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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‣ Deletion of the trpc4 gene and its role in simple and complex strategic learning

William D. Klipec; Phuong Nguyen; Bridget Deeney; Claire Williamson; Kami Wenzel; Jessica Stumme; Marissa Collins; Abby Drish; Laura Swenson; Eric Ostertag; Donald C. Cooper
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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  we tested TRPC4 KO and normal wild type (WT) rats. TRPC4 KO and WT rats exhibited no differences in Y-­maze learning or simple discrimination learning. Furthermore, on a more complex serial reversal shift task designed  to assess strategic learning where the reward and non-­reward cues were repeatedly reversed between training sessions both TRPC4 KO and WT rats   performed equally well. Finally, we found no   performance differences when using a conditional reversal shift task where a tone signals the reversal of reward and non-reward cues within sessions. These data suggest that although TRPC4 channels may play a role in social interaction/anxiety  they exert a minimal role in simple and complex strategic learning.

‣ Clean Coal and Spirulina maxima (Cyanobacteria) Production through Alkaline-Seawater

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
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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%, respectively, and clean coal will be produced. S. maxima biomass production cost was 3.35 times lower in PSWS medium than that of the standard. This method will be used for carbon sequestration and low cost biomass production.

‣ INCF Lithuanian Workshop on Neuroscience and Information Technology

Aušra Saudargiene
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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. Aušra Saudargiene (Department of Informatics, Vytautas Magnus University, Kaunas, and Faculty of Natural Sciences, Vilnius University, Lithuania) and INCF. 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; discussion about the strategies for forming an INCF national node, and the benefits of having such a node in Lithuania (Appendix A: Program; Appendix B: Abstracts).

‣ Grid Potential Analysis and Docking Studies on a Dataset of N-Arylsulfonyl-3-AcetylIndoles as Anti-HIV Agent

Surendra Kumar; Meena Tiwari
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
A grid potential analysis employing the AutoGPA module in MOE2009.10 was performed on a dataset of 42 molecules of N-arylsulfonyl-3-acetylindoles as anti-HIV agent. The molecular docking simulations were also employed to position the inhibitors to their binding site to determine the most appropriate binding mode for different conformations of molecule. The uniqueness of AutoGPA module is that it automatically builds the 3D-QSAR model on the pharmacophore based molecular alignment. The best AutoGPA 3D-QSAR model obtained in the present study gives the cross-validated q2 value of 0.588 and r2pred value of 0.701 among the fifty six 3D-QSAR model developed. Furthermore, the steric and electrostatic contour maps for AutoGPA model along with the 3D structure of protein (binding residue of active site) inlaid were obtained to better understand the structural requirements against HIV and interaction between binding residues of protein and inhibitors. The study shows that hydrophobic and hydrogen bonding potential groups are favorable for optimization of parent nucleus for better activity.

‣ Protocol for Metatranscriptomic analysis of Intestinal Microbiota

Valeriy Poroyko; Alvaro G. Hernandez; John C. Alverdy; Donald C. Liu
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 70×75 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 non-ribosomal reads is ~17%. Hence we described a robust technique for metranscriptomic studies of animal intestinal microbiota. The double stranded cDNAs, prepared following this protocol, are suitable for pyrosequencing (454, Illumina), clone library construction or could be used to archive and store metaranscriptomic samples.

‣ Neural Information Processing: between synchrony and chaos

Josep L. Rossello; Vincent Canals; Antoni Morro
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 associated with both ordered and disordered states. Here we show an explanation of which processes are related to chaotic and synchronized states based on the study of in-silico implementation of biologically plausible neural systems. The measurements obtained reveal that synchronized cells (that can be understood as ordered states of the brain) are related to non-linear computations, while uncorrelated neural ensembles are excellent information transmission systems that are able to implement linear transformations (as the realization of convolution products) and to parallelize neural processes. From these results we propose a plausible meaning for Hebbian and non-Hebbian learning rules as those biophysical mechanisms by which the brain creates ordered or chaotic ensembles depending on the desired functionality. The measurements that we obtain from the hardware implementation of different neural systems endorse the fact that the brain is working with two different states...

‣ Integrative Approach - New Level Knowledge of Functions: Opportunities and Prospects

Vladimir M. Pokrovskii
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 methodology for scientific analysis to other organism systems.

‣ Segmenting DNA sequence into words based on statistical language model

Wang Liang
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 “words” 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 ‘probability approach to word segmentation’ 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.

‣ Mining PubMed for Biomarker-Disease Associations to Guide Discovery

Walter J. Jessen; Katherine T. Landschulz; Thomas G. Turi; Rachel Y. Reams
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
Biomedical knowledge is growing exponentially; however, meta-knowledge around the data is often lacking. PubMed is a database comprising more than 21 million citations for biomedical literature from MEDLINE and additional life science journals dating back to the 1950s. To explore the use and frequency of biomarkers across human disease, we mined PubMed for biomarker-disease associations. We then ranked the top 100 linked diseases by relevance and mapped them to medical subject headings (MeSH) and, subsequently, to the Disease Ontology. To identify biomarkers for each disease, we queried Covance BioPathways, an online data resource that maps commercial biomarker assays to biological and disease pathways. We then integrated pathways-based information to describe both known and potential biomarkers as well as disease-associated genes/proteins for select diseases. This approach identifies therapeutic areas with candidate or validated biomarkers, and highlights those areas where a paucity of biomarkers exists.

‣ The persistent impact of incidental experience

Matthew Wilder; Matt Jones; Alaa Ahmed; Tim Curran; Michael Mozer
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 reflect optimal adaptation to a dynamic environment exhibiting varying rates of change. The theory predicts a heavy-tailed decaying influence of past experience, consistent with our data, and suggests that individual incidental experiences are catalogued in a temporally extended memory utilized to optimize subsequent behavior.

‣ Non-linear Effects in Asymmetric Catalysis: Whys and Wherefores

Sosale Chandrasekhar
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 of “quasi-equilibrium”: in this, although overall equilibrium is attained, the product-spread is far from equilibrium. Thus, both the linear and NLE cases of chiral catalysis represent departures from equilibrium (which requires that the product e.e. = 0). Interesting similarities exist with models of non-equilibrium systems, the NLE cases apparently being analogs of open systems just after the bifurcation point has been crossed.

‣ Climate Change and Disease Simulation

Somnath Jha
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
Climate change has manifested differential impacts on various components of the earth system. The impact of climate change is not merely limited to the climatic variable. Climate change has resulted in complex, unforeseen consequences in the biosphere of earth. The silent but gradual changes arise out of varied responses of disease-causing organism to the combination of the disease-conducive environmental variables. The change is the same for both the target hosts plant as well as the animal kingdom. There is an urgent need to look into the changing disease dynamics and the disease pathogen genome sensitivity to the changes in climatic variables. The long memory of genetic makeup of disease pathogen to capture, inherit and evolve or mutate the changed or impacted gene due to climate change in generation after generation may invite a cascading effect on the next generation of biosphere. These silent but gradual changes in the genome of disease organism are rarely investigated or included in simulation models. This also enhances the risk of quantification of uncertainties of various disease simulation models. Thus, chances and lists of black swan events in life and food insecurity are on the rise.

‣ Diet transition to a high-fat diet for 3 weeks reduces brain omega-3-fatty acid levels, alters BDNF signaling and induces anxiety & depression-like behavior in adult rats

Sandeep Sharma; Yumei Zhuang; Fernando Gomez-Pinilla
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 for 3 weeks. Anxiety and depression-like behaviors were assessed by using open field (OF) and elevated plus maze (EPM). Molecular assessments were performed in the frontal cortex and hippocampus as dysfunctions in these brain regions are main contributors towards depression, anxiety-like behavior and stress. Results: We found that the HFD increased vulnerability for anxiety and depression-like behavior, and that these modifications harmonized with changes in the anxiety-related neuropeptide Y (NPY)-1 receptor. The HFD reduced levels of brain-derived neurotrophic factor (BDNF)...

‣ 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

Samuel Bogoch; Elenore S. Bogoch
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 obtained, permitted solid-phase synthesis of Replikin vaccines in seven days, which blocked H5N1 in chickens. The information also now provides up to two years of time to thoroughly test and distribute vaccines to high risk individuals in the countries identified; thus for the first time, a quantitative genomic Replikins method to both predict initial outbreaks and to prevent the development of a pandemic.

‣ Quantum probabilities in competing lizard communities

Diederik Aerts; Marek Czachor; Bart D'Hooghe; Maciej Kuna; Barry Sinervo; Sandro Sozzo
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 ‘paradox of the plankton’ 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 involve probabilistic incompatibilities, analogous to those occurring in quantum mechanics. Here, using experimental data collected from 1990 to 2011 on the RPS cycles of lizards, we show that the incompatibilities are indeed unavoidable, and the data cannot be reconstructed from a single Kolmogorovian probability space. We then prove that the effect is genuinely quantum probabilistic, i.e. all the probabilities can be formulated in terms of a single density matrix and a set of non-commuting projectors. This formal quantum structure is dormant in games where probabilities of strategies do not entangle with probabilities of payoffs...

‣ Nucleic acid - protein fingerprints. Novel protein classification based on nucleic acid - protein recognition

Alexander Krylov; Renad Zhdanov
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 "nucleic acid-protein fingerprints". 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 to 12 bases, and we have obtained unexpected result that tetranucleotide one is long enough for specific protein binding. This 4-mer can contain two universal bases - 5-nitroindole nucleoside analogue (Ni) and only two meaningful bases, like A, G, T and C. The result obtained opens a way for constructing the simplest protein binding microarray. This microarray consists of 16 meaningful dinucleotides, like AA, AG, CT, GG etc. Physical sequences of all the nucleotides were NiNiAA, etc, where Ni is bound to gel through the amino linker. We prepared such an array and tested it for specific binding of several DNA/RNA binding proteins...

‣ Inference of population splits and mixtures from genome-wide allele frequency data

Joseph K. Pickrell; Jonathan K. Pritchard
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 data; in contrast, we infer many migration events. While some of the migration events that we find have been detected previously, many have not. For example, in the human data we infer that Cambodians trace approximately 16% of their ancestry to a population ancestral to other extant East Asian populations. In the dog data, we infer that both the boxer and basenji trace a considerable fraction of their ancestry (9% and 25%, respectively) to wolves subsequent to domestication, and that East Asian toy breeds (the Shih Tzu and the Pekingese) result from admixture between modern toy breeds and ``ancient" Asian breeds. Software implementing the model described here...

‣ In silico design of potent agonists for human PPAR γ

Navya Pallapotu; Divya M; Kanipakam Hema; Amineni Umamaheswari
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
Peroxisome proliferator-activated receptor (PPAR γ) acts as a key regulator on adipocyte differentiation and glucose homeostasis. PPAR γ has been implicated in the pathology of type 2 diabetes. As human PPAR γ activity is considered important in improving insulin sensitivity, in silico screening was carried out to find potent agonists for human PPAR γ protein. The co-crystal structure of PPAR γ, solved through X-Ray diffraction method was retrieved from the protein data bank. Four PPAR γ agonists selected from literature were submitted to subsequent 2D searching protocol using Ligand.Info, which yielded 1699 structural analogs. The PPAR γ co-crystal structure and ligand dataset were preprocessed using protein preparation wizard and LigPrep, respectively. Further, docking was performed by using three phased docking protocol of Maestro v9.2 that implements Glide v5.7. The obtained thirteen leads through docking were compared with the existing inhibitors and seven leads with good binding affinity with PPAR γ were proposed. The binding orientations of the seven leads were coinciding well with the native co-crystal structure of human PPAR γ. Thus, the proposed seven leads can be suggested as potential agonists for improving insulin sensitivity in the treatment of type 2 diabetes mellitus if synthesized and validated in animal models

‣ In-silico identification of potential antagonists for human Casein kinase II subunit alpha' (CK2α2)

Kanipakam Hema; Harika Meduru; Navya Pallapotu; Amineni Umamaheswari
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
Human CK2α2 is an enzyme that belongs to the Serine/Threonine protein kinase family which is involved in signal transduction. Over expression of CK2α2 causes kidney cancer therefore, human CK2α2 has been identified as a drug target for the development of potential antagonists against cancer therapy. The existing human CK2α2 inhibitors in clinical practice are having side effects like fatigue, diarrhea, nausea, anorexia and vomiting. High-throughput virtual screening is one of the most common method used to identify lead compounds was implemented in the present study to identify potential inhibitors of human CK2α2. The co-crystal structure of human CK2α2 was retrieved from the protein data bank. A 2D similarity search was performed for available five human CK2α2 inhibitors (Apigenin, VX680, Sunitinib, SUI4813 and CCK) taken from PDB and PubMed to acquire 1942 structural analogs. The 3D structural conversion and multiple confirmations for 1942 compounds were generated using LigPrep. The docking and scoring calculations were performed using Glide v5.7 which includes high throughput virtual screening (HTVS), Standard precision (SP) docking and extra precision (XP) docking. Obtained 39 leads were compared with docking scores of the existing inhibitors and proposed six leads having good binding affinity. The binding orientation of CK2α2-lead 1complex was correlating with native co-crystal structure. Hence...

‣ Dispersal of _Aedes aegypti_: field study in temperate areas and statistical approach

Paula Bergero; Carlos A. Ruggerio; Rubén Lombardo; Nicolás Schweigmann; Hernán Solari
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 oviposition activity were determined: a corridor surrounding the urbanized area, a second region between 10m and 25m and the third region extending from 30m to 45m from the urbanization. The landscape (plant cover) and the human activity in the area appear to have an influence in the dispersal of _Aedes aegypti_.