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1. MIRIAM Identifiers and Resources / 2. Existing Identifier Schemes Nature Precedings
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.
(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
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*100 Semi-supercentenarians and older as a proposed sample set for the Archon Genomics X PRIZE Validation Protocol* Nature Precedings
Thomas Perls; Nir Barzilai.
The "Archon Genomics X PRIZE Validation Protocol":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 >=105 years as the source of DNAs for the competition.

Tipo: Manuscript Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Data Standards.
Ano: 2011 URL: http://precedings.nature.com/documents/5756/version/1
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11-amino-5-N-methyl-7-fluorine- quindoline derivatives: The Potential Anti-angiogenic Agents Targeting G-quadruplex Structure in Vascular Endothelial Cell Growth Factor Nature Precedings
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's promoter and the...
Tipo: Manuscript Palavras-chave: Cancer.
Ano: 2008 URL: http://precedings.nature.com/documents/1946/version/1
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11[beta]-hydroxysteroid dehydrogenase-type 2 evolved from an ancestral 17[beta]-hydroxysteroid dehydrogenase-type 2 Nature Precedings
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...
Tipo: Manuscript Palavras-chave: Cancer; Developmental Biology; Pharmacology; Bioinformatics; Evolutionary Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/4649/version/1
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12x coverage 454/Sanger Hybrid Assembly of Cucumber (Cucumis sativus L. cv.Borszczagovski) genome - the most efficient way to begin post genomic era Nature Precedings
Rafał Wóycicki; Justyna Witkowicz; Magdalena Pawełkowicz; Ewa Siedlecka; Wojciech Gutman; Wojciech Pląder; Anna Seroczyńska; Mieczysław Śmiech; Katarzyna Niemirowicz-Szczytt; Stanisław Karpiński; 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. 
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 15’196 contigs of 197 Mbp length and N50 27’086 bp and 4’157 scaffolds of 224 Mbp length...
Tipo: Poster Palavras-chave: Biotechnology; Genetics & Genomics; Bioinformatics; Plant Biology.
Ano: 2010 URL: http://precedings.nature.com/documents/5466/version/1
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14-3-3ζ is Amplified, Overexpressed and Possesses Oncogenic Activities in Head and Neck Squamous Cell Carcinoma Nature Precedings
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
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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 Nature Precedings
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
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17 years of integrated research, monitoring, and management of HWA and hemlock ecosystems at Delaware Water Gap National Recreation Area Nature Precedings
Richard Evans.
Delaware Water Gap National Recreation Area (“the park”) 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 “Outstanding Natural Features” having “high intrinsic or unique values.” 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
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1st INCF Workshop on Genetic Animal Models for Brain Diseases Nature Precedings
Olaf Riess; Holm Graessner.
The INCF Secretariat organized a workshop to focus on the “role of neuroinformatics in the processes of building, evaluating, and using genetic animal models for brain diseases” in Stockholm, December 13–14, 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
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1st INCF Workshop on Global Portal Services for Neuroscience Nature Precedings
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
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1st INCF Workshop on Needs for Training in Neuroinformatics Nature Precedings
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
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1st INCF Workshop on Neuroanatomical Nomenclature and Taxonomy Nature Precedings
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
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1st INCF Workshop on NeuroImaging Database Integration Nature Precedings
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
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1st INCF Workshop on Sustainability of Neuroscience Databases Nature Precedings
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
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2011 German Escherichia coli O104:H4 outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles Nature Precedings
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 & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6109/version/2
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2011 German Escherichia coli outbreak: Alignment-free whole-genome phylogeny by feature frequency profiles Nature Precedings
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 & Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2011 URL: http://precedings.nature.com/documents/6109/version/1
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2011 German Escherichia coli outbreak: Prophage analysis of close-assembled TY2482 against 55989 using PHAST Nature Precedings
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 & Genomics; Microbiology; Bioinformatics.
Ano: 2011 URL: http://precedings.nature.com/documents/6110/version/1
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21 Tesla Micro-MRI of Rat Skin Nature Precedings
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. 

*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
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21 Tesla MRI Microimaging of Rat Heart by Superparamagnetic Antimyoglobin Bound Nanoparticles Nature Precedings
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
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21 Tesla MRI Microimaging of Rat Heart by Superparamagnetic Antimyoglobin Bound Nanoparticles Nature Precedings
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
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