Últimos itens adicionados do Acervo: Proceedings Nature

Nature é uma das mais prestigiosas e antigas revistas científicas do mundo: sua primeira edição é de 4 de novembro de 1869. Entre as inúmeras descobertas científicas publicadas na Nature estão a dos raios X, da estrutura em dupla hélice do ADN e o buraco na camada de ozônio.

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‣ Neural Substrates of Chronic Pain in the Thalamocortical Circuit

Antonio G. Zippo; Riccardo M. Storchi; Maurizio Valente; Gian Carlo Caramenti; Gabriele E. M. Biella
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 disconnection syndrome and hypothesize potential novel therapeutic appraisal.

‣ The Semantic Automated Discovery and Integration (SADI) Web service Design-Pattern, API and Reference Implementation

Mark Wilkinson; Benjamin Vandervalk; Luke McCarthy
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Background. 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. Description. SADI – Semantic Automated Discovery and Integration – 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 bioinformatics and other scientific domains. Using Semantic Web technologies at every level of the Web services “stack”, SADI services consume and produce instances of OWL Classes following a small number of very straightforward best-practices. In addition, we provide codebases that support these best-practices, and plug-in tools to popular developer and client software that dramatically simplify deployment of services by providers, and the discovery and utilization of those services by their consumers. Conclusions. SADI Services are fully compliant with...

‣ A Draft Sequence of the Puerto Rican Parrot Genome (Amazona vittata) – a Genome Project funded by a Local Community Effort

Taras K. Oleksyk
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 (<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 longest contig at 75,003, and 148,255 long fragment library of scaffolds with N50=19,470 with the longest at 206,462 bp length. Further sequencing is needed to generate enough coverage of the genome and close the assembly gaps. To our knowledge, this is the first genome project to be initiated and supported by local community fundraising efforts, and represents a model for the future of de novo genome projects for conservation genetics of nonhuman species.

‣ Milk is for Children, Colostrum silage is for calves.

Mara Helena Saalfeld; Daniela Brayer Pereira; Kathleen Krüguer Silveira; Marcia Gularte; Julia Valente; Renata Schramm; Fábio Leivas Leite
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 the development of the calves. Calves fed with this product had a significant higher weight gain comparing to the ones fed with milk. Then the milk can be used for human consumption.

‣ Hacking the JPEG/PDF tree format

Joseph Hughes
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
We have been illustrating the relationships between species and genes as trees for over a century. Whilst in the early years of morphological and molecular phylogenetics, embedding illustrations into manuscripts might have been the most appropriate way to disseminate knowledge, this has resulted in the locking up of phylogenetic hypotheses into the pages of journals and books without an easy way to access this information. As a result, most phylogenetic knowledge is lost upon publication. I will explain the reasons for re-using published trees, discuss ways to liberate this information and avoid these problems in the future.

‣ In silico designing of activator for human IGF2 protein for effective cardiovascular disease therapeutics

M Sandhya rani; Manne Munikumar; Amineni Umamaheswari
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
Insulin like growth factor-II (IGF2) is a member of IGF family, the main role of IGF2 is as a growth hormone during gestation or fetal development. Ischematic stroke, atherosclerosis and pathological cardiac hypertrophy are associated with low circulating levels of IGF2. 5-aza-2’-deoxycytidine increases the activity of IGF2, due to high toxicity of 5aza2’deoxycytidine, some silenced genes are also expressed that cause various cancer diseases. In the present study an in silico approach was used to design the potential activator for IGF2 without side effects to treat cardiovascular diseases. Ligand binding sites were predicted using CASTp for drug target. 361 ligand analogs for 5-aza-2’-deoxycytidine were identified through virtual screening from Ligand.Info database. Docking studies were performed using Schrodinger software (2010) generated 13 lead agonists for human IGF2. Docking complexes of 13 lead agonists and 5aza2’deoxycytidine with IGF2 were compared and four leads with better affinity, ADME properties and lower XPGscore than 5-aza-2’-deoxycytidine were proposed as potential activators. Lead‘1’ (mizoribine), the best ranked activator (XPG score -7.181) having good binding affinity...

‣ Serine biosynthesis with one carbon catabolism represents a novel pathway for ATP generation in cells using alternative glycolysis with zero net ATP production

Alexei Vazquez; Elke K. Markert; Zoltan N. Oltvai
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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, in cells using the standard- or the net zero ATP glycolysis pathways a significant portion of the glycolysis flux is always associated with ATP generation, and the ratio between the flux rates of the two pathways determines the rate of ATP generation and lactate and alanine secretion during glycolysis.

‣ Early exposure to environmental toxin contributes to neuronal vulnerability and axonal pathology in a model of familial ALS

Grace Lee; Christopher A. Shaw
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 results cumulatively confirm earlier findings that exposure to an environmental toxin is sufficient to produce the disease phenotype and indicate a role for gene-environment interaction in some forms of the disease.

‣ On the Hydrides of B, C, N, O and F

Michael J. Bucknum; Eduardo A. Castro
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 structure-type thus.

‣ Towards an Open Taxonomy

Roderic Page
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
Taxonomy is in many ways still predigital. Most taxonomic databases are little more than digitized index cards linking names to often-cryptic bibliographic citations, oblivious to the growing volume of scientific literature that is now online. A growing fraction of taxonomic literature is becoming freely available, either through adoption of Open Access publishing models, or through digitizing efforts such as the Biodiversity Heritage Library. Yet much of the most basic information about biodiversity, namely taxonomic description, remains either behind a pay wall, or only available in paper form. This talk sketches the goal of an "Open Taxonomy." The first step towards this goal is digitally linking scientific names to the primary literature using standard identifiers such as DOIs. I argue that until we make serious inroads into this task, taxonomic knowledge will remain in a ghetto largely ignored by the wider scientific community.

‣ A similarity criterion for forest growth curves

Georgii A. Alexandrov; Georgy S. Golitsyn
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 rates of non-structural carbohydrate supply and demand. Since the rate of supply is much higher than the rate of demand, the flow of non-structural carbohydrates achieves the tips of branches and enables the radial growth of crown. Proceeding from these ideas, we derived the similarity criterion which supposedly captures the “essence of growth” that emerges from the geometric similarity of tree crowns.

‣ Computer aided drug design studies to explore novel antagonist of human myotrophin

Sandeep Swargam; K Mahesh; Amineni Umamaheswari
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
Human myotrophin is the smallest ankyrin repeat protein implicated as a factor to induce cardiac hypertrophy. Activation of myotrophin was observed during acute myocardial infarction (MI). In acute coronary syndrome (ACS) patients, myotrophin acts as a self-governing predictor of major adverse cardiac events (MACE). Therefore, human myotrophin serves as an effective drug target for discovery of new potential drugs. Recent human myotropin inhibitors have poor pharmalogical properties leading to intolerable side effects. Hence, ligand based virtual screening protocol of CADD method was persuaded in the present study to propose new class potential myotrophin inhibitors. Docking was done by using Schrödinger software suite 2010 (maestro v9.1), docked complexes were validated and enumerated to find out the best lead, top twenty docked complexes were selected, analyzed through LIGPLOT for their binding orientations. Finally ten top ranked leads were reported based on the XPGscore, better binding affinity and good pharmacological properties compared to existing inhibitors. Lead ‘1’ (Mitoxantrone) showed lowest XPGscore (-8.4k cal/mol) and good van der Waal interaction, hydrophobic interactions with the residues Lys-24...

‣ Where Is Scientific Evidence in Support of Refuge Size Reduction for Pyramided Bt Crops?

Andrei Alyokhin
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
Genetically modified plants expressing insecticidal Cry proteins originating from a soil-dwelling bacterium Bacillus thuringiensis (Bt) provide a powerful tool for managing insect pests. Unfortunately, insect ability to develop resistance to insecticidal proteins potentially jeopardizes its long-term efficiency. Review of registration materials submitted by plant biotech industry to the U.S. Environmental Protection Agency and the existing scientific literature shows that currently available evidence in support of reducing refuge for the pyramided genetically modified corn plants to 5% of the total crop area is essentially limited to predictions of a single unpublished mathematical model developed “in-house” by the industry scientists. Additional research and a more extensive (and open) scientific discussion will be of great benefit for ensuring sustainable use of this technology.

‣ The carbon allotrope glitter as n-diamond and i-carbon nanocrystals

Michael J. Bucknum; Eduardo A. Castro
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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.

‣ Levy flights are not evolved behavior

Jay Willis; Lucas Merckelbach
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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, '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 directed movement. Gliders are autonomous underwater vehicles (AUV), propelled by a buoyancy engine^5^.The principle of operation is that by alternating positive and negative buoyancy, the winged AUV glides through the ocean in an undulating path, resurfacing after a pre-programmed number of undulations. During the periods at the surface, which typically last 15 minutes, GPS is used for positioning before and after transmission of data via a satellite link, whereas underwater the trajectory is deadreckoned from measured heading...

‣ Coupling perception and action using probabilistic control

Constantin A. Rothkopf; Paul Schrater
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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). 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 a virtual reality setup so as to change the uncertainty of the ballʼs position in parametric ways. Specifically, the contrast of the ball changes as a function of the heading angle towards the ball along the subjectʼs momentary trajectory. Subjects adjusted their interception strategy within an average of 26 trials and are consistently able to catch these balls. For the classic interception task it has been shown that the optimal strategy for constant velocities and certain noise distributions is indeed the constant bearing angle strategy. The complex observation functions used in the human experiments above require modeling the task as a POMDP. We use an approximate solution technique based on Markov Chain Monte Carlo to solve the control task and compare this to the solution in which the system first finds the most likely position of the target and then acts upon this percept. This computational strategy corresponds to certainty equivalent control and is shown to be suboptimal in this task. We conclude that humans are able to carry out complex control tasks that require computing with uncertainties relating sensory input...

‣ In-silico analysis of human IGFBP-4 involved in cardiovascular diseases

Manne MuniKumar; Kavali Roopesh; Amineni Umamaheswari
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
Cardiovascular disease is the major cause of disability and premature death throughout the world and contributes substantially to the escalating costs of health care. Insulin like growth factor binding protein 4 (IGFBP-4) mainly belongs to the family of IGFB protein. Over expression of IGFBP-4 leads to cardiovascular diseases namely stroke, acute myocardial infarction and heart failure. IGFBP-4 serves as an effective drug target against cardiovascular disease. Hence, ligand based virtual screening was pursued in the present study to propose potential inhibitors of IGFBP-4. Two published inhibitors were selected to initiate high throughput virtual screening from small molecule databases namely, NCI, ChemBank, ChemPDB, AKos GmbH, Asinex Ltd and KEGG ligand. The structures listed through database search were docked with IGFBP-4 using virtual screening workflow of Maestro v9.2. Three leads that showed better binding affinity and good correlation than two published inhibitors were proposed as potential IGFBP-4 inhibitors. The three proposed leads showed good pharmacological properties in comparison to the two existing inhibitors for next generation drug designing against cardiovascular diseases.

‣ The BRIF (Bioresource Research Impact Factor) as a tool for improving bioresource sharing in biomedical research

Laurence Mabile; Raymond Dalgleish; Gudmundur A. Thorisson; Mylène Deschênes; Robert Hewitt; Jane Carpenter; Elena Bravo; Pierre-Antoine Gourraud; Paul Hofman; Jennifer Harris; Maria Angeles Munoz-Fernandes; Anne Cambon-Thomsen
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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.

‣ In silico design of novel leads for inhibition of human beta-2-microglobulin

Pallapotu Navya; Dibyabhaba Pradhan; Amineni Umamaheswari
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
Human myotrophin is the smallest ankyrin repeat protein implicated as a factor to induce cardiac hypertrophy. Activation of myotrophin was observed during acute myocardial infarction (MI). In acute coronary syndrome (ACS) patients, myotrophin acts as a self-governing predictor of major adverse cardiac events (MACE). Therefore, human myotrophin serves as an effective drug target for discovery of new potential drugs. Recent human myotropin inhibitors have poor pharmacological properties leading to intolerable side effects. Hence, ligand based virtual screening protocol of CADD method was pursued in the present study to propose new class potential myotrophin inhibitors. Docking was done by using Schrödinger software suite 2010 (maestro v9.1), docked complexes were validated and enumerated to find out the best lead, the top twenty docked complexes were selected and analyzed through LIGPLOT for their binding orientations. Finally, the ten top ranked leads were reported based on the XPGscore, better binding affinity and good pharmacological properties compared to existing inhibitors. Lead ‘1’ (Mitoxantrone) showed lowest XPGscore (-8.4k cal/mol) and good van der Waal interaction, hydrophobic interactions with the residues Lys-24...

‣ Identification of new leads for human IGFBP-2: a therapeutic target for cardiovascular diseases

Kanipakam Hema; I Vani Priyadarshini; Amineni Umamaheswari
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
IGFBP-2, the largest member of insulin-like growth factor binding proteins family, is under-expressed in hazardous cardiovascular diseases like obesity and type II diabetes mellitus, which upon aging leads to heart stroke. Therefore, IGFBP-2 has been proposed as a possible target for the development of novel leads for cardiovascular disease therapy. High-throughput virtual screening, one of the most common methods used to identify lead compounds was implemented here to identify potential IGFBP-2 activators. The NMR (nuclear magnetic resonance) structure of human IGFBP-2 was retrieved from the protein data bank. A 2D similarity search was performed for known IGFBP-2 activator TPA to acquire 383 structural analogs. The 3D structural conversion and multiple confirmations for 383 compounds were generated using LigPrep with ADME constraints. The docking and scoring calculations were performed using Glide v5.7. The extra precision (XP) docking reported 35 leads and ranked based on XP Gscore. Eleven leads having better XP Gscore compared to TPA were proposed as potential IGFBP-2 activators. Lead ’1’ (3,11-dihydroxyl-13-methyl-6,7,8,9,11,12,13,14,15,16-decahydro-cyclopenta [a] phenon) showed highest XP Gscore of -7.239 kcal/mol...