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    BALL-SNPgp--from genetic variants toward computational diagnostics (2016)
    Oxford University Press
    Details
    Publikationsdatum: 2016-06-16
    Beschreibung: : In medical research, it is crucial to understand the functional consequences of genetic alterations, for example, non-synonymous single nucleotide variants (nsSNVs). NsSNVs are known to be causative for several human diseases. However, the genetic basis of complex disorders such as diabetes or cancer comprises multiple factors. Methods to analyze putative synergetic effects of multiple such factors, however, are limited. Here, we concentrate on nsSNVs and present BALL-SNPgp, a tool for structural and functional characterization of nsSNVs, which is aimed to improve pathogenicity assessment in computational diagnostics. Based on annotated SNV data, BALL-SNPgp creates a three-dimensional visualization of the encoded protein, collects available information from different resources concerning disease relevance and other functional annotations, performs cluster analysis, predicts putative binding pockets and provides data on known interaction sites. Availability and implementation: BALL-SNPgp is based on the comprehensive C ++ framework Biochemical Algorithms Library (BALL) and its visualization front-end BALLView. Our tool is available at www.ccb.uni-saarland.de/BALL-SNPgp . Contact: ballsnp@milaman.cs.uni-saarland.de
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 2
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    Linking stage-resolved population models with field observations: an integrated approach on population dynamics of Pseudocalanus elongatus in the German Bight (2011)
    Oxford University Press
    Details
    Publikationsdatum: 2011-12-13
    Beschreibung: The population dynamics of Pseudocalanus elongatus have been investigated within the framework of the GLOBEC-Germany project to gain a better understanding of its life cycle and population dynamics and to estimate secondary production in the North Sea. During an intensive field study in the German Bight between February and October 2004, experiments on reproduction were performed and data on length of copepodids and abundance were collected to characterize the population in the southern North Sea. This data set was used to update the literature-based parameterization of a population model for P. elongatus to investigate the population dynamics, life history and production in the German Bight. The ability of data to improve population models is also discussed. Pseudocalanus elongatus was found to be a major contributor to carbon uptake contributing about one-third of copepod production. Though the spatial variability in field observations was not reflected by the model, the simulation matched data within one order of magnitude at most stations. The high-resolution field observations and experiments mainly improved the parameterization of the reproductive parameters. Mortality is found to be a critical parameter due to its influence on population size. Using constant rates, though based on observation-derived estimates, seems not to capture realistic variability. Our study confirms the need for experimental and field data to build a robust parameterization for concentration-based population models.
    Print ISSN: 0142-7873
    Digitale ISSN: 1464-3774
    Thema: Biologie
    Publiziert von Oxford University Press
    Standort Signatur Einschränkungen Verfügbarkeit
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  • 3
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    Nosocomial Transmission of Extensively Drug-Resistant Tuberculosis in a Rural Hospital in South Africa (2012)
    Oxford University Press
    Details
    Publikationsdatum: 2012-12-18
    Beschreibung: Background.  Extensively drug-resistant tuberculosis (XDR-tuberculosis) is a global public health threat, but few data exist elucidating factors driving this epidemic. The initial XDR-tuberculosis report from South Africa suggested transmission is an important factor, but detailed epidemiologic and molecular analyses were not available for further characterization. Methods.  We performed a retrospective, observational study among XDR-tuberculosis patients to identify hospital-associated epidemiologic links. We used spoligotyping, IS 6110 -based restriction fragment–length polymorphism analysis, and sequencing of resistance-determining regions to identify clusters. Social network analysis was used to construct transmission networks among genotypically clustered patients. Results.  Among 148 XDR-tuberculosis patients, 98% were infected with human immunodeficiency virus (HIV), and 59% had smear-positive tuberculosis. Nearly all (93%) were hospitalized while infectious with XDR-tuberculosis (median duration, 15 days; interquartile range: 10–25 days). Genotyping identified a predominant cluster comprising 96% of isolates. Epidemiologic links were identified for 82% of patients; social network analysis demonstrated multiple generations of transmission across a highly interconnected network. Conclusions.  The XDR-tuberculosis epidemic in Tugela Ferry, South Africa, has been highly clonal. However, the epidemic is not the result of a point-source outbreak; rather, a high degree of interconnectedness allowed multiple generations of nosocomial transmission. Similar to the outbreaks of multidrug-resistant tuberculosis in the 1990s, poor infection control, delayed diagnosis, and a high HIV prevalence facilitated transmission. Important lessons from those outbreaks must be applied to stem further expansion of this epidemic.
    Print ISSN: 0022-1899
    Digitale ISSN: 1537-6613
    Thema: Medizin
    Publiziert von Oxford University Press im Namen von The Infectious Diseases Society of America (IDSA).
    Standort Signatur Einschränkungen Verfügbarkeit
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