GOSim – an R-package for computation of information theoretic GO similarities between terms and gene products

<p>Abstract</p> <p>Background</p> <p>With the increased availability of high throughput data, such as DNA microarray data, researchers are capable of producing large amounts of biological data. During the analysis of such data often there is the need to further explore the similarity of genes not only with respect to their expression, but also with respect to their functional annotation which can be obtained from Gene Ontology (GO).</p> <p>Results</p> <p>We present the freely available software package <it>GOSim</it>, which allows to calculate the functional similarity of genes based on various information theoretic similarity concepts for GO terms. <it>GOSim </it>extends existing tools by providing additional lately developed functional similarity measures for genes. These can e.g. be used to cluster genes according to their biological function. Vice versa, they can also be used to evaluate the homogeneity of a given grouping of genes with respect to their GO annotation. <it>GOSim </it>hence provides the researcher with a flexible and powerful tool to combine knowledge stored in GO with experimental data. It can be seen as complementary to other tools that, for instance, search for significantly overrepresented GO terms within a given group of genes.</p> <p>Conclusion</p> <p><it>GOSim </it>is implemented as a package for the statistical computing environment <it>R </it>and is distributed under GPL within the CRAN project.</p

Validation of Phonon Physics in the CDMS Detector Monte Carlo

The SuperCDMS collaboration is a dark matter search effort aimed at detecting the scattering of WIMP dark matter from nuclei in cryogenic germanium targets. The CDMS Detector Monte Carlo (CDMS-DMC) is a simulation tool aimed at achieving a deeper understanding of the performance of the SuperCDMS detectors and aiding the dark matter search analysis. We present results from validation of the phonon physics described in the CDMS-DMC and outline work towards utilizing it in future WIMP search analyses.Comment: 6 Pages, 5 Figures, Proceedings of Low Temperature Detectors 14 Conferenc

Effect of the GaAsP shell on optical properties of self-catalyzed GaAs nanowires grown on silicon

We realize growth of self-catalyzed core-shell GaAs/GaAsP nanowires (NWs) on Si substrates using molecular-beam epitaxy. Transmission electron microscopy (TEM) of single GaAs/GaAsP NWs confirms their high crystal quality and shows domination of the zinc-blende phase. This is further confirmed in optics of single NWs, studied using cw and time-resolved photoluminescence (PL). A detailed comparison with uncapped GaAs NWs emphasizes the effect of the GaAsP capping in suppressing the non-radiative surface states: significant PL enhancement in the core-shell structures exceeding 2000 times at 10K is observed; in uncapped NWs PL is quenched at 60K whereas single core-shell GaAs/GaAsP NWs exhibit bright emission even at room temperature. From analysis of the PL temperature dependence in both types of NW we are able to determine the main carrier escape mechanisms leading to the PL quench

Downy mildew warning systems for vineyards cultivated under plastic covering - influence on yield and quality

Poste

Search for inelastic dark matter with the CDMS II experiment

Results are presented from a reanalysis of the entire five-tower data set acquired with the Cryogenic Dark Matter Search (CDMS II) experiment at the Soudan Underground Laboratory, with an exposure of 969 kg-days. The analysis window was extended to a recoil energy of 150 keV, and an improved surface-event background-rejection cut was defined to increase the sensitivity of the experiment to the inelastic dark matter (iDM) model. Three dark matter candidates were found between 25 keV and 150 keV. The probability to observe three or more background events in this energy range is 11%. Because of the occurrence of these events the constraints on the iDM parameter space are slightly less stringent than those from our previous analysis, which used an energy window of 10-100 keV.Comment: 10 pages, 10 figures, minor changes to match published version, conclusion unchange

Fermi Large Area Telescope Observations of the Cosmic-Ray Induced gamma-ray Emission of the Earth's Atmosphere

We report on measurements of the cosmic-ray induced gamma-ray emission of Earth's atmosphere by the Large Area Telescope onboard the Fermi Gamma-ray Space Telescope. The LAT has observed the Earth during its commissioning phase and with a dedicated Earth-limb following observation in September 2008. These measurements yielded 6.4 x 10^6 photons with energies >100MeV and ~250hours total livetime for the highest quality data selection. This allows the study of the spatial and spectral distributions of these photons with unprecedented detail. The spectrum of the emission - often referred to as Earth albedo gamma-ray emission - has a power-law shape up to 500 GeV with spectral index Gamma = 2.79+-0.06.Comment: Accepted for publication in PR