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  • Oxford University Press  (240)
  • 2015-2019  (141)
  • 1990-1994  (40)
  • 1985-1989  (37)
  • 1965-1969  (20)
  • 1935-1939  (2)
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  • 1
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    A modified S-DIMM+: applying additional height grids for characterizing daytime seeing profiles (2018)
    Oxford University Press
    Details
    Publication Date: 2018-06-15
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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  • 2
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    Deep crustal seismic reflection images from the Dharwar craton, Southern India—evidence for the Neoarchean subduction (2017)
    Oxford University Press
    Details
    Publication Date: 2017-10-09
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Royal Astronomical Society.
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  • 3
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    Ca II absorbers in the Sloan Digital Sky Survey: element abundances and dust (2015)
    Oxford University Press
    Details
    Publication Date: 2015-08-02
    Description: We present measurements of element abundance ratios and dust in Ca ii absorbers identified in Sloan Digital Sky Survey DR7+DR9. In an earlier paper we formed a statistical sample of 435 Ca ii absorbers and postulated that their statistical properties might be representative of at least two populations of absorbers. Here, we show that if the absorbers are roughly divided into two subsamples with Ca ii rest equivalent widths larger and smaller than $W_0^{\lambda 3934} = 0.7$ Å, they are then representative of two physically different populations. Comparisons of abundance ratios between the two Ca ii absorber populations indicate that the weaker $W_0^{\lambda 3934}$ absorbers have properties consistent with halo-type gas, while the stronger absorbers have properties intermediate between halo- and disc-type gas. We also show that, on average, the dust-extinction properties of the overall sample is consistent with a Large Magellanic Cloud or Small Magellanic Cloud dust law, and the stronger absorbers are nearly six times more reddened than their weaker counterparts. The absorbed-to-unabsorbed composite flux ratio at rest  = 2200 Å is $\mathcal {R} \approx 0.73$ and E ( B – V )  0.046 for the stronger Ca ii absorbers ( $W_0^{\lambda 3934} \ge 0.7$ Å), and $\mathcal {R} \approx 0.95$ and E ( B – V )  0.011 for the weaker Ca ii absorbers ( $W_0^{\lambda 3934} 〈 0.7$ Å).
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 4
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    QVZ: lossy compression of quality values (2015)
    Oxford University Press
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    Publication Date: 2015-09-22
    Description: Motivation: Recent advancements in sequencing technology have led to a drastic reduction in the cost of sequencing a genome. This has generated an unprecedented amount of genomic data that must be stored, processed and transmitted. To facilitate this effort, we propose a new lossy compressor for the quality values presented in genomic data files (e.g. FASTQ and SAM files), which comprise roughly half of the storage space (in the uncompressed domain). Lossy compression allows for compression of data beyond its lossless limit. Results: The proposed algorithm QVZ exhibits better rate-distortion performance than the previously proposed algorithms, for several distortion metrics and for the lossless case. Moreover, it allows the user to define any quasi-convex distortion function to be minimized, a feature not supported by the previous algorithms. Finally, we show that QVZ-compressed data exhibit better performance in the genotyping than data compressed with previously proposed algorithms, in the sense that for a similar rate, a genotyping closer to that achieved with the original quality values is obtained. Availability and implementation: QVZ is written in C and can be downloaded from https://github.com/mikelhernaez/qvz . Contact: mhernaez@stanford.edu or gmalysa@stanford.edu or iochoa@stanford.edu 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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  • 5
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    Unveiling Vela - time variability of Na I D lines in the direction of the Vela supernova remnant (2015)
    Oxford University Press
    Details
    Publication Date: 2015-11-25
    Description: High-resolution spectral profiles of Na i D lines from the interstellar medium towards 64 stars in the direction of the Vela supernova remnant are presented. This survey conducted mostly between 2011 and 12 complements an earlier survey of the same stars by Cha & Sembach done in the 1993–96 period. The interval of 15–18 yr provides a base line to search for changes in the interstellar profiles. Dramatic disappearance of strong absorption components at low radial velocity is seen towards three stars – HD 63578, HD 68217, HD 76161 – over 15–18 yr; HD 68217 and HD 76161 are associated with the Vela SNR but HD 63578 is likely associated with the wind bubble of 2 Velorum. The vanishing of these cold neutral clouds in the short time of 15–18 yr needs some explanation. Other changes are seen in high-velocity Na D components.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Specificity of the ModA11, ModA12 and ModD1 epigenetic regulator N6-adenine DNA methyltransferases of Neisseria meningitidis (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-03
    Description: Phase variation (random ON/OFF switching) of gene expression is a common feature of host-adapted pathogenic bacteria. Phase variably expressed N 6 -adenine DNA methyltransferases (Mod) alter global methylation patterns resulting in changes in gene expression. These systems constitute phase variable regulons called phasevarions. Neisseria meningitidis phasevarions regulate genes including virulence factors and vaccine candidates, and alter phenotypes including antibiotic resistance. The target site recognized by these Type III N 6 -adenine DNA methyltransferases is not known. Single molecule, real-time (SMRT) methylome analysis was used to identify the recognition site for three key N. meningitidis methyltransferases: ModA11 (exemplified by M.NmeMC58I) (5'-CGY m6 A G-3'), ModA12 (exemplified by M.Nme77I, M.Nme18I and M.Nme579II) (5'-AC m6 A CC-3') and ModD1 (exemplified by M.Nme579I) (5'-CC m6 A GC-3'). Restriction inhibition assays and mutagenesis confirmed the SMRT methylome analysis. The ModA11 site is complex and atypical and is dependent on the type of pyrimidine at the central position, in combination with the bases flanking the core recognition sequence 5'-CGY m6 A G-3'. The observed efficiency of methylation in the modA11 strain (MC58) genome ranged from 4.6% at 5'-GCGC m6 A GG-3' sites, to 100% at 5'-ACGT m6 A GG-3' sites. Analysis of the distribution of modified sites in the respective genomes shows many cases of association with intergenic regions of genes with altered expression due to phasevarion switching.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 7
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    Two Host Clades, Two Bacterial Arsenals: Evolution through Gene Losses in Facultative Endosymbionts (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-30
    Description: Bacterial endosymbiosis is an important evolutionary process in insects, which can harbor both obligate and facultative symbionts. The evolution of these symbionts is driven by evolutionary convergence, and they exhibit among the tiniest genomes in prokaryotes. The large host spectrum of facultative symbionts and the high diversity of strategies they use to infect new hosts probably impact the evolution of their genome and explain why they undergo less severe genomic erosion than obligate symbionts. Candidatus Hamiltonella defensa is suitable for the investigation of the genomic evolution of facultative symbionts because the bacteria are engaged in specific relationships in two clades of insects. In aphids, H. defensa is found in several species with an intermediate prevalence and confers protection against parasitoids. In whiteflies, H. defensa is almost fixed in some species of Bemisia tabaci , which suggests an important role of and a transition toward obligate symbiosis. In this study, comparisons of the genome of H. defensa present in two B. tabaci species (Middle East Asia Minor 1 and Mediterranean) and in the aphid Acyrthosiphon pisum revealed that they belong to two distinct clades and underwent specific gene losses. In aphids, it contains highly virulent factors that could allow protection and horizontal transfers. In whiteflies, the genome lost these factors and seems to have a limited ability to acquire genes. However it contains genes that could be involved in the production of essential nutrients, which is consistent with a primordial role for this symbiont. In conclusion, although both lineages of H. defensa have mutualistic interactions with their hosts, their genomes follow distinct evolutionary trajectories that reflect their phenotype and could have important consequences on their evolvability.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    The ESO UVES advanced data products quasar sample - VI. Sub-damped Lyman {alpha} metallicity measurements and the circumgalactic medium (2016)
    Oxford University Press
    Details
    Publication Date: 2016-04-10
    Description: The circumgalactic medium (CGM) can be probed through the analysis of absorbing systems in the line of sight to bright background quasars. We present measurements of the metallicity of a new sample of 15 sub-damped Lyman α absorbers (sub-DLAs, defined as absorbers with 19.0 〈 log N(H I) 〈 20.3) with redshift 0.584 ≤ z abs ≤ 3.104 from the ESO Ultra-Violet Echelle Spectrograph (UVES) Advanced Data Products Quasar Sample (EUADP). We combine these results with other measurements from the literature to produce a compilation of metallicity measurements for 92 sub-DLAs as well as a sample of 362 DLAs. We apply a multi-element analysis to quantify the amount of dust in these two classes of systems. We find that either the element depletion patterns in these systems differ from the Galactic depletion patterns or they have a different nucleosynthetic history than our own Galaxy. We propose a new method to derive the velocity width of absorption profiles, using the modelled Voigt profile features. The correlation between the velocity width V 90 of the absorption profile and the metallicity is found to be tighter for DLAs than for sub-DLAs. We report hints of a bimodal distribution in the [Fe/H] metallicity of low redshift ( z 〈 1.25) sub-DLAs, which is unseen at higher redshifts. This feature can be interpreted as a signature from the metal-poor, accreting gas and the metal-rich, outflowing gas, both being traced by sub-DLAs at low redshifts.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Following Up on Smallholder Farmers and Supermarkets in Kenya (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-10
    Description: In many developing countries, supermarkets are expanding rapidly. This affects farmers’ marketing options. Previous studies have analyzed welfare effects of smallholder participation in supermarket channels from a static perspective, using cross-section data. We develop a conceptual framework and use panel data to better understand participation and impact dynamics. The analysis focuses on vegetable producers in Kenya. Participation in supermarket channels is associated with income gains. However, many farmers have dropped out of the supermarket channel due to various constraints. The initial income gains cannot be sustained when returning to the traditional market. Organizational support may be needed to avoid widening income disparities.
    Keywords: L24 - Contracting Out ; Joint Ventures ; Technology Licensing, O12 - Microeconomic Analyses of Economic Development, O13 - Agriculture ; Natural Resources ; Energy ; Environment ; Other Primary Products, Q12 - Micro Analysis of Farm Firms, Farm Households, and Farm Input Markets, Q13 - Agricultural Markets and Marketing ; Cooperatives ; Agribusiness, Q18 - Agricultural Policy ; Food Policy
    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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  • 10
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    36 new, high-probability, damped Ly{alpha} absorbers at redshift 0.42 〈 z 〈 0.70 (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-26
    Description: Quasar damped Lyα (DLA) absorption-line systems with redshifts z  〈 1.65 are used to trace neutral gas over approximately 70 per cent of the most recent history of the Universe. However, such systems fall in the UV and are rarely found in blind UV spectroscopic surveys. Therefore, it has been difficult to compile a moderate-sized sample of UV DLAs in any narrow cosmic time interval. However, DLAs are easy to identify in low-resolution spectra because they have large absorption rest equivalent widths. We have performed an efficient strong-Mg  ii -selected survey for UV DLAs at redshifts z  = [0.42, 0.70] using Hubble Space Telescope 's low-resolution ACS-HRC-PR200L prism. This redshift interval covers ~1.8 Gyr in cosmic time, i.e. t   [7.2, 9.0] Gyr after the big bang. A total of 96 strong Mg  ii absorption-line systems identified in Sloan Digital Sky Survey spectra were successfully observed with the prism at the predicted UV wavelengths of Lyα absorption. We found that 35 of the 96 systems had a significant probability of being DLAs. One additional observed system could be a very high $N_{\rm H\,\small {I}}$ DLA ( $N_{\rm H\,\small {I}} \sim 2\times 10^{22}$ atoms cm –2 or possibly higher), but since very high $N_{\rm H\,\small {I}}$ systems are extremely rare, it would be unusual for this system to be a DLA given the size of our sample. Here we present information on our prism sample, including our best estimates of $N_{\rm H\,\small {I}}$ and errors for the 36 systems fitted with DLA profiles. This list is valuable for future follow-up studies of low-redshift DLAs in a small redshift interval, although such work would clearly benefit from improved UV spectroscopy to more accurately determine their neutral hydrogen column densities.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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