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  • 1
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    The young cluster NGC 2282: a multiwavelength perspective (2015)
    Oxford University Press
    Details
    Publication Date: 2015-10-22
    Description: We present the analysis of the stellar content of NGC 2282, a young cluster in the Monoceros constellation, using deep optical BVI and INT Photometric Hα Survey (IPHAS) photometry along with infrared (IR) data from UKIRT Infrared Deep Sky Survey and Spitzer -IRAC. Based on the stellar surface density analysis using nearest neighbourhood method, the radius of the cluster is estimated as ~3.15 arcmin. From optical spectroscopic analysis of eight bright sources, we have classified three early B-type members in the cluster, which includes, HD 289120, a previously known B2V-type star, a Herbig Ae/Be star (B0.5 Ve) and a B5 V star. From spectrophotometric analyses, the distance to the cluster has been estimated as ~1.65 kpc. The K -band extinction map is estimated using nearest neighbourhood technique, and the mean extinction within the cluster area is found to be A V ~ 3.9 mag. Using IR colour–colour criteria and Hα-emission properties, we have identified a total of 152 candidate young stellar objects (YSOs) in the region, of which, 75 are classified as Class II, nine are Class I YSOs. Our YSO catalogue also includes 50 Hα-emission line sources, identified using slitless spectroscopy and IPHAS photometry data. Based on the optical and near-IR colour–magnitude diagram analyses, the cluster age has been estimated to be in the range of 2–5 Myr, which is in agreement with the estimated age from disc fraction (~58 per cent). Masses of these YSOs are found to be ~0.1–2.0 M . Spatial distribution of the candidate YSOs shows spherical morphology, more or less similar to the surface density map.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    The DES Science Verification weak lensing shear catalogues (2016)
    Jarvis, M., Sheldon, E., Zuntz, J., Kacprzak, T., Bridle, S. L., Amara, A., Armstrong, R., Becker, M. R., Bernstein, G. M., Bonnett, C., Chang, C., Das, R., Dietrich, J. P., Drlica-Wagner, A., Eifler, T. F., Gangkofner, C., Gruen, D., Hirsch, M., Huff, E. M., Jain, B., Kent, S., Kirk, D., Mac; Crann, N., Melchior, P., Plazas, A. A., Refregier, A., Rowe, B., Rykoff, E. S., Samuroff, S., Sanchez, C., Suchyta, E., Troxel, M. A., Vikram, V., Abbott, T., Abdalla, F. B., Allam, S., Annis, J., Benoit-Levy, A., Bertin, E., Brooks, D., Buckley-Geer, E., Burke, D. L., Capozzi, D., Carnero Rosell, A., Carrasco Kind, M., Carretero, J., Castander, F. J., Clampitt, J., Crocce, M., Cunha, C. E., D'Andrea, C. B., da Costa, L. N., De; Poy, D. L., Desai, S., Diehl, H. T., Doel, P., Fausti Neto, A., Flaugher, B., Fosalba, P., Frieman, J., Gaztanaga, E., Gerdes, D. W., Gruendl, R. A., Gutierrez, G., Honscheid, K., James, D. J., Kuehn, K., Kuropatkin, N., Lahav, O., Li, T. S., Lima, M., March, M., Martini, P., Miquel, R., Mohr, J. J., Neilsen, E., Nord, B., Ogando, R., Reil, K., Romer, A. K., Roodman, A., Sako, M., Sanchez, E., Scarpine, V., Schubnell, M., Sevilla-Noarbe, I., Smith, R. C., Soares-Santos, M., Sobreira, F., Swanson, M. E. C., Tarle, G., Thaler, J., Thomas, D., Walker, A. R., Wechsler, R. H.
    Oxford University Press
    Details
    Publication Date: 2016-06-13
    Description: We present weak lensing shear catalogues for 139 square degrees of data taken during the Science Verification (SV) time for the new Dark Energy Camera (DECam) being used for the Dark Energy Survey (DES). We describe our object selection, point spread function estimation and shear measurement procedures using two independent shear pipelines, im3shape and ngmix , which produce catalogues of 2.12 million and 3.44 million galaxies, respectively. We detail a set of null tests for the shear measurements and find that they pass the requirements for systematic errors at the level necessary for weak lensing science applications using the SV data. We also discuss some of the planned algorithmic improvements that will be necessary to produce sufficiently accurate shear catalogues for the full 5-yr DES, which is expected to cover 5000 square degrees.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 3
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    RNA-Redesign: a web server for fixed-backbone 3D design of RNA (2015)
    Oxford University Press
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    Publication Date: 2015-07-02
    Description: RNA is rising in importance as a design medium for interrogating fundamental biology and for developing therapeutic and bioengineering applications. While there are several online servers for design of RNA secondary structure, there are no tools available for the rational design of 3D RNA structure. Here we present RNA-Redesign ( http://rnaredesign.stanford.edu ), an online 3D design tool for RNA. This resource utilizes fixed-backbone design to optimize the sequence identity and nucleobase conformations of an RNA to match a desired backbone, analogous to fundamental tools that underlie rational protein engineering. The resulting sequences suggest thermostabilizing mutations that can be experimentally verified. Further, sequence preferences that differ between natural and computationally designed sequences can suggest whether natural sequences possess functional constraints besides folding stability, such as cofactor binding or conformational switching. Finally, for biochemical studies, the designed sequences can suggest experimental tests of 3D models, including concomitant mutation of base triples. In addition to the designs generated, detailed graphical analysis is presented through an integrated and user-friendly environment.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 4
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    Primerize: automated primer assembly for transcribing non-coding RNA domains (2015)
    Oxford University Press
    Details
    Publication Date: 2015-07-02
    Description: Customized RNA synthesis is in demand for biological and biotechnological research. While chemical synthesis and gel or chromatographic purification of RNA is costly and difficult for sequences longer than tens of nucleotides, a pipeline of primer assembly of DNA templates, in vitro transcription by T7 RNA polymerase and kit-based purification provides a cost-effective and fast alternative for preparing RNA molecules. Nevertheless, designing template primers that optimize cost and avoid mispriming during polymerase chain reaction currently requires expert inspection, downloading specialized software or both. Online servers are currently not available or maintained for the task. We report here a server named Primerize that makes available an efficient algorithm for primer design developed and experimentally tested in our laboratory for RNA domains with lengths up to 300 nucleotides. Free access: http://primerize.stanford.edu .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 5
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    An RNA Mapping DataBase for curating RNA structure mapping experiments (2012)
    Oxford University Press
    Details
    Publication Date: 2012-11-11
    Description: : We have established an RNA mapping database (RMDB) to enable structural, thermodynamic and kinetic comparisons across single-nucleotide-resolution RNA structure mapping experiments. The volume of structure mapping data has greatly increased since the development of high-throughput sequencing techniques, accelerated software pipelines and large-scale mutagenesis. For scientists wishing to infer relationships between RNA sequence/structure and these mapping data, there is a need for a database that is curated, tagged with error estimates and interfaced with tools for sharing, visualization, search and meta-analysis. Through its on-line front-end, the RMDB allows users to explore single-nucleotide-resolution mapping data in heat-map, bar-graph and colored secondary structure graphics; to leverage these data to generate secondary structure hypotheses; and to download the data in standardized and computer-friendly files, including the RDAT and community-consensus SNRNASM formats. At the time of writing, the database houses 53 entries, describing more than 2848 experiments of 1098 RNA constructs in several solution conditions and is growing rapidly. Availability: Freely available on the web at http://rmdb.stanford.edu Contact: rhiju@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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  • 6
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    The deep geology of South India inferred from Moho depth and Vp/Vs ratio (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-18
    Description: We present a comprehensive study of thickness and composition of the crust; and the nature of crust–mantle boundary beneath Southern India using P -wave receiver function from 119 seismic stations. Data from distributed network of seismograph location encompass geological domains like mid to late Archean Dharwar craton, Archean and Proterozoic metamorphic terrains, Proterozoic basin, rifted margins and escarpments, and Deccan volcanics. Except for the mid to lower crust exhumed Archean terrains (of West Dharwar and Southern Granulite) all other geological domains have crustal thickness in the range 33–40 km. In the western Dharwar, crustal thickness increases from ~40 km in the north to over 50 km in the south. The Archean domain of granulite terrain is thicker (40–45 km) and more mafic compared to its counterpart in south deformed at 550 Ma. Most of the crustal blocks have low to moderate Vp / Vs (1.72–1.76) representing a felsic to intermediate composition. Exception to the above include Archean granulite terrain with high Vp / Vs (1.76–1.81) suggestive of more mafic crust beneath them. When accounted for the paleo burial depth of 15–25 km, the study suggests a possible Himalaya–Tibet like scenario beneath the mid-late Archean in southwestern Dharwar and north granulite terrain whose deeper crust has progressively densified. This led to a gradational crust–mantle transition that is otherwise sharp elsewhere. The study suggests a more homogenized and felsic nature of the Precambrian crust beneath the terrains formed after 2.6 Ga, possibly due to delamination of the mafic lower crust. Our study does not suggest any distinction between late Archean and Proterozoic crust. The Deccan volcanism at 65 Ma does not appear to have altered the crustal character beneath it and is similar to the adjoining late Archean east Dharwar craton. The western Ghat escarpment and the coastal plain formed due to separation of India from Madagascar are underlain by mafic lower crust.
    Keywords: Seismology
    Print ISSN: 0956-540X
    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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  • 7
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    Functional evaluation of BRCA2 variants mapping to the PALB2-binding and C-terminal DNA-binding domains using a mouse ES cell-based assay (2012)
    Oxford University Press
    Details
    Publication Date: 2012-08-28
    Description: Single-nucleotide substitutions and small in-frame insertions or deletions identified in human breast cancer susceptibility genes BRCA1 and BRCA2 are frequently classified as variants of unknown clinical significance (VUS) due to the availability of very limited information about their functional consequences. Such variants can most reliably be classified as pathogenic or non-pathogenic based on the data of their co-segregation with breast cancer in affected families and/or their co-occurrence with a pathogenic mutation. Biological assays that examine the effect of variants on protein function can provide important information that can be used in conjunction with available familial data to determine the pathogenicity of VUS. In this report, we have used a previously described mouse embryonic stem (mES) cell-based functional assay to characterize eight BRCA2 VUS that affect highly conserved amino acid residues and map to the N-terminal PALB2-binding or the C-terminal DNA-binding domains. For several of these variants, very limited co-segregation information is available, making it difficult to determine their pathogenicity. Based on their ability to rescue the lethality of Brca2- deficient mES cells and their effect on sensitivity to DNA-damaging agents, homologous recombination and genomic integrity, we have classified these variants as pathogenic or non-pathogenic. In addition, we have used homology-based modeling as a predictive tool to assess the effect of some of these variants on the structural integrity of the C-terminal DNA-binding domain and also generated a knock-in mouse model to analyze the physiological significance of a residue reported to be essential for the interaction of BRCA2 with meiosis-specific recombinase, DMC1.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 8
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    Near-infrared studies of V5558 Sgr: an unusually slow nova with multiple outbursts (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-21
    Description: We present near-infrared (1–2.5 μm) JHK photospectroscopic results of the unusually slow nova V5558 Sgr (2007). V5558 Sgr showed a slow climb to maximum that lasted for about 60 d and then underwent at least five strong secondary outbursts. We have analysed the optical light curve to derive large t 2 and t 3 values of 281 ± 3 and 473 ± 3 d, respectively. An alternate approach is adopted to derive a distance estimate of 1.55 ± 0.25 kpc as conventional maximum magnitude–rate of decline relation may not be applicable for a slow nova. In the pre-maxima stage, the spectra showed narrow (FWHM ~ 400–550 km s –1 ) and strong emission lines of Paschen and Brackett series with prominent P-Cygni components. In the later phase, the spectra show significant changes with the development of strong and broad (~1000 km s –1 ) emission lines of H i , He i , O i and N i and some uncommon Fe ii emission lines. No evidence of dust formation is seen. V5558 Sgr has been shown to be a rare hybrid nova showing a transition from He/N to Fe ii type from optical spectra. However, the near-infrared data do not show such a transition and we discuss this anomalous behaviour. A recombination analysis of the Brackett lines allows us to constrain the electron density and emission measure during the early optically thick phase and to estimate the mass of the ejecta to be (6.0 ± 1.5) 10 –4 M , assuming a filling factor of unity, from later observations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Near-infrared studies of V5558 Sgr: an unusually slow nova with multiple outbursts (2014)
    Oxford University Press
    Details
    Publication Date: 2014-12-29
    Description: We present near-infrared (1–2.5 μm) JHK photospectroscopic results of the unusually slow nova V5558 Sgr (2007). V5558 Sgr showed a slow climb to maximum that lasted for about 60 d and then underwent at least five strong secondary outbursts. We have analysed the optical light curve to derive large t 2 and t 3 values of 281 ± 3 and 473 ± 3 d, respectively. An alternate approach is adopted to derive a distance estimate of 1.55 ± 0.25 kpc as conventional maximum magnitude–rate of decline relation may not be applicable for a slow nova. In the pre-maxima stage, the spectra showed narrow (FWHM ~ 400–550 km s –1 ) and strong emission lines of Paschen and Brackett series with prominent P-Cygni components. In the later phase, the spectra show significant changes with the development of strong and broad (~1000 km s –1 ) emission lines of H i , He i , O i and N i and some uncommon Fe ii emission lines. No evidence of dust formation is seen. V5558 Sgr has been shown to be a rare hybrid nova showing a transition from He/N to Fe ii type from optical spectra. However, the near-infrared data do not show such a transition and we discuss this anomalous behaviour. A recombination analysis of the Brackett lines allows us to constrain the electron density and emission measure during the early optically thick phase and to estimate the mass of the ejecta to be (6.0 ± 1.5) 10 –4 M , assuming a filling factor of unity, from later observations.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    Localizing Ashkenazic Jews to Primeval Villages in the Ancient Iranian Lands of Ashkenaz (2016)
    Oxford University Press
    Details
    Publication Date: 2016-04-21
    Description: The Yiddish language is over 1,000 years old and incorporates German, Slavic, and Hebrew elements. The prevalent view claims Yiddish has a German origin, whereas the opposing view posits a Slavic origin with strong Iranian and weak Turkic substrata. One of the major difficulties in deciding between these hypotheses is the unknown geographical origin of Yiddish speaking Ashkenazic Jews (AJs). An analysis of 393 Ashkenazic, Iranian, and mountain Jews and over 600 non-Jewish genomes demonstrated that Greeks, Romans, Iranians, and Turks exhibit the highest genetic similarity with AJs. The Geographic Population Structure analysis localized most AJs along major primeval trade routes in northeastern Turkey adjacent to primeval villages with names that may be derived from "Ashkenaz." Iranian and mountain Jews were localized along trade routes on the Turkey’s eastern border. Loss of maternal haplogroups was evident in non-Yiddish speaking AJs. Our results suggest that AJs originated from a Slavo-Iranian confederation, which the Jews call "Ashkenazic" (i.e., "Scythian"), though these Jews probably spoke Persian and/or Ossete. This is compatible with linguistic evidence suggesting that Yiddish is a Slavic language created by Irano-Turko-Slavic Jewish merchants along the Silk Roads as a cryptic trade language, spoken only by its originators to gain an advantage in trade. Later, in the 9th century, Yiddish underwent relexification by adopting a new vocabulary that consists of a minority of German and Hebrew and a majority of newly coined Germanoid and Hebroid elements that replaced most of the original Eastern Slavic and Sorbian vocabularies, while keeping the original grammars intact.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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