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Yeast Features: Identifying Significant Features Shared Among Yeast Proteins for Functional Genomics
Provedor de dados: 17
Autores: Michel Dumontier; James R. Green; Ashkan Golshani; Myron L. Smith; Nadereh  Mir-Rashed; Md  Alamgir; Veronika  Eroukova; Frank Dehne; James  J. Cheetham.
Background&amp;#xd;&amp;#xa;High throughput yeast functional genomics experiments are revealing associations among tens to hundreds of genes using numerous experimental conditions. To fully understand how the identified genes might be involved in the observed system, it is essential to consider the widest range of biological annotation possible. Biologists often start their search by collating the annotation provided for each protein within databases such as the Saccharomyces Genome Database, manually comparing them for similar features, and empirically assessing their significance. Such tasks can be automated, and more precise calculations of the significance can be determined using established probability measures....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2311/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

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

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

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

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

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

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

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

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

Using the Gene Ontology to Annotate Biomedical Journal Articles
Provedor de dados: 17
Autores: Michael Bada; Lawrence Hunter.
We are creating a gold-standard corpus of manually annotated full-text biomedical journal articles toward natural-language-processing applications.  Central to this is our use of entire ontologies of the Open Biomedical Ontologies initiative as well as other terminologies as term sources, in contrast to most other such annotation projects, which have used small, ad hoc schemas.  In addition to the standard difficulties in such annotation projects, each of the terminologies we have used has idiosyncrasies and ambiguities that present further challenges to consistent, high-quality annotation of these articles.  In this paper we present and discuss the most salient of these with regard to the Gene Ontology that we have encountered and addressed in our...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3556/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

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

Varicella notification in immigrants: a brief report from Ferrara, Italy
Provedor de dados: 17
Autores: Alessandro Cucchi; Silvia Atti; Mauro Bergamini.
Background and Aim of the work - We conducted a survey of varicella cases&amp;#x27; notifications in the immigrant population in the province of Ferrara, Italy.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Materials and Methods &amp;#x2013; We collected notifications of infectious disease between 2002 and 2006. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results and discussion - At the end of 2006, the 4.5% (14252 subjects) of total population of the province of Ferrara and its province was represented of immigrants from foreign countries. In this context, between 2002 and 2006, a total of 1969 cases of varicella, including 3.1% related to migrants, were reported. Among immigrants, there were 36 cases in males, and 26 in females. The cases were notified in the 64.5% by the...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/3361/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

The Heterochromatin Protein 1 positively regulates euchromatic gene expression by RNA binding
Provedor de dados: 17
Autores: Piacentini Lucia; Laura Fanti; Rodolfo Negri; Valerio Del Vescovo; Alessandro Fatica; Sergio Pimpinelli.
HP1 is a well known conserved protein involved in heterochromatin formation and gene silencing in different species including humans1-4. A general model has been proposed for heterochromatin formation and epigenetic gene silencing in different species that implies an essential role for HP1. According to the model, histone methyltransferase enzymes (HMTases) methylate the histone H3 at lysine 9 (H3-MeK9), creating selective binding sites for itself and the chromodomain of HP15. This complex is thought to form a higher order chromatin state that represses gene activity. It has also been found that HP1 plays a role in telomere capping6. Surprisingly, recent data have suggested an association of HP1 in gene activity7-10 but the nature of this interaction is...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2687/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

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

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

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

Vestibular effects on cerebral blood flow
Provedor de dados: 17
Autores: Jorge Serrador; F. Owen Black; Todd Schlegel; Scott Wood.
Humans demonstrate a number of unique adaptations that allow the maintenance of blood pressure and brain blood flow after transition to the upright position. While these adaptations maintain heart-level mean arterial pressure similar to supine values, the brain remains ~30 cm above the heart, resulting in a ~25% decrease in perfusion pressure. To maintain brain blood flow, the cerebral vessels must dilate in response to this change in position. While several physiological systems are involved in adaptation to the upright posture, including cerebral autoregulation, the unique role that the vestibular system plays in helping to maintain brain blood flow is just beginning to be elucidated. Since the vestibular system not only assists in balance control and...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2413/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

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

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

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

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

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

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

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

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

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

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

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

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

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

Visualization of the Phosphoproteomic Data from AfCS with the Google Motion Chart Gadget
Provedor de dados: 17
Autores: Huilei Xu; Avi Ma&amp;#x27;ayan.
Results from multivariate molecular biological experiments become increasingly complex. Hence, the challenge of projecting high-dimensional data onto few dimensions for effective data visualization is becoming increasingly important in Systems Biology. Effective data visualization can summarize the activity of many variables over time as well as display relationships between variables. Dynamic interactive visualization tools can provide scientists with ways of visually identifying relationship and patterns, and improve communication of results on the web and in presentations. For this, interactive systems with animation have great potential since they add dimensions to static images limited to two dimensions. Interactivity and animation is particularly...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3074/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

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

Towards realising Darwin&amp;#x2019;s dream: setting the trees free
Provedor de dados: 17
Autores: Roderic Page.
The fact that all living organisms are related by common descent is one of the central principles of modern biology.  Since the early 1990&amp;#x27;s the amount of data available to evolutionary biologists has exploded, and Elsevier&amp;#x2019;s journal _Molecular Phylogenetics and Evolution_, has become the largest single publisher of evolutionary trees (phylogenies). These trees and their supporting data potentially form a tremendous resource for biologists, with applications in genomics, evolutionary biology, biodiversity, and public health. However, most published trees are not available in any public database, but instead languish as images, &amp;#x22;locked up&amp;#x22; in the pages of journals. A long term solution to this problem is to invert the...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2217/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

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

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

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

Translating Environmental Science into Policy and Action
Provedor de dados: 17
Autores: Lee M. Talbot.
Background/Question/Methods:  Many ecologists are skilled at identifying environmental problems and defining solutions, but not at achieving concrete action to implement those insights.  The question, then, is how to help ecologists translate environmental science into policy and action.  Most ecologists&amp;#x27; education and training do not prepare them to be effective in the policy arena, much less in ways to achieve action.  Ecologists find disincentives in the form of the academic attitude that somehow the application of science is inferior to so-called &amp;#x22;pure science.&amp;#x22;  This ivory tower holdover has been largely discredited in the context of environmental issues, and the discipline of conservation biology exists explicitly to foster...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3606/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

The Teleost Taxonomy Ontology
Provedor de dados: 17
Autores: Peter E. Midford; James P. Balhoff; Wasila Dahdul; Cartik R. Kothari; Hilmar Lapp; John Lundberg; Paula Mabee; Todd J. Vision; Monte Westerfield.
The Teleost Taxonomy Ontology (TTO) is an ontology of taxonomic groups and associated names for fish (not just teleosts). This ontology has served as a source of names and taxonomic structure within the Phenoscape project since early 2008. Although the TTO is based on Eschmeyer&amp;#x27;s Catalog of Fishes (CoF) and incorporates all valid species and genus names, it is also extended by the curation needs of the Phenoscape project. Names of fossil taxa not included in the CoF as well as references to specimens identi&amp;#xc;ed only to genus (e.g., _Eigenmannia sp._ (Fink and Fink 1981)) are incorporated into the TTO as required by the curation needs of the Phenoscape project. As Phenoscape receives updates to the CoF, a tool called TTOUpdate merges the...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4629/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

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

Sensitivity Analysis of Self-Identified Race and Ethnicity (SIRE): Screening for Single Nucleotide Polymorphisms.
Provedor de dados: 17
Autores: Toni P. Miles; Stephen Hanson; LaCreis Kidd; Avonne Connor; Saeed A. Jortani.
Within the realm of medical care, Self-Identified Race and Ethnicity (SIRE) categories are promoted as an inexpensive tool to identify underlying genotypic diversity. Scientific opinion is divided about the adequacy of SIRE to serve this function. If genetic diversity can guide medical decisions, it is important to know the effectiveness of genetic screening via SIRE. Proper development of self-reported measures such as SIRE requires sensitivity and specificity studies. These types of formal evaluation are largely absent for SIRE. To begin this formal process, we estimate the sensitivity of SIRE in screening for variant Single Nucleotide Polymorphism (SNP). Our results indicate that the current use of SIRE is inadequate to screen for selected...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/1524/version/1

The activating receptors 2B4 and NTB-A, but not CRACC are subject to ligand-induced down-regulation on human natural killer cells
Provedor de dados: 17
Autores: Stephan Meinke; Carolin B&amp;#xf6;hm; Sibel Durlanik; Carsten Watzl.
Activation of natural killer cells can be mediated by different receptors. Stimulation of the receptors 2B4, NTB-A and CRACC, members of the SLAM-related receptor family, induces cytotoxicity and cytokine production. The surface expression of 2B4 and other activating natural killer cell receptors is down-modulated after receptor engagement, which results in a weaker response to consecutive stimulation. We tested whether this regulatory mechanism applies to all SLAM-related receptors expressed by primary human natural killer cells. After co-culture with target cells expressing the respective ligands different effects on receptor surface expression were observed. While 2B4 ex-pression was strongly reduced, NTB-A showed less prominent down-modulation and the...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4917/version/1

The transmission dynamics of syphilis and the CDC&amp;#x2019;s elimination plan
Provedor de dados: 17
Autores: Romulus Breban; Virginie Supervie; Justin Okano; Raffaele Vardavas; Sally Blower.
The Centers for Disease Control (CDC) is currently attempting to eliminate syphilis in the United States (US); to ensure that their control strategies will be effective it is important to understand the transmission dynamics of syphilis. Epidemics of certain infectious diseases (e.g., influenza) can rise and fall with a well-defined periodicity; this cycling behavior is important because it can have significant implications for the design and effectiveness of control strategies. Here we discuss the methodology that has been used to identify epidemic cycles in longitudinal data sets, and the endogenous and exogenous mechanisms that generate cycling. We then examine the recently proposed hypothesis that syphilis epidemics cycle. This hypothesis was proposed...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/1373/version/1

Reply to &amp;#x201c;Limusaurus and bird digit identity&amp;#x201d;
Provedor de dados: 17
Autores: Xing Xu; James Clark; Jonah  Choiniere; David Hone; Corwin Sullivan.
Vargas et al. agree with us that a lateral shift in theropod dinosaur digits occurred prior to the origin of birds, but contend that it occurred as a single &amp;#x201c;frameshift&amp;#x201d; with little outward change to the three main digits involved^1^.  We consider the digital morphology of Limusaurus, other ceratosaurs, and non-avian tetanurans to provide evidence that the shift was stepwise, and that a stepwise shift better explains theropod manual morphology than a hidden frameshift.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6375/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

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

The association between having a household member with a cancer-related limitation and human papillomavirus vaccine uptake
Provedor de dados: 17
Autores: Tabatha N. Offutt-Powell; Rohit P. Ojha; Joseph Tota; Karan P. Singh.
OBJECTIVE: To evaluate the association between having a household member with a cancer-related limitation (physical, mental, or emotional) and human papillomavirus (HPV) vaccine uptake among females aged 9 &amp;#x2013; 17 years. &amp;#xd;&amp;#xa;METHODS: We analyzed 2008 National Health Interview Survey for our cross-sectional analysis. All households with females aged 9 &amp;#x2013; 17 years were eligible for inclusion in our analysis. Our outcomes of interest included HPV vaccine initiation (&amp;#x2265;1 dose) and series completion (full 3 doses). A dichotomous variable indicating a cancer-related limitation for a household member was created if at least one adult in the household responded to having a limitation caused by cancer. We used...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4925/version/1

The Earliest Perfect Flower
Provedor de dados: 17
Autores: Xin Wang; Shaolin Zheng.
Despite of angiosperms in the Yixian Formation (&amp;#x3e;125 Ma, early Cretaceous), there is no perfect flower typical of angiosperms to date. Here we report _Euanthus dilaensis_ gen. et sp. nov as the earliest perfect flower known to date. The flower includes tepals, androecium and gynoecium. The anthers are globose in form, with bristles atop and in situ round-triangular pollen grains. The gynoecium is composed of probably two carpels with plumose stigmas and a carpel-enclosing receptacle. The discovery of _Euanthus_ increases the diversity of early angiosperms, and indicates that perfect flowers occurred as early as 125 Ma ago.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1320/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

Why do many animals move with a predominance of roughly forward directions?
Provedor de dados: 17
Autores: Kevin Duffy.
Animal movements can influence their ecology and demographics. Animal movements are often characterized by path structures with directional persistence. The extent to which directional persistence improves forage success is investigated in this paper using theoretical simulations. It is shown that a movement strategy with directional persistence enables simulated animals to find more forage as compared to a random movement strategy. Situations where resources are chosen with certainty (optimally) are even more successful. Choosing resource with certainty cannot result in directional persistence. However, in cases where animals choose with certainty adjacent cells with resource but continue in their existing direction if none of these have resources then...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/5156/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

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

Systems Biology Graphical Notation:  Process Description language Level 1
Provedor de dados: 17
Autores: Stuart L. Moodie; Nicolas  Le Novere; Emek Demir; Huaiyu  Mi; Falk  Schreiber.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialized notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/3721/version/3

Suggested actions from the Melbourne HVP Information Seminar
Provedor de dados: 17
Autores: Richard Cotton; Myles Axton; Agnes Bankier; Bernard Brais; Lawrence Cavedon; Desir&amp;#xe9;e du Sart; Peter George; David Goldgar; Terence Harrison; Marienne Hibbert; John Hopper; Finlay Macrae; Christine M. O&amp;#x2019;Keefe; David Ravine; Ravi Savarirayan; Les Sheffield; Tim Smith; Nicola Stokes; Vijaya Sundararajan; David Thorburn; Ingrid Winship.
The Human Variome Project (HVP; www.humanvariomeproject.org) was initiated at a meeting in June 2006 and addressed the problems of collecting genetic information and generated 96 recommendations (http://www.nature.com/ng/journal/v39/n4/full/ng0407-423.html) to overcome these, with the focus on Mendelian disease. A considerable number of projects have been added, to those that have been ongoing for a number of years, since that meeting. Also, a planning meeting is to be held May 25-29, 2008 in Spain (http://www.humanvariomeproject.org/HVP2008/).&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A dramatic boost has been given to the HVP by the preparedness and action of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT; www.insight-group.org), to,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1784/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

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

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

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

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

Targeting Human Dendritic Cells with Lewis X Modified Liposomes
Provedor de dados: 17
Autores: Lucie Kalvodova; Yongmin Zhang.
In this short report, we demonstrate that liposomes bearing the Lewis X trisaccharide on the surface (&amp;#x201c;Awesosomes&amp;#x201d;) efficiently target human dendritic cells. We chose a glycolipid with Lewis X trisaccharide headgroup to facilitate the targeted liposome uptake via the DC-SIGN internalization pathway. While no uptake of Awesosomes was detected with wild-type human HEK293 cells, HEK293 cells transfected with human DC-SIGN internalized Awesosomes extensively. In samples of human blood-derived leukocytes, the extent of uptake of Awesosomes correlated with the expression of DC-SIGN, which is a dendritic cells marker. There was a marked difference in the uptake of Awesosomes and plain liposomes by DC-SIGN expressing dendritic cells. There...
Tipo: Manuscript
Palavras-chave: Immunology; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4764/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

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

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

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

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

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

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

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

Screening Lactic Acid Bacteria for Antimicrobial Compound Production
Provedor de dados: 17
Autores: Khalisanni Khalid; Lee  Hung Kiong.
Lactic Acid Bacteria was known as potential probiotic used in food industries and dairy products and probable to produce antimicrobial compound that inhibit variety of microorganisms. The objectives of the research are to determine the optimum condition and glucose utilization in relation to antimicrobial compound production. Two species of Lactic Acid Bacteria namely Lactococcus and Lactobacillus were used as probiotic. The Lactic Acid Bacteria were fermentated in different medium, initial substrate pH and incubation temperature for the production of antimicrobial compound. The test organisms such as E.coli and Salmonella were selected as test organisms. Amongst the two species of Lactic Acid Bacteria, Lactococcus produced the highest amount of...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3326/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

Self-organization of intrinsically disordered proteins with folded N-termini
Provedor de dados: 17
Autores: Philip C. Simister; Fred Schaper; Nicola O&amp;#x27;Reilly; Simon McGowan; Stephan M. Feller.
Thousands of human proteins lack recognizable tertiary structure in most of their chains. Here we hypothesize that some use their structured N-terminal domains (SNTDs) to organise the remaining protein chain via intramolecular interactions, generating partially structured proteins. This model has several attractive features: as protein chains emerge, SNTDs form spontaneously and serve as nucleation points, creating more compact shapes. This reduces the risk of protein degradation or aggregation. Moreover, an interspersed pattern of SNTD-docked regions and free loops can coordinate assembly of sub-complexes in defined loop-sections and enables novel regulatory mechanisms, for example through posttranslational modifications of docked regions.
Tipo: Manuscript
Palavras-chave: Cancer; Immunology; Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5124/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

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

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

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

The model of proteolysis
Provedor de dados: 17
Autores: Piotr Dittwald; Anna Gambin.
This document presents the original approach for estimating parameters of proteolysis process. Data used to fit the model are taken from mass&amp;#xd;&amp;#xa;spectrometric experiments. For parameters estimation the Levenberg-Marquadt algorithm is used. The motivation for model is a hypothesis&amp;#xd;&amp;#xa;that discrimination between cancer patients and healthy donors can be based on activity of peptide cleaving enzymes (i.e. peptidases).
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4400/version/1

RAB family gene expression in breast cancer cells under influence of paclitaxel
Provedor de dados: 17
Autores: Jolanta Rzymowska; Tadeusz Malewski; Piotr Maj; Andrzej Wilkolaski.
The aim of this study was to investigate the role of paclitaxel on RAB family of genes in primary breast cancer cell lines. The cancer breast cells obtained from 40 women during mastectomy were used to address this issue. The group included patients with intraductal breast cancer - lesions in I or II advancement level by TNM classification and G1-G2 by Bloom classification. (tumor dimensions up to 2.0 cm without metastases to lymph nodes). Cytostatic drugs before surgery were not administered to these patients. The cultures were conducted in 25 cm^2^ plastic containers at RPMI medium with addiction of 10% fetal bovine serum (FBS) at the standard conditions. After reaching concentration levels of 10 000/ml of the cells, the cultures were treated with 60...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6227/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

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

Words make people think, ... but pictures make people feel: The effect negative vs. positive images on charitable behavior
Provedor de dados: 17
Autores: Carolina  Perez Due&amp;#xf1;as; Maria Fernanda Rivas; Olusegun A. Oyediran; Alberto Acosta; Pablo Bra&amp;#xf1;as Garza.
We ran an experiment where the subjects initially played a four-round dictator game, after which each subject was shown either a set of positive images or a set of negative images. Finally the subjects played another four-round dictator game.&amp;#xd;&amp;#xa;The effect of the sign of images shown is clear on the players&amp;#x2019; behaviors: positive images have moderate effects on charitable behavior while negative images dramatically increase charity.&amp;#xd;&amp;#xa;We could therefore infer from our experimental results that showing negative images of the Haitian and Chilean catastrophes to the international public would have significant positive impacts on international donations to the victims and the rebuilding programs in both countries.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4287/version/1

Temporal trends in groundwater levels from Saskatchewan, Canada
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Groundwater resources play a key role in supplying water for domestic, industrial, agricultural, and ecological functions on the Canadian prairies. The current study investigates potential temporal trends in groundwater levels for the Canadian province of Saskatchewan over the past several decades. Overall, the large majority of areally distributed stations throughout Saskatchewan with increasing groundwater level time trends suggests that this hydrogeological resource is growing in quantity and is not under current threat from depletion.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6696/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

Worm-like carbon shell chains produced from wood
Provedor de dados: 17
Autores: Kyoko Suzuki; Hidetoshi Kita; Yukie Saito; Tsutomu Suzuki; Kazuhisa Sato; Toyohiko Konno.
Large-scale utilization of wood which command absolute majority in biomass for functional carbon precursors contributes to reduce greenhouse effect. Wood char generally has a limit on material usage because of its non-graphitic structure^1^, so we developed a new functional wood char by iron-, or nickel-catalyzed carbonization, which has a graphite-like structure with mesopores good for electroconductivity and liquid phase adsorption capacity for macro molecules^2-5^. However the fine structure of the wood char is still not clear. Here we report more than 70 wt % of iron-catalyzed wood char is filled with chained carbon shells formed by 3~20 defective stacking layers of carbon hexagonal planes, which look like nanometer-sized worms swarm. We name them...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6519/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

Top-down and bottom-up informatics: who has the high ground?
Provedor de dados: 17
Autores: Vincent S. Smith; Dave Roberts.
Recent years have seen the emergence of several major initiatives supporting the development of biodiversity informatics infrastructures. In Europe examples include: EDIT &amp;#x2013; the European Distributed Institute of Taxonomy; LifeWatch &amp;#x2013; a biodiversity analytical platform integrating observatories, databases, processing and computational capacity; and SYNTHESYS &amp;#x2013; funding researcher access to a network of taxonomic collections, laboratories and libraries. These European projects alone represent a spend of approximately 35 Million Euros, with funding contingent on the collaboration of numerous geographically dispersed institutional partners. In this presentation we will review the major informatics products of these initiatives;...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4592/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

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

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

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

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

Transforming growth factor-beta 1 (tgf-&amp;#x3b2;1) induces angiogenesis through vascular endothelial growth factor (vegf)-mediated apoptosis
Provedor de dados: 17
Autores: Giovanni Ferrari; B D. Cook; Vitaly Terushkin; Giuseppe Pintucci; Paolo Mignatti.
VEGF and TGF-[beta]1 induce angiogenesis but have opposing effects on endothelial cells. VEGF protects endothelial cells from apoptosis; TGF-[beta]1 induces apoptosis. We have previously shown that VEGF / VEGF receptor-2 (flk-1) signaling mediates TGF-[beta]1 induction of apoptosis. This finding raised an important question: Does this mechanism stimulate or inhibit angiogenesis? Here we report that VEGF-mediated apoptosis is required for TGF-[beta]1 induction of angiogenesis. In vitro the apoptotic effect of TGF-[beta]1 on endothelial cells is rapid and followed by a long period in which the cells are refractory to apoptosis induction by TGF-[beta]1. Inhibition of VEGF / flk-1 signaling abrogates formation of vessel-like structures by TGF-[beta]1 with an...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2008
URL: http://precedings.nature.com/documents/1758/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

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

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

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

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

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

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

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

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

Virtual screening for NS5B inhibitors of Hepatitis C virus
Provedor de dados: 17
Autores: Amjesh  R; Achuthsankar  S. Nair; Sugunan V.S.
Hepatitis C Virus (HCV) infection is a serious cause of chronic liver disease worldwide with more than 170 million infected individuals at a risk of developing significant morbidity and mortality. To date there is no effective drug for the treatment or vaccine to prevent this infection. The present study aims to discover novel inhibitors which target an allosteric binding site of RNA dependent RNA polymerase enzyme of HCV. A structure based virtual screening of Zinc database by computational docking and the post docking analysis of energy calculations and interactions followed by ADMET studies were conducted. Our study revealed 10 compounds which has more potential than the existing inhibitor to be considered as lead compounds.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7055/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

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

The Brain in Business: The Case for Organisational Cognitive Neuroscience?
Provedor de dados: 17
Autores: Nick Lee; Michael J. R. Butler; Carl Senior.
The application of cognitive neuroscientific techniques to understanding social behaviour has resulted in many discoveries. Yet advocates of the &amp;#x2018;social cognitive neuroscience&amp;#x2019; approach maintain that it suffers from a number of limitations. The most notable of these is its distance from any form of real-world applicability. One solution to this limitation is &amp;#x2018;Organisational Cognitive Neuroscience&amp;#x2019; &amp;#x2013; the study of the cognitive neuroscience of human behaviour in, and in response to, organizations. Given that all of us will spend most of our lives in some sort of work related organisation, organisational cognitive neuroscience allows us to examine the cognitive underpinnings of social behaviour that...
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2159/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

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

Selective insectivory in _Nymphaea nouchali_ Burm. f.
Provedor de dados: 17
Autores: Pundarikakshudu Tetali; Shrikant Sutar; Sujata Tetali.
Carnivorous plants comprise roughly 0.24 percent of the flowering plants, or 640 species represented in 12 families. Yet they are regarded as _miracula naturae_. Over fifty percent of these taxa are represented in a single family, namely Lentibulariaceae. Carnivorous plants are generally insectivorous, and carnivory in flowering plants is generally found in taxa that are adapted to nutrient-deficient habitats. The extra nutrients such plants acquire by special ways serve merely as supplements. The origin and evolution of carnivorous plants is a mystery in the phylogenetic tree of angiosperms, they often appear without a clear linkage. Here, we report that _Nymphaea nouchali_ Burm. f. (a cultivar of var. cernua), a large aquatic member of the family...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1817/version/1

SED-ML Script Language
Provedor de dados: 17
Autores: Frank Bergmann.
The Simulation Experiment Description Markup Language (SED-ML) is a XML format describing simulation experiments, so that they can be easily exchanged independent of software tools that created them. This document describes the SED-ML Script, a Python based shorthand that makes it easy to create / edit SED-ML documents.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6105/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

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

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

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

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

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

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

The potential of Manitoba chokecherry as a source of high natural antioxidants
Provedor de dados: 17
Autores: Wende Li; Farah S. Hosseinian; Arnold W. Hydamaka; Lynda Lowry; Trust Beta.
Consumption of fruits and vegetables is shown to be beneficial for protecting health and preventing some chronic diseases such as cancer, cardiovascular disease, and stroke. The positive health effects have been mainly due to the contributions of their natural antioxidant capacity. Chokecherry (Prunus virginiana), a unique fruit, is a member of the Rose family and native to North America. Here we demonstrate that chokecherry fruit with strong antioxidant capacity is available in Manitoba, and that its potent antioxidant potential can be developed for health benefits in value-added applications.These findings are useful for developing novel value-added antioxidant products from chokecherry because of its phytochemical profile associated with health...
Tipo: Manuscript
Palavras-chave: Cancer; Chemistry; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1529/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

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

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

Trichoscopy criteria for diagnosing female androgenic alopecia.
Provedor de dados: 17
Autores: Adriana Rakowska; Monika Slowinska; Elzbieta Kowalska-Oledzka; Malgorzata Olszewska; Lidia Rudnicka.
Differential diagnosis of chronic hair loss remains a challenge in dermatology. The aim of the study was to evaluate the value of a new scalp visualization technique, trichoscopy, in differential diagnosis of hair loss. Trichoscopy was performed in 131 females (59 with androgenic alopecia, 33 with chronic telogen effluvium, 39 healthy controls). Based study results, a standardized trichoscopy report was developed and diagnostic criteria for female androgenic alopecia were established. Major criteria: increased number of yellow dots and thin hairs, as well as decreased average hair thickness in frontal area. Minor criteria: increased frontal area to occiput ratio of single-hair units (&amp;#x3e;2:1), vellus hairs (&amp;#x3e;1.5:1) and follicles with...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/1913/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

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

Second-Hand Stress: Neurobiological Evidence for a Human Alarm Pheromone
Provedor de dados: 17
Autores: Lilianne R. Mujica-Parodi; Helmut H. Strey; Blaise Frederick; Robert Savoy; David D. Cox; Yevgeny Botanov; Denis Tolkunov; Denis Rubin; Jochen Weber.
Alarm pheromones are airborne chemical signals, released by an individual into the environment, which transmit warning of danger to conspecifics via olfaction. Using fMRI, we provide the first neurobiological evidence for a human alarm pheromone. Individuals showed activation of the amygdala in response to sweat produced by others during emotional stress, with exercise sweat as a control; behavioral data suggest facilitated evaluation of ambiguous threat.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2561/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

Why Intelligent People Live Longer
Provedor de dados: 17
Autores: Robert Hauser; Alberto Palloni.
Numerous studies find a positive relationship between cognitive ability, IQ as measured in childhood or youth, and subsequent survival. Explanations range from the idea that low ability is an indicator of adverse systemic events in early life to the idea that high cognitive functioning is required continuously to maintain health and reduce threats to survival. The Wisconsin Longitudinal Study (WLS) has followed a large cohort of Wisconsin high school seniors from ages 18 to 69. As expected, in the WLS survival varies positively with adolescent IQ. However, rank in high school class accounts completely for the relationship between IQ and survival, and it has a much larger effect on survival. These findings suggest that cognitive functioning improves...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4340/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

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

The impact of Bt cotton on poor households in rural India
Provedor de dados: 17
Autores: Arjunan Subramanian; Matin Qaim.
The impact of genetically modified (GM) crops on the poor in developing countries is still the subject of controversy. While previous studies have examined direct productivity effects of _Bacillus thuringiensis_ (Bt) cotton and other GM crops, little is known about wider socioeconomic outcomes. We develop a microeconomic modeling approach and use comprehensive survey data from India to analyze welfare and distribution effects in a typical village economy. Bt cotton adoption increases aggregate employment with interesting gender implications. Likewise, aggregate household incomes rise, including for poor and vulnerable farmers, suggesting that Bt cotton contributes to poverty reduction and rural development.
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1812/version/1

The 2010 Scientific Strategic Plan of the Global HIV Vaccine Enterprise: A Roadmap for the Future
Provedor de dados: 17
Autores: Alan Bernstein; Peter Piot.
HIV/AIDS is arguably the most significant health challenge facing the world today. The 2008 numbers tell the story: 33.4 million were living with HIV, 2 million people died of AIDS and 2.7 million people were newly infected. Despite impressive scientific advances in developing over two dozen drugs to treat HIV infections, there is still no cure. In addition, only about one-third of those who need drugs have access to therapy.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In 2003, recognizing the enormity of the scientific and humanitarian challenge of HIV/AIDS, two-dozen leading investigators and major funding organizations formed the Global HIV Vaccine Enterprise, a voluntary alliance of independent organizations committed to working together to accelerate the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4803/version/2

Review: Dystroglycan in the Nervous System
Provedor de dados: 17
Autores: Matthias Samwald.
Dystroglycan is part of a large complex of proteins, the dystrophin-glycoprotein complex, which has been implicated in the pathogenesis of muscular dystrophies for a long time.  Besides muscular degeneration many patients manifest symptoms of neurological and cognitive dysfunction. Newer findings suggest that dystroglycan is implicated in brain development, synapse formation and plasticity, nerve-glia interactions and maintenance of the blood-brain barrier.&amp;#xd;&amp;#xa;Most research so far has focused on the functions of dystroglycan in muscle and neuromuscular junctions, while its role in the brain and interneuronal synapses has been largely neglected. &amp;#xd;&amp;#xa;This review will give an overview of the biochemistry of dystroglycan, its...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/196/version/1

Temperature factor analysis of outer membrane &amp;#x3b2;-stranded porin crystal structures suggests the pore is not uniformly rigid
Provedor de dados: 17
Autores: S. Krishnaswamy; Abhishek Kumar.
Outer membrane beta-stranded porins form a diverse and complex set of proteins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective using atomic temperature factors or B-factors. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. Structures of six porins (four 16 stranded beta barrel porins and two 8 stranded beta barrel porins) were taken from the PDB for the analysis based on resolution (better than 3.0 &amp;#xc5;) and R-factor (&amp;#x3c; 0.23). The residue distribution and mobility distribution was found to be characteristic of each of the porins. The mobility and residue...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2495/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

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

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

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

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

Trans-Disciplinary Protein Binding Of Drug: Docking Approach
Provedor de dados: 17
Autores: Ajeet Ajeet.
The purpose of present work is to introduce the binding of existing drugs to the trans-disciplinary protein with the help of docking procedures. Docking procedures allows virtually screening a database of compounds and predict the strongest binder based on various scoring functions. This work has been performed with the help of Molegro Virtual docker, in which two drugs are docked with their corresponding and non-corresponding (trans-disciplinary) protein. Results reveals that the protein-ligand interaction energy, hydrogen bond energy and  MolDock scores provided by molegro virtual docker, between legands (Levodopa and Acyclovir) and trans-disciplinary proteins have been equivalent or even better than that of between legands and corresponding proteins.
Tipo: Manuscript
Palavras-chave: Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6702/version/1

Towards Context Driven Modularization of Large Biomedical Ontologies
Provedor de dados: 17
Autores: Pinar Wennerberg; Sonja Zillner.
Formal knowledge about human anatomy, radiology or diseases is necessary to support clinical applications such as medical image search. This machine processable knowledge can be acquired from biomedical domain ontologies, which however, are typically very large and complex models.  Thus, their straightforward incorporation into the software applications becomes difficult. In this paper we discuss first ideas on a statistical approach for modularizing large medical ontologies and we prioritize the practical applicability aspect. The underlying assumption is that the application relevant ontology fragments, i.e. modules, can be identified by the statistical analysis of the ontology concepts in the domain corpus. Accordingly, we argue that most frequently...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3522/version/1

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

Secondary water pore formation for proton transport in a ClC exchanger revealed by an atomistic molecular dynamics simulation
Provedor de dados: 17
Autores: Youn Jo Ko; Won Ho Jo.
Several prokaryotic ClC proteins have been demonstrated to function as exchangers that transport both chloride ions and protons simultaneously in opposite directions. However, the path of the proton through the ClC exchanger and how the protein brings about the coupled movement of both ions are still unknown. In the present work, we demonstrate that a previously unknown secondary water pore is formed inside a ClC exchanger by using an atomistic molecular dynamics (MD) simulation. From the systematic simulations, it was determined that the glutamate residue exposed to the intracellular solution, E203, plays an important role as a trigger for the formation of the secondary water pore. Based on our simulation results, we conclude that protons in the ClC...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/2168/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

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

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

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

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

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

Sex-Related Moral Behavior
Provedor de dados: 17
Autores: Alberto Priori; Manuela Fumagalli; Sara Marceglia; Roberta  Ferrucci; Francesca Mameli; Stefano Zago; Sergio Barbieri; Giuseppe Sartori; Stefano Cappa.
The moral sense is one of the most complex aspects of the human mind. While neurobiological, cognitive and behavioural gender-related differences are increasingly studied and verified, the common belief that morality differs between men and women has not been experimentally investigated. We assessed the impact of gender on moral choices by testing thirty men and thirty women with the Moral Sense Task (MST) (Greene _et al_. 2001, 2004; Koenigs _et al_. 2007).  Whereas the two genders did not differ in utilitarian responses to non-moral dilemmas (NM) and to impersonal moral dilemmas (MI), men gave significantly more utilitarian answers to personal moral dilemmas (MP; i.e. that action whose endorsement involves highly emotional decision).  These results...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1467/version/1

Third-codon transversion rate-based _Nymphaea_ basal angiosperm phylogeny -- concordance with developmental evidence
Provedor de dados: 17
Autores: Xiaohan Yang; Gerald A. Tuskan; Timothy J. Tschaplinski; (Max) Zong-Ming Cheng.
Flowering plants (angiosperms) appeared on Earth rather suddenly approximately 130 million years ago and underwent a massive expansion in the subsequent 10-12 million years. Current molecular phylogenies have predominantly identified _Amborella_, followed by _Nymphaea_ (water lilies) or _Amborella_ plus _Nymphaea_, in the ANITA clade (_Amborella_, Nymphaeales, Illiciaceae, Trimeniaceae and Austrobaileyaceae) as the earliest angiosperm. However, developmental studies suggest that the earliest angiosperm had a 4-cell/4-nucleus female gametophyte and a diploid endosperm represented by _Nymphaea_, suggesting that _Amborella_, having an 8-cell/9-nucleus female gametophyte and a triploid endosperm, cannot be representative of the basal angiosperm. This...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/320/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

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

Solubilization of M2 Transmembrane Peptide of Influenza A in Pure Water: Implications for Emergence of Proteins and Protein-embedded Primeval Membranes in Unsalted Oceans
Provedor de dados: 17
Autores: Jianxing Song; Linlin  Miao.
We demonstrated that M2 transmembrane peptide, one of the most hydrophobic sequences in nature, can be solublized to at least ~100 &amp;#xb5;M in unsalted water without any lipid molecules. Strikingly, the M2 peptide also forms a highly-helical conformation in water which remains almost unchanged even at 95 &amp;#xba;C, as characterized by CD spectroscopy. Our result has critical implications in understanding emergence of proteins and protein-embedded primeval membranes in unsalted oceans.
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6773/version/1

Synthesis and characterization of chemically modified sago starch with potential biomedical application (Presented at ChemFerence-2010 at IIT Kanpur, 13 July 2010)
Provedor de dados: 17
Autores: Akhilesh  V. Singh.
This study was undertaken to assess the potential of highly substitute acetylated sago starch (SS) to be used  as a platform for controlled drug delivery. The acetylated sago starch was synthesized and the two parameters i.e.  duration of reaction and temperature were optimized. FT-IR spectra showed the corresponding group attachment in the modified form. XRD pattern exhibits change in the physical nature i.e. from crystalline to amorphous.  Swelling, hydration and viscosity value exhibits decrease in the respective values in comparison to its native  form which is due a to decrease in its hydrophilic value.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/5768/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

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

Study of Sea level changes with Leckie method of the Abderaz Formation (Middle Turonian-Early Campanian) at type section based on foraminifera
Provedor de dados: 17
Autores: Meysam Shafiee Ardestani; Abbas  Abbasi.
In this research the Abderaz Formation at its type section with an age of Turonian-early Campanian and a thickness of 300 m containing.light grey shale and marls was investigated. Statistical Studise of the morphotype groups of planktonic foraminifera shows that the majority of them are of shallow water forms (SWF) and deep water forms (DWF) and planktonic to benthic ratio is high indicating specific condition of oligotrophy and sedimentation in a relatively deeper marine condition
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4359/version/1

The History, Development and Impact of Computed Imaging in Neurological Diagnosis and Neurosurgery: CT, MRI, and DTI
Provedor de dados: 17
Autores: Aaron G. Filler.
A steady series of advances in physics, mathematics, computers and clinical imaging science have progressively transformed diagnosis and treatment of neurological and neurosurgical disorders in the 115 years between the discovery of the X-ray and the advent of high resolution diffusion based functional MRI. The story of the progress in human terms, with its battles for priorities, forgotten advances, competing claims, public battles for Nobel Prizes, and patent priority litigations bring alive the human drama of this remarkable collective achievement in computed medical imaging.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3267/version/5

Theoretical study on the gas and solution phase enthalpies, free energies, and equilibrium constants for the isomerization of [1.1]paracyclophane derivatives as potential molecular switches
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Theoretical studies were conducted on the predicted gas and solution phase thermodynamic properties for isomerization of various [1.1]paracyclophane derivatives to their corresponding transannular[4+4] adducts at representative levels of density functional and composite method theory. Calculations suggest the [1.1]paracyclophane to transannular[4+4] adduct isomerizations are not likely amenable to thermodynamic solvent tuning for the methylene, ether, and thioether bridged derivatives using a broad range of nonpolar and polar aprotic and polar protic implicit solvation models, but may be receptive towards solvent tuning for the amine bridged analogs. Varying the nature of the cyclophanic bridging atoms and the electron withdrawing/releasing character of...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5332/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

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

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

Reciprocal homeostatic reactions to chronic excitatory synaptic receptor inactivation in developing cerebral cortex networks
Provedor de dados: 17
Autores: Michael A. Corner.
Chronic blockade of actively excitatory glutamatergic synaptic receptors in co-cultured organotypic rodent neocortex explants leads to a compensatory up-regulation of otherwise inactive input channels so as to maintain almost normal levels of ongoing bursts of action potentials. We report here that this homeostatic return of spontaneous (now kainate receptor driven) firing is accompanied by a reciprocal down-regulation of blocked AMPA and NMDA receptors, such that the developing cortical network is protected against becoming hyperactive when those synaptic inputs are again able to transmit normally.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1260/version/3

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

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

Studies of Histidine, Phenylalanine Complexes of Oxovanadium(IV) Derived from Acetylacetone
Provedor de dados: 17
Autores: Rajeev Singh Yadav.
Schiff base complexes of oxovanadium(IV) with amino acids and acetylacetone were synthesized and characterized by elemental analysis, conductivity measurements, spectral and magnetic data. The complexes were found to be non-electrolytes and stoichiometry shown 1:1. The spectral and magnetic data were suggesting the square pyramidal geometry
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4378/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

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

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

Striatal neuroinflammation promotes parkinsonism in rats
Provedor de dados: 17
Autores: Dong-Young Choi; Randy Hunter; Mei Liu; Wayne Cass; Jignesh Pandya; Patrick Sullivan; Eun-Joo Shin; Hyoung-Chun Kim; Don Gash; Guoying Bing.
The specific role of neuroinflammation in the pathogenesis of Parkinson&amp;#x27;s disease remains to be fully elucidated. By infusing lipopolysaccharide (LPS) into the striatum, we investigated the effect of neuroinflammation on the dopamine nigrostriatal pathway. Here, we report that LPS-induced neuroinflammation in the striatum causes progressive degeneration of the dopamine nigrostriatal system, which is accompanied by motor impairments resembling parkinsonism. Our results indicate that neurodegeneration is associated with defects in the mitochondrial respiratory chain related to extensive S-nitrosylation/nitration of mitochondrial proteins. Mitochondrial injury was prevented by treatment of L-N^6^-(l-iminoethyl)-lysine, an inducible nitric oxide...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1970/version/1

Spontaneous glomerular deposition of immunoglobulins for ACE (Angiotensin Converting Enzyme) induces spontaneous nephropathy in diabetogenic rats
Provedor de dados: 17
Autores: Seikoh Nishida; Tamaki Sasaki; Yasushi Hirokawa; Michihiro Matsuki; Tsutomu Nohno.
We first discovered autoantibodies to ACE (angiotensin converting enzyme) in patients with type 2 diabetes mellitus^1^. The antibodies were positive for 64.5% of the patients with diabetes and were positive in 83.3% in the early stage of clinical diabetic nephropathy. In addition, in genetically diabetogenic OLETF (Otsuka Long-Evans Tokushima Fatty) rats^2^, one of the characteristics of which strain is spontaneous nephropathy resembling those of human type 2 diabetes, and in control LETO rats^2^, immunization with rabbit lung ACE developed glomerulopathy similar to that seen in diabetics^3^. Also, in normal New Zealand white rabbits, immunization with the rabbit lung ACE induced glomerular changes similar to those seen in diabetic nephropathy^3^. In this...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2009
URL: http://precedings.nature.com/documents/3275/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

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

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

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

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core (Release 1 Candidate)
Provedor de dados: 17
Autores: Michael Hucka; Frank Bergmann; Stefan Hoops; Sarah M. Keating; Sven Sahle; Darren J. Wilkinson.
This is the specification for _Release 1 Candidate_ of *SBML Level 3 Version 1 Core*, an electronic model representation format for systems biology.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. SBML is defined neutrally with respect to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML. This document contains many examples of SBML models written in XML.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa; More information about SBML and this specification is available online at &amp;#x22;http://sbml.org/Documents/Specifications/...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4123/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

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

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

Translational neuroscience requires better design and analysis of preclinical studies
Provedor de dados: 17
Autores: Stanley E. Lazic.
Animal models are often used to obtain a better understanding of psychiatric, neurodegenerative, and neurodevelopmental disorders. Despite many years of research, these models have not led to many novel therapies or treatments. Translating results between species will always be difficult, and it is argued that inappropriate statistical analyses, failure to identify the experimental unit, lack of random assignment to treatment conditions, and unblinded assessment of outcomes contribute to the low rate of translating preclinical in vivo studies into successful therapies. It is known that these shortcomings can generate biased estimates, too many false positives and false negatives, and unreproducible results. These issues have been raised repeatedly, but...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/6987/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

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

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

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

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

The water clock of Proteus mirabilis paces colony periodic and synchronous swarming
Provedor de dados: 17
Autores: Elodie Lahaye; Frederic Jamme; Olivier Sire.
For decades, the origin of the concentric ring pattern of bacterial swarming colonies has puzzled microbiologists. Thanks to _in situ_ and real time infrared microspectroscopy and the brilliance of the infrared beam at SOLEIL synchrotron, we demonstrate here that _Proteus mirabilis_ swarming is paced by a periodic variation of the water activity at colony&amp;#x27;s edge. This periodic variation originates a phase transition within the extracellular matrix water H bond network which switches on and off the exopolysaccharides viscoelasticity and, consequently, the ability of bacterial cells to swarm. A dynamic behaviour emerges from the global properties of the multicellular entity which here relies on the ability of the bacterial cells to tune exoproducts...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4455/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 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

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

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

The role of ongoing dendritic oscillations in single-neuron dynamics
Provedor de dados: 17
Autores: Michiel Remme; Mate Lengyel; Boris  Gutkin.
The dendritic tree contributes significantly to the elementary computations a neuron performs while converting its synaptic inputs into action potential output. Traditionally, these computations have been characterized as temporally local, near-instantaneous mappings from the current input of the cell to its current output, brought about by somatic summation of dendritic contributions that are generated in spatially localized functional compartments. However, recent evidence about the presence of oscillations in dendrites suggests a qualitatively different mode of operation: the instantaneous phase of such oscillations can depend on a long history of inputs, and under appropriate conditions, even dendritic oscillators that are remote may interact through...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3335/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

The History, Development and Impact of Computed Imaging in Neurological Diagnosis and Neurosurgery: CT, MRI, and DTI
Provedor de dados: 17
Autores: Aaron G. Filler.
A steady series of advances in physics, mathematics, computers and clinical imaging science have progressively transformed diagnosis and treatment of neurological and neurosurgical disorders in the 115 years between the discovery of the X-ray and the advent of high resolution diffusion based functional MRI. The story of the progress in human terms, with its battles for priorities, forgotten advances, competing claims, public battles for Nobel Prizes, and patent priority litigations bring alive the human drama of this remarkable collective achievement in computed medical imaging.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3267/version/3

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

The genetic equidistance result of molecular evolution is independent of mutation rates
Provedor de dados: 17
Autores: Shi Huang.
The genetic equidistance result shows that sister species are approximately equidistant to an outgroup as measured by DNA or protein dissimilarity.  The equidistance result is the most direct evidence, and remains the only evidence, for the constant mutation rate interpretation of this result, known as the molecular clock.  However, data independent of the equidistance result have steadily accumulated in recent years that often violate a constant mutation rate.  Many have automatically inferred non-equidistance whenever a non-constant mutation rate was observed, based on the unproven assumption that the equidistance result is an outcome of constant mutation rate.  Here it is shown that the equidistance result remains valid even when different species can...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1733/version/1

The Open Practises E-Science Network (OPEN)
Provedor de dados: 17
Autores: Cameron  Neylon.
A grant proposal submitted for support to fund a research network focussed on identifying and dealing with the practical issues of enabling open practise in research. The text of the proposal was written by a large number of people and coordinated by Cameron Neylon.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1370/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

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

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

Structural requirements for the binding affinity of some small, non&amp;#x2013;peptide C5a receptor antagonists
Provedor de dados: 17
Autores: Haiying Xie; Weiming  Wang; Ziqiang  Xie; Hong  Chen; Kexian  Chen.
Complement anaphylatoxin 5a (C5a) has been recognized as a potent therapeutic target for anti-inflammatory therapy, thus, blocking the action of C5a on its binding receptors may provide an effective treatment of a variety of inflammatory diseases. However, there have been few clinically available non-peptide C5a receptor antagonists disclosed at present. In pursuit of better anti-inflammatory drugs, quantitative structure&amp;#x2013;activity relationship studies were carried out in a series of non-peptide C5a receptor antagonists with binding activity using different physicochemical descriptors. The conventional best 2D-QSAR models were developed using a training set of 35 molecules and an external test set of 8 molecules by genetic function approximation...
Tipo: Manuscript
Palavras-chave: Chemistry; Immunology; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6630/version/1

Selective bias in temporal bisection task by number exposition
Provedor de dados: 17
Autores: Carmelo Mario Vicario.
Temporal experience can be modulated by a number of environmental factors such as quantity. Here I show that merely looking at numbers causes a bias in imaginative (but not perceptual) time bisection task that depends on the number&amp;#x2019;s magnitude. This suggests that automatic shifts of spatial attention to the left and right side, as a result of exposure to numbers, modulates temporal as well as spatial behaviour (2,3,4). This finding suggests that the representation of time and space produce certain patterns in neural maps that are decoded by means of the similar neural mechanisms.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1479/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

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

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

The cultural epigenetics of psychopathology: The missing heritability of complex diseases found?
Provedor de dados: 17
Autores: Rodrick Wallace.
We extend a cognitive paradigm for gene expression to the epigenetic epidemiology of mental disorders, recognizing the fundamental role that culture plays in human biology as another heritage mechanism parallel to, and interacting with, the more familiar genetic and epigenetic systems. In the mathematical model, culture acts as another tunable epigenetic catalyst that both directs developmental trajectories and becomes convoluted with individual ontology via a mutually interacting crosstalk mediated by a social interaction that is itself culturally driven. We call for the incorporation of embedding culture as an essential component of the epigenetic regulation of human mental development and its dysfunctions, bringing what is perhaps the central reality of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3894/version/1

Striatal Enriched Protein Tyrosine Phosphatase mediates Ethanol inhibition of NMDA Receptor Activity
Provedor de dados: 17
Autores: Peter H. Wu; Ronald K. Freund; William R. Procotor; Susan M. Goebel-Goody; Michael D. Browning; Paul J. Lombroso.
We demonstrated previously that ethanol inhibition of NMDA receptor (NMDAR) function is accompanied by a reduction in tyrosine phosphorylation of Tyr^1472^ on the NR2B subunit, and this action of ethanol is attenuated by a broad spectrum tyrosine phosphatase inhibitor. Here we examined whether this ethanol inhibition of NMDAR activity was due to the actions of STriatal Enriched protein tyrosine Phosphatase (STEP) which has been shown to regulate NMDAR internalization by dephosphorylating Tyr^1472^ on the NR2B subunit. Using whole-cell recordings of pharmacologically isolated NMDAR-mediated excitatory post-synaptic currents (NMDA EPSCs) from hippocampal CA1 pyramidal neurons, we show that intracellular infusion of a substrate-trapping inactive form of STEP...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2473/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

Reflect: Augmented Browsing for the Life Scientist
Provedor de dados: 17
Autores: Evangelos Pafilis; Se&amp;#xe1;n I. O&amp;#x27;Donoghue; Lars J. Jensen; Heiko Horn; Michael Kuhn; Nigel P. Brown; Reinhard Schneider.
Anyone who regularly reads life science literature often comes across names of genes, proteins, or small molecules that they would like to know more about. To make this process easier, we have developed a new, free service called Reflect (&amp;#x22;http://reflect.ws&amp;#x22;:http://reflect.ws) that can be installed as a plug-in to Firefox or Internet Explorer. Reflect tags gene, protein, and small molecule names in any web page, typically within a few seconds, and without affecting document layout. Clicking on a tagged gene or protein name opens a popup showing a concise summary that includes synonyms, database identifiers, sequence, domains, 3D structure, interaction partners, subcellular location, and related literature. Clicking on a tagged small...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3212/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

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

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

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

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

Threshold Decline in Mesoamerican Coral Growth and Resiliency
Provedor de dados: 17
Autores: Jessica Carilli; Richard Norris.
Caribbean coral reefs have been massively altered in recent decades due to human impacts, resulting in a dramatic reduction of live coral cover but quantitative data before the 1970s have not been available to assess how these changes came about1,2,3. We produced master chronologies of growth rates in massive Montastrea faveolata corals from the Mesoamerican reef tract that provide a method for extending records of coral health further back into the past. Our records reveal a unique reduction in growth rate associated with the 1998 coral bleaching event that has no parallel in the past 75 to 150 years. Of 92 cores collected from live coral heads in 2006-2007, 94% have severely reduced growth rates and 14% exhibit partial mortality scars in 1998-1999...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2115/version/1

Signi&amp;#xfb01;cance tests for comparing digital gene  expression pro&amp;#xfb01;les
Provedor de dados: 17
Autores: Leonardo Varuzza; Arthur Gruber; Carlos A. B. Pereira.
Most of the statistical tests currently used to detect differentially expressed genes are based on asymptotic results, and perform poorly for low expression tags. Another problem is the common use of a single canonical cutoff for the significance level (p-value) of all the tags, without taking into consideration the type II error and the highly variable character of the sample size of the tags.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;  This work reports the development of two significance tests for the comparison of digital expression profiles, based on frequentist and Bayesian points of view, respectively. Both tests are exact, and do not use any asymptotic considerations, thus producing more correct results for low frequency tags than the chi-square test. The...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2002/version/2

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

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

Skeletal Evidence for Leprosy in India by the Second Millenium B.C.
Provedor de dados: 17
Autores: Gwendolyn Robbins; Veena Tripathy; VN Misra; RK Mohanty; VS Shinde; Kelsey Gray; Malcolm Schug.
Leprosy is a chronic infectious disease caused by _Mycobacterium leprae_ that affects almost 500,000 people worldwide^1^. The timing of first infection, geographic origin, and pattern of transmission of the disease are unknown^1-3^. Comparative genomics research has recently suggested _M. leprae_ evolved in East Africa or South Asia before spreading to Europe and the rest of the World^4-5^. The earliest accepted textual evidence indicates that leprosy existed in India by at least 600 B.C. and was known in Europe by 400 B.C.^6-7^. The earliest skeletal evidence was dated 300-200 B.C. in Egypt^8^ and Thailand^9^. Here, we report the presence of lepromatous leprosy in skeletal remains from Balathal, a Chalcolithic site (2300-1550 B.C.) in India^10-11^. A...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2009
URL: http://precedings.nature.com/documents/2745/version/1

Slug-based epithelial-mesenchymal transition gene signature is associated with prolonged time to recurrence in glioblastoma
Provedor de dados: 17
Autores: Wei-Yi Cheng; Jessica J. Kandel; Darrell J. Yamashiro; Peter Canoll; Dimitris Anastassiou.
Background&amp;#xd;&amp;#xa;We previously identified a precise stage-associated gene expression signature of coordinately expressed genes, including the transcription factor Slug (SNAI2) and other epithelial mesenchymal transition (EMT) markers, present in samples from publicly available gene expression datasets in multiple cancer types. The expression levels of the co-expressed genes vary in a continuous and coordinate manner across the samples, ranging from absence of expression to strong co-expression of all genes. These data suggest that tumor cells may pass through an EMT like process of mesenchymal transition to varying degrees.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Findings&amp;#xd;&amp;#xa;Here we show that this signature in glioblastoma multiforme...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6544/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

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

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

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

The human genome is composed of viral DNA: Viral homologues of the protein products cause Alzheimer&amp;#x27;s disease and others via autoimmune mechanisms.
Provedor de dados: 17
Autores: Christopher J. Carter.
The human genome is composed of millions of fragmented contiguous viral DNA sequences, dating from the dawn of evolution and reflecting retroviral insertions over millions of years of coexistence. Herpes and other viral insertion points correspond to the locations of over 120 Alzheimer&amp;#x27;s disease susceptibility genes and to linkage hotspots. The greater the number of pathogen matches, the more important the gene. These DNA sequences are translated into short contiguous 5-12 amino acid stretches (vatches), identical in viruses and man, and in other pathogens implicated in Alzheimer&amp;#x27;s disease (_Borrelia_, _Chlamydia_, _Helicobacter_, _C. Neoformans_ , _P. Gingivalis_). _C. Neoformans_, which has been associated with a rare but curable form...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4765/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

Structure and function prediction of human homologue hABH5 of _E. coli_ ALKB5 using in silico approach
Provedor de dados: 17
Autores: Mr. Shankaracharya; Saibal Das; Ambarish Sharan Vidyarthi.
Newly discovered human homologues of ALKB protein have shown the activity of DNA damaging drugs, used for cancer therapy. Little is known about the structure and function of hABH5, 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 modeler 9v7 to predict the 3D structure of the hABH5 protein. 3-D model of hABH5, ALKBH5.B99990005.pdb was predicted and evaluated. Validation results showed 96.8% residues in favor and an additional allowed region of the Ramachandran plot. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, conserved pattern of Pro158-X-Asp160-Xn-His266 in the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5597/version/2

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

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

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

Stochastic Resonance Can Drive Adaptive Physiological Processes
Provedor de dados: 17
Autores: Bradly J. Alicea.
Stochastic resonance (SR) is a concept from the physics and engineering communities that has applicability to both systems physiology and other living systems. In this paper, it will be argued that stochastic resonance plays a role in driving behavior in neuromechanical systems. The theory of stochastic resonance will be discussed, followed by a series of expected outcomes, and two tests of stochastic resonance in an experimental setting. These tests are exploratory in nature, and provide a means to parameterize systems that couple biological and mechanical components. Finally, the potential role of stochastic resonance in adaptive physiological systems will be discussed.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3301/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

Underlying Mathematics in Diversification of Human Olfactory Receptors in Different Loci
Provedor de dados: 17
Autores: Sk. Sarif  Hassan; Pabitra  Pal Choudhury; Arunava Goswami.
As per conservative estimate, approximately (51-105) Olfactory Receptors (ORs) loci are present in human genome occurring in clusters. These clusters are apparently unevenly spread as mosaics over 21 pair of human chromosomes. Olfactory Receptor (OR) gene families which are thought to have expanded for the need to provide recognition capability for huge number of pure and complex odorants. ORs form the largest known multi-gene family in the human genome. Recent studies have shown that 388 full length and 414 OR pseudo-genes are present in these OR genomic clusters. In this paper, the authors report a classification method for all human ORs based on their sequential quantitative information like presence of poly strings of nucleotides bases, long range...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5475/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

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

Visual Molecular Dynamics Investigations of the Impact of Hydrophobic Nanoparticles on Prognosis  of Alzheimer&amp;#x2019;s Disease and Cancers
Provedor de dados: 17
Autores: I. C. Baianu; M Charles; V. I. Prisecaru.
The possible impact of hydrophobic lectin nanoparticles on the prognosis and progression of Alzheimer&amp;#x27;s disease (AD) and cancers was investigated by Visual Molecular Dynamics (VMD) computer modeling programs available from the Beckmann Advanced Research Institute at the University of Illinois at Urbana. Our results indicate the possibility of impeding pathological aggregation of certain proteins such as modified tau- or beta-amyloid that are currently being considered as possible causes of Alzheimer&amp;#x27;s disease. VMD programs serve as useful tools for investigation hydrophobic protein aggregation that may play a role in aging of human populations.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience; Pharmacology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7111/version/2

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

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

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

Without magic bullets: the biological basis for public health interventions against protein folding disorders
Provedor de dados: 17
Autores: Rodrick Wallace.
Protein folding disorders of aging like Alzheimer&amp;#x27;s and Parkinson&amp;#x27;s diseases currently present intractable medical challenges. &amp;#x27;Small molecule&amp;#x27; interventions - drug treatments - often have, at best, palliative impact, failing to alter disease course. The design of individual or population level interventions will likely require a deeper understanding of protein folding and its regulation than currently provided by contemporary &amp;#x27;physics&amp;#x27; or culture-bound medical magic bullet models. Here, a topological rate distortion analysis is applied to the problem of protein folding and regulation that is similar in spirit to Tlusty&amp;#x27;s (2010a) elegant exploration of the genetic code. The formalism produces...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4847/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

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

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

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

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

Rabbit Muscle Actin Polymerization changes by Ultraviolet &amp;#x2013;B radiation
Provedor de dados: 17
Autores: Anita Mukherjee; Arun Kumar Attri.
Increase in Ultraviolet-B flux from the Sun has the potential to alter the protein in mammals. Rabbit muscle was processed and filtered to extract G-actin, which was tested for its protein concentration before exposing to UV-B. It was found that polymerization of actin does get affected exposure of actin monomers to UV-B radiation. Inside the cell, there are many actin binding proteins which might be playing crucial role in G-actin to F-actin formation.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2766/version/1

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

Remote estimation of carbon dioxide uptake of terrestrial ecosystems
Provedor de dados: 17
Autores: Martin F. Garbulsky.
The estimation of the carbon balance in ecosystems, regions, and the biosphere is currently one of the main concerns in the study of the ecology of global change. Current remote sensing methodologies for estimating gross primary productivity are not satisfactory because they rely too heavily on (i) the availability of climatic data, (ii) the definition of land-use cover, and (iii) the assumptions of the effects of these two factors on the radiation-use efficiency of vegetation (RUE). A new methodology is urgently needed that will actually assess RUE and overcome the problems associated with the capture of fluctuations in carbon absorption in space and over time. Remote sensing techniques such as the widely used reflectance vegetation indices (e.g., NDVI,...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/977/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 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

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

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

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

The biotechnological perspective of Beta-Glucosidases
Provedor de dados: 17
Autores: Israr  Khan; Muhammad waheed Akhtar.
Biotechnology is the art and science of making and technology to process biological materials for the welfare of human being. This discussion includes the beta glucosidase classification, its structure, application, and recent research interests in relation to its significance and comparison with eukaryotic Beta glucosidases including plant, animal and yeast as well. The study also comprise of the various stress factors and modifications thereby the organism to cope it. The focus of the study is on the various kinetics principles and their full potential exploitation to increase the activity of the enzyme. As such making the enzyme a potent vehicle for various industrial, pharmaceutical and research purposes. It also include the various glycosylhydrolases...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4945/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

Variation in _PNPLA3_ is associated with outcomes in alcoholic liver disease
Provedor de dados: 17
Autores: Chao Tian; Renee P. Stokowski; David Kershenobich; Dennis G. Ballinger; David A. Hinds.
Two recent genome-wide association studies have described associations of SNP variants in _PNPLA3_ with nonalcoholic fatty liver and plasma liver enzyme levels in population based cohorts. We investigated the contributions of these variants to clinical outcomes in Mestizo subjects with a history of excessive alcohol consumption. We show that non-synonymous variant rs738409[G] (I148M) in _PNPLA3_ is strongly associated with alcoholic liver disease and progression to alcoholic cirrhosis (unadjusted OR = 2.25, P = 1.7x10^-10^; ancestry-adjusted OR = 1.79, P = 1.9x10^-5^).
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3254/version/1

Vocal Bursts Communicate Discrete Emotions: Evidence for New Displays
Provedor de dados: 17
Autores: Emiliana Simon-Thomas; Disa Sauter; Lara Sinicropi-Yao; Anna Abramson; Dacher Keltner.
Studies of emotion signaling have proven critical to scientific advances in understanding emotion, informing claims about the evolutionary origins of different emotions1, the central and peripheral nervous system correlates of emotion 2 3 and even which states warrant consideration in emotion taxonomies 4. An initial wave of empirical studies of emotion-related facial expression5 and vocalization 6 7 has concentrated almost exclusively on a limited set of emotions - anger, disgust, fear, sadness, surprise, happiness, and tenderness. More recent work on emotional facial expressions has expanded this framework, documenting reliable displays of other emotions like embarrassment and shame 8, pride 9, and love and desire 10 . Here, we present two studies that...
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1356/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

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 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

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

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

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

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

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

Reduced contribution of the ipsilateral primary motor cortex to force modulation with short-term motor learning in humans: An NIRS study
Provedor de dados: 17
Autores: Kenichi Shibuya; Masako Iwadate; Tomoko Sadamoto.
How is muscle force modulated during hand exercise? Oxygenation in the contralateral primary motor cortex (M1) has been observed to vary considerably across trials of repetitive handgrip exercise. No linear relationship was observed between the average value of oxygenation determined by a block design study and the force of the handgrip. We found reduced oxygenation in the ipsilateral M1 and unchanged oxygenation in the contralateral M1 during repetitive static handgrip exercises (40% and 60% maximal voluntary contraction; 10 s exercise/75 s rest; 5 sets), which might be due to short-term motor learning. These results support the hypothesis that the ipsilateral M1 might functionally compensate for the contralateral M1 in force modulation during unilateral...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1865/version/1

&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

The Predominance of Electric Transport in Synaptic Transmission
Provedor de dados: 17
Autores: Hamid Reza Noori.
The quantitative description of the motion of neurotransmitters in the synaptic cleft appears to be one of the most difficult problems in the modeling of synapses. Here we show in contradiction to the common view, that this process is merely governed by electric transport than diffusion forces.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2304/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

Voltage-sensitive dye imaging reveals tonotopic organization of auditory cortex spontaneous activity
Provedor de dados: 17
Autores: Brandon J. Farley; Arnaud Norena.
Imaging neural activity across a large (several mm) cortical area with high temporal and spatial resolution is desirable, for example in the auditory system to measure cortical processing across a broad frequency spectrum. Voltage-sensitive dye imaging (VSDI) has a unique combination of properties making this possible, but so far studies have been limited to studying simple sparsely-presented sensory stimuli. We demonstrate the feasibility of long-acquisition VSDI (using the dye RH-1691) in auditory cortex while presenting complex time-varying acoustic stimuli or silence. Using a dense array of partially-overlapping 50 ms tone pips (8 frequencies per octave spanning six octaves), we obtained high-resolution spectrotemporal receptive fields (STRFs)...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5820/version/1

Sodium Benzoate as Promoter in the Soap Flotation of Phosphate Minerals
Provedor de dados: 17
Autores: Mihir DM; Vijay Kumar P; Prabhulingaiah Gowda.
In the present study we show that sodium benzoate substantially improves the efficiency of Soap LDO collector in the flotation of phosphate minerals.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6572/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

Why are Male IQ Scores More Variable?
Provedor de dados: 17
Autores: Bernard Strauss; Jacob Strauss.
The male female difference in the variance of quantitative traits including IQ can be accounted for by the observation of the concentration of genes involved in brain development on the X chromosome and by the mechanism of sex determination in mammals. Females have two X chromosomes with one randomly inactivated. Males have a single X chromosome, which results in increased variance. It is shown that these factors are sufficient to account for the observed differences.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3238/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

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

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

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

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

Valid and efficient formula for free energy difference from nonequilibrium work
Provedor de dados: 17
Autores: Liao Y. Chen.
Atomic force microscopes and optical tweezers afford direct probe into the inner working of single biomolecules by mechanically unfolding them.^1-15^ Critical to the success of this type of probe is to correctly extract the free energy differences between the various conformations of a protein/nucleic acid along its forced unfolding pathways. Current studies rely on the Jarzynski equality^16^ (JE) or its undergirding Crooks fluctuation theorem^17^ (CFT), even though questions remain on its validity^17-19^ and on its accuracy.^13,20-21^ The validity of JE relies on the assumption of microscopic reversibility.^17,18^ The dynamics of biomolecules, however, is Langevin stochastic in nature. The frictional force in the Langevin equation breaks the time reversal...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1911/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

Young children do not integrate visual and haptic information
Provedor de dados: 17
Autores: Monica Gori; Michela Del Viva; Giulio Sandini; David C. Burr.
Several studies have shown that adults integrate visual and haptic information (and information from other modalities) in a statistically optimal fashion, weighting each sense according to its reliability. To date no studies have investigated when this capacity for cross-modal integration develops. Here we show that prior to eight years of age, integration of visual and haptic spatial information is far from optimal, with either vision or touch dominating totally, even in conditions where the dominant sense is far less precise than the other (assessed by discrimination thresholds). For size discrimination, haptic information dominates in determining both perceived size and discrimination thresholds, while for orientation discrimination vision dominates. By...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1521/version/1

Seasonal changes in brain serotonin transporter binding in short 5-HTTLPR-allele carriers but not in long-allele homozygotes
Provedor de dados: 17
Autores: Jan Kalbitzer; David Erritzoe; Klaus K. Holst; Finn  A. Nielsen; Lisbeth Marner; Szabolcs Lehel; Tine Arentzen; Terry L. Jernigan; Gitte  M. Knudsen.
Several findings suggest seasonal variations in the serotonin (5-HT) system. We sought evidence for seasonal variation in the serotonin transporter (5-HTT). We found that length of daylight time in minutes correlates negatively with 5-HTT binding in the putamen and the caudate, with a similar tendency in the thalamus, but no such association in the midbrain. In the putamen, an anatomical region with a dense serotonin innervation that is implicated in processing of aversive stimuli, we found a significant gene*daylight effect with a negative correlation between the 5-HTT binding and daylight time in carriers of the short 5-HTTLPR allele, but not in carriers of the long allele. The neurobiological endophenotype identified here directly links activation...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2259/version/1

When does right functional hemispheric lateralization arise? Evidence from preterm infants
Provedor de dados: 17
Autores: Giovanni Mento; Agnese Suppiej; Patrizia Bisiacchi.
In recent years, magnetic resonance imaging (MRI) has allowed researchers to individuate an earlier morphological development of the right hemisphere compared to the left hemisphere before birth. Anatomical asymmetry, however, does not necessarily mean functional asymmetry and whether the anatomical differences between hemispheres at this early age are paralleled by functional specializations is still unknown. Here we show electrophysiological evidence of an early functional right lateralization for pitch processing arising by 30 gestational weeks, not before, in preterm newborns.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3204/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

Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case
Provedor de dados: 17
Autores: Jos&amp;#xe9; Luiz Rybarczyk; Mauro A. A. Castro; Rodrigo J. S. Dalmolin; Jos&amp;#xe9; C. F. Moreira; Leonardo G. Brunnet; Rita M. C. de Almeida.
A genome modular classification that associates cellular processes to modules could lead to a method to quantify the differences in gene expression levels in different cellular stages or conditions: the transcriptogram, a powerful tool for assessing cell performance, would be at hand. Here we present a computational method to order genes on a line that clusters strongly interacting genes, defining functional modules associated with gene ontology terms. The starting point is a list of genes and a matrix specifying their interactions, available at large gene interaction databases. Considering the Saccharomyces cerevisiae genome we produced a succession of plots of gene transcription levels for a fermentation process. These plots discriminate the fermentation...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3869/version/1

The BRIF (Bioresource Research Impact Factor) as a tool for improving bioresource sharing in biomedical research
Provedor de dados: 17
Autores: Laurence Mabile; Raymond Dalgleish; Gudmundur  A. Thorisson; Myl&amp;#xe8;ne Desch&amp;#xea;nes; Robert Hewitt; Jane Carpenter; Elena Bravo; Pierre-Antoine Gourraud; Paul Hofman; Jennifer Harris; Maria Angeles Munoz-Fernandes; Anne Cambon-Thomsen.
The central aim of the BRIF (Bioresource Research Impact Factor) initiative is to construct a quantitative parameter to evaluate bioresources, modeled to some degree on the Journal Impact Factor (JIF), and to provide guidance and methodology for optimizing recognition of bioresources, their use and their sharing at international level. To implement this concept an international working group has been set up. Specific tasks have been assigned to several sub-groups: BRIF digital identifier schemes; BRIF parameters, measures and indicators; journal guidelines for resource citing and referencing; policies for bioresource access and sharing. These are discussed in the present manuscript.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Pharmacology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6568/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

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

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

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

Regulation of Phosphatase Homologue of Tensin Protein Expression by Bone Morphogenetic Proteins in Prostate Epithelial Cells
Provedor de dados: 17
Autores: Travis Jerde; Zhong Wu; Dan Theodorescu; Wade Bushman.
Phosphatase homologue of tensin (PTEN) is the key endogenous inhibitor of phosphoinositide signaling and is the most commonly mutated gene in human prostate cancer. The bone morphogenetic proteins (BMPs) are secreted developmental signaling molecules known to promote differentiation in the prostate. BMP ligands have been shown to inhibit prostate cancer cell line proliferation and tumor growth and expression of BMPs, BMP ligands, receptors and signaling effectors are diminished in prostate cancer. A previous report in the colon led us to investigate the potential mechanistic relationship between PTEN and BMP signaling in prostate epithelial cells. We show here that BPM signaling positively regulates PTEN in normal and malignant prostate cells by increasing...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4311/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

The Roles of Membrane Rafts in CD32A-Mediated Phagocytosis
Provedor de dados: 17
Autores: Timothy P. Tolentino; Periasamy Selvaraj; Cheng Zhu.
Membrane rafts are highly dynamic heterogeneous sterol- and sphingolipid-rich micro-domains on cell surfaces. They are generally believed to provide residency for cell surface molecules (e.g., adhesion and signaling molecules) and scaffolding to facilitate the functions of these molecules such as membrane trafficking, receptor transport, cell signaling, and endocytosis.&amp;#xd;&amp;#xa;The governing, or overall hypothesis, for this project is that membrane rafts provide residency for Fc[gamma]RIIA (CD32A) on K562 cells, and that by doing so they provide a platform from which Fc[gamma]RIIA initiate or carry out their functions, which include migration, signaling, phagocytic synapse formation, and internalization of IgG opsonized...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1191/version/1

Treemap Versus BPA (Again): A Response to Dowling
Provedor de dados: 17
Autores: Roderic Page; Michael Charleston.
TreeMap is a computer program for analysing host-parasite cospeciation. We respond to Dowling&amp;#x2019;s (Cladistics, 18: 416-435) recent comparison of TreeMap and Brooks Parsimony Analysis (BPA) by showing that Dowling&amp;#x2019;s comparison suffers from several mistakes and flaws. We discuss the problems with both BPA and TreeMap, and show that BPA incorrectly counts the true number coevolutionary events more often than TreeMap 1. We also discuss the two main limitations of TreeMap 1 correctly identified by Dowling, namely its inability to handle widespread parasites, and its coarse optimality criterion (the number of cospeciation events). We suggest a simple fix for widespread parasites. The newly released TreeMap 2 uses a more sensitive optimality...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1030/version/1

Variability and community organization in moderately exposed tropical rocky shore algal communities as influenced by different consumer groups
Provedor de dados: 17
Autores: Edison Macusi.
Tropical rocky shores have been described as diverse and having a complex variety of consumers. This wide array of consumers has been studied to shed light on the different roles of consumers, particularly grazers on rocky shores and how they affect the relative abundance and distribution of sessile algal prey. One of the aims of ecology is to clarify factors that regulate and structure the abundance, growth and relationship of predators and preys in each habitat. Grazing is known as one of the most important determinants of growth and distribution of rocky shore communities. In this study a comparison between the different effects of fishes, crabs and molluscan herbivores on the relative abundances of microalgae and macroalgae from micro (hundreds of...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2267/version/1

Two &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 arguments regarding the genetic code are applied to the classification of tertiary irregular protein symmetries. Unlike the genetic case, two protein folding codes are found, a &amp;#x27;normal&amp;#x27; globular and a &amp;#x27;pathological&amp;#x27; amyloid version. The underlying normal &amp;#x27;protein folding code error 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 three additional subminor handles. The basic amyloid folding code error network appears to be more complicated, of genus two, giving the eightfold symmetry of the steric zipper. Like many before us, we conjecture that the elaborate...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4665/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

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

Spatiotemporal dynamics of complex ecological networks: Power-law scaling and implications for conservation planning
Provedor de dados: 17
Autores: Christopher Wright.
Spatial constraints on the topology of complex networks are just beginning to be appreciated, both theoretically^1-3^ and in concrete examples like the Internet^4^ and global air transportation network^5^. Ecological networks, composed of habitat patches connected by species dispersal, are intrinsically spatial and show promise as a tool for conservation planning; but while habitat-loss effects on ecological networks have been simulated, such effects have not been directly measured in ecological networks varying over time^6-8^. In this study, I used satellite remote sensing to study ecological networks composed of wetland habitat in the Prairie Pothole Region (PPR) of North America. I find power-law scaling of important topological properties as a function...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2532/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

The likelihood that two proteins interact might depend on the proteins&amp;#x27; age
Provedor de dados: 17
Autores: Pedro Beltrao.
It has been previously shown [1] that _S. cerevisiae_ proteins preferentially interact with proteins of the same estimated likely time of origin.  To study this observation further, the protein interaction networks of _S. cerevisiae_ and _H. sapiens_ were analyzed taking into account an estimate for the age of the proteins in these species.  These estimates were obtained by studying the presence and absence of putative orthologs in other eukaryotic species. In this work preliminary results are described that point to a dependence of the likelihood of protein interaction on the proteins&amp;#x2019; age. The probability of two proteins interactions was found to be linearly dependent on the time the proteins have co-existed in the species.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/22/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

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

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

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

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

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

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

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

Validated, Ultra Violet Spectroscopy method for the Dissolution study of Mycophenolate mofetil immediate release 500mg tablets
Provedor de dados: 17
Autores: Surajpal P. Verma; Ozair Alam; Pooja Mullick; Nadeem Siddiqui; Suroor A. Khan.
A simple, selective and precise dissolution method was developed and validated for the Mycophenolate mofetil immediate release tablets. The method employed dissolution medium 0.1N HCl (pH1.2) and volume 900ml with USP-II apparatus (Paddle). Detection was made by measuring the absorbance on UV at the [lambda]~max~ 250nm. The method show the linearity in the range of conc. 5[micro]g/ml to 40[micro]g/ml with r^2^=0.999. The method is also validated as per International Conference of Harmonization guidelines. The method showed the specificity with standard deviation 0.00. The method is repeatable, selective and accurate for the dissolution study of Mycophenolate mofetil immediate release tablets.
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2250/version/1

Structural and functional validation of Microsystin synthetases
Provedor de dados: 17
Autores: Swapnil G. Sanmukh; Waman N. Paunikar.
The structure and function prediction for the Microsystin synthetases from Microsystis aerogenosa (LNSAMB) were carried out for verifying the authenticity of the sequenced genes. The genes for Microsystin synthetases (mcyA, mcyB, mcyD and mcyE,), were predicted by the application of computational methods and Bioinformatics web tools. The probable function prediction for the proteins was done by using Bioinformatics web tools like CDD-BLAST, INTERPROSCAN, PFAM and COGs by searching protein databases for the presence of conserved domains. While tertiary structures were constructed using PS2 Server- Protein Structure Prediction server. This study revealed structural and functional validation of sequenced genes.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6835/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

Structural basis for the activation of peroxisome proliferator-activated receptor-gamma by telmisartan
Provedor de dados: 17
Autores: Yasushi Amano; Tomohiko Yamaguchi; Kazuki Ohno; Tatsuya Niimi; Masaya Orita; Hitoshi Sakashita; Makoto Takeuchi.
Telmisartan, a selective angiotensin receptor blocker, has been recently shown to act as a partial agonist for peroxisome proliferator-activated receptor-gamma (PPAR&amp;#x3b3;). To understand the activation mechanism of PPAR&amp;#x3b3; by telmisartan, we determined the ternary complex structure of PPAR&amp;#x3b3;, telmisartan and coactivator peptide from SRC1 at 2.25 &amp;#xc5; resolution. The overall fold of PPAR&amp;#x3b3; is almost identical to previously-determined complex structures with agonists. However, telmisartan exhibits an unexpected binding mode, devoid of some essential hydrogen bonds for full activation of PPAR&amp;#x3b3;.
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/5265/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

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

Return of Kosi river induced by Tibet earthquake
Provedor de dados: 17
Autores: Saumitra Mukherjee.
Seismotectonics and change in river courses were correlated. Following the elastic rebound theory before the occurrence of the earthquake the subsurface rocks accumulate the energy by the tectonic movement. The Kosi river barrage was broken due to the tectonic forces accumulation in the south of Tibet Himalayas. Kosi river originates from Tibetan Himalayas and any disturbance in Tibet plateau has the potential to change the river course.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2278/version/2

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

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

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

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

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

&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

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

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

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

The True Colours of Carbon
Provedor de dados: 17
Autores: Sebastian Thomas; Ove O. H. G. Hoegh-Guldberg; Andrew Griffiths; Paul Dargusch; John Bruno.
Carbon offset projects in developing countries are one of the principal mechanisms designed to reduce greenhouse gas emissions and promote sustainable development yet have critical limitations in both areas. Here we present a framework for categorizing carbon offset projects according to four general approaches to the reduction of greenhouse gas emissions: (1) efficiency (&amp;#x27;Brown&amp;#x27;); innovation (&amp;#x27;Red&amp;#x27;), terrestrial sequestration (&amp;#x27;Green&amp;#x27;) or sequestration in aquatic environments (&amp;#x27;Blue&amp;#x27;). Analysis of the 6109 CDM projects currently in the CDM &amp;#x22;pipeline&amp;#x22; reveals that 99% are Brown or Red, and only 1% are Green or Blue, yet Green and Blue projects typically offer a far...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5099/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

Targeted delivery of anti-inflammatory therapy to rheumatoid tissue by fusion proteins containing an IL-4-linked synovial targeting peptide
Provedor de dados: 17
Autores: Sarah E. Wythe; Danielle DiCara; Taher E. I. Taher; Ciara M. Finucane; Rita Jones; Y. K. Stella Man; Michele Bombardieri; Ahuva Nissim; Stephen J. Mather; Yuti Chernajovsky; Costantino Pitzalis.
We provide first-time evidence that the synovial endothelium-targeting peptide (SyETP) CKSTHDRLC successfully delivers conjugated IL-4 to human rheumatoid synovium transplanted into SCID mice. SyETP, previously isolated by in vivo phage display and shown to preferentially localize to synovial xenografts, was linked by recombinant technology to hIL-4 via an MMP-cleavable sequence. Both IL-4 and the MMP-cleavable sequence were shown to be functional. IL-4-SyETP augmented production of IL-1ra by synoviocytes stimulated with IL-1[beta] in a dose-dependent manner. In vivo imaging confirmed increased retention of SyETP-linked-IL-4 in synovial grafts which was enhanced by increasing number of copies (one to three) in the constructs. Strikingly, SyETP delivered...
Tipo: Manuscript
Palavras-chave: Biotechnology; Immunology.
Ano: 2011
URL: http://precedings.nature.com/documents/6399/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

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 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

The circadian system alters thermoregulation depending on the time of day and feeding condition
Provedor de dados: 17
Autores: Kei Nagashima; Ken Tokizawa; Yuki Uchida.
The circadian rhythm of body temperature (Tb) is a well-known phenomenon. However, it is unknown how the circadian system affects thermoregulation. Food deprivation in mice induces a greater reduction of Tb particularly in the light phase. We examined the role of the clock gene and the suprachiasmatic nucleus (SCN) during induced hypothermia. At 20C with fasting, mice increased their metabolic heat production in the dark phase and maintained T~b~, whereas in the light phase, heat production was less, resulting in hypothermia. Under these conditions, neuronal activity in the SCN, assessed by cFos expression, increased only in the light phase. The differences between the phases in Clock mutant mice were less marked. The neural network between the SCN and...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2940/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

Sequence-specific Solution Structures of the Four Isosequential Pairs of Single-stranded DNAs and RNAs
Provedor de dados: 17
Autores: Subhrangsu  Chatterjee; Wimal  Pathmasiri; Jyoti Chattopadhyaya.
The role of the sequence-context in the self-organization of four single-stranded (ss) isosequential pairs of DNAs (1 &amp;#x2013; 4) and RNAs (5 &amp;#x2013; 8), [d/r-(5&amp;#x27;C^1^A^2^X^3^G^4^Y^5^A^6^C^7^): X^3^ = A or C, Y^5^ = A or C; sequence variations: 2^2^ = 4], has been elucidated by NMR-constrained Molecular Dynamics (MD) simulations (2 ns). Following sequence-specific observations have been made from the solution NMR and the NMR constrained MD simulation study: (i) Analysis of the NOESY footprints, mainly (H8/H6)~n~ to (H1&amp;#x27; and H3&amp;#x27;)~n-1~ contacts, of ssDNAs (1 - 4) and ssRNAs (5 &amp;#x2013; 8) in the aqueous medium have shown that all ssDNAs (1 - 4) and ssRNAs (5 - 8) adopt right handed stacked helical structures in the NMR...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1685/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

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

Workshop report: 1st INCF Workshop on Mouse and Rat Brain Digital Atlasing Systems
Provedor de dados: 17
Autores: Jyl Boline; Michael Hawrylycz; Robert W. Williams.
The goal of this workshop was to survey current activities and plans related to development of mouse and rat brain digital atlasing systems. The workshop discussed needs for and types of coordinated action that will ensure rapid progress, compatibility, and dissemination with use of novel technological approaches. The report summarizes the state-of-the-art in the field and provides recommendations for actions.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/1046/version/1

Shear stress activation of nitric oxide synthase and increased NO levels in human red blood cells
Provedor de dados: 17
Autores: Pinar Ulker; Nazmi Yaras; Ciler Celik-Ozenci; Herbert Meiselman; Oguz Baskurt.
Since the discovery of nitric oxide (NO) as a vasoactive molecule, red blood cells (RBC) have been considered to participate in NO-mediated control of the circulation. The classical role attributed to RBC was scavenging of NO, thereby impacting the local bioavailability of this important regulator of vascular tone^1^. RBC have been shown to be a source of NO, primarily via its transport bound to haemoglobin^2, 3^. Under specific conditions, haemoglobin plays an active role in converting NO derivatives (e.g., nitrite) to NO^4, 5^, with this NO originating from RBC being an effective modulator of vascular smooth muscle tone^6^. Interestingly, RBC contain a NO synthase (NOS) protein^7^, can actively synthesize NO using L-arginine as a substrate^8^, and can...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4608/version/1

Vitamin C insufficiency causes the stress-induced sudden death through the induction of extensive heart injury.
Provedor de dados: 17
Autores: Jae Seung Kang; Sung Joon Kim; Seyeon Bae; Joo Myung Kong; Na-Eun Lee; Hyung Gun Maeng; Yong Sung Kim; Hang Rae Kim; Hyemin Kim; Yong-Jin Kim; Seung-Pyo Lee; Kyung-Hee Kim; Daehee Kim; Dae-Won Sohn; Byung Joo Cho; Young Il Hwang; Wang Jae Lee.
Vitamin C scavenges toxic free radicals as an antioxidant, and oxidative stress is considered as a major contributor inducing damage to cardiomyocytes in heart diseases. Also, it is well-known that stress provokes oxidative stress and induces cardiac sudden death. Here we show the effects of vitamin C on the prevention of cardiac damage by stress in gulo(-/-) mice which cannot synthesize vitamin C. Vitamin C-insufficient gulo(-/-) mice under stress showed prominent cardiac damage and expired within 2 weeks. It was accompanied with structural changes in the heart, cardiac dysfunction and severe emphysema. These changes were caused by the elevation of pro-inflammatory cytokines, especially TNF-&amp;#x3b1;, the activation of MMP-2/MMP-9, an increase in...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4320/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

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

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

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

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

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

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

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

Structural Analysis of Outer Membrane Beta-stranded Porins using Temperature Factor
Provedor de dados: 17
Autores: Abhishek Kumar.
Computational and statistical analysis has formed a large component of the biophysical efforts put forth to understand protein structure and function, due to the diversity and complexity of their structure. Outer membrane proteins form a diverse and complex set of proteins. Of these, porins which allow passage of molecules across the membrane interface have been analyzed here from a biophysical and structural perspective. The objective of this study is to analyze the structural organization of porins using atomic temperature factor as a parameter. Generally atomic temperature factors of molecules from crystal structures indicate the degree of mobility or disorder seen in the crystal structure. As good crystal structures have fewer possibilities of errors...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7016/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

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

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

The persistent impact of incidental experience
Provedor de dados: 17
Autores: Matthew Wilder; Matt Jones; Alaa Ahmed; Tim Curran; Michael Mozer.
As we perform daily activities-- driving to work, unlocking the office door, grabbing a coffee cup-- our actions seem automatic and preprogrammed. Nonetheless, routine, well-practiced behavior is continually modulated by incidental experience: in repetitive experimental tasks, recent (~4) trials reliably influence performance and action choice. Psychological theories downplay the significance of sequential effects, explaining them as rapidly decaying perturbations of behavior with no long-term consequences. We challenge this traditional perspective in two studies designed to probe the impact of more distant experience, finding evidence for effects spanning up to a thousand intermediate events. We present a normative theory in which these persistent effects...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/6942/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

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

Understanding economical outcomes with the mental number line
Provedor de dados: 17
Autores: Carmelo Vicario.
With this study we provide evidence that the cognitive processes involved in addition/subtraction, mapped along the mental number line, seem to mediate our understanding of trading verbs. When left-to-right culture participants read &amp;#x22;loss&amp;#x22; verbs, cognitive activation moves &amp;#x22;leftward&amp;#x22; as in arithmetical subtraction, while reading &amp;#x22;gain&amp;#x22; verbs activates a mental rightward space as in addition. &amp;#xd;&amp;#xa;          We test this hypothesis by asking to a group of participants to use their left and right hand in judging (as correct of not) the syntactic form of several verbs meaning financial outcomes. Results show that processing &amp;#x201c;gain verbs&amp;#x201d; was associated with shorter...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5775/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

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

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

Systems level analysis of transgenerational spermatogenic inheritance predicts biomarkers and underlying pathways
Provedor de dados: 17
Autores: Abhay Sharma.
Transgenerational spermatogenic inheritance of adult male acquired CNS gene expression characteristics has recently been discovered using a Drosophila systems model. In this novel mode of inheritance, transcriptomic alteration induced by the neuroactive drug pentylenetetrazole (PTZ) has been found to leak to future generations. Here, the available microarray gene expression data pertaining to CNS and/or testis of exposed F0 and the resulting F1 and F2 generations has been pooled and analyzed in an unbiased manner at four levels, namely, biological processes and pathways, protein interactome networks, miRNA-targets, and microarray expression profile similarities. Enrichment for processes related to translation, energy metabolism, cell proliferation, cell...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3312/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

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

Visual consciousness tracked with direct intracranial recording from early visual cortex in humans
Provedor de dados: 17
Autores: Naotsugu Tsuchiya; Jeffrey Chung; Dawn Eliashiv; Ralph Adolphs; Adam Mamelak.
A fundamental question in cognitive neuroscience is how neuronal representations are related to conscious experience.&amp;#xd;&amp;#xa;Two key questions are: where in the brain such representations are located, and at what point in time they correlate with conscious experience. In line with this issue, a hotly debated question is whether primary visual cortex (V1) contributes to visual consciousness, or whether this depends only on higher-order cortices. Here we investigated this issue by recording directly from early visual cortex in two neurosurgical patients undergoing epilepsy monitoring with intracranial electrocorticogram (ECoG) electrodes that covered early visual cortices, including the dorsal and ventral banks of the calcarine sulcus. We used...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6040/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

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

The &amp;#x201c;Minimum Information about an ENvironmental Sequence&amp;#x201d; (MIENS) specification
Provedor de dados: 17
Autores: Pelin  Yilmaz; Renzo Kottmann; Dawn Field; Rob Knight; James R. Cole; Linda Amaral-Zettler; Jack A. Gilbert; Ilene Karsch-Mizrachi; Anjanette  Johnston; Guy Cochrane; Robert  Vaughan; Christopher Hunter; Joonhong Park; Norman Morrison; Phillipe Rocca-Serra; Peter Sterk; Mani Arumugam; Laura Baumgartner; Bruce W. Birren; Martin J. Blaser; Vivien Bonazzi; Peer Bork; Pier Luigi Buttigieg; Patrick Chain; Elizabeth K. Costello; Heather Huot-Creasy; Peter Dawyndt; Todd DeSantis; Noah Fierer; Jed Fuhrman; Rachel E. Gallery; Richard A. Gibbs; Michelle Gwinn Giglio; Inigo San Gil; Elizabeth M. Glass; Antonio Gonzalez; Jeffrey I. Gordon; Robert Guralnick; Wolfgang Hankeln; Sarah Highlander; Philip Hugenholtz; Janet Jansson; Jerry Kennedy; Dan Knights; Omry Koren; Justin Kuczynski; Nikos Kyrpides; Robert Larsen; Christian L. Lauber; Teresa Legg; Ruth E. Ley; Catherine  A. Lozupone; Wolfgang Ludwig; Donna Lyons; Eamonn  Maguire; Barbara A. Meth&amp;#xe9;; Folker Meyer; Sara Nakielny; Karen E. Nelson; Diana Nemergut; Josh D. Neufeld; Norman R. Pace; Giriprakash Palanisamy; J&amp;#xf6;rg Peplies; Jane Peterson; Joseph Petrosino; Lita Proctor; Jeroen Raes; Sujeevan Ratnasingham; Jacques Ravel; David A. Relman; Susanna Assunta-Sansone; Lynn Schriml; Erica Sodergren; Aym&amp;#xe9; Spor; Jesse Stombaugh; James M. Tiedje; Doyle V. Ward; George M. Weinstock; Doug Wendel; Owen White; Andreas Wilke; Jennifer Wortmann; Frank Oliver Gl&amp;#xf6;ckner.
We present the Genomic Standards Consortium&amp;#x2019;s (GSC) &amp;#x201c;Minimum Information about an ENvironmental Sequence&amp;#x201d; (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5252/version/1

Towards an Ontological Representation of Resistance: The Case of MRSa
Provedor de dados: 17
Autores: Albert Goldfain; Lindsay G. Cowell; Barry Smith.
This paper addresses a family of issues surrounding the biological phenomenon of resistance and its representation in realist ontologies. Resistance terms from various existing ontologies are examined and found to be either overly narrow, inconsistent, or&amp;#xd;&amp;#xa;otherwise problematic. We propose a more coherent ontological representation using the antibiotic resistance in Methicillin-Resistant _Staphylococcus aureus_ (MRSa) as a case study.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3474/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

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

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

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

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

The last Charrua Indian; (Uruguay): analysis of the remains of Chief Vaimaca Per&amp;#xfa;.
Provedor de dados: 17
Autores: Monica Sans; Gonzalo Figueiro; Carlos Sanguinetti; Lourdes Echarte-Rafaelli; Cecilia Portela; Luis Taranto; Carlos Pizzarossa; Roberto Oliver; Rosana Manikowski; Isabel Barreto; Pedro C. Hidalgo; Guido Berro.
Uruguay is the only Latin American country that at present lacks Native populations and little is known about its prehistoric populations. In the construction of National identity, the unique reference to Natives is about Charra Indians, one of the most important ethnic groups that lived in the territory and exterminated in the 1830s. In 1833, four survivors were taken to be exhibited and studied in France, becoming martyrs and a symbol of their nation. The skeletal remains of Chief Per&amp;#xfa; were preserved and studied mainly by Rivet1; these are the only remains certainly identified as belonging to a Charr&amp;#xfa;a. In 2002, the French government returned the remains to Uruguay, where they were buried with honours at the National Pantheon. Before...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/4415/version/1

Vestibular stimulation reduces unrealistic optimism
Provedor de dados: 17
Autores: Corinne Tamagni; Antonella  Palla; Peter  Krummenacher; Deborah  Vitacco; Elisabeth  Huberle; Dominik  Straumann; Stefan  C. A. Hegemann; Ryan McKay; Peter Brugger.
Unrealistic optimism (UO) refers to the tendency of healthy people to underestimate their risk of future misfortune. Just as left-ear caloric irrigation attenuates anosognosia (denial of manifest illness) in clinical patients, we found that it also reduces UO about future health risks in healthy individuals. This finding demonstrates asymmetric hemispheric involvement in emotion regulation and self-evaluation, and suggests that a similar neuropsychological process underpins anosognosia and healthy optimism.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4519/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

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

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

Regulating Nanomedicine: A European perspective
Provedor de dados: 17
Autores: Joel D&amp;#x27;Silva; Geert Van Calster.
The potential impact of nanomedicine is foreseen to radically change health care; however it also challenges existing perceptions, dynamics and standards relating to ethics, safety and governance. This commentary briefly highlights aspects and approaches pertaining to nanomedical regulation in the European Union.
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2388/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

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

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

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

Synaptic modification and entrained phase are phase dependent in STDP
Provedor de dados: 17
Autores: Gang Zhao.
Synapse strength can be modified in an activity dependent manner, in which the temporal relationship between pre- and post-synaptic spikes plays a major role. This spike timing dependent plasticity (STDP) has profound implications in neural coding, computation and functionality, and this line of research is booming in recent years. Many functional roles of STDP have been put forward. Because the STDP learning curve is strongly nonlinear, initial state may have great impacts on the eventual state of the system. However, this feature has not been explored before. This paper proposes two possible functional roles of STDP by considering the influence of initial state in modeling studies. First, STDP could lead to phase-dependent synaptic modification that have...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1921/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 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

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

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

Reduced glutathione and cysteine hydrochloride on crossbred bull semen
Provedor de dados: 17
Autores: P Perumal.
Over the last few years, good quality freezable semen was not utilized effectively due to less knowledge about the freezability of semen. One reason is the lack of sufficient antioxidants in the seminal plasma and semen extender. The antioxidant content is reduced during the cryopreservation process and causes premature cryo-capacitation and modification of sperm membrane structure upon thawing. So the study of pre-freezing and post thaw seminal parameters like viability, motility, acrosomal integrity, lipid peroxide assay, vanguard distance traveled by sperm, mitochondrial membrane potential, velocity and motility parameters (CASA) and field fertility trial helped to assess the effectiveness of the additives. The conception rate was better in reduced...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/6998/version/1

Tap Water vs. Bottled Water in a Footprint Integrated Approach
Provedor de dados: 17
Autores: Stefano Botto.
A Footprint Integrated approach was used to assess and compare the impact on the environment and on the resources of tap water (TW) and pet-bottled natural mineral water (BW). A set of BW from six Italian companies was analyzed. This set covers about the 10% (by volume) of the total marketed bottled waters in Italy. TW is the public water available in Siena (Italy). The functional unit is a volume of water of 1.5 L.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;An ad hoc Footprint methodology was defined, integrating Ecological Footprint (EF), Water Footprint (WF) and Carbon Footprint (CF). A Life Cycle Assessment (LCA) was performed, in order to derive the material and energy inputs and outputs of each upstream and downstream process required by the two ways of...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3407/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

Variability In The Ecoraces Of Tropical Tasar Sillkworm Antheraea Mylitta  Drury
Provedor de dados: 17
Autores: Ajit Kumar Sinha.
Tropical tasar silkworm, Antheraea mylitta Drury is exploited in countries for commercial silk production and improved varieties of these silkworms can be evolved by employing various breeding techniques. As the insect has established itself in various forms of ecological populations (Commonly called as ecoraces) in different geographical niches of the country depending on food plants and micro-environmental conditions available to them, the species exists in the form of nearly 44 ecoraces (Singh and Srivastava,1997, Srivastava,2002 and Srivastava et at. 2007) distributed over different states. However, due to free interbreeding in nature for centuries, the fauna is highly heterogeneous.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Tasar culture is a forest based...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6161/version/1

Soybean Composition Database from NIR, NMR and GC-MS Analyses
Provedor de dados: 17
Autores: I. C. Baianu.
This novel Soybean Composition Database from the AFC-NMR &amp;#x26; NIR Spectroscopy Facility of the College of ACES at the University of Illinois at Urbana includes more than 12,000 NIR measurements on soybeans from the International Soybean Germplasm Collection, such as those received from Peking at the National Soybean Collection.&amp;#xd;&amp;#xa;Excel files (.xls) of our novel spectroscopic data are currently available for all 80,000 + NIR and FT-NMR measurements; such data are made available from an ultra-fast and secure supercomputer server utilizing the current version of the Scientific-Linux OS-based software. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A detailed account is also presented of our high-resolution nuclear magnetic resonance (HR-NMR) and...
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/6201/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

The Traveling Salesman Problem in the Natural Environment
Provedor de dados: 17
Autores: Flip Phillips; Thomas O&amp;#x27;Connell; Oliver W. Layton.
Is it possible for humans to navigate in the natural environment wherein the path taken between various destinations is &amp;#x27;optimal&amp;#x27; in some way? In the domain of optimization this challenge is traditionally framed as the &amp;#x22;Traveling Salesman Problem&amp;#x22; (TSP). What strategies and ecological considerations are plausible for human navigation? When given a two-dimensional map-like presentation of the destinations, participants solve this optimization exceptionally well (only 2-3% longer than optimum)^1, 2^. In the following experiments we investigate the effect of effort and its environmental affordance on navigation decisions when humans solve the TSP in the natural environment. Fifteen locations were marked on two outdoor...
Tipo: Manuscript
Palavras-chave: Neuroscience; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4960/version/1

Some Computational Aspects of Essential Properties of Evolution and Life
Provedor de dados: 17
Autores: Hector Zenil; James A. R. Marshall.
While evolution has inspired algorithmic methods of heuristic optimisation, little has been done in the way of using concepts of computation to advance our understanding of salient aspects of biological evolution. We argue that under reasonable assumptions, interesting conclusions can be drawn that are of relevance to behavioural evolution. We will focus on two important features of life--robustness and fitness optimisation--which, we will argue, are related to algorithmic probability and to the thermodynamics of computation, subjects that may be capable of explaining and modelling key features of living organisms, and which can be used in understanding and formulating algorithms of evolutionary computation.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6867/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

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 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

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

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

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

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

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

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

Remarks on the number of tubulin dimers per neuron and implications for Hameroff-Penrose Orch OR
Provedor de dados: 17
Autores: Danko Georgiev.
Stuart Hameroff has wrongly estimated that a typical brain neuron has 10^7^ tubulin dimers and wrongly attributed this result to Yu and Baas, J. Neurosci. 1994; 14: 2818-2829. In this letter we show that Hameroff&amp;#x2019;s estimate is based on misunderstanding of the results provided by Yu and Baas, who actually measured the total microtubule length in a single axonal projection with length of 56 &amp;#x3bc;m in a differentiating in vitro stage 3 embryonic hippocampal neuron. In order to visualize how big Hameroff&amp;#x2019;s error is, we have reconstructed two of the studied by Yu and Baas embryonic hippocampal neurons with Neuromantic v1.6.3 and compared them with previously published reconstructions of adult hippocampal neurons. Correct calculations...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3860/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

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

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

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

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

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

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

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

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

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

Rapid antigen detection using the liquid sample as a lens and self-mixer for light scattering detection
Provedor de dados: 17
Autores: Antonio Garcia; John Schneider.
Superhydrophobic surfaces, both natural and artificial, cause aqueous drops to bead on them. The most water-repellent surfaces produce nearly perfect spheres with very little contact between water, solutes, and surface due to the roughness of the surface ^1^. However, a related phenomenon that has not been well appreciated until recently, is that colloidal particles in the aqueous drop remain highly mobile, and smaller-sized colloids migrate to the drop surface due to both the driving force of evaporation and the expanded liquid/air interface ^2-3^. A newly identified, third useful optical property resulting from the suspension of an aqueous drop by the superhydrophobic surface is that a spheroidal lens is created. Without any additional energy or...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4754/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

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

Use of inadequate data and methodological errors lead to a dramatic overestimation of the water footprint of Jatropha curcas
Provedor de dados: 17
Autores: Wouter  Maes; Wouter M. J. Achten; Bart Muys.
In their recent article, Gerbens-Leenes et al. (1) calculated the water footprint (WF, the amount of water required to produce 1 GJ of energy) of several bioenergy crops. One of the most remarkable findings of this study was the very high water footprint of this species, which has serious management consequences. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;However, these results are in apparent contrast with recent findings on this species. We present evidence that several errors were made by the authors when calculating the water footprint of jatropha, which has lead to a dramatic overestimation. These errors include weaknesses concerning the data used for the calculation of the water footprint, as well as flaws in the calculation method, as we demonstrate in the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Earth &amp; Environment; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3410/version/1

Reduction of adipose tissue mass by the angiogenesis inhibitor ALS-L1023
Provedor de dados: 17
Autores: Michung Yoon; Hyunhee Lee; Yeonhee Hong; Dongmin Park; Jaeho Oh; Byung-Young Park; Hee Lee; Eun kyu Park; Jong Cheon Hahm; Min-Young Kim.
Objective: Angiogenesis has been demonstrated to modulate adipogenesis and obesity. This study was undertaken to determine whether the botanical drug ALS-L1023 (ALS), which exhibits antiangiogenic activity, can regulate adipose tissue growth in high-fat-diet-induced obese mice.Materials and Methods: The effects of ALS on angiogenesis and extracellular matrix remodeling were measured using in vitro assays. The effects of ALS on adipose tissue growth was investigated in nutritionally obese mice. Results: ALS inhibited angiogenesis in a concentration-dependent manner in the tube formation assay and the VEGF-induced proliferation assay using human umbilical vein endothelial cells. ALS also suppressed matrix metalloproteinase (MMP) activity in vitro. ALS...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6256/version/1

Synchronized Mammalian Cells in Culture: A Comparison of Normal and KB Cancer Cell Growth
Provedor de dados: 17
Autores: I. C. Baianu.
Experimentation and tests with cells in culture and cell synchronization or synchrony are important in order to be able to make both reliable and high-sensitivity measurements. This is also very important for mechanistic studies of cell division control, oncogenesis and tumor growth. A comparison is made in this article between the initially synchronized cell growth of rabbit and KB cells in synchronized cultures.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7128/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

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

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

Study of planktonic morphotype of the Abderaz Formation at type section, Iran
Provedor de dados: 17
Autores: Meysam Shafiee Ardestani.
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.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3189/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

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

Temporal trends in annual water yields from the Mackenzie, Saskatchewan-Nelson, Churchill, and Missouri-Mississippi River watersheds in western and northern Canada
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Historical temporal trends in annual water yields were examined at 109 hydrometric monitoring stations in the Mackenzie, Saskatchewan-Nelson, Churchill, and Missouri-Mississippi River watersheds from the western Canadian provinces of Alberta, Saskatchewan, and northeastern British Columbia, as well as the Northwest Territories and the eastern portion of the Yukon territory. Effective drainage areas range in size from 325 to 1,680,000 (mean=65,600; median=9,300) km^2^, with associated hydrometric record lengths ranging between 18 and 97 (mean=41; median=38) years. Approximately three-quarters of the stations have no significant trend in average annual flow, with about equal numbers of stations exhibiting significant temporal increases or decreases in annual...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5342/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

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

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

Ustilago and the accidental domestication of maize
Provedor de dados: 17
Autores: Juan Pablo Martinez-Soriano; Katia Avina-Padilla.
Maize is the essential crop of the Americas. Maize appeared suddenly about 8,500 years ago as domesticated teosinte; however, there is no evidence (genetical, archaeological, linguistic or ethnobotanical) able to support a gradual transformation from the teosinte ear into the corn ear. Teosinte has never been cultivated by Americans, nor did they ever attempt to domesticate it. Its grains were not used as food, making unrealistic the assumption that prehispanics created something edible from seeds that were not so. Plant domestication is a slow process in almost every known crop but maize evolution might not be the case. Teosinte has a brittle cob, whereas maize forms solid ones that do not release their seeds 2. The latter are soft, while in teosinte they...
Tipo: Manuscript
Palavras-chave: Plant Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3240/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

The Hepatocellular Hypoxia Criteria:2&amp;#x2019;Nitroimidazole Effect on Hepatocyte Carbohydrate Metabolizing Enzymes
Provedor de dados: 17
Autores: Rakesh Sharma.
Aim:  to understand the 2&amp;#x2019;-nitroimidazole induced hypoxia and liver cell interaction, we proposed a &amp;#x201c;Hapatocellular Hypoxia Criteria&amp;#x201d;. Hypothesis: The nitroimidazole induced metabolic energy loss and oxygen depletion (hypoxia) in liver cell mitochondria causes the phagocytosis.  Based on it, ten control subjects with 2&amp;#x2019;-nitroimidazole therapy were studied for their carbohydrate metabolizing enzymes in serum and hepatocellular enzymes in liver biopsy tissues.  Materials and Methods: Proven ten control subjects were studied for hypoxia by enzyme assays.  The 2&amp;#x2019;nitroimidazole treated paired ten subjects were studied for hypoxia using enzyme assays and hepatocellular cytomorphology by electron microscopy....
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2738/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

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

The History, Development and Impact of Computed Imaging in Neurological Diagnosis and Neurosurgery: CT, MRI, and DTI
Provedor de dados: 17
Autores: Aaron G. Filler.
A steady series of advances in physics, mathematics, computers and clinical imaging science have progressively transformed diagnosis and treatment of neurological and neurosurgical disorders in the 115 years between the discovery of the X-ray and the advent of high resolution diffusion based functional MRI. The story of the progress in human terms, with its battles for priorities, forgotten advances, competing claims, public battles for Nobel Prizes, and patent priority litigations bring alive the human drama of this remarkable collective achievement in computed medical imaging.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3267/version/1

Weight Stigma and Educators&amp;#x27; Perceptions of Children&amp;#x27;s Psychological Symptoms
Provedor de dados: 17
Autores: John Pryor; Laura Reber.
Objective: To investigate whether weight stigma influences educators&amp;#x27; judgments about psychological symptoms in children.Design: Experimental study manipulating the weight status of children with school problems and examining implicit and explicit anti-fat attitudes as potential moderators of stigmatizing judgments.Subjects: 188 pre-service educators.Measurements: Attributions of laziness as primary dependent variable plus measures of implicit and explicit anti-fat attitudes as potential moderators.Results: Educators were more likely to attribute laziness to overweight children with school problems. Implicit anti-fat attitudes moderated this effect.Conclusion: Spontaneous anti-fat attitudes were importantly related to educators&amp;#x27; biases in...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2133/version/1

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

Ten reasons NOT to fix the numerical value of the Avogadro constant
Provedor de dados: 17
Autores: Nigel Wheatley.
This discussion paper, circulated in advance of the 17th meeting of the Consultative Committee for Amount of Substance, addresses the proposed redefinition of the mole in terms of a fixed numerical value for the Avogadro constant. It gives ten reasons why the Avogadro constant should not be given a fixed numerical value in the International System of Units, noting that there would be no metrological benefit from such a change, and that the proposed redefinition would be more conceptually complex that the current one and divorced from practical measurement and historical background. As the conditions for redefinition of the kilogram have not been met, and no mise en pratique has been produced for the proposed new definition, the paper concludes that the...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/5828/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

Role of intellectual property rights in biotechnology and pharmaceutical industries
Provedor de dados: 17
Autores: Ajeet Ajeet.
The main objective of this review is to highlight and explore the inter-relationship and the functioning of the intellectual property right in the pharmaceutical and biotechnology industry. The rising tide of patent applications can be witnessed globally in this industry as the need for such protection and licensing has become imperative so as to safeguard the rights of the inventor and also to encourage and promote new talents, inventions and innovations which can be a boon for the economy. The field of biotechnology is an upcoming science which is still at the initial stage of establishing  a foundation but it promises a revolution in the fields of  medicine, agriculture, pharmaceuticals and industrial sector amongst  other sectors of the economy along...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2012
URL: http://precedings.nature.com/documents/7065/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

Viral organization of human proteins
Provedor de dados: 17
Autores: Stefan Wuchty.
A compilation of experimentally verified interactions between HIV-1 and human proteins allows insights into the intricate interplay between viral and host proteins on a large scale.We find that HIV-1 predominantly targets rich-clubs, human proteins that are not only well connected but also strongly intertwined among each other. These assemblies of proteins putatively serve as an infection gateway, allowing the virus to take control of the human host by reaching protein pathways and diversified cellular functions in a pronounced and focused way. In particular, HIV-1 utilizes its small number of proteins in a combinatorial manner, exerting a significant influence on pathways that deal with transcriptional, translational and degradation processes....
Tipo: Manuscript
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2041/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

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

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

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

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

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

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

The stroboscopic human vision
Provedor de dados: 17
Autores: Maarten A. Bouman.
When the frequency of seeing light from a pair of point flashes is beyond the probability summation of the separate flashes, the surplus is due to the successful interaction of subliminal responses from the different flashes. Experiments with various distances and various periods of the pair show thet successful interaction occurs when in each of two successive time-quanta of 0.04 seconds and in each of two adjacent distinct receptor groups at least one subliminal receptor response occurs. An autonomous source produces the time-quanta. It serves the time-processing of the central nervous system and of the motor system. Posdsibly, action potentials from the purkinje cells of the myocardium play a role. Hyper acuity in direction and in depth, flicker fusion,...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4663/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

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

Understanding Consciousness: An Online Workshop on Contemporary Theories
Provedor de dados: 17
Autores: Alfredo Pereira Jr; Jonathan Edwards; Dietrich Lehmann; Chris Nunn; Arnold Trehub; Max Velmans.
An invited workshop on &amp;#x2018;Theories of Consciousness&amp;#x2019; was organized in the format of a Nature Network closed group during the second semester of 2009. There were presentations by each of 15 authors active in the field, followed by debate with other presenters and invitees. A week was allocated to each of the theories proposed; general discussion threads were also opened from time to time, as seemed appropriate. We (who had been participants in the workshop) offer here an account of the principal outcomes. It can be regarded as a contemporary, &amp;#x2018;state of the art&amp;#x2019; snapshot of thinking in this field.
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4348/version/1

The Antarctic &amp;#x27;ozone hole&amp;#x27; combined with no sea ice causes severe oxidative damage in echinoid embryos
Provedor de dados: 17
Autores: Kathryn  N. Lister; Miles Lamare; David Burritt.
Over the past three decades, the &amp;#x27;ozone hole&amp;#x27; has caused a transient increase in the levels of ultraviolet B radiation (UV-B, 280 to 320 nm) reaching Antarctic coastal marine ecosystems^1^. The direct effect of this enhanced UV-B on pelagic organisms remains unclear, for few studies have examined in situ the responses of Antarctic marine organisms in direct relation to the &amp;#x27;ozone hole&amp;#x27;. Here we show that the presence of the &amp;#x27;ozone hole&amp;#x27; over McMurdo Sound, Antarctica, during a two-week period in 2008 resulted in unequivocal increases in oxidative damage and developmental abnormality in embryos of the sea urchin _Sterechinus neumayeri_ Meissner (Echinoidea: Echinidae) growing in open waters. We show that...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2906/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

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

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

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

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

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

VO: Vaccine Ontology
Provedor de dados: 17
Autores: Yongqun He; Lindsay Cowell; Alexander  D. Diehl; Harry  Mobley; Bjoern  Peters; Alan  Ruttenberg; Richard  H. Scheuermann; Ryan R. Brinkman; Melanie  Courtot; Chris Mungall; Zuoshuang  Xiang; Fang Chen; Thomas  Todd; Lesley  Colby; Howard  Rush; Trish  Whetzel; Mark  A. Musen; Brian  D. Athey; Gilbert  S. Omenn; Barry  Smith.
The collaborative, community-based Vaccine Ontology (VO) was developed to promote vaccine data standardization, integration, and computer-assisted reasoning. Currently VO covers a variety of aspects of the vaccine domain, with an emphasis on classification of vaccines and vaccine components, and on host immune response to vaccines. VO can be used for a number of applications, e.g., ontology-based vaccine literature mining through collaboration with the National Center for Integrative Biomedical Informatics (NCIBI).
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3553/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

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

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

Young and Early Career Investigators: Report from a Global HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: Dan H. Barouch; Thumbi  Ndung&amp;#x2019;u; Galit  Alter; Timothy  Cardozo; Bhavna  Chohan; Jacques  Fellay; Nicole  Frahm; Jonathan Fuchs; Alasdair Leslie; Yong Liu; Penny  L. Moore; Raul  Rabadan.
The scientific challenges facing HIV-1 vaccine development are unprecedented in the history of vaccinology. As a result, investigators, funders, and other stakeholders generally agree that &amp;#x201c;game-changing&amp;#x201d; ideas are required. While innovation can certainly arise from investigators at all career stages, young and early-career investigators, defined as those under 40 years of age or within 10 years of their final degree or clinical training, are especially key contributors of novel and transformative ideas. Young and early-career investigators bring energy, enthusiasm, and fresh perspectives that are unbiased by prevailing dogma and that are essential to scientific progress.
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4800/version/2

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

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

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

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

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

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

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

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

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

The Origin and Evolution of Viruses as Molecular Organisms
Provedor de dados: 17
Autores: Claudiu I. Bandea.
Viruses are the most abundant life forms and the repertoire of viral genes is greater than that of cellular genes. It is also evident that viruses have played a major role in driving cellular evolution, and yet, viruses are not part of mainstream biology, nor are they included in the Tree of Life. A reason for this major paradox in biology is the misleading dogma of viruses as viral particles and their enigmatic evolutionary origin. This article presents an alternative view about the nature of viruses based on their properties during the intracellular stage of their life cycle, when viruses express features comparable to those of many parasitic cellular species. Supporting this view about the nature of viruses is a novel hypothetical evolutionary model for...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3886/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

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

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

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

The role of acute inflammation at the peritoneal cavity-enhanced adhesion formation
Provedor de dados: 17
Autores: Roberta Corona; Karina Mailova; Maria Mercedes Binda; Ron Schonman; Jasper Verguts; Philippe Robert Koninckx.
_Objective_: To investigate the role of acute inflammation of the peritoneal cavity in adhesion formation. &amp;#xd;&amp;#xa;_Design_: Prospective randomized, controlled trial &amp;#xd;&amp;#xa;_Setting_: University laboratory research center&amp;#xd;&amp;#xa;_Animals_: 9-10 weeks old BALB/c female mice &amp;#xd;&amp;#xa;_Interventions_: In our laparoscopic mouse model acute inflammation of the peritoneal cavity and adhesion formation were evaluated in a control group with CO2 pneumoperitoneum (PP)-enhanced adhesions, in CO2 PP plus manipulation-enhanced adhesions and in the latter group + dexamethasone-reduced adhesions. Adhesions and acute inflammation were assessed by neoangiogenesis, diapedesis and leukocytes accumulation on the 2nd day after surgery....
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4788/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

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

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

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

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

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

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

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

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

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

Solving the protein folding problems
Provedor de dados: 17
Autores: Robert P. Bywater.
The protein folding problem persists in being the major unsolved problem in biophysics and molecular biology. The most immediate obstacle to its solution is said to be the immense combinatorial difficulty of finding the global minimum energy structure, due to the galactic number of possible rotamer states for the polypeptide backbone and its sidechains, the so-called Levinthal paradox1. Much attention has been paid to the topography of the free energy surface that the folding polypeptide has to negotiate in order to find this minimum and the notion of a funnel-shaped topography has been proposed2. While this has achieved wide acceptance, providing insight into the possible shape of the free energy surface, it still does not solve the problem. In this work...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4730/version/1

Stronger inflammatory/cytotoxic T cell response in women identified by microarray analysis
Provedor de dados: 17
Autores: Anura Hewagama; Dipak Patel; Sushma Yarlagadda; Faith M. Strickland; Bruce  C. Richardson.
Women develop chronic inflammatory autoimmune diseases like lupus more often than men. The mechanisms causing the increased susceptibility are incompletely understood, although estrogen is believed to contribute. Chronic immune stimulation characterizes many autoimmune disorders. We hypothesized that repeated stimulation may cause a different T cell immune response in women than men. Microarray approaches were used to compare gene expression in T cells from healthy men and women with and without repeated stimulation. Four days following a single stimulation only 25% of the differentially expressed, gender-biased genes were expressed at higher levels in the women. In contrast, following restimulation 72% were more highly expressed in women. Immune response...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology.
Ano: 2008
URL: http://precedings.nature.com/documents/2690/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

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

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

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

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

Serine biosynthesis with one carbon catabolism represents a novel pathway for ATP generation in cells using alternative glycolysis with zero net ATP production
Provedor de dados: 17
Autores: Alexei Vazquez; Zoltan N. Oltvai.
Recent experimental evidence indicates that some cancer cells have an alternative glycolysis pathway with net zero ATP production, implying that upregulation of glycolysis in these cells may not be related to the generation of ATP. Here we use a genome-scale model of human cell metabolism to investigate the potential metabolic alterations in cells using net zero ATP glycolysis. We uncover a novel pathway for ATP generation that involves reactions from the serine biosynthesis and one-carbon metabolism pathways. This pathway has a predicted two-fold higher flux rate in cells using net zero ATP glycolysis than those using standard glycolysis and generates twice as much ATP with significantly lower rate of lactate- but higher rate of alanine secretion. Thus,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6123/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

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

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

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

Spherulites of A[beta]~42~ in vitro and in Alzheimer&amp;#x27;s disease
Provedor de dados: 17
Autores: Christopher Exley; Emily House; Joanna F. Collingwood; Mark R. Davidson; Danielle Cannon; Athene M. Donald.
Several amyloid-forming proteins and peptides, including insulin^1^, [beta]-lactoglobulin^2^ and albumin^3^, form spherulites in vitro under non-physiological solution conditions. These micrometer-sized, roughly spherical structures are composed of ordered arrays of [beta] sheets of amyloid fibrils in radial arrangements which, characteristically, show a typical Maltese cross pattern of light extinction under the polarizing microscope. The physiological significance, if any, of these amyloid super assemblies is unknown although in Alzheimer&amp;#x27;s disease there is the suggestion that senile plaques composed primarily of [beta] sheets of A[beta]~42~ are spherulitic^4^. Herein we describe the first observation of the formation in vitro of spherulites of...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3982/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

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

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

The genetic equidistance result of molecular evolution is independent of mutation rates
Provedor de dados: 17
Autores: Shi Huang.
The well-established genetic equidistance result shows that sister species are approximately equidistant to a simpler outgroup as measured by DNA or protein dissimilarity.  The equidistance result is the most direct evidence, and remains the only evidence, for the constant mutation rate interpretation of this result, known as the molecular clock.  However, data independent of the equidistance result have steadily accumulated in recent years that often violate a constant mutation rate.  Many have automatically inferred non-equidistance whenever a non-constant mutation rate was observed, based on the unproven assumption that the equidistance result is an outcome of constant mutation rate.  Here it is shown that the equidistance result remains valid even when...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1733/version/2

The Unfolded Protein Response and its potential role in Huntington&amp;#x27;s disease
Provedor de dados: 17
Autores: Ravi  K. R. Kalathur; Kamesh Ayasolla; Matthias E. Futschik.
Huntington&amp;#x27;s disease (HD) is a progressive, neurodegenerative disease with fatal outcome. Although the disease-causing gene (huntingtin) has been known for some time, the exact cause of neuronal cell death is still unknown. One potential mechanism contributing to the massive loss of neurons in the brain of HD patients might be the unfolded protein response (UPR), which is activated by accumulation of misfolded proteins in the endoplasmatic reticulum (ER). As an adaptive response to counter-balance accumulation of un- or misfolded proteins, the UPR upregulates transcription of chaperones, temporarily attenuates new translation, and activates protein degradation via the proteasome. However, it is known that persistent ER stress and activated UPR can...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7145/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

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

The Relationship between Physical Activity and Body Mass Index: Issues in Model Specification
Provedor de dados: 17
Autores: Gizachew Tiruneh.
*Objective*: To investigate the best statistical models that describe the effect of physical activity on BMI.&amp;#xd;&amp;#xa;*Design*: Cross-sectional analyses of physical activity and BMI data. &amp;#xd;&amp;#xa;*Subjects*: 107 obese, overweight, and healthy college students (mean duration of physical activity for the normal, overweight, and obese students: 89, 59, and 24 months, respectively; mean BMI for the normal, overweight, and obese students: 21.61, 27.07, and 35.54 kg/m2, respectively).&amp;#xd;&amp;#xa;*Measurements*: Inverse linear, inverse logarithmic, and inverse logistics models were used to analyze survey data for physical activity (measured by both frequency and duration of exercise) and BMI. Gender, age, and physical intensity variables...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/2758/version/5

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

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

Representation of Sounds in Auditory Cortex of Awake Rats (Dissertation)
Provedor de dados: 17
Autores: Tom&amp;#xe1;&amp;#x161; Hrom&amp;#xe1;dka.
This thesis is divided into six chapters (following Introduction). Each chapter was intended to be self-contained, so they do not have to be read in the order they are presented.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Second chapter (Sec. 2) contains a detailed description of experimental techniques: surgery, recording, and training techniques we used in awake head-fixed rats. We have also included a detailed description of all sets of stimuli we used to probe neurons, analytical methods used to analyze data, and description of computational models used in other parts of the thesis.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Third chapter (Sec. 3) focuses on description of single-neuron responses in primary auditory cortex of awake head-fixed rats. The primary...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2464/version/1

The Control Fallacy: Why OA Out-Innovates the Alternative
Provedor de dados: 17
Autores: John Wilbanks.
This article examines the relationship between Open Access to the scholarly literature and innovation. It traces the ideas of &amp;#x22;end to end&amp;#x22; network principles in the Internet and the World Wide Web and applies them to the scholarly biomedical literature. And the article argues for the importance of relieving not just price barriers but permission barriers.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1808/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

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

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

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

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

The Relationship between Physical Activity and Body Mass Index: Issues in Model Specification
Provedor de dados: 17
Autores: Gizachew Tiruneh.
*Objective:* To investigate the best statistical models that describe the effect of physical activity on BMI.&amp;#xd;&amp;#xa;*Design:* Cross-sectional analyses of physical activity and BMI data.Subjects: 107 obese, overweight, and healthy college students (mean duration of physical activity for the normal, overweight, and obese students: 89, 59, and 24 months, respectively; mean BMI for the normal, overweight, and obese students: 21.61, 27.07, and 35.54 kg/m^2^, respectively).&amp;#xd;&amp;#xa;*Measurements:* Inverse linear, inverse logarithmic, and inverse logistics models were used to analyze survey data for physical activity (measured by both frequency and duration of exercise) and BMI. Gender, age, and physical intensity variables were also...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2758/version/2

Suitability of dysphonia measurements for telemonitoring of Parkinson&amp;#x2019;s disease
Provedor de dados: 17
Autores: Max A. Little; Patrick E. McSharry; Eric J. Hunter; Jennifer Spielman; Lorraine O. Ramig.
We present an assessment of the practical value of existing traditional and non-standard measures for discriminating healthy people from people with Parkinson?s disease (PD) by detecting dysphonia. We introduce a new measure of dysphonia, Pitch Period Entropy (PPE), which is robust to many uncontrollable confounding effects including noisy acoustic environments and normal, healthy variations in voice frequency. We collected sustained phonations from 31 people, 23 with PD. We then selected 10 highly uncorrelated measures, and an exhaustive search of all possible combinations of these measures finds four that in combination lead to overall correct classification performance of 91.4%, using a kernel support vector machine. In conclusion, we find that...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2298/version/1

Stomatin-like Protein 2 Links Mitochondria to T-Cell Receptor Signalosomes at the Immunological Synapse and Enhances T-Cell Activation
Provedor de dados: 17
Autores: Mark G. Kirchhof; Luan A. Chau; Caitlin D. Lemke; Santosh Vardhana; Peter J. Darlington; Maria E. Marquez; Roy Taylor; Kamilia Rizkalla; Isaac Blaca; Michael L. Dustin; Joaquin Madrenas.
T cell activation through the antigen receptor (TCR) requires sustained signalling from microclusters in the peripheral region of the immunological synapse (IS). The bioenergetics of such prolonged signaling have been linked to the redistribution of mitochondria to the IS. Here, we report that stomatin-like protein-2 (SLP-2) plays an important role in this process by bridging polarized mitochondria to these signaling TCR microclusters or signalosomes in the IS in a polymerized actin-dependent manner. In this way, SLP-2 helps to sustain TCR-dependent signalling and enhances T cell activation.
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1068/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

SBML Level 3 Package Proposal: Flux
Provedor de dados: 17
Autores: Frank Bergmann; Brett G. Olivier.
This document describes  an easy to implement  package for storing information related &amp;#xd;&amp;#xa;to flux balance analysis of  SBML  Level  3 models  (the  FBA  package). In addition,  &amp;#xd;&amp;#xa;we  provide  an  example  of  how  this package  may be  implemented and  used as  a SBML&amp;#xd;&amp;#xa;Level 2 annotation.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4236/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

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

Regulation and feedback of cholesterol metabolism
Provedor de dados: 17
Autores: Alexander Mazein; Steven Watterson; Holly C. Gibbs; Wayne Hsieh; Mohammed Ba Abdullah; Mathieu Blanc; William J. Griffiths; Tom C. Freeman; Peter Ghazal.
Cholesterol biosynthesis serves as a central metabolic hub for numerous biological processes in health and disease. An integrative knowledge representation of how the cholesterol pathway is structured and how it interacts with other pathway systems is lacking. Here we provide using Systems Biology Graphical Notation the research synthesis of a process diagram integrating the regulatory and feedback systems for cholesterol synthesis.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6315/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

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

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

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

Sparse bayesian step-filtering for high-throughput analysis of molecular machine dynamics
Provedor de dados: 17
Autores: Max A. Little; Nick S. Jones.
Nature has evolved many molecular machines such as kinesin, myosin, and the rotary flagellar motor powered by an ion current from the mitochondria. Direct observation of the step-like motion of these machines with time series from novel experimental assays has recently become possible. These time series are corrupted by molecular and experimental noise that requires removal, but classical signal processing is of limited use for recovering such step-like dynamics. This paper reports simple, novel Bayesian filters that are robust to step-like dynamics in noise, and introduce an L1-regularized, global filter whose sparse solution can be rapidly obtained by standard convex optimization methods. We show these techniques outperforming classical filters on...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4318/version/1

The study on estimation of time since death with proton magnetic resonance spectroscopy under different temperature
Provedor de dados: 17
Autores: Tiantong Yang; Li Zhenwei; Wu Yue; Liu Liang; Zheng Na.
Estimation of the time of death (post-mortem interval, PMI) is occasionally a critical issue in adjudication of a criminal or civil action. But no objective and precise means has been derived for estimating PMI.One reason for this outcome may be the fact that most of these methods attempted to characterize PMI by a few or even just one specific parameter&amp;#x27;s variable in constant ambient temperature. It is crucial that we reduce or eliminate the effect of temperature variation in the estimation of PMI. Here we show the first results by using proton magnetic resonance spectroscopy (1H-MRS) technique to determine the order of degradation of certain substances, present in the brain tissue of a rabbit model, under different temperatures; our goal is to...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2007
URL: http://precedings.nature.com/documents/1363/version/1

Where is the &amp;#x2018;Jennifer Aniston neuron&amp;#x2019;?
Provedor de dados: 17
Autores: Dorian Aur.
It is generally believed that spike timing features (firing rate, ISI) are the main characteristics that can be related to neural code. Contrary to this common belief, spike directivity, a new measure that quantifies transient charge density dynamics within action potentials (APs) provides better results in discriminating different categories of visual object recognition. Specifically, intracranial recordings from medial temporal lobe (MTL) of epileptic patients have been analyzed using firing rate, interspike intervals and spike directivity. A comparative statistical analysis of the same spikes from four selected neurons shows that electrical micro-mapped features in neurons display higher separability to input images compared to spike timing features. If...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5345/version/2

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

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

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

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

Two cases of mother-infant cannibalism in orangutans
Provedor de dados: 17
Autores: David F. Dellatore; C. D. Waitt; Ivona Foitova.
Two unrelated female orangutans (_Pongo abelii_) were observed on different occasions cannibalizing the remains of their infants, a behavior never before reported in apes. Both orangutans are free-ranging ex-captive individuals in an area of forest which also hosts large numbers of visiting tourists. The cannibalism events appear to have been aberrant behavior, perhaps due to stress and the environmental conditions of the area.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1998/version/1

Screening of certain Ayurvedic plants extracts against E. turcicum
Provedor de dados: 17
Autores: Kaushal Kumar Bhati; R. Prasad; Rajesh Singh.
The use of chemicals against pathogens is environmentally dangerous, so use of natural inhibitors for disease management is needed. In this work we screen botanical extracts from ayurvedic plants for their antifungal properties against economically important plant fungal pathogen. As a test fungal pathogen, we select E. turcicum, a potent fungal pathogen responsible for Northern leaf corn blight of Maize. This fungal pathogen was challenged by the leaf extract prepared from certain Ayurvedic plants and these observations have shown a promising future in biocontrol of fungus by using such environmentally friendly&amp;#xd;&amp;#xa;antifungal agents.
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Pharmacology; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6199/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

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

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

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

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

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

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

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

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

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

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

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

The novel adiponectin-resistin (AR) and insulin resistance (IR~AR~) indexes
Provedor de dados: 17
Autores: Cia-Hin Lau; Sekaran Muniandy.
Serum hypoadiponectinemia and hyperrestinemia independently links insulin resistance to type 2 diabetes (T2DM) and metabolic syndrome (MS). Thus, the aim of this study was propose a novel adiponectin-resistin (AR) index by unifying the effect of adiponectin and resistin. Then, a novel insulin resistance (IR~AR~) index was proposed by taking into account the AR index. Serum adiponectin and resistin levels as well as other insulin resistance, T2DM and MS risk factors were tested. Experimental results showed the AR index was more stronger correlated with insulin resistance risk factors and had stronger association (df=5; F=51.154; P&amp;#x3c;0.001) with T2DM and MS susceptibility rather than the serum adiponectin (df=5; F=15.680; P&amp;#x3c;0.001) and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4191/version/1

Universal fractal scaling of self-organized networks
Provedor de dados: 17
Autores: Paul J. Laurienti; Karen E. Joyce; Qawi K. Telesford; Jonathan H. Burdette; Satoru Hayasaka.
There is an abundance of literature on complex networks describing a variety of relationships among units in social, biological, and technological systems. Such networks, consisting of interconnected nodes, are often self-organized, naturally emerging without any overarching designs on topological structure yet enabling efficient interactions among nodes. Here we show that the number of nodes and the density of connections in such self-organized networks exhibit a power law relationship. We examined the size and connection density of 46 self-organizing networks of various biological, social, and technological origins, and found that the size-density relationship follows a fractal relationship spanning over 6 orders of magnitude. This finding indicates that...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4894/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

Spatiotemporal dynamics of complex ecological networks: Power-law scaling and implications for conservation planning
Provedor de dados: 17
Autores: Christopher Wright.
Spatial constraints on the topology of complex networks are just beginning to be appreciated, both theoretically and in concrete examples like the Internet and global air transportation network. Ecological networks, composed of habitat patches connected by species dispersal, are intrinsically spatial and show promise as a tool for conservation planning; but while habitat-loss effects on ecological networks have been simulated, such effects have not been directly measured in ecological networks varying over time. In this study, I used satellite remote sensing to study ecological networks composed of wetland habitat in the Prairie Pothole Region (PPR) of North America. I find power-law scaling of important topological properties as a function of dispersal...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2532/version/2

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

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

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

Studies on Regioselective Binding Mode of Steroid Molecules in Homology Modeled Cytochrome P450-2C11
Provedor de dados: 17
Autores: Hamed I. Ali; Morio Yamada; Hukihisa Fujita; Eiichi Akaho.
In this study, we investigated the regioselective binding mode of steroid molecules and structure requirements for steroid molecules for 16[alpha]-hydroxylation by Cytochrome P450-2C11. Docking study by using the homology Cytochrome P450-2C11 indicated that 16[alpha]-hydroxylation is favored with steroidal molecules possessing the following components, 1) a bent A-B ring configuration (5[beta]-reduced), 2) C-3[alpha]-hydroxyl group, 3) C-17[beta]-acetyl group, and 4) methyl group at both the C-18 and C-19. These respective steroid components requirements such as A-B ring configuration and functional groups at C-3 and C-17 were defined as the inhibitory contribution factor. Overall results by rat CYP2C11 revealed that steroidal structure requirements...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3541/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

Up-expression of GAD65 in the Amygdala of the Rat Model of Chroric Immobilization Stress with Elevated Blood Glucose
Provedor de dados: 17
Autores: Xiao-Jing Li; Wei Zhang; Bing Liang; Xiang Zheng; Xue Zhou.
It is believed that the hypothalamus is the regulating center for blood glucose levels, but how chronic stress leads to hyperglycemia is not known. In this experiment, we use the chronic immobilization stressed rat as a model, and found that only rats with increased expression of GAD65 in the amygdala have an elevated level of blood glucose. Considering there are fiber tracks between the amygdala and hypothalamus, including GABAergic projections, this result suggests that the changes in GAD65 expression in the amygdala may correlate with the changes in blood glucose levels, and point to the importance of the the amygdala in blood glucose regulation.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5885/version/1

SED-ML: Nested Simulation Proposal
Provedor de dados: 17
Autores: Frank T. Bergmann.
This document describes a second version of the proposal for nested simulation experiments for SED-ML (http://sed-ml.org). The proposal has been updated to include the feedback received in the meantime and has been enhanced by examples. A full implementation is available with libSedML (http://libsedml.sf.net) and the SED-ML Web Tools (http://sysbioapps.dyndns.org/SED-ML_Web_Tools/)
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/4257/version/2

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

Structural basis of the allosteric trigger of the Hsp70 chaperone proteins.
Provedor de dados: 17
Autores: Akash Bhattacharya; Alexander Kurochkin; Grover Yip; Eric Bertelsen; Erik Zuiderweg.
This work solves a decades-old dilemma that stood in the way of understanding the allosteric mechanism of Hsp70 (heat shock 70 kDa) chaperone proteins. Hsp70s are central to protein folding, refolding, and trafficking in organisms ranging from Archae to Homo Sapiens, both at normal and at stressed cellular conditions. Hsp70s are comprised of two main domains: a 44 kDa N-terminal nucleotide-binding domain (NBD), and a 25 kDa substrate-binding domain (SBD) that harbors the substrate binding site. The nucleotide binding site in the NBD and the substrate binding site in the SBD are allosterically linked: ADP binding promotes substrate binding, while ATP binding promotes substrate release. It has long been a goal of structural biology to characterize the nature...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1978/version/1

Range-based techniques for discovering optimality and analyzing scaling relationships in neuromechanical systems
Provedor de dados: 17
Autores: Bradly J. Alicea.
In this paper, a method for decoupling the neuromuscular function of a set of limbs from the role morphology plays in regulating the performance of an activity is introduced. This method is based on two previous methods: the rescaled range analysis specific to time series data, and the use of scaling laws. A review of the literature suggests that limb geometry can either facilitate or constrain performance as measured experimentally. Whether limb geometry is facilitatory or acts as a constraint depends on the size differential between arm morphology and the underlying muscle. &amp;#x22;Changes in size and shape&amp;#x22; are theoretically extrapolations of morphological geometry to other members of a population or species, to other species, or to...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2845/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

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

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

The Predominance of Electric Transport in Synaptic Transmission
Provedor de dados: 17
Autores: Hamid Reza Noori.
The quantitative description of the motion of neurotransmitters in the synaptic cleft appears to be one of the most difficult problems in the modeling of synapses. Here we show in contradiction to the common view, that this process is merely governed by electric transport than diffusion forces.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2304/version/2

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

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

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

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

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

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

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

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

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

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

Workshop report: 1st INCF Workshop on Large-scale Modeling of the Nervous System
Provedor de dados: 17
Autores: Mikael Djurfeldt; Anders Lansner.
The goal of this workshop was to survey current demands, ongoing activities, and plans relating to development of tools for scalable neural network simulation. Areas covered included software components for preprocessing/model setup, as well&amp;#xd;&amp;#xa;as for storage, analysis, and visualization of results. Participants discussed the need for coordinated action in the field with regard to model, method and tool development. The reports a description of the state-of-art in the field as well as recommendations for actions to facilitate infrastructure developments.
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2007
URL: http://precedings.nature.com/documents/262/version/1

Synaptic state matching: a dynamical architecture for predictive internal representation and feature perception
Provedor de dados: 17
Autores: Saeed Tavazoie.
Here we consider the possibility that a fundamental function of sensory cortex is the generation of an internal simulation of sensory environment in real-time. A logical elaboration of this idea leads to a dynamical neural architecture that oscillates between two fundamental network states, one driven by external input, and the other by recurrent synaptic drive in the absence of sensory input. Synaptic strength is modified by a proposed synaptic state matching (SSM) process that ensures equivalence of spike statistics between the two network states. Remarkably, SSM, operating locally at individual synapses, generates accurate and stable network-level predictive internal representations, enabling pattern completion and unsupervised feature detection from...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/6282/version/2

_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

Translational Oncogenomics and Human Cancer Interactome Networks:
Provedor de dados: 17
Autores: I. C. Baianu.
An overview of translational, human oncogenomics, transcriptomics and cancer interactomic networks is presented together with basic concepts and potential, new applications to Oncology and Integrative Cancer Biology. Novel translational oncogenomics research is rapidly expanding through the application of advanced technology, research findings and computational tools/models to both pharmaceutical and clinical problems. A self-contained presentation is adopted that covers both fundamental concepts and the most recent biomedical, as well as clinical, applications. Sample analyses in recent clinical studies have shown that gene expression data can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6190/version/1

Targeted Assembly of Short Sequence Reads
Provedor de dados: 17
Autores: Rene L. Warren; Robert A. Holt.
As next-generation sequence (NGS) production continues to increase, analysis is becoming a significant bottleneck. However, in situations where information is required only for specific sequence variants, it is not necessary to assemble or align whole genome data sets in their entirety.  Rather, NGS data sets can be mined for the presence of sequence variants of interest by localized assembly, which is a faster, easier, and more accurate approach. We present TASR, a streamlined assembler that interrogates very large NGS data sets for the presence of specific variants, by only considering reads within the sequence space of input target sequences provided by the user. The NGS data set is searched for reads with an exact match to all possible short words...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5524/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

The Modified Pharaoh Approach: Stingless bees mummify beetle parasites alive
Provedor de dados: 17
Autores: Mark K. Greco; Dorothee Hoffmann; Anne Dollin; Michael Duncan; Robert Spooner-Hart; Peter Neumann.
Social insect colonies usually live in nests, which are often invaded by parasitic species. Workers from these colonies use different defence strategies to combat invaders. Nevertheless, some parasitic species are able to bypass primary colony defences due to their morphology and behaviour. In particular, some beetle nest invaders cannot be killed or removed by workers of social bees, thus creating the need for alternative social defence strategies to ensure colony survival. Here we show, using Diagnostic Radioentomology, that stingless bee workers _Trigona carbonaria_, immediately mummify invading destructive nest parasites _Aethina tumida_ alive, with a mixture of resin, wax and mud, thereby preventing severe damage to the colony. In sharp contrast to...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2591/version/2

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

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

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

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

Statistical Tests for Detecting Differential RNA-Transcript Expression from Read Counts
Provedor de dados: 17
Autores: Oliver Stegle; Philipp Drewe; Regina Bohnert; Karsten Borgwardt; Gunnar R&amp;#xe4;tsch.
As a fruit of the current revolution in sequencing technology, transcriptomes can now be analyzed at an unprecedented level of detail. These advances have been exploited for detecting differential expressed genes across biological samples and for quantifying the abundances of various RNA transcripts within one gene. However, explicit strategies for detecting the hidden differential abundances of RNA transcripts in biological samples have not been defined. In this work, we present two novel statistical tests to address this issue: a &amp;#x27;gene structure sensitive&amp;#x27; Poisson test for detecting differential expression when the transcript structure of the gene is known, and a kernel-based test called Maximum Mean Discrepancy when it is unknown. We...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4437/version/1

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

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

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

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

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

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

Transcriptomic analysis implicates ribosomal and energy metabolic pathways in antiepileptic drug action in a Drosophila model
Provedor de dados: 17
Autores: Priyanka Singh; Farhan Mohammad; Abhay Sharma.
Mechanisms of long term action of antiepileptic drugs (AEDs), used in treating epilepsy and many other neurological and psychiatric disorders, are poorly understood. Recently, a novel Drosophila transcriptomic model of locomotor plasticity induced by chronic pentylenetetrazole (PTZ), a chemoconvulsant commonly used to model epileptogenesis and test AEDs in rodents, has been described. In this model, two of the five AEDs tested, sodium valproate (NaVP) and levetiracetam (LEV), not ethosuximide (ETH), gabapentin (GBP) and vigabatrin (VGB), ameliorate development of chronic PTZ induced locomotor alteration. Here, we describe transcriptomic effect of the AEDs in the fly model. Singular treatment with ETH, GBP and VGB in general caused downregulation of genes....
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3396/version/1

Successful outdoor cultivation of a photosensitive wild strain of edible Pleurotus ostreatus (Fr.) Kummel (Oyster mushroom) from the Western Ghats region of Goa
Provedor de dados: 17
Autores: Nandkumar N. Kamat; N. V. Desilva; K. R. Phadte.
There is considerable interest in identifying wild tropical strains of oyster mushrooms&amp;#xd;&amp;#xa;useful for cultivation, strain improvement and systematic breeding programme. During&amp;#xd;&amp;#xa;routine surveys to identify such strains from Goa&amp;#x2019;s western ghats, an interesting wild form of Pleurotus ostreatus was found growing on logs of wild Mangifera indica L a novel habitat for the species reported for the first time. After obtaining and screening several pure isolates, a fertile strain BA-50/GUOMS was selected for cultivation under natural outdoor conditions. Spawn prepared on wheat grains was produced within 11 days and was used to ramify sterilized paddy straw as substrate using standard polybag technique. Spawn run was...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology; Earth &amp; Environment; Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4213/version/1

Thermal characterization of Plasmodium falciparum species specific proteins in Indian geographical area.
Provedor de dados: 17
Autores: Mohit Bhardwaj; Leena Bharadwaj; Kritika Trigunayat; Madan Mohan Trigunayat.
The paper reveals thermal characteristics of _P.falciparum_ species specific proteins. These proteins determine why _P. vivex_ species are dominant over _P.falciparum_ in Indian geographical area. Outside human host plasmodium parasite survives in poikilothermal mosquitoes. Climatic temperature conditions greatly affect native state of _P.falciparum_ species specific proteins in mosquitoes. Study of climatic temperature conditions in Indian geographical area reveals that Pfsd protein for _Plasmodium falciparum_ can remain in native state between &amp;#x2265;7 degree centigrade and &amp;#x2264;42.6 degree centigrade temperature conditions. While their best optimum functions (activity) was noted between 25.3 degree centigrade to 33degree centigrade. Pfsd...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4565/version/1

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

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

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

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

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

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

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

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

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

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

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

The Strauss-Kahn Syndrome
Provedor de dados: 17
Autores: Robert Skopec.
Accumulating evidence shows that the central nervous system (CNS) regulates the activity of the immune system. Concerning the role of immune system in cancer, psychosocial influences on immune function provide a mechanism of association between psychosocial factors (like interpersonal aggression) and cancer prognosis. Social conflicts between males, involving high aggression stress and threat (psychosocial conflicts) produce both an allostatic state and allostatic load. The costs for aggressors (Hawks) and victims (losers) tested under semi laboratory conditions are quite different. Testosterone does not cause aggression, only exaggerates the pre-existing pattern and response to environmental triggers of aggression. The individual&amp;#x27;s personality...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2011
URL: http://precedings.nature.com/documents/6456/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

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

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

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

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

When Spandrels Become Arches: Neural crosstalk and the evolution of consciousness
Provedor de dados: 17
Autores: Rodrick Wallace.
Once cognition is recognized as having a &amp;#x27;dual&amp;#x27; information source, the information theory chain rule implies that isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to the rapid, shifting global neural broadcasts of consciousness. The argument is quite analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in neurons and neuronal subsystems. Astrobiological implications are obvious.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6115/version/2

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

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

Validation of a Multivariate Serum Profile for Epithelial Ovarian Cancer Using a Prospective Multi-Site Collection
Provedor de dados: 17
Autores: Partha Seshaiah; Greg P. Bertenshaw; Tzong-Hao Chen; Katharine J. Bergstrom; Jinghua Zhao; James P. Mapes; Laurie L. Stephen; Suraj Amonkar; Michael E. McCollum; Brigitte E. Miller; Lynda D. Roman; Beth Y. Karlan; Eva Chalas; Paul A. DiSilvestro; James F. Barter; James W. Orr; Glenn E. Bigsby; Robert W. Holloway; Ronald D. Alvarez; Ping F. Yip; Brian C. Mansfield.
In previous studies we described the use of a retrospective collection of ovarian cancer and benign disease samples, in combination with a large set of multiplexed immunoassays and a multivariate pattern recognition algorithm, to develop an 11-biomarker classification profile that is predictive for the presence of epithelial ovarian cancer.  In this study, customized, Luminex-based multiplexed immunoassay kits were GMP-manufactured and the classification profile was refined from 11 to 8 biomarkers (CA-125, epidermal growth factor receptor, CA 19-9, C-reactive protein, tenascin C, apolipoprotein AI, apolipoprotein CIII, and myoglobin).  The customized kits and the 8-biomarker profile were then validated in a double-blinded manner using prospective samples...
Tipo: Manuscript
Palavras-chave: Cancer; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4667/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

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

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

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

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

Representing an Object by Interchanging What with Where
Provedor de dados: 17
Autores: Jong-Hoon Ahn; Yillbyung Lee.
Exploring representations is a fundamental step towards understanding vision. The visual system carries two types of information along separate pathways: One is about what it is and the other is about where it is. Initially, the what is represented by a pattern of activity that is distributed across millions of photoreceptors, whereas the where is &amp;#x27;implicitly&amp;#x27; given as their retinotopic positions. Many computational theories of object recognition rely on such pixel-based representations, but they are insufficient to learn spatial information such as position and size due to the implicit encoding of the where information. &amp;#xd;&amp;#xa;Here we try transforming a retinal image of an object into its internal image via interchanging the...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1686/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

The efficacy of working memory training in improving crystallized intelligence
Provedor de dados: 17
Autores: Tracy Alloway; Ross Alloway.
Crystallized intelligence (Gc) is thought to reflect skills acquired through knowledge and experience and is related to verbal ability, language development^1^ and academic success^2^. Gc, together with fluid intelligence (Gf), are constructs of general intelligence^3^. While Gc involves learning, knowledge and skills, Gf refers to our ability in tests of problem-solving, pattern matching, and reasoning. Although there is evidence that Gf can be improved through memory training in adults^4^, the efficacy of memory training in improving acquired skills, such as Gc and academic attainment, has yet to be established. Furthermore, evidence of transfer effects from gains made in the trained tasks is sparse^5^. Here we demonstrate improvements in Gc and academic...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3697/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

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

Water and the Biology of Prions and Plaques
Provedor de dados: 17
Autores: Graham K. Steel; Phillippa M. Wiggins.
This  is  an  attempt  to  account  for  the  insolubility  and/or  aggregation  of  prions  and plaques  in  terms  of  a  model  of  water  consisting  of  an  equilibrium  between  high &amp;#xd;&amp;#xa;density  and  low  density microdomains. Hydrophobic molecules,  including proteins, &amp;#xd;&amp;#xa;accumulate  selectively  into  stable  populations,  enriched  in  high  density  water,  at &amp;#xd;&amp;#xa;charged  sites on  biopolymers.  In enriched  high density water, proteins are probably &amp;#xd;&amp;#xa;partially unfolded and may precipitate  out when  released. All extracellular matrices &amp;#xd;&amp;#xa;contain such charged polymers. Prions, which have been shown to accumulate in soils &amp;#xd;&amp;#xa;and  clays  containing...
Tipo: Manuscript
Palavras-chave: Microbiology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1381/version/1

The 2010 Scientific Strategic Plan of the Global HIV Vaccine Enterprise: A Roadmap for the Future
Provedor de dados: 17
Autores: Alan Bernstein; Peter Piot.
HIV/AIDS is arguably the most significant health challenge facing the world today. The 2008 numbers tell the story: 33.4 million were living with HIV, 2 million people died of AIDS and 2.7 million people were newly infected. Despite impressive scientific advances in developing over two dozen drugs to treat HIV infections, there is still no cure. In addition, only about one-third of those who need drugs have access to therapy.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In 2003, recognizing the enormity of the scientific and humanitarian challenge of HIV/AIDS, two-dozen leading investigators and major funding organizations formed the Global HIV Vaccine Enterprise, a voluntary alliance of independent organizations committed to working together to accelerate the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4803/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

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

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

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

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

Why not &amp;#x22;do simple things in a simple way&amp;#x22;: Use of the Pap test as the first step in screening genetic stability for human cultured stem cell therapy?
Provedor de dados: 17
Autores: Katherine Athayde Teixeira de Carvalho; Ana Carolina Irioda; Larissa Zocche; Carolina Maria Costa de Oliveira Souza; Reginaldo J. Ferreira; Eduardo Aliprandini; Ricardo C Cunha; Julio C Francisco; Luiz Cesar Guarita-Souza; Mariester Malvezzi; Miriam Beltrame; Lismary Mesquita; Diogo Kuczera; Rafael Vargas.
The aim of this study was to analyze adipose tissue-derived mesenchymal stem cells (AT-MSCs) using the Pap test as a first screening step to evaluate genetic stability. Human adipose tissue from six healthy female donors was obtained from elective liposuction procedures. The cells were isolated, cultivated at P2/P3, characterized by flow cytometric analysis, and differentiation induced. The AT-MSCs were stained by Papanicolaou staining and analyzed according to the Bethesda classification, and viability-apoptosis relationships were evaluated. The results of the Pap test for Sample I indicated high-grade alterations consistent with genetic instability; for Samples II-V, atypical cells of undetermined significance; and for Sample VI, normal cells. These...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5676/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

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

THE EFFECT OF HEPARIN ON THE CELL CYCLE IN HUMAN B-LYMPHOBLASTS: AN IN VITRO STUDY
Provedor de dados: 17
Autores: Ayse Aksoy; Erol Erduran; Yusuf Gedik.
Heparin has an apoptotic effect in addition to its anticoagulant, anti-inflammatory, antihypertensive, and antiproliferative effects. In this study, we detected the effect of heparin on the cell cycle of lymphoblasts by flow cytometry (FCM) and tried to determine which phase in the cell cycle of lymphoblasts contains heparin-sensitive points. Twelve children with newly diagnosed acute lymphoblastic leukemia (ALL) were included in the study. Lymphoblasts were incubated in different levels of heparin concentrations (0, 10, and 20 U/mL) and the percentages of lymphoblasts at each phase of the cell cycle were simultaneously measured by FCM at 0, 1, and 2 hours (h). The percentages of lymphoblasts at the G2/M and S phases were significantly increased in 20 U/mL...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1989/version/1

The use of Web Ontology Language (OWL) to Combine Extant Controlled Vocabularies in Biodiversity Informatics Appears Redundant
Provedor de dados: 17
Autores: Roger D. Hyam.
Implementation of PESI requires data to be combined from multiple source databases. Some of the shared fields in the source databases used different controlled vocabularies of terms. OWL DL was investigated as a mechanism to build an extensible, shared ontology of species occurrence terms that permitted the source database to continue using and extending their own vocabularies whilst formally mapping to a more generic shared vocabulary. The merits of this approach were explored and it was concluded that the building of such a complex mapping ontology probably wasn&amp;#x27;t worthwhile. The level of semantic complexity involved outweighed the costs of simply imposing a flat list of well defined terms onto data suppliers. The main problem with exiting...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5168/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

Validated, Ultra Violet Spectroscopy Method for the Dissolution Study of Mycophenolate Mofetil Immediate Release 500mg Tablets
Provedor de dados: 17
Autores: Surajpal Verma; Ozair Alam; Pooja Mullick; Nadeem Siddiqui; Suroor Khan.
A simple, selective and precise dissolution method was developed and validated for the Mycophenolate mofetil immediate release tablets. The method employed dissolution medium 0.1N HCl (pH1.2) and volume 900ml with USP-II apparatus (Paddle). Detection was made by measuring the absorbance on UV at the &amp;#x3bb;~max~ 250nm. The method show the linearity in the range of conc. 5[mu]g/ml to 40[mu]g/ml with r^2^=0.999. The method is also validated as per International Conference of Harmonization guidelines. The method showed the specificity with standard deviation 0.00. The method is repeatable, selective and accurate for the dissolution study of Mycophenolate mofetil immediate release tablets.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/3084/version/1

Sandy bottom communities at the end of a cold (1971-1975) and warm (1997-1998) regime in the California Current:  impacts of high and low plankton production
Provedor de dados: 17
Autores: John S. Oliver; Stacy L. Kim; Peter N. Slattery; James  A. Oakden; Kamille K. Hammerstrom; Ethan M. Barnes.
There were highly significant changes in the structure of benthic infaunal communities at the end of the last cold regime (1976) compared to the end of the last warm regime (1999) in the California Current. The warm regime is characterized by much lower plankton production, which we argue is the primary cause of the degraded infaunal community at the end of the warm regime. In 1997-98, we resampled a depth gradient along a subtidal, high-energy sandy beach (6-24m) in Monterey Bay that was sampled for five years at the end of the last cold regime (1971-75). There was a dramatic decline in the total number species, number of individuals, and biomass by the end of the warm period. There was no overlap in benthic assemblages at all water depths between the...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2103/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

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

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

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

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

The realities of storing carbon dioxide - A response to CO2 storage capacity issues raised by Ehlig-Economides &amp;#x26; Economides
Provedor de dados: 17
Autores: Andy Chadwick; Dan Smith; Chris Hodrien; Sue Hovorka; Eric Mackay; Simon Mathias; Bryan Lovell; Francois Kalaydjian; Graeme Sweeney; Sally Benson; Jim Dooley; Casie Davidson.
In a recent publication, Ehlig-Economides &amp;#x26; Economides (2010) have sought to demonstrate that carbon dioxide capture and storage (CCS) is not technically or economically feasible, based on a supposed lack of underground storage capacity. We consider this to be a serious misrepresentation of the scientific, engineering and operational facts surrounding CCS. Ehlig-Economides &amp;#x26; Economides raise a number of storage related issues: reservoir boundaries, capacity, pressure management, storage integrity, dissolution and storage in depleted reservoirs. We take each one in turn, highlighting specific errors in the paper but also drawing attention to more general background issues. Finally, we discuss in more detail some inconsistencies in the...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4500/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

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

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

Towards a model of non-equilibrium binding of a metal ion in a biological system
Provedor de dados: 17
Autores: James Beardmore; Christopher Exley.
We have used a systems biology approach to address the hitherto insoluble problem of the quantitative analysis of non-equilibrium binding of aqueous metal ions by competitive ligands in heterogeneous media. To-date, the relative proportions of different metal complexes in aqueous media have only been modelled at chemical equilibrium and there are no quantitative analyses of the approach to equilibrium1. While these models have improved our understanding of how metals are used in biological systems they cannot account for the influence of kinetic factors in metal binding, transport and fate2. Here we have modelled the binding of aluminium in blood serum by the iron transport protein transferrin (Tf) as it is widely accepted that the biological fate of this...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2025/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

Why are women smaller than men? When anthropology meets evolutionary biology
Provedor de dados: 17
Autores: Priscille Touraille; Pierre-Henri Gouyon.
There are large variations of size among humans but in all populations, men are larger on average than women. For most biologists this fact can be easily explained by the same processes that explain the size dimorphism in large mammals in general and in apes in particular. Due to fights between males for the possession of females, sexual selection has favoured bigger males. Indeed, this factor certainly explains why males are selected for being large but lets aside the question of selection on the female side. Actually, it has been shown that larger females are also favoured by natural selection. This is particularly relevant for women because their probability of dying when giving birth is then reduced. In this paper, the common view that size dimorphism...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1832/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

Role of the porous structure of the bioceramic scaffolds in bone tissue engineering
Provedor de dados: 17
Autores: Wang Zhen; Chang Jiang; Bai Feng; Sun Xiaojiang; Lu Jianxi; Lin Li; Lei Chen; Dai Rong.
The porous structure of biomaterials plays a critical role in improving the efficiency of biomaterials in tissue engineering. Here we fabricate successfully porous bioceramics with accurately controlled pore parameters, and investigate the effect of pore parameters on the mechanical property, the cell seeding proliferation and the vascularization of the scaffolds. This study shows that the porosity play an important role on the mechanical property of the scaffolds, which is affected not only by the macropores size, but also by the interconnections of the scaffolds. Larger pores are beneficial for cell growth in scaffolds. In contrast, the interconnections do not affect cell growth much. The interconnections appear to limit the number of blood vessels...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4148/version/1

Systema Naturae. Classification of living things.
Provedor de dados: 17
Autores: Alexey Shipunov.
Original classification of living organisms containing four kingdoms (Monera, Protista, Vegetabilia and Animalia), 60 phyla and 253 classes, is presented.
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/241/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

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

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

Reinforcement learning in populations of spiking neurons
Provedor de dados: 17
Autores: Robert Urbanczik; Walter Senn.
Population coding is widely regarded as a key mechanism for achieving reliable behavioral responses in the face of neuronal variability. But in standard reinforcement learning a flip-side becomes apparent. Learning slows down with increasing population size since the global reinforcement becomes less and less related to the performance of any single neuron. We show that, in contrast, learning speeds up with increasing population size if feedback about the populationresponse modulates synaptic plasticity in addition to global reinforcement. The two feedback signals (reinforcement and population-response signal) can be encoded by ambient neurotransmitter concentrations which vary slowly, yielding a fully online plasticity rule where the learning of a...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1976/version/1

Rapid estimation of Brilliant Blue concentrations in soil by diffuse reflectance spectroscopy
Provedor de dados: 17
Autores: Christina Bogner; Iris Schmiedinger; Bernd Huwe.
Brilliant Blue is often used to trace water movement in soils. Its concentration in soil samples is usually determined by extraction &amp;#x2013; a laborious procedure with varying accuracy. We show that Brilliant Blue can be estimated directly by visible diffuse reflectance spectroscopy. We build a PLSR (partial least squares regression) model for the concentration range of 0.1 to 15 mg Brilliant Blue per g soil with an RMSE (root mean square error of prediction) of 1 mg g-1 and an R2adj of 0.9. However, as the method is based on visible spectra, prediction accuracy can be altered by variations in soil colour between calibration and prediction data sets.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4293/version/1

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies
Provedor de dados: 17
Autores: Leming D. Shi; Wendell D. Jones; Roderick V. Jensen; Stephen C. Harris; Roger G. Perkins; Federico M. Goodsaid; Lei Guo; Lisa J. Croner; Cecilie Boysen; Hong Fang; Shashi Amur; Wenjun Bao; Catalin C. Barbacioru; Vincent Bertholet; Xiaoxi Megan Cao; Tzu-Ming Chu; Patrick J. Collins; Xiao-hui Fan; Felix W. Frueh; James C. Fuscoe; Xu Guo; Jing Han; Damir Herman; Huixiao Hong; Ernest S. Kawasaki; Quan-Zhen Li; Yuling Luo; Yunqing Ma; Nan Mei; Ron L. Peterson; Raj K. Puri; Feng Qian; Richard Shippy; Zhenqiang Su; Yongming Andrew Sun; Hongmei Sun; Brett Thorn; Yaron Turpaz; Charles Wang; Sue-Jane Wang; Janet A. Warrington; James C. Willey; Jie Wu; Qian Xie; Liang Zhang; Lu Zhang; Sheng Zhong; Russell D. Wolfinger; Weida Tong.
Reproducibility is a fundamental requirement in scientific experiments and clinical contexts.  Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs).  In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values.  We recommend the use of FC...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/306/version/2

Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome
Provedor de dados: 17
Autores: Michael D. Barton; Balazs Papp; Daniel Delneri; Stephen G. Oliver; Magnus Rattray; Casey M. Bergman.
Proteins vary in their cost to the cell and natural selection may favour the use of proteins that are cheaper to produce. We develop a novel approach to estimate the amino acid biosynthetic cost based on genome-scale metabolic models, and directly investigate the effects of biosynthetic cost on transcriptomic, proteomic and metabolomic data in _Saccharomyces cerevisiae_. We find that our systems approach to formulating biosynthetic cost produces a novel measure that explains similar levels of variation in gene expression compared with previously reported cost measures. Regardless of the measure used, the cost of amino acid synthesis is weakly associated with transcript and protein levels, independent of codon usage bias. In contrast, energetic costs...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1841/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

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

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

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

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

Tumor induction by disruption of the Dnmt1, PCNA and UHRF1 interactions.
Provedor de dados: 17
Autores: Eric Hervouet; Lisenn Lalier; Emilie Debien; Mathilde Cheray; Audrey Geairon; Helene Rogniaux; Francois Vallette; Pierre-Francois  Cartron.
The low level of DNA methylation in tumors compared to the level of DNA methylation in their normal-tissue counterparts or global DNA hypomethylation was one of the first epigenetic alterations to be found in human cancer^1,2^. While the contribution of genome hypomethylation in cancer development and progression is explained by several mechanisms: chromosomal instability, loss of imprinting, and reactivation of transposable elements^3, 4^, the molecular causes of genome hypomethylation remain unclear. Indeed, despite the central roles of the DNA methyltransferases (Dnmts) in the establishment and maintenance of the DNA methylation, no clear consensus appears between the reduction of the Dnmts expression and the genome hypomethylation in human cancers^5^....
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/2509/version/1

Waist Circumference predicting Cardiovascular Disease in Korean Men and Women
Provedor de dados: 17
Autores: Sun Ha Jee; Sat Byul Park.
Objective: Obesity and cardiovascular disease (CVD) are closely related and have become increasingly prevalent in Korea. Asians are more prone to obesity-related co-morbidities than Caucasians, even at lower body mass index (BMI) and/or smaller waist circumference (WC) values. Nevertheless, little is known regarding the association of WC with the risk of CVD in non-Caucasian populations. The authors conducted a prospective cohort study of WC and the risk of CVD in the Korean Heart Study.Methods: We examined the association of WC to CVD incidence among 53,026 Korean adults (30,152 men, 22,874 women) with no history of CVD and/or cancer. During a mean follow-up of 8.6 years, 2,722 incident cases of atherosclerotic cardiovascular disease (ASCVD) including...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4609/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

The Dryad Digital Repository: Published evolutionary data as part of the greater data ecosystem
Provedor de dados: 17
Autores: Todd Vision.
Here we describe the motivation and workings of Dryad, a digital repository for data underlying published articles in the biosciences, that grew out of a grassroots effort to support a joint data archiving policy adopted by a consortium of journals in ecology and evolutionary biology.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4595/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

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

The existence of species rests on a metastable equilibrium  between inbreeding and outbreeding
Provedor de dados: 17
Autores: Etienne Joly.
Background: Speciation corresponds to the progressive establishment of reproductive barriers between groups of individuals derived from an ancestral stock. Since Darwin did not believe that reproductive barriers could be selected for, he proposed that most events of speciation would occur through a process of separation and divergence, and this point of view is still shared by most evolutionary biologists today. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: I do, however, contend that, if so much speciation occurs, it must result from a process of natural selection, whereby it is advantageous for individuals to reproduce preferentially within a group and reduce their breeding with the rest of the population, leading to a model whereby new species arise not...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5003/version/4

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

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

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

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

SNPxGE2: a database for human 3-way SNP-expression associations
Provedor de dados: 17
Autores: Yupeng Wang; Sandeep J. Joseph; Xinyu Liu; Michael Kelly; Romdhane Rekaya.
Recently, gene co-expression relationships have been found to be often conditional and dynamic. Besides, many studies have suggested that single nucleotide polymorphisms (SNPs) have impacts on gene expression variations in human populations. The SNPxGE2 database contains the computationally predicted human 3-way SNP-expression associations, that is, the differential co-expression between 2 genes is associated with a genotype/SNP. This data was generated from a large scale association study that was based on the HapMap data, which covered 269 individuals from 4 human populations, 701,202 SNPs and 15,000 gene expression profiles. Two models of 3-way SNP-expression associations were considered: gap/substitution and on/off. The implementation was carried out...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5704/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

Variety in evolutionary strategies favours biodiversity in habitats of moderate productivity
Provedor de dados: 17
Autores: Simon Pierce.
The mechanism whereby biodiversity varies between habitats differing in productivity is a missing link between ecological and evolutionary theory with vital implications for biodiversity conservation, management and the assessment of ecosystem services. A unimodal, humped-back relationship, with biodiversity greatest at intermediate productivities, is evident when plant, animal and microbial communities are compared across productivities in nature. However, the mechanistic, evolutionary basis of this observation remains enigmatic. We show, for natural and semi-natural plant communities across a range of bioclimatic zones, that biodiversity is greatest where communities include species with widely divergent values for phenotypic traits involved in resource...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6618/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

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

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

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

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

TLR-9 Expression in Human Bronchial Epithelial Cells induced with Lipopolysaccharide
Provedor de dados: 17
Autores: Sangeetha Dharmalingam; Shanmuga Saravanabhavan.
The study conducted here was to investigate the gene and protein expression of Toll like receptor 9 when human bronchial epithelial cells were induced by lipopolysaccharide. TLRs are pattern recognition receptor (PRR) which plays a key role in innate immunity. They recognise the molecules that are shared by pathogens but distinguishes from the host which is referred to as pathogen associated molecular patterns (PAMPs). The HBECs were first cultured and once it becomes confluent they were induced with 10ng/ml of LPS. In order to find out whether the gene was expressed in the cells, the RNA was isolated and RT-PCR was carried out. Before carrying out the RT-PCR, RNA gel electrophoresis was carried out to show the 28S and 18S bands. Once the gene expression...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4701/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

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

Smoking-induced long-lasting modifications of human platelet serotonin catabolism through a MAO epigenetic regulation
Provedor de dados: 17
Autores: Jean-Marie Launay; Muriel  Del Pino; Gilles Chironi; Jacques Callebert; Katell Peoc&amp;#x27;h; Jean-Louis M&amp;#xe9;gnien; Jacques Mallet; Alain  Simon; Francine Rendu.
Postulating that serotonin, secreted from smoking-activated platelets, could be involved in smoking-induced vascular modifications, we studied 115 men distributed in smokers (S), former smokers (FS) and never smokers (NS). The platelet serotonin content was similar in S and NS but lower in FS. This was unexpected because the monoamine oxidase (MAO) activity, which catabolizes serotonin, was inhibited during smoking. However, the amount of platelet MAO was higher in S and FS than in NS. The persistent elevated MAO amount in FS prompted us to study the methylation of its gene promoter in an additional series of patients: it was markedly lower for S and FS vs. NS due to cigarette smoke-induced increase of nucleic acid demethylase activity. This...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2113/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

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

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

_Trichoderma pseudokoningii_ Rifai isolation from Egyptian immunocompromised cattle with _Mycobacterium bovis_ infection
Provedor de dados: 17
Autores: Helmy Torky; Eman Khalifa.
Recently, _Trichoderma_ species have emerged as potent fungal pathogens in immunocompromised humans. We report the first three cases of _Trichoderma pseudokoningii_ Rifai pulmonary infection in the Egyptian tuberculous dairy cattle with _Mycobacterium bovis_, from the heart of a generalized bovine TB in a cow over 5 years old, a mediastinal lymph node of pulmonary TB in a cow of 3 years old, and a lung of mixed pulmonary and digestive BTB in a cow of 4 years old. We have also developed a pathogenisity test technique for _Trichoderma pseudokoningii_ Rifai infection in 3 G. pigs by intraperitoneal injection of 2 G. pigs with mixed infection of _Mycobacterium bovis_ and _Trichoderma pseudokoningii_ Rifai; death of both animals 14 days, thereafter, and by...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2012
URL: http://precedings.nature.com/documents/6928/version/1

Weight, Length, and Growth in Cutbow Trout (Oncorhynchus mykiss x clarkii)
Provedor de dados: 17
Autores: David Parker; Thomas Avers; Michael Courtney.
Background:  The cutbow trout (Oncorhynchus mykiss x clarkii) is a fertile hybrid of rainbow and cutthroat trout.  Little published length-weight data is available for this hybrid, and a standard weight curve is not established.  Eleven Mile Reservoir is a clear mountain reservior in Colorado with a surface area of 13.4 square kilometers, an average depth of 10 m, and a maximum depth of 41 m.  80,000 cutbow trout were stocked through the ice in late winter before samples were taken.&amp;#xd;&amp;#xa;Materials and Methods: Angling provided 171 samples which were weighed and measured (total length and fork length).  Dressed weight was also determined with the scales, head, and entrails removed.  Estimates of parameters a and b in the model, W(L) = aLb, were...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/6432/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

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

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

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

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

Visualising a scienti&amp;#xfb01;c article
Provedor de dados: 17
Autores: Roderic Page.
This paper describes my entry in the Elsevier Grand Challenge &amp;#x22;Knowledge Enhancement in the Life Sciences&amp;#x22; contest.  The entry takes a collection of fulltext issues of _Molecular Phylogenetics and Evolution_ as the starting point, then extracts citation links to both papers and data, such as Genbank sequences and specimens, together with geotagged localities, and builds a &amp;#x22;web&amp;#x22; of objects linked by typed relationships. Each object (such as a publication, a sequence, a specimen, a taxon name, etc.) is treated equally, so that you can take a publication and see what taxa it refers to, or take the taxon and find all the publications that refer to the taxon. Although the database has been seeded with some articles from...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2579/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 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

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

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

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

Semiempirical, Hartree-Fock, density functional, and second order Moller-Plesset perturbation theory methods do not accurately predict ionization energies and electron affinities of short- through long-chain [n]acenes
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Vertical, well-to-well, and adiabatic ionization energies (IEs) and electron affinities (EAs) were calculated for the n=1-10 [n]acenes using a wide range of semiempirical, Hartree-Fock, density functional, and second order Moller-Plesset perturbation theory model chemistries. None of the model chemistries examined were able to accurately predict the IEs or EAs for both short- through mid-length [n]acenes, as well as for extrapolations to the polymeric limit, when compared to available experimental and benchmark theoretical data. Provided a minimal basis set size is employed, basis set effects on predicted IEs and EAs are not significant relative to the choice of model chemistry. The poor IE/EA prediction performance for the parent [n]acenes likely extends...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6578/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

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

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

Theoretical studies on the all-anti zigzag geometries of perfluoro-n-alkyl chains
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Theoretical investigations were conducted on the gas phase all-anti zigzag geometries of C~3~ through C~7~ perfluoro-n-alkanes and the perfluoro-n-octanoate anion using various semiempirical, density functional theory, and composite method approaches. The major theoretical methods are in agreement that the gas phase zigzag geometry of &amp;#x3e;=C~3~ perfluoro-n-alkyl chains is a transition state between the left and right handed helical/twisted global minima. For the C~3~ perfluoropropyl group, a slightly twisted (about 1 to 2 degree central F-C-C-F dihedral angle) near zigzag conformation exists as a global minimum, whereas helical global minima are obtained for C~4~ and longer perfluoroalkyl chains. The left to right handed helix inversion activation...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5061/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

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

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

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

Simcluster: clustering enumeration gene expression data on the simplex space
Provedor de dados: 17
Autores: Ricardo Z. N. V&amp;#xea;ncio; Leonardo A. B. Varuzza; Carlos Pereira; Helena Brentani; Ilya Shmulevich.
Transcript enumeration methods such as SAGE, MPSS, and sequencing-by-synthesis EST &amp;#x22;digital northern&amp;#x22;, are important high-throughput techniques for digital gene expression measurement. As other counting or voting processes, these measurements constitute compositional data exhibiting properties particular to the simplex space where the summation of the components is constrained. These properties are not present on regular Euclidean spaces, on which hybridization-based microarray data is often modeled. Therefore, pattern recognition methods commonly used for microarray data analysis may be non-informative for the data generated by transcript enumeration techniques since they ignore certain fundamental properties of this...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/202/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

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

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

Solving mazes with memristors: a massively-parallel approach
Provedor de dados: 17
Autores: Yuriy V. Pershin; Massimiliano  Di Ventra.
Solving mazes is not just a fun pastime. Mazes are prototype models in graph theory, topology, robotics, traffic optimization, psychology, and in many other areas of science and technology. However, when maze complexity increases their solution becomes cumbersome and very time consuming. Here, we show that a network of memristors - resistors with memory - can solve such a non-trivial problem quite easily. In particular, maze solving by the network of memristors occurs in a massively parallel fashion since all memristors in the network participate simultaneously in the calculation. The result of the calculation is then recorded into the memristors&amp;#x2019; states, and can be used and/or recovered at a later time. Furthermore, the network of memristors...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5748/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

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

Regulated peristalsis into the acidic region of the _Drosophila_ larval midgut is controlled by a novel component of the Autonomic Nervous System
Provedor de dados: 17
Autores: Dennis Richard LaJeunesse; Brooke Ann Johnson; Jason Presnell; Kathleen K. Catignas; Grzegorz Zapotoczny.
The underlying cellular and molecular mechanisms that regulate and coordinate critical physiological processes such as peristalsis are complex, often cryptic, and involve the integration of multiple tissues and organ systems within the organism. We have identified a completely novel component of the larval autonomic nervous system in the _Drosophila_ larval midgut that is essential for the peristaltic movement of food from the anterior midgut into the acidic region of the midgut. We have named this region the Superior Cupric Autonomic Nervous System or SCANS. Located at the junction of the anterior and the acidic portions of the midgut, the SCANS is characterized by a cluster of a novel neuro-enteroendocrine cells that we call Lettuce Head Cells, a valve,...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3873/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

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

Universal Features in the Genome-level Evolution of Protein Domains
Provedor de dados: 17
Autores: Marco Cosentino Lagomarsino; Alessandro L. Sellerio; Philip D. Heijning; Bruno Bassetti.
Protein domains are found on genomes with notable statistical distributions, which bear a high degree of similarity.  Previous work has shown how these distributions can be accounted for by simple models, where the main ingredients are probabilities of duplication, innovation, and loss of domains. However, no one so far has addressed the issue that these distributions follow definite trends depending on protein-coding genome size only.  We present a stochastic duplication/innovation model, falling in the class of so-called Chinese Restaurant Processes, able to explain this feature of the data.  Using only two universal parameters, related to a minimal number of domains and to the relative weight of innovation to duplication, the model reproduces two...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1376/version/2

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

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

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

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

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

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

Requirement of Activation for Hepatitis B Virus Infection
Provedor de dados: 17
Autores: Michael Bruns; Claudia Maenz.
Although _in vitro_ models of human hepatitis B virus replication are established, so far none could approximate infection efficiency as expected from _in vivo_ observations. Susceptibility for HBV infections has only been reported for primary hepatocytes of human, chimpanzee or Tupaia belangeri and the cell line HepaRG. Here we show that the insusceptible human hepatoma cell line HepG2 can be infected, when the virus was beforehand activated by passage over whole duck liver cell cultures. That suggests an activation step to be performed by specialized liver cells.
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2007
URL: http://precedings.nature.com/documents/221/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

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

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

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

The Central Enigma of Consciousness
Provedor de dados: 17
Autores: Chris C. King.
Abstract: The nature and physical basis of consciousness remains the central enigma of the scientific description of reality in the third millennium. This paper seeks to examine the phenomenal nature of subjective consciousness and elucidate a possible biophysical basis for its existence, in terms of a form of quantum anticipation based on entangled states driven by chaotic sensitivity of global brain dynamics during decision-making processes. Evidence is presented for the evolutionary emergence of chaotic excitation as a universal sense organ in the founding eucaryotes, which then became used in a context-sensitive manner by complex central nervous systems, leading to the dynamical brain.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2465/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

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

TreeBASE2: Rise of the Machines
Provedor de dados: 17
Autores: Rutger A. Vos; Hilmar Lapp; William H. Piel; Val Tannen.
TreeBASE is a public repository of peer-reviewed phylogenetic knowledge. Researchers submit their results to TreeBASE when they are writing a manuscript based on them for publication in a suitable journal. The submitted data are assigned permanent, unique identifiers and web addresses that authors can refer to in their article. Anyone can locate and access the data once the study has been published by TreeBASE and by the targeted journal.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A prototype of this system has served the phylogenetics community well for a number of years, accumulating the results of thousands of studies. The usage model was that of a silo where data could only be accessed through a web browser, and only be downloaded in representations that...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4600/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

Research Objects: Towards Exchange and Reuse of Digital Knowledge
Provedor de dados: 17
Autores: Sean Bechhofer; David De Roure; Matthew Gamble; Carole Goble; Iain Buchan.
What will researchers be publishing in the future? Whilst there is little question that the Web will be the publication platform, as scholars move away from paper towards digital content, there is a need for mechanisms that support the production of self-contained units of knowledge and facilitate the publication, sharing and reuse of such entities.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;  In this paper we discuss the notion of _research objects_, semantically rich aggregations of resources, that can possess some scientific intent or support some research objective. We present a number of principles that we expect such objects and their associated services to follow.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4626/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

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

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

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

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

Standardized Model for Repeated Social Defeat Stress vs. Sensory Contact Model: similarities and differences, strengths and weaknesses
Provedor de dados: 17
Autores: Natalia N. Kudryavtseva.
Of all the models used by behavioral neuroscience the biosocial models are gaining in popularity among the scientists who study the consequences of chronic social conflicts and social stress in animals. One of such models, the Standardized Model for Repeated Social Defeat Stress (SMRSDS) (Golden et al., 2011) has been widely applied to produce important results on the molecular mechanisms of the social defeat stress (Berton et al., 2006). SMRSDS is a modified version of the Sensory Contact Model (SCM) (Kudryavtseva, 1991), which has been used by different laboratories in its original or modified forms for elucidating implications of chronic social conflicts. The basic design and justification of the SCM different stages are described in detail in the...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6411/version/1

Sensorimotor states affect choice in the magnitude judgment of ambiguous durations
Provedor de dados: 17
Autores: Carmelo M. Vicario; Enea Francesco Pavone; Giorgio Fuggetta.
The statistics of the environment seem to exert optimal influence on the organization of functions subserving decision making. In order to make decisions about ambiguous sensory information, predictive coding models suggest that brain generate a template against which to match observed sensory evidence. Here we challenge this notion providing evidence that stochastic choices about the magnitude judgment of visual duration are triggered by bottom-up sensorimotor information.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3264/version/1

The unique mouse pollination in an orchid species
Provedor de dados: 17
Autores: Yong Wang; Yang Zhang; Xiao-Kai Ma; Li Dong.
The Chinese orchid, _Cymbidium serratum_, is pollinated by the wild mountain mouse _Rattus fulvescens_. The flowers use both odor and colour as attractants, and provide labellum as food reward for the pollinators. The mice pollinate the flowers during their endeavour to eat the labellums.
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1824/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

Speciation of chilean Rhinocryptidae (Avian) based on their behaviour
Provedor de dados: 17
Autores: Alejandro Correa Rueda; Jorge Mpodozis.
The current classification of the chilean representatives of the passerine family Rhinocryptidae includes eight species. Three of them contain subspecies that don&amp;#x2019;t exhibit clear differences. Moreover, differences among two lineages of _Scytalopus_ genera and two species of _Pteroptochos_ are very scarce. We propose  a new methodology  based on ecological and behavioural patterns in order to understand the concept of speciation in this group of birds. According to our results, we postulate that there is not a cut criteria to establish differences among three sister lineages of current classification. This way the methodology developed by us does not allow to establish divergence for a given common ancestor. Our methodology allows to establish...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1597/version/2

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

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

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

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

Understanding Genomic Evolution of Olfactory Receptors through Fractal and Mathematical Morphology
Provedor de dados: 17
Autores: Sk. Sarif Hassan; Pabitra Pal Choudhury; B. S. Dayasagar; Shantanav Chakraborty; Ranita  Guha; Arunava Goswami.
Fractals and Mathematical Morphology are immensely used to study many problems in different branches of science and technology including the domain of Biology. There are many more unrevealed facts and figures of genes and genome in Computational Biology. In this paper, our objective is to explore how the evolutionary network is associated among Human, Chimpanzee and Mouse with regards to their genomic information. We are about to explore their genomic evolution through the quantitative measures of fractals and morphology. We have considered olfactory receptors for our case study. These olfactory receptors do function in different species with subtle differences in the structures of DNA sequences. Those subtle differences can be exposed through intricate...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5674/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

Statistical analysis of protein molecules
Provedor de dados: 17
Autores: Kushal Shah.
In this paper, entropy and auto-correlation values of main chain dihedral angles of 22,356 protein molecules are calculated and found to lie within a well-specified range for most proteins. Also, the entropy values obey a Gaussian distribution, which indicates that entropy plays a crucial role in evolution and conservation of protein tertiary structures. A comparison of the auto-correlation values of the dihedral angles of the entire protein molecule with those of the alpha helices and beta sheets indicates that random coils play an important role in determining the tertiary structure of protein molecules.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6298/version/1

Structures, enthalpies of formation, and ionization energies for the parent and binary mixed carbon, silicon, nitrogen, and phosphorus cubane derivatives: A G4MP2 theoretical study
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Gas phase standard state (298.15 K, 1 atm) structures, enthalpies of formation, and ionization energies (IEs) were calculated at the G4MP2 composite method level of theory for the parent and binary mixed carbon, silicon, nitrogen, and phosphorus cubane derivatives. Increasing nitrogen content increases the enthalpies of formation for the carbon-nitrogen, nitrogen-phosphorus, and silicon-nitrogen binary cubanes, with the opposite enthalpies of formation trend for increasing phosphorus content within the carbon-phosphorus, nitrogen-phosphorus, and silicon-phosphorus derivatives. Varying carbon/silicon content in the carbon-silicon cubanes results in no general trends for enthalpies of formation. Isomerization enthalpies within the homolog groups having more...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5154/version/1

The INCF Digital Atlasing Program: Report on Digital Atlasing Standards in the Rodent Brain
Provedor de dados: 17
Autores: Michael Hawrylycz; Jyl Boline; Albert Burger; Tsutomu Hashikawa; G. Allan Johnson; Maryann Martone; Lydia Ng; Jonathan Nissanov; Luis Puelles; Seth Ruffins; Fons Verbeek; Ilya Zaslavsky.
The goal of the INCF Digital Atlasing Program is to provide the vision and direction necessary to make the rapidly growing collection of multidimensional data of the rodent brain (images, gene expression, etc.) widely accessible and usable to the international research community. This Digital Brain Atlasing Standards Task Force was formed in May 2008 to investigate the state of rodent brain digital atlasing, and formulate standards, guidelines, and policy recommendations.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Our first objective has been the preparation of a detailed document that includes the vision and specific description of an infrastructure, systems and methods capable of serving the scientific goals of the community, as well as practical issues for...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics; Data Standards.
Ano: 2009
URL: http://precedings.nature.com/documents/4000/version/1

The Cognitive Atlas: Employing Interaction Design Processes to Facilitate Collaborative Ontology Creation
Provedor de dados: 17
Autores: Eric Miller; Christian Seppa; Aniket Kittur; Fred W. Sabb; Russell A. Poldrack.
The Cognitive Atlas is a collaborative knowledge-building project that aims to develop an ontology that characterizes the current conceptual framework among researchers in cognitive science and neuroscience. The project objectives from the beginning focused on usability, simplicity, and utility for end users. Support for Semantic Web technologies was also a priority in order to support interoperability with other neuroscience projects and knowledge bases. Current off-the-shelf semantic web or semantic wiki technologies, however, do not often lend themselves to simple user interaction designs for non-technical researchers and practitioners; the abstract nature and complexity of these systems acts as point of friction for user interaction, inhibiting...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4532/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

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

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

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

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

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

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

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

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

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

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

The Feasibility of Neuroimaging Methods in Marketing Research
Provedor de dados: 17
Autores: Nick Lee; Carl Senior; Michael Butler; Ricardo Fuchs.
On July 17, 1990, President George Bush issued &amp;#x201c;Proclamation #6158&amp;#x201d; which boldly declared the following ten years would be called the &amp;#x201c;Decade of the Brain&amp;#x201d; (Bush, 1990). Accordingly, the research mandates of all US federal biomedical institutions worldwide were redirected towards the study of the brain in general and cognitive neuroscience specifically. In 2008, one of the greatest legacies of this &amp;#x201c;Decade of the Brain&amp;#x201d; is the impressive array of techniques that can be used to study cortical activity. We now stand at a juncture where cognitive function can be mapped in the time, space and frequency domains, as and when such activity occurs. These advanced techniques have led to discoveries...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2836/version/1

Tendril, adhesive disc and super adhesive effect of climbing plant
Provedor de dados: 17
Autores: Wenli Deng.
Understanding the super adhesion mechanism of biological system is of great scientific interest and a prerequisite for bioinspired design of adhesive systems. To investigate the versatile climbing plant requires the development of new methods. Here I present strategies to fully study the super adhesive effect of climbing plant _Parthenocissus tricuspidata_ by the first time measuring the mass and the attached area of single adhesive disc, by further determining the microscopic structure and the adhesive strength of single adhesive disc and by finally elucidating the adhesion mechanism in cellular and molecular level using the classical theories and the proposed new hypothesis and model. I have measured that a single mature adhesive disc has an average mass...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1513/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

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

Solvent Induced Disulfide Bond Formation in 2,5-dimercapto-1,3,4-thiadiazole
Provedor de dados: 17
Autores: Palanisamy Kalimuthu; Palraj Kalimuthu; S. Abraham John.
Disulfide bond formation is the decisive event in the protein folding to determine the conformation and stability of protein. To achieve this disulfide bond formation in vitro, we took 2,5-dimercapto-1,3,4-thiadiazole (DMcT) as a model compound. We found that disulfide bond formation takes place between two sulfhydryl groups of DMcT molecules in methanol. UV-Vis, FT-IR and mass spectroscopic as well as cyclic voltammetry were used to monitor the course of reaction. We proposed a mechanism for the solvent induced disulfide bond formation on the basis of the results we obtained.
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/734/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

The interplay of descriptor-based computational analysis with pharmacophore modeling builds the basis for a novel classification scheme for feruloyl esterases
Provedor de dados: 17
Autores: D.B.R.K. Gupta Udatha; Irene  Kouskoumvekaki; Lisbeth Olsson; Gianni  Panagiotou.
One of the most intriguing groups of enzymes, the feruloyl esterases (FAEs), is ubiquitous in both simple and complex organisms. FAEs have gained importance in biofuel, medicine and food industries due to their capability of acting on a large range of substrates for cleaving ester bonds and synthesizing high-added value molecules through esterification and transesterification reactions. During the past two decades extensive studies have been carried out on the production and partial characterization of FAEs from fungi, while much less is known about FAEs of bacterial or plant origin. Initial classification studies on FAEs were restricted on sequence similarity and substrate specificity on just four model substrates and considered only a handful of FAEs...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4762/version/1

The cultural epigenetics of psychopathology: The missing heritability of complex diseases found?
Provedor de dados: 17
Autores: Rodrick Wallace.
We extend a cognitive paradigm for gene expression to the epigenetic epidemiology of mental disorders, recognizing the fundamental role that culture plays in human biology as another heritage mechanism parallel to, and interacting with, the more familiar genetic and epigenetic systems. In the mathematical model, culture acts as another tunable epigenetic catalyst that both directs developmental trajectories and becomes convoluted with individual ontology via a mutually interacting crosstalk mediated by a social interaction that is itself culturally driven. We call for the incorporation of embedding culture as an essential component of the epigenetic regulation of human mental development and its dysfunctions, bringing what is perhaps the central reality of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3894/version/2

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

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

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

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

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

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

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

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

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

The Role of Neuregulin 1 in Schizophrenia:  A Bioinformatics Approach
Provedor de dados: 17
Autores: Alvaro M. Dias; Vinicius V. M. C. Maracaja-Coutinho; Artur A. Q. L. Lopo.
*Context:* Notwithstanding the great number of studies on the etiology and pathophysiology of schizophrenia, both issues remain far from being fully understood. Schizophrenia seems to be related to several biochemical abnormalities, which point to a multi-factor etiology and pathophysiology, as well as to the perspective that several etiologically diverse disorders might coexist within this nosographic entity. On the other hand, identical twins reveal a high concordance for schizophrenia. From that standpoint, the perspective that structurally-related proteins may play an important and yet non-deterministic role seems attractive. Among these proteins, it is suggestive that Neuregulin 1 exerts a pivotal role. &amp;#xd;&amp;#xa;*Objective:* This paper aims...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3905/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

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

SBML Level 3 Package Proposal: Annotation
Provedor de dados: 17
Autores: Dagmar Waltemath; Neil Swainston; Allyson L. Lister; Frank Bergmann; Ron Henkel; Stefan Hoops; Michael Hucka; Nick Juty; Sarah Keating; Christian Knuepfer; Falko Krause; Camille Laibe; Wolfram Liebermeister; Catherine Lloyd; Goksel Misirli; Marvin Schulz; Morgan Taschuk; Nicolas Le Nov&amp;#xe8;re.
The annotation of Systems Biology Markup Language (SBML) models with semantic terms has been supported for a number of years. The prevalence of such annotated models is growing, with repositories such as Biomodels.net and an increasing number of software tools supporting and encouraging their use and development.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;With the increasing use of semantic annotations in the context of systems biology modeling has come the realization that the current Core SBML specification defining their use contains limitations that reduce the scope of metadata that can be captured in such models.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;SBML Level 3 provides the facility to propose and develop optional extensions to the Core specification. One such...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5610/version/1

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies
Provedor de dados: 17
Autores: Leming Shi; Wendell D. Jones; Roderick V. Jensen; Stephen C. Harris; Roger G. Perkins; Federico M. Goodsaid; Lei Guo; Lisa J. Croner; Cecilie Boysen; Hong Fang; Shashi Amur; Wenjun Bao; Catalin C. Barbacioru; Vincent Bertholet; Xiaoxi Megan Cao; Tzu-Ming Chu; Patrick J. Collins; Xiao-hui Fan; Felix W. Frueh; James C. Fuscoe; Xu Guo; Jing Han; Damir Herman; Huixiao Hong; Ernest S. Kawasaki; Quan-Zhen Li; Yuling Luo; Yunqing Ma; Nan Mei; Ron L. Peterson; Raj K. Puri; Feng Qian; Richard Shippy; Zhenqiang Su; Yongming Andrew Sun; Hongmei Sun; Brett Thorn; Yaron Turpaz; Charles Wang; Sue-Jane Wang; Janet A. Warrington; James C. Willey; Jie Wu; Qian Xie; Liang Zhang; Lu Zhang; Sheng Zhong; James J. Chen; Russell D. Wolfinger; Weida Tong.
Reproducibility is a fundamental requirement in scientific experiments and clinical contexts.  Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs).  In this study we demonstrate that (1) such discordance may stem from ranking and selecting DEGs solely by statistical significance (P) derived from widely used simple t-tests; (2) when fold change (FC) is used as the ranking criterion, the lists become much more reproducible, especially when fewer genes are selected; and (3) the instability of short DEG lists based on P cutoffs is an expected mathematical consequence of the high variability of the t-values.  We recommend the use of FC...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/306/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

&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

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

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

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

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

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

Visualization of Minute Mechanical-Excitation/Relaxation Wave-front Propagation in Myocardial Tissue
Provedor de dados: 17
Autores: Hiroshi Kanai; Motonao Tanaka.
Unlike the case of skeletal muscle, the direction of myocardial contraction does not coincide with the direction of work necessary to eject the intraventricular blood, contributing to great complexity of the wall deformation sequence of cardiac contraction. The advent of advanced techniques (CT^1^, MRI^2,3^, SPECT^4^, echocardiology^5-9^, electrocardiography^10^, and magnetocardiography^11,12^) has enabled to the evaluation of cardiac function and disorders by the measurement of blood flow, pressure, electrical reaction process, and other factors. However, complexity of the contraction sequence is still not fully understood because the dynamic mechanical excitation process, which directly correlates with contraction, cannot be accurately measured based on...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4931/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

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

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

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

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

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

The inherent occurrence of complex intron-rich spliceosomal split genes, including regulatory and splicing elements, within pre-biotic random genetic sequences
Provedor de dados: 17
Autores: Ashwini Bhasi; Bipin Balan; Brajendra Kumar; Sudar  Senapathy; Periannan Senapathy.
Growing evidence indicates that complex intron-rich split genes and an advanced spliceosome existed in the earliest eukaryote, and possibly the first life form. We sought to examine how these split genes could have originated in the prebiotic system. We previously found that split coding sequences for complex proteins occur in abundance in random DNA sequences (P. Senapathy, et al, accompanying paper). This study demonstrates that a full complement of exons, introns and regulatory and splicing elements could have also occurred inherently within pre-biotic chemistry by chance. By comparing the characteristics of split genes found in computer-generated random genetic sequences with those of several extant eukaryotes, we show that an abundance of intron-rich...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2010
URL: http://precedings.nature.com/documents/5385/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 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

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

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

TATA binding protein binds to single stranded DNA: A new model for eukaryotic transcription
Provedor de dados: 17
Autores: Rostem J. Irani.
Although the players mediating the initiation of eukaryotic transcription appear to be known, the mechanism is not. In this paper we report findings on the interaction between the TATA box binding protein (TBP) and DNA, using a novel optical technology, that point to a potential plausible physical mechanism, and at the same time tie together a number of otherwise disparate observations. TBP plays a central and ubiquitous role in initiating eukaryotic transcription, binding to promoters with and without the canonical 5&amp;#x2019; TATA(A/T)A(A/T)(G/A) 3&amp;#x2019; motif1. It also tends to bind to double-stranded DNA promiscuously, and though affinity is lower, the number of binding opportunities is greater. TBP-DNA complexes have been characterized...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4139/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

The Freezing Rotation Illusion
Provedor de dados: 17
Autores: Max R. D&amp;#xfc;rsteler.
The freezing rotation illusion arises when a figure is continuously rotating in front of a back and forth rotating ground. The term &amp;#x201c;freezing rotation&amp;#x201d; designates the decrease in the perceived rotation speed of a figure when the figure and the ground are turning in equal directions.  Subjects had to estimate the rotation speed of a continuously turning figure while the ground was either turning opposite to or with the figure. Their estimations of the figure&amp;#x2019;s speed were significantly lower, when the ground was moving in the same direction as the figure.  In control experiments subjects had to estimate the ground&amp;#x2019;s speed while the figure was turning opposite to or with the ground. Overall, their estimations of the...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/371/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

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

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

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

Searching for better flu surveillance? A brief communication arising from Ginsberg et al. Nature 457, 1012-1014 (2009)
Provedor de dados: 17
Autores: Donald R. Olson; Atar Baer; Michael  A. Coletta; Lana  Deyneka; Ryan  Gentry; Amy  Ising; Erin  L. Murray; Marc  Paladini; Justin  Pendarvis; Karl  Soetebier; Kevin J. Konty; Jill  Schulmann; Jeffrey  Engel; Julia  Gunn; Robert  T. Rolfs; Farzad  Mostashari.
Through retrospectively analyzing billions of internet search queries, Ginsberg et al. identified a collection of specific searches that track the course of influenza-like illness (ILI) reported by the US Centers for Disease Control and Prevention (CDC). Prospective monitoring during 2007-2008 found high correlation between Google estimates and CDC-reported ILI, with next-day timeliness compared to the 1-2 week delay reported in traditional CDC ILI surveillance. The assertion by Ginsberg et al., however, that internet search term estimates enable public health officials to respond better to seasonal and pandemic influenza does not take into account the current practice of public health, or the state of the art in electronic disease surveillance.
Tipo: Manuscript
Palavras-chave: Microbiology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3493/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

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

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

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

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

Towards a cognitive definition of colour vision
Provedor de dados: 17
Autores: Peter Skorupski; Lars Chittka.
In recent years, colour vision abilities have been rather generously awarded to vari-ous invertebrates and even bacteria. This uncertainty of when to diagnose colour vi-sion stems in part from confusing what colour vision can do with what it is. What col-our vision can do is discriminate wavelength independent of intensity. However, if we take this as a definition of what colour vision is, then we might indeed be obliged to conclude that some plants and bacteria have colour vision. Moreover, there is a simi-lar confusion of what are necessary and what are sufficient mechanisms and behav-ioural abilities for colour vision. To humans, seeing in colour means seeing an image in which objects/lights have chromatic attributes - in contrast to the sensation that...
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1766/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

The response of two legume crops (hyacinth bean and Kidney bean) to the parasitism of field dodder (_Cuscuta campestris_)
Provedor de dados: 17
Autores: Awad F. Farah.
Abstract: Microscopic examinations and chemical studies were performed to study the response of two legume crops, hyacinth bean (_Lablab purpureus L._) Sweet and kidney bean (_phaseolus vulgaris L._) to the filed dodder (FD) (_Cuscuta campestris Yuncker_) parasitism. Hyacinth bean, showing no effective resistance mechanisms,was found to be a highly susceptible host to FD. However, kidney bean, displaying resistant reactions towards the parasitism of FD,was found to be an incompatible host.The possible reasons for the resistance of kidney bean to FD were anatomical (hypersensitivity) and chemical (high contents of phenolic acids and lignin) stimulated defence mechanisms, which developed during the actual intrusion of FD haustorial cells inside its tissues.
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4207/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

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

The &amp;#x201c;Minimum Information about an ENvironmental Sequence&amp;#x201d; (MIENS) specification
Provedor de dados: 17
Autores: Pelin  Yilmaz; Renzo Kottmann; Dawn Field; Rob Knight; James R. Cole; Linda Amaral-Zettler; Jack A. Gilbert; Ilene Karsch-Mizrachi; Anjanette  Johnston; Guy Cochrane; Robert  Vaughan; Christopher Hunter; Joonhong Park; Norman Morrison; Phillipe Rocca-Serra; Peter Sterk; Mani Arumugam; Laura Baumgartner; Bruce W. Birren; Martin J. Blaser; Vivien Bonazzi; Peer Bork; Pier Luigi Buttigieg; Patrick Chain; Elizabeth K. Costello; Heather Huot-Creasy; Peter Dawyndt; Todd DeSantis; Noah Fierer; Jed Fuhrman; Rachel E. Gallery; Richard A. Gibbs; Michelle Gwinn Giglio; Inigo San Gil; Elizabeth M. Glass; Antonio Gonzalez; Jeffrey I. Gordon; Robert Guralnick; Wolfgang Hankeln; Sarah Highlander; Philip Hugenholtz; Janet Jansson; Jerry Kennedy; Dan Knights; Omry Koren; Justin Kuczynski; Nikos Kyrpides; Robert Larsen; Christian L. Lauber; Teresa Legg; Ruth E. Ley; Catherine  A. Lozupone; Wolfgang Ludwig; Donna Lyons; Eamonn  Maguire; Barbara A. Meth&amp;#xe9;; Folker Meyer; Sara Nakielny; Karen E. Nelson; Diana Nemergut; Josh D. Neufeld; Norman R. Pace; Giriprakash Palanisamy; J&amp;#xf6;rg Peplies; Jane Peterson; Joseph Petrosino; Lita Proctor; Jeroen Raes; Sujeevan Ratnasingham; Jacques Ravel; David A. Relman; Susanna Assunta-Sansone; Lynn Schriml; Erica Sodergren; Aym&amp;#xe9; Spor; Jesse Stombaugh; James M. Tiedje; Doyle V. Ward; George M. Weinstock; Doug Wendel; Owen White; Andreas Wilke; Jennifer Wortmann; Frank Oliver Gl&amp;#xf6;ckner.
We present the Genomic Standards Consortium&amp;#x2019;s (GSC) &amp;#x201c;Minimum Information about an ENvironmental Sequence&amp;#x201d; (MIENS) standard for describing marker genes. Adoption of MIENS will enhance our ability to analyze natural genetic diversity across the Tree of Life as it is currently being documented by massive DNA sequencing efforts from myriad ecosystems in our ever-changing biosphere.
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Genetics &amp; Genomics; Microbiology; Bioinformatics; Earth &amp; Environment; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/5252/version/2

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

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

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

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

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

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

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

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

Structure and function prediction of human homologue hABH5 of _E. coli_ ALKB5 using in silico approach
Provedor de dados: 17
Autores: shankaracharya shankaracharya; Saibal Das; Ambarish Sharan Vidyarthi.
Newly discovered human homologues of ALKB protein have shown the activity of DNA damaging drugs, used for cancer therapy. Little is known about the structure and function of hABH5, 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 modeler 9v7 to predict the 3D structure of the hABH5 protein. 3-D model of hABH5, ALKBH5.B99990005.pdb was predicted and evaluated. Validation results showed 96.8% residues in favor and an additional allowed region of the Ramachandran plot. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, conserved pattern of Pro158-X-Asp160-Xn-His266 in the...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5597/version/1

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

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

Some Secrets of Fluorescent Proteins: Distinct Bleaching in Various Mounting Fluids and Photoactivation of cyan fluorescent proteins at YFP-Excitation
Provedor de dados: 17
Autores: Johannes Schmid; Naila Malkani.
Background&amp;#xd;&amp;#xa;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 specific proteins or cells or to determine protein interactions. In the latter case, the quantum physical phenomenon of fluorescence resonance energy transfer (FRET) is exploited by specific microscopy techniques to visualize proximity of proteins.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methodology/Principal Findings&amp;#xd;&amp;#xa;When we applied a commonly used FRET microscopy technique - the increase in donor (CFP)-fluorescence after bleaching of acceptor fluorophores (YFP), we obtained good signals in live cells, but very...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/4517/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

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

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

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

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

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

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

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

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

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

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

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

Satellite Images Show the Movement of Floating _Sargassum_ in the Gulf of Mexico and Atlantic Ocean
Provedor de dados: 17
Autores: Jim Gower; Stephanie King.
The question of the origin, distribution and fate of the floating seaweed _Sargassum_ has fascinated sailors and scientists from the time of Columbus. Observations from ships are hampered by the large and variable area over which _Sargassum_ is dispersed. Here we use satellite imagery to present the first mapping of the full distribution and movement of the population of _Sargassum_ in the Gulf of Mexico and western Atlantic in the years 2002 to 2008. For the first time, we show a seasonal pattern in which _Sargassum_ originates in the northwest Gulf of Mexico in spring of each year, is advected into the Atlantic in about July, appearing east of Cape Hatteras as a &amp;#x22;Sargassum jet&amp;#x22;, and ending northeast of the Bahamas in February of the...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1894/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

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

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

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

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

Sociability is decreased following deletion of the _trpc4_ gene
Provedor de dados: 17
Autores: Kristin C. Rasmus; Jun-Gang  Wang; Andrew L. Varnell; Eric M. Ostertag; Donald C. Cooper.
Shyness and social anxiety are predominant features of some psychiatric disorders including autism, schizophrenia, anxiety and depression. Understanding the cellular and molecular determinants of sociability may reveal therapeutic approaches to treat individuals with these disorders and improve their quality of life. Previous experiments from our laboratory have identified selective mRNA and protein expression of a nonselective cation channel known as the canonical transient receptor potential channel 4 (TRPC4s) in brain regions implicated in emotional regulation and anxiety. TRPC4 is highly expressed in the corticolimbic regions of the mammalian brain. We hypothesized that robust corticolimbic expression of TRPC4 may regulate the brain&amp;#x2019;s...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6367/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

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

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

Visual computation of surface lightness: Local contrast vs. frames of reference
Provedor de dados: 17
Autores: Alan Gilchrist; Ana Radonjic.
Seeing black, white and gray surfaces, called lightness perception, might seem simple because white surfaces reflect 90% of the light they receive while black surfaces reflect only 3%, and the human retina is composed of light sensitive cells. The problem is that, because illumination varies from time to time and from place to place, any amount of light can be reflected from any shade of gray. Thus the amount of light reflected by an object, called luminance, says nothing about its lightness. Experts agree that the lightness of a surface can be computed only by using the surrounding context, but they disagree about how the context is used. We have tested an image in which two major classes of theory, contrast theories and frame-of-reference theories, make...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4244/version/1

The Synthesis of Resveratrol (Thesis)
Provedor de dados: 17
Autores: Dustin Sprouse.
The purpose of this research experiment was to perform and improve the synthesis of resveratrol (CAS: 501-36-0). Resveratrol (trans-3,4&amp;#x27;,5-trihydroxystilbene), a natural polyphenolic, non-flavonoid antioxidant, is a phytoalexin found naturally in many plants. The compound was synthesized using the decarbonylative Heck reaction. The modified four-step reaction generated poor yields but the spectra indicate that the overall resveratrol compound was obtained. Several improvements were made to help increase yield.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4685/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

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

The chronotron: a neuron that learns to fire temporally-precise spike patterns
Provedor de dados: 17
Autores: R&amp;#x103;zvan V. Florian.
In many cases, neurons process information carried by the precise timing of spikes. Here we show how neurons can learn to generate specific temporally-precise output spikes in response to input spike patterns, thus processing and memorizing information that is fully temporally coded, both as input and as output. We introduce two new supervised learning rules for spiking neurons with temporal coding of information (chronotrons), one that is analytically-derived and highly efficient, and one that has a high degree of biological plausibility. We show how chronotrons can learn to classify their inputs and we study their memory capacity.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5190/version/1

The study of the umbilical system in planktonic foraminifera in relation with depth of the Abderaz Formation at type section, IRAN
Provedor de dados: 17
Autores: Meysam Shafiee Ardestani; Ebrahim Ghasemi-Nejad.
Prospect of changes in such umbilical structures as Lip, Portici and Tegilla throughout Turonian-Campanian was also investigated. The phylogenic trend show that Lip structure in primary morphogroups turns gradually to tegilla in more developed forms in which the opening become also entirely umbilical. Statistical an analysis showed that the trends of changes are correlatable with increase in water depth while a decrease in depth result in development of lip in the planktonic foraminifera studied. The changes are considered to be in accord with Pascal law.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3206/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

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

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

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

Tutorial: Query Federation with SWObjects
Provedor de dados: 17
Autores: Eric Prud&amp;#x27;hommeaux; Helena Deus; M. Scott Marshall.
Query federation is a way to make use of distributed data sources on the Web, including many SPARQL endpoints as well as relational databases. SWObjects makes use of mapping rules represented as SPARQL Constructs to dynamically rewrite the terms and predicates of a SPARQL query into corresponding terms in another vocabulary and connect the resulting query with the appropriate service for answering the query. SWObjects can also rewrite SPARQL queries in SQL, effectively including relational databases alongside SPARQL endpoints in a linked data federation. The author of SWObjects, Eric Prud&amp;#x27;hommeaux, is the W3C staff contact for the W3C Health Care and Life Sciences Interest Group (HCLS IG) and will give the tutorial via a teleconference connection,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5538/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

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

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

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

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

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

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

Systema Naturae. Classification of living things.
Provedor de dados: 17
Autores: Alexey Shipunov.
Original classification of living organisms containing four kingdoms (Monera, Protista, Vegetabilia and Animalia), 60 phyla and 254 classes, is presented. The classification is based on latest available information.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/241/version/2

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

Study on the effect of toxicity under highly arsenic prone zone in Nadia district of West Bengal in India
Provedor de dados: 17
Autores: Tanmoy Rana; Samar Sarkar; Tapan K. Mandal; Subhasis Batabyal; Bakul K. Datta; Sumanta De; Sourav Sikdar.
The present study was carried out on the basis of status of arsenic in soil, drinking water and plants, blood, urine and faeces of animals at arsenic prone zone. Within the ambit with the environment, the examination of animals was taken into consideration. They were screened and categorised on the degree of As toxicity. For field works animals were randomly selected from arsenic prone zone. The external manifestation indicated a complex syndrome and characteristic signs such as increased heart rate and respiratory rate, red urine, congested mucous membrane, anorexia, absence of ruminal motility, diarrhoea with blood, polyuria and unusual weight loss. The haematobiochemical changes such as low Hb level, decreased level of TEC, TLC and increased level ALT,...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2992/version/1

The folding fingerprint of visual cortex reveals the timing of human V1 and V2
Provedor de dados: 17
Autores: Justin Ales; Thom Carney; Stanley A. Klein.
Primate neocortex contains over 30 visual areas. Recent techniques such as functional magnetic resonance imaging (fMRI) have successfully identified many of these areas in the human brain, but have been of limited value for revealing the temporal dynamics between adjacent visual areas, a critical component of understanding visual cognition. The voltages recorded at the scalp, electroencephalography (EEG), is a direct measure of neural activity that reflects the summed activity across all brain areas. Identifying the cortical sources that contribute to the EEG is a difficult problem. We developed an anatomically constrained dipole search method that solves the traditional problems by combining fMRI, EEG and many stimuli that activate small cortical regions....
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/716/version/1

Upstream Stimulatory Factor (USF) and CCAAT/Enhancer Binding Protein &amp;#x3b4; (C/EBP&amp;#x3b4;) Compete for overlapping Sites in the Negative Regulatory Region of the HIV-1 LTR
Provedor de dados: 17
Autores: Torik T. A. Ayoubi; Sandra M. P. Meulemans; Wim W. J. M. Van de Ven.
Human immunodeficiency virus type 1 (HIV-1) is a human retrovirus and the causative agent of the acquired immunodeficiency syndrome. Genetic analysis has revealed that the HIV-1 LTR contains a potential negative regulatory element (NRE) with an E box, the recognition sequence for the helix-loop-helix (HLH) family of transcription factors. Furthermore, the upstream stimulatory factor (USF) has been implicated as a negative regulator of HIV-1 expression. Here, we report that the NRE is a composite element and that both C/EBP&amp;#x3b4; and USF can specifically bind to the NRE. The recognition sequence for C/EBP&amp;#x3b4; overlaps with the E box in the NRE of HIV-1. Competition experiments showed that either USF or C/EBP&amp;#x3b4; binds to this NRE but not...
Tipo: Manuscript
Palavras-chave: Immunology; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1212/version/1

Soybean Composition Database from NIR, NMR and GC-MS Analyses- (v.3)
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng You; Jun Guo; Doina M. Costescu; V. I. Prisecaru.
This novel Soybean Composition Database from the AFC-NMR &amp;#x26; NIR Spectroscopy Facility of the College of ACES at the University of Illinois at Urbana includes more than 12,000 NIR measurements on soybeans from the International Soybean Germplasm Collection, such as those received from Peking at the National Soybean Collection.&amp;#xd;&amp;#xa;Excel files (.xls) of our novel spectroscopic data are currently available for all 80,000 + NIR and FT-NMR measurements; such data are made available from an ultra-fast and secure supercomputer server utilizing the current version of the Scientific-Linux OS-based software. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A detailed account is also presented of our high-resolution nuclear magnetic resonance (HR-NMR) and...
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/6201/version/3

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

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

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

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

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

Simulation of Two Dimensional Ultraviolet (2DUV) Spectroscopy of Amyloid Fibrils
Provedor de dados: 17
Autores: Jun Jiang; Darius Abramavicius; Cyril Falvo; Benjamin Bulheller; Jonathan Hirst; Shaul Mukamel.
Revealing the structure and aggregation mechanism of amyloid fibrils is essential for the treatment of over 20 diseases related to protein misfolding. Coherent two dimensional (2D) infrared spectroscopy is a novel tool that provides a wealth of new insight into the structure and dynamics of biomolecular systems. Recently developed ultrafast laser sources are extending multidimensional spectroscopy into the ultraviolet (UV), and this opens up new opportunities for probing fibrils. In a simulation study, we show that 2DUV spectra of the backbone of a 32-residue &amp;#x3b2;-amyloid (A&amp;#x3b2;(9-40)) fibril associated with Alzheimer&amp;#x27;s disease, and two intermediate prefibrillar structures carry characteristic signatures of fibril size and geometry...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4369/version/1

Specification of spatial relationships in directed graphs of cell signaling networks
Provedor de dados: 17
Autores: Azi Lipshtat; Susana R. Neves; Ravi Iyengar.
Graph theory provides a useful and powerful tool for the analysis of cellular signaling networks. Intracellular components such as cytoplasmic signaling proteins, transcription factors and genes are connected by links, representing various types of chemical interactions that result in functional consequences. However, these graphs lack important information regarding the spatial distribution of cellular components. The ability of two cellular components to interact depends not only on their mutual chemical affinity but also on co-localization to the same subcellular region.  Localization of components is often used as a regulatory mechanism to achieve specific effects in response to different receptor signals.  Here we describe an approach for...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2038/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

Steroidal anti inflammatory drug betamethasone significantly alters level of striatal dopamine in a rat model of Parkinson&amp;#x2019;s disease
Provedor de dados: 17
Autores: Mehdi Shafiee Ardestani; Hasan Mehrab; Amin Geravand; Nasir Mohajer; Mostafa Saffari.
Many scientific efforts have been well done to investigate the effects of anti inflammatory agents on the degenerative brain diseases such as Parkinson&amp;#x2019;s (PD) or Alzheimer&amp;#x2019;s disease and their affiliated sings. Previously we showed the effectiveness of steroids on rigidity of PD and in the study for further mechanistic investigation of that observation the microdialysis technique was employed to determine the striatal dopamine changes in parkinsonian rats after administration of betamethasone (0.12, 0.24 mg/kg) respectively. Our findings showed us the significant increase in the striatal dopaminergic neurotransmission (P&amp;#x3c;0.05) after administration of betamethasone comparing to the controls. These observations suggest a new...
Tipo: Manuscript
Palavras-chave: Chemistry; Immunology; Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2330/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 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

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

Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation
Provedor de dados: 17
Autores: Benjamin Bouvier; Raik Gr&amp;#xfc;nberg; Michael Nilges; Frederic Cazals.
The accurate description of protein-protein interfaces remains a challenging task. Traditional criteria, based on atomic contacts or changes in solvent accessibility, tend to over or underpredict the interface itself and cannot discriminate active from less relevant parts. A recent simulation study by Mihalek and co-authors (2007, JMB 369, 584-95) concluded that active residues tend to be `dry&amp;#x27;, that is, insulated from water fluctuations. We show that patterns of `dry&amp;#x27; residues can, to a large extent, be predicted by a fast, parameter-free and purely geometric analysis of protein interfaces. We introduce the shelling order of Voronoi facets as a straightforward quantitative measure of an atom&amp;#x27;s depth inside an interface. We...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1522/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

Visualization of and Access to CloudSat Vertical Data through Google Earth
Provedor de dados: 17
Autores: Aijun Chen; Gregory  Leptoukh; Liping Di; Steven Kempler; Christopher Lynnes.
Online tools, pioneered by the Google Earth (GE), are facilitating the way in which scientists and general public interact with geospatial data in real three dimensions. However, even in Google Earth, there is no method for depicting vertical geospatial data derived from remote sensing satellites as an orbit curtain seen from above. Here, an effective solution is proposed to automatically render the vertical atmospheric data on Google Earth. The data are first processed through the Giovanni system, then, processed to be 15-second vertical data images. A generalized COLLADA model is devised based on the 15-second vertical data profile. Using the designed COLLADA models and satellite orbit coordinates, a satellite orbit model is designed and implemented in...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/595/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

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

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

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

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

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

Small critical RNAs in the scrapie agent
Provedor de dados: 17
Autores: Steve Simoneau; Marie-Madeleine Ruchoux; Nicolas Vignier; Pierre Lebon; Sophie Freire; Emmanuel Comoy; Jean-Philippe Deslys; Jean-Guy Fournier.
Unconventional infectious agents cause transmissible spongiform encephalopathy (TSE) diseases including scrapie and bovine spongiform encephalopathy (BSE) in animals and Creutzfeldt-Jakob disease in humans. The protein only hypothesis claims that the TSE agent is composed solely of the protein called prion (PrP^sc^)^1^. This protein is the misfolded form of a host-encoded cellular protein, PrP^c^ exerting presumably a vital role at the synapse^2^. Even though now widely accepted, the prion concept fails to provide in certain circumstances^3-6^, a satisfying interpretation of the infectious phenomenon. Using the 263K scrapie-hamster model, we conducted a transmission study to search for a putative prion-associated factor indispensable for infectivity. Here...
Tipo: Manuscript
Palavras-chave: Microbiology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3344/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

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

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

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

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

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

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

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

Reductive Biotransformation of Ethyl Acetoacetate: A Comparative Studies using Free and Immobilized Whole Yeast Cells
Provedor de dados: 17
Autores: Amit  R. Kumbhar; Vaibhav V.  Kulkarni; Madhav B. Pande; Sachin S. Laddha.
Bioreduction of ethyl acetoacetate with free and immobilized yeast whole cell was achieved by using water and sucrose combination. After detachment from immobilized beads under basic condition, the corresponding ethyl(S)-(+)-3-hydroxybutanoate was isolated with 98 to 100% yield. Immobilized beads of yeast whole cell were prepared at different temperature which affects the morphology and physiology of the beads for the diffusion of the enzyme, which shown the maximum conversion of the substrate to products as compared to the free yeast whole cell.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/2087/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

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

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

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

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

_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

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

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

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

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

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

Successive Induction in Larval Zebrafish
Provedor de dados: 17
Autores: John Staddon; Robert Macphail; Stephanie Padilla.
Activating one reflex often facilitates another, antagonistic one. Since Charles Sherrington first identified successive induction more than 100 years ago, it has been demonstrated in a wide range of species, from aphids to grasshoppers to dogs and humans. We show a particularly orderly example in zebrafish (Danio rerio) larvae and identify the simple dynamic process that seems to underlie it.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3659/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

The use of DCEEG to estimate functional and metabolic state of nervous tissue of the brain at hyper- and hypoventilation
Provedor de dados: 17
Autores: Sergey Murik.
A pilot study has been made of the simultaneous DC potential and total slow electrical activity changes during modeling various metabolic and  functional states of the human brain. The multi-electrode DCEEG recordings have been performed during the hyperventilation (frequent deep one-minute long breathing motions) and  the hypoventilation (voluntary breath holding). It has been shown that the ischemic state occurring in hyperventilation is accompanied by the negative shift of DC potential and increase in the  EEG rhythms amplitude. A distention of brain vessels during hypoventilation (voluntary breath-hold) and an improvement of blood supply and thus improvement of vital and functional state of neurons gave rise to an increase in the EEG rhythm amplitude...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6638/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

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Provedor de dados: 17
Autores: Michael Hucka; Andrew M. Finney; Stefan Hoops; Sarah M. Keating; Nicolas Le Novere.
Not applicable
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/58/version/1

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

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

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

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

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

Requirement of RIZ1 for cancer prevention by methyl-balanced diet
Provedor de dados: 17
Autores: Wenyun Zhou; Sergio Alonso; Daisaku Takai; Shelly C. Lu; Fumiichiro Yamamoto; Manuel Perucho; Shi Huang.
The typical Western diet is not balanced in methyl nutrients that regulate the level of the methyl donor S-adenosylmethionine (SAM) and its derivative metabolite S-adenosylhomocysteine (SAH), which in turn may control the activity of certain methyltransferases.  Feeding rodents with amino acid defined and methyl-imbalanced diet decreases hepatic SAM and causes liver cancers. RIZ1 (PRDM2 or KMT8) is a tumor suppressor and functions in transcriptional repression by methylating histone H3 lysine 9.  Here we show that a methyl-balanced diet conferred additional survival benefits compared to a tumor-inducing methyl-imbalanced diet only in mice with wild type RIZ1 but not in mice deficient in RIZ1.  While absence of RIZ1 was tumorigenic in mice fed the balanced...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics.
Ano: 2008
URL: http://precedings.nature.com/documents/1732/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

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

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

Treatment of Alzheimer&amp;#x27;s Disease with Anti-Homocysteic acid Antibody
Provedor de dados: 17
Autores: Tohru Hasegawa; Nobuyuki Mikoda; Masashi Kitazawa; Frank M. LaFerla.
Homocysteic acid (HA) may play an important role in Alzhiemer disease (AD) as we previously reported that HA induced accumulation of intraneuronal A[beta]42. In this study, we first analyzed HA levels in a mouse model of AD. 4-month old pre-pathologic 3xTg-AD mice exhibited higher levels of HA in the hippocampus as compared to age-matched nontransgenic, suggesting that HA accumulation may precede both A[beta] and tau pathologies. To further determine the pathogenic role of HA in AD, we treated young 3xTg-AD mice with vitamin B6-deficient food for 3 weeks to induce the production of HA in the brain. Concominantly, mice received either saline or anti-HA antibody intraventricularly using a guide cannula every 3 days. Mice received anti-HA antibody...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2301/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: Cancer; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3521/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

Reciprocal homeostatic reactions to chronic excitatory synaptic receptor inactivation in developing cerebral cortex networks
Provedor de dados: 17
Autores: Michael A. Corner.
Chronic blockade of actively excitatory glutamatergic synaptic receptors in co-cultured organotypic rodent neocortex explants leads to a compensatory up-regulation of otherwise inactive input channels so as to maintain almost normal levels of ongoing bursts of action potentials. We report here that this homeostatic return of spontaneous (now kainate receptor driven) firing is accompanied by a reciprocal down-regulation of blocked AMPA and NMDA receptors, such that the developing cortical network is protected against becoming hyperactive when those synaptic inputs are again able to transmit normally.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1260/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

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

The Relationship between Physical Activity and Body Mass Index: Issues in Model Specification
Provedor de dados: 17
Autores: Gizachew Tiruneh.
*Objective:* To investigate the best statistical models that describe the effect of physical activity on BMI.&amp;#xd;&amp;#xa;*Design:* Cross-sectional analyses of physical activity and BMI data.Subjects: 107 obese, overweight, and healthy college students (mean duration of physical activity for the normal, overweight, and obese students: 89, 59, and 24 months, respectively; mean BMI for the normal, overweight, and obese students: 21.61, 27.07, and 35.54 kg/m^2^, respectively).&amp;#xd;&amp;#xa;*Measurements:* Inverse linear, inverse logarithmic, and inverse logistics models were used to analyze survey data for physical activity (measured by both frequency and duration of exercise) and BMI. Gender, age, and physical intensity variables were also...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2758/version/3

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

Tuberculosis vaccine strain _Mycobacterium bovis_ BCG Russia is a natural _recA_ mutant
Provedor de dados: 17
Autores: Peter M. Keller; Erik C. Boettger; Peter Sander.
The current tuberculosis vaccine is a live vaccine derived from _Mycobacterium bovis_ and attenuated by serial _in vitro_ passaging. All vaccine substrains in use stem from one source, strain Bacille Calmette-Gu&amp;#xe9;rin. However, they differ in regions of genomic deletions, antigen expression levels, immunogenicity, and protective efficacy. As a RecA phenotype increases genetic stability and may contribute restricting the ongoing evolution of the various BCG substrains, we aimed to inactivate _recA_ by allelic replacement in BCG vaccine strains representing different phylogenetic lineages (Pasteur, Frappier, Denmark, Russia). Homologous gene replacement was successful in three out of four strains. However, only illegitimate recombination was observed...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1576/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

The Baseline for Response Latency Distributions
Provedor de dados: 17
Autores: Ferm&amp;#xed;n Moscoso del Prado Mart&amp;#xed;n.
Response latency - the time taken to initiate or complete an action or task - is one of the principal measures used to investigate the mechanisms subserving human and animal cognitive processes. The right tails of response latency distributions have received little attention in experimental psychology. This is because such very long latencies have traditionally been considered irrelevant for psychological processes, instead, they are expected to reflect &amp;#x27;contingent&amp;#x27; neural events unrelated to the experimental question. Most current theories predict the right tail of response latency distributions to decrease exponentially. In consequence, current standard practice recommends discarding very long response latencies as...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3622/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

Segmenting DNA sequence into words based on statistical language model
Provedor de dados: 17
Autores: Wang Liang.
This paper presents a novel method to segment/decode DNA sequences based on n-gram statistical language model. Firstly, we find the length of most DNA &amp;#x201c;words&amp;#x201d; is 12 to 15 bps by analyzing the genomes of 12 model species. The bound of language entropy of DNA sequence is about 1.5674 bits. After building an n-gram biology languages model, we design an unsupervised &amp;#x2018;probability approach to word segmentation&amp;#x2019; method to segment the DNA sequences. The benchmark of segmenting method is also proposed. In cross segmenting test, we find different genomes may use the similar language, but belong to different branches, just like the English and French/Latin. We present some possible applications of this method at last.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6939/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

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

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

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

Reconstruction of an in silico metabolic model of _Arabidopsis thaliana_ through database integration
Provedor de dados: 17
Autores: Karin Radrich; Yoshimasa Tsuruoka; Paul Dobson; Albert Gevorgyan; Neil Swainston; Jean-Marc Schwartz.
The number of genome-scale metabolic models has been rising quickly in recent years, and the scope of their utilization encompasses a broad range of applications from metabolic engineering to biological discovery. However the reconstruction of such models remains an arduous process requiring a high level of human intervention. Their utilization is further hampered by the absence of standardized data and annotation formats and the lack of recognized quality and validation standards.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Plants provide a particularly rich range of perspectives for applications of metabolic modeling. We here report the first effort to the reconstruction of a genome-scale model of the metabolic network of the plant _Arabidopsis thaliana_,...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3309/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

Screening of actinobacteria for antimicrobial activities by a modified &amp;#x22;Cross-Streak&amp;#x22; method
Provedor de dados: 17
Autores: Nandkumar Kamat; Sonashia Velho-Pereira.
New molecule discovery from natural sources, such as that of actinobacteria, has proved to be an interesting area in antibiotic research, as most of these antibiotics are difficult to synthesize. Out of 30 actinobacterial cultures screened for antimicrobial activity, 28 cultures were found to produce active products against various pathogenic microorganisms such as Gram-negative, Gram-positive bacteria and yeast, using a &amp;#x2018;modified cross streak method.&amp;#x27; The modified method helped in easy quantification of results and also in ruling out probable mutual antibiosis. 53%, 13% and 10% of tested actinobacterial strains belonging to Streptomyces, Micromonospora and Actinomadura genera, respectively, showed the ability of producing antimicrobial...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Immunology; Microbiology; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6765/version/1

Thermal Carbon Dioxide Splitting: A Summary of the Peer-Reviewed Scientific Literature
Provedor de dados: 17
Autores: Sierra Rayne.
Increasing concentrations of carbon dioxide (CO~2~) in the atmosphere have stimulated significant global research and development efforts regarding the reduction in CO~2~ 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 CO~2~ (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;CO~2~ 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...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1741/version/2

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

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

The Evolution of Homochirality
Provedor de dados: 17
Autores: Rodrick Wallace.
It is possible to reconsider the origin of biological homochirality in a novel way by formally invoking the standard groupoid approach to stereochemistry in a thermodynamic context that generalizes Landau&amp;#x27;s spontaneous symmetry breaking arguments. On Earth, limited metabolic free energy may have served as a low temperature analog to &amp;#x27;freeze&amp;#x27; the system in the lowest energy state, i.e., the set of simplest homochiral transitive groupoids representing reproductive chemistries. These engaged in a Darwinian competition until a single configuration survived. Subsequent path dependent evolutionary process locked in this initial condition, in spite of increases in available metabolic free energy. Astrobiological outcomes, given higher...
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Molecular Cell Biology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/3902/version/2

Theoretical studies on the pK~a~ values of perfluoroalkyl carboxylic acids: Non-helical conformation acidity constants for n-perfluorooctanoic acid (n-PFOA)
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
A molecular mechanics force field method (MMFF94) systematic rotor conformational search was conducted on the well known environmental contaminant n-perfluorooctanoic acid (n-PFOA). The  MMFF94 conformational search yielded 2915 separate low- through high-energy conformers of n-PFOA. Ranking of these structures gave the 94 lowest MMFF94 energy conformations that were subjected to subsequent density functional theory (DFT) computational investigations at the B3LYP/6-311++G(d,p) level of theory. Application of a thermodynamic cycle approach, coupled with aqueous and gas phase DFT calculations on the molecular and anionic forms for each of the 94 lowest energy n-PFOA conformers, gave estimated acidity constants (pK~a~ values) for a final converged set of...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3837/version/1

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Provedor de dados: 17
Autores: Michael Hucka; Andrew M. Finney; Stefan Hoops; Sarah M. Keating; Nicolas Le Novere.
With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models.  The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2007
URL: http://precedings.nature.com/documents/58/version/2

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

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

Standard operating procedures (SOP) in experimental stroke research: SOP for middle cerebral artery occlusion in the mouse
Provedor de dados: 17
Autores: Ulrich Dirnagl; Members of the MCAO-SOP Group.
Recently, systematic reviews have found quantitative evidence that low study quality may have introduced a bias into preclinical stroke research. Monitoring, auditing, and standard operating procedures (SOPs) are already key elements of quality control in randomized clinical trials and will hopefully be widely adopted by preclinical stroke research in the near future. Increasingly, funding bodies and review boards overseeing animal experiments are taking a proactive stance, and demand auditable quality control measures in preclinical research. Every good quality control system is based on its SOPs. This article introduces the concept of quality control and presents for the first time an SOP in experimental stroke research.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3492/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

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

Structures at the Atomic Level of Cobalt, Zinc and Lead Niobates
Provedor de dados: 17
Autores: Raji Heyrovska.
The author has found in recent years that bond lengths are exact sums of the radii of adjacent atoms and or ions, where the ions have Golden ratio based radii. This work was prompted by the exciting observation last year of the Golden ratio in the magnetic properties of cobalt niobate. It is shown here that in cobalt and zinc niobates, cobalt, zinc and oxygen ions have Golden ratio based ionic radii, whereas in lead niobate, all atoms have covalent radii. Also, the angles at the single bond oxygen anion and atom are close to 1080, as in a pentagon.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6059/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

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

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

Water soluble carbon nanotubes affect growth of the common gram (Cicer arietinum)
Provedor de dados: 17
Autores: Shweta Tripathi; Sumit Kumar Sonkar; Abhishek Kumar; M.Y. Khan; Sabyasachi  Sarkar.
Multi-walled Carbon nanotube, its role and implications in biological systems are currently under evaluation and became interesting for many researchers primarily working on the interface of chemistry, physics and biology.  However, concerns about the potential toxicity of multi-walled carbon nanotubes have been raised. To carry such affords, herein we investigate the effects of carboxylic acid functionalized water soluble carbon nanotube (wsCNT) on the growth of gram Cicer arietinum plant. The growth of gram plants was observed with and without the presence of wsCNT to demonstrate that carboxylated functionalized multi-walled carbon nanotubes showed better growth and under more wsCNT, the growth was enhanced without showing apparent toxicity. Although...
Tipo: Manuscript
Palavras-chave: Chemistry; Plant Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/4056/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

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

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

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

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

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

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

Review of Immunoinformatic approaches to in-silico B-cell epitope prediction
Provedor de dados: 17
Autores: Rick Reitmaier.
In this paper, the current state of in-silico, B-cell epitope prediction is discussed.   Recommendations for improving some of the approaches encountered are outlined, along with the presentation of an entirely novel technique, which uses molecular mechanics for epitope classification, evaluation and prediction.
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/353/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

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

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

Stop-and-go kinetics in amyloid fibrillation
Provedor de dados: 17
Autores: Jesper Ferkinghoff-Borg; Jesper Fonslet; Christian B. Andersen; Sandeep Krishna; Simone Pigolotti; Hisashi Yagi; Yuji Goto; Daniel Erik Otzen; Mogens H. Jensen.
Many human diseases are associated with protein aggregation and fibrillation. Using glucagon as a model system for protein fibrillation we show that fibrils grow in an intermittent fashion, with periods of growth followed by long pauses. Remarkably, even if the intrinsic transition rates vary considerably in each experiment, the probability of being in the growing (stopping) state is very close to 1/4 (3/4), suggesting the presence of 4 independent conformations of the fibril tip. We discuss this possibility in terms of existing structural knowledge.
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4279/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

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

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

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

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

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

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

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

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

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

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

The neural bases of distracter-resistant working memory
Provedor de dados: 17
Autores: Tor Wager; Rachel Insler; Edward Smith.
A major difference between humans and other animals is our capacity to maintain information in working memory (WM) while performing secondary tasks, which enables sustained, complex cognition. A common assumption is that the lateral prefrontal cortex (PFC) is critical for WM performance in the presence of distracters, but direct evidence is scarce. We assessed the relationship between fMRI activity and WM performance within-subjects, with performance matched across Distracter and No-distracter conditions. Activity in ventrolateral PFC during WM encoding and maintenance positively predicted performance in both conditions, whereas activity in the pre-supplementary motor area (pre-SMA) predicted performance only under distraction. Other parts of dorsolateral...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5526/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

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

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

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

Seasonal patterns of presentation in primary malignant brain tumors and metastases based on a retrospective neuropathologic database
Provedor de dados: 17
Autores: Sepehr Ehsani; Sidney E. Croul; Keith Knight; Tim-Rasmus Kiehl.
Seasonal variation in the occurrence of several classes of cancer has been observed in the past. However, evidence for such trends in adult central nervous system tumors is scant. We have analyzed the monthly occurrence rates of glioblastomas as well as carcinomas metastatic to the brain in 6,154 neurosurgical patients in Toronto selected from the University Health Network neuropathologic database over a seven-year period (July 2001 to June 2008). The electronic repository was representative of the patient population in southern Ontario, and the case accession dates in the database reflected the onset patterns of the selected tumor groups. A modification to Nam&amp;#x27;s alternative method to the Roger test was developed to statistically quantify the...
Tipo: Manuscript
Palavras-chave: Cancer; Neuroscience; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2969/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/8

SARS-CoV Regulates Immune Function-Related Gene Expressions in Human Monocytic Cells
Provedor de dados: 17
Autores: Wan-Jiung(Wan-Chung) Hu; Yu-Ting Yen; Sher Singh; Chuan-Liang Kao; Betty A. Wu-Hsieh.
Background: Severe Acute Respiratory Syndrome (SARS) is characterized by acute respiratory distress (ARDS) and pulmonary fibrosis, and the monocyte/macrophage is the key player in the pathogenesis of SARS.&amp;#xd;&amp;#xa; &amp;#xd;&amp;#xa;Methods: In this study, we compared the transcriptional profiles of SARS coronavirus (SARS-CoV) infected monocytic cells against that infected by coronavirus 229E (CoV-229E). Total RNA was extracted from infected DC-SIGN transfected monocytes (THP-1-DC-SIGN) at 6 and 24 h after infection and the gene expression was profiled by oligonucleotide-based microarray. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: Analysis of immune-related gene expression profiles showed that 24 h after SARS-CoV infection, (i)...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5908/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

Theoretical studies on the pK~a~ values of perfluoroalkyl carboxylic acids: Chain helicity
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Semiempirical, ab initio, and density functional theory (DFT) studies were conducted on a homologous series of straight chain perfluoroalkyl carboxylic acids (PFCAs) ranging in chain length from C~1~ (trifluoroacetic acid; TFA) to C~9~ (perfluorodecanoic acid). Regardless of perfluoroalkyl chain length and computational method and level employed, no significant change in the electrostatic or steric characteristics of the carboxylate head group was found between C~2~ and C~9~. Application of a thermodynamic cycle to calculations at the B3LYP/6-311++G(3df,2p) level provided an accurate prediction of the experimental monomeric pK~a~ for TFA. At this &amp;#x2013; and similar &amp;#x2013; levels of theory, monomeric pK~a~ values of longer straight chain PFCAs...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3829/version/1

Successful use of axonal transport for drug delivery by synthetic molecular vehicles
Provedor de dados: 17
Autores: Aaron G. Filler; Garth Whiteside; Mark Bacon; Martyn Frederickson; Franklyn A. Howe; Miri K. Rabinowitz; Alan J. Sokoloff; Terrence Deacon; Chris Abell; Raj Munglani; John R. Griffiths; B. Anthony Bell; Andrew Lever.
We report the use of axonal transport to achieve intraneural drug delivery. We constructed a novel tripartite complex of an axonal transport facilitator conjugated to a linker molecule bearing up to a hundred reversibly attached drug molecules. The complex efficiently enters nerve terminals after intramuscular or intradermal administration and travels within axonal processes to neuron cell bodies. The tripartite agent provided 100-fold amplification of saturable neural uptake events, delivering multiple drug molecules per complex. _In vivo_, analgesic drug delivery to systemic and to non-targeted neural tissues was greatly reduced compared to existing routes of administration, thus exemplifying the possibility of specific nerve root targeting and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2164/version/1

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

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

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 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

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

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

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

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

Systems biology of energetic and atomic costs in the yeast transcriptome, proteome, and metabolome
Provedor de dados: 17
Autores: Michael D. Barton; Balazs Papp; Daniela Delneri; Stephen G. Oliver; Magnus Rattray; Casey M. Bergman.
Background: Every protein has a variable atomic and energetic cost to the cell based on the synthesis of its constituent amino acids. Quantifying the cost of amino acid synthesis is challenging, however natural selection is expected to favour the use of proteins whose constituents are cheaper to produce in terms of energetic and atomic cost.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Results: We develop a systems biology approach to estimate the cost of amino acid synthesis based on genome-scale metabolic models, and directly investigate the effects of the cost of amino acid synthesis on transcriptomic, proteomic and metabolomic data in Saccharomyces cerevisiae. We used our two new and six previously reported measures of amino acid cost in conjunction with codon...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1841/version/2

The concentration of homocysteine-derived disulfides in human coronary artery
Provedor de dados: 17
Autores: Mauro Iuliano; Gaetano De Tommaso; Liberato Ciavatta; Raffaele Ragone.
*Background* &amp;#xd;&amp;#xa;Based on previous findings, we have estimated that, in injured coronary artery tissue, the low molecular weight disulfides homocystine and cysteine-homocysteine, otherwise identified as oxidized homocysteine equivalents (OHcyE), may achieve a total concentration that is higher than the aqueous solubility of homocystine at room temperature. In order to verify whether or not OHcyE could reach their saturation limit in the vascular tissue, we have measured the solubility of homocystine in physiological-like condition.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Materials and methods* &amp;#xd;&amp;#xa;The solubility of homocystine has been measured in aqueous sodium chloride solutions at 37 &amp;#xb0;C by differential pulse polarography...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/1436/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

Voluntary universal testing and treatment is unlikely to lead to HIV elimination: a modeling analysis
Provedor de dados: 17
Autores: Bradley  G. Wagner; Sally Blower.
Recently Granich et al. at the World Health Organization (WHO) concluded, using mathematical modeling, that HIV epidemics could be eliminated within a decade. They assumed all individuals would be tested annually and every infected individual (regardless of stage of infection) would be put on treatment. Based on this modeling study the WHO is considering using universal testing and treatment as an HIV elimination strategy. Here we examine the study by Granich et al. and assess its validity. We present new analyses of their model by varying assumptions and parameter values. We find that under certain very optimistic assumptions HIV elimination would be (theoretically) possible, but it would take at least 70 years. To obtain this result we assumed ~65% of...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3917/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

The study of the umbilical system in planktonic foraminifera in relation with depth of the Ziarat-kola section at the Maastrichtian, Central Alborz, IRAN
Provedor de dados: 17
Autores: Meysam Shafiee Ardestani; Behnaz Balmaki; Massod Asgharian.
The main aim of this research is study of the planktonic foraminifera morphogroups distinction genus to perform by changing the umbilicus area in Ziarat-kola section to find novel results. Therefore, original objection at this research considers the cause of organizing umbilicus structures (Lip, Portici, Tegilla) at this protests. it seems that phylogeny trend entirely the changes of planktonic foraminifera changing from lip at primary morphogroup to tegilla at development shape which continued this phylogeny trend opening become entirely umbilicus that this trend accompanied to increasing deep. Therefore, the study of planktonic foraminifera morphotype, and recognizing, the obtained results from planktonic foraminifera analysis percent and their...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3342/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

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

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

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

Spindle oscillations are generated in the dorsal thalamus and modulated by the thalamic reticular nucleus
Provedor de dados: 17
Autores: Chun-Hua Liu; Yi Ping Guo; Xian-Kai Meng; Yan-Qin Yu; Ying Xiong; Li-Xia Gao; Ying-Shing Chan; Jufang He.
Spindle waves occur during the early stage of slow wave sleep and are thought to arise in the thalamic reticular nucleus (TRN), causing inhibitory postsynaptic potential spindle-like oscillations in the dorsal thalamus that are propagated to the cortex. We have found that thalamocortical neurons exhibit membrane oscillations that have spindle frequencies, consist of excitatory postsynaptic potentials, and co-occur with electroencephalographic spindles. TRN lesioning prolonged oscillations in the medial geniculate body (MGB) and auditory cortex (AC). Injection of GABA~A~ antagonist into the MGB decreased oscillation frequency, while injection of GABA~B~ antagonist increased spindle oscillations in the MGB and cortex. Thus, spindles originate in the dorsal...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2313/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

Schizophrenia is a TH2 dominant autoimmune disease possibly against acetylcholine receptors of CNS
Provedor de dados: 17
Autores: Wanchung(Wan-Jiung) Hu.
Schizophrenia is a very common psychiatric disorder. However, its etiology and pathogenesis is still unknown. Current theory saying that neurotransmitter imbalance such as serotonin or dopamine only provides limited effectiveness in schizophrenia treatment by drugs changing serotonin and dopamine concentration. Despite of such treatment, majority of schizophrenia patients still have very poor prognosis. Thus, the neurotransmitter imbalance theory is not correct. Here, I propose that schizophrenia is actually a TH2 dominant autoimmune disorder. The candidate of autoantigen could be acetylcholine receptors of CNS. My theory can explain the positive as well as negative symptoms of schizophrenia. By microarray analysis of PBMCS, one-tenth of the total 519...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Immunology; Neuroscience; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6978/version/1

Technological Solutions for Energy Security and Sustainability
Provedor de dados: 17
Autores: Paul J. Werbos.
This paper addresses the question: how can we minimize the expected time between now and the time when we achieve three measures of sustainability and security together -- independence from oil in cars and trucks, very deep reductions in greenhouse gas emissions and deep reductions in natural gas for electricity? Specific new technologies and metrics for progress are discussed, in context, linked to new information from IEEE, NSF, the State of the Future project and other sources.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2131/version/1

Tuning and regulating the repertoire of glycan determinants
Provedor de dados: 17
Autores: Rodrick Wallace; Deborah Wallace.
We apply Tlusty&amp;#x27;s information-theoretic index theorem analysis of the genetic code to the glycome, using a cognitive paradigm by which external information sources constrain and tune the glycan code error network, in the context of available metabolic energy. The model suggests spontaneous symmetry breaking of the glycan code as a function of metabolic energy intensity, an effect that may be currently present, or embedded in evolutionary trajectory, recording large-scale ecosystem resilience shifts in energy availability such as the aerobic transition. Once focused on a subset of the glycan error code network however, the glycan production machinery must then be regulated by an elaborate cognitive process to ensure that what is produced matches...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Ecology; Molecular Cell Biology; Pharmacology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5932/version/2

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

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

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

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

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

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

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

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

Unique features of Plasmids among different Citrobacter species
Provedor de dados: 17
Autores: Swapnil G. Sanmukh; Waman N. Paunikar.
The _Citrobacter_ plasmids are supposed to represent the host genetic association within the living bacterial cell. The plasmids impart various beneficial characteristics to the host, helping it to retain suitable characteristics for adaptation as well as evolution. The study aims at understanding the role of prophage in influencing host functional characteristics by horizontal gene transfer or as whole plasmids. The  _Citrobacter_ plasmid can be understood by analyzing many hypothetical protein sequences within its genome. Our study included 82 hypothetical proteins in 5 _Citrobacter_ plasmids genomes. The function predictions in 31 hypothetical proteins and 3-D structures were predicted for 11 protein sequences using PS2 server. The probable function...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6836/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

Studies on the Accumulation of Chromium in Fenugreek
Provedor de dados: 17
Autores: Xanthate D S; Murthy Ch V R; Rajan S C S; Sekhar D M R.
Studying Cr uptake by Fenugreek, we note that the maximum concentration of Cr takes place in the shells of the pods followed by leaves, stems and seeds in that order. Interestingly, applied higher doses of Cr does not increase accumulation of Cr in the stems, rather Cr content in the stems levels off. However, the maximum dispersal/distribution of Cr taken up is in the leaves.
Tipo: Manuscript
Palavras-chave: Pharmacology; Plant Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6763/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

Structural and functional glycosphingolipidomics by glycoblotting with aminooxy-functionalized gold nanoparticle
Provedor de dados: 17
Autores: Noriko Nagahori; Midori Abe; Shin-Ichiro Nishimura.
Glycosphingolipids (GSLs) synthesized in Golgi apparatus by sequential transfer of sugar residues to a ceramide lipid anchor are ubiquitously distributing on vertebrate plasma membranes. Standardized method allowing for high throughput structural profiling and functional characterization of living cell surface GSLs is of growing importance because they function as crucial signal transduction molecules in various processes of dynamic cellular recognitions. However, methods are not available for amplification of GSLs, while the genomic scale PCR amplification permits large-scale mammalian proteomic analysis.&amp;#x3000;Here we communicate such an approach to a novel &amp;#x22;omics&amp;#x22;, namely glycosphingolipidomics based on the glycoblotting method....
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/2034/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

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

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

Siberian flood basalt magmatism and Mongolia-Okhotsk slab dehydration
Provedor de dados: 17
Autores: Alexei V. Ivanov; Konstantin D. Litasov.
Experimental data combined with numerical calculations suggest that fast subducting slabs are cold enough to carry into the deep mantle a significant portion of the water in antigorite, which transforms with increasing depth to phase A and then to phase E and/or wadsleyite by solid-solid phase transition. Clathrate hydrates and ice VII are also stable at PT conditions of cold slabs and represent other potential phases for water transport into the deep mantle. Some cold slabs are expected to deflect while crossing the 410 km and stagnate in transition zone being unable to penetrate through 660 km discontinuity. In this way slabs can move a long way beneath continents after long-lived subduction. With time, the stagnant slabs are heated to the temperature of...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1489/version/1

The Genetic Signature of Perineuronal Oligodendrocytes
Provedor de dados: 17
Autores: Sara Szuchet; Joseph A. Nielsen; Gabor Lovas; Javier Martinez de Velasco; Dragan Maric; Lynn D. Hudson.
Oligodendrocytes in the central nervous system can be categorized as precursors, myelin-forming, and non-myelinating perineuronal cells. The function of perineuronal oligodendrocytes is unknown; it was proposed that following injury, they may remyelinate denuded axons. We investigated these cells&amp;#x27; potential. A combination of cell-specific tags, microarray technology and bioinformatics tools to identify gene expression differences between these subpopulations allowed us to capture the genetic signature of perineuronal oligodendrocytes. Here we report that perineuronal oligodendrocytes are configured for a dual role. As cells that embrace neuronal somata, they integrate a repertoire of transcripts designed to create their own code for communicating...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1821/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

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

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

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

Topological network alignment uncovers biological function and phylogeny
Provedor de dados: 17
Autores: Oleksii Kuchaiev; Tijana Milenkovic; Vesna Memisevic; Wayne Hayes; Natasa Przulj.
Sequence comparison and alignment has had an enormous impact on our understanding of evolution, biology, and disease. Comparison and alignment of biological networks will likely have a similar impact. Existing network alignments use information external to the networks, such as sequence, because no good algorithm for purely topological alignment has yet been devised. In this paper, we present a novel algorithm based solely on network topology, that can be used to align any two networks. We apply it to biological networks to produce by far the most complete topological alignments of biological networks to date. We demonstrate that both species phylogeny and detailed biological function of individual proteins can be extracted from our alignments....
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4089/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

Wikipedia as an encyclopaedia of life
Provedor de dados: 17
Autores: Roderic Page.
In his 2003 essay E O Wilson outlined his vision for an &amp;#x201c;encyclopaedia of life&amp;#x201d; comprising &amp;#x201c;an electronic page for each species of organism on Earth&amp;#x201d;, each page containing &amp;#x201c;the scientific name of the species, a pictorial or genomic presentation of the primary type specimen on which its name is based, and a summary of its diagnostic traits.&amp;#x201d; Although the &amp;#x201c;quiet revolution&amp;#x201d; in biodiversity informatics has generated numerous online resources, including some directly inspired by Wilson&amp;#x27;s essay (e.g., &amp;#x22;http://ispecies.org&amp;#x22;:http://ispecies.org, &amp;#x22;http://www.eol.org&amp;#x22;:http://www.eol.org), we are still some way from the goal of having...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4242/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

Sensory Contact Model: Protocol, Control, Applications
Provedor de dados: 17
Autores: N.N. Kudryavtseva.
Among the models that become more and more popular in behavioral neuroscience are biosocial models, which allow studying the consequences of chronic social conflicts and social stress in animals. The sensory contact model appears to represent one of such models. Repeated experience of aggression or social defeats in daily agonistic interactions in male mice of different strains leads to the formation of opposing kinds of social behavior: one attributable to winners (aggressors) and another attributable to losers (defeated males, victims of aggression). A large variety of behavioral pathologies which develop in male mice in these conditions (anxious depression, catalepsy, social withdrawal, pronounced aggression, anxiety, hyperactivity, cognitive...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3299/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

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

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

Variant calling comparison CASAVA1.8 and GATK
Provedor de dados: 17
Autores: Denis C. Bauer.
This work aims at addressing the question of whether the new CASAVA1.8, which boasts improvements such as local realignments of reads, is at par with the well accepted pipeline of BWA mapping, duplicate removal, local realignment, re-calibration and variant calling using GATK. We therefore compare the two methods on chromosome 21 of a Yoruba trio and compare the results to the genotype identified by the 1000 genomes project. &amp;#xd;&amp;#xa;We &amp;#xfb01;nd that the mapping performance is the same for CASAVA1.8 and the academic pipeline, resulting in a mean coverage of about 22. CASAVA1.8 and GATK both call about 70.000 SNPs per individual of which 80% overlap between CASAVA1.8, GATK and the 1000 genomes project. This stands in contrast to the indel...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6107/version/1

The Systems Biology Markup Language (SBML): Language Specification for Level 3 Version 1 Core
Provedor de dados: 17
Autores: Michael Hucka; Frank T. Bergmann; Stefan Hoops; Sarah M. Keating; Sven Sahle; James C. Schaff; Lucian P. Smith; Darren J. Wilkinson.
This is the final specification for _Release 1_ of *SBML Level 3 Version 1 Core*, an electronic model representation format for systems biology.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;SBML is oriented towards describing biological processes of the sort common in research on a number of topics, including metabolic pathways, cell signaling pathways, and many others. SBML is defined neutrally with respect to programming languages and software encoding; however, it is oriented primarily towards allowing models to be encoded using XML. This document contains many examples of SBML models written in XML.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;More information about SBML and this specification is available online at...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/4959/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

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

Water Quality and Pollution Status of Lararpur Reservoir with Special Reference to Bacterial Contamination
Provedor de dados: 17
Autores: Subhash C. Pandey; Sadhna M. Singh; Subrata  Pani; Arti Malhosia.
Laharpur dam was constructed in the southwest of Bhopal city, M.P., India with an objective to store water for irrigational purpose. At the time of planning and construction of the reservoir it was in the outskirts of township but now, with the expansion of the city the reservoir has come well within the settlement. The developmental activities and occupancy in the area is exerting pressure on the water body. Surface water in urban water bodies almost always contains some degree of contamination. This is due to exposure to animals, humans, aquatic life, etc. In addition to this, variety of other human activities resulted in increasing the bacterial concentration of reservoir. Many of these bacteria are pathogenic and spread diseases like typhoid,...
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3645/version/1

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

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

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

Spiral Tissue Microarrays as Next Evolutionary Step in the High-density Tissue Microarray Technology
Provedor de dados: 17
Autores: Junya Fukuoka; Matthias Hofer; Takashi Hori; Tomonori Tanaka; Sayaka Tominaga; Ryo Ohsawa; Takeshi Uemura; Lucian Chirieac.
Tissue microarray (TMA) is a well-established technique that connects basic research with clinical applications that allow the validation of many pathobiologic events from gene expression dysregulation to genomic aberrations. However, conventional TMAs have several limitations such as limited representation of tissue heterogeneity, destruction of donor tissue blocks due to coring and usage of particular specimens that have limited evaluable material (tissue from thin specimens or needle biopsies). We have developed a novel method, which we termed &amp;#x22;Spiral TMA&amp;#x22; that generates TMAs that allow for improved representation of the donor tissue while keeping the architectural details of the donor block intact. This technology is ideal for...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4831/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

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

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

Role of CellML and FieldML in VPH/Physiome Applications
Provedor de dados: 17
Autores: Peter J. Hunter.
Discusses the use of the VPH/Physiome markup languages in VPH applications.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5911/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

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

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

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

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

Review of the Carbon Dioxide Splitting Patent Literature
Provedor de dados: 17
Autores: Sierra Rayne.
Increasing concentrations of carbon dioxide in the atmosphere have stimulated significant global research and development efforts regarding the reduction in 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 carbon dioxide (i.e., sequestration), there is considerable worldwide interest for dissociating waste stream carbon dioxide molecules into their constituent carbon and oxygen atoms (&amp;#x22;CO2 splitting&amp;#x22;) as a final &amp;#x22;end-of-pipe&amp;#x22; treatment option. This document presents a review of on-point issued and applied for patents in the field of carbon dioxide splitting. The findings suggest patents in this area...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1739/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

Role of chondroitin sulfate proteoglycans (CSPGs) in synaptic plasticity and neurotransmission in mammalian spinal cord.
Provedor de dados: 17
Autores: Arsen S. Hunanyan; Guillermo Garcia-Alias; Joel M. Levine; James W. Fawcett; Lorne M. Mendell; Victor L. Arvanian.
Chronic unilateral hemisection (HX) of the adult rat spinal cord diminishes conduction through intact fibers in the ventrolateral funiculus (VLF) contralateral to HX. Intraspinal injections of Chondroitinase-ABC, known to digest chondroitin sulfate proteoglycans (CSPGs) in the vicinity of injury, prevented this decline of axonal conduction. This was associated with improved locomotor function. We further injected three purified CSPGs into the lateral column of the uninjured cord at T10: NG2 and neurocan, which increase in the vicinity of a spinal injury, and aggrecan, which decreases. Intraspinal injection of NG2 acutely depressed axonal conduction through the injection region in a dose dependent manner. Similar injections of saline, aggrecan, or neurocan...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3681/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

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

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

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

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

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

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

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

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

The Proteomics World is Flat: Dependence of Regulation upon Abundance
Provedor de dados: 17
Autores: David Good; Roman Zubarev.
The long-standing assumption that proteins divide into house-keeping and cell-specific groups was recently struck down after discovering that the vast majority of expressed proteins are shared across cell lines. Here, we tested a related hypothesis that abundant proteins are less regulated than low-abundance ones. Meta-analysis of published data revealed that protein regulation is only weakly dependent upon the protein abundance, thus providing support to cell characterization by the &amp;#x22;top&amp;#x22; proteome.
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/6412/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

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

Rethinking Leucine Zipper &amp;#x2013; a ubiquitous signal transduction motif
Provedor de dados: 17
Autores: Yaroslav Nikolaev; Konstantin Pervushin.
In this essay we attempt to reconsider the concept of the &amp;#x201c;Leucine Zipper&amp;#x201d; (LZ) protein oligomerization motif. Reasoning on the wealth of existing data, we suggest that despite of the structural similarity with highly stable extended &amp;#x201c;Coiled Coil&amp;#x201d; motifs, on the functional level short and moderately stable &amp;#x201c;Leucine Zippers&amp;#x201d; might stand out as a distinct group. Namely, this family of oligomerization motifs facilitates combinatorial protein-protein recognition in the course of signal transduction events, thus going beyond the structural role of the extended &amp;#x201c;Coiled Coils&amp;#x201d;. Summarizing the existing knowledge on stability, specificity and folding of Leucine Zippers we...
Tipo: Manuscript
Palavras-chave: Cancer; Immunology; Molecular Cell Biology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3271/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; 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

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

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

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 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

Toxicological Assessment of Herbal Medicine in Rats
Provedor de dados: 17
Autores: Ramar Perumal Samy; Vincent  TK Chow.
Protein profiles analysis of liver, kidney and spleen by SDS-PAGE in aqueous leaf extract of Tragia involucrata L. (Euphorbiaceae) was injected intraperitoneally in albino rats for 30 days. The variation of protein changes was recorded. In liver, the aqueous leaf extracts treated (1500 mg/kg body/weight) group did not exhibit a marked increase in any of the polypeptides over control. But in the case of other treatments (250, 500, 1000 and 2000 mg/kg body weight doses) the profile showed significant increases in the accumulation of all polypeptides that were quantified using densitometry. This concludes that the aqueous leaf extract influenced the accumulation of polypeptide in higher concentration. Extra polypeptides may be responsible for the protective...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6026/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

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

Robustness of self-organised systems to changes in individual level behaviour: an example from real and simulated self-organised snail aggregations
Provedor de dados: 17
Autores: Richard Stafford; Mark S. Davies; Gray A. Williams.
Perfect behaviours that are optimal to the environment an agent operates within rarely exist in real animals or in robotic systems. The costs (be they biological or economic) of building sensors and processing the information they capture become excessive compared to the small advantages that occur from the modifications of behaviour. Many self-organised systems are thought to change their properties as a result of changes in individual behaviour. Here, using both natural systems and computer simulations, we demonstrate that intertidal snail aggregations slightly decrease in size when individuals forage for shorter periods due to hotter and more desiccating conditions &amp;#x2013; a non-optimal behaviour for the snails since aggregation reduces desiccation...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3922/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

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

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

Trichoplax, the simplest known animal, contains an estrogen-related receptor: Implications for the evolution of vertebrate and invertebrate estrogen receptors
Provedor de dados: 17
Autores: Michael E. Baker.
Although, as their names imply, vertebrate and invertebrate estrogen receptors [ERs] and estrogen-related receptors [ERRs] are related transcription factors, their evolutionary relationships to each other are not fully understood.  We searched recently sequenced genome of _Trichoplax_, the simplest known animal, and genomes from three lophotrochozoans: _Capitella_, a worm, _Helobdella robusta_, a leech, and _Lottia gigantea_, a snail, to elucidate the origins and evolution of ERs and ERRs.  BLAST found an ERR in _Trichoplax_, but no ER.  BLAST searches of the lophotrochozaons found ERRs in all three and invertebrate ERs in _Capitella_ and _Lottia_, but not in _Helobdella_.  These database searches and a phylogenetic analyses indicate that invertebrate ERs...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1863/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

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

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

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

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

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

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

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

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

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

The Olfactory Nervous System Of Terrestrial And Aquatic Vertebrates
Provedor de dados: 17
Autores: Ashiq Hussain.
Animals in their natural milieu are surrounded by odors. These odors are rich source of information, and are perceived by sophisticated olfactory systems, that have evolved over time. The sense of smell helps species to localize prey, evade predators, explore food and recognize viable mates. In humans, memoirs, thoughts, emotions, and associations are more readily reached through the sense of smell than through any other channel. This suggests that olfactory processing is imperative and may differ fundamentally from processing in other sensory modalities. The molecular age in olfaction initiated in 1991 with the significant discovery of a large, multigene family of olfactory receptors in rat by Linda Buck and Richard Axel (Buck and Axel, 1991). The first...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6642/version/1

The biological cost of consciousness
Provedor de dados: 17
Autores: Bernard J. Baars.
Some philosophers maintain that consciousness as subjective experience has no biological function. However, conscious brain events seem very different from unconscious ones. The cortex and thalamus support the reportable qualitative contents of consciousness. Subcortical structures like the cerebellum do not. Likewise, attended sensory stimuli are typically reportable as conscious, while memories of those stimuli are not so reportable until they are specifically recalled.  &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Reports of conscious experiences in normal humans always involve subjectivity and an implicit observing ego. Unconscious brain events are not reportable, even under optimal conditions of report. While there are claimed exceptions to these points, they...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6775/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

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

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

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

X-ray phase contrast imaging of biological specimens with tabletop synchrotron radiation
Provedor de dados: 17
Autores: Stefan Kneip; Chris McGuffey; Franklin Dollar; Michael S. Bloom; Vladimir Chvykov; Galina Kalintchenko; Karl Krushelnick; Anatoly Maksimchuk; Stuart P. D. Mangles; Takeshi Matsuoka; Zulfikar Najmudin; Charlotte A. J. Palmer; Joerg Schreiber; Will Schumaker; Alexander G. R. Thomas; Victor Yanovsky.
Since their discovery in 1896, x-rays have had a profound impact on science, medicine and technology. Here we show that the x-rays from a novel tabletop source of bright coherent synchrotron radiation can be applied to phase contrast imaging of biological specimens, yielding superior image quality and avoiding the need for scarce or expensive conventional sources.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Microbiology.
Ano: 2011
URL: http://precedings.nature.com/documents/5946/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

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

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

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

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

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

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

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

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

Taking shortcuts with OWL using safe macros
Provedor de dados: 17
Autores: Christopher J. Mungall; Alan Ruttenberg; David Osumi-Sutherland.
Accurate representation of complex domains such as biology demands&amp;#xd;&amp;#xa;powerful and expressive ontology languages such as OWL. However, the&amp;#xd;&amp;#xa;complex nested class expressions required for modeling can be a&amp;#xd;&amp;#xa;hindrance to ontology authoring and adoption. These class expressions&amp;#xd;&amp;#xa;can appear opaque to domain experts, and even users proficient in OWL&amp;#xd;&amp;#xa;can benefit from some kind of syntactic sugar or &amp;#x22;short-cut&amp;#x22;&amp;#xd;&amp;#xa;strategy, especially when authoring large ontologies.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;One solution is to have domain experts fill in simple templates (for&amp;#xd;&amp;#xa;example, in Excel) and translate the results into more complex...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5292/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

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

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

Stress responsive miR-23a attenuates skeletal muscle atrophy by targeting MAFbx /atrogin-1
Provedor de dados: 17
Autores: Shogo Wada; Yoshio Kato; Mitsuharu Okutsu; Shigeru Miyaki; Katsuhiko Suzuki; Zhen Yan; Hiroshi Asahara; Takashi Ushida; Takayuki Akimoto.
Muscle atrophy occurs in many pathological states and results primarily from accelerated protein degradation by the ubiquitin-proteasome pathway. We used dexamethasone to induce muscle wasting and investigated the role of a microRNA (miRNA) in the control of muscle-specific E3 ubiquitin ligase MAFbx/atrogin-1. Here we show that miR-23a suppresses MAFbx/atrogin-1 translation by binding to 3&amp;#x27;UTR of the mRNA. Furthermore, ectopic expression of miR-23a is sufficient to protect myocytes from atrophy in vitro and in vivo in response to dexamethasone treatment, and heat stress-induced miR-23a protects muscle from dexamethasone-induced muscle atrophy. Our surprising discovery of the physiological role of miR-23a in preventing the atrophy program should...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2175/version/1

Reducing the Probability of False Positive Research Findings by Pre-Publication Validation - Experience with a Large Multiple Sclerosis Database
Provedor de dados: 17
Autores: Martin M. Daumer; Ulrike U. Held; Katja K. Ickstadt; Moritz M. Heinz; Siegfried S. Schach; George G. Ebers.
*Objective*&amp;#xd;&amp;#xa;We have assessed the utility of a pre-publication validation policy in reducing the probability of publishing false positive research findings. &amp;#xd;&amp;#xa;*Study design and setting*&amp;#xd;&amp;#xa;The large database of the Sylvia Lawry Centre for Multiple Sclerosis Research was split in two parts: one for hypothesis generation and a validation part for confirmation of selected results. We present case studies from 5 finalized projects that have used the validation policy and results from a simulation study.&amp;#xd;&amp;#xa;*Results*&amp;#xd;&amp;#xa;In one project, the &amp;#x22;relapse and disability&amp;#x22; project as described in section II (example 3), findings could not be confirmed in the validation part of...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/433/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

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

Structural Modeling and Validation of Rep protein of Begomovirus Strains (TLCBV and TYLCTHV)
Provedor de dados: 17
Autores: Rajneesh Prajapat; Vivek Bajpai; Rajarshi Kumar Gaur.
Homology modeling involves taking a known sequence with an unknown structure and mapping it against a known structure of one or several similar (homologous) proteins. It would be expected that two proteins of similar origin and function would have reasonable structural similarity. Therefore it is possible to use the known structure as a template for modeling the structure of the unknown structure. Proteins that share the same function generally have similar structures. During alignment if two proteins show maximum sequence identity they also show a similar folding pattern. This principal has became the foundation of homology modeling. &amp;#xd;&amp;#xa;The Geminivirus taxonomic group of plant viruses is characterized by geminate particles and genomes...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5617/version/1

The largest reservoir of mitochondrial introns is a relic of an ancestral split gene
Provedor de dados: 17
Autores: Cyril Ferandon; Serge Moukha; Philippe Callac; Jean-Pierre Benedetto; Michel Castroviejo; Gerard Barroso.
In eukaryotes, introns are located in nuclear and organelle genes from several kingdoms (ref. 1-4). Large introns (0.1 to 5 kbp) are frequent in mitochondrial genomes of plant and fungi (ref. 1,5) but scarce in Metazoa, despite these organisms are grouped with fungi among Opisthokonts. Introns are classified in two main groups (I and II) according to their RNA secondary structure involved in the intron self-splicing mechanism (ref. 5,6). Most of the group I introns carry a &amp;#x22;Homing Endonuclease Gene&amp;#x22; (ref. 7-9) encoding a DNA endonuclease acting in the transfer and site specific integration &amp;#x22;homing&amp;#x22;) and allowing the intron spreading and gain after lateral transfer even between species from different kingdoms (ref....
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Microbiology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4373/version/1

Return of Kosi river induced by Tibet earthquake
Provedor de dados: 17
Autores: Saumitra Mukherjee.
Seismotectonics and change in river courses were correlated. Following the elastic rebound theory before the occurrence of the earthquake the subsurface rocks accumulate the energy by the tectonic movement. The Kosi river barrage was broken due to the tectonic forces accumulation in the south of Tibet Himalayas. Kosi river originates from Tibetan Himalayas and any disturbance in Tibet plateau has the potential to change the river course.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2278/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

Widespread Mitochondrial Disease in North American Bison
Provedor de dados: 17
Autores: Thomas H. Pringle.
North American bison have rebounded from near-extinction in the nineteenth century but from such small inbred founding populations that once-rare deleterious nuclear gene alleles and mitochondrial haplotypes are now at high frequencies. The initial bottleneck was compounded by decades of unnatural selection affecting bison conservation genomics and undercutting restoration initiatives. The genomics era began in late 2010 for bison and sister species yak with the release of 102 whole mitochondrial genomes, displacing earlier control region and microsatellite data not extending to coding regions. This allows detection of both sporadic and sub-clade level mutations in mitochondrially encoded proteins and tRNAs by comparative genomics methods: deleterious...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/5645/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

Standard operating procedures (SOP) in experimental stroke research: SOP for middle cerebral artery occlusion in the mouse
Provedor de dados: 17
Autores: Ulrich Dirnagl; Members of the MCAO-SOP Group.
Recently, systematic reviews have found quantitative evidence that low study quality may have introduced a bias into preclinical stroke research. Monitoring, auditing, and standard operating procedures (SOPs) are already key elements of quality control in randomized clinical trials and will hopefully be widely adopted by preclinical stroke research in the near future. Increasingly, funding bodies and review boards overseeing animal experiments are taking a proactive stance, and demand auditable quality control measures in preclinical research. Every good quality control system is based on its SOPs. This article introduces the concept of quality control and presents for the first time an SOP in experimental stroke research.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/3492/version/3

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

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

Trichoplax, the simplest known animal, contains an estrogen-related receptor but no estrogen receptor: Implications for estrogen receptor evolution
Provedor de dados: 17
Autores: Michael E. Baker.
Although, as their names imply, estrogen receptors [ERs] and estrogen-related receptors [ERRs] are related transcription factors, their evolutionary relationships to each other are not fully understood.  To elucidate the origins and evolution of ERs and ERRs, we searched for their orthologs in the recently sequenced genome of _Trichoplax_, the simplest known animal, and in the genomes of three lophotrochozoans: _Capitella_, an annelid worm, _Helobdella robusta_, a leech, and _Lottia gigantea_, a snail.  BLAST searches found an ERR in _Trichoplax_, but no ER.  BLAST searches also found ERRs in all three lophotrochozoans and invertebrate-like ERs in _Capitella_ and _Lottia_, but not in _Helobdella_.  Unexpectedly we find that the _Capitella_ ER sequence is...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2170/version/1

Web 2.0 and the ever elusive balance between information explosion and data mining
Provedor de dados: 17
Autores: Abhay Krishna.
In a fascinating tussle of perspectives in Volume 6 and issue no 3 of april 2008 Frontiers in Ecology and Evolution, Martin A Nu&amp;#xf1;ez and Gregory M Crustinger enlist ways to brace up with the recent literature. They advocate that PhD students should choose a well studied system to have better chances of success. On the other side of this fascinating tussle Daniel Simberloff and Nathan J Sanders agree with there enthusiastic case and approaches for bracing up with the recent literature. However, they disagree with the play safe strategy of start-ups in ecology and evolution.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;For me this tussle of perspectives is really fascinating. It underlines the story of our times. In the times of information explosion, should...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1959/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

Ultrasonicated synthesis of 1-(2-hydroxyaryl)-3-(pyrrolidin-1-yl)-prop-2-en-1-ones and their antimicrobial screening
Provedor de dados: 17
Autores: Sharad Shelke; Mahendra Sonawane; Bhausaheb Karale; Charnshing Gill.
Abstract: A facile synthesis of title compounds has been carried out under ultrasound irradiation. The main advantages of the present procedure are shorter reaction time and higher yield. Products have been characterized by IR, PMR, CMR, GCMS study and screened for their antimicrobial activity.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2009
URL: http://precedings.nature.com/documents/2855/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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Using Metaneva for Structuring, Managing and Retrieving Animal Data in the Cognitive Neurosciences
Provedor de dados: 17
Autores: Dirk Derom; Randall A. Schmidt; Ian McLeod; Bruce A. Hewitt.
Contemporary cognitive neuroscience data sets are characterized by a lack of a standardized ontology, leading to shortcomings in data reports and data sharing along with possibly outdated modular models of functional brain mechanisms. Neuroinformatics is actively addressing these hiatuses, developing detailed and more powerful workbenches. However, the structuring of data is largely neglected due to the intrinsically different data sets in the neurosciences. Here we present a workbench called Metaneva addressing the need of data structures for the improvement of both data storage and data retrieval. We hereby present both our data structuring approach and the system developed specifically for the storage and retrieval of this Metaneva specific data...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4146/version/1

Skin Typing and High Resolution MRI of Human Skin: Multiple Contrast Approach for Image Characterization
Provedor de dados: 17
Autores: Rakesh R. Sharma.
Background and objectives:    &amp;#xd;&amp;#xa;The ex vivo magnetic resonance microimaging (MRM) image characteristics are reported in human skin excised samples. &amp;#xd;&amp;#xa;Design and methods:&amp;#xd;&amp;#xa;Human excised skin samples were imaged using custom coil placed inside 500 MHz NMR imager for high resolution microimaging. Skin in vivo- and ex vivo MRI images were processed for characterization of different skin structures. Contiguous cross-sectional T1-weighted 3D spin echo MRI, T2-weighted 3D spin echo MRI and proton density images were compared with skin histopathology and NMR peaks. In all skin specimens, epidermis and dermis thickening and hair follicle size was measured using MRM.  &amp;#xd;&amp;#xa;Results:...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4161/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

Transforming the Axiomisation of Ontologies: The Ontology Pre-Processor Language
Provedor de dados: 17
Autores: Mikel Ega&amp;#xf1;a Aranguren; Robert Stevens; Erick Antezana.
As ontologies are developed there is a common need to transform them, especially from those that are axiomatically lean to those that are axiomatically rich. Such transformations often require large numbers of axioms to be generated that affect many different parts of the ontology. This paper describes the Ontology Pre-Processor Language (OPPL), a domain-specific macro language, based in the Manchester OWL Syntax, for manipulating ontologies written in OWL. OPPL instructions can add/remove entities, and add/remove axioms (semantics or annotations) to/from entities in an OWL ontology. OPPL is suitable for applying the same change to different ontologies or at different development stages, and for keeping track of the changes made (e.g. in pipelines). It is...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/4006/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

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

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

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

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

Temporal dynamics of travelling theta wave activity in infants responding to visual looming
Provedor de dados: 17
Autores: Ruud F. R. van der Weel; Audrey van der Meer.
A fundamental property of most animals is the ability to see whether an object is approaching on a direct collision course and, if so, when it will collide. Using high-density electroencephalography in 5- to 11-month-old infants and a looming stimulus approaching under three different accelerations, we investigated how the young human nervous system extracts and processes information for impending collision. Here we show that infants&amp;#x27; looming related brain activity is characterized by theta oscillations. Source analyses reveal clear localised activity in the visual cortex. Analysing the temporal dynamics of the source waveform, we provide evidence that the temporal structure of different looming stimuli is sustained during processing in the more...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2917/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

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

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

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

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

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

The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data
Provedor de dados: 17
Autores: Colin Batchelor; Thomas Bittner; Karen Eilbeck; Chris Mungall; Jane Richardson; Rob Knight; Jesse Stombaugh; Craig Zirbel; Eric Westhof; Neocles Leontis.
Biomedical Ontologies are intended to integrate diverse biomedical data to enable intelligent data-mining and facilitate translation of basic research into useful clinical knowledge. We present the first version of RNAO, an ontology for integrating RNA 3D structural, biochemical and sequence data. While each 3D data file depicts the structure of a specific molecule, such data have broader significance as representatives of classes of homologous molecules, which, while differing in sequence, generally share core structural features of functional importance. Thus, 3D structure data gain value by being linked to homologous sequences in genomic data and databases of sequence alignments. Likewise genomic data can increase in value by annotation of shared...
Tipo: Manuscript
Palavras-chave: Chemistry; Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3561/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

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

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

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

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

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

The architecture of predator-prey and the relationship between complexity and stability
Provedor de dados: 17
Autores: Karen Luz Burgoa Rosso; Jose Alberto Nogales Vera; Lucas Faria; Iraziet Charret; Chrystian Paixao.
Theoretical studies predict that the stability of an ecosystem is negatively correlated with its complexity, measured by the number of interacting species. On the other hand, empirical evidence indicates that food webs are highly interconnected. In this manuscript we present results on the stability two-level predator-prey food webs. We analyzed exhaustively all possible topologies of connections among species. Our findings show that those food webs fall into two classes with clearly distinct stability properties. In one of them stability is negatively correlated with complexity, and in the other group stability is positively correlated. For a positive relationship our results reveals highly structured food webs. The positive or negative relationship is...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2010
URL: http://precedings.nature.com/documents/4396/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

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

Trigohexagonite: A Rare Quaternary Stoichiometry Network
Provedor de dados: 17
Autores: Michael J. Bucknum; Bin Wen; Doletha M. E. Szebenyi; E.A. Castro.
A rare quaternary stoichiometry network of high hexagonal symmetry (P-6m2) is described. A set of hexagonal fractional crystallographic coordinates, for both an idealized network, and optimized boron and carbon allotropic realizations are described along with their band structures. Both should be metallic phases.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1650/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

Study of Fish Weight Loss in Solar Dryer Across Different Agro-Ecological Zones of Nigeria
Provedor de dados: 17
Autores: Julius Olokor; Emeka Ugoala; Adenike Ibitoye.
Drying sessions were conducted across Nigeria to study the interaction between fish weight loss and the meteorological parameters. Correlation analyses using weight loss values show that latitude is strongly related (r =+0.96) to weight loss of fish inside the dryer while altitude had a weak relationship (r = +0.24) with weight loss. The results show that New Bussa recorded more weight loss of fish than Jos, despite their uniform latitude. Weight loss records in Jos, was however better than those of Warri and Ibadan.
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3018/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/1

Socio-economic determinants of anthropometric measures of abdominal adiposity among older people in England
Provedor de dados: 17
Autores: Jose Iparraguirre; Sam SzeLam.
Objective: to look into the socio-economic determinants of levels of three anthropometric measures of abdominal adiposity among older people in England -body mass index, waist circumference (WC), and waist-hip ratio (WHR)- and of changes along two health risk classifications: the World Health Organisation classification based on BMI levels and the WHO combined classification based on BMI and waist circumference measurements.&amp;#xd;&amp;#xa;Design: quantile regression and multinomial analysis using data from the English Longitudinal Study of Ageing (ELSA), wave 2 (2004-05) and wave 4 (2008-09)&amp;#xd;&amp;#xa;Results: The quantile analysis on levels led to disparate results depending on the wave, which would question results previously published based on...
Tipo: Manuscript
Palavras-chave: Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/6897/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 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 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

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

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

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

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

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

Reading the Neural Code: What do Spikes Mean for Behavior?
Provedor de dados: 17
Autores: Dorian Aur; Mandar  Jog.
The present study reveals the existence of an intrinsic spatial code within neuronal spikes that predicts behavior. As rats learnt a T-maze procedural task, simultaneous changes in temporal occurrence of spikes and spike directivity are evidenced in &amp;#x201c;expert&amp;#x201d; neurons.  While the number of spikes between the tone delivery and the beginning of turn phase reduced with learning, the generated spikes between these two events acquired behavioral meaning that is of highest value for action selection. Spike directivity is thus a hidden feature that reveals the semantics of each spike and in the current experiment, predicts the correct turn that the animal would subsequently make to obtain reward. Semantic representation of behavior can then be...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/61/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

The Nuclear Imaging Uncertainty Principle. Do Nuclear Cameras Really Work?
Provedor de dados: 17
Autores: Richard Fleming; Gordon Harrington.
The introduction of the Heisenberg Uncertainty principle and Nuclear Cardiology occurred simultaneously in 1925-1927. Thirty years later the Anger gamma camera would allow for a more sophisticated radioactive isotope counting to determine the presence or absence of disease. When employed with technetium-99m isotopes, ischemic heart disease can be inferred by differences in visual appearance of cardiac images. These gestalts of imaging results have been separated from the quantitative information recorded by the cameras computer. We investigated whether current camera and computer systems are sophisticated enough to quantify differences between images to be clinically relevant. Our study demonstrated that efforts to &amp;#x22;sharpen&amp;#x22; image...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/5013/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

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

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

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

Spike processing model of the brain
Provedor de dados: 17
Autores: Robert Brown.
The timing of a spike within a specific time period is used to identify a place in space (input terminal) and/or sense changes in energy or position in the environment, and is used to determine the motion of an actuator or the activation of a place in space (output terminal). The timing of a spike is specified by a sensor or a time delay memory cell that is preset (predetermined) or set through experience (empirical). Time delay memory cells are arranged in decoding networks that activate specific output terminals based upon the timing of incoming spike trains, or arranged in encoding networks that generate spike trains from activated input terminals. These spike trains form semi-axes that can transmit large quantities of information in one direction...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/5621/version/1

The computational magic of the ventral stream
Provedor de dados: 17
Autores: Tomaso Poggio.
I argue that the sample complexity of (biological, feedforward) object recognition is mostly due to geometric image transformations and conjecture that a main goal of the ventral stream &amp;#x2013; V1, V2, V4 and IT &amp;#x2013; is to learn-and-discount image transformations.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In the first part of the paper I describe a class of simple and biologically plausible memory-based modules that learn transformations from unsupervised visual experience. The main theorems show that these modules provide (for every object) a signature which is invariant to local affine transformations and approximately invariant for other transformations. I also prove that,&amp;#xd;&amp;#xa;in a broad class of hierarchical architectures, signatures...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/6117/version/3

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

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

Systems Biology Graphical Notation: Entity Relationship language Level 1
Provedor de dados: 17
Autores: Nicolas Le Nov&amp;#xe8;re; Stuart Moodie; Anatoly Sorokin; Falk Schreiber; Huaiyu Mi.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2010
URL: http://precedings.nature.com/documents/3719/version/2

The Size-Weight Illusion Is Not an Illusion When Picking the Best Objects to Throw
Provedor de dados: 17
Autores: Qin Zhu; Geoffrey Bingham.
Heaviness perception involves a misperception of weight known, since the 19th century, as the Size-Weight Illusion ^1^. The larger of two objects of equal mass is reported to be lighter than the smaller when they are lifted. The illusion has been found to be reliable and robust. It persists even when people know that the masses are equal and handle objects properly ^2^. It has been exhibited by children of only 2 years of age ^3,4^. All this suggests that the effect might be intrinsic to humans. Although different hypotheses have been advanced to account for the illusion over the 100+ years it has been studied ^5-11^, its origin remains unknown. More recently, people&amp;#x27;s perception of optimal objects for long distance throwing was found to exhibit a...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4584/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

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

Trypsin digest of cancer cells surface stimulates anti-tumor immune response better than cancer cells themselves
Provedor de dados: 17
Autores: Petr Lokhov; Balashova Elena.
Antigens expressed on the surface of cancer cells are accessible targets for both humoral and cell-mediated immune responses, and are therefore potential candidates for vaccine development. Treating surface of live human breast adenocarcinoma cells (MCF-7) with trypsin yields a digest that contains 0.7% of total cell protein. Despite this difference, the trypsin digest stimulates in cytotoxicity assays anti-tumor response which kills 10-40% more cancer cells than those stimulated with cells themselves. From these results, we concluded that trypsin digest obtained from live cancer cells contains the essential antigens to induce an immune-mediated anti-tumor effect, and therefore, is candidate for anti-tumor vaccine development.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4895/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

The Relationship between Physical Activity and Body Mass Index: Issues in Model Specification
Provedor de dados: 17
Autores: Gizachew Tiruneh.
*Objective*: To investigate the best statistical models that describe the effect of physical activity on BMI.&amp;#xd;&amp;#xa;*Design*: Cross-sectional analyses of physical activity and BMI data. &amp;#xd;&amp;#xa;*Subjects*: 107 obese, overweight, and healthy college students (mean duration of physical activity for the normal, overweight, and obese students: 89, 59, and 24 months, respectively; mean BMI for the normal, overweight, and obese students: 21.61, 27.07, and 35.54 kg/m2, respectively).&amp;#xd;&amp;#xa;*Measurements*: Inverse linear, inverse logarithmic, and inverse logistics models were used to analyze survey data for physical activity (measured by both frequency and duration of exercise) and BMI. Gender, age, and physical intensity variables...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2758/version/4

Ten Simple Rules for Searching and Organizing the Scientific Literature
Provedor de dados: 17
Autores: Denis C. Bauer.
The exponentially increasing number of published papers (1.4 million per year by one estimate) makes it more and more difficult for us to manage the flood of scientific information. Each of us has acquired some protocol to find and organize journal articles and other references over the course of our careers. Most of those protocols are likely to have been formed by old routines or idleness rather than a structured approach to save time and frustration over the long run. Furthermore, with the Web 2.0 revolution, new ways of handling information are emerging (O&amp;#x2019;Reilly 2005). For example, traditional standalone tools for reference management like EndNote  are being supplemented by centralized resources like RefWorks  and social bookmarking sites...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3867/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

Using causal models to distinguish between neurogenesis-dependent and -independent effects on behaviour
Provedor de dados: 17
Autores: Stanley E. Lazic.
There has been a substantial amount of research on the relationship between hippocampal neurogenesis and behaviour over the past fifteen years, but the causal role that new neurons have on cognitive and affective behavioural tasks is still far from clear. This is partly due to the difficulty of manipulating levels of neurogenesis without inducing off-target effects, which might also influence behaviour. In addition, the analytical methods typically used do not directly test whether neurogenesis mediates the effect of an intervention on behaviour. Previous studies may have incorrectly attributed changes in behavioural performance to neurogenesis because the role of known (or unknown) neurogenesis-independent mechanisms were not formally taken into...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2012
URL: http://precedings.nature.com/documents/6988/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

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

Transpiration in plants: A thermodynamic imperative
Provedor de dados: 17
Autores: Carmen Noemi Hernandez Candia; Karo Michaelian.
In this article we determine the importance of transpiration in plants at three different levels of organization: the plant itself, the ecosystem, and the biosphere, all in terms of entropy production due to transpiration. We propose that transpiration is a thermodynamic imperative rather than a physiological burden for the plant. Plants have not replaced their prevalent metabolism C3 with those of less loss of water, C4 or CAM. We argue that the fact that plants retain higher rates of transpiration along evolution could be explained using thermodynamic criteria.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Plant Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5463/version/1

Statistical Modeling of Epistasis and Linkage Decay using Logic Regression
Provedor de dados: 17
Autores: Thomas  B. Parker; Peter Szucs; Walt  F. Mahaffee; Jean-Luc Jannink; John A. Henning.
Logic regression has been recognized as a tool that can identify and model non-additive genetic interactions using Boolean logic groups. Logic regression, TASSEL-GLM and SAS-GLM were compared for analytical precision using a previously characterized model system to identify the best genetic model explaining epistatic interaction of vernalization-sensitivity in barley. A genetic model containing two molecular markers identified in vernalization response in barley was selected using logic regression while both TASSEL-GLM and SAS-GLM included spurious associations in their models. The results also suggest the logic regression can be used to identify dominant/recessive relationships between epistatic alleles through its use of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1386/version/2

The oldest amputation on a Neolithic human skeleton in France
Provedor de dados: 17
Autores: Cecile Buquet-Marcon; Charlier Philippe; Samzun Anaick.
While &amp;#x27;surgical&amp;#x27; practices such as trepanations are well attested since the first stages of the European Neolithic, the amputation of limbs in Prehistoric periods has not been well-documented until the case presented here. The particularly well-preserved remains of an aged male were recently uncovered in the Neolithic site (4900-4700 BC) of Buthiers-Boulancourt in the vicinity of Paris, France. It was already noticed in situ that the distal part of the left humerus was abnormal and this led us to the hypothesis of a partially healed &amp;#x27;surgical&amp;#x27; amputation.The further investigations reported here confirm a traumatic origin and a partial cicatrisation after surgery, indicating that the patient survived. It also proves the...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2007
URL: http://precedings.nature.com/documents/1278/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

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

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

Without magic bullets: the biological basis for public health interventions against protein folding disorders
Provedor de dados: 17
Autores: Rodrick Wallace.
Protein folding disorders of aging like Alzheimer&amp;#x27;s and Parkinson&amp;#x27;s diseases currently present intractable medical challenges. &amp;#x27;Small molecule&amp;#x27; interventions - drug treatments - often have, at best, palliative impact, failing to alter disease course. The design of individual or population level interventions will likely require a deeper understanding of protein folding and its regulation than currently provided by contemporary &amp;#x27;physics&amp;#x27; or culture-bound medical magic bullet models. Here, a topological rate distortion analysis is applied to the problem of protein folding and regulation that is similar in spirit to Tlusty&amp;#x27;s (2010a) elegant exploration of the genetic code. The formalism produces...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Molecular Cell Biology; Neuroscience; Pharmacology.
Ano: 2010
URL: http://precedings.nature.com/documents/4847/version/2

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

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

The E3 ubiquitin ligase c-IAP1 regulates PCSK9-mediated LDLR degradation: Linking the TNF-&amp;#x3b1; pathway to cholesterol uptake
Provedor de dados: 17
Autores: Weiming Xu; Lizhi Liu.
Proprotein convertase subtilisin/kexin type 9 (PCSK9), in addition to LDLR (low-density lipoprotein receptor) and APOB (apolipoprotein B), is one of three loci implicated in autosomal dominant hypercholesterolaemia (ADH)^1^. A number of PCSK9 gain-of-function mutations and loss-of-function mutations have been identified from families afflicted with ADH with hypercholesterolaemia or hypocholesterolaemia, respectively^1-4^. In humans, the main function of PCSK9 appears to be the post-transcriptional regulation of the number of cell-surface LDL receptors^5-7^. To date, only LDLR and its closest family members VLDLR and ApoER2 have been shown to bind with PCSK9^8,9^. To find new binding partners for PCSK9, we used a shotgun proteomic method to analyse the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4554/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

Strategies for identifying exact structure of neural circuits with broad light microscopy connectivity probes
Provedor de dados: 17
Autores: Yuriy Mishchenko.
Dissecting the structure of neural circuits in the brain is one of the central problems of neuroscience. Until present day, the only way to obtain complete and detailed reconstructions of neural circuits was thought to be the serial section Electron Microscopy, which could take decades to complete a small circuit. In this paper, we develop a mathematical framework that allows performing such reconstructions much faster and cheaper with existing light microscopy and genetic tools. In this framework, a collection of genetically targeted light probes of connectivity is prepared from different animals and then used to systematically deduce the circuit&amp;#x27;s connectivity. Each measurement is represented as mathematical constraint on the circuit...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2669/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

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

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

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

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

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

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

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

SNOMED CT&amp;#x2019;s Ontological Commitment
Provedor de dados: 17
Autores: Stefan Schulz; Ronald Cornet.
SNOMED CT is a clinical terminology that describes the meaning of terms by logical axioms. This requires an ontological commitment, i.e. precise agreements about the ontological nature of the entities referred to. We provide evidence that SNOMED implicitly supports at least three different kinds of commitments, viz. (i) independently existing entities, (ii) representational artifacts, and (iii) clinical situations. Our analysis shows how the truth-value of a sentence changes according to one of these perspectives. We argue that a clear understanding of to what kind of entities SNOMED CT concepts extend is crucial for the proper use and maintenance of SNOMED CT.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3465/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

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

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

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

What is the function of the C1-C3 adrenergic group in the medulla?
Provedor de dados: 17
Autores: John Smythies.
This brief communication discusses a much neglected topic in functional neuroanatomy-the possible function(s) of the adrenergic system in the brain.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1291/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; 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

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

Wikis in scholarly publishing
Provedor de dados: 17
Autores: Daniel Mietchen; Gregor Hagedorn; Konrad U. F&amp;#xf6;rstner; M Fabiana Kubke; Claudia Koltzenburg; Mark J. Hahnel; Lyubomir Penev.
Scientific research is a process concerned with the creation, collective accumulation, contextualization, updating and maintenance of knowledge. Wikis provide an environment that allows to collectively accumulate, contextualize, update and maintain knowledge in a coherent and transparent fashion. Here, we examine the potential of wikis as platforms for scholarly publishing. In the hope to stimulate further discussion, the article itself was drafted on &amp;#x22;Species-ID&amp;#x22;:http://species-id.net/w/index.php?title=Wikis_in_scholarly_publishing&amp;#x26;oldid=3815 - a wiki that hosts a prototype for wiki-based scholarly publishing - where it can be updated, expanded or otherwise improved.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5891/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/1

SNP analysis reveals an evolutionary acceleration of the human-specific microRNAs
Provedor de dados: 17
Autores: Qipeng Zhang; Ming Lu; Qinghua Cui.
MicroRNAs are one class of important gene regulators at the post-transcriptional level by binding to the 3&amp;#x2019;UTRs of target mRNAs. It has been reported that human microRNAs are evolutionary conserved and show lower single nucleotide polymorphisms (SNPs) than their flanking regions. However, in this study, we report that the human-specific microRNAs show a higher SNP density than both the conserved microRNAs and other control regions, suggesting rapid evolution and positive selection has occurred in these regions. Furthermore, we observe that the human-specific microRNAs show greater SNPs minor allele frequency and the SNPs in the human-specific microRNAs show fewer effects on the stability of the microRNA secondary structure, indicating that the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2127/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

Systems Biology Graphical Notation: Process Diagram Level 1
Provedor de dados: 17
Autores: Nicolas Le Novere; Stuart Moodie; Anatoly Sorokin; Michael Hucka; Falk Schreiber; Emek Demir; Huaiyu Mi; Yukiko Matsuoka; Katja Wegner; Hiroaki Kitano.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2320/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

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

Scaffolder - Software for Reproducible Genome Scaffolding.
Provedor de dados: 17
Autores: Michael D. Barton; Hazel A. Barton.
Background: Assembly of short-read sequencing data can result in a fragmented non-contiguous series of genomic sequences. Therefore a common step in a genome project is to join neighboring sequence regions together and fill gaps in the assembly using additional sequences. This scaffolding step, however, is non-trivial and requires manually editing large blocks of nucleotide sequence. Joining these sequences together also hides the source of each region in the final genome sequence. Taken together, these considerations may make reproducing or editing an existing genome build difficult.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methods: The software outlined here, &amp;#x201c;Scaffolder,&amp;#x201d; is implemented in the Ruby programming language and can be...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5779/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

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

The Computational Magic of the Ventral Stream: Towards a Theory
Provedor de dados: 17
Autores: Tomaso A. Poggio.
I conjecture that the sample complexity of object recognition is mostly due to geometric image transformations and that a main goal of the ventral stream &amp;#x2013; V1, V2, V4 and IT &amp;#x2013; is to learn-and-discount image transformations. The most surprising implication of the theory emerging from these assumptions is that the computational goals and detailed properties of cells in the ventral stream follow from symmetry properties of the visual world through a process of unsupervised correlational learning.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;From the assumption of a hierarchy of areas with receptive fields of increasing size the theory predicts that the size of the receptive fields determines which transformations are learned during development and...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6117/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

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

The use of Web Ontology Language (OWL) to Combine Extant Controlled Vocabularies in Biodiversity Informatics Appears Redundant
Provedor de dados: 17
Autores: Roger D. Hyam.
Implementation of PESI requires data to be combined from multiple source databases. Some of the shared fields in the source databases used different controlled vocabularies of terms. OWL DL was investigated as a mechanism to build an extensible, shared ontology of species occurrence terms that permitted the source database to continue using and extending their own vocabularies whilst formally mapping to a more generic shared vocabulary. The merits of this approach were explored and it was concluded that the building of such a complex mapping ontology probably wasn&amp;#x27;t worthwhile. The level of semantic complexity involved outweighed the costs of simply imposing a flat list of well defined terms onto data suppliers. The main problem with exiting...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5168/version/2

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

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

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

Towards a cognitive definition of colour vision
Provedor de dados: 17
Autores: Peter Skorupski; Lars Chittka.
In recent years, colour vision abilities have been rather generously awarded to vari-ous invertebrates and even bacteria. This uncertainty of when to diagnose colour vi-sion stems in part from confusing what colour vision can do with what it is. What col-our vision can do is discriminate wavelength independent of intensity. However, if we take this as a definition of what colour vision is, then we might indeed be obliged to conclude that some plants and bacteria have colour vision. Moreover, there is a simi-lar confusion of what are necessary and what are sufficient mechanisms and behav-ioural abilities for colour vision. To humans, seeing in colour means seeing an image in which objects/lights have chromatic attributes - in contrast to the sensation that...
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1766/version/2

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

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

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

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

Skin Typing and High Resolution MRI of Human Skin: Multiple Contrast Approach for Image Characterization
Provedor de dados: 17
Autores: Rakesh R. Sharma.
Background and objectives:    &amp;#xd;&amp;#xa;The ex vivo magnetic resonance microimaging (MRM) image characteristics are reported in human skin excised samples. &amp;#xd;&amp;#xa;Design and methods:&amp;#xd;&amp;#xa;Human excised skin samples were imaged using custom coil placed inside 500 MHz NMR imager for high resolution microimaging. Skin in vivo- and ex vivo MRI images were processed for characterization of different skin structures. Contiguous cross-sectional T1-weighted 3D spin echo MRI, T2-weighted 3D spin echo MRI and proton density images were compared with skin histopathology and NMR peaks. In all skin specimens, epidermis and dermis thickening and hair follicle size was measured using MRM.  &amp;#xd;&amp;#xa;Results:...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4161/version/2

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

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

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

The origin of vertebrates and their symmetry, segmentation, chord and tubular nervous system
Provedor de dados: 17
Autores: Alexander Ermolenko; Elena A. Perepada.
Development of vertebrata begins with formation of a multicellular organism by ordered repeated division of a reproductive cell and nondisjunction of the new formed cells, which have kept connection by means of the extracellular matrix. Further there is a consecutive formation of organisms due to aggregation of similar structures: blastaea; segmentella, supersegmentella. Supersegmentella gave development to tunicates, hemichordates, chordates like lancelet and to predecessors of vertebrata. Segmentation of organisms is determined by aggregation of supergastraeas into one integrated. Symmetry is determined by structure-forming quality of extracellular matrix. Symmetry of primary organisms was radial; then radial-bilateral, and the first plane of symmetry...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4164/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

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

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

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

The Bond Between a Horse and a Human
Provedor de dados: 17
Autores: Debbie Crews.
The bond that exists between a horse and human was examined using EEG from the horse and human simultaneously. Three volunteers ranging from novice to elite horse experience participated with an unfamiliar horse. The elite participant was also recorded with her own horse. A dose-response effect was tested using 6 conditions requiring increasing interaction between the horse and human (baseline - apart, standing together, petting, grooming, sitting, and riding). EEG was recorded from 10 locations on the horse and the human. EEG brain maps illustrated that increasing interaction between the horse and human showed more synchronous EEG. The elite horse person showed greater synchronization with her own familiar horse. Perhaps these findings illustrate the bond...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3454/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

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

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

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

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

Visual Molecular Dynamics Investigations of the Impact of Hydrophobic Nanoparticles on Prognosis  of Alzheimer&amp;#x2019;s Disease and Cancers
Provedor de dados: 17
Autores: I. C. Baianu; M Charles; V. I. Prisecaru.
The possible impact of hydrophobic lectin nanoparticles on the prognosis and progression of Alzheimer&amp;#x27;s disease (AD) and cancers was investigated by Visual Molecular Dynamics (VMD) computer modeling programs available from the Beckmann Advanced Research Institute at the University of Illinois at Urbana. Our results indicate the possibility of impeding pathological aggregation of certain proteins such as modified tau- or beta-amyloid that are currently being considered as possible causes of Alzheimer&amp;#x27;s disease. VMD programs serve as useful tools for investigation hydrophobic protein aggregation that may play a role in aging of human populations.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Neuroscience; Pharmacology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7111/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

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

The Calbindin-D28k binding site on inositol monophosphatase may allow inhibition independent of the lithium site of action
Provedor de dados: 17
Autores: Galila Agam; Miriam Eisenstein; Itshak Levi; Yael Askira; Orna Almog; Chaim Gilon; Amnon Hoffman; Yftah Talgan; Joseph Fanous.
Among numerous reported biochemical effects the lithium-inhibitable enzyme inositol-monophosphatase (IMPase) remains a viable target for lithium&amp;#x27;s therapeutic mechanism of action. Calbindin-D28k (calbindin) interacts with IMPase enhancing its activity. In the present study in silico modeling of IMPase-calbindin binding using the program MolFit indicated that the 55-66 amino acid segment of IMPase anchors calbindin via Lys59 and Lys61 with a glutamate in between (Lys-Glu-Lys motif). The model further suggested that the Lys-Glu-Lys motif interacts with residues Asp24 and Asp26 of calbindin. Indeed, we found that differently from wildtype calbindin, IMPase was not activated by mutated calbindin in which Asp24 and Asp26 were replaced by alanine....
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6323/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

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

Salmonella typhimurium harboring plasmid expressing interleukin-12 induced attenuation of infection and protective immune responses
Provedor de dados: 17
Autores: Yong Keun Park; Yoon Won Suck; Lee Seung Seok.
IL-12 is known to be an essential cytokine which appears to provide protective immunity against intracellular bacteria, such as Salmonella. In this study, we investigated the possibility of developing a vaccine using IL-12 against virulent Salmonella. We used the host defense system activated by cytokine IL-12. The highly virulent Salmonella strain (Salmonella typhimurium UK-1) was transformed with cytokine-expressing plasmids. These live, wild-type pathogens were used as vaccine strains without undergoing any other biological or genetic attenuating processes. The newly developed strains induced partial protection from infections (30-40%). Of note, the interleukin-12 transformed pathogen was safe upon immunization with low doses (103 CFU), induced IgG...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/3413/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

`The frozen accident&amp;#x27; as an evolutionary adaptation: A rate distortion theory perspective on the dynamics and symmetries of genetic coding mechanisms
Provedor de dados: 17
Autores: James  F. Glazebrook; Rodrick  Wallace.
We survey some interpretations and related issues concerning the frozen hypothesis due to F. Crick and how it can be explained in terms of several natural mechanisms involving error correction codes, spin glasses, symmetry breaking and the characteristic robustness of genetic networks.  The approach to most of these questions involves using elements of Shannon&amp;#x27;s rate distortion theory incorporating a semantic system which is meaningful for the relevant alphabets and vocabulary implemented in transmission of the genetic code. We apply the fundamental homology between information source uncertainty with the free energy density of a thermodynamical system with respect to transcriptional regulators and the communication channels of sequence/structure...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5717/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/7

Reversal of an immunity associated plant cell death program by the growth regulator auxin
Provedor de dados: 17
Autores: Suresh Gopalan.
One form of plant immunity against pathogens involves a rapid host programmed cell death at the site of infection accompanied by resistance, termed the hypersensitive response (HR). Here it is shown that the HR programmed cell death program initiated by the bacterial type III secretion system dependent proteinaceous elicitor harpin from Erwinia amylovora can be reversed till very late in the process by the plant growth regulator auxin. Early inhibition or late reversal of this cell death program does not affect marker genes tightly correlated with local and systemic resistance. Cross-regulation between cell death programs and growth regulators is prevalent in different kingdoms. Thus, the concept that cell death program can be reversed till late provides a...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology; Molecular Cell Biology; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1347/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

Stem Cell Antigen CD34 In Native And Engineered Form Alter Its Binding Ability To Stromal Cells And Ligands: A Classical Example Of Clinical Benefits Of Therapeutic Genetic Engineering Of Stem Cells In Transplantation
Provedor de dados: 17
Autores: Gurudutta Gangenahalli; Vimal Kumar  Singh; Rajendra Prasad  Tripathi; Yogesh Kumar Verma; Pallavi  Gupta; Neeraj Kumar Satija.
CD34 is a highly glycosylated surface-expressed sialomucin and, because it is present on hematopoietic stem cells (HSCs), has demonstrated immense clinical utility in their enumeration in aphaeresis products, immunoaffinity purification for transplantation, and disease monitoring.  The success of CD34 based reagents in identifying hematopoietic progenitors led to the assumption that CD34 is expressed on cells with regenerative potential and is sufficient for hematopoietic reconstitution in marrow-ablated recipients. However, its role has not been identified in substantial detail. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;With the advent of the fact that CD34 binds adapter protein like CRK-L in cytosol and CD34 knock out studies identified a a signaling role,...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5454/version/1

Towards a Taxonomically Intelligent Phylogenetic Database
Provedor de dados: 17
Autores: Roderic Page.
This note outlines some of the key intellectual obstacles that stand in the way of creating a usable phylogenetic database. These challenges include the need to accommodate multiple taxonomic names and classifications, and the need for tools to query trees in biologically meaningful ways. Until these problems are addressed, and a taxonomically intelligent phylogenetic database created, much of our phylogenetic knowledge will languish in the pages of journals.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1028/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

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

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

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

Single cell fertilizer (SCF): Evidence to prove that bio-molecules are potent nutrient for plant growth
Provedor de dados: 17
Autores: Sribir Sen; Amit  Kr. Roy; Sayan Choudhury; Shibu Ghosh; Somenath Das; Sohini Roy; Rajib Ghosh; Dipankar Dey; Deben Pathak; Sanjeev Upadhyay; Isita Chattopadhya.
Fertilizers of various kinds are used for the cultivation of crop plants for hyper production of plant based food materials. The study used bio-molecules made in a bacterial cell. The experimental results showed tremendous effect on plant growth. These cellular molecules were made by treating the bacterial cells with   lysozyme and protenase K. The   wet/weight was increased in multiple folds compared to that of control sets. The fold of increase was 4.79 for rice, 2.77 for wheat, 1.89 for gram and 1.89 for pea when bacterial cellular molecules were used as fertilizer.
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/2816/version/1

Transformation of metabolism with age and lifestyle in Antarctic seals: a case study of systems biology approach to cross-species microarray experiment
Provedor de dados: 17
Autores: Andrey Ptitsyn; Shane Kanatous.
*_Background:_* The metabolic transformation that changes Weddell seal pups born on land into aquatic animals is not only interesting for the study of general biology, but it also provides a model for the acquired and congenital muscle disorders which are associated with oxygen metabolism in skeletal muscle. However, the analysis of gene expression in seals is hampered by the lack of specific microarrays and the very limited annotation of known Weddell seal (_Leptonychotes weddellii_) genes.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*_Results:_* Muscle samples from newborn, juvenile, and adult Weddell seals were collected during an Antarctic expedition. Extracted RNA was hybridized on Affymetrix Human Expression chips. Preliminary studies showed a detectable...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3380/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

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

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

The universal &amp;#x22;shape&amp;#x22; of human languages: spectral analysis beyond speech
Provedor de dados: 17
Autores: Fermin Moscoso del Prado.
A common recommendation for linguists is that, when analyzing language, they should take a &amp;#x22;man-from-mars&amp;#x22;, know-nothing, perspective to describe the structures that they observe, if possible limiting themselves to the mechanical application of a set of well-defined techniques and criteria. Unfortunately, the complex nature of linguistic structures makes it difficult to adopt such a detached perspective. A language, as represented by a corpus of text, can be described macroscopically by the symbolic periodogram of the corpus, analogous to the spectrograms commonly used for describing speech. Here, I show that the periodogram exhibits a universal &amp;#x22;shape&amp;#x22; from human languages, and this shape originates in known properties...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6097/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

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

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

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

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

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

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

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

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

Strong and weak competitors can coexist in the same niche
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The competitive exclusion principle postulates that two trophically identical but fitness different species can not stably coexist in the same niche. However, this principle contradicts the observed nature&amp;#x27;s species richness. This fact is known as the biodiversity paradox. Here, using a simple cellular automaton model, we mechanistically show how two trophically identical, but fitness different species may stably coexist in the same niche. As environment is stable and any trade-offs are absent in this model, it strongly violates the competitive exclusion principle.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7107/version/2

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

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

We Need A Web For Data
Provedor de dados: 17
Autores: John Wilbanks.
The Web has many forums for sharing personal data, but not for scientific data and not in a way that allows the data to be accessed by &amp;#x22;machines as users.&amp;#x22; A Web of data could add tremendous value by integrating disparate disciplines or conduct data-driven queries. Doing this is very complex and requires more robust standards than currently exist. The intended user for most data is not a person; it is a software application that can manipulate the data into something useful for humans. Such software could be &amp;#x22;search engines, analytic software, visualization tools, database back ends, and more.&amp;#x22; This need creates a much different requirement for standards than those that were developed for displaying web data to people....
Tipo: Manuscript
Palavras-chave: Biotechnology; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5499/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

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

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

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

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

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

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

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

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

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

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

Tumor suppressors p53, p63, and p73 inhibit migrating cancer stem cells by increasing the expression of stem cell suppressing miRNAs
Provedor de dados: 17
Autores: Lakshmanane Boominathan.
ZEB1/2 has been shown to suppress the expression of the tumor suppressors E-cadherin, TA-p73, INK4b, CDKN1a, and thereby promotes epithelial to mesenchymal transition, invasion, and metastasis.  I have recently shown that p53-dependent miRs, such as miR-192, 215, 145, 203, 200b/c, 183, suppress the expression of ZEB1/2.  Another recent study showed that ZEB1/2 suppresses the expression of miR-200b/c, miR-203, &amp;#x26; miR-183, which in turn, inhibit the expression of stem cell factors, such as Sox-2, Klf-4, and BMI.  ZEB1/2, by inhibiting the expression of stem cell factors suppressing miRs, it up regulates the expression of stem cell factors.  By up regulating the stem cell factors and down regulating metastasis suppressors, ZEB1/2 promotes both...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4385/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

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

Thermal signatures of human pheromones in sexual and reproductive behaviour
Provedor de dados: 17
Autores: Andrea Mazzatenta; Gian Luca Romani; Luca Tommasi; Arcangelo Merla.
Chemically mediated sexual communication in humans has been largely neglected due to its non-conscious and relatively concealed nature. However, menstrual cycle synchronisation, puberty onset in young pre-pubertal girls exposed to their stepfather, and consanguinity avoidance suggest a function in the physiological regulation of sexual and reproductive behaviour in humans. These phenomena are related to activation of the limbic system by pheromones. On the basis of sexually dimorphic activation of brain hypothalamic areas and the control of body temperature via the hypothalamus, our hypothesis is that human sexual pheromones can induce thermal effects that can be revealed by high-resolution thermal infrared imaging. Here we show that in women, male sexual...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4477/version/1

TreeRipper: towards a fully automated optical tree  recognition software
Provedor de dados: 17
Autores: Joseph Hughes.
Relationships between species, genes and genomes have been printed as trees for over a century. Whilst this may have been the best format for exchanging and sharing phylogenetic hypotheses during the 20th century, the worldwide web now provides faster and automated ways of transferring and sharing phylogenetic knowledge. However, novel software is needed to defrost these published phylogenies for the 21st century. &amp;#xd;&amp;#xa;TreeRipper is a command line c++ program for the fully-automated recognition of multifurcating phylogenetic trees. The program accepts a range of input image formats  (PNG, JPG/JPEG, GIF, TIFF or PDF ). Then follows a number of cleaning steps to detect lines, remove node labels, patch-up broken lines and corners and detect line...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Earth &amp; Environment; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4997/version/1

Translational Oncogenomics and Human Cancer Interactome Networks
Provedor de dados: 17
Autores: I. C. Baianu.
An overview of translational, human oncogenomics, transcriptomics and cancer interactomic networks is presented together with basic concepts and potential, new applications to Oncology and Integrative Cancer Biology. Novel translational oncogenomics research is rapidly expanding through the application of advanced technology, research findings and computational tools/models to both pharmaceutical and clinical problems. A self-contained presentation is adopted that covers both fundamental concepts and the most recent biomedical, as well as clinical, applications. Sample analyses in recent clinical studies have shown that gene expression data can be employed to distinguish between tumor types as well as to predict outcomes. Potentially important applications...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Genetics &amp; Genomics; Immunology; Molecular Cell Biology; Pharmacology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6190/version/2

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

The Multigeneic _Rhg1_ Locus: A Model For The Effects on Root Development, Nematode Resistance and Recombination Suppression.
Provedor de dados: 17
Autores: David A. Lightfoot; Ali Srour; Jawad Afzal; Navinder Saini.
Soybean (Glycine max L. Merr.) resistance to populations (HgType) of _Heterodera glycines I._, the soybean cyst nematode (SCN), requires a functional allele at rhg1. An apoptosis-like response in the giant cells formed around the nematode results 24-48 h after feeding commences. This study aimed to identify the role of the three genes within the rhg1 locus, a receptor like kinase (RLK), a laccase and an ion anti-porter. Used were near isogeneic lines (NILs) that contrasted at their rhg1 alleles. Features of the rhg1 locus, the candidate genes and their nascent transcripts and proteins in roots were elucidated. First, evidence for a syntenic gene cluster was found and the effectiveness of SNP probes for distinguishing the homeolog sequence variant on...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Plant Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2726/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

The saltational model for the dawn of H. sapiens, chin, adolescence phase, complex language and modern behavior
Provedor de dados: 17
Autores: Omer Faruk NOYAN; Sahin CAKIR.
A new model may contribute to resolve the origin problem of  H. sapiens. According to our new viewpoint, Neandertals were neither one of our direct ancestors nor a different species.  Their origin was not in Europe 150-200 or 300 thousand years ago. As for the origin of H. sapiens, it was neither in Africa roughly 2 million years ago nor roughly 200 thousand years ago. In other words, both the Multiregional model and the recent African origin model seem wrong. Our own species arose in the Middle East approximately 150 thousand years ago and split into two subspecies: Moderns and Neandertals.  Rapid and radial expansion of H. sapiens from the origin implies a revolution (see Figure 1). Complex language, modern behavior and even adolescence phase plus chin...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics.
Ano: 2007
URL: http://precedings.nature.com/documents/579/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/1

Understanding Hydrogen-Bond Patterns in Proteins using a Novel Statistical Model
Provedor de dados: 17
Autores: Ofer Rahat; Uri Alon; Yaakov Levy; Gideon Schreiber.
Proteins are built from basic structural elements and their systematic characterization is of interest. Searching for recurring patterns in protein contact maps, we found several network motifs, patterns that occur more frequently in experimentally determined protein contact maps than in randomized contact maps with the same properties. Some of these network motifs correspond to sub-structures of alpha helices, including topologies not previously recognized in this context. Other motifs characterize beta-sheets, again some of which appear to be novel. This topological characterization of patterns serves as a tool to characterize proteins, and to reveal a high detailed differences map for comparing protein structures solved by X-ray crystallography, NMR and...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1490/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

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

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

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

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

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

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

Strategies for recovering exact structure of neural circuits with broadly targeted fluorescent connectivity probes
Provedor de dados: 17
Autores: Yuriy Mishchenko.
We present a framework for reconstructing structure of complete neural circuits&amp;#xd;&amp;#xa;in the brain using collections of independent measurements of connectivity&amp;#xd;&amp;#xa;performed with existing anatomical or functional fluorescent probes, and&amp;#xd;&amp;#xa;designed to provide complementary information about neural circuit&amp;#x2019;s structure&amp;#xd;&amp;#xa;by targeting slightly different its parts either in deterministic or stochastic&amp;#xd;&amp;#xa;succession. We discuss specific implementation of this procedure using&amp;#xd;&amp;#xa;synaptic fluorescent marker GRASP and Cre/Lox system Brainbow to collect&amp;#xd;&amp;#xa;ensemble of observations of the sets of synapses between stochastically labeled&amp;#xd;&amp;#xa;samples...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2669/version/2

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

Rapid Dissolution of Lignocellulosic Plant Materials in an Ionic Liquid
Provedor de dados: 17
Autores: Sierra Rayne; Giuseppe Mazza.
Concerns regarding the non-renewable nature of, and pollution from, petroleum derived energy and commercial products has led to the concept of a biomass economy. As part of this vision for a society based on sustainable biomaterials, proposed biorefineries need to tackle the challenges of taking a wide diversity of raw biomass and rapidly and effectively transforming it into functionalizable platform molecules that can be derivatized into industrial and consumer products, or converted into biofuels. A substantial research effort is underway focussed on degrading biomass into smaller constituents using a variety of physical, chemical, and biological processes. One promising technology for the solubilization of biomass is ionic liquids (ILs), which has...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment; Plant Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/637/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

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

Systems Biology Markup Language (SBML) Level 2: Structures and Facilities for Model Definitions
Provedor de dados: 17
Autores: Michael Hucka; Stefan Hoops; Sarah M. Keating; Nicolas Le Nov&amp;#xe8;re; Sven Sahle; Darren Wilkinson.
With the rise of Systems Biology as a new paradigm for understanding biological processes, the development of quantitative models is no longer restricted to a small circle of theoreticians. The dramatic increase in the number of these models precipitates the need to exchange and reuse both existing and newly created models. The Systems Biology Markup Language (SBML) is a free, open, XML-based format for representing quantitative models of biological interest that advocates the consistent specification of such models and thus facilitates both software development and model exchange.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Principally oriented towards describing systems of biochemical reactions, such as cell signalling pathways, metabolic networks and gene...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2008
URL: http://precedings.nature.com/documents/2715/version/1

To every man his own language: Are we all Darwin&amp;#x2019;s children?
Provedor de dados: 17
Autores: Shantanu Ghosh.
Although current theories of language evolution have examined both molecular evolution as well as functional connectivity of the cortex in humans as well as other primates, a description of language as pre-adaptation open to natural selection has eluded us so far. Here I review the evidence in favor of natural selection that trigger growth and plasticity of the prefrontal cortex in humans and its links to the mirror neuron system. Evolvability of recursive mechanisms as the hallmark of evolution of symbolic communication in humans is also investigated. The polymorphism of genes like ASPM, Microcephalin and FOXP2 in the evolution of language as an emergent property has also been examined.
Tipo: Manuscript
Palavras-chave: Evolutionary Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1375/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

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

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

To be resistant or tolerant: the evolution of mixed defence strategies
Provedor de dados: 17
Autores: Etzel Garrido; Juan Fornoni.
Theory predicts that resistance and tolerance represent mutually exclusive strategies of host defence. However, empirical evidence reveals that individual hosts simultaneously allocate resources to both mechanisms. Understanding the maintenance of this defence pattern remains controversial because empirical evidence is at odds with theoretical assumptions. Here, we present a novel host-enemy dynamic that considers: the differential effect of each defence strategy upon the evolutionary response of natural enemies; the process of local adaptation of the natural enemies to their hosts and the effect of negative and positive frequency-dependent selection acting on resistance and tolerance respectively. Our analysis suggests that a mixed pattern of defence...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4791/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

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

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

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

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

Young and Early Career Investigators: Report from a Global HIV Vaccine Enterprise Working Group
Provedor de dados: 17
Autores: Dan H. Barouch; Thumbi  Ndung&amp;#x2019;u; Galit  Alter; Timothy  Cardozo; Bhavna  Chohan; Jacques  Fellay; Nicole  Frahm; Jonathan Fuchs; Alasdair Leslie; Yong Liu; Penny  L. Moore; Raul  Rabadan.
The scientific challenges facing HIV-1 vaccine development are unprecedented in the history of vaccinology. As a result, investigators, funders, and other stakeholders generally agree that &amp;#x201c;game-changing&amp;#x201d; ideas are required. While innovation can certainly arise from investigators at all career stages, young and early-career investigators, defined as those under 40 years of age or within 10 years of their final degree or clinical training, are especially key contributors of novel and transformative ideas. Young and early-career investigators bring energy, enthusiasm, and fresh perspectives that are unbiased by prevailing dogma and that are essential to scientific progress.
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4800/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

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

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

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

Selfish and Altruistic Bacterial Populations Maximize Fitness Under Stress by Local Segregation
Provedor de dados: 17
Autores: Juan Keymer; Peter Galajda; Juliana Malinverni; Roberto Kolter; Guillaume Lambert; David Liao; Robert Austin.
Landscapes in ecology have a profound influence on the adaption and evolution of competing populations for resources. We are interested in how altruistic populations survive in the presence of selfish individuals in a non-stirred, closed and complex nutrient landscape. Well-stirred (landscape-free) but closed environments have a depressing future when selfish individuals arise in a population, a fate known as the tragedy of the Commons. Over-exploitation of a well-stirred communal habitat by selfish individuals which do not follow rules of communal self-regulation ends up in the elimination (extinction) of both the original altruistic inhabitants and the selfish population. In the context of bacterial population, the Commons tragedy that occurs is the...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/1713/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

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

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

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

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

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

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

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

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

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

Using open access literature to guide full-text query formulation
Provedor de dados: 17
Autores: Heather A. Piwowar; Wendy W. Chapman.
*Background* &amp;#xd;&amp;#xa;Much scientific knowledge is contained in the details of the full-text biomedical literature.  Most research in automated retrieval presupposes that the target literature can be downloaded and preprocessed prior to query. Unfortunately, this is not a practical or maintainable option for most users due to licensing restrictions, website terms of use, and sheer volume.  Scientific article full-text is increasingly queriable through portals such as PubMed Central, Highwire Press, Scirus, and Google Scholar.  However, because these portals only support very basic Boolean queries and full text is so expressive, formulating an effective query is a difficult task for users.  We propose improving the formulation of full-text queries...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4267/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

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

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

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

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

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

Slow in Motion but Smart in Learning and Memory: Behavioral Changes in Adult NR3A Knockout Mice
Provedor de dados: 17
Autores: Shan Ping Yu; Mingke Song; Osama Mohamad; Ling Wei.
The expression of NMDA receptor subunit NR3A is high in the neonatal brain but low in adults. However, its functional role in the adult brain is obscure. Using wild-type (WT) and NR3A knockout (KO) mice, we show here that NR3A plays imperative roles in multiple behavioral functions in adults. NR3A deletion produced a slow locomotor phenotype with enhanced memory capacities. Hippocampal slices from juvenile and adult NR3A KO mice showed greater long-term potentiation (LTP) compared to WT slices. NR3A deletion resulted in increased expression and phosphorylation of calmodulin-dependent kinase II (CaMKII). CaMKII inhibition abrogated the enhanced LTP in NR3A KO slices. NR3A KO mice were also more sensitive to acute and chronic pain. These data reveal for the...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6079/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

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

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

Recent trends in US patent grants and issues to be considered
Provedor de dados: 17
Autores: George M. Garrity; Charles T. Parker.
The life sciences have changed radically since the Convention on Biological Diversity first opened for signatures in 1992. Traditional organism-based approaches to discovery and use of genetic resources have been supplanted by molecular approaches. Biodiversity prospecting is more likely to be a programmatic bioinformatics activity rather than an activity conducted by field scientists. Access to genetic resources is no longer centered on a hunt for novel species. Rather, the hunt is for novel genes and metabolic pathways that can be cloned into well-understood expression systems and readily scaled-up for industrial production. Information about contemporary research, development, and manufacturing practices needs to be addressed, especially when those...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4998/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

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

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

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

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

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

The Neuroanatomic Basis of the Acupuncture Principal Meridians
Provedor de dados: 17
Autores: Peter Dorsher.
Acupuncture involves treating illness by inserting needles at specified body locations (acupoints). The Principal meridians are pathways that join acupoints with related physiologic effects. Despite nearly 5000 years of continuous clinical study, an accepted anatomic or physiologic basis for acupuncture&amp;#x27;s clinical effects has remained elusive. Some acupoints overlie peripheral nerves, and fMRI studies demonstrate that acupoints have specific effects on central nervous system processing. Traditional Chinese Medicine (TCM) founders described the body&amp;#x27;s viscera based on anatomic dissections yet not a discrete nervous system. By applying computer graphics and virtual human imaging techniques to human developmental neuroanatomy, this paradox...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3795/version/1

The Shape and Dimensionality of Phylogenetic Tree-Space Based on Mitochondrial Genomes
Provedor de dados: 17
Autores: James C. Wilgenbusch; Wen Huang; Kyle A. Gallivan.
Phylogenetic analyses of large and diverse data sets generally result in large sets of competing phylogenetic trees. Consensus tree methods used to summarize sets of competing trees discard important information regarding the similarity and distribution of competing trees. A more fine grain approach is to use a dimensionality reduction method to project tree-to-tree distances in 2D or 3D space. In this study, we systematically evaluate the performance of several  nonlinear dimensionality reduction (NLDR) methods on tree-to-tree distances obtained from independent nonparametric bootstrap analyses of genes from three mid- to large-sized mitochondrial genome alignments.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4605/version/1

The carbon allotrope glitter as n-diamond and i-carbon nanocrystals
Provedor de dados: 17
Autores: Michael J. Bucknum; Eduardo A. Castro.
Diffraction data taken from nanocrystalline n-diamond and i-carbon forms is fit to a so-called glitter model, in which the geometry of the C lattice has been optimized by density functional theory (DFT). A calculated theoretical diffraction pattern for glitter is shown to be a close fit to the experimental data for these novel C forms.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6489/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

XML in Motion from Genome to Drug
Provedor de dados: 17
Autores: C. Gopi Mohan.
Information technology (IT) has emerged as a central to the solution of contemporary genomics and drug discovery problems. Researchers involved in genomics, proteomics, transcriptional profiling, high throughput structure determination, and in other sub-disciplines of bioinformatics have direct impact on this IT revolution. As the full genome sequences of many species, data from structural genomics, micro-arrays, and proteomics became available, integration of these data to a common platform require sophisticated bioinformatics tools. Organizing these data into knowledgeable databases and developing appropriate software tools for analyzing the same are going to be major challenges. XML (eXtensible Markup Language) forms the backbone of biological data...
Tipo: Manuscript
Palavras-chave: Chemistry; Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/287/version/1

Systems Biology Graphical Notation: Activity Flow language Level 1
Provedor de dados: 17
Autores: Huaiyu Mi; Falk Schreiber; Nicolas Le Nov&amp;#xe9;re; Stuart Moodie; Anatoly Sorokin.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialized notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3724/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

Unnatural Selection: A new formal approach to punctuated equilibrium in economic systems
Provedor de dados: 17
Autores: Rodrick Wallace.
Generalized Darwinian evolutionary theory has emerged as central to the description of economic process (e.g., Aldrich et. al., 2008). Here we demonstrate that, just as Darwinian principles provide necessary, but not sufficient, conditions for understanding the dynamics of social entities, in a similar manner the asymptotic limit theorems of information theory provide another set of necessary conditions that constrain the evolution of socioeconomic process. These latter constraints can, however, easily be formulated as a statistics-like analytic toolbox for the study of empirical data that is consistent with a generalized Darwinism, and this is no small thing.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5612/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

Range of motion in intervertebral joints: why we don&amp;#x2019;t trust DinoMorph
Provedor de dados: 17
Autores: Michael P. Taylor.
Attempts to quantitatively reconstruct the range of motion of sauropod necks are intrinsically flawed because of ubiquitous distortion in preserved cervical vertebrae.  This is true even for specimens that are usually considered particularly well preserved, such as the Carnegie Diplodocus and the Berlin Giraffatitan.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6878/version/1

Theoretical studies on the pK~a~ values of perfluoroalkyl carboxylic acids: Non-helical conformation acidity constants for n-perfluorooctanoic acid (n-PFOA)
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
A molecular mechanics force field method (MMFF94) systematic rotor conformational search was conducted on the well known environmental contaminant n-perfluorooctanoic acid (n-PFOA). The  MMFF94 conformational search yielded 2915 separate low- through high-energy conformers of n-PFOA. Ranking of these structures gave the 94 lowest MMFF94 energy conformations that were subjected to subsequent density functional theory (DFT) computational investigations at the B3LYP/6-311++G(d,p) level of theory. Application of a thermodynamic cycle approach, coupled with aqueous and gas phase DFT calculations on the molecular and anionic forms for each of the 94 lowest energy n-PFOA conformers, gave estimated acidity constants (pK~a~ values) for a final converged set of...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3837/version/2

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

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

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

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

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

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

The Broad Spectrum HDAC Inhibitor PCI-24781 Induces Caspase- and ROS-Dependent Apoptosis and is Synergistic with Bortezomib in Lymphoma
Provedor de dados: 17
Autores: Savita  Bhalla; Sriram Balasubramanian; Kevin David; Mint Sirisawad; Joseph  Buggy; Lauren Mauro; Sheila Prachand; Richard Miller; Leo Gordon; Andrew Evens.
We investigated the cytotoxicity and biology of the novel broad-spectrum hydroxamic acid-based histone deacetylase inhibitor (HDACi), PCI-24781. PCI-24781 was studied alone and combined with bortezomib in Hodgkin lymphoma (L428) and non-Hodgkin&amp;#x27;s lymphoma cell lines (Ramos, HF1, SUDHL4). PCI-24781 induced dose-dependent apoptosis that was associated with prominent G0/G1 arrest, decreased S-phase, increased p21 protein expression, and production of reactive oxygen species (ROS). Furthermore, PCI-24781-induced apoptosis was shown to be ROS- and caspase-dependent. Combined PCI-24781 and bortezomib exposure resulted in strong synergistic apoptosis in all cell lines (combination indices 0.19-0.6). Furthermore, compared to either agent alone,...
Tipo: Manuscript
Palavras-chave: Cancer; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/1999/version/1

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

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

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

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

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

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

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

Strong and weak competitors can coexist in the same niche
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
The competitive exclusion principle postulates that two trophically identical but fitness different species can not stably coexist in the same niche. However, this principle contradicts the observed nature&amp;#x27;s species richness. This fact is known as the biodiversity paradox. Here, using a simple cellular automaton model, we mechanistically show how two trophically identical, but fitness different species may stably coexist in the same niche. As environment is stable and any trade-offs are absent in this model, it strongly violates the competitive exclusion principle.
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7107/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

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

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

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

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

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

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

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

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

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

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

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

Trichoderma reesei derived cellulase activity in three N,N-dimethylethanolammonium akylcarboxylate ionic liquids
Provedor de dados: 17
Autores: Sierra Rayne; Giuseppe Mazza.
The activity and denaturation extent of cellulase from Trichoderma reesei (E.C. # 3.2.1.4) was investigated in three representative N,N-dimethylethanolammonium akylcarboxylate ionic liquids. Significant cellulase activity and absence of enzyme unfolding was found in all concentrations of N,N-dimethylethanolammonium acetate (DMEAA), including the pure liquid. Activities in 20% and 40%  (v/v) solutions of DMEAA were equal to citrate buffer controls. Lower enzymatic activities and denaturation were observed in solutions of the corresponding formate and octanoate ionic liquids, although cellulose hydrolysis still proceeded at a substantial rate. The results provide the first proof-of-principle that cellulose can be enzymatically hydrolyzed in the presence of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry.
Ano: 2007
URL: http://precedings.nature.com/documents/632/version/1

Where did Words Come from? A Linking Theory of Sound Symbolism and Natural Language Evolution
Provedor de dados: 17
Autores: Jamie Reilly; David Biun; Wind Cowles; Jonathan Peelle.
Where did words come from? The traditional view is that the relation between the sound of a word and its meaning is arbitrary. An alternative hypothesis, known as sound symbolism, holds that form-meaning correspondence is systematic. Numerous examples of sound symbolism exist across natural language phyla. Moreover, cross-linguistic similarities suggest that sound symbolism represents a language universal. For example, many unrelated languages affix an &amp;#x22;ee&amp;#x22; sound to words in order to emphasize size distinctions or express affection (e.g., look at the teeny weeny baby); other such phonetic universals are evident for object mass, color, brightness, and aggression. We hypothesize that sound symbolism reflects sensitivity to an ecological law...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2369/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

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

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

Transduction Pathways Regulating The Trophic effects of Saccharomyces boulardii in Rat small intestinal mucosa
Provedor de dados: 17
Autores: Jean-Paul Buts; Nadine De Keyser.
_S . boulardii_ is a probiotic yeast widely prescribed in a lyophilized form that determines in human and rat small intestine several effects including endoluminal secretion of enzymes and of polyamines, stimulation of microvillous enzymes, of sIgA ,increased production of the receptor for polymeric immunoglobulins by crypt cells, and enhanced D-glucose uptake.&amp;#xd;&amp;#xa;Aim: The objective of this study was to determine the pathway(s) by which these effects generated by the yeast are transduced into the cell.&amp;#xd;&amp;#xa;Methods: Litters of 6 growing Wistar rats each (30 days post partum) were treated with _S .boulardii_ (50[micro]g per g body wt) or with saline during 72 hours. For each animal, the cytosol was prepared from the whole mucosa...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Microbiology.
Ano: 2009
URL: http://precedings.nature.com/documents/3061/version/1

The hypothesis of basic phenotype modules
Provedor de dados: 17
Autores: Thomas von Zelewsky.
The evolutionary events that allowed the rapid occurrence of metazoa are still enigmatic. The presumably oldest metazoan fossils are microscopic and occur just above 635 Ma, at the beginning of the Ediacaran period. Upon condition that the lack of macrofossils in the lower Ediacaran strata is real, the assumption of a sudden appearance of already complex, but still small animals that flourished during the first half of the Ediacaran is a reasonable option. Consequently, the emergence of the first macrofossils with metazoan affinity in mid Ediacaran strata would indicate a second leap in animal evolution. Here, these apparent leaps are explained in terms of a new concept of evolvability that is based on well definable developmental modules: A system based...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4189/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

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

WikiPathways: Community Curation of Biological Pathways
Provedor de dados: 17
Autores: Alexander Pico.
Assembling biological pathways from information in scientific literature and biological databases is a challenging task. Building a pathway requires domain knowledge from specialists in various biological research areas. Furthermore, research is generating new biological knowledge continuously, making pathway curation an ongoing and dynamic process. To facilitate this process we developed &amp;#x22;WikiPathways&amp;#x22;:http://www.wikipathways.org ^1^, a wiki where users can curate pathways, using an easy to use pathway drawing tool. WikiPathways currently has over 1200 registered users and contains more than 1300 pathways for various organisms, spanning human, mouse, zebrafish, fruit fly, worm, yeast, plants and bacteria. WikiPathways is entering a phase...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/5361/version/1

The Symmetrical Immune Network Theory and a New HIV Vaccine Concept
Provedor de dados: 17
Autores: Geoffrey  W. Hoffmann.
The symmetrical immune network theory is based on Jerne&amp;#x2019;s network hypothesis. An improved version of the theory is presented. The theory is characterized by symmetrical stimulatory, inhibitory and killing interactions between idiotypic and antiidiotypic immune system components. In this version killing is ascribed to IgM antibodies, while IgG antibodies are stimulatory. In the symmetrical immune network theory T cells make specific T cell factors, that have a single V region, and are cytophilic for non-specific accessory cells (A cells, including macrophages and monocytes) and play a role in the system switching between stable steady states. A recurring theme in the theory is the concept of co selection. Co-selection is the mutual positive...
Tipo: Manuscript
Palavras-chave: Immunology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4228/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/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

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

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

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

Subjective Experiences of Space and Time: Self, Sensation, and Phenomenal Time
Provedor de dados: 17
Autores: Ram Lakhan Pandey Vimal.
The investigation of subjective experiences (SEs) of space and time is at the core of consciousness research.  The term &amp;#x2018;space&amp;#x2019; includes the subject and objects.  The SE of subject, I-ness, is defined as &amp;#x2018;Self&amp;#x2019;.  The SEs of objects, subject&amp;#x2019;s external body, and subject&amp;#x2019;s internal states such as feelings, thoughts, and so on can be investigated using the proto-experience (PE)-SE framework.  The SE of time is defined as &amp;#x2018;phenomenal time&amp;#x2019; (which includes past, present and future) and the SE of space as &amp;#x2018;phenomenal space&amp;#x2019;. The three non-experiential materialistic models are as follows: (I) The quantum-dissipation model [25] can connect the discrete...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2272/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

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

Single Cancer Cell Detection by Near Infrared Microspectroscopy, Infrared Chemical Imaging and Fluorescence Microspectroscopy
Provedor de dados: 17
Autores: I. C. Baianu; Schuyler S. Korban; Doina M. Costescu.
Novel techniques are currently being developed and established for the accurate chemical analysis and detection of single cancer cells, single embryos and single seeds by Fourier Transform Near Infrared (FT-NIR) Microspectroscopy, Fourier Transform Infrared (FT-IR), Fluorescence and High-Resolution NMR (HR-NMR). The first FT-NIR chemical images of biological systems approaching 1micron resolution are here reported. 400 and 500 MHz, H-1 NMR analyses were carried out that allowed the selection of mutagenized embryos. Detailed chemical analyses are being demonstrated to be also possible by FT-NIR Chemical Imaging/ Microspectroscopy of single cancer cells. FT-NIR Microspectroscopy and Chemical Imaging are also shown to be potentially important in Functional...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Developmental Biology; Molecular Cell Biology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6207/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

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

Vesicles and lamella: outcome of the changing formation path of a sodium N-lauroylsarcosinate hydrate/1-decanol/water system
Provedor de dados: 17
Autores: Nasima Akter; Faizal Mohamed; Shahidan Radiman; Mohammad I. H. Reza.
Vesicles are closed bilayers that enclose a part of the continuous phase inside the core. In spherical shape, they attain the minimum free energy state. Conversely, lamella with maximum free energy remain in planer bilayer shape in the colloidal dispersion. Even with the same amphiphile concentration the colloidal structures depend on different parameters, many of these already addressed in different reports. However, the effect of mixing procedure as a formation path is unidentified. Here we reported water in 1-decanol and 1-decanol in water; these two different mixing procedures yield vesicles and lamella at the same point of the phase diagram of a sodium N-lauroylsarcosinate hydrate/1-decanol/water system. It was found that the favorable and unfavorable...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/6760/version/1

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

Reward sharpens orientation coding independently on attention
Provedor de dados: 17
Autores: Stefano Baldassi; Claudio Simoncini.
Rewarding improves performance. Is it due to modulations of the output modules of the neural systems or are there mechanisms favoring more &amp;#x27;generous&amp;#x27; inputs? Some recent study included V1 in the the circuitry of reward-based modulations, but the effects of reward can easily be confused with effects of attention. Here we address this issue with a psychophysical dual task to control attention while orientation sensitivity on targets associated to different levels of reward is measured. We found that different reward rates improve orientation discrimination and sharpen the internal response distributions. Data are unaffected by changing attentional load nor by dissociating the feature of the reward cue from the feature relevant for the task....
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3023/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

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

The effects of anti-sense interleukin-5 gene transferred by recombinant adeno-associated virus in allergic rats
Provedor de dados: 17
Autores: Daxiong Zeng; Yong Cao; Qingfeng Song; Chao Cao; Xiansheng Liu; Yongjian Xu; Weining Xiong.
The accumulation and infiltration of eosinophils in airways is one of the most important characteristics of asthma, and is mediated partly by secretion of IL-5 from Th2 lymphocytes. It is well known that interleukin-5 (IL-5) played an important role in the regulation of eosinophils. In this study, an anti-sense IL-5 gene transferred by recombinant adeno-associated virus (rAAV-ASIL-5) was prepared to transfect allergic rats. It was found that the expression of IL-5 protein in plasma and BALF were inhibited significantly. The rAAV-ASIL-5-mediated suppression of total cell counts in peripheral blood and BALF were also observed. Moreover, rAAV-ASIL-5 remarkably reduced the eosinophil counts in peripheral blood and BALF, as well as the expression of ECP protein...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2036/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

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

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

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

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

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

The monoclonal antibody nBT062 conjugated to maytansinoids has potent and selective cytotoxicity against CD138 positive multiple myeloma cells _in vitro_ and _in vivo_
Provedor de dados: 17
Autores: Hiroshi Ikeda; Teru Hideshima; Robert J. Lutz; Hiroshi Yasui; Yutaka Okawa; Tanyel Kiziltepe; Sonia Vallet; Samantha Pozzi; Loredana Santo; Giulia Perrone; Mariateresa Fulciniti; Yu-Tzu Tai; Diana Cristea; Noopur S. Raje; Christoph Uherek; Benjamin D&amp;#xe4;lken; Silkie Aigner; Frank Osterroth; Nikhil C. Munshi; Paul Richardson; Kenneth C. Anderson.
CD138 (Syndecan1) is highly expressed on multiple myeloma (MM) cells. In this study, we examined the anti-MM effect of murine/human chimeric CD138-specific monoclonal antibody (mAb) nBT062 conjugated with highly cytotoxic maytansinoid derivatives _in vitro_ and _in vivo_. These agents significantly inhibited growth of CD138-positive MM cell lines and primary tumor cells from MM patients, without cytotoxicity against peripheral blood mononuclear cells from healthy volunteers. In MM cells, they induced G2/M cell cycle arrest followed by apoptosis associated with cleavage of PARP and caspase-3, -8 and -9. Non-conjugated nBT062 completely blocked cytotoxicity induced by nBT062-maytansinoid conjugate, confirming that binding is required for inducing...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2374/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

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

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

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

Soil Carbon in Agroforestry Systems: An Unexplored Treasure?
Provedor de dados: 17
Autores: P. K. Ramachandran Nair; Vimala D. Nair; Emanuela Gama-Rodrigues; Rasmo Garcia; Solomon Haile; David S. Howlett; B. Mohan Kumar; M.-Rosa Mosquera-Losada; Subhrajit Saha; Asako Takimoto; Rafael Tonucci.
Soil organic matter (SOM), which contains more reactive organic carbon (C) than any other single terrestrial pool, plays a major role in determining C storage in ecosystems and regulating atmospheric concentrations of carbon dioxide (CO2)^1^. Agroforestry, the practice of growing trees and crops in interacting combinations on the same unit of land^2^, primarily by resource-poor smallholder farmers in developing countries, is recognized as a strategy for soil carbon sequestration (SCS) under the Clean Development Mechanism (CDM) of the Kyoto Protocol^3^. The understanding about C storage and dynamics under agroforestry systems (AFS), however, is minimal. Our studies under various AFS in diverse ecological conditions in five countries showed that tree-based...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/4061/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.
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

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

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

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

The &amp;#x27;consciousness&amp;#x27; of the living state: Extending the Baars global broadcast model across physiological subsystems
Provedor de dados: 17
Autores: Rodrick Wallace.
For the broad spectrum of cognitive biological phenomena having &amp;#x27;dual&amp;#x27; information sources, isolation from crosstalk between them requires more metabolic free energy than permitting correlation. This allows an evolutionary exaptation leading to dynamic global broadcasts at multiple scales, similar to the well-studied exaptation of noise to trigger stochastic resonance amplification in physiological systems. Entropy gradient models adapted from nonequilibrium thermodynamics lead to an index theorem in which analytic solutions of empirical equations describe different possible topological modes. Not only is the living state characterized by cognition at every scale and level of organization, but by multiple, shifting, tunable, cooperative...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Ecology; Immunology; Molecular Cell Biology; Neuroscience; Pharmacology; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6898/version/2

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

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

Structures at the Atomic Level of Cobalt, Zinc and Lead Niobates (with an Appendix: Atomic structure of cobalt niobate crystal)
Provedor de dados: 17
Autores: Raji Heyrovska.
The author has found in recent years that bond lengths are exact sums of the radii of adjacent atoms and or ions, where the ions have Golden ratio based radii. This work was prompted by the exciting observation last year of the Golden ratio in the magnetic properties of cobalt niobate. It is shown here that in cobalt and zinc niobates, cobalt, zinc and oxygen ions have Golden ratio based ionic radii, whereas in lead niobate, all atoms have covalent radii. Also, the angles at the single bond oxygen anion and atom are close to 1080, as in a pentagon.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6059/version/2

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

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

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

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

Role and immunomodulatory profile of histamine receptors by H1 and H2 antagonists
Provedor de dados: 17
Autores: Trivendra Tripathi; Mohd. Shahid; Mashiatullah Siddiqui; Rahat Khan.
The present study was designed to delineate the immunomodulatory role of histamine receptors (H1- and H2-) on induction of antibody response to sheep red blood cells (SRBC), as well as the antibody generation profile, in rabbit system, systemically. The rabbits in two groups received pheniramine (H1-receptor antagonist) and ranitidine (H2-receptor antagonist), respectively, via intramuscular route and were immunized with SRBC intravenously to evaluate suppression or enhancement of antibody responses in sem. A third, control group, received vehicle and were immunized in a similar manner. Histamine released from effector cells (mast cells and basophils) _in vivo_ during inflammatory reactions could influence a detectable antibody response to SRBC as early as...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/1547/version/1

Sonic Layer Depth estimated from XBT temperatures and climatological salinities
Provedor de dados: 17
Autores: TVS Udaya Bhaskar; Debadatta  Swain.
Sonic layer depth (SLD) plays an important role in antisubmarine warfare in terms of identifying the shadow zones for submarine safe parking. SLD is estimated from sound velocity profiles (SVP) which is in turn obtained from temperature and salinity (T/S) profiles. Given the limited availability of salinity data in comparison to temperature, SVPs need to be obtained from alternate methods. In the present work, to make use of voluminous temperature data sets from XBT, CTD and other source for estimating SLD, we propose a method of utilizing XBT measurements and World Ocean Atlas climatological salinities to compute SVP and then extract SLD. This approach is demonstrated by utilizing T/S data from Argo floats in the Arabian Sea (40&amp;#xb0; &amp;#x2013;...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6534/version/1

Transient-mediated fate determination in a transcriptional circuit of HIV
Provedor de dados: 17
Autores: Leor Weinberger; Roy D. Dar; Michael Simpson.
Steady-state behavior and bistability have been proposed as mechanisms for decision-making in gene circuits. However, transient gene expression has also been proposed to control cell fate with the decision arbitrated by the lifetime of the expression transient. Here, we report that transcriptional positive-feedback plays a critical role in determining HIV infected cell-fate by extending the duration of Tat expression transients far beyond what protein half-life modulation can achieve. To directly quantify feedback strength and its effects on the duration of Tat transcriptional pulses, we exploit the noise inherent to gene-expression and measure shifts in the autocorrelation of expression noise. The results indicate that transcriptional positive-feedback...
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1198/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

The genetics of colored sequence synesthesia: Evidence of linkage to chromosome 16q and genetic heterogeneity for the condition
Provedor de dados: 17
Autores: Stephanie S. Nelson; Nili Avidan; Anand K. Sarma; Rejnal Tushe; Dianna M. Milewicz; Kwanghyuk Lee; Molly Bray; Suzanne M. Leal; David M. Eagleman.
Synesthesia is a perceptual condition in which normal sensory stimulation can trigger anomalous sensory experiences. For example, synesthetes may experience colors in response to sounds, tastes in response to words, or smells in response to touch. We here focus on colored sequence synesthesia, in which color experiences are triggered by learned ordinal sequences such as letters, numbers, weekdays and months. Although synesthesia has been noted in the scientific literature for over a century, it is understood only at the level of the phenomenology, and not at the molecular and neural levels. We have performed a linkage analysis to identify the first genetic loci responsible for the increased neural crosstalk underlying colored sequence synesthesia. Our...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3987/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

Tautomeric Equilibria Studies by Mass Spectrometry
Provedor de dados: 17
Autores: Patricia E. Allegretti; Mercedes M. Schiavonni; Eduardo A. Castro; Jorge J. Furlong.
Tautomerism in organic chemistry has been extensively studied in condensed phase by spectrometric methods, mainly by IR and NMR techniques. Mass spectrometry studies start 40 years ago but just recently it has been recognized the importance of the mass spectral data for the study of tautomerism in the gas phase.&amp;#xd;&amp;#xa;Mass spectrometry can provide valuable information in regard to tautomeric equilibria when studying mass spectra among the members of different families of organic compounds.&amp;#xd;&amp;#xa;The relevance of the mass spectral data resides on several facts but there are two that are of key importance:&amp;#xd;&amp;#xa;1-&amp;#x9;Mass spectral fragmentation assignments should be tautomer specific since the corresponding abundances...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/1842/version/1

The carbon allotrope glitter as n-diamond and i-carbon nanocrystals
Provedor de dados: 17
Autores: Michael J. Bucknum; Eduardo A. Castro.
Diffraction data taken from nanocrystalline n-diamond and i-carbon forms is fit to a so-called glitter model, in which the geometry of the C lattice has been optimized by density functional theory (DFT). A calculated theoretical diffraction pattern for glitter is shown to be a close fit to the experimental data for these novel C forms.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6489/version/2

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

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

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

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

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

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

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

The Gramene Genetic Diversity Module: a resource for genotype-phenotype association analysis in grass species
Provedor de dados: 17
Autores: Charles Chen; Genevieve DeClerck; Terry Casstevens; Ken Youens-Clark; Jon Zhang; Doreen Ware; Pankaj Jaiswal; Susan McCouch; Edward Buckler.
The Genetic Diversity module of the Gramene database (&amp;#x22;http://www.gramene.org/diversity&amp;#x22;:http://www.gramene.org/diversity) is specifically designed to handle data from high-throughput sequencing and array-based genotyping plateforms. Empowered by the Genomic Diversity and Phenotype Data Model, Gramene Genetic Diversity module provides live database connectivities of RFLP, SSR and SNP allele data, information about QTL, passport data for wild and cultivated germplasm from rice, maize, wheat, and _Arabidopsis_, and quantitative phenotypic data for some of these accessions. Large datasets of SNP variation are searchable via genomic positions of interest by SNP Query tool on a sequenced genome; and, trait associations, patterns of linkage...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4645/version/1

Using Satellite Images in Determination of Malaria Outbreaks Potential Region
Provedor de dados: 17
Autores: Abolfazl Ahmadian Marj; Mohammad Reza Mobasheri; Mohammad Javad Valadanzouje; Yousef Rezaie; Mohammad Reza Abaie.
Malaria outbreaks are affecting nearly 40 percent of the earth&amp;#x27;s population most of whom are living in tropical and subtropical zones. Malaria is an infectious disease that is being transferred by the female mosquito of the species Anopheles. The life cycle of the malaria parasite develops in the anopheline and in the human body. These parasites require suitable environmental parameters in order to complete their development cycles within the mosquito. These parameters are temperature, humidity, vegetation and water. A temperature range of 25&amp;#xb0;C to 35&amp;#xb0;C and relative humidity range of 50 to 80 percent is suitable for developing malaria outbreaks. As the fly-range of the mosquito is limited to 2 to 4 kilometers and since water pools...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2325/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

Relation Ontology II
Provedor de dados: 17
Autores: Cristian Cocos.
Conceived as follow-up to recent efforts destined to supply .owl ontologies with relational tools of greater complexity, the present article focuses on four main paths, all of them consisting in providing biomedical ontologies with formal means to express (1) deviations from normality, (2) topological connectedness, (3) inherence and (4) causality and function.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2479/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

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

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

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

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

The demonstration of the invariant lipid-free composition and the mechanism varying energy and the main components of some mammal meats consisting of muscle and adipose tissue
Provedor de dados: 17
Autores: Mitsugu Inoue; Kazuyo Tsugita.
Background: The assumption of an invariant fat-free or lipid-free composition is prerequisite for most methods of the estimation of body composition in mammals including human but has not been theoretically demonstrated.&amp;#xd;&amp;#xa;Objective: To demonstrate theoretically and practically the invariant lipid-free composition and to understand the mechanism varying the main components of muscle and adipose tissue which have intimate relationships to lipid accumulation or obesity in mammals. &amp;#xd;&amp;#xa;Design:  Whether the combinations of correlations among energy and main components in the hypothetical lipid-ratio variation model (L-varied model), which reflects the invariant lipid-free composition, are consistent with those in the practical...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3832/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

South Dakota Diversity of Temperature: Pictures from Statistical Analysis
Provedor de dados: 17
Autores: Boris Shmagin; Dennis Todey.
The regional diversity of monthly temperature was analyzed based on long-term data obtained for South Dakota (SD) from the High Plains Regional Climate Center. Multidimensional statistical methods were used and the principal results presented as a sequence of 2- and 3-dimensional scatterplot pictures depicting the quantitative results. &amp;#xd;&amp;#xa;System hierarchical model of landscape was used for research tasks formulation. Initial matrixes for three research tasks were compiled for the state. The first set of initial matrices of time series {Xt*n}, where t = number of years and n = number of meteorological stations, contains two matrixes: X1(67*29) and X2(33*94). The second set -{Xt*m}, where t = number of years and m = number of months in a year:...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/1082/version/1

The universe of normal and cancer cell line responses to anticancer treatment: Lessons for cancer therapy
Provedor de dados: 17
Autores: Alexei Vazquez.
According to the Surveillance Epidemiology and End Results report, 1,479,350 men and women will be diagnosed with and 562,340 will die of cancer of all sites in 2009, indicating that about 40% of the cancer patients do not respond well to current anticancer therapies. Using tumor and normal tissue cell lines as a model, we show this high mortality rate is rooted in inherent features of anticancer&amp;#xd;&amp;#xa;treatments. We obtain that, while on average anticancer treatments exhibit a two fold higher efficacy when applied to cancer cells, the response distribution of cancer and normal cells significantly overlap. Focusing on specific treatments, we provide evidence indicating that the therapeutic index is proportional to the fraction of cancer cell...
Tipo: Manuscript
Palavras-chave: Cancer; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5785/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

The beauty of the mammalian vascular system
Provedor de dados: 17
Autores: Julio Gil; Rafael Lahoz-Beltra; Miguel  Gimeno; Jes&amp;#xfa;s Laborda; Javier Nubiala.
Beauty is a characteristic of objects that provides a perceptual experience of pleasure. In nature, aesthetic appreciation thereof has given rise to the mathematical search for good series (e.g. the Fibonacci series) and proportions (e.g. the Golden proportion) as important elements of beauty. In 1928 the mathematician George David Birkhoff introduced a formula for aesthetic measurement of an object. Birkhoff equation defines the aesthetic value as the amount of order divided by the complexity of the product. These two features can be measured easily in poetry, music, painting, architecture, etc. In the fine arts, it is the artist who manipulates both these features, but how does nature manage order and complexity in living organisms or their parts? Here...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2976/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

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

Shaping neurons: how morphological constraints affect axonal polarity
Provedor de dados: 17
Autores: Catherine Villard; Annie Andrieux.
Neuronal differentiation is under the tight control of biochemical and physical information arising from micro-environment. Here, through a panel of poly-L-lysine micropatterns, we wished to assay how external geometrical constraints of neurons may modulate axonal polarization. Constraints applied to either the cell body or to the neurite directions revealed the existence of a differential mechanical tension between the nascent axon and other neurites. Also, we show that centrosome location is not predictive of axonal polarization but responds to the force exerted by the nascent axon. Using curved trajectories for neurite growth inhibited axonal differentiation and prevented formation of multiple axons normally induced by cytochalasin or taxol treatments....
Tipo: Manuscript
Palavras-chave: Developmental Biology; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6021/version/1

The Oxidative Reaction of Potassium Permanganate with Mycolic Acids Leads to a Unique Diagnostic Pattern for Mycobacterium Tuberculosis
Provedor de dados: 17
Autores: Mohsen khatami.
In an oxidative reaction, potassium permanganate reacts with the mycolic acid component of _M.tuberculosis_ and gives rise to a unique saponified pattern specific for _M.tuberculosis_. This brown orange pattern makes it possible to identify _M.tuberculosis_ in a typical laboratory sample. The method avoids the complexity of other methods with special regard to save time and costs.
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2365/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

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

Swine Influenza A Evolution via Recombination - Genetic Drift Reservoir
Provedor de dados: 17
Autores: Henry L. Niman.
The looming influenza pandemic has focused attention^1-4^ on the rapid evolution of H5N1 and other human and avian serotypes.  The basic tenets of influenza genetics^5^ define gradual changes as drifts caused by point mutations created by a polymerase that lacks a proof reading function.  More abrupt changes have been linked to reassortment, which shuffles the eight sub-genomic segments of the influenza genome in dually infected host. The complex evolution of these viruses has created a challenge in vaccine development.  Swine influenza isolates from 2003 and 2004 have been identified^6^ that have acquired a human influenza gene, PB1.  My analysis of the eight gene segments found large portions of two genes, PB2 and PA, which were identical matches with...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics.
Ano: 2007
URL: http://precedings.nature.com/documents/385/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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Reduced GABA-B/GIRK-mediated regulation of the VTA following a single exposure to cocaine
Provedor de dados: 17
Autores: Brian Cadle; Andrew Varnell; Donald C. Cooper.
In this paper, Arora and colleagues expand on their previous work on GIRK channels in the ventral tegmental area (VTA) presenting evidence that a single exposure to cocaine reduces inhibitory GABAergic transmission to dopamine (DA) neurons in the ventral tegmental area. Mice receiving i.p. injections of cocaine saw a short lived (1-5 days) decrease in GABAb mediated G-protein coupled inwardly-rectifying potassium (GIRK) currents in DA neurons in the VTA. This decrease parallels an NMDA-mediated increase in the frequency of glutamatergic neurotransmission. Chronic cocaine injections had no additional effects beyond those seen with single injections. Though they found no change in mRNA levels for GABAb receptors, GIRK channels, or RGS-2 (a G-protein...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6771/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

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

Roman roads: The hierarchical endosymbiosis of cognitive modules
Provedor de dados: 17
Autores: Rodrick Wallace.
Serial endosymbiosis theory provides a unifying paradigm for examining the interaction of cognitive modules at vastly different scales of biological, social, and cultural organization. A trivial but not unimportant model associates a dual information source with a broad class of cognitive processes, and punctuated phenomena akin to phase transitions in physical systems, and associated coevolutionary processes, emerge as consequences of the homology between information source uncertainty and free energy density. The dynamics, including patterns of punctuation similar to ecosystem resilience transitions, are largely dominated by the availability of &amp;#x27;Roman roads&amp;#x27; constituting channels for the transmission of information between modules.
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience; Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3892/version/1

Trophoblastic hormones direct early human embryogenesis
Provedor de dados: 17
Autores: Miguel J. Gallego; Prashob Porayette; Maria M. Kaltcheva; Richard L. Bowen; Sivan Vadakkadath Meethal; Craig S. Atwood.
Division of the human zygote leads to the formation of the blastocyst that contains human embryonic stem cells (hESC) which develop into the embryo.  Little is known about the physiological signals that direct hESC division and differentiation during early embryogenesis.  A number of growth factors, including the pregnancy-associated hormone human chorionic gonadotropin (hCG), are secreted by trophoblasts^1-3^ that lie adjacent to the embryoblast in the blastocyst, but it is not known whether these growth factors directly signal the epiblast.  Here we show that hCG promotes the division of embryoblast-derived inner mass cells (hESC), and their differentiation during blastulation and neurulation.  Inhibition of LH/hCG receptor (LHCGR) signaling with...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2671/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

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

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

Reciprocal homeostatic reactions to chronic excitatory synaptic receptor inactivation in developing cerebral cortex networks
Provedor de dados: 17
Autores: Michael A. Corner.
Chronic blockade of actively excitatory glutamatergic synaptic receptors in co-cultured organotypic rodent neocortex explants leads to a compensatory up-regulation of otherwise inactive input channels so as to maintain almost normal levels of ongoing bursts of action potentials. We report here that this homeostatic return of spontaneous (now kainate receptor driven) firing is accompanied by a reciprocal down-regulation of blocked AMPA and NMDA receptors, such that the developing cortical network is protected against becoming hyperactive when those synaptic inputs are again able to transmit normally.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1260/version/2

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

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

Reassessing the Lineage Fusion Hypothesis for the Origin of Double Membrane Bacteria
Provedor de dados: 17
Autores: Kristen S. Swithers; Gregory P. Fournier; J. Peter Gogarten; Pascal Lapierre.
In 2009, James Lake introduced a new hypothesis in which reticulate phylogeny reconstruction is used to elucidate the origin of Gram-negative bacteria.  The presented data supported the Gram-negative bacteria originating from an ancient endosymbiosis between the Actinobacteria and Clostridia.  His conclusion was based on a presence-absence analysis of protein families that divided all prokaryotes into five groups: Actinobacteria, Double Membrane bacteria (DM), Clostridia, Archaea and Bacilli.  Of these five groups, the DM are by far the largest and most diverse group compared to the other groupings.  While the fusion hypothesis for the origin of double membrane bacteria is enticing, we show that the signal supporting an ancient symbiosis is lost when the...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5812/version/1

Study of Echinoids of Gurpi formation, Iran
Provedor de dados: 17
Autores: Behnaz Balmaki; Masoud  Asgharian Rostami.
In order to detailed study of Echinoids, some samples are collected from Brown limestone member of Seimare from Gurpi Formation with 213 meter thickness which located in the vicinity of Ilam province; settling over Ilam Formation continuously. Paleontological results indicated Campanian - maastrichtian age at this section. Detailed analysis of the 300 samples led to recognition of Bivalve especially Bivalve of Lofa, Brachiopods and five species of Echinoids such as: _Salenia nutrix_, _Globator bleicheri_, _Orthopsis miliarisi_, _Goniopygus superbus_, and _Conulus douville_
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3839/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

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

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

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

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

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

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

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

Regrowing the adult brain: NF-&amp;#x3ba;B controls functional circuit formation and tissue homeostasis in the dentate gyrus
Provedor de dados: 17
Autores: Yvonne Imielski; Jens C. Schwamborn; Patrick L&amp;#xfc;ningschr&amp;#xf6;r; Peter Heimann; Magdalena Holzberg; Hendrikje Werner; Oliver Leske; Andreas W. P&amp;#xfc;schel; Sylvie Memet; Rolf Heumann; Alain Israel; Christian Kaltschmidt; Barbara Kaltschmidt.
Cognitive decline during aging is correlated with a continuous loss of cells within the brain and especially within the hippocampus, which could be regenerated by adult neurogenesis. Here we show that genetic ablation of NF-&amp;#x3ba;B resulted in severe defects in the neurogenic region (dentate gyrus) of the hippocampus. Despite increased stem cell proliferation, axogenesis, synaptogenesis and neuroprotection were hampered, leading to disruption of the mossy fiber pathway and to atrophy of the dentate gyrus during aging. Here, NF-&amp;#x3ba;B controls the transcription of FOXO1 and PKA, regulating axogenesis. Structural defects culminated in behavioral impairments in pattern separation. Re-activation of NF-&amp;#x3ba;B resulted in integration of newborn...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6096/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

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

Universal fractal scaling of self-organized networks
Provedor de dados: 17
Autores: Paul J. Laurienti; Karen E. Joyce; Qawi K. Telesford; Jonathan H. Burdette; Satoru Hayasaka.
There is an abundance of literature on complex networks describing a variety of relationships among units in social, biological, and technological systems. Such networks, consisting of interconnected nodes, are often self-organized, naturally emerging without any overarching designs on topological structure yet enabling efficient interactions among nodes. Here we show that the number of nodes and the density of connections in such self-organized networks exhibit a power law relationship. We examined the size and connection density of 46 self-organizing networks of various biological, social, and technological origins, and found that the size-density relationship follows a fractal relationship spanning over 6 orders of magnitude. This finding indicates that...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4894/version/2

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

Standard operating procedures (SOP) in experimental stroke research: SOP for middle cerebral artery occlusion in the mouse
Provedor de dados: 17
Autores: Ulrich Dirnagl; Members of the MCAO-SOP Group.
Recently, systematic reviews have found quantitative evidence that low study quality may have introduced a bias into preclinical stroke research. Monitoring, auditing, and standard operating procedures (SOPs) are already key elements of quality control in randomized clinical trials and will hopefully be widely adopted by preclinical stroke research in the near future. Increasingly, funding bodies and review boards overseeing animal experiments are taking a proactive stance, and demand auditable quality control measures in preclinical research. Every good quality control system is based on its SOPs. This article introduces the concept of quality control and presents for the first time an SOP in experimental stroke research.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/3492/version/2

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

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

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

Strong violation of the competitive exclusion principle
Provedor de dados: 17
Autores: Lev V. Kalmykov; Vyacheslav L. Kalmykov.
Bacteria and plants are able to form population waves as a result of their consumer behaviour and propagation. A soliton-like interpenetration of colliding population waves was assumed but not proved earlier. Here we show how and why colliding population waves of trophically identical but fitness different species can interpenetrate through each other without delay. We have hypothesized and revealed here that the last mechanism provides a stable coexistence of two, three and four species, competing for the same limiting resource in the small homogeneous habitat under constant conditions and without any fitness trade-offs. We have explained the mystery of biodiversity mechanistically because (i) our models are bottom-up mechanistic, (ii) the revealed...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Microbiology; Bioinformatics; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6667/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

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

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

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

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

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

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

Singlet-triplet excitation energies of substituted benzenes: A G4 theoretical study
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Singlet-triplet adiabatic (AE~S-T~) and well-to-well (WWE~S-T~) excitation energies of variously substituted phenyl cations were calculated at the G4 level of theory. The G4 E~S-T~ estimates range from 19 to 40 kJ/mol higher than prior density functional theory based predictions for these cations, and suggest that E~S-T~ and ground state multiplicity structure-property trends for phenyl cations previously proposed in the literature may be incorrect. Among the substituents considered, meta-substituted phenyl cations with electron donating groups have singlet ground states, and are not isoenergetic with the corresponding triplet states as previously claimed. Depending on the functional group, ortho- or para- substituted phenyl cations may also be ground...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6449/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

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

Repurposing of Meropenem and Nadifloxacin for Treatment of Burn Patients?
Provedor de dados: 17
Autores: Joseph G. Moloughney; Janice D. Thomas; Christie E. Costa; Karla S. Bullon; James Spencer; Jeffrey H. Toney.
The escalating number of multidrug resistant pathogens has demanded the swift development of new and potent antibiotics (ref. 2). Metallo-[beta]-lactamases (MBLs) continue to evolve, rendering the latest generation of carbapenem antibiotics useless (ref. 8). SPM-1, a recently discovered MBL, was isolated from a juvenile leukemia patient residing in a hospital in San Palo, Brazil just prior to the patient succumbing to septicemia brought on by Pseudomonas aeruginosa expressing SPM-1 (ref. 8). Screening of the Johns Hopkins Compound library of 1,514 FDA or FAD approved drugs (ref. 1) identified a novel SPM-1 inhibitor that is synergistically compatible with meropenem. Using clinically achievable concentrations, meropenem coupled with nadifloxacin inhibits...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3761/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

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

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

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

Signaling via Alk5 Controls Ontogeny of Lung Clara Cells
Provedor de dados: 17
Autores: Yiming Xing; Changgong Li; Aimin Li; Somyoth Sridurongrit; Caterina Tiozzo; Saverio Bellusci; Zea Borok; Vesa Kaartinen; Parviz Minoo.
Clara cells, together with ciliated and pulmonary neuroendocrine cells, make up the epithelium of the bronchioles along the conducting airways. Clara cells are also known as Progenitor/Stem cells during lung regeneration after injury. The mechanisms of Clara cell differentiation are largely unknown. Transforming growth factor-beta is a multifunctional molecule with roles in normal development and disease pathogenesis. In this study, we deleted the TGF-&amp;#x3b2; type I receptor, Alk5 in the embryonic lung epithelium using Gata5-Cre mice. Absence of Alk5 blocked Clara cell differentiation but had no effect on ciliated or pulmonary neuroendocrine cells. Hairy/Enhancer of Split-1, which is expressed in Clara cell putative &amp;#x22;progenitors&amp;#x22; was...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3036/version/1

Vermiculiphily: Larvae Pollinating Orchids!
Provedor de dados: 17
Autores: Pankaj Kumar; Gopal S. Rawat.
Orchids are truly extraordinary organisms exhibiting a wide range of pollination mechanism, many of which awaits discovery. Epipactis veratrifolia is a terrestrial orchid that has been reported to be pollinated by various species of hoverflies in Israel1,2. This orchid is known to emit the smell of aphid pheromone that attracts hoverflies, which lay eggs inside the flower and in the process pollinate them. Recently, we observed a species of hoverfly (Ischiodon scutellaris) pollinate the same orchid species in the Western Himalaya while laying eggs inside the flowers. Ischiodon scutellaris is being reported for the first time as pollinator of this orchid. However, all flowers don&amp;#x2019;t get pollinated, even though insects visit them and lay eggs...
Tipo: Manuscript
Palavras-chave: Ecology; Plant Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6295/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

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

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

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

Two Rules on the Protein-Ligand Interaction
Provedor de dados: 17
Autores: Xiaodong Pang; Linxiang Zhou; Lily Zhang; Lina Xu; Xinyi Zhang.
So far, we still lack a clear molecular mechanism to explain the protein-ligand interaction on the basis of electronic structure of a protein. By combining the calculation of the full electronic structure of a protein along with its hydrophobic pocket and the perturbation theory, we found out two rules on the protein-ligand interaction. One rule is the interaction only occurs between the lowest unoccupied molecular orbitals (LUMOs) of a protein and the highest occupied molecular orbital (HOMO) of its ligand, not between the HOMOs of a protein and the LUMO of its ligand. The other rule is only those residues or atoms located both on the LUMOs of a protein and in a surface pocket of a protein are activity residues or activity atoms of the protein and the...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2008
URL: http://precedings.nature.com/documents/2728/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

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

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

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

Tracking patterns of body mass index and triceps skinfold thickness from childhood to young adulthood: a 12-year prospective cohort study in Slovenia
Provedor de dados: 17
Autores: Gregor Starc; Janko Strel.
OBJECTIVE: To examine tracking patterns of body mass index (BMI), triceps skinfold thickness (TSF), height and weight from childhood to young adulthood in a rapidly developing society.DESIGN: Prospective 12-year cohort study of the Slovenian children, born during 1990-1991.SUBJECTS: A subsample of 4 833 Slovenian children from the 1990-1991 national cohort (n = 21 777) who were included in the SLOFIT monitoring system from 1997 to 2008, with complete data at age 7 and 18 y.MEASUREMENTS: Height, weight and TSF were measured at ages 7, 11, 14 and 18 y. The IOTF BMI cutoff points were used to identify overweight and obesity. RESULTS: Height, weight, and BMI at age 18 y were well predicted from childhood and grew more predictable with age, while TSF was not....
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2902/version/1

Statistical Modeling of Epistasis and Linkage Decay using Logic Regression
Provedor de dados: 17
Autores: Thomas Parker; P Sz&amp;#x171;cs; W F. Mahaffee; John A. Henning.
Logic regression has been recognized as a tool that can identify and model non-additive genetic interactions using Boolean logic groups. Logic regression, TASSEL-GLM and SAS-GLM were compared for analytical precision using a previously characterized model system to identify the best genetic model explaining epistatic interaction for vernalization-sensitivity in barley. A genetic model containing two molecular markers identified in vernalization response in barley was selected using logic regression while both TASSEL-GLM and SAS-GLM included spurious associations in their models. The results also suggest the logic regression can be used to identify dominant/recessive relationships between epistatic alleles through its use of conjugate operators.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2007
URL: http://precedings.nature.com/documents/1386/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

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

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

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

The sound of concepts: The link between auditory and conceptual brain systems
Provedor de dados: 17
Autores: Markus Kiefer; Eun-Jin Sim; B&amp;#xe4;rbel Herrnberger; Jo Grothe; Klaus Hoenig.
Concepts in long-term memory are important building blocks of human cognition and are the basis for object recognition, language and thought. While it is well accepted that concepts are comprised of features related to sensory object attributes, it is still unclear how these features are represented in the brain. Of central interest is whether concepts are essentially grounded in perception. This would imply a common neuroanatomical substrate for perceptual and conceptual processing. Here we show using functional magnetic resonance imaging and recordings of event-related potentials that acoustic conceptual features rapidly recruit auditory areas even when implicitly presented through visual words. Recognizing words denoting objects for which acoustic...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1216/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

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

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

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

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

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

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

Theoretical studies in the molecular Platonic solids: Pure and mixed carbon, nitrogen, phosphorus, and silicon tetrahedranes
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Calculations were conducted at the G4MP2 and G4 composite method levels of theory on the 35 potential carbon, nitrogen, silicon, and phosphorus tetrahedrane derivatives with the general form C~a~N~b~Si~c~P~d~H~(4-b-d)~ (where a+b+c+d=4). At both levels of theory, optimized electronic ground state neutral singlet gas phase (298.15 K, 1 atm) geometries were obtained for 24 of the 35 possible C/N/Si/P tetrahedrane derivatives. Corresponding enthalpies of formation were calculated using the atomization method. Triplet state neutral tetrahedron starting geometries for all compounds either resulted in cage opening or failed to converge. Only 9 cationic and 3 anionic forms converged to stable geometries that retained the tetrahedron cage and were absent imaginary...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6299/version/1

The Entropic Landscape of proteins revealing protein folding mechanism
Provedor de dados: 17
Autores: Kentaro Onizuka.
It has long since been a mystery why most proteins fold within a flash of time into particular structures out of astronomically large numbers of possible conformations. Even more confusing is that protein folding in vivo is played out in rich solution containing various organic and non-organic, big and small molecules and ions which would potentially bind the protein molecules and prevent them folding. A possible answer to these mysteries might be, &amp;#x22;Nature have favoured such proteins that quickly fold in rich solution through natural selection&amp;#x22;. Then what mechanism of folding has been favoured? Here I show how to decipher protein sequences to reveal the folding mechanism. The entropic landscape of a protein sequence tells which region of...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2719/version/1

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

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

Remote preconditioning by aortic constriction: affords cardioprotection as classical or other remote ischemic preconditioning? Role of iNOS
Provedor de dados: 17
Autores: Ashish Sharma; Arshee Munajjam; Bhawna Vaishnav; Richa Sharma; Kunal Kishore; Ashok Sharma; Akash Sharma; Divya Sharma; Rita Kumari; Ashish Tiwari; B.P. Srinivasan; Shyam Agarwal.
Dose remote preconditioning by aortic constriction (RPAC) affords cardioprotection similar to classical or other remote ischemic preconditioning stimulus? Moreover study was also designed to investigate role of inducible nitric oxide synthase in remote preconditioning by aortic constriction. There are sufficient evidences that &amp;#x22;ischemic preconditioning&amp;#x22; has surgical applications and afford clinically relevant cardioprotection. Transient occlusion of circumflex artery, renal artery, limb artery or mesenteric artery preconditions the myocardium against ischemia reperfusion injury in case of ischemic heart disease leading to myocardial infraction. Here abdominal aorta was selected to produce RPAC. Four episodes of Ischemia-reperfusion of 5...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5494/version/1

Reservoir of Bacterial Exotoxin Genes in the Environment
Provedor de dados: 17
Autores: Veronica Casas; Joseph Magbanua; Gerico  Sobrepe&amp;#xf1;a; Stanley Maloy.
This is the first report of an environmental reservoir of a bacterial exotoxin gene harbored in an atypical host in the environment. Screening bacterial isolates from the environment via sea-specific PCR identified an isolate with a DNA sequence  &amp;#x3e;95% identical to the Staphylococcus aureus enterotoxin A gene (_sea_). 16S DNA sequence comparisons identified the environmental isolate as a Pseusodomonad. Laboratory studies confirmed that this Pseudomonad is psychrophilic. The results indicate that the _sea_ gene is present in an alternative bacterial host, providing the first evidence for an environmental reservoir of exotoxin genes in bacteria. Transfer of these genes between phage and alternative bacterial hosts may promote the evolution of novel...
Tipo: Manuscript
Palavras-chave: Ecology; Microbiology.
Ano: 2008
URL: http://precedings.nature.com/documents/2065/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

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

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

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

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

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

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

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

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

Scaling of soaring seabirds and its implication for the maximum size of flying pterosaurs
Provedor de dados: 17
Autores: Katsufumi Sato; Kentaro Q. Sakamoto; Yutaka Watanuki; Akinori Takahashi; Nobuhiro Katsumata; Charles-Andre Bost; Henri Weimerskirch.
The flight ability of animals is restricted by the scaling effects imposed by physical and physiological factors. In comparisons of the power available from muscle and the mechanical power required to fly, theoretical studies have predicted that the margin between the powers should decrease with body size and that flying animals have a maximum body size. However, predicting an absolute value of this upper limit has been difficult because wing morphology and flight styles vary among species. Albatrosses and petrels have long, narrow, aerodynamically efficient wings and are considered to be soaring birds. Here, using animal-borne accelerometers, we show that scaling analyses of wing-flapping frequencies in these seabirds indicate that the maximum size limit...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/2605/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

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

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

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

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

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

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

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

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

The modulation of alpha-wave amplitude in human EEG by the intention to act with a motor response
Provedor de dados: 17
Autores: Kuno Kirschfeld.
The most conspicuous signal in the human EEG is the so-called alpha wave, oscillations in the frequency range of 8 to 12 Hz. Visual stimulation of the retina suppresses the amplitude of alpha waves (Berger effect), and increased attention can reduce them. Here I show that one more parameter significantly affects the amplitudes of alpha waves: the intention to act by a motor response. Together with data from the literature, these results show that alpha waves are not part of the visual processing network but rather part of a long-range neuromodulatory network. The modulation modifies latencies in perception or motor response. The relevant mechanisms are located in early cortical visual areas; their activity may contribute to hemodynamic changes in these...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3720/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/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

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

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

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

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

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

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

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

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

Transcriptional coupling of neighbouring genes and gene expression noise: evidence that gene orientation and non-coding transcripts are modulators of noise
Provedor de dados: 17
Autores: Guang-Zhong Wang; Martin J. Lercher; Laurence D. Hurst.
For some genes, notably essential genes, expression when expression is needed is vital hence low noise in expression is favourable. For others noise is necessary for coping with stochasticity or for providing dice-like mechanisms to control cell fate.  But how is noise in gene expression modulated?  We hypothesise that gene orientation may be crucial, as for divergently organized gene pairs expression of one gene could affect chromatin of a neighbour thereby reducing noise. Transcription of antisense non-coding RNA from a shared promoter is similarly argued to be a noise-reduction mechanism.   Stochastic simulation models confirm the expectation.  The model correctly predicts: that protein coding genes with bi-promoter architecture, including those with a...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4792/version/1

Snca and Bdnf gene expression in the VTA and raphe nuclei of midbrain in chronically victorious and defeated male mice
Provedor de dados: 17
Autores: Natalia N. Kudryavtseva; Natalia P. Bondar; Ul&amp;#x27;yana A. Boyarskikh; Maxim L. Filipenko.
The study aimed to analyze the mRNA levels of Snca and Bdnf genes in the ventral tegmental area (VTA) and raphe nuclei of the midbrain in male mice that had each won or defeated 20 encounters in daily agonistic interactions. Groups of animals that had the same winning and losing track record followed by a no-fight period for 14 days were also studied. Snca mRNA levels were increased in the raphe nuclei in the losers and in the VTA of the winners. After fighting deprivation Snca mRNA levels were decreased to the control level in both groups. Snca mRNA levels were similar to the control level in the VTA of the losers and in the raphe nuclei of the winners. However Snca gene expression was increased in these areas after no-fight period in the winners and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4327/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

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

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

Reaction Attempts Book
Provedor de dados: 17
Autores: Jean-Claude Bradley; Khalid Mirza; Andrew Lang; Tim Bohinski; David Bulger; Alisha Merchant; Emily Messner; Marshall Moritz; Shannon Oseback; Rikesh Parikh; Mitesh Shah.
This book is a compilation of Ugi reactions attempted for the UsefulChem Project mainly in the Bradley laboratory at Drexel University. This includes failed, inconclusive or in progress reactions as well as those where a product was successfully isolated and characterized. The entries are sorted alphabetically based on reactants. Links are provided to the relevant lab notebook pages.  Future editions will include contributions from other sources as well.
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2010
URL: http://precedings.nature.com/documents/4416/version/1

Studies on Endogenous Hormonal Changes during Grain Development in Wheat Genotypes (PhD Thesis)
Provedor de dados: 17
Autores: Sridhar Gutam.
Pot culture experiment was conducted in the Rabi seasons of 2001 and 2002 in order to study the genotypic differences in grain growth rates and endogenous hormonal contents in the developing grains. The hexaploid new plant types and extant variety and other tetraploids are taken up for the study. The data on yield and yield components show that the tetraploids had higher ear number per plant but lesser number of seeds per ear and lower seed weight per ear. The most important yield component 1000-grain yield was also possessed by hexaploids. The mean plant height was found to be higher in hexaploids over tetraploids in general, and among them DL- 1266-1 and DL-1266-2 (new plant types) recorded higher plant height. Similarly, the ear length was also higher...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4821/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

Thermal characterization of Plasmodium falciparum species specific proteins in Indian geographical area.
Provedor de dados: 17
Autores: Mohit Bhardwaj; Leena Bharadwaj; Kritika Trigunayat; Madan Mohan Trigunayat.
The paper reveals thermal characteristics of _P.falciparum_ species specific proteins. These proteins determine why _P. vivex_ species are dominant over _P.falciparum_ in Indian geographical area. Outside human host plasmodium parasite survives in poikilothermal mosquitoes. Climatic temperature conditions greatly affect native state of _P.falciparum_ species specific proteins in mosquitoes. Study of climatic temperature conditions in Indian geographical area reveals that Pfsd protein for _Plasmodium falciparum_ can remain in native state between &amp;#x2265;7 degree centigrade and &amp;#x2264;42.6 degree centigrade temperature conditions. While their best optimum functions (activity) was noted between 25.3 degree centigrade to 33degree centigrade. Pfsd...
Tipo: Manuscript
Palavras-chave: Ecology; Molecular Cell Biology; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4565/version/2

The Necessity of Darwin
Provedor de dados: 17
Autores: Stanley K. Sessions; Herbert C. Macgregor.
February 12th, 2009 was Charles Darwin&amp;#x27;s 200th birthday, and November 2009 represents the 150th anniversary of the publication of his transformative book, The Origin of Species. It seems a good time to look back and assess Darwin&amp;#x27;s legacy within the perspective of current knowledge of genetics, cytogenetics, and molecular biology in general. Although a comprehensive understanding of evolution would no doubt have emerged eventually, it is difficult to imagine how anyone could have matched Darwin&amp;#x2019;s prodigious and sustained efforts, as well as his talent for explaining things in simple terms.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2887/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

Word Activation Forces Map Word Networks
Provedor de dados: 17
Autores: Jun Guo; Hanliang Guo; Zhanyi Wang.
Words associate with each other in a manner of intricate clusters^1-3^. Yet the brain capably encodes the complex relations into workable networks^4-7^ such that the onset of a word in the brain automatically and selectively activates its associates, facilitating language understanding and generation^8-10^. One believes that the activation strength from one word to another forges and accounts for the latent structures of the word networks. This implies that mapping the word networks from brains to computers^11,12^, which is necessary for various purposes^1,2,13-15^, may be achieved through modeling the activation strengths. However, although a lot of investigations on word activation effects have been carried out^8-10,16-20^, modeling the activation...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5764/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

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

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

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

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

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

Substrate entering and product leaving trajectories predict an engulfing dynamic for the major conformational change of the &amp;#x3b2;-lactam acylase
Provedor de dados: 17
Autores: Xi Huang; Jun Yin; Wei-Hong Jiang; Zixin Deng; Guo-Ping Zhao.
It is still a major challenge to acquire insight into the conformational changes between the ground state and the transition state of an enzyme, although conformational fluctuation within interconverting conformers has been widely investigated (1-4). Here, we utilize different enzymatic reactions in b-lactam acylase to figure out the substrate/product trajectories in the enzyme, thereby probing the overall conformational changes in transition state. First, an auto-proteolytic intermediate of cephalosporin acylase (EC 3.5.1.11) with partial spacer segment was identified. As a final proteolytic step, the deletion of this spacer segment was revealed to be a first-order reaction, suggesting an intramolecular Ntn mechanism for the auto-proteolysis. Accordingly,...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2514/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

The Rise of Consortia
Provedor de dados: 17
Autores: Neil E. Caporaso; Siiri N. Bennett.
We provide some observations on the role of consortia in GWAS. We include 2 surveys (addressed to GWAS Investigators and to GWAS Consortia) sent to GWAS investigators in the spring of 2011. Tables and figures derived from the data are included. We also provide a summary table with some basic data on 110 consortia. We invite the community to visit the WikiGene site (http://www.wikigenes.org/GWAS/consortia.html) where this data may be further corrected and updated.
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics.
Ano: 2011
URL: http://precedings.nature.com/documents/6680/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

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

Talin1 Promotes Prostate Cancer Invasion and Metastasis via AKT Signaling and Anoikis Resistance
Provedor de dados: 17
Autores: Shinichi Sakamoto; Richard McCann; Natasha Kyprianou.
Talin1 is an integrin regulatory protein that mediates integrin interactions with the extracellular matrix (ECM). This study investigated the significance of talin1 in prostate cancer progression to metastasis in vitro and in vivo. Talin1 overexpression enhanced prostate cancer cell adhesion, migration and invasion by activating survival signals and anoikis resistance. ShRNA-mediated talin1 loss led to a significant suppression of prostate cancer cell migration and transendothelial invasion in vitro and a significant inhibition of prostate cancer metastasis in vivo. Talin1 regulates cell survival signals via phosphorylation of focal adhesion kinase (FAK) and AKT. Targeting AKT activation led to a significant reduction of talin1-mediated prostate cancer...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3059/version/1

Variation in _PNPLA3_ is associated with outcomes in alcoholic liver disease
Provedor de dados: 17
Autores: Chao Tian; Renee P. Stokowski; David Kershenobich; Dennis G. Ballinger; David A. Hinds.
Two recent genome-wide association studies have described associations of SNP variants in _PNPLA3_ with nonalcoholic fatty liver and plasma liver enzyme levels in population based cohorts. We investigated the contributions of these variants to clinical outcomes in Mestizo subjects with a history of excessive alcohol consumption. We show that non-synonymous variant rs738409[G] (I148M) in _PNPLA3_ is strongly associated with alcoholic liver disease and progression to alcoholic cirrhosis (unadjusted OR = 2.25, P = 1.7x10^-10^; ancestry-adjusted OR = 1.79, P = 1.9x10^-5^).
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics.
Ano: 2009
URL: http://precedings.nature.com/documents/3254/version/2

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

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

Simulation Experiment Description Markup Language (SED-ML) : Level 1 Version 1
Provedor de dados: 17
Autores: Dagmar Waltemath; Frank T. Bergmann; Richard Adams; Nicolas Le Novere.
The Simulation Experiment Description Markup Language (SED-ML) is an XML-based format for encoding simulation experiments, following the requirements defined in the MIASE guidelines. SED-ML allows one to define the model to use, the experimental task to run, and which result to produce.
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5846/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

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

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

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

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

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

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

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

Real-time imaging of the medullary circuitry involved in the generation of spontaneous muscle sympathetic nerve activity in awake human subjects
Provedor de dados: 17
Autores: Vaughan Macefield; Luke Henderson.
In order to understand the central neural processes involved in blood pressure regulation we recorded muscle sympathetic nerve activity (MSNA) via a tungsten microelectrode in the common peroneal nerve while performing functional Magnetic Resonance Imaging (fMRI) of the brainstem at 3T. Blood Oxygen Level Dependent (BOLD) changes in signal intensity were measured over 4 s every 8 s (200) volumes. Using the MSNA as the input model, we found that increases in sympathetic outflow were associated with robust increases in signal intensity in the region of the rostal ventrolateral medulla (RVLM). Reciprocal decreases in signal intensity occurred in the regions of the nucleus tractus solitarius (NTS) and caudal ventrolateral medulla (CVLM). We show for the first...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2356/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

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

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

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

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

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

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

Selective loss of GABAB receptors in orexin/hypocretin-producing neurons results in disrupted sleep/wakefulness architecture
Provedor de dados: 17
Autores: Takeshi Sakurai; Taizo Matsuki; Hitomi Takahira; Noriko Hirashima; Thomas Kilduff; Satoshi Kunita; Satoru Takahashi; Ken-ichi Yagami; Bernard Bettler; Masashi Yanagisawa; Mika Nomiyama.
We generated mice with a selective loss of GABAB receptors in orexin neurons. Orexin neurons in these GABAB1&amp;#x3c;sup&amp;#x3e;-/-(orexin)&amp;#x3c;/sup&amp;#x3e; mice showed reduced responsiveness to GABA&amp;#x3c;sub&amp;#x3e;A&amp;#x3c;/sub&amp;#x3e; receptor agonists due to a compensatory increase in GABAA receptor-mediated inhibition. This increased GABA&amp;#x3c;sub&amp;#x3e;A&amp;#x3c;/sub&amp;#x3e; receptor-mediated inhibition of orexin neurons is due to orexin-1 receptor-mediated activation of local GABAergic interneurons. Surprisingly, orexin neurons were also less responsive to glutamate, apparently because the augmented GABA&amp;#x3c;sub&amp;#x3e;A&amp;#x3c;/sub&amp;#x3e; receptor-mediated inhibition increases the membrane conductance and...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1195/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

When Spandrels Become Arches: Neural crosstalk and the evolution of consciousness
Provedor de dados: 17
Autores: Rodrick Wallace.
Once cognition is recognized as having a &amp;#x27;dual&amp;#x27; information source, the information theory chain rule implies that isolating coresident information sources from crosstalk requires more metabolic free energy than permitting correlation. This provides conditions for an evolutionary exaptation leading to the rapid, shifting global neural broadcasts of consciousness. The argument is quite analogous to the well-studied exaptation of noise to trigger stochastic resonance amplification in neurons and neuronal subsystems. Astrobiological implications are obvious.
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Neuroscience; Bioinformatics; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6115/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

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

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

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

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

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

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

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

Rapid pre-gel visualization of proteins with mass spectrometry compatibility
Provedor de dados: 17
Autores: Marco A. Mata-Gomez; Matthew T. Yasui; Robert Winkler.
Despite all of the prophecies of doom, gel electrophoresis is still prevalent in modern proteomic workflows. However, the currently used protein staining methods represent a serious bottleneck for a quick subsequent protein analysis using mass spectrometry. Substituting traditional protein stains by pre-gel derivatization with visible and mass spectrometry compatible reagents eliminates several processing steps and drastically reduces the sample preparation time. A defined chemistry permits seamless integration of such covalent protein staining methods into standardized bioinformatic pipelines. Using Uniblue A we could covalently stain simple to complex protein samples within 1 minute. Protein profiles on the gels were not compromised and MS/MS based...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/5163/version/1

The Starving Cell: Metabolic Syndrome as an Adaptive Process
Provedor de dados: 17
Autores: Beatrice A. Golomb.
Metabolic syndrome (MetS) is commonly presumed to stem from obesity, with both propelled by energy surfeit: positive balance of calories consumed to energy expended. A complementary thesis is proposed: that episodes of cell energy deficit (not expressly calorie deficit) drive MetS &amp;#x2013; the &amp;#x201c;Starving Cell.&amp;#x201d; &amp;#xd;&amp;#xa;Risk factors for MetS include hypoxemia from sleep apnea, severe calorie debt, mitochondrial dysfunction, oxidative stress; and sleep restriction, illness, surgery, trauma, cold. Each fosters inadequate cell energy, hampering production or boosting demand. MetS factors support energy: glucose, triglycerides, abdominal/visceral fat &amp;#x2013; and blood pressure, sustaining perfusion. Additional...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6535/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

Using Ontology Fingerprints to evaluate genome-wide association study results
Provedor de dados: 17
Autores: Lam C. Tsoi; Michael Boehnke; Richard L. Klein; W. Jim Zheng.
We describe an approach to characterize genes or phenotypes via ontology fingerprints which are composed of Gene Ontology (GO) terms overrepresented among those PubMed abstracts linked to the genes or phenotypes. We then quantify the biological relevance between genes and phenotypes by comparing their ontology fingerprints to calculate a similarity score. We validated this approach by correctly identifying genes belong to their biological pathways with high accuracy, and applied this approach to evaluate GWA study by ranking genes associated with the lipid concentrations in plasma as well as to prioritize genes within linkage disequilibrium (LD) block.  We found that the genes with highest scores were: ABCA1, LPL, and CETP for HDL; LDLR, APOE and APOB for...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3615/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

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

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

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

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

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

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

Stochastic and regulatory role of chromatin silencing in genomic response to environmental changes
Provedor de dados: 17
Autores: Jung Kyoon Choi; Sohyun Hwang; Young-Joon Kim.
Phenotypic diversity and fidelity can be balanced by controlling stochastic molecular mechanisms. Epigenetic silencing is one that has a critical role in stress response. Here we show that in yeast, incomplete silencing increases stochastic noise in gene expression, probably owing to unstable chromatin structure. Telomere position effect is suggested as one mechanism. Expression diversity in a population achieved in this way may render a subset of cells to readily respond to various acute stresses. By contrast, strong silencing tends to suppress noisy expression of genes, in particular those involved in life cycle control. In this regime, chromatin may act as a noise filter for precisely regulated responses to environmental signals that induce huge...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1612/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

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

Remote estimation of carbon dioxide uptake of terrestrial ecosystems
Provedor de dados: 17
Autores: Martin F. Garbulsky; Josep Pe&amp;#xf1;uelas; Dario Papale; Iolanda Filella.
The estimation of the carbon balance in ecosystems, regions, and the biosphere is currently one of the main concerns in the study of the ecology of global change. Current remote sensing methodologies for estimating gross primary productivity are not satisfactory because they rely too heavily on (i) the availability of climatic data, (ii) the definition of land-use cover, and (iii) the assumptions of the effects of these two factors on the radiation-use efficiency of vegetation (RUE). A new methodology is urgently needed that will actually assess RUE and overcome the problems associated with the capture of fluctuations in carbon absorption in space and over time. Remote sensing techniques such as the widely used reflectance vegetation indices (e.g., NDVI,...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/977/version/2

The non-obligatory role of endothelial cells in the relaxation of arterial smooth muscle by acetylcholine
Provedor de dados: 17
Autores: Igor Buchwalow; Sona Cacanyiova; Joachim Neumann; Vera Samoilova; Werner Boecker; Frantisek Kristek.
The concept of Endothelium Derived Relaxing Factor (EDRF), put forward by Furchgott in the earlier 80s of the past century, implies that nitric oxide (NO) produced by NO synthase (NOS) in the endothelium in response to acetylcholine (ACh) passively diffuses to the underlying vascular smooth muscle cells (VSMC) thereby reducing vascular tension. It was thought that VSMC do not express NOS by themselves, but to the time of those studies immunohistochemical techniques were not what they are now. State-of-the-art immunohistochemistry permits nowadays to localize NOS both to the endothelium and to VSMC. However, the principal question remained unanswered, is the NO generation by VSMC physiologically relevant? We hypothesized that the destruction of the vascular...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1884/version/1

Re-evaluating the list of high-production chemicals predicted to become Arctic contaminants
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
The large number of historical and current organic chemicals in commerce, and the ability of these compounds to make their way from industrial to remote regions, has resulted in concerted efforts to predict which chemicals have the capacity to migrate from where they are used/disposed to areas such as the Arctic. A suite of 120 high production volume chemicals has been recently screened from an initial dataset of &amp;#x3e;100,000 compounds and listed as potential Arctic contaminants. In the current work, we critically assess members of this proposed list for their possible rapid reactivity in environmental systems that would prevent substantial accumulation or transport in the environment and accumulation in vivo, as well as whether the investigated...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4436/version/1

Rescue with an anti-inflammatory peptide of chickens infected H5N1 avian flu
Provedor de dados: 17
Autores: Masaki M. Imai; Alan A. Okada; Hidechika H. Okada; Ekowati E. Handharyani; Yasuhiro Tsukamoto; Kazuhide K. Adachi; Noriko N. Okada; Retno Damajanti R. D. Soejoedono.
Chickens suffering from avian flu caused by H5N1 influenza virus are destined to die within 2 days due to a systemic inflammatory response. Since HVJ infection (1,2) and influenza virus infection (3,4) cause infected cells to activate homologous serum complement, the systemic inflammatory response elicited could be attributed to the unlimited generation of C5a anaphylatoxin of the complement system, which is a causative peptide of serious inflammation. In monkeys inoculated with a lethal dose of LPS (4 mg/kg body weight), inhibition of C5a by an inhibitory peptide termed AcPepA (5) rescued these animals from serious septic shock which would have resulted in death within a day (6). Therefore, we tested whether AcPepA could also have a beneficial effect on...
Tipo: Manuscript
Palavras-chave: Immunology; Microbiology; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/3425/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

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

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

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

Single gene-based distinction of individual microbial genomes from a mixed population of microbial cells
Provedor de dados: 17
Autores: Manu Tamminen; Marko Virta.
Background: Recent progress in environmental microbiology has revealed vast populations of microbes in any given habitat that cannot be detected by conventional culturing strategies. The use of sensitive genetic detection methods such as CARD-FISH and in situ PCR have been limited by the cell wall permeabilization requirement that cannot be performed similarly on all cell types without lysing some and leaving some unpermeabilized. Furthermore, the detection of low copy targets such as genes present in single copies in the microbial genomes, has remained problematic.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Methodology/Principal Findings: We describe an emulsion-based procedure to trap individual microbial cells into picoliter-volume polyacrylamide droplets that...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/4761/version/1

Suggested actions from the Melbourne HVP Information Seminar
Provedor de dados: 17
Autores: Richard Cotton; Myles Axton; Agnes Bankier; Bernard Brais; Lawrence Cavedon; Desir&amp;#xe9;e du Sart; Peter George; David Goldgar; Terence Harrison; Marienne Hibbert; John Hopper; Finlay Macrae; Christine M. O&amp;#x2019;Keefe; David Ravine; Ravi Savarirayan; Les Sheffield; Tim Smith; Nicola Stokes; Vijaya Sundararajan; David Thorburn; Ingrid Winship.
The Human Variome Project (HVP; www.humanvariomeproject.org) was initiated at a meeting in June 2006 and addressed the problems of collecting genetic information and generated 96 recommendations (http://www.nature.com/ng/journal/v39/n4/full/ng0407-423.html) to overcome these, with the focus on Mendelian disease. A considerable number of projects have been added, to those that have been ongoing for a number of years, since that meeting. Also, a planning meeting is to be held May 25-29, 2008 in Spain (http://www.humanvariomeproject.org/HVP2008/).&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A dramatic boost has been given to the HVP by the preparedness and action of the International Society for Gastrointestinal Hereditary Tumours (InSiGHT; www.insight-group.org), to,...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1784/version/2

Ventral Posterior Complex of the Thalamus
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 ventral posterior complex of the thalamus (VP), 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 VP were compared to the values of the macro/parent-structure, in this case the thalamus, 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...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2055/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

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

Universality of a mesenchymal transition signature in invasive solid cancers
Provedor de dados: 17
Autores: Dimitris Anastassiou.
In this brief communication, additional computational validation is provided consistent with the unifying hypothesis that a shared biological mechanism of mesenchymal transition, reflected by a precise gene expression signature, may be present in all types of solid cancers when they reach a particular stage of invasiveness.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6862/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

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

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

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

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

Resveratrol Increases Intracellular NAD+ Levels Through Up regulation of The NAD+ Synthetic Enzyme Nicotinamide Mononucleotide Adenylyltransferase
Provedor de dados: 17
Autores: Ross S. Grant.
Resveratrol is a polyphenol with major health benefits that is thought to operate through direct activation of the &amp;#x27;anti-aging&amp;#x27; enzyme SIRT1. However recent reports have challenged this &amp;#x27;direct-activation&amp;#x27; hypothesis, suggesting the mechanism by which resveratrol increases SIRT1 function is still unknown. We report for the first time that resveratrol induces a dose dependent increase in activity of the NAD+ synthetic enzyme nicotinamide mononucleotide adenylyl transferase (NMNAT1). Activation of NMNAT1 by resveratrol in cultured primary human astrocytes and neurons increased NAD+ levels by up to 5 fold. As SIRT1 requires NAD+ as a substrate to perform its gene silencing function, higher NAD+ levels will enhance SIRT1...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2010
URL: http://precedings.nature.com/documents/4421/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

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

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

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

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

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

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

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

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

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

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

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

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

The Future of the Journal? Integrating research data with scientific discourse
Provedor de dados: 17
Autores: Anita de Waard.
To advance the pace of scientific discovery we propose a conceptual format that forms the basis of a truly new way of publishing science. In our proposal, all scientific communication objects (including experimental workflows, direct results, email conversations, and all drafted and published information artifacts) are labeled and stored in a great, big, distributed data store (or many distributed data stores that are all connected). Each item has a set of metadata attached to it, which includes (at least) the person and time it was created, the type of object it is, and the status of the object including intellectual property rights and ownership. Every researcher can (and must) deposit every knowledge item that is produced in the lab into this...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4742/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

Study of Molecular Mechanism of Antibiotic susceptibility against Polymicrobial Oral infection
Provedor de dados: 17
Autores: Deepak Dwivedi.
Abstract&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Introduction- Antibiotic to treat dental caries infection are routinely prescribed. Bacteria have increased resistance to the currently recommended antibiotics. The purpose of this investigation was to perform antibiotic susceptibility on a panel pathogenic strain of bacteria isolated step by step from dental caries infection. &amp;#xd;&amp;#xa;Materials and Methods-Bacteria were isolated from caries site of patients and cultivated identified at the species level. Each of 150 species of bacteria was tested for antibiotics susceptibility to a five antibiotics using Etest. Antibiotic used were Amoxicillin, Cloxocillin, Erythromycin, Tetracycline, Penicillin-V.&amp;#xd;&amp;#xa;Results- The percentages of Resistance...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/5291/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

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

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

Report on trial of SatScan tray scanner system by SmartDrive Ltd.
Provedor de dados: 17
Autores: Vladimir  Blagoderov; Ian Kitching; Thomas Simonsen; Vincent Smith.
Smartdrive Ltd.  has developed a prototype imaging system, SatScan, that captures digitised images of large areas while keeping smaller objects in focus at very high resolution. The system was set up in the Sackler Biodiversity Imaging laboratory of Natural History Museum on March 8, 2010 for a one-month trial. A series of projects imaging parts of the entomological, botanical and palaeoentomological collection were conducted to assess the systems utility for museum collection management and biodiversity research. The technical and practical limitations of the system were investigated as part of this process.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4486/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

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

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

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

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

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

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

Searching the World-Wide-Web using nucleotide and peptide sequences
Provedor de dados: 17
Autores: Natarajan Ganesan; Nicholas F. Bennett; Bala Kalyanasundaram; Mahe Velauthapillai; Richard Squier.
*Background:* No approaches have yet been developed to allow instant searching of the World-Wide-Web by just entering a string of sequence data. Though general search engines can be tuned to accept &amp;#x2018;processed&amp;#x2019; queries, the burden of preparing such &amp;#x2018;search strings&amp;#x2019; simply defeats the purpose of quickly locating highly relevant information. Unlike &amp;#x2018;sequence similarity&amp;#x2019; searches that employ dedicated algorithms (like BLAST) to compare an input sequence from defined databases, a direct &amp;#x2018;sequence based&amp;#x2019; search simply locates quick and relevant information about a blunt piece of nucleotide or peptide sequence. This approach is particularly invaluable to all biomedical...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2492/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

Using open access literature to guide full-text query formulation
Provedor de dados: 17
Autores: Heather A. Piwowar; Wendy W. Chapman.
*Background*&amp;#xd;&amp;#xa;Much scientific knowledge is contained in the details of the full-text biomedical literature.  Most research in automated retrieval presupposes that the target literature can be downloaded and preprocessed prior to query. Unfortunately, this is not a practical or maintainable option for most users due to licensing restrictions, website terms of use, and sheer volume.  Scientific article full-text is increasingly queriable through portals such as PubMed Central, Highwire Press, Scirus, and Google Scholar.  However, because these portals only support very basic Boolean queries and full text is so expressive, formulating an effective query is a difficult task for users.  We propose improving the formulation of full-text queries...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4267/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

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

The legacy of bio-molecules as a bio-fertilizer: Context of single cell fertilizer Isolation and partial characterization of an amylolytic bacterium
Provedor de dados: 17
Autores: Sribir Sen; Anwesha Banerjee; Sanghamitra Sanyal.
Repeated cultivation of crop plants is the reason for the depletion of nutrients in an agricultural land. Therefore, modern procedures of agriculture cascaded with the addition of organic and inorganic fertilizers, the use of insecticides and pesticides, the addition of proper water, etc. Various inorganic molecules are used as fertilizers. However, the use of organic manures is also in practice. They have many roles such as improving soil porosity, air holding capacity, water holding capacity, structure, texture, etc. Agricultural scientists suggest using organic molecules for many reasons. Bio-fertilizers of many kinds are used by farmers of all nations. However, these fertilizers are unable to cause tremendous effects on the growth and development of...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2012
URL: http://precedings.nature.com/documents/6774/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

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

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

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

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

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

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

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

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

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

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

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

Systems Biology Graphical Notation:  Process Description language Level 1
Provedor de dados: 17
Autores: Stuart L. Moodie; Nicolas  Le Novere; Anatoly  Sorokin; Huaiyu  Mi; Falk  Schreiber.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3721/version/1

Study of Molecular Mechanism of Antibiotic susceptibility against Polymicrobial Oral infection
Provedor de dados: 17
Autores: Deepak Dwivedi.
Abstract&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Introduction- Antibiotic to treat dental caries infection are routinely prescribed. Bacteria have increased resistance to the currently recommended antibiotics. The purpose of this investigation was to perform antibiotic susceptibility on a panel pathogenic strain of bacteria isolated step by step from dental caries infection. &amp;#xd;&amp;#xa;Materials and Methods-Bacteria were isolated from caries site of patients and cultivated identified at the species level. Each of 150 species of bacteria was tested for antibiotics susceptibility to a five antibiotics using Etest. Antibiotic used were Amoxicillin, Cloxocillin, Erythromycin, Tetracycline, Penicillin-V.&amp;#xd;&amp;#xa;Results- The percentages of Resistance...
Tipo: Manuscript
Palavras-chave: Microbiology.
Ano: 2010
URL: http://precedings.nature.com/documents/5291/version/2

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

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

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

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

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

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

Wellcome Trust Policy on Data Management and Sharing
Provedor de dados: 17
Autores: David Carr.
The Wellcome Trust&amp;#x27;s policy statement on data management and sharing, which was originally published in January 2007 and revised in August 2010.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6007/version/1

Singlet-triplet excitation energies of R~1~R~2~Si=Si silylene derivatives: A G4/W1BD theoretical study
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Well-to-well (WWE~S-T~) and adiabatic (AE~S-T~) singlet-triplet excitation energies were calculated at the Gaussian-4 (G4) and W1BD levels of theory for a suite of mono- and disubstituted R~1~R~2~Si=Si silylene derivatives (where R~1~/R~2~=H, CH~3~, NH~2~, OH, and F), as well as H~2~C=Si and HN=Si. Reasonable agreement was obtained with prior E~S-T~ estimates at the CCSD(T)/6-311++G(d,p)//QCISD/6-31G(d) and B3LYP/AUG-cc-pVTZ//B3LYP/6-31+G(d) levels of theory. The G4/W1BD E~S-T~ are systematically higher than these prior estimates by between 1 to 5 kcal/mol, averaging positive deviations of about 1-2 and 3-4 kcal/mol from the CCSD(T) and B3LYP estimates, respectively. Qualitative ground state multiplicity agreement between the four levels of theory was...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2011
URL: http://precedings.nature.com/documents/6465/version/1

Variability of Mauna Loa melt inclusions
Provedor de dados: 17
Autores: Pietro Armienti; Daniela Gasperini.
A major element of variability of olivine melt inclusions in Mauna Loa lavas is here proved to be strictly related to olivine crystallization at inclusion walls, at low pressure and decreasing temperature.  &amp;#xd;&amp;#xa;In so doing it is probably worth it to interpret trace elements and isotope variability in these olivine trapped liquids as the effect of disequilibrium (isotope) fractionation. In this respect, the accurate analytical work performed by Sobolev et al. (2011) does not document the presence of a heterogeneous source, rather representing a tool to explore poorly documented aspects of magmatic crystallization that are controlled by the kinetics of liquid-solid phase transition.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/6582/version/1

The Modified Pharaoh Approach: Stingless bees mummify beetle parasites alive
Provedor de dados: 17
Autores: Mark K. Greco; Peter Neumann; Dorothee Hoffmann; Anne Dollin; Michael Duncan; Robert Spooner-Hart.
Social insect colonies usually live in nests, which are often invaded by parasitic species^1^. Workers from these colonies use different defence strategies to combat invaders^1^. Nevertheless, some parasitic species are able to bypass primary colony defences due to their morphology and behaviour^1-3^. In particular, some beetle nest invaders cannot be killed or removed by workers of social bees^2-5^, thus creating the need for alternative social defence strategies to ensure colony survival. Here we show, using Diagnostic Radioentomology^6^, that stingless bee workers _Trigona carbonaria_, immediately mummify invading destructive nest parasites _Aethina tumida_ alive, with a mixture of resin, wax and mud, thereby preventing severe damage to the colony. In...
Tipo: Manuscript
Palavras-chave: Biotechnology; Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2591/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

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

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

Where is the &amp;#x2018;Jennifer Aniston neuron&amp;#x2019;?
Provedor de dados: 17
Autores: Dorian Aur; Peter N. Steinmetz.
It is generally believed that spike timing features (firing rate, ISI) are the main characteristics that can be related to neural code. Contrary to this common belief, spike directivity, a new measure that quantifies transient charge density dynamics within action potentials (APs) provides better results in discriminating different categories of visual object recognition. Specifically, intracranial recordings from medial temporal lobe (MTL) of epileptic patients have been analyzed using firing rate, interspike intervals and spike directivity. A comparative statistical analysis of the same spikes from four selected neurons shows that electrical micro-mapped features in neurons display higher separability to input images compared to spike timing features. If...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5345/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

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

Using Trees: Myrmecocystus Phylogeny and Character Evolution and New Methods for Investigating Trait Evolution and Species Delimitation (PhD Dissertation)
Provedor de dados: 17
Autores: Brian C. O&amp;#x27;Meara.
1) Rates of phenotypic evolution have changed throughout the history of life, producing variation in levels of morphological, functional, and ecological diversity among groups. Testing for the presence of these rate shifts is a key component of evaluating hypotheses about what causes them. General predictions regarding changes in phenotypic diversity as a function of evolutionary history and rates are developed, and tests are derived to evaluate rate changes. Simulations show that these tests are more powerful than existing tests using standardized contrasts. &amp;#xd;&amp;#xa;2) Species delimitation and species tree inference are difficult problems in the case of recent divergences, especially when different loci have different histories. I quantify the...
Tipo: Manuscript
Palavras-chave: Ecology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2261/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

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

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

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

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

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

The nitrite anion: the key intermediate in alkyl nitrates degradative mechanism.
Provedor de dados: 17
Autores: Loris Grossi.
Alkyl nitrates, _in vivo_, are metabolized to yield nitric oxide, and thiol groups are considered necessary cofactors. This statement is based on studies that underline how these species potentiate hemodynamic responsiveness to nitrates in patients with ischemic heart disease. However, the role of thiols might be mediated by the formation of corresponding S-nitrosothiols, and a redox process is responsible for the nitrates&amp;#x27; degradation: an enzyme, probably the cytochrome P450, is involved _in vivo_. Here, we report evidence that, in vitro, no reaction between thiols and alkyl nitrates takes place, but that stronger reducing agents, such as iron (II) derivatives, are necessary: alkoxy radicals and the nitrite anion are the reaction intermediates....
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2007
URL: http://precedings.nature.com/documents/235/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

Respiratory, postural and spatio-kinetic motor stabilization, internal models, top-down timed motor coordination and expanded cerebello-cerebral circuitry: a review
Provedor de dados: 17
Autores: John R. Skoyles.
Human dexterity, bipedality, and song/speech vocalization in Homo are reviewed within a motor evolution perspective in regard to &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;(i) brain expansion in cerebello-cerebral circuitry, &amp;#xd;&amp;#xa;(ii) enhanced predictive internal modeling of body kinematics, body kinetics and action organization, &amp;#xd;&amp;#xa;(iii) motor mastery due to prolonged practice, &amp;#xd;&amp;#xa;(iv) task-determined top-down, and accurately timed feedforward motor adjustment of multiple-body/artifact elements, and &amp;#xd;&amp;#xa;(v) reduction in automatic preflex/spinal reflex mechanisms that would otherwise restrict such top-down processes. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Dual-task interference and developmental neuroimaging...
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2092/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

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

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

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

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

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

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

Relationship of arterial and exhaled CO2 during elevated artificial pneumoperitoneum pressure for introduction of the first trocar.
Provedor de dados: 17
Autores: Octavio H. M. Hypolito; Joao-Luiz Azevedo; Susana A. Miyahira; Fabiana Scarpelli; Otavio M. Becker Junior; Afonso   C. C. G. Machado; Otavio C. Azevedo; Glicia C. Azevedo; Bianca Marigliani; Jose F. Borborema; Linda  Bernardes; Gustavo P. S. Miguel.
The present study evaluated the correlation between arterial CO2  and exhaled CO2 during brief high-pressure pneumoperitoneum. Patients were randomly distributed into two groups:  P12 group (n=30) received a maximum intraperitoneal pressure of 12mmHg, and P20 group (n=37) received a maximum intraperitoneal pressure of 20mmHg. Arterial CO2 was evaluated by radial arterial catheter and exhaled CO2 was measured by capnometry at the following time points: before insufflation, once intraperitoneal pressure reached 12mmHg , 5 minutes after intraperitoneal pressure reached 12mmHg for the P12 group or 20mmHg for the P20 group,  and 10 minutes after intraperitoneal pressure reached 12mmHg for the P12 group or when intraperitoneal pressure  had decreased from 20mmHg...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2011
URL: http://precedings.nature.com/documents/6538/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

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

Sensory adaptation in the light of information and energy
Provedor de dados: 17
Autores: Nikon Rasumov; Jeremy Niven; Michael Baker; Simon Laughlin.
Signal processing in neurons is constrained by internal noise and energy consumption. Neural systems often invest energy in amplifying signals to protect them against internal noise. There is no general expression for the trade-off between energy and information, because it is strongly dependent on the properties of signal, noise and underlying mechanism. We present the first analysis of this energy-information trade-off in a specific system, the R1-6 photoreceptors of the blowfly, Calliphora vicina. These photoreceptors adapt to light level by adjusting their transduction gain (number of light-gated channels opened per photon) and potassium conductance. By combining experimental measures of photoreceptor impedances, transfer functions and signal quality...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5805/version/1

The Sonic Hedgehog Pathway Stimulates Prostate Tumor Growth by Paracrine Signaling and Recaptures Embryonic Gene Expression in Tumor Myofibroblasts
Provedor de dados: 17
Autores: Aubie Shaw; Jerry Gipp; Wade Bushman.
The Hedgehog (Hh) pathway contributes to prostate cancer growth and progression. The presence of robust Shh expression in both normal prostate and localized cancer challenged us to explain the unique growth promoting effect in cancer. We show here that paracrine Hh signaling exerts a non-cell autonomous effect on xenograft tumor growth and that Hh pathway activation in myofibroblasts alone is sufficient to stimulate tumor growth. Nine genes regulated by Hh in the mesenchyme of the developing prostate were found to be regulated in the stroma of Hh over-expressing xenograft tumors. Correlation analysis of gene expression in matched specimens of benign and malignant human prostate tissue revealed a partial 5 gene fingerprint of Hh-regulated expression in...
Tipo: Manuscript
Palavras-chave: Cancer; Developmental Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3682/version/1

The genetic equidistance result of molecular evolution is independent of mutation rates
Provedor de dados: 17
Autores: Shi Huang.
The well-established genetic equidistance result shows that sister species are approximately equidistant to a simpler outgroup as measured by DNA or protein dissimilarity.  The equidistance result is the most direct evidence, and remains the only evidence, for the constant mutation rate interpretation of this result, known as the molecular clock.  However, data independent of the equidistance result have steadily accumulated in recent years that often violate a constant mutation rate.  Many have automatically inferred non-equidistance whenever a non-constant mutation rate was observed, based on the unproven assumption that the equidistance result is an outcome of constant mutation rate.  Here it is shown that the equidistance result remains valid even when...
Tipo: Manuscript
Palavras-chave: Ecology; Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1733/version/3

USP4 is regulated by Akt phosphorylation and deubiquitylates TGF-beta type I receptor
Provedor de dados: 17
Autores: Long Zhang; Fangfang Zhou; Yvette Drabsch; Ewa  Snaar-Jagalska; Craig Mickanin; Huizhe Huang; Kelly-Ann Sheppard; Chris Lu; Peter ten Dijke.
Stability and membrane localization of Transforming growth factor-&amp;#x3b2; (TGF-&amp;#x3b2;) type I receptor (T&amp;#x3b2;RI) is essential for controlling TGF-&amp;#x3b2; signaling. T&amp;#x3b2;RI is targeted for ubiquitination-mediated degradation by Smad7/Smurf2 complex. However, it is unclear whether polyubiquitin modified T&amp;#x3b2;RI can be reversed. Here we performed a genome-wide gain of function screen and identified ubiquitin-specific protease (USP) 4 as a strong inducer of TGF-&amp;#x3b2; signaling. Putative oncogenic USP4 was found to interact with T&amp;#x3b2;RI as deubiquitinating enzyme thus maintains T&amp;#x3b2;R1 levels at the plasma membrane. Depletion of USP4 mitigates TGF-&amp;#x3b2;-induced breast cancer cell migration, epithelial...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Pharmacology.
Ano: 2012
URL: http://precedings.nature.com/documents/6804/version/1

Stress impairs decision-making in rats
Provedor de dados: 17
Autores: Lauren K. Jones; Taejib Yoon; Jeansok J. Kim.
Stress influences various types of memory, but its effects on other cognitive functions are relatively unknown. We investigated the effects of uncontrollable stress on subsequent decision-making in rats, using a computer vision-based water foraging choice task. Stress impaired the animals&amp;#x27; ability to bias their responses toward the larger reward when transitioning from equal to unequal quantities, and this stress effect was dependent on the amygdala.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2923/version/1

Systems Biology Graphical Notation: Entity Relationship language Level 1 (Version 1.2)
Provedor de dados: 17
Autores: Nicolas Le Novere; Emek Demir; Huaiyu Mi; Stuart Moodie; Alice Villeger.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/5902/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

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

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

Synergistic Induction of NR4A Orphan Nuclear Receptors by LPS and cAMP in Murine Macrophage Cells
Provedor de dados: 17
Autores: Harish Shandilya; Sidney M. Morris.
Although NR4A orphan nuclear receptors have been implicated in inflammatory gene expression and atherosclerosis, there is little information regarding their regulation by combinations of stimuli likely to be found in vivo, such as LPS and inducers of cAMP. LPS rapidly induced Nur77 and NOR1 mRNAs but had little effect on expression of Nurr1 mRNA. All three NR4As were rapidly induced by 8-bromo-cAMP and remained elevated for at least 8 h. Maximum induction of NOR1 by 8-bromo-cAMP was much greater than with LPS, but maximum induction of Nur77 was similar with both agents. Whereas Nurr1 mRNA had very little response to LPS, it was strongly induced by 8-bromo-cAMP, and Nurr1 mRNA levels remained elevated for at least 20 h. The combination of 8-bromo-cAMP and...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/663/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

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

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

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

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

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

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

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

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

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

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

Sensory Transduction and Subjective Experience: Expression of eight genes in three senses suggests a radical model of consciousness
Provedor de dados: 17
Autores: Chris C. King.
Recent research into whole genome mapping of the mouse brain has made possible direct investigation of the brain expression of unusual genes. A search of the Allen Brain Atlas database has provided genetic and neuro-anatomical evidence for widespread specific expression in the brain of eight genes specific to sensory transduction, in vision, hearing and touch. A novel biophysical model is proposed for the function of these proteins, in generating the internal model of experiential reality.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1473/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

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

The use of coral as a graft in a large cortical bone defect
Provedor de dados: 17
Autores: Hassan Z. Eskandar; Wan Zulmi; Abdul Hamid Suzina; Abd Rani Samsudin.
The use of coral as space filler in a large cortical bone defect was studied. Twelve Australian White Rabbit were divided into 8 and 12 week group. All rabbits were operated to create a 2.5cm defect in right tibia and replaced with coral; partially covered with the free autologous non-vascularized periosteum harvested from contralateral tibia. The coral was transfixed and the leg was immobilized with Plaster of Paris. At the end of 8th and 12th week, all the rabbits were assessed clinically, radiologically and sacrified for histology evaluation. Bony union achieved in 3 out of 5 rabbits at 8th week while 3 out of 4 at 12th supported by radiological studies. Histological examination showed healing at coral-cortical junction by callus formation with...
Tipo: Manuscript
Palavras-chave: Biotechnology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/2264/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

Sequential Allocation and Balancing Prognostic Factors in a Psychiatric Clinical Trial
Provedor de dados: 17
Autores: Victor Fossaluza; Juliana B. Diniz; Basilio B. Pereira; Euripedes C. Miguel; Carlos  A. B. Pereira.
In controlled clinical trials, each of several prognostic factors should be balanced across the trial arms. Traditional restricted randomization may be proved inadequate especially with small sample sizes. In psychiatric disorders such as obsessive compulsive disorder (OCD), small trials prevail. Therefore, procedures to minimize the chance of imbalance between treatment arms are advisable. This paper describes a minimization procedure specifically designed for a clinical trial that evaluates treatment efficacy for OCD patients. Aitchison&amp;#x27;s compositional distance was used to calculate vectors for each possibility of allocation in a covariate adaptive method. Two different procedures were designed to allocate patients in small blocks or...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2102/version/1

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

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

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

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

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

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

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

The Normal Fetal Heart Rate Study: Analysis Plan
Provedor de dados: 17
Autores: Martin Daumer; Michael Scholz; Anne-Laure Boulesteix; Stephanie Pildner von Steinburg; Sven Schiermeier; Wolfgang Hatzmann; K T M Schneider.
Recording of fetal heart rate via CTG monitoring has been routinely performed as an important part of antenatal and subpartum care for several decades. The current guidelines of the FIGO (ref1) recommend a normal range of the fetal heart rate from 110 to 150 bpm. However, there is no agreement in the medical community whether this is the correct range (ref2). We aim to address this question by computerized analysis (ref 3) of a high quality database (HQDb, ref 4) of about one billion electronically registered fetal heart rate measurements from about 10,000 pregnancies in three medical centres over seven years. In the present paper, we lay out a detailed analysis plan for this evidence-based project in the vein of the validation policy of the Sylvia Lawry...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/980/version/2

The universal &amp;#x22;shape&amp;#x22; of human languages: spectral analysis beyond speech
Provedor de dados: 17
Autores: Fermin Moscoso del Prado.
A common recommendation for linguists is that, when analyzing language, they should take a &amp;#x22;man-from-mars&amp;#x22;, know-nothing, perspective to describe the structures that they observe, if possible limiting themselves to the mechanical application of a set of well-defined techniques and criteria. Unfortunately, the complex nature of linguistic structures makes it difficult to adopt such a detached perspective. A language, as represented by a corpus of text, can be described macroscopically by the symbolic periodogram of the corpus, analogous to the spectrograms commonly used for describing speech. Here, I show that the periodogram exhibits a universal &amp;#x22;shape&amp;#x22; from human languages, and this shape originates in known properties...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6097/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

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

Speciation of chilean Rhinocryptidae (Avian) based on their behaviour
Provedor de dados: 17
Autores: Alejandro Correa Rueda; Jorge Mpodozis.
The current classification of the chilean representatives of the passerine family Rhinocryptidae includes eight species. Three of them contain subspecies that don&amp;#x27;t exhibit clear differences. Moreover, differences among two lineages of _Scytalopus_ genera and two species of _Pteroptochos_ are cryptic. We propose a new methodology based on ecological and behavioural patterns in order to understand the concept of speciation in this group of birds. According to our results, we postulate that there is not a cut criteria to establish differences among three sister lineages of current classification. This way the methodology developed by us does not allow to establish divergence for a given common ancestor. Our methodology allows to establish comparison...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1597/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

Tendril, adhesive disc and super adhesive effect of climbing plant
Provedor de dados: 17
Autores: Wenli Deng.
Understanding the super adhesion mechanism of biological system is of great scientific interest and a prerequisite for bioinspired design of adhesive systems. To investigate the versatile climbing plant requires the development of new methods. Here I present strategies to fully study the super adhesive effect of climbing plant _Parthenocissus tricuspidata_ by the first time measuring the mass and the attached area of single adhesive disc, by further determining the microscopic structure and the adhesive strength of single adhesive disc and by finally elucidating the adhesion mechanism in cellular and molecular level using the classical theories and the proposed new hypothesis and model. I have measured that a single mature adhesive disc has an average mass...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1513/version/2

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

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

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

Technical Comments on &amp;#x201c;Greater Transportation Energy and GHG Offsets from BioelectricityThan Ethanol&amp;#x201d;
Provedor de dados: 17
Autores: Y-H Percival Zhang; Joe Rollin.
Campbell et al. [Report in Science 2009 (May 22),  324, 1055] analyzed two scenarios where bioenergy crops were used for transportation &amp;#x2013; (1) cellulosic ethanol production by biorefineries for internal combustion engines and (2) bioelectricity generation by power stations for electric motors. Their study suggests the latter approach offers more efficient energy utilization than the former.  We argue that the evaluation of a transportation system must be based on complicated metrics rather than only one or two factors. We suggest another out-of-the-box solution biomass carbohydrate-to-hydrogen-to-electricity as a key component of the future transportation sector.
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3725/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/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

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

The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation
Provedor de dados: 17
Autores: Mark Wilkinson; Benjamin Vandervalk; Luke McCarthy.
Background.  &amp;#xd;&amp;#xa;The complexity and inter-related nature of biological data poses a difficult challenge for data and tool integration.  There has been a proliferation of interoperability standards and projects over the past decade, none of which has been widely adopted by the bioinformatics  community.  Recent attempts have focused on the use of semantics to assist integration, and Semantic Web technologies are being welcomed by this community.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Description. &amp;#xd;&amp;#xa;SADI &amp;#x2013; Semantic Automated Discovery and Integration &amp;#x2013; is a lightweight set of fully standards-compliant Semantic Web service design patterns that simplify the publication of services of the type commonly found in...
Tipo: Manuscript
Palavras-chave: Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6550/version/1

Using MicroPET Imaging in Quantitative Verification of Acupuncture Effect in Ischemia Stroke Treatment
Provedor de dados: 17
Autores: Xiaoyan  Shen; Hongtu Tang; Jia Li; Ting Xiang; Huafeng Liu; Weichuan  Yu.
While acupuncture has survived several thousand years&amp;#x2019; evolution of medical practice, its function still remains as a myth from the view point of modern medicine. Our goal in this paper is to quantitatively understand the function of acupuncture in ischemia stroke treatment. We carried out a comparative study using the Sprague Dawley rat animal model. We induced the focal cerebral ischemia in the rats using the middle cerebral artery occlusion (MCAO) procedure. For each rat from the real acupuncture group (n = 40), sham acupoint treatment group (n = 54), and blank control group (n = 16), we acquired 3-D FDG-microPET images at baseline, after MCAO, and after treatment (i.e., real acupuncture, sham acupoint treatment, or resting according to the...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4128/version/1

Screening for the optimal siRNA targeting a novel gene (HA117) and construction and evaluation of a derivative recombinant adenovirus
Provedor de dados: 17
Autores: Youhua Xu; Gaihuan Zheng; Yuxia Guo; Xianqing Jin; Qing Luo.
We found a novel gene named as HA117 in our previous research. At this study, we screened for an optimal siRNA targeting the novel gene HA117 using the pSOS-HUS method, verified the results of pSOS-HUS siRNA screening for optimal affinity for the target gene, and constructed and evaluated a recombinant adenovirus carrying the DNA template for transcription of the optimal HA117 siRNA. The pSOS-HUS vector method was successfully utilized as a rapid and effective screen for an optimal siRNA for a target gene. Among five pairs of DNA templates, siRNA transcribed from HAi5 gave the strongest interference with the novel gene HA117; a HAi5-carrying recombinant adenovirus (Ad-HAi5) was successfully constructed and evaluated, laying a foundation for the further...
Tipo: Manuscript
Palavras-chave: Cancer; Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5301/version/1

Topological Characterization of Protein-Protein Interaction Networks in Human and Mouse
Provedor de dados: 17
Autores: Bipin Singh.
The elucidation of the cell&amp;#x27;s large-scale organization is a primary challenge for post-genomic biology, and understanding the structure and topological properties of protein-protein interaction networks offers an important starting point for such studies. We compare the protein-protein interaction network of the human and mouse, aiming to uncover the network&amp;#x27;s generic large-scale properties and the impact of the protein&amp;#x27;s function and cellular localization on the network topology. We show that both human and mouse protein-protein interaction supports a scale-free, topology with hierarchical modularity, indicating that these features represent a robust and generic property of the protein interactions network. We also find strong...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6126/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

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

Serine biosynthesis with one carbon catabolism represents a novel pathway for ATP generation in cells using alternative glycolysis with zero net ATP production
Provedor de dados: 17
Autores: Alexei Vazquez; Elke K. Markert; Zoltan N. Oltvai.
Recent experimental evidence indicates that some cancer cells have an alternative glycolysis pathway with net zero ATP production, implying that upregulation of glycolysis in these cells may not be related to the generation of ATP. Here we use a genome-scale model of human cell metabolism to investigate the potential metabolic alterations in cells using net zero ATP glycolysis. We uncover a novel pathway for ATP generation that involves reactions from the serine biosynthesis and one-carbon metabolism pathways. This pathway has a predicted two-fold higher flux rate in cells using net zero ATP glycolysis than those using standard glycolysis and generates twice as much ATP with significantly lower rate of lactate- but higher rate of alanine secretion. Thus,...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6123/version/2

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

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

Simulations of Antigenic Variability in Influenza A
Provedor de dados: 17
Autores: Nuno Fachada; Vitor V. Lopes; Agostinho C. Rosa.
Computational models of the immune system (IS) and pathogenic agents have several applications, such as theory testing and validation, or as a complement to first stages of drug trials. One possible application is the prediction of the lethality of new Influenza A strains, which are constantly created due to antigenic drift and shift. Here, we present several simulations of antigenic variability in Influenza A using an agent-based approach, where low level molecular antigen-antibody interactions are explicitly described. Antigenic drift and shift events are analyzed regarding the virulence of emergent strains against the IS. Results are discussed from a qualitative point of view taking into account recent and generally recognized immunology and influenza...
Tipo: Manuscript
Palavras-chave: Immunology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2303/version/1

The maximum sustainable yield leads to extinction of species in most single and multispecies fisheries
Provedor de dados: 17
Autores: Tarzan Legovi&amp;#x107;; Jasminka Klanj&amp;#x161;&amp;#x10d;ek; Sun&amp;#x10d;ana Ge&amp;#x10d;ek.
The Commission of the European Communities passed a resolution in 2006 to implement sustainability in EU fisheries through application of the maximum sustainable yield (MSY) based policy. It is shown here that attempts to reach MSY will lead towards extinction of species for every fishery that includes fishing of at least one trophic level which is directly or indirectly used as food for a higher trophic level. Because this condition is met by most single and multispecies fisheries, attempts to reach MSY should be discouraged instead of being legally prescribed as a goal. Based upon above result advice is given on how to manage a fishery which will not drive species to extinction.
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/2910/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

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

The Five Stars of Online Journal Articles  &amp;#x2013; an article evaluation framework
Provedor de dados: 17
Autores: David Shotton.
I propose five factors &amp;#x2013; peer review, open access, enriched content, available datasets and machine-readable metadata &amp;#x2013; as the Five Stars of Online Journal Articles, a constellation of five independent criteria within a multi-dimensional publishing universe against which online journal articles can be evaluated, to see how well they match up to current visions for research communications. Achievement along each of these publishing axes can vary, analogous to the different stars within the constellation shining with varying luminosities. I suggest a five-point scale for each by which a journal article can be evaluated, and a diagrammatic representation for such evaluations.  While the criteria adopted for these scales are somewhat...
Tipo: Manuscript
Palavras-chave: Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/6542/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

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

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

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

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

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

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

Ultrasonic frogs show extraordinary sex differences in auditory frequency sensitivity
Provedor de dados: 17
Autores: Jun-Xian Shen; Zhi-Min Xu; Zu-Lin Yu; Shuai Wang; De-Zhi Zheng.
Acoustic communication plays an important role in the reproductive behavior of anurans. Males of concave-eared torrent frog (_Odorrana tormota_) have ultrasonic communication capacity 1, 2, but it is unknown whether females communicate with ultrasound. Here we show that _O. tormota_ exhibits great sex differences in the auditory frequency sensitivity. Acoustic playback experiments demonstrated that the male&amp;#x27;s advertisement calls evoke gravid females&amp;#x27; positive phonotaxis and vocal responses, whereas ultrasonic components of the male&amp;#x27;s calls (frequencies above 20 kHz) do not elicit female phonotaxis or vocalization. The behavioral study was complemented by electrophysiological recordings from the auditory midbrain and by laser...
Tipo: Manuscript
Palavras-chave: Neuroscience; Evolutionary Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/5337/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

Reduction of circulating histone toxicity is a major function of C-reactive protein after extensive tissue damage
Provedor de dados: 17
Autores: Cheng-Hock Toh; Florence Baluwa; Nan Zhang; Joanna Manson; Caroline Dar; Susan Siyu Wang; Tingting Liu; Simon Abrams; Karim Brohi; Anja Kipar; Weiping Yu; Jecko Thachil; Yasir Alhamdi; guozheng Wang.
C-reactive protein (CRP) is a major acute phase protein. Although known to interact with chromatin, nucleosomes and histones, its functional roles are not clearly understood. Using both in vitro and in vivo models and samples from patients, this study demonstrates for the first time that CRP plays important roles in reducing the toxic effects of histones released into the circulation after extensive cell death. CRP protects endothelial cells by preventing histone integration into the cell membrane and thus reducing Ca2+ influx. In vivo, circulating histones cause endothelial damage, increased microvascular permeability, coagulation activation and IL-6 secretion. The latter induces CRP production in hepatocytes to form a negative feedback loop, a possible...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6264/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

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

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

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

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

Visual perception of colourful petals reminds us of classical fragments
Provedor de dados: 17
Autores: Sophia Rhizopoulou; Apostolis Argiropoulos; Emmanuel Spanakis; Demetris Gikas; Nikos Alexandredes; Danae Koukos; Demetrios Anglos.
Colour has attracted the interest and attention of many of the most gifted intellects of all time. Ideas of early thinkers were not -and could not have been- grasped on a scientific level without knowledge of a kind that lay far in the future. One character that is being considered is the colourful surfaces of living tissues, which could hardly have been visualized without a corresponding reference to the microscale parallel. Millions of years before man made manipulated synthetic structures, biological systems were using nanoscale architecture to produce striking optical effects. Here we show the microsculpture of the adaxial surface of flower petals from the asphodel, the Stork&amp;#x27;s-bill and the common poppy by using optical, scanning electron and...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2008
URL: http://precedings.nature.com/documents/1523/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

Structural dynamics and divergence of the polygalacturonase gene family in land plants
Provedor de dados: 17
Autores: Soon-Jae Kwon; Jae-Han Son; Kyong-Cheul Park; Hae-Young Oh; Pyeung-Hyeun Kim; Woo-Hyeon Byeon; Nam-Soo Kim.
A distinct feature of eukaryotic genomes is the presence of gene families. The polygalacturonase (PG) (EC3.2.1.15) gene family is one of the largest gene families in plants. PG is a pectin-digesting enzyme with a glycoside hydrolase 28 domain. It is involved in numerous plant developmental processes. The evolutionary processes accounting for the functional divergence and the specialized functions of PGs in land plants are unclear. Here, phylogenetic and gene structure analysis of PG genes in algae and land plants revealed that land plant PG genes resulted from differential intron gain and loss, with the latter event predominating. PG genes in land plants contained 15 homologous intron blocks and 13 novel intron blocks. Intron position and phase were not...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Plant Biology; Evolutionary Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1608/version/1

Semiotic Dynamics Solves the Symbol Grounding Problem
Provedor de dados: 17
Autores: Luc L. Steels; Martin Loetzsch; Michael S. Spranger.
Language requires the capacity to link symbols (words, sentences) through the intermediary of internal representations to the physical world, a process known as symbol grounding. One of the biggest debates in the cognitive sciences concerns the question how human brains are able to do this. Do we need a material explanation or a system explanation? John Searle&amp;#x27;s well known Chinese Room thought experiment, which continues to generate a vast polemic literature of arguments and counter-arguments, has argued that autonomously establishing internal representations of the world (called &amp;#x27;intentionality&amp;#x27; in philosophical parlance) is based on special properties of human neural tissue and that consequently an artificial system, such as an...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2007
URL: http://precedings.nature.com/documents/1234/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

Technical Note: The Use of RNA-interference as a Tool to Find Proteins Involved in Melanosome Formation or Transport
Provedor de dados: 17
Autores: Eva M. Amsen; Daniela Rotin.
Melanosomes are lysosome-related organelles that produce and transport the pigment melanin within melanocytes. Mutations in proteins required for melanosome transport and formation lead to a range of pigmentation defects, manifested at the cellular level as perinuclear clustering of melanosomes, or reduced sorting of melanosomal cargo such as tyrosinase-related protein 1 (TYRP1). A pilot screen was carried out to investigate whether a combination of cellular imaging and RNA interference could be used to identify new proteins involved in pigmentation pathways. In this study, eleven genes known to play a role in melanosome transport/formation or other pigmentation properties were knocked down in mouse melanocytes with shRNAmir constructs. The investigated...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3419/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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The Correlation between Sleep and Creativity
Provedor de dados: 17
Autores: Valeria Drago; Debora Aric&amp;#xf2;; Kenneth Heilman; Paul Foster; John Williamson; Pasquale Montagna; Raffaele Ferri.
Fredrich August von Kekule, a famous German chemist, was attempting to determine the shape of the benzene molecule, which was known to have six carbon atoms. In 1865, reflecting upon his discovery of the hexagonal-ring like structure, he asserted that the solution came to him in a dream1; however, it is not clear if he was in rapid eye movement (REM) sleep dreaming or if he was in non-REM (NREM) sleep imagery. It is possible to think of this type of discoveries as an expression of creativity, i.e. the ability to use existing pieces of information and combine them in novel patterns leading to greater understanding and new solutions. Preliminary support of the role of sleep in creative thinking comes from a recent study by Wagner et al.2; these authors asked...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4266/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

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

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

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

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

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

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

The Effect of a Reduced-Calorie Diet on alpha-2 Adrenergic Receptor Responsiveness in Abdominal Adipose Tissue in Obese Men During Exercise
Provedor de dados: 17
Autores: Roy R. Estrada; Joseph O. Schmelz; David Turbow; Edith Neumann.
There is at present an imperfect understanding of the effect of diet on availability of inhibitory receptors in fat cells during exercise among obese men. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Objective:* The purpose of this study was to determine whether diet results in downregulation of alpha-2 adrenergic receptor ([alpha]~2-AR~) messenger RNA (mRNA), improving metabolism in exercise in obese men. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Design:* One group, pre-test, post-test design.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Measurements:* Subcutaneous abdominal adipose tissue was tested for physiologic response, such as changes in catecholamines and other markers of lipolysis measured during periods of exercise, before and after a 12-week diet. Plasma markers of...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1838/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 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

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

The Inhibitory Fc[gamma] Receptor is Unnecessary for IVIG Efficacy
Provedor de dados: 17
Autores: Danila Leontyev; Yulia Katsman; Xue-Zhong Ma; Donald R. Branch.
Intravenous gamma globulin (IVIG) is used as an effective therapy for many different autoimmune and inflammatory diseases. The current paradigm for the mechanism underpinning anti-inflammatory effects links IVIG administration to increased expression and activity of the inhibitory Fc[gamma] receptor (Fc[gamma]RIIB) on splenic macrophages. This hypothesis has been disputed in the literature. Here we show that IVIG administered in the context of passive antibody-mediated thrombocytopenia to be therapeutically efficacious in both splenectomized and unmanipulated Balb/c mice despite no upregulation of Fc[gamma]RIIB mRNA in the spleen. Moreover, IVIG effectively ameliorated immune thrombocytopenia (ITP) in Fc[gamma]RIIB-deficient Balb/c mice, but not in...
Tipo: Manuscript
Palavras-chave: Immunology.
Ano: 2010
URL: http://precedings.nature.com/documents/4635/version/1

Weight change and quality of life in a community-based population
Provedor de dados: 17
Autores: Saskia P. J. Verkleij; Marcel C. Adriaanse; Gerrie C. W. Wendel-Vos; Albertine J. Schuit.
*Objectives:* This study investigates the longitudinal association between 5-year weight change and quality of life (QoL) in Dutch men and women.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Design:* A prospective cohort study (1998, 2000, 2003) in a population based sample. Subjects: 2,414 men and women from the Maastricht region of the Netherlands.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;*Measurements:* QoL outcomes were measured by the RAND-36 (eight subscales and two overall composite scores, physical and mental health (PCS and MCS)). Weight was measured on a scale. Weight change was calculated as change in weight between 1998 and 2003. In addition, 5-year weight change was also categorized in three groups: weight losers, weight maintainers, and weight gainers. All...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2583/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

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

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

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

Social Processing of Discrete Emotions in Humans
Provedor de dados: 17
Autores: Jacob Vigil.
I asked human observers to rate capacity and trustworthiness trait impressions of, and to indicate affiliative and avoidant dispositions, and felt emotive responses toward social objects. I show that interpersonal dispositions and emotive responses are systematically associated with variation in perceived levels of these trait impressions. The findings suggest that perception and expression of cues that signal capacity and trustworthiness of reciprocating altruism may underlie discrete affect behaviors in humans.
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2725/version/1

Testing a new intervention to enhance road safety
Provedor de dados: 17
Autores: Rainer Spiegel; Roger Kalla; Frank Spiegel; Michael Strupp.
By 2020, it is estimated that road accidents will have moved from ninth to third in the worldwide ranking of burden of disease, as assessed in the disability adjusted life years (DALY)^1,2^. Therefore, it is vital to find effective methods to enhance road safety. Speed limits and traffic calming have the potential to reduce injuries due to road accidents^3,4^. Many drivers, however, do not adhere to speed limits^1-7^. Several studies have shown that adherence to speed limits can be explained by the theory of planned behaviour ^5-7^ and that it is possible to focus on drivers&amp;#x27; intentions via self-report questionnaires. It is often difficult, however, to reach the majority of drivers on accident-prone locations with self-report questionnaires. This...
Tipo: Manuscript
Palavras-chave: Neuroscience; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/2231/version/1

The phyogenetic principles of mma: A hypothetical biostratigraphic model
Provedor de dados: 17
Autores: Alfred Czarnetzki; Dirk von Rautenfeld; Madjid Samii.
Two erectoid hominids from Sarstedt prompted a detailed examination of the course of the impressions of the Arteria meningea media and their characteristics within the line of hominidae.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/6993/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

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

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

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

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

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

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

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

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

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

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

Silent Spring - the lost call
Provedor de dados: 17
Autores: Michael J. Quinn; Mary Ann Ottinger.
The &amp;#x22;silence&amp;#x22; in Rachel Carson&amp;#x27;s Silent Spring1 alludes to the demise of bird populations through reproductive problems and death resulting from exposure to the pesticides of that time, many of which are endocrine active. Endocrine disrupting chemicals (EDCs) are compounds which may interfere with the endocrine system, producing effects that may disrupt the physiologic function of hormones. Early research on EDC exposure in humans and wildlife has focused mainly on reproductive effects of estrogenic chemicals, however recent studies have revealed that effects of estrogenic as well as non-estrogen active chemicals are often more far reaching than the reproductive system, and even mild exposures experienced early in development may...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology; Earth &amp; Environment.
Ano: 2008
URL: http://precedings.nature.com/documents/1492/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

Whisker&amp;#x27;s Directional Selectivity: Orientation Columns in the Barrel Field?
Provedor de dados: 17
Autores: Vassiliy Tsytsarev; Daniel Pope; Elena Pumbo; Alexander Yablonskii; Michael Hofmann.
Using voltage-sensitive dye optical imaging methods, we visualized neural activity in the rat barrel cortex in response to the deflection of a single whisker in different directions. Obtained data indicates that fast movements of single whiskers in varying directions correlate with different patterns of activation in the somatosensory cortex. A functional map was created based on the voltage-sensitive dye optical signal. This supports prior research that vibrissae deflections cause responses in different cortical neurons within the barrel field according to the direction of the deflection. By analogy with the orientation columns in the visual cortex, directionally-biased single whisker responses to different directions of deflection could be a possible...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4254/version/1

Yeast surface 2-hybrid to detect protein-protein interactions via the secretory pathway as a platform for antibody discovery
Provedor de dados: 17
Autores: Xuebo Hu; Sungkwon Kang; Xiaoyue Chen; Charles B. Shoemaker; Moonsoo M. Jin.
High throughput methods to measure protein-protein interactions will facilitate uncovering pairs of unknown interactions as well as designing new interactions. We have developed a platform to detect protein interactions on the surface of yeast, where one protein (bait) is covalently anchored to the cell wall and the other (prey) is expressed in secretory form. The prey is released either outside of the cells or remains on the cell surface by its binding to the bait. The strength of their interaction is measured by antibody binding to the epitope tag fused to the prey or direct readout of split fluorescence protein complementation. Our novel &amp;#x27;yeast surface 2-hybrid&amp;#x27; system was found to differentiate 6-log difference in binding affinities...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2008
URL: http://precedings.nature.com/documents/2067/version/1

Whisker&amp;#x27;s Directional Selectivity: Orientation Columns in the Barrel Field?
Provedor de dados: 17
Autores: Vassiliy Tsytsarev; Daniel Pope; Elena Pumbo; Alexander Yablonskii; Michael Hofmann.
Using voltage-sensitive dye optical imaging methods, we visualized neural activity in the rat barrel cortex in response to the deflection of a single whisker in different directions. Obtained data indicates that fast movements of single whiskers in varying directions correlate with different patterns of activation in the somatosensory cortex. A functional map was created based on the voltage-sensitive dye optical signal. This supports prior research that vibrissae deflections cause responses in different cortical neurons within the barrel field according to the direction of the deflection. By analogy with the orientation columns in the visual cortex, directionally-biased single whisker responses to different directions of deflection could be a possible...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4254/version/2

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

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

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

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

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

The effect of noise correlations in populations of diversely tuned neurons
Provedor de dados: 17
Autores: Alexander S. Ecker; Philipp Berens; Andreas S. Tolias; Matthias Bethge.
The amount of information encoded by networks of neurons critically depends on the correlation structure of their activity. Neurons with similar stimulus preferences tend to have higher noise correlations than others. In homogeneous populations of neurons this limited range correlation structure is highly detrimental to the accuracy of a population code. Therefore, reduced spike count correlations under attention, after adaptation or after learning have been interpreted as evidence for a more efficient population code. Here we analyze the role of limited range correlations in more realistic, heterogeneous population models. We use Fisher information and maximum likelihood decoding to show that reduced correlations do not necessarily improve encoding...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6170/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

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

Tumor-associated EGFR over-expression specifically activates Stat3 and Smad7 resulting in desensitization of TGF-&amp;#x3b2; signaling
Provedor de dados: 17
Autores: Rodney Luwor; Lauren Taylor; Bo Wang; Hong-Jian  Zhu.
Transforming Growth Factor-[beta] (TGF-[beta]) and Epidermal Growth Factor (EGF) signaling pathways are both independently implicated as key regulators in tumor formation and progression. Here, we demonstrate that activation of the tumor-associated and over-expressed EGFR desensitizes TGF-[beta] signaling and its cytostatic regulation through specific Stat3 activation and Smad7 induction. In normal and tumor human cell lines, reduction of TGF-[beta]-mediated Smad2 phosphorylation, nuclear translocation and Smad3 target gene activation were observed where EGFR is over-expressed, but not in cells which expressed EGFR at normal levels. The EGFR downstream signaling molecules phosphatidyinositol-3 Kinase (PI3K) or mitogen-activated protein kinase/ERK kinase...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1535/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

Recombinant Mitochondrial Transcription Factor A with N-terminal Mitochondrial Transduction Domain Increases Respiration and Mitochondrial Gene Expression in G11778A Leber&amp;#x27;s Hereditary Optic Neuropathy Cybrid Cells
Provedor de dados: 17
Autores: Shilpa Iyer; Ravindar R. Thomas; Francisco R. Portell; Lisa D. Dunahm; Caitlin K. Quigley; James P. Bennett.
Diseases involving mitochondrial defects usually manifest themselves in high-energy, post-mitotic tissues such as brain, retina, skeletal and cardiac muscle and frequently cause deficiencies in mitochondrial bioenergetics. We have developed a scalable procedure to produce recombinant human mitochondrial transcription factor A (TFAM) modified with an N-terminal protein transduction domain (PTD) and mitochondrial localization signal (MLS) that allow it to cross membranes and enter mitochondria through its &amp;#x22;mitochondrial transduction domain&amp;#x22; (MTD,=PTD+MLS). _In vitro_ studies in a classic mitochondrial disease cell model demonstrated that Alexa488-labeled MTD-TFAM rapidly entered the mitochondrial compartment. MTD-TFAM treatment of these...
Tipo: Manuscript
Palavras-chave: Biotechnology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2084/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

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

Traditional wisdom confirmed by scientific research: Jatropha species from Mexico is non-toxic
Provedor de dados: 17
Autores: Harinder P. S. Makkar; Vikas Kumar; Olubisi Oyeleye; Akinwale Oluwasegun Akinleye; Miguel A. Angulo-Escalante; Klaus Becker.
The seeds of _Jatropha platyphylla_, available on the pacific coast from Sinaloa to Michoac&amp;#xe1;n including the Nayarit and Jalisco states in Mexico, are consumed by local communities after roasting them in a manner similar to that used for peanuts. The kernels and kernel meal of _J. platyphylla_ were found to be free of phorbol esters but the kernel meal contained antinutritional factors: trypsin inhibitor, lectins and phytate at levels similar to those in _J. curcas_ kernel meal. However, trypsin inhibitor and lectins are heat labile so this explains why the local people can eat roasted seeds without ill effect. The fatty acid profile of _J. platyphylla_ oil was similar to that of _J. curcas_ and the kernels of both these species contained _ca_ 58%...
Tipo: Manuscript
Palavras-chave: Plant Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4155/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

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

Relationship between depth and morphology of foraminifera in Abderaz Formation, IRAN
Provedor de dados: 17
Autores: Meysam Shafiee Ardestani; Masoud  Asgharian rostami; Behzad  Balmaki; Behnaz  Balmaki.
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. In the present study the depth of Abderaz Formation was determined using planktonic morphotypes. As Results of the study all changes in test...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/4264/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

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

Role of cardiac resynchronization therapy in the development of new-onset atrial fibrillation:  A single-center prospective study.
Provedor de dados: 17
Autores: Gaetano Santulli; Massimo Chiariello; Cristofaro d&amp;#x27;Ascia; Salvatore d&amp;#x27;Ascia.
Albeit several studies examined the association between cardiac resynchronization therapy (CRT) and atrial fibrillation (AF) in heart failure (HF), results are still unclear and quite conflicting. We thereby designed a single-center prospective study to determine whether CRT has a favorable effect on the incidence of new-onset AF in a homogeneous population of patients with non-ischemic idiopathic dilated cardiomyopathy and severe heart failure HF. We enrolled 58 patients, AF na&amp;#xef;ve when received CRT. After 1 year of follow-up our population was subdivided into responders (72.4%) and non (27.6%), so to compare the incidence of AF after 1, 2 and 3 years of follow-up in these two groups. Already after 1 year, there is a significant (p&amp;#x3c;0.05)...
Tipo: Manuscript
Palavras-chave: Ecology; Pharmacology; Bioinformatics; Earth &amp; Environment.
Ano: 2012
URL: http://precedings.nature.com/documents/7137/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

Studies on Utilizing the Three Famous International Index Systems to Evaluate Scientific Research Level of Higher Learning Institutions
Provedor de dados: 17
Autores: Xun Liu; Changyu  Huang; Wei-Liang Qian; Yong-Chang  Huang.
Science Citation Index (SCI), The Engineering Index (EI) and Index to Scientific &amp;#x26; Technical Proceeding (ISTP) are widely accepted and used to evaluate the scientific research level of higher learning institutions by many country&amp;#x27;s science and technology field currently. After research, we point out the blemishes in this method and put forward the problems that need to be noticed, and then, under current conditions, bring forward brand-new standard and method to estimate research level, efficiency, fund exploitation and so on. One shouldn&amp;#x27;t over-emphasize the total amount of papers collected in SCI, EI &amp;#x26; ISTP when evaluating the scientific research level of higher learning institutions, whereas using...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4835/version/1

Seeing faces: evidence suggesting cortical disinhibition in the genesis of visual hallucinations.
Provedor de dados: 17
Autores: Giuseppe Iaria; Christopher Fox; Jason Barton.
The neural mechanisms responsible for triggering visual hallucinations are poorly understood. Here, we report a unique patient whose hallucinations consist exclusively of faces, and which could be reliably precipitated by looking at trees. Using functional Magnetic Resonance Imaging (fMRI), we found that, while face hallucinations was associated with increased neural activity in a number of cortical regions, including low-level visual areas, there was significant decreased activity in the right fusiform face area, a region that is empirically defined by increase activity during veridical perception of faces. These findings indicate key differences in how hallucinatory and veridical perceptions lead to the same phenomenological experience of seeing faces,...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/1827/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

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

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

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

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

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

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

_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

The spread of antimalarial drug resistance: A mathematical model with practical implications for ACT drug policies
Provedor de dados: 17
Autores: Wirichada Pongtavornpinyo; Shunmay Yeung; Ian Hastings; Arjen Dondorp; Nicholas Day; Nicholas White.
Most malaria-endemic countries are implementing a change in antimalarial drug policy to artemisinin combination therapy (ACT). The impact of different drug choices and implementation strategies is uncertain. A comprehensive model was constructed incorporating important epidemiological and biological factors and used to illustrate the spread of resistance in low and high transmission settings. The model predicts robustly that in low transmission settings drug resistance spreads faster than in high transmission settings, and that in low transmission areas ACTs slows the spread of drug resistance to a partner drug, especially at high coverage rates. This effect decreases exponentially with increasing delay in deploying the ACT and decreasing rates of...
Tipo: Manuscript
Palavras-chave: Microbiology; Pharmacology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1539/version/1

The Diet of the Rhinolophidae in the &amp;#x201c;Kabylia of the Babors&amp;#x201d; Region, Northern Algeria
Provedor de dados: 17
Autores: Ahmim Mourad; Moali  Aissa.
Many bats of the Rhinolophidae family are currently threatened all over the world. In Algeria they are represented by six species listed in the IUCN red list and whose hunting habits and diet are, at best, poorly known. This paper describes the diet composition of four of these species (Rhinolophus ferrumequinum, R. hipposideros, R. euryale and R. blasii) in the Bejaia and Jijel districts, and in Kabylia of the Babors region, in northern Algeria. Between March 2007 and January 2008 guano was sampled every fortnight in the different sites used by the species and preys remains identified under microscope. Results show that these Algerian Rhinolophidae prey on three groups of Arthropodes (Insects, Chilopodes and Spiders) whose frequencies vary from one...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Ecology.
Ano: 2012
URL: http://precedings.nature.com/documents/6822/version/1

Waveomics: bringing experimental data to online collaboration
Provedor de dados: 17
Autores: Neil Swainston.
Systems biology offers an interdisciplinary approach to scientific research that typically involves the collaboration of teams of experimentalists and mathematical modellers. While the importance of data standards has been recognised in facilitating exchange of data between the parties, challenges still remain regarding the practicalities of disseminating experimental data.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;The introduction of novel web-based tools aimed at promoting collaborative work has provided a platform upon which scientific applications can be built. The recently released Google Wave protocol provides a facility for real-time collaboration between teams of researchers.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This work introduces a customized Robot that...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4795/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

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

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

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

Visualization of and Access to CloudSat Vertical Data through Google Earth
Provedor de dados: 17
Autores: Aijun Chen; Gregory  Leptoukh; Liping Di; Denis  Nadeau; John Farley; Christopher Lynnes; Steven Kempler.
Online tools, pioneered by the Google Earth (GE), are facilitating the way in which scientists and general public interact with geospatial data in real three dimensions. However, even in Google Earth, there is no method for depicting vertical geospatial data derived from remote sensing satellites as an orbit curtain seen from above. Here, an effective solution is proposed to automatically render the vertical atmospheric data on Google Earth. The data are first processed through the Giovanni system, then, processed to be 15-second vertical data images. A generalized COLLADA model is devised based on the 15-second vertical data profile. Using the designed COLLADA models and satellite orbit coordinates, a satellite orbit model is designed and implemented in...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2007
URL: http://precedings.nature.com/documents/595/version/2

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

Steroid substrate-induced epimerase mechanism in the active site of the human 11&amp;#x3b2;-hydroxysteroid dehydrogenase type 1
Provedor de dados: 17
Autores: Olivier Hennebert; Matthieu Montes; Alain Favre-Reguillon; Henry Chermette; Clotilde Ferroud; Robert Morfin.
Cytochrome P4507B1 7[alpha]-hydroxylates dehydroepiandrosterone (DHEA), epiandrosterone (EpiA) and 5[alpha]-androstane-3[beta],17[beta]-diol (Adiol). 11[beta]-Hydroxysteroid dehydrogenase type 1 (11[beta]-HSD1) interconverts 7[alpha]- and 7[beta]- forms. Whether the inter-conversion proceeds through oxido-reductive steps or epimerase activity is investigated. Experiments using ^3^H-labeled 7[beta]-hydroxy-DHEA, 7[beta]-hydroxy-EpiA and 7[beta]-hydroxy-Adiol show the ^3^H-label to accumulate in 7-oxo-DHEA trap but neither in 7-oxo-EpiA nor 7-oxo-Adiol traps. Computed models of 7-oxygenated steroids dock in the active site of 11[beta]-HSD1 either in a flipped or turned form relative to cortisone and cortisol. 7-Oxo-steroid reduction in 7[alpha]- or...
Tipo: Manuscript
Palavras-chave: Chemistry; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/1861/version/1

Treatment of Alzheimer&amp;#x27;s Disease with Anti-Homocysteic acid Antibody
Provedor de dados: 17
Autores: Tohru Hasegawa; Nobuyuki Mikoda; Masashi Kitazawa; Frank M. LaFerla.
Homocysteic acid (HA) may play an important role in Alzhiemer disease (AD) as we previously reported that HA induced accumulation of intraneuronal A[beta]42. In this study, we first analyzed HA levels in a mouse model of AD. 4-month old pre-pathologic 3xTg-AD mice exhibited higher levels of HA in the hippocampus as compared to age-matched nontransgenic, suggesting that HA accumulation may precede both A[beta] and tau pathologies. To further determine the pathogenic role of HA in AD, we treated young 3xTg-AD mice with vitamin B6-deficient food for 3 weeks to induce the production of HA in the brain. Concominantly, mice received either saline or anti-HA antibody intraventricularly using a guide cannula every 3 days. Mice received anti-HA antibody...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2301/version/2

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

Taking shortcuts with OWL using safe macros
Provedor de dados: 17
Autores: Christopher J. Mungall; Alan Ruttenberg; David Osumi-Sutherland.
Accurate representation of complex domains such as biology demands powerful and expressive ontology languages such as OWL. However, the complex nested class expressions required for modeling can be a hindrance to ontology authoring and adoption. These class expressions can appear opaque to domain experts, and even users proficient in OWL can benefit from some kind of syntactic sugar or &amp;#x22;short-cut&amp;#x22; strategy, especially when authoring large ontologies.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;One solution is to have domain experts fill in simple templates (for example, in Excel) and translate the results into more complex axioms, but this has the disadvantage of being disconnected from full ontology authoring and reasoning...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/5292/version/2

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

Unlocking biomarker discovery: Large scale application of aptamer proteomic technology for early detection of lung cancer
Provedor de dados: 17
Autores: Rachel M. Ostroff; William L. Bigbee; Wilbur Franklin; Larry Gold; Mike Mehan; York E. Miller; Harvey I. Pass; William N. Rom; Jill M. Siegfried; Alex Stewart; Jeffrey J. Walker; Joel L. Weissfeld; Stephen Williams; Dom Zichi; Edward N. Brody.
Lung cancer is the leading cause of cancer deaths, because ~84% of cases are diagnosed at an advanced stage. Worldwide in 2008, ~1.5 million people were diagnosed and ~1.3 million died &amp;#x2013; a survival rate unchanged since 1960. However, patients diagnosed at an early stage and have surgery experience an 86% overall 5-year survival. New diagnostics are therefore needed to identify lung cancer at this stage. Here we present the first large scale clinical use of aptamers to discover blood protein biomarkers in disease with our breakthrough proteomic technology. This multi-center case-control study was conducted in archived samples from 1,326 subjects from four independent studies of non-small cell lung cancer (NSCLC) in long-term tobacco-exposed...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Molecular Cell Biology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4537/version/1

Ultrasound-targeted microbubble destruction enhances AAV mediated gene transfection: human RPE cells in vitro and the rat retina in vivo
Provedor de dados: 17
Autores: Hongli Li; Xiaozhi Zheng; Huiping Wang; Fan Li; Ying Wu; Lianfang Du.
The present study was performed to investigate the efficacy and safety of Ultrasound-targeted microbubble destruction (UTMD) mediated rAAV2-EGFP to cultured human retinal pigment epithelium (RPE) cells _in vitro_ and the rat retina _in vivo_. _In vitro_ study, cultured human RPE cells were exposed to US under different conditions with or without microbubbles. Furthermore, the effect of UTMD to rAAV2-EGFP itself and the cells were evaluated. _In vivo_ study, gene transfer was examined by injecting rAAV2-EGFP into the subretinal space of the rats with or without microbubbles and then exposed to US. We investigated EGFP expression _in vivo_ via stereomicroscopy and performed quantitative analysis by Axiovision 3.1 software. HE staining and frozen sections...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/2898/version/1

Systemic similarity analysis of compatibility drug-induced multiple pathway patterns _in vivo_
Provedor de dados: 17
Autores: Zhong Wang; Zhan-jun Zhang; Yi Wang; Yiyu Cheng; Weida Tong; Yongyan Wang.
A major challenge in post-genomic research is to understand how physiological and pathological phenotypes arise from the networks of expressed genes and to develop powerful tools for translating the information exchanged between gene and the organ system networks. Although different expression modules may contribute independently to different phenotypes, it is difficult to interpret microarray experimental results at the level of single gene associations. The global effects and response pathways of small molecules in cells have been investigated, but the quantitative details of the activation mechanisms of multiple pathways _in vivo_ are not well understood. Similar response networks indicate similar modes of action, and gene networks may appear to be...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/1688/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

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

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

Recombination modulates how selection affects linked sites in Drosophila
Provedor de dados: 17
Autores: Suzanne  E. McGaugh; Caiti S. Smukowski; Brenda Manzano-Winkler; Tiffany  L. Himmel; Mohamed A. F. Noor.
One of the most influential observations in molecular evolution has been a strong association between regional recombination rate and amount of nucleotide polymorphism in those genomic regions, interpreted as evidence for ubiquitous natural selection. The alternative explanation, that recombination is mutagenic, has been rejected by the absence of a similar association between regional recombination rate and nucleotide divergence between species. However, many recent studies show that recombination rates are often very different even in closely related species, questioning whether an association between recombination rate and divergence between species has been tested satisfactorily. To circumvent this problem, we directly surveyed recombination across...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Evolutionary Biology.
Ano: 2012
URL: http://precedings.nature.com/documents/7005/version/1

Range-based techniques for discovering optimality and analyzing scaling relationships in neuromechanical systems
Provedor de dados: 17
Autores: Bradly J. Alicea.
In this paper, a method for decoupling the neuromuscular function of a set of limbs from the role morphology plays in regulating the performance of an activity is introduced. This method is based on two previous methods: the rescaled range analysis specific to time series data, and the use of scaling laws. A review of the literature suggests that limb geometry can either facilitate or constrain performance as measured experimentally. Whether limb geometry is facilitatory or acts as a constraint depends on the size differential between arm morphology and the underlying muscle. &amp;#x22;Changes in size and shape&amp;#x22; are theoretically extrapolations of morphological geometry to other members of a population or species, to other species, or to...
Tipo: Manuscript
Palavras-chave: Neuroscience; Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/2845/version/2

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

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

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

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

Transparent Exopolymer Particles (TEP): an overlooked factor in the process of biofilm formation in aquatic environments
Provedor de dados: 17
Autores: Tom Berman; Uta Passow.
We hypothesize that transparent exopolymer particles (TEP), present in high concentrations in most sea and freshwaters, are critical agents for biofilm initiation and development in many natural and anthropogenic aquatic environments. These gel-like particles appear in many forms; amorphous blobs, clouds, sheets, filaments or clumps ranging in size from ~2 to ~200 &amp;#xb5;m. TEP are mostly polysaccharide, negatively charged, very sticky and are frequently colonized by bacteria. TEP may be considered a &amp;#x22;planktonic&amp;#x22; subgroup of exopolymeric substances (EPS), widely studied in biofilm research. Recognition of TEP involvement in biofilm formation has important implications for a comprehensive understanding of the complexities of this...
Tipo: Manuscript
Palavras-chave: Biotechnology; Microbiology.
Ano: 2007
URL: http://precedings.nature.com/documents/1182/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

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

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

Structural changes in intestinal enteroendocrine cells after ileal interposition in normal rats
Provedor de dados: 17
Autores: Gilmara S. Aguiar-Yamaguchi; Jo&amp;#xe3;o-Luiz M. C. Azevedo; Marcelo C. Carlini; Paolo H. B. Lourenco; Wellington Cardia; Maria T. S. Alves; Aparecida E. Hirata; Lucas P. F. F. Leal; Bianca Marigliani; Linda O. A. Bernardes; Karina F. Neves; Rudy N. Rocha; Jos&amp;#xe9;-Francisco Borborema; Jo&amp;#xe3;o-Luiz C. Azevedo; Otavio C. Azevedo; Gustavo P. S. Miguel.
INTRODUCTION: No therapeutic approach has significantly impacted the progression of diabetes. As early improvement of glicaemic control is observed after bariatric surgeries, there is currently a search for surgical procedures that can promote euglycemia also in non-obese patients. Glicaemic 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. The interposition of ileal segment to a more anterior region (proximal jejunum) can promote a greater stimulation of the L cells by poorly digested food, increasing the production of GLP-1 and reflecting on glicaemic control.&amp;#xd;&amp;#xa;AIMS: To investigate long-term histological modifications of...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6683/version/1

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

Safe Functional Inference for Uncharacterized Viral Proteins
Provedor de dados: 17
Autores: Yaniv Loewenstein; Michal Linial.
The explosive growth in the number of sequenced genomes has created a flood of protein sequences with unknown structure and function. A routine protocol for functional inference on an input query sequence is based on a database search for homologues. Searching a query against a non-redundant database using BLAST (or more advanced methods, e.g. PSI-BLAST) suffers from several drawbacks: (i) a local alignment often dominates the results; (ii) the reported statistical score (i.e. E-value) is often misleading; (iii) incorrect annotations may be falsely propagated. &amp;#xd;&amp;#xa;Several systematic methods are commonly used to assign sequences with functions on a genomic scale. In Pfam (1) and resources alike, statistical profiles (HMMs) are built from...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2187/version/1

Using Biotic Interaction Networks for Prediction in Biodiversity and Emerging Diseases
Provedor de dados: 17
Autores: Christopher R. Stephens; Joaquin Gim&amp;#xe9;nez Heau; Camila Gonz&amp;#xe1;lez-Rosas; Carlos N. Ibarra-Cerde&amp;#xf1;a; Victor S&amp;#xe1;nchez-Cordero.
Networks offer a powerful tool for understanding and visualizing inter-species interactions within an ecology. Previously considered examples, such as trophic networks, are just representations of experimentally observed direct interactions. However, species interactions are so rich and complex it is not feasible to directly observe more than a small fraction. In this paper, using data mining techniques, we show how potential interactions can be inferred from geographic data, rather than by direct observation. An important application area for such a methodology is that of emerging diseases, where, often, little is known about inter-species interactions, such as between vectors and reservoirs. Here, we show how using geographic data, biotic interaction...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1495/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

Vestibular effects on cerebral blood flow
Provedor de dados: 17
Autores: Jorge Serrador; F. Owen Black; Todd Schlegel; Scott Wood.
Withdrawn.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2413/version/2

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

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

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

Shelling the Voronoi interface of protein-protein complexes predicts residue activity and conservation
Provedor de dados: 17
Autores: Benjamin Bouvier; Raik Gr&amp;#xfc;nberg; Michael Nilges; Frederic Cazals.
The accurate description and analysis of protein-protein interfaces remains a challenging task. Traditional definitions, based on atomic contacts or changes in solvent accessibility, tend to over- or underpredict the interface itself and cannot discriminate active from less relevant parts.&amp;#xd;&amp;#xa;We here extend a fast, parameter-free and purely geometric definition of protein interfaces and introduce the shelling order of Voronoi facets as a novel measure for an atom&amp;#x27;s depth inside the nterface. Our analysis of 54 protein-protein complexes reveals a strong correlation between Voronoi Shelling Order (VSO) and water dynamics. High Voronoi Shelling Order coincides with residues that were found shielded from bulk water fluctuations in a...
Tipo: Manuscript
Palavras-chave: Chemistry; Molecular Cell Biology; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/1522/version/2

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

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

The development of a simple basal area increment model
Provedor de dados: 17
Autores: Georg Erich Kindermann.
In most cases forest practice in Austria use yield tables to predict the growth of their forests. Common yield tables show the increment of pure even-aged stands which are treated in a way the table developer recommends. The usage of these tables in stands which are either uneven-aged, mixed or treated in another way, may lead to inaccurate predictions. To avoid these problems, forest growth models have been developed. Until now they are not widely used in Austria. One reason may be, that most of the models need some input parameters which are usually not gathered by companies. In this work a basal area increment per hectare model has been developed which is based on the input parameters: diameter at breast height, height to diameter ratio, top height at...
Tipo: Manuscript
Palavras-chave: Ecology; Bioinformatics; Plant Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6301/version/1

Transcriptional memory emerges from cooperative histone modifications
Provedor de dados: 17
Autores: Hans Binder; Lydia Steiner; Thimo Rohlf; Sonja Prohaska; Joerg Galle.
Background&amp;#xd;&amp;#xa;Transcriptional regulation in cells makes use of diverse mechanisms to ensure that functional states can be maintained and adapted to variable environments; among them are chromatin-related mechanisms. While mathematical models of transcription factor networks controlling development are well established, models of transcriptional regulation by chromatin states are rather rare despite they appear to be a powerful regulatory mechanism.&amp;#xd;&amp;#xa;Results&amp;#xd;&amp;#xa;We here introduce a mathematical model of transcriptional regulation governed by histone modifications. This model describes binding of protein complexes to chromatin which are capable of reading and writing histone marks. Molecular interactions between...
Tipo: Manuscript
Palavras-chave: Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6507/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

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

_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

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

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

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

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

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

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

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

SBML Reaction Finder: Retrieve and extract specific reactions from the BioModels database
Provedor de dados: 17
Autores: Maxwell L. Neal; Herbert M. Sauro.
Summary: The SBML Reaction Finder (SRF) application leverages the deep semantic annotations in the BioModels database to provide efficient retrieval and extraction of individual reactions from SBML models. We hope that the SRF will be useful to quantitative modelers who seek to accelerate their modeling efforts by reusing previously published representations of specific chemical reactions.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Availability and Implementation: The SRF is open source, coded in Java, and distributed under the Mozilla Pubic License Version 1.1. Windows, Macintosh and Linux distributions are available for download at &amp;#xd;&amp;#xa;http://sourceforge.net/projects/sbmlrxnfinder.&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/7028/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

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

Rsp5 promotes Gene Activation mediated by 9aaTAD Transcription Factors Oaf1 and Gal4
Provedor de dados: 17
Autores: Joachim Lipp; Manfred Koranda; Martin Piskacek.
Nine-amino-acid transactivation domain, 9aaTAD, defines a large superfamily of yeast and mammals transcription factors. The transactivation of the 9aaTAD has been addressed to multiple general co-activators TAF9, MED15, CBP and p300. We demonstrate for the 9aaTAD transcription factors Oaf1 and Gal4 functional and physical interaction with E3-Ubiquitin Ligase Rsp5. The Rsp5-associations with RNA polymerase II and TFIID were reported previously.
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/3968/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

Reaction time to judge the temporal inequality of digits numbers
Provedor de dados: 17
Autores: Carmelo M. Vicario.
Several studies had consistently lighted mechanisms about the relation between spatial and numerical cognition; parallel to this, a separate research line begin to document similar relationships for the representation of time and quantity as well. However there are still few studies that explore cognitive mechanisms subserving this relation. Starting from the evidence of the SNARC effect (Dehaene et al., 1993), here we investigate about the presence of similar effect in the processing of temporal and numerical information. We studied the effects of numerical exposure when participants are asked to perform a visual detection task in which temporal information is explicitly or implicitly conveyed. The main result shows that, during explicit timing, low...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2797/version/1

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

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

Synaptic state matching: a dynamical architecture for predictive internal representation and feature perception
Provedor de dados: 17
Autores: Saeed Tavazoie.
Here we consider the possibility that a fundamental function of sensory cortex is the generation of an internal simulation of sensory environment in real-time. A logical elaboration of this idea leads to a dynamical neural architecture that oscillates between two fundamental network states, one driven by external input, and the other by recurrent synaptic drive in the absence of sensory input. Synaptic strength is modified by a proposed synaptic state matching (SSM) process that ensures equivalence of spike statistics between the two network states. Remarkably, SSM, operating locally at individual synapses, generates accurate and stable network-level predictive internal representations, enabling pattern completion and unsupervised feature detection from...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6282/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

The anti-angiogenic herbal composition Ob-X inhibits adipose tissue growth in obese mice
Provedor de dados: 17
Autores: Min-Young Kim; Jong Cheon Hahm; Byung-Young Park; Hee Suk Lee; Eun kyu Park; Michung Yoon; Jinmi Lee; Yeonhee Hong; Seolwha Choi; Hyunghee Lee.
Objective: The growth and development of adipose tissue are thought to be associated with angiogenesis and extracellular matrix remodeling. Since the composition of the herbal extract called Ob-X has been shown to have both anti-angiogenic and matrix metalloproteinase (MMP)-inhibiting activities, we hypothesized that growth of adipose tissue can be regulated by Ob-X. Materials and Methods: The effects of Ob-X on angiogenesis and extracellular matrix remodeling were measured using in vitro and ex vivo assays. The effects of Ob-X on adipose tissue growth were investigated with nutritionally obese mice. Results: Ob-X inhibited angiogenesis in a dose-dependent manner in the human umbilical vein endothelial cell (HUVEC) tube formation assay in vitro and the rat...
Tipo: Manuscript
Palavras-chave: Biotechnology.
Ano: 2009
URL: http://precedings.nature.com/documents/2970/version/1

Simple reverse genetics approach to elucidating the biosynthetic pathway of complex thiopeptide nocathiacin
Provedor de dados: 17
Autores: Maochen Wei; Jing Deng; Shuzhen Wang; Nan Liu; Yijun Chen.
Biothythetic pathway of the most drugable thiopeptide nocathiacin has been elucidated by applying reverse genetics method based on its structural features. The present study provides an efficient approach for an easy access to the biosynthetic gene clusters of complex bioactive peptides that are ribosomally synthesized with extensive posttranslational modifications.
Tipo: Manuscript
Palavras-chave: Biotechnology; Genetics &amp; Genomics; Microbiology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/4740/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&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

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

The Role of Cognitive Dissonance in Social Networks
Provedor de dados: 17
Autores: Henrique Akiba; Alvaro Machado Dias; Eduardo Oda; Ricardo Ikeda; Mauri Oliveira.
Context:&amp;#xd;&amp;#xa;The principles behind the process of creating new, spontaneous sequences out of previously ordered non-declarative stimuli have been scarcely addressed and, for such reason, remain highly unknown. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;Objective:&amp;#xd;&amp;#xa;This paper has four interconnected goals: &amp;#xd;&amp;#xa;(1) Introduce a new software-based neuropsychological test that can be used as a means to assess key aspects of the way people order and reorder non-declarative stimuli, based upon cognitive dissonance principles; (2) introduce a mathematical approach to the latter in ordering/re-ordering of non-declarative stimuli; &amp;#xd;&amp;#xa;(3) assess whether the principles of cognitive dissonance in ordering/re-ordering...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6682/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

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

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

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

The river-refuge hypothesis and other contributions of Marcio Ayres to conservation science
Provedor de dados: 17
Autores: Liliana D&amp;#xe1;valos; Miguel A. Pinedo-Vasquez.
For more than a century, biogeographers have sought to explain the large number of species found in Amazonian forests. The role of rivers as barriers to dispersal was recognized early on and this was the first evolutionary hypothesis to explain Amazonian diversity. Most of the recent debate on speciation in the Amazon has focused on the role of Pleistocene refugia. The methods of refuge biogeography helped shape early conservation priorities in Amazonia, although actual plans did not directly depend on the conceptual strengths or weaknesses of refugia biogeography. These approaches viewed people mostly as threats, though not always explicitly. Based on his work on primate distribution Marcio Ayres formulated a synthetic speciation theory, the river-refuge...
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/5142/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

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

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

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

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

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

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

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

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

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

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

&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

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

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

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

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

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

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

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

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

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

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

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

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

Soluble oligomerization provides a beneficial fitness effect on destabilizing mutations.
Provedor de dados: 17
Autores: Shimon Bershtein; Eugene Shakhnovich.
Protein stability is widely recognized as a major evolutionary constraint. However, the relation between mutation-induced perturbations of protein stability and biological fitness has remained elusive. Here we explore this relation by introducing a selected set of mostly destabilizing mutations into an essential chromosomal gene of E.coli encoding dihydrofolate reductase (DHFR) to determine how changes in protein stability, activity and abundance affect fitness. Several mutant strains showed no growth while many exhibited fitness higher than wild type. Overexpression of chaperonins (GroEL/ES) buffered the effect of mutations by rescuing the lethal phenotypes and worsening better-fit strains. Changes in stability affect fitness by mediating the abundance of...
Tipo: Manuscript
Palavras-chave: Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Evolutionary Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/6219/version/1

The Normal Fetal Heart Rate Study: Analysis Plan
Provedor de dados: 17
Autores: Martin Daumer; Michael Scholz; Anne-Laure Boulesteix; Stephanie Pildner von Steinburg; Sven Schiermeier; Wolfgang Hatzmann; K T M Schneider.
Recording of fetal heart rate via CTG monitoring has been routinely performed as an important part of antenatal and subpartum care for several decades. The current guidelines of the FIGO (ref1) recommend a normal range of the fetal heart rate from 110 to 150 bpm. However, there is no agreement in the medical community whether this is the correct range (ref2). We aim to address this question by computerized analysis (ref 3) of a high quality database (HQDb, ref 4) of about one billion electronically registered fetal heart rate measurements from about 10,000 pregnancies in three medical centres over seven years. In the present paper, we lay out a detailed analysis plan for this evidence-based project in the vein of the validation policy of the Sylvia Lawry...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2007
URL: http://precedings.nature.com/documents/980/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

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

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

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

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

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

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

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

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

Systems Biology Graphical Notation:  Process Description language Level 1
Provedor de dados: 17
Autores: Stuart L. Moodie; Nicolas  Le Novere; Emek Demir; Huaiyu Mi; Alice Villeger.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialized notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics; Data Standards.
Ano: 2011
URL: http://precedings.nature.com/documents/3721/version/4

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

The importance of decadal-scale climate variability to wind-driven modulation of hypoxia in Chesapeake Bay
Provedor de dados: 17
Autores: Malcolm E. Scully.
Millions of dollars are spent annually to reduce nutrient loading to Chesapeake Bay, with a fundamental goal of reducing the extent and severity of low dissolved oxygen (hypoxia) during the summertime months^1^. Yet despite recent reductions in nutrient loading, large volumes of the Bay continue to be impacted by hypoxia and anoxia during the summer months^2-3^. One obstacle to assessing efforts to improve water quality in the Bay and other estuarine systems is a complete understanding of the physical processes that modulate dissolved oxygen and the long-term variability of these processes. Here I analyze a 58-year data set of estimated hypoxic volume in the Bay^2^ and demonstrate the importance that wind direction plays in controlling the extent and...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3308/version/1

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 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

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

Theoretical studies on the pK~a~ values of perfluoroalkyl carboxylic acids
Provedor de dados: 17
Autores: Sierra Rayne; Kaya Forest.
Computational studies were conducted using the major levels of semiempirical, ab initio, density functional theory (DFT), and the CBS-Q//B3 method and various solvation models on a homologous series of straight chain perfluoroalkyl carboxylic acids (PFCAs) ranging in chain length from C~1~ (trifluoroacetic acid) to C~9~ (n-perfluorodecanoic acid) as well as the monomethyl branched C~7~ (n-perfluorooctanoic acid; n-PFOA) isomers. Regardless of perfluoroalkyl chain length and theoretical method employed, application of a computational thermodynamic cycle indicated no significant change in the estimated aqueous monomeric pK~a~ values between C~1~ and C~9~, all having a relatively constant pK~a~ of about 0 that is in agreement with earlier predictions and...
Tipo: Manuscript
Palavras-chave: Chemistry; Earth &amp; Environment.
Ano: 2010
URL: http://precedings.nature.com/documents/3829/version/2

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

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

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

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

Versatile Control System for Automated Single-Molecule Optical Tweezers Investigations
Provedor de dados: 17
Autores: Steven J. Koch; Richard C. Yeh.
We present a versatile control system to automate single-molecule biophysics experiments. This method combines low-level controls into various functional, user-configurable modules, which can be scripted in a domain-specific instruction language. The ease with which the high-level parameters can be changed accelerates the development of a durable experiment for the perishable single-molecule samples. Once the experimental parameters are tuned, the control system can be used to repeatedly manipulate other single molecules in the same way, which is necessary to accumulate the statistics needed to report results from single-molecule studies. This system has been implemented for an optical tweezers instrument for single-molecule manipulations, with real-time...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4284/version/1

Toxicity prediction of anti tuberculosis active molecules
Provedor de dados: 17
Autores: Sajeev  R; Abdul  Jaleel.U.C.
Abstract&amp;#xd;&amp;#xa;The aim of the work was to understand the toxicity, physically significant descriptors and pharmaceutically relevant properties of some imidazoles obtained from the open sources that may found to be active against tuberculosis. At present five azoles were modeled for the prediction and calculation of descriptors that were carried out by means of computational approach [1].&amp;#xd;&amp;#xa;
Tipo: Manuscript
Palavras-chave: Chemistry; Microbiology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6236/version/1

Three mutations in SASH1 cause the pathogenesis of dyschromatosis universalis hereditaria (DUH)
Provedor de dados: 17
Autores: Qinghe Xing; Dingan Zhou; Zhiyun Wei.
Dyschromatosis universalis hereditaria (DUH) is a rare genodermatosis characterized by hyper- and hypopigmented macules which form a reticulate or mottled pattern. The causal gene and the precise pathogenesis of DUH have been unclear since the disease was initially reported in 1933. However, we found three heterozygous mutations encoding amino acid substitutions in SASH1 in each of three nonconsanguineous DUH families. Immunohistochemistry and melanin staining showed distribution heterogenicity of melanocytes, predominantly melanized melanocytes in the epidermal tissues of a DUH patient. Specifically, we identified that mutations of SASH1 can up-regulate resident melanogenic proteins, transport proteins of melanosome, and induce increased mobility of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Molecular Cell Biology.
Ano: 2011
URL: http://precedings.nature.com/documents/5629/version/1

The computational magic of the ventral stream
Provedor de dados: 17
Autores: Tomaso Poggio.
I argue that the sample complexity of (biological, feedforward) object recognition is mostly due to geometric image transformations and conjecture that a main goal of the ventral stream &amp;#x2013; V1, V2, V4 and IT &amp;#x2013; is to learn-and-discount image transformations.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;In the first part of the paper I describe a class of simple and biologically plausible memory-based modules that learn transformations from unsupervised visual experience. The main theorems show that these modules provide (for every object) a signature which is invariant to local affine transformations and approximately invariant for other transformations. I also prove that,&amp;#xd;&amp;#xa;in a broad class of hierarchical architectures, signatures...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2011
URL: http://precedings.nature.com/documents/6117/version/2

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

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

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

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

Simple SVM based whole-genome segmentation
Provedor de dados: 17
Autores: Justin Bedo; Geoff Macintyre; Izhak Haviv; Adam Kowalczyk.
We present a support vector machine (SVM) based framework for DNA segmentation into binary classes. Two applications are explored: transcription start site prediction and transcription factor binding prediction. Experiments demonstrate our approach has significantly better performance than other methods on both tasks.
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3811/version/1

Soybean Composition Database from NIR, NMR and GC-MS Analyses
Provedor de dados: 17
Autores: I. C. Baianu; Tiefeng You; Jun Guo; Doina M. Costescu; V. I. Prisecaru.
This novel Soybean Composition Database from the AFC-NMR &amp;#x26; NIR Spectroscopy Facility of the College of ACES at the University of Illinois at Urbana includes more than 12,000 NIR measurements on soybeans from the International Soybean Germplasm Collection, such as those received from Peking at the National Soybean Collection.&amp;#xd;&amp;#xa;Excel files (.xls) of our novel spectroscopic data are currently available for all 80,000 + NIR and FT-NMR measurements; such data are made available from an ultra-fast and secure supercomputer server utilizing the current version of the Scientific-Linux OS-based software. &amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;A detailed account is also presented of our high-resolution nuclear magnetic resonance (HR-NMR) and...
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/6201/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

Spiders (Araneae) from Agricultural fields near foothill of Satpura Mountain ranges of Amravati District, Maharashtra, India.
Provedor de dados: 17
Autores: Nanduwarghat E. Warghat; Anil J. Gaur; Navin  R. Sharma; Sudhir G. Chirde; Gajendra S. Pachalore; Mamata R. Chandrakar.
This paper deals with the study of spider distribution in agricultural fields adjoining the Satpura Mountain Ranges of the Amravati district. The total collection of spiders comprises 12 families, 37 genera and 76 species. The Araneidae and Thomisidae families were dominant, followed by Saltisidae from the selected agricultural area. Lycosidae and Tetragnathidae were also found in a decreasing number of species due to their specific habitation. The analysis of guild structure revealed six feeding guilds. Orb web weavers and Ambushers constituted the dominant feeding guild representing 33% and 22% of the total collection respectively. Stalkers and ground runners represent 20% and 17% and foliage hunters and sheet web weavers represent 5% and 3%...
Tipo: Manuscript
Palavras-chave: Ecology.
Ano: 2011
URL: http://precedings.nature.com/documents/5912/version/1

Survey of the diagenesis process and effect these process on reservoir quality of the Kangan formation in South Pars Field
Provedor de dados: 17
Autores: Gholamreza Hosseinyar; Hossein Rahimpour-Bonab; Ashkan Asadi Esksndar; Masoud Asgharian Rostami.
Kangan and Upper Dalan formations are forming reservoir sequence of the South Pars field. Litology of the kangan formation is carbonate and (limestone and dolomite with anhydrite intervals), so digenetic processes were very active in this formation and these processes have changeed the reservoir quality. Importances of the digenetic process are including dissolution, calcite cements, dolomitization, anhydritization, physical and chemical compaction and fracturing.
Tipo: Manuscript
Palavras-chave: Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3529/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

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

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

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

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

The land surface water and energy budgets over the Tibetan Plateau
Provedor de dados: 17
Autores: Li Xu.
Tibetan Plateau plays an important role in the Asian Monsoon and global general circulation system. Due to the lack of quantitative observations and complicated cold season processes in high elevation terrain, however, the land surface water and energy budgets are still unexplored over this special region. In this study, the water and energy balances are analyzed in detail based on recently released land surface &amp;#x201c;reanalysis&amp;#x201d; data produced by NASA Global Land Data Assimilation System by three different land models, which first ingest all available ground and satellite data into the data assimilation system over the Tibetan Plateau. The major land surface energy and water components in the annual variability are compared. The model and...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5587/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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

The Physical Mechanism in Epilepsy - Understanding the Transition to Seizure
Provedor de dados: 17
Autores: Dorian Aur.
The occurrence of seizures is a rare event with a very low probability of incidence.  Therefore, a new paradigm is required to understand how epileptic seizures are generated. Specifically, analytical models and experimental data analysis show that the process underlying seizure generation is a severe dysfunctional regulation of neuronal activity inside the epileptogenic region. Translated into significant changes of endogenous electric field, this dysfunction acts at fundamental level of charge dynamics and leads to chaotic diffusion and electrical resonances within clustered regions with high frequency oscillations (HFO). Since the altered regulation can be modeled by perturbed Hamiltonian systems with many degrees of freedom that describe the motion of...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/5398/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

Structure based de novo design of IspD inhibitors as anti-tubercular agents
Provedor de dados: 17
Autores: Rohith Anand Varikoti; Rahul P. Gangwal; Gaurao V. Dhoke; Venkata Krishnan Ramaswamy; Abhay T. Sangamwar.
Tuberculosis is one of the leading contagious diseases, caused by Mycobacterium tuberculosis. Despite improvements in anti-tubercular agents, it remains one of the most prevalent infectious diseases worldwide, responsible for a total of 1.6 million deaths annually. The emergence of multidrug resistant strains highlighted the need of discovering novel drug targets for the development of anti-tubercular agents. 2-C-methyl-D-erythritol-4-phosphate cytidyltransferase (IspD) is an enzyme involved in MEP pathway for isoprenoid biosynthesis, which is considered an attractive target for the discovery of novel antibiotics for its essentiality in bacteria and absence in mammals. In the present study, we have employed structure based drug design approach to develop...
Tipo: Manuscript
Palavras-chave: Chemistry.
Ano: 2012
URL: http://precedings.nature.com/documents/7088/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

Signi&amp;#xfb01;cance tests for comparing digital gene  expression pro&amp;#xfb01;les
Provedor de dados: 17
Autores: Leonardo Varuzza; Arthur Gruber; Carlos A. B. Pereira.
Most of the statistical tests currently used to detect differentially expressed genes are based on asymptotic results, and perform poorly for low expression tags. Another problem is the common use of a single canonical cutoff for the significance level (p-value) of all the tags, without taking into consideration the type II error and the highly variable character of the sample size of the tags.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;  This work reports the development of two significance tests for the comparison of digital expression profiles, based on frequentist and Bayesian points of view, respectively. Both tests are exact, and do not use any asymptotic considerations, thus producing more correct results for low frequency tags than the chi-square test. The...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Bioinformatics.
Ano: 2008
URL: http://precedings.nature.com/documents/2002/version/3

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

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

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

The effect of personality on reasoning
Provedor de dados: 17
Autores: Ascensi&amp;#xf3;n Fumero; Carlos Santamar&amp;#xed;a; Phil Johnson-Laird.
The ability to reason depends on intelligence, but preferences for different sorts of reasoning may depend on an individual&amp;#x2019;s personality. The possibility is unlikely if reasoning is akin to a formal proof in logic.  But, such effects are predicted from the theory that reasoning is a semantic process of envisaging possibilities consistent with the meanings of premises and knowledge. According to the standard &amp;#x2018;big five&amp;#x2019; model of personality, individuals differ in their openness to experience and in their conscientiousness.  Certain inferential problems are ambiguous, e.g., if a pilot falls from a plane without a parachute then the pilot dies; this pilot didn&amp;#x2019;t die; how come? A deductive response is: the pilot...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2099/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

Systems Biology Graphical Notation: Entity Relationship language Level 1
Provedor de dados: 17
Autores: Nicolas Le Nov&amp;#xe8;re; Stuart Moodie; Anatoly Sorokin; Falk Schreiber; Huaiyu Mi.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3719/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

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

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

Rapid extinction of cocaine craving: toward a novel cue exposure therapy
Provedor de dados: 17
Autores: Serge H. Ahmed; George F. Koob.
Cocaine does not only evoke intense rewarding sensations but also induces craving for more cocaine. This latter effect is especially obvious in addicted individuals and is thought to contribute together with other factors to trigger relapse after abstinence. Cocaine-induced craving can be studied in animals in the drug reinstatement model. In this model, responding for the drug (e.g., pressing a lever) is first extinguished by discontinuing drug reinforcement and then reinstated by drug priming (i.e., non-contingent re-exposure to the drug) or stress. Importantly, during reinstatement testing, responses continue to be unrewarded as during extinction and, therefore, reflect genuine drug seeking. Here we show that reinstatement of cocaine seeking can be...
Tipo: Manuscript
Palavras-chave: Neuroscience; Pharmacology.
Ano: 2009
URL: http://precedings.nature.com/documents/2980/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

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

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

Three Dimensional Quantitative Structure-Activity Relationships of Sulfonamides Binding Monoclonal Antibody by Comparative Molecular Field Analysis
Provedor de dados: 17
Autores: Zhanhui  Wang; Xingyuan Cao; Zhenpeng  Kai; Ross C. Beier; Congming Wu; Haiyang Jiang; Linli Cheng; Jianzhong Shen; Xinling Yang.
The three-dimensional quantitative structure-activity relationship (3D-QSAR) model of sulfonamide analogs binding a monoclonal antibody (MabSMR) produced against sulfamerazine, was carried out by comparative molecular field analysis (CoMFA). The affinities of MabSMR, expressed as Log10IC50, for 17 sulfonamide analogs were determined by competitive fluorescence polarization immunoassay (FPIA). Removal of two outliers from the initial set of 17 sulfonamide analogs improved the predictability of the models. The 3D-QSAR model of 15 sulfonamides resulted in q2cv values of 0.600, and r2 values of 0.995, respectively. This novel study combining FPIA with CoMFA demonstrates that multidisciplinary research can be used as a useful tool to investigate...
Tipo: Manuscript
Palavras-chave: Biotechnology; Chemistry; Pharmacology.
Ano: 2008
URL: http://precedings.nature.com/documents/2646/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

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

Sulfur-bound biomarkers of a Monterey shale and a Greenland lake sediment
Provedor de dados: 17
Autores: Joshua G. Stern.
Seeking to reconstruct the biogeochemical processes that produced organic sulfur compounds in two unique depositional environments, we used the nickel boride desulfurization reaction to release hydrocarbons from sulfur-bound macromolecules not otherwise amenable to chromatographic analysis. We desulfurized two geochemical extracts: one sample is a Monterey shale of late Miocene age, and the other sample is a surface sediment from the Greenland lake Brayas&amp;#xf8;. Both samples contained organic sulfur compounds, but the Monterey shale was biologically and thermally modified after deposition. A comparison of the free and sulfur-bound hydrocarbons from each sample revealed a precursor-product relationship between tocopherol and pristane, for Monterey....
Tipo: Manuscript
Palavras-chave: Chemistry; Ecology; Earth &amp; Environment.
Ano: 2009
URL: http://precedings.nature.com/documents/3325/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: Ecology; Genetics &amp; Genomics; Microbiology; Molecular Cell Biology.
Ano: 2008
URL: http://precedings.nature.com/documents/1738/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

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

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

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

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

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

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

The Etiology of Depression in Parkinson&amp;#x27;s Disease
Provedor de dados: 17
Autores: Dafhna Sourani; Renana Eitan; Gadi  Oelman.
Although a high percentage of Parkinson&amp;#x27;s disease (PD) patients suffer from depression in addition to their motor disabilities, the etiology of this depression is unknown. Within the framework of the monoamine deficiency hypothesis of depression, we present a neuronal circuitry that accounts for depression in PD. Using behavioral and direct neuronal circuitry measurements we show that the habenula mediates the coupling between the dopaminergic and the serotonergic systems and argue that alterations in basal ganglia activity cause habenula hyperactivity that result with depression in PD. Behavioral results from novelty suppressed feeding and force swim tests, as well as direct circuitry measures with manganese enhanced MRI indicate (i)...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2010
URL: http://precedings.nature.com/documents/4804/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

The History, Development and Impact of Computed Imaging in Neurological Diagnosis and Neurosurgery: CT, MRI, and DTI
Provedor de dados: 17
Autores: Aaron G. Filler.
A steady series of advances in physics, mathematics, computers and clinical imaging science have progressively transformed diagnosis and treatment of neurological and neurosurgical disorders in the 115 years between the discovery of the X-ray and the advent of high resolution diffusion based functional MRI. The story of the progress in human terms, with its battles for priorities, forgotten advances, competing claims, public battles for Nobel Prizes, and patent priority litigations bring alive the human drama of this remarkable collective achievement in computed medical imaging.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3267/version/2

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

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

The NCBO OBOF to OWL Mapping
Provedor de dados: 17
Autores: Dilvan A. Moreira; Christopher J. Mungall; Nigam H. Shah; Stuart Aitken; John-Day Richter; Timothy Redmond; Mark A. Musen.
Two of the most significant formats for biomedical ontologies are the Open Biomedical Ontologies Format (OBOF) and the Web Ontology Language (OWL). To make it possible to translate ontologies between these two representation formats, the National Center for Biomedical Ontology (NCBO) has developed a mapping between the OBOF and OWL formats as well as inter-conversion software. The goal was to allow the sharing of tools, ontologies, and associated data between the OBOF and Semantic Web communities.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;OBOF does not have a formal grammar, so the NCBO had to capture its intended semantics to map it to OWL.&amp;#xd;&amp;#xa;&amp;#xd;&amp;#xa;This official NCBO mapping was used to make all OBO Foundry ontologies available in OWL....
Tipo: Manuscript
Palavras-chave: Bioinformatics.
Ano: 2009
URL: http://precedings.nature.com/documents/3938/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

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

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

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

Seeing the invisible: The scope and limits of unconscious processing in binocular rivalry
Provedor de dados: 17
Autores: Zhicheng Lin; Sheng He.
When an image is presented to one eye and a very different image is presented to the corresponding location of the other eye, they compete for conscious representation, such that only one image is visible at a time while the other is suppressed. Called binocular rivalry, this phenomenon and its deviants have been extensively exploited to study the mechanism and neural correlates of consciousness. In this paper, we propose a framework, the unconscious binding hypothesis, to distinguish unconscious processing from conscious processing. According to this framework, the unconscious mind not only encodes individual features but also temporally binds distributed features to give rise to cortical representation, but unlike conscious binding, such unconscious...
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2246/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

The disease mutation A77V in Ryanodine receptor RyR2 induces changes in energy conduction pathways in the protein
Provedor de dados: 17
Autores: Burak Erman; Nazan Walpoth.
Energetically responsive residues of the 217 amino acid N-terminal domain of the cardiac Ryanodine receptor RyR2 are identified by a simple elastic net model. These residues lie along a hydrogen bonded path through the protein. The evolutionarily conserved residues of the protein are all located on this path or in its close proximity. All of the residues of the path are either located on the two Mir domains of the protein or are hydrogen bonded to them. Two calcium binding residues, E171 and E173, are proposed as potential binding residues, based on insights gained from the elastic net analysis of another calcium channel receptor, the inositol 1,4,5-triphosphate receptor, IP3R. Analysis of the disease causing A77V mutated RyR2 showed that the path is...
Tipo: Manuscript
Palavras-chave: Molecular Cell Biology; Bioinformatics.
Ano: 2011
URL: http://precedings.nature.com/documents/6678/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

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

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

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

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

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

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

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

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

Working memory: Is it the new IQ?
Provedor de dados: 17
Autores: Tracy Packiam Alloway; Ross G. Alloway.
Working memory, our ability to process and remember information, is linked to a range of cognitive activities from reasoning tasks to verbal comprehension. There is also extensive evidence of the relationship between working memory and learning outcomes. However, some researchers suggest that working memory is simply a proxy for IQ and does not make a unique contribution to learning outcomes. Here we show that children&amp;#x27;s working memory skills at 5 years of age was the best predictor of reading, spelling, and math outcomes six years later. IQ, in contrast, accounted for a smaller portion of unique variance to reading and math skills, and was not a significant predictor of spelling performance. Our results demonstrate that working memory is not a...
Tipo: Manuscript
Palavras-chave: Ecology; Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2343/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

Why Do Glucocorticoids Produce Potent and Persistent Diuresis Only in Subjects with Volume Overload Other Than Euvolemia
Provedor de dados: 17
Autores: Chao Liu; Kunshen Liu.
Background: The role of glucocorticoids in body fluid control is full of controversy. It is well documented that glucocorticoids could produce potent and persistent diuresis in congestive heart failure. But, the diuretic effect was not reported in patients with euvolemia.     &amp;#xd;&amp;#xa;Objective: To test the hypothesis that the diuresis induced by glucocorticoids is systemic volume dependent. &amp;#xd;&amp;#xa;Methods: The diuretic effect of glucocorticoids in rats with various systemic volume statuses (i.e. systemic volume depletion, euvolemia, and systemic volume overload, respectively) was recorded. &amp;#xd;&amp;#xa;Results: Glucocorticoids only produced potent and persistent diuresis in the rats with systemic volume...
Tipo: Manuscript
Palavras-chave: Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/5559/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

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

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

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

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

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

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

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

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

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

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

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

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

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

Why overlearned sequences are special: distinct neural networks in the right hemisphere for ordinal sequences
Provedor de dados: 17
Autores: Vani Pariyadath; Sara J. Churchill; David M. Eagleman.
Written and spoken words activate left hemisphere areas involved in language processing. However, we here show that overlearned sequences (e.g. letters, numbers, weekdays, months) involve an unexpected right hemispheric activation in both the middle temporal gyrus and temporoparietal junction. Our findings offer a framework for understanding neuropsychological patterns seen in conditions such as synesthesia, in which anomalous perceptual experiences are triggered by overlearned sequences, and also in semantic dementia, in which left hemisphere damage disrupts word knowledge even while sequences can be spared.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2008
URL: http://precedings.nature.com/documents/2452/version/1

Tracing blastomere fate choices of early embryos in single cell culture
Provedor de dados: 17
Autores: Yunhan Hong; Haobin Zhao; Ni Hong; Zhendong Li; Meisheng Yi; Rong Liu; Mingyou Li; Yan Yan; Yongming Yuan; Chang Ming Li; Ruowen Ge; Jianxin Song.
Blastomeres of early vertebrate embryos undergo numerous fate choices for division, motility, pluripotency maintenance and restriction culminating in various cell lineages. Tracing blastomere fate choices at the single cell level in vitro has not been possible because of the inability to isolate and cultivate early blastomeres as single cells. Here we report the establishment of single cell culture system in the fish medaka, enabling the isolation and cultivation of individual blastomeres from 16- to 64-cell embryos for fate tracing at the single cell level in vitro. Interestingly, these blastomeres immediately upon isolation exhibit motility, lose synchronous divisions and even stop dividing in &amp;#x2265;50% cases, suggesting that the widely accepted...
Tipo: Manuscript
Palavras-chave: Biotechnology; Developmental Biology; Molecular Cell Biology.
Ano: 2010
URL: http://precedings.nature.com/documents/4907/version/1

Unique for human centromeric regions of interphase chromatin homing (CENTRICH) govern dynamic features of chromatin fractal globules
Provedor de dados: 17
Autores: Gennadi Glinsky.
We report the results of the genome-wide alignment of inter- and intra-chromosomal chromatin interactions within the context of interphase chromatin binding to nuclear lamina and nucleolus. For all human chromosomes, a significant correlation exists between binding of chromosomal loci to nuclear lamina and segregation into spatially-defined distinct compartments of genome-wide chromatin interactions identified by Hi-C method. We report identification of near-centromeric intergenic regions on human chromosomes (chr2; chr10; chr17; chr1), which are highly enriched for interphase chromatin homing sites and function as attractors of long-range physical interactions (Centromeric Regions of Interphase Chromatin Homing, CENTRICH). CENTRICH are engaged in 397-1526...
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Developmental Biology; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics.
Ano: 2012
URL: http://precedings.nature.com/documents/6756/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

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

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

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

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

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

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

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

TMEPAI, a transmembrane TGF-&amp;#x3b2;-inducible protein, sequesters Smad proteins in TGF-&amp;#x3b2; signaling
Provedor de dados: 17
Autores: Susumu Itoh; Yukihide Watanabe; Kiyotoshi Satoh; Masako Inamitsu; Liang Shi; Naoko Nakano; Aya Tanaka; Eliza Wiercinska; Hiroshi Shibuya; Peter ten Dijke; Mitsuyasu Kato.
Transforming growth factor-[beta] (TGF-[beta]) is a multifunctional cytokine of key importance for controlling embryogenesis and tissue homeostasis. How TGF-[beta] signals are attenuated and terminated is not well understood. Here, we show that TMEPAI, a direct target gene of TGF-[beta] signaling, antagonizes TGF-[beta] signaling by interfering with TGF-[beta] type I receptor (T[beta]RI)-induced R-Smad phosphorylation. TMEPAI can directly interact with R-Smads via a Smad interaction motif (SIM). TMEPAI competes with Smad anchor for receptor activation (SARA) for R-Smad binding, thereby sequestering R-Smads from T[beta]RI kinase activation. In mammalian cells, ectopic expression of TMEPAI inhibited TGF-[beta]-induced PAI-1 production, whereas specific...
Tipo: Manuscript
Palavras-chave: Cancer; Molecular Cell Biology.
Ano: 2007
URL: http://precedings.nature.com/documents/1403/version/1

TRPC4 ion channel protein is selectively expressed in a subpopulation of dopamine neurons in the ventral tegmental area
Provedor de dados: 17
Autores: Kurt R. Illig; Andrew  L. Varnell; Eric M. Ostertag; William  D. Klipec; Donald  C. Cooper.
The nonselective cation channel TRPC4 has been shown to be present in high abundance in the corticolimbic regions of the brain and play a pivotal role in modulating cellular excitability due to their involvement in intracellular Ca^2+^ regulation. Recently we reported their involvement in socialization and regulating anxiety-like behaviors in rats. Given the important role for dopamine in modulating emotions involved in social anxiety we investigated whether TRPC4 protein and mRNA was found on dopaminergic neurons of the ventral tegmental area (VTA). Using emulsion autoradiography we found that TRPC4 mRNA is indeed present in the VTA and the substantia nigra. Additionally, immunohistochemistry verified it&amp;#x2019;s presence on a subpopulation of...
Tipo: Manuscript
Palavras-chave: Genetics &amp; Genomics; Neuroscience; Pharmacology.
Ano: 2011
URL: http://precedings.nature.com/documents/6577/version/1

The History, Development and Impact of Computed Imaging in Neurological Diagnosis and Neurosurgery: CT, MRI, and DTI
Provedor de dados: 17
Autores: Aaron G. Filler.
A steady series of advances in physics, mathematics, computers and clinical imaging science have progressively transformed diagnosis and treatment of neurological and neurosurgical disorders in the 115 years between the discovery of the X-ray and the advent of high resolution diffusion based functional MRI. The story of the progress in human terms, with its battles for priorities, forgotten advances, competing claims, public battles for Nobel Prizes, and patent priority litigations bring alive the human drama of this remarkable collective achievement in computed medical imaging.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/3267/version/4

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

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

Replacement and late formation of atmospheric N2 on undifferentiated Titan by impacts
Provedor de dados: 17
Autores: Yasuhito Sekine; Hidenori Genda; Seiji Sugita; Toshihiko Kadono; Takafumi Matsui.
Saturn&amp;#x2019;s moon, Titan, has remarkable surface features&amp;#x2014;a massive N2 atmosphere and hydrological cycle of CH4&amp;#x2014;that are often compared with that of Earth^1^. However, the origin and evolution of Titan&amp;#x2019;s atmosphere remains largely unknown. The proposed formation mechanisms for Titan&amp;#x2019;s N2 require a prolonged, warm proto-atmosphere during accretion^2-4^. These mechanisms accordingly would not have worked efficiently if Titan stayed cold, as indicated by the incompletely differentiated interior observed by Cassini^5^. Because formation of a massive secondary atmosphere on a planetary body would associate with a major differentiation of its sold body during accretion^6&amp;#x2013;8^, the presence of such an...
Tipo: Manuscript
Palavras-chave: Earth &amp; Environment.
Ano: 2011
URL: http://precedings.nature.com/documents/5880/version/1

Structural and Dynamic Studies of Amino Acids, Proteins and Nucleic Acids By Chemical-Hyperspectral Imaging, FT-IR/NIR, Vibro-Rotational Spectroscopy, Plasma, Microwave and Neutron Spectroscopy
Provedor de dados: 17
Autores: I. C. Baianu.
A detailed review of structural and dynamic studies of amino acids, proteins and nucleic acids by spectroscopic techniques: microwaves,  near infrared, UV, X-rays and neutrons, including also EXAFS, chemical-hyperspectral imaging and fluorescence correlation spectroscopy and FLIM, FRAP imaging with references, instrumentation diagrams and  application examples for several related areas.
Tipo: Manuscript
Palavras-chave: Biotechnology; Cancer; Chemistry; Genetics &amp; Genomics; Molecular Cell Biology; Bioinformatics; Data Standards.
Ano: 2012
URL: http://precedings.nature.com/documents/7079/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

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

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

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

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

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

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

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

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

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

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

The Relationship between Physical Activity and Body Mass Index: Issues in Model Specification
Provedor de dados: 17
Autores: Gizachew Tiruneh.
*Objective:* To investigate the best statistical models that describe the effect of physical activity on BMI.&amp;#xd;&amp;#xa;*Design:* Cross-sectional analyses of physical activity and BMI data.Subjects: 107 obese, overweight, and healthy college students (mean duration of physical activity for the normal, overweight, and obese students: 89, 59, and 24 months, respectively; mean BMI for the normal, overweight, and obese students: 21.61, 27.07, and 35.54 kg/m^2^, respectively).&amp;#xd;&amp;#xa;*Measurements:* Inverse linear, inverse logarithmic, and inverse logistics models were used to analyze survey data for physical activity (measured by both frequency and duration of exercise) and BMI. Gender, age, and physical intensity variables were also...
Tipo: Manuscript
Palavras-chave: Developmental Biology.
Ano: 2009
URL: http://precedings.nature.com/documents/2758/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

Systems Biology Graphical Notation:  Process Description language Level 1
Provedor de dados: 17
Autores: Stuart L. Moodie; Nicolas  Le Novere; Emek Demir; Huaiyu  Mi; Falk  Schreiber.
Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialised notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical...
Tipo: Manuscript
Palavras-chave: Biotechnology; Bioinformatics.
Ano: 2010
URL: http://precedings.nature.com/documents/3721/version/2

Vision senses number directly
Provedor de dados: 17
Autores: John Ross; David C. Burr.
We have recently suggested that numerosity is a primary sensory attribute, showing that it is strongly susceptible to adaptation. Here we use the Method of Single Stimuli (MSS) to show that observers can extract a running average of the numerosity of a succession of stimuli and hold it in mind for use as a standard of comparison for subsequent stimuli. Accuracy and precision of judgments are high and not reduced by potentially misleading variables like texture density or display area.
Tipo: Manuscript
Palavras-chave: Neuroscience.
Ano: 2009
URL: http://precedings.nature.com/documents/2792/version/1

Suppression of cell cycle progression by Jun dimerization protein (JDP2) involves down-regulation of cyclin A2
Provedor de dados: 17
Autores: Jianzhi Pan; Koji Nakade; Satoko Masuzaki; Hitomi Hasegawa; Yu-Chang Huang; Takehide Murata; Atsushi Yoshiki; Naoto Yamaguchi; Yuichi Obata; Kazunari K. Yokoyama.
We report here a novel role for Jun dimerization protein-2 (JDP2) as a regulator of the progression of normal cells through the cell cycle. To determine the role of JDP2 in vivo, we generated Jdp2 knock-out (Jdp2KO) mice by targeting exon 1 to disrupt the site of initiation of transcription. The healing of wounded skin of Jdp2KO mice proceeded more rapidly than that of control mice and more proliferating cells were found at wound margins. Fibroblasts derived from embryos of Jdp2KO mice proliferated more rapidly and formed more colonies than wild-type fibroblasts. JDP2 was recruited to the promoter of the gene for cyclin A2 (ccna2) at a previously unidentified AP-1 site. Cells lacking Jdp2 had elevated levels of cyclin A2 mRNA. Moreover, reintroduction of...
Tipo: Manuscript
Palavras-chave: Cancer.
Ano: 2009
URL: http://precedings.nature.com/documents/3840/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

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