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  • 1
    Publication Date: 2015-04-16
    Description: Seismic full waveform inversion (FWI) has been applied to simple elastic problems with certain symmetries, such as isotropic, transverse isotropic or vertical transversely isotropic media. In this study, the FWI concept is extended to the most general anisotropic case with 21 independent elastic material parameters and no symmetry plane (triclinic). Beside a short description of the 3-D finite-difference scheme to solve the forward problem and the FWI optimization algorithm, we present a sensitivity study for a simple anisotropic medium. This test problem consists of a homogenous triclinic anisotropic full space, which contains 21 spatially separated spheres. In each sphere one component of the elastic tensor deviates by 5 per cent from the background medium. The resolution of the different spheres, ambiguities between the different elastic parameters, as well as the effect of the acquisition geometry can be systematically investigated. Due to the high computational costs of the triclinic forward problem a few compromises have to be made regarding the acquisition geometries. Point sources are replaced by plane wave sources which lead to a limitation of incidence angles and therefore a strong decrease in resolution of the nondiagonal elastic tensor components. It is shown that, despite these limitations, a tomographic acquisition geometry would be able to resolve to some extent a monoclinic symmetry via FWI. Restricting the acquisition geometries (e.g. VSP combined with reflection seismic or reflection seismic only) significantly reduces the number of resolvable tensor elements in strict dependence of the covered incidence angles.
    Keywords: Marine Geosciences and Applied Geophysics
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 2
    Publication Date: 2015-05-24
    Description: When an unbiased estimator of the likelihood is used within a Metropolis–Hastings chain, it is necessary to trade off the number of Monte Carlo samples used to construct this estimator against the asymptotic variances of the averages computed under this chain. Using many Monte Carlo samples will typically result in Metropolis–Hastings averages with lower asymptotic variances than the corresponding averages that use fewer samples; however, the computing time required to construct the likelihood estimator increases with the number of samples. Under the assumption that the distribution of the additive noise introduced by the loglikelihood estimator is Gaussian with variance inversely proportional to the number of samples and independent of the parameter value at which it is evaluated, we provide guidelines on the number of samples to select. We illustrate our results by considering a stochastic volatility model applied to stock index returns.
    Print ISSN: 0006-3444
    Electronic ISSN: 1464-3510
    Topics: Biology , Mathematics , Medicine
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  • 3
    Publication Date: 2015-02-15
    Description: Gamma-ray bursts (GRBs) are the most energetic phenomena in the Universe; believed to result from the collapse and subsequent explosion of massive stars. Even though it has profound consequences for our understanding of their nature and selection biases, little is known about the dust properties of the galaxies hosting GRBs. We present analysis of the far-infrared properties of an unbiased sample of 20 BeppoSAX and Swift GRB host galaxies (at an average redshift of z  = 3.1) located in the Herschel Astrophysical Terahertz Large Area Survey, the Herschel Virgo Cluster Survey, the Herschel Fornax Cluster Survey, the Herschel Stripe 82 Survey and the Herschel Multi-tiered Extragalactic Survey, totalling 880 deg 2 , or ~3 per cent of the sky in total. Our sample selection is serendipitous, based only on whether the X-ray position of a GRB lies within a large-scale Herschel survey – therefore our sample can be considered completely unbiased. Using deep data at wavelengths of 100–500 μm, we tentatively detected 1 out of 20 GRB hosts located in these fields. We constrain their dust masses and star formation rates (SFRs), and discuss these in the context of recent measurements of submillimetre galaxies and ultraluminous infrared galaxies. The average far-infrared flux of our sample gives an upper limit on SFR of 〈114 M yr –1 . The detection rate of GRB hosts is consistent with that predicted assuming that GRBs trace the cosmic SFR density in an unbiased way, i.e. that the fraction of GRB hosts with SFR 〉 500 M yr –1 is consistent with the contribution of such luminous galaxies to the cosmic star formation density.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 4
    Publication Date: 2015-01-16
    Description: Phosphatases are crucial enzymes in health and disease, but the knowledge of their biological roles is still limited. Identifying substrates continues to be a great challenge. To support the research on phosphatase–kinase–substrate networks we present here an update on the human DEPhOsphorylation Database: DEPOD ( http://www.depod.org or http://www.koehn.embl.de/depod ). DEPOD is a manually curated open access database providing human phosphatases, their protein and non-protein substrates, dephosphorylation sites, pathway involvements and external links to kinases and small molecule modulators. All internal data are fully searchable including a BLAST application. Since the first release, more human phosphatases and substrates, their associated signaling pathways (also from new sources), and interacting proteins for all phosphatases and protein substrates have been added into DEPOD. The user interface has been further optimized; for example, the interactive human phosphatase–substrate network contains now a ‘highlight node’ function for phosphatases, which includes the visualization of neighbors in the network.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 5
    Publication Date: 2013-01-17
    Print ISSN: 0260-1230
    Electronic ISSN: 1464-3766
    Topics: Biology
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  • 6
    Publication Date: 2012-09-27
    Description: The conserved bacterial anticodon nuclease (ACNase) RloC and its phage-excluding homolog PrrC comprise respective ABC-adenosine triphosphatase (ATPase) and ACNase N- and C-domains but differ in three key attributes. First, prrC is always linked to an ACNase silencing, DNA restriction–modification (R–M) locus while rloC rarely features such linkage. Second, RloC excises its substrate’s wobble nucleotide, a lesion expected to impede damage reversal by phage transfer RNA (tRNA) repair enzymes that counteract the nick inflicted by PrrC. Third, a distinct coiled-coil/zinc-hook (CC/ZH) insert likens RloC’s N-region to the universal DNA damage checkpoint/repair protein Rad50. Previous work revealed that ZH mutations activate RloC’s ACNase. Data shown here suggest that RloC has an internal ACNase silencing/activating switch comprising its ZH and DNA-break-responsive ATPase. The existence of this control may explain the lateral transfer of rloC without an external silencer and supports the proposed role of RloC as an antiviral contingency acting when DNA restriction is alleviated under genotoxic stress. We also discuss RloC’s possible evolution from a PrrC-like ancestor.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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  • 7
    Publication Date: 2016-02-06
    Description: We use new near-infrared spectroscopic observations to investigate the nature and evolution of the most luminous Hα emitters at z ~ 0.8–2.23, which evolve strongly in number density over this period, and compare them to more typical Hα emitters. We study 59 luminous Hα emitters with L Hα 〉  $L_{\rm H\alpha }^{\ast }$ , roughly equally split per redshift slice at z ~ 0.8, 1.47 and 2.23 from the HiZELS and CF-HiZELS surveys. We find that, overall, 30 ± 8 per cent are active galactic nuclei [AGNs; 80 ± 30 per cent of these AGNs are broad-line AGNs, BL-AGNs], and we find little to no evolution in the AGN fraction with redshift, within the errors. However, the AGN fraction increases strongly with Hα luminosity and correlates best with L Hα / $L_{\rm H\alpha }^{\ast }(z)$ . While L Hα  ≤  $L_{\rm H\alpha }^{\ast }(z)$ Hα emitters are largely dominated by star-forming galaxies (〉80 per cent), the most luminous Hα emitters ( $L_{\rm H\alpha } 〉 10L_{\rm H\alpha }^{\ast }(z)$ ) at any cosmic time are essentially all BL-AGN. Using our AGN-decontaminated sample of luminous star-forming galaxies, and integrating down to a fixed Hα luminosity, we find a factor of ~1300 evolution in the star formation rate density from z  = 0 to 2.23. This is much stronger than the evolution from typical Hα star-forming galaxies and in line with the evolution seen for constant luminosity cuts used to select ‘ultraluminous’ infrared galaxies and/or sub-millimetre galaxies. By taking into account the evolution in the typical Hα luminosity, we show that the most strongly star-forming Hα-selected galaxies at any epoch ( $L_{\rm H\alpha } 〉 L^{\ast }_{\rm H\alpha }(z)$ ) contribute the same fractional amount of 15 per cent to the total star formation rate density, at least up to z  = 2.23.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 8
    Publication Date: 2013-10-09
    Description: Full waveform tomography (FWT) is a powerful velocity building method to exploit the full richness of seismic waveforms in complex media. Most applications today neglect the frequency-dependent amplitude decrease and phase velocity dispersion caused by intrinsic attenuation. In this study, we present a numerical investigation of the influence of attenuation on the recovered velocity model. Based on the generalized standard linear solid as rheological model, we incorporate attenuation into a 2-D time-domain acoustic FWT scheme. Attenuation is considered here as a modelling and not an inversion parameter. We investigate two reflection seismic experiments: (1) a visco-acoustic 1-D model and (2) a visco-acoustic version of the Marmousi model to which realistic quality factors are assigned. In the presence of soft rocks with pronounced absorption we observe a poor recovery of the velocity model when attenuation effects are not taken into account in the modelling. By considering an appropriate attenuation model in the forward modelling of the FWT, the accuracy of the reconstructed velocity model improves significantly in both cases. Even a homogeneous background quality factor model might allow a satisfactory recovery of the velocity model, provided that it is a quite good representation of the shallow structures. Our results suggest to consider attenuation as a smooth background modelling parameter in reflection seismic configurations to improve velocity model building by a purely acoustic inversion scheme.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 9
    Publication Date: 2012-03-20
    Description: Purpose: The PathVisio-Validator plugin aims to simplify the task of producing biological pathway diagrams that follow graphical standardized notations, such as Molecular Interaction Maps or the Systems Biology Graphical Notation. This plugin assists in the creation of pathway diagrams by ensuring correct usage of a notation, and thereby reducing ambiguity when diagrams are shared among biologists. Rulesets, needed in the validation process, can be generated for any graphical notation that a developer desires, using either Schematron or Groovy. The plugin also provides support for filtering validation results, validating on a subset of rules, and distinguishing errors and warnings. Availability: The PathVisio-Validator plugin works with versions of PathVisio 2.0.11 and later on Windows, Mac OS X and Linux. The plugin along with the instructions, example rulesets for Groovy and Schematron, and Java source code can be downloaded at http://pathvisio.org/wiki/PathVisioValidatorHelp . The software is developed under the open-source Apache 2.0 License and is freely available for both commercial and academic use. Contact: chandankmit@gmail.com ; augustin@mail.nih.gov 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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  • 10
    Publication Date: 2015-01-10
    Description: Lentiviral vectors almost universally use heterologous internal promoters to express transgenes. One of the most commonly used promoter fragments is a 1.2-kb sequence from the human ubiquitin C ( UBC ) gene, encompassing the promoter, some enhancers, first exon, first intron and a small part of the second exon of UBC . Because splicing can occur after transcription of the vector genome during vector production, we investigated whether the intron within the UBC promoter fragment is faithfully transmitted to target cells. Genetic analysis revealed that more than 80% of proviral forms lack the intron of the UBC promoter. The human elongation factor 1 alpha ( EEF1A1 ) promoter fragment intron was not lost during lentiviral packaging, and this difference between the UBC and EEF1A1 promoter introns was conferred by promoter exonic sequences. UBC promoter intron loss caused a 4-fold reduction in transgene expression. Movement of the expression cassette to the opposite strand prevented intron loss and restored full expression. This increase in expression was mostly due to non-classical enhancer activity within the intron, and movement of putative intronic enhancer sequences to multiple promoter-proximal sites actually repressed expression. Reversal of the UBC promoter also prevented intron loss and restored full expression in bidirectional lentiviral vectors.
    Keywords: Synthetic Biology and Assembly Cloning, Recombinant DNA expression
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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