. The garnet inclusion-bearing spinel harzburgite from Lashaine (Tanzania) provides the first evidence for the existence of ultra-high spinel zone and is explained as recrystallized minerals hosting the interacted residue of ancient oceanic lithosphere subducted into the great depth of more than 220km. These previously unexpected findings are generating great challenges to phase...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1898/version/1

Natural evidence for garnet-spinel transition (GST) in the Earth&amp;#x27;s mantle
Provedor de dados: 17
Autores: BenXun Su.
This study based on compiled world-wide garnet peridotite data confirms the GST in high P and T conditions, which was obtained from Al-free experimental system (MgO-Cr~2~O~3~-SiO~2~) by Klemme (2004). A new spinel-phase peridotite zone, garnet peridotite discontinuous zone, is defined, and another GST, although no experimental data, is principally and presumably proposed to exist. The garnet inclusion-bearing spinel harzburgite from Lashaine (Tanzania) provides the first evidence for the existence of ultra-high spinel zone and is explained as recrystallized minerals hosting the interacted residue of ancient oceanic lithosphere subducted into the great depth of more than 220km. These previously unexpected findings are generating great challenges to phase...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1898/version/2

Natural Language Query in the Biochemistry and Molecular Biology Domains Based on Cognition Search&amp;#x2122;
Provedor de dados: 17
Autores: Elizabeth J. Goldsmith; Saurabh Mendiratta; Radha Akella; Kathleen Dahlgren.
Motivation: With the tremendous growth in scientific literature, it is necessary to improve upon the standard pattern matching style of the available search engines. Semantic NLP may be the solution to this problem. Cognition Search (CSIR) is a natural language technology. It is best used by asking a simple question that might be answered in textual data being queried, such as MEDLINE. CSIR has a large English dictionary and semantic database. Cognition&amp;#x2019;s semantic map enables the search process to be based on meaning rather than statistical word pattern matching and, therefore, returns more complete and relevant results. The Cognition Search engine uses downward reasoning and synonymy which also improves recall. It improves precision through...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2315/version/1

Natural Radiation Induced Developmental Disability: An Avian Model
Provedor de dados: 17
Autores: Jeni Chandar Padua; Basil Rose MR.
Radiation exposure during gestation causes mutation in the fetus leading to birth defects in the newborn. On a survey of the coastal villages of Kanyakumari District, Tamilnadu, India, high levels of background radiation were detected, which was suggestive of inducing mutations, and congenital abnormalities in the exposed population. To substantiate the dangerous impact of such natural radioactive emissions, we have established an avian model of irradiation-induced birth defect in chicks hatched from eggs exposed to natural radioactive beach sand. The hatched experimental chicks exhibited severe locomotor disability and extreme malformations. Our study proves for the first time, that natural beach sand radiation induces severe developmental abnormalities....
Tipo: Manuscript
Palavras-chave: Developmental Biology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6191/version/1

Natural Selection: A Deselection vs Proselection Analysis
Provedor de dados: 17
Autores: Raymond Hardy.
Since the dawn of Darwinian evolution theory evolutionists have assumed that evolution favors adaptive traits. In this analysis article the author explores the usefulness of assuming that natural selection works only by disfavoring deleterious traits.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1787/version/1

Natural Selection _In Utero_ Contributes to the Male Longevity Deficit in Contemporary Human Populations
Provedor de dados: 17
Autores: Ralph Catalano.
Much literature invokes natural selection to explain the pervasive deficit in the average lifespan of men compared to women.^1^ The explanation assumes that mothers, not fathers, provisioned children over much of human existence, and that women who lived long enough to help their children and grand children survive to reproductive age had more grandchildren and great-grandchildren than did shorter-lived women.^2^ Although this argument implies that natural selection would conserve mutations that conferred longevity on mothers but not fathers,^3,4^ it offers no explanation of the considerable changes over historic time in the male longevity deficit thereby implying that these arise solely from culture.^5^ I show, however, that natural selection _in utero_...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3915/version/1

Natural Selection of Paths in Networks
Provedor de dados: 17
Autores: Chrisantha Fernando; Vera Vasas; E&amp;#xf6;rs Szathm&amp;#xe1;ry; Philip Husbands.
We present a novel algorithm that exhibits natural selection of paths in a network. If each node and weighted directed edge has a unique identifier, a path in the network is defined as an ordered list of these unique identifiers. We take a population perspective and view each path as a genotype. If each node has a node phenotype then a path phenotype is defined as the list of node phenotypes in order of traversal. We show that given appropriate path traversal, weight change and structural plasticity rules, a path is a unit of evolution because it can exhibit multiplicative growth (i.e. change it&amp;#x2019;s probability of being traversed), and have variation and heredity. Thus, a unit of evolution need not be a spatially distinct physical individual. The...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5535/version/1

NCBO Overview and Biositemaps
Provedor de dados: 17
Autores: Patricia L. Whetzel.
none
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6355/version/1

Near Infrared Microspectroscopy, Fluorescence Microspectroscopy, Infrared Chemical Imaging and  High-Resolution Nuclear Magnetic Resonance Analysis of Soybean Seeds, Embryos and Single Cells
Provedor de dados: 17
Autores: I. C. Baianu; Schyler S.  Korban; Tiefeng You.
Chemical analysis of soybean seeds, somatic embryos and single cells were carried out by Fourier Transform Infrared (FT-IR), Fourier Transform Near Infrared (FT-NIR) Microspectroscopy, Fluorescence and High-Resolution NMR (HR-NMR). The first FT-NIR chemical images of biological systems approaching 1 micron (1&amp;#x3bc;) resolution are presented here. Chemical images obtained by FT-NIR and FT-IR Microspectroscopy are presented for oil in soybean seeds and somatic embryos under physiological conditions. FT-NIR spectra of oil and proteins were obtained for volumes as small as 2&amp;#x3bc;3. Related, HR-NMR analyses of oil contents in somatic embryos are also presented here with nanoliter precision. Such 400 MHz 1H NMR analyses allowed the selection of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6200/version/1

Near Infrared Reflectance Spectroscopy (NIRS) Determination of Isoflavone Contents for Selected Soybean Accessions
Provedor de dados: 17
Autores: I. C. Baianu; Jun  Guo; Tiefeng  You; Randall   L. Nelson.
Soybean isoflavones are of considerable interest in relation to their possible health effects in human diets. The rapid and economical determination of soybean isoflavone concentrations is essential for the investigation and development of soybean health foods as well as the selection of soybean seeds with optimal isoflavone levels for such foods. Fourier transforms near infrared reflectance spectroscopy (FT-NIRS) calibrations were developed for the rapid and cost-effective analysis of isoflavones in soybean seeds. FT-NIRS measurements were carried out in quadruplicate for 50 soybean lines selected from the USDA Soybean Germplasm Collection. The selected soybean seeds provided a wide range of isoflavone concentrations (from 0.3 to 6.0 mg/g) that is...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7048/version/1

Neem leaf glucosamine stimulates Interleukin-2 (IL-2) in swiss albino mice
Provedor de dados: 17
Autores: Santhosh Kumar Venugopalan; Navaratnam Viswesharan; Rajasekaran Aiyalu; Nair N K.
Neem leaf glucosamine-mediated immune stimulation was studied in male swiss albino mice. Mice were treated with three doses of Neem leaf glucosamine (266, 400 and 800 &amp;#xb5;g/30gm mouse, intraperitoneal injection) one dose per week for four weeks. At doses of 266, 400 and 800 &amp;#xb5;g/30gm mouse a significant increase in Interleukin-2 in mice serum was observed when compared to the control group and also an increase in relative organ weight of the thymus was observed but there was a mild increase in liver and kidney weights. The immune stimulatory response of Neem leaf glucosamine was also observed in T-lymphocyte proliferation. Overall, Neem leaf glucosamine showed a stimulatory effect on immune functions in mice. The immunostimulatory effect of...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5923/version/1

Network-based analyses of Huntington&amp;#x2019;s Disease
Provedor de dados: 17
Autores: Ravi K. Kalathur; Matthias  E. Futschik.
The use of high-throughput technologies has provided us with large amounts of data for _Huntington&amp;#x27;s disease_ (HD), especially at the gene and protein levels. As phenotypic changes in HD may not just be due to the activity of individual genes but interrelated alterations of whole molecular networks, it is important to systematically analyse and represent accumulated data in a network-based approach.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: To analyse and visualise protein interaction networks through a dedicated database to HD, we have established &amp;#x22;HDNetDB&amp;#x22;: http://hdnetdb.sysbiolab.eu. This platform will not only help to understand molecular mechanisms better, but also assist in identifying potential molecular markers...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7090/version/1

Networking Phylogeny for Indo-European and Austronesian Languages
Provedor de dados: 17
Autores: Philippe Blanchard; Filippo Petroni; Maurizio Serva; Dimitri Volchenkov.
Harnessing cognitive abilities of many individuals, a language evolves upon their mutual interactions establishing a persistent social environment to which language is closely attuned. Human history is encoded in the rich sets of linguistic data by means of symmetry patterns that are not always feasibly represented by trees. Here we use the methods developed in the study of complex networks to decipher accurately symmetry records on the language phylogeny of the Indo-European and the Austronesian language families, considering, in both cases, the samples of fifty different languages. In particular, we support the Anatolian theory of Indo-European origin and the &amp;#x2018;express train&amp;#x2019; model of Austronesian expansion from South-East Asia, with...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3156/version/1

Networking Phylogeny for Indo-European and Austronesian Languages
Provedor de dados: 17
Autores: Philippe Blanchard; Filippo Petroni; Maurizio Serva; Dimitri Volchenkov.
Harnessing cognitive abilities of many individuals, a language evolves upon their mutual interactions establishing a persistent social environment to which language is closely attuned. Human history is encoded in the rich sets of linguistic data by means of symmetry patterns that are not always feasibly represented by trees. Here we use the methods developed in the study of complex networks to decipher accurately symmetry records on the language phylogeny of the Indo-European and the Austronesian language families, considering, in both cases, the samples of fifty different languages. In particular, we support the Anatolian theory of Indo-European origin and the &amp;#x2018;express train&amp;#x2019; model of Austronesian expansion from South-East Asia, with...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3156/version/2

Networks, Extinction and Paleocommunity Food Webs
Provedor de dados: 17
Autores: Peter Roopnarine.
Food webs represent trophic interactions among species in communities. Those interactions both structure and are structured by species richness, ecological diversity, and evolutionary processes. Geological and macroevolutionary timescales are therefore important to the understanding of food web dynamics, and there is a need for the consideration of paleocommunity food webs. The fossil record presents challenges in this regard, but the problem can be approached with combinatoric analysis and network theory. This paper is an introduction to the aspects of those disciplines relevant to the study of paleo-food webs, and explores a probabilistic and numerical approach.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4433/version/2

Networks of intergenic long-range enhancers and snpRNAs drive castration-resistant phenotype of prostate cancer and contribute to pathogenesis of multiple common human disorders
Provedor de dados: 17
Autores: Anna Glinskii; Shuang Ma; Jun Ma; Denise Grant; Chang-Uk  Lim; Ian Guest; Stewart Sell; Ralph Buttyan; Gennadi Glinsky.
Biological and mechanistic relevance of intergenic disease-associated genetic loci (IDAGL) containing highly statistically significant disease-linked SNPs remains unknown. Here we present the experimental and clinical evidence revealing important role of IDAGL in human diseases. Targeted RT-PCR screen coupled with sequencing of purified PCR products detects widespread transcription at multiple intergenic disease-associated genomic loci (IDAGL) and identifies 96 small non-coding trans-regulatory RNAs of ~ 100-300 nt in length containing SNPs associated with 21 common human disorders (snpRNAs). Functionality of snpRNAs is supported by multiple independent lines of experimental evidence demonstrating their cell-type-specific expression and evolutionary...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6069/version/1

Neural activity dissociation between thought-based and perception-based response conflict
Provedor de dados: 17
Autores: Antao Chen; Xu Lei; Xiting Huang; Qinglin Zhang; Qiang Liu; Yongxiu Lai; Dezhong Yao; Hong Li.
Based on the idea that intentions have different penetrability to perception and thought (Fodor, 1983), four Stroop-like tasks, AA, AW, WA, and WW are used, where the A represents an arrow and the CPPR (closest processing prior to response) is perception, and the W represents a word and the CPPR is thought. Event-related brain potentials were recorded as participants completed these tasks, and sLORETA (standardized low resolution brain electromagnetic tomography) was used to localize the sources at specific time points. These results showed that there is an interference effect in the AA and WA tasks, but not in the AW or WW tasks. The activated brain areas related to the interference effect in the AA task were the PFC and ACC, and PFC activation took place...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1269/version/1

Neural Basis of Motivation Lateralizes with Motor Control
Provedor de dados: 17
Autores: Geoffrey Brookshire; Daniel Casasanto.
According to decades of research on affective motivation in the human brain, approach motivational states are subserved by the left hemisphere and avoidance states by the right hemisphere. Here we show that hemispheric specialization for motivation reverses with handedness. This covariation provides initial support for the Sword and Shield Hypothesis, according to which hemispheric laterality of affective motivation is causally linked to motor control for the dominant and non-dominant hands.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6585/version/1

Neural Coding of Green Flash in Retinal Bipolar Pathways
Provedor de dados: 17
Autores: Caiping Hu.
What visual information do the graded potentials among retinal bipolar pathways actually transmit from photoreceptors to ganglion cells? The answer does not exist. Even the graded electric signals have not been understood completely. Here, this paper tries to analyze the encoding mechanisms of graded signals among the parallel bipolar pathways in response to brief green flash. The typical ON, OFF and ON-OFF bipolar cells simultaneously abstracted vectors from green flash stimulus with sine-like functions on their dendritic plane. Atypical bipolar cell had the synchronously monopolar response in contrast to the bipolar responses of typical bipolar cells, they also annotated green flash with facilitated stochastic (asynchronous and rate-coded) responses....
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/6786/version/1

Neural Information Processing: between synchrony and chaos
Provedor de dados: 17
Autores: Josep  L. Rossello; Vincent Canals; Antoni Morro.
The brain is characterized by performing many different processing tasks ranging from elaborate processes such as pattern recognition, memory or decision-making to more simple functionalities such as linear filtering in image processing. Understanding the mechanisms by which the brain is able to produce such a different range of cortical operations remains a fundamental problem in neuroscience. Some recent empirical and theoretical results support the notion that the brain is naturally poised between ordered and chaotic states. As the largest number of metastable states exists at a point near the transition, the brain therefore has access to a larger repertoire of behaviours. Consequently, it is of high interest to know which type of processing can be...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/6935/version/1

Neural Mechanisms of Selective Auditory Attention in Rats (Dissertation)
Provedor de dados: 17
Autores: Lung-Hao Tai; Anthony M. Zador.
How does attention modulate sensory representations? In order to probe the underlying neural mechanisms, we established a simple rodent model of modality-specific attention. Rats were trained to perform distinct auditory two-tone discrimination and olfactory odor discrimination in a two alternative choice (2AC) paradigm. &amp;#xd;&amp;#xa;To determine auditory cortex&amp;#x2019;s role in this frequency discrimination task, we used GABA-A receptor agonist muscimol to transiently and reversibly inactivate auditory cortexes bilaterally in rats performing simple interleaved auditory and olfactory discrimination. With olfactory discrimination performance serving as internal control for motivation and decision making capability, we found only auditory two-tone...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2355/version/1

Neural Modulation by Rhythm Induced Temporal Expectations
Provedor de dados: 17
Autores: Gustavo Rohenkohl; Anna  Dal Molin; Anna C. Nobre.
Time is an essential dimension of our experience, framing human behaviour at scales ranging from the millisecond organization of motor actions to circadian rhythms cycle, and beyond.  Nevertheless, the mechanisms by which the brain keeps time and uses temporal information to organise behaviour remain unknown. Whereas the principles of the organisation of spatial cognition in the human brain are emerging, the same is not true for temporal cognition. The current study tested the influence of temporal expectations on attentional orienting to moving targets.  In this task, a ball appeared at the left side of a screen and moved across the screen in steps following either a regular or irregular rhythm. After reaching an occluding band, the ball was temporarily...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2956/version/1

Neural Networks, Cell Genome and Interactome Nonlinear Dynamic Models
Provedor de dados: 17
Autores: I. C. Baianu.
Operational logic and bioinformatics models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes are proposed. &amp;#x141;ukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks. An algebraic formulation of variable &amp;#x27;next-state functions&amp;#x27; is extended to a &amp;#x141;ukasiewicz Topos with an n-valued &amp;#x141;ukasiewicz Algebraic Logic subobject classifier description that represents non-random and nonlinear network activities as well as their transformations in...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6206/version/1

Neural Substrates of Chronic Pain in the Thalamocortical Circuit
Provedor de dados: 17
Autores: Antonio G. Zippo; Riccardo M. Storchi; Maurizio Valente; Gian Carlo Caramenti; Gabriele E. M. Biella.
Chronic pain (CP), a pathological condition with a large repertory of signs and symptoms, has no recognizable neural functional common hallmark shared by its diverse expressions. The aim of the present research was to identify potential dynamic markers shared in CP models, by using simultaneous electrophysiological extracellular recordings from the rat ventrobasal thalamus and the primary somatosensory cortex. We have been able to extract a neural signature attributable solely to CP, independent from of the originating conditions. This study showed disrupted functional connectivity and increased redundancy in firing patterns in CP models versus controls, and interpreted these signs as a neural signature of CP. In a clinical perspective, we envisage CP as...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6548/version/1

Neurodegeneration: Potential Causes, Prevention, and Future Treatment Options
Provedor de dados: 17
Autores: Zhongtao Zhang.
Here I advance a hypothesis that neurodegeneration is a natural process associated with aging due to the loss of genetic redundancy following a mathematical model R(t) = R0(1-&amp;#x3b1;e(&amp;#x3b2;C+&amp;#x3b3;I+&amp;#x3b4;Et)t), where the calorie intake (C) and immune response (I) play critical roles. The early onset of neurodegenerative diseases such as Alzheimer&amp;#x2019;s disease is due to metabolic imbalance or chronic immune reactions to various infections. Therefore, the potential treatment options for neurodegenerative diseases are to modulate metabolism and immune response.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6324/version/1

Neurogenesis and astrogenesis contribute to vestibular compensation in the neurectomized adult cat: cellular and behavioral evidence
Provedor de dados: 17
Autores: Sophie Dutheil; Jean Michel Brezun; Jacques Leonard; Michel Lacour; Brahim Tighilet.
Neurogenesis occurs in some regions of the adult mammalian brain and gives rise to neurons integrated into functional networks. In pathological or postlesional conditions, neurogenesis and astrogenesis can also occur, as demonstrated in the deafferented vestibular nuclei after unilateral vestibular neurectomy in the adult cat. Here we report that in cats infused with an antimitotic drug, cytosine-[beta]-D arabinofuranoside (AraC), the number of GAD67 and GFAP immunoreactive cells is increased, despite the total mitotic activity blockade observed in the deafferented vestibular nuclei after unilateral vestibular neurectomy. At the behavioral level, recovery of posturo-locomotor function was drastically delayed, and no alteration of the horizontal spontaneous...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2957/version/1

Neuron impairment or loss in brain may be responsible for type 2 diabetes and essential hypertension
Provedor de dados: 17
Autores: Xiang Zheng; Xue Zhou.
Type 2 diabetes and essential hypertension are both very common chronic diseases. Type 2 diabetes is often associated with hypertension, but the exact causes of them are unknown. Here, based on recent investigations, we will look at the pathogenesis of these two diseases in a new light.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4187/version/1

Neuronal plasticity: cell-based strategy for target identification and validation
Provedor de dados: 17
Autores: Ana Mingorance-Le Meur; Timothy P. O&amp;#x27;Connor.
While growing neurites are relatively plastic during development, their plasticity levels drop rapidly as neurons mature and become integrated into neuronal networks. As a consequence, the central nervous system ability to reorganize itself in response to injury or disease is insufficient. One of the main limitations for the design of therapeutic strategies to enhance neurite sprouting following neurological diseases is our poor understanding of the mechanisms underlying neurite structural plasticity. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To overcome this limitation, we have implemented a strategy to identify, characterize and validate the most therapeutically relevant drug targets to modulate neuronal plasticity. This strategy is based on the hypothesis...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2780/version/1

Neuroscience and eating disorders: the role of the medial temporal lobe
Provedor de dados: 17
Autores: Giuseppe Riva.
Evidence from psychology and neuroscience indicates that our spatial experience, including the bodily one, involves the integration of different sensory inputs within two different reference frames egocentric (body as reference of first-person experience) and allocentric (body as object in the physical world). Even if functional relations between these two frames are usually limited, they influence each other during the interaction between long- and short-term memory processes in spatial cognition. If, for some reasons, this process is impaired, the egocentric sensory inputs are no more able to update the contents of the allocentric representation of the body: the subject is locked to it.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In our perspective, subjects with...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4235/version/1

New checksum functions for Biopython
Provedor de dados: 17
Autores: Sebastian Bassi; Virginia Gonzalez.
Checksum algorithms are used in biological databases for integrity check and identification purposes. CRC64 is the only checksum algorithm already included in Biopython. This work proposes two new implementation of known algorithms (GCG Checksum and SEGUID). There is also an application based on SEGUID: Looking for redundancy between two FASTA files full of protein sequences based only in sequence information, by comparing the SEGUIDs of both files.&amp;#xd;&amp;#xa;The code is shown in the manuscript and may be available at Biopython.org.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/278/version/1

New discovery of the oldest maize weevils in the world from Jomon potteries, Japan
Provedor de dados: 17
Autores: Hiroki Obata; Aya Manabe; Naoko Nakamura; Tomokazu Onishi; Yasuko Senba.
The maize weevil (_Sitophilus zeamais_) and rice weevil (_Sitophilus oryzae_) are two of the most damaging insects for stored grains, and are characteristic species of ancient Japan. Both species and the granary weevil (_Sitophilus granarius_) are common elsewhere in the world, but the natural distribution of maize and rice weevils is restricted to the Old World^1^. Japanese archaeological records contain a few maize weevil fossils after the Middle Yayoi period (ca. 2000 aBP)^2^. However, since evidence of weevils was discovered as impressions in Jomon potsherds in 2004^3^, many weevil impressions have been found. The oldest is from the Late Jomon (ca. 4000 to 3200 aBP). These findings and other archaeological evidence suggest that the maize weevil invaded...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4407/version/1

New Equations for Atomic Mass, Mass per Nucleon and Mass defects of Elements in Terms of Rest Mass Based Neutron Numbers
Provedor de dados: 17
Autores: Raji Heyrovska.
Conventional neutron numbers are based on the approximations that the mass of the electron is zero and that those of the proton and neutron are each equal to unity. It was shown, by using the exact rest masses, that the neutron numbers are actually one or two less than the conventional ones for atomic masses greater than 108. Presented here are new equations for the atomic mass, mass per nucleon and mass defects for the most abundant stable isotope (or the one with the longest half life) of each of the 118 elements of the Periodic Table.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4547/version/1

New Evidence for Early Silk in the Indus Civilization
Provedor de dados: 17
Autores: Irene L. Good; Jonathan Mark Kenoyer; Richard H. Meadow.
Silk is an important economic fiber, and is generally considered to have been the exclusive cultural heritage of China. Silk weaving is evident from the Shang period, though the earliest evidence for silk textiles in ancient China dates to more than a millennium earlier. New study of fibers from Harappan bronze artifacts reveals surprising early evidence for knowledge of silkworking in South Asia, the earliest evidence in the world for any silk outside China, and roughly contemporaneous with the earliest Chinese evidence for silk. This important new finding brings into question the traditional historical notion of sericulture as being an exclusively Chinese invention.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1900/version/1

New fungal sources for &amp;#x3b1;-L-Rhamnosidase: an important enzyme used in the synthesis of drugs and drug precursors
Provedor de dados: 17
Autores: Vinita  Yadav; Kapil Deo Singh Yadav.
Two fungal strains were isolated and tentatively identified as Penicillium VY and Aspergillus VY. All the isolated species show the maximum production on third day in a liquid culture media. The pH optimum was found to be 10.0 for Penicillium VY and 11.0 for Aspergillus VY. The temperature optima were 50&amp;#xba;C in both the cases. The enzyme produced by Penicillium VY was found to be stable in the pH range 3.0-7.0 and 3.0&amp;#x2013;6.0 in case of Aspergillus VY. The enzyme does not loose activity up to 40&amp;#xba; C in case of Penicillium VY and 40&amp;#xba;C in case of Aspergillus VY if exposed for 1 h.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2560/version/1

New insight into DNA damage by cisplatin at the atomic scale
Provedor de dados: 17
Autores: Raji Heyrovska.
Cisplatin is cis-diamminedichloroplatinum (II) of chemical formula, Pt(NH3)Cl2, abbreviated as cis-DDP and known commercially as platinol. It is used widely as an anticancer drug for various types of cancer, ever since its discovery two centuries ago and has become a target of extensive researches. Transplatin, trans-DDP on the other hand, is found to be less or ineffective to treat cancers. Cisplatin is known to interact mainly with the N(7) nitrogen of guanine in nucleic acids, after a water molecule takes away one of the chlorines by hydrolysis. This initiates the damage of nucleic acids and eventually leads to apoptosis. However the way how this happens and why transplatin is less effective is not completely clear. Here the author brings some new...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6891/version/1

New Lewis Structures through the application of the Hypertorus Electron Model
Provedor de dados: 17
Autores: Omar Yepez.
The hypertorus electron model is applied to the chemical bond. As a consequence, the bond topology can be determined. A linear correlation is found between the normalized bond area and the bond energy. The normalization number is a whole number. This number is interpreted as the Lewis&amp;#x27;s electron pair. A new electron distribution in the molecule follows. This discovery prompts to review the chemical bond, as it is understood in chemistry and physics.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5336/version/1

New methods for analyzing serological data with applications to influenza surveillance
Provedor de dados: 17
Autores: Wilfred Ndifon.
Two important challenges to the use of serological assays for influenza surveillance include the substantial amount of experimental effort involved, and the inherent noisiness of serological data. Here, informed by the observation that log-transformed serological data (obtained from the hemagglutination-inhibition assay) exist in an effectively one-dimensional space, computational methods are developed for accurately and efficiently recovering unmeasured serological data from a sample of measured data, and systematically minimizing noise found in the measured data. Careful application of these methods would enable the collection of better-quality serological data on a greater number of circulating influenza viruses than is currently possible, and improve...
Tipo: Manuscript
Palavras-chave: Immunology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3820/version/1

New source for L-iditol and taxanes
Provedor de dados: 17
Autores: Liu Xi-Kui; Liu Jian-Jun.
We describe the first report of the recovery of L-iditol and Taxane from an angiosperm- Yunnanopilia longistaminata (W.Z.Li) C.Y.Wu et D.Z.Li (Opiliaceae). Two taxane compounds and L-iditol were isolated from the tender burgeon of Yunnanopilia longistaminata, and their structure were identified as Taxayunnansin B, Taxumairol E and L-iditol on the basis of NMR and MS spectrum, respectively. It is a new plant source for L-iditol and taxanes.
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1502/version/1

New species from the deep Pacific suggest that carnivorous sponges date back to the Early Jurassic
Provedor de dados: 17
Autores: Jean Vacelet; Michelle Kelly.
Some deep-sea poecilosclerid sponges (Porifera) have developed a carnivorous feeding habit that is very surprising in sponges^1^. As shown by the typical morphology of their spicules, they most probably evolved from &amp;#x22;normal sponges&amp;#x22; under the difficult conditions of a deep-sea environment. Such evolution, which implies the loss of the diagnostic character of the phylum Porifera, i.e. a filter feeding habit through a complex aquiferous system, should be of great interest in the understanding of the origin of metazoans. Some scenarios, based on the hypothesis of the paraphyly of Porifera, allege that metazoans could derive from a sponge filter-feeding body plan. A difficulty, however, is to imagine the transition from a sponge grade of...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2327/version/1

New Spontaneous Model of Fibrodysplasia Ossificans Progressiva
Provedor de dados: 17
Autores: Bruce Rothschild; Larry Martin; Robert Timm.
We report the first known example of spontaneous, naturally occurring fibrodysplasia ossificans progressiva (FOP) in a mammal. The Southeast Asian mouse deer of the genus _Tragulus_ (Artiodactyla: Tragulidae) have an osseous sheath covering the lower back and upper thigh region consistent with the clinical definition of FOP. This heterotophic bone deposition is sex related apparently with a genetic basis - it only occurs in males and is lacking in females; it is present in all adults males, including both wild obtained and zoo bred animals. _Tragulus_ may offer the opportunity to examine many of the disease&amp;#x27;s most significant attributes experimentally.
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1541/version/1

Newer Methods of Nanoparticle Synthesis: Nitroimidazole properties with Nanometal oxides in Polymer Cages as Drug-Biomarker Monitors
Provedor de dados: 17
Autores: Rakesh Sharma.
Nitroimidazoles are radiosensitizers and hypoxia detecting chemosensitizers. Intially nitroimidazoles were single dose antibiotic drugs. Recently, nitroimidazole derivatives have emerged as multifunctional &amp;#x201c;drug-biomarker monitors&amp;#x201d; chemical compounds with importance in treatment of tumors, monitoring hypoxia and safer imaging contrast agents to monitor the therapeutic progress.  Additionally, the number of nitroimidazole derivatives is growing and identified their importance as multifunctional nanoparticles. The nanoparticle synthesis scheme of nitroimidazole was proposed as nitroimidazole caged with paramagnetic metal oxide inside polymer coating and labeled with marker radiolebels or biomolecules. We report the step by step...
Tipo: Presentation
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3952/version/1

neXtProt, a new knowledgebase  on human proteins
Provedor de dados: 17
Autores: Lydie Lane.
In September 2008, the UniProt/Swiss-Prot group achieved a major milestone: the first complete manual annotation of what is believed to be the full set of human proteins (derived from ~20&amp;#x27;300 genes). This corpus of data is already quite rich in information pertinent to modern biomolecular medical research, but made us realize how large is the gap in our knowledge of human proteins in terms of functional information as well as protein characterization (PTMs, protein/protein interactions, subcellular locations, etc). This gap resides not only in the available experimental information, but also in the way this information has been stored, which is far from being sufficient to help researchers making sense of what all these human proteins do in our...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5104/version/1

Niche Overlap and Diet Breadth: Can bumble bee (Bombus spp.) foraging behavior reveal species vulnerabilities?
Provedor de dados: 17
Autores: Rosemary Malfi; T&amp;#x27;ai Roulston.
Within the last two decades, notable shifts have taken place within the bumble bee (_Bombus_ spp.) communities of North America: some species have experienced substantial, rapid declines, while others appear to be stable or even experiencing range expansion. Studies from the UK and Europe implicate the loss of natural habitat and associated floral resources in overall bumble bee declines and species losses. Research also indicates that loss of host plants disproportionately impacts species with narrower diet breadths, and that these species are more likely to be long-tongued (presumably due to the reduction of long-tubed floral hosts). In contrast, species with more generalized diets have been shown to be more abundant. In this study we examined resource...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6482/version/1

Nicotinic &amp;#x3b1;7 acetylcholine receptor-mediated currents are not modulated by the tryptophan metabolite kynurenic acid in adult hippocampal interneurons
Provedor de dados: 17
Autores: Peter  Dobelis; Andrew L. Varnell; Kevin J. Staley; Donald  C. Cooper.
The &amp;#xa0;tryptophan &amp;#xa0;metabolite, &amp;#xa0;kynurenic &amp;#xa0;acid (KYNA), &amp;#xa0;is &amp;#xa0;classically &amp;#xa0;known &amp;#xa0;to &amp;#xa0;be &amp;#xa0;an antagonist &amp;#xa0;of ionotropic&amp;#xa0;glutamate&amp;#xa0;receptors. Within the last decade several reports have been published suggesting that KYNA also blocks nicotinic acetylcholine receptors (nAChRs) containing the &amp;#x3b1;7 subunit (&amp;#x3b1;7*).  Most of these reports involve either indirect measurements of KYNA effects on &amp;#x3b1;7 nAChR function, or are reports of KYNA effects in complicated in vivo systems. &amp;#xa0;However, a recent report investigating KYNA interactions with &amp;#x3b1;7 nAChRs failed to detect an interaction using direct measurements of...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6277/version/1

NIR Calibrations for Soybean Seeds and Soy Food Composition Analysis: Total Carbohydrates, Oil, Proteins and Water Contents
Provedor de dados: 17
Autores: I. C. Baianu; Jun Guo.
Conventional chemical analysis techniques are expensive, time consuming, and often destructive. The non-invasive Near Infrared (NIR) technology was introduced over the last decades for wide-scale, inexpensive chemical analysis of food and crop seed composition (see Williams and Norris, 1987; Wilcox and Cavins, 1995; Buning and Diller, 2000 for reviews of the NIR technique development stage prior to 1998, when Diode Arrays were introduced to NIR). NIR spectroscopic measurements obey Lambert and Beer&amp;#x2019;s law, and quantitative measurements can be successfully made with high speed and ease of operation. NIR has been used in a great variety of food applications. General applications of products analyzed come from all sectors of the food industry...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6611/version/1

NIR Calibrations for Soybean Seeds and Soy Food Composition Analysis: Total Carbohydrates, Oil, Proteins and Water Contents [v.2]
Provedor de dados: 17
Autores: I. C. Baianu; Jun Guo; Randall L. Nelson; Tiefeng You; Doina M. Costescu.
Conventional chemical analysis techniques are expensive, time consuming, and often destructive. The non-invasive Near Infrared (NIR) technology was introduced over the last decades for wide-scale, inexpensive chemical analysis of food and crop seed composition (see Williams and Norris, 1987; Wilcox and Cavins, 1995; Buning and Diller, 2000 for reviews of the NIR technique development stage prior to 1998, when Diode Arrays were introduced to NIR). NIR spectroscopic measurements obey Lambert and Beer&amp;#x2019;s law, and quantitative measurements can be successfully made with high speed and ease of operation. NIR has been used in a great variety of food applications. General applications of products analyzed come from all sectors of the food industry...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6611/version/2

NIR Spectroscopy and Microspectroscopy Analysis of Intact Soybean Seeds for Food Applications through Composition Improvements. Version 2.0
Provedor de dados: 17
Autores: Tiefeng You; I. C. Baianu.
The soybean-derived products are among the most important agricultural products in the USA and the world. Conventional analytical methods for soybean composition analysis are both time consuming and costly. Faster and less expensive methods are required for most practical applications. To improve the accuracy, reliability and sensitivity of NIR, major advancements in instrumentation, as well as, data analysis / calibration methodology are required. Novel NIR instruments, such as DA-NIR and FT-NIR spectrometers developed in recent years have the potential for improving significantly the quantification of soybean composition at a reasonable cost. We present representative calibrations and data for intact soybean composition analysis obtained at the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6253/version/1

Nitric oxide synthase in skeletal muscle fibres of patients with type 2 diabetes
Provedor de dados: 17
Autores: Karla Punkt; Katharina Kandt; Andreas Oberbach; Volker Adams; Igor Buchwalow; Matthias Blueher.
Muscle-derived nitric oxide (NO) mediates fundamental physiological actions on skeletal muscle including glucose uptake into muscle cells. Recently, we have shown that the altered glucose metabolism in skeletal muscle of patients with type 2 diabetes (T2D) is associated with changes in the metabolic profile of individual muscle fibres, but fibre-type specific changes in NO synthase (NOS) expression in skeletal muscle of T2D patients remain to be elucidated. Here we investigated fibre-type related NOS expression in vastus lateralis muscle of T2D patients compared with healthy individuals with normal glucose tolerance (NGT). Cytophotometrical assay and Western blotting did not reveal any quantitative differences between NOS expression in muscles from NGT and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7049/version/1

Nitrogen Fixation and Translocation in Sugarcane
Provedor de dados: 17
Autores: Takuji Ohyama; Atsushi Momose; Norikuni Ohtake; Kuni Sueyoshi; Takashi Sato; Yasuhiro Nakanishi; Shoichiro Akao.
World sugarcane production is increasing rapidly as a biofuel. In some areas in Brazil, sugarcane has been grown continually over very long periods without N fertiliser inputs. Therefore, the occurrence of N fixation has been suspected. However, quantitative studies seeking to identify the N~2~ fixation sites in the plant and to record the translocation of fixed N around the plant have not yet established. A ^15^N~2~ gas tracer experiment was conducted using young sugarcane plants to investigate the sites of N~2~ fixation and also to explore the possibility of translocation of the fixed N among the plant&amp;#x27;s major organs. Young sugarcane plants (_Saccharum officinarum_ L.) about 40 cm high and some 14 days after sprouting from a stem cutting were...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2360/version/1

NMR and Electron Microscopy Studies of Soybean Seeds, Soybean Proteins, and Oil for Improved Utilization in Foods and Feeds
Provedor de dados: 17
Autores: Doina M. Costescu; I. C. Baianu.
NMR, NIR and EM techniques are suitable methods of measuring protein and oil content in soybeans. After completion of a measurement with NMR or NIR, a soybean sample could be either replanted or consummated. NMR techniques involved in the present work are based on the response of nuclei, as nuclear spin flips, when set in a 7.05T magnetic field and excited with rf pulses of 300 MHz. NIR spectroscopy is based on outer electron molecular vibrations, when excited with radiation of frequency 1012 -4&amp;#xd7;1014Hz, and &amp;#xf06c;=2.5Om-750 nm. &amp;#xd;&amp;#xa;TEM and ESEM techniques are bulk and surface analysis techniques, respectively, working with electron beams of 15KV, and image resolution in the range of nm&amp;#x2019;s. ESEM is based on the...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6192/version/1

No evidence for a recent genetic bottleneck in the endangered Sheko cattle breed (African Bos taurus) revealed by microsatellite analysis
Provedor de dados: 17
Autores: Hailu Dadi; Joram Mwacharo; Markos Tibbo; Yukimizu Takahashi; Koh Nomura; Hirofumi  Hanada; Takashi Amano.
Sheko is African taurine cattle, valued for its milk yield, adaptation to humid tsetse infested environment and trypanotolerance. We used 30 microsatellite markers in analyzing 30 DNA samples. We found high genetic diversity and no genetic bottlenecks in endangered Sheko cattle. Sheko cattle have not undergone recent genetic bottlenecks, in spite of drastic reduction in its overall demographic population size. The results were supported by three statistical methods: &amp;#xd;&amp;#xa;(i) detection of heterozygosity excess &amp;#xd;&amp;#xa;(ii) a mode-shift indicator of allele distribution pattern &amp;#xd;&amp;#xa;(iii) the ratio of the number of alleles to the range of allele size, M-ratio test. This breed reflects historical and cultural identity of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3925/version/1

Noise, cycles, and noisy cycles in finite populations
Provedor de dados: 17
Autores: Mario Pineda-Krch.
Periodic predator-prey dynamics in constant environments are usually taken as indicative of deterministic limit cycles. It is known, however, that demographic stochasticity in finite populations can also give rise to regular population cycles, even when the corresponding deterministic models predict a stable equilibrium. The existence of quasi-cycles substantially expands the scope for natural patterns of periodic population oscillations caused by ecological interactions, thereby complicating the conclusive interpretation of such patterns. It is, however, feasible and straightforward to accurately distinguish between the two types of cycle through the combined analysis of autocorrelations and marginal distributions of population sizes. By confronting these...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/48/version/1

Non-linear Effects in Asymmetric Catalysis: Whys and Wherefores
Provedor de dados: 17
Autores: Sosale Chandrasekhar.
It is argued that the titled non-linear effects (NLE) may arise whenever the order of the reaction in the chiral catalyst in greater than 1. In a fundamental departure from previous approaches, this is mathematically elaborated for the second order case. (NLE may also be observed if the chiral catalyst forms non-reacting dimers in a competing equilibrium; practically, however, this implies the in situ resolution of the catalyst.) The amplification of enantiomeric excess by NLE implies a relative (although modest) reduction in the entropy of mixing. The consequent increase in free energy apparently indicates a non-equilibrium process. It is suggested, based on arguments involving the chemical potential, that kinetically-controlled reactions lead to a state...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/6947/version/1

Nonlinear Models of Neural and Genetic Network Dynamics
Provedor de dados: 17
Autores: I. C. Baianu.
A categorical and &amp;#x141;ukasiewicz-Topos framework for &amp;#x141;ukasiewicz LM-Algebraic Logic models of nonlinear dynamics in complex functional systems such as neural networks, genomes and cell interactomes is proposed. &amp;#x141;ukasiewicz Algebraic Logic models of genetic networks and signaling pathways in cells are formulated in terms of nonlinear dynamic systems with n-state components that allow for the generalization of previous logical models of both genetic activities and neural networks.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7114/version/1

Non-linear Regression Approaches in ABC
Provedor de dados: 17
Autores: Michael G. B. Blum.
In this talk, we consider different methods of parameter inference for ABC. Derivations of the asymptotic bias and variance of the standard ABC estimators indicates that ABC may achieve poor performance when the dimension of the summary statistics is large. The linear adjustment introduced by Beaumont et al. (2002) is found to achieve better performance when there is a nearly homoscedastic relationship between the summary statistics and the parameter of interest. To provide a more flexible adjustment method, we propose two innovations. The new method fits 1/a heteroscedatic rather than a homoscedastic regression model and consider 2/non linear instead of linear regression. The new algorithm is compared to the state-of-the-art approximate Bayesian methods...
Tipo: Presentation
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5954/version/1

Non-specific binding of antibodies in immunohistochemistry: Fakes and facts
Provedor de dados: 17
Autores: Igor Buchwalow; Vera  Samoilova; Werner Boecker; Markus  Tiemann.
Protocols for blocking non-specific antibody (Ab) binding in immunohistochemistry are based on rather contradictory and outdated reports.  This prompted us to prove, whether non-specific Ab binding may really lead to unwanted background staining in routinely processed cell and tissue probes.  In this study, the probes were fixed and processed according to routine protocols with and without a blocking step (goat serum or BSA).  Surprisingly, all Ab in probes processed without a blocking step did not show any propensity towards non-specific binding that might lead to background staining, thus implying that endogenous Fc receptors do not retain their ability to bind Fc portion of Ab after standard fixation.  Likewise in routinely fixed probes, we did not find...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2011
URL: http://precedings.nature.com/documents/5892/version/1

Non-viral delivery and optimized optogenetic stimulation of retinal ganglion cells led to behavioral restoration of vision
Provedor de dados: 17
Autores: Ling Gu; Shivaranjani Shivalingaiah; Mathew Ficinski; Edward Wong; Samarendra Mohanty.
Stimulation of retinal neurons using optogenetics via use of chanelrhodopsin-2 (ChR2) has opened up a new direction for restoration of vision for treatment of retinitis pigmentosa (RP). Here, we report non-viral in-vivo electroporation of degenerated retina of adult RP-mice with ChR2-plasmids and subsequent in-vivo imaging of retina to confirm expression. Further, we demonstrate that in addition to efficient non-viral delivery of ChR2 to a specific retinal layer, threshold level of stimulation light needs to be delivered onto the retina for achieving successful behavioral outcome. Measurement of intensity of light reaching the retina of RP-mouse models along with geometrical optics simulation of light propagation in the eye is reported in order to...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/6869/version/1

Normalization and Matching of Chemical Compound Names
Provedor de dados: 17
Autores: Martin Golebiewski; Jasmin &amp;#x160;ari&amp;#x107;; Henriette Engelken; Meik Bittkowski; Ulrike Wittig; Wolfgang M&amp;#xfc;ller; Isabel Rojas.
The identification of a chemical compound solely based on its name requires comprehensive chemical knowledge and often extensive searches in chemical databases. However, it is crucial for the integration of biochemical data extracted from the literature, since many publications exclusively describe a compound by its name. We have developed an application which matches synonymic names of chemical compounds and thereby facilitates the bundling of corresponding data referring to the same compound.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The tool that we have developed is based on natural language processing (NLP) methods and applies rules to systematically normalize chemical compound names. Matching of synonymous names is achieved by comparison of the normalized...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3322/version/1

Normalization And Matching Of Chemical Compound Names
Provedor de dados: 17
Autores: Martin Golebiewski; Meik Bittkowski; Henriette Slogsnat; Jasmin Saric; Isabel Rojas; Wolfgang M&amp;#xfc;ller.
We have developed ChemHits (http://sabio.h-its.org/chemHits/), an application which detects and matches synonymic names of chemical compounds. The tool is based on natural language processing (NLP) methods and applies rules to systematically normalize chemical compound names. Subsequently, matching of synonymous names is achieved by comparison of the normalized name forms. The tool is capable of normalizing a given name  of a chemical compound and matching it against names in (bio-)chemical databases, like SABIO-RK, PubChem, ChEBI or KEGG, even when there is no exact name-to-name-match.
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6505/version/1

Not a slow snail: Rapid rise of environmental awareness and ecological insights regarding invasive island apple snails (Pomacea insularum)
Provedor de dados: 17
Autores: Romi Burks; Jess Van Dyke.
*_Background/Question/Methods_*&amp;#xd;&amp;#xa;Exotic invaders routinely move faster than scientific publication processes.  Lacking aerial dispersal stages, snails generally match descriptions of slow colonizers.  However, reminiscent of the pace with which zebra mussels gained notoriety, a growing sense of urgency has emerged from management communities regarding established populations of exotic, invasive island apple snails (_Pomacea insularum_).  Recently separated by mitochondrial markers as a related, yet distinct, species, _P. insularum_ sits poised to follow along the invasive trajectory of its better known relative, the golden apple snail (_P. canaliculata_).  Literature studies examining mechanisms that promote invasiveness suggest family...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3853/version/1

Novel approaches, including systems biology, to HIV vaccine research and development: Report from a Global HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: Bali  Pulendran; Rino Rappuoli; Alan Aderem; the Working Group convened by the Global HIV Vaccine Enterprise.
The Global HIV Vaccine Enterprise convened a two-day workshop on August 10-11 2009, at the Fred Hutchison Cancer Research Center offices in Seattle, WA, to discuss the application of novel approaches,including systems biology, to HIV vaccine research and development. The goals of this Working Group were to identify key scientific issues and opportunities that have emerged since the Enterprise Scientific Strategic Plan1 was published in 2005, and to make recommendations to Enterprise stakeholders.
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4798/version/2

Novel approaches, including systems biology, to HIV vaccine research and development: Report from a Global HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: Bali  Pulendran; Rino Rappuoli; Alan Aderem; the Working Group convened by the Global HIV Vaccine Enterprise.
The Global HIV Vaccine Enterprise convened a two-day workshop on August 10-11 2009, at the Fred Hutchison Cancer Research Center offices in Seattle, WA, to discuss the application of novel approaches,including systems biology, to HIV vaccine research and development. The goals of this Working Group were to identify key scientific issues and opportunities that have emerged since the Enterprise Scientific Strategic Plan1 was published in 2005, and to make recommendations to Enterprise stakeholders.
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4798/version/1

Novel associations for hypothyroidism include known autoimmune risk loci
Provedor de dados: 17
Autores: Nicholas Eriksson; Joyce  Y. Tung; Amy K. Kiefer; David A. Hinds; Uta Francke; Joanna L. Mountain; Chuong B. Do.
Hypothyroidism is the most common thyroid disorder, affecting about 5% of the general population.  Here we present the first large genome-wide association study of hypothyroidism, in 2,564 cases and 24,448 controls from the customer base of 23andMe, Inc., a personal genetics company.  We identify four genome-wide significant associations, two of which are well known to be involved with a large spectrum of autoimmune diseases: rs6679677 near _PTPN22_ and rs3184504 in _SH2B3_ (p-values 3.5e-13 and 3.0e-11, respectively).  We also report associations with rs4915077 near _VAV3_ (p-value 8.3e-11), another gene involved in immune function, and rs965513 near _FOXE1_ (p-value 3.1e-14).  Of these, the association with _PTPN22_ confirms a recent small candidate gene...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6055/version/1

Novel Cell type-specific aptamer-siRNA delivery system for HIV-1 therapy
Provedor de dados: 17
Autores: Jiehua Zhou; Haitang Li; Shirley Li; John Zaia; John Rossi.
The successful use of small interfering RNAs (siRNAs) for therapeutic purposes requires safe and efficient delivery to specific cells and tissues. Here we demonstrate cell type-specific delivery of anti-HIV siRNAs via fusion to an anti-gp120 aptamer. The envelope glycoprotein is  expressed on the surface of HIV-1 infected cells, allowing binding and interalization of the aptamer-siRNA chimeric molecules. We demonstrate that the anti-gp120 aptamer-siRNA chimera is specifically taken up by cells expressing HIV-1 gp120, and the appended siRNA is processed by Dicer, releasing an anti-tat/rev siRNA which in turn inhibits HIV replication. We show for the first time a dual functioning aptamer-siRNA chimera in which both the aptamer and the siRNA portions have...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1299/version/1

Novel determinants describe chaperonin substrate proteins
Provedor de dados: 17
Autores: Emanuele Raineri; Paolo Ribeca; Luis Serrano; Tobias Maier.
Molecular chaperones ensure that their substrate proteins reach the functional native state and prevent their aggregation. The bacterial GroEL/ES chaperonin system is understood in great detail on a structural, mechanistic and functional level. Its substrate proteins in E. coli have been identified and characterized. However, a long standing and yet unresolved question in the field is: what makes a protein a chaperone substrate?&amp;#xd;&amp;#xa;Here we demonstrate with a bioinformatics-based approach that a simple set of criteria is sufficient to describe the GroEL substrate proteome to unprecedented accuracy. We define two novel parameters differentiating GroEL substrates from other cellular proteins: evolutionary rate and hydrophobicity. We demonstrate...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2968/version/2

Novel developments in SBGN-ED and applications
Provedor de dados: 17
Autores: Tobias Czauderna; Eva Grafahrend-Belau; Astrid Junker; Anja Hartmann; Matthias Klapperst&amp;#xfc;ck; Falk Schreiber.
Systems Biology Graphical Notation (SBGN, http://sbgn.org) [1] is an emerging standard for graphical representations of biochemical and cellular processes studied in systems biology. Three different views (Process Description, Entity Relationship, and Activity Flow) cover several aspects of the represented processes in different levels of detail. SBGN helps to communicate biological knowledge more efficient and accurate between different research communities in the life sciences. However, to support SBGN, methods and tools for editing, validating, and translating of SBGN maps are necessary.&amp;#xd;&amp;#xa;We present methods for these tasks and novel developments in SBGN-ED (www.sbgn-ed.org) [2], a tool which allows to create all three types of SBGN maps...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6415/version/1

Novel mutations in the toll like receptor genes cause hyporesponsiveness to Mycobacterium avium subsp. paratuberculosis infection
Provedor de dados: 17
Autores: Mangesh Bhide; Rastislav Mucha; Ivan Mikula Jr.; Lucia Kisova; Rostislav Skrabana; Michal Novak; Ivan Mikula Sr.
Toll like receptors play a central role in the recognition of pathogen associated molecular patterns (PAMPs). Mutations in TLR1, TLR2 and TLR4 genes may change the PAMP reorganization ability which causes altered responsiveness to the bacterial pathogens. A case control study, performed to assess the association between TLR gene mutations and susceptibility to Mycobacterium avium subsp. paratuberculosis (MAP), revealed novel mutations (TLR1 - Ser150Gly and Val220Met; TLR2 - Phe670Leu) that hindered either PAMP recognition or further downstream TLR pathway activation. A cytokine expression experiments (IL-4, IL-8, IL-10, IL-12 and IFN-&amp;#x3b3;) in the challenged mutant and wild type moDCs (mocyte derived dendritic cells) confirmed the negative impact of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2637/version/1

Novel network pharmacology methods for drug mechanism of action identification, pre-clinical drug screening and drug repositioning
Provedor de dados: 17
Autores: Jianghui Xiong.
The high rates of failure in oncology drug clinical trials highlight the problems of using pre-clinical data to predict the clinical effects of drugs. Here we present two methodology innovations on network pharmacology modeling. (1) We hypothesize that the gene network associated with cancer outcome in heterogeneous patient populations could serve as a reference for identifying drug effects. We proposed a novel in vivo genetic interaction between genes as &amp;#x2018;synergistic outcome determination&amp;#x2019;, in a similar way to &amp;#x2018;synthetic lethality&amp;#x2019;. We scanned above genetic interactions based on microarray profiling for cancer prognosis, and identified a cluster of important yet epigenetically regulated gene modules. By...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6455/version/1

Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for  Composition Improvements
Provedor de dados: 17
Autores: I. C. Baianu; Valentin  Prisecaru.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions.  Conventional &amp;#x201c;wet chemistry&amp;#x201d; analytical methods are time-consuming and costly.  As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry.  Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6231/version/1

Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for  Composition Improvements.  (v.3)
Provedor de dados: 17
Autores: Valentin  Prisecaru; I. C. Baianu.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions.  Conventional &amp;#x201c;wet chemistry&amp;#x201d; analytical methods are time-consuming and costly.  As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry.  Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6231/version/3

Novel NIR Spectroscopy Correlation Approach to Amino Acid Analysis of Soybean Proteins for  Composition Improvements.  (Version 2.0)
Provedor de dados: 17
Autores: Valentin  Prisecaru; I. C. Baianu.
Amino acid NIR calibrations were developed in our Physical Chemistry of Foods Laboratory of the University of Illinois at Urbana for three selected amino acid groups that include essential amino acids for identified soybean accessions.  Conventional &amp;#x201c;wet chemistry&amp;#x201d; analytical methods are time-consuming and costly.  As a result, soybean breeders and researchers have an imperative need to utilize faster and less expensive methods. NIR Spectroscopy is a rapid and inexpensive method for composition analysis for academia and industry.  Recent advancements in instrumentation design, such as the application of the Diode Array (DA) technique and the Fourier Transform (FT) IR and NIR techniques, have significantly improved overall instrument...
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6231/version/2

Novel phytosynthesis of nanoparticles using Indigeneous Australian Plants
Provedor de dados: 17
Autores: N V K V Prasad Tollamadugu; S R Venkata Kambala; Benjamin Convery; Ravi Naidu.
Nanoparticles are considered to be the building blocks of nanotechnology. Biosynthesis of nanoparticles using plant material is an exciting and relatively new developing research area in nanobiotechnology. In the present study, Eucalyptus leaves were collected from Olive pink botanical garden, Alice Springs, Australia and were used to synthesize silver nanoparticles. Cubical structured and well monodispersed silver nanoparticles were formed with an average size of 50nm. The formed silver nanoparticles are found to have promising applications in medicine as good antimicrobial agents. To the best of our knowledge this is the first report on exploiting indigeneous Australian plant sources for the synthesis of metallic nanoparticles.
Tipo: Poster
Palavras-chave: Developmental Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6307/version/1

Novel protein antigen (JHP940) from the genomic plasticity region of Helicobacter pylori induces TNF-alpha and Interleukin- 8 secretion by human macrophages
Provedor de dados: 17
Autores: Niyaz Ahmed; Ayesha Alvi; Mohammed Rizwan.
Plasticity region of the H. pylori genome comprises strain specific gene loci. We performed genotyping and functional biology of one such locus (jhp940) that was previously found to be functionally unknown but present in gastric cancer associated strains from many different countries. We found its geographic prevalence to be independent of cagA presence and disease status. Cloning, expression and purification of the JHP940 revealed a novel, ~36kDa protein in biologically active form. The same induced strong and significant levels of TNF-alpha and Interleukin-8 in human macrophages. Induction of these cytokines by JHP940 points to its putative role in chronic gastric inflammation and various other outcomes of H. pylori infection including gastric cancer.
Tipo: Poster
Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/864/version/1

Novel role of substance-p as a systemic wound messenger to mobilize mesenchymal stem cell from bone marrow and be engaged in the wound healing epithelial layer
Provedor de dados: 17
Autores: Hyun Sook Hong; Jung Sun Lee; Young Sam Kwon; Eun Kyung Lee; Woosung Ahn; Jae Chan Kim; Youngsook Son.
Tissue injury may bring up the systemic participation of bone marrow stem cells in the repair. In this study, we report that substance-p is a systemically acting messenger to mobilize mesenchymal stem cell (MSC) probably from the bone marrow and be engaged in the wound healing process. This was supported by the injury-inducible substance-p detection in the tissue and the peripheral blood and subsequent MSC mobilization in the alkali-burn rabbit eye model, whose kinetics were dependent on the wound size. Furthermore, i.v. injection of exogenous substance-p stimulated MSC mobilization in the uninjured rabbits and those mobilized cells showed multipotent differentiation capacity. We demonstrated that earlier substance-p elevation in the circulation by...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1309/version/1

Novel Techniques for Microspectroscopy and Chemical Imaging Analysis of Soybean Seeds and Embryos
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng  You; Doina M. Costescu.
Novel methodologies are currently being evaluated for the Chemical Analysis of soybean seeds as well as developing mature soybean embryos by FT-IR/NIR Microspectroscopy. This is the first report of FT-NIR Chemical Images obtained with 1 micron resolution. NIR spectra of Proteins, Oil and DNA fibers are obtained for regions as small as 1&amp;#x3bc;^2^.
Tipo: Poster
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6591/version/2

Novel Techniques for Microspectroscopy and Chemical Imaging Analysis of Soybean Seeds and Embryos
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng  You; Doina M. Costescu.
Novel methodologies are currently being&amp;#xd;&amp;#xa;evaluated for the Chemical Analysis of&amp;#xd;&amp;#xa;soybean seeds as well as developing &amp;#xd;&amp;#xa;mature soybean embryos by FT-IR/NIR Microspectroscopy. This is the first report of FT-NIR Chemical Images obtained with 1 micron resolution. NIR spectra of Proteins, Oil and DNA fibers are obtained for regions as small as 1&amp;#x3bc;^2^.
Tipo: Poster
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Molecular Cell Biology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6591/version/1

NPO:  Ontology for Cancer Nanotechnology Research
Provedor de dados: 17
Autores: Dennis Thomas; Rohit Pappu; Nathan Baker.
We present the design and development of NanoParticle Ontology (NPO). The ontology is implemented in the Ontology Web Language (OWL).  The domain terms in NPO currently represent entities, which describe knowledge about physical, chemical, and functional properties of nanoparticles characterized in cancer nanotechnology research. The upper-level of NPO is formed using terms from the Basic Formal Ontology (BFO).
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3515/version/1

NPO:  Ontology for Cancer Nanotechnology Research
Provedor de dados: 17
Autores: Dennis Thomas; Rohit Pappu; Nathan Baker.
We present the design and development of NanoParticle Ontology (NPO). The ontology is implemented in the Ontology Web Language (OWL).  The domain terms in NPO currently represent entities, which describe knowledge about physical, chemical, and functional properties of nanoparticles characterized in cancer nanotechnology research. The upper-level of NPO is formed using terms from the Basic Formal Ontology (BFO).
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3514/version/1

NPY Levels In Type 1 Diabetic Men of Different Duration.
Provedor de dados: 17
Autores: Riccardo Volpi; Anna Araldi; Simona Cataldo; Maria Grazia Magotti; Luigi Capretti; Vittorio Coiro; Claudio Giumelli; Teore Ferri; Roberta Minelli; Lavinia Volpi; Paolo Chiodera.
Background: The aim of the present study was to evaluate whether the different duration of type 1 diabetes mellitus influences basal NPY secretion. Design: The NPY concentrations were measured in sixty-eight men with insulin-dependent diabetes mellitus (IDDM) (duration: group 1 (n.21) &amp;#x3c;5 years (range 2-4 years); group 2 (n.24) &amp;#x3e;5 years and &amp;#x3c;10 years (range: 6-9 years); group 3 (n.29) &amp;#x3e;10 years (range: 11-14 years)) and in age matched normal control subjects (n. 30). Results: The NPY levels were significantly lower in group 3 than in group 2 and 1 and in the control group, in group 2 than in group 1 and in the control group and in group 1 than control group. Conclusion: These results support the view that the duration of...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6731/version/1

Nuclear DNA and protein content evaluation in Taxus plant cell cultures using multiparameter flow cytometry
Provedor de dados: 17
Autores: Vishal Gaurav; Amit Shavit; Susan C. Roberts.
Plant cell cultures of Taxus provide the most reliable production methods for the anti-cancer drug paclitaxel. In order to comprehend the inherent culture heterogeneity and production variability in cell cultures, it is essential that the cellular metabolism is studied at the genomic level. Genomic stability in plant cell cultures is crucial as it affects cell growth and division, metabolite accumulation and protein synthesis. A rapid and efficient method to prepare nuclei suspensions from aggregated cell cultures of Taxus was employed. Methods were subsequently developed to simultaneously stain them for DNA and protein content using Propidium Iodide and Fluorescein Isothiocyanate respectively. Flow cytometry was used to analyze and quantify the DNA...
Tipo: Poster
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3809/version/1

Nuclear Medicine and Early Discovery of Disease
Provedor de dados: 17
Autores: I. C. Baianu.
There is an urgent need for the early detection of diseases such as Alzheimer&amp;#x2019;s (AD) and Cancers in order to enable their successful treatment. Cancer is the second major cause of death after Heart Disease, and AD is the third major cause of death with major consequences for the society.&amp;#xd;&amp;#xa;Three major Nuclear Medicine techniques that are established for diagnostic and research purposes are: Positron Emission Tomography (PET) CAT/CT and Nuclear Magnetic Resonance Imaging (NMRI/MRI). These nuclear medicine techniques are discussed together with their clinical and research applications to early diagnosis of Alzheimer&amp;#x27;s Disease (AD) and cancers. Novel approaches to early detection and modeling of AD and cancers are then...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6196/version/1

Nucleic acid - protein fingerprints. Novel protein classification based on nucleic acid - protein recognition
Provedor de dados: 17
Autores: Alexander Krylov; Renad Zhdanov.
Protein chemistry uses protein description and classification based on molecular mass and isoelectric point as general features. Enzymes are also compared by enzymatic reaction constants, namely Km and kcat values. Proteins are also studied by binding to different oligonucleotides. Here we suggest a simple experimental method for such a comparison of DNA binding proteins, which we call &amp;#x22;nucleic acid-protein fingerprints&amp;#x22;. The experimental design of the method is based on an use of short oligonucleotides immobilized inside microarray of hydrogel cells - biochip. As a first stage, we solved a simple experimental task: what is the shortest single strand oligonucleotide to be recognized by protein? We tested binding of oligonucleotides from 2...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2012
URL: http://precedings.nature.com/documents/6955/version/1

Nucleosome-mediated cooperativity between transcription factors
Provedor de dados: 17
Autores: Leonid A. Mirny.
Cooperative binding of transcription factors (TFs) to cis-regulatory regions (CRRs) is essential for precision of gene expression in development and other processes. The classical model of cooperativity requires direct interactions between TFs, thus constraining the arrangement of TFs sites in a CRR. On the contrary, genomic and functional studies demonstrate a great deal of flexibility in such arrangements with variable distances, numbers of sites, and identities of the involved TFs. Such flexibility is inconsistent with the cooperativity by direct interactions between TFs. Here we demonstrate that strong cooperativity among non-interacting TFs can be achieved by their competition with nucleosomes. We find that the mechanism of nucleosome-mediated...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2796/version/1

Nucleotide repeats in mitochondrial genome determine human lifespan
Provedor de dados: 17
Autores: Konstantin Popadin; Georgii Bazykin.
Direct nucleotide repeats can facilitate deletions of segments of mitochondrial genome1, leading to a wide range of neuromuscular disorders1,2 as well as aging2,3 in humans. We hypothesized that the number of the direct perfect repeats in human mitochondrial genomes influences longevity through the formation of harmful mtDNA deletions in the somatic cells. The analysis of the complete mitochondrial genomes of 762 unrelated Japanese individuals4-6 reveals a negative correlation between the abundance of the direct perfect repeats and the expected longevity. This association is largely due to the disruption of the common repeat (8470,13447) by a point mutation 8473C which occurred at the origin of the D4a haplogroup characterized by extreme longevity in...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2399/version/1

Nuisance Signal in Resting-State fMRI Study
Provedor de dados: 17
Autores: Xi-Nian Zuo; Michael P. Milham.
We systematically presented various nuisance signals in resting-state fMRI (R-fMRI) dataset. First, we examined the impact of different extraction methods on the default-mode pattern seeded by posterior cingulate cortex (PCC). Second, we compared their differences in test-retest reliability. Finally, we speculated the equivalence of removing global mean signal to removing gray matter mean signal.
Tipo: Presentation
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4352/version/1

Numbers, not value, motivate cooperation in humans and orangutans
Provedor de dados: 17
Autores: Ellen E. Furlong; John E. Opfer.
Cooperation among competitors-whether sharing the burden of wind resistance in the Tour de France, forming price-fixing cartels in economic markets, or adhering to arms-control agreements in international treaties-seldom spreads in proportion to the potential benefits. To gain insight into the minds of uncooperative agents, economists and social psychologists have used the prisoner&amp;#x27;s dilemma task to examine factors leading to cooperation among competitors. Two types of factors have emerged in these studies: the relative rewards of defecting versus cooperating and breakdowns in trust, forgiveness and communication. The generalizability of economic and social psychological factors, however, relies on the assumption that agents&amp;#x27; comparisons...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/1392/version/1

Obesity as a perceived social signal
Provedor de dados: 17
Autores: Manasee Mankar; Radhika Joshi; Prajakta Belsare; Maithili Jog; Milind Watve.
Fat accumulation has been classically considered as a means of energy storage. Obese people are theorized as metabolically &amp;#x2018;thrifty&amp;#x2019;, saving energy during times of food abundance. However, recent research has highlighted many neuro-behavioral and social aspects of obesity, with a suggestion that obesity, abdominal obesity in particular, may have evolved as a social signal. We tested here whether body proportions, and abdominal obesity in particular, are perceived as signals revealing personality traits. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Faceless drawings of three male body forms namely lean, muscular and feminine, each with and without abdominal obesity were shown in a randomized order to a group of 222 respondents. A list of 30...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2711/version/1

Obesity care pathway
Provedor de dados: 17
Autores: Phillipa Hobson; Abdallah Mangoud.
This paper recognises that obesity is a growing problem within the UK with Britain with one of the highest rates for overweight children in Europe and with one in three adults predicted to be obese by 2012. Within the UK, nearly 25 per cent of men and women are now obese which has created enormous implications for health service providers (NICE, 2006). This paper focuses specifically on North East Lincolnshire where life expectancy is less than the national average with males (76) and females (80.8). Within North East Lincolnshire we developed an evidence-based adult obesity care pathway based on the NICE obesity guidance, incorporating local referral criteria and input. The pathway is benefiting patients by helping to reduce obesity through an increase in...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4718/version/1

Objective dysphonia quantification in vocal fold paralysis: comparing nonlinear with classical measures
Provedor de dados: 17
Autores: Max A. Little; Declan A. E. Costello; Meredydd L. Harries.
Clinical acoustic voice recording analysis is usually performed using classical perturbation measures including jitter, shimmer and noise-to-harmonic ratios. However, restrictive mathematical limitations of these measures prevent analysis for severely dysphonic voices. Previous studies of alternative nonlinear random measures addressed wide varieties of vocal pathologies. Here, we analyze a single vocal pathology cohort, testing the performance of these alternative measures alongside classical measures.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We present voice analysis pre- and post-operatively in unilateral vocal fold paralysis (UVFP) patients and healthy controls, patients undergoing standard medialisation thyroplasty surgery, using jitter, shimmer and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3106/version/1

Obtaining New Insights for Biodiversity Conservation from Broad-Scale  Citizen Science Data
Provedor de dados: 17
Autores: Steve Kelling; Daniel Fink; Wesley M. Hochachka; Marshall J. Iliff; Brian L. Sullivan; Christopher L. Wood; Arthur Munson; Mirek Riedewald.
Increasing public engagement in volunteer science1, either through data collection2 or processing3, is both raising public awareness of science and gathering useful information for scientists.  While the payoffs of citizen science4 are potentially large, achieving them requires new approaches to data management and analysis that can only result from strong cross-disciplinary collaborations.  This is especially true in ecology and conservation biology, where historically the understanding of species&amp;#x2019; responses to environmental change has been constrained by the limited spatial5 or temporal scale6 of available data.  Here we describe collaborative research in ecology, computer science, and statistics to generate essential information for...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3967/version/1

Occurrence Of Ascidian _Molgula Sp_. From The Coastal Waters Of Visakhapatnam, India
Provedor de dados: 17
Autores: Veena Shettigar; Kaladharan P.
A specimen of solitary ascidian _Molgula sp._, collected from seaweeds growing at Thotlakonda beach, Visakhapatnam is reported for the first time from Visakhapatnam coast of Indian waters.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4953/version/2

Occurrence Of Ascidian _Molgula Sp_. From The Coastal Waters Of Visakhapatnam, India
Provedor de dados: 17
Autores: Veena Shettigar; Kaladharan P.
A specimen of solitary ascidian _Molgula sp._, collected from seaweeds growing at Thotlakonda beach, Visakhapatnam is reported for the first time from Visakhapatnam coast of Indian waters.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4953/version/1

Occurrence of Gastroliths in _Baurusuchus_ (Baurusuchidae, Mesoeucrocodylia) from Adamantina Formation, Bauru Basin
Provedor de dados: 17
Autores: Felipe M. Vasconcellos; Leonardo Morato; Thiago Marinho; Ismar S. Carvalho.
The fossil record of Baurusuchidae Mesoeucrocodylia in the General Salgado county and its surroundings is one of the best regarding preservation, completeness and articulation of skull and skeleton remains, including specimens that shown even the most delicate bone structures and cartilaginous tissues. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;One of them, UFRJ DG 288-R, has preserved its skull and about 80% of its skeleton. During the removal of the rock matrix, on what should be the specimen&amp;#x2019;s abdominal region, together with fragments of gastralia were observed some small well-polished weathered angulous to subrounded clasts, presumed to be gastroliths. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;These xenoliths occur in a restrict cluster, where at least...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1950/version/1

Octanol/water distribution coefficients of the C~1~ through C~7~ perfluoro-n-alkyl sulfonates: Comparison of the IEFPCM-UFF, CPCM, and SMD solvation models
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
The octanol/water distribution coefficients (log D~ow~) of the C~1~ through C~7~ perfluoro-n-alkyl sulfonates (PFSAs) were calculated using the M062X/6-311++G(d,p) and MP2/6-311++G(d,p)//M062X/6-311++G(d,p) levels of theory and the IEFPCM-UFF, CPCM, and SMD solvation models. At both levels of theory with all solvation models, absolute log D~ow~ calculated for the straight chain C~1~ through C~7~ PFSAs display a substantial negative bias against available experimental data and expected trends by several log units. However, the SMD solvation model achieves accurate relative log D~ow~ accuracy, yielding fragmental contributions of a -CF~2~- group towards the log D~ow~ of 0.51+/-0.02 to 0.54+/-0.01 units (-3.0+/-0.1 to -3.1+/-0.1 kJ/mol), in good agreement...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5103/version/1

Oculomotor Nucleus
Provedor de dados: 17
Autores: Allen Institute for Brain Science; Josh J. Burnell; Lydia L. Ng; Angela L. Guillozet-Bongaarts.
This report contains a gene expression summary of the oculomotor nucleus, derived from the Allen Brain Atlas (ABA) in situ hybridization mouse data set. The structure&amp;#x27;s location and morphological characteristics in the mouse brain are described using the Nissl data found in the Allen Reference Atlas. Using an established algorithm, the expression values of the oculomotor nucleus were compared to the values of the macro/parent-structure, in this case the midbrain, for the purpose of extracting regionally selective gene expression data. The genes with the highest ranking selectivity ratios were manually curated and verified. 50 genes were then selected and compiled for expression characterization. The experimental data for each gene may be accessed...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2094/version/1

ODIN: An Advanced Interface for the Curation of Biomedical Literature
Provedor de dados: 17
Autores: Fabio Rinaldi; Simon Clematide; Gerold Schneider; Martin Romacker; Therese Vachon.
We present *ODIN* (Ontogene Document INspector): a system for interactive curation of biomedical&amp;#xd;&amp;#xa;literature, developed within the scope of the &amp;#x22;*SASEBio* project&amp;#x22;:http://www.ontogene.org/projects/sasebio/ (Semi-Automated Semantic Enrichment of the Biomedical Literature), as a collaboration between the &amp;#x22;OntoGene group&amp;#x22;:http://www.ontogene.org/ at the University of Zurich and the NITAS/TMS group of Novartis Pharma AG. The purpose of the system is to allow a human annotator/curator to leverage upon the results of an advanced text mining system in order to enhance the speed and effectiveness of the annotation process. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The OntoGene system takes as input a document (e.g a...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5169/version/1

Off-line memory reprocessing in a recurrent neuronal network formed by unsupervised learning
Provedor de dados: 17
Autores: Jenia Jitsev; Christoph von der Malsburg.
In the visual cortex, memory traces for complex objects are embedded into a scaffold of feed-forward and recurrent connectivity of the hierarchically organized visual pathway. Strong evidence suggests that consolidation of the memory traces in such a memory network depends on an off-line reprocessing done in the sleep state or during restful waking. It remains largely unclear, what plasticity mechanisms are involved in this consolidation process and what changes are induced in the network during memory reprocessing in the off-line regime. Here we focus on the functional consequences off-line reprocessing has in a hierarchical recurrent neuronal network that learns different person identities from natural face images in an unsupervised manner. Due to the...
Tipo: Presentation
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5776/version/1

Off-target response to decoy oligodeoxynucleotide treatment
Provedor de dados: 17
Autores: Ewan J. D. Robson; Aaron R. Jeffs; Michael R. Eccles.
*Background:* The transcription factor PAX2 regulates key developmental processes, including mediation of resistance to apoptosis. Inappropriate PAX2 expression has been implicated in facilitating tumour survival, and we have previously shown that siRNA-mediated blockade of PAX2 signalling at the transcript level in EJ bladder carcinoma cells promotes cell death. In this study, we attempted to disrupt PAX2 transcriptional activity in EJ cells by using a decoy oligodeoxynucleotide (ODN). &amp;#xd;&amp;#xa;*Results:* We could not show an interaction between PAX2 and our PAX2 decoy ODN, and in both &amp;#xd;&amp;#xa;PAX2-positive EJ and PAX2-negative HEK293 control cells, decoy and control ODN transfection resulted in a marked retardation of cell growth,...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2281/version/1

Oilseed Rape straw for Cultivation of Oyster Mushroom
Provedor de dados: 17
Autores: Gholamali Peyvast; Ahmad Nowroozi; Jamal-Ali Olfati.
Oyster mushroom [_Pleurotus ostreatus_ var. _sajor caju_ (Fr.) Singer] cultivation can play an important role in managing organic waste. It can be cultivated on a wide rang of substrates containing lignin and cellulose. Oyster mushroom was grown on five substrates: Rise straw (Oryza sativa L. var. Alikazemi), Rise straw + Oilseed Rape straw (Brassica napus var. Hyola 401) (75:25 dw /dw), Rise straw + Oilseed Rape straw (50:50 dw /dw), Rise straw + Oilseed Rape straw (25:75 dw /dw) and Oilseed Rape straw alone. Oilseed Rape straw alone and Rise straw + Oilseed Rape straw (25:75 dw /dw) were best for fruit body production of P. ostreatus. Time to fruiting for P. ostreatus was also shorter on Oilseed Rape straw. Protein content of the fruit bodies obtained...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2069/version/1

Omics Data Sharing - BioSharing: on Data Policies&amp;#x2019;s Plans and Reporting Standards
Provedor de dados: 17
Autores: Susanna-Assunta Sansone.
Several data preservation, management and sharing policies have emerged in response to increased funding for high-throughput approaches in major genomics and functional genomics bioscience domain; and nowadays, several funding agencies also require inclusion of data-sharing plans in grant applications. But despite some commonalities, the policies are heterogeneous by nature, given the different types of communities served and the data types they generate. In parallel, an escalating number of community-driven standardization efforts (including biocurators, database developers and experimentalists, vendors etc), operate to develop minimal requirements checklists, ontologies, and file-formats to support the harmonization of the reporting process, so that...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5049/version/1

On ARS-interacting multifunctional protein p18
Provedor de dados: 17
Autores: Viktor Deineko.
Nine aminoacyl-tRNA synthetases with three auxiliary components are forming a multisynthetase complex which is essential component of protein biosynthesis machinery. The smallest auxiliary component p18 takes part in biosynthesis channeling. It is also a regulator of p53 and has tumor suppressing function. Particular structure of this protein is still unknown. Here methods of structural bioinformatics were applied to generate a model of p18 spatial structure suitable for further research. The structure was created using homology modeling. DNA-binding residues of p18 were also derived both from raw sequence and from three-dimensional structure model.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1593/version/1

On Asymmetry in Biology and Nature
Provedor de dados: 17
Autores: I. C. Baianu.
Symmetry has attracted a substantial amount of effort because considerable simplifications are possible in the mathematical and physical treatment of phenomena and natural systems that possess a certain degree of symmetry. Among physical and chemical systems the most widely known are those related to crystals and fluids. Whereas crystals have a lattice structure and a symmetry caused by &amp;#x2018;perfect&amp;#x2019; order which can be classified by mathematical symmetry groups, most fluids have an average isotropic, highly-disordered &amp;#x2018;structure&amp;#x2019; that is often considered to be random.Asymmetry is widely encountered in Biology and ecological systems- from amino acids to trees forests, and tribes, from physiological processes to...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics; Earth &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7134/version/1

On attraction of slime mould Physarum polycephalum to plants with sedative properties
Provedor de dados: 17
Autores: Andrew Adamatzky.
A plasmodium of acellular slime mould Physarum polycephalum is a large single cell with many nuclei. Presented to a configuration of attracting and repelling stimuli a plasmodium optimizes its growth pattern and spans the attractants, while avoiding repellents, with efficient network of protoplasmic tubes. Such behaviour is interpreted as computation and the plasmodium as an amorphous growing biological computer. Till recently laboratory prototypes of slime mould computing devices (Physarum machines) employed rolled oats and oat powder to represent input data. We explore alternative sources of chemo-attractants, which do not require a sophisticated laboratory synthesis. We show that plasmodium of P. polycephalum prefers sedative herbal tablets and dried...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5985/version/1

On biological homochirality
Provedor de dados: 17
Autores: Rodrick Wallace.
Generalizing Landau&amp;#x27;s spontaneous symmetry breaking arguments using the standard groupoid approach to stereochemistry allows reconsideration of the origin of biological homochirality. On Earth, limited metabolic free energy density may have served as a low temperature analog to &amp;#x27;freeze&amp;#x27; the system into the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in Darwinian competition until a single configuration survived. Subsequent path dependent evolutionary process licked in this initial condition. Astrobiological outcomes, in the presence of higher initial metabolic free energy densities, could well be considerably richer, perhaps of mixed chirality. One result would be a...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3902/version/1

On optical detection of densely labeled synapses in neuropil and mapping  connectivity with combinatorially multiplexed fluorescent synaptic markers
Provedor de dados: 17
Autores: Yuriy Mishchenko.
We propose a new method for mapping neural connectivity optically, by utilizing  Cre/Lox system Brainbow to tag synapses of different  neurons with random  mixtures of different  fluorophores, such as GFP, YFP, etc., and then detecting patterns of fluorophores at different synapses using light microscopy (LM). Such patterns will immediately report the pre- and post-synaptic cells at each synaptic connection, without tracing neural projections from individual synapses to corresponding cell bodies. We simulate fluorescence from a population of densely labeled synapses in a block of hippocampal neuropil, completely reconstructed from electron microscopy data, and show that high-end LM is able to detect such patterns with over 95% accuracy. We conclude,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4144/version/1

On Real-Time Synthetic Primate Vision
Provedor de dados: 17
Autores: Andrew A. Dankers; Nick Barnes; Walter F. Bischof; Alex Zelinsky.
The primate vision system exhibits numerous capabilities. Some important basic visual competencies include: 1) a consistent representation of visual space across eye movements; 2) egocentric spatial perception; 3) coordinated stereo fixation upon and pursuit of dynamic objects; and 4) attentional gaze deployment. We present a synthetic vision system that incorporates these competencies.We hypothesize that similarities between the underlying synthetic system model and that of the primate vision system elicit accordingly similar gaze behaviors. Psychophysical trials were conducted to record human gaze behavior when free-viewing a reproducible, dynamic, 3D scene. Identical trials were conducted with the synthetic system. A statistical comparison of synthetic...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1241/version/1

On the 7-azaindole in acetonitrile anhydrous solutions as an inappropriate photophysical model for DNA base pairs
Provedor de dados: 17
Autores: Javier Catal&amp;#xe1;n.
Multiple Hydrogen-bonding is a fundamental issue to explain base-pairing in DNA structures, which was firstly described by Watson and Crick^1^ using stable keto tautomer forms. In their analysis, they considered the possibility of mutations via proton transfer reactions within a base pair. Such reactions can be induced by electronic excitation, for example, adenine-cytosine mispairing may be caused by double-proton phototautomerism.^2^ The 7-azaindole (7AI) doubly-hydrogen bonded dimer was firstly proposed as a suitable model for explaining the DNA base mispairing owing to excited state two-proton phototautomerization in 1969 by Taylor _et al_.^3^ The concerted nature of this excited state biprotonic transfer has been strongly supported by available...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3089/version/1

On the close relationship between speciation, inbreeding and recessive mutations.
Provedor de dados: 17
Autores: Etienne Joly.
Whilst the principle of adaptive evolution is unanimously recognised as being caused by the process of natural selection favouring the survival and/or reproduction of individuals having acquired new advantageous traits, a consensus has proven much harder to find regarding the actual origin of species. Indeed, since speciation corresponds to the establishment of reproductive barriers, it is difficult to see how it could bring a selective advantage because it amounts to a restriction in the opportunities to breed with as many and/or as diverse partners as possible. In this regard, Darwin himself did not believe that reproductive barriers could be selected for, and today most evolutionary biologists still believe that speciation can only occur through a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5003/version/3

On the Coding of Negative Quantities in Cortical Circuits
Provedor de dados: 17
Autores: Dana Ballard; Janneke Jehee.
Mullers Law of specific nerve energies introduced the idea that nerves transmit information about specific sensory features. This concept has been refined by the notion of &amp;#x27;labeled lines,&amp;#x27; specific cells that capture sub-features of a sensory or motor stimulus, such as Hubel and Weisel&amp;#x27;s opponent color cells. Such features can be visualized as coding a signed quantity that has positive and negative components that are encoded with separate nerve cells. We show that there are two important consequences when learning receptive field using signed codings in circuits. The first is that in feedback circuits even simple operations need to be distributed across multiple distinct pathways. The second consequence is that such pathways are...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1938/version/1

On The Dangers Of Aligning RNA Sequences Using &amp;#x201c;Conserved&amp;#x201d; Motifs
Provedor de dados: 17
Autores: Roderic Page.
Aligning RNA sequences can be a challenging task. Automatic sequence alignment programs typically align sequences only with respect to primary sequence, and as a result may yield spurious alignments. Incorporating information on RNA secondary structure can improve the alignment, but this must usually be done by hand. One approach to aligning RNA sequences uses &amp;#x22;conserved motifs&amp;#x22;, however relying on these motifs may lead to gross errors of alignment if, in fact, those motifs are not conserved.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1029/version/1

On the difference between exclosures and enclosures in ecology and the environment
Provedor de dados: 17
Autores: Raf Aerts; Jan Nyssen; Mitiku Haile.
Rehabilitation of degraded land in arid and semiarid environments often involves excluding livestock from degraded sites, creating what are usually but unfortunately not consistently, called _exclosures_.  Their main objective is to allow native vegetation to regenerate as a means of providing fodder and woody biomass, to reduce soil erosion and to increase rain water infiltration.  We are concerned that some of the alternative names for this practice that are reported in the international literature, including _closed area_, _area closure_ and _enclosure_, may lead to confusion and misunderstanding, especially when these are used as synonyms.  Here we aim to illustrate the difference between exclosures and enclosures using recent ecological and...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2308/version/1

On the dimensionality of the Avogadro constant and the definition of the mole
Provedor de dados: 17
Autores: Nigel Wheatley.
There is a common misconception among educators, and even some metrologists, that the Avogadro constant _N_~A~ is (or should be) a pure number, and not a constant of dimension *N*^&amp;#x2013;1^ (where *N* is the dimension amount of substance). Amount of substance is measured, and has always been measured, as ratios of other physical quantities, and not in terms of a specified pure number of elementary entities. Hence the Avogadro constant has always been defined in terms of the unit of amount of substance, and not vice versa. The proposed redefinition of the mole in terms of a fixed value of the Avogadro constant would cause additional conceptual complexity for no metrological benefit.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5138/version/1

On the Doubly hydrogen bonded dimer of 7-azaindole (0.1 M) as a model for DNA base pairs in acetonitrile solutions at rt
Provedor de dados: 17
Autores: Javier Catalan.
Multiple H-bonded base-pairing as a fundamental element of DNA structure was first described by Watson and Crick using stable keto tautomer forms. In their analysis, they considered the possibility of mutations via tautomeric proton transfer shifts. Among other phenomena, such shifts can be caused by electronic excitation; for example, anomalous adenine-cytosine pairing may be a result of two-proton phototautomerism. One suitable model base pair for two-proton translocating tautomerization is the C2h dimer of 7-azaindole (7AI) proposed by Taylor et al. in 1969. The most salient contribu&amp;#xac;tion of their work was that the double proton transfer in such a dimer occurs in a concerted manner. After the strong controversy raised in 1995 by the proposal of...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1926/version/1

On the exotic fishes given to... geometry
Provedor de dados: 17
Autores: Yury L. Voytekhovsky.
Polyhedral forms are extremely widespread both in animate and inanimate nature. Thus,  crystals occur as polyhedra only. Besides, these forms are quite common with various primitive organisms, i.e. icosahedral viruses, radiolaria and algae. Here we discuss the cases of exotic Boxfish and Porcupinefish. The specific morphology of the Boxfish reveals in polygonal osseous blades, covering its body. As for the Porcupinefish, its polyhedral approximation was observed via certain geometrical techniques applied. Namely, their spine bases were considered the Delaunay point (R, r)-systems. Consequently, the respective Dirichlet tiling proved to be quasifullerenes and analogous to the Boxfish morphology. This unexpected geometrical dualism of the two families...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2191/version/1

On the Hydrides of B, C, N, O and F
Provedor de dados: 17
Autores: Michael J. Bucknum; Eduardo A. Castro.
This paper reports a productive discussion of bonding principles in the non-metallic 2nd row hydrides. It suggests the inversion of a bonding character, potentially from hydrides of B &amp;#x26; C, which may display unsaturation and electronic deficiency accompanied by electronic delocalization in 1D or 2D or 3D. Contrasted with the opposite possibility, within the finite number of hydrides of N, O and F, that display apparently extensive H-bonding and subsequently proton delocalization in 1D and 2D (in HF &amp;#x26; ice polymorphs, respectively), and now potentially in 3D in a corresponding hydride of N called Rice&amp;#x27;s blue material, or perhaps polyimidogen. Where polyimidogen is a crystalline NH lattice that is a polymorph of the ammonium azide...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/2541/version/3

On the Hydrides of B, C, N, O and F
Provedor de dados: 17
Autores: Michael J. Bucknum; Eduardo A. Castro.
This paper reports a productive discussion of bonding principles in the non-metallic 2nd row hydrides. It suggests the inversion of a bonding character, potentially from hydrides of B &amp;#x26; C, which may display unsaturation and electronic deficiency accompanied by electronic delocalization in 1D or 2D or 3D. Contrasted with the opposite possibility, within the finite number of hydrides of N, O and F, that display apparently extensive H-bonding and subsequently proton delocalization in 1D and 2D (in HF &amp;#x26; ice polymorphs, respectively), and now potentially in 3D in a corresponding hydride of N called Rice&amp;#x27;s blue material, or perhaps polyimidogen. Where polyimidogen is a crystalline NH lattice that is a polymorph of the ammonium azide...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/2541/version/2

On the nucleotide distribution in bacterial DNA sequences
Provedor de dados: 17
Autores: Marcelo Sobottka; Andrew Glenn Hart.
It is probable that the distributional structure of DNA sequences arises from the accumulation of many successive stochastic events such as nucleotide deletions, insertions, substitutions and elongations [1, 2, 3, 4, 5, 6, 7]. Although the existence of long-range correlations in non-coding portions of DNA sequences is well established [8, 9, 10, 11], first order Markov chains might well capture aspects of their nucleotide distributions [12]. Here we propose a hidden Markov model based on a coupling of an urn process with a Markov chain to approximate the distributional structure of primitive DNA sequences. Then, by supposing that a bacterial DNA sequence can be derived from uniformly distributed mutations of some primitive DNA, we use the model to explain...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5245/version/1

On the origin of the mitochondrial genetic code: Towards a unified mathematical framework for the management of genetic information
Provedor de dados: 17
Autores: Diego Luis Gonzalez; Simone Giannerini; Rodolfo Rosa.
The origin of the genetic code represents one of the most challenging problems in molecular evolution. The genetic code is an important universal feature of extant organisms and indicates a common ancestry of different forms of life on earth. Known variants of the genetic code can be mainly divided in mitochondrial and nuclear classes. Here we provide a new insight on the origin of the mitochondrial genetic code: we found that its degeneracy distribution can be explained by using a mathematical approach recently developed for the description of the Euplotes nuclear variant of the genetic code. The results point to a primeval mitochondrial genetic code composed of four base codons, which we call tesserae, that, among other features, exhibit outstanding...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7136/version/1

On the Origin of Western Diet Pathologies
Provedor de dados: 17
Autores: John Schloss.
The ratio of the two sulfur-containing amino acids, methionine (Met) and cysteine (Cys), may be a determining factor for which foods contribute to longevity and health. It is shown here that substantially more Met than Cys is consistently found in foods, such as dairy and meat products, thought to contribute to pathologies associated with the Western Diet.
Tipo: Manuscript
Palavras-chave: Cancer; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4641/version/1

On the reliability of Bayesian posterior clade probabilities in phylogenetic analysis
Provedor de dados: 17
Autores: Graham Jones.
This article discusses possible reasons why posterior clade probabilities obtained from Bayesian phylogenetic analyses might be inaccurate. It attempts to list all possible sources of uncertainty and error in Bayesian phylogenetic analysis. The choice of priors on trees has been suggested by several authors as a cause of inaccurate posterior clade probabilities. I argue strongly for using priors based on biological knowledge. Two possible sources of bias which do not seem to have been published before are also discussed. One is a computational problem and the other related to majority rule consensus trees.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1494/version/1

On the social induction of Alzheimer&amp;#x27;s disease: An index theorem aging model for amyloid formation
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
The central &amp;#x27;risk factor&amp;#x27; for Alzheimer&amp;#x27;s disease (AD) is age. From first principles, we construct a mathematical model of protein folding and its in vivo regulation that gives this result in a natural manner. We extend the basic approach using topological information theory methods, and examine a case history of socially-induced premature aging in the United States.
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6012/version/1

On the status of the Michaelis-Menten equation and its implications for enzymology
Provedor de dados: 17
Autores: Sosale Chandrasekhar.
The Michaelis-Menten equation (MME) is considered to be the fundamental equation describing the rates of enzyme-catalysed reactions, and thus the &amp;#x27;physicochemical key&amp;#x27; to understanding all life processes. It is the basis of the current view of enzymes as generally proteinaceous macromolecules that bind the substrate reversibly at the active site, and convert it to the product in a relatively slow overall sequence of bonding changes (&amp;#x27;turnover&amp;#x27;). The manifested &amp;#x27;saturation kinetics&amp;#x27;, by which the rate of the enzymic reaction (essentially) increases linearly with the substrate concentration ([S]) at low [S] but reaches a plateau at high [S], is apparently modelled by the MME. However, it is argued herein...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1637/version/1

Oncogenic Product HMGA1a Might Function as an Aberrant Splicing Inducer of Estrogen Receptor [alpha] in Breast Cancer
Provedor de dados: 17
Autores: Kenji Ohe; Toshiaki Utsumi; Akila Mayeda.
Estrogen receptor (ER)-[alpha]46 is known as an important isoform for ER[alpha]. It inhibits the function of full length ER[alpha] in MCF-7 mammary carcinoma cells and associated with cell cycle arrest. On the other hand, the oncogene _HMGA1_ (formally _HMG I/Y_) is known to have increased expression in mammary carcinoma correlating with the degree of malignancy. We present here that HMGA1a (HMG I) induces the exon skipped product, ER[alpha]46 mRNA, by tethering U1 snRNP to an upstream pseudo 5&amp;#x27; splice site, which is quite analogous to the PSI-mediated splicing regulation of _Drosophila_ P-element.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4104/version/1

One lump or two?
Provedor de dados: 17
Autores: Kieran Smallbone.
We investigate methods for modelling metabolism within populations of cells. Typically one represents the interaction of  a cloned population of cells with their environment as though it were one large cell. The question is as to whether any dynamics are lost by this assumption, and as to whether it might be more appropriate to instead model each cell individually. We show that it is sufficient to model at an intermediate level of granularity, representing the population as two interacting lumps of tissue.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4033/version/1

OneStop:JWS Online&amp;#x27;s access point to SBML,SBGN and MIRIAM compliant annotation
Provedor de dados: 17
Autores: Franco B. Du Preez; Stuart Owen; Katherine Wolstencroft; Olga Krebs; Wolfgang M&amp;#xfc;ller; Carole Goble; Jacky L. Snoep.
We have developed an online model constructor and validator called OneStop, which is compliant with SBGN, SBML and MIRIAM standards. Key features of OneStop are: 1) a human readable input form (in addition to SBML upload and saving); 2) live visualization (SBGN graphics) of the reaction network during the construction phase; and 3) online access from any machine with a compatible browser. Sophisticated error feedback simplifies the debugging process during model construction significantly and guides the efforts of new users in a step by step fashion. OneStop is seamlessly integrated with the JWS Online model repository and simulator and also facilitates the importation of models from the BioModels database. In addition, OneStop is part of the SysMO-SEEK...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6349/version/1

Online Human Health Risk Assessment &amp;#x26; Management: An in-silico approach
Provedor de dados: 17
Autores: Lavkush Dwivedi.
Dreamed quality of life can be achieved by good health and further restored and maintained by the identification of health-related issues and their effective management. Human health risk assessment &amp;#x26; management (HHRAM) approaches are applied for doing so. As internet is now increasingly being used by citizens as a major source of health information, the HHRAM approach was developed in the present study which could predict and manage online the health risks associated with any possible health hazard present in an Indian scenario. The approach is communicated to the entire population through the developed website www.healthrisk.co.in.&amp;#xd;&amp;#xa;The study was completed in three phases (1) Preparation of online health risk assessment...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5357/version/1

Online Training of New Curators
Provedor de dados: 17
Autores: Marc E. Gillespie; Bijay Jassal.
The basic information in Reactome is provided by bench biologists who are experts on a particular pathway, the Reactome Team is always working hard to drive engagement. This engagement between experts, curators, editors and reviewers requires maintenance and improvement, and in this sense Reactome is itself a model for large biocuration projects that are driven by community engagement.  &amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;This tutorial will highlight issues from the perspective of online training participants, the trainer&amp;#x27;s and the audience&amp;#x27;s. From the audience perspective the tutorial will introduce the concepts that drive the Reactome data model, cover the basic steps that a researcher would have to follow in order to breakdown a...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3420/version/1

ONS Open Melting Point Collection
Provedor de dados: 17
Autores: Jean-Claude Bradley; Andrew S. I. D. Lang; Antony J. Williams; Evan Curtin.
This book represents a PDF version of Dataset ONSMP029 (2706 unique compounds, 7413 measurements) from a project to collect and curate melting points made available as Open Data. This particular collection was selected from the application of a threshold to favor the likelihood of reliability. Specifically, the entire range of averaged values for a data point was set to 0.01 C to 5 C, with at least two different measurements within this range.  Measurements were pooled and processed from the following sources: Alfa Aesar, MDPI, Bergstrom, PhysProp, DrugBank, Bell, Oxford MSDS, Hughes, Griffiths and the Chemical Information Validation Spreadsheet.  Links to all the information sources and web services are available from the Open Melting Point Resource page:...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6229/version/1

OntoCAT - a simpler way to access ontology resources
Provedor de dados: 17
Autores: Tomasz Adamusiak; Tony Burdett; K Joeri van der Velde; Niran Abeygunawardena; Despoina Antonakaki; Helen Parkinson; Morris Swertz.
OntoCAT is an open source package developed to simplify the task of querying heterogeneous ontology resources. It supports local ontologies in OBO and OWL format as well as public repositories NCBO BioPortal and EBI Ontology Lookup Service (OLS). It is available from &amp;#x22;http://ontocat.sourceforge.net&amp;#x22;:http://ontocat.sourceforge.net
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4666/version/1

OntoCAT - an integrated programming toolkit for common ontology application tasks
Provedor de dados: 17
Autores: Tomasz Adamusiak; Natalja Kurbatova; Morris A. Swertz; Helen  Parkinson.
OntoCAT provides high level abstraction for interacting with ontology resources including local ontology files in standard OWL and OBO formats (via OWL API) and public ontology repositories: EBI Ontology Lookup Service (OLS) and NCBO BioPortal. Each resource is wrapped behind easy to learn Java, Bioconductor/R and REST web service commands enabling reuse and integration of ontology software efforts despite variation in technologies.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6121/version/1

OntoFox:
Provedor de dados: 17
Autores: Zuoshuang Xiang; Yongqun He.
OntoFox (&amp;#x22;http://ontofox.hegroup.org/&amp;#x22;:http://ontofox.hegroup.org/) is a web server that facilitates ontology development by automatically fetching ontology terms and their annotations from existing ontologies and saving the results in importable RDF/OWL format. OntoFox is developed based on the MIREOT principle. Currently OntoFox can fetch ontology annotations from &amp;#x3e;10 existing ontologies. OntoFox provides an efficient approach to promote ontology sharing and interoperability.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3528/version/1

Ontologies for use in Systems Biology: SBO, KiSAO and TEDDY
Provedor de dados: 17
Autores: Nick Juty; Nicolas Le Nov&amp;#xe8;re; Dagmar Waltemath; Christian Knuepfer.
The use of computational modelling in the description and analysis of biological systems is at the heart of Systems Biology. Besides the information stored in a core model, there is increasingly a need to provide additional semantic information: to identify model components, to assist in biological interpretation of models, to define simulation conditions and to describe simulation results. This information deficit can be addressed through the use of ontologies. We describe here three ontologies created specifically to address the needs of the Systems Biology community in each sub-division, and illustrate their practical use with the &amp;#x27;Repressilator&amp;#x27; model (Elowitz and Leibler, 2000).
Tipo: Poster
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5122/version/1

Ontology for Biomedical Investigations
Provedor de dados: 17
Autores: Bjoern Peters; The OBI Consortium.
The goal of OBI is to enable a formal representation of biomedical investigations that captures the experimental evidence on which their findings are based. The scope of OBI includes: materials made in and produced for investigations, research objectives, experimental protocols, roles of people in investigations and processing and publication of data gathered in investigations. Use of OBI will allow comparison of experimental data from the wide array of scientific disciplines represented by domain experts in the OBI consortium. OBI follows the principles laid out by the OBO foundry, and integrates tightly with other foundry candidate ontologies, such as GO (www.geneontology.org) and ChEBI (www.ebi.ac.uk/chebi/) whose terms are used to describe biological...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3623/version/1

Ontology Mapping of PATO to YATO for the improvement of interoperability of quality description
Provedor de dados: 17
Autores: Hiroshi Masuya; Nobuhiko Tanaka; Kazunori Waki; Tatsuya Kushida; Kouji Kozaki; Riichiro Mizoguchi.
To facilitate broad interoperability for phenotype information between different ontological frameworks, we developed a reference ontology, PATO2YATO_Quality, with the careful mapping of terms of PATO which is a quality ontology commonly used for biological phenotype annotation to the latest top-level ontology, YATO, which represents advanced modeling of quality-related concepts.  As a result, YATO framework enabled to describe changes of phenotypic qualities along the courses of time in ontologically correct way and sophisticated classification and representation of interrelationships among quality-related concepts to provide fully integration of qualitative values and quantitative values obtained from phenotyping experiments and advanced representation...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3508/version/1

Ontology (Science)
Provedor de dados: 17
Autores: Barry Smith.
Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type &amp;#x2013; the Gene Ontology (GO) being the most conspicuous example &amp;#x2013; are a _part of science_. Initial evidence for the truth of this proposition (which some will find self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology develop&amp;#xac;ment work being undertaken in support of scientific research. Ontologies created by...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2027/version/2

Ontology (Science)
Provedor de dados: 17
Autores: Barry Smith.
Increasingly, in data-intensive areas of the life sciences, experimental results are being described in algorithmically useful ways with the help of ontologies. Such ontologies are authored and maintained by scientists to support the retrieval, integration and analysis of their data. The proposition to be defended here is that ontologies of this type &amp;#x2013; the Gene Ontology (GO) being the most conspicuous example &amp;#x2013; are a _part of science_. Initial evidence for the truth of this proposition (which some will find self-evident) is the increasing recognition of the importance of empirically-based methods of evaluation to the ontology development work being undertaken in support of scientific research. The ontologies created by scientists...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2027/version/1

Ontology-&amp;#xad;based Tools to Enhance the Curation Workflow
Provedor de dados: 17
Autores: Trish Whetzel.
In order to effectively search, retrieve, and analyze data oftentimes it is curated and tagged with ontology terms.  However, the amount of effort to curate the existing set of data resources is beyond the limits of purely manual curation.  We present three ontology-based tools developed by the National Center for Biomedical Ontology to enhance the curation workflow: Ontology Widgets, Notes, and the Annotator.  The Ontology Widgets provide a mechanism to use ontologies in Web-based forms without the need to locally parse and store the ontology.  The widgets provide a variety of functionality including term autocompletion and ontology visualization.  The Ontology Widgets are implemented for all BioPortal ontologies, including those from the OBO Foundry and...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5213/version/1

Ontology-based Assisted Curation of Biomedical Data
Provedor de dados: 17
Autores: Conrad Plake.
Manual curation of biomedical data is highly accurate but time consuming, and does not scale with the ever increasing growth of biomedical literature. Text mining as a high-throughput computational technique scales well but requires human expertise to produce highly accurate results. Ontologies can help organizing large quantities of unstructured information. Here we present three systems, namely GoGene, GoPubMed and GoWeb, employing biomedical ontologies and show how they can assist manual curation of biomedical data.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;GoGene associates all genes from different model organisms to concepts of the Gene Ontology (GO) and the Medical Subject Headings (MeSH). The hierarchical structures of both terminologies support clustering...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3122/version/1

Ontology-Based Queries over Cancer Data
Provedor de dados: 17
Autores: Alejandra Gonzalez-Beltran.
The ever-increasing amount of data in biomedical research, and in cancer research in particular, needs to be managed to support efficient data access, exchange and integration. Existing software infrastructures, such as caGrid, support access to distributed information annotated with a domain ontology. However, caGrid&amp;#x27;s current querying functionality depends on the structure of individual data resources without exploiting the semantic annotations. In this paper, we present the design and development of an ontology-based querying functionality that consists of: the generation of OWL2 ontologies from the underlying data resources&amp;#x2019; metadata and a query rewriting and translation process based on reasoning, which converts a query at the...
Tipo: Presentation
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5406/version/1

Ontology-based Trial Management System (ObTiMA)
Provedor de dados: 17
Autores: Mathias Brochhausen; Gabriele Weiler; Fatima Schera; Jochen Rauch; Norbert Graf; Stephan Kiefer.
The ACGT project which aims to foster the sharing of research result from both, clinical and molecular research for the benefit of cancer patients uses ontology-driven semantic services. One novelty ACGT provides is a tool named ObTiMA which allows to build questionnaires directly from the ACGT Master Ontology. This will facilitate the process of creating Case Report Forms. Furthermore, the clinical data collected is already annotated in the terms of the ontology.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3753/version/1

Ontology-driven International Maize Information System (IMIS) for Phenotypic and Genotypic Data Exchange
Provedor de dados: 17
Autores: Rosemary Shrestha; Hector Sanchez; Claudio Ayala; Peter Wenzl; Elizabeth Arnaud.
The Consultative Group on International Agricultural Research (CGIAR; http://www.cgiar.org/) centres have developed the International Crop Information System (ICIS; http://www.icis.cgiar.org) for the management and integration of global information on genetic resources, and germplasm improvement for any crop. The Maize breeding programs at CIMMYT (http://beta.cimmyt.org/) have different software tools to manage phenotypic, genotypic, and environmental information for their experiments generated worldwide. These tools have the capacity of collecting information in the field, wet lab, and store it into different relational databases. The IMIS (http://imis.cimmyt.org/confluence/display/IMIS/Crop+Finder) is an implementation of the ICIS, which is a...
Tipo: Poster
Palavras-chave: Bioinformatics; Plant Biology; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5029/version/1

Open Biomedical Ontologies Applied to Prostate Cancer
Provedor de dados: 17
Autores: James A. Overton; Cesare Romagnoli; Rethy Chhem.
This paper surveys preliminary results from the Interdisciplinary Prostate Ontology Project (IPOP), in which ontologies from the Open Biomedical Ontologies (OBO) library have been used to annotate clinical reports about prostate cancer. First we discuss why we rejected several controlled vocabularies, including SNOMED, DICOM, and RadLex, preferring instead to use the OBO library. We then briefly describe the database-backed website we have created around the relevant OBO ontologies, and provide excerpts of reports from radiology, surgery, and pathology which we have hyperlinked to the ontology terms. This method allows us to discover which relevant terms exist in the OBO library, and which do not. The final section of this paper discusses these gaps in the...
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3570/version/1

Open Biomedical Ontologies Applied to Prostate Cancer
Provedor de dados: 17
Autores: James A. Overton; Cesare Romagnoli; Rethy Chhem.
In this presentation we survey preliminary results from the Interdisciplinary Prostate Ontology Project (IPOP), in which ontologies from the Open Biomedical Ontologies (OBO) library have been used to annotate clinical reports about prostate cancer. First we discuss why we rejected several controlled vocabularies, including SNOMED, DICOM, and RadLex, preferring instead to use the OBO library. We then briefly describe the database-backed website we have created around the relevant OBO ontologies, and provide excerpts of reports from radiology, surgery, and pathology which we have hyperlinked to the ontology terms. This method allows us to discover which relevant terms exist in the OBO library, and which do not. The final section of this paper discusses these...
Tipo: Presentation
Palavras-chave: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3589/version/1

Open Chemistry
Provedor de dados: 17
Autores: Peter Murray-Rust.
An invited article on Open Chemistry discussing the importance of Open Access and Open Data and stressing the emerging role of the blogosphere
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2007
URL: http://precedings.nature.com/documents/1200/version/1

Open Data in Science
Provedor de dados: 17
Autores: Peter Murray-Rust.
Open Data (OD) is an emerging term in the process of defining how scientific data may be published and re-used without price or permission barriers. Scientists generally see published data as belonging to the scientific community, but many publishers claim copyright over data and will not allow its re-use without permission. This is a major impediment to the progress of scholarship in the digital age. This article reviews the need for Open Data, shows examples of why Open Data are valuable and summarizes some early initiatives in formalizing the right of access to and re-use of scientific data.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1526/version/1

Open Notebook Science Challenge: Solubilities of Organic Compounds in Organic Solvents
Provedor de dados: 17
Autores: Jean-Claude Bradley; Cameron Neylon; Rajarshi Guha; Antony J. Williams; Bill Hooker; Andrew S. I. D. Lang; Brent Friesen; Tim Bohinski; David Bulger; Matthew Federici; Jenny Hale; Jenna Mancinelli; Khalid B. Mirza; Marshall J. Moritz; Daniel Rein; Cedric Tchakounte; Hai T. Truong.
This book contains the results of the Open Notebook Science Solubility Challenge. All experimental measurements are provided with a link to either the laboratory notebook page where the experiment was carried out or to a literature reference.  The Challenge was sponsored by Submeta, Nature and Sigma-Aldrich.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4243/version/2

Open Notebook Science Challenge: Solubilities of Organic Compounds in Organic Solvents
Provedor de dados: 17
Autores: Jean-Claude Bradley; Cameron Neylon; Rajarshi Guha; Antony J. Williams; Bill Hooker; Andrew S. I. D. Lang; Brent Friesen; Tim Bohinski; David Bulger; Matthew Federici; Jenny Hale; Jenna Mancinelli; Khalid B. Mirza; Marshall J. Moritz; Daniel Rein; Cedric Tchakounte; Hai T. Truong.
This book contains the results of the Open Notebook Science Solubility Challenge. All experimental measurements are provided with a link to either the laboratory notebook page where the experiment was carried out or to a literature reference.  The Challenge was sponsored by Submeta, Nature and Sigma-Aldrich.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4243/version/3

Open Notebook Science Challenge: Solubilities of Organic Compounds in Organic Solvents
Provedor de dados: 17
Autores: Jean-Claude Bradley; Cameron Neylon; Rajarshi Guha; Antony J. Williams; Bill Hooker; Andrew S. I. D. Lang; Brent Friesen; Tim Bohinski; David Bulger; Matthew Federici; Jenny Hale; Jenna Mancinelli; Khalid B. Mirza; Marshall J. Moritz; Daniel Rein; Cedric Tchakounte; Hai T. Truong.
This book contains the results of the Open Notebook Science Solubility Challenge. All experimental measurements are provided with a link to either the laboratory notebook page where the experiment was carried out or to a literature reference.  The Challenge was sponsored by Submeta, Nature and Sigma-Aldrich.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4243/version/1

Open Notebook Science - Falcipain-2 Preliminary Results
Provedor de dados: 17
Autores: Jean-Claude Bradley; Philip Rosenthal; Rajarshi Guha; Khalid Mirza; Jiri Gut.
This talk was presented by Jean-Claude Bradley at the American Chemical Society meeting in Philadelphia on August 20, 2008. An introduction to Open Notebook Science is presented followed by an illustration of how ONS can be used in drug discovery. New data relating to the anti-malarial activity of Ugi products on 2 falcipain-2 docking sites is detailed. The docking calculations were provided by Rajarshi Guha and the enzyme and in vitro assays on Plasmodium falciparum were provided by Phil Rosenthal and Jiri Gut. Most of the syntheses were carried out by Khalid Mirza in the Bradley group.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Screencast available at:...
Tipo: Presentation
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2216/version/1

Open Notebook Science: Perspectives from a newbie
Provedor de dados: 17
Autores: Cameron Neylon.
My group is using an electronic lab notebook based on a Blog format that is being developed in collaboration with the group of Professor Jeremy Frey. Here I discuss how this led to the adoption of an open notebook science approach in my group as well as some of the consequences, both positive and negative, of adopting such an approach.
Tipo: Presentation
Palavras-chave: Biotechnology.
Ano: 2007
URL: http://precedings.nature.com/documents/1130/version/1

Open Notebook Science Using Blogs and Wikis
Provedor de dados: 17
Autores: Jean-Claude Bradley.
The first half is a summary of how the Bradley group at Drexel University is doing Open Notebook Science with the UsefulChem project to synthesize and test novel anti-malarial compounds.  Graduate student Dave Strumfels&amp;#x27; code to compute kinetics from JCAMP NMR reaction profiles is then highlighted.  Finally screenshots are shown of a building on Nature Island in Second Life where Beth Ritter-Guth and Eloise Pasteur have helped to set up a poster room with NMR spectra, molecules and an organic chemistry quiz that can be activated by clicking on an obelisk. &amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Chemistry.
Ano: 2007
URL: http://precedings.nature.com/documents/39/version/1

Open Science: Tools, approaches, and implications
Provedor de dados: 17
Autores: Shirley Wu; Cameron Neylon.
The Pacific Symposium on Biocomputing is an annual meeting whose topics are determined by proposals submitted by members of the community. This document is the proposal for a session on Open Science, submitted for consideration for the PSB meeting in 2009.
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1633/version/1

Open Source Drug Discovery
Provedor de dados: 17
Autores: Jyoti Yadav; OSDD  Consortium.
Tuberculosis is a ravaging disease killing one person in every 1.5 minutes in India alone. Someone in the world is newly infected with TB bacilli every second. Overall, one-third of the world&amp;#x27;s population is currently infected with the TB bacillus. Left untreated, each person with active TB disease will infect on average between 10 and 15 people every year. 450 000 new MDR-TB cases are estimated to occur every year. Estimated 5% of TB patients are HIV infected. Although the complete genome sequence of the causative pathogen _Mycobacterium tuberculosis_ was published about a decade ago and many years of painstaking efforts have been invested, we are still far from having a good, fast acting drug and vaccine which confers long lasting protection....
Tipo: Poster
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2537/version/1

Open Source Kinesin-1 Stochastic Simulation and Gliding Assay Tracking Software
Provedor de dados: 17
Autores: Lawrence J. Herskowitz; Anthony L. Salvagno; Brian P. Josey; Andy Maloney; Steven J. Koch.
Kinesin-1 (conventional kinesin) is a homodimeric motor protein important for axonal transport. It has been well studied through ensemble and single-molecule assays. However, the enzymatic stepping cycle is complex, with many rate constants that are modulated by interaction of the two motor domains. This makes it difficult to predict how changes in a given rate constant may affect observable properties such as processivity, velocity, or stall force. We have written a simulation of kinesin walking using a Stochastic Simulation Algorithm. The model allows for interactions between the heads, and includes states that are not considered part of the normal cycle. This adds to the complexity of the model but also allows for probing rare events, such as those that...
Tipo: Poster
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4468/version/1

Open Standards and Resources in Systems Biology: collaborative scale-up toward virtual life
Provedor de dados: 17
Autores: Nicolas Le Novere.
The practise of Systems Biology relies on interfaces. Interfaces&amp;#xd;&amp;#xa;between the entities we study: the paradigm moved from a physical&amp;#xd;&amp;#xa;object centric view toward a relationship-centric one; interfaces&amp;#xd;&amp;#xa;between tools: From the retrieval of the primary data to the fine&amp;#xd;&amp;#xa;analysis of a model&amp;#x27;s behaviour, one uses many tools, more or less&amp;#xd;&amp;#xa;well connected; interfaces between individuals: To build any&amp;#xd;&amp;#xa;non-trivial mechanistic model requires to merge existing work and&amp;#xd;&amp;#xa;gather external expertise.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;If we want these interfaces to be generic enough to allow for anybody&amp;#xd;&amp;#xa;to leverage on existing...
Tipo: Presentation
Palavras-chave: Biotechnology; Data Standards.
Ano: 2006
URL: http://precedings.nature.com/documents/10/version/1

OpenCell - Status and plans
Provedor de dados: 17
Autores: Alan Garny.
Update on the current status of OpenCell (&amp;#x22;www.opencell.org&amp;#x22;:http://www.opencell.org) and discussion of our plans for a new version of OpenCell.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5131/version/1

OpenCOR
Provedor de dados: 17
Autores: Alan Garny.
A description of the OpenCOR project. What has been done so far, the choices that were made, etc., as well as the direction in which we are heading.
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5898/version/1

Openness as Infrastructure
Provedor de dados: 17
Autores: John Wilbanks.
Openness at the layer of cultural works and data is the key to the data infrastructure we need to accelerate science. This article lays out three key elements of data infrastructure - collaboration, classification, and openness - which draw us inevitably towards the long-claimed, but rarely-achieved, goal of the scientific method: to make claims that are reproducible under similar circumstances by someone other than the claimant, to be reproducible.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6032/version/1

Opposite effects of two zinc(II) dithiocarbamates on NF-kB pathway
Provedor de dados: 17
Autores: Boris Cvek; Zdenek Dvorak; Jan Taraba; Lukas Muller; Radim Vrzal; Jitka Ulrichova.
Inhibiting nuclear factor-kappaB (NF-kB) activation in anticancer and antiinflammatory therapy is of topical interest. Current research in molecular biology has dramatically advanced in the understanding of the cellular events involved in NF-kB induction. Dithiocarbamates, in particular diethyldithiocarbamate and pyrrolidinedithiocarbamate, have been known and widely used as strong inhibitors of NF-kB signaling pathway for more than ten years. Their activity is frequently thought to be due to chelating of zinc or copper present in serum supplemented in the culture medium. Zinc(II) diethyldithiocarbamate (Et2Zn) and zinc(II) dibenzyldithiocarbamate (Bz2Zn) were prepared by direct synthesis in aqueous millieu. They were structurally characterized by X-ray...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Molecular Cell Biology; Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/735/version/1

Optical and Electrical Properties of Multi-Walled Carbon Nanotubes Functionalized with Oxadiazole Chromophores
Provedor de dados: 17
Autores: Bo-Zhang Yu; Ji-Fei Ma; Hu-Lin Li; Ya-Fei Zhang; Wen-Xin La.
Multi-walled carbon nanotubes (MWCNTs) functionalized with oxadiazole chromophores, 2-(4-aminophenyl)-5-naphthyl-1,3,4-oxadiazole (APND) was prepared by an amide linkage. The resultant MWCNTs-APND and APND were characterized by using FT IR, ^1^H NMR, and XRD analysis to give their structural and crystal information, supporting the successful modification. UV-Vis absorption spectrum of MWCNTs-APND was broadened and significantly red-shifted, and its emission peak was narrower than that of APND, which provided direct evidence for reaction of APND with surface of MWCNTs via [pi]-stacking. The electrical properties demonstrated that there was a perfect ohmic behaviour for membrane of APND, and the thin films of MWCNTs-APND had the same nonlinear properties as...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/2749/version/1

Optimal control circuitry design for the digital p53 dynamics in cancer cell and apoptosis
Provedor de dados: 17
Autores: Rosario M. Ardito Marretta.
Experimental work and theoretical models deduce a &amp;#x22;digital&amp;#x22; response of the p53 transcription factor when genomic integrity is damaged. The mutual influence of p53 and its antagonist, the Mdm2 oncogene, is closed in feedback. This paper proposes an aerospace architecture for translating the p53/Mdm2/DNA damage network into a digital circuitry in which the optimal control theory is applied for obtaining the requested dynamic evolutions of some considered cell species for repairing a DNA damage. The purpose of this paper is not to improve the analysis of the actual mathematical models but to demonstrate the usefulness of such digital circuitry design capable to predict and detect the cell species dynamics for finding more information...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2870/version/1

Optimal decision bounds for probabilistic population codes and time varying evidence
Provedor de dados: 17
Autores: Jan Drugowitsch; Rub&amp;#xe9;n Moreno-Bote; Alexandre Pouget.
Decision making under time constraints requires the decision maker to trade off between making quick, inaccurate decisions and gathering more evidence for more accurate, but slower decisions. We have previously shown that, under rather general settings, optimal behavior can be described by a time-dependent decision bound on the decision maker&amp;#x2019;s belief of being correct (Drugowitsch, Moreno-Bote, Pouget, 2009). In cases where the reliability of sensory information remains constant over time, we have shown how to design diffusion models (DMs) with time-changing boundaries that feature such behavior. Such theories can be easily mapped onto simple neural models of decision making with two perfectly anti-correlated neurons, where they predict the...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5821/version/1

Optimal encoding of interval timing in expert percussionists
Provedor de dados: 17
Autores: David Burr; Guido Chicchini; Roberto Arrighi; Marco Giusti; Luca Cecchetti.
We measured temporal reproduction in expert drummers, string-musicians and non-musical subjects. While duration reproduction of the controls showed a characteristic regression to the mean, drummers responded veridically. This behavior is well explained by a model that combines optimally the sensory estimate for duration (more precise in drummers) with a prior, given by the average of the past few trials. These results highlight the efficiency and adaptability of sensori-motor mechanisms estimating temporal duration.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5588/version/1

Optimal Population Coding, Revisited
Provedor de dados: 17
Autores: Philipp Berens; Alexander S. Ecker; Sebastian Gerwinn; Andreas S. Tolias; Matthias Bethge.
Cortical circuits perform the computations underlying rapid perceptual decisions within a few dozen milliseconds with each neuron emitting only a few spikes. Under these conditions, the theoretical analysis of neural population codes is challenging, as the most commonly used theoretical tool &amp;#x2013; Fisher information &amp;#x2013; can lead to erroneous conclusions about the optimality of different coding schemes. Here we revisit the effect of tuning function width and correlation structure on neural population codes based on ideal observer analysis in both a discrimination and reconstruction task. We show that the optimal tuning function width and the optimal correlation structure in both paradigms strongly depend on the available decoding time in a...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5513/version/1

Optimal storage and recall with biologically plausible synapses
Provedor de dados: 17
Autores: Cristina Savin; Mate Lengyel.
Synaptic plasticity is widely accepted to underlie learning and memory. Yet, models of associative networks with biologically plausible synapses fail to match brain performance: memories stored in such networks are quickly overwritten by ongoing plasticity (Amit &amp;#x26; Fusi 1996, Fusi et al 2007). Metaplasticity - the process by which neural activity changes the ability of synapses to exhibit further plasticity - is believed to increase memory capacity (Fusi et al 2005). However, it remains unclear if neurons can make use of this additional information during recall. In particular, previous attempts at reading out information in metaplastic synapses using heuristic recall dynamics led to rather poor performance (Huang &amp;#x26; Amit...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5818/version/1

Optimising Blue Fluorescent Protein (BFP) for use as a mammalian reporter gene in parallel with Green Fluorescent Protein (GFP).
Provedor de dados: 17
Autores: Etienne Joly.
To obtain an optimised form of BFP for use as a reporter gene in mammalian cells, the brightest available GFP form, EGFP, was mutated at 5 different positions, yielding 8 different mutagenised forms of BFP. The intensity of the fluorescent signals attained in mammalian cells with all these various versions of BFP was analysed by flow cytometry of transiently transfected COS 7 cells. The best mutant obtained can be detected readily both by flow cytometry and fluorescence microscopy, even when expressed together with GFP. To explore whether cellular localization could enhance the fluorescence signals any further, plasmid constructs were made to target optimised versions of GFP and BFP to the nucleus, the endoplasmic reticulum (ER) and the cell surface....
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2007
URL: http://precedings.nature.com/documents/1259/version/1

Optimization of the Ugi reaction using parallel synthesis and automated liquid handling
Provedor de dados: 17
Autores: Jean-Claude Bradley; Khalid Mirza; Kevin Owens; Tom Osborne; Antony Williams.
The Ugi reaction has proved to be a convenient way to quickly create diverse libraries of compounds. It involves the reaction of an amine, an aldehyde, a carboxylic acid and an isonitrile typically in methanol at room temperature. The Ugi reaction has often been used as a tool in the synthesis of pharmacologically active molecules. It has been observed that Ugi products sometimes precipitate in pure form from the reaction mixture. This is a very fortunate outcome since the reaction can then be easily scaled up without requiring costly purification procedures such as chromatography. It would be most beneficial to optimize the Ugi product yield as obtained directly from filtering the reaction mixture without further treatment. To this end we utilized a...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2237/version/1

Optimization-Based Peptide Mass Fingerprinting for Protein Mixture Identification
Provedor de dados: 17
Autores: Zengyou He; Chao Yang; Can Yang; Robert Z Qi; Jason Po-Ming Tam; Weichuan Yu.
*Motivation:* In current proteome research, peptide sequencing is probably the most widely used method for protein mixture identification. However, this peptide-centric method has its own disadvantages such as the immense volume of tandem Mass Spectrometry (MS) data for sequencing peptides. With the fast development of technology, it is possible to investigate other alternative techniques.  Peptide Mass Fingerprinting (PMF) has been widely used to identify single purified proteins for more than 15 years. Unfortunately, this technique is less accurate than peptide sequencing method and cannot handle protein mixtures, which hampers the widespread use of PMF technique. If we can remove these limitations, PMF will become a useful tool in protein mixture...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2268/version/1

Optimizing automated preprocessing streams for brain morphometric comparisons across multiple primate species
Provedor de dados: 17
Autores: Daniel Mietchen; Robert Dahnke; Christian Gaser.
INTRODUCTION&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;MR techniques have delivered images of brains from a wide array of species, ranging from invertebrates to birds to elephants and whales. However, their potential to serve as a basis for comparative brain morphometric investigations has rarely been tapped so far (Christidis and Cox, 2006; Van Essen &amp;#x26; Dierker, 2007), which also hampers a deeper understanding of the mechanisms behind structural alterations in neurodevelopmental disorders (Kochunov et al., 2010).  One of the reasons for this is the lack of computational tools suitable for morphometrci comparisons across multiple species. In this work, we aim to characterize this gap, taking primates as an...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4511/version/2

Optimizing automated preprocessing streams for brain morphometric comparisons across multiple primate species
Provedor de dados: 17
Autores: Daniel Mietchen; Robert Dahnke; Christian Gaser.
Introduction: MR techniques have delivered images of a wide array of species, ranging from invertebrates to birds to elephants and whales. However, their potential to serve as a basis for comparative brain morphometric investigations has rarely been tapped so far (Christidis and Cox, 2006; Van Essen &amp;#x26; Dierker, 2007). In order to address one of the potential reasons behind this, we tested various automated segmentation streams (using CARET, FSL and lab-written code) that have been mainly designed for applications in humans, with the aim of optimizing them for comparisons across multiple species.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: T1-weighted MR images from individuals representing 11 primate species have been acquired by Rilling and Insel...
Tipo: Poster
Palavras-chave: Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4511/version/1

Optogenetic control of genetically-targeted pyramidal neuron activity in prefrontal cortex
Provedor de dados: 17
Autores: Michael  V. Baratta; Shinya Nakamura; Peter Dobelis; Matthew B. Pomrenze; Samuel D. Dolzani; Donald  C. Cooper.
A salient feature  of  prefrontal  cortex  organization  is  the  vast diversity  of  cell types  that  support  the  temporal   integration   of   events   required   for   sculpting future   responses.   A   major   obstacle   in   understanding   the   routing   of   information   among   prefrontal   neuronal   subtypes   is   the   inability   to   manipulate   the   electrical   activity   of genetically defined cell types over behaviorally relevant timescales and activity patterns.  To address these constraints, we present here a simple approach for selective activation of prefrontal excitatory   neurons   in   both   in   vitro   and   in   vivo   preparations.   Rat   prelimbic pyramidal neurons   were   genetically   targeted   to   express   a...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/7102/version/1

Optogenetics in primates: monkey see monkey look
Provedor de dados: 17
Autores: Mehrdad Jazayeri; Zachary Lindbloom-Brown; Gregory Horwitz.
Optogenetics has emerged as a powerful tool for studying the neural basis of simple behaviors in rodents and small animals. In the primate model, however, optogenetics has had limited utility because optical methods have not been able to drive behavior. Here, we report that monkeys reliably shift their gaze toward the receptive field of optically driven channelrhodopsin-2-expressing V1 neurons. This result establishes optogenetics as a viable means for the causal analysis of behavior in the primate model.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6736/version/1

Organic consequences of ileal transposition in rats with diet-induced obesity
Provedor de dados: 17
Autores: Lucas P. F. F. Leal; Joao Luiz  M. C. Azevedo; Gilmara  S. Aguiar-Yamaguchi; Wellington  Cardia; Bianca  Marigliani; Karina  F. Neves; Paolo  H. B. Louren&amp;#xe7;o; Marcelo  C. Carlini; Joao  L. C. Azevedo; Ot&amp;#xe1;vio  C. Azevedo; Gui  M. Ko; Gustavo  P. S.  Miguel; Valderez  B. V.  Lapchick.
INTRODUCTION: The clinical management of metabolic syndrome - especially diabetes mellitus type 2 - is notoriously complex due to the progressive nature of this disease. At present, there is a need for a surgical procedure that is effective for the treatment of diabetes mellitus type 2, even in non-obese individuals. The isolated ileal transposition theory could lead to an effective alternative therapy. This intervention has not yet been performed in humans, and there are no reports of its use in an experimental model of diet-induced metabolic syndrome.&amp;#xd;&amp;#xa; OBJECTIVES: The objective of this study is to evaluate the physiological effects of ileal transposition in rats with diet-induced metabolic syndrome. The effects of this procedure on...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6122/version/1

Organic Control of Oilseed Rape Pests through Natural Pesticides and Mixed Cultivation with Turnip Rape
Provedor de dados: 17
Autores: Tobias Ludwig; Eva Jansen; Benjamin Trost; Julia Mayer; Stefan K&amp;#xfc;hne; Herwart B&amp;#xf6;hm.
A mixed cropping system of rapeseed and 10 % turnip rape as trap crop was compared with oilseed rape in pure stand to demonstrate the reduction of infestation by insect pests. Furthermore the application of bio-pesticides like pyrethrum/rape oil (Spruzit&amp;#xae; Neu), spinosad (SpinTor), diatomeen earth (SiO~2~) /sunflower-oil and rock powder/water was tested. Oilseed rape showed a higher infestation by stem weevils (_Ceutorhynchus_ spp.) in the mixed cropping system compared to rapeseed in pure stand. The reduction of the pollen beetle (_Meligethes aeneus_) on the rapeseed buds resulted from higher attractiveness of turnip rape as a consequence of advanced growth. The faster development of turnip rape seems to be the important key of successful pollen...
Tipo: Presentation
Palavras-chave: Chemistry; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5741/version/1

Organising metabolic networks: cycles in flux distributions
Provedor de dados: 17
Autores: Maur&amp;#xed;cio V. Kritz; Marcelo T. dos Santos; Sebasti&amp;#xe1;n Urrita; Jean-Marc Schwartz.
Metabolic networks are among the most widely studied biological systems. The topology and interconnections of metabolic reactions have been well described for many species, but are not sufficient to understand how their activity is regulated in living organisms. The principles directing the dynamic organisation of reaction fluxes remain poorly understood. Cyclic structures are thought to play a central role in the homeostasis of biological systems and in their resilience to a changing environment. In this work, we investigate the role of fluxes of matter cycling in metabolic networks. First, we introduce a methodology for the computation of cyclic and acyclic fluxes in metabolic networks, adapted from an algorithm initially developed to study cyclic fluxes...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3932/version/1

Orienting Attention Based on Long-Term Memory Improves Perceptual Discriminations
Provedor de dados: 17
Autores: E. Zita Patai; Jennifer Summerfield; Anling Rao; Anna C. Nobre.
The role of attentional orienting in daily life is to selectively deploy both behavioural and neural resources towards events, based on continually changing task goals and expectations, in order to optimize performance. In the following experiment, we show that attentional orienting is influenced by long-term memories in a perceptual discrimination task. In the learning phase, participants were trained on 120 ecologically valid natural scenes, of which 80 contained a target. Their task was to locate the target (a small key) on the screen by clicking on it with the mouse. One or two days later, participants completed a cued perceptual discrimination task. The same scenes that were studied before, but without any targets,  were presented as cues (50 ms...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2960/version/1

Origin and diversification of steroids: Co-evolution of enzymes and nuclear receptors
Provedor de dados: 17
Autores: Michael E. Baker.
Recent sequencing of amphioxus and sea urchin genomes has provided important data for understanding the origins of enzymes that synthesize adrenal and sex steroids and the receptors that mediate physiological response to these vertebrate steroids.  Phylogenetic analyses reveal that CYP11A and CYP19, which are involved in the synthesis of adrenal and sex steroids, first appear in the common ancestor of amphioxus and vertebrates.  This correlates with recent evidence for the first appearance in amphioxus of receptors with close similarity to vertebrate steroid receptors.  Other CYP450 enzymes involved in steroid synthesis can be traced back to invertebrates, in which they have at least two functions: detoxifying xenobiotics and catalyzing the synthesis of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4674/version/1

Origin of biological information: Inherent occurrence of intron-rich split genes, coding for complex extant proteins, within pre-biotic random genetic sequences
Provedor de dados: 17
Autores: Periannan Senapathy; Brajendra Kumar; Chandan K. Singh; Sudar Senapathy; Bipin Balan; Raj Kuppuswami.
The origin of biological information is an unexplained phenomenon. Prior research in resolving the origin of proteins, based on the assumption that the first genes were contiguous prokaryotic sequences has not succeeded. Rather, it has been established that contiguous protein-coding genes do not exist in practically any amount of random genetic sequences. We found that complex eukaryotic proteins could be inherently encoded in split genes that could exist by chance within mere micrograms to milligrams of random DNA. Using protein amino acid sequence variability, codon degeneracy, and stringent exon-length restriction, we demonstrate that split genes for proteins of extant eukaryotes occur extensively in random genetic sequences. The results provide...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5384/version/1

Origin of nanosized diamonds in interstellar space and low-pressure-temperature Earth rocks
Provedor de dados: 17
Autores: Sergei Simakov.
Nanosized diamond particles in the interstellar space and in the Earth rocks related with water presence. In the paper proposed the model of the nanosized diamond particle formation from oxidized water-carbon dioxide gaseous mixtures.
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/4064/version/1

Origin of the Jews and the Arabs: Date of their Most Recent Common Ancestor is Written in their Y-Chromosomes - However, There Were Two of Them
Provedor de dados: 17
Autores: Anatole A. Klyosov.
A pattern of Y-chromosomal mutations in 37 and 67 marker haplotypes of the Jews and the Arabs indicates that their most recent common ancestor in haplogroup J1 (subclade J1e*) and that (a different one) in haplogroup J2 (subclade J2a*) lived 4300+/-500 years before present (ybp) and 4175+/-510 ybp, respectively, that is practically at the same time. Then a split between the Jewish and the Arabic lineages in both J1 and J2 haplogroups occurred, which is clearly visible on the respective haplotype trees. The data show that a common ancestor of Cohanim (Jewish High Priests) of haplogroup J1 lived 1070+/-170 ybp, while a common ancestor of Cohanim in haplogroup J2 lived 3300+/-400 ybp.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/4206/version/1

Ornithine decarboxylase activity, a clinical biomarker for evaluating cancer chemopreventive efficacy of phytomolecules
Provedor de dados: 17
Autores: Nusrat Masood; Vijaya Dubey; Suaib Luqman.
Biomarkers of cancer have made a strong traipse in predicting the disease pattern and contributed significantly to the understanding of tumour state, progression, characteristics and response to therapies. Polyamines such as putrescine, spermine and spermidine are cationic biomolecules essential for the cell cycle function and serve as excellent biomarkers of tumour progression. The polyamine biosynthesis is tightly regulated by ornithine decarboxylase, a highly inducible enzyme specific to pH, temperature, time and substrate concentration. The expression of this enzyme is very high during cell transformation and tumour progression leading to elevated level of polyamines. To measure the activity of ornithine decarboxylase an improved, easy, simple,...
Tipo: Poster
Palavras-chave: Cancer; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6643/version/1

Osmotic stress and water isotope effects in kinesin-1 gliding motility assays
Provedor de dados: 17
Autores: Steven J. Koch; Andy Maloney; Lawrence J. Herskowitz.
The osmotic pressure and kinetic properties of water play important roles in biomolecular interactions.  As pointed out by Parsegian, Rand, and Rau, these crucial roles are often overlooked[1].  In some fields, osmotic stress and isotope effects have been exploited for probing the role water plays in binding interactions of biomolecules.  To our knowledge, there have been no studies of osmotic stress and water isotope effects for kinesin, and only a handful for myosin.  We&amp;#x27;re currently using the gliding motility assay to see whether we can extract new information about kinesin-1 / microtubule interactions by changing osmotic stress and water isotopes.  We will describe our open-source, automated analysis platform for extracting microtubule gliding...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4479/version/1

Overcoming high temperature inhibition of flower formation and fruit production without bees
Provedor de dados: 17
Autores: Albert Liptay; Ron A. Salzman; Jerry H. Stoller; Michael D. Orzolek.
Flower formation in the Cucurbitaceae family is compromised at high temperatures; both male and female flowers and therefore fruit productivity are greatly reduced as the growing temperatures for these vegetable crops are increased above 26C. This intractable phenomenon has been documented both with outdoor field experiments at various latitudes on the eastern seaboard in the USA and in a laboratory, temperature-regulated setting. We now report that an agricultural product, FP, which has been, and is used globally on many commercial crops to increase flower number and strength during blossom formation and development, overcomes the apparent refractory floral initiation and development at high temperatures. This is a new and unexpected finding....
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3707/version/1

Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates
Provedor de dados: 17
Autores: Bjoern Peters; Alan Ruttenberg; Jason Greenbaum; Melanie Courtot; Ryan Brinkman; Patricia Whetzel; Daniel Schober; Susanna Assunta Sansone; Richard Scheuerman; Philippe Rocca-Serra.
The developers of the Ontology of Biomedical Investigations (OBI) primarily use Prot&amp;#xe9;g&amp;#xe9; for editing. However, adding many classes with similar patterns of logical definition is time consuming, error prone, and requires the editor to have some expertise in OWL. Therefore, the process is poorly suited for a large number of domain experts who have limited experience Prot&amp;#xe9;g&amp;#xe9; and ontology development. We have developed a procedure to ease this task and allow such domain experts to add terms to the ontology in a way that both effectively includes complex logical definitions yet requires minimal manual intervention by OBI developers. The procedure is based on editing a Quick Term Template in a spreadsheet format which is...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3970/version/1

Overexpression of an isoform of AML1 in acute leukemia and its potential role in leukemogenesis
Provedor de dados: 17
Autores: Xiangrong Liu; Qing Zhang; Dong-er Zhang; Chunlin Zhou; Haiyan Xing; Zhen Tian; Qing Rao; Min Wang; Jianxiang Wang.
AML1/RUNX1 is a critical transcription factor in hematopoietic cell differentiation and proliferation. From the _AML1_ gene, at least three isoforms, _AML1a_, _AML1b_ and _AML1c_, are produced through alternative splicing. AML1a interferes with the function of AML1b/1c, which are often called AML1. In the current study, we found a higher expression level of _AML1a_ in ALL patients in comparison to the controls. Additionally, AML1a represses transcription from promotor of macrophage-colony simulating factor receptor (M-CSFR) mediated by AML1b, indicating that AML1a antagonized the effect of AML1b. In order to investigate the role of _AML1a_ in hematopoiesis and leukemogenesis _in vivo_, bone marrow mononuclear cells (BMMNCs) from mice were transduced with...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1795/version/1

Overexpression of the leukotriene C4 synthase gene in mice reproduces human aspirin-induced asthma
Provedor de dados: 17
Autores: Hirokuni Hirata; Kyoko Honda; Yasutsugu Fukushima; Masafumi Arima; Takeshi Tokuhisa; Takeshi Fukuda.
The pathogenesis of aspirin-induced asthma (AIA) is presumed to involve the aspirin /non-steroidal anti-inflammatory drug (NSAID)-induced abnormal metabolism of arachidonic acid, resulting in an increase in 5-lopoxygenase (5-LO) metabolites, particularly leukotriene C4 (LTC4)&amp;#x3000;which is a highly potent bronchial constrictor. However, the role of LTC4 in the development of AIA has yet to be conclusively demonstrated. To elucidate the effect of LTC4 on the development of AIA, we generated LTC4 synthase (Ltc4s) gene transgenic (LTC4S-Tg) mice. In contrast to wild-type (WT) mice, LTC4S-Tg mice displayed NSAID-induced airway obstruction that was associated with increases of LTC4 and Th2 cytokines in lung tissue. This is the first study to demonstrate...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4751/version/1

Over-Imitation in the Kalahari Desert and the Origins of Human Cultural Cognition
Provedor de dados: 17
Autores: Mark Nielsen; Keyan Tomaselli.
Children grow up in environments saturated with tools and objects which they must learn to use. One of the most efficient ways in which children do this is by imitating. Recent work has shown that, in contrast to non-human primates, when young children learn by imitating they focus more on reproducing the specific actions used than the actual outcomes achieved. From about 18 months of age children will routinely copy arbitrary and unnecessary actions. This puzzling behaviour is called &amp;#x27;over-imitation&amp;#x27;. By documenting similarities exhibited by children from a large, industrialised city and children from remote Bushman communities in southern Africa, we provide here the first indication that over-imitation is a universal human trait. We...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3049/version/1

Overnight weight loss: relationship with sleep structure and heart rate variability
Provedor de dados: 17
Autores: Walter Moraes; Dalva Poyares; Christian Guilleminault; Agostinho Rosa; Marco Tulio Mello; Adriana Rueda; Sergio Tufik.
Background: Weight loss can be caused by a loss of body mass due to metabolism and by water loss as unsensible water loss, sweating, or excretion in feces and urine. Although weight loss during sleep is a well-known phenomenon, it has not yet been studied in relation to sleep structure or autonomic tonus during sleep. Our study is proposed to be a first step in assessing the relationship between overnight weight loss, sleep structure, and HRV (heart rate variability) parameters.Methods: Twenty-five healthy volunteers received a 487 kcal meal and 200 ml water before experiment. Volunteers were weighed before and after polysomnography. Absolute and relative weight indices were calculated. Time and frequency domain analysis of heart rate variability was...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2342/version/1

Overview of BioSharing
Provedor de dados: 17
Autores: Susanna-Assunta Sansone.
Research communities, funding agencies, and journals participate in the development of reporting standards for the bioscience domain to ensure that shared experiments are reported with enough information to be comprehensible and (in principle) reproducible, compared or integrated (Field, Sansone et al., Science, 2009). Similar trends in both the regulatory arena and commercial science.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Proliferation of standards is a positive sign of stakeholders&amp;#x2019; engagement, but how much do we know about these standards? Which ones are mature and stable enough to use or recommend? Which tools and databases implement which standard? Etc...&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The BioSharing catalogue (www.biosharing.org) aims...
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6151/version/1

Overweight, Obesity and Socio-economic Change among Tangkhul Naga Tribal Women of Manipur, North East India
Provedor de dados: 17
Autores: N.K. Mungreiphy; Satwanti Kapoor.
Background: The prevalence of overweight and obesity is increasing worldwide at an alarming rate. Although in countries like India, which is multi-ethnic having multi socio-economic levels, is typically known for high prevalence of under nutrition, significant proportions of overweight and obese now coexist with the undernourished. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Objectives: The study aims to find the prevalence of overweight and obesity, and its association with socio-economic change among Tangkhul Naga women of Manipur, North East India and also to compare with other female populations of India.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: A cross-sectional study was carried out among 346 Tangkhul Naga tribal women of Manipur, age ranging from 20 to...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1947/version/1

Oxidation numbers as Social Security Numbers: Are they predictive or postdictive?
Provedor de dados: 17
Autores: Hannes Raebiger; Stephan Lany; Raffaele Resta; Alex Zunger.
The Oxidation Number (ON) of an atom within a molecule or solid is a well defined quantity in chemistry (assuming a consistent set of rules are followed), with a long and distinguished history of usefulness. The question revisited recently [1&amp;#x2013;3] is whether it carries a predictive physical meaning in its own right beyond being an unquestionably convenient label. For example, whereas the color of compounds physically reflects the relative energetic positions of occupied vs. unoccupied, dipolecoupled energy levels, can the color be explained [4] by the oxidation state of the central ion? Can the different colors of various Mn compounds be predicted or explained in terms of their oxidation numbers [e.g. pink Mn(II) vs. black Mn(IV) vs. purple...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/4012/version/1

Oxidative Stress and Mitochondrial Injury in Chronic Multisymptom Conditions:  From Gulf War Illness to Autism Spectrum Disorder
Provedor de dados: 17
Autores: Beatrice A. Golomb.
Background: Overlapping chronic multisymptom illnesses (CMI) include Chronic Fatigue Syndrome (CFS), fibromyalgia, irritable bowel syndrome, multiple chemical sensitivity, and Gulf War illness (GWI), and subsets of autism spectrum disorder (ASD). GWI entails a more circumscribed set of experiences that may provide insights of relevance to overlapping conditions.&amp;#xd;&amp;#xa;Objectives: To consolidate evidence regarding a role for oxidative stress and mitochondrial dysfunction (OSMD), as primary mediators in CMI, using GWI as a departure point.&amp;#xd;&amp;#xa;Methods: Exposure relations, character, timecourse and multiplicity of symptoms, and objective correlates of GWI are compared to expectation for OSMD. Objective correlates of OSMD in GWI and...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6847/version/1

Oxytocin makes us trusting but not gullible
Provedor de dados: 17
Autores: Mo&amp;#xef;ra Mikolajczak; Anthony Lane; James Gross; Philippe de Timary; Olivier Luminet.
Originally known for its role in childbirth and lactation, oxytocin (OT) has recently proved to play a key role in social behavior. Deprived of OT, humans are unable to recognize and to bond to their peers. Inversely, once boosted with OT, people become more caring, trusting and generous. Effect-sizes on trust and generosity were sufficiently large that OT started to be perceived as a natural drug that would make people credulous. But could OT really impede judgment and lead individuals to trust untrustworthy peers? Here we show that oxytocin makes people trusting, but not gullible. Namely, OT did not have a trust-enhancing effect on people who interacted with seemingly unreliable peers. These results emphasize that the effect of OT is much more...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3790/version/1

P300- like event related potential amplitude in rats is a correlate of conditioned reinforcement
Provedor de dados: 17
Autores: William D. Klipec; Steven Faux.
We have developed a methodology for recording a robust P300 event related potential  (ERP) in rats. In these experiments a contingency shaped model of the human &amp;#x201c;oddball&amp;#x2019;  paradigm was employed in which rats were shaped to press a lever for food reinforcement signaled by the click of the pellet dispenser. A target tone cued the insertion of the lever that retracted after 1&amp;#xad;sec or immediately following a single reinforced  response, while a non&amp;#xad;target tone was randomly presented. Brain activity was recorded through stainless steel electrodes implanted 1mm below the skull. Here, we compared the amplitude of the P300 response to the click of the pellet dispenser to the amplitude of the P300 response to the target and...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/7100/version/1

p53 independent epigenetic-differentiation treatment in xenotransplant models of acute myeloid leukemia
Provedor de dados: 17
Autores: Yogen Saunthararajah; Quteba Ebrahem; Soledad Negrotto; Reda Mahfouz; Kevin Link; Zhenbo Hu; Xiaorong Gu; Anjali Advani; Matt Kalaycio; Ronald Sobecks; Mikkael Sekeres; Edward Copelan; Tomas Radivoyevitch; Jaroslaw Maciejewski; James C. Mulloy, PhD; Kwok-Peng Ng.
Suppression of apoptosis by TP53 mutation contributes to resistance of acute myeloid leukemia (AML) to conventional cytotoxic treatment. Using differentiation to induce irreversible cell cycle exit in AML cells could be a p53-independent treatment alternative, however, this possibility requires evaluation. In vitro and in vivo regimens of the cytosine analogue decitabine that deplete the chromatin modifying enzyme DNA methyl-transferase 1 (DNMT1) without phosphorylating p53 or inducing early apoptosis were determined. These decitabine regimens but not equimolar DNA-damaging cytarabine up regulated the key late differentiation factors CEBP&amp;#x3b5; and p27/CDKN1B, induced cellular differentiation, and terminated AML cell-cycle, even in...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5780/version/1

p53 Response to DNA Damage in S-phase
Provedor de dados: 17
Autores: David Reisman; Paula Takahashi; Amanda Polson.
p53 induces the transcription of genes that negatively regulate progression of the cell cycle in response to DNA damage or other cellular stressors, and thus participates in maintaining genome stability. Under stress conditions, p53 must be activated to prohibit the replication of cells containing damaged DNA. However, in normal, non-stressed cells, p53 activity must be inhibited. Previous studies have demonstrated that p53 transcription is activated before or during early S-phase in cells progressing from G0/G1 into S-phase. In that this is not what would be predicted from a gene involved in growth arrest and apoptosis, in this study, we provide evidence that this induction occurs to provide available p53 mRNA in order to prepare the cell for DNA damage...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4403/version/1

p63, p73, &amp;#x26; p53 are Negative Regulators of Epithelial to Mesenchymal Transition (EMT), Invasion &amp;#x26; Metastasis
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
It has recently been shown that microRNAs, such as miRs-145,192, and 215, are regulated by the tumor suppressor p53 through their p53REs.  Considering miRs-145, 192, and 215 promoters contain p53REs suggests that they could be transcriptional targets of p63 and p73 as well.  Remarkably, bioinformatics analysis of miRs-145, 192, and 215 targets suggests that they target ZEB2, suggesting that p53, p63, and p73 by increasing the expression of miRs-192, 215, &amp;#x26; 145, they could inhibit the expression of ZEB2.  ZEB2 has been shown to function as a repressor of the tumor suppressor E-cadherin, suggesting that p53, p73, and p63 by suppressing the expression of ZEB2 through their transcriptional target miRs, they could increase the expression of E-cadherin....
Tipo: Poster
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4109/version/1

Pachydermoperiostosis-Like Disease In Captive Red Ruffled Lemurs (Varecia Variegatus Rubra)
Provedor de dados: 17
Autores: Bruce Rothschild; Donald Neiffer; Steve Marks.
Pachydermatoperiostosis, a rare form of hypertrophic osteoarthropathy, is of unknown etiology and previously thought limited to humans. The only periosteal reaction previously reported in prosimians is related to renal disease. Notation of hypertrophic osteoarthritis in three prosimians led to recognition that this was the first non-human documentation of the disease. Three related red ruffed lemurs (Varecia variegatus rubra) had diaphyseal periosteal reaction classic for hypertrophic osteoarthropathy. Workup was negative for known underlying causes and for the secondary hyperparathyroidism which produces bone alterations in black Eulemur macao, black and white Varecia variegatatus varigatus and ringtail Lemur catta lemurs. Recognition of facial coarsening...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6374/version/1

Paclitaxel delivery by micro/nano encapsulation using layer-by-layer assembly
Provedor de dados: 17
Autores: Girish Kumar Gupta; Vikas Jain; Prabhat Ranjan Mishra.
A novel formulation of paclitaxel (PTX) has been developed by providing multilayer assembly over drug loaded porous CaCO3 microparticles (CaCO3 MP) using combination of biocompatible and biodegradable polyelectrolytes (PE&amp;#x2019;s). PTX was encapsulated into the nanopores of preformed CaCO3 MP prepared by the co-precipitation method. Infrared (IR) and X-ray diffraction (XRD) provides evidences that PTX has been encapsulated into nanopores of CaCO3 MP and not crystallized on the surface. PTX loaded CaCO3 MP (CaCO3-PTX) was found to be highly stabilized against thermal decomposition as evinced by thermo gravimetric analysis (TGA) indicating decomposition at 600&amp;#xb0;C and 250&amp;#xb0;C for CaCO3-PTX and PTX respectively. The multilayer assembly over...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2812/version/1

PAL:  A Perl Script for Rapidly Identifying the Active Site of Large Protein Families
Provedor de dados: 17
Autores: Andres A. Larrea; Pablo A. Larrea.
In the post-genomic era, with an ever-increasing amount of sequence information, it is critical to develop tools that assist in sifting through all the data to identify information amidst the noise.  The two main steps in determining the functional sites in proteins are aligning a large set of homologous sequences and analyzing this large file to identify highly conserved residues.  Although a number of tools exist for generating high quality alignments rapidly there are much fewer tools available for rapidly identifying conserved cores within that multiple sequence alignment. PAL, is a Perl script that rapidly identifies conserved residues present in a large alignment file.  The strengths of PAL are: speed, flexibility and ease of use.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/917/version/1

Palaeobathymetry of the Abderaz Formation using foraminifera, Iran
Provedor de dados: 17
Autores: Meysam Shafiee Ardestani; Ebrahim Ghasemi-Nejad.
Abderaz Formation at its type section with an age of Turonian-early Campanian and a thickness of 300 m contains light grey shale and marl. The study of the planktonic foraminifera in isolated form led to differentiate three morphotype groups. The first group is characterized by trochospiral tests usually indicate shallow waters, the second group contains forms with strong ornamentations and the primary keels representing mid waters and finally compact trochospiral tests with keels known as deep water indices are included in the third group. Studies on the morphotypes showed a regressive cycle for Abderaz Formation. Also the planktonic to benthic ratio was calculated using Depth = e^(3.58718 + (0.03534 &amp;#xd7; %*p)^ equilibrium which explains that at the...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2787/version/1

Paleoecology of the Maastrichtian and Danian sediment at North of Central Alborz, Iran, based on Planktonic foraminifera
Provedor de dados: 17
Autores: Behnaz Balmaki.
In order to study the fossil contents of the Ziarat-kola section for biostratigraphical purposes the 212 meters was sampled at Central Alborz. The sequence is mainly made up of monotonous grey- green to light grey marl. Based on Planktonic foraminifera age of Maastrichtian-Danian is determined to the section.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Four zones were determined by the benthic foraminifera morphogroup for showing oxygen and productivity change. The approximate low oxygen and high food supply has been indicates zone of one that increase infauna to epifauna morphotype percent is low (nearness 60% infouna, 40% epifauna). In zone two, with due attention to equal percent of Epifauna ratio to infauna, intermediate oxygen and food supply is anticipated....
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4475/version/1

Paleolinguistics brings more light on the earliest history of the traditional Eurasian pulse crops
Provedor de dados: 17
Autores: Aleksandar M. Mikic; Aleksandar P. Medovic; Branko T. Cupina; Vojislav M. Mihailovic; Aleksandra M. Ignjatovic-Cupina; Vuk B. Djordjevic; Borislav D. J. Kobiljski.
Traditional pulse crops such as pea, lentil, field bean, bitter vetch, chickpea and common vetch originate from Middle East, Mediterranean and Central Asia^1^. They were a part of human diets in hunter-gatherers communities^2^ and are one of the most ancient cultivated crops^3,4^. Europe has always been rich in languages^5^, with individual families still preserving common vocabularies related to agriculture^6,7^. The evidence on the early pulse history witnessed by the attested roots in diverse Eurasian proto-languages remains insufficiently clarified and its potential for supporting archaeobotanical findings is still non-assessed. Here we show that the paleolinguistic research may contribute to archaeobotany in understanding the role traditional Eurasian...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5837/version/1

Pancreas islets in metabolic signaling - focus on the &amp;#x3b2;-cell
Provedor de dados: 17
Autores: Jakob Suckale; Michele Solimena.
Taken together the Islets of Langerhans form a nutrient sensing network spread throughout the pancreas. They are tightly connected to the source organ - the intestine - and the target organs - liver, muscle, and fat cells. The expression of a unique set of proteins enables [beta] cells, the most frequent islet cell type, to detect elevated blood glucose levels and secrete insulin accordingly. Neighbouring [beta]-cells achieve tighter regulation of glucose-induced insulin secretion by coordination through cell surface proteins. They also adjust their secretory pathway capacity and &amp;#xfb02;ow to avoid being damaged. The immediate reaction of the [beta] cell to nutrients is regulated by translational mechanisms, while longer term adaptations involve...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1724/version/1

Pancreas islets in metabolic signaling - focus on the &amp;#x3b2;-cell
Provedor de dados: 17
Autores: Jakob Suckale; Michele Solimena.
Taken together the Islets of Langerhans form a nutrient sensing network spread throughout the pancreas. They are tightly connected to the source organ - the intestine - and the target organs - liver, muscle, and fat cells. The expression of a unique set of proteins enables [beta] cells, the most frequent islet cell type, to detect elevated blood glucose levels and secrete insulin accordingly. Neighbouring [beta]-cells achieve tighter regulation of glucose-induced insulin secretion by coordination through cell surface proteins. They also adjust their secretory pathway capacity and &amp;#xfb02;ow to avoid being damaged. The immediate reaction of the [beta] cell to nutrients is regulated by translational mechanisms, while longer term adaptations involve...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1724/version/2

Pandemic (H1N1) 2009 Cluster Analysis: A Preliminary Assessment
Provedor de dados: 17
Autores: Charles Wick; Michael Stanford; Rabih Jabbour; Samir Deshpande; Patrick McCubbin; Evan Skowronski; Alan Zulich.
Pandemic (H1N1) 2009 virus has been causing major concerns around the world because of its epidemic potential, rapid dissemination, rate of mutations, and the number of fatalities. One way to gain an advantage over this virus is to use existing rapid bioinformatics tools to examine easily and inexpensively generated genetic sequencing data. We have used the protein sequences deposited with the National Center for Biotechnology Information (NCBI) for data mining to study the relationship among the Pandemic (H1N1) 2009 proteins. There are 11 proteins in the Pandemic (H1N1) 2009 virus, and analysis of sequences from 65 different locations around the globe has resulted in two major clusters. These clusters illustrate the Pandemic H1N1 2009 virus is already...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3773/version/1

Para-(benzoyl)-phenylalanine as a potential inhibitor against leptospirosis
Provedor de dados: 17
Autores: Dibyabhaba  Pradhan; Vani Priyadarshini; Manne Munikumar; Amineni  Umamaheswari.
Leptospirosis is a zoonotic disease of global concern caused by Leptospira interrogans. Subtractive genomic approach, metabolic pathway analysis and multi strain genome comparisons of Leptospira interrogans serovars had proposed 88 common drug targets from 5,124 genes of serovar Copenhageni and 4,727 genes of serovar Lai. Three potential drug targets (lpxC, lpxD and lpxB) were identified from Lipid A biosynthesis process of lipopolysaccharide (LPS) biosynthesis pathway. Lipid A is one of the three components of LPS that contains multiple hydrophobic fatty acid chains which anchor the LPS into the bacterial membrane. Designing inhibitory drug molecules targeting Lipid A biosynthesis would dissolve the structural integrity of membrane structure leading to...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5636/version/1

Parallel genome assembly from pre-biotic split-genes: A solution for the mosaic genome conundrum
Provedor de dados: 17
Autores: Periannan Senapathy; Brajendra Kumar; Jeffrey Mattox; Sudar  Senapathy.
The classical concept that all complex life evolved from a simple bacterium-like life form has been questioned by comparative genomics and proteomics. Several discoveries, including the occurrence of entirely new genes in unexpected life forms without any precursors, and the random mosaic distribution of genes across organisms in higher taxa undermine the principal assertions of this theory. We present a new model of the pre-biotic parallel evolution of eukaryotic genomes starting with the structurally complex split genes, which are far more probable of supporting biological information and of occurring in random DNA sequences than contiguous genes. By comparing the mosaic patterns of simulated genomes and extant genomes, we show that genomes arising from...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5387/version/1

Parallel routes of human carcinoma development: Implications of the age-specific incidence data
Provedor de dados: 17
Autores: James Brody.
The multi-stage hypothesis suggests that cancers develop through a single defined series of genetic alterations. This hypothesis was first suggested over 50 years ago based upon age-specific incidence data. However, recent molecular studies of tumors indicate that multiple routes exist to the formation of cancer, not a single route. This parallel route hypothesis has not been tested with age-specific incidence data.To test the parallel route hypothesis, I formulated it in terms of a mathematical equation, confirmed this equation with computer simulations, then tested whether this equation was consistent with age-specific incidence data compiled by the Surveillance Epidemiology and End Results (SEER) cancer registries since 1973. I used the chi-squared...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3080/version/1

Parameter Estimation for Hidden Markov models with Intractable Likelihoods
Provedor de dados: 17
Autores: Ajay  Jasra; Thomas A. Dean; Sumeetpal  S. Simgh; Gareth W. Peters.
In this talk I consider sequential Monte Carlo (SMC) methods for hidden Markov models. In the scenario for which the conditional density of the observations given the latent state is intractable we give a simple ABC approximation of the model along with some basic SMC algorithms for sampling from the associated filtering distribution. Then, we consider the problem of smoothing, given access to a batch data set. We present a simulation technique which combines forward only smoothing (Del Moral et al, 2011) and particle Markov chain Monte Carlo (Andrieu et al 2010), for an algorithm which scales linearly in the number of particles.
Tipo: Presentation
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5957/version/1

Paraoxonase 1 Polymorphism p.Q192R in Patients With Dementia
Provedor de dados: 17
Autores: Tomasz Krzywkowski.
PON1 PCR-RFLP polymorphism frequency and enzyme activity were determined in 223 patients with dementia (94 with AD, 55 with VaD and 74 with MD) and in 100 age and sex matched controls without dementia. I found no statistical significance of genotype frequencies between analyzed groups. &amp;#xd;&amp;#xa;Paraoxonase 1 activity was lower in patients carrying the R allele in locus 192 as compared with the R allele non-carriers. The results showed statistically significant association between PON1 polymorphism and enzyme activity and thus can suggest an important relationship between different isoforms of PON1, enzyme activity and dementia.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6333/version/1

Parental Selection for Productivity Improvement in Indian Tropical Tasar Silkworm, Antheraea mylitta Drury (Lepidoptera: Saturniidae)
Provedor de dados: 17
Autores: Dr. Manohar Reddy Rangareddygari.
Global demand for Vanya silks in general and tasar silk in particular, call-for sustainable utilization of the country&amp;#x2019;s seri-biodiversity potential. Viability and productivity proportion of tasarculture in terms of seeds, cocoons and essentially raw silk, need attention for its vital role in reforming the livelihood and economic condition of tribal farmers. The conventional approaches on basic stock maintenance, commercial seed production, selective use of parental races or parents for heterosis and heterobeltiosis, method of backcrossing to exploit the traits of commercial importance and applying the advantage of genotype x environment (G x E) interactions are indispensable. In spite of current knowledge on sophisticated transgenic silkworm,...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6331/version/1

Parenteral administration of hCG (Human Choriogonadotropin) and fat loss as assessed by Dual energy X-ray absorptiometry (DXA) in experimental animals.
Provedor de dados: 17
Autores: Daniel Belluscio; Ezequiel Klimovsky; Alejandro Kaniuk; Sergio Vaney.
Our studies suggest that in experimental animals, submitted to a hypocaloric diet, the intrarectal administration of hCG (Human Chorionic Gonadotropin) decreases body fat and increases lean mass content in relative values to a greater extent that control animals who did not receive hCG.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/7074/version/1

Parkinson&amp;#x2019;s disease is a TH17 dominant autoimmune disorder against accumulated alpha-synuclein
Provedor de dados: 17
Autores: Wanchung(Wanjiung) Hu.
Parkinson&amp;#x2019;s disease is a very common neurodegenerative disorder. Patients usually undergo destruction of substantia nigra to develop typical symptoms such as resting tremor, hypokinesia, and rigidity. However, the exact mechanism of Parkinson&amp;#x2019;s disease is still unknown, so it is called idiopathic Parkinsonism. According to my microarray analysis of peripheral blood leukocytes and substantia nigra brain tissue, I propose that Parkinson&amp;#x2019;s disease is actually a TH17 dominant autoimmune disease. The autoantigen is mainly alpha-synuclein. After knowing the exact disease pathophysiology, we can develop better drugs to prevent or control the detrimental disorder.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6176/version/1

ParMap, an Algorithm for the Identification of Complex Genomic Variations in Nextgen Sequencing Data
Provedor de dados: 17
Autores: Hossein Khiabanian; Pieter  Van Vlierberghe; Teresa Palomero; Adolfo  A. Ferrando; Raul Rabadan.
Next-generation sequencing produces high-throughput data, albeit with greater error and shorter reads than traditional Sanger sequencing methods. This complicates the detection of genomic variations, especially, small insertions and deletions. Here we describe ParMap, a statistical algorithm for the identification of complex genetic variants using partially mapped reads in nextgen sequencing data. We also report ParMap&amp;#x2019;s successful application to the mutation analysis of chromosome X exome-captured leukemia DNA samples.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4145/version/1

Parrot proventricular dilatation disease: a possible model of Guillain-Barre&amp;#x301; syndrome?
Provedor de dados: 17
Autores: Giacomo Rossi; Lorenzo Crosta; Stefano Pesaro.
Proventricular Dilatation Disease (PDD) affects parrots with clinico-pathological aspects similar to those of the Guillain-Barre&amp;#x301; syndrome (GBS), a human neurophathy. We observed that in sera of PPD-affected parrots antibodies to gangliosides were detectable, similarly to that observed for GBS, and that quantification of such antibodies could be diagnostic for PDD. Then, we proved that administration of purified gangliosides to parrots, elicited autoimmune response and a pathological outcome similar to that of natural PDD. We propose this model not only for better studying PDD, but also as the basis for developing a reliable animal model of GBS.
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/2590/version/1

Partial Dissociation and Hydration Quantitatively Explain the Properties of Aqueous Electrolyte Solutions and hence Empirical Activity Concepts are Unnecessary
Provedor de dados: 17
Autores: Raji Heyrovska.
The author shows that Arrhenius&amp;#x27;s theory of partial electrolytic dissociation was immaturely displaced about eight decades ago by the empirical concept of ionic activities and the assumption of complete dissociation of electrolytes at all concentrations. The latter brought the theory of electrolytes over the next decades into a complicated state without any physical significance. Therefore, the author started a systematic investigation of the available data and could completely restore the original theory of partial dissociation. Now solution properties can be easily understood and quantitatively explained in terms of absolute concentrations and volumes of ions and ion pairs and hydration.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6416/version/1

PathExpand: Extending biological pathways using molecular interaction networks
Provedor de dados: 17
Autores: Enrico Glaab; Anais Baudot; Natalio Krasnogor; Alfonso Valencia.
We present a methodology for extending pre-defined protein sets representing cellular pathways and processes by mapping them onto a protein-protein interaction network, and extending them to include densely interconnected interaction partners. The added proteins display distinctive network topological features and molecular function annotations, and can be proposed as putative new components, and/or as regulators of the communication between the different cellular processes. Finally, these extended pathways and processes are used to analyze their enrichment in cancer mutated genes. Significant associations between mutated genes and certain processes are identified, enabling an analysis of the influence of previously non-annotated cancer mutated genes.
Tipo: Presentation
Palavras-chave: Cancer; Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5639/version/1

Pathogenesis of AD is similar to that of uremic encephalopathy of Homocysteic acid.
Provedor de dados: 17
Autores: Tohru Hasegawa; Masayoshi Ichiba; Takeshi Tabira.
Homocysteic acid (HA) has been established as a pathogen in Alzheimer&amp;#x27;s disease (AD) in 3xTg-AD model mice. However, it is not established whether HA is involved in the AD pathogenesis in humans. We investigated the relationship between urinary HA levels and Mini-Mental State Examination (MMSE) scores in patients with AD (n = 110, normal =22, AD=88) and found a positive, statistically significant relationship between the two variables (r = 0.39, p =0.00003, n = 110). This relationship was stronger in females. (r = 0.47, p = 0.00008, n = 65 in females; r = 0.39, p = 0.02, n =45 in males). The difference in the urinary HA level between normal and AD females was statistically significant (normal:18.4 + 10.6vsAD: 9.1 + 7.2 mM,p&amp;#x3c;0.01), but...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5833/version/1

Pathogenetic role of tissue factor in graft-versus-host disease
Provedor de dados: 17
Autores: Li Quan; Li Weiming; Zhang Jian; Zou Ping.
Graft-versus-host disease (GVHD) is a serious complication after allogeneic stem cell transplantation, the mechanism of it is still not elucidated. Recent findings suggest that host endothelial cells are a target of alloreactive donor cytotoxic T lymphocytes in GVHD and tissue factor (TF) plays an important role not only in coagulation-inflammation cycle, but also in transplant immunology. We postulate TF expression in vascular endothelial cells(VEC) may play an pivotal role in the pathogenesis of GVHD. TF gene andprotein expression in target organs of GVHD in aGVHD mice was significantly elevated compared to that of controls as determined by real-time PCR and Western blotting. Allogeneic CD4^+^T cell and CD8^+^T cells enhanced TF, VCAM-1, TNF-[alpha],...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2248/version/1

PathwayAnalyser: A Systems Biology Tool for Flux Analysis of Metabolic Pathways
Provedor de dados: 17
Autores: Karthik Raman; Nagasuma Chandra.
Stoichiometric and constraint-based analyses of metabolic pathways have been gaining ground in the recent past with the increase in the quality and number of pathway databases available and the curation of genome-scale metabolic models. Genome-scale metabolic models of several organisms such as _Escherichia coli_, _Saccharomyces cerevisiae_ and _Staphylococcus aureus_ have already been constructed. Flux Balance Analysis (FBA) and Minimisation of Metabolic Adjustment (MoMA) are two of the popular techniques for the constraint-based analysis of metabolic pathways.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We have developed a computational tool, PathwayAnalyser, for the analysis of metabolic pathways, particularly by FBA and MoMA. PathwayAnalyser interfaces with the...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1868/version/1

Patterns in soil ammonia-oxidizer response to global change
Provedor de dados: 17
Autores: Kathryn M. Docherty; Brendan Bohannan; Audrey Niboyet; Xavier LeRoux.
Background/Question/Methods&amp;#xd;&amp;#xa;The Domains Archaea and Bacteria contain the vast majority of Earth&amp;#x2019;s biodiversity and biomass, and their members play critical, often exclusive, roles in many biogeochemical cycles and ecosystem services. Human-induced global change, particularly with respect to increased nitrogen deposition, has the potential to drastically alter how soil nitrifying communities perform their biogeochemical function. Additionally, multi-factor global change can alter how microbial communities interact with each other and with the associated plant communities. This study, performed in the context of the long-term Jasper Ridge Global Change Experiment (JRGCE) in a California grassland ecosystem, examines how...
Tipo: Presentation
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5508/version/1

PDBWiki
Provedor de dados: 17
Autores: Henning Stehr; Jose Duarte; Michael Lappe; Jong Bhak; Dan Bolser.
*Background:* The success of community projects such as Wikipedia has recently prompted a discussion about the applicability of such tools in the life sciences. However, there is currently no consensus about how best to achieve this goal.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Methodology/Principal Findings:* Here we present a community knowledge base for the annotation of biological molecular structures that addresses some of these issues. This Wiki-style database consists of one structured page for each entry in the the Protein Data Bank (PDB) and allows users to attach categorised comments and discussions to the entries. The core data for each entry is shown as a summary and can be used for searching and navigation via categories. A user-editable list of...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3123/version/1

PECAn: workflow management for data assimilation and forecasting
Provedor de dados: 17
Autores: David LeBauer; Dan Wang; Xiaohui Feng; Michael Dietze.
*Background/Question/Methods*  Ecosystem models use physiological traits and environmental data to model land-air carbon exchange. Such models can integrate heterogeneous ecological and environmental data, but rarely account for the contribution of each input to the overall uncertainty in model output. Quantifying uncertainty in each model input and propagating uncertainty through model ensembles directly estimates overall uncertainty in model output. Identification of data that would most effectively constrain uncertainty can also be directly inferred by processing output. Real-time data assimilation and forecasting benefits from a method that is transparent, scalable, and adaptable. A tool that manages these steps while tracking the provenance of data...
Tipo: Presentation
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5533/version/1

Peduncle inheritance behavior in Antheraea mylitta. D. - An interesting observation
Provedor de dados: 17
Autores: Mazumdar  Rama Rao; Santosh Kumar Tiwari.
In eco-racial hybridization of Antheraea mylitta D.( Raily X Daba ) the occurrence of long peduncle with two and more rings were found to be an interesting observation against Daba cultivar. Preliminary studies indicate to incorporate the peduncle structure in breeding programs apart from investigating its impact on physiological behavior of the insect.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6293/version/1

Pegs and Ropes: Geometry at Stonehenge
Provedor de dados: 17
Autores: Anthony Johnson; Alberto Pimpinelli.
A recent computer-aided-design investigation of the Neolithic 56 Aubrey Hole circuit at Stonehenge has led to the discovery of an astonishingly simple geometrical construction for drawing an approximately regular 56-sided polygon, feasible with a compass and straightedge. In the present work, we prove analytically that the aforementioned construction yields as a byproduct, an extremely accurate method for approximating a regular heptagon, and we quantify the accuracy that prehistoric surveyors may have ideally attained using simple pegs and ropes. We compare this method with previous approximations, and argue that it is likely to be at the same time the simplest and most accurate. Implications of our findings are discussed.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2153/version/1

Pendent Drops at Elevated P &amp;#x26; T
Provedor de dados: 17
Autores: Apostolos Georgiadis; Geoffrey Maitland; Martin Trusler; Sergei Kazarian; Alexander Bismarck.
Within the scope of producing clean fossil fuels by simultaneously tackling greenhouse gas emissions, the interfacial tension of partially miscible phases containing CO~2~ is being investigated with the pendant drop method. Emphasis is given to measurements at elevated pressures and temperatures, analogous to reservoir conditions. A high pressure apparatus consisting of a view cell and high pressure capillary fittings is used for creating pendent drops at the desired conditions. A computer aided Drop Shape Analysis system is used for capturing images of such drops, which are then analysed for the interfacial tension calculation of the two phases with the KRUSS DSA software. The results acquired from the initial measurements conducted for the H~2~O/CO~2~...
Tipo: Poster
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2636/version/1

Pepper yellow leaf curl Indonesia virus, a new bipartite begomovirus species that belongs to distinct clade of Old World geminiviruses
Provedor de dados: 17
Autores: Pradeep  Sharma1,2; J. Sakata2; Y. Shibuya2; Masato  Ikegami2.
Begomoviruses are currently emerging as a major threat to vegetable production in many tropical and subtropical regions worldwide. Pepper yellow leaf curl disease (PepYLCD) has been noticed in many Capsicum annum L. producing regions from East Asia especially from Indonesia and causes devastating damage to pepper crop production since 2000. In this study we have cloned and sequenced complete nucleotide of begomoviruses from pepper exhibiting leaf curling and bright yellowing symptoms. Besides, we also determined the occurrence of disease on tomato evoking leaf curl symptoms and ageratum with yellow vein type of symptoms. On the basis of genome organization and sequence homology, these viruses were designated as Pepper yellow leaf curl Indonesia virus...
Tipo: Poster
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4162/version/1

Peptides as potent antimicrobials tethered to a solid surface: Implications for medical devices
Provedor de dados: 17
Autores: Ivan A. Gonzalez; XiXi Wong; Dilhari DeAlmeida; Raymond B. Yurko; Simon C. Watkins; Kazi Islam; Ronald C. Montelaro; Ahmed El-Ghannam; Timothy A. Mietzner.
Medical devices are an integral part of therapeutic management; despite their importance, they carry a significant risk of microbial infection. Bacterial attachment to a medical device is established by a single, multiplying organism, leading to subsequent biofilm formation. To date, no preventative measures have impacted the incidence of device-related infection. We report the bidirectional covalent coupling of an engineered cationic antimicrobial peptide (eCAP), WLBU2, to various biological surfaces is accomplished. These surfaces included (i) a carbohydrate-based gel matrix, (ii) a complex polymeric plastic bead, and (iii) a silica-calcium phosphate nanocomposite associated with bone reconstruction. WLBU2-conjugated surfaces are shown to retain potent...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/1967/version/1

Perceptual deficits and inattention in schizophrenia
Provedor de dados: 17
Autores: John R. Skoyles; Bernt C. Skottun.
A number of investigators have found perceptual deficits in schizophrenic subjects. It has also been indicated that those with schizophrenia suffer from reduced attention. This raises the possibility that their perceptual deficits may wholly or in part reflect attentional effects. The present study used computer simulations to examine the potential effects of inattention on performance measures determined with three psychophysical methods: the Two Alternative Forced Choice (2-AFC) Staircase Method, the Two Alternative Forced Choice (2-AFC) Fixed Stimuli Method, and the Yes/No Method. It is shown that both 2-AFC methods are susceptible to attentional effects but, in contrast, the Yes/No Method may allow for the differentiation of attentional effects from...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1584/version/1

Performance of the ALOGPS 2.1 program for octanol-water partition coefficient prediction with organic chemicals on the Canadian Domestic Substances List
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
The KOWWIN and ALOGPS octanol-water partition coefficient (K~ow~) estimation software programs were compared for their capacity to accurately predict log K~ow~ values of 1596 organic compounds on the publicly available Domestic Substances List (DSL) from Environment Canada for which experimental data is available. KOWWIN contained a significantly lower number and magnitude of prediction errors compared to ALOGPS, particularly at experimental log K~ow~ values &amp;#x3c;2. Substantial predictive differences were observed between the two programs for 9093 compounds not having experimental K~ow~ data on the Canadian DSL. Predictive differences of up to 40 log K~ow~ units were found between KOWWIN and ALOGPS, and in some cases, the discrepancies were...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3882/version/1

Performance of the ALOGPS 2.1 program for octanol-water partition coefficient prediction with organic chemicals on the Canadian Domestic Substances List
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
The KOWWIN and ALOGPS octanol-water partition coefficient (K~ow~) estimation software programs were compared for their capacity to accurately predict log K~ow~ values of 1545 organic compounds on the publicly available Domestic Substances List (DSL) from Environment Canada for which experimental data is available. Approximately equivalent log K~ow~ error statistics were observed between KOWWIN and ALOGPS against available experimental data. Substantial predictive differences were observed between the two programs for 6529 compounds not having experimental K~ow~ data on the Canadian DSL. Predictive differences of up to 40 log K~ow~ units were found between KOWWIN and ALOGPS, and in some cases, the discrepancies were sufficiently large that strongly opposing...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/3882/version/2

Performance of the Charniak-Lease parser on biological text using different training corpora
Provedor de dados: 17
Autores: Alison V. Callahan; Michel Dumontier.
POS tagging is used as the first step in many NLP workflows, although the accuracy of tag assignment frequently goes unchecked. We hypothesize that changing the training corpora for a parser will affect its POS tagging of a target corpus. To this end we train the Charniak-Lease parser on the WSJ corpus and two biomedical corpora and evaluate its output to MedPost, a POS tagger with a reported 97% accuracy on biomedical text. Our findings indicate that using biomedical training corpora significantly improves performance, but that minor differences in the biomedical training corpora have a significant effect on the correctness of POS tagging. Specifically, the tagging of hyphenated words and verbs was affected. This work suggests that the choice of training...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2310/version/1

Performance of the M062X density functional against the ISOL set of benchmark isomerization energies for large organic molecules
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase standard state (298.15 K, 1 atm) isomerization energies were calculated using the M062X functional with the QZVP, 6-311++G(d,p), 6-311++G(2d,2p), and cc-pVTZ basis sets against the 24 reactions in the ISOL set of benchmark isomerization energies for large organic molecules. The M062X functional appears to offer comparable isomerization energy prediction performance to the best performing currently available dispersion corrected functionals against this benchmark dataset.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5183/version/1

Performance of the major semiempirical, ab initio, and density functional theory methods in evaluating isomerization enthalpies for linear to branched heptanes
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
The gas phase standard state (298.15 K, 1 atm) isomerization enthalpy prediction performance of the major semiempirical, ab initio, and density functional levels of theory was investigated using the linear to branched heptanes. The M062X density functional, MP2 (and higher) levels of Moller-Plesset perturbation theory, and the CBS and Gaussian-n composite methods are best suited for thermodynamic studies of alkane derivative isomerizations expected during the processing of petroleum, biomass, coal, or other fuels. Where large molecular systems prohibit the use of higher levels of theory, the PM6 and PDDG semiempirical methods may offer an appropriate computational cost-accuracy compromise. Non-M062X density functionals are not recommended for theoretical...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4865/version/1

Persistence of Edge-State in Stacked Graphene and Nano-Graphene Materials
Provedor de dados: 17
Autores: Kikuo Harigaya.
Nano-carbon materials are investigated intensively. In this paper, the edge-state in nanographene materials with zigzag edges is studied theoretically. In particular, while the inter-layer interactions are considered, we prove that edge states exist at the energy of the Dirac point in the doubly stacked nanographene, and in the case of the infinitely-wide lower layer case. This property applies both for the A-B and A-C stackings.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3878/version/1

Persistent BioPerl
Provedor de dados: 17
Autores: Hilmar Lapp.
I present BioSQL, a generic and highly extensible relational model for storing biological sequences, sequence clusters, genes, sequence features, sequence and feature annotation, and ontology terms. BioSQL also represents the interoperable persistence API among the Bio* life science programming toolkits (BioPerl, Biojava, Biopython, BioRuby), each of which has a language-binding to the BioSQL schema. I specifically present the Bioperl-db software, which in a transparent manner makes BioPerl objects persistent using BioSQL.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1233/version/1

Persisters show heritable phenotype and generate bacterial heterogeneity and noise in protein expression
Provedor de dados: 17
Autores: Jaison Jacob.
Persisters are a small subpopulation of bacteria that survive a lethal concentration of antibiotic without antibiotic resistance genes. Isolation of persisters from normally dividing population is considered difficult due to their slow growth, low numbers and phenotypic shift i.e. when re-grown in antibiotic free medium, they revert to parent population. Inability to isolate persisters is a major hindrance in this field of research. Here we reject the &amp;#x2018;phenotypic shift&amp;#x2019; phenomenon exhibited by persisters. Persisters, on the other hand, exhibit a heritable phenotype and can be easily isolated from a normally dividing population that allows their selective growth. Rather than a single subset, they comprise many distinct subgroups each...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/1411/version/2

Persisters show heritable phenotype and generate bacterial heterogeneity and noise in protein expression
Provedor de dados: 17
Autores: Jaison Jacob.
Persisters are a small subpopulation of bacteria that survive a lethal concentration of antibiotic without antibiotic resistance genes. Isolation of persisters from normally dividing population is considered difficult due to their slow growth, low numbers and phenotypic shift i.e. when re-grown in antibiotic free medium, they revert to parent population. Inability to isolate persisters is a major hindrance in this field of research. Here we reject the &amp;#x2018;phenotypic shift&amp;#x2019; phenomenon exhibited by persisters. Persisters, on the other hand, exhibit a heritable phenotype and can be easily isolated from a normally dividing population that allows their selective growth. Rather than a single subset, they comprise many distinct subgroups each...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2007
URL: http://precedings.nature.com/documents/1411/version/1

PERSPECTIVES OF NANODIAMOND FORMATION FROM THE ORGANIC MATTER  AT  LOW P-T PARAMETERS
Provedor de dados: 17
Autores: Sergei Simakov.
The perspectives of nanosized diamond particles formation at metastable P-T parameters from organic matter at hydrothermal conditions is discussed. From the known data it&amp;#x2019;s possible to conclude that we could provide the hydrothermal syntheses of nanodiamonds from the water-oil or water-alcohol-oil solutions.
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4924/version/1

Perspectives on Gene-Environment Interplay in Psychiatry
Provedor de dados: 17
Autores: Michael Rutter.
Sir Michael Rutter began the symposium with a broad overview of gene-environment interplay.&amp;#xd;&amp;#xa;He described the goals of studying such interactions and pointed to the inherent challenges.  He concluded by stressing the need for a variety of strategies for research. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To watch Sir Rutter&amp;#x2019;s presentation, please see the Panel 1 &amp;#x22;Google Video posting.&amp;#x22;:http://video.google.com/videoplay?docid=-3097337289947323438&amp;#x26;hl=en Panel 1 also features welcoming remarks by Dr. Mildred Cho and Professor Hank Greely, both of Stanford University. &amp;#xd;&amp;#xa;
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2657/version/1

pFAR plasmids: New Eukaryotic Expression Vectors for Gene Therapy, devoid of Antibiotic Resistance Markers
Provedor de dados: 17
Autores: Corinne Marie; Magali Richard; Gaelle Vandermeulen; Mickael Quiviger; Veronique Preat; Daniel Scherman.
Efficient production of eukaryotic expression vectors requires the selection of plasmid-containing bacteria. To avoid the risk of dissemination of antibiotic resistance markers, we developed a new system to produce a family of plasmids Free of Antibiotic Resistance genes, called pFARs. The strategy is based on the suppression of a chromosomal nonsense mutation by a plasmid-borne function. The amber mutation was introduced into the Escherichia coli thyA gene that encodes a thymidylate synthase required for dTMP synthesis, resulting in thymidine auxotrophy. In parallel, a small plasmid vector that carries an amber suppressor t-RNA gene was entirely synthesised. The introduction of pFAR plasmids into an optimised thyA mutant restored normal growth to the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2395/version/1

Phagocytic Activity and Hexose Monophosphate Shunt Activity of Cultured Human Kupffer Cells upon Zymosan, Erythrocytes, Amoebic Trophozoits, Latex Beads and Nitroimidazole
Provedor de dados: 17
Autores: Rakesh Sharma; Vijay S. Singh.
Phagocytic function of human Kupffer cells was altered by the addition of nitroimidazole and amoebic trophozoits. The hypothesis was that phagocytic activity was dependent on the nature of additives in culture. The Kupffer cells were fractionated and lysosomes were isolated for enzyme estimations in presence of additives. Phagocytic activity function of human Kupffer cells was altered by the addition of nitroimidazole and amoebic trophozoits in Kupffer cell culture. The human Kupffer cells showed take up of zymosan particles larger than 1 micron in diameter and inert interaction with latex particles. The liver endothelial cells or phagocytes constitute a second line of defense in the liver for the phagoctosis function. The nitroimidazole slowed down the...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4300/version/1

Phantom Pain Reduction by Non-ionizing Electromagnetic Treatment
Provedor de dados: 17
Autores: Istvan Bokkon.
Based on our years of experience testing a technique called non-ionizing Electromagnetic-Own-Signal-Treatment (EMOST), here, we present our preliminary results for phantom pain reduction by this method under clinical circumstances. Our preliminary results showed not only a reduction in phantom pain in patients but also a marked improvement in their sleep and mood quality after the treatments. Here, we also suggest that some of the important effects of our method may be achieved via the redox balance of the body and redox-related neural plasticity. However, low-frequency and intensity electromagnetic fields can potentially provide useful methods for the treatment of various problematic disorders and can play important roles in public health of the 21st...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4989/version/1

Pharmacophore Modeling and Binding Analysis for targeting Mycobacterium tuberculosis MurC ligase
Provedor de dados: 17
Autores: Yogesh N; Jignesh P; Vivek K; C Gopi Mohan.
Despite the availability of effective chemotherapy and the moderately protective vaccine, new anti-Tuberculosis agents are urgently needed to decrease the global incidence of Tuberculosis (TB). The resumption of TB, mainly caused by the emergence of multidrug-resistant (MDR) and extensively drug-resistant (XDR) strains and HIV epidemics, led to an increased need to understand the molecular mechanisms of drug action and drug resistance, which should provide significant insight into the development of newer compounds.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Based on this ground, computational studies of Mtb-MurC enzyme inhibition were carried out to find out novel lead molecules against the same.
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4163/version/1

PharmGKB:  Capturing knowledge to catalyze pharmacogenomics research
Provedor de dados: 17
Autores: Russ B. Altman.
This is a powerpoint presentation made initially at the Cold Spring Harbor meeting on Pharmacogenomics, November 2006.  It discusses the PharmGKB (http://www.pharmgkb.org/) and how we are building a pipeline for annotation of knowledge.  In particular, we are focusing on pathway knowledge, &amp;#x22;Very important Pharmacogene&amp;#x22; annotations, and curation of the pharmacogenomics literature.  We are building an ontology-based system to capture and aggregate knowledge, for use by our curators.
Tipo: Presentation
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Pharmacology.
Ano: 2006
URL: http://precedings.nature.com/documents/8/version/1

Phase organization of circadian oscillators in extended gate and oscillator models
Provedor de dados: 17
Autores: Gang Zhao.
The suprachiasmatic nuclei (SCN) control daily oscillations in physiology and behavior. The gate-oscillator model captures function heterogeneity in SCN and has been successful in reproducing many features of SCN. This paper investigates the mechanism of phase organization in the gate-oscillator model and finds that only stable fixed points of the phase transition function are essential to phase organization. Extending the model with a dead zone of the phase transition function and the propagation delay of the gate signal which represents the spatial structure of SCN, the author discusses how the experimentally reported phase distribution, including phase splitting of animals in LL condition, and fixed phase difference between neurons of SCN could be...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3642/version/1

Phenex: Ontological Annotation of Phenotypic Diversity
Provedor de dados: 17
Autores: James P. Balhoff; Wasila M. Dahdul; Cartik R. Kothari; Hilmar Lapp; John G. Lundberg; Paula Mabee; Peter E. Midford; Monte Westerfield; Todd J. Vision.
Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. Thus, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.&amp;#xd;&amp;#xa;Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4068/version/1

Phenex: Ontological Annotation of Phenotypic Diversity
Provedor de dados: 17
Autores: James P. Balhoff; Wasila M. Dahdul; Cartik R. Kothari; Hilmar Lapp; John G. Lundberg; Paula Mabee; Peter E. Midford; Monte Westerfield; Todd J. Vision.
Phenex is a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic variation using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Despite the centrality of the phenotype to so much of biology, traditions for communicating information about phenotypes are idiosyncratic to different disciplines. Phenotypes seem to elude standardized descriptions due to the variety of traits that compose them and the difficulty of capturing the complex forms and subtle differences among organisms that we can readily observe. Consequently, phenotypes are refractory to attempts at data integration that would allow computational...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4636/version/1

Phenoscape: Ontologies for Large Multi-species Phenotype Datasets
Provedor de dados: 17
Autores: Peter Midford; Paula Mabee; Todd Vision; Hilmar Lapp; Jim Balhoff; Wasila Dahdul; Cartik Kothari; John Lundberg; Monte Westerfield.
The Phenoscape project is developing ontologies and tools to integrate morphological and genomic data to address comparative questions in evolutionary biology. We are currently curating 81 publications describing ~5000 phenotypic characters in 4,000 species of Ostariophysian fishes, and will be making our database of ontology-based annotations concurrently with this meeting via a web-based interface at &amp;#x22;http://kb.phenoscape.org&amp;#x22;:http://kb.phenoscape.org.
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3594/version/1

Phenotypes, Social Constructionism and the Spurious Finding
Provedor de dados: 17
Autores: Nancy Press.
Dr. Press discussed behavioral genetics through the lens of social constructionism.  She also discussed the phenomenon of medicalization, focusing on the example of smoking as a behavior.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To watch Dr. Press&amp;#x27;s presentation, please see the &amp;#x22;Google Video posting&amp;#x22;:http://video.google.com/videoplay?docid=522910112497476586&amp;#x26;hl=en.
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2568/version/1

Phenotypic Plasticity and the Invasiveness of Three _Taraxacum_ Species
Provedor de dados: 17
Autores: Jing Luo; John Cardina.
*Background/Question/Methods* &amp;#xd;&amp;#xa;Many factors have been found to be associated with the success of invasive species. Phenotypic plasticity, the ability of a plant genotype to respond to different environmental conditions by producing different phenotypes, is thought to play an important role plant invasions. In three major experiments, I tested the hypothesis that the invasive _Taraxacum officinale_ (common dandelion) and its non-invasive congener _T. laevigatum_ will exhibit different phenotypic plasticity in germination, growth, and reproduction. I also proposed that their responses to various environments could be used to assess the invasive behavior of a potential crop species: _T....
Tipo: Poster
Palavras-chave: Ecology; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3767/version/1

Phonology is Fundamental in Skilled Reading
Provedor de dados: 17
Autores: Jane Ashby.
There is controversy about the importance of phonology in skilled reading. Event-related potential (ERP) evidence from the initial moments of visual word recognition indicates that processing sub-lexical phonology is fundamental to skilled reading. The early timecourse of this phonological activation explains the predictive power of phonological awareness for early reading development, affirms the importance of phonological processing in learning to read, and illuminates the persistent challenges of dyslexia.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2254/version/1

Phosphate rich organic manure as fertiliser
Provedor de dados: 17
Autores: DMR Sekhar; Y Dassin; Lutfi  Momani; Abu  Hamatteh.
Certain types of rock phosphates of sedimentary origin are applied to acidic soils as fertilizer directly. Recent research in India showed that high grade rock phosphate in fine size when used as a mix with organic manure works as efficiently as di-ammonium phosphate (DAP) in alkaline soils. The rock phosphate from Jhamarkotra, India (sedimentary origin), Egypt (sedimentary origin) and South Africa (volcanic origin) showed good agronomic efficiency when used as Phosphate Rich Organic Manure (PROM). Further PROM shows equal residual effect. The results of efficiency of PROM made using two grades (+ 24% P2O5 and 34% P2O5) of rock phosphate mineral from Jordan show that low grade rock phosphate slimes are as effective as high grade phosphate concentrate when...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/2411/version/1

Phosphatidylserine polarization is required for proper Cdc42 localization and for development of cell polarity.
Provedor de dados: 17
Autores: Gregory Fairn; Sergio Grinstein.
We used genetically-encoded fluorescent probes to visualize the distribution of phosphatidylserine (PS) in live S. cerevisiae. The majority of the PS was found to reside in the cytosolic leaflet of the plasma membrane. Remarkably, PS was polarized, accumulating in bud necks, the bud cortex and the tips of mating projections. Polarization required vectorial delivery of PS-enriched secretory and recycling vesicles. Rapid dissipation of the PS gradient is prevented by the slow diffusion of lipids along the plasmalemmal inner leaflet, estimated by photobleaching recovery measurements to be over an order of magnitude slower than in mammalian cells. In mutants lacking PS-synthase the absence of PS was associated with, and likely responsible for impaired...
Tipo: Manuscript
Palavras-chave: Microbiology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4232/version/1

Photoelectrochemical properties of melanin
Provedor de dados: 17
Autores: Arturo Solis; Maria E. Lara; Luis E. Rendon.
Melanin is to the animal kingdom like chlorophyll to the vegetal kingdom(1). Melanin collects energy from lower-energy radiation sources, kicks electrons into excited states, initiating a process that would end up producing chemical energy, similar to the way in which photosynthesis supplies energy to plants. However, the precise roles of melanin during this process are unknown. Here we show that the increase in the electron-transfer properties of melanin is independent of the energy of the incident photons. We found in controlled in vivo assays that melanin has the remarkable capability of converting lower-energy radiation towards a more useful form of energy. Furthermore, we found that melanin can break up water molecules and giving up energy suggesting...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2007
URL: http://precedings.nature.com/documents/1312/version/1

Photometric properties of microfossil shells
Provedor de dados: 17
Autores: Stergios Zarkogiannis; Ruediger Henrich.
The chromatic characteristics of fossil planktonic foraminifera were measured with the use of an opticoelectric microscope and a new aspect of their nature has been revealed.
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4037/version/1

Photoprotection in Southern Ocean phytoplankton: missing key to low primary productivity
Provedor de dados: 17
Autores: Gary Griffith; Ross Vennell.
The Southern Ocean is considered a zone of high nutrients and low chlorophyll (HNLC). Despite the year round availability of nutrients, phytoplankton biomass remains low. Key modes of control are now thought to be light, grazing, iron and supply of silicic acid^1^. Physiological photoprotective mechanisms used by phytoplankton to regulate photosynthesis versus rapid light fluctuations have not been considered important. In diatoms and haptophytes, which are the major component of phytoplankton biodiversity in the Southern Ocean, the one step de-epoxidation of diadinoxanthin (Dd) into diatoxanthin (Dt) of the Dd-cycle constitutes the main photoprotective mechanism^2,3^. Here we show that Southern Ocean diatoms and haptophytes have higher concentrations of...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5377/version/1

p-hydroxybenzoic acid inhibited photosynthetic efficiency, yield and non-photochemical fluorescence quenching in Lactuca sativa
Provedor de dados: 17
Autores: M. Iftikhar Hussain; Luis Gonzalez; Manuel Joaquin Reigosa.
The p-hydroxybenzoic acid (BA) is a widespread phenolic compound often cited as allelochemical [1], released into soil by root exudates of _Avena fatua_ [2], leaf leachates, and decomposed plant tissues of _Triticum aestivum_ L. [3]. Because of the herbicidal potential of BA on crops [4] and weed species [5], commercially available BA was tested on photosynthetic efficiency, yield and non-photochemical fluorescence quenching in _Lactuca sativa_ in a glass house study. The stock solution (3mM) of BA was made in Methanol: Water (20:80). Methanol was evaporated in a rotary vaporizer and stock solution was adjusted to concentration of 1.5 mM. Lettuce (_Lactuca sativa_ L. cv. Great Lakes California) seeds were grown in perlite culture in plastic pots, irrigated...
Tipo: Poster
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4573/version/1

Phyloclimatic Modelling Can Estimate Ancestral Areas
Provedor de dados: 17
Autores: Chris Yesson; Alastair Culham.
Ancestral area selection is traditionally based on geographic patterns analyzed alongside phylogenetic data. The approach assumes consistent climate and will only select areas from within present day distributions. The combination of observed distribution and inferred climate preferences have been used to determine the potential distribution of species in the past, present and future. The heritability of environmental niches, based on climate preferences, has been demonstrated, and ancestral niches have been reconstructed using phylogenetic techniques. These techniques can be combined to estimate ancestral areas. Ancestral area selection via environmental preference differs from traditional methods, as areas which are outside the current observed...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/478/version/1

Phyloclimatic Modelling: Phylogenies, Palaeo-climate and Environmental Preferences
Provedor de dados: 17
Autores: Chris Yesson; Alastair Culham.
A new technique is demonstrated for the interpretation of the role played by climate in plant diversity through the optimisation of climate variables on phylogenetic trees. This is achieved by calculating climate preferences for individual species based on established bioclimatic modelling techniques using point&amp;#xd;&amp;#xa;distribution data from distributed sources. We demonstrate a new technique for optimising the component parameters on phylogenetic trees. These parameters can be re-combined into&amp;#xd;&amp;#xa;bioclimatic models for ancestral nodes throughout the phylogenetic tree. The combination of DNA-sequence data and the fossil record is used to establish time-calibrated phylogenies. Using these chronograms, bioclimatic models can in turn...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/145/version/1

PhyloCSF: a comparative genomics method to distinguish protein-coding and non-coding regions
Provedor de dados: 17
Autores: Michael F. Lin; Irwin Jungreis; Manolis Kellis.
As high-throughput transcriptome sequencing provides evidence for novel transcripts in many species, there is a renewed need for accurate methods to classify small genomic regions as protein-coding or non-coding. We present PhyloCSF, a novel comparative genomics method that analyzes a multi-species nucleotide sequence alignment to determine whether it is likely to represent a conserved protein-coding region, based on a formal statistical comparison of phylogenetic codon models. We show that PhyloCSF&amp;#x27;s classification performance in 12-species _Drosophila_ genome alignments exceeds all other methods we compared in a previous study, and we provide a software implementation for use by the community. We anticipate that this method will be widely...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4784/version/1

Phylogenetic Codivergence Supports Coevolution of Mimetic Heliconius Butterflies
Provedor de dados: 17
Autores: Jennifer Hoyal Cuthill; Michael Charleston.
The unpalatable and warning-patterned butterflies _Heliconius erato_ and _Heliconius melpomene_ provide the best studied example of mutualistic M&amp;#xfc;llerian mimicry, thought &amp;#x2013; but rarely demonstrated &amp;#x2013; to promote coevolution. Some of the strongest available evidence for coevolution comes from phylogenetic codivergence, the parallel divergence of ecologically associated lineages. Early evolutionary reconstructions suggested codivergence between mimetic populations of _H. erato_ and _H. melpomene_, and this was initially hailed as the most striking known case of coevolution. However, subsequent molecular phylogenetic analyses found discrepancies in phylogenetic branching patterns and timing (topological and temporal incongruence)...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6829/version/1

Phylogeny of conserved adenines in linkers of Group-I introns
Provedor de dados: 17
Autores: Natarajan Ganesan; Chandrasekhar Kesavan.
We have analyzed the linkers in group-I introns, a characteristic region that is crucial to the folding and splicing process of the folded RNA, in seventy sequences spreading across r-RNA, t-RNA and organelle genes from various organisms including algae, fungi and protozoa. The study revealed a high degree of consensus of specific adenine residues in J3/4, J6/7 and J8/7 stems of the linker regions that were required to stabilize the local orientation, either as single residue or by forming unusual base pairs along with divalent metal ions. Conservation of these residues in the Group-I intron linkers suggests their significant contribution to the folded structure whose bonding and geometry recruit metal ions to interact in stabilizing the folded nature of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2909/version/1

Phyloinformatics in the age of Wikipedia
Provedor de dados: 17
Autores: Roderic Page.
This talk describes a mapping between the NCBI taxonomy database and Wikipedia. These two databases were chosen because the NCBI taxonomy contains all the taxa for which sequences are publicly available, and for many taxa Wikipedia is the first site returned in a Google search on that taxon&amp;#x27;s scientific name. The NCBI web pages for nearly 53,000 NCBI taxa now have a link to the corresponding page in Wikipedia.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4583/version/1

Phylontal: Using Phylogenies to Align Phenotype Ontologies
Provedor de dados: 17
Autores: Peter Midford.
Phylontal is a simple approach to generating alignments of ontologies or constructs based on controlled vocabularies that correspond to tips on a phylogeny.  The method requires only a downpass (tips to root) and thus constructing alternative alignments from multiple or uncertain phylogenies may be relatively inexpensive.
Tipo: Poster
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4628/version/1

Physiological Mechanisms Underlying Motion-Induced Blindness
Provedor de dados: 17
Autores: Camilo Libedinsky; Tristram Savage; Margaret Livingstone.
Visual disappearance illusions - such as motion-induced blindness (MIB) - are commonly used to study the neural underpinnings of visual perception. In such illusions a salient visual target becomes perceptually invisible. Previous studies are inconsistent regarding the role of primary visual cortex (V1) in these illusions. Here we provide physiological and psychophysical evidence supporting a role for V1 in generating MIB.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1506/version/1

Phytochemical Approach and Bioanalytical Strategy to Develop Chaperone-Based Medications
Provedor de dados: 17
Autores: Bernd B. K. Kastenholz.
Currently, no pharmaceuticals for the etiological treatment of degenerative protein-misfolding diseases (e.g., ALS, Alzheimer&amp;#x2019;s or prion diseases) are commercially available. Therefore, in this technical note theoretical considerations and practical approaches concerning the development of chaperone-based medications from medicinal plants (e.g., Ginkgo biloba) are reviewed and discussed in detail. Phytochaperones and other agents isolated from medicinal plants are proposed to serve as the general basis of drug development in protein-misfolding diseases.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Neuroscience; Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/1431/version/1

Phytochemical Approach and Bioanalytical Strategy to Develop Chaperone-Based Medications
Provedor de dados: 17
Autores: Bernd Kastenholz.
Currently, no pharmaceuticals for the etiological treatment of degenerative protein-misfolding diseases (e.g., ALS, Alzheimer&amp;#x2019;s or prion diseases) are commercially available. Therefore, in this technical note theoretical considerations and practical approaches concerning the development of chaperone-based medications from medicinal plants (e.g., Ginkgo biloba) are reviewed and discussed in detail. Phytochaperones and other agents isolated from medicinal plants are proposed to serve as the general basis of drug development in protein-misfolding diseases.
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1431/version/2

Picturing the genetic code
Provedor de dados: 17
Autores: A.W.F. Edwards.
The 64 codons of the genetic code are arranged on a six-set Edwards-Venn diagram in such a way that the amino-acids are advantageously displayed.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2007
URL: http://precedings.nature.com/documents/682/version/1

PID: The Pathway Interaction Database
Provedor de dados: 17
Autores: Carl F. Schaefer; Kira Anthony; Shiva Krupa; Jeffrey Buchoff; Matthew Day; Timo Hannay; Kenneth H. Buetow.
The Pathway Interaction Database (PID, &amp;#x22;http://pid.nci.nih.gov&amp;#x22;:http://pid.nci.nih.gov) is a freely available collection of curated and peer-reviewed pathways composed of human molecular signaling and regulatory events and key cellular processes. Created in a collaboration between the U.S. National Cancer Institute and Nature Publishing Group, the database serves as a research tool for the cancer research community and others interested in cellular pathways, such as neuroscientists, developmental biologists, and immunologists. PID offers a range of search features to facilitate pathway exploration. Users can browse the predefined set of pathways or create interaction network maps centered on a single molecule or cellular process of...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2243/version/1

PIM1-dependent phosphorylation of Histone H3 at Serine 10 is required for MYC-dependent transcriptional activation and oncogenic transformation.
Provedor de dados: 17
Autores: Salvatore Oliviero; Alessio Zippo; Alessandra De Robertis; Riccardo Serafini.
The serine/threonine kinase PIM1, cooperates with MYC in cell cycle progression and tumorigenesis. However, the nature of this cooperation remains elusive. Here we show that PIM1 contributes to the transcriptional activation of MYC-target genes by phosphorylating the histone H3 nucleosome at Serine 10 (H3S10). Recombinant PIM1 directly phosphorylates H3S10 on the nucleosome _in vitro_. Following growth factor stimulation, PIM1 accumulates in the nucleus where it forms a complex with the MYC/MAX dimer via the MYC BoxII domain (MBII). Immunofluorescence analysis coupled with _in vivo_ run-on shows a high degree of PIM1 and MYC co-localization in the nucleus at sites of active transcription. Expression profile analysis revealed that PIM1 contributes to the...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/100/version/1

Pioneer Discovery of secondary gold deposits-unique bacterioforms andplacers in north Goa from deep coremetabiosphere
Provedor de dados: 17
Autores: Nandkumar M. Kamat.
Bacterioform secondary gold deposits were discovered in tilloid overlaying archaean base rock (metagraywacke) in Sanvordem rock formation, at the depth of 65 metres in north Goa , India and were confirmed optically as microbiogenic Gold. Multiple and unique forms were seen. This is claimed to be first report of bacterioform Gold in deep cores in Goa, India and Asia.
Tipo: Presentation
Palavras-chave: Biotechnology; Chemistry; Ecology; Genetics &amp; Genomics; Microbiology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5497/version/1

PLA Microparticles for Pulmonary Delivery of AntiTB drugs: Biodistribution study
Provedor de dados: 17
Autores: Rahul Kumar  Verma; Jatinder Kaur; Awadh Bihari Yadav; Kauslender  Kumar; Amit Misra.
A dry powder inhalable (DPI) microparticles comprising anti-tuberculosis drugs incorporated in biodegradable polymers was developed for the treatment of pulmonary tuberculosis (P. Muttil _et al_. 2007). Poly L-lactic acid (PLA) microparticles incorporating a high payload of rifabutin and isoniazid were fabricated by spray drying (Buchi 190). Microparticles were composed of PLA and the drugs (rifabutin and isoniazid) at a 2:1:1 weight ratio. Microparticles of desired high encapsulation efficiency and sustained release characteristics were produced having a diameter range of 2-10 &amp;#xb5;m (Malvern Mastersizer 2000). Differential scanning calorimetry (DSC) was carried out to study drug polymer interaction. The time course of tissue biodistribution...
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2448/version/1

Plant functional constraints on foliar N:P ratios in a tropical forest landscape
Provedor de dados: 17
Autores: Carlos A. Sierra.
Although large scale analyses of foliar N:P ratios suggest and overall pattern of P limitation in tropical forests, analyses within the biome are less indicative of a consistent pattern of nutrient limitation. High tree species diversity and soil heterogeneity are important factors driving the variability of foliar chemistry in the tropics; however, this variability could be reduced at the level of the functional characteristics of the species present at a site. In this study it is hypothesized that foliar N:P ratios would be more constrained when the species are grouped according to functional characteristics, and would reveal patterns of nutrient limitation. The study was conducted in a tropical forest landscape of the Porce region in Colombia, which...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3185/version/1

Plant Functional Types and Plant Trait Measurements in the Eastern Ghats, South India
Provedor de dados: 17
Autores: K. Anupama; A. Stephen; S. Aravajy; G. Orukaimani.
Classifying terrestrial plant species on the basis of function rather than on taxonomy facilitates addressing ecological questions at the scale of ecosystems, landscapes or Biomes. The concept of plant functional types (PFTs) helps handle taxonomic diversity, as it groups together species that share common attributes with respect to, e.g. life-form, phenology and bioclimatic limits. For some time now, large international efforts promoted by the IGBP-GCTE programme are underway to measure for a large number of species a shortlist of significant plant traits that would underlie such functional plant classification systems. The idea here is to help address vegetation responses to and vegetation effects on environmental changes such as climate changes, but...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/941/version/1

Plant Impacts on Competition Between Tidal Marsh Microbes
Provedor de dados: 17
Autores: Ariana Sutton-Grier; Allyson Bullock; Jason Keller; Cindy Gilmour; Pat Megonigal.
*Background/Question/Methods* &amp;#xd;&amp;#xa;Wetlands can store a lot of carbon in soils, but wetland microbial respiration also releases a great deal of carbon dioxide (CO~2~) and methane (CH~4~). These gases combined are responsible for ~80% of the radiative climate forcing.  Understanding the controls on microbial respiration and the importance of different metabolic pathways has important climate change implications. Plants affect microbial respiration in wetlands by impacting the available soil carbon pool and the redoximorphic conditions of the soil environment. These plant impacts in turn affect microbial competition. In this study we were particularly interested in determining the role of soil carbon quality versus environmental factors in...
Tipo: Presentation
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3630/version/1

Plant Metabolic Pathways in MetaCyc and SolCyc
Provedor de dados: 17
Autores: Anuradha Pujar; Ron Caspi; Naama Menda; Isaak Tecle; Peter Karp; Lukas Mueller.
MetaCyc is a metabolic encyclopedia of experimentally validated biochemical pathways curated from scientific literature, that spans all organisms, with an emphasis on plants and microbes. The Pathway tools is a complex curation software suite that enables curation of reactions, construction of pathways and annotation with one or more representative enzymes, that include information such as substrate specificity, kinetic properties, activators, inhibitors, cofactor requirements, genes if cloned and links to external databases. In addition curators are able to provide concise, review-level summaries and extensive literature citations. The present database release includes more than 1200 pathways from more than 1549 organisms, 7312 reactions, 5127 enzymes,...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3192/version/1

Plant regulation of microbial enzyme production in situ
Provedor de dados: 17
Autores: Colin Averill; Adrien C. Finzi.
Soil extracellular enzymes regulate the rate at which complex organic forms of nitrogen (N) become bio-available. Much research has focused on the limitations to heterotrophic enzyme production via lab incubations, but little has been done to understand the limitations to enzyme production in situ. We created root and symbiotic mycelia exclusion treatments using mesh in-growth bags in the field to isolate the effect of roots and other portions of the microbial community on enzyme production. When fertilized with complex protein N we found increases in N-degrading enzyme concentrations only when root in-growth was allowed. No response was observed when complex N was added to root-free treatments. Expanding on economic rules of microbial element limitation...
Tipo: Poster
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6353/version/1

Plant species diversity and genetic diversity interactively influence community properties and ecosystem processes
Provedor de dados: 17
Autores: Kerri M. Crawford; Jennifer  A. Rudgers.
Background/Questions/Methods:  Biodiversity is a critical element of community properties and ecosystem processes.  Both plant species richness and genetic diversity positively affect processes ranging from primary production, ecosystem stability, and the maintenance of diversity.  In nature, it is likely that species diversity and genetic diversity interactively affect how communities are structured and ecosystems function.  However, the relative contribution of species diversity and genetic diversity to ecological processes has been rarely documented, and potential interactions between the two levels of diversity have not been investigated.  Here, I report results from a common garden experiment conducted in a coastal freshwater dune habitat at Sleeping...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5242/version/1

Plant Transcription Factors @ uni-potsdam.de
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n; Ingo Dreyer; Slobodan Ruzicic; Bernd Mueller-Roeber.
We present the Plant Transcription Factor Database (PlnTFDB), and the putative complete set of TFs in the algae _Chlamydomonas reinhardtii_, _Ostreococcus tauri_ and the vascular plants _Oryza sativa_ and _Arabidopsis thaliana_.
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/243/version/1

Plants at risk from climate change
Provedor de dados: 17
Autores: Chris Yesson; Alastair Culham.
The popular garden flower Cyclamen grows natively in the Mediterranean.  Climate change could make the region unsuitable for 18/21 species in 50 years time.  Ant-dispersed Cyclamen can&amp;#x2019;t hope to migrate to suitable new areas without assistance.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Background: The impact of global climate change on plant distribution, speciation and extinction is of current concern. Examining species climatic preferences via bioclimatic niche modelling is a key tool to study this impact. There is an established link between bioclimatic niche models and phylogenetic diversification. A next step is to examine future distribution predictions from a phylogenetic perspective. We present such a study using Cyclamen (Myrsinaceae), a group...
Tipo: Poster
Palavras-chave: Ecology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/150/version/1

Plants switch photosystem at high temperature to protect photosystem II
Provedor de dados: 17
Autores: Yasuo Yamauchi; Yukihiro Kimura; Seiji Akimoto; Yoko Marutani; Masaharu Mizutani; Yukihiro Sugimoto.
Plants are often exposed to temperatures of around 40^o^C. These temperatures can cause serious damage to photosystems, yet plants can survive with minimum damage. Here, we show that plants switch photosystem to protect photosystem II (PSII) at 40^o^C. Using wheat and Arabidopsis seedlings, we investigated the mechanisms of heat-derived damage in the dark and avoidance of damage in the light. Heat treatment at 40^o^C in the dark caused serious damage to PSII: the maximum quantum yield of PSII (Fv/Fm) and oxygen evolution rapidly decreased. The damage was due to the degradation of the D1 protein (shown by immuno-chemical analysis) and the disturbance of energy transfer in PSII core chlorophyll-binding proteins CP43 and CP47 (shown by time-resolved...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6168/version/1

Plasma amino acid profile is altered by visceral fat accumulation and is a predictor of visceral obesity in humans
Provedor de dados: 17
Autores: Takayuki Tanaka; Yuko Ishizaka; Toru Mitushima; Mizuki Tani; Akiko Toda; Eiichi Toda; Minoru Okada; Hiroshi Yamamoto; Minoru Yamakado.
Background: The plasma amino acid profile can be a useful indicator in clinical settings because it changes in response to various metabolic alternations. However, the association between the plasma amino acid profile and body fat accumulation has not been evaluated in humans.Objective: This study aimed to relate plasma amino acids to visceral fat accumulation in humans because excess visceral fat raises the odds ratio of developing metabolic syndrome.Design: A total of 1,449 subjects (985 males and 464 females) who had undergone a comprehensive health screening were enrolled in this study. The visceral fat area (VFA) was determined in each subject using CT imaging. Subjects were then divided into two groups according to VFA: high-VFA (&amp;#x2265;100 cm2,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5560/version/1

Plasmodium falciparum has rare correlation properties
Provedor de dados: 17
Autores: Kushal Shah.
A plot of the correlation function of a given DNA sequence has certain characteristic features common to almost all organisms. One common feature is that the correlation values at distances that are multiples of three is higher than correlation values at other distances. Because of this such a correlation plot can be divided into two or three curves with different scalings. P. falciparum has a rare correlation property which is probably unique. I have analyzed genomes of many bacteria, fungi and protozoa and found that P. falciparum is the only organism whose DNA sequence correlation plot can be divided into four curves with different scalings. This property is neither shared by other species of the Plasmodium genus nor by other AT rich genomes. This could...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6817/version/1

PlnTFDB: Plant Transcription Factor Database &amp;#x2013; Update
Provedor de dados: 17
Autores: Diego Mauricio Ria&amp;#xf1;o-Pach&amp;#xf3;n; Luiz Gustavo Guedes Correa; Bernd Mueller-Roeber.
PlnTFDB is a publicly available computational resource comprising putative complete sets of transcription factors from plants. The original database listed the putative complete sets of TFs from five different green plant (viridiplantae) species. Up to date, summer 2007, PlnTFDB have had more than one hundred thousand hits from more than one thousand different clients, showing the importance that this resource had acquired for the plant community. In this first major update, we extended the coverage of the database to additional completed viridiplantae genomes, i.e., the moss _Physcomitrella patens_ and the rice _Oryza sativa_ spp _indica_. The scope of PlnTFDB was broadened to encompass other eukaryote photosynthetic organisms, such as the rhodophyte...
Tipo: Poster
Palavras-chave: Ecology; Bioinformatics; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1094/version/1

PMEM of carabid beetles in the agro-ecosystem: Prospects and problems
Provedor de dados: 17
Autores: Kai  U. Priesnitz; Ullrich  Benker.
The comparison of carabid communities sampled at three different field sites during 5 years of ecological biosafety research provides useful information for the design of a post market environmental monitoring of this arthropod family. Each evaluated field site demonstrated a unique composition of carabid species. A baseline for the carabid beetle communities would therefore be necessary for each field site to detect any changes in its composition over time. Aside from the influence of the location, the impacts of weather, the date of sampling and of course the chosen sampling method have to be considered. A standardized method is a basic requirement for a replicable assessment. The number of traps per square meter, and the size and the design of the traps...
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4445/version/1

PML-RAR&amp;#x3b1; enhances autophagic activity through inhibiting Akt/mTOR pathway
Provedor de dados: 17
Autores: Guo-Qiang Chen; Ying Huang; Xu-Yun Zhao; Ting-Ting Chen; Jia-Kai Hou; Jing Zhang; Jie Yang; Scott C. Kogan.
Autophagy is a highly conserved, closely-regulated homeostatic cellular activity that allows for the bulk degradation of long-lived proteins and cytoplasmic organelles. Its roles in cancer initiation and progression and in determining the response of tumor cells to anticancer therapy are complicated, and the potential significance of autophagy in the pathogenesis and therapeutic response of acute myeloid leukemia has a little investigation. Here, we demonstrate that induction of acute promyelocytic leukemia (APL)-specific PML-RAR&amp;#x3b1; but not PLZF-RAR&amp;#x3b1;/NPM-RAR&amp;#x3b1; fusion protein up-regulates constitutive autophagic activation in leukemic and non-leukemic cells. The significant increase of autophagic activity is also found in the...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5250/version/1

PocketMatch: A new algorithm to compare binding sites in protein structures
Provedor de dados: 17
Autores: Yeturu Kalidas; Nagasuma Chandra.
Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental&amp;#xd;&amp;#xa;requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring  functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of&amp;#xd;&amp;#xa;the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2142/version/1

PocketMatch: A new algorithm to compare binding sites in protein structures
Provedor de dados: 17
Autores: Yeturu Kalidas; Nagasuma Chandra.
Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental&amp;#xd;&amp;#xa;requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring  functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of&amp;#xd;&amp;#xa;the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2142/version/2

Polar Mapper: a computational tool for integrated visualization of protein interaction networks and mRNA expression data
Provedor de dados: 17
Autores: Joana P. Gon&amp;#xe7;alves; M&amp;#xe1;rio Gr&amp;#xe3;os; Andre X. C. N. Valente.
Polar Mapper is a computational application for exposing the architecture of protein interaction networks. It facilitates the system-level analysis of mRNA expression data in the context of the underlying protein interaction network. Preliminary analysis of a human protein interaction network and comparison of yeast oxidative stress and heat shock gene expression responses are addressed as case studies.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2663/version/1

Polycentric networks and resilience in urban systems: A comparison of Baltimore and Seattle
Provedor de dados: 17
Autores: Michele Romolini; Morgan Grove.
Numerous studies have demonstrated that successful resource management requires collaboration among many groups. While most research has been conducted on rural resource management, collaborative management is now recognized as an important strategy in densely settled urban areas. Cities generally consist of many fragmented land parcels under different types of use and ownership, which produces a large and diverse group of stakeholders with an interest in resource management decisions. Past research has shown that 1) natural resource stewardship organizations play an important role in both managing natural resources and building social capital; 2) successful outcomes often rely on effective collaborations through organizational networks; 3) there are...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5222/version/1

Polyelectrolyte multilayer assembly bearing ketoprofen for transdermal delivery
Provedor de dados: 17
Autores: Rachna Gupta; Preeti Yadav; Subhini A. Saraf.
A novel microencapsulation technology based on layer-by-layer assembly has been extensively studied and used for controlled delivery of drug microcrystal having poor aqueous solubility and low bioavailability. A non-steroidal anti-inflammatory drug ketoprofen (KF)was selected for encapsulation using biodegradable and biocompatible polyions and synergistically the fabricated system was embedded in gel matrix for topical application. Topical application of the drugs at the pathological sites offer potential advantages of delivering the drug directly to the site of action and thus producing high tissue concentrations of the drug.
Tipo: Poster
Palavras-chave: Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3849/version/1

Polyethylenimine-Modified Multiwalled Carbon Nanotubes for Plasmid DNA Gene Delivery
Provedor de dados: 17
Autores: Bo-Zhang  Yu; Ji-Fei Ma; Wen-Xin Li.
An efficient molecular delivery technique based on the transporting high-molecular-weight PEI 600K-modified multiwalled carbon nanotubes (PEI 600K-MWCNTs) into cell membranes is reported. The PEI 600K-MWCNTs exhibit low cytotoxicity and its associated plasmid DNA (pDNA) is delivered to cells efficiently, and the green fluorescent protein (GFP) levels up to 18 times higher than that of naked DNA were observed.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/2753/version/1

Polymerase-endonuclease amplification reaction for large-scale enzymatic production of antisense oligonucleotide
Provedor de dados: 17
Autores: Xiaolong Wang; Deming Gou.
Synthetic oligonucleotides are contaminated with highly homologous failure sequences. Oligonucleotide synthesis is difficult to scale up because it requires expensive equipments, hazardous chemicals, and tedious purification process. Here we report a novel thermocyclic reaction, polymerase-endonuclease amplification reaction (PEAR), for the amplification of oligonucleotides. A target oligonucleotide and a tandem repeated antisense probe are subjected to repeated cycles of denaturing, annealing, elongation and cleaving, in which thermostable DNA polymerase elongation and strand slipping generate duplex tandem repeats, and thermostable endonuclease (PspGI) cleavage releases monomeric duplex oligonucleotides. Each round of PEAR achieves &amp;#x3e;100-fold...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3711/version/1

Polymorphic (NH): As Polyimidogen and Ammonium Azide Structure-types
Provedor de dados: 17
Autores: Michael J. Bucknum.
This paper reports a productive discussion of bonding principles in the non-metallic 2nd row hydrides. It suggests the inversion of a bonding character, potentially from hydrides of B &amp;#x26; C, which may display unsaturation and electronic deficiency accompanied by electronic delocalization in 1D or 2D or 3D. Contrasted with the opposite possibility, within the finite number of hydrides of N, O and F, that display apparently extensive H-bonding and subsequently proton delocalization in 1D and 2D (in HF &amp;#x26; ice polymorphs, respectively), and now potentially in 3D in a corresponding hydride of N called Rice&amp;#x27;s blue material, or perhaps polyimidogen. Where polyimidogen is a crystalline NH lattice that is a polymorph of the ammonium azide...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/2541/version/1

Polymorphisms of CYP1A1 I462V and GSTM1 genotypes and lung cancer susceptibility in Mongolian
Provedor de dados: 17
Autores: Fuhou Chang; Zhi-Xie Zhang; Jia Ma; Jun QI; Min-jie Wang; Qin Yin; Guang Wang.
Aim: To study the genotype of cytochrome P450 1A1(CYP1A1) I462V and glutathions S-transferase M1( GSTM1) and the relationship of the genetic polymorphism of them with the susceptibility of lung cancer in Mongolia of China. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: Allele-specific PCR and a multiplex PCR were employed to identify the genotypes of I462V of CYP1A1 and GSTM1 in a case-control study of 210 lung cancer patients with bronchoscopy diagnosis and 210 matched controls free of malignancy.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: The frequencies of the variant CYP1A1(Val/Val) genotypes and GSTM1(-) in lung cancer groups were higher than that in control groups (15.24% vs 7.4% and 56.67% vs 40.95% ). The individuals who carried with CYP1A1(Val/Val)...
Tipo: Manuscript
Palavras-chave: Cancer; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3336/version/1

Polymorphisms of the _ENPP1_ gene are not associated with type 2 diabetes or obesity in the Chinese Han population
Provedor de dados: 17
Autores: Teng Zhao; Di Zhang; Yun Liu; Daizhan Zhou; Zhuo Chen; Sheng Li; Lan Yu; Simin Liu; Zuofeng Zhang; Guoyin Feng; Lin He; He Xu.
*Objective:* Type 2 Diabetes mellitus is a metabolic disorder characterized by chronic hyperglycemia and with a major feature of insulin resistance. Genetic association studies have suggested that _ENPP1_ might play a potential role in susceptibility to type 2 diabetes and obesity. Our study aimed to examine the association between _ENPP1_ and type 2 diabetes and obesity.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Design:* Association study between two SNPs, rs1044498 (K121Q) and rs7754561 of ENPP1 and diabetes and obesity in the Chinese Han population.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Subjects:* 1912 unrelated patients (785 male and 1127 female with a mean age 63.8 &amp;#xb1; 9 years), 236 IFG/IGT subjects (83 male and 153 female with a mean age 64 &amp;#xb1;...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/1742/version/1

Polymorphisms of TSER and MTHFR are associated with prognosis of fluoropyrimidine-based therapy in colorectal cancer patients
Provedor de dados: 17
Autores: Jong Woo Kim; Jae Ho  Lee; Seung Ho Hong; Su Jin Bae; Young Do Kwon; Doyeun Oh; Nam Keun Kim.
This study was designed to investigate the influence of TSER and MTHFR polymorphisms on the clinical outcomes of patients with colorectal cancer receiving 5-FU-based chemotherapy. Genomic DNA was isolated from 103 frozen or paraffin-embedded tissues of colorectal cancer patients. The genotypes of two common polymorphisms were determined by PCR-RFLP. Patient prognoses were compared with genotype groups and analyzed according to tumor location. Polymorphisms of TSER and MTHFR 677C&amp;#x3e;T were not significantly associated with clinicopathological factors. There were no differences in prognosis between genotypes or functional groups when the TSER and MTHFR groups were considered separately. However, analysis of combined genotypes of the TSER and the MTHFR...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3741/version/1

Population development of beet cyst nematodes and their damage potential to sugar beets under different temperature regimes
Provedor de dados: 17
Autores: Bart Vandenbossche; Bj&amp;#xf6;rn Niere; Stefan Vidal.
_Heterodera schachtii_, the white beet cyst nematode, is considered as one of the most important nematode pests on sugar beet and is present in most sugar-beet growing areas. The yellow beet cyst nematode, _Heterodera betae_, is less prevalent but has also been found damaging beet crops. However, knowledge about the damage potential and population dynamics of the yellow beet cyst nematode is limited. The amount of damage inflicted by nematodes is dependent on different factors. An important factor influencing the sugar beet yield decline by beet cyst nematodes is the soil temperature. Relationships between soil temperature, _H. schachtii_ population densities and sugar beet yields have been reported previously. Until present, most studies have been...
Tipo: Presentation
Palavras-chave: Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5744/version/1

Population Dynamics
Provedor de dados: 17
Autores: Ron W. Nielsen.
Explicit assumption that the use of natural resources promoting and sustaining growth is proportional to the number of people living on the planet at any given time leads to a model, which reproduces the population data remarkably well.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/2983/version/1

Population genetic structure of the pelagic goby, Sufflogobius bibarbatus, in the Northern Benguela ecosystem, based on PCR-RFLP analysis of the mitochondrial control region and the ND 3 and 4 region (Dissertation).
Provedor de dados: 17
Autores: Pallagae M. C. S. De Silva.
Polymorphism within the mitochondrial NADH-3,4 dehydrogenase(ND-3/4) and control region (D-Loop) was studied by polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) analysis of Sufflogobius bibarbatus (Pelagic Goby) population in the Northern Benguela ecosystem. Three major geographical areas representing the north-south axis (Ludritz, Walvis Bay and North of Ambrose Bay) were selected. Polymorphism was detected using three and two restriction enzymes respectively in ND- 3 / 4 and D-Loop regions, and a total number of 25 composite haplotypes were identified. The most common haplotype accounted for 36% of 238 individuals. Recorded haplotype diversities were quite high, ranging 0.70 to 0.86.The highest haplotype diversity was found...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3007/version/1

Population genomics of domestic and wild yeasts
Provedor de dados: 17
Autores: David M. Carter; Gianni Liti; Alan M. Moses; Leopold Parts; Stephen A. James; Robert P. Davey; Ian N. Roberts; Anders Blomberg; Jonas Warringer; Austin Burt; Vassiliki Koufopanou; Isheng J. Tsai; Casey M. Bergman; Douda Bensasson; Michael J. T. O&amp;#x27;Kelly; Alexander van Oudenaarden; David B. H. Barton; Elizabeth Bailes; Matthew Jones; Michael A. Quail; Ian Goodhead; Sarah Sims; Frances Smith; Richard Durbin; Edward Louis.
The natural genetics of an organism is determined by the distribution of sequences of its genome. Here we present one- to four-fold, with some deeper, coverage of the genome sequences of over seventy isolates of the domesticated baker&amp;#x27;s yeast, _Saccharomyces cerevisiae_, and its closest relative, the wild _S. paradoxus_, which has never been associated with human activity. These were collected from numerous geographic locations and sources (including wild, clinical, baking, wine, laboratory and food spoilage). These sequences provide an unprecedented view of the population structure, natural (and artificial) selection and genome evolution in these species. Variation in gene content, SNPs, indels, copy numbers and transposable elements provide...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1988/version/1

Populational analysis of Saccharomyces cerevisiae strains from different appellations of origin and grape varieties by microsatellite analysis.
Provedor de dados: 17
Autores: Leonor Pereira; Filomena L. Duarte; Paulo T. Ramos; Maria F. Alem&amp;#xe3;o; Paula Gomes; Ana C. Gomes; Susana  Sousa; Sofia Machado; Manuel Santos; Margarida Casal; Dorit Schuller.
The objective of the present study was to evaluate populational relationships among Saccharomyces cerevisiae strains isolated from some of the Portuguese most important grapevine varieties in different appellations of origin, using polymorphic microsatellites.  &amp;#xd;&amp;#xa;One hundred ninety two grape samples were collected during the 2006 and 2007 harvest season in the Vinho Verde (grape varieties: Arinto, Alvarinho, Avesso, Loureiro, Touriga Nacional) Bairrada (grape varieties: Arinto, Baga, Castel&amp;#xe3;o Franc&amp;#xea;s, Maria Gomes, Touriga Nacional) Alentejo (grape varieties, Aragon&amp;#xea;s, Trincadeira, Touriga Nacional), Terras do Sado (grape variety Castel&amp;#xe3;o) Bucelas (grape variety Arinto) and Estremadura (grape varieties:...
Tipo: Poster
Palavras-chave: Ecology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2290/version/1

Populous: A Tool For Populating OWL Ontologies From Templates
Provedor de dados: 17
Autores: Simon Jupp.
We present Populous, a tool for gathering content with which to populate an ontology. Domain experts need to add content, that is often repetitive in its form, but without having to tackle the underlying ontological representation. Populous presents users with a table based form in which columns are constrained to take values from particular ontologies; the user can select a concept from an ontology via its meaningful label to give a value for a given entity attribute.&amp;#xd;&amp;#xa;Populated tables are mapped to patterns that can then be used to automatically generate the ontology&amp;#x27;s content. Populous&amp;#x27;s contribution is in the knowledge gathering stage of ontology development. It separates knowledge gathering from the conceptualisation...
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5419/version/1

Porous Chitsan-Gelatin Scaffolds Embedded with PLGA Nanoparticles for Bone Repair
Provedor de dados: 17
Autores: Vijay Kumar Nandagiri; Piergiergio Gentile; Valeria Chiono; Clara Muttu; Gianluca Ciardelli; Franco Maria Montevecchi; Ziebun Ramtoola.
Bone regeneration can be accelerated by localized delivery of appropriate growth factors/bio active molecules. Localized delivery can be achieved by incorporating bioactive molecules within biodegradable particulate carrier system followed by embed them in a suitable porous scaffolds. These carrier system facilitates the impregnated growth factor(s) to release at a desirable rate and concentration, and to linger at injury sites for a sufficient time to recruit progenitors and stimulate tissue healing processes. In this study, an attempt has been made to engraft the porous chitosan-gelatin scaffolds with PLGA nanoparticles for localized delivery of bioactive components. Scaffolds loaded with PLGA nanoparticles were subjected to physical and mechanical...
Tipo: Poster
Palavras-chave: Developmental Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4728/version/1

Positive and Negative Congruency Effects in Masked Priming: A Neuro-computational Model Based on Representation Strength and Attention
Provedor de dados: 17
Autores: Ahmad Sohrabi; Robert L. West.
Positive priming effects have been found with a short time between the prime and the target, while negative priming effects (i.e., a congruent prime causes longer RTs) have been found with a long time between the prime and the target. In the current study, positive and negative priming effects were found using stimuli that have strong and weak representations, respectively, without changing the time between prime and target. A model was developed that fits our results. The model also fits a wide range of previous results in this area. In contrast to other approaches our model depends on attentional neuro-modulation not motor self-inhibition.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2415/version/1

Positive Darwinian Selection And The Birth Of An Olfactory Receptor Clade In Teleost Fish
Provedor de dados: 17
Autores: Ashiq Hussain; Luis Saraiva; Sigrun Korsching.
Trace amine-associated receptors (TAARs) in mammals recently have been shown to function as olfactory receptors. We have delineated the taar gene family in jawless, cartilaginous and bony fish (zero, two, and more than hundred genes, respectively). We conclude that taar genes are evolutionary much younger than the related OR and ORA/V1R olfactory receptor families, which are present already in lamprey, a jawless vertebrate. The two cartilaginous fish genes appear to be ancestral for two taar classes, each with mammalian and bony fish (teleost) representatives. Unexpectedly, a whole new clade, class III, of taar genes originated even later, within the teleost lineage. Taar genes from all three classes are expressed in subsets of zebrafish olfactory receptor...
Tipo: Poster
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6448/version/1

Post Market Monitoring of GM Herbicide-Tolerant Crops
Provedor de dados: 17
Autores: Alan M. Dewar.
As soon as humans adopted agriculture as the principle means of feeding themselves, they have had an effect on the environment, and by implication, also on biodiversity. It is not possible to grow crops in an intensive manner without doing so, but it is necessary to do so to feed the population. In this respect, the use of herbicides or other weed control practices (e.g. hand-hoeing) inevitably will have an effect on biodiversity, whether those methods are used in conventional, organic or genetically modified herbicide-tolerant (GMHT) crops. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Recent literature from the UK following the Farm Scale Evaluations (FSE) of the environmental impact of GMHT oilseed rape, maize and sugar beet suggests that the recommended weed...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4462/version/1

Posterior parietal cortex controls spatial attention through modulation of anticipatory alpha rhythms
Provedor de dados: 17
Autores: Paolo Capotosto; Claudio Babiloni; Gian Luca Romani; Maurizio Corbetta.
A dorsal fronto-parietal network, including regions in intra-parietal sulcus (IPS) and frontal eye field (FEF), has been hypothesized to control the allocation of spatial attention to environmental stimuli. One putative mechanism of control is the de-synchronization of electroencephalography (EEG) alpha rhythms (~8-12 Hz) in parieto-occipital cortex in anticipation of a visual target. We show that brief interference by transcranial magnetic stimulation (rTMS) with preparatory activity in right IPS or right FEF while subjects attend to a spatial location impairs identification of target stimuli ~2 seconds later. Moreover, the visual deficit relates to the disruption of anticipatory (pre-stimulus) alpha desynchronization and its topography in...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1563/version/1

Post-market monitoring: legal framework in Brazil and first results
Provedor de dados: 17
Autores: Marcia A. Melo; Ederson  A. Kido; Paulo P. Andrade.
Brazil is presently (2010) the second largest producer of Genetically Modified (GM) crops. The legal framework to support both research activities and the commercial release of Genetically Modified Organisms (GMOs) is, however, very recent, as the Biosafety Law dates back from 2005. After the indispensable risk analysis, done by National Technical Committee for Biosafety (CTNBio), a GM plant can be approved for commercial release. Nevertheless, as stated in the Normative Resolution nr. 5 (NR-5), 2008, the post-market monitoring is mandatory. However, the first GM crop in Brazil, the herbicide tolerant soybean, was harvested in 2005. The CTNBio asked, then, for a monitoring plan and the applicant designed a complex study focused on case-specific monitoring....
Tipo: Poster
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4528/version/1

Post-meiotic apozygotic combinatory process in sugar beet (Beta vulgaris L.)
Provedor de dados: 17
Autores: Evgenii Levites; Svetlana Kirikovich.
The effect of colchicine on phenotypic classes ratio of the enzyme locus controlling alcohol dehydrogenase (ADH1) in sugar beet agamospermous progenies was analyzed. The obtained data are indicative of the thing that colchicine causes polytenization of homological chromosome regions carrying marker locus Adh1 alleles. Theoretical calculation of the formation of egg cell frequencies and those of further development of cells entering embryogenesis without fertilization, also the diminution calculation of excessive chromosome regions carrying marker locus alleles have been made. The coincidence of theoretical and experimental ratios of phenotypic classes indicates the existence of a post-meiotic apozygotic combinatory process in plants.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6738/version/1

Potential and environmental concerns of ethanol production from sugarcane molasses in Pakistan
Provedor de dados: 17
Autores: Tahir Rashid; Zafar Altaf.
Energy security and climate change imperatives require large-scale substitution of petroleum-based fuels as well as improved vehicle efficiency4. Biofuels have become one of the fastest growing markets in the world - at 15% growth a year. In fact, until recently, Pakistan was the second largest exporter of sugarcane ethanol to the European Union - a preferential status we have since lost because of WTO obligations and dumping complaints. Several distilleries have planned to close down in light of this fact. Instead of curbing production of fuel ethanol, however, we should redirect it to the domestic market. Pakistan produces around 2 million tons molasses annually and over 90% is exported earning only $47 million. This quantity of molasses will produce...
Tipo: Manuscript
Palavras-chave: Biotechnology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1499/version/1

Potential effects of pollen from stacked Bt maize on non-target Lepidoptera in agrarian systems
Provedor de dados: 17
Autores: Mechthild  Schuppener; Alan J. Slusarenko; Stefan  Rauschen.
The cultivation of genetically engineered (GE) maize expressing Lepidopteran specific Bt proteins poses potential risk for non-target butterflies. Pollen is dispersed by wind in the surroundings of maize fields, deposited on weeds and taken up by non-target butterfly lavae. While MON810 contains low concentrations of Bt protein in pollen, this is not necessarily true for new GE maize lines.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Species appropriate for a post market environmental monitoring (PMEM) should (i) have a small host range to ensure a comprehensive inventory, (ii) be representative and (iii) be common in agrarian landscapes. Rare species seem to be inappropriate (Aviron et al. 2009). We selected the Small Tortoiseshell (_Aglais urticae_) and the...
Tipo: Poster
Palavras-chave: Earth &amp; Environment; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4491/version/1

Potential Impacts of Tailings and Tailings Cover Fertilization on Arsenic Mobility in Surface and Ground Waters
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
A number of mining sites worldwide, particularly gold mines, have tailings management facilities (TMFs) that contain high levels of arsenic. Current closed mine site regulatory agencies tend to prefer revegetation of TMFs as part of the mandated reclamation activities. At many sites, often in polar regions, vegetation is difficult to establish either directly on the tailings or on the coarse-rock covers due to nutrient poor soils, phytotoxicity problems, and/or a less than optimum climate. Addition of phosphorus-based fertilizers to the tailings and/or cover material is commonly considered in order to promote the revegetation process and &amp;#x2013; ideally &amp;#x2013; allow the site owners to discharge their closure duties as rapidly as possible....
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1740/version/1

Potential pathways of indole acetic acid (IAA) biosynthesis in Euphorbia abyssinica
Provedor de dados: 17
Autores: Raf Aerts; Els Prinsen; Bart Muys.
Desert candle (_Euphorbia abyssinica_ J.F. Gmel.) (further referred to as EAG) is a succulent tree of dry deciduous and evergreen montane forest, woodland and shrub savanna.  It occurs widely throughout dryland Africa, where it is appreciated as a live fence because it is easily propagated from untreated mature branch cuttings.&amp;#xd;&amp;#xa;Earlier we argued that the ability of large EAG branches to regenerate with ease in dry soil may be related to the natural plant growth regulator hormone indole acetic acid (IAA) contained in the latex of the plant.  EAG latex samples from northern Ethiopia (n = 3) that were chemically analyzed contained on average 0.06 mg/l latex, as well as the IAA metabolites indole lactate (ILA) and indole ethanol (IEt).  One...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2212/version/1

Potential role of 2,2&amp;#x27;-biphenylquinones in the carcinogenic/anti-cancer activity of dioxins
Provedor de dados: 17
Autores: Sierra Rayne.
Modes of carcinogenicity for the well-known environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) have been investigated over the past several decades. However, the mechanisms underlying TCDD carcinogenicity are still unclear. Recent work also suggests TCDD may have anti-cancer activity. Based on established photochemical generation of reactive 2,2&amp;#x27;-biphenylquinone intermediates from dioxins, a novel toxicological mechanism for TCDD that may be operative is proposed. 2,2&amp;#x27;-Biphenylquinones may be obtained via biochemical activation of dioxins such as TCDD, and these intermediates may play a role in expressing both the carcinogenic and anti-cancer activities of this important contaminant class. The broader research community...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1929/version/1

Potential Use of Folate-polyethylene glycol (PEG)-Appended Dendrimer (G3) Conjugate with alpha-Cyclodextrin as DNA Carriers to Tumor Cells
Provedor de dados: 17
Autores: Taishi Higashi; Ayumi Yoshimitsu; Haruna Ikeda; Masayo Arizono; Kenjiro Hattori; Tomoko Takeuchi; Fumitoshi Hirayama; Kaneto Uekama; Hidetoshi Arima; Keiichi Motoyama.
We previously reported that polyamidoamine STARBURST dendrimer (generation 3, G3) (dendrimer) conjugate with alpha-cyclodextrin (alpha-CyD) having an average degree of substitution of 2.4 of alpha-CyD (alpha-CDE) provided remarkable aspects as novel carriers for DNA and siRNA. To develop novel alpha-CDE derivatives with tumor cell specificity, we prepared folate-appended alpha-CDEs (Fol-alpha-CDEs) and folate-polyethylene glycol (PEG)-appended alpha-CDEs (Fol-PalphaCs) with the various degrees of substitution of folate (DSF), and evaluated in vitro and in vivo gene transfer activity, cytotoxicity, cellular association and physicochemical properties. In vitro gene transfer activity of Fol-alpha-CDEs (G3, DSF 2, 5 or 7) was lower than that of &amp;#x3b1;-CDE...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2011
URL: http://precedings.nature.com/documents/6488/version/1

Power laws, memory capacity, and self-tuned critical branching in an LIF model with binary synapses
Provedor de dados: 17
Autores: Christopher T. Kello; Bryan Kerster.
Both fluctuations and distributions of spontaneous neural spiking activity have been observed to closely follow a variety of power laws. Multiple explanations have been offered for each observation, but few lead to mechanisms that encompass their widespread occurrence. A canonical, leaky integrate-and-fire model is presented in which synapses are updated based on the timing of pre- and post-synaptic spikes in order to maintain a state of critical branching. Results showed that 1) the self-tuning algorithm maintained critical branching under a range of parameters; 2) power laws were obtained in spiking activity fluctuations (1/f scaling), size distributions of network bursts (neural avalanches), and temporal correlations in interspike intervals (Allan...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5893/version/1

Power-law behavior reveals phase transitions in landscape controls of fire regimes
Provedor de dados: 17
Autores: Donald McKenzie; Maureen C. Kennedy.
In low-severity fire regimes of the American West and elsewhere, landscape memory of fire events is registered in fire-scarred trees, with temporal record lengths often exceeding 200 years^1-5^. Understanding the environmental controls on historical wildfires, and how they changed across spatial scales, is difficult because there are no surviving explicit records of either weather or vegetation (fuels). We show how power laws associated with fire-event time series arise in limited domains of parameters that represent critical transitions in the controls on landscape fire. We used stochastic simulations iteratively with Monte Carlo inference to replicate the spatio-temporal structure of historical fire-scar records in forested watersheds of varying...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6222/version/1

P-POD, The Princeton Protein Orthology Database, as a Tool for Identifying Gene Function
Provedor de dados: 17
Autores: Michael S. Livstone; Rose Oughtred; Sven Heinicke; Fan Kang; Benjamin Vernot; Aiton Goldman; Dannie Durand; David Botstein; Kara Dolinski.
P-POD, the Princeton Protein Orthology Database, classifies proteins from model organisms and medically-important organisms into families of homologs and provides curated evidence from the literature addressing these relationships.  The web page for each protein family includes a phylogenetic tree, sequence alignment, and cross-references to disease-related papers from SGD, papers describing complementation experiments, and OMIM gene and disease information.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;As participants in the Gene Ontology Consortium&amp;#x2019;s Reference Genome project, we seek to provide a consistent centralized method to identify orthologous proteins.  We have expanded P-POD to include the protein complement of the twelve Reference Genomes.  In...
Tipo: Poster
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3119/version/1

Practical experiences in concurrent, collaborative ontology building using Collaborative Prot&amp;#xe9;g&amp;#xe9;
Provedor de dados: 17
Autores: Daniel Schober; James Malone; Robert Stevens.
Creation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by the distribution of the ontology&amp;#x2019;s developers. An obvious solution therefore is to build collaboration into ontology development tools. Such support necessarily includes both the technical means to perform editing operations upon an ontology, but also support for the communication that makes collaboration such a vital part of much ontology development. To investigate the distributed, collaborative ontology engineering process and the corresponding capabilities of the Collaborative Protege 3 (CP) tool, members of the OntoGenesis network came together and enriched the Ontology of Biomedical Investigations (OBI) with new...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3517/version/1

Practical experiences in concurrent, collaborative ontology building using Collaborative Prot&amp;#xe9;g&amp;#xe9;
Provedor de dados: 17
Autores: Daniel Schober; James Malone; Robert Stevens.
Creation of an ontology according to some common plan is best accomplished collaboratively. This is sometimes contradicted by the distribution of the ontology&amp;#x2019;s developers. An obvious solution therefore is to build collaboration into ontology development tools. Such support necessarily includes both the technical means to perform editing operations upon an ontology, but also support for the communication that makes collaboration such a vital part of much ontology development. To investigate the distributed, collaborative ontology engineering process and the corresponding capabilities of the Collaborative Protege 3 (CP) tool, members of the OntoGenesis network came together and enriched the Ontology of Biomedical Investigations (OBI) with new...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3517/version/2

Pramipexole protective effect on rotenone induced neurotoxicity in mice
Provedor de dados: 17
Autores: Mohamed M. Salama; Dina El-Tantawy; Sahar A. El-Dakroury; Hasan Abd-Elghaffar; Sara El-Dosouky; Abdelaziz A. Ghanem; Seham A. Gad-Elhak.
Introduction: &amp;#xd;&amp;#xa;Pramipexole is a new dopaminergic drug which has been approved for PD treatment. However, we tried to find a new capacity for this drug rather than symptomatic effect. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Materials and Methods: &amp;#xd;&amp;#xa;A chronic rotenone model with daily oral dose of 30mg/kg was induced in mice. Pramipexole was tried in a new approach where the treatment began in the middle of rotenone course with oral dose 1mg/kg/day of pramipexole. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: &amp;#xd;&amp;#xa;Further analysis of behavioral tests and immunohistochemistry revealed success of pramipexole in improving the rotenone intoxicated mice. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Conclusion:...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6640/version/1

Pre and post fire carbon dynamics in a Florida Scrub oak
Provedor de dados: 17
Autores: Rosvel Bracho; Cassondra Thomas; Jiahong Li; Thomas Powell; C. Ross Hinkle.
Scrub oak is a xeromorphic shrub ecosystem discontinuously distributed in coastal and inland Florida. It supports a high biodiversity which includes a large number of endangered and threatened species.  Its structural features are maintained by a fire return cycle of 7 to 10 years which maintains the biodiversity. Management of fire prone ecosystems such as this raises the question of whether the management strategy contributes to the system being a carbon sink or carbon source over the long-term.  We used eddy covariance and biometric approaches to measure carbon dynamics in a Florida scrub oak ecosystem located at Kennedy Space Center in east Central Florida from April 2004 to December 2007. The study site was controlled burned in February 2006. Two...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5223/version/1

Prebiotic Organic Globules
Provedor de dados: 17
Autores: Marie-Paule Bassez; Yoshinori Takano.
Analogs of organic globules observed in carbonaceous chondrite meteorites and in interplanetary dust particles and of rod to spherical structures observed in terrestrial archean microstructures have been synthesized in our experiments conducted with proton irradiation on a mixture of simple inorganic constituants, CO, N2 and H2O. Our analyses of these laboratory organic globules show that the proton irradiation residue contains proteinous and non-proteinous amino acid precursors. On the basis of morphology, of hydrothermal and mineral environment, we suggest that the meteoritic organic globules and the archean carbon microstructures could be composed of amino acid precursors.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4694/version/1

Prebiotic Organic Microstructures
Provedor de dados: 17
Autores: Marie-Paule BASSEZ; Yoshinori  TAKANO; Kensei KOBAYASHI.
Micro- and sub-micrometer spheres, tubules and fiber-filament soft structures have been synthesized in our experiments conducted with 3 MeV proton irradiations of a mixture of simple inorganic constituents, CO, N2 and H2O. We analysed the irradiation products, with scanning electron microscopy (SEM) and atomic force microscopy (AFM). These laboratory organic structures produced wide variety of proteinous and non-proteinous amino acids after HCl hydrolysis. The enantiomer analysis for D-, L- alanine confirmed that the amino acids were abiotically synthesized during the laboratory experiment. Considering hydrothermal activity, the presence of CO2 and H2, of a ferromagnesian silicate mineral environment, of an Earth magnetic field which was much less intense...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/4694/version/2

Precipitation in Aberdeen, SD: data analysis approach
Provedor de dados: 17
Autores: Boris Shmagin; Carol A. Johnston; Dennis Todey.
The daily, monthly and annual sum of precipitation was analyzed for station Aberdeen-Airport, South Dakota (NOAA COOP #390020) with traditional normative statistical descriptions of precipitation variability and with methods of data analysis. The goal for research was formulated as finding a way to forecast extremes, such as the flooding of Aberdeen in May 2007 after a 30-hour, 8.42 inch rain event. Daily data were available, analyzed and cannot be considered as having any use for the forecast. The observations of 1423 monthly sums of precipitation have the following characteristics: mean = 1.802 in.; geometric mean = 0.856 in.; median = 1.26 in.; minimum = 0.0; maximum = 12.39 in. Simplified Fourier analysis was performed for monthly data, and 31 cyclic...
Tipo: Poster
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3197/version/1

Precipitation in Aberdeen, SD: data analysis approach
Provedor de dados: 17
Autores: Boris Shmagin.
Daily, monthly, and annual sums of precipitation for Aberdeen, South Dakota, from 1890-2008 were analyzed using univariate and multivariate statistical methods (primary statistical analysis, factor analysis, time-series analysis: shift detection and simplified Fourier analysis - SFA) and provided descriptions of the variability (stochastic and cyclic or oscillatory) for monthly and annual sums of precipitation. The goal was to describe the natural variability in three scales, then to use this to forecast extremes, such as the spring 2007 flooding event that occurred in Aberdeen.  The part of the variability that may be explained for sums of precipitation seasonality by factor model is 57%. The single time series relations of the main cyclic component to...
Tipo: Poster
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3197/version/2

Precise Atomic Structures of Three Novel Nanomaterials in Nanotechnology, Biomedicine and Cosmology: Graphene, Boron Nitride and Coronene
Provedor de dados: 17
Autores: Raji Heyrovska; Lakshmi Atchison; Sara Narayan.
Nanomaterials are currently of great importance in science, technology and commercial applications. Since these materials are atomic layer thick and are a few square nanometers of area, a knowledge of their precise atomic structures will help in the exact understanding of the properties at the nanoscale and in the fabrication and design of the nanomaterials for their many uses. Their known inter-atomic distances have been used here to obtain the exact atomic radii of the component atoms and thereby their precise atomic structures, for the first time. Considered here are three nanomaterials with hexagonal structures, but of quite different properties, namely, graphene (an electrical conductor), boron nitride (an insulator) and coronene (indicators of life...
Tipo: Poster
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4357/version/1

Precise Atomic Structures of two Important Molecules in Biochemistry:
Provedor de dados: 17
Autores: Raji Heyrovska; Saraswathi Narayan; Lakshmi Atchison.
This work celebrates the &amp;#x201c;International Year of Chemistry &amp;#x2013; 2011&amp;#x201d;, by providing &amp;#x201c;for the first time&amp;#x201d;, the structures at the atomic level of two important molecules, namely, ascorbic acid and aspirin. Ascorbic acid, also known as vitamin C, was discovered as a cure for scurvy which claimed many human lives and hence got its name. It is also supposed to be an antioxidant and to prevent flu. Aspirin is synthesized from salicylic acid and is widely used as a remedy for flu and has other medical uses such as saving the lives of cardiac patients as an anticoagulant of blood. The biochemistry and chemistry of both these compounds have been evolving for nearly a century ever since their discoveries. Here, the...
Tipo: Poster
Palavras-chave: Chemistry; Developmental Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5966/version/1

Precise Molecular Structures of Cysteine, Cystine, Hydrogen-Bonded Dicysteine, Cysteine Dipeptide, Glutathione and Acetyl Cysteine Based on Additivity of Atomic Radii
Provedor de dados: 17
Autores: Raji Heyrovska.
Structures of molecules are usually represented by arbitrary line drawings, ball and stick or space filling models. In recent years, the author found that using the appropriate radii of atoms and ions, bond lengths in inorganic, organic and biomolecules and of hydrogen bonds are exact sums of the radii of the adjacent atoms and or ions. This additivity of atomic radii was shown to hold also for the bond lengths in the twenty essential amino acids. On this basis, the atomic structures of the very important molecules mentioned in the title, have been presented here for the first time. It is hoped that these precise structures and their dimensions will shed new light into their role in biochemistry, pharmaceutical chemistry, environmental chemistry,...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6692/version/1

Precise Similarity of Many Human Proteins to Proteins of Prokarya
Provedor de dados: 17
Autores: Roy Britten.
&amp;#x9; Proteins originated in early forms of life and have long survived, because they have always been required. Some recognizably similar proteins are found in all sequence comparisons between species, no matter how distant, including prokaryotes and eukaryotes. Reported  here are observations on the relationships of human  proteins to the proteins of  458 prokaryotes for which protein libraries are available. Each of these libraries includes a protein that matches a human protein with a BLAST score of 573 or more, indicating excellent conservation of  certain amino acid sequences. A majority of these proteins also match a yeast protein and other eukaryote proteins with comparable accuracy, indicating that protein conservation is responsible in most...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/800/version/1

Precocious activation of APC/C-Cdh1 at pre-anaphase causes genome instability
Provedor de dados: 17
Autores: Ayumu Yamamoto; Takashi Ushimaru; Takanori Ohyoshi; Asuka Suzuki; Kazuhiro Toda; Masaru Ueno; Masahiro Uritani.
Faithful chromosome segregation and thereby accurate gene transmission are crucial for all organisms. Until proper attachment of the mitotic spindle to the kinetochore is established, the ubiquitin ligase (E3) Cdc20-activated APC/C (anaphase promoting complex/cyclosome) is repressed by the spindle assembly checkpoint (SAC) and sister chromatin cohesion is protected. Mutants defective in SAC fail to arrest at metaphase even in the presence of damaged microtubules. Interestingly, a similar phenomenon occurs in yeast cells defective in Bub2, a negative factor of the mitotic exit network (MEN), which is required for telophase onset, although its precise molecular mechanism is unknown. Here, we show that chromosome missegregation occurs frequently in...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1603/version/1

Predictability engenders more efficient neural responses
Provedor de dados: 17
Autores: David M. Eagleman; Vani Pariyadath; Sara J. Churchill.
The neural response to a stimulus diminishes with repeated presentations, a phenomenon known as repetition suppression. We here use neuroimaging to demonstrate that repetition suppression appears to be a special case of &amp;#x22;prediction suppression&amp;#x22;--that is, the brain shows diminishing activity when subsequent stimuli in a train are predictable. This demonstration supports the hypothesis that the brain dynamically leverages prediction to minimize energy consumption.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2847/version/1

Predicting patterns of stress and mortality in intertidal invertebrates:  applications of biophysical ecology in a changing world
Provedor de dados: 17
Autores: Brian Helmuth; Michael Kearney; Gianluca Sar&amp;#xe1;.
Background, Questions and Methods&amp;#xd;&amp;#xa;Recent studies have emphasized that local and geographic patterns of species distributions can be set by a variety of factors related to weather and climate, including exposure to lethal environmental conditions, indirect effects on consumers and competitors, and sublethal effects of physiological stress on growth and reproduction.  Predicting where, when and with what magnitude these impacts are most (and least) likely to occur is imperative if we are to effectively plan for (i.e. adapt to) the effects of climate change.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;We developed a series of methods for translating patterns of environmental &amp;#x201c;signals&amp;#x201d; into organismal responses in intertidal...
Tipo: Presentation
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5211/version/1

Predicting Prostate Cancer Aggressiveness through a Nanoparticle Test
Provedor de dados: 17
Autores: Qun Huo; Shannon Sullivan; Hillari Hallquist; Sally Litherland; David Decker; Inoel Rivera-Ramirez.
Prostate cancer (PCa) is the most common malignancy and the second leading cause of cancer death in American men. Due to the lack of accurate tests to distinguish aggressive cancer from indolent tumor, prostate cancer is often over-treated. Post-surgery pathology analysis revealed that 30% of tumors removed by radical prostatectomy are deemed clinically insignificant and would not have required such invasive treatment.^1^ Over-diagnosis and treatment of low-risk prostate cancer has serious and long-lasting side effect: as high as 70% of the patients who receive radical prostatectomy treatment will suffer a loss of sexual potency that cannot be remedied by drugs such as sildenafil citrate.^2^ We herein report a simple nanoparticle-serum protein adsorption...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6409/version/1

Predicting Protein-Disease Relationships Using Sequence, Physicochemical Properties, and Molecular Function Information
Provedor de dados: 17
Autores: Predrag Radivojac; Kang Peng; Wyatt T. Clark; Brandon J. Peters; Amrita Mohan; Sean M. Boyle; Sean D. Mooney.
One of the most important tasks of modern bioinformatics is the development of computational tools that can be used to understand and treat human disease. To date, a variety of methods have been explored and algorithms for predicting whether a protein is involved in disease are gaining in their utility. Here, we describe an algorithm for detecting protein-disease associations based on the human protein-protein interaction network, known gene-disease associations, protein sequence, and protein functional information at the molecular level. Our method, PhenoPred (&amp;#x22;www.phenopred.org&amp;#x22;:www.phenopred.org), is supervised: first, we map each protein onto the spaces of disease and functional terms based on distance to all annotated proteins in the...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2239/version/1

Predicting species abundance distributions by simultaneously using number and biomass as units of measurement
Provedor de dados: 17
Autores: Peter A. Henderson; Anne E. Magurran.
The universal observation that some species in an ecological community are common, but many more are rare, is neatly encapsulated in a species abundance distribution (SAD)1. However, the shape of the distribution can depend on the currency used to measure abundance 2. Here we show how the SADs for numerical abundance and biomass are related and how this relationship can be used to predict the form of the SAD. When plotted in log numerical abundance, log biomass space, species points lie within an approximately triangular area the limits of which are set by body size range, and the upper limit of abundance in both metrics. Under the simplifying, but reasonable, assumption that the observed scatter of species within this region is random, the shape of the...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/1405/version/1

Predicting Temporal Patterns In The Environment: Toward Primitive Mechanisms Of Learning, Memory, And Generalization
Provedor de dados: 17
Autores: Matthew C. Jones; Tim Curran; Michael C. Mozer; Matt Wilder.
Across a wide range of cognitive tasks, recent experience influences subsequent behavior. For example, when individuals repeatedly perform a speeded two-alternative choice task, response latencies vary dramatically based on the immediately preceding sequence. These sequential dependencies (SDs) have been interpreted as adaptation to the statistical structure of an uncertain, changing environment (e.g., Jones &amp;#x26; Sieck, 2003; Mozer, Kinoshita, &amp;#x26; Shettel, 2007; Yu &amp;#x26; Cohen, 2009), and can shed light on how individuals learn and represent structure in binary stimulus sequences. Heretofore, theories have posited that SDs arise from rapidly (exponentially) decaying memory traces of various environmental statistics (e.g., Cho et al.,...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5796/version/1

Predicting the Congener-Specific Environmental Behaviour of Perfluorinated Acid Contaminants Using Semi-Empirical Computational Methods
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest; Ken J. Friesen.
Perfluorinated acids (PFAs) are contaminants detected worldwide in a range of abiotic and biotic environmental matrices. The two major classes of PFAs include the perfluorinated carboxylic acids (PFCAs) and perfluorinated sulfonic acids (PFSAs), both of which are considered persistent and potentially bioaccumulative. Current research and regulatory efforts are focussed on the straight-chain members of each PFA class and homologue group, primarily because these congeners are the major components of technical mixtures and are also available as pure standards. However, the numerous potential branched congeners in each PFA class represent a poorly understood family of environmental contaminants whose environmental and toxicological properties may be more...
Tipo: Poster
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1956/version/1

Prediction Of Cancer Possibility By Pattern Recognition And Statistical Study Of Expression Of Gene Level Of Cancer Cells
Provedor de dados: 17
Autores: Medhavi Mallick; Devang Odedra.
The activity of the p53 tumor-suppressor protein has a key role in controlling both cancer and aging: under activity encourages the growth of cancer, and over activity can accelerate the aging process. The p53 protein is a tumor suppressor encoded by a gene whose disruption is associated with approximately 50 to 55 percent of human cancers. The p53 protein acts as a checkpoint in the cell cycle, either preventing or initiating programmed cell death (Apoptosis). p53 regulating genes MDM2, PARP, Oncogenicras, and p21 etc play a crucial role in tumor suppression.
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5624/version/1

Prediction of Evolutionarily important catalytic amino acid of Mycobacterium tuberculosis O-Succinylbenzoate synthase through in silico mutational analysis
Provedor de dados: 17
Autores: Babajan B; Chaitanya M; Anuradha CM; Suresh Kumar Chitta.
The emergence of tuberculosis resistant to multiple, first- and second-line antibiotics poses challenges to a global control strategy that relies on standard drug treatment regimens. The high drug-resistant strains of Mycobacterium tuberculosis (Mtb) have been implicated in outbreaks and have been found throughout the world; a comprehensive understanding, the magnitude of this threat requires an accurate assessment of the worldwide burden of resistance. In an attempt to design anti-TB drugs, the target chosen is a key enzyme of Mtb, O-Succinylbenzoate synthase (OSBS), which is an attractive target for its role in electron transport chain as OSBS is not available in humans.  An attempt has been to built the 3-D structure of Mtb-OSBS using online Swiss model...
Tipo: Poster
Palavras-chave: Biotechnology; Microbiology; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3776/version/1

Prediction of Functional Sites in SCOP Domains using Dynamics Perturbation Analysis
Provedor de dados: 17
Autores: Judith D. Cohn; Dengming Ming; Michael E. Wall.
Dynamics perturbation analysis (DPA) finds regions in a protein structure where proteins are &amp;#x22;ticklish&amp;#x22;, i.e., where interactions cause a large change in protein dynamics. Previously, such regions were shown to predict the location of native binding sites in a docking test set, but the more general applicability of DPA to the prediction of functional sites in proteins was not shown. Here we describe the results of applying an accelerated algorithm, called Fast DPA, to predict functional sites in over 50,000 SCOP domains.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2209/version/1

Prediction of novel inhibitors for human RNase1 involved in cardiovascular disease through in silico screening
Provedor de dados: 17
Autores: Kanipakam Hema; Sadnala Giribabu; Sandeep Swargam; Amineni Umamaheswari.
Human pancreatic ribonuclease (RNase1) is a small digestive and pyramidine specific enzyme secreted by the pancreas. RNase1 contributes in the regulation of extracellular RNA by hydrolyzing RNA phosphodiester bonds. High levels of RNase1 in cardiovascular disease patients project the enzyme as an attractive drug target. The known RNase1 inhibitors, citric acid and U1S were searched for structural analogs from Ligand.info database to compile 783 ligands. The ligands&amp;#x27; 3D structures and their tautomeric states were generated using LigPrep. The 3424 prepared conformations were subjected to QikProp analysis and filtered based on Lipinski rule of five and zero reactive functional group.  The 3376 conformations with good ADME (absorption, desorption,...
Tipo: Poster
Palavras-chave: Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6527/version/1

Prediction of Soil Organic Properties in a Diverse Population of Ohio Soils Using Near Infrared Reflectance Spectroscopy Analysis
Provedor de dados: 17
Autores: Warren Dick; Aditi Sengupta.
A Near Infrared Spectroscopy (NIRS) method was used to predict soil organic carbon and amino sugar concentrations, and &amp;#x3b2;-Glucosidase and &amp;#x3b2;-Glucosaminidase activity in 184 diverse soils of Ohio. The measured variable values were calibrated to NIR spectral data with partial least squares regression analysis. The multivariate models developed were validated using the full cross validation method and the test set method with a test set size of 50 samples. Statistical analysis of the spectral data was done using the multivariate analysis software Unscrambler 8.0 (CAMO Inc). The first differential transformation of the NIR region (1100-2498 nm) gave good results. The NIRS method predicted well the organic carbon (OC) and amino sugar...
Tipo: Poster
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6248/version/1

Prediction of specific virus outbreaks made from the increased concentration of a new class of virus genomic peptides, replikins.
Provedor de dados: 17
Autores: Samuel Bogoch; Elenore S. Bogoch.
Advance warning of pathogen outbreaks has not been possible heretofore. A new class of genomic peptides associated with rapid replication was discovered and named replikins. Software was designed to analyze replikins quantitatively. Replikin concentration changes were measured annually prior to, and &amp;#x201c;real time&amp;#x201d; every few days during, the 2009 H1N1 influenza pandemic. Replikins were seen by both linear sequence representation and three-dimensional X-ray diffraction, and found to expand on the virus hemagglutinin surface prior to and during the H1N1 pandemic.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A highly significant increased concentration of virus replikins was found a) retrospectively in three pandemics from 1918 to 1999 (14,227...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6279/version/1

Predictive context biases perceptual selection during binocular rivalry
Provedor de dados: 17
Autores: Rachel N. Denison; Michael A. Silver.
Prediction may be a fundamental principle of sensory processing, such that the brain continuously generates predictions about forthcoming sensory information. However, little is known about how prediction contributes to the selection of a conscious percept from among competing alternatives. Here, we used binocular rivalry to investigate the effects of prediction on perceptual selection. In binocular rivalry, incompatible images presented to the two eyes result in a perceptual alternation between the images, even though the visual stimuli remain constant. If predictive signals influence the competition between neural representations of rivalrous images, this influence should generate a bias in perceptual selection that depends on predictive context. To...
Tipo: Poster
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5816/version/1

Predictive Models of Insulin Resistance Derived from Simple Morphometric and Metabolic Measurements Related to Obesity in Baboons.
Provedor de dados: 17
Autores: Alberto Chavez; Amalia Gastaldelli; Juan Carlos Lopez-Alvarenga; Rodolfo Guardado-Mendoza; Michelle Leland; M. Elizabeth Tejero; GianPio Sorice; Alberto Davalli; Raul Bastarrachea; Anthony Comuzzie; Ralph DeFronzo; Franco Folli.
Non-human primates are valuable models for the study of insulin resistance and human obesity. In baboons, insulin sensitivity levels can be evaluated directly with the euglycemic clamp and is highly predicted by adiposity, metabolic markers of obesity and impaired glucose metabolism (i.e. percent body fat by DXA and hemoglobin A1C). However, a simple method to screen and identify obese insulin resistant baboons for inclusion in interventional studies is not available. We characterized a population of obese nondiabetic, insulin resistant baboons using the euglycemic clamp technique and used a multivariate linear regression analysis (after adjustment for gender) to test three different predictive models for insulin sensitivity. In the first model, abdominal...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2429/version/1

Preen Gland-Secreted Alkanols Enhance Male Attractiveness in Parrots
Provedor de dados: 17
Autores: Jian-Xu Zhang; Wei Wei; Jin-Hua Zhang.
The skin glands are widely used in pheromone production throughout the vertebrate worlds. Growing evidences show that birds also have chemical communication, but the uropygial (also called preen or oil) glands, serving as only specialized skin glands of birds, have no sex pheromones characterized. Here, by combining GC-MS analysis and bioassay, we show with the budgerigar, Melopsittacus undulatus, that birds can used the preen gland-secreted volatiles (a blend of octadecanol, nonadecanol and eicosanol for male budgerigars) spread over body plumage when preening to convey sex information. Here, we first report the avian pheromones derived from the uropyginal gland and suggests that the gland has broader implications than previously known (e.g. plumage...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2305/version/1

Pregnancy Obstructs Involution Stage II of the Mammary Gland in Cows: General Biological Implications
Provedor de dados: 17
Autores: Gabriel Leitner; Ana-Maria Anug; Uzi  Merin; Nissim Silanikove.
*Background*&amp;#xd;&amp;#xa;Repeated research findings over the last 4 decades show that involution of mammary glands in dairy cows did not regress to same extend as that noticed in other mammalian species.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Methodology/Principal Findings*&amp;#xd;&amp;#xa;We took an advantage of a rare event in the normal modern dairy farming: A cow that was false-positively identified as being pregnant was &amp;#x22;dried up&amp;#x22; (i.e., induced into involution) conventionally about 60 before her expected parturition. This cow was culled, and samples of her mammary gland tissue were examined for gross histology. In this study we demonstrate for the first time that modern dairy cow may undergo extensive obliteration of the...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Immunology.
Ano: 2007
URL: http://precedings.nature.com/documents/846/version/2

Pregnancy Obstructs Involution Stage II of the Mammary Gland in Cows: General Biological Implications
Provedor de dados: 17
Autores: Nissim Silanikove; Gabriel Leitner; Ana-Maria Anug; Uzi  Merin.
*Background*&amp;#xd;&amp;#xa;Repeated research findings over the last 4 decades show that involution of mammary glands in dairy cows did not regress to same extend as that noticed in other mammalian species.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Methodology/Principal Findings*&amp;#xd;&amp;#xa;We took an advantage of a rare event in the normal modern dairy farming: A cow that was false-positively identified as being pregnant was &amp;#x22;dried up&amp;#x22; (i.e., induced into involution) conventionally about 60 before her expected parturition. This cow was culled, and samples of her mammary gland tissue were examined for gross histology. In this study we demonstrate for the first time that modern dairy cow may undergo extensive obliteration of the...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology; Immunology.
Ano: 2007
URL: http://precedings.nature.com/documents/846/version/1

Prehistoric psychotropic consumption in Andean Chilean mummies
Provedor de dados: 17
Autores: Juan P. Ogalde; Bernardo T. Arriaza; Elia Soto.
Hallucinogenic plants are often regarded as the main source of psychoactive drugs in antiquity to reach deep altered states of consciousness^1,2^. Many researchers believe this was particularly true during the Tiwanaku empire expansion, circa (500-1000 A.D.), along the Atacama Desert of Chile. Highly decorated snuffing tablets and tubes are often found as grave goods during this period^3,4,5,6,7,8^. Until now the type of drugs consumed in this paraphernalia has been unclear. From the modern city of Arica, naturally mummified human bodies with abundant hair provided a unique opportunity to test for hallucinogenic plants consumed in Andean prehistory. Analysis by gas chromatography and mass spectrometry demonstrated the presence of harmine. The...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/1368/version/1

Preincision Processing of Cyclobutane Pyrimidine Dimers in Escherichia coli
Provedor de dados: 17
Autores: Sunirmal Paul; Mitsumasa Hashimoto; Opinder Bhanot; Yoke Kow; Moon-shong Tang.
In both prokaryotes and eukaryotes cyclobutane pyrimidine dimers (CPD) formed by UV-irradiation are repaired mainly by the nucleotide excision repair (NER) pathway. Evidence has been presented that CPDs are repaired more rapidly and efficiently in vivo than when using purified NER components in vitro, and raises the possibility that CPD can be processed at the preincision stage before being removed by NER pathway. We investigated this hypothesis in E. coli cells and found that the phosphodiester bonds in CPDs are indeed incised (for the sake of simplicity we term this result as CPD*) in a time-dependent fashion in NER-proficient cells. This CPD preincision processing also occurs in NER-deficient uvrB- and uvrC-, but not in uvrA-mutant cells, and in...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1709/version/1

PRELIMINARY BASELINE SURVEY OF AVIFAUNAL DIVERSITY IN JIMMA ZONE, SOUTH-WESTERN ETHIOPIA
Provedor de dados: 17
Autores: Haile Yineger; Kitessa  Hundera; Bruktawit Abdu; Tifases Beyene; James Kuria Ndungu&amp;#x27;; Cagan Hakki  Sekercioglu; Olivier Honnay; Bart Muys; Raf Aerts; Luc Lens.
Multidimensional poverty, which is deeply-rooted within least-developed African countries like Ethiopia, is forcing local people to heavily rely on natural resources for their subsistent livelihoods. As a result, remaining wilderness areas in tropical Africa which support huge but little known biological diversity, are subject to extensive habitat loss, fragmentation and degradation in turn causing loss of plant and animal species and ecosystem services provided by them. Coffee forest fragment within the Jimma Zone of Ethiopia cannot be expected to be an exception to such scenario. Taking this persistent problem into consideration, we carried out a preliminary survey of bird biodiversity in selected areas of Jimma Zone during a short term bird ringing...
Tipo: Poster
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4185/version/1

Preliminary results of a semi-empirical study on the structure and reactivity of the Paroxetine drug
Provedor de dados: 17
Autores: Giuseppe Lubes.
Paroxetine is a widely consumed drug with antidepressant and anxiolytic activity prescribed in the treatment of related disorders, such as obsessive-compulsive disorder, panic fits, social phobias and post-traumatic stress. Molecular modelling analyses show that both semi-empirical methods (PM3 and AM1) give us approximated the same values of heat of formation, Total energy, binding energy, nuclear energy, Dipole moment, HOMO and LUMO energies, etc. And the Paroxetine molecule has a large negative heat of formation indicating that it is a molecule thermodynamically stable.
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3047/version/1

Present and future of proteomics data curation at the PRIDE database
Provedor de dados: 17
Autores: Juan Antonio Vizcaino; Henning Hermjakob; Lennart Martens.
Significant progress has been made in improving the accessibility and utility of the large amounts of generated high-throughput proteomics data by the introduction of publicly available proteomics repositories. One such repository is PRIDE (the &amp;#x2018;PRoteomics IDEntifications&amp;#x2019; database, &amp;#x22;http://www.ebi.ac.uk/pride&amp;#x22;:http://www.ebi.ac.uk/pride). PRIDE stores mass spectrometry related data, including peptide and protein identifications, mass spectra and valuable additional metadata.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;At present, data curation in PRIDE is limited to data submission support. The format in which all submissions need to take place is PRIDE XML. Mass spectrometry derived data is very heterogeneous in terms of...
Tipo: Poster
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3222/version/1

Preservation of C Hexagons in C Allotrope Transformations
Provedor de dados: 17
Autores: Michael J. Bucknum; Eduardo A. Castro.
In this Letter is described the analogous hexagon preserving C allotrope transformations of graphite to diamond, as a packing of C spheres on the one hand, and alternatively C nanotubes to the C allotrope hexagonite, as a packing of C cylinders on the other hand.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6481/version/1

Pressure buildup during CO2 injection in brine aquifers using the Forchheimer equation
Provedor de dados: 17
Autores: Simon A. Mathias; Paul E. Hardisty; Mark R. Trudell; Robert W. Zimmerman.
If geo-sequestration of CO2 is to be employed as a key emissions reduction method in the global effort to mitigate climate change, simple yet robust screening of the risks of disposal in brine aquifers will be needed. There has been significant development of simple analytical and semi-analytical techniques to support screening analysis and performance assessment for potential carbon sequestration sites. These techniques have generally been used to estimate the size of CO2 plumes for the purpose of leakage rate estimation. A common assumption has been that both the fluids and the geological formation are incompressible. Consequently, calculation of pressure distribution requires the specification of an arbitrary radius of influence. In this talk, a new...
Tipo: Presentation
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2634/version/1

Prevalence and Patterns of Microarray Data Sharing
Provedor de dados: 17
Autores: Heather A. Piwowar; Wendy W. Chapman.
Sharing research data is a cornerstone of science. Although many tools and policies exist to encourage data sharing, the prevalence with which datasets are shared is not well understood. We report our preliminary results on patterns of sharing microarray data in public databases.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The most comprehensive method for measuring occurrences of public data sharing is manual curation of research reports, since data sharing plans are usually communicated in free text within the body of an article. Our early findings from manual curation of 100 papers suggest that 30% of investigators publicly share their full microarray datasets. Of these, 70% of the datasets are deposited at NCBI&amp;#x27;s Gene Expression Omnibus (GEO) database,...
Tipo: Poster
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1701/version/1

Prevalence of sarcopenia and sarcopenic obesity in Korean adults: The Korean Sarcopenic Obesity Study (KSOS)
Provedor de dados: 17
Autores: Tae Nyun Kim; Sae Jeong Yang; Hye Jin Yoo; Kang Il Lim; Hyun Joo Kang; Wook Song; Ji A Seo; Sin Gon Kim; Nan Hee Kim; Sei Hyun Baik; Dong Seop Choi; Kyung Mook Choi.
*Context:* Sarcopenic obesity (SO), a combination of excess weight and reduced muscle mass and/or strength, is suggested to be associated with an increased risk of adverse health outcomes. &amp;#xd;&amp;#xa;*Objectives:* To examine the prevalence and characteristics of Sarcopenic and SO defined by using different indices such as Appendicular Skeletal muscle Mass (ASM)/height^2^ and Skeletal Muscle Index (SMI (%): skeletal muscle mass (kg)/weight (kg) &amp;#xd7; 100) for Korean adults. &amp;#xd;&amp;#xa;*Methods:* 591 participants were recruited from the Korean Sarcopenic Obesity Study (KSOS) which is an ongoing prospective observational cohort study. Analysis was conducted in 526 participants (328 women, 198 men) who had complete data on body composition...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2915/version/1

Preventing hereditary cancers caused by opportunistic carcinogens
Provedor de dados: 17
Autores: Bernard Friedenson.
Objectives&amp;#xd;&amp;#xa;Previous studies reported inherited BRCA1/2 deficits appear to cause cancer by impairing normal protective responses to some carcinogens. Opportunistic carcinogens can exploit these deficits by causing chronic inflammation, constant cell death and replacement in a mutagenic environment, DNA crosslinking or double strand breaks. Some of the resulting cancers may be prevented if BRCA1/2 specific carcinogens are identified.&amp;#xd;&amp;#xa;Methods&amp;#xd;&amp;#xa;The literature was systematically searched for carcinogens capable of exploiting deficits in BRCA1/2 pathways. Search criteria were common exposure, available information, required BRCA1/2 pathway repairs, increased risks for any cancer, and effects on stem...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6636/version/1

Preventing hereditary cancers caused by opportunistic carcinogens
Provedor de dados: 17
Autores: Bernard Friedenson.
Objectives&amp;#xd;&amp;#xa;Previous studies reported inherited BRCA1/2 deficits can cause cancer by impairing normal protective responses.   Opportunistic carcinogens can exploit these deficits by causing chronic inflammation, constant cell death and replacement in a mutagenic environment, DNA crosslinking or double strand breaks.  Some of the resulting cancers may be prevented if opportunistic carcinogens are identified.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods&amp;#xd;&amp;#xa;The literature was systematically searched for carcinogens capable of exploiting deficits in BRCA1/2 pathways.   Search criteria were common exposure, available information, required BRCA1/2 pathway repairs, increased risks for any cancer, and effects on stem...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6668/version/1

Prey capture and meat-eating by the wild colobus monkey _Rhinopithecus bieti_ in Yunnan, China
Provedor de dados: 17
Autores: Baoping Ren; Dayong Li; Zhijin Liu; Hua Wu; Ming Li.
If it is true that extant primates evolved from an insectivorous ancestor, then primate entomophagy would be a primitive trait. Many taxa, however, have undergone a dietary shift from entomophagy to phytophagy, evolving a specialised gut and dentition and becoming exclusive herbivores. The exclusively herbivorous taxa are the Malagasy families Indriidae and Lepilemuridae, and the Old World Monkey subfamily Colobinae, and among these meat-eating has not been observed except as an anomaly, with the sole exception of the Hanuman langur (_Semnopithecus entellus_), which feeds on insects seasonally, and a single observation of a nestling bird predated by wild Sichuan snub-nosed monkeys (_Rhinopithecus roxellana_). Here, we describe the regular capture of...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/3021/version/1

Primate phylogeny: molecular evidence for a pongid clade excluding humans and a prosimian clade containing tarsiers
Provedor de dados: 17
Autores: Shi Huang.
Interpretations of molecular data by the modern evolution theory are often sharply inconsistent with paleontological results.  This is to be expected since the theory is only true for microevolution and yet fossil records are mostly about macroevolution.  The maximum genetic diversity (MGD) hypothesis is a more coherent and complete account of evolution that has yet to meet a single contradiction.  Here, molecular data were analyzed based on the MGD to resolve key questions of primate phylogeny.  A new method was developed from a novel result predicted by the MGD: genetic non-equidistance to a simpler taxon only in slow but not in fast evolving sequences given non-equidistance in time.  This &amp;#x2018;slow clock&amp;#x2019; method showed that humans are...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3794/version/1

Principal basis for enzyme power
Provedor de dados: 17
Autores: Alexander G. Foigel.
The reaction rate enhancement that enzymes produce had not been fully appreciated. The object of the article is to present the mechanism of the enormous catalytic power of the enzymes. I conclude that during substrate conversion to product the enzyme transfers firstly some additional small reactant group that must be initially presented in the active site of the enzyme to bound substrate (i) ; the enzyme regenerates during second substrate group transfer (ii);  the active enzyme acts as a reactant of the enzymatic reaction (iii). The detailed chemical mechanisms of enzymatic reactions, such as a the well-studied reaction of the serine proteases family, the peptide bond hydrolysis catalyzed by  &amp;#x3b1;-chymotrypsin, and the glyceraldehyde-3-phosphate...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2406/version/1

Principles for the post-GWAS functional characterisation of risk loci
Provedor de dados: 17
Autores: Matthew L. Freedman; Alvaro N. A. Monteiro; Simon A. Gayther; Gerhard A. Coetzee; Angela Risch; Christoph Plass; Graham Casey; Mariella De Biasi; Chris Carlson; Dave Duggan; Michael James; Pengyuan Liu; Jay W.  Tichelaar; Haris G. Vikis; Ming You; Ian G. Mills.
Several challenges lie ahead in assigning functionality to susceptibility SNPs. For example, most effect sizes are small relative to effects seen in monogenic diseases, with per allele odds ratios usually ranging from 1.15 to 1.3. It is unclear whether current molecular biology methods have enough resolution to differentiate such small effects. Our objective here is therefore to provide a set of recommendations to optimize the allocation of effort and resources in order to maximize the chances of elucidating the functional contribution of specific loci to the disease phenotype. It has been estimated that 88% of currently identified disease-associated SNPs are intronic or intergenic. Thus, in this paper we will focus our attention on the analysis of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5162/version/2

Principles for the post-GWAS functional characterisation of risk loci
Provedor de dados: 17
Autores: Alvaro N. A. Monteiro; Gerhard A. Coetzee; Matthew L. Freedman; Mariella De Biasi; Graham Casey; Dave Duggan; Angela Risch; Christoph Plass; Pengyuan Liu; Michael James; Haris G. Vikis; Jay W.  Tichelaar; Ming You; Simon A. Gayther; Ian G. Mills.
Several challenges lie ahead in assigning functionality to susceptibility SNPs. For example, most effect sizes are small relative to effects seen in monogenic diseases, with per allele odds ratios usually ranging from 1.15 to 1.3. It is unclear whether current molecular biology methods have enough resolution to differentiate such small effects. Our objective here is therefore to provide a set of recommendations to optimize the allocation of effort and resources in order maximize the chances of elucidating the functional contribution of specific loci to the disease phenotype. It has been estimated that 88% of currently identified disease-associated SNP are intronic or intergenic. Thus, in this paper we will focus our attention on the analysis of non-coding...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5162/version/1

PrionOme: A database of prions and other sequences relevant to prion phenomena
Provedor de dados: 17
Autores: Djamel Harbi; Marimuthu Parthiban; Deena Gendoo; Sepehr Ehsani; Manish Kumar; Gerold Schmitt-Ulms; Ramanathan Sowdhamini; Paul M. Harrison.
Prions are units of propagation of an altered state of a protein or proteins. Prions can propagate from cell to cell, and from organism to organism, through cooption of other protein copies. Prions contain no necessary nucleic acids, and are important both as both pathogenic agents, and as a potential force in epigenetic phenomena. The original prions were derived from a misfolded form of the mammalian Prion Protein PrP. Infection by these prions causes neurodegenerative diseases. Other prions cause non-Mendelian inheritance in budding yeast, and sometimes act as diseases of yeast. We have compiled a database of &amp;#x3e;2000 prion-related sequences, called the PrionOme. The database comprises seven PrionOme classification categories: prionogenic...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6430/version/1

Proapoptotic Bid Association with Mre11-Rad50-Nbs1 Complex is Indispensable for Checkpoint Activation after DNA Damage
Provedor de dados: 17
Autores: Van B. T. Ta; Karel Bezstarosti; Jeroen A. A. Demmers; Timurs Maculins; Karlyn Schellekens; Dik C. C. van Gent; Stephan P. Persengiev.
The proapoptotic protein Bid is phosphorylated by ATM after double strand breaks (DSBs) induction and induces S-phase arrest by a mechanism that remains to be elucidated. Here we show that in mammalian cells, Bid is associated with Mre11, a subunit of the Mre11-Rad50-Nbs1 (MRN) complex. We demonstrate that Bid activation is abrogated in Mre11 and Nbs1 deficient primary mouse fibroblasts and cells from patients with ataxia talangiectasia-like disorder. Bid depletion by RNA interference inhibited the S-phase checkpoint activation and G2/M arrest after genotoxic insult, but had no effect on MRN complex formation. Our results explain the mechanism of Bid phosphorylation by ATM in response to DNA damage and suggest that Bid functions as a link between the MRN...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1203/version/1

ProbCD: enrichment analysis accounting for categorization uncertainty
Provedor de dados: 17
Autores: Ricardo V&amp;#xea;ncio; Ilya Shmulevich.
As in many other areas of science, systems biology makes extensive use of statistical association and significance estimates in contingency tables, a type of categorical data analysis known in this field as enrichment (also over-representation or enhancement) analysis. In spite of efforts to create probabilistic annotations, especially in the Gene Ontology context, or to deal with uncertainty in high throughput-based datasets, current enrichment methods largely ignore this probabilistic information since they are mainly based on variants of the Fisher Exact Test. We developed an open-source R package to deal with probabilistic categorical data analysis, ProbCD, that does not require a static contingency table. The contingency table for&amp;#xd;&amp;#xa;the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/369/version/1

Probing the connectivity of neural circuits at single-neuron resolution using high-throughput DNA sequencing
Provedor de dados: 17
Autores: Hassana Oyibo; Gang  Cao; Huiqing Zhan; Alex Koulakov; Lynn Enquist; Joshua Dubnau; Anthony  Zador.
There is growing excitement in determining the complete connectivity diagram of the brain&amp;#x2014;the &amp;#x22;connectome&amp;#x22;. So far, the complete connectome has been established for only one organism, C. elegans, with 302 neurons connected by about 7000 synapses&amp;#x2014;and even this was a heroic task, requiring over 50 person-years of labor. Like all current approaches, this reconstruction was based on microscopy. Unfortunately, microscopy is poorly suited to the study of neural connectivity because brains are macroscopic structures, whereas synapses are microscopic. Nevertheless, there are several large-scale projects underway to scale up high-throughput microscopic approaches to the connectome.&amp;#xd;&amp;#xa;Here we present a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6452/version/1

Process Makna - A Semantic Wiki for Scientific Workflows
Provedor de dados: 17
Autores: Adrian Paschke; Zhili Zhao.
Virtual e-Science infrastructures supporting Web-based scientific workflows are an example for knowledge-intensive collaborative and weakly-structured processes where the interaction with the human scientists during process execution plays a central role. In this paper we propose the lightweight dynamic user-friendly interaction with humans during execution of scientific workflows via the low-barrier approach of Semantic Wikis as an intuitive interface for non-technical scientists. Our Process Makna Semantic Wiki system is a novel combination of a business process management system adapted for scientific workflows with a Corporate Semantic Web Wiki user interface supporting knowledge intensive human interaction tasks during scientific workflow execution.
Tipo: Presentation
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5633/version/1

Processing of insect retrotransposons by self-cleaving ribozymes
Provedor de dados: 17
Autores: Dana J. Ruminski; Chiu-Ho T. Webb; Nathan J. Riccitelli; Andrej Luptak.
We show that several classes of insect non-LTR retrotransposons harbor self-cleaving ribozymes of the HDV family at their 5&amp;#x2032; termini. In Drosophila the R2 ribozymes exhibit highly differential in vivo expression and robust in vitro activity, modulated by an upstream sequence originating from the insertion site. Our data suggest a role for self-cleaving ribozymes in co-transcriptional processing of retrotransposons with implications for downstream events, including translation and retrotransposition.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4333/version/1

PrOCoil - Advances in predicting two- and three-stranded coiled coils
Provedor de dados: 17
Autores: Carsten C. Mahrenholz*; Ingrid G. Abfalter*; Ulrich Bodenhofer; Rudolf Volkmer; Sepp Hochreiter.
*Overview* | Coiled coils are usually described as consisting of two up to seven &amp;#x3b1;-helices that are wrapped around each other. They can associate as either homomeric or heteromeric structures and bind in parallel or antiparallel topologies. Another characteristic of all coiled coils is the periodic recurrence of a sequence [abcdefg]n called heptad repeat, where n denotes the heptad number. In these repeats, a and d are hydrophobic amino acids at core positions crucial for the tertiary structure. In contrast, the polar positions b, c, and f are hydrophilic and e and g are charged residues.&amp;#xd;&amp;#xa;Due to their ability to oligomerize, coiled coils are involved in a variety of important cellular functions, either on their own or as part of...
Tipo: Poster
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4677/version/1

ProDGe: investigating protein-protein interactions at the domain level
Provedor de dados: 17
Autores: Finja B&amp;#xfc;chel; Clemens Wrzodek; Florian Mittag; Andreas Dr&amp;#xe4;ger; Adrian Schr&amp;#xf6;der; Andreas Zell.
An important goal of systems biology is the identification and investigation of known and predicted protein-protein interactions to obtain more information about new cellular pathways and processes. Proteins interact via domains, thus it is important to know which domains a protein contains and which domains interact with each other. Here we present the Java^TM^ program ProDGe (Protein Domain Gene), which visualizes existing and suggests novel domain-domain interactions and protein-protein interactions at the domain level. The comprehensive dataset behind ProDGe consists of protein, domain and interaction information for both layers, collected and combined appropriately from UniProt, Pfam, DOMINE and IntAct. Based on known domain interactions, ProDGe...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6188/version/1

Production of Transgenic Cloned Miniature Pigs with Membrane-bound Human Fas Ligand (FasL) by Somatic Cell Nuclear Transfer
Provedor de dados: 17
Autores: Jae Goo Seol; Soo Hyun Kim; Dong-Il Jin; Seung Pyo Hong; Ji Yeon Yoo; Ki Myung Choi; Young Chul Park; Yun Jin Yun; Kwang Wook Park; Jae Young Heo.
Cell-mediated xenograft rejection, including NK cells and CD8+ CTL, is a major obstacle in successful pig-to-human xenotransplantation. Human CD8+ CTL and NK cells display high cytotoxicity for pig cells, mediated at least in part by the Fas/FasL pathway. To prevent cell-mediated xenocytotoxicity, a membrane-bound form of human FasL (mFasL) was generated as an inhibitor for CTL and NK cell cytotoxicity that could not be cleaved by metalloproteinase to produce putative soluble FasL. We produced two healthy transgenic pigs harboring the mFasL gene via somatic cell nuclear transfer (SCNT). In a cytotoxicity assay using transgenic clonal cell lines and transgenic pig ear cells, the rate of CD8+ CTL-mediated cytotoxicity was significantly reduced in transgenic...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4539/version/1

Productivity and forage quality of a phytodiverse semi-natural grassland &amp;#xb;under various management regimes
Provedor de dados: 17
Autores: Tatiana  From; Ute K. Petersen; Johannes Isselstein.
Grassland management experiment (GrassMan) was set up in 2008 on a permanent semi-natural grassland in the Solling uplands, Germany. The main research focus is on the ecosystem functioning of the phytodiverse grassland (e.g. productivity and forage quality, water and nutrient fluxes). The aim of our study was to analyse the effects of vegetation composition and functional diversity on productivity and forage quality of the semi-natural permanent grassland. Variation in sward composition was achieved by herbicide application and resulted in three sward types: control sward type (without herbicide application), monocot-reduced and dicot-reduced. Further management factors included different nutrient input levels (without fertilizer and 180-30-100 kg/ha of...
Tipo: Poster
Palavras-chave: Ecology; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6622/version/1

Progress report: SBML  Level 3 package FBA
Provedor de dados: 17
Autores: Brett G. Olivier; Frank T. Bergmann.
The SBML Level 3 &amp;#x22;FBA&amp;#x22; package is a proposal for an extension to the current Level 3 Core specification that allows for the description and annotation of constraint based models.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This allows one to e.g. store information related to flux balance analysis in SBML Level 3 models.
Tipo: Presentation
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5033/version/1

Progression of Parkinson&amp;#x2019;s disease pathology is reproduced by intragastric administration of rotenone in mice
Provedor de dados: 17
Autores: Francisco J. Pan-Montojo; Oleg Anichtchik; Yanina Dening; Lilla  Knells; Stefan Pursche; Roland  Jung; Gabriele Gille; Maria Grazia Spillantini; Heinz Reichmann; Richard H. W. Funk.
In Parkinson&amp;#x2019;s disease patients pathology follows a characteristic pattern involving inter alia the enteric nervous system, the dorsal motor nucleus of the vagus, the intermediolateral nucleus of the spinal cord and the substantia nigra, providing the basis for the neuropathological staging of the disease. Here we report that intragastrically administered rotenone, a commonly used pesticide that inhibits mitochondrial Complex I, is able to reproduce PD pathological staging as found in patients. Our results show that low doses of chronically and intragastrically administered rotenone induce PD pathology in all the above-mentioned nervous system structures in wild-type mice. Interestingly, HPLC analysis showed no rotenone levels in the systemic...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3352/version/2

Progression of Parkinson&amp;#x2019;s disease pathology is reproduced by intragastric administration of rotenone in mice
Provedor de dados: 17
Autores: Francisco J. Pan-Montojo; Oleg Anichtchik; Yanina Dening; Lilla  Knells; Stefan Pursche; Roland  Jung; Sandra  Jackson; Gabrielle Gille; Maria Grazia Spillantini; Heinz  Reichmann; Richard H. W. Funk.
In Parkinson&amp;#x2019;s disease patients pathology follows a characteristic pattern involving inter alia the enteric nervous system, the dorsal motor nucleus of the vagus, the intermediolateral nucleus of the spinal cord and the substantia nigra, providing the basis for the neuropathological staging of the disease. Here we report that intragastrically administered rotenone, a commonly used pesticide that inhibits mitochondrial Complex I, is able to reproduce PD pathological staging as found in patients. Our results show that low doses of chronically and intragastrically administered rotenone induce PD pathology in all the above-mentioned nervous system structures in wild-type mice. Interestingly, HPLC analysis showed no rotenone levels in the systemic...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/3352/version/3

Progression of Parkinson&amp;#x2019;s disease pathology is reproduced by intragastric administration of rotenone in mice
Provedor de dados: 17
Autores: Francisco J. Pan-Montojo; Oleg Anichtchik; Yanina Dening; Lilla  Knells; Stefan Pursche; Roland  Jung; Gabriele Gille; Maria Grazia Spillantini; Heinz Reichmann; Richard H. W. Funk.
In Parkinson&amp;#x2019;s disease patients pathology follows a characteristic pattern involving inter alia the enteric nervous system, the dorsal motor nucleus of the vagus, the intermediolateral nucleus of the spinal cord and the substantia nigra, providing the basis for the neuropathological staging of the disease. Here we report that intragastrically administered rotenone, a commonly used pesticide that inhibits mitochondrial Complex I, is able to reproduce PD pathological staging as found in patients. Our results show that low doses of chronically and intragastrically administered rotenone induce PD pathology in all the above-mentioned nervous system structures in wild-type mice. Interestingly, HPLC analysis showed no rotenone levels in the systemic...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3352/version/1

Projected Climate Change Impacts on Grape Growing in the Okanagan Valley, British Columbia, Canada
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest; Ken J. Friesen.
A statistical analysis was conducted on long-term climate records in the Okanagan Valley wine grape growing region of British Columbia, Canada. No observable trends for average annual temperatures were found in the region. Analyses of monthly mean and extreme temperatures show wide spatial and temporal heterogeneity, indicating that future studies using downscaling of global climate models for this region will require resolutions on the order of several kilometers. Mean winter temperatures are increasing throughout the valley, and extreme minimum temperatures are also increasing during the winter at the central and northern sites which have historically presented the most risk of winter damage to grapevines. Only the most southern and northern sub-regions...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3162/version/1

Projected Climate Change Impacts on Grape Growing in the Okanagan Valley, British Columbia, Canada
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest; Ken J. Friesen.
A statistical analysis was conducted on long-term climate records in the Okanagan Valley wine grape growing region of British Columbia, Canada. No observable trends for average annual temperatures were found in the region. Analyses of monthly mean and extreme temperatures show wide spatial and temporal heterogeneity, indicating that future studies using downscaling of global climate models for this region will require resolutions on the order of several kilometers. Mean winter temperatures are increasing throughout the valley, and extreme minimum temperatures are also increasing during the winter at the central and northern sites which have historically presented the most risk of winter damage to grapevines. Only the most southern and northern sub-regions...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/3162/version/2

Proliferating Cell Nuclear Antigen (PCNA) allows the automatic identification of follicles in microscopic images of human ovarian tissue
Provedor de dados: 17
Autores: Tom Kelsey; Benedicta Caserta; Luis Castillo; Hamish Wallace; Francisco C&amp;#xf3;ppola Gonz&amp;#xe1;lvez.
Background: Human ovarian reserve is defined by the population of non-growing follicles (NGFs) in the ovary. Direct estimation of ovarian reserve involves the identification of NGFs in prepared ovarian tissue. Previous studies involving human tissue have used hematoxylin and eosin (HE) stain, with NGF populations estimated by human examination either of tissue under a microscopic, or of images taken of this tissue.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;Methods: In this study we replace HE with Proliferating Cell Nuclear Antigen (PCNA), and automate the identification and enumeration of NGFs that appear in the resulting microscopic images. We compared the automated estimates to those obtained by human experts, with the gold standard taken to be the average of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4418/version/1

Prolonged maturation of prefrontal white matter in chimpanzees
Provedor de dados: 17
Autores: Tomoko  Sakai; Daichi Hirai; Akichika Mikami; Juri  Suzuki; Yuzuru  Hamada; Masaki Tomonaga; Masayuki Tanaka; Takako Miyabe-Nishiwaki; Haruyuki Makishima; Masato Nakatsukasa; Tetsuro Matsuzawa.
Delayed maturation in the prefrontal cortex, a brain region associated with complex cognitive processing, has been proposed to be specific to humans. However, we found, using a longitudinal design, that prefrontal white matter volume in chimpanzees increased gradually with age, and the increase appears to continue beyond the onset of puberty, as in humans. This provides the first evidence for a prolonged period of prefrontal connection elaboration in great apes.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4411/version/1

PROM Khad an efficient source of P to replace the costly chemical Phosphatic Fertilizer
Provedor de dados: 17
Autores: DMR Sekhar; MK Katewa; MS Shaktawat.
The subsidy on phosphate fertilizers rose to an unacceptable level while alternate cost effective technologies are available. Fertilizer industry needs to develop innovative products using the recent advances in the agricultural sciences. Manure producing industries to be supplied rock phosphate mineral (at subsidized costs) as being supplied to chemical fertilizers industries suitable to produce PROM Khad (Phosphate Rich Organic Manure).
Tipo: Manuscript
Palavras-chave: Biotechnology; Earth &amp; Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/6848/version/1

Promoter regions of many neural- and nutrition-related genes have experienced positive selection during human evolution
Provedor de dados: 17
Autores: Ralph Haygood; Olivier Fedrigo; Brian Hanson; Ken-Daigoro Yokoyama; Gregory Wray.
Surveys of protein-coding sequences for evidence of positive selection in humans and chimpanzees have flagged surprisingly few genes known to be involved in neural or nutritional processes, despite the pronounced differences between humans and chimpanzees in behavior, cognition, and diet. It may be that most such differences are due to changes in gene regulation rather than protein structure. Here, we present the first survey of promoter (5&amp;#x27;-flanking) regions, which are rich in _cis_-regulatory sequences, for signatures of positive selection in humans. Our results indicate that positive selection has targeted the regulation of many genes known to be involved in neural development and function, both in the brain and elsewhere in the nervous system,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/69/version/1

Proof of principle for shotgun DNA mapping by unzipping
Provedor de dados: 17
Autores: Lawrence J. Herskowitz; Anthony L. Salvagno; R. Andy Maloney; Linh N. Le; Steven J. Koch.
Ability to map polymerases and nucleosomes on chromatin is important for understanding the impact of chromatin remodeling on key cellular processes.  Current methods (such as ChIP and ChIP-chip) have produced a wealth of information that demonstrates this importance, but key information is elusive in these ensemble methods.  We&amp;#x2019;re pursuing a new single-molecule chromatin mapping method based on unzipping native chromatin molecules with optical tweezers.  The first step we are taking towards this ability is shotgun DNA mapping (SDM).  This is the ability to identify the genomic location of a random DNA fragment based on its naked DNA unzipping forces compared with simulated unzipping forces of a published genome.  We show that ~32 separate...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/2808/version/2

Proof of principle for shotgun DNA mapping by unzipping
Provedor de dados: 17
Autores: Lawrence J. Herskowitz; Anthony L. Salvagno; R. Andy Maloney; Linh N. Le; Steven J. Koch.
Ability to map polymerases and nucleosomes on chromatin is important for understanding the impact of chromatin remodeling on key cellular processes.  Current methods (such as ChIP and ChIP-chip) have produced a wealth of information that demonstrates this importance, but key information is elusive in these ensemble methods.  We&amp;#x2019;re pursuing a new single-molecule chromatin mapping method based on unzipping native chromatin molecules with optical tweezers.  The first step we are taking towards this ability is shotgun DNA mapping (SDM).  This is the ability to identify the genomic location of a random DNA fragment based on its naked DNA unzipping forces compared with simulated unzipping forces of a published genome.  We show that ~32 separate...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/2808/version/1

Propofol Induction Reduces the Capacity for Neural Information Integration: Implications for the Mechanism of Consciousness and General Anesthesia
Provedor de dados: 17
Autores: UnCheol  Lee; Seunghwan Kim; Gyu-Jeong Noh; Byung-Moon Choi; George A. Mashour.
The cognitive unbinding paradigm suggests that the synthesis of cognitive information is attenuated by general anesthesia. Here, we investigated the functional organization of brain activities in the conscious and anesthetized states, based on characteristic functional segregation and integration of electroencephalography (EEG). EEG recordings were obtained from 14 subjects undergoing induction of general anesthesia with propofol. We quantified changes in mean information integration capacity in each band of the EEG. After induction with propofol, mean information integration capacity was reduced most prominently in the gamma band of the EEG (p=0.0001). Furthermore, we demonstrate that loss of consciousness is reflected by the breakdown of the...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1244/version/2

Proposing a life cycle land use impact calculation methodology
Provedor de dados: 17
Autores: Wouter M. J. Achten; Erik Mathijs; Bart Muys.
The Life Cycle Assessment (LCA) community is yet to come to a consensus on a methodology to incorporate land use in LCA, still struggling with what exactly should be assessed and which indicators should be used. To solve this problem we start from concepts and models describing how ecosystems function and sustain, in order to understand how land use affects them. Earlier our research group presented a methodology based on the ecosystem exergy concept. This concept as based on the hypothesis that ecosystems develop towards more effective degradation of exergy fluxes passing through the system and is derived from two axioms: the principles of (i) maximum exergy storage and the (ii) maximum exergy dissipation. This concept aiming at the area of protection...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2340/version/3

Proposing a life cycle land use impact calculation methodology
Provedor de dados: 17
Autores: Wouter M. J. Achten; Erik Mathijs; Bart Muys.
The Life Cycle Assessment (LCA) community is yet to come to a consensus on a methodology to incorporate land use in LCA, still struggling with what exactly should be assessed and which indicators should be used. To solve this problem we start from concepts and models describing how ecosystems function and sustain, in order to understand how land use affects them. Earlier our research group presented a methodology based on the ecosystem exergy concept. This concept as based on the hypothesis that ecosystems develop towards more effective degradation of exergy fluxes passing through the system and is derived from two axioms: the principles of (i) maximum exergy storage and the (ii) maximum exergy dissipation. This concept aiming at the area of protection...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2340/version/2

Proposing a life cycle land use impact calculation methodology
Provedor de dados: 17
Autores: Wouter M. J. Achten; Pieter Vandenbempt; Patrick Lema&amp;#xee;tre; Erik Mathijs; Bart Muys.
The Life Cycle Assessment (LCA) community is yet to come to a consensus on a methodology to incorporate land use in LCA. Earlier our research group presented a methodology based on the ecosystem exergy concept. The ecosystem exergy concept suggests that ecosystems develop towards more effective degradation of energy fluxes passing through the system. The concept is argued to be derivable from two axioms: the principles of (i) maximum exergy storage and the (ii) maximum exergy dissipation. In this paper we present a methodology to assess impacts of human induced land use occupation, in which we make a difference between functional and structural land use impacts. The methodology follows a dynamic multi-indicator approach looking at mid-point impacts on soil...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2340/version/1

Pro-social motive promotes early understanding of false belief
Provedor de dados: 17
Autores: Tomoko Matsui; Yui Miura.
Ever since Premack &amp;#x26; Woodruff&amp;#x27;s classic article^1^, which introduced the term &amp;#x22;theory of mind&amp;#x22;, researchers have claimed that strategic deception is the most natural behavioural consequence of understanding false belief. Here we challenge that claim, and provide evidence for the first time that the earliest manifestation of false belief understanding in human development is found in young children&amp;#x27;s emerging pro-social behaviours. In a modified false belief task, children were asked either to choose one protagonist they should help to find the object (the pro-social context), or to choose one they need to deceive so that none of the protagonists can find the object (the competitive context). The results show...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1695/version/1

Prospect and importance of green mulching on the soil status of tropical tasar plantation fields in India
Provedor de dados: 17
Autores: Rangareddygari Manohar Reddy; Ramkumar -.
The soils of tropical tasar plantation fields in general are sloppy and are primarily deficient of nutrition due to top soil erosion and constant leaf productivity exploitation to rear tasar silk insect, Antheraea mylitta Drury. The rainfed field of Terminalia tomentosa (W&amp;#x26;A) plantation has been evaluated for soil fortification with green mulching through legumes, Sun hemp (Crotalaria juncea), Daincha (Sesbania aculeata), Green gram (Vigna radiatus) and Black gram (Vigna mungo) during rainy season. The mulching has enhanced the water holding, moisture retention, electrical conductivity, organic carbon, nitrogen (N) and potassium (K) and reduced the bulk density and pore space of soil. Among the legumes, Sun hemp has shown higher improvement of...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6388/version/1

Protection from avian influenza H5N1 virus infection with antibody-impregnated filters
Provedor de dados: 17
Autores: Yoichiro Kamiyama; Kazuhide Adachi; Ekowati Handharyani; Retno Damajanti Soejoedono; Takayuki Kusano; Marie Inai; Masaya Tsukamoto; Seizaburo Kashiwagi; Yasuhiro Tsukamoto.
There is worldwide concern over the possibility of a new influenza pandemic originating from the highly pathogenic avian H5N1 influenza viruses. We herein demonstrate that functional air filters impregnated with ostrich antibodies against the hemagglutinin of the H5N1 virus protect chickens from death by H5N1 transmission. These results suggest that the use of ostrich antibody-impregnated filters might be a powerful way to prevent the transmission of H5N1.
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4548/version/1

Protective effect of (-) &amp;#x3b1;-bisabolol on markers of oxidative stress in erythrocytes subjected to oxidative insult
Provedor de dados: 17
Autores: Suaib  Luqman; Suchita  Srivastava.
(-)-&amp;#x3b1;-bisabolol is a sesquiterpene alcohol found as a major component of essential oil of chamomile (Matricaria recutita L., Chamomilla recutita L., Matricaria chamomilla L.; Family Asteraceae). Chamomile, one of the most ancient and widely recognized herbs to mankind, has been used traditionally for centuries as an anti-inflammatory, antispasmodic, carminative, mild astringent and healing medicine. It is also known to be very helpful as an external agent for encouraging the rapid healing of ulcers and burns without infection, as well as persistent skin problems such as eczema and psoriasis. Since clinical trials and human studies are limited, we have investigated the effect of (-)-&amp;#x3b1;-bisabolol on markers of oxidative stress in human...
Tipo: Poster
Palavras-chave: Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6903/version/1

Protective vaccination in the horse against _Streptococcus equi_ with recombinant antigens
Provedor de dados: 17
Autores: Bengt Guss; Margareta Flock; Lars Frykberg; Andrew Waller; Carl Robinson; Ken Smith; Jan-Ingmar Flock.
_Streptococcus equi_ subspecies _equi_ (_S. equi_) is a clonal, equine host-adapted pathogen of global importance that causes a highly contagious suppurative lymphodendopathy of the head and neck, more commonly known as Strangles. The disease is highly prevalent, can be severe and spread easily by visibly infected animals or by carrier animals that show no clinical signs of disease. Antibiotic treatment is usually ineffective. However, the majority of horses develop immunity to re-infection, suggesting that vaccination should be a feasible way to prevent the infection. Live attenuated vaccine strains of _S. equi_ are available but adverse reactions have been reported and they suffer from a short duration of immunity. Thus, a safe and effective vaccine...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/2985/version/1

Protein and DNA evolution: Statistics and combinatorics are the rules of the game
Provedor de dados: 17
Autores: Arunava Goswami; Srimoyee Duttagupta; Chirantan Chakraborty; Amita Pal; Pabitra Pal Choudhury; Sk Sarif Hassan.
Let us assume AVMAYDRYVAIC or MAYDRYVAICCP, most important signature domain of&amp;#xd;&amp;#xa;olfactory receptor (OR) gene family assembled in evolution following simplest possible laws of statistics which says the addition of V after A in AVMAYDRYVAIC or addition of A after M are independent events. There are 20 amino acids present in nature so the probability of joint occurrence of such events is 1/400. Therefore for making a contiguous string of&amp;#xd;&amp;#xa;AVMAYDRYVAIC or MAYDRYVAICCP, the probability would be 1 out of 2012. Over millions of years of evolution this has certainly happened and that is why we see such a signature sequence in OR1D2, OR1D subfamily member 2 as per &amp;#x22;HORDE...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4859/version/1

Protein Data Integration through Ontologies
Provedor de dados: 17
Autores: Amandeep S. Sidhu.
In this paper, we consider the challenges of information integration in proteomics from the prospective of researchers using information technology as an integral part of their discovery process. Specifically, data integration, meta-data specification, data provenance and data quality are discussed here. Here we review existing protein data integration methods and propose the use of common vocabulary for protein data integration using ontologies.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4062/version/1

Protein folding disorders: Toward a basic biological paradigm
Provedor de dados: 17
Autores: Rodrick Wallace.
Mechanistic &amp;#x27;physics&amp;#x27; models of protein folding fail to account for the observed spectrum of protein folding and aggregation disorders, suggesting that a more appropriately biological paradigm will be needed for understanding the etiology, prevention, and treatment of these diseases.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4344/version/1

Protein folding disorders: Toward a basic biological paradigm
Provedor de dados: 17
Autores: Rodrick Wallace.
Mechanistic &amp;#x27;physics&amp;#x27; models of protein folding fail to account for the observed spectrum of protein folding and aggregation disorders, suggesting that a cognitive paradigm for protein folding regulation will be needed for understanding the etiology, prevention, and treatment of these diseases.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4344/version/2

Protein Ontology and Community Curation
Provedor de dados: 17
Autores: Cecilia Arighi.
The Protein Ontology (PRO) is designed as a formal and well-principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from the classification of proteins, on the basis of evolutionary relationships at the homeomorphic level, to the representation of the multiple protein forms of a gene, such as those resulting from alternative splicing, cleavage and/or post-translational modifications. As an ontology, PRO differs from a database in that it provides description about the protein types and their relationships. In this way PRO can be integrated with or cross-referenced by other ontologies and/or databases. The representation of specific protein entities in PRO allows precise definition of objects in pathways,...
Tipo: Presentation
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3169/version/1

Protein Regge Trajectories, Phase Coexistence and Loop Aetiology in Alzheimers Disease
Provedor de dados: 17
Autores: Antti Niemi; Andrey Krokhotin.
Alzheimer&amp;#x27;s disease has a devastating impact on its victims by causing severe neurodegeneration in the brain that leads to a certain death. Only in a small number of cases can the origin be traced to a variety of genetic mutations, for the greater part the reasons for its onset are unclear.The defining factor is the formation of extracellular senile amyloid plaques in the brain, but therapeutic approaches to remove them remain to be shown effective in humans. Here we investigate physical processes that are involved in the release of the extracellular amyloid, by scrutinizing the intracellular domain of its precursor protein. We identify a phenomenon that has never before been discussed in the context of protein research: Like ice and water...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6030/version/1

Proteins of the XMRV retrovirus implicated in chronic fatigue syndrome and prostate cancer are homologous to human proteins relevant to both diseases.
Provedor de dados: 17
Autores: Christopher Carter.
The XMRV retrovirus has been implicated in chronic fatigue syndrome and prostate cancer. A homology search comparing retroviral with human proteins revealed short contiguous amino acid strings (typically 5-8 aa) matching human proteins whose dysfunction might be expected to cause fatigue, including mitochondrial proteins related to oxidative phosphorylation, glutamate receptors and their synaptic scaffolds, muscular acetylcholine receptor scaffolds and structural proteins, components of the immune system, and phosphatidylinositol signalling inter alia. Viral proteins are also homologous to members of the oestrogen, peroxisome proliferator, and CREB activated receptor networks, all of which are implicated in prostate cancer, and to a protein, SRCAP, that...
Tipo: Manuscript
Palavras-chave: Cancer; Immunology; Microbiology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4669/version/1

Proteomics in the Light of Integral Value Transformations
Provedor de dados: 17
Autores: Sk. S.  Hassan; P. Pal  Choudhury.
In this paper, Proteomics have been studied in the light of Integral Value Transformations (IVTs) which was introduced by Sk. S. Hassan et al in 2010. For case study, a Human olfactory receptor OR1D2 protein sequence has been taken and then different IVTs have been used to evolve OR1D2 into some other proteomic like sequences. It has been observed that some of the generated sequences have been mapped to another olfactory receptor in Human or in some other species. Also it has been corroborated through fractal dimension that some of the fundamental protein properties have been nearly intact, even after the mapping. This study will help to comprehend the proteomic evolutionary network with the help of IVTs.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6100/version/1

Protocol for Metatranscriptomic analysis of Intestinal Microbiota
Provedor de dados: 17
Autores: Valeriy Poroyko; Alvaro G. Hernandez; John C. Alverdy; Donald C. Liu.
The objective of this publication is to provide the detailed protocol for metartancriptomisc studies of animal intestinal microbiota. The protocol describes isolation of high quality microbial community RNA from the mammalian intestinal content, subsequent mRNA enrichment, cDNA synthesis and sequencing. Twelve libraries were prepared, pooled in equimolar concentrations into a single library and sequenced on one GS Titanium 70&amp;#xd7;75 picotiter plate, following this protocol. The total number of reads obtained for 12 libraries was 1,155,062 (average 96,000 per library) and the combined size of 12 libraries was 521 million bases (average 43 million bases per library). The reported size of non-ribosomal RNA library fraction is ~15%, the fraction of...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2012
URL: http://precedings.nature.com/documents/6934/version/1

Providing a Realist Perspective on the eyeGENE Database System
Provedor de dados: 17
Autores: Werner Ceusters.
One of the achievements of the eyeGENE Network is a repository of DNA samples of patients with inherited eye diseases and an associated database that tracks key elements of phenotype and genotype information for each patient. Although its database structure serves its direct research needs, eyeGENE has set a goal of enhancing this structure to become increasingly well integrated with medical information standards over time. This goal should be achieved by ensuring semantic interoperability with other information systems but without adopting the incoherencies and inconsistencies found in available biomedical standards. Therefore, eyeGENE&amp;#x2019;s current pragmatic perspective with focus on data and information, rather than what the information is about,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3467/version/1

PSA Dynamics traditionally evaluated with an inadequate formula
Provedor de dados: 17
Autores: Hans-J&amp;#xfc;rg Gerber.
The PSA doubling time is usually calculated from measured PSA values with an inadequate formula that tacitly assumes the absence of that process, which it is supposed to reveal. We present a modified calculational procedure which is optimized to unveil a weak second exponential process in the presence of a strong first one, using early screening data. The notion of Break Even Time (BET) indicates the stages of the processes.
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3930/version/1

Psychiatric and Behavioral Genetics: A Useful Distinction?
Provedor de dados: 17
Autores: Joachim Hallmayer.
Dr. Hallmayer began with a discussion of the Nuffield Council on Bioethics&amp;#x27; work on genetics, mental disorders and human behavior.  He further explored psychiatric genetics and urged against the oversimplification of dynamic interactions. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To watch Dr. Hallmayer&amp;#x2019;s presentation, please see the &amp;#x22;Google Video posting.&amp;#x22;:http://video.google.com/videoplay?docid=-5387564337084407366&amp;#x26;hl=en&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;To watch the deliberative discussion concluding the first Symposium panel, please see the &amp;#x22;Google Video posting.&amp;#x22;:http://video.google.com/videoplay?docid=3871777823134971240&amp;#x26;hl=en
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2619/version/1

Psychiatric Genetics: Methods, Findings and Ethical Issues
Provedor de dados: 17
Autores: Kenneth Kendler.
This talk has 4 major sections. First, I review the basic definition of a complex trait, especially as it applies to psychiatric disorders. Second, I outline the 4 basic paradigms of psychiatric genetics: simple genetic epidemiology, advanced genetic epidemiology, gene-finding methods and molecular genetics. Third, I review a few basic facts about psychiatric genetics - the level of heritabilities found for most common disorders and the difficulties the field has had in obtaining replicated evidence for single gene effects. Finally, I briefly review three conceptual/philosophical issues that relate to psychiatric genetics: i) why do people become much more concerned in learning about possible genetic influences on personality or risk for depression than...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2623/version/1

PTOMSM: A modified version of Topological Overlap Measure used for predicting Protein-Protein Interaction Network
Provedor de dados: 17
Autores: Xun Huang.
A variety of methods are developed to integrating diverse biological data to predict novel interaction relationship between proteins. However, traditional integration can only generate protein interaction pairs within existing relationships. Therefore, we propose a modified version of Topological Overlap Measure to identify not only extant direct PPIs links, but also novel protein interactions that can be indirectly inferred from various relationships between proteins. Our method is more powerful than a na&amp;#xef;ve Bayesian-network-based integration in PPI prediction, and could generate more reliable candidate PPIs. Furthermore, we examined the influence of the sizes of training and test datasets on prediction, and further demonstrated the effectiveness...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4107/version/1

Public awareness of cancer in Britain: a population-based survey of adults
Provedor de dados: 17
Autores: K Robb; S Stubbings; A Ramirez; U Macleod; J Austoker; J Waller; S Hiom; J Wardle.
*_Objective:_* To assess public awareness of cancer warning signs, anticipated delay, and perceived barriers to seeking medical advice in the British population. &amp;#xd;&amp;#xa;Methods: We carried out a population-based survey using face-to-face, computer-assisted interviews to administer the Cancer Awareness Measure (CAM), a newly-developed, validated measure of cancer awareness.  The sample included 2216 adults (970 male and 1246 female) recruited as part of the Office for National Statistics Opinions Survey using stratified probability sampling.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*_Results:_*  Awareness of cancer warning signs was low when open-ended (recall) questions were used and higher with closed (recognition) questions; but on either measure,...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3817/version/1

Publishing Interactive Articles: Integrating Journals And Biological Databases
Provedor de dados: 17
Autores: Karen Yook; Arun  Rangarajan; Hans-Michael Muller; Paul Sternberg; Tracey DePellegrin-Connelly; Tim Schedl; Mike Cherry; William  Gelbart; Juancarlos Chan; Stephen  Haenel; Lolly  Otis; Sharon Faelten; Marek S. Skrzypek; Steven Marygold.
In collaboration with the journal GENETICS, we&amp;#x27;ve developed and launched a pipeline by which interactive full-text HTML/PDF journal articles are published with named entities linked to corresponding resource pages in &amp;#x22;WormBase&amp;#x22;:http://www.wormbase.org/ (WB). Our interactive articles allow a reader to click on over ten different data type objects (gene, protein, transgene, etc.) and be directed to the relevant webpage. This seamless connection from the article to summaries of data types promotes a deeper level of understanding for the na&amp;#xef;ve reader, and incisive evaluation for the sophisticated reader. Further, this collaboration allows us to identify and collect information before the publication of the article. The...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5146/version/1

Publishing re-usable phylogenetic trees, in theory and practice
Provedor de dados: 17
Autores: Brian O&amp;#x27;Meara; Jamie Whitacre; Ross Mounce; Dan F. Rosauer; Rutger A. Vos; Arlin Stoltzfus.
Sharing and re-use of data are essential to the progressive and self-correcting nature of science. In recognition of this principle, journals and funding agencies have adopted policies to encourage sharing of information (&amp;#x27;data&amp;#x27;), including empirical data as well as computed inferences such as phylogenetic trees. &amp;#xd;&amp;#xa;Here we summarize an ongoing analysis of 1) current practices for sharing phylogenetic trees and associated data; 2) current barriers to effective sharing and reuse of such data; and 3) prospects for reducing these barriers to promote more widespread sharing and re-use. Currently, the technical infrastructure is available to support (with some limitations) rudimentary archiving in conjunction with manuscript...
Tipo: Presentation
Palavras-chave: Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6048/version/1

Purification and physicochemical studies of metalloprotease, cotinifolin from Euphorbia cotinifolia
Provedor de dados: 17
Autores: Reetesh Kumar.
A detailed procedure for the purification of cotinifolin from the latex of Euphorbia cotinifolia using ion exchange chromatography and hydrophobic interaction chromatography is described.&amp;#xd;&amp;#xa;Various biochemical characteristics of cotinifolin and other enzymatic properties along with spectroscopic parameters like circular dichorism and fluorescence have been reported. Cotinifolin is stable over a wide range of pH and under extreme conditions of chaotrops and organic solvents where most proteins lost their functions.  Further studies on the identification of physiological substrates, biophysical and structural studies will give insight into the utility of the enzyme in the biotechnological industries and protein engineering.
Tipo: Presentation
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6397/version/1

Pyrolysis of asphaltenes and biomarkers for the fingerprinting of the _Amoco Cadiz_ oil spill after 23 years
Provedor de dados: 17
Autores: Jean Oudot; Fr&amp;#xe9;d&amp;#xe9;ric Chaillan.
The chemical composition of the petroleum products accidently or deliberately released in the environment varies considerably with time under the action of biological (biodegradation) and physico-chemical (photo-oxidation) processes. It becomes more and more difficult to trace the origin of the oil spilled. A technique widely used  for monitoring ancient oil pollutions is the study of oil biomarkers like terpanes and steranes^1,2^. Here we show that the geochemical technique of asphaltenes pyrolysis can be successfully applied to environmental samples. This method allows the reconstitution of the original oil from the asphaltenes fraction of severely degraded oil residues. We applied the two techniques: biomarkers analysis and pyrolysis of asphaltenes to...
Tipo: Manuscript
Palavras-chave: Chemistry; Microbiology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2975/version/1

Pyrosequencing/Sanger Plant Genome Assembly (Limitations, Problems And Solutions) - On The Way To Cucumber (Cucumis sativus L. cv. Borszczagowski) Draft Genome Sequence Publishing
Provedor de dados: 17
Autores: Rafal Woycicki; Zbigniew Przybecki.
Genome sequencing give us an opportunity to broaden the range and improve the quality of omics studies. New sequencing technologies make it possible to achieve the sequencing reads fast and cheap. Since the assembly step of such next generation reads is still not well standardized it is the most cumbersome part of sequencing projects.&amp;#xd;&amp;#xa;We focus here on the wide range of approaches undertaken to assemble the draft cucumber (Cucumis sativus L. cv. Borszczagowski) genome done by using 12x coverage of pyrosequencing Titanium chemistry shotgun paired and unpaired reads combined with Sanger reads.
Tipo: Poster
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4630/version/1

QSAR &amp;#x26; DOCKING APPROACH - POTENTIAL WAY TO NEW DRUG  DEVELOPMENT
Provedor de dados: 17
Autores: Ajeet Ajeet.
With today&amp;#x27;s need for discovering and developing new drug molecules, it is necessary to accept ways to save time and wet lab essentials.  To this end, the QSAR and molecular docking approach is used widely by us.  This poster describes steps for developing a new or modified moiety of a drug molecule.&amp;#xd;&amp;#xa;
Tipo: Poster
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7071/version/1

QSAR and Docking Studies of Gallic Acid Derivatives for Anticancer and Immunomodulatory Activity
Provedor de dados: 17
Autores: Dharmendra Kumar Yadav; Feroz Khan; Arvind Singh  Negi.
Immuno-modulation is the process of alteration in immune response due to foreign intrusion of molecules inside the body. In the present communication QSAR and molecular docking studies for immuno-modulatory activity of derivatives of gallic acid were performed. Molecular docking studies showed higher binding affinity with INF&amp;#x3b1;-2, IL-6, and IL-4 receptors. Binding site residues indicate hydrogen bonds formation with gallic acid derivative compounds G-3, G-4, G-5, G-6, G-7 and G-10. Further screening through quantitative structure activity relationship model establishes the immuno-modulatory activity of the compounds G-4, G-7, G-9, G-10, G-12 and G-13. Activity was predicted through a robust statistical model, developed by forward feed multiple...
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Chemistry; Pharmacology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6620/version/1

QSAR studies on Withanolide analogs for anticancer activity
Provedor de dados: 17
Autores: Dharmendra Kumar  Yadav; Feroz  Khan; Rajender S.  Sangwan.
Withanolides are a group of pharmacologically active compounds present in most prodigal amounts in roots and leaves of Withania somnifera (Indian ginseng), one of the most important medicinal plants of Indian systems of medicine. Withanolides are basically steroidal lactones (highly oxygenated C-28 phytochemicals) and similar to ginsenosides activity. Some of the withanolides that have been reported possess immunomodulatory, and anticancer activities. In the present investigation, a quantitative structure activity relationship (QSAR) model based on forward stepwise multiple linear regression (MLR) has been developed against the MCF7, MCF7/BUS, and SK-Br-3 human solid tumor breast cancer cell lines. Relationship correlation coefficient (r2) and cross...
Tipo: Poster
Palavras-chave: Cancer; Chemistry; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6617/version/1

Quadruple context-free L-System mathematical tools as origin of biological evolution
Provedor de dados: 17
Autores: Arunava Goswami; Pabitra Pal Choudhury; Rajneesh Singh; Sk. Sarif Hassan.
It is well known that A, T, G, C annealed together early in evolution and the long stretch of DNA was found which ultimately resulted into chromosomes of different organisms.  But it is unclear till date how exons, introns, conserved protein domains was formed. Using the DNA sequences of the largest known gene-family present in human genome, i.e., olfactory receptors and simplest possible quadruple context-free L-Systems, we show that conserved protein domains and intergenic regions which lies at the heart of the biological evolution started with a sixteen base-pairs stretch of DNA.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4851/version/1

Quality decay and shelf-life study of fresh celery (Apium graveolens L.) grown under different nitrogen fertilization
Provedor de dados: 17
Autores: Valeria Rizzo; Giuseppe  Muratore; Marco Antonio Russo; Riccardo Iacona; Adalgisa Belligno.
Nitrogen fertilization is useful and widespread to obtain higher growth and quality of productions. To evaluate the influence of nitrogen-rich fertilizers on the quality characteristics, shelf-life tests of celery grown with two levels (80-120 kg ha-1) of two different nitrogen fertilizers were performed. Celery plants were selected and packed in two plastic films (anti-fog polyolefin and micro-perforated polypropylene). Nitrate contents, weight loss, hardness, changes in colour parameters and total phenols, were studied in both packaging solutions during storage. Results showed that celery fertilized with organic nitrogen and packed in anti-fog polyolefin reached a shelf-life of 37 days. Not treated sample packed in micro-perforated polypropylene was not...
Tipo: Manuscript
Palavras-chave: Biotechnology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4180/version/1

Quantification of Cell Movement Reveals Distinct Edge Motility Types During Cell Spreading
Provedor de dados: 17
Autores: Benjamin J. Dubin-Thaler; Jake M. Hofman; Harry V. Xenias; Ingrid A. Spielman; Anna H. Shneidman; Lawrence David; Hans-Guenther Dobereiner; Chris Wiggins; Michael  P. Sheetz.
Actin-based motility is central to cellular processes such as migration, bacterial engulfment, and cancer metastasis, and requires precise spatial and temporal regulation of the cytoskeleton. We studied one such process, fibroblast spreading, which involves three temporal phases: early, middle, and late spreading, distinguished by differences in cell area growth. In these studies, aided by improved algorithms for analyzing edge movement, we observed that each phase was dominated by a single, kinematically and biochemically distinct cytoskeletal organization, or motility type. Specifically, early spreading was dominated by periodic blebbing; continuous protrusion occurred predominantly during middle spreading; and periodic contractions were prevalent in...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/391/version/1

Quantification of growth hormone in serum by isotope dilution mass spectrometry
Provedor de dados: 17
Autores: Cristian Arsene; Andr&amp;#xe9;  Henrion; Nina Diekmann; Jenny Manolopoulou; Martin Bidlingmaier.
Inter-assay variation of antibody based routine tests is hampering comparability of measurement results for growth hormone (GH) between different laboratories and decision making in clinical practice. Here it is demonstrated, that quantification of GH by isotope dilution mass spectrometry (IDMS) constitutes a way to precise and reliable results which can be referred to in evaluation of  performance of commercial test kits. With the IDMS method developed, tryptic cleavage products YSFLQNPQTSLCFSESIPTPSNR (T6) and LEDGSPR (T12) of GH are quantified by LC/MS-MS using the isotopically labeled forms of the peptides as internal standards. The GH cleavage fragments are obtained by whole-serum tryptic proteolysis and then extracted from the resulting mixture by...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/4050/version/1

Quantification of miRNAs and Their Networks in the light of Integral Value Transformations
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; Arunava  Goswami; Vrushali Fangal.
MicroRNAs (miRNAs) which are on average only 21-25 nucleotides long are key post-transcriptional regulators of gene expression in metazoans and plants. A proper quantitative understanding of miRNAs is required to comprehend their structures, functions, evolutions etc. In this paper, the nucleotide strings of miRNAs of three organisms namely Homo sapiens (hsa), Macaca mulatta (mml) and Pan troglodytes (ptr) have been quantified and classified based on some characterizing features. A network has been built up among the miRNAs for these three organisms through a class of discrete transformations namely Integral Value Transformations (IVTs), proposed by Sk. S. Hassan et al [1, 2].  Through this study we have been able to nullify or justify one given nucleotide...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6035/version/1

Quantification of miRNAs and Their Networks in the light of Integral Value Transformations
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; Arunava  Goswami; Navonil De Sarkar; Vrushali Fangal.
MicroRNAs (miRNAs) which are on average only 21-25 nucleotides long are key post-transcriptional regulators of gene expression in metazoans and plants. A proper quantitative understanding of miRNAs is required to comprehend their structures, functions, evolutions etc. In this paper, the nucleotide strings of miRNAs of three organisms namely Homo sapiens (hsa), Macaca mulatta (mml) and Pan troglodytes (ptr) have been quantified and classified based on some characterizing features. A network has been built up among the miRNAs for these three organisms through a class of discrete transformations namely Integral Value Transformations (IVTs), proposed by Sk. S. Hassan et al [1, 2].  Through this study we have been able to nullify or justify one given nucleotide...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6035/version/2

Quantitation of 55 Common Human Plasma Proteins in Healthy Young Adults and Correlation with Body Mass Index and Dietary Patterns
Provedor de dados: 17
Autores: Bibiana  Garcia-Bailo; Darren Brenner; Daiva Nielsen; Hyeon-Joo Lee; Christoph Borchers; Alaa  Badawi; Mohamed Karmali; Ahmed El-Sohemy.
Plasma biomarkers are a useful tool for monitoring dietary exposures and the development of chronic disease. Measuring multiple biomarkers at once provides a more complete characterization of phenotype than measuring single markers. Certain dietary patterns have been associated with increased risk of obesity. Adhering to a &amp;#x2018;Western&amp;#x2019; dietary pattern, characterized by high consumption of meat products and low fruit and vegetable consumption, may put individuals at a higher risk of becoming overweight or obese than a &amp;#x2018;Prudent&amp;#x2019; or an &amp;#x2018;Eastern&amp;#x2019; dietary pattern. A novel mass spectrometry-based multiple reaction monitoring (MRM) proteomics assay was used to quantitate 55 common plasma proteins that...
Tipo: Presentation
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5322/version/1

Quantitative detection of cereal geminiviruses
Provedor de dados: 17
Autores: Nadine Drechsler; Antje  Habeku&amp;#xdf;; Thomas Thieme; J&amp;#xf6;rg Schubert.
The Geminiviruses _Wheat dwarf virus_ (WDV) and _Barley dwarf virus_ (BDV) cause symptoms such as dwarfing, stunting and yellowing in infected cereals and can lead to reduced yield and even death of the plant. Both viruses are transmitted by the leafhopper _Psammotettix alienus_ Dahlb. in a persistent  non propagative manner. WDV is reported in Germany since the early 1990s. In the future an increase of infections is predicted due to global warming which leads to prolonged active periods of the vector in autumn. Furthermore infected plants can hibernate and serve as source of infection in spring.   &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;For the first time quantitative PCR assays were developed which allow the sensitive detection and quantification of WDV and...
Tipo: Presentation
Palavras-chave: Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5735/version/1

Quantitative detection of _Potato virus Y_ in potato plants and aphids - Discussion of diverse applications in potato research
Provedor de dados: 17
Autores: Anja H&amp;#xfc;hnlein; J&amp;#xf6;rg Schubert; Thomas Thieme; Edgar Schliephake.
Every year potato growers worldwide complain about severe yield losses caused by _Potato virus Y_ (PVY). Therefore, PVY along with _Potato leafroll virus_ belongs to the most important potato viruses. There are three main strains of PVY: PVY^O^, PVY^N^ and PVY^C^. However, also recombinant forms exist such as PVY^N^Wilga and PVY^NTN^, both of which increase in importance due to their potential to displace the non-recombinant strains at a high percentage. They appear also in mixed infections. In recent years PCR and qPCR assays were developed to differentiate PVY isolates. In order to identify PVY isolates by PCR often large amplicons have to be generated which requires the input of expensive enzymes. On the other hand, qPCR assays until now do not allow...
Tipo: Presentation
Palavras-chave: Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5734/version/1

Quantitative Models for Efficient Cloning of Different Vectors with Various Clone sites
Provedor de dados: 17
Autores: Gang Zhang; Anurag Tandon.
We developed an efficient &amp;#x22;Combinatorial Strategy&amp;#x201d; for cloning different vectors with various clone sites. 1) Using originally existed clone sites from circular vectors to prepare the inserts, and if no appropriate sites are available, performing SDM to create compatible sites, to achieve maximal correct digestion of the inserts. 2) Different vectors were digested with various restriction endonucleases, and then dephosphorylated with CIP. 3) Top10 competent cells were used for transformation to increase the transformant colonies. Our results showed that, when blunt sites, or a Xba I site was adopted for ligation, the percentages of positive clones were about 50%. Whereas, when different sites, including one blunt and another Pst I...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Immunology; Microbiology; Molecular Cell Biology; Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/6965/version/1

Quantitative MRI and MR Spectroscopy of Multiple Sclerosis, Alzheimer&amp;#x2019;s Disease, Epilepsy and Cancer Microimaging Techniques
Provedor de dados: 17
Autores: Rakesh Sharma.
Clinical MRI and MRS have promise in molecular imaging. Microimaging techniques offer a promising research tool to get noninvasive data in monitoring the effect of drugs.
Tipo: Presentation
Palavras-chave: Biotechnology; Cancer; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3485/version/1

Quantitative Preparative Native Continuous Polyacrylamide Gel Electrophoresis (QPNC-PAGE)
Provedor de dados: 17
Autores: Bernd Kastenholz.
QPNC-PAGE, or quantitative preparative native continuous polyacrylamide gel electrophoresis, is a high-resolution technique applied in biochemistry and bioinorganic chemistry to separate proteins by isoelectric point. This variant of gel electrophoresis is used by biologists to isolate active or native metalloproteins in biological samples and to resolve properly and improperly folded metal cofactor-containing proteins in complex protein mixtures.
Tipo: Poster
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1782/version/1

Quantization makes relativity compatible with superluminal phenomena
Provedor de dados: 17
Autores: Qi-Ren Zhang.
News shocked the physicist society that neutrinos may move faster than light. Most physicists affirm that this is impossible, according to the well-established relativity. Some try to find a new theory other than relativity to explain the phenomena. In the following we show it may be explained within relativity, if the quantum theory is also taken into account.
Tipo: Manuscript
Palavras-chave: Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/6887/version/1

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species
Provedor de dados: 17
Autores: I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn &amp;#x2013;algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata.  Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7083/version/2

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species
Provedor de dados: 17
Autores: I. C. Baianu.
Previous theoretical or general approaches to the problems of Quantum Genetics and Molecular Evolution are considered in this article from the point of view of Quantum Automata Theory first published by the author in 1971 and further developed in several recent articles. The representation of genomes and Interactome networks in categories of many-valued logic LMn &amp;#x2013;algebras that are naturally transformed during biological evolution, or evolve through interactions with the environment provide a new insight into the mechanisms of molecular evolution, as well as organismal evolution, in terms of sequences of quantum automata.  Phenotypic changes are expressed only when certain environmentally-induced quantum-molecular changes are coupled with an...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Developmental Biology; Ecology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Evolutionary Biology; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7083/version/1

Quantum probabilities in competing lizard communities
Provedor de dados: 17
Autores: Diederik Aerts; Marek Czachor; Bart D&amp;#x27;Hooghe; Maciej Kuna; Barry Sinervo; Sandro Sozzo.
Despite predictive success, population dynamics and evolutionary game theory still pose fundamental problems. Violation of the competitive exclusion principle in plankton communities provides an example. A promising solution of this &amp;#x2018;paradox of the plankton&amp;#x2019; comes from theories involving cyclic competition, an evolutionary analogue of the classical rock-paper-scissors (RPS) game. However, modeling probabilistic RPS structures, one encounters a fundamental difficulty: the pairs rock-scissors, scissors-paper, and paper-rock possess representations in separate Kolmogorovian probability spaces, but a single global probability space for entire triplets does not exist. Populations that take part in cyclic competition should therefore...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6954/version/1

Quantum stochasticity and neuronal computations
Provedor de dados: 17
Autores: Peter Jedlicka.
The nervous system probably cannot display macroscopic quantum (i.e. classically impossible) behaviours such as quantum entanglement, superposition or tunnelling (Koch and Hepp, Nature 440:611, 2006). However, in contrast to this quantum &amp;#x2018;mysticism&amp;#x2019; there is an alternative way in which quantum events might influence the brain activity. The nervous system is a nonlinear system with many feedback loops at every level of its structural hierarchy. A conventional wisdom is that in macroscopic objects the quantum fluctuations are self-averaging and thus not important. Nevertheless this intuition might be misleading in the case of nonlinear complex systems. Because of a high sensitivity to initial conditions, in chaotic systems the...
Tipo: Presentation
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3702/version/1