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| Registros recuperados: 3.453 | |
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| Delphine Dauga. |
| The curation process is significantly slowed down by missing information in the articles analyzed (for example, the identity of the clones used to generate ISH probes, the precise sequences tested in reporter assays, etc..). To help authors ensure in the future that necessary information is present in their article, we defined the Article Minimum Information Standard (AMIS) guidelines. This standard describes for each experiment the mandatory information that should be mentioned in literature articles to facilitate the curation process. These guidelines extend the minimal information defined by the MISFISHIE format (Deutsch at al. 2008, _Nature Biotechnology_). This standard was deduced from the ANISEED curation pipeline (Tassy, Dauga, Daian, Sobral et al.... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Data Standards. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/5054/version/1 |
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| Andreas Mayr; Djork-Arne Clevert; Sepp Hochreiter. |
| One of the main topics in systems biology is to model genetic pathways. Genes of a pathway, which show linear dependencies of their expression values, are easy to identify to belong to the pathway. However, if feedback loops or signal cascades are present, gene expression values of pathway genes can be nonlinearly dependent on the expression values of other genes in the pathway. In this situation such genes are hard to detect as belonging to the pathway because nonlinearity and noise must be distinguished.

We propose an algorithm to infer nonlinear network elements in pathways from microarray data. Our model assumes, that gene expression values, belonging to one pathway, are mainly driven by one single latent factor. We... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2010 |
URL: http://precedings.nature.com/documents/4715/version/1 |
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| Bernd Kastenholz; Basil Horst; Jürgen 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 (> 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 |
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| Varala Sravani; I Vani Priyadarshini; Amineni Umamaheswari. |
| The Leukocyte Immunoglobulin-like Receptors (LILRs) are a family of receptors that was broadly expressed on all leukocytes and have the ability to regulate their function. The increased levels of human LILRA3 in rheumatoid arthritis patients leads to stroke. In quest of designing novel inhibitors against LILRA3 an accurate homology model for the protein was based on crystal structures of 1GOX and 3P2T using Modeller 9V9. The use of multiple templates for structure prediction led us to propose a structure comprising all 439 amino acids of human LILRA3 for the first time. The best model was selected based on GA341 and DOPE score and further assessed through ProSA and PROCHECK. The validated structure was subjected to CASTp analysis ligand binding site... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics; Plant Biology. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6532/version/1 |
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| 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 |
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| Valentina Carapella; Vicente Grau; Pras Pathmanathan; Kevin Burrage. |
| Cardiac motion is a vital process as it sustains the pumping of blood in the body. For this reason motion abnormalities are often associated with severe cardiac pathologies. Clinical imaging techniques, such as MRI, are powerful in assessing motion abnormalities but their connection with pathology often remains unknown.

Computational models of cardiac motion, integrating imaging data, would thus be of great help in linking tissue structure (i.e. cells organisation into fibres and sheets) to motion abnormalities and to pathology. Current models, though, are not able yet to correctly predict realistic cardiac motion in the healthy or diseased heart.

Our hypothesis is that a more realistic... |
| Tipo: Poster |
Palavras-chave: Bioinformatics. |
| Ano: 2011 |
URL: http://precedings.nature.com/documents/6594/version/1 |
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| Kentaro Hayashi; Vincent Piras; Masaru Tomita; Masa Tsuchiya; Kumar Selvarajoo. |
| The Tumor Necrosis Factor-α (TNF-α), 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-α 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-α stimulated transcription factors NF-κB 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 |
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| 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 |
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| 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'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 & Genomics; Neuroscience. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/2202/version/1 |
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| Sierra Rayne; Kaya Forest. |
| Enthalpies of formation (Δ~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 Δ~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 |
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| Conrad Plake. |
| Manual curation of biomedical data is highly accurate but time consuming, and does not scale with the ever increasing growth of biomedical literature. Text mining as a high-throughput computational technique scales well but requires human expertise to produce highly accurate results. Ontologies can help organizing large quantities of unstructured information. Here we present three systems, namely GoGene, GoPubMed and GoWeb, employing biomedical ontologies and show how they can assist manual curation of biomedical data.

GoGene associates all genes from different model organisms to concepts of the Gene Ontology (GO) and the Medical Subject Headings (MeSH). The hierarchical structures of both terminologies support clustering... |
| Tipo: Presentation |
Palavras-chave: Bioinformatics. |
| Ano: 2009 |
URL: http://precedings.nature.com/documents/3122/version/1 |
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| 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 'snapshot' 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 |
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| 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 & Environment. |
| Ano: 2008 |
URL: http://precedings.nature.com/documents/1909/version/1 |
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| 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 |
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| 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 & 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 & ice polymorphs, respectively), and now potentially in 3D in a corresponding hydride of N called Rice'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 |
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| Alessandro Cucchi; Silvia Atti; Mauro Bergamini. |
| Background and Aim of the work - We conducted a survey of varicella cases' notifications in the immigrant population in the province of Ferrara, Italy.

Materials and Methods – We collected notifications of infectious disease between 2002 and 2006. 

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 |
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| Registros recuperados: 3.453 | |
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