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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‣ Isoglitter

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

‣ Biophysical Mechanisms Supporting Conscious Perception: Prospects for an Artificial Astrocyte

Alfredo Pereira Jr
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 to integrate spatially distributed information. The amplitude-modulated calcium waveform in astrocytes is a multiscale phenomenon, simultaneously operating on temporal scales of milliseconds and seconds, as well as in micro and macro spatial scales. Oscillatory synchrony, constructive wave interference and communication by means of ionic antennas are proposed to constitute a neuro-astroglial self-organizing mechanism of perceptual integration and feeling of the integrated information content. A pilot experiment of a single artificial astrocyte is suggested...

‣ Cationic State Distributions over Chlorophyll Pairs in Photosystem I and II

Keisuke Saito; Hiroshi Ishikita
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
Photosystem I (PSI) and II (PSII) possess chlorophyll pairs P~A~/P~B~ and P~D1~/P~D2~, respectively. These chlorophylls are the primary electron donors in the light-induced electron transfer. After the electron transfer, the radical cation remains on these chlorophyll pairs, forming [P~A~/P~B~]^·+^ and [P~D1~/P~D2~]^·+^. The positive charge distributions over the two chlorophylls were reported to be 10/90-50/50 for P~A~^·+^/P~B~^·+^ [1,2] and 70/30-80/20 for P~D1~^·+^/P~D2~^·+^ [3,4]. To clarify the origin of the distributions, we calculated ratios of P~A~^·+^/P~B~^·+^ and P~D1~^·+^/P~D2~^·+^ with a quantum mechanical/molecular mechanical (QM/MM) approach and the redox potentials (_E_~m~) of monomeric chlorophylls P~A~, P~B~, P~D1~, and P~D2~ with an electrostatic continuum-model approach, using the crystal structures of PSI [5] and PSII [6]. 1) Our QM/MM calculation reproduced the experimentally measured ratios of P~A~^·+^/P~B~^·+^ [1,2] and P~D1~^·+^/P~D2~^·+^ [3,4]. The calculated ratios were strongly correlated with the calculated _E_~m~ values. 2) We analyzed residues on puseudo-symmetrical subunit pairs PsaA/PasB and D1/D2 that shifted _E_~m~ of P~A~...

‣ Potential Use of Folate-polyethylene glycol (PEG)-Appended Dendrimer (G3) Conjugate with alpha-Cyclodextrin as DNA Carriers to Tumor Cells

Taishi Higashi; Ayumi Yoshimitsu; Haruna Ikeda; Masayo Arizono; Kenjiro Hattori; Tomoko Takeuchi; Fumitoshi Hirayama; Kaneto Uekama; Hidetoshi Arima; Keiichi Motoyama
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 α-CDE (G3) in KB cells, folate receptor (FR)-overexpressing cancer cells. Of the three Fol-PalphaCs (G3, DSF 2, 5 or 7), Fol-PalphaC (G3, DSF 5) had the highest gene transfer activity in KB cells. The activity of Fol-PalphaC (G3, DSF 5) was significantly higher than that of alpha-CDE (G3) in KB cells, but not in A549 cells, FR-negative cells. Negligible cytotoxicity of the pDNA complex with Fol-PalphaC (G3, DSF 5) was observed in KB cells or A549 cells up to a charge ratio of 100/1 (carrier/pDNA). The cellular association of the pDNA complex with Fol-PalphaC (G3...

‣ 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.

‣ Accurate estimation of homologue-specific DNA concentration-ratios in cancer samples allows long-range haplotyping

Scott L. Carter; Matthew Meyerson; Gad Getz
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 segments of distinct copy number and modeling the four distinct genotypes in each segment. We describe general methods for fitting these models to data which are suit- able for both SNP microarrays and massively parallel sequencing data. In addition, we demonstrate a specially tailored error-model for interpretation of systematic variations arising in microarray platforms. The ability to directly determine haplotypes from cancer samples represents an opportunity to expand reference panels of phased chromosomes...

‣ Emergence of macroscopic simplicity from the Tumor Necrosis Factor-alpha signaling dynamics

Kentaro Hayashi; Vincent Piras; Masaru Tomita; Masa Tsuchiya; Kumar Selvarajoo
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 activation of the third group of genes is not mainly due to the poor rate of mRNA decay process, rather, the law of signaling flux conservation stipulates the presence of secondary signaling, such as feedback mechanism or autocrine signaling, is crucial. Although the living system is perceived as sophisticated and complex, notably, our work reveals the presence of simple governing principles in cell population dynamics.

‣ Introduction to the Baltimore Ecosystem Study, Long-Term Ecological Research Project, Phase III

Steward T. A. Pickett
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
The Baltimore Ecosystem Study (BES) is one of two urban Long-Term Ecological Research (LTER) projects in the United States. It began its third funding cycle in 2011. Although the project continues key measurements that were started in 1997 at the inception of the research, the third phase is characterized by a new conceptual framework. Phase III of BES focuses on metropolitan Baltimore, Maryland, as a system poised for transition from a "sanitary city" -- characterized by engineered environmental solutions, management via discrete disciplines, and government control to a "sustainable city" -- which would be characterized by additional biological solutions, collaborative management, and polycentric and multi-level governance. In such a situation, the guiding research question becomes, "What are the effects of adaptive processes aimed at sustainability in the Baltimore socio-ecological system?" Adaptive processes are those social and biophysical features and actions which allow a complex system to adjust to changing internal and external drivers. The full proposal and other details of BES can be discovered on the project website: www.beslter.org

‣ Human Heart Development Pathways

Samuel Sklar; Alexander Pico
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
This pathway has been largely adapted from an article by Deepak Srivastava, Cell. 2006 Sep 22;126(6):1037-48. In this pathway are known transcription factors, miRNAs and regulatory proteins that impact the regional specificity of the human heart. Activating signals are indicated by arrows while inhibitory signals are indicated by T-bars. Special thanks to Kim Cordes for her assistance in revising this pathway, based on recent heart development research. A live version of the pathway can be found at http://www.wikipathways.org/index.php/Pathway:WP1591

‣ Normalization And Matching Of Chemical Compound Names

Martin Golebiewski; Meik Bittkowski; Henriette Slogsnat; Jasmin Saric; Isabel Rojas; Wolfgang Müller
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Poster
Português
We have developed ChemHits (http://sabio.h-its.org/chemHits/), an application which detects and matches synonymic names of chemical compounds. The tool is based on natural language processing (NLP) methods and applies rules to systematically normalize chemical compound names. Subsequently, matching of synonymous names is achieved by comparison of the normalized name forms. The tool is capable of normalizing a given name of a chemical compound and matching it against names in (bio-)chemical databases, like SABIO-RK, PubChem, ChEBI or KEGG, even when there is no exact name-to-name-match.

‣ SABIO-RK: Access to Biochemical Reaction Kinetics Data

Martin Golebiewski
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Conferência ou Objeto de Conferência
Português
SABIO-RK (http://sabio.h-its.org/) is a curated database for biochemical reaction kinetics data drawn from different sources: from literature or direct submission by experimenters. The system offers standardized data by the use of controlled vocabularies and annotations pointing to other resources and biological ontologies. SABIO-RK can be accessed either manually via a web-based search interface or automatically via web services that allow direct data access by other tools. Both interfaces support the export of the data together with its annotations in SBML (Systems Biology Markup Language) complying with the MIRIAM (Minimal Information Requested In the Annotation of biochemical Models) standard. New RESTful web services, as well as a new browser interface both offer extended functionality, such as hierarchical search for data based on organism taxonomy or tissue and cell type ontology. SABIO-RK facilitates the exchange of kinetic data between experimentalists and modelers, and thereby supports the setup of quantitative computer models. The web services and the degree of data integration make it well suited for its integration into applications using or requiring kinetic data, such as systems biology modeling platforms.

‣ Transcriptional memory emerges from cooperative histone modifications

Hans Binder; Lydia Steiner; Thimo Rohlf; Sonja Prohaska; Joerg Galle
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
Background 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. Results 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 these complexes and DNA or histones create a regulatory switch of transcriptional activity possessing a regulatory memory. The regulatory states of the switch depend on the activity of histone (de-) methylases, the structure of the DNA-binding regions of the complexes, and the number of histones contributing to binding. We apply our model to transcriptional regulation by trithorax- and polycomb- complex binding. By analyzing data on pluripotent and lineage-committed cells we verify basic model assumptions and provide evidence for a positive effect of the length of the modified regions on the stability of the induced regulatory states and thus on the transcriptional memory. Conclusions Our results provide new insights into epigenetic modes of transcriptional regulation. Moreover...

‣ Antiviral Effects of a Synthetic Aluminium-Magnesium Silicate on Avian Influenza Virus

Madike Ezeibe; Anthony Egbuji; Obianuju Okoroafor; James Eze; Omadi Ijabo; Augustine Ngene; Ikechukwu Eze; Joeseph Ugonabo; Mary Sanda; Ijeoma Mbuko
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 ± 5.48 %. Viral titres reduced significantly (P from HA, 73 ± 32.72 to 1.4 ±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 ± 4.38 to 130 ±17.27 hours. When incubation with AMS was repeated on portions of the same sample, MDT increased from 64 to 104 hours with the portion incubated once. Two AIV portions on which incubation with AMS was repeated could not kill chick embryos.

‣ Design and construction of a new Drosophila species, D.synthetica, by synthetic regulatory evolution

Eduardo Moreno
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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's "Biological Species Concept"^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 "transgenic organisms" towards "synthetic species", such as Drosophila synthetica, constitutes a safety mechanism to avoid hybridization with wild type populations and preserve natural biodiversity^16-18^. Drosophila synthetica is the first transgenic organism that cannot hybridize with the original wild type population but remains fertile when crossed with other transgenic animals.

‣ Cunningham: a BLAST Runtime Estimator

James R. White; Malcolm Matalka; W. Florian Fricke; Samuel V. Angiuoli
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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’s going to take is kind of depressing, and you could waste a day of work trying to run a job that would never finish. If you feel the same way we do, then check out Cunningham, a tool we designed to estimate BLAST runtimes for shotgun sequence datasets using sequence composition statistics. We’ve trained its models on real metagenomic sequence data using the Amazon EC2 cloud, and it will provide a relatively quick estimate for datasets with up to tens of millions of sequences. It’s not perfect, but it’ll give you at least some idea of expected runtime...

‣ CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.1

James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets: A) Qiime – 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; B) UCHIME – a tool for rapid identification of chimeric 16S sequence fragments; C) Mothur – a C++-based software package for 16S analysis; D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations. CloVR-16S accepts as input raw multiplex 454-pyrosequencer output (i.e. pooled pyrotagged sequences from multiple samples), or alternatively, pre-processed sequences from multiple samples in separate files. This protocol became first available in CloVR beta version 0.7.

‣ CloVR-Metagenomics: Functional and taxonomic microbial community characterization from metagenomic whole-genome shotgun (WGS) sequences – standard operating procedure, version 1.0

James R. White; Cesar Arze; Malcom Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
The CloVR-Metagenomics pipeline employs several well-known tools and protocols for the analysis of metagenomic whole-genome shotgun (WGS) sequence datasets: A) UCLUST – a C++-based software package for clustering redundant DNA sequences and removing artificial 454 replicates; B) BLASTX and BLASTN for functional and taxonomic assignment of sequences, respectively; C) Metastats and custom R scripts to generate additional statistical and graphical evaluation. 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, which are used for comparative analysis. This protocol is available in CloVR beta version 0.5 and 0.6.

‣ CloVR-Microbe: Assembly, gene finding and functional annotation of raw sequence data from single microbial genome projects – standard operating procedure, version 1.0

Kevin Galens; James R. White; Cesar Arze; Malcolm Matalka; Michelle Gwinn Giglio; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 HiSeq sequencing platforms or of combinations of Sanger and Roche/454 sequence data. The pipeline output consists of results and summary files generated during the different pipeline steps. Annotated sequence files are generated that are compatible with common genome browser tools and can be submitted to the GenBank repository at NCBI. This protocol is available in CloVR beta versions 0.5 and 0.6.

‣ CloVR-16S: Phylogenetic microbial community composition analysis based on 16S ribosomal RNA amplicon sequencing – standard operating procedure, version 1.0

James R. White; Cesar Arze; Malcolm Matalka; The CloVR Team; Owen White; Samuel V. Angiuoli; W. Florian Fricke
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
The CloVR-16S pipeline employs several well-known phylogenetic tools and protocols for the analysis of 16S rRNA sequence datasets: A) Mothur – 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); B) The Ribosomal Database (RDP) naïve Bayesian classifier assigns each 16S sequence to a reference taxonomy with associated empirical probabilities based on oligonucleotide frequencies; C) Qiime – a python-based workflow package, allowing for sequence processing and phylogenetic analysis using different methods including phylogenetic distance (UniFrac) for within-(alpha diversity) and between-(beta diversity) sample analysis; D) Metastats and custom R scripts used to generate additional statistical and graphical evaluations. Though some of the different protocols used in CloVR-16S overlap in purpose (e.g. OTU clustering), the end-user benefits from their overall complementary nature as they focus on different aspects of the phylogenetic analysis. CloVR-16S accepts as input raw multiplex 454-pyrosequencer output...

‣ Worm-like carbon shell chains produced from wood

Kyoko Suzuki; Hidetoshi Kita; Yukie Saito; Tsutomu Suzuki; Kazuhisa Sato; Toyohiko Konno
Fonte: Nature Preceedings Publicador: Nature Preceedings
Tipo: Manuscript
Português
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 "carbon shell chains". The discussion of the formation mechanism reveals that the wood cell wall plays an important role for their efficient production. They are stable at 1800 ºC under vacuum, but in air, burn under 600 ºC, and are perfectly conversed into hydrogen and carbon monoxide in a short time by steam at 900 ºC. The control of their decomposition will bring out a new talent in the wood char as a big source of supply for nano-graphite or nano-graphene...