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  • Articles  (57)
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  • 1
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    Repeat- and error-aware comparison of deletions (2015)
    Oxford University Press
    Details
    Publication Date: 2015-09-11
    Description: Motivation: The number of reported genetic variants is rapidly growing, empowered by ever faster accumulation of next-generation sequencing data. A major issue is comparability. Standards that address the combined problem of inaccurately predicted breakpoints and repeat-induced ambiguities are missing. This decisively lowers the quality of ‘consensus’ callsets and hampers the removal of duplicate entries in variant databases, which can have deleterious effects in downstream analyses. Results: We introduce a sound framework for comparison of deletions that captures both tool-induced inaccuracies and repeat-induced ambiguities. We present a maximum matching algorithm that outputs virtual duplicates among two sets of predictions/annotations. We demonstrate that our approach is clearly superior over ad hoc criteria, like overlap, and that it can reduce the redundancy among callsets substantially. We also identify large amounts of duplicate entries in the Database of Genomic Variants, which points out the immediate relevance of our approach. Availability and implementation: Implementation is open source and available from https://bitbucket.org/readdi/readdi Contact: roland.wittler@uni-bielefeld.de or t.marschall@mpi-inf.mpg.de 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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  • 2
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    Migrating Scarps as a Significant Driver for Cometary Surface Evolution (2019)
    Wiley
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    Publication Date: 2019
    Description: Abstract Rosetta observations of 67P/Churyumov‐Gerasimenko (67P) reveal that most changes occur in the fallback‐generated smooth terrains, vast deposits of granular material blanketing the comet's northern hemisphere. These changes express themselves both morphologically and spectrally across the nucleus, yet we lack a model that describes their formation and evolution. Here we present a self‐consistent model that thoroughly explains the activity and mass loss from Hapi's smooth terrains. Our model predicts the removal of dust via re‐radiated solar insolation localized within depression scarps that are substantially more ice‐rich than previously expected. We couple our model with numerous Rosetta observations to thoroughly capture the seasonal erosion of Hapi's smooth terrains, where local scarp retreat gradually removes the uppermost dusty mantle. As sublimation‐regolith interactions occur on rocky planets, comets, icy moons and KBOs, our coupled model and observations provide a foundation for future understanding of the myriad of sublimation‐carved worlds.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 3
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    Fractures on comet 67P/Churyumov-Gerasimenko observed by Rosetta/OSIRIS (2015)
    Wiley
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    Publication Date: 2015-06-27
    Description: The OSIRIS experiment onboard the Rosetta spacecraft currently orbiting comet 67P/Churyumov-Gerasimenko has yielded unprecedented views of a comet's nucleus. We present here the first ever observations of meter-scale fractures on the surface of a comet. Some of these fractures form polygonal networks. We present an initial assessment of their morphology, topology, and regional distribution. Fractures are ubiquitous on the surface of the comet's nucleus. Furthermore, they occur in various settings and show different topologies suggesting numerous formation mechanisms, which include thermal insolation weathering, orbital-induced stresses, and possibly seasonal thermal contraction. However, we conclude that thermal insolation weathering is responsible for creating most of the observed fractures based on their morphology and setting in addition to thermal models that indicate diurnal temperature ranges exceeding 200 K and thermal gradients of ~15 K/min at perihelion are possible. Finally, we suggest that fractures could be a facilitator in surface evolution and long-term erosion.
    Print ISSN: 0094-8276
    Electronic ISSN: 1944-8007
    Topics: Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 4
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    Extreme Magnesium Isotope Fractionation at Outcrop Scale Records the Mechanism and Rate at which Reaction Fronts Advance (2015)
    Oxford University Press
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    Publication Date: 2015-01-21
    Description: Isotopic fractionation of cationic species during diffusive transport provides a novel means of constraining the style and timing of metamorphic transformations. Here we document a major (~1) decrease in the Mg isotopic composition of the reaction front of an exhumed contact between rocks of subducted crust and serpentinite in the Syros mélange zone. This isotopic perturbation extends over a notable length scale (~1 m), implicating diffusion of Mg through an intergranular fluid network over a period of ~100 kyr. These novel observations confirm models of diffusion-controlled growth of reaction zones formed between rocks of contrasting compositions, such as found at the slab–mantle interface in subduction zones. The results also demonstrate that diffusive processes can result in exotic stable isotope compositions of major elements with implications for mantle xenoliths and complex intrusions.
    Print ISSN: 0022-3530
    Electronic ISSN: 1460-2415
    Topics: Geosciences
    Published by Oxford University Press
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  • 5
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    Isotopic compositions of sulfides in exhumed high‐pressure terranes: Implications for sulfur cycling in subduction zones (2019)
    Wiley
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    Publication Date: 2019
    Description: Abstract Subduction is a key component of Earth's long‐term sulfur cycle; however, the mechanisms that drive sulfur from subducting slabs remain elusive. Isotopes are a sensitive indicator of the speciation of sulfur in fluids, sulfide dissolution‐precipitation reactions, and inferring fluid sources. To investigate these processes, we report δ34S values determined by secondary ion mass spectroscopy (SIMS) in sulfides from a global suite of exhumed high‐pressure rocks. Sulfides are classified into two petrogenetic groups: 1. Metamorphic, which represent closed‐system (re)crystallization from protoliths‐inherited sulfur, and 2. Metasomatic, which formed during open system processes, such as an influx of oxidized sulfur. δ34S values for metamorphic sulfides tend to reflect their precursor compositions: −4.3 to +13.5 ‰ for metabasic rocks, and −32.4 to −11.0 ‰ for metasediments. Metasomatic sulfides exhibit a range of δ34S from −21.7 to +13.9 ‰. We suggest that sluggish sulfur‐self diffusion prevents isotopic fractionation during sulfide breakdown, and that slab fluids inherit the isotopic composition of their source. We estimate a composition of −11 to +8 ‰ for slab fluids, a significantly smaller range than observed for metasomatic sulfides. Large fractionations during metasomatic sulfide precipitation from sulfate‐bearing fluids, and an evolving fluid composition during reactive transport may account for the entire ~36 ‰ range of metasomatic sulfide compositions. Thus, we suggest that sulfate is likely the dominant sulfur species in slab‐derived fluids.
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 6
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    Boron Isotope Analysis of Silicate Glass with Very Low Boron Concentrations by Secondary Ion Mass Spectrometry (2014)
    Wiley
    Details
    Publication Date: 2014-03-23
    Description: Here we present an improved method for the determination of the boron isotopic composition of volcanic glasses with boron concentrations of as low as 0.4–2.5 μg g −1 , as is typical for mid-ocean ridge basalt glasses. The analyses were completed by secondary ion mass spectrometry using a Cameca 1280 large-radius ion microprobe. Transmission and stability of the instrument and analytical protocol were optimised, which led to an improvement of precision and reduction of surface contamination and analysis time compared with earlier studies. Accuracy, reproducibility (0.4–2.3‰, 2 RSD), measurement repeatability (2 RSE = 2.5–4.0‰ for a single spot with [B] = 1 μg g −1 ), matrix effects (〈〈 0.5‰ among komatiitic, dacitic and rhyolitic glass), machine drift (no internal drift; long-term drift: ~ 0.1‰ hr −1 ), contamination (~ 3–8 ng g −1 ) and machine background (0.093 s −1 ) were quantified and their influence on samples with low B concentrations was determined. The newly developed set-up was capable of determining the B isotopic composition of basaltic glass with 1 μg g −1 B with a precision and accuracy of ± 1.5‰ (2 RSE) by completing 4–5 consecutive spot analyses with a spatial resolution of 30 μm x 30 μm. Samples with slightly higher concentrations (≥ 2.5 μg g −1 ) can be analysed with a precision of better than ± 2‰ (internal 2 RSE) with a single spot analysis, which takes 32 min. This article is protected by copyright. All rights reserved.
    Print ISSN: 1639-4488
    Electronic ISSN: 1751-908X
    Topics: Geosciences
    Published by Wiley
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  • 7
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    Development and evolution of detachment faulting along 50km of the Mid-Atlantic Ridge near 16.5°N (2014)
    Wiley
    Details
    Publication Date: 2014-11-19
    Description: A multifaceted study of the slow-spreading Mid-Atlantic Ridge (MAR) at 16.5ºN provides new insights into detachment faulting and its evolution through time. The survey included regional multibeam bathymetry mapping, high-resolution mapping using AUV Sentry , seafloor imaging using the TowCam system, and an extensive rock-dredging program. At different times, detachment faulting was active along ∼50km of the western flank of the study area, and may have dominated spreading on that flank for the last 5 Ma. Detachment morphologies vary and include a classic corrugated massif, non-corrugated massifs, and back-tilted ridges marking detachment breakaways. High-resolution Sentry data reveal one other detachment morphology; a low-angle, irregular surface in the regional bathymetry is shown to be a finely corrugated detachment surface (corrugation wavelength of only tens of meters and relief of just a few meters). Multi-scale corrugations are observed 2-3km from the detachment breakaway suggesting that they formed in the brittle layer, perhaps by anastomosing faults. The thin wedge of hanging wall lavas that covers a low-angle (6º) detachment footwall near its termination are intensely faulted and fissured; this deformation may be enhanced by the low-angle of the emerging footwall. Active detachment faulting currently is limited to the western side of the rift valley. Nonetheless, detachment fault morphologies also are present over a large portion of the eastern flank on crust 〉 2 Ma indicating that within the last 5 Ma parts of the ridge axis have experienced periods of two-sided detachment faulting. This article is protected by copyright. All rights reserved.
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 8
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    Emplacement and High‐Temperature Evolution of Gabbros of the 16.5°N Oceanic Core Complexes (Mid‐Atlantic Ridge): Insights Into the Compositional Variability of the Lower Oceanic Crust (2019)
    Wiley
    Details
    Publication Date: 2019
    Description: Abstract This study reports the composition of the oceanic crust from the 16.5°N region of the Mid‐Atlantic Ridge, a spreading ridge segment characterized by a complex detachment fault system and three main oceanic core complexes (southern, central, and northern OCCs). Lithologies recovered from the core complexes include both greenschist facies and weathered pillow basalt, diabase, peridotite, and gabbro, while only weathered and fresh pillow basalt was dredged from the rift valley floor. The gabbros are compositionally bimodal, with the magmatic crust in the region formed by scattered intrusions of chemically primitive plutonic rocks (i.e., dunites and troctolites), associated with evolved oxide‐bearing gabbros. We use thermodynamic models to infer that this distribution is expected in regions where small gabbroic bodies are intruded into mantle peridotites. The occurrence of ephemeral magma chambers located in the lithospheric mantle enables large proportions of the melt to be erupted after relatively low degrees of fractionation. A large proportion of the dredged gabbros reveal evidence for deformation at high‐temperature conditions. In particular, chemical changes in response to deformation and the occurrence of very high‐temperature ultramylonites (〉1000 °C) suggest that the deformation related to the oceanic detachment commenced at near‐solidus conditions. This event was likely associated with the expulsion of interstitial, evolved magmas from the crystal mush, a mechanism that enhanced the formation of disconnected oxide‐gabbro seams or layers often associated with crystal‐plastic fabrics in the host gabbros. This granulite‐grade event was soon followed by hydrothermal alteration revealed by the formation of amphibole‐rich veins at high‐temperature conditions (~900 °C).
    Electronic ISSN: 1525-2027
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by Wiley on behalf of American Geophysical Union (AGU).
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  • 9
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    Early solar system. Early accretion of water in the inner solar system from a carbonaceous chondrite-like source (2014)
    American Association for the Advancement of Science (AAAS)
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    Publication Date: 2014-11-02
    Description: Determining the origin of water and the timing of its accretion within the inner solar system is important for understanding the dynamics of planet formation. The timing of water accretion to the inner solar system also has implications for how and when life emerged on Earth. We report in situ measurements of the hydrogen isotopic composition of the mineral apatite in eucrite meteorites, whose parent body is the main-belt asteroid 4 Vesta. These measurements sample one of the oldest hydrogen reservoirs in the solar system and show that Vesta contains the same hydrogen isotopic composition as that of carbonaceous chondrites. Taking into account the old ages of eucrite meteorites and their similarity to Earth's isotopic ratios of hydrogen, carbon, and nitrogen, we demonstrate that these volatiles could have been added early to Earth, rather than gained during a late accretion event.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Sarafian, Adam R -- Nielsen, Sune G -- Marschall, Horst R -- McCubbin, Francis M -- Monteleone, Brian D -- New York, N.Y. -- Science. 2014 Oct 31;346(6209):623-6. doi: 10.1126/science.1256717. Epub 2014 Oct 30.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA. asarafian@whoi.edu. ; Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA. ; Department of Geology and Geophysics, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA. Department of Earth and Planetary Sciences, American Museum of Natural History, New York, NY 10024, USA. School of Earth Sciences, University of Bristol, Bristol BS8 1RJ, UK. ; Institute of Meteoritics, University of New Mexico, Albuquerque, NM 87131, USA.〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/25359971" target="_blank"〉PubMed〈/a〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 10
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    Arc magmas sourced from mélange diapirs in subduction zones (2012)
    Springer Nature
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    Publication Date: 2012-11-30
    Description: Nature Geoscience 5, 862 (2012). doi:10.1038/ngeo1634 Authors: Horst R. Marschall & John C. Schumacher
    Print ISSN: 1752-0894
    Electronic ISSN: 1752-0908
    Topics: Geosciences
    Published by Springer Nature
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