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  • 2010-2014  (58)
  • 1985-1989  (22)
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  • 1
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    MHD instabilities in accretion mounds - II. 3D simulations (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-17
    Description: We investigate the onset of pressure-driven toroidal-mode instabilities in accretion mounds on neutron stars by 3D magnetohydrodynamic (MHD) simulations using the pluto MHD code. Our results confirm that for mounds beyond a threshold mass, instabilities form finger-like channels at the periphery, resulting in mass-loss from the magnetically confined mound. Ring-like mounds with hollow interior show the instabilities at the inner edge as well. We perform the simulations for mounds of different sizes to investigate the effect of the mound mass on the growth rate of the instabilities. We also investigate the effect of such instabilities on observables such as cyclotron resonant scattering features and timing properties of such systems.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    MHD instabilities in accretion mounds - I. 2D axisymmetric simulations (2013)
    Oxford University Press
    Details
    Publication Date: 2013-03-16
    Description: We have performed stability analysis of axisymmetric accretion mounds on neutron stars in high-mass X-ray binaries by 2D magnetohydrodynamic (MHD) simulations with the pluto MHD code. We find that the mounds are stable with respect to interchange instabilities, but the addition of excess mass destabilizes the equilibria. Our simulations confirm that accretion mounds are unstable with respect to MHD instabilities beyond a threshold mass. We investigate both filled and hollow mounds and for the latter also compute the expected profile of cyclotron resonance scattering features (CRSF). In comparison to the CRSF from filled mounds reported in our earlier work, hollow mounds display wider and more complex line profiles.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    CTCFBSDB 2.0: a database for CTCF-binding sites and genome organization (2012)
    Oxford University Press
    Details
    Publication Date: 2012-12-20
    Description: CTCF is a highly conserved transcriptional regulator protein that performs diverse functions such as regulating gene expression and organizing the 3D structure of the genome. Here, we describe recent updates to a database of CTCF-binding sites, CTCFBSDB ( http://insulatordb.uthsc.edu/ ), which now contains almost 15 million CTCF-binding sequences in 10 species. Since the original publication of the database, studies of the 3D structure of the genome, such as those provided by Hi-C experiments, have suggested that CTCF plays an important role in mediating intra- and inter-chromosomal interactions. To reflect this important progress, we have integrated CTCF-binding sites with genomic topological domains defined using Hi-C data. Additionally, the updated database includes new features enabled by new CTCF-binding site data, including binding site occupancy and the ability to visualize overlapping CTCF-binding sites determined in separate experiments.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Bayesian Network Webserver: a comprehensive tool for biological network modeling (2013)
    Oxford University Press
    Details
    Publication Date: 2013-10-19
    Description: : The Bayesian Network Webserver (BNW) is a platform for comprehensive network modeling of systems genetics and other biological datasets. It allows users to quickly and seamlessly upload a dataset, learn the structure of the network model that best explains the data and use the model to understand relationships between network variables. Many datasets, including those used to create genetic network models, contain both discrete (e.g. genotype) and continuous (e.g. gene expression traits) variables, and BNW allows for modeling hybrid datasets. Users of BNW can incorporate prior knowledge during structure learning through an easy-to-use structural constraint interface. After structure learning, users are immediately presented with an interactive network model, which can be used to make testable hypotheses about network relationships. Availability and implementation: BNW, including a downloadable structure learning package, is available at http://compbio.uthsc.edu/BNW . (The BNW interface for adding structural constraints uses HTML5 features that are not supported by current version of Internet Explorer. We suggest using other browsers (e.g. Google Chrome or Mozilla Firefox) when accessing BNW). Contact: ycui2@uthsc.edu 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
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  • 5
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    Single-cell genomics reveals organismal interactions in uncultivated marine protists (2011)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2011-05-10
    Description: Whole-genome shotgun sequence data from three individual cells isolated from seawater, followed by analysis of ribosomal DNA, indicated that the cells represented three divergent clades of picobiliphytes. In contrast with the recent description of this phylum, we found no evidence of plastid DNA nor of nuclear-encoded plastid-targeted proteins, which suggests that these picobiliphytes are heterotrophs. Genome data from one cell were dominated by sequences from a widespread single-stranded DNA virus. This virus was absent from the other two cells, both of which contained non-eukaryote DNA derived from marine Bacteroidetes and large DNA viruses. By using shotgun sequencing of uncultured marine picobiliphytes, we revealed the distinct interactions of individual cells.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Yoon, Hwan Su -- Price, Dana C -- Stepanauskas, Ramunas -- Rajah, Veeran D -- Sieracki, Michael E -- Wilson, William H -- Yang, Eun Chan -- Duffy, Siobain -- Bhattacharya, Debashish -- New York, N.Y. -- Science. 2011 May 6;332(6030):714-7. doi: 10.1126/science.1203163.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Bigelow Laboratory for Ocean Sciences, West Boothbay Harbor, ME 04575, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/21551060" target="_blank"〉PubMed〈/a〉
    Keywords: Animals ; Aquatic Organisms/classification/*genetics/*physiology/virology ; Bacteria/classification/genetics/isolation & purification ; Cell Communication ; Cell Separation ; DNA Viruses/classification/genetics/isolation & purification ; DNA, Bacterial/analysis/genetics ; DNA, Ribosomal/genetics ; DNA, Single-Stranded ; DNA, Viral/analysis/genetics ; Eukaryota/classification/*genetics/*physiology/virology ; *Genome ; Heterotrophic Processes ; Likelihood Functions ; Molecular Sequence Data ; Phylogeny ; Plankton/classification/genetics/physiology/virology ; Plastids/genetics/metabolism ; Proteins/chemistry/genetics ; *Seawater ; Single-Cell Analysis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 6
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    Cyanophora paradoxa genome elucidates origin of photosynthesis in algae and plants (2012)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2012-02-22
    Description: The primary endosymbiotic origin of the plastid in eukaryotes more than 1 billion years ago led to the evolution of algae and plants. We analyzed draft genome and transcriptome data from the basally diverging alga Cyanophora paradoxa and provide evidence for a single origin of the primary plastid in the eukaryote supergroup Plantae. C. paradoxa retains ancestral features of starch biosynthesis, fermentation, and plastid protein translocation common to plants and algae but lacks typical eukaryotic light-harvesting complex proteins. Traces of an ancient link to parasites such as Chlamydiae were found in the genomes of C. paradoxa and other Plantae. Apparently, Chlamydia-like bacteria donated genes that allow export of photosynthate from the plastid and its polymerization into storage polysaccharide in the cytosol.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Price, Dana C -- Chan, Cheong Xin -- Yoon, Hwan Su -- Yang, Eun Chan -- Qiu, Huan -- Weber, Andreas P M -- Schwacke, Rainer -- Gross, Jeferson -- Blouin, Nicolas A -- Lane, Chris -- Reyes-Prieto, Adrian -- Durnford, Dion G -- Neilson, Jonathan A D -- Lang, B Franz -- Burger, Gertraud -- Steiner, Jurgen M -- Loffelhardt, Wolfgang -- Meuser, Jonathan E -- Posewitz, Matthew C -- Ball, Steven -- Arias, Maria Cecilia -- Henrissat, Bernard -- Coutinho, Pedro M -- Rensing, Stefan A -- Symeonidi, Aikaterini -- Doddapaneni, Harshavardhan -- Green, Beverley R -- Rajah, Veeran D -- Boore, Jeffrey -- Bhattacharya, Debashish -- MSP-14226/Canadian Institutes of Health Research/Canada -- New York, N.Y. -- Science. 2012 Feb 17;335(6070):843-7. doi: 10.1126/science.1213561.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Ecology, Evolution, and Natural Resources, Rutgers University, New Brunswick, NJ 08901, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/22344442" target="_blank"〉PubMed〈/a〉
    Keywords: Biological Evolution ; Cyanobacteria/genetics ; Cyanophora/*genetics ; *Evolution, Molecular ; Gene Transfer, Horizontal ; Genes, Bacterial ; *Genome, Plant ; Molecular Sequence Data ; Photosynthesis/*genetics ; Phylogeny ; Symbiosis
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 7
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    Antimetastatic nanoparticle [Applied Biological Sciences] (2013)
    National Academy of Sciences
    Details
    Publication Date: 2013-04-24
    Description: Although biomedical applications of nanotechnology, which typically involve functionalized nanoparticles, have taken significant strides, biological characterization of unmodified nanoparticles remains underinvestigated. Herein we demonstrate that unmodified gold nanoparticles (AuNPs) inhibit the proliferation of cancer cells in a size- and concentration-dependent manner by abrogating MAPK-signaling. In addition, these AuNPs reverse epithelial-mesenchymal...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
    Published by National Academy of Sciences
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  • 8
    Electronic Resource
    Electronic Resource
    Harmonic generation in nondegenerate semiconductors at low lattice temperature (1988)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 64 (1988), S. 4554-4561 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The characteristics of second harmonic generation (SHG) in covalent semiconductors at low lattice temperatures are studied here over a wide range of the bias field, beginning from a weakly heated carrier ensemble up to the onset of impurity breakdown giving due consideration to the effect of recombination of the nonequilibrium carriers in the presence of shallow attractive traps. The calculations are carried out for a parabolic law of dispersion and a scalar effective mass. The results confirm that the recombination effects bring in both qualitative and quantitative changes in the SHG characteristics throughout the entire range of the bias field. Like the situation around room temperatures, the curves for the efficiency of SHG versus the bias field at low lattice temperatures also exhibit maximum, thus illustrating the optimum bias field for which the generation can be most efficient. Depending upon the lattice temperature and the material, the recombination effects may bring in a second maximum in the characteristics of SHG. The results are found to be useful for the determination of some capture parameters. The inadequacies of the theory are pointed out and the scope for further refinement is discussed.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.341257
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  • 9
    Electronic Resource
    Electronic Resource
    Coplanar-waveguide excitation of magnetostatic surface waves (1987)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 62 (1987), S. 4322-4324 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The theory of excitation of magnetostatic surface waves with a coplanar-waveguide (CPW) transmission line has been developed. An expression for an equivalent radiation admittance relating the energy carried away by magnetostatic surface waves to electromagnetic energy propagating along the CPW line has been obtained. The input admittance of an open-circuited yttrium iron garnet (YIG)-loaded CPW transmission line has been computed with gap width of CPW and YIG film thickness as parameters.
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.339063
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  • 10
    Electronic Resource
    Electronic Resource
    Determination of recombination center position from the temperature dependence of minority carrier lifetime in the base region of p-n junction solar cells (1985)
    [S.l.] : American Institute of Physics (AIP)
    Journal of Applied Physics 57 (1985), S. 2942-2947 
    Details
    ISSN: 1089-7550
    Source: AIP Digital Archive
    Topics: Physics
    Notes: The minority carrier lifetime (τ) in the base region of n+-p silicon solar cells has been measured in the temperature range ∼77–400 °K using the open-circuit voltage decay technique. The injection level has been maintained constant in the entire temperature region. Experiment and theory agree in a small temperature region if τn0 (minority carrier lifetime in heavily doped p silicon) is assumed to be temperature independent. However, an excellent fit between experimental and theoretical results is obtained if τn0 is assumed to vary as exp[−(Eτn0/kT)].
    Type of Medium: Electronic Resource
    URL: http://dx.doi.org/10.1063/1.335234
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