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  • 1
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    500 days of SN 2013dy: spectra and photometry from the ultraviolet to the infrared (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-14
    Description: SN 2013dy is a Type Ia supernova (SN Ia) for which we have compiled an extraordinary data set spanning from 0.1 to ~ 500 d after explosion. We present 10 epochs of ultraviolet (UV) through near-infrared (NIR) spectra with Hubble Space Telescope /Space Telescope Imaging Spectrograph, 47 epochs of optical spectra (15 of them having high resolution), and more than 500 photometric observations in the BVrRiIZYJH bands. SN 2013dy has a broad and slowly declining light curve ( m 15 ( B ) = 0.92 mag), shallow $\mathrm{Si}\,\small {II}\,\lambda 6355$ absorption, and a low velocity gradient. We detect strong C ii in our earliest spectra, probing unburned progenitor material in the outermost layers of the SN ejecta, but this feature fades within a few days. The UV continuum of SN 2013dy, which is strongly affected by the metal abundance of the progenitor star, suggests that SN 2013dy had a relatively high-metallicity progenitor. Examining one of the largest single set of high-resolution spectra for an SN Ia, we find no evidence of variable absorption from circumstellar material. Combining our UV spectra, NIR photometry, and high-cadence optical photometry, we construct a bolometric light curve, showing that SN 2013dy had a maximum luminosity of $10.0^{+4.8}_{-3.8} \times 10^{42}$  erg s –1 . We compare the synthetic light curves and spectra of several models to SN 2013dy, finding that SN 2013dy is in good agreement with a solar-metallicity W7 model.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    Spectropolarimetry of the Type IIb SN 2008aq (2016)
    Oxford University Press
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    Publication Date: 2016-07-13
    Description: We present optical spectroscopy and spectropolarimetry of the Type IIb SN 2008aq 16-d and 27-d post-explosion. The spectrum of SN 2008aq remained dominated by Hα P Cygni profile at both epochs, but showed a significant increase in the strength of the helium features, which is characteristic of the transition undergone by supernovae between Type IIb and Type Ib. Comparison of the spectra of SN 2008aq to other Type IIb SNe (SN 1993J, SN 2011dh, and SN 2008ax) at similar epochs revealed that the helium lines in SN 2008aq are much weaker, suggesting that its progenitor was stripped to a lesser degree. SN 2008aq also showed significant levels of continuum polarization at p cont = 0.70 (±0.22) per cent in the first epoch, increasing to p cont = 1.21 (±0.33) per cent by the second epoch. Moreover, the presence of loops in the q – u planes of Hα and He i in the second epoch suggests a departure from axial symmetry.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    Genetic and epigenetic variants contributing to clofarabine cytotoxicity (2013)
    Oxford University Press
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    Publication Date: 2013-09-08
    Description: 2-chloro-2-fluoro-deoxy-9-D-arabinofuranosyladenine (Clofarabine), a purine nucleoside analog, is used in the treatment of hematologic malignancies and as induction therapy for stem cell transplantation. The discovery of pharmacogenomic markers associated with chemotherapeutic efficacy and toxicity would greatly benefit the utility of this drug. Our objective was to identify genetic and epigenetic variants associated with clofarabine toxicity using an unbiased, whole genome approach. To this end, we employed International HapMap lymphoblastoid cell lines (190 LCLs) of European (CEU) or African (YRI) ancestry with known genetic information to evaluate cellular sensitivity to clofarabine. We measured modified cytosine levels to ascertain the contribution of genetic and epigenetic factors influencing clofarabine-mediated cytotoxicity. Association studies revealed 182 single nucleotide polymorphisms (SNPs) and 143 modified cytosines associated with cytotoxicity in both populations at the threshold P ≤ 0.0001. Correlation between cytotoxicity and baseline gene expression revealed 234 genes at P ≤ 3.98 x 10 –6 . Six genes were implicated as: (i) their expression was directly correlated to cytotoxicity, (ii) they had a targeting SNP associated with cytotoxicity, and (iii) they had local modified cytosines associated with gene expression and cytotoxicity. We identified a set of three SNPs and three CpG sites targeting these six genes explaining 43.1% of the observed variation in phenotype. siRNA knockdown of the top three genes ( SETBP1, BAG3, KLHL6 ) in LCLs revealed altered susceptibility to clofarabine, confirming relevance. As clofarabine's toxicity profile includes acute kidney injury, we examined the effect of siRNA knockdown in HEK293 cells. siSETBP1 led to a significant change in HEK293 cell susceptibility to clofarabine.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 4
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    nhmmer: DNA homology search with profile HMMs (2013)
    Oxford University Press
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    Publication Date: 2013-09-20
    Description: : Sequence database searches are an essential part of molecular biology, providing information about the function and evolutionary history of proteins, RNA molecules and DNA sequence elements. We present a tool for DNA/DNA sequence comparison that is built on the HMMER framework, which applies probabilistic inference methods based on hidden Markov models to the problem of homology search. This tool, called nhmmer, enables improved detection of remote DNA homologs, and has been used in combination with Dfam and RepeatMasker to improve annotation of transposable elements in the human genome. Availability: nhmmer is a part of the new HMMER3.1 release. Source code and documentation can be downloaded from http://hmmer.org . HMMER3.1 is freely licensed under the GNU GPLv3 and should be portable to any POSIX-compliant operating system, including Linux and Mac OS/X. Contact: wheelert@janelia.hhmi.org
    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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    Farmers' exposure to risk and their temporary water trading (2015)
    Oxford University Press
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    Publication Date: 2015-02-06
    Description: In this article, the role of water markets in helping farmers manage the risk of water shortage is studied. Using farm survey data from Australia's southern Murray–Darling Basin, one of the most active water markets in the world, we tested the relationship between farmers' exposure to risk and their decisions to purchase and sell water allocations (temporary water) on the market. Farmers experiencing higher variability in profit and facing more downside risk purchased greater volumes of water allocations in general. Purchasing water allocations on the market is found to be a risk-reducing strategy, in particular for farmers in the horticultural sector. There is only very weak evidence to support the notion that selling water allocations is associated with reduced risk exposure.
    Print ISSN: 0165-1587
    Electronic ISSN: 1464-3618
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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  • 6
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    The Dfam database of repetitive DNA families (2016)
    Oxford University Press
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    Publication Date: 2016-01-07
    Description: Repetitive DNA, especially that due to transposable elements (TEs), makes up a large fraction of many genomes. Dfam is an open access database of families of repetitive DNA elements, in which each family is represented by a multiple sequence alignment and a profile hidden Markov model (HMM). The initial release of Dfam, featured in the 2013 NAR Database Issue, contained 1143 families of repetitive elements found in humans, and was used to produce more than 100 Mb of additional annotation of TE-derived regions in the human genome, with improved speed. Here, we describe recent advances, most notably expansion to 4150 total families including a comprehensive set of known repeat families from four new organisms (mouse, zebrafish, fly and nematode). We describe improvements to coverage, and to our methods for identifying and reducing false annotation. We also describe updates to the website interface. The Dfam website has moved to http://dfam.org . Seed alignments, profile HMMs, hit lists and other underlying data are available for download.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Measuring Price Elasticities of Demand and Supply of Water Entitlements Based on Stated and Revealed Preference Data (2015)
    Oxford University Press
    Details
    Publication Date: 2015-12-13
    Description: Estimates of price elasticities of water entitlements (known as permanent water or water rights in the United States) are complicated by data limitations and problems of endogeneity. To overcome these issues, we develop an approach to generate stated preference data and combine them with revealed preference data to estimate price elasticities from various types of water entitlement sales in the southern Murray-Darling Basin, Australia. Our results suggest that price elasticities of demand and supply of high security water entitlements are inelastic in the relevant market price range between AUD ${{\$}}$ 1,700 to ${{\$}}$ 2,100 per mega-liter, and that supply is relatively more inelastic than demand. For lower reliability water entitlements, the price elasticity of demand is estimated to be even more inelastic than high security water entitlements. The price elasticity of supply for general security water entitlements is similar to high security water entitlements, while the supply of low reliability water entitlements is extremely inelastic for our data set. The comparison between the stated and revealed preference data provides strong evidence of support for a data fusion approach; nevertheless, some differences in water sale preferences were found for irrigators choosing not to sell all of their water. The consistency of our results signals support for the use of this methodology in other water basins around the world.
    Keywords: Q21 - Demand and Supply, Q25 - Water
    Print ISSN: 0002-9092
    Electronic ISSN: 1467-8276
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition , Economics
    Published by Oxford University Press
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  • 8
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    The early phases of the Type Iax supernova SN 2011ay (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-30
    Description: We present a detailed study of the early phases of the peculiar supernova (SN) 2011ay based on BVRI photometry obtained at Konkoly Observatory, Hungary, and optical spectra taken with the Hobby–Eberly Telescope at McDonald Observatory, Texas. The spectral analysis carried out with syn++ and synapps confirms that SN 2011ay belongs to the recently defined class of SNe Iax, which is also supported by the properties of its light and colour curves. The estimated photospheric temperature around maximum light, T phot  ~ 8000 K, is lower than in most SNe Ia, which results in the appearance of strong Fe ii features in the spectra of SN 2011ay, even during the early phases. We also show that strong blending with metal features (those of Ti ii , Fe ii , Co ii ) makes the direct analysis of the broad spectral features very difficult, and this may be true for all SNe Iax. We find two alternative spectrum models that both describe the observed spectra adequately, but their photospheric velocities differ by at least ~3000 km s –1 . The quasi-bolometric light curve of SN 2011ay has been assembled by integrating the ultraviolet–optical spectral energy distributions. Fitting a modified Arnett model to L bol ( t ), the moment of explosion and other physical parameters, i.e. the rise time to maximum, the 56 Ni mass and the total ejecta mass are estimated as t rise  ~ 14 ± 1 d, M Ni  ~ 0.22 ± 0.01 M and M ej  ~ 0.8 M , respectively.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Genetic variants and cellular stressors associated with exfoliation syndrome modulate promoter activity of a lncRNA within the LOXL1 locus (2015)
    Oxford University Press
    Details
    Publication Date: 2015-10-23
    Description: Exfoliation syndrome (XFS) is a common, age-related, systemic fibrillinopathy. It greatly increases risk of exfoliation glaucoma (XFG), a major worldwide cause of irreversible blindness. Coding variants in the lysyl oxidase-like 1 ( LOXL1 ) gene are strongly associated with XFS in all studied populations, but a functional role for these variants has not been established. To identify additional candidate functional variants, we sequenced the entire LOXL1 genomic locus (~40 kb) in 50 indigenous, black South African XFS cases and 50 matched controls. The variants with the strongest evidence of association were located in a well-defined 7-kb region bounded by the 3'-end of exon 1 and the adjacent region of intron 1 of LOXL1 . We replicated this finding in US Caucasian (91 cases/1031 controls), German (771 cases/1365 controls) and Japanese (1484 cases/1188 controls) populations. The region of peak association lies upstream of LOXL1-AS1 , a long non-coding RNA (lncRNA) encoded on the opposite strand of LOXL1 . We show that this region contains a promoter and, importantly, that the strongly associated XFS risk alleles in the South African population are functional variants that significantly modulate the activity of this promoter. LOXL1-AS1 expression is also significantly altered in response to oxidative stress in human lens epithelial cells and in response to cyclic mechanical stress in human Schlemm's canal endothelial cells. Taken together, these findings support a functional role for the LOXL1-AS1 lncRNA in cellular stress response and suggest that dysregulation of its expression by genetic risk variants plays a key role in XFS pathogenesis.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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    Taking care of business in a flash : constraining the time-scale for low-mass satellite quenching with ELVIS (2015)
    Oxford University Press
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    Publication Date: 2015-10-15
    Description: The vast majority of dwarf satellites orbiting the Milky Way and M31 are quenched, while comparable galaxies in the field are gas rich and star forming. Assuming that this dichotomy is driven by environmental quenching, we use the Exploring the Local Volume in Simulations (ELVIS) suite of N -body simulations to constrain the characteristic time-scale upon which satellites must quench following infall into the virial volumes of their hosts. The high satellite quenched fraction observed in the Local Group demands an extremely short quenching time-scale (~2 Gyr) for dwarf satellites in the mass range M * ~ 10 6 –10 8 M . This quenching time-scale is significantly shorter than that required to explain the quenched fraction of more massive satellites (~8 Gyr), both in the Local Group and in more massive host haloes, suggesting a dramatic change in the dominant satellite quenching mechanism at M * 10 8 M . Combining our work with the results of complementary analyses in the literature, we conclude that the suppression of star formation in massive satellites ( M * ~ 10 8 –10 11 M ) is broadly consistent with being driven by starvation, such that the satellite quenching time-scale corresponds to the cold gas depletion time. Below a critical stellar mass scale of ~10 8 M , however, the required quenching times are much shorter than the expected cold gas depletion times. Instead, quenching must act on a time-scale comparable to the dynamical time of the host halo. We posit that ram-pressure stripping can naturally explain this behaviour, with the critical mass (of M * ~ 10 8 M ) corresponding to haloes with gravitational restoring forces that are too weak to overcome the drag force encountered when moving through an extended, hot circumgalactic medium.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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