Bioinformatics tools for analysing viral genomic data

The field of viral genomics and bioinformatics is experiencing a strong resurgence due to high-throughput sequencing (HTS) technology, which enables the rapid and cost-effective sequencing and subsequent assembly of large numbers of viral genomes. In addition, the unprecedented power of HTS technologies has enabled the analysis of intra-host viral diversity and quasispecies dynamics in relation to important biological questions on viral transmission, vaccine resistance and host jumping. HTS also enables the rapid identification of both known and potentially new viruses from field and clinical samples, thus adding new tools to the fields of viral discovery and metagenomics. Bioinformatics has been central to the rise of HTS applications because new algorithms and software tools are continually needed to process and analyse the large, complex datasets generated in this rapidly evolving area. In this paper, the authors give a brief overview of the main bioinformatics tools available for viral genomic research, with a particular emphasis on HTS technologies and their main applications. They summarise the major steps in various HTS analyses, starting with quality control of raw reads and encompassing activities ranging from consensus and de novo genome assembly to variant calling and metagenomics, as well as RNA sequencing

The Supernova Relic Neutrino Background

An upper bound to the supernova relic neutrino background from all past Type II supernovae is obtained using observations of the Universal metal enrichment history. We show that an unambiguous detection of these relic neutrinos by the Super-Kamiokande detector is unlikely. We also analyze the event rate in the Sudbury Neutrino Observatory (where coincident neutrons from anti-nu_e + D --> n + n + e+ might enhance background rejection), and arrive at the same conclusion. If the relic neutrino flux should be observed to exceed our upper bound and if the observations of the metal enrichment history (for z<1) are not in considerable error, then either the Type II supernova rate does not track the metal enrichment history or some mechanism may be responsible for transforming anti-nu_{mu,tau} --> anti-nu_e.Comment: Matches version accepted for publication in Phys. Rev.

Absorptive capacity and market orientation in public service provision

This is an Accepted Manuscript of an article published by Taylor & Francis Group in Journal of Strategic Marketing on 05.04.2012, available online at: http://www.tandfonline.com/10.1080/0965254X.2011.643915The application of market orientation to public organisations does not adequately account for the unique features of this context. Drawing on absorptive capacity literature, this is the first study to examine the role of the organisation's learning environment on the market orientation-performance interface for two opposing public management contexts. The research involved a national survey questionnaire to 1060 internal and external public leisure service providers in England. Empirical testing through structural equation modelling revealed that not all dimensions of market orientation are universally positive and marketing scholars should seek to examine and understand market orientation in the context of the organisation and its learning mechanisms, as absorptive capacity has clear and different moderation effects under different management contexts. © 2012 Copyright Taylor and Francis Group, LLC

Abelian Magnetic Monopole Dominance in Quark Confinement

We prove Abelian magnetic monopole dominance in the string tension of QCD. Abelian and monopole dominance in low energy physics of QCD has been confirmed for various quantities by recent Monte Carlo simulations of lattice gauge theory. In order to prove this dominance, we use the reformulation of continuum Yang-Mills theory in the maximal Abelian gauge as a deformation of a topological field theory of magnetic monopoles, which was proposed in the previous article by the author. This reformulation provides an efficient way for incorporating the magnetic monopole configuration as a topological non-trivial configuration in the functional integral. We derive a version of the non-Abelian Stokes theorem and use it to estimate the expectation value of the Wilson loop. This clearly exhibits the role played by the magnetic monopole as an origin of the Berry phase in the calculation of the Wilson loop in the manifestly gauge invariant manner. We show that the string tension derived from the diagonal (abelian) Wilson loop in the topological field theory (studied in the previous article) converges to that of the full non-Abelian Wilson loop in the limit of large Wilson loop. Therefore, within the above reformulation of QCD, this result (together with the previous result) completes the proof of quark confinement in QCD based on the criterion of the area law of the full non-Abelian Wilson loop.Comment: 33 pages, Latex, no figures, version accepted for publication in Phys. Rev. D (additions of sec. 4.5 and references, and minor changes

Precision Measurement of the Proton and Deuteron Spin Structure Functions g2 and Asymmetries A2

We have measured the spin structure functions g2p and g2d and the virtual photon asymmetries A2p and A2d over the kinematic range 0.02 < x < 0.8 and 0.7 < Q^2 < 20 GeV^2 by scattering 29.1 and 32.3 GeV longitudinally polarized electrons from transversely polarized NH3 and 6LiD targets. Our measured g2 approximately follows the twist-2 Wandzura-Wilczek calculation. The twist-3 reduced matrix elements d2p and d2n are less than two standard deviations from zero. The data are inconsistent with the Burkhardt-Cottingham sum rule if there is no pathological behavior as x->0. The Efremov-Leader-Teryaev integral is consistent with zero within our measured kinematic range. The absolute value of A2 is significantly smaller than the sqrt[R(1+A1)/2] limit.Comment: 12 pages, 4 figures, 2 table

Measurement of the Proton and Deuteron Spin Structure Functions g2 and Asymmetry A2

We have measured the spin structure functions g2p and g2d and the virtual photon asymmetries A2p and A2d over the kinematic range 0.02 < x < 0.8 and 1.0 < Q^2 < 30(GeV/c)^2 by scattering 38.8 GeV longitudinally polarized electrons from transversely polarized NH3 and 6LiD targets.The absolute value of A2 is significantly smaller than the sqrt{R} positivity limit over the measured range, while g2 is consistent with the twist-2 Wandzura-Wilczek calculation. We obtain results for the twist-3 reduced matrix elements d2p, d2d and d2n. The Burkhardt-Cottingham sum rule integral - int(g2(x)dx) is reported for the range 0.02 < x < 0.8.Comment: 12 pages, 4 figures, 1 tabl

Measurements of the Q2Q^2-Dependence of the Proton and Neutron Spin Structure Functions g1p and g1n

The structure functions g1p and g1n have been measured over the range 0.014 < x < 0.9 and 1 < Q2 < 40 GeV2 using deep-inelastic scattering of 48 GeV longitudinally polarized electrons from polarized protons and deuterons. We find that the Q2 dependence of g1p (g1n) at fixed x is very similar to that of the spin-averaged structure function F1p (F1n). From a NLO QCD fit to all available data we find $\Gamma_1^p - \Gamma_1^n =0.176 \pm 0.003 \pm 0.007$ at Q2=5 GeV2, in agreement with the Bjorken sum rule prediction of 0.182 \pm 0.005.Comment: 17 pages, 3 figures. Submitted to Physics Letters

Evolution of CDC42, a putative virulence factor triggering meristematic growth in black yeasts

The cell division cycle gene (CDC42) controlling cellular polarization was studied in members of Chaetothyriales. Based on ribosomal genes, ancestral members of the order exhibit meristematic growth in view of their colonization of inert surfaces such as rock, whereas in derived members of the order the gene is a putative virulence factor involved in expression of the muriform cell, the invasive phase in human chromoblastomycosis. Specific primers were developed to amplify a portion of the gene of 32 members of the order with known position according to ribosomal phylogeny. Phylogeny of CDC42 proved to be very different. In all members of Chaetohyriales the protein sequence is highly conserved. In most species, distributed all over the phylogenetic tree, introns and 3rd codon positions are also invariant. However, a number of species had paralogues with considerable deviation in non-coding exon positions, and synchronous variation in introns, although non-synonomous variation had remained very limited. In some strains both orthologues and paralogues were present. It is concluded that CDC42 does not show any orthologous evolution, and that its paralogues haves the same function but are structurally relaxed. The variation or absence thereof could not be linked to ecological changes, from rock-inhabiting to pathogenic life style. It is concluded that eventual pathogenicity in Chaetothyriales is not expressed at the DNA level in CDC42 evolution

Large enhancement of deuteron polarization with frequency modulated microwaves

We report a large enhancement of 1.7 in deuteron polarization up to values of 0.6 due to frequency modulation of the polarizing microwaves in a two liters polarized target using the method of dynamic nuclear polarization. This target was used during a deep inelastic polarized muon-deuteron scattering experiment at CERN. Measurements of the electron paramagnetic resonance absorption spectra show that frequency modulation gives rise to additional microwave absorption in the spectral wings. Although these results are not understood theoretically, they may provide a useful testing ground for the deeper understanding of dynamic nuclear polarization.Comment: 10 pages, including the figures coming in uuencoded compressed tar files in poltar.uu, which also brings cernart.sty and crna12.sty files neede