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  • Oxford University Press  (47)
  • 2015-2019  (39)
  • 1990-1994  (8)
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  • 1
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    Comparison of haplotype-based statistical tests for disease association with rare and common variants (2016)
    Oxford University Press
    Details
    Publication Date: 2016-07-16
    Description: Recent literature has highlighted the advantages of haplotype association methods for detecting rare variants associated with common diseases. As several new haplotype association methods have been proposed in the past few years, a comparison of new and standard methods is important and timely for guidance to the practitioners. We consider nine methods—Haplo.score, Haplo.glm, Hapassoc, Bayesian hierarchical Generalized Linear Model (BhGLM), Logistic Bayesian LASSO (LBL), regularized GLM (rGLM), Haplotype Kernel Association Test, wei-SIMc-matching and Weighted Haplotype and Imputation-based Tests. These can be divided into two types—individual haplotype-specific tests and global tests depending on whether there is just one overall test for a haplotype region (global) or there is an individual test for each haplotype in the region. Haplo.score is the only method that tests for both; Haplo.glm, Hapassoc, BhGLM and LBL are individual haplotype-specific, while the rest are global tests. For comparison, we also apply a popular collapsing method—Sequence Kernel Association Test (SKAT) and its two variants—SKAT-O (Optimal) and SKAT-C (Combined). We carry out an extensive comparison on our simulated data sets as well as on the Genetic Analysis Workshop (GAW) 18 simulated data. Further, we apply the methods to GAW18 real hypertension data and Dallas Heart Study sequence data. We find that LBL, Haplo.score (global test) and rGLM perform well over the scenarios considered here. Also, haplotype methods are more powerful (albeit more computationally intensive) than SKAT and its variants in scenarios where multiple causal variants act interactively to produce haplotype effects.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 2
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    SLA-PGN-primed dendritic cell-based vaccination induces Th17-mediated protective immunity against experimental visceral leishmaniasis: a crucial role of PKC{beta} (2016)
    Oxford University Press
    Details
    Publication Date: 2016-05-27
    Description: Emergence of drug resistance during visceral leishmaniasis (VL) is a major obstacle imposed during successful therapy. An effective vaccine strategy against this disease is therefore necessary. Our present study exploited the SLA (soluble leishmanial antigen) and PGN (peptidoglycan) stimulated bone marrow-derived dendritic cells (DCs) as a suitable vaccine candidate during experimental VL. SLA-PGN-stimulated DCs showed a significant decrease in hepatic and splenic parasite burden, which were associated with increased production of nitric oxide and pro-inflammatory cytokines such as IL-12, IFN- and IL-17. Elevated level of IL-17 was accompanied with the generation of more Th17 cells. Further studies on DC provided the evidence that these SLA-PGN-stimulated DCs played an important role in providing necessary cytokines such as IL-6, IL-23 and TGF-β for the generation of Th17 cells. Interestingly, inhibition of protein kinase C-β (PKCβ) in DCs led to decreased production of Th17 polarizing cytokines, causing reduction of the Th17 population size. Altogether, our finding highlighted the important role of DC-based PKCβ in regulation of the function and generation of Th17 cells.
    Print ISSN: 0928-8244
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 3
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    Scanning electron microscopy of scale microstructures in Channa barca, a poorly known snake head fish in regard to taxonomy (2015)
    Oxford University Press
    Details
    Publication Date: 2015-10-10
    Description: Scanning electron microscopy has been identified as an important approach in studying scale microstructures in fish with reference to taxonomy. In this article, a detailed microstructural analysis of the scales of Channa barca , a poorly known snakehead fish was carried out the location of focus, inter-radial distance, average width and inter-circular space of anterior circulii; inter-circular distance and dentition in lateral circulii; the shape, spacing, length of lepidonts in anterior circulii and the number and width of radii were compared with those of a related species, Channa aurantimaculata . The location of the focus was found to be similar to those of the gachua group of the genus Channa but was different from those of the marulius group. There were major similarities—though with a few notable differences—in scale microstructures between C. barca and the aforementioned closely related species C. aurantimaculata , indicating that scale microstructure analysis has the potential to distinguish even closely related fish species . While several of the microstructural features of the scale were found to be similar to those of the gachua group, others were closer in nature to those of the marulius group. Some microstructural characteristics, however, were found to be totally different from those of both gachua and marulius groups. All of these characteristic features of scale microstructure in C. barca are discussed with reference to taxonomic significance.
    Print ISSN: 0022-0744
    Electronic ISSN: 1477-9986
    Topics: Electrical Engineering, Measurement and Control Technology , Natural Sciences in General , Physics
    Published by Oxford University Press on behalf of The Japanese Electron Microscopy Society.
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  • 4
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    ISQuest: finding insertion sequences in prokaryotic sequence fragment data (2015)
    Oxford University Press
    Details
    Publication Date: 2015-10-21
    Description: Motivation: Insertion sequences (ISs) are transposable elements present in most bacterial and archaeal genomes that play an important role in genomic evolution. The increasing availability of sequenced prokaryotic genomes offers the opportunity to study ISs comprehensively, but development of efficient and accurate tools is required for discovery and annotation. Additionally, prokaryotic genomes are frequently deposited as incomplete, or draft stage because of the substantial cost and effort required to finish genome assembly projects. Development of methods to identify IS directly from raw sequence reads or draft genomes are therefore desirable. Software tools such as Optimized Annotation System for Insertion Sequences and IScan currently identify IS elements in completely assembled and annotated genomes; however, to our knowledge no methods have been developed to identify ISs from raw fragment data or partially assembled genomes. We have developed novel methods to solve this computationally challenging problem, and implemented these methods in the software package ISQuest. This software identifies bacterial ISs and their sequence elements—inverted and direct repeats—in raw read data or contigs using flexible search parameters. ISQuest is capable of finding ISs in hundreds of partially assembled genomes within hours, making it a valuable high-throughput tool for a global search of IS elements. We tested ISQuest on simulated read libraries of 3810 complete bacterial genomes and plasmids in GenBank and were capable of detecting 82% of the ISs and transposases annotated in GenBank with 80% sequence identity. Contact : abiswas@cs.odu.edu
    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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    Stability of Curcuma longa rhizome lectin: Role of N-linked glycosylation (2016)
    Oxford University Press
    Details
    Publication Date: 2016-02-26
    Description: Curcuma longa rhizome lectin, a mannose-binding protein of non-seed portions of turmeric, is known to have antifungal, antibacterial and α-glucosidase inhibitory activities. We studied the role of complex-type glycans attached to asparagine (Asn) 66 and Asn 110 to elucidate the role of carbohydrates in lectin activity and stability. Apart from the native lectin, the characteristics of a deglycosylated Escherichia coli expressed lectin, high-mannose oligosaccharides at both asparagines and its glycosylation mutants N66Q and N110Q expressed in Pichia pastoris , were compared to understand the relationship between glycosylation and activity. Far UV circular dichroism (CD) spectra, fluorescence emission maximum, hemagglutination assay show no change in secondary or tertiary structures or sugar-binding properties between wild-type and aforementioned recombinant lectins under physiological pH. But reduced agglutination activity and loss of tertiary structure are observed in the acidic pH range for the deglycosylated and the N110Q protein. In thermal and guanidine hydrochloride (GdnCl)-induced unfolding, the wild-type and high-mannose lectins possess higher stability compared with the deglycosylated recombinant lectin and both mutants, as measured by a higher T m of denaturation or a greater free energy change, respectively. Reversibility experiments after thermal denaturation reveal that deglycosylated proteins tend to aggregate during thermal inactivation but the wild type shows a much greater recovery to the native state upon refolding. These results suggest that N-glycosylation in turmeric lectin is important for the maintenance of its proper folding upon changes in pH, and that the oligosaccharides help in maintaining the active conformation and prevent aggregation in unfolded or partially folded molecules.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 6
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    Pseudo-real principal G-bundles over a real curve (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-24
    Description: We consider stable and semistable principal bundles over a smooth projective real algebraic curve, equipped with a real or pseudo-real structure in the sense of Atiyah. After fixing appropriate topological invariants, one can build a suitable gauge theory, and show that the resulting moduli spaces of pseudo-real bundles are connected. This in turn allows one to describe the various fixed point varieties on the complex moduli spaces under the action of the real involutions on the curve and the structure group.
    Print ISSN: 0024-6107
    Electronic ISSN: 1469-7750
    Topics: Mathematics
    Published by Oxford University Press
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  • 7
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    DES13S2cmm: the first superluminous supernova from the Dark Energy Survey (2015)
    Papadopoulos, A., D'Andrea, C. B., Sullivan, M., Nichol, R. C., Barbary, K., Biswas, R., Brown, P. J., Covarrubias, R. A., Finley, D. A., Fischer, J. A., Foley, R. J., Goldstein, D., Gupta, R. R., Kessler, R., Kovacs, E., Kuhlmann, S. E., Lidman, C., March, M., Nugent, P. E., Sako, M., Smith, R. C., Spinka, H., Wester, W., Abbott, T. M. C., Abdalla, F., Allam, S. S., Banerji, M., Bernstein, J. P., Bernstein, R. A., Carnero, A., da Costa, L. N., De; Poy, D. L., Desai, S., Diehl, H. T., Eifler, T., Evrard, A. E., Flaugher, B., Frieman, J. A., Gerdes, D., Gruen, D., Honscheid, K., James, D., Kuehn, K., Kuropatkin, N., Lahav, O., Maia, M. A. G., Makler, M., Marshall, J. L., Merritt, K. W., Miller, C. J., Miquel, R., Ogando, R., Plazas, A. A., Roe, N. A., Romer, A. K., Rykoff, E., Sanchez, E., Santiago, B. X., Scarpine, V., Schubnell, M., Sevilla, I., Soares-Santos, M., Suchyta, E., Swanson, M., Tarle, G., Thaler, J., Tucker, L. D., Wechsler, R. H., Zuntz, J.
    Oxford University Press
    Details
    Publication Date: 2015-03-26
    Description: We present DES13S2cmm, the first spectroscopically-confirmed superluminous supernova (SLSN) from the Dark Energy Survey (DES). We briefly discuss the data and search algorithm used to find this event in the first year of DES operations, and outline the spectroscopic data obtained from the European Southern Observatory (ESO) Very Large Telescope to confirm its redshift ( z  = 0.663 ± 0.001 based on the host-galaxy emission lines) and likely spectral type (Type I). Using this redshift, we find $M^{\rm peak}_U=-21.05^{+0.10}_{-0.09}$ for the peak, rest-frame U -band absolute magnitude, and find DES13S2cmm to be located in a faint, low-metallicity (sub-solar), low stellar-mass host galaxy (log ( M /M ) = 9.3 ± 0.3), consistent with what is seen for other SLSNe-I. We compare the bolometric light curve of DES13S2cmm to 14 similarly well-observed SLSNe-I in the literature and find that it possesses one of the slowest declining tails (beyond +30 d rest-frame past peak), and is the faintest at peak. Moreover, we find the bolometric light curves of all SLSNe-I studied herein possess a dispersion of only 0.2–0.3 mag between +25 and +30 d after peak (rest frame) depending on redshift range studied; this could be important for ‘standardizing’ such supernovae, as is done with the more common Type Ia. We fit the bolometric light curve of DES13S2cmm with two competing models for SLSNe-I – the radioactive decay of 56 Ni, and a magnetar – and find that while the magnetar is formally a better fit, neither model provides a compelling match to the data. Although we are unable to conclusively differentiate between these two physical models for this particular SLSN-I, further DES observations of more SLSNe-I should break this degeneracy, especially if the light curves of SLSNe-I can be observed beyond 100 d in the rest frame of the supernova.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Lateral variation of crustal attenuation properties from southern Tibet to eastern Nepal Himalaya (2019)
    Oxford University Press
    Details
    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Lateral variations of body wave, coda wave, intrinsic and scattering attenuation have been investigated using 114 local earthquakes which were recorded in eastern Nepal Himalaya and southern Tibet from October 2001 to March 2003. The extended coda normalization method and single isotropic scattering model are used to estimate the quality factor of body waves (〈span〉Qp〈/span〉, 〈span〉Qs〈/span〉) and coda wave (〈span〉Qc〈/span〉), respectively. We have divided the entire area into two zones such as eastern Nepal Himalaya and southern Tibet to explore the attenuation characteristics laterally. We have used all crustal events within hypocentral distance of 100 km. The observations are made at six different central frequencies such as 2, 4, 6, 8, 10 and 12 Hz. For both regions 〈span〉Q〈/span〉 values are found to be frequency dependent. Subsequently, we separate out the contributions of both intrinsic (〈span〉Qi〈/span〉) and scattering (〈span〉Qsc〈/span〉) attenuation parameters using the Wennerberg approach. It is observed that the intrinsic attenuation prevails over scattering attenuation in eastern Nepal Himalaya at all the frequency ranges while for southern Tibet scattering attenuation dominates at higher frequencies (〉8Hz). The similarity between 〈span〉Qc〈/span〉 and 〈span〉Qi〈/span〉 is noted for both areas, which confirms that the decay of coda wave is primarily due to the intrinsic dissipation. Intrinsic attenuation is found to be higher in southern Tibet, which could be associated with the partial melting, fluid trapped in the crust or high heat flow that exists below the region. The results correlate with the underlying geo-tectonical model as well as with the structural complexities present beneath the study area. The obtained values in this study are well comparable with other results reported for similar tectonic regime.〈/span〉
    Print ISSN: 2051-1965
    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
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    Lateral variation of crustal attenuation properties from southern Tibet to eastern Nepal Himalaya (2019)
    Oxford University Press
    Details
    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉Lateral variations of body wave, coda wave, intrinsic and scattering attenuation have been investigated using 114 local earthquakes which were recorded in eastern Nepal Himalaya and southern Tibet from October 2001 to March 2003. The extended coda normalization method and single isotropic scattering model are used to estimate the quality factor of body waves (〈span〉Qp, Qs〈/span〉) and coda wave (〈span〉Qc〈/span〉) respectively. We have divided the entire area into two zones such as eastern Nepal Himalaya and southern Tibet to explore the attenuation characteristics laterally. We have used all crustal events within hypocentral distance of 100 km. The observations are made at six different central frequencies such as 2, 4, 6, 8, 10 and 12 Hz. For both regions 〈span〉Q〈/span〉 values are found to be frequency dependent. Subsequently we separate out the contributions of both intrinsic (〈span〉Qi〈/span〉) and scattering (〈span〉Qsc〈/span〉) attenuation parameters using usingWennerberg (1993) approach. It is observed that the intrinsic attenuation prevails over scattering attenuation in eastern Nepal Himalaya at all the frequency ranges while for southern Tibet scattering attenuation dominates at higher frequencies (〉8Hz). The similarity between 〈span〉Qc〈/span〉 and 〈span〉Qi〈/span〉 is noticed for both areas which confirms that the decay of coda wave is primarily due to the intrinsic dissipation. Intrinsic attenuation is found to be higher in southern Tibet which could be associated with the partial melting, fluid trapped in the crust, or high heat flow that exists below the region. The results correlate with the underlying geo-tectonical model as well as with the structural complexities present beneath the study area. The obtained values in this study are well comparable with other results reported for similar tectonic regime.〈/span〉
    Print ISSN: 2051-1965
    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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  • 10
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    Accurate estimations of electromagnetic transitions of Sn iv for stellar and interstellar media (2018)
    Oxford University Press
    Details
    Publication Date: 2018-04-21
    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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