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  • 1
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    In:  Phys. Earth Plan. Int., Potsdam, ZIPE, vol. 153, no. 4, pp. 175-180, pp. 2156, (ISBN: 0-12-018847-3)
    Publication Date: 2005
    Keywords: Aftershocks ; Earthquake ; Statistical investigations ; Seismicity ; power ; law ; decay ; PEPI ; Seismicity ; Earthquake ; Precursors ; Non-linear effects ; Least-squares
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  • 2
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    In:  Geophys. J. Int., Potsdam, ZIPE, vol. 125, no. 32, pp. 857-868, pp. 2156, (ISBN: 0-12-018847-3)
    Publication Date: 1996
    Keywords: Stress ; Inversion ; Fault plane solution, focal mechanism ; GJI
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  • 3
    Publication Date: 2015-12-18
    Description: Motivation: The Oxford Nanopore MinION sequencer, currently in pre-release testing through the MinION Access Programme (MAP), promises long reads in real-time from an inexpensive, compact, USB device. Tools have been released to extract FASTA/Q from the MinION base calling output and to provide basic yield statistics. However, no single tool yet exists to provide comprehensive alignment-based quality control and error profile analysis—something that is extremely important given the speed with which the platform is evolving. Results: NanoOK generates detailed tabular and graphical output plus an in-depth multi-page PDF report including error profile, quality and yield data. NanoOK is multi-reference, enabling detailed analysis of metagenomic or multiplexed samples. Four popular Nanopore aligners are supported and it is easily extensible to include others. Availability and implementation : NanoOK is an open-source software, implemented in Java with supporting R scripts. It has been tested on Linux and Mac OS X and can be downloaded from https://github.com/TGAC/NanoOK . A VirtualBox VM containing all dependencies and the DH10B read set used in this article is available from http://opendata.tgac.ac.uk/nanook/ . A Docker image is also available from Docker Hub—see program documentation https://documentation.tgac.ac.uk/display/NANOOK . Contact: richard.leggett@tgac.ac.uk 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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  • 4
    Publication Date: 2015-02-10
    Description: How Darwin's “endless forms most beautiful” have evolved remains one of the most exciting questions in biology. The significant variety of bacterial shapes is most likely due to the specific advantages they confer with respect to the diverse environments they occupy. While our understanding of the mechanisms generating relatively simple shapes has improved tremendously in the last few years, the molecular mechanisms underlying the generation of complex shapes and the evolution of shape diversity are largely unknown. The emerging field of bacterial evolutionary cell biology provides a novel strategy to answer this question in a comparative phylogenetic framework. This relatively novel approach provides hypotheses and insights into cell biological mechanisms, such as morphogenesis, and their evolution that would have been difficult to obtain by studying only model organisms. We discuss the necessary steps, challenges, and impact of integrating “evolutionary thinking” into bacterial cell biology in the genomic era. The molecular mechanisms underlying the evolution of bacterial shape diversity are largely unknown. The emerging field of bacterial evolutionary cell biology provides a novel strategy to answer this question in a comparative phylogenetic framework. We discuss the necessary steps, challenges, and impact of integrating “evolutionary thinking” into bacterial cell biology in the genomic era.
    Print ISSN: 0265-9247
    Electronic ISSN: 1521-1878
    Topics: Biology , Medicine
    Published by Wiley
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  • 5
    Publication Date: 2014-02-20
    Description: : Illumina’s recently released Nextera Long Mate Pair (LMP) kit enables production of jumping libraries of up to 12 kb. The LMP libraries are an invaluable resource for carrying out complex assemblies and other downstream bioinformatics analyses such as the characterization of structural variants. However, LMP libraries are intrinsically noisy and to maximize their value, post-sequencing data analysis is required. Standardizing laboratory protocols and the selection of sequenced reads for downstream analysis are non-trivial tasks. NextClip is a tool for analyzing reads from LMP libraries, generating a comprehensive quality report and extracting good quality trimmed and deduplicated reads. Availability and implementation: Source code, user guide and example data are available from https://github.com/richardmleggett/nextclip/ . Contact: Richard.Leggett@tgac.ac.uk 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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  • 6
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Geophysical journal international 125 (1996), S. 0 
    ISSN: 1365-246X
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences
    Notes: The tectonic stress orientation is estimated in the lithosphere of northern Sicily, the southern Tyrrhenian sea and southern Calabria, and in the Wadati-Benioff zone below the Tyrrhenian, by inversion of fault-plane solutions of earthquakes covering a magnitude range from 2.5 to 7.1. Focal mechanisms of 97 earthquakes are taken from the literature, after a critical evaluation of their data quality. an average misfit of F= 13° indicates that the set of all shallow (〈50km) earthquakes is generated by a heterogeneous stress field. For three subsets, based on regional and magnitude separation, F was small enough (2.8°〈inlineGraphic alt="leqslant R: less-than-or-eq, slant" extraInfo="nonStandardEntity" href="urn:x-wiley:0956540X:GJI857:les" location="les.gif"/〉F〈inlineGraphic alt="leqslant R: less-than-or-eq, slant" extraInfo="nonStandardEntity" href="urn:x-wiley:0956540X:GJI857:les" location="les.gif"/〉 5.9°) to support the assumption of a homogeneous stress direction; for an additional subset, with F= 7.4°, such a condition is close to being fulfilled even though some heterogeneity appears to be present. The number of earthquakes in these subsets ranged from nine to 22, and the uncertainties of the principal stress directions were generally of the order of 20° at the 90 per cent confidence level. The earthquakes with M〈inlineGraphic alt="geqslant R: gt-or-equal, slanted" extraInfo="nonStandardEntity" href="urn:x-wiley:0956540X:GJI857:ges" location="ges.gif"/〉 5 define a regional stress field with the greatest principal stress, σ1, dipping at a shallow angle to the south. In north-eastern Sicily and south-western Calabria the stress field estimated by earthquakes is extensional, with σ3 in a direction of WNW, and a near-vertical σ1, in agreement with the graben tectonics mapped geologically in this area. In western Sicily the σ1 direction is oriented WNW, but this result is judged less reliable than the others, based on the broader confidence limits of the solution and the average misfit of 7.4°. The earthquakes in the Wadati-Benioff zone define σ1 dipping at about 70° to the NW, subparallel to the zone, with σ2 horizontal and striking parallel to the zone.
    Type of Medium: Electronic Resource
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  • 7
    Electronic Resource
    Electronic Resource
    Oxford, UK : Blackwell Publishing Ltd
    Geophysical journal international 108 (1992), S. 0 
    ISSN: 1365-246X
    Source: Blackwell Publishing Journal Backfiles 1879-2005
    Topics: Geosciences
    Notes: A statistical model of the microearthquake occurrence in the Messina area, assuming periodic transitions among several Generalized Poisson states, is proposed. Four states are defined, of different duration, cluster mean rate and earthquake interdependence level. Their sequence is cyclically repeated with annual period. The findings of this work can be seen as a generalization of the approach of Bender (1984) who considered transition phenomena of the seismic temporal pattern among distinct states of the Simple Poisson type. Further, the investigation aims at identifying possible factors leading to the observed periodic changes in the earthquake statistical parameters and to the main ‘deviations’ of experimental data from the model. The rainfall and regional tectonic stress patterns appear to be reasonable candidates for explaining the microearthquake periodicity and the most relevant anomaly of the observed seismic temporal pattern with respect to the model, respectively.
    Type of Medium: Electronic Resource
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  • 8
    Publication Date: 1992-01-01
    Print ISSN: 0956-540X
    Electronic ISSN: 1365-246X
    Topics: Geosciences
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  • 9
    Publication Date: 2014-09-05
    Description: We report an atomistic molecular dynamics determination of the phase diagram of a rigid-cage model of C 36 . We first show that free energies obtained via thermodynamic integrations along isotherms displaying “van der Waals loops,” are fully reproduced by those obtained via isothermal-isochoric integration encompassing only stable states. We find that a similar result also holds for isochoric paths crossing van der Waals regions of the isotherms, and for integrations extending to rather high densities where liquid-solid coexistence can be expected to occur. On such a basis we are able to map the whole phase diagram of C 36 , with resulting triple point and critical temperatures about 1770 K and 2370 K, respectively. We thus predict a 600 K window of existence of a stable liquid phase. Also, at the triple point density, we find that the structural functions and the diffusion coefficient maintain a liquid-like character down to 1400–1300 K, this indicating a wide region of possible supercooling. We discuss why all these features might render possible the observation of the melting of C 36 fullerite and of its liquid state, at variance with what previously experienced for C 60 .
    Print ISSN: 0021-9606
    Electronic ISSN: 1089-7690
    Topics: Chemistry and Pharmacology , Physics
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  • 10
    Publication Date: 2007-08-01
    Print ISSN: 1069-3513
    Electronic ISSN: 1555-6506
    Topics: Geosciences
    Published by Springer
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