ALBERT

All Library Books, journals and Electronic Records Telegrafenberg

X
feed icon rss

Your email was sent successfully. Check your inbox.

An error occurred while sending the email. Please try again.

Proceed reservation?

Export
  • 1
    facet.materialart.
    Unknown
    A process approach to inferences of causation: empirical research from vaccine cases in the USA (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-12
    Description: In law, inferences of causation are sometimes made through a structured process in which multiple participants play various roles, and make decisions concerning various logical components of the overall inference (such as legal rules, policy objectives, presumptions, evidence, burdens of proof and findings of fact). This article illustrates such a process using empirical research into compensation decisions in the USA for injuries allegedly caused by vaccinations. Empirical research into actual legal processes is essential, in order to discover how various players approach their sub-tasks of decision-making. It also provides insights for areas outside of law, such as non-monotonic logic, cognitive science, sociology and artificial intelligence.
    Print ISSN: 1470-8396
    Electronic ISSN: 1470-840X
    Topics: Mathematics , Law
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 2
    facet.materialart.
    Unknown
    An integrative somatic mutation analysis to identify pathways linked with survival outcomes across 19 cancer types (2016)
    Oxford University Press
    Details
    Publication Date: 2016-06-01
    Description: Motivation: Identification of altered pathways that are clinically relevant across human cancers is a key challenge in cancer genomics. Precise identification and understanding of these altered pathways may provide novel insights into patient stratification, therapeutic strategies and the development of new drugs. However, a challenge remains in accurately identifying pathways altered by somatic mutations across human cancers, due to the diverse mutation spectrum. We developed an innovative approach to integrate somatic mutation data with gene networks and pathways, in order to identify pathways altered by somatic mutations across cancers. Results: We applied our approach to The Cancer Genome Atlas (TCGA) dataset of somatic mutations in 4790 cancer patients with 19 different types of tumors. Our analysis identified cancer-type-specific altered pathways enriched with known cancer-relevant genes and targets of currently available drugs. To investigate the clinical significance of these altered pathways, we performed consensus clustering for patient stratification using member genes in the altered pathways coupled with gene expression datasets from 4870 patients from TCGA, and multiple independent cohorts confirmed that the altered pathways could be used to stratify patients into subgroups with significantly different clinical outcomes. Of particular significance, certain patient subpopulations with poor prognosis were identified because they had specific altered pathways for which there are available targeted therapies. These findings could be used to tailor and intensify therapy in these patients, for whom current therapy is suboptimal. Availability and implementation: The code is available at: http://www.taehyunlab.org . Contact: jhcheong@yuhs.ac or taehyun.hwang@utsouthwestern.edu or taehyun.cs@gmail.com Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 3
    facet.materialart.
    Unknown
    FlyNet: a versatile network prioritization server for the Drosophila community (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-02
    Description: Drosophila melanogaster (fruit fly) has been a popular model organism in animal genetics due to the high accessibility of reverse-genetics tools. In addition, the close relationship between the Drosophila and human genomes rationalizes the use of Drosophila as an invertebrate model for human neurobiology and disease research. A platform technology for predicting candidate genes or functions would further enhance the usefulness of this long-established model organism for gene-to-phenotype mapping. Recently, the power of network prioritization for gene-to-phenotype mapping has been demonstrated in many organisms. Here we present a network prioritization server dedicated to Drosophila that covers ~95% of the coding genome. This server, dubbed FlyNet, has several distinctive features, including (i) prioritization for both genes and functions; (ii) two complementary network algorithms: direct neighborhood and network diffusion; (iii) spatiotemporal-specific networks as an additional prioritization strategy for traits associated with a specific developmental stage or tissue and (iv) prioritization for human disease genes. FlyNet is expected to serve as a versatile hypothesis-generation platform for genes and functions in the study of basic animal genetics, developmental biology and human disease. FlyNet is available for free at http://www.inetbio.org/flynet .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 4
    facet.materialart.
    Unknown
    The period ratio distribution of Kepler's candidate multiplanet systems (2015)
    Oxford University Press
    Details
    Publication Date: 2015-02-26
    Description: We calculate and analyse the distribution of period ratios observed in systems of Kepler exoplanet candidates including studies of both adjacent planet pairs and all planet pairs. These distributions account for both the geometrical bias against detecting more distant planets and the effects of incompleteness due to planets missed by the data reduction pipeline. In addition to some of the known features near first-order mean-motion resonances (MMRs), there is a significant excess of planet pairs with period ratios near 2.2. The statistical significance of this feature is assessed using Monte Carlo simulation. We also investigate the distribution of period ratios near first-order MMR and compare different quantities used to measure this distribution. We find that beyond period ratios of ~2.5, the distribution of all period ratios follows a power law with an exponent –1.26 ± 0.05. We discuss implications that these results may have on the formation and dynamical evolution of Kepler -like planetary systems–systems of sub-Neptune/super-Earth planets with relatively short orbital periods.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 5
    facet.materialart.
    Unknown
    Antibiotic stress-induced modulation of the endoribonucleolytic activity of RNase III and RNase G confers resistance to aminoglycoside antibiotics in Escherichia coli (2014)
    Oxford University Press
    Details
    Publication Date: 2014-04-15
    Description: Here, we report a resistance mechanism that is induced through the modulation of 16S ribosomal RNA (rRNA) processing on the exposure of Escherichia coli cells to aminoglycoside antibiotics. We observed decreased expression levels of RNase G associated with increased RNase III activity on rng mRNA in a subgroup of E. coli isolates that transiently acquired resistance to low levels of kanamycin or streptomycin. Analyses of 16S rRNA from the aminoglycoside-resistant E. coli cells, in addition to mutagenesis studies, demonstrated that the accumulation of 16S rRNA precursors containing 3–8 extra nucleotides at the 5’ terminus, which results from incomplete processing by RNase G, is responsible for the observed aminoglycoside resistance. Chemical protection, mass spectrometry analysis and cell-free translation assays revealed that the ribosomes from rng -deleted E. coli have decreased binding capacity for, and diminished sensitivity to, streptomycin and neomycin, compared with wild-type cells. It was observed that the deletion of rng had similar effects in Salmonella enterica serovar Typhimurium strain SL1344. Our findings suggest that modulation of the endoribonucleolytic activity of RNase III and RNase G constitutes a previously uncharacterized regulatory pathway for adaptive resistance in E. coli and related gram-negative bacteria to aminoglycoside antibiotics.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 6
    facet.materialart.
    Unknown
    YeastNet v3: a public database of data-specific and integrated functional gene networks for Saccharomyces cerevisiae (2013)
    Oxford University Press
    Details
    Publication Date: 2013-12-29
    Description: Saccharomyces cerevisiae , i.e. baker’s yeast, is a widely studied model organism in eukaryote genetics because of its simple protocols for genetic manipulation and phenotype profiling. The high abundance of publicly available data that has been generated through diverse ‘omics’ approaches has led to the use of yeast for many systems biology studies, including large-scale gene network modeling to better understand the molecular basis of the cellular phenotype. We have previously developed a genome-scale gene network for yeast, YeastNet v2, which has been used for various genetics and systems biology studies. Here, we present an updated version, YeastNet v3 (available at http://www.inetbio.org/yeastnet/ ), that significantly improves the prediction of gene–phenotype associations. The extended genome in YeastNet v3 covers up to 5818 genes (~99% of the coding genome) wired by 362 512 functional links. YeastNet v3 provides a new web interface to run the tools for network-guided hypothesis generations. YeastNet v3 also provides edge information for all data-specific networks (~2 million functional links) as well as the integrated networks. Therefore, users can construct alternative versions of the integrated network by applying their own data integration algorithm to the same data-specific links.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 7
    facet.materialart.
    Unknown
    Site-Specific Structural Constraints on Protein Sequence Evolutionary Divergence: Local Packing Density versus Solvent Exposure (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-04
    Description: Protein sequences evolve under selection pressures imposed by functional and biophysical requirements, resulting in site-dependent rates of amino acid substitution. Relative solvent accessibility (RSA) and local packing density (LPD) have emerged as the best candidates to quantify structural constraint. Recent research assumes that RSA is the main determinant of sequence divergence. However, it is not yet clear which is the best predictor of substitution rates. To address this issue, we compared RSA and LPD with site-specific rates of evolution for a diverse data set of enzymes. In contrast with recent studies, we found that LPD measures correlate better than RSA with evolutionary rate. Moreover, the independent contribution of RSA is minor. Taking into account that LPD is related to backbone flexibility, we put forward the possibility that the rate of evolution of a site is determined by the ease with which the backbone deforms to accommodate mutations.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 8
    facet.materialart.
    Unknown
    Skin microrelief profiles as a cutaneous aging index (2016)
    Oxford University Press
    Details
    Publication Date: 2016-10-08
    Description: An objective measurement of cutaneous topographical information is important for quantifying the degree of skin aging. Our aim was to improve methods for measuring microrelief patterns using a three-dimensional analysis based on silicone replicas and scanning electron microscope (SEM). Another objective was to compare the results with those obtained using a two-dimensional analysis method based on dermoscopy. Silicone replicas were obtained from forearms, dorsum of the hands and fingers of 51 volunteers. Cutaneous profiles obtained by SEM with silicone replicas showed more consistent correlations with age than data obtained by dermoscopy. This indicates the advantage of three-dimensional topography analysis using silicone replicas and SEM over the widely used dermoscopic assessment. The cutaneous age was calculated using stepwise linear regression, and the result was 57.40–9.47  x  (number of furrows on dorsum of the hand)  x  (width of furrows on dorsum of the hand).
    Print ISSN: 0022-0744
    Electronic ISSN: 1477-9986
    Topics: Electrical Engineering, Measurement and Control Technology , Natural Sciences in General , Physics
    Published by Oxford University Press on behalf of The Japanese Electron Microscopy Society.
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 9
    facet.materialart.
    Unknown
    Pathway-based approach using hierarchical components of collapsed rare variants (2016)
    Oxford University Press
    Details
    Publication Date: 2016-09-02
    Description: Motivation: To address ‘missing heritability’ issue, many statistical methods for pathway-based analyses using rare variants have been proposed to analyze pathways individually. However, neglecting correlations between multiple pathways can result in misleading solutions, and pathway-based analyses of large-scale genetic datasets require massive computational burden. We propose a Pathway-based approach using HierArchical components of collapsed RAre variants Of High-throughput sequencing data (PHARAOH) for the analysis of rare variants by constructing a single hierarchical model that consists of collapsed gene-level summaries and pathways and analyzes entire pathways simultaneously by imposing ridge-type penalties on both gene and pathway coefficient estimates; hence our method considers the correlation of pathways without constraint by a multiple testing problem. Results: Through simulation studies, the proposed method was shown to have higher statistical power than the existing pathway-based methods. In addition, our method was applied to the large-scale whole-exome sequencing data with levels of a liver enzyme using two well-known pathway databases Biocarta and KEGG. This application demonstrated that our method not only identified associated pathways but also successfully detected biologically plausible pathways for a phenotype of interest. These findings were successfully replicated by an independent large-scale exome chip study. Availability and Implementation: An implementation of PHARAOH is available at http://statgen.snu.ac.kr/software/pharaoh/ . Contact: tspark@stats.snu.ac.kr Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
  • 10
    facet.materialart.
    Unknown
    Capillary oscillations at the exit of a nozzle (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-16
    Description: We compute the natural frequencies for the oscillation of the free boundary of a perfect incompressible fluid in the presence of capillary forces and partially in contact with a solid container. First, we study the case when the fluid occupies the domain { ( x , y ): y ≤ h ( x , t )} with h ( x , t )=0 for | x | 〉 a and h ( x , t ) the free boundary for | x | ≤ a . We deduce an integrodifferential evolutionary equation for the linearized free boundary and impose two different boundary conditions: the condition that the contact line between free boundary and the solid is pinned and the condition that the contact line can move vertically with a contact angle /2. For both cases, we compute the natural oscillation frequencies for the free surface and compare the results with the frequencies of oscillation in the absence of solid walls. Secondly, we study the effect of having two parallel solid walls at | x | = b + a on the natural frequencies of oscillation of the free boundary.
    Print ISSN: 0272-4960
    Electronic ISSN: 1464-3634
    Topics: Mathematics
    Published by Oxford University Press
    Location Call Number Expected Availability
    BibTip Others were also interested in ...
    PAPER CURRENT
Close ⊗
This website uses cookies and the analysis tool Matomo. More information can be found here...