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  • 1
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    H{alpha} kinematics of S4G spiral galaxies - II. Data description and non-circular motions (2015)
    Oxford University Press
    Details
    Publication Date: 2015-06-05
    Description: We present a kinematical study of 29 spiral galaxies included in the Spitzer Survey of Stellar Structure in Galaxies, using Hα Fabry–Perot (FP) data obtained with the Galaxy Hα Fabry–Perot System instrument at the William Herschel Telescope in La Palma, complemented with images in the R band and in Hα. The primary goal is to study the evolution and properties of the main structural components of galaxies through the kinematical analysis of the FP data, complemented with studies of morphology, star formation and mass distribution. In this paper we describe how the FP data have been obtained, processed and analysed. We present the resulting moment maps, rotation curves, velocity model maps and residual maps. Images are available in fits format through the NASA/IPAC Extragalactic Database and the Centre de Données Stellaires. With these data products we study the non-circular motions, in particular those found along the bars and spiral arms. The data indicate that the amplitude of the non-circular motions created by the bar does not correlate with the bar strength indicators. The amplitude of those non-circular motions in the spiral arms does not correlate with either arm class or star formation rate along the spiral arms. This implies that the presence and the magnitude of the streaming motions in the arms is a local phenomenon.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 2
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    Disentangling the effect of parental care, food supply, and offspring decisions on the duration of the postfledging period (2015)
    Oxford University Press
    Details
    Publication Date: 2015-11-20
    Description: The postfledging dependence period (PFDP) is a crucial stage in the development of altricial birds. This period is regulated by parental investment, in terms of food provisioning and protection, and the demands of young associated with their development and physical condition. We examine the relative role of parental investment, food provisioning, and offspring decisions on the PFDP regulation in the Spanish imperial eagle ( Aquila adalberti ) by comparing the PFDP timing among young from non-manipulated territories, food supplemented territories, and birds translocated by hacking methods in the absence of adults and with ad libitum food supply. We found that extra food homogenized the nutritional condition of young and reduced the length of the first stage of PFDP, which is related to flight development and thus dependent on body condition. However, hacked birds did not reduce this stage despite ad libitum food, likely due to the lack of parental stimulus to develop advanced flights. Although the presence of adults might accelerate young becoming independent, hacked birds did not extend significantly the whole PFDP and all birds eventually started dispersal. Thereby, the PFDP regulation was primarily under offspring control, and modulated secondarily by parental effects independently of food provisioning and laying date. The length of this period seems to be constrained mainly by the inherent benefits of early dispersal on ultimate fitness in accordance with ontogenic hypotheses. In addition, hacking was shown to be an effective translocation method when properly used, without negative drawbacks for young development during the PFDP.
    Print ISSN: 1045-2249
    Electronic ISSN: 1465-7279
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Context-specific metabolic network reconstruction of a naphthalene-degrading bacterial community guided by metaproteomic data (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-27
    Description: Motivation: With the advent of meta-‘omics’ data, the use of metabolic networks for the functional analysis of microbial communities became possible. However, while network-based methods are widely developed for single organisms, their application to bacterial communities is currently limited. Results: Herein, we provide a novel, context-specific reconstruction procedure based on metaproteomic and taxonomic data. Without previous knowledge of a high-quality, genome-scale metabolic networks for each different member in a bacterial community, we propose a meta-network approach, where the expression levels and taxonomic assignments of proteins are used as the most relevant clues for inferring an active set of reactions. Our approach was applied to draft the context-specific metabolic networks of two different naphthalene-enriched communities derived from an anthropogenically influenced, polyaromatic hydrocarbon contaminated soil, with (CN2) or without (CN1) bio-stimulation. We were able to capture the overall functional differences between the two conditions at the metabolic level and predict an important activity for the fluorobenzoate degradation pathway in CN1 and for geraniol metabolism in CN2. Experimental validation was conducted, and good agreement with our computational predictions was observed. We also hypothesize different pathway organizations at the organismal level, which is relevant to disentangle the role of each member in the communities. The approach presented here can be easily transferred to the analysis of genomic, transcriptomic and metabolomic data. Contact: fplanes@ceit.es or mferrer@icp.csic.es 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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  • 4
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    Improving initial conditions for cosmological N-body simulations (2016)
    Oxford University Press
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    Publication Date: 2016-07-29
    Description: In cosmological N -body simulations, the representation of dark matter as discrete ‘macroparticles’ suppresses the growth of structure, such that simulations no longer reproduce linear theory on small scales near k Nyquist . Marcos et al. demonstrate that this is due to sparse sampling of modes near k Nyquist and that the often-assumed continuum growing modes are not proper growing modes of the particle system. We develop initial conditions (ICs) that respect the particle linear theory growing modes and then rescale the mode amplitudes to account for growth suppression. These ICs also allow us to take advantage of our very accurate N -body code abacus to implement second-order Lagrangian perturbation theory (2LPT) in configuration space. The combination of 2LPT and rescaling improves the accuracy of the late-time power spectra, halo mass functions, and halo clustering. In particular, we achieve 1 per cent accuracy in the power spectrum down to k Nyquist , versus k Nyquist /4 without rescaling or k Nyquist /13 without 2LPT, relative to an oversampled reference simulation. We anticipate that our 2LPT will be useful for large simulations where fast Fourier transforms are expensive and that rescaling will be useful for suites of medium-resolution simulations used in cosmic emulators and galaxy survey mock catalogues. Code to generate ICs is available at https://github.com/lgarrison/zeldovich-PLT .
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Triggered star formation in a merging, gas-rich dwarf galaxy around NGC 7241 (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-08
    Description: Using multiwavelength kinematic and photometric data we have analysed the gaseous and stellar properties of a previously uncharacterized low-mass star-forming companion and newly discovered stellar stream seen projected against the edge-on spiral galaxy NGC 7241. The companion object was identified serendipitously as an offset velocity component in H α Fabry–Perot observations along the line of sight to NGC 7241, and is most prominent visually in UV and blue wavelengths. Its occulting position with respect to NGC 7241 allows measurement of its dust extinction properties which are then combined with photometric spectral energy distribution fitting and long-slit spectroscopy to study star formation (SF) in this gas-rich accreting dwarf galaxy. The dynamical properties of the stream and companion suggest that they may likely be remnants of the same low-mass progenitor dwarf galaxy which is being disrupted during its accretion on to NGC 7241 – with the companion's recent SF triggered during its passage with the disc of NGC 7241. This is supported by the companion's metallicity and SF rates, the asymmetric SF in the disc of NGC 7241, as well as the coincident velocity of the extraplanar H i filament and the star-forming companion. In contrast, mass estimates from dynamical modelling of NGC 7241 rule out an interaction between NGC 7241 and UGC 11964 (the other large spiral galaxy in the group) within the last ~3 Gyr – making such an interaction a poor candidate for inducing the recent SF in the system. Together, the data for this system offer a window into how SF proceeds in low-mass mergers.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Intergalactic magnetic field spectra from diffuse gamma-rays (2015)
    Oxford University Press
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    Publication Date: 2015-05-16
    Description: Non-vanishing parity-odd correlators of gamma-ray arrival directions observed by Fermi -LAT indicate the existence of a helical intergalactic magnetic field with strength B ~ 10 –14  G on ~10 Mpc scales. We successfully test this hypothesis using more stringent cuts of the data, Monte Carlo simulations with Fermi -LAT time exposure information, separate analyses for the Northern and Southern galactic hemispheres, and confirm predictions made in Tashiro & Vachaspati. With some further technical assumptions, we show how to reconstruct the magnetic helicity spectrum from the parity-odd correlators.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 7
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    MC-2D: An Efficient and Scalable Multicoupon Scheme (2015)
    Oxford University Press
    Details
    Publication Date: 2015-03-27
    Description: Electronic multicoupons are the digital version of paper-based booklet of coupons, which allow a customer to obtain goods or services from a merchant typically with discounts or gifts. In this paper, we propose a multicoupon scheme for multi-merchant environments that enhances the security and the efficiency as regards the previous solution that deals with this kind of scenario. On one hand, our scheme meets basic security requirements (unforgeability, reuse detection), but also unsplittability. This fact will help to increase the trust on the part of merchants. On the other hand, we focus on achieving a high degree of privacy for customers (anonymity, unlinkability, confidentiality) that will contribute to gaining the trust of the involved customers. Moreover, we provide measures to protect honest parties from dishonest participants, keeping in mind the scalability and efficiency of the multicoupon scheme, to attract customers and merchants. In addition, we show by implementation that our proposal outperforms previous solutions of this kind.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 8
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    The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases (2016)
    Oxford University Press
    Details
    Publication Date: 2016-01-07
    Description: The MetaCyc database ( MetaCyc.org ) is a freely accessible comprehensive database describing metabolic pathways and enzymes from all domains of life. The majority of MetaCyc pathways are small-molecule metabolic pathways that have been experimentally determined. MetaCyc contains more than 2400 pathways derived from 〉46 000 publications, and is the largest curated collection of metabolic pathways. BioCyc ( BioCyc.org ) is a collection of 5700 organism-specific Pathway/Genome Databases (PGDBs), each containing the full genome and predicted metabolic network of one organism, including metabolites, enzymes, reactions, metabolic pathways, predicted operons, transport systems, and pathway-hole fillers. The BioCyc website offers a variety of tools for querying and analyzing PGDBs, including Omics Viewers and tools for comparative analysis. This article provides an update of new developments in MetaCyc and BioCyc during the last two years, including addition of Gibbs free energy values for compounds and reactions; redesign of the primary gene/protein page; addition of a tool for creating diagrams containing multiple linked pathways; several new search capabilities, including searching for genes based on sequence patterns, searching for databases based on an organism's phenotypes, and a cross-organism search; and a metabolite identifier translation service.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 9
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    Influence of syntectonic sedimentation and décollement rheology on the geometry and evolution of orogenic wedges: analogue modeling of the Kuqa fold‐and‐thrust belt (NW China) (2019)
    Wiley
    In: Tectonics
    Details
    Publication Date: 2019
    Description: Abstract Contractional deformation in the outer parts of fold‐and‐thrust belts is in part controlled by the presence of syntectonic sediments and multiple décollements (e.g. the Apennines, the Appalachians, the Pyrenees, the Zagros, or the Sub‐Andean and Kuqa fold‐and‐thrust belts). To better understand the influence of these parameters in the kinematic evolution of fold‐and‐thrust systems, we carried out an experimental study including four 3D sandbox models inspired by one of the previously mentioned prototypes, the Kuqa fold‐and‐thrust belt. This belt contains two décollements: a weak synorogenic salt layer; and a deeper, preorogenic and frictionless décollement (i.e., organic‐rich shales) showing along strike variations of rheology. The experimental results show that increasing synkinematic sedimentation rate: (i) generates a progressive change from distributed to localized deformation and, (ii) delays the development of frontal contractional structures detached on the salt, favoring the formation and reactivation of more hinterland thrusts and backthrusts. With respect to the rheology, our study reveals that as the viscosity of the prekinematic décollement increases: (i) the deformation propagates more slowly towards the foreland and, (ii) the underlying thrust stack becomes broader and lower and has a gentler thrust taper angle. The rheology of the prekinematic décollement defines the distribution and geometry of the structures detached on it that in turn influence the development of overlying, salt‐detached structures. Subsalt structures can: (i) determine the areal extent of the salt and therefore of any fold‐and‐thrust system detached on it and, (ii) hamper or even prevent the progressive foreland propagation of deformation above the salt.
    Print ISSN: 0278-7407
    Electronic ISSN: 1944-9194
    Topics: Geosciences
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 10
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    Global scombrid life history dataset (2016)
    Wiley
    In: Ecology
    Details
    Publication Date: 2016
    Description: Abstract The scombrids (Family Scombridae), commonly known as tunas, bonitos, Spanish mackerels, and mackerels, play an important role as predators and prey in coastal and oceanic marine ecosystems, and sustain some of the most important fisheries in the world. Knowledge of their basic biology and life history traits, such as growth, age and maturity, is fundamental to sustainably manage these species, and maintain their critical role in marine ecosystems. Given the economic and social importance of their fisheries in many regions throughout the world, numerous life history studies have been conducted in the last century. Despite efforts to create global repositories of life history parameters, e.g. FishBase, many life history studies remain scattered and not readily accessible. Here, we compiled 667 life history studies published between 1933 and 2012 describing the growth, age, and reproductive biology of the 51 species of scombrids distributed around the world and create a standardized life history dataset including maximum size, longevity, growth, maturity, fecundity, spawning season and frequency, and egg size information. We created this dataset to promote the best use of the existing life history information and with the intention of providing a data resource suitable to test large‐scale ecological hypotheses on life history strategies and life history evolution, as well as support the management and conservation of this important group of commercially exploited species. We envisage the large repository of standardized life history data compiled will make this endeavor more effective and robust by providing a valuable resource that can help address many research questions. This article is protected by copyright. All rights reserved.
    Print ISSN: 0012-9658
    Electronic ISSN: 1939-9170
    Topics: Biology
    Published by Wiley on behalf of The Ecological Society of America (ESA).
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