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16338 research data, page 1 of 1634

Genome-Wide Identification of Susceptibility Alleles for Viral Infections through a Population Genetics Approach

Viruses have exerted a constant and potent selective pressure on human genes throughout evolution. We utilized the marks left by selection on allele frequency to identify viral infection-associated allelic variants. Virus diversity (the number of different viruses in a geographic region) was used to measure virus-driven selective pressure. Results showed an excess of variants correlated with virus diversity in genes involved in immune response and in the biosynthesis of glycan structures func...

Sequence composition information of the Zebrafish/Drosophila melanogaster test set.

The sequence composition is along the mature miRNAs and their flanking regions. A, B. Sequence composition for the 3′ and 5′ mature miRNAs, respectively. C. Sequence composition for the combined data set, including both 3′ and 5′ mature miRNAs. Note that position triplets (prior to the mature miRNA for 3′ samples, after the mature miRNA for 5′ samples and symmetrically at both ends of the mature miRNA for all samples) in this dataset are also very likely to contain Uracil, as was the case wi...

Scatter plot of the melanoma sample dataset of Haqq et al.

Berretta, Regina; Moscato, Pablo (2010)
Publisher: Figshare
This is the same set of samples of Figure 4 and we have used the same color coding. We are now using the modified statistical complexity measures M-skin and M-metastasis II. As expected, normal skin samples (in green) have a low value of the M-skin measure. Interestingly, most of the nevi samples (in yellow) have an intermediate value of the M-skin measure, and most of the primary and metastatic samples have even larger values of M-skin. This result, together with our observation and analysis...

A Statistical Method for the Detection of Alternative Splicing Using RNA-Seq

Deep sequencing of transcriptome (RNA-seq) provides unprecedented opportunity to interrogate plausible mRNA splicing patterns by mapping RNA-seq reads to exon junctions (thereafter junction reads). In most previous studies, exon junctions were detected by using the quantitative information of junction reads. The quantitative criterion (e.g. minimum of two junction reads), although is straightforward and widely used, usually results in high false positive and false negative rates, owning to th...

A Systems Biology Approach Uncovers Cellular Strategies Used by Methylobacterium extorquens AM1 During the Switch from Multi- to Single-Carbon Growth

BackgroundWhen organisms experience environmental change, how does their metabolic network reset and adapt to the new condition? Methylobacterium extorquens is a bacterium capable of growth on both multi- and single-carbon compounds. These different modes of growth utilize dramatically different central metabolic pathways with limited pathway overlap.Methodology/Principal FindingsThis study focused on the mechanisms of metabolic adaptation occurring during the transition from succinate growth...

HIV-1 Subtype C-Infected Individuals Maintaining High Viral Load as Potential Targets for the “Test-and-Treat” Approach to Reduce HIV Transmission

The first aim of the study is to assess the distribution of HIV-1 RNA levels in subtype C infection. Among 4,348 drug-naïve HIV-positive individuals participating in clinical studies in Botswana, the median baseline plasma HIV-1 RNA levels differed between the general population cohorts (4.1–4.2 log10) and cART-initiating cohorts (5.1–5.3 log10) by about one log10. The proportion of individuals with high (≥50,000 (4.7 log10) copies/ml) HIV-1 RNA levels ranged from 24%–28% in the general HIV-p...

Effect of AITC on C. elegans lifespan at 25°C.

L1- or L4- after the concentration unit µM or mM indicates that nematodes were treated with AITC from either L1 or L4 stage on, respectively.a, Percent differences of the mean lifespan compared with that of the control.b, P values were calculated by log-rank test (vs 0 µM).

Percentage of Ppt1-deficient embryos displaying axonal defects.

Parentheses, the number of stage 16–17 embryos assayed.n/d: not determined.