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  • Springer Nature  (40,053)
  • Oxford University Press  (30,734)
  • American Association for the Advancement of Science (AAAS)
  • 2010-2014  (74,883)
  • 1980-1984
  • 1925-1929
  • 2013  (45,573)
  • 2011  (29,310)
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  • 2010-2014  (74,883)
  • 1980-1984
  • 1925-1929
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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
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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
    Type: Article , isiRev
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  • 3
    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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  • 4
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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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  • 5
    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
    Type: Article
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  • 6
    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
    Type: Article
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  • 7
    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
    Type: Article
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    Format: application/msword
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  • 8
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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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  • 9
    Publication Date: 2013-06-17
    Print ISSN: 1552-4450
    Electronic ISSN: 1552-4469
    Topics: Biology , Chemistry and Pharmacology
    Published by Springer Nature
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  • 10
    Publication Date: 2013-05-12
    Print ISSN: 1552-4450
    Electronic ISSN: 1552-4469
    Topics: Biology , Chemistry and Pharmacology
    Published by Springer Nature
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  • 11
  • 12
    Publication Date: 2013-05-22
    Print ISSN: 1476-1122
    Electronic ISSN: 1476-4660
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 13
    Publication Date: 2013-11-21
    Print ISSN: 1476-1122
    Electronic ISSN: 1476-4660
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 14
    Publication Date: 2011-10-24
    Print ISSN: 1476-1122
    Electronic ISSN: 1476-4660
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 15
    Publication Date: 2013-05-22
    Print ISSN: 1476-1122
    Electronic ISSN: 1476-4660
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Natural Sciences in General , Physics
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  • 16
    Publication Date: 2013-05-24
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 17
    Publication Date: 2011-04-03
    Print ISSN: 1748-3387
    Electronic ISSN: 1748-3395
    Topics: Biology , Chemistry and Pharmacology , Physics
    Published by Springer Nature
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  • 18
    Publication Date: 2011-10-24
    Print ISSN: 1476-1122
    Electronic ISSN: 1476-4660
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Natural Sciences in General , Physics
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  • 19
    Publication Date: 2013-01-23
    Print ISSN: 0028-0836
    Electronic ISSN: 1476-4687
    Topics: Biology , Chemistry and Pharmacology , Medicine , Natural Sciences in General , Physics
    Published by Springer Nature
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  • 20
    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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  • 21
    Publication Date: 2013-09-07
    Description: The magnetism of graphene has remained divergent and controversial due to absence of reliable experimental results. Here we show the intrinsic magnetism of graphene edge states revealed based on unidirectional aligned graphene sheets derived from completely carbonized SiC crystals. It is found that ferromagnetism, antiferromagnetism and diamagnetism along with a probable superconductivity exist in the graphene with irregular zigzag edges. A phase diagram is constructed to show the evolution of the magnetism. The ferromagnetic ordering curie-temperature of the fundamental magnetic order unit (FMOU) is 820 ± 80 K. The antiferromagnetic ordering Neel temperature of the FMOUs belonging to different sublattices is about 54 ± 2 K. The diamagnetism is similar to that of graphite and can be well described by the Kotosonov's equation. Our experimental results provide new evidences to clarify the controversial experimental phenomena observed in graphene and contribute to a deeper insight into the nature of magnetism in graphene based system. Scientific Reports 3 doi: 10.1038/srep02599
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 22
    Publication Date: 2013-09-07
    Description: The detection, differentiation and visualization of compounds such as gases, liquids or ions are key challenges for the design of selective optical chemosensors. Optical chemical sensors employ a transduction mechanism that converts a specific analyte recognition event into an optical signal. Here we report a novel concept for fluoride ion sensing where a porous crystalline framework serves as a host for a fluorescent reporter molecule. The detection is based on the decomposition of the host scaffold which induces the release of the fluorescent dye molecule. Specifically, the hybrid composite of the metal-organic framework NH2-MIL-101(Al) and fluorescein acting as reporter shows an exceptional turn-on fluorescence in aqueous fluoride-containing solutions. Using this novel strategy, the optical detection of fluoride is extremely sensitive and highly selective in the presence of many other anions. Scientific Reports 3 doi: 10.1038/srep02562
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 23
    Publication Date: 2013-09-07
    Description: Despite the pathological importance of fibrin clot formation, little is known about the structure of these clots because X-ray and nuclear magnetic resonance (NMR) analyses are not applicable to insoluble proteins. In contrast to previously reported anti-fibrin monoclonal antibodies (mAbs), our anti-fibrin clot mAb (clone 102–10) recognises an uncovered region that is exposed only when a fibrin clot forms. The epitope of the 102–10 mAb was mapped to a hydrophobic region on the Bβ chain that interacted closely with a counterpart region on the γ chain in a soluble state. New anti-Bβ and anti-γ mAbs specific to peptides lining the discovered region appeared to bind exclusively to fibrin clots. Furthermore, the radiolabelled 102–10 mAb selectively accumulated in mouse spontaneous tumours, and immunohistochemistry using this mAb revealed greater fibrin deposition in World Health Organization (WHO) grade 4 glioma than in lower-grade gliomas. Because erosive tumours are apt to cause micro-haemorrhages, even early asymptomatic tumours detected with a radiolabelled 102-10 mAb may be aggressively malignant. Scientific Reports 3 doi: 10.1038/srep02604
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 24
    Publication Date: 2013-09-07
    Description: An electrical pumped microscopic active display with integration of plasmonic polarizer and light-emitting-diode is proposed. Thanks to the strong polarized emission through the rectangular nanoholes, well designed pixels with respect to different polarizations are engineered, which give rise to flexible and controllable active display. As results, polarization multiplexed letter encoding, single and double gray-scale images and animation movies are successfully realized. Our results demonstrate a new strategy in electro-optical integration and indicate potential applications in designing new type of microscopic electro-optical devices. Scientific Reports 3 doi: 10.1038/srep02603
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 25
    Publication Date: 2013-09-07
    Description: We compare the three most commonly used scanning probe techniques to obtain a reliable value of the work function in graphene domains of different thickness. The surface potential (SP) of graphene is directly measured in Hall bar geometry via a combination of electrical functional microscopy and spectroscopy techniques, which enables calibrated work function measurements of graphene domains in ambient conditions with values Φ1LG ~4.55 ± 0.02 eV and Φ2LG ~ 4.44 ± 0.02 eV for single- and bi-layer, respectively. We demonstrate that frequency-modulated Kelvin probe force microscopy (FM-KPFM) provides more accurate measurement of the SP than amplitude-modulated (AM)-KPFM. The discrepancy between experimental results obtained by different techniques is discussed. In addition, we use FM-KPFM for contactless measurements of the specific components of the device resistance. We show a strong non-Ohmic behavior of the electrode-graphene contact resistance and extract the graphene channel resistivity. Scientific Reports 3 doi: 10.1038/srep02597
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 26
    Publication Date: 2013-09-07
    Description: The non-canonical NF-κB pathway is crucial for the immune system. A critical event in activation of the non-canonical pathway is the attenuation of NF-κB-inducing kinase (NIK) degradation, which is promoted by continuous polyubiquitination of NIK catalyzed by the NIK ubiquitin-ligase complex composed of cellular inhibitor of apoptosis protein 1 and 2 (cIAP1/2), TNF receptor-associated factor 2 (TRAF2), and TRAF3. However, the molecular mechanism of stimulation-dependent NIK stabilization remains poorly understood. Here, we show that A20, a ubiquitin-editing enzyme, promotes efficient activation of the non-canonical pathway independent of its catalytic activity. A20 directly binds to cIAP1 through the seventh zinc finger of A20, resulting in dissociation of the TRAF2/TRAF3 interaction, thereby inactivating the ligase complex to stabilize NIK. Given that A20 negatively regulates the canonical pathway, A20 is likely involved in the molecular switch that promotes the transition from canonical to non-canonical activation for proper control of the immune system. Scientific Reports 3 doi: 10.1038/srep02568
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 27
    Publication Date: 2013-09-07
    Description: Plasmon-enhanced photocurrent generation and water oxidation from visible to near-infrared wavelengths NPG Asia Materials 5, e61 (September 2013). doi:10.1038/am.2013.42 Authors: Kosei Ueno & Hiroaki Misawa
    Keywords: gold nanorodlocalized surface plasmon resonancenear-infrared lightphotoelectric conversionplasmonic chemistrywater oxidation
    Print ISSN: 1884-4049
    Electronic ISSN: 1884-4057
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 28
    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
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 29
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    Oxford University Press
    Publication Date: 2013-09-08
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 30
    Publication Date: 2013-09-08
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 31
    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.
    Print ISSN: 0959-6658
    Electronic ISSN: 1460-2423
    Topics: Biology , Medicine
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  • 32
    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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  • 33
    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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  • 34
    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
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  • 35
    Publication Date: 2013-09-08
    Description: Article The Broca area is located in the human prefrontal cortex and is involved in voluntary speech. Hage and Nieder now show that a monkey homologue of Broca’s area is similarly responsible for monkey volitional vocalizations. Nature Communications doi: 10.1038/ncomms3409 Authors: Steffen R. Hage, Andreas Nieder
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 36
    Publication Date: 2013-09-08
    Description: Article B lymphocytes respond to stimulation by proliferating and differentiating. Here the authors quantify and model the responses of B lymphocytes to TLR and CD40-dependent stimulation, and find that the latter induces a more complex response to signals of varying strength. Nature Communications doi: 10.1038/ncomms3406 Authors: E.D. Hawkins, M.L. Turner, C.J. Wellard, J.H.S. Zhou, M.R. Dowling, P.D. Hodgkin
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 37
    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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  • 38
    Publication Date: 2013-09-08
    Description: Erratum Nature Communications doi: 10.1038/ncomms3309 Authors: Ralph P. Schneider, Ianire Garrobo, Miguel Foronda, Jose A. Palacios, Rosa M. Marión, Ignacio Flores, Sagrario Ortega, Maria A. Blasco
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 39
    Publication Date: 2013-09-08
    Description: Article It has long been suggested, but never shown, than nanometre-sized particles precede mineral formation in magmatic systems. Here, Helmy et al. demonstrate that platinum and arsenic self-organize to nanoparticle precursors in magmatic liquids before mineral crystallization. Nature Communications doi: 10.1038/ncomms3405 Authors: Hassan M. Helmy, Chris Ballhaus, Raúl O.C. Fonseca, Richard Wirth, Thorsten Nagel, Marian Tredoux
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 40
    Publication Date: 2013-09-08
    Description: Article Messenger RNAs and their associated proteins are transported from the nucleus through highly selective nuclear pore complexes. Using ultrahigh resolution single-molecule imaging, the authors visualise the path taken by each messenger RNA as it negotiates the pore’s selectivity filter. Nature Communications doi: 10.1038/ncomms3414 Authors: Jiong Ma, Zhen Liu, Nicole Michelotti, Sethuramasundaram Pitchiaya, Ram Veerapaneni, John R. Androsavich, Nils G. Walter, Weidong Yang
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 41
    Publication Date: 2013-09-08
    Description: Article TRPA1 is a transient receptor potential channel family member and is involved in the detection of nociceptive stimuli. Zhou et al. identify an alternative splice variant of TRPA1, which increases TRPA1 plasma expression and channel function, and enhances pain-like behaviour in mice. Nature Communications doi: 10.1038/ncomms3399 Authors: Yiming Zhou, Yoshiro Suzuki, Kunitoshi Uchida, Makoto Tominaga
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 42
    Publication Date: 2013-09-08
    Description: Corrigendum Nature Communications doi: 10.1038/ncomms3358 Authors: Qilong Wang, Xiaoying Zhuang, Jingyao Mu, Zhong-Bin Deng, Hong Jiang, Lifeng Zhang, Xiaoyu Xiang, Baomei Wang, Jun Yan, Donald Miller, Huang-Ge Zhang
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 43
    Publication Date: 2013-09-08
    Description: Article Despite its importance for non-volatile memory, the origin of resistive switching in a metal insulator-metal structure is unclear. Park et al. fabricate such a structure inside a transmission electron microscope to show that switching occurs via oxygen-vacancy migration, which changes the conduction channels. Nature Communications doi: 10.1038/ncomms3382 Authors: Gyeong-Su Park, Young Bae Kim, Seong Yong Park, Xiang Shu Li, Sung Heo, Myoung-Jae Lee, Man Chang, Ji Hwan Kwon, M. Kim, U-In Chung, Regina Dittmann, Rainer Waser, Kinam Kim
    Electronic ISSN: 2041-1723
    Topics: Biology , Chemistry and Pharmacology , Natural Sciences in General , Physics
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  • 44
    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.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 45
    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.
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  • 46
    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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  • 47
    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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  • 48
    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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  • 49
    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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  • 50
    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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  • 51
    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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  • 52
    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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  • 53
    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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  • 54
    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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  • 55
    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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  • 56
    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.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 57
    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.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 58
    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.
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
    Published by Oxford University Press on behalf of The Deutsche Geophysikalische Gesellschaft (DGG) and the Royal Astronomical Society (RAS).
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  • 59
    Publication Date: 2013-09-11
    Description: Insects face the challenge of integrating multi-sensory information to control their flight. Here we study a ‘streamlining’ response in honeybees, whereby honeybees raise their abdomen to reduce drag. We find that this response, which was recently reported to be mediated by optic flow, is also strongly modulated by the presence of air flow simulating a head wind. The Johnston's organs in the antennae were found to play a role in the measurement of the air speed that is used to control the streamlining response. The response to a combination of visual motion and wind is complex and can be explained by a model that incorporates a non-linear combination of the two stimuli. The use of visual and mechanosensory cues increases the strength of the streamlining response when the stimuli are present concurrently. We propose this multisensory integration will make the response more robust to transient disturbances in either modality. Scientific Reports 3 doi: 10.1038/srep02614
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
    Published by Springer Nature
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  • 60
    Publication Date: 2013-09-11
    Description: A novel 3D hexadecanuclear heteropolyoxozincate organic framework, IFMC-200, has been successfully synthesized based on a late transition metal-oxygen cluster. IFMC-200 not only represents the first example of (3,4,24)-connected framework but also contains the first 24-connected single metal cluster in a crystal structure. It exhibits superior thermal stability, good water-stability, and even insensitivity to the existence of acid and base within a certain range of pH values. Furthermore, it performs as a heterogeneous crystalline Lewis acid catalyst with good activity for the conversion of long-chain fatty acids rather than short-chain ones, and high recycling efficiency for esterification reaction of fatty acids with alcohols to produce biodiesel. Scientific Reports 3 doi: 10.1038/srep02616
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 61
    Publication Date: 2013-09-11
    Description: Hybrid materials made from all inorganic components are intriguing in many fields, because they have shown in-depth potential use for electronic and optoelectronic applications including solar cells, gas sensors, photodetectors, and field effect transistors. Hybrid materials made from SnO2 nanoparticles on SnSe nanosheets have been synthesized via a facile, lost-cost and safe solution method, and have been demonstrated as promising multifunctional materials in various prototype devices, including gas sensors, photodetectors, and field effect transistors. Scientific Reports 3 doi: 10.1038/srep02613
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 62
    Publication Date: 2013-09-11
    Description: The simplification of current vaccine administration regimes is of crucial interest in order to further sustain and expand the high impact of vaccines for public health. Most vaccines including the vaccine against hepatitis B need several doses to achieve protective immunization. In order to reduce the amount of repetitive injections, depot-based approaches represent a promising strategy. We present the application of novobiocin-sensitive biohybrid hydrogels as a depot for the pharmacologically controlled release of a vaccine against hepatitis B. Upon subcutaneous implantation of the vaccine depot into mice, we were able to release the vaccine by the oral administration of the stimulus molecule novobiocin resulting in successful immunization of the mice. This material-based vaccination regime holds high promises to replace classical vaccine injections conducted by medical personnel by the simple oral uptake of the stimulus thereby solving a major obstacle in increasing hepatitis B vaccination coverage. Scientific Reports 3 doi: 10.1038/srep02610
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 63
    Publication Date: 2013-09-11
    Description: Glyphosate usage is increasing worldwide and the application schemes of this herbicide are currently changing. Amphibians migrating through arable fields may be harmed by Glyphosate applied to field crops. We investigated the population-based temporal coincidence of four amphibian species with Glyphosate from 2006 to 2008. Depending on a) age- and species-specific main migration periods, b) crop species, c) Glyphosate application mode for crops, and d) the presumed DT50 value (12 days or 47 days) of Glyphosate, we calculated up to 100% coincidence with Glyphosate. The amphibians regularly co-occur with pre-sowing/pre-emerging Glyphosate applications to maize in spring and with stubble management prior to crop sowing in late summer and autumn. Siccation treatment in summer coincides only with early pond-leaving juveniles. We suggest in-depth investigations of both acute and long-term effects of Glyphosate applications on amphibian populations not only focussed on exposure during aquatic periods but also terrestrial life stages. Scientific Reports 3 doi: 10.1038/srep02622
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 64
    Publication Date: 2013-09-11
    Description: Polymeric composite films with a high loading of nano-size silicates can hardly meet the increasingly stringent fireproof and smoke-free requirements during burning. Thus, it is desirable to prepare pure clay films that can block air, heat, and flame. Here we report an organic-free clay film capable of both flame- and heat-shielding. The film was prepared from the self-assembly of nanometer-thick silicate platelets derived from the exfoliation of natural clays. The self-assembled film has a highly regular multilayered nanostructure over a large area and an appreciable volume of air entrapped in between. The combination of regular structure and substantial air volume contributes to the low thermal conductivity and flame blocking property of the film. It was demonstrated that the film can shield flame over hour duration and prevent temperature rising on the backside of film. This remarkable clay film has a myriad of uses including gas barrier, heat insulator, and fireproof devices. Scientific Reports 3 doi: 10.1038/srep02621
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 65
    Publication Date: 2013-09-11
    Description: State-of-the art computers need high performance transistors, which consume ultra-low power resulting in longer battery lifetime. Billions of transistors are integrated neatly using matured silicon fabrication process to maintain the performance per cost advantage. In that context, low-cost mono-crystalline bulk silicon (100) based high performance transistors are considered as the heart of today's computers. One limitation is silicon's rigidity and brittleness. Here we show a generic batch process to convert high performance silicon electronics into flexible and semi-transparent one while retaining its performance, process compatibility, integration density and cost. We demonstrate high-k/metal gate stack based p-type metal oxide semiconductor field effect transistors on 4 inch silicon fabric released from bulk silicon (100) wafers with sub-threshold swing of 80 mV dec−1 and on/off ratio of near 104 within 10% device uniformity with a minimum bending radius of 5 mm and an average transmittance of ~7% in the visible spectrum. Scientific Reports 3 doi: 10.1038/srep02609
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 66
    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.
    Print ISSN: 1470-8396
    Electronic ISSN: 1470-840X
    Topics: Mathematics , Law
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  • 67
    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.
    Print ISSN: 1470-8396
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  • 68
    facet.materialart.
    Unknown
    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.
    Print ISSN: 1470-8396
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  • 69
    facet.materialart.
    Unknown
    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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  • 70
    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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  • 71
    Publication Date: 2013-09-12
    Description: Imaging single epidermal growth factor receptors (EGFR) in intact cells is presently limited by the available microscopy methods. Environmental scanning electron microscopy (ESEM) of whole cells in hydrated state in combination with specific labeling with gold nanoparticles was used to localize activated EGFRs in the plasma membranes of COS7 and A549 cells. The use of a scanning transmission electron microscopy (STEM) detector yielded a spatial resolution of 3 nm, sufficient to identify the locations of individual EGFR dimer subunits. The sizes and distribution of dimers and higher order clusters of EGFRs were determined. The distance between labels bound to dimers amounted to 19 nm, consistent with a molecular model. A fraction of the EGFRs was found in higher order clusters with sizes ranging from 32–56 nm. ESEM can be used for quantitative whole cell screening studies of membrane receptors, and for the study of nanoparticle-cell interactions in general. Scientific Reports 3 doi: 10.1038/srep02626
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 72
    Publication Date: 2013-09-12
    Description: Ubiquitin is involved in almost every cellular process, and it is also known to be a stress-inducible protein. Based on previous reports that many types of cancer display an elevated level of ubiquitin, we hypothesized that this increased amount of ubiquitin is essential for the growth of cancer cells and that, consequently, the downregulation of ubiquitin may be a potential anti-cancer treatment. We first found that the level of ubiquitin can be effectively downregulated via knockdown of a polyubiquitin gene, Ubb, with siRNA (Ubb-KD) and then demonstrated its anti-cancer effects in several cancer cell lines and xenograft mice. Ubb-KD resulted in the attenuation of TNFα-induced NF-κB activation, the stabilization of the tumor suppressor p53, and stress-sensitization. Taken together, downregulation of ubiquitin through Ubb-KD is a potential anti-cancer treatment by inhibiting ubiquitination at multiple sites related to oncogenic pathways and by weakening the ability of cancer cells to overcome increased stress. Scientific Reports 3 doi: 10.1038/srep02623
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 73
    Publication Date: 2013-09-12
    Description: NAD kinase (NADK) is a crucial enzyme for production of NADP+. ATP-specific NADK prefers ATP to inorganic polyphosphate [poly(P)] as a phosphoryl donor, whereas poly(P)/ATP-NADK utilizes both ATP and poly(P), and is employed in industrial mass production of NADP+. Poly(P)/ATP-NADKs are distributed throughout Gram-positive bacteria and Archaea, whereas ATP-specific NADKs are found in Gram-negative α- and γ-proteobacteria and eukaryotes. In this study, we succeeded in conferring the ability to utilize poly(P) on γ-proteobacterial ATP-specific NADKs through a single amino-acid substitution; the substituted amino-acid residue is therefore important in determining the phosphoryl-donor specificity of γ-proteobacterial NADKs. We also demonstrate that a poly(P)/ATP-NADK created through this method is suitable for the poly(P)-dependent mass production of NADP+. Moreover, based on our results, we provide insight into the evolution of bacterial NADKs, in particular, how NADKs evolved from poly(P)/ATP-NADKs into ATP-specific NADKs. Scientific Reports 3 doi: 10.1038/srep02632
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 74
    Publication Date: 2013-09-12
    Description: Mass production of high-quality graphene nanosheets (GNs) is essential for practical applications. We report that oxidation of graphite by low concentration KMnO4 at relatively high temperature (60°C) leads to edge-selectively oxidized graphite (EOG) which preserves the high crystalline graphitic structure on its basal planes while the edges are functionalized by oxygen-containing groups. Long-chain tetradecyl-ammonium salt (C14N+) could be spontaneously intercalated into EOG to form intercalated EOG-C14N+ compounds. Gentle and short-time sonication of EOG-C14N+ in toluene can full exfoliate EOG into edge-oxidized graphene nanosheets (EOGNs) with concentration of 0.67 mg/ml, monolayer population up to 90% and lateral size from 1 μm to 〉100 μm. The EOG and EOGN films show excellent electrical conductance, which is far superior to their graphene oxide (GO) counterparts. Our method provides an efficient way to produce high-quality GNs, and the resultant EOG also can be directly used for production of multifunctional materials and devices. Scientific Reports 3 doi: 10.1038/srep02636
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 75
    Publication Date: 2013-09-12
    Description: Society's techno-social systems are becoming ever faster and more computer-orientated. However, far from simply generating faster versions of existing behaviour, we show that this speed-up can generate a new behavioural regime as humans lose the ability to intervene in real time. Analyzing millisecond-scale data for the world's largest and most powerful techno-social system, the global financial market, we uncover an abrupt transition to a new all-machine phase characterized by large numbers of subsecond extreme events. The proliferation of these subsecond events shows an intriguing correlation with the onset of the system-wide financial collapse in 2008. Our findings are consistent with an emerging ecology of competitive machines featuring ‘crowds’ of predatory algorithms, and highlight the need for a new scientific theory of subsecond financial phenomena. Scientific Reports 3 doi: 10.1038/srep02627
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 76
    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.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
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  • 77
    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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  • 78
    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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  • 79
    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.
    Print ISSN: 0024-6093
    Electronic ISSN: 1469-2120
    Topics: Mathematics
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  • 80
    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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  • 81
    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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    Electronic ISSN: 1469-2120
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  • 82
    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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  • 83
    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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  • 84
    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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  • 85
    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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  • 86
    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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  • 87
    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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  • 88
    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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  • 89
    Publication Date: 2013-09-13
    Description: Metastatic SW620 colon cancer cells are primed for death when detached and can be sensitized to anoikis by the BH3-mimetic ABT-737 Cell Death and Disease 4, e801 (September 2013). doi:10.1038/cddis.2013.328 Authors: A Maamer-Azzabi, O Ndozangue-Touriguine & J Bréard
    Keywords: anoikiscolon cancerBcl-2 familymetastasisABT-737
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
    Published by Springer Nature
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  • 90
    Publication Date: 2013-09-13
    Description: Smac mimetic and demethylating agents synergistically trigger cell death in acute myeloid leukemia cells and overcome apoptosis resistance by inducing necroptosis Cell Death and Disease 4, e802 (September 2013). doi:10.1038/cddis.2013.320 Authors: L Steinhart, K Belz & S Fulda
    Keywords: apoptosisnecroptosisSmacleukemiaRIP1
    Electronic ISSN: 2041-4889
    Topics: Biology , Medicine
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  • 91
    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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  • 92
    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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  • 93
    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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  • 94
    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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  • 95
    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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  • 96
    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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  • 97
    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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  • 98
    Publication Date: 2013-09-13
    Description: (2S,3S)-2,3-Butanediol ((2S,3S)-2,3-BD) is a potentially valuable liquid fuel and an excellent building block in asymmetric synthesis. In this study, cofactor engineering was applied to improve the efficiency of (2S,3S)-2,3-BD production and simplify the product purification. Two NADH regeneration enzymes, glucose dehydrogenase and formate dehydrogenase (FDH), were introduced into Escherichia coli with 2,3-BD dehydrogenase, respectively. Introduction of FDH resulted in higher (2S,3S)-2,3-BD concentration, productivity and yield from diacetyl, and large increase in the intracellular NADH concentration. In fed-batch bioconversion, the final titer, productivity and yield of (2S,3S)-2,3-BD on diacetyl reached 31.7 g/L, 2.3 g/(L·h) and 89.8%, the highest level of (2S,3S)-2,3-BD production thus far. Moreover, cosubstrate formate was almost totally converted to carbon dioxide and no organic acids were produced. The biocatalytic process presented should be a promising route for biotechnological production of NADH-dependent microbial metabolites. Scientific Reports 3 doi: 10.1038/srep02643
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 99
    Publication Date: 2013-09-13
    Description: Optical coherence tomography (OCT) may revolutionize fundamental investigation and clinical management of age-related macular degeneration and other eye diseases. However, quantitative OCT interpretation is hampered due to uncertain sub-cellular correlates of reflectivity in the retinal pigment epithelium (RPE) and photoreceptor. The purpose of this study was twofold: 1) to test OCT correlates in the RPE, and 2) to demonstrate the feasibility of longitudinal OCT monitoring of sub-cellular RPE dynamics. A high resolution OCT was constructed to achieve dynamic imaging of frog eyes, in which light-driven translocation of RPE melanosomes occurred within the RPE cell body and apical processes. Comparative histological examination of dark- and light-adapted eyes indicated that the RPE melanin granule, i.e., melanosome, was a primary OCT correlate. In vivo OCT imaging of RPE melanosomes opens the opportunity for quantitative assessment of RPE abnormalities associated with disease, and enables longitudinal investigation of RPE kinetics correlated with visual function. Scientific Reports 3 doi: 10.1038/srep02644
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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  • 100
    Publication Date: 2013-09-13
    Description: Our brain is known to automatically optimize effort expenditure during motor coordination, such that for example, during bimanual braking of a bicycle, a well-oiled brake will automatically be used more than a corroded, heavy brake. But how does our brain infer the effort expenditure? All previous motor coordination models have believed that the effort in a task is known precisely to our brain, solely from the motor commands it generates. Here we show that this belief is incorrect. Through experiments and simulation we exhibit that in addition to the motor commands, the returning haptic signals play a crucial role in the inference of the effort during a force sharing task. Our results thus elucidate a previously unknown sensory-motor association that has major ramifications for our understanding of motor coordination and provides new insights into how sensory modifications due to ergonomics, stroke and disease can affect motor coordination in humans. Scientific Reports 3 doi: 10.1038/srep02648
    Electronic ISSN: 2045-2322
    Topics: Natural Sciences in General
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