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  • Wiley  (12)
  • Oxford University Press  (8)
  • 2010-2014  (20)
  • 1945-1949
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  • 2014  (20)
  • 1
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    Active Faults and Nuclear Power Plants (2014)
    Wiley
    Details
    Publication Date: 2014-01-29
    Description: The destruction of the Fukushima Daiichi Nuclear Power Plant (NPP) following the March 2011 Tohoku earthquake and tsunami brought into sharp focus the susceptibility of NPPs to natural hazards. This is not a new issue—seismic hazard has affected the development of plants in the United States, and volcanic hazard was among the reasons for not commissioning the Bataan NPP in the Philippines [ Connor et al ., 2009].
    Print ISSN: 0096-3941
    Electronic ISSN: 2324-9250
    Topics: Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 2
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    On the Relevance of Two-Dimensional Models for Radiation of Statistical Sources in Stratified Media (2014)
    Wiley
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    Publication Date: 2014-10-09
    Description: We present analytical closed-form expressions for the radiation patterns of 2D line sources and 3D point dipoles embedded in a general multi-layered configuration. While the former are simplified model sources, used as a preliminary analytical step toreduce derivation complexity, the latter have been shown experimentally to reproduce the electromagnetic behaviour of many elementary statistical sources. By decomposing the sources to current elements generating pure transverse electric (TE) or transverse magnetic (TM) polarized radiation, we arrive at a unified format for the radiation pattern expression for all sources considered. Analyzing the common 1D (characteristic) Green's function, we show that the normalized TE-polarized emission of model 2D electric line sources reproduces exactly the measured TE-polarized radiation of statistical (3D) dipoles with random in-plane orientation; the connection between the TM-polarized emission of the two species is discussed, and physical interpretation is provided via the unified expression. These results specify the precise relations between the 2D and 3D models, providing intuition as well as guidelines for proper usage of simplified 2D results for analysis of realistic 3D statistical configurations.
    Print ISSN: 0048-6604
    Electronic ISSN: 1944-799X
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
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    Bayesian distances and extinctions for giants observed by Kepler and APOGEE (2014)
    Oxford University Press
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    Publication Date: 2014-10-22
    Description: We present a first determination of distances and extinctions for individual stars in the first release of the APOKASC catalogue, built from the joint efforts of the Apache Point Observatory Galactic Evolution Experiment ( APOGEE ) and the Kepler Asteroseismic Science Consortium (KASC). Our method takes into account the spectroscopic constraints derived from the APOGEE Stellar Parameters and Chemical Abundances Pipeline, together with the asteroseismic parameters from KASC. These parameters are then employed to estimate intrinsic stellar properties, including absolute magnitudes, using the Bayesian tool param . We then find the distance and extinction that best fit the observed photometry in Sloan Digital Sky Survey (SDSS), 2MASS, and WISE passbands. The first 1989 giants targetted by APOKASC are found at typical distances between 0.5 and 5 kpc, with individual uncertainties of just ~1.8 per cent. Our extinction estimates are systematically smaller than provided in the Kepler Input Catalogue and by the Schlegel et al. maps. Distances to individual stars in the NGC 6791 and NGC 6819 star clusters agree to within their credible intervals. Comparison with the APOGEE red clump and SAGA catalogues provide another useful check, exhibiting agreement with our measurements to within a few per cent. Overall, present methods seem to provide excellent distance and extinction determinations for the bulk of the APOKASC sample. Approximately one third of the stars present broad or multiple-peaked probability density functions and hence increased uncertainties. Uncertainties are expected to be reduced in future releases of the catalogue, when a larger fraction of the stars will have seismically determined evolutionary status classifications.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    Pediatric Brain Tumor Cell Lines (2014)
    Wiley
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    Publication Date: 2014-09-13
    Description: Pediatric brain tumors as a group, including medulloblastomas, gliomas and atypical teratoid rhabdoid tumors (ATRT) are the most common solid tumors in children and the leading cause of death from childhood cancer. Brain tumor-derived cell lines are critical for studying the biology of pediatric brain tumors and can be useful for initial screening of new therapies. Use of the appropriate brain tumor cell line for experiments is important, as results may differ depending on tumor properties, and can thus affect the conclusions and applicability as a model. Despite reports in the literature of over 60 pediatric brain tumor cell lines, the majority of published papers utilize only a small number of these cell lines. Here we list the approximately 60 currently-published pediatric brain tumor cell lines and summarize some of their central features as a resource for scientists seeking pediatric brain tumor cell lines for their research. J. Cell. Biochem. © 2014 Wiley Periodicals, Inc.
    Electronic ISSN: 0091-7419
    Topics: Biology , Chemistry and Pharmacology , Medicine
    Published by Wiley
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  • 5
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    Selection on Horizontally Transferred and Duplicated Genes in Sinorhizobium (Ensifer), the Root-Nodule Symbionts of Medicago (2014)
    Oxford University Press
    Details
    Publication Date: 2014-05-25
    Description: Structural variation, including variation in gene copy number and presence or absence of genes, is a widespread and important source of genomic variation. We used whole-genome DNA sequences from 48 strains of Sinorhizobium (recently renamed Ensifer ), including 20 strains of Sinorhizobium meliloti and 12 strains of S. medicae that were the focus of the analyses, to study the fitness effects of new structural variants created by duplication and horizontal gene transfer. We find that derived duplicated and horizontally transferred (HT) genes segregate at lower frequency than synonymous and nonsynonymous nucleotide variants in S. meliloti and S. medicae . Furthermore, the relative frequencies of different types of variants are more similar in S. medicae than in S. meliloti , the species with the larger effective population size . These results are consistent with the hypothesis that most duplications and HT genes have deleterious effects. Diversity of duplications, as measured by segregating duplicated genes per gene, is greater than nucleotide diversity, consistent with a high rate of duplication. Our results suggest that the vast majority of structural variants found among closely related bacterial strains are short-lived and unlikely to be involved in species-wide adaptation.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    Impact of sequencing depth in ChIP-seq experiments (2014)
    Oxford University Press
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    Publication Date: 2014-05-20
    Description: In a chromatin immunoprecipitation followed by high-throughput sequencing (ChIP-seq) experiment, an important consideration in experimental design is the minimum number of sequenced reads required to obtain statistically significant results. We present an extensive evaluation of the impact of sequencing depth on identification of enriched regions for key histone modifications (H3K4me3, H3K36me3, H3K27me3 and H3K9me2/me3) using deep-sequenced datasets in human and fly. We propose to define sufficient sequencing depth as the number of reads at which detected enrichment regions increase 〈1% for an additional million reads. Although the required depth depends on the nature of the mark and the state of the cell in each experiment, we observe that sufficient depth is often reached at 〈20 million reads for fly. For human, there are no clear saturation points for the examined datasets, but our analysis suggests 40–50 million reads as a practical minimum for most marks. We also devise a mathematical model to estimate the sufficient depth and total genomic coverage of a mark. Lastly, we find that the five algorithms tested do not agree well for broad enrichment profiles, especially at lower depths. Our findings suggest that sufficient sequencing depth and an appropriate peak-calling algorithm are essential for ensuring robustness of conclusions derived from ChIP-seq data.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Physical Properties of Ambient and Laboratory Generated Secondary Organic Aerosol (2014)
    Wiley
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    Publication Date: 2014-06-03
    Description: The size and thickness of organic aerosol particles collected by impaction in five field campaigns were compared to those of laboratory generated secondary organic aerosols (SOA). Scanning transmission x-ray microscopy (STXM) was used to measure the total carbon absorbance (TCA) by individual particles as a function of their projection areas on the substrate. Particles with higher viscosity/surface tension can be identified by a steeper slope on a plot of TCA vs. size because they flatten less upon impaction. The slopes of the ambient data are statistically similar indicating a small range of average viscosities/surface tensions across five field campaigns. Steeper slopes were observed for the plots corresponding to ambient particles, while smaller slopes were indicative of the laboratory generated SOA. This comparison indicates that ambient organic particles have higher viscosities/surface tensions than those typically generated in laboratory SOA studies.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 8
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    DiSWOP: a novel measure for cell-level protein network analysis in localized proteomics image data (2014)
    Oxford University Press
    Details
    Publication Date: 2014-01-29
    Description: Motivation : New bioimaging techniques have recently been proposed to visualize the colocation or interaction of several proteins within individual cells, displaying the heterogeneity of neighbouring cells within the same tissue specimen. Such techniques could hold the key to understanding complex biological systems such as the protein interactions involved in cancer. However, there is a need for new algorithmic approaches that analyze the large amounts of multi-tag bioimage data from cancerous and normal tissue specimens to begin to infer protein networks and unravel the cellular heterogeneity at a molecular level. Results : The proposed approach analyzes cell phenotypes in normal and cancerous colon tissue imaged using the robotically controlled Toponome Imaging System microscope. It involves segmenting the 4',6-diamidino-2-phenylindole-labelled image into cells and determining the cell phenotypes according to their protein–protein dependence profile. These were analyzed using two new measures, Difference in Sums of Weighted cO-dependence/Anti-co-dependence profiles (DiSWOP and DiSWAP) for overall co-expression and anti-co-expression, respectively. These novel quantities were extracted using 11 Toponome Imaging System image stacks from either cancerous or normal human colorectal specimens. This approach enables one to easily identify protein pairs that have significantly higher/lower co-expression levels in cancerous tissue samples when compared with normal colon tissue. Availability and implementation: http://www2.warwick.ac.uk/fac/sci/dcs/research/combi/research/bic/diswop . Contact: v.n.kovacheva@warwick.ac.uk or Nasir.Rajpoot@ieee.org 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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  • 9
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    UNDERSTANDING PROTECTED AREA RESILIENCE: A MULTI-SCALE, SOCIAL-ECOLOGICAL APPROACH (2014)
    Wiley
    Details
    Publication Date: 2014-09-09
    Description: Protected Areas (PAs) remain central to the conservation of biodiversity. PAs were originally conceived as areas that would be set aside to maintain a natural state free from human influence. However, global environmental change, growing anthropogenic influence, and increasing globalisation of society have made it clear that PAs can no longer be thought of as 'ecological islands' that function independently of the broader social-ecological system in which they are located. For PAs to be resilient (and to contribute to broader social-ecological resilience) they must be able to adapt to changing social and ecological conditions over time in a way that supports the long-term persistence of populations, communities, and ecosystems of conservation concern. We propose a framework for understanding PAs and their long-term persistence, as a form of land-use embedded in social-ecological systems, with feedbacks from the local to the global scale. We develop approaches to thinking of PAs as multi-scale social-ecological systems in three ways. First, we combine elements of resilience analysis and the closely related social-ecological systems framework of Ostrom to develop a new conceptual outline for thinking about PA resilience. Second, we highlight the cross-scale influences and feedbacks on PAs that exist from the local to the global scale, contextualizing PAs within multi-scale social-ecological 'functional landscapes'. Such functional landscapes are integral to understanding and managing the long-term sustainability of individual PAs. Third, we illustrate our conceptual contribution with three case studies that highlight cross-scale feedbacks and social-ecological interactions in the functioning of PAs and in relation to regional resilience. Our analysis suggests that while ecological, economic and social processes are often directly relevant to PAs at finer scales, at broader scales the dominant processes that shape and alter PA resilience are primarily social and economic. # doi:10.1890/13-2113.1
    Print ISSN: 1051-0761
    Electronic ISSN: 1939-5582
    Topics: Biology
    Published by Wiley on behalf of The Ecological Society of America (ESA).
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  • 10
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    Selection on Horizontally Transferred and Duplicated Genes in Sinorhizobium (Ensifer), the Root-Nodule Symbionts of Medicago (2014)
    Oxford University Press
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    Publication Date: 2014-05-01
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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