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  • 1
    Publication Date: 2015-03-26
    Description: Deep focus earthquakes within the underthrust Indian lower crust beneath the Himalaya occur in very specific regions and have distinct source characteristics. The study of the source mechanisms of these earthquakes provides valuable constraints on the kinematics of deformation of the underthrust Indian Plate, and its influence on the active deformation of the overlying Himalayan wedge. One of the most significant regions of these deep focus earthquakes is beneath the Sikkim and Bhutan Himalaya. We study the source characteristics of the 2011 September 18 ( M w 6.9) deep focus Sikkim main shock and its major aftershocks using global, regional and local waveform data. We determined the focal mechanism of the main shock using moment tensor inversion of global P and SH waveforms, and ascertained the earthquake fault plane using rupture directivity from regional P -wave spectra. The main shock originated at 53 ± 4 km depth and ruptured at least 20 km thickness of the underthrust Indian lower crust. Faulting occurred on a near vertical dextral strike-slip fault oriented NW-SE (strike 127°, dip 81° and rake 167°), oblique to the local strike of the Himalayan arc. The rupture initiated from the SE end of the fault and propagated to the northwest. The main shock was followed by 20 small-to-moderate aftershocks ( m b  〉 3.0), which we relocated using phase arrival times. We computed the focal mechanisms of the larger ones ( m b  ≥ 3.5) using local waveform inversion. We find that all aftershocks originated SE of the main shock, between depths of 12 and 50 km, and have dominantly strike-slip mechanisms. Our results, combined with the source mechanisms of earthquakes from previous studies, reveals that the entire underthrust Indian crust is seismogenic and deforms by dextral strike-slip motion on oblique structures beneath the Sikkim and Bhutan Himalaya. These active oblique structures with transverse motion possibly mark the western boundary of the clock-wise rotating ‘microplates’ in northeast India observed from GPS geodesy.
    Keywords: Seismology
    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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  • 2
    Publication Date: 2015-03-29
    Description: Deep focus earthquakes within the underthrust Indian lower crust beneath the Himalaya occur in very specific regions and have distinct source characteristics. The study of the source mechanisms of these earthquakes provides valuable constraints on the kinematics of deformation of the underthrust Indian Plate, and its influence on the active deformation of the overlying Himalayan wedge. One of the most significant regions of these deep focus earthquakes is beneath the Sikkim and Bhutan Himalaya. We study the source characteristics of the 2011 September 18 ( M w 6.9) deep focus Sikkim main shock and its major aftershocks using global, regional and local waveform data. We determined the focal mechanism of the main shock using moment tensor inversion of global P and SH waveforms, and ascertained the earthquake fault plane using rupture directivity from regional P -wave spectra. The main shock originated at 53 ± 4 km depth and ruptured at least 20 km thickness of the underthrust Indian lower crust. Faulting occurred on a near vertical dextral strike-slip fault oriented NW-SE (strike 127°, dip 81° and rake 167°), oblique to the local strike of the Himalayan arc. The rupture initiated from the SE end of the fault and propagated to the northwest. The main shock was followed by 20 small-to-moderate aftershocks ( m b  〉 3.0), which we relocated using phase arrival times. We computed the focal mechanisms of the larger ones ( m b  ≥ 3.5) using local waveform inversion. We find that all aftershocks originated SE of the main shock, between depths of 12 and 50 km, and have dominantly strike-slip mechanisms. Our results, combined with the source mechanisms of earthquakes from previous studies, reveals that the entire underthrust Indian crust is seismogenic and deforms by dextral strike-slip motion on oblique structures beneath the Sikkim and Bhutan Himalaya. These active oblique structures with transverse motion possibly mark the western boundary of the clock-wise rotating ‘microplates’ in northeast India observed from GPS geodesy.
    Keywords: Seismology
    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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  • 3
    Publication Date: 2013-12-21
    Description: Inherited retinal diseases are a group of clinically and genetically heterogeneous disorders for which a significant number of cases remain genetically unresolved. Increasing knowledge on underlying pathogenic mechanisms with precise phenotype–genotype correlation is, however, critical for establishing novel therapeutic interventions for these yet incurable neurodegenerative conditions. We report phenotypic and genetic characterization of a large family presenting an unusual autosomal dominant retinal dystrophy. Phenotypic characterization revealed a retinopathy dominated by inner retinal dysfunction and ganglion cell abnormalities. Whole-exome sequencing identified a missense variant (c.782A〉C, p.Glu261Ala) in ITM2B coding for Integral Membrane Protein 2B, which co-segregates with the disease in this large family and lies within the 24.6 Mb interval identified by microsatellite haplotyping. The physiological role of ITM2B remains unclear and has never been investigated in the retina. RNA in situ hybridization reveals Itm2b mRNA in inner nuclear and ganglion cell layers within the retina, with immunostaining demonstrating the presence of the corresponding protein in the same layers. Furthermore, ITM2B in the retina co-localizes with its known interacting partner in cerebral tissue, the amyloid β precursor protein, critical in Alzheimer disease physiopathology. Interestingly, two distinct ITM2B mutations, both resulting in a longer protein product, had already been reported in two large autosomal dominant families with Alzheimer-like dementia but never in subjects with isolated retinal diseases. These findings should better define pathogenic mechanism(s) associated with ITM2B mutations underlying dementia or retinal disease and add a new candidate to the list of genes involved in inherited retinal dystrophies.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
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  • 4
    Publication Date: 2015-07-31
    Description: The paper deals with a theoretical model for interacting dark energy (DE). The interaction between the cold dark matter (dust) and the DE has been assumed to be non-gravitational in nature. Exact analytic cosmological solutions are obtained both for constant and variable EoS for DE. It is found that, for very small value of the coupling parameter (in the interaction term), the model asymptotically extends up to cold dark matter, while the model can enter into the phantom domain asymptotically, if the coupling parameter is not so small. Both the solutions are then analysed with 194 Supernovae Type Ia data. The best-fitting parameters are shown with 1 and 2 confidence intervals. Finally, we have discussed the cosmographic parameters for both the cases.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 5
    Publication Date: 2016-07-29
    Description: The advent of space-based observatories such as Convection, Rotation and planetary Transits ( CoRoT ) and Kepler has enabled the testing of our understanding of stellar evolution on thousands of stars. Evolutionary models typically require five input parameters, the mass, initial helium abundance, initial metallicity, mixing length (assumed to be constant over time), and the age to which the star must be evolved. Some of these parameters are also very useful in characterizing the associated planets and in studying Galactic archaeology. How to obtain these parameters from observations rapidly and accurately, specifically in the context of surveys of thousands of stars, is an outstanding question, one that has eluded straightforward resolution. For a given star, we typically measure the effective temperature and surface metallicity spectroscopically and low-degree oscillation frequencies through space observatories. Here we demonstrate that statistical learning, using artificial neural networks, is successful in determining the evolutionary parameters based on spectroscopic and seismic measurements. Our trained networks show robustness over a broad range of parameter space, and critically, are entirely computationally inexpensive and fully automated. We analyse the observations of a few stars using this method and the results compare well to inferences obtained using other techniques. This method is both computationally cheap and inferentially accurate, paving the way for analysing the vast quantities of stellar observations from past, current, and future missions.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 6
    Publication Date: 2016-04-10
    Description: Mycobacterium phlei , a nontuberculosis mycobacterial species, was first described in 1898–1899. We present the complete genome sequence for the M. phlei CCUG21000 T type strain and the draft genomes for four additional strains. The genome size for all fiveis 5.3 Mb with 69.4% Guanine-Cytosine content. This is 0.35 Mbp smaller than the previously reported M. phlei RIVM draft genome. The size difference is attributed partly to large bacteriophage sequence fragments in the M. phlei RIVM genome. Comparative analysis revealed the following: 1) A CRISPR system similar to Type 1E ( cas 3) in M. phlei RIVM; 2) genes involved in polyamine metabolism and transport ( potAD , potF ) that are absent in other mycobacteria, and 3) strain-specific variations in the number of -factor genes. Moreover, M. phlei has as many as 82 mce (mammalian cell entry) homologs and many of the horizontally acquired genes in M. phlei are present in other environmental bacteria including mycobacteria that share similar habitat. Phylogenetic analysis based on 693 Mycobacterium core genes present in all complete mycobacterial genomes suggested that its closest neighbor is Mycobacterium smegmatis JS623 and Mycobacterium rhodesiae NBB3, while it is more distant to M. smegmatis mc2 155.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 7
    Publication Date: 2015-07-09
    Description: We provide the genome sequences of the type strains of the polychlorophenol-degrading Mycobacterium chlorophenolicum (DSM43826), the degrader of chlorinated aliphatics Mycobacterium chubuense (DSM44219) and Mycobacterium obuense (DSM44075) that has been tested for use in cancer immunotherapy. The genome sizes of M. chlorophenolicum , M. chubuense , and M. obuense are 6.93, 5.95, and 5.58 Mb with GC-contents of 68.4%, 69.2%, and 67.9%, respectively. Comparative genomic analysis revealed that 3,254 genes are common and we predicted approximately 250 genes acquired through horizontal gene transfer from different sources including proteobacteria. The data also showed that the biodegrading Mycobacterium spp. NBB4, also referred to as M. chubuense NBB4, is distantly related to the M. chubuense type strain and should be considered as a separate species, we suggest it to be named Mycobacterium ethylenense NBB4. Among different categories we identified genes with potential roles in: biodegradation of aromatic compounds and copper homeostasis. These are the first nonpathogenic Mycobacterium spp. found harboring genes involved in copper homeostasis. These findings would therefore provide insight into the role of this group of Mycobacterium spp. in bioremediation as well as the evolution of copper homeostasis within the Mycobacterium genus.
    Electronic ISSN: 1759-6653
    Topics: Biology
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  • 8
    Publication Date: 2014-06-06
    Description: The -ray flare of PKS 1222+216, observed in 2010 June, is interpreted as an outcome of jet dynamics at recollimation zone. We obtained the -ray light curves in three different energy bands, namely 100–300 MeV, 300 MeV–1 GeV and 1–3 GeV from observations by the Fermi -LAT (Large Area Telescope). We also use the Swift -XRT (X-Ray Telescope) flux from 0.3–10 keV obtained from archival data. We supplement these with the 0.07–0.4 TeV observations with MAGIC (Major Atmospheric Gamma-ray Imaging Cherenkov) telescope, available in the literature. The detection of source at very high energy ( E  〉 100 GeV) with a differential photon spectral index of 2.7 ± 0.3 and the rapid variability associated with it suggests that the emission arises from a compact region located beyond the broad line emitting region. The plausible -ray emission mechanism can then be inverse Compton scattering of IR photons from obscuring torus. Further, the decay time of LAT flare cannot be explained by considering simple radiative loss mechanisms. Hence, to interpret the LAT light curves, we develop a model where the broad-band emission originates from a compact region, arising plausibly from the compression of jet matter at the recollimation zone. The flare is then expressed as an outcome of jet deceleration probably associated with this focusing effect. Based on this model, the rise of the LAT flare is attributed to the opening of emission cone followed by the decay resulting from jet deceleration. The parameters of the model are further constrained by reproducing the broad-band spectral energy distribution of the source obtained during the flare episode. Our study suggests that the particle energy density exceeds magnetic energy density by a large factor which in turn may cause rapid expansion of the emission region. However, near equipartition can be achieved towards the end of LAT flare during which the compact emission region would have expanded to the size of jet cross-section.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 9
    Publication Date: 2014-07-04
    Description: Motivation: Counting the frequencies of k -mers in read libraries is often a first step in the analysis of high-throughput sequencing data. Infrequent k -mers are assumed to be a result of sequencing errors. The frequent k -mers constitute a reduced but error-free representation of the experiment, which can inform read error correction or serve as the input to de novo assembly methods. Ideally, the memory requirement for counting should be linear in the number of frequent k -mers and not in the, typically much larger, total number of k -mers in the read library. Results: We present a novel method that balances time, space and accuracy requirements to efficiently extract frequent k -mers even for high-coverage libraries and large genomes such as human. Our method is designed to minimize cache misses in a cache-efficient manner by using a pattern-blocked Bloom filter to remove infrequent k -mers from consideration in combination with a novel sort-and-compact scheme, instead of a hash, for the actual counting. Although this increases theoretical complexity, the savings in cache misses reduce the empirical running times. A variant of method can resort to a counting Bloom filter for even larger savings in memory at the expense of false-negative rates in addition to the false-positive rates common to all Bloom filter-based approaches. A comparison with the state-of-the-art shows reduced memory requirements and running times. Availability and implementation: The tools are freely available for download at http://bioinformatics.rutgers.edu/Software/Turtle and http://figshare.com/articles/Turtle/791582 . Contact: rajatroy@cs.rutgers.edu or schliep@cs.rutgers.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 10
    Publication Date: 1970-04-01
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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