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  • 2010-2014  (4)
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  • 1
    Publication Date: 2012-12-21
    Description: Motivation: Gene expression experiments aim to accurately quantify thousands of transcripts in parallel. Factors posterior to RNA extraction can, however, impair their accurate representation. RNA degradation and differences in the efficiency of amplification affect raw intensity measurements using Affymetrix expression arrays. The positional intensity decay of specifically hybridized probes along the transcript they intend to interrogate is used to estimate the RNA quality in a sample and to correct probe intensities for the degradation bias. This functionality, for which no previous software solution is available, is implemented in the R/Bioconductor package AffyRNADegradation presented here. Availability: The package is available via Bioconductor at the URL http://bioconductor.org/packages/release/bioc/html/AffyRNA Degradation.html Contact: Fasold@izbi.uni-Leipzig.de Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 2
    Publication Date: 2013-03-13
    Description: Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next-generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2014-07-04
    Description: In June 2013, central Europe was hit by a century flood affecting the Danube and Elbe catchments after a 4 day period of heavy precipitation and causing severe human and economic loss. In this study model analysis and observational data are investigated to reveal the key atmospheric processes that caused the heavy precipitation event. The period preceding the flood was characterised by a weather regime associated with cool and unusual wet conditions resulting from repeated Rossby wave breaking (RWB). During the event a single RWB established a reversed baroclinicity in the low to mid-troposphere in central Europe with cool air trapped over the Alps and warmer air to the north. The upper-level cut-off resulting from the RWB instigated three consecutive cyclones in eastern Europe that unusually tracked westward during the days of heavy precipitation. Continuous large-scale slantwise ascent in so-called "equatorward ascending" warm conveyor belts (WCBs) associated with these cyclones is found as the key process that caused the 4 day heavy precipitation period. Fed by moisture sources from continental evapotranspiration, these WCBs unusually ascended equatorward along the southward sloping moist isentropes. Although "equatorward ascending" WCBs are climatologically rare events, they have great potential for causing high impact weather.
    Print ISSN: 1561-8633
    Electronic ISSN: 1684-9981
    Topics: Geography , Geosciences
    Published by Copernicus on behalf of European Geosciences Union (EGU).
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  • 4
    Publication Date: 2014-01-20
    Description: In June 2013 Central Europe was hit by a century flood affecting the Danube and Elbe catchments after a 4 day period of heavy precipitation and causing severe human and economic loss. In this study model analysis and observational data are investigated to reveal the key atmospheric processes that caused the heavy precipitation event. The period preceeding the flood was characterised by a weather regime associated with cool and unusual wet conditions resulting from repeated Rossby wave breaking (RWB). During the event a single RWB established a reversed baroclinicity in the low to mid troposphere in Central Europe with cool air trapped over the Alps and warmer air to the North. The upper-level cut-off resulting from the RWB instigated three consecutive cyclones in eastern Europe that unusually tracked westward during the days of heavy precipitation. Continuous large-scale slantwise ascent in so-called "upside down" warm conveyor belts (WCBs) associated with these cyclones is found as the key process that caused the 4 day heavy precipitation period. Fed by moisture sources from continental evapotranspiration, these WCBs unusually ascended equatorward along the southward sloping moist isentropes. Although "upside down" WCBs are climatologically rare events, they have great potential for causing high impact weather.
    Electronic ISSN: 2195-9269
    Topics: Geography , Geosciences
    Published by Copernicus on behalf of European Geosciences Union (EGU).
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