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  • Oxford University Press  (78,388)
  • 2010-2014  (78,388)
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  • 1
    Publication Date: 2020-11-20
    Description: Siwi caldera, in the Vanuatu arc (Tanna island), is a rare volcanic complex where both persistent eruptive activity (Yasur volcano)and rapid block resurgence (Yenkahe horst) can be investigated simultaneously during a post-caldera stage. Here we provide new constraints on the feeding system of this volcanic complex, based on a detailed study of the petrology, geochemistry and volatile content of Yasur^Siwi bulk-rocks and melt inclusions, combined with measurements of the chemical composition and mass fluxes of Yasur volcanic gases. Major and trace element analyses of Yasur^ Siwi volcanic rocks, together with literature data for other volcanic centers, point to a single magmatic series and possibly long-lived feeding of Tanna volcanism by a homogeneous arc basalt. Olivine-hosted melt inclusions show that the parental basaltic magma, which produces basaltic-trachyandesites to trachyandesites by 50^70% crystal fractionation, is moderately enriched in volatiles ( 1wt % H2O, 0·1wt % S and 0·055 wt % Cl). The basaltic-trachyandesite magma, emplaced at between 4^5 km depth and the surface, preserves a high temperature (1107 158C) and constant H2O content ( 1wt %) until very shallow depths, where it degasses extensively and crystallizes. These conditions, maintained over the past 1400 years of Yasur activity, require early water loss during basalt differentiation, prevalent open-system degassing, and a relatively high heat flow ( 109W). Yasur volcano releases on average 13·4 103 tons d 1 of H2O and 680 tons d 1 of SO2, but moderate amounts of CO2 (840 tons d 1), HCl (165 tons d 1), and HF (23 tons d 1). Combined with melt inclusion data, these gas outputs constrain a bulk magma degassing rate of 5 107 m3 a 1, about a half of which is due to degassing of the basaltic-trachyandesite. We compute that 25 km3 of this magma have degassed without erupting and have accumulated beneath Siwi caldera over the past 1000 years, which is one order of magnitude larger than the accumulated volume uplift of the Yenkahe resurgent block. Hence, basalt supply and gradual storage of unerupted degassed basaltictrachyandesite could easily account for (or contribute to) the Yenkahe block resurgence.
    Description: Published
    Description: 1077-1105
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 2.4. TTC - Laboratori di geochimica dei fluidi
    Description: JCR Journal
    Description: restricted
    Keywords: Vanuatu arc ; Yasur ; gas fluxes ; volatiles ; melt inclusions ; resurgent block ; volcano thermal budget ; 04. Solid Earth::04.04. Geology::04.04.12. Fluid Geochemistry ; 04. Solid Earth::04.08. Volcanology::04.08.01. Gases ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
    Type: article
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  • 2
    Publication Date: 2020-11-26
    Description: So far, the role of appendicularians in the biogeochemical cycling of organic matter has been largely overlooked. Appendicularians represent only a fraction of total mesozooplankton biomass, however these ubiquitous zooplankters have very high filtration and growth rates compared to copepods, and produce numerous fecal pellets and filtering houses contributing to export production by aggregating small marine particles. To study their quantitative impact on biogeochemical flux, we have included this group in the biogeochemical flux model, using a recently developed ecophysiological model. One-dimensional annual simulations of the pelagic ecosystem including appendicularians were conducted with realistic surface forcing for the year 2000, using data from the DyFAMed open ocean station. The appendicularian grazing impact was generally low, but appendicularians increased detritus production by 8% and export production by 55% compared to a simulation without appendicularians. Therefore, current biogeochemical models lacking appendicularians probably under, or misestimate the detritus and export production by omitting the pathway from small-sized plankton to fast sinking detritus. Detritus production and export rates are 60% lower than the estimates from mesotrophic sites, showing that appendicularians’ role is lower but still significant in oligotrophic environments. The simulated annual export at 200 m exceeds sediment trap values by 44%, suggesting an intense degradation during the sinking of appendicularian detritus, supported by observations made at other sites. Thus, degradation and grazing of appendicularian detritus need better quantification if we are to accurately assess the role of appendicularia in export flux.
    Description: EU-FP6 project SESAME GOCE-036949
    Description: Published
    Description: 855-872
    Description: 3.7. Dinamica del clima e dell'oceano
    Description: JCR Journal
    Description: reserved
    Keywords: BFM ; zooplankton ; 03. Hydrosphere::03.01. General::03.01.01. Analytical and numerical modeling ; 03. Hydrosphere::03.01. General::03.01.07. Physical and biogeochemical interactions ; 03. Hydrosphere::03.04. Chemical and biological::03.04.01. Biogeochemical cycles ; 03. Hydrosphere::03.04. Chemical and biological::03.04.04. Ecosystems
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 3
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    Oxford University Press
    In:  EPIC3Journal of Experimental Botany, Oxford University Press, ISSN: 0022-0957
    Publication Date: 2019-07-17
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
    Publication Date: 2017-04-04
    Description: Crystal-rich lithic clasts occurring in volcanic deposits are key tools to understand processes of storage, cooling, and fractionation of magmas in pre-eruptive volcanic systems. These clasts, indeed, represent snapshots of the magma-chamber/host-rock interface before eruptions and provide information on crystallization, differentiation, and degrees of interaction between magma and wall-rocks. In this study, with the aim to shed light on magma-carbonate interaction and CO2 emission in volcanic areas, we focused on the petrology of cumulate and skarn rocks by using as case study a suite of mafic and calcite-bearing lithic clasts from the Colli Albani Volcanic District. By means of phase relations, bulk rock chemistry, phase compositions, and stable isotope data we have recognized different types of cumulates and skarns. Cumulates containing either clinopyroxene±olivine associated with Cr-bearing spinel or glass+phlogopite have been divided in primitive and differentiated, respectively. Primitive cumulates originate at the interface between a relatively primitive magma and carbonate-bearing rocks and show evidences of olivine instability (i.e. heteradcumulate texture) due to carbonate assimilation. Differentiated cumulates, characterized by Ca-rich olivines, phlogopite, and glass containing calcite, form from a differentiated magma in a system open to CaO-contamination. Skarns has been divided in exoskarns, characterized by xenomorphic texture and abundant calcite, and endoskarns, characterized by hypidiomorphic texture, Ca-Tschermak-rich mineral phases, and interstitial glass. Exoskarns formed by means of solid state reactions in a dolostone protolith whereas endoskarns crystallized at subliquidus temperature from a silicate melt that experienced exoskarns assimilation. Our study evidences that magma-carbonate interaction can not be considered a one step process exhausting just after the formation of skarn shells. Magma and carbonate rocks, when in contact, continuously interact leading to the formation of exoskarns, endoskarns, cumulates (primitive and differentiated ones), and differentiated melts. Finally, by means of oxygen and carbon isotope compositions of calcite in equilibrium with skarns, we demonstrate that carbonate assimilation represents a source of massive CO2 degassing mechanism due to the consumption of calcite and removing of CO2 during the decarbonation process.
    Description: Sapienza Universita' di Roma INGV-DPC [Project V 3.1, Colli Albani].
    Description: Published
    Description: 2307-2332
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: JCR Journal
    Description: reserved
    Keywords: magma/carbonate interaction ; CO2 degassing ; c umulate and skarn ; Colli Albani ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 5
    Publication Date: 2017-04-04
    Description: Stromboli is known for its persistent degassing and rhythmic strombolian activity occasionally punctuated by paroxysmal eruptions. The basaltic pumice and scoria emitted during paroxysms and strombolian activity, respectively, differ in their textures, crystal contents and glass matrix compositions, which testify to distinct conditions of crystallization, degassing and magma ascent. We present here an extensive dataset on major elements and volatiles (CO2, H2O, S and Cl) in olivine-hosted melt inclusions and embayments from pyroclasts emplaced during explosive eruptions of variable magnitude. Magma saturation pressures were assessed from the dissolved amounts of H2O and CO2 taking into account the melt composition evolution. Both pressures and melt inclusion compositions indicate that (1) Ca-basaltic melts entrapped in high-Mg olivines (Fo89–90) generate Stromboli basalts through crystal fractionation, and (2) the Stromboli plumbing system can be imaged as a succession of magma ponding zones connected by dikes. The 7–10 km interval, where magmas are stored and differentiate, is periodically recharged by new magma batches, possibly ranging from Ca-basalts to basalts, with a CO2-rich gas phase. These deep recharges promote the formation of bubbly basalt blobs, which are able to intrude the shallow plumbing system (2–4 km), where CO2 gas fluxing enhances H2O loss, crystallization and generation of crystal-rich, dense, degassed magma. Chlorine partitioning into the H2O–CO2-bearing gas phase accounts for its efficient degassing (≥69%) under the open-system conditions of strombolian activity. Paroxysms, however, are generated through predominantly closed-system ascent of basaltic magma batches from the deep storage zone. In this situation crystallization is negligible and sulfur exsolution starts at ≤170 MPa. Chlorine remains dissolved in the melt until lower pressures, only 16% being lost upon eruption. Finally, we propose a continuum in explosive eruption energy, from strombolian activity to large paroxysmal events, ultimately controlled by variable pressurization of the deep feeding system associated with magma and gas recharges.
    Description: Published
    Description: 603-626
    Description: 2.3. TTC - Laboratori di chimica e fisica delle rocce
    Description: 3.5. Geologia e storia dei vulcani ed evoluzione dei magmi
    Description: JCR Journal
    Description: reserved
    Keywords: Stromboli ; melt inclusions ; magmatic volatiles ; CO2 fluxing ; magma degassing ; 04. Solid Earth::04.04. Geology::04.04.05. Mineralogy and petrology ; 04. Solid Earth::04.08. Volcanology::04.08.03. Magmas
    Repository Name: Istituto Nazionale di Geofisica e Vulcanologia (INGV)
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  • 6
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    Oxford University Press
    In:  EPIC3Ocean Acidification, Oxford, Oxford University Press, pp. 291-311, ISBN: 978-0-19-959109-1
    Publication Date: 2014-04-15
    Repository Name: EPIC Alfred Wegener Institut
    Type: Inbook , peerRev
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  • 7
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    Oxford University Press
    In:  EPIC3Journal of Plankton Research, Oxford University Press, 34(5), pp. 399-415, ISSN: 0142-7873
    Publication Date: 2019-07-17
    Description: This study investigates the relationships between the spring phytoplankton community and environmental factors in the Brazil-Malvinas confluence region. Phytoplankton community composition was determined by the high performance liquid chromatography/CHEMTAX approach, complemented with microscopic examination. Abiotic factors included temperature, salinity, dissolved inorganic macronutrients (ammonium, nitrite, nitrate, phosphate and silicate), water column stability and upper mixed layer depth (UMLD). These environmental variables were reasonably informative to explain the variability of the phytoplankton communities (44% of variation explained). Cluster and canonical correspondence analyses allowed discrimination of four zones (coastal, Sub-Antarctic, tropical and intermediate zones), also identifiable in the T–S diagrams and in the nutrient spatial distribution patterns. The presence of nutrient-rich Sub-Antarctic waters was a major oceanographic feature, associated with diatoms and dinoflagellates. However, in the Sub-Antarctic zone, biomass was particularly low, probably as a result of grazing pressure, as suggested by chemical and biological indicators. In contrast, in oligotrophic tropical waters, phytoplankton was mainly composed by small nanoflagellates and cyanobacteria. A large intermediate zone was also dominated by nanoflagellates, mainly Phaeocystis antarctica, probably favored by strong water column stability. The coastal zone exhibited fairly similar conditions to those in the intermediate zone, but with deeper UMLD, a favorable condition for diatom growth. These results emphasize the importance of the properties of water masses and also biological processes such as grazing in structuring phytoplankton communities in the region.
    Repository Name: EPIC Alfred Wegener Institut
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  • 8
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Conservation Physiology 1 (2013): cot006, doi:10.1093/conphys/cot006.
    Description: Large whales are subjected to a variety of conservation pressures that could be better monitored and managed if physiological information could be gathered readily from free-swimming whales. However, traditional approaches to studying physiology have been impractical for large whales, because there is no routine method for capture of the largest species and there is presently no practical method of obtaining blood samples from free-swimming whales. We review the currently available techniques for gathering physiological information on large whales using a variety of non-lethal and minimally invasive (or non-invasive) sample matrices. We focus on methods that should produce information relevant to conservation physiology, e.g. measures relevant to stress physiology, reproductive status, nutritional status, immune response, health, and disease. The following four types of samples are discussed: faecal samples, respiratory samples (‘blow’), skin/blubber samples, and photographs. Faecal samples have historically been used for diet analysis but increasingly are also used for hormonal analyses, as well as for assessment of exposure to toxins, pollutants, and parasites. Blow samples contain many hormones as well as respiratory microbes, a diverse array of metabolites, and a variety of immune-related substances. Biopsy dart samples are widely used for genetic, contaminant, and fatty-acid analyses and are now being used for endocrine studies along with proteomic and transcriptomic approaches. Photographic analyses have benefited from recently developed quantitative techniques allowing assessment of skin condition, ectoparasite load, and nutritional status, along with wounds and scars from ship strikes and fishing gear entanglement. Field application of these techniques has the potential to improve our understanding of the physiology of large whales greatly, better enabling assessment of the relative impacts of many anthropogenic and ecological pressures.
    Description: This work was supported by the United States Office of Naval Research (award #N000141110435 to K.E.H., award #N000141110540 to R.M.R., and award #N0001412WX20890 to L.C.Y. and C.E.D.); the United Kingdom Natural Environmental Research Council (supporting A.J.H.); the National Center for Research Resources, a component of the United States National Institutes of Health (NIH; supporting C.E.D.); the NIH Roadmap for Medical Research (UL1 RR024146 supporting C.E.D.); The Hartwell Foundation (supporting C.E.D.) and the 2012 Marine Mammal Breath Workshop, which was funded by the National Oceanic and Atmospheric Administration’s Marine Mammal Health and Stranding Response Program.
    Keywords: Blow ; Biopsy dart ; Cetacea ; Faecal samples ; Non-invasive ; Visual health assessment
    Repository Name: Woods Hole Open Access Server
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  • 9
    Publication Date: 2022-05-25
    Description: © 2010 The Authors. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial License. The definitive version was published in ICES Journal of Marine Science: Journal du Conseil 67 (2010): 365-378, doi:10.1093/icesjms/fsp262.
    Description: A commercial acoustic system, originally designed for seafloor applications, has been adapted for studying fish with swimbladders. The towed system contains broadband acoustic channels collectively spanning the frequency range 1.7–100 kHz, with some gaps. Using a pulse-compression technique, the range resolution of the echoes is ~20 and 3 cm in the lower and upper ranges of the frequencies, respectively, allowing high-resolution imaging of patches and resolving fish near the seafloor. Measuring the swimbladder resonance at the lower frequencies eliminates major ambiguities normally associated with the interpretation of fish echo data: (i) the resonance frequency can be used to estimate the volume of the swimbladder (inferring the size of fish), and (ii) signals at the lower frequencies do not depend strongly on the orientation of the fish. At-sea studies of Atlantic herring demonstrate the potential for routine measurements of fish size and density, with significant improvements in accuracy over traditional high-frequency narrowband echosounders. The system also detected patches of scatterers, presumably zooplankton, at the higher frequencies. New techniques for quantitative use of broadband systems are presented, including broadband calibration and relating target strength and volume-scattering strength to quantities associated with broadband signal processing.
    Description: The research was supported by the US Office of Naval Research, grants number N00014-04-1-0440 and N00014-04-1-0475, NOAA/CICOR cooperative agreement NA17RJ1223, NOAA/ National Marine Fisheries Service, and the J. Seward Johnson Chair of the WHOI Academic Programs Office.
    Keywords: Acoustic scattering ; Broadband ; Echosounder ; Fish ; Resonance
    Repository Name: Woods Hole Open Access Server
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  • 10
    Publication Date: 2022-05-25
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): W82-W87, doi:10.1093/nar/gks418.
    Description: Amplicon sequencing of the hypervariable regions of the small subunit ribosomal RNA gene is a widely accepted method for identifying the members of complex bacterial communities. Several rRNA gene sequence reference databases can be used to assign taxonomic names to the sequencing reads using BLAST, USEARCH, GAST or the RDP classifier. Next-generation sequencing methods produce ample reads, but they are short, currently ∼100–450 nt (depending on the technology), as compared to the full rRNA gene of ∼1550 nt. It is important, therefore, to select the right rRNA gene region for sequencing. The primers should amplify the species of interest and the hypervariable regions should differentiate their taxonomy. Here, we introduce TaxMan: a web-based tool that trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. It allows interactive plotting of taxa, both amplified and missed in silico by the primers used. Additionally, using the trimmed sequences improves the speed of sequence matching algorithms. The smaller database greatly improves run times (up to 98%) and memory usage, not only of similarity searching (BLAST), but also of chimera checking (UCHIME) and of clustering the reads (UCLUST). TaxMan is available at http://www.ibi.vu.nl/programs/taxmanwww/.
    Description: University of Amsterdam under the research priority area ‘Oral Infections and Inflammation’ (to B.W.B.); National Science Foundation [NSF/BDI 0960626 to S.M.H.]; the European Union Seventh Framework Programme (FP7/ 2007-2013) under ANTIRESDEV grant agreement no 241446 (to E.Z.).
    Repository Name: Woods Hole Open Access Server
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  • 11
    Publication Date: 2022-05-25
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Briefings in Bioinformatics 15 (2014): 783-787, doi:10.1093/bib/bbt010.
    Description: The extremely high error rates reported by Keegan et al. in ‘A platform-independent method for detecting errors in metagenomic sequencing data: DRISEE’ (PLoS Comput Biol 2012;8:e1002541) for many next-generation sequencing datasets prompted us to re-examine their results. Our analysis reveals that the presence of conserved artificial sequences, e.g. Illumina adapters, and other naturally occurring sequence motifs accounts for most of the reported errors. We conclude that DRISEE reports inflated levels of sequencing error, particularly for Illumina data. Tools offered for evaluating large datasets need scrupulous review before they are implemented.
    Description: National Institutes of Health [1UH2DK083993 to M.L.S.]; National Science Foundation [BDI- 096026 to S.M.H.].
    Keywords: Next-generation sequencing ; Sequencing error ; Adapter ligation ; PCR ; Quality score
    Repository Name: Woods Hole Open Access Server
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  • 12
    Publication Date: 2022-05-25
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial License. The definitive version was published in Journal of Plankton Research 32 (2010): 1355-1368, doi:10.1093/plankt/fbq062.
    Description: Increasing availability and extent of biological ocean time series (from both in situ and satellite data) have helped reveal significant phenological variability of marine plankton. The extent to which the range of this variability is modified as a result of climate change is of obvious importance. Here we summarize recent research results on phenology of both phytoplankton and zooplankton. We suggest directions to better quantify and monitor future plankton phenology shifts, including (i) examining the main mode of expected future changes (ecological shifts in timing and spatial distribution to accommodate fixed environmental niches vs. evolutionary adaptation of timing controls to maintain fixed biogeography and seasonality), (ii) broader understanding of phenology at the species and community level (e.g. for zooplankton beyond Calanus and for phytoplankton beyond chlorophyll), (iii) improving and diversifying statistical metrics for indexing timing and trophic synchrony and (iv) improved consideration of spatio-temporal scales and the Lagrangian nature of plankton assemblages to separate time from space changes.
    Description: This study was supported by NSF grants to R.J.: OCE-0727033, 0815838 and 0732152. NSF grants to A.C.T.: OCE-0535386, 0815051 and 0814413. NSF grant to J.A.R.: OCE 0815336.
    Keywords: Plankton ; Phenology ; Life history ; Climate change
    Repository Name: Woods Hole Open Access Server
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  • 13
    Publication Date: 2022-05-25
    Description: © The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution-Noncommercial 2.5 License. The definitive version was published in Genome Biology and Evolution 2 (2010): 304, doi:10.1093/gbe/evq022.
    Description: Reduction of various biological processes is a hallmark of the parasitic lifestyle. Generally, the more intimate the association between parasites and hosts the stronger the parasite relies on its host's physiology for survival and reproduction. However, some systems have been held to be indispensable, for example, the core pathways of carbon metabolism that produce energy from sugars. Even the most hardened anaerobes that lack oxidative phosphorylation and the tricarboxylic acid cycle have retained glycolysis and some downstream means to generate ATP. Here we describe the deep-coverage genome resequencing of the pathogenic microsporidiian, Enterocytozoon bieneusi, which shows that this parasite has crossed this line and abandoned complete pathways for the most basic carbon metabolism. Comparing two genome sequence surveys of E. bieneusi to genomic data from four other microsporidia reveals a normal complement of 353 genes representing 30 functional pathways in E. bieneusi, except that only 2 out of 21 genes collectively involved in glycolysis, pentose phosphate, and trehalose metabolism are present. Similarly, no genes encoding proteins involved in the processing of spliceosomal introns were found. Altogether, E. bieneusi appears to have no fully functional pathway to generate ATP from glucose. Therefore, this intracellular parasite relies on transporters to import ATP from its host.
    Description: This work was supported by grants from the Canadian Institutes for Health Research (MOP-84265), the National Institutes of Health (NIH AI31788, R21 AI52792, and R21 AI064118), and the National Science Foundation (MCB- 0135272). N.C. is a Scholar of the Canadian Institute for Advanced Research and is supported by a fellowship from the Swiss National Science Foundation (NSF) (PA00P3- 124166). D.E. is supported by the Swiss NSF. P.J.K. is a Fellow of the Canadian Institute for Advanced Research and a Senior Scholar of the Michael Smith Foundation for Health Research.
    Keywords: Microsporidia ; Parasite ; Glycolysis ; Carbon metabolism ; Reduction ; Evolution
    Repository Name: Woods Hole Open Access Server
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  • 14
    Publication Date: 2022-05-25
    Description: Author Posting. © The Authors, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 197 (2014): 697-704, doi:10.1093/gji/ggu048.
    Description: After the 1960 M9.5 Valdivia, Chile earthquake, three types of geodetic observations were made during four time periods at nearby locations. These post-seismic observations were previously explained by post-seismic afterslip on the downdip extension of the 1960 rupture plane. In this study, we demonstrate that the post-seismic observations can be explained alternatively by volumetric viscoelastic relaxation of the asthenosphere mantle. In searching for the best-fitting viscosity model, we invert for two variables, the thickness of the elastic lithosphere, He, and the effective Maxwell decay time of the asthenosphere mantle, TM, assuming a 100-km-thick asthenosphere mantle. The best solutions to fit the observations in four sequential time periods, 1960–1964, 1960–1968, 1965–1973 and 1980–2010, each yield a similar He value of about 65 km but significantly increasing TM values of 0.7, 6, 10 and 80 yr, respectively. We calculate the corresponding viscoelastic Coulomb stress increase since 1960 on the future rupture plane of the 2010 M8.8 Maule, Chile earthquake. The calculated viscoelastic stress increase on the 2010 rupture plane varies gradually from 13.1 bars at the southern end to 0.1 bars at the northern end. In contrast, the stress increase caused by an afterslip model has a similar spatial distribution but slightly smaller values of 0.1–3.2 bars on the 2010 rupture plane.
    Description: This work was supported by a MIT/WHOI Joint Program Student Fellowship and a Graduate Student Fellowship from the WHOI Deep Ocean Exploration Institute (MD), as well as NSF Grant OCE-1141785 and a Deerbrook Foundation Award (JL).
    Keywords: Seismic cycle ; Transient deformation ; Seismicity and tectonics ; Subduction zone processes ; Dynamics: seismotectonics ; South America
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  • 15
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    Oxford University Press
    In:  EPIC3Geophysical Journal International, Oxford University Press, 193(3), pp. 1399-1414, ISSN: 0956-540X
    Publication Date: 2019-07-16
    Description: The Boreas Basin is located in the Norwegian-Greenland Sea between Northeast Greenland and Svalbard. Towards the east, it is bounded by the ultraslow mid-ocean Knipovich Ridge. Here, we present a 340-km-long seismic refraction line acquired during the expedition ARK-XXIV/3 of research vessel Polarstern in 2009, using 18 ocean bottom seismometers. It crosses the central Boreas Basin from the Knipovich Ridge to the Northeast Greenland margin. Thus, the line provides the first reliable crustal structure information of this basin. In addition, the gravity data acquired parallel to the seismic refraction line are used to calculate a 2.5-D gravity model. The P-wave velocity model shows an unusual ∼3-km-thin oceanic crust with seismic velocities less than 6.3 km s−1, indicating the absence of a significant oceanic layer 3. Mantle velocities vary between 7.5 kms−1 in the uppermost mantle and 8.0 km s−1 at approximately 15 km depth. The low velocities within the upper mantle may be explained by 13 per cent serpentinisation, which is negligible at about 15 km depth. Furthermore, the S-wave velocity model shows low Vp/Vs ratios in the mantle, indicating a highly serpentinised mantle at shallow depths. The gravity model has crustal densities between 2.3 and 2.9 g cm−3, which also point towards the absence of a significant thick oceanic layer 3. The results of our seismic refraction line and other geophysical data indicate that the entire Boreas Basin opened at ultraslow spreading rates since at least ∼28 Ma. No evidence for an extinct spreading ridge in the centre of the Boreas Basin was found.
    Repository Name: EPIC Alfred Wegener Institut
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  • 16
    Publication Date: 2022-05-26
    Description: © The Author(s), 2013. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 5 (2013): 2368-2381, doi:10.1093/gbe/evt179.
    Description: The dinoflagellates are an evolutionarily and ecologically important group of microbial eukaryotes. Previous work suggests that horizontal gene transfer (HGT) is an important source of gene innovation in these organisms. However, dinoflagellate genomes are notoriously large and complex, making genomic investigation of this phenomenon impractical with currently available sequencing technology. Fortunately, de novo transcriptome sequencing and assembly provides an alternative approach for investigating HGT. We sequenced the transcriptome of the dinoflagellate Alexandrium tamarense Group IV to investigate how HGT has contributed to gene innovation in this group. Our comprehensive A. tamarense Group IV gene set was compared with those of 16 other eukaryotic genomes. Ancestral gene content reconstruction of ortholog groups shows that A. tamarense Group IV has the largest number of gene families gained (314–1,563 depending on inference method) relative to all other organisms in the analysis (0–782). Phylogenomic analysis indicates that genes horizontally acquired from bacteria are a significant proportion of this gene influx, as are genes transferred from other eukaryotes either through HGT or endosymbiosis. The dinoflagellates also display curious cases of gene loss associated with mitochondrial metabolism including the entire Complex I of oxidative phosphorylation. Some of these missing genes have been functionally replaced by bacterial and eukaryotic xenologs. The transcriptome of A. tamarense Group IV lends strong support to a growing body of evidence that dinoflagellate genomes are extraordinarily impacted by HGT.
    Description: J.H.W. was supported by the NSF IGERT Program in Comparative Genomics at the University of Arizona (grant number DGE-0654435). This work was supported by grants from the National Science Foundation (grant numbers OCE-0723498, EF-0732440) and funding provided by the BIO5 Institute at the University of Arizona to J.D.H.
    Keywords: Gene innovation ; Alexandrium tamarense Group IV ; Phylogenetic profile ; Phylogenomics ; De novo transcriptome assembly ; Mitochondrial metabolism
    Repository Name: Woods Hole Open Access Server
    Type: Article
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  • 17
    Publication Date: 2022-05-26
    Description: Author Posting. © Author, 2014. This article is posted here by permission of The Royal Astronomical Society for personal use, not for redistribution. The definitive version was published in Geophysical Journal International 198 (2014): 622-636, doi: 10.1093/gji/ggu121.
    Description: The robust statistical model of a Gaussian core contaminated by outlying data that underlies robust estimation of the magnetotelluric (MT) response function has been re-examined. The residuals from robust estimators are systematically long tailed compared to a distribution based on the Gaussian, and hence are inconsistent with the robust model. Instead, MT data are pervasively described by the alpha stable distribution family whose variance and sometimes mean are undefined. A maximum likelihood estimator (MLE) that exploits the stable nature of MT data is formulated, and its two-stage implementation in which stable parameters are first fit to the data and then the MT responses are solved for is described. The MLE is shown to be inherently robust, but differs from the conventional robust estimator because it is based on a model derived from the data, while robust estimators are ad hoc, being based on the robust model that is inconsistent with actual data. Propriety versus impropriety of the complex MT response was investigated, and a likelihood ratio test for propriety and its null distribution was established. The Cramér-Rao lower bounds for the covariance matrix of proper and improper MT responses were specified. The MLE was applied to exemplar long period and broad-band data sets from South Africa. Both are shown to be significantly stably distributed using the Kolmogorov–Smirnov goodness of fit and Ansari-Bradley non-parametric dispersion tests. Impropriety of the MT responses at both sites is pervasive, hence the improper Cramér-Rao bound was used to estimate the MLE covariance. The MLE is shown to be nearly unbiased and well described by a Gaussian distribution based on bootstrap simulation. The MLE was compared to a conventional robust estimator, establishing that the standard errors of the former are systematically smaller than for the latter and that the standardized differences between them exhibit excursions that are both too frequent and too large to be described by a Gaussian model. This is ascribed to pervasive bias of the robust estimator that is to some degree obscured by their systematically large confidence bounds. Finally, a series of topics for further investigation is proposed.
    Description: This work was supported by NSF grant EAR0809074.
    Keywords: Time series analysis ; Numerical approximations and analysis ; Fractals and multifractals ; Probability distributions ; Magnetotellurics
    Repository Name: Woods Hole Open Access Server
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  • 18
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Journal of Plankton Research 36 (2014): 943-955, doi:10.1093/plankt/fbu029.
    Description: The mechanisms by which phytoplankton cope with stressors in the marine environment are neither fully characterized nor understood. As viruses are the most abundant entities in the global ocean and represent a strong top-down regulator of phytoplankton abundance and diversity, we sought to characterize the cellular response of two marine haptophytes to virus infection in order to gain more knowledge about the nature and diversity of microalgal responses to this chronic biotic stressor. We infected laboratory cultures of the haptophytes Haptolina ericina and Phaeocystis pouchetii with CeV-01B or PpV-01B dsDNA viruses, respectively, and assessed the extent to which host cellular responses resemble programmed cell death (PCD) through the activation of diagnostic molecular and biochemical markers. Pronounced DNA fragmentation and activation of cysteine aspartate-specific proteases (caspases) were only detected in virus-infected cultures of these phytoplankton. Inhibition of host caspase activity by addition of the pan-caspase inhibitor z-VAD-fmk did not impair virus production in either host–virus system, differentiating it from the Emiliania huxleyi-Coccolithovirus model of haptophyte–virus interactions. Nonetheless, our findings point to a general conservation of PCD-like activation during virus infection in ecologically diverse haptophytes, with the subtle heterogeneity of cell death biochemical responses possibly exerting differential regulation on phytoplankton abundance and diversity.
    Description: Funding to J.L.R, R.-A.S. and A.L. was provided by the Norwegian Research Council for the “VIPMAP” (nr. 186142) and “HAPTODIV” (nr. 190307) projects, and by the European Research Council Advanced Grant ERC-AG-LS8 “Microbial Network Organisation” (MINOS, project number 250254). J.L.R. received a FRIBIO overseas research fellowship from the Norwegian Research Council. K.D.B. and B.V.M. were supported by funding from the United States National Science Foundation (OCE-1061883).
    Keywords: Caspase ; DNA fragmentation ; IETD ; Phycodnaviridae ; z-VAD-fmk ; Haptophyte
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  • 19
    Publication Date: 2022-05-26
    Description: © The Author(s), 2014. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology and Evolution 6 (2014): 2210-2217, doi:10.1093/gbe/evu177.
    Description: The alpha subunits of voltage-gated calcium channels (Cavs) are large transmembrane proteins responsible for crucial physiological processes in excitable cells. They are assisted by three auxiliary subunits that can modulate their electrical behavior. Little is known about the evolution and roles of the various subunits of Cavs in nonbilaterian animals and in nonanimal lineages. For this reason, we mapped the phyletic distribution of the four channel subunits and reconstructed their phylogeny. Although alpha subunits have deep evolutionary roots as ancient as the split between plants and opistokonths, beta subunits appeared in the last common ancestor of animals and their close-relatives choanoflagellates, gamma subunits are a bilaterian novelty and alpha2/delta subunits appeared in the lineage of Placozoa, Cnidaria, and Bilateria. We note that gene losses were extremely common in the evolution of Cavs, with noticeable losses in multiple clades of subfamilies and also of whole Cav families. As in vertebrates, but not protostomes, Cav channel genes duplicated in Cnidaria. We characterized by in situ hybridization the tissue distribution of alpha subunits in the sea anemone Nematostella vectensis, a nonbilaterian animal possessing all three Cav subfamilies common to Bilateria. We find that some of the alpha subunit subtypes exhibit distinct spatiotemporal expression patterns. Further, all six sea anemone alpha subunit subtypes are conserved in stony corals, which separated from anemones 500 MA. This unexpected conservation together with the expression patterns strongly supports the notion that these subtypes carry unique functional roles.
    Keywords: Voltage-gated calcium channel ; Ion channel ; Cnidaria ; Nematostella vectensis ; Evolution of nervous system
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  • 20
    Publication Date: 2022-05-26
    Description: © The Author(s), 2012. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Nucleic Acids Research 40 (2012): 7132-7149, doi:10.1093/nar/gks467.
    Description: The capacity of microorganisms to respond to variable external conditions requires a coordination of environment-sensing mechanisms and decision-making regulatory circuits. Here, we seek to understand the interplay between these two processes by combining high-throughput measurement of time-dependent mRNA profiles with a novel computational approach that searches for key genetic triggers of transcriptional changes. Our approach helped us understand the regulatory strategies of a respiratorily versatile bacterium with promising bioenergy and bioremediation applications, Shewanella oneidensis, in minimal and rich media. By comparing expression profiles across these two conditions, we unveiled components of the transcriptional program that depend mainly on the growth phase. Conversely, by integrating our time-dependent data with a previously available large compendium of static perturbation responses, we identified transcriptional changes that cannot be explained solely by internal network dynamics, but are rather triggered by specific genes acting as key mediators of an environment-dependent response. These transcriptional triggers include known and novel regulators that respond to carbon, nitrogen and oxygen limitation. Our analysis suggests a sequence of physiological responses, including a coupling between nitrogen depletion and glycogen storage, partially recapitulated through dynamic flux balance analysis, and experimentally confirmed by metabolite measurements. Our approach is broadly applicable to other systems.
    Description: Office of Science (BER), U.S. Department of Energy [DE-FG02-07ER64388 to D.S. and DE-FG02- 08ER64511 to M.H.S.]; National Aeronautics and Space Administration, NASA Astrobiology Institute [NNA08CN84A to D.S.].
    Repository Name: Woods Hole Open Access Server
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  • 21
    Publication Date: 2013-09-07
    Description: The predicted effect of effective population size on the distribution of fitness effects and substitution rate is critically dependent on the relationship between sequence and fitness. This highlights the importance of using models that are informed by the molecular biology, biochemistry, and biophysics of the evolving systems. We describe a computational model based on fundamental aspects of biophysics, the requirement for (most) proteins to be thermodynamically stable. Using this model, we find that differences in population size have minimal impact on the distribution of population-scaled fitness effects, as well as on the rate of molecular evolution. This is because larger populations result in selection for more stable proteins that are less affected by mutations. This reduction in the magnitude of the fitness effects almost exactly cancels the greater selective pressure resulting from the larger population size. Conversely, changes in the population size in either direction cause transient increases in the substitution rate. As differences in population size often correspond to changes in population size, this makes comparisons of substitution rates in different lineages difficult to interpret.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 22
    Publication Date: 2013-09-08
    Description: O -GlcNAcylation is an inducible, highly dynamic and reversible post-translational modification, mediated by a unique enzyme named O -linked N -acetyl- d -glucosamine ( O -GlcNAc) transferase (OGT). In response to nutrients, O -GlcNAc levels are differentially regulated on many cellular proteins involved in gene expression, translation, immune reactions, protein degradation, protein–protein interaction, apoptosis and signal transduction. In contrast to eukaryotic cells, little is known about the role of O -GlcNAcylation in the viral life cycle. Here, we show that the overexpression of the OGT reduces the replication efficiency of Kaposi's sarcoma-associated herpesvirus (KSHV) in a dose-dependent manner. In order to investigate the global impact of O -GlcNAcylation in the KSHV life cycle, we systematically analyzed the 85 annotated KSHV-encoded open reading frames for O -GlcNAc modification. For this purpose, an immunoprecipitation (IP) strategy with three different approaches was carried out and the O -GlcNAc signal of the identified proteins was properly controlled for specificity. Out of the 85 KSHV-encoded proteins, 18 proteins were found to be direct targets for O -GlcNAcylation. Selected proteins were further confirmed by mass spectrometry for O -GlcNAc modification. Correlation of the functional annotation and the O -GlcNAc status of KSHV proteins showed that the predominant targets were proteins involved in viral DNA synthesis and replication. These results indicate that O -GlcNAcylation plays a major role in the regulation of KSHV propagation.
    Print ISSN: 0959-6658
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  • 23
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    Oxford University Press
    Publication Date: 2013-09-08
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  • 24
    Publication Date: 2013-09-08
    Print ISSN: 0959-6658
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  • 25
    Publication Date: 2013-09-08
    Description: Galectins are potent adhesion/growth-regulatory effectors with characteristic expression profiles. Understanding the molecular basis of gene regulation in each case requires detailed information on copy number of genes and sequence(s) of their promoter(s). Our report reveals plasticity in this respect between galectins and species. We here describe occurrence of a two-gene constellation for human galectin (Gal)-7 and define current extent of promoter-sequence divergence. Interestingly, cross-species genome analyses also detected single-copy display. Because the regulatory potential will then be different, extrapolations of expression profiles are precluded between respective species pairs. Gal-4 coding in chromosomal vicinity was found to be confined to one gene, whereas copy-number variation also applied to Gal-9. The example of rat Gal-9 teaches the lesson that the presence of multiple bands in Southern blotting despite a single-copy gene constellation is attributable to two pseudogenes. The documented copy-number variability should thus be taken into consideration when studying regulation of galectin genes, in a species and in comparison between species.
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  • 26
    Publication Date: 2013-09-08
    Description: In studying the molecular basis for the potent immune activity of previously described gamma and delta inulin particles and to assist in production of inulin adjuvants under Good Manufacturing Practice, we identified five new inulin isoforms, bringing the total to seven plus the amorphous form. These isoforms comprise the step-wise inulin developmental series amorphous -〉 alpha-1 (AI-1) -〉 alpha-2 (AI-2) -〉 gamma (GI) -〉 delta (DI) -〉 zeta (ZI) -〉 epsilon (EI) -〉 omega (OI) in which each higher isoform can be made either by precipitating dissolved inulin or by direct conversion from its precursor, both cases using regularly increasing temperatures. At higher temperatures, the shorter inulin polymer chains are released from the particle and so the key difference between isoforms is that each higher isoform comprises longer polymer chains than its precursor. An increasing trend of degree of polymerization is confirmed by end-group analysis using 1 H nuclear magnetic resonance spectroscopy. Inulin isoforms were characterized by the critical temperatures of abrupt phase-shifts (solubilizations or precipitations) in water suspensions. Such (aqueous) "melting" or "freezing" points are diagnostic and occur in strikingly periodic steps reflecting quantal increases in noncovalent bonding strength and increments in average polymer lengths. The (dry) melting points as measured by modulated differential scanning calorimetry similarly increase in regular steps. We conclude that the isoforms differ in repeated increments of a precisely repeating structural element. Each isoform has a different spectrum of biological activities and we show the higher inulin isoforms to be more potent alternative complement pathway activators.
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  • 27
    Publication Date: 2013-09-08
    Description: The methylotrophic yeast, Pichia pastoris , is an important organism used for the production of therapeutic proteins. Previously, we have reported the glycoengineering of this organism to produce human-like N -linked glycans but up to now no one has addressed engineering the O -linked glycosylation pathway. Typically, O -linked glycans produced by wild-type P. pastoris are linear chains of four to five α-linked mannose residues, which may be capped with β- or phospho-mannose. Previous genetic engineering of the N-linked glycosylation pathway of P. pastoris has eliminated both of these two latter modifications, resulting in O -linked glycans which are linear α-linked mannose structures. Here, we describe a method for the co-expression of an α-1,2-mannosidase, which reduces these glycans to primarily a single O -linked mannose residue. In doing so, we have reduced the potential of these glycans to interact with carbohydrate-binding proteins, such as dendritic cell-specific intercellular adhesion molecule-3-grabbing non-integrin. Furthermore, the introduction of the enzyme protein- O -linked-mannose β-1,2- N -acetylglucosaminyltransferase 1, resulted in the capping of the single O -linked mannose residues with N -acetylglucosamine. Subsequently, this glycoform was extended into human-like sialylated glycans, similar in structure to α-dystroglycan-type glycoforms. As such, this represents the first example of sialylated O -linked glycans being produced in yeast and extends the utility of the P. pastoris production platform beyond N -linked glycosylated biotherapeutics to include molecules possessing O -linked glycans.
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  • 28
    Publication Date: 2013-09-08
    Description: Neurons and other cells require intracellular transport of essential components for viability and function. Previous work has shown that while net amyloid precursor protein (APP) transport is generally anterograde, individual vesicles containing APP move bi-directionally. This discrepancy highlights our poor understanding of the in vivo regulation of APP-vesicle transport. Here, we show that reduction of presenilin (PS) or suppression of gamma-secretase activity substantially increases anterograde and retrograde velocities for APP vesicles. Strikingly, PS deficiency has no effect on an unrelated cargo vesicle class containing synaptotagmin, which is powered by a different kinesin motor. Increased velocities caused by PS or gamma-secretase reduction require functional kinesin-1 and dynein motors. Together, our findings suggest that a normal function of PS is to repress kinesin-1 and dynein motor activity during axonal transport of APP vesicles. Furthermore, our data suggest that axonal transport defects induced by loss of PS-mediated regulatory effects on APP-vesicle motility could be a major cause of neuronal and synaptic defects observed in Alzheimer's Disease (AD) pathogenesis. Thus, perturbations of APP/PS transport could contribute to early neuropathology observed in AD, and highlight a potential novel therapeutic pathway for early intervention, prior to neuronal loss and clinical manifestation of disease.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
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  • 29
    Publication Date: 2013-09-08
    Description: With age, muscle mass and integrity are progressively lost leaving the elderly frail, weak and unable to independently care for themselves. Defined as sarcopenia, this age-related muscle atrophy appears to be multifactorial but its definite cause is still unknown. Mitochondrial dysfunction has been implicated in this process. Using a novel transgenic mouse model of mitochondrial DNA (mtDNA) double-strand breaks (DSBs) that presents a premature aging-like phenotype, we studied the role of mtDNA damage in muscle wasting. We caused DSBs in mtDNA of adult mice using a ubiquitously expressed mitochondrial-targeted endonuclease, mito- Pst I. We found that a short, transient systemic mtDNA damage led to muscle wasting and a decline in locomotor activity later in life. We found a significant decline in muscle satellite cells, which decreases the muscle's capacity to regenerate and repair during aging. This phenotype was associated with impairment in acetylcholinesterase (AChE) activity and assembly at the neuromuscular junction (NMJ), also associated with muscle aging. Our data suggests that systemic mitochondrial dysfunction plays important roles in age-related muscle wasting by preferentially affecting the myosatellite cell pool.
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  • 30
    Publication Date: 2013-09-09
    Description: Populations of widely distributed species encounter and must adapt to local environmental conditions. However, comprehensive characterization of the genetic basis of adaptation is demanding, requiring genome-wide genotype data, multiple sampled populations, and an understanding of population structure and potential selection pressures. Here, we used single-nucleotide polymorphism genotyping and data on numerous environmental variables to describe the genetic basis of local adaptation in 21 populations of teosinte, the wild ancestor of maize. We found complex hierarchical genetic structure created by altitude, dispersal events, and admixture among subspecies, which complicated identification of locally beneficial alleles. Patterns of linkage disequilibrium revealed four large putative inversion polymorphisms showing clinal patterns of frequency. Population differentiation and environmental correlations suggest that both inversions and intergenic polymorphisms are involved in local adaptation.
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  • 31
    Publication Date: 2013-09-10
    Description: We present a methodology for infrasonic remote sensing of winds in the stratosphere that does not require discrete ground-truth events. Our method uses measured time delays between arrays of sensors to provide group velocities (referred to here as celerities) and then minimizes the difference between observed and predicted celerities by perturbing an initial atmospheric specification. Because we focus on interarray propagation effects, it is not necessary to simulate the full propagation path from source to receiver. This feature allows us to use a relatively simple forward model that is applicable over short-regional distances. By focusing on stratospheric returns, we show that our non-linear inversion scheme converges much better if the starting model contains a strong stratospheric duct. Using the Horizontal Wind Model (HWM)/Mass Spectrometer Incoherent Scatter (MSISE) empirical climatology as a starting model, we demonstrate that the inversion scheme is robust to large uncertainties in backazimuth, but that uncertainties in the measured trace velocity and celerity require the use of prior constraints to ensure suitable convergence. The inversion of synthetic data, using realistic estimates of measurement error, shows that our scheme will nevertheless improve upon a starting model under most scenarios. The inversion scheme is applied to infrasound data recorded from a large event on 2010 December 25, which is presumed to be a bolide, using data from a nine-element infrasound network in Utah. We show that our recorded data require a stronger zonal wind speed in the stratosphere than is present in the HWM profile, and are more consistent with the Ground-to-Space (G2S) profile.
    Print ISSN: 0956-540X
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    Topics: Geosciences
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  • 32
    Publication Date: 2013-09-10
    Description: Coda- Q is a stochastic parameter reflecting the heterogeneities of medium that seismic waves travel through. We confirmed that coda- Q would vary with the stress loaded to an elastic medium using numerical simulations of seismic wave propagation. When the stress is loaded, cracks in the crust could either close or newly open. The closure and opening of the cracks are not random but depending on the magnitude and the direction of the stress and the crack aspect ratio. The cracks in the medium after loading stress could be aligned in a specific orientation, and elastic wave velocity field would become anisotropic due to the alignment of specific crack orientations. Elastic wave velocity is in general faster along the direction corresponding with the crack orientation while slower along the perpendicular direction. In the numerical simulation, the effect of anisotropy in elastic wave velocity field due to the selective closure and opening of the cracks is calculated using a 2-D finite difference method assuming elastic wave velocity to be a function of the magnitude of loaded stress. The coda- Q calculated from seismic waves simulated for a model varies when the averaged normal stress changes. Our simulation indicated that the sensitivity of coda- Q –1 , that is the reciprocal of the coda- Q , would be 1.0 10 –2 (1.0 MPa –1 ) against the magnitude of the confining pressure and 1.0 10 –3 (1.0 deg –1 ) against the direction of principal stress. We would like to conclude that coda- Q , a stochastic parameter reflecting heterogeneities of subsurface medium, could become a quantitative state indicator of the stress field of the medium where seismic waves propagate through. Spatiotemporal variation of coda- Q reflects change in the stress field in the crust.
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  • 33
    Publication Date: 2013-09-10
    Description: How do body-wave traveltimes constrain the Earth's radial (1-D) seismic structure? Existing 1-D seismological models underpin 3-D seismic tomography and earthquake location algorithms. It is therefore crucial to assess the quality of such 1-D models, yet quantifying uncertainties in seismological models is challenging and thus often ignored. Ideally, quality assessment should be an integral part of the inverse method. Our aim in this study is twofold: (i) we show how to solve a general Bayesian non-linear inverse problem and quantify model uncertainties, and (ii) we investigate the constraint on spherically symmetric P -wave velocity ( V P ) structure provided by body-wave traveltimes from the EHB bulletin (phases Pn , P , PP and PKP ). Our approach is based on artificial neural networks, which are very common in pattern recognition problems and can be used to approximate an arbitrary function. We use a Mixture Density Network to obtain 1-D marginal posterior probability density functions (pdfs), which provide a quantitative description of our knowledge on the individual Earth parameters. No linearization or model damping is required, which allows us to infer a model which is constrained purely by the data. We present 1-D marginal posterior pdfs for the 22 V P parameters and seven discontinuity depths in our model. P -wave velocities in the inner core, outer core and lower mantle are resolved well, with standard deviations of ~0.2 to 1 per cent with respect to the mean of the posterior pdfs. The maximum likelihoods of V P are in general similar to the corresponding ak135 values, which lie within one or two standard deviations from the posterior means, thus providing an independent validation of ak135 in this part of the radial model. Conversely, the data contain little or no information on P -wave velocity in the D '' layer, the upper mantle and the homogeneous crustal layers. Further, the data do not constrain the depth of the discontinuities in our model. Using additional phases available in the ISC bulletin, such as PcP , PKKP and the converted phases SP and ScP , may enhance the resolvability of these parameters. Finally, we show how the method can be extended to obtain a posterior pdf for a multidimensional model space. This enables us to investigate correlations between model parameters.
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  • 34
    Publication Date: 2013-09-10
    Description: We have developed a network optimization method for regional-scale microseismic monitoring networks and applied it to optimize the densification of the existing seismic network in northeastern Switzerland. The new network will build the backbone of a 10-yr study on the neotectonic activity of this area that will help to better constrain the seismic hazard imposed on nuclear power plants and waste repository sites. This task defined the requirements regarding location precision (0.5 km in epicentre and 2 km in source depth) and detection capability [magnitude of completeness M c  = 1.0 ( M L )]. The goal of the optimization was to find the geometry and size of the network that met these requirements. Existing stations in Switzerland, Germany and Austria were considered in the optimization procedure. We based the optimization on the simulated annealing approach proposed by Hardt & Scherbaum, which aims to minimize the volume of the error ellipsoid of the linearized earthquake location problem ( D -criterion). We have extended their algorithm to: calculate traveltimes of seismic body waves using a finite difference ray tracer and the 3-D velocity model of Switzerland, calculate seismic body-wave amplitudes at arbitrary stations assuming the Brune source model and using scaling and attenuation relations recently derived for Switzerland, and estimate the noise level at arbitrary locations within Switzerland using a first-order ambient seismic noise model based on 14 land-use classes defined by the EU-project CORINE and open GIS data. We calculated optimized geometries for networks with 10–35 added stations and tested the stability of the optimization result by repeated runs with changing initial conditions. Further, we estimated the attainable magnitude of completeness ( M c ) for the different sized optimal networks using the Bayesian Magnitude of Completeness (BMC) method introduced by Mignan et al. The algorithm developed in this study is also applicable to smaller optimization problems, for example, small local monitoring networks. Possible applications are volcano monitoring, the surveillance of induced seismicity associated with geotechnical operations and many more. Our algorithm is especially useful to optimize networks in populated areas with heterogeneous noise conditions and if complex velocity structures or existing stations have to be considered.
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  • 35
    Publication Date: 2013-09-10
    Description: Fluid injection in and withdrawal from wells are basic procedures in mining activities and deep resources exploitation, such as oil and gas extraction, permeability enhancement for geothermal exploitation and waste fluid disposal. All of these activities have the potential to induce seismicity, as exemplified by the 2006 Basel earthquake ( M L 3.4). Despite several decades of experience, the mechanisms of induced seismicity are not known in detail, which prevents effective risk assessment and/or mitigation. In this study, we provide an interpretation of induced seismicity based on computation of Coulomb stress changes that result from fluid injection/withdrawal at depth, mainly focused on the interpretation of induced seismicity due to stimulation of a geothermal reservoir. Seismicity is, theoretically, more likely where Coulomb stress changes are larger. For modeling purposes, we simulate the thermodynamic evolution of a system after fluid injection/withdrawal. The associated changes in pressure and temperature are subsequently considered as sources of incremental stress changes, which are then converted to Coulomb stress changes on favourably oriented faults, taking into account the background regional stress. Numerical results are applied to the water injection that was performed to create the fractured reservoir at the enhanced-geothermal-system site, Soultz-sous-Forets (France). Our approach describes well the observed seismicity, and provides an explanation for the different behaviors of a system when fluids are injected or withdrawn.
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  • 36
    Publication Date: 2013-09-10
    Description: We report on a broad-band high-resolution attenuation model for the North China Craton and surrounding regions based on regional Lg -wave data. Vertical broad-band waveforms recorded at 39 stations from 176 crustal earthquakes are collected to extract the Lg -wave amplitude spectra between 0.05 and 10.0 Hz. We use the dual-station method to generate a preliminary Q Lg model and use it as the initial model. Then, we combine the dual- and single-station data together to jointly invert the Q Lg distribution and Lg source excitation functions. These inversions are conducted independently at individual frequencies without using any a priori assumption about the frequency dependences in Q Lg and source terms. The maximum spatial resolution is approximately 1° x 1° in well-covered areas for frequencies between 0.05 and 2.0 Hz. The Q Lg image is then used to determine the relationship between the attenuation and different geological structures. Results show an average Q 0 (1 Hz Q Lg ) of 374 for the entire North China Craton with an increasing trend from east to west. Average Q 0 values are 337, 361 and 421 for the east, central and west blocks, respectively. For the surrounding regions, the Eastern Tibetan plateau has a very low Q 0 of 188, while the Northeast China Plate and the Tianshan–Xingmeng fold belts are characterized by high Q 0 values of 506 and 424, respectively. We also investigate regional variations of the Lg attenuation in low-frequency band between 0.2 and 1.0 Hz.
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  • 37
    Publication Date: 2013-09-10
    Description: We present a systematic study on the influence of pressure (0.1–600 MPa), temperature (750–1200 °C), carbon dioxide fugacity (log f CO 2  = –4.41 to 3.60) and time (2–12 hr) on the chemical and physical properties of carbonate rock. Our experiments aim to reproduce the conditions at the periphery of magma chamber where carbonate host rock is influenced by, but not readily assimilated by, magma. This permits the investigation of the natural conditions at which circulating fluids/gases promote infiltration reactions typical of metasomatic skarns that can involve large volumes of subvolcanic carbonate basements. Results show that, providing that carbon dioxide is retained in the pore space, decarbonation does not proceed at any magmatic pressure and temperature. However, when the carbon dioxide is free to escape, decarbonation can occur rapidly and is not hindered by a low initial porosity or permeability. Together with carbon dioxide and lime, portlandite, a mineral commonly found in voluminous metasomatic skarns, readily forms during carbonate decomposition. Post-experimental analyses highlight that thermal microcracking, a result of the highly anisotropic thermal expansion of calcite, exerts a greater influence on rock physical properties (porosity, ultrasonic wave velocities and elastic moduli) than decarbonation. Our data suggest that this will be especially true at the margins of dykes or magma bodies, where temperatures can reach up to 1200 °C. However, rock compressive strength is significantly reduced by both thermal cracking and decarbonation, explained by the relative weakness of lime + portlandite compared to calcite, and an increase in grain size with increasing temperature. Metasomatic skarns, whose petrogenetic reactions may involve a few tens of cubic kilometres, could therefore represent an important source of volcanic instability.
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  • 38
    Publication Date: 2013-09-10
    Description: The scattering of plane SH waves incident on a circular sectorial canyon is considered. An accurate region-matching technique is applied to derive a rigorous series solution. Appropriate wavefunctions are employed to describe antiplane motions. Judicious basis functions, involving Gegenbauer polynomials, are well utilized to correctly capture the singular behaviour in stress fields near the canyon bottom. The enforcement of matching conditions on the auxiliary boundary leads to the determination of unknown coefficients. Plotted results demonstrate the influence of pertinent parameters on surface and subsurface motions. Both steady-state and transient results are included. The solution technique proposed achieves a considerable reduction in the computational effort, facilitating benchmark computations. The derived series solution enriches the limited list of series solutions presently known for canyon problems related to SH -wave scattering.
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  • 39
    Publication Date: 2013-09-10
    Description: We present 3-D models of the P- and S -wave velocity distributions in the crust and uppermost mantle beneath Sicily, Calabria (Southern Italy), and surrounding submerged areas, obtained by tomographic inversion of traveltimes of regional body waves phases. Our method combines double-difference tomographic inversion with a post-processing procedure [Weighted Average Model method (WAM)]. This procedure was applied to a set of models consistent with the experimental data. We tested the ability of the WAM procedure to mitigate the uncertainty associated with the arbitrary nature of the many input parameters required for each inversion. The local reliability and resolution of the obtained models have been assessed through: synthetic tests, experimental tests carried out with independent data sets and unconventional tests based on the analysis of the internal consistency of the P - and S -velocity models. The tomographic images provide a detailed sketch of P- and S- wave velocity anomalies. These clearly show the shape of the Sicilian-Maghrebian belt beneath Sicily and Calabrian Arc at different depths. Low V P and Vs bodies are imaged beneath Stromboli and Marsili volcanoes in the southern Tyrrhenian, whereas high and low seismic velocities alternate beneath the Etna giving inferences on the possible depth of the mantle melting feeding the volcano. In the upper crust, the main sedimentary basins and tectonic features are also well imaged. Finally, tomographic cross sections show the trend of the Moho in the study area, where its depth ranges between 35 and 40 km beneath the Sicilian belt and between 15 and 22 km in the southern Tyrrhenian basin and Ionian Sea.
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  • 40
    Publication Date: 2013-09-10
    Description: We used two tracks of ALOS PALSAR images to investigate the focal mechanism and slip distribution of the 2011 March 24, M W 6.8 Burma strike-slip earthquake. Three different SAR techniques, namely conventional interferometry, SAR pixel offsets (SPO) and multiple-aperture InSAR (MAI), were employed to obtain the coseismic surface deformation fields along the ~30 km length of the fault rupture. Along-track measurements from SPO and MAI techniques show a high correlation, and were subsequently used to precisely determine the location and extent of the surface fault trace. The best-fitting fault model geometry derived from an iterative inversion technique suggests that the rupture occurred on a near-vertical sinistral strike-slip fault west of the Nam Ma fault with a strike of 70°. A maximum slip of 4.2 m occurs at a depth of 2.5 km, with significant slip constrained only to the upper 10 km of the crust.
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  • 41
    Publication Date: 2013-09-10
    Description: Knowledge of the mantle reflectivity structure is highly dependent on our ability to efficiently extract, and properly interpret, small seismic arrivals. Among the various data types and techniques, long-period SS/PP precursors and high-frequency receiver functions are routinely utilized to increase the confidence of the recovered mantle stratifications at distinct spatial scales. However, low resolution and a complex Fresnel zone are glaring weaknesses of SS precursors, while over-reliance on receiver distribution is a formidable challenge for the analysis of converted waves from oceanic regions. A promising high frequency alternative to receiver functions is P ' P ' precursors, which are capable of resolving mantle structures at vertical and lateral resolution of ~5 and ~200 km, respectively, owing to their spectral content, shallow angle of incidence and near-symmetric Fresnel zones. This study presents a novel processing method for both SS (or PP) and P ' P ' precursors based on deconvolution, stacking, Radon transform and depth migration. A suite of synthetic tests is performed to quantify the fidelity and stability of this method under different data conditions. Our multiresolution survey of the mantle at targeted areas near Nazca-South America subduction zone reveal both olivine and garnet related transitions at depths below 400 km. We attribute a depressed 660 to thermal variations, whereas compositional variations atop the upper-mantle transition zone are needed to explain the diminished or highly complex reflected/scattered signals from the 410 km discontinuity. We also observe prominent P ' P ' reflections within the transition zone, and the anomalous amplitudes near the plate boundary zone indicate a sharp (~10 km thick) transition that likely resonates with the frequency content of P ' P ' precursors. The migration of SS precursors in this study shows no evidence of split 660 reflections, but potential majorite–ilmenite (590–640 km) and ilmenite–perovskite transitions (740–750 km) are identified based on similarly processed high-frequency P ' P ' precursors. Additional findings of severely scattered energy in the lithosphere and distinct lower mantle reflections at ~800 km could be potentially important but require further verifications. Overall, our improved imaging methods and the strong sensitivity of P ' P ' precursors to the existence, depth, sharpness and strength of reflective structures offer significant future promise for the understanding of mantle mineralogy and dynamics.
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  • 42
    Publication Date: 2013-09-10
    Description: Time-dependent probabilistic seismic hazard assessment requires a stochastic description of earthquake occurrences. While short-term seismicity models are well-constrained by observations, the recurrences of characteristic on-fault earthquakes are only derived from theoretical considerations, uncertain palaeo-events or proxy data. Despite the involved uncertainties and complexity, simple statistical models for a quasi-period recurrence of on-fault events are implemented in seismic hazard assessments. To test the applicability of statistical models, such as the Brownian relaxation oscillator or the stress release model, we perform a systematic comparison with deterministic simulations based on rate- and state-dependent friction, high-resolution representations of fault systems and quasi-dynamic rupture propagation. For the specific fault network of the Lower Rhine Embayment, Germany, we run both stochastic and deterministic model simulations based on the same fault geometries and stress interactions. Our results indicate that the stochastic simulators are able to reproduce the first-order characteristics of the major earthquakes on isolated faults as well as for coupled faults with moderate stress interactions. However, we find that all tested statistical models fail to reproduce the characteristics of strongly coupled faults, because multisegment rupturing resulting from a spatiotemporally correlated stress field is underestimated in the stochastic simulators. Our results suggest that stochastic models have to be extended by multirupture probability distributions to provide more reliable results.
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  • 43
    Publication Date: 2013-09-10
    Description: Stress waves, known as acoustic emissions (AEs), are released by localized inelastic deformation events during the progressive failure of brittle rocks. Although several numerical models have been developed to simulate the deformation and damage processes of rocks, such as non-linear stress–strain behaviour and localization of failure, only a limited number have been capable of providing quantitative information regarding the associated seismicity. Moreover, the majority of these studies have adopted a pseudo-static approach based on elastic strain energy dissipation that completely disregards elastodynamic effects. This paper describes a new AE modelling technique based on the combined finite-discrete element method (FEM/DEM), a numerical tool that simulates material failure by explicitly considering fracture nucleation and propagation in the modelling domain. Given the explicit time integration scheme of the solver, stress wave propagation and the effect of radiated seismic energy can be directly captured. Quasi-dynamic seismic information is extracted from a FEM/DEM model with a newly developed algorithm based on the monitoring of internal variables (e.g. relative displacements and kinetic energy) in proximity to propagating cracks. The AE of a wing crack propagation model based on this algorithm are cross-analysed by traveltime inversion and energy estimation from seismic recordings. Results indicate a good correlation of AE initiation times and locations, and scaling of energies, independently calculated with the two methods. Finally, the modelling technique is validated by simulating a laboratory compression test on a granite sample. The micromechanical parameters of the heterogeneous model are first calibrated to reproduce the macroscopic stress–strain response measured during standard laboratory tests. Subsequently, AE frequency–magnitude statistics, spatial clustering of source locations and the evolution of AE rate are investigated. The distribution of event magnitude tends to decay as power law while the spatial distribution of sources exhibits a fractal character, in agreement with experimental observations. Moreover, the model can capture the decrease of seismic b value associated with the macrorupture of the rock sample and the transition of AE spatial distribution from diffuse, in the pre-peak stage, to strongly localized at the peak and post-peak stages, as reported in a number of published laboratory studies. In future studies, the validated FEM/DEM-AE modelling technique will be used to obtain further insights into the micromechanics of rock failure with potential applications ranging from laboratory-scale microcracking to engineering-scale processes (e.g. excavations within mines, tunnels and caverns, petroleum and geothermal reservoirs) to tectonic earthquakes triggering.
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  • 44
    Publication Date: 2013-09-10
    Description: We used strong-motion records from the 2012 May 20 and 29 Emilia-Romagna earthquakes ( M w 6.1 and 5.9, respectively) and four aftershocks with magnitudes ranging between 4.9 and 5.5 to analyse the S -wave spectral amplitude decay with distance and estimate acceleration source functions and site effects. The data set consists of six earthquakes, 44 stations and 248 records with hypocentral distances in the range 10 〈 r  〈 100 km. We rotated the accelerograms to calculate transverse and radial components of the acceleration spectrum. We found non-parametric attenuation functions that describe the spectral amplitude decay of SH and SV waves with distance at 60 different frequencies between 0.1 and 40 Hz. These attenuation functions provide an estimate of the quality factor Q at each frequency analysed. Assuming that geometrical spreading is 1/ r for r  ≤ r x and 1/( r x r ) 0.5 for r  〉 r x with r x  = 60 km and normalizing at 15 km (the recording distance where the attenuation functions start to decay), we find that the average Q for SH waves can be approximated by Q SH  = 82 ± 1 f  1.2±0.02 and by Q SV  = 79 ± 1 f  1.24±0.03 for SV waves in the frequency range 0.10 ≤ f  ≤ 10.7 Hz. At higher frequencies, 11.8 ≤ f  ≤ 40 Hz, the frequency dependence of Q weakens and is approximated by Q SH  = 301 ± 1 f   0.36±0.04 and Q SV  = 384 ± 1 f  0.28±0.04 . These results indicate that the S -wave attenuation is radially isotropic at local distances in the epicentral area. Nevertheless, we used these attenuation parameters separately to correct the radial (with Q SV ) and transverse (with Q SH ) components of the acceleration spectra and to separate source and site effects using a non-parametric spectral inversion scheme. We found that the source function of the main event and the bigger aftershocks show enhanced low frequency radiation between 0.4 and 3.0 Hz. We converted the source functions into far-field source acceleration spectra and interpreted the resulting source spectra in terms of Brune's model. The stress drops obtained range between approximately 0.9 and 2.9 MPa. Although all the recording stations used are located in the Po Plain, the site functions obtained from the spectral inversion show important amplification variability between the sites. We compared these site functions with the average horizontal to vertical spectral ratios calculated for each station, and we found consistent results for most stations.
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  • 45
    Publication Date: 2013-09-12
    Description: The tension between the meaning of causality in science and law or public policy is well-known; however, defendants in product liability cases or industries that might be affected by a government regulation may try to convince the factfinder to require evidence of a causal relationship that meets the standards of science. From the perspective of public health, however, people may be exposed unnecessarily to a health risk during the time period between the establishment of reasonably strong evidence of a causal relationship and the overwhelming evidence required for scientific causality. The Bayesian paradigm enables one to update information from epidemiologic studies as they accumulate, providing estimates of the probability that the relative risk of a particular harm from exposure exceeds a threshold value, e.g. 2.0 or 4.0 that is sufficient to meet the preponderance of the evidence standard or to support a health initiative. In order to diminish the role of the initial prior distribution, which may be quite subjective, the first case-control study or an analysis of adverse event and case reports is used to determine two prior distributions. One is the most favourable to the defendant, or industry that might be regulated, which is consistent with the previous data. The other is centred on or near the estimated relative risk from the first study. The method is applied to the studies that linked aspirin use to Reye syndrome and demonstrates that the evidence of a causal association was sufficiently strong in 1982, when the Food and Drug Administration first proposed that the public be warned of the risk, to support the regulation. Thus, lives would have been saved had the warning been given at the end of 1982 rather than in early 1985.
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  • 46
    Publication Date: 2013-09-12
    Description: In law, inferences of causation are sometimes made through a structured process in which multiple participants play various roles, and make decisions concerning various logical components of the overall inference (such as legal rules, policy objectives, presumptions, evidence, burdens of proof and findings of fact). This article illustrates such a process using empirical research into compensation decisions in the USA for injuries allegedly caused by vaccinations. Empirical research into actual legal processes is essential, in order to discover how various players approach their sub-tasks of decision-making. It also provides insights for areas outside of law, such as non-monotonic logic, cognitive science, sociology and artificial intelligence.
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  • 47
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    Oxford University Press
    Publication Date: 2013-09-12
    Description: Situations of causal factual uncertainty are relatively common in law. The problems and difficulties regarding ‘factual causation’ in law point to the need of ‘evidence’ and ‘proof’ models that are adequate and capable to accommodate the tests and methodologies used to explain and demonstrate it in a legal context. Given the configuration of the situations of causal factual uncertainty and the available ‘evidence’ and ‘proof’ models, I argue that it is justified to use an ‘argumentative-narrative’ model for ‘proving causation’ in law. However, considering that each model of ‘evidence’ and ‘proof’ reveals a different kind of ‘rationality’ that can still be viewed in different ways, I also argue that we must try to match the perspective we have on the ‘rationality’ behind the chosen model of ‘evidence’ and ‘proof’ with the ‘rationality’ underlying ‘causation’ in law.
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  • 48
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    Oxford University Press
    Publication Date: 2013-09-12
    Description: At least in some cases, the values confronted in legal decision-making appear to be incommensurable. Some legal theorists resist incommensurability because they fear that this presents an overwhelming obstacle to rational decision-making. By offering a close analysis of proportionality and, more particularly, measures of proportional value satisfaction, I show that this fear is unfounded. Comparative measures of proportional value satisfaction do not require the values to be commensurable. However, assuming incommensurability presents us with the problem of public significance in the proportional satisfaction of values. When two values are commensurable, this public significance is provided by the mediating effects of the overarching third value that provides the common measure of the values. However, when this common measure is removed, then the public significance of value satisfaction must be otherwise achieved. This is why I propose an equal proportional value satisfaction as the most appropriate proportionality maximand. Under equal proportional value satisfaction, the proportional satisfaction of any one value has significance for each and every other value. This kind of public significance is interpersonal rather than impersonal (or second-personal rather than third-personal). The article then shows that the legal process that is most appropriate to equal proportionality is a process that implements defeasible legal rules.
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  • 49
    Publication Date: 2013-09-12
    Description: In order to allocate the risk between parties in legal adjudication, we use evidentiary techniques with the main device among them being the standard of proof (SoP). The traditional view holds the grade of probability to be the parameter that shifts when moving to different standards. However, as soon as we dig slightly deeper, an incoherent picture is being revealed. In this article, I challenge the accepted view and try to show that it faces insurmountable problems concerning the rationality, the grammatical consistency and the impact of the SoP for the acceptability of verdicts. At the end of the article, I shortly discuss the theory of epistemological contextualism and propose a framework that allows rational distinctions to be drawn between different standards of proof. In the second part of this project (forthcoming), I will defend a contextualist view according to which shifting parameter is not the grade of (aleatory) probability, but instead the Set of Epistemic Defeaters in play.
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  • 50
    Publication Date: 2013-09-13
    Description: There is much interest in using high-throughput DNA sequencing methodology to monitor microorganisms, complex plant and animal communities. However, there are experimental and analytical issues to consider before applying a sequencing technology, which was originally developed for genome projects, to ecological projects. Many of these issues have been highlighted by recent microbial studies. Understanding how high-throughput sequencing is best implemented is important for the interpretation of recent results and the success of future applications. Addressing complex biological questions with metagenomics requires the interaction of researchers who bring different skill sets to problem solving. Educators can help by nurturing a collaborative interdisciplinary approach to genome science, which is essential for effective problem solving. Educators are in a position to help students, teachers, the public and policy makers interpret the new knowledge that metagenomics brings. To do this, they need to understand, not only the excitement of the science but also the pitfalls and shortcomings of methodology and research designs. We review these issues and some of the research directions that are helping to move the field forward.
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  • 51
    Publication Date: 2013-09-13
    Description: We believe that undergraduate biology students must acquire a foundational background in computing including how to formulate a computational problem; develop an algorithmic solution; implement their solution in software and then test, document and use their code to explore biological phenomena. Moreover, by learning these skills in the first year, students acquire a powerful tool set that they can use and build on throughout their studies. To address this need, we have developed a first-year undergraduate course that teaches students the foundations of computational thinking and programming in the context of problems in biology. This article describes the structure and content of the course and summarizes assessment data on both affective and learning outcomes.
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  • 52
    Publication Date: 2013-09-13
    Description: Bioinformatics is an integral part of modern life sciences. It has revolutionized and redefined how research is carried out and has had an enormous impact on biotechnology, medicine, agriculture and related areas. Yet, it is only rarely integrated into high school teaching and learning programs, playing almost no role in preparing the next generation of information-oriented citizens. Here, we describe the design principles of bioinformatics learning environments, including our own, that are aimed at introducing bioinformatics into senior high school curricula through engaging learners in scientifically authentic inquiry activities. We discuss the bioinformatics-related benefits and challenges that high school teachers and students face in the course of the implementation process, in light of previous studies and our own experience. Based on these lessons, we present a new approach for characterizing the questions embedded in bioinformatics teaching and learning units, based on three criteria: the type of domain-specific knowledge required to answer each question (declarative knowledge, procedural knowledge, strategic knowledge, situational knowledge), the scientific approach from which each question stems (biological, bioinformatics, a combination of the two) and the associated cognitive process dimension (remember, understand, apply, analyze, evaluate, create). We demonstrate the feasibility of this approach using a learning environment, which we developed for the high school level, and suggest some of its implications. This review sheds light on unique and critical characteristics related to broader integration of bioinformatics in secondary education, which are also relevant to the undergraduate level, and especially on curriculum design, development of suitable learning environments and teaching and learning processes.
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  • 53
    Publication Date: 2013-09-13
    Description: The aim of this paper is to study the relations between the Hausdorff dimensions of k -quasilines and the theory of extremal quasiconformal mappings. We show that there is an open and dense subset (Strebel points) of the universal Teichmüller space T (H) such that, for every [ f ] in the set, the Hausdorff dimension of the k -quasiline determined by [ f ] is strictly less than 1 + k 2 . We also show that there are some points [ f ] != [id] outside the open and dense set in the universal Teichmüller space such that the Hausdorff dimension of the quasiline determined by [ f ] is 1. Moreover, some results on the Hausdorff dimensions of the quasilines varying in the asymptotic Teichmüller space are also obtained.
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  • 54
    Publication Date: 2013-09-13
    Description: Next-generation sequencing (NGS) is increasingly being adopted as the backbone of biomedical research. With the commercialization of various affordable desktop sequencers, NGS will be reached by increasing numbers of cellular and molecular biologists, necessitating community consensus on bioinformatics protocols to tackle the exponential increase in quantity of sequence data. The current resources for NGS informatics are extremely fragmented. Finding a centralized synthesis is difficult. A multitude of tools exist for NGS data analysis; however, none of these satisfies all possible uses and needs. This gap in functionality could be filled by integrating different methods in customized pipelines, an approach helped by the open-source nature of many NGS programmes. Drawing from community spirit and with the use of the Wikipedia framework, we have initiated a collaborative NGS resource: The NGS WikiBook. We have collected a sufficient amount of text to incentivize a broader community to contribute to it. Users can search, browse, edit and create new content, so as to facilitate self-learning and feedback to the community. The overall structure and style for this dynamic material is designed for the bench biologists and non-bioinformaticians. The flexibility of online material allows the readers to ignore details in a first read, yet have immediate access to the information they need. Each chapter comes with practical exercises so readers may familiarize themselves with each step. The NGS WikiBook aims to create a collective laboratory book and protocol that explains the key concepts and describes best practices in this fast-evolving field.
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  • 55
    Publication Date: 2013-09-13
    Description: A new uniqueness result for a general n th order differential equation is obtained. We show that some previous results follow immediately from our theorem.
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  • 56
    Publication Date: 2013-09-13
    Description: Consider a discrete uniformly elliptic divergence form equation on the d ≥3 dimensional lattice Z d with random coefficients. In Conlon and Spencer [ Trans. Amer. Math. Soc. , http://www.math.lsa.umich.edu/~conlon/paper/hom10.pdf ], rate of convergence results in homogenization and estimates on the difference between the averaged Green's function and the homogenized Green's function for random environments which satisfy a Poincaré inequality were obtained. Here, these results are extended to certain environments in which correlations can have arbitrarily small power law decay. These environments are simply related via a convolution to environments which do satisfy a Poincaré inequality.
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  • 57
    Publication Date: 2013-09-13
    Description: In this paper, we prove that, for any a , M N with ( a , M ) = 1, there are infinitely many Carmichael numbers m such that m a mod M .
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  • 58
    Publication Date: 2013-09-13
    Description: We give a topological analogue for openness of a criterion for flatness that originates with Auslander. Over a normal base of dimension n , failure of openness is detected by a vertical component in the n th fibred power of the morphism.
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  • 59
    Publication Date: 2013-09-13
    Description: Investigated are regular maps from real algebraic varieties into real Fermat varieties. It is proved that under some natural assumptions, all such maps are null homotopic.
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  • 60
    Publication Date: 2013-09-13
    Description: Let ( M , g ) be a complete non-compact Riemannian manifold. We consider operators of the form g + V , where g is the non-negative Laplacian associated with the metric g , and V a locally integrable function. Let be a Riemannian covering, with Laplacian g and potential . If the operator + V is non-negative on ( M , g ), then the operator is non-negative on . In this note, we show that the converse statement is true provided that is a co-amenable subgroup of 1 ( M ).
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  • 61
    Publication Date: 2013-09-13
    Description: Peak interpolation is concerned with a foundational kind of mathematical task: building functions in a fixed algebra A , which have prescribed values or behaviour on a fixed closed subset (or on several disjoint subsets). In this paper, we do the same but now A is an algebra of operators on a Hilbert space. We briefly survey this noncommutative peak interpolation , which we have studied with coauthors in a long series of papers, and whose basic theory now appears to be approaching its culmination. This programme developed from, and is based partly on, theorems of Hay and Read whose proofs were spectacular, but therefore inaccessible to an uncommitted reader. We give short proofs of these results, using recent progress in noncommutative peak interpolation, and conversely give examples of the use of these theorems in peak interpolation. For example, we prove a useful new noncommutative peak interpolation theorem.
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  • 62
    Publication Date: 2013-09-13
    Description: We show how a parameterized family of maps of the spine of a manifold can be used to construct a family of homeomorphisms of the ambient manifold which have the inverse limits of the spine maps as global attractors. We describe applications to unimodal families of interval maps, to rotation sets, and to the standard family of circle maps.
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  • 63
    Publication Date: 2013-09-13
    Description: For every prime p , we give infinitely many examples of torsors under abelian varieties over Q that are locally trivial but not divisible by p in the Weil–Châtelet group. We also give an example of a locally trivial torsor under an elliptic curve over Q that is not divisible by 4 in the Weil–Châtelet group. This gives a negative answer to a question of Cassels.
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  • 64
    Publication Date: 2013-09-13
    Description: We show that at least of the zeros of the Riemann zeta-function are simple, assuming the Riemann hypothesis. This was previously established by Conrey, Ghosh and Gonek [ Proc. London Math. Soc. 76 (1998) 497–522] under the additional assumption of the generalized Lindelöf hypothesis. We are able to remove this hypothesis by careful use of the generalized Vaughan identity.
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  • 65
    Publication Date: 2013-09-13
    Description: We construct an infinite family of hyperbolic, homologically thin knots that are not quasi-alternating. To establish the latter, we argue that the branched double-cover of each knot in the family does not bound a negative-definite 4-manifold with trivial first homology and bounded second Betti number. This fact depends in turn on information from the correction terms in Heegaard Floer homology, which we establish by way of a relationship to, and calculation of, the Turaev torsion.
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  • 66
    Publication Date: 2013-09-13
    Description: We observe that E -resultant of a very ample rank 2 vector bundle E on a real projective curve (with no real points) is nonnegative when restricted to the space of real sections. Moreover, we show that if E has a section vanishing at exactly two points and the degree d of E satisfies d ( d – 6) ≥ 4( g – 1), then this polynomial cannot be written as a sum of squares.
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  • 67
    Publication Date: 2013-09-13
    Description: Let G be one of the Ricci-flat holonomy groups SU( n ), Sp( n ), Spin(7) or G 2 , and M a compact manifold of dimension 2 n , 4 n , 8 or 7, respectively. We prove that the natural map from the moduli space of torsion-free G -structures on M to the moduli space of Ricci-flat metrics is open, and that the image is a smooth manifold. For the exceptional cases G = Spin(7) and G 2 , we extend the result to asymptotically cylindrical manifolds.
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  • 68
    Publication Date: 2013-09-13
    Description: We improve the results of Booker and Krishnamurthy ( Compos. Math. 147 (2011) 669–715) by allowing restricted sets of poles among the unramified twists. This allows for a clean statement of the GL(2) converse theorem which includes all cases of Eisenstein series.
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  • 69
    Publication Date: 2013-09-13
    Description: Let G be a solvable subgroup of the automorphism group Aut( X ) of a compact Kähler manifold X of complex dimension n , and let N ( G ) be the normal subgroup of G consisting of elements with null entropy. Let us denote by G * the image of G under the natural map from Aut( X ) to GL( V , R ), where V is the Dolbeault cohomology group H 1, 1 ( X , R ). Assume that the Zariski closure of G * in GL( V C ) is connected. The main aim of this paper is to show that, when the rank r ( G ) of the quotient group G / N ( G ) is equal to n – 1 and the identity component of Aut( X ) is trivial, then the normal subgroup N ( G ) of G is finite. This affirmatively answers a question in Invent. Math. posed by D.-Q. Zhang.
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  • 70
    Publication Date: 2013-09-16
    Description: The dihedral angle formed at junctions between two plagioclase grains and a grain of augite is only very rarely in textural equilibrium in gabbros from kilometre-scale crustal layered intrusions. The median of a population of these disequilibrium angles, cpp , varies systematically within a single layered intrusion, remaining constant over large stretches of stratigraphy with significant increases and decreases associated with the addition or reduction respectively of the number of phases on the liquidus of the bulk magma. The stepwise changes in cpp are present in the Upper Zone of the Bushveld Complex, the Megacyclic Unit I of the Sept Iles Intrusion, and the Layered Series of the Skaergaard intrusion. The plagioclase-bearing cumulates of Rum have a bimodal distribution of cpp , dependent on whether the cumulus assemblage includes clinopyroxene. The presence of the stepwise changes is independent of the order of arrival of cumulus phases and of the composition of either the cumulus phases or the inferred composition of the interstitial liquid. The only parameter that behaves in an exactly analogous manner to cpp is the rate of change in enthalpy with temperature ( H / T ) during crystallization. Both H / T and cpp increase with the addition of a liquidus phase, and decrease with the removal of a liquidus phase. The replacement of one phase by another has little effect on H / T and no discernible effect on cpp . An increase of H / T results in an increase in the fraction of the total enthalpy budget that is the latent heat of crystallization (the fractional latent heat). It also increases the mass crystallized in each incremental temperature drop (the crystal productivity). These increases of both fractional latent heat and crystal productivity are likely to cause an increase in the time taken to form three-grain junctions in the mush via thermal buffering of a thickened mushy layer. We suggest these are the underlying causes of stepwise increases in cpp . Stepwise changes in the geometry of three-grain junctions in fully solidified gabbros thus provide a clear microstructural marker for the progress of fractionation down the liquid line of descent in layered intrusions.
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  • 71
    Publication Date: 2013-09-16
    Description: High-resolution sampling in monogenetic fields has the potential to reveal fine-scale heterogeneity of the mantle, a feature that may be overwhelmed by larger fluxes of magma, or missed by under-sampling. The Quaternary Auckland Volcanic Field (AVF) in northern New Zealand is a basaltic field of 51 small-volume volcanic centres, and is one of the best-sampled examples of a monogenetic volcanic field. We present data for 12 centres in the volcanic field. These show the large compositional variations between volcanoes as well as through single eruptive sequences. Whole-rock compositions range from subalkaline basalt in the larger centres, through alkali basalt to nephelinite in the smallest centres. Fractional crystallization has had a limited effect in many of the centres, but high-pressure clinopyroxene crystallization may have occurred in others. Three end-members are observed in Pb isotope space, indicating that distinct mantle source components are involved in the petrogenesis of the magmas. Whole-rock multi-element patterns show that the larger centres have prominent positive Sr anomalies and lack K anomalies, whereas the smaller centres have prominent negative K anomalies and lack Sr anomalies. The melting parameters and compositions of the sources involved are modelled using trace element ratios and multi-element patterns, and three components are characterized: (1) fertile peridotite with a Pb-isotope composition similar to Pacific mid-ocean ridge basalt; (2) eclogite domains with a HIMU-like isotope composition dispersed within the fertile peridotite; (3) slightly depleted subduction-metasomatized peridotitic lithospheric mantle (containing c . 3% subduction fluids). Modelling shows that melting in the AVF begins in garnet-bearing fertile asthenosphere (with preferential melting of eclogite domains) and that melts are variably diluted by melts of the lithospheric source. The U–Th isotope compositions of the end-members in the AVF show 230 Th excess [( 230 Th/ 232 Th) ratios of 1·11–1·38], with the samples of lower ( 230 Th/ 232 Th) exhibiting higher ( 238 U/ 232 Th), which we attribute to the dilution effect of the melts from the lithospheric mantle source. Modelling reveals a correlation between melting in the asthenosphere, the degree of melting and incorporation of the metasomatized lithospheric mantle source, and the resultant size of the volcanic centre. This suggests that the scale of the eruption may essentially be controlled by asthenospheric mantle dynamics.
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  • 72
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2013-09-16
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  • 73
    Publication Date: 2013-09-16
    Description: The origin of mafic and ultramafic sills exhibiting different whole-rock compositional profiles (e.g. I-, C-, D-, M- and S-shaped profiles) remains controversial. We have addressed this issue by revisiting three ~100 m thick Siberian dolerite sills (Vavukansky, Kuz’movsky and Vilyuysky) that display remarkable internal differentiation. The Vavukansky sill has an M-shaped profile with prominent basal and top reversals showing inward increases in whole-rock MgO, Mg-number [100Mg/(Mg + Fe)] and normative An content [100An/(An + Ab)], followed by the Layered and Upper Border Series with inward decreases in these indices. The Kuz’movsky and Vilyuysky sills both show S-shaped profiles similar to the Vavukansky sill, but lack a top reversal. These whole-rock M- and S-shaped profiles are accompanied by similar profiles in mineral compositions. Plagioclase and, to a lesser extent, olivine show systematic inward increases in An content and Mg-number, respectively, across basal and top reversals. These compositional trends are followed by inward decreases in these ratios in the interiors of the Vavukansky and Kuz’movsky sills. Currently accepted models attribute whole-rock M- and S-shaped compositional profiles to crystal settling, compositional convection or compaction operating in closed systems. Our observations challenge these traditional interpretations because variations in mineral compositions observed in marginal reversals cannot result from closed-system fractionation. We suggest instead that initially the sills evolved as open systems that were slowly inflated by magmas that became gradually more primitive with time. The inflation was accompanied by in situ crystallization that preserved the preceding fractionation history of the injected magmas by forming basal and top reversals with minerals becoming more primitive inwards. This process culminated with rapid inflation of the sills to their current size owing to a major influx of primitive magma. Subsequently, magma flow through the sills ceased and they evolved as closed systems by fractional crystallization. This resulted in the Layered and Upper Border Series with minerals becoming more evolved inwards. This model can be extended to explain other compositional profiles and petrological features in mafic and ultramafic sills.
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  • 74
    facet.materialart.
    Unknown
    Oxford University Press
    Publication Date: 2013-09-16
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  • 75
    Publication Date: 2013-09-16
    Description: The genomes of related species contain valuable information on the history of the considered taxa. Great apes in particular exhibit variation of evolutionary patterns along their genomes. However, the great ape data also bring new challenges, such as the presence of incomplete lineage sorting and ancestral shared polymorphisms. Previous methods for genome-scale analysis are restricted to very few individuals or cannot disentangle the contribution of mutation rates and fixation biases. This represents a limitation both for the understanding of these forces as well as for the detection of regions affected by selection. Here, we present a new model designed to estimate mutation rates and fixation biases from genetic variation within and between species. We relax the assumption of instantaneous substitutions, modeling substitutions as mutational events followed by a gradual fixation. Hence, we straightforwardly account for shared ancestral polymorphisms and incomplete lineage sorting. We analyze genome-wide synonymous site alignments of human, chimpanzee, and two orangutan species. From each taxon, we include data from several individuals. We estimate mutation rates and GC-biased gene conversion intensity. We find that both mutation rates and biased gene conversion vary with GC content. We also find lineage-specific differences, with weaker fixation biases in orangutan species, suggesting a reduced historical effective population size. Finally, our results are consistent with directional selection acting on coding sequences in relation to exonic splicing enhancers.
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  • 76
    Publication Date: 2013-09-16
    Description: Genetic control of male or female gonad development displays between different groups of organisms a remarkable diversity of "master sex-determining genes" at the top of the genetic hierarchies, whereas downstream components surprisingly appear to be evolutionarily more conserved. Without much further studies, conservation of sequence has been equalized to conservation of function. We have used the medaka fish to investigate the generality of this paradigm. In medaka, the master male sex-determining gene is dmrt1bY , a highly conserved downstream regulator of sex determination in vertebrates. To understand its function in orchestrating the complex gene regulatory network, we have identified targets genes and regulated pathways of Dmrt1bY. Monitoring gene expression and interactions by transgenic fluorescent reporter fish lines, in vivo tissue-chromatin immunoprecipitation and in vitro gene regulation assays revealed concordance but also major discrepancies between mammals and medaka, notably amongst spatial, temporal expression patterns and regulations of the canonical Hedgehog and R-spondin/Wnt/Follistatin signaling pathways. Examination of Foxl2 protein distribution in the medaka ovary defined a new subpopulation of theca cells, where ovarian-type aromatase transcriptional regulation appears to be independent of Foxl2. In summary, these data show that the regulation of the downstream regulatory network of sex determination is less conserved than previously thought.
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  • 77
    Publication Date: 2013-09-16
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  • 78
    Publication Date: 2013-09-17
    Description: We present measurements of higher order clustering of galaxies in the latest release of the Canada–France–Hawaii Telescope Legacy Survey (CFHTLS)-Wide. We construct a series of volume-limited sample of galaxies containing more than one million galaxies over the redshift range 0.2 〈  z  〈 1 in the four independent fields of the CFHTLS-Wide. Using a counts-in-cells technique we measure the variance ${\bar{\xi }}_2$ and the hierarchical moments $S_{n}= {{\bar{\xi }}_n / {\bar{\xi }}_2^{n-1}}$ (3 ≤  n  ≤ 5) as a function of redshift and angular scale. We find that the measured field-to-field scatter in our estimators is in excellent agreement with analytical predictions. At small scales, corresponding to the highly non-linear regime, we find tentative evidence at the 1 level that the hierarchical moments increase with redshift. At large scales, corresponding to the weakly non-linear regime, our measurements are marginally consistent with perturbation theory predictions for standard cold dark matter cosmology using a simple linear bias. The predictions of perturbation theory tend to slightly overestimate our measurements, which may be a signature of non-linear bias.
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  • 79
    Publication Date: 2013-09-17
    Description: We estimate cosmic microwave background (CMB) polarization power spectra and temperature–polarization cross-spectra, from the 9-year data of the Wilkinson Microwave Anisotropy Probe ( WMAP ). Foreground cleaning is implemented using minimum variance linear combinations of the coefficients of needlet decompositions of sky maps for all WMAP channels, to produce maps for CMB temperature anisotropies ( T -mode) and polarization ( E and B -modes), for nine different years of observation. The final power spectra are computed from averages of all possible cross-year power spectra obtained using foreground-cleaned maps for the different years. Our analysis technique yields a measurement of the EE spectrum that is in excellent agreement with theoretical expectations from the current cosmological model. By comparison, the publicly available WMAP EE power spectrum is higher on average (and significantly higher than the predicted EE spectrum from the current best fit) at scales larger than about a degree, an excess that is not confirmed by our analysis. Our TE and TB measurements are in good agreement overall with the WMAP ones and are compatible with the theoretical expectations, although a few data points are off by a few standard deviations, and yield a reduced 2 somewhat above expectation. As predicted for a standard cosmological model with low tensor-to-scalar ratio, the EB and BB power spectra obtained in our analysis are compatible with zero.
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  • 80
    Publication Date: 2013-09-17
    Description: We present optical integral field unit observations of two gas pillars surrounding the Galactic young massive star cluster NGC 3603. The high S/N and spectral resolution of these data have allowed us to accurately quantify the Hα, [N ii ] and [S ii ] emission line shapes, and we find a mixture of broad (FWHM ~ 70–100 km s –1 ) and narrow (〈50 km s –1 ) components. The broad components are found close to the edges of both pillars, suggesting that they originate in turbulent mixing layers (TMLs) driven by the effect of the star cluster wind. Both pillars exhibit surprisingly high ionized gas densities of 〉10 000 cm –3 . In one pillar we found that these high densities are only found in the narrow component, implying that they must originate from deeper within the pillar than the broad component. From this, together with our kinematical data, we conclude that the narrow component traces a photoevaporation flow, and that the TML forms at the interface with the hot wind. On the pillar surfaces, we find a consistent offset in radial velocity between the narrow (brighter) components of Hα and [N ii ] of ~5–8 km s –1 , for which we were unable to find a satisfactory explanation. We urge the theoretical community to simulate mechanical and radiative cloud interactions in more detail to address the many unanswered questions raised by this study.
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  • 81
    Publication Date: 2013-09-17
    Description: By exploiting the data base of early-type galaxy (ETG) members of the WINGS survey of nearby clusters, we address here the long debated question of the origin and shape of the Fundamental Plane (FP). Our data suggest that different physical mechanisms concur in shaping and ‘tilting’ the FP with respect to the virial plane (VP) expectation. In particular, a ‘hybrid solution’ in which the structure of galaxies and their stellar population are the main contributors to the FP tilt seems to be favoured. We find that the bulk of the tilt should be attributed to structural non-homology, while stellar population effects play an important but less crucial role. In addition, our data indicate that the differential FP tilt between the V and K band is due to a sort of entanglement between structural and stellar population effects, for which the inward steepening of colour profiles ( V  –  K ) tends to increase at increasing the stellar mass of ETGs. The same kind of analysis applied to the ATLAS 3 D and Sloan Digital Sky Survey (SDSS) data in common with WINGS ( WSDSS throughout the paper) confirms our results, the only remarkable difference being the less important role that our data attribute to the stellar mass-to-light-ratio (stellar populations) in determining the FP tilt . The ATLAS 3 D data also suggest that the FP tilt depends as well on the dark matter (DM) fraction and on the rotational contribution to the kinetic energy ( V rot /), thus again pointing towards the above-mentioned ‘hybrid solution’. We show that the global properties of the FP, i.e. its tilt and tightness, can be understood in terms of the underlying correlation among mass, structure and stellar population of ETGs, for which, at increasing the stellar mass, ETGs become (on average) ‘older’ and more centrally concentrated. Finally, we show that a Malmquist-like selection effect may mimic a differential evolution of the mass-to-light ratio for galaxies of different masses. This should be taken into account in the studies investigating the amount of the so-called ‘downsizing’ phenomenon.
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  • 82
    Publication Date: 2013-09-17
    Description: I present a new algorithm, Curved-sky grAvitational Lensing for Cosmological Light conE simulatioNS ( calclens ), for efficiently computing weak gravitational lensing shear signals from large N -body light cone simulations over a curved sky. This new algorithm properly accounts for the sky curvature and boundary conditions, is able to produce redshift-dependent shear signals including corrections to the Born approximation by using multiple-plane ray tracing and properly computes the lensed images of source galaxies in the light cone. The key feature of this algorithm is a new, computationally efficient Poisson solver for the sphere that combines spherical harmonic transform and multigrid methods. As a result, large areas of sky (~10 000 square degrees) can be ray traced efficiently at high resolution using only a few hundred cores. Using this new algorithm and curved-sky calculations that only use a slower but more accurate spherical harmonic transform Poisson solver, I study the convergence, shear E-mode, shear B-mode and rotation mode power spectra. Employing full-sky E/B-mode decompositions, I confirm that the numerically computed shear B-mode and rotation mode power spectra are equal at high accuracy (1 per cent) as expected from perturbation theory up to second order. Coupled with realistic galaxy populations placed in large N -body light cone simulations, this new algorithm is ideally suited for the construction of synthetic weak lensing shear catalogues to be used to test for systematic effects in data analysis procedures for upcoming large-area sky surveys. The implementation presented in this work, written in c and employing widely available software libraries to maintain portability, is publicly available at http://code.google.com/p/calclens .
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  • 83
    Publication Date: 2013-09-17
    Description: Quasar accretion disc winds observed via broad absorption lines (BALs) in the UV produce strong continuous absorption in X-rays. The X-ray absorber is believed to serve critically as a radiative shield to keep the outflow ionizations low enough for radiative driving. However, previous studies have shown that ‘mini-BAL’ and narrow absorption line (NAL) outflows have dramatically less X-ray absorption than BALs. Here, we examine X-ray and rest-frame UV spectra of eight mini-BAL quasars with outflow speeds in the range 0.1–0.2c to test the hypothesis that these extreme speeds require a strong shield. We find that the X-ray absorption is weak or moderate, with neutral-equivalent column densities N H  〈 few 10 22 cm –2 , consistent with mini-BALs at lower speeds. We use photoionization models to show that the amount of shielding consistent with our data is too weak to control the outflow ionizations and, therefore, it is not important for the acceleration. Shielding in complex geometries also seems unlikely because the alleged shield would need to extinguish the ionizing far-UV flux while avoiding detection in X-rays and the near-UV. We argue that the outflow ionizations are kept moderate, instead, by high gas densities in small clouds. If the mini-BALs form at radial distances of the order of R ~ 2 pc from the central quasar (broadly consistent with theoretical models and with the mini-BAL variabilities observed here and in previous work), and the total column densities in the mini-BAL gas are N H 10 21 cm –2 , then the total radial extent of outflow clouds is only R clouds 3 x 10 13 cm in cases of no/weak shielding or R clouds 3 x 10 14 cm behind the maximum shield allowed by our data. This implies radial filling factors R clouds / R 5 x 10 – 6 or 5 x 10 – 5 for the unshielded or maximally shielded cases, respectively. Compared to the transverse sizes 8 x 10 15 cm (based on measured line depths), the outflows have shapes like thin ‘pancakes’ viewed face-on, or they occupy larger volumes like a spray of many dense clouds with a small volume filling factor. These results favour models with magnetic confinement in magnetic disc winds. To the extent that BALs, mini-BALs and NALs probe the same general outflow phenomenon, our result for dense substructures should apply to all three outflow types.
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  • 84
    Publication Date: 2013-09-17
    Description: The estimated stellar masses of galaxies are widely used to characterize how the galaxy population evolves over cosmic time. If stellar masses can be estimated in a robust manner, free from any bias, global diagnostics such as the stellar mass function can be used to constrain the physics of galaxy formation. We explore how galaxy stellar masses, estimated by fitting broad-band spectral energy distributions (SEDs) with stellar population models, can be biased as a result of commonly adopted assumptions for the star formation and chemical enrichment histories, recycled fractions and dust attenuation curves of galaxies. We apply the observational technique of broad-band SED fitting to model galaxy SEDs calculated by the theoretical galaxy formation model GALFORM, isolating the effect of each of these assumptions. We find that, averaged over the entire galaxy population, the common assumption of exponentially declining star formation histories does not, by itself, adversely affect stellar mass estimation. However, we also show that this result does not hold when considering galaxies that have undergone a recent burst of star formation. We show that fixing the metallicity in SED fitting or using sparsely sampled metallicity grids can introduce mass-dependent systematics into stellar mass estimates. We find that the common assumption of a star–dust geometry corresponding to a uniform foreground dust screen can cause the stellar masses of dusty model galaxies to be significantly underestimated. Finally, we show that stellar mass functions recovered by applying SED fitting to model galaxies at high redshift can differ significantly in both shape and normalization from the intrinsic mass functions predicted by a given model. In particular, the effects of dust can reduce the normalization at the high-mass end by up to 0.6 dex in some cases. Given these differences, our methodology of using stellar masses estimated from model galaxy SEDs offers a new, self-consistent way to compare model predictions with observations. We conclude that great care should be taken when comparing theoretical galaxy formation models to observational results based on the estimated stellar masses of high-redshift galaxies.
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  • 85
    Publication Date: 2013-09-17
    Description: We analyse the 2D correlation function of the Sloan Digital Sky Survey-III Baryon Oscillation Spectroscopic Survey (BOSS) CMASS sample of massive galaxies of the ninth data release to measure cosmic expansion H and the angular diameter distance D A at a mean redshift of 〈 z 〉 = 0.57. We apply, for the first time, a new correlation function technique called clustering wedges μ ( s ). Using a physically motivated model, the anisotropic baryonic acoustic feature in the galaxy sample is detected at a significance level of 4.7 compared to a featureless model. The baryonic acoustic feature is used to obtain model-independent constraints cz / H / r s = 12.28 ± 0.82 (6.7 percent accuracy) and D A / r s =  9.05 ± 0.27 (3.0 per cent) with a correlation coefficient of –0.5, where r s is the sound horizon scale at the end of the baryonic drag era. We conduct thorough tests on the data and 600 simulated realizations, finding robustness of the results regardless of the details of the analysis method. Combining this with r s constraints from the cosmic microwave background, we obtain H (0.57) = 90.8 ± 6.2 km s –1 Mpc –1 and D A (0.57) = 1386 ± 45 Mpc. We use simulations to forecast results of the final BOSS CMASS data set. We apply the reconstruction technique on the simulations demonstrating that the sharpening of the anisotropic baryonic acoustic feature should improve the detection as well as tighten constraints of H and D A by ~30 per cent on average.
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  • 86
    Publication Date: 2013-09-17
    Description: We present an analysis of Chandra archival, pre-explosion data of the positions of three nearby (〈25 Mpc) Type Ia supernovae, SN2011iv, SN2012cu and SN2012fr. No sources corresponding to the progenitors were found in any of the observations. Combining all sources with well-defined backgrounds does not reveal any evidence for X-ray emission from the progenitors either. We calculated upper limits on the bolometric luminosities of the progenitors, under the assumption that they were black bodies with effective temperatures between 30 and 150 eV, corresponding to ‘canonical’ supersoft X-ray sources. The upper limits of SN2012fr straddle the Eddington luminosity of canonical supersoft sources, but fainter canonical supersoft sources cannot be ruled out by this study. We also compare our upper limits with known compact binary supersoft X-ray sources. This study is a continuation of the campaign to directly detect or constrain the X-ray characteristics of pre-explosion observations of nearby Type Ia supernova progenitors; with the results reported in Nielsen, Voss & Nelemans (see reference in Introduction), the number of nearby Type Ia supernovae for which pre-explosion images are available in the Chandra archive is now 13 and counting.
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  • 87
    Publication Date: 2013-09-17
    Description: In this work, we report the Photodetector Array Camera and Spectrometer (PACS) 100 μm/160 μm detections of a sample of 42 GALEX -selected and far-infrared (FIR)-detected Lyman break galaxies (LBGs) at z  ~ 1 located in the Cosmic Evolution Survey (COSMOS) field and analyse their ultraviolet (UV) to FIR properties. The detection of these LBGs in the FIR indicates that they have a dust content high enough so that its emission can be directly detected. According to a spectral energy distribution (SED) fitting with stellar population templates to their UV-to-near-IR observed photometry, PACS-detected LBGs tend to be bigger ( R eff  ~ 4.1 kpc), more massive [log ( M * /M ) ~ 10.7], dustier [ E s ( B  –  V ) ~ 0.40], redder in the UV continuum (β ~ –0.60) and UV-brighter [log ( L UV /L ) ~ 10.1] than PACS-undetected LBGs. PACS-detected LBGs at z  ~ 1 are mostly disc-like galaxies and are located over the green valley and red sequence of the colour–magnitude diagram of galaxies at their redshift. By using their UV and IR emission, we find that PACS-detected LBGs tend to be less dusty and have slightly higher total star formation rates (SFRs) than other PACS-detected UV-selected galaxies within the same redshift range. As a consequence of the selection effect due to the depth of the FIR observations employed, all our PACS-detected LBGs have total IR luminosities, L IR , higher than 10 11 L and thus are luminous IR galaxies. However, none of the PACS-detected LBGs are in the ultra-luminous IR galaxy (ULIRG) regime, L IR  ≥ 10 12 L , where the FIR observations are complete. The finding of ULIRGs-LBGs at higher redshifts ( z  ~ 3) suggests an evolution of the FIR emission of LBGs with cosmic time. In an IRX–β diagram, PACS-detected LBGs at z  ~ 1 tend to be located around the relation for local starburst similarly to other UV-selected PACS-detected galaxies at the same redshift. Consequently, the dust-correction factors obtained with their UV continuum slope allow us to determine their total SFR, unlike at higher redshifts. However, the dust attenuation derived from UV to NIR SED fitting overestimates the total SFR for most of our PACS-detected LBGs in an age-dependent way: the overestimation factor is higher in younger galaxies. This is likely due to the typical degeneracy between dust attenuation and age in the SED fitting with synthetic templates and highlights the importance of the FIR measurements in the analysis of star-forming galaxies at intermediate redshifts.
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  • 88
    Publication Date: 2013-09-17
    Description: We study 23 previously published Kepler targets to perform a consistent grid-based Bayesian asteroseismic analysis and compare our results to those obtained via the Asteroseismic Modelling Portal. We find differences in the derived stellar parameters of many targets and their uncertainties. While some of these differences can be attributed to systematic effects between stellar evolutionary models, we show that the different methodologies deliver incompatible uncertainties for some parameters. Using non-adiabatic models and our capability to measure surface effects, we also investigate the dependency of these surface effects on the stellar parameters. Our results suggest a dependence of the magnitude of the surface effect on the mixing length parameter which also, but only minimally, affects the determination of stellar parameters. While some stars in our sample show no surface effect at all, the most significant surface effects are found for stars that are close to the Sun's position in the Hertzsprung–Russell diagram.
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  • 89
    Publication Date: 2013-09-17
    Description: We present evidence for a strong relationship between galaxy size and environment for the quiescent population in the redshift range 1 〈  z  〈 2. Environments were measured using projected galaxy overdensities on a scale of 400 kpc, as determined from ~96 000 K -band-selected galaxies from the UKIDSS Ultra Deep Survey (UDS). Sizes were determined from ground-based K -band imaging, calibrated using space-based CANDELS HST observations in the centre of the UDS field, with photometric redshifts and stellar masses derived from 11-band photometric fitting. From the resulting size–mass relation, we confirm that quiescent galaxies at a given stellar mass were typically ~50 per cent smaller at z  ~ 1.4 compared to the present day. At a given epoch, however, we find that passive galaxies in denser environments are on average significantly larger at a given stellar mass. The most massive quiescent galaxies ( M *  〉 2 10 11  M ) at z  〉 1 are typically 50 per cent larger in the highest density environments compared to those in the lowest density environments. Using Monte Carlo simulations, we reject the null hypothesis that the size–mass relation is independent of environment at a significance 〉4.8 for the redshift range 1 〈  z  〈 2. In contrast, the evidence for a relationship between size and environment is much weaker for star-forming galaxies.
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  • 90
    Publication Date: 2013-09-17
    Description: We present the results from the Very Large Array radio continuum total power and polarized intensity observations of Stephan's Quintet at 1.43 and 4.86 GHz, along with complementary 4.85- and 8.35-GHz Effelsberg observations. Our study shows a large envelope of radio emission encompassing all the member galaxies and hence a large volume of intergalactic matter. Infall of the galaxy NGC 7318B produces a ridge of intergalactic, polarized emission, for which the magnetic field strength has been estimated as 11.0 ± 2.2 μG, with an ordered component of 2.6 ± 0.8 μG. The energy density of the field within the ridge area is of the same order as estimates of the thermal component, implying that the magnetic field has a significant role in the dynamics of the intergalactic matter. We also report that the tidal dwarf galaxy candidate SQ-B possesses a strong and highly anisotropic magnetic field, with a total strength equal to 6.5 ± 1.9 μG and an ordered component reaching 3.5 ± 1.2 μG, which is comparable to that found in normal-sized galaxies.
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  • 91
    Publication Date: 2013-09-17
    Description: We present a simple and efficient phenomenological model for the two-dimensional two-point galaxy correlation function that works well over a wide range of scales, from large scales down to scales as small as 25 h –1 Mpc. Our model incorporates non-linear effects and a scale-dependent galaxy bias on small scales, and it allows the redshift-space distortions to be scale and direction dependent. We validate our model using LasDamas mock catalogues and apply it to the Sloan Digital Sky Survey (SDSS) Data Release Seven (DR7) luminous red galaxies (LRGs). Using only the monopole and quadrupole of the correlation function measured from the SDSS DR7 LRGs, we obtain improved measurements H ( z ) r s ( z d )/ c  = 0.0433 ± 0.0042, D A ( z )/ r s ( z d ) = 6.59 ± 0.46 and f ( z ) 8 ( z ) = 0.429 ± 0.089 at z  = 0.35, using the scale range 25 〈  s  〈 120 h –1 Mpc. We expect our results and model to be useful in tightening dark energy and gravity constraints from the full analysis of current and future galaxy clustering data.
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  • 92
    Publication Date: 2013-09-17
    Description: We study the formation and evolution of filamentary configurations of dark matter haloes in voids. Our investigation uses the high-resolution cold dark matter simulation CosmoGrid to look for void systems resembling the VGS_31 elongated system of three interacting galaxies that was recently discovered by the Void Galaxy Survey inside a large void in the Sloan Digital Sky Survey galaxy redshift survey. H  i data revealed these galaxies to be embedded in a common elongated envelope, possibly embedded in intravoid filament. In the CosmoGrid simulation we look for systems similar to VGS_31 in mass, size and environment. We find a total of eight such systems. For these systems, we study the distribution of neighbour haloes, the assembly and evolution of the main haloes and the dynamical evolution of the haloes, as well as the evolution of the large-scale structure in which the systems are embedded. The spatial distribution of the haloes follows that of the dark matter environment. We find that VGS_31-like systems have a large variation in formation time, having formed between 10 Gyr ago and the present epoch. However, the environments in which the systems are embedded evolved to resemble each other substantially. Each of the VGS_31-like systems is embedded in an intravoid wall, that no later than z  = 0.5 became the only prominent feature in its environment. While part of the void walls retain a rather featureless character, we find that around half of them are marked by a pronounced and rapidly evolving substructure. Five haloes find themselves in a tenuous filament of a few h –1 Mpc long inside the intravoid wall. Finally, we compare the results to observed data from VGS_31. Our study implies that the VGS_31 galaxies formed in the same (proto)filament, and did not meet just recently. The diversity amongst the simulated halo systems indicates that VGS_31 may not be typical for groups of galaxies in voids.
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  • 93
    Publication Date: 2013-09-17
    Description: Using 3D numerical hydrodynamical simulations, we show that jets launched prior to Type Ia supernova (SN Ia) explosion in the core-degenerate (CD) scenario can account for the appearance of two opposite lobes (‘Ears’) along the symmetry axis of the SN remnant (SNR). In the double-degenerate (DD) and CD scenarios the merger of the two degenerate compact objects is very likely to lead to the formation of an accretion disc, that might launch two opposite jets. In the CD scenario, these jets interact with the envelope ejected during the preceding common envelope phase. If explosion occurs shortly after the merger process, the exploding gas and the jets will collide with the ejected nebula, leading to SNR with axisymmetric components including ‘Ears’. We also explore the possibility that the jets are launched by the companion white dwarf prior to its merger with the core. This last process is similar to the one where jets are launched in some pre-planetary nebulae. The SNR ‘Ears’ in this case are formed by a spherical SN Ia explosion inside an elliptical planetary nebula-like object. We compare our numerical results with two SNRs – Kepler and G299.2–2.9.
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  • 94
    Publication Date: 2013-09-17
    Description: Low-mass star-forming regions are more complex than the simple spherically symmetric approximation that is often assumed. We apply a more realistic infall/outflow physical model to molecular/continuum observations of three late Class 0 protostellar sources with the aims of (a) proving the applicability of a single physical model for all three sources and (b) deriving physical parameters for the molecular gas component in each of the sources. We have observed several molecular species in multiple rotational transitions. The observed line profiles were modelled in the context of a dynamical model which incorporates infall and bipolar outflows, using a three-dimensional radiative transfer code. This results in constraints on the physical parameters and chemical abundances in each source. Self-consistent fits to each source are obtained. We constrain the characteristics of the molecular gas in the envelopes as well as in the molecular outflows. We find that the molecular gas abundances in the infalling envelope are reduced, presumably due to freeze-out, whilst the abundances in the molecular outflows are enhanced, presumably due to dynamical activity. Despite the fact that the line profiles show significant source-to-source variation, which primarily derives from variations in the outflow viewing angle, the physical parameters of the gas are found to be similar in each core.
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  • 95
    Publication Date: 2013-09-17
    Description: We present predictions for hydrogen and helium emission line luminosities from circumstellar matter around Type Ia supernovae (SNe Ia) using time dependent photoionization modelling. Early high-resolution ESO/Very Large Telescope (VLT) optical echelle spectra of the SN Ia 2000cx were taken before and up to ~70 d after maximum to probe the existence of such narrow emission lines from the supernova. We detect no such lines, and from our modelling place an upper limit on the mass-loss rate for the putative wind from the progenitor system, $\skew4\dot{M}\lesssim 1.3\times 10^{-5} \,{\rm M}_{\odot }\,{\rm yr}^{-1}$ , assuming a speed of 10 km s –1 and solar abundances for the wind. If the wind would be helium-enriched and/or faster, the upper limit on $\skew4\dot{M}$ could be significantly higher. In the helium-enriched case, we show that the best line to constrain the mass-loss would be He i 10 830. In addition to confirming the details of interstellar Na i and Ca ii absorption towards SN 2000cx as discussed by Patat et al., we also find evidence for 6613.56 Å diffuse interstellar band absorption in the Milky Way. We also discuss measurements of the X-ray emission from the interaction between the supernova ejecta and the wind and we re-evaluate observations of SN 1992A obtained ~16 d after maximum by Schlegel & Petre. We find an upper limit of $\skew4\dot{M}\sim 1.3\times 10^{-5} \,{\rm M}_{\odot }\,{\rm yr}^{-1}$ which is significantly higher than that estimated by Schlegel & Petre. These results, together with the previous observational work on the normal SNe Ia 1994D and 2001el, disfavour a symbiotic star in the upper mass-loss rate regime (so-called Mira-type systems) from being the likely progenitor scenario for these SNe. Our model calculations are general, and can also be used for the subclass of SNe Ia that do show circumstellar interaction, e.g. the recent PTF 11kx. To constrain hydrogen in late-time spectra, we present ESO/VLT and ESO/New Technology Telescope optical and infrared observations of SNe Ia 1998bu and 2000cx in the nebular phase, 251-388 d after maximum. We see no signs of hydrogen line emission in SNe 1998bu and 2000cx at these epochs, and from the absence of Hα with a width of the order of ~10 3 km s –1 , we argue from modelling that the mass of such hydrogen-rich gas must be 0.03 M for both supernovae. Comparing similar upper limits with recent models of Pan et al., it seems that hydrogen-rich donors with a separation of 5 times the radius of the donor may be ruled out for the five SNe Ia 1998bu, 2000cx, 2001el, 2005am and 2005cf. Larger separation, helium-rich donors, or a double-degenerate origin for these supernovae seems more likely. Our models have also been used to put the limit on hydrogen-rich gas in the recent SN 2011fe, and for this supernova, a double-degenerate origin seems likely.
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  • 96
    Publication Date: 2013-09-17
    Description: We build differential-reddening maps for 66 Galactic globular clusters (GCs) with archival Hubble Space Telescope WFC/ACS F 606 W and F 814 W photometry. Because of the different GC sizes (characterized by the half-light radius R h ) and distances to the Sun, the WFC/ACS field of view (200 arcsec x 200 arcsec) coverage ( R obs ) lies in the range 1 R obs / R h 15 for about 85 per cent of the sample, with about 10 per cent covering only the inner ( R obs R h ) parts. We divide the WFC/ACS field of view across each cluster in a regular cell grid and extract the stellar-density Hess diagram from each cell, shifting it in colour and magnitude along the reddening vector until matching the mean diagram. Thus, the maps correspond to the internal dispersion of the reddening around the mean. Depending on the number of available stars (i.e. probable members with adequate photometric errors), the angular resolution of the maps range from 7 arcsec x 7 arcsec to 20 arcsec x 20 arcsec. We detect spatially variable extinction in the 66 GCs studied, with mean values ranging from 〈E(B-V)〉0.018 (NGC 6981) up to 〈E(B-V)〉0.016 (Palomar 2). Differential-reddening correction decreases the observed foreground reddening and the apparent distance modulus but, since they are related to the same value of E ( B  –  V ), the distance to the Sun is conserved. Fits to the mean-ridge lines of the highly extincted and photometrically scattered GC Palomar 2 show that age and metallicity also remain unchanged after the differential-reddening correction, but measurement uncertainties decrease because of the reduced scatter. The lack of systematic variations of 〈E(B-V)〉 with both the foreground reddening and the sampled cluster area indicates that the main source of differential reddening is interstellar.
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  • 97
    Publication Date: 2013-09-17
    Description: We present a physically motivated semi-analytic model to understand the clustering of high-redshift Lyman α emitters (LAEs). We show that the model parameters constrained by the observed luminosity functions can be used to predict large-scale bias and angular correlation function of LAEs. These predictions are shown to reproduce the observations remarkably well. We find that average masses of dark matter haloes hosting LAEs brighter than the threshold narrow-band magnitude ~25 are ~10 11 M . These are smaller than that of typical Lyman break galaxies (LBGs) brighter than a similar threshold continuum magnitude by a factor of ~10. This results in a smaller clustering strength of LAEs compared to LBGs. However, using the observed relationship between the UV continuum and Lyman α luminosity of LAEs, we show that both LAEs and LBGs belong to the same parent galaxy population with narrow-band techniques having greater efficiency in picking up galaxies with low UV luminosity. We also show that the lack of evidence for the presence of the one-halo term in the observed LAE angular correlation functions can be attributed to a sub-Poisson distribution of LAEs in dark matter haloes as a result of their low halo occupations.
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  • 98
    Publication Date: 2013-09-17
    Description: We present a detailed analysis of spectral line profiles in Type Ia supernova (SN Ia) spectra. We focus on the feature at ~3500–4000 Å, which is commonly thought to be caused by blueshifted absorption of Ca H&K. Unlike some other spectral features in SN Ia spectra, this feature often has two overlapping (blue and red) components. It is accepted that the red component comes from photospheric calcium. However, it has been proposed that the blue component is caused by either high-velocity calcium (from either abundance or density enhancements above the photosphere of the supernova, SN) or Si ii 3858. By looking at multiple data sets and model spectra, focusing on spectra near maximum brightness, we conclude that the blue component of the Ca H&K feature is caused by Si ii 3858 for most SNe Ia, although high-velocity calcium is likely important for some SNe. The strength of the Si ii 3858 feature varies strongly with the light-curve shape of an SN. As a result, the velocity measured from a single-Gaussian fit to the full line profile correlates with light-curve shape. The velocity of the Ca H&K component of the profile does not correlate with light-curve shape, contrary to previous claims. We detail the pitfalls of assuming that the blue component of the Ca H&K feature is caused by calcium, with implications for our understanding of SN Ia progenitors, explosions and cosmology.
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  • 99
    Publication Date: 2013-09-17
    Description: Subject of this paper is the statistical properties of ellipticity alignments between galaxies evoked by their coupled angular momenta. Starting from physical angular momentum models, we bridge the gap towards ellipticity correlations, ellipticity spectra and derived quantities such as aperture moments, comparing the intrinsic signals with those generated by gravitational lensing, with the projected galaxy sample of Euclid in mind. We investigate the dependence of intrinsic ellipticity correlations on cosmological parameters and show that intrinsic ellipticity correlations give rise to non-Gaussian likelihoods as a result of non-linear functional dependences. Comparing intrinsic ellipticity spectra to weak lensing spectra we quantify the magnitude of their contaminating effect on the estimation of cosmological parameters and find that biases on dark energy parameters are very small in an angular momentum-based model in contrast to the linear alignment model commonly used. Finally, we quantify whether intrinsic ellipticities can be measured in the presence of the much stronger weak lensing induced ellipticity correlations, if prior knowledge on a cosmological model is assumed.
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  • 100
    Publication Date: 2013-09-17
    Description: In this paper, I present a new method that has been developed for determining the brightness of a cloudless night sky, on the basis of widely available amateur observations of comets. The tests show the correctness of the method, which makes it possible to determine the level of light pollution, defined as the brightness of the artificial sky glow, through the use of the archival observations of comets. The use of data bases of comet observations in Poland in the period 1994–2009 has led to a positive verification of the known model map of the brightness of the night sky. Also, it has been possible to find changes in the level of light pollution in this period, at the selected observation sites.
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