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  • 1
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    The High Time Resolution Universe survey - XI. Discovery of five recycled pulsars and the optical detectability of survey white dwarf companions (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-12
    Description: We present the discovery of a further five recycled pulsar systems in the mid-Galactic latitude portion of the High Time Resolution Universe survey. The pulsars have rotational periods ranging from 2 to 66 ms, and four are in binary systems with orbital periods between 10.8 h and 9 d. Three of these binary systems are particularly interesting; PSR J1227–6208 has a pulse period of 34.5 ms and the highest mass function of all pulsars with near-circular orbits. The circular orbit suggests that the companion is not another neutron star, so future timing experiments may reveal one of the heaviest white dwarfs ever found (〉1.3 M ). Timing observations of PSR J1431–4715 indicate that it is eclipsed by its companion which has a mass indicating it belongs to the redback class of eclipsing millisecond pulsars. PSR J1653–2054 has a companion with a minimum mass of only 0.08 M , placing it among the class of pulsars with low-mass companions. Unlike the majority of such systems, however, no evidence of eclipses is seen at 1.4 GHz.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    Abundance and Distribution of Transposable Elements in Two Drosophila QTL Mapping Resources (2013)
    Oxford University Press
    Details
    Publication Date: 2013-09-16
    Description: Here we present computational machinery to efficiently and accurately identify transposable element (TE) insertions in 146 next-generation sequenced inbred strains of Drosophila melanogaster . The panel of lines we use in our study is composed of strains from a pair of genetic mapping resources: the Drosophila Genetic Reference Panel (DGRP) and the Drosophila Synthetic Population Resource (DSPR). We identified 23,087 TE insertions in these lines, of which 83.3% are found in only one line. There are marked differences in the distribution of elements over the genome, with TEs found at higher densities on the X chromosome, and in regions of low recombination. We also identified many more TEs per base pair of intronic sequence and fewer TEs per base pair of exonic sequence than expected if TEs are located at random locations in the euchromatic genome. There was substantial variation in TE load across genes. For example, the paralogs derailed and derailed-2 show a significant difference in the number of TE insertions, potentially reflecting differences in the selection acting on these loci. When considering TE families, we find a very weak effect of gene family size on TE insertions per gene, indicating that as gene family size increases the number of TE insertions in a given gene within that family also increases. TEs are known to be associated with certain phenotypes, and our data will allow investigators using the DGRP and DSPR to assess the functional role of TE insertions in complex trait variation more generally. Notably, because most TEs are very rare and often private to a single line, causative TEs resulting in phenotypic differences among individuals may typically fail to replicate across mapping panels since individual elements are unlikely to segregate in both panels. Our data suggest that "burden tests" that test for the effect of TEs as a class may be more fruitful.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Longline hook testing in the mouths of pelagic odontocetes (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-06
    Description: Several species of odontocete cetaceans depredate bait and catch and, as a result, become hooked and entangled in pelagic longline fisheries. The present study measured how selected commercial longline hooks, including "weak hooks", behaved within odontocete mouths. Five hooks (Mustad-16/0, Mustad-18/0, Mustad J-9/0, Korean 16, and Korean 18) were tested on three species of odontocetes known to interact with longline fisheries—short-finned pilot whales ( Globicephala macrorhynchus ), Risso's dolphins ( Grampus griseus ), and false killer whales ( Pseudorca crassidens ). Specimens were secured to a stanchion, hooks were placed in the mouth at multiple positions along the dorsal lip, and the force required to pull each hook free was measured. The soft tissue lips of these odontocetes were capable of resisting forces up to 250 kg before failing. The polished steel M-16, M-18, and J-9 hooks straightened at forces between 50 and 225 kg, depending on hook gauge. When straightened, these hooks exposed the sharpened barb, which sliced through the lip tissue, usually releasing the hook intact. The K-16 and K-18 hooks behaved very differently, breaking at higher forces (110–250 kg) and consistently just at the barb; usually, there was measurable soft-tissue loss and often shards of the hook were retained within those soft tissues. The different behaviours of these two hook types—the M and J type polished steel vs . the K type carbon steel—were consistent across all species tested. Mechanical tests were also conducted to determine if hooks could fracture the mandible of these same odontocetes. Only the M-18 and K-18 hooks had sufficiently large gapes to hook around the mandible, and both hook types fractured bone in short-finned pilot whales and Risso's dolphins. These results support other lines of evidence indicating that longline hooks can cause serious injury to these species, and suggest possible steps to mitigate these impacts.
    Print ISSN: 1054-3139
    Electronic ISSN: 1095-9289
    Topics: Biology , Geosciences , Physics
    Published by Oxford University Press
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  • 4
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    The Power to Detect Quantitative Trait Loci Using Resequenced, Experimentally Evolved Populations of Diploid, Sexual Organisms (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-22
    Description: A novel approach for dissecting complex traits is to experimentally evolve laboratory populations under a controlled environment shift, resequence the resulting populations, and identify single nucleotide polymorphisms (SNPs) and/or genomic regions highly diverged in allele frequency. To better understand the power and localization ability of such an evolve and resequence (E&R) approach, we carried out forward-in-time population genetics simulations of 1 Mb genomic regions under a large combination of experimental conditions, then attempted to detect significantly diverged SNPs. Our analysis indicates that the ability to detect differentiation between populations is primarily affected by selection coefficient, population size, number of replicate populations, and number of founding haplotypes. We estimate that E&R studies can detect and localize causative sites with 80% success or greater when the number of founder haplotypes is over 500, experimental populations are replicated at least 25-fold, population size is at least 1,000 diploid individuals, and the selection coefficient on the locus of interest is at least 0.1. More achievable experimental designs (less replicated, fewer founder haplotypes, smaller effective population size, and smaller selection coefficients) can have power of greater than 50% to identify a handful of SNPs of which one is likely causative. Similarly, in cases where s ≥ 0.2, less demanding experimental designs can yield high power.
    Print ISSN: 0737-4038
    Electronic ISSN: 1537-1719
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    Particle nucleation in the tropical boundary layer and its coupling to marine sulfur sources (1998)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 1998-10-02
    Description: New particle formation in a tropical marine boundary layer setting was characterized during NASA's Pacific Exploratory Mission-Tropics A program. It represents the clearest demonstration to date of aerosol nucleation and growth being linked to the natural marine sulfur cycle. This conclusion was based on real-time observations of dimethylsulfide, sulfur dioxide, sulfuric acid (gas), hydroxide, ozone, temperature, relative humidity, aerosol size and number distribution, and total aerosol surface area. Classic binary nucleation theory predicts no nucleation under the observed marine boundary layer conditions.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Clarke -- Davis -- Kapustin -- Eisele -- Chen -- Paluch I -- Lenschow -- Bandy -- Thornton -- Moore -- Mauldin -- Tanner -- Litchy -- Carroll -- Collins -- Albercook -- New York, N.Y. -- Science. 1998 Oct 2;282(5386):89-92.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉A. D. Clarke, V. N. Kapustin, K. Moore, M. Litchy, School of Ocean and Earth Science and Technology, University of Hawaii, Honolulu, HI, USA. D. Davis, F. Eisele, G. Chen, School of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atl.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/9756483" target="_blank"〉PubMed〈/a〉
    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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    A population of fast radio bursts at cosmological distances (2013)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2013-07-06
    Description: Searches for transient astrophysical sources often reveal unexpected classes of objects that are useful physical laboratories. In a recent survey for pulsars and fast transients, we have uncovered four millisecond-duration radio transients all more than 40 degrees from the Galactic plane. The bursts' properties indicate that they are of celestial rather than terrestrial origin. Host galaxy and intergalactic medium models suggest that they have cosmological redshifts of 0.5 to 1 and distances of up to 3 gigaparsecs. No temporally coincident x- or gamma-ray signature was identified in association with the bursts. Characterization of the source population and identification of host galaxies offers an opportunity to determine the baryonic content of the universe.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Thornton, D -- Stappers, B -- Bailes, M -- Barsdell, B -- Bates, S -- Bhat, N D R -- Burgay, M -- Burke-Spolaor, S -- Champion, D J -- Coster, P -- D'Amico, N -- Jameson, A -- Johnston, S -- Keith, M -- Kramer, M -- Levin, L -- Milia, S -- Ng, C -- Possenti, A -- van Straten, W -- New York, N.Y. -- Science. 2013 Jul 5;341(6141):53-6. doi: 10.1126/science.1236789.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Jodrell Bank Centre for Astrophysics, School of Physics and Astronomy, University of Manchester, Manchester, UK. thornton@jb.man.ac.uk〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/23828936" target="_blank"〉PubMed〈/a〉
    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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    Efficient Software for Multi-marker, Region-Based Analysis of GWAS Data (2016)
    Genetics Society of America (GSA)
    Details
    Publication Date: 2016-04-08
    Description: Genome-wide association studies (GWAS) have associated many single variants with complex disease, yet the better part of heritable complex disease risk remains unexplained. Analytical tools designed to work under specific population genetic models are needed. Rare variants are increasingly shown to be important in human complex disease, but most existing GWAS data do not cover rare variants. Explicit population genetic models predict that genes contributing to complex traits and experiencing recurrent, unconditionally deleterious, mutation will harbor multiple rare, causative mutations of subtle effect. It is difficult to identify genes harboring rare variants of large effect that contribute to complex disease risk via the single marker association tests typically used in GWAS. Gene/region-based association tests may have the power detect associations by combining information from multiple markers, but have yielded limited success in practice. This is partially because many methods have not been widely applied. Here, we empirically demonstrate the utility of a procedure based on the rank truncated product (RTP) method, filtered to reduce the effects of linkage disequilibrium. We apply the procedure to the Wellcome Trust Case Control Consortium (WTCCC) data set, and uncover previously unidentified associations, some of which have been replicated in much larger studies. We show that, in the absence of significant rare variant coverage, RTP based methods still have the power to detect associated genes. We recommend that RTP-based methods be applied to all existing GWAS data to maximize the usefulness of those data. For this, we provide efficient software implementing our procedure.
    Electronic ISSN: 2160-1836
    Topics: Biology
    Published by Genetics Society of America (GSA)
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  • 8
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    The Atacama Cosmology Telescope: dusty star-forming galaxies and active galactic nuclei in the Southern survey (2014)
    Oxford University Press
    Details
    Publication Date: 2014-03-09
    Description: We present a catalogue of 191 extragalactic sources detected by the Atacama Cosmology Telescope (ACT) at 148 and/or 218 GHz in the 2008 Southern survey. Flux densities span 14 –1700 mJy, and we use source spectral indices derived using ACT-only data to divide our sources into two subpopulations: 167 radio galaxies powered by central active galactic nuclei (AGN) and 24 dusty star-forming galaxies (DSFGs). We cross-identify 97 per cent of our sources (166 of the AGN and 19 of the DSFGs) with those in currently available catalogues. When combined with flux densities from the Australia Telescope 20 GHz survey and follow-up observations with the Australia Telescope Compact Array, the synchrotron-dominated population is seen to exhibit a steepening of the slope of the spectral energy distribution from 20 to 148 GHz, with the trend continuing to 218 GHz. The ACT dust-dominated source population has a median spectral index, α 148–218 , of 3.7 $^{+0.62}_{-0.86}$ , and includes both local galaxies and sources with redshift around 6. Dusty sources with no counterpart in existing catalogues likely belong to a recently discovered subpopulation of DSFGs lensed by foreground galaxies or galaxy groups.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Synthesis of a Family of Spirocyclic Scaffolds: Building Blocks for the Exploration of Chemical Space (2013)
    American Chemical Society (ACS)
    Details
    Publication Date: 2013-06-27
    Description: The Journal of Organic Chemistry DOI: 10.1021/jo400738b
    Print ISSN: 0022-3263
    Electronic ISSN: 1520-6904
    Topics: Chemistry and Pharmacology
    Published by American Chemical Society (ACS)
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  • 10
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    3D visualization of additive occlusion and tunable full-spectrum fluorescence in calcite (2016)
    Springer Nature
    Details
    Publication Date: 2016-11-19
    Description: 3D visualization of additive occlusion and tunable full-spectrum fluorescence in calcite Nature Communications, Published online: 18 November 2016; doi:10.1038/ncomms13524 Introducing organic guests to a crystal is a convenient way to tailor its properties. Here, the authors occlude fluorescent dyes within calcite to reveal that additives can occupy distinct zones of a crystal, and strategically embed green, blue, and red dyes to create white fluorescent calcite.
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
    Published by Springer Nature
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