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  • 1
    Publication Date: 2012-07-10
    Description: The aim of this paper is to analyse a numerical method to solve transient eddy current problems with input current intensities as data, formulated in terms of the magnetic field in a bounded domain including conductors and dielectrics. To this end, we introduce a time-dependent weak formulation and prove its well-posedness. We propose a finite element method for space discretization based on the Nédélec edge elements on tetrahedral meshes, for which we obtain error estimates. Then we introduce a backward Euler scheme for time discretization and prove error estimates for the fully discrete problem, too. Furthermore, a magnetic scalar potential is introduced to deal with the curl-free condition in the dielectric domain, which leads to an important saving in computational effort. Finally, the method is applied to solve two problems: a test with a known analytical solution and an application to electromagnetic forming.
    Print ISSN: 0272-4979
    Electronic ISSN: 1464-3642
    Topics: Mathematics
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  • 2
    Publication Date: 2015-01-16
    Description: BioModels ( http://www.ebi.ac.uk/biomodels/ ) is a repository of mathematical models of biological processes. A large set of models is curated to verify both correspondence to the biological process that the model seeks to represent, and reproducibility of the simulation results as described in the corresponding peer-reviewed publication. Many models submitted to the database are annotated, cross-referencing its components to external resources such as database records, and terms from controlled vocabularies and ontologies. BioModels comprises two main branches: one is composed of models derived from literature, while the second is generated through automated processes. BioModels currently hosts over 1200 models derived directly from the literature, as well as in excess of 140 000 models automatically generated from pathway resources. This represents an approximate 60-fold growth for literature-based model numbers alone, since BioModels’ first release a decade ago. This article describes updates to the resource over this period, which include changes to the user interface, the annotation profiles of models in the curation pipeline, major infrastructure changes, ability to perform online simulations and the availability of model content in Linked Data form. We also outline planned improvements to cope with a diverse array of new challenges.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 3
    Publication Date: 2016-01-22
    Description: We present the discovery of the highest velocity C iv broad absorption line to date in the z = 2.47 quasar SDSS J023011.28+005913.6, hereafter J0230. In comparing the public DR7 and DR9 spectra of J0230, we discovered an emerging broad absorption trough outflowing at ~60 000 km s –1 , which we refer to as trough A. In pursuing follow up observations of trough A, we discovered a second emergent C iv broad absorption trough outflowing at ~40 000 km s –1 , namely trough B. In total, we collected seven spectral epochs of J0230 that demonstrate emergent and rapidly (~10 d in the rest-frame) varying broad absorption. We investigate two possible scenarios that could cause these rapid changes: bulk motion and ionization variability. Given our multi-epoch data, we were able to rule out some simple models of bulk motion, but have proposed two more realistic models to explain the variability of both troughs. Trough A is likely an augmented ‘crossing disc’ scenario with the absorber moving at 10 000 〈 v (km s –1 ) 〈 18 000. Trough B can be explained by a flow-tube feature travelling across the emitting region at 8000 〈 v (km s –1 ) 〈 56 000. If ionization variability is the cause for the changes observed, trough A's absorber has n e ≥ 724 cm –3 and is at r equal ≥ 2.00 kpc, or is at r 〈 2.00 kpc with no constraint on the density; trough B's absorber either has n e ≥ 1540 cm –3 and is at r equal ≥ 1.37 kpc, or is at r 〈 1.37 kpc with no constraint on the density.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 4
    Publication Date: 2013-10-08
    Description: We analyse the energetics of the major radio flare of 2005 October 8 in GRS 1915+105. The flare is of particular interest because it is one of the most luminous and energetic radio flares from a Galactic black hole that has ever been observed. The motivation is twofold. One, to learn more about the energetics of this most extreme phenomenon and its relationship to the accretion state. The second is to verify if the calibrated estimates of the energy of major radio flares (based on the peak low frequency optically thin flux) derived from flares in the period 1996–2001 in Punsly & Rodriguez, PR13 hereafter, can be used to estimate plasmoid energy beyond this time period. We find evidence that the calibrated curves are still accurate for this strong flare. Furthermore, the physically important findings of PR13 are supported by the inclusion of this flare: the flare energy is correlated with both the intrinsic bolometric X-ray luminosity, L bol , ~1 h before ejection and L bol averaged over the duration of the ejection of the plasmoid and L bol is highly elevated relative to historic levels just before and during the ejection episode. A search of the data archives reveal that only the 2005 October 8 flare and those in PR13 have adequate data sampling to allow estimates of both the energy of the flare and the X-ray luminosity before and during flare launch.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 5
    Publication Date: 2014-08-14
    Description: Seasonal drought, typical of temperate and Mediterranean environments, creates problems in establishing plantations and affects development and yield, and it has been widely studied in numerous species. Forestry fast-growing species such as Eucalyptus spp. are an important resource in such environments, selected clones being generally used for production purposes in plantations in these areas. However, use of mono-specific plantations increases risk of plant loss due to abiotic stresses, making it essential to understand differences in an individual clone's physiological responses to drought stress. In order to study clonal differences in drought responses, nine Eucalyptus globulus (Labill.) clones (C14, C46, C97, C120, C222, C371, C405, C491 and C601) were gradually subjected to severe drought stress (〈14% of field capacity). A total of 31 parameters, physiological (e.g., photosynthesis, gas exchange), biochemical (e.g., chlorophyll content) and hormonal (abscisic acid [ABA] content), were analysed by classic and multivariate techniques. Relationships between parameters were established, allowing related measurements to be grouped into functional units (pigment, growth, water and ABA). Differences in these units showed that there were two distinct groups of E. globulus clones on the basis of their different strategies when faced with drought stress. The C14 group (C14, C120, C405, C491 and C601) clones behave as water savers, maintaining high water content and showing high stomatal adjustment, and reducing their aerial growth to a great extent. The C46 group (C46, C97, C222 and C371) clones behave as water spenders, reducing their water content drastically and presenting osmotic adjustment. The latter maintains the highest growth rate under the conditions tested. The method presented here can be used to identify appropriate E. globulus clones for drought environments, facilitating the selection of material for production and repopulation environments.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
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  • 6
    Publication Date: 2016-05-22
    Description: We report the discovery of KELT-10b, the first transiting exoplanet discovered using the KELT-South telescope. KELT-10b is a highly inflated sub-Jupiter mass planet transiting a relatively bright V = 10.7 star (TYC 8378-64-1), with T eff = 5948 ± 74 K, log g = $4.319_{-0.030}^{+0.020}$ and [Fe/H] = $0.09_{-0.10}^{+0.11}$ , an inferred mass M * = $1.112_{-0.061}^{+0.055}$ M and radius R * = $1.209_{-0.035}^{+0.047}$ R . The planet has a radius R p = $1.399_{-0.049}^{+0.069}$ R J and mass M p = $0.679_{-0.038}^{+0.039}$ M J . The planet has an eccentricity consistent with zero and a semimajor axis a = $0.052\,50_{-0.000\,97}^{+0.000\,86}$ au. The best-fitting linear ephemeris is T 0 = 2457 066.720 45 ± 0.000 27 BJD TDB and P = 4.166 2739 ± 0.000 0063 d. This planet joins a group of highly inflated transiting exoplanets with a larger radius and smaller mass than that of Jupiter. The planet, which boasts deep transits of 1.4 per cent, has a relatively high equilibrium temperature of T eq = $1377_{-23}^{+28}$  K, assuming zero albedo and perfect heat redistribution. KELT-10b receives an estimated insolation of $0.817_{-0.054}^{+0.068}$ x 10 9  erg s –1  cm –2 , which places it far above the insolation threshold above which hot Jupiters exhibit increasing amounts of radius inflation. Evolutionary analysis of the host star suggests that KELT-10b may not survive beyond the current subgiant phase, depending on the rate of in-spiral of the planet over the next few Gyr. The planet transits a relatively bright star and exhibits the third largest transit depth of all transiting exoplanets with V 〈 11 in the Southern hemisphere, making it a promising candidate for future atmospheric characterization studies.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 7
    Publication Date: 2013-06-09
    Description: Using data obtained with the Australia Telescope Compact Array (ATCA), we have characterized the amount, spatial distribution and kinematics of the molecular gas in the merging, double-nucleus type 2 quasar (QSO) SDSS J002531.46–104022.2 (hereafter SDSS J0025–10) at z  = 0.30 using the CO(1–0) transition. This is one of the scarce examples of quasar host galaxies where the CO emission has been resolved spatially at any redshift. We infer a molecular gas mass $M_{\rm H_2}=(6\pm 1)\times 10^9$ M , which is distributed in two main reservoirs separated by ~9 kpc. It has been found that ~60 per cent of the gas is in the central region, associated with the QSO nucleus and/or the intermediate region between the two nuclei. The other 40 per cent is associated with the northern tidal tail and is therefore unsettled. With its high infrared (IR) luminosity L IR  = (1.1 ± 0.3)  x 10 12 L , SDSS J0025–10 is an analogue of local luminous infrared galaxies (LIRGs with high L IR 〉 several x 10 11 L ) and ultraluminous infrared galaxies (ULIRGs). The clear evidence for an ongoing major merger of two gas-rich progenitors, the high L IR dominated by a starburst, the massive reservoir of molecular gas, with a large fraction still unsettled, and the quasar activity are all properties consistent with a transition phase in the (U)LIRG–optical QSO evolutionary scenario. We propose that we are observing the system during a particular transient phase, prior to more advanced mergers where the nuclei have already coalesced. We argue that a fraction of the molecular gas reservoir is associated with a tidal dwarf galaxy identified in the optical Hubble Space Telescope image at the tip of the northern tidal tail. The formation of such structures is predicted by simulations of colliding galaxies.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 8
    Publication Date: 2012-12-20
    Description: Here, we present WormQTL ( http://www.wormqtl.org ), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype–phenotype linkage and association mapping based on but not limited to R/qtl ( http://www.rqtl.org ). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researchers.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 9
    Publication Date: 2013-12-21
    Description: Tumor-derived exosomes are emerging as local and systemic cell-to-cell mediators of oncogenic information through the horizontal transfer of mRNAs, microRNAs and proteins during tumorigenesis. The exosomal content has been described as biologically active when taken up by the recipient cell. Identifying the specific molecular cargo of exosomes will help to determine their function in specific steps of the tumorigenic process. Here we evaluate whether Np73 is selectively packaged in tumor-derived exosomes, its function in the acceptor cells in vitro and in vivo and its prognosis potential in cancer. Np73 messenger is enriched in tumor-derived exosomes, suggesting its active sorting in these microvesicles. We observed the transmission of this exosome cargo to different cell types and how it confers proliferation potential and chemoresistance to the acceptor cells in vitro and in animal models. Finally, our data support the potential prognostic value of exosomal Np73 in colon cancer patients.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 10
    Publication Date: 2013-11-29
    Description: Motivation: Bisulfite sequencing (BS-seq) has emerged as the gold standard to study genome-wide DNA methylation at single-nucleotide resolution. Quality control (QC) is a critical step in the analysis pipeline to ensure that BS-seq data are of high quality and suitable for subsequent analysis. Although several QC tools are available for next-generation sequencing data, most of them were not designed to handle QC issues specific to BS-seq protocols. Therefore, there is a strong need for a dedicated QC tool to evaluate and remove potential technical biases in BS-seq experiments. Results: We developed a package named BSeQC to comprehensively evaluate the quality of BS-seq experiments and automatically trim nucleotides with potential technical biases that may result in inaccurate methylation estimation. BSeQC takes standard SAM/BAM files as input and generates bias-free SAM/BAM files for downstream analysis. Evaluation based on real BS-seq data indicates that the use of the bias-free SAM/BAM file substantially improves the quantification of methylation level. Availability and implementation: BSeQC is freely available at: http://code.google.com/p/bseqc/ . Contact: wl1@bcm.edu 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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