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Yeast Features: Identifying Significant Features Shared Among Yeast Proteins for Functional Genomics Nature Precedings
Michel Dumontier; James R. Green; Ashkan Golshani; Myron L. Smith; Nadereh Mir-Rashed; Md Alamgir; Veronika Eroukova; Frank Dehne; James J. Cheetham.
Background
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
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Can Plant-Made Copper Chaperones Heal Early Alzheimer’s Disease? Nature Precedings
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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Inhibition of central insulin-receptor signaling by S961 causes hyperglycemia and glucose intolerance in rats Nature Precedings
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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Emergence of macroscopic simplicity from the Tumor Necrosis Factor-alpha signaling dynamics Nature Precedings
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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Prey capture and meat-eating by the wild colobus monkey _Rhinopithecus bieti_ in Yunnan, China Nature Precedings
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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Motor Nucleus of the Trigeminal Nerve Nature Precedings
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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Life fingerprints of nuclear reactions in the body of animals Nature Precedings
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
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A G4/W1BD theoretical study into the gas phase enthalpies of formation for potential high energy materials Nature Precedings
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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Biological taxonomy and ontology development: scope and limitations Nature Precedings
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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Effect of temperature on waterflea Daphnia magna (Crustacea:Cladocera) Nature Precedings
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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Using the Gene Ontology to Annotate Biomedical Journal Articles Nature Precedings
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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Polymorphic (NH): As Polyimidogen and Ammonium Azide Structure-types Nature Precedings
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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Cross-Product Extensions of the Gene Ontology Nature Precedings
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 & Genomics; Bioinformatics.
Ano: 2009 URL: http://precedings.nature.com/documents/3496/version/1
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Varicella notification in immigrants: a brief report from Ferrara, Italy Nature Precedings
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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Improving cellular cancer vaccines Nature Precedings
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
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The Heterochromatin Protein 1 positively regulates euchromatic gene expression by RNA binding Nature Precedings
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 & Genomics; Molecular Cell Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/2687/version/1
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Methanogen consortium metabolism characteristic analysis of Illinois basin by real time monitor method Nature Precedings
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
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Aqueous phase hydration and hydrate acidity of perfluoroalkyl and n:2 fluorotelomer aldehydes Nature Precedings
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 & Environment.
Ano: 2010 URL: http://precedings.nature.com/documents/4520/version/1
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Incident light orientation lets C4 monocotyledonous leaves make light work differently Nature Precedings
Ana S. Soares; Simon P. Driscoll; Till K. Pellny; Enrique Olmos; Maria Arrabaça; 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'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 & Genomics; Earth & Environment; Plant Biology.
Ano: 2008 URL: http://precedings.nature.com/documents/1672/version/1
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Pregnancy Obstructs Involution Stage II of the Mammary Gland in Cows: General Biological Implications Nature Precedings
Gabriel Leitner; Ana-Maria Anug; Uzi Merin; Nissim Silanikove.
*Background*
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.

*Methodology/Principal Findings*
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 "dried up" (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
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