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  • 1
    Publikationsdatum: 2015-08-08
    Beschreibung: : As sequencing becomes cheaper and more widely available, there is a greater need to quickly and effectively analyze large-scale genomic data. While the functionality of AVIA v1.0, whose implementation was based on ANNOVAR, was comparable with other annotation web servers, AVIA v2.0 represents an enhanced web-based server that extends genomic annotations to cell-specific transcripts and protein-level functional annotations. With AVIA’s improved interface, users can better visualize their data, perform comprehensive searches and categorize both coding and non-coding variants. Availability and implementation : AVIA is freely available through the web at http://avia.abcc.ncifcrf.gov . Contact : Hue.Vuong@fnlcr.nih.gov Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 2
    Publikationsdatum: 2015-08-08
    Beschreibung: : As new methods for multivariate analysis of genome wide association studies become available, it is important to be able to combine results from different cohorts in a meta-analysis. The R package MultiMeta provides an implementation of the inverse-variance-based method for meta-analysis, generalized to an n -dimensional setting. Availability and implementation: The R package MultiMeta can be downloaded from CRAN. Contact: dragana.vuckovic@burlo.trieste.it ; vi1@sanger.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Digitale ISSN: 1460-2059
    Thema: Biologie , Informatik , Medizin
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 3
    Publikationsdatum: 2015-08-12
    Beschreibung: We performed a detailed analysis of elemental abundances, dust features, and polycyclic aromatic hydrocarbons (PAHs) in the C-rich planetary nebula (PN) Wray16-423 in the Sagittarius dwarf spheroidal galaxy, based on a unique data set taken from the Subaru/HDS, MPG/ESO FEROS, HST /WFPC2, and Spitzer /IRS. We performed the first measurements of Kr, Fe, and recombination O abundance in this PN. The extremely small [Fe/H] implies that most Fe atoms are in the solid phase, considering into account the abundance of [Ar/H]. The Spitzer /IRS spectrum displays broad 16–24 μm and 30 μm features, as well as PAH bands at 6–9 and 10–14 μm. The unidentified broad 16–24 μm feature may not be related to iron sulphide (FeS), amorphous silicate, or PAHs. Using the spectral energy distribution model, we derived the luminosity and effective temperature of the central star, and the gas and dust masses. The observed elemental abundances and derived gas mass are in good agreement with asymptotic giant branch nucleosynthesis models for an initial mass of 1.90 M and a metallicity of Z  = 0.004. We infer that respectively about 80, 50, and 90 per cent of the Mg, S, and Fe atoms are in the solid phase. We also assessed the maximum possible magnesium sulphide (MgS) and iron-rich sulphide (Fe50S) masses and tested whether these species can produce the band flux of the observed 30 μm feature. Depending on what fraction of the sulphur is in sulphide molecules such as CS, we conclude that MgS and Fe50S could be possible carriers of the 30 μm feature in this PN.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 4
    Publikationsdatum: 2015-08-12
    Beschreibung: We investigate the evolution of the H β + [O iii ] and [O ii ] luminosity functions from z  ~ 0.8 to ~5 in four redshift slices per emission line using data from the High- z Emission Line Survey (HiZELS). This is the first time that the H β + [O iii ] and [O ii ] luminosity functions have been studied at these redshifts in a self-consistent analysis. This is also the largest sample of [O ii ] and H β + [O iii ] emitters (3475 and 3298 emitters, respectively) in this redshift range, with large comoving volumes ~1  x  10 6  Mpc –3 in two independent volumes (COSMOS and UDS), greatly reducing the effects of cosmic variance. The emitters were selected by a combination of photometric redshift and colour–colour selections, as well as spectroscopic follow-up, including recent spectroscopic observations using DEIMOS and MOSFIRE on the Keck Telescopes and FMOS on Subaru. We find a strong increase in L * and a decrease in * for both H β + [O iii ] and [O ii ] emitters. We derive the [O ii ] star formation history of the Universe since z  ~ 5 and find that the cosmic star formation rate density (SFRD) rises from z  ~ 5 to ~3 and then drops towards z  ~ 0. We also find that our star formation history is able to reproduce the evolution of the stellar mass density up to z  ~ 5 based only on a single tracer of star formation. When comparing the H β + [O iii ] SFRDs to the [O ii ] and H α SFRD measurements in the literature, we find that there is a remarkable agreement, suggesting that the H β + [O iii ] sample is dominated by star-forming galaxies at high- z rather than AGNs.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 5
    Publikationsdatum: 2015-08-12
    Beschreibung: We present a ‘two-fluid’ implementation of dust in smoothed particle hydrodynamics (SPH) in the test particle limit. The scheme is able to handle both short and long stopping times and reproduces the short friction time limit, which is not properly handled in other implementations. We apply novel tests to verify its accuracy and limitations, including multidimensional tests that have not been previously applied to the drag-coupled dust problem and which are particularly relevant to self-gravitating protoplanetary discs. Our tests demonstrate several key requirements for accurate simulations of gas–dust mixtures. First, in standard SPH particle jitter can degrade the dust solution, even when the gas density is well reproduced. The use of integral gradients, a Wendland kernel and a large number of neighbours can control this, albeit at a greater computational cost. Secondly, when it is necessary to limit the artificial viscosity we recommend using the Cullen & Dehnen switch, since the alternative, using α ~ 0.1, can generate a large velocity noise up to v   0.3 c s in the dust particles. Thirdly, we find that an accurate dust density estimate requires 〉400 neighbours, since, unlike the gas, the dust particles do not feel regularization forces. This density noise applies to all particle-based two-fluid implementations of dust, irrespective of the hydro solver and could lead to numerically induced fragmentation. Although our tests show accurate dusty gas simulations are possible, care must be taken to minimize the contribution from numerical noise.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 6
    Publikationsdatum: 2015-08-12
    Beschreibung: Halo abundance matching has been used to construct a one-parameter mapping between galaxies and dark matter haloes by assuming that halo mass and galaxy luminosity (or stellar mass) are monotonically related. While this approach has been reasonably successful, it is known that galaxies must be described by at least two parameters, as can be seen from the two-parameter Fundamental Plane on which massive early-type galaxies lie. In this paper, we derive a connection between initial dark matter density perturbations in the early Universe and present-day virialized dark matter haloes by assuming simple spherical collapse combined with conservation of mass and energy. We find that z  = 0 halo concentration, or alternatively the inner slope of the halo density profile α, is monotonically and positively correlated with the collapse redshift of the halo. This is qualitatively similar to the findings of some previous works based on numerical simulations, with which we compare our results. We then describe how the halo mass and concentration (or inner slope α) can be used as two halo parameters in combination with two parameters of early-type galaxies to create an improved abundance matching scheme. In a forthcoming paper, we will show an application of this scheme to galaxies on the Fundamental Plane.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 7
    Publikationsdatum: 2015-08-12
    Beschreibung: Large surveys have shown that red galaxies are preferentially aligned with their haloes, while blue galaxies have a more isotropic distribution. Since haloes generally align with their filaments, this introduces a bias in the measurement of the cosmic shear from weak lensing. It is therefore vitally important to understand why this difference arises. We explore the stability of different disc orientations within triaxial haloes. We show that, in the absence of gas, the disc orientation is most stable when its spin is along the minor axis of the halo. Instead when gas cools on to a disc, it is able to form in almost arbitrary orientation, including off the main planes of the halo (but avoiding an orientation perpendicular to the halo's intermediate axis). Substructure helps gasless galaxies reach alignment with the halo faster, but has less effect on galaxies when gas is cooling on to the disc. Our results provide a novel and natural interpretation for why red, gas poor galaxies are preferentially aligned with their halo, while blue, star-forming, galaxies have nearly random orientations, without requiring a connection between galaxies’ current star formation rate and their merger history.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 8
    Publikationsdatum: 2015-08-09
    Beschreibung: In this work, we investigate the bifurcations of relative equilibria in the gravitational potential of asteroids. A theorem concerning a conserved quantity, which is about the eigenvalues and number of relative equilibria, is presented and proved. The conserved quantity can restrict the number of non-degenerate equilibria in the gravitational potential of an asteroid. It is concluded that the number of non-degenerate equilibria in the gravitational field of an asteroid varies in pairs and is an odd number. In addition, the conserved quantity can also restrict the kinds of bifurcations of relative equilibria in the gravitational potential of an asteroid when the parameter varies. Furthermore, studies have shown that there exist transcritical bifurcations, quasi-transcritical bifurcations, saddle–node bifurcations, saddle–saddle bifurcations, binary saddle–node bifurcations, supercritical pitchfork bifurcations, and subcritical pitchfork bifurcations for the relative equilibria in the gravitational potential of asteroids. It is found that for the asteroid 216 Kleopatra, when the rotation period varies as a parameter, the number of relative equilibria changes from 7 to 5 to 3 to 1, and the bifurcations for the relative equilibria are saddle–node bifurcations and saddle–saddle bifurcations.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 9
    Publikationsdatum: 2015-08-09
    Beschreibung: We examine the relationship between star formation and active galactic nuclei (AGN) activity by constructing matched samples of local (0 〈  z  〈 0.6) radio-loud and radio-quiet AGN in the Herschel -Astrophysical Terahertz Large Area Survey fields. Radio-loud AGN are classified as high-excitation and low-excitation radio galaxies using their emission lines and WISE 22-μm luminosity. AGN accretion and jet powers in these active galaxies are traced by [O iii ] emission-line and radio luminosity, respectively. Star formation rates (SFRs) and specific star formation rates (SSFRs) were derived using Herschel 250-μm luminosity and stellar mass measurements from the Sloan Digital Sky Survey–Max Planck Institute for Astrophysics-John Hopkins University catalogue. In the past, star formation studies of AGN have mostly focused on high-redshift sources to observe the thermal dust emission that peaks in the far-infrared, which limited the samples to powerful objects. However, with Herschel we can expand this to low redshifts. Our stacking analyses show that SFRs and SSFRs of both radio-loud and radio-quiet AGN increase with increasing AGN power but that radio-loud AGN tend to have lower SFR. Additionally, radio-quiet AGN are found to have approximately an order of magnitude higher SSFRs than radio-loud AGN for a given level of AGN power. The difference between the star formation properties of radio-loud and -quiet AGN is also seen in samples matched in stellar mass.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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  • 10
    Publikationsdatum: 2015-08-09
    Beschreibung: We assemble a sample of 24 hydrogen-poor superluminous supernovae (SLSNe). Parameterizing the light-curve shape through rise and decline time-scales shows that the two are highly correlated. Magnetar-powered models can reproduce the correlation, with the diversity in rise and decline rates driven by the diffusion time-scale. Circumstellar interaction models can exhibit a similar rise–decline relation, but only for a narrow range of densities, which may be problematic for these models. We find that SLSNe are approximately 3.5 mag brighter and have light curves three times broader than SNe Ibc, but that the intrinsic shapes are similar. There are a number of SLSNe with particularly broad light curves, possibly indicating two progenitor channels, but statistical tests do not cleanly separate two populations. The general spectral evolution is also presented. Velocities measured from Fe  ii are similar for SLSNe and SNe Ibc, suggesting that diffusion time differences are dominated by mass or opacity. Flat velocity evolution in most SLSNe suggests a dense shell of ejecta. If opacities in SLSNe are similar to other SNe Ibc, the average ejected mass is higher by a factor 2–3. Assuming  = 0.1 cm 2 g –1 , we estimate a mean (median) SLSN ejecta mass of 10 M (6 M ), with a range of 3–30 M . Doubling the assumed opacity brings the masses closer to normal SNe Ibc, but with a high-mass tail. The most probable mechanism for generating SLSNe seems to be the core collapse of a very massive hydrogen-poor star, forming a millisecond magnetar.
    Print ISSN: 0035-8711
    Digitale ISSN: 1365-2966
    Thema: Physik
    Publiziert von Oxford University Press
    Standort Signatur Erwartet Verfügbarkeit
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