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  • 11
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    Pergamon Press
    In:  Oxford, Pergamon Press, vol. 13, no. 3, pp. 632 pp., (ISBN 0-8493-0068-1)
    Publication Date: 1988
    Keywords: Earthquake ; Earthquake precursor: prediction research ; Earthquake hazard ; Geol. aspects ; Geodesy
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  • 12
    Publication Date: 2015-11-26
    Description: Human lactate dehydrogenase (LDH) has attracted attention as a potential target for cancer therapy and contraception. In this study, we reconstituted human lactic acid fermentation in Saccharomyces cerevisiae , with the goal of constructing a yeast cell-based LDH assay system. pdc null mutant yeast (mutated in the endogenous pyruvate decarboxylase genes) are unable to perform alcoholic fermentation; when grown in the presence of an electron transport chain inhibitor, pdc null strains exhibit a growth defect. We found that introduction of the human gene encoding LDHA complemented the pdc growth defect; this complementation depended on LDHA catalytic activity. Similarly, introduction of the human LDHC complemented the pdc growth defect, even though LDHC did not generate lactate at the levels seen with LDHA. In contrast, the human LDHB did not complement the yeast pdc null mutant, although LDHB did generate lactate in yeast cells. Expression of LDHB as a red fluorescent protein (RFP) fusion yielded blebs in yeast, whereas LDHA-RFP and LDHC-RFP fusion proteins exhibited cytosolic distribution. Thus, LDHB exhibits several unique features when expressed in yeast cells. Because yeast cells are amenable to genetic analysis and cell-based high-throughput screening, our pdc /LDH strains are expected to be of use for versatile analyses of human LDH.
    Print ISSN: 0021-924X
    Electronic ISSN: 1756-2651
    Topics: Biology , Chemistry and Pharmacology
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  • 13
    Publication Date: 2015-06-14
    Description: Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are key s to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a ‘ blackbox preprocessing ’ to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory. Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein – DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the ‘ blackbox preprocessing ’ ). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein – DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein – protein complex and a protein – RNA complex, which is biologically known as a protein – RNA mimicry case. Availability and implementation: The PROSTA-inter web-server is publicly available at http://www.cbrc.kaust.edu.sa/prosta/ . Contact: xin.gao@kaust.edu.sa
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
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  • 14
    Publication Date: 2013-10-01
    Description: Shear-wave splitting (SWS) analysis using SKS , SKKS , and PKS (hereafter collectively called XKS ) phases is one of the most commonly used techniques in structural seismology. In spite of the apparent simplicity in performing SWS measurements, large discrepancies in published SWS parameters (fast direction and splitting time) suggest that a significant portion of splitting parameters has been incorrectly determined. Here, based on the popularly used minimization of transverse energy technique, we present a procedure that combines automatic data processing and careful manual screening, which includes adjusting the XKS window used for splitting analysis, modifying band-pass filtering corner frequencies, and verifying and (if necessary) changing the quality ranking of the measurements. Using real and synthetic data, we discuss causes and diagnostics of a number of common problems in performing SWS analysis, and suggest possible remedies. Those problems include noise in the XKS window being mistaken as signal, non- XKS seismic arrivals in the XKS window, excessive use of null ranking, measurements from misoriented sensors and from sensors with mechanical problems, and inappropriate dismissal of usable measurements.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
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  • 15
    Publication Date: 2015-05-13
    Description: Peters et al. (1) raise several questions about early chicken domestication in northern China (2), including the claim that the climate would have been unsuitable for red jungle fowl. However, northern China was much warmer and more humid with much more extensive forest coverage during the early Holocene, as shown...
    Keywords: Letters
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 16
    Publication Date: 2014-11-05
    Description: We study the magnetotransport properties of monolayer graphene grown on SiC substrates. At low magnetic fields, a parabolic magnetoresistance (MR) is observed. With increasing magnetic field, however, this parabolic MR is changed to a linear field dependence that does not show signs of saturation for magnetic fields up to 9 T. At a fixed field, the value of the linear MR decreases with increasing temperature, with its value as large as 80% under 9 T at room temperature. Furthermore, the Hall mobility is found to be suppressed when the sample is annealed at 390 K under a helium atmosphere, with this suppression causing a decrease of the observed linear MR. The decrease in the linear MR shows a linear dependence on Hall mobility, which is indicative of the application of the monolayer graphene. We attribute the observed linear MR to a classical origin owing to the close relation between the MR and Hall mobility.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
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  • 17
    Publication Date: 2015-04-28
    Description: A metal-semiconductor-metal (MSM) structure ultraviolet photodetector has been fabricated from amorphous InGaZnO (a-IGZO) film at room temperature. The photodetector can work without consuming external power and show a responsivity of 4 mA/W. The unbiased photoresponse characteristic is attributed to the hole-trapping process occurred in the electrode/a-IGZO interface, and a physical model based on band energy theory is proposed to explain the origin of the photoresponse at zero bias in our device. Our findings may provide a way to realize unbiased photoresponse in the simple MSM structure.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
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  • 18
    Publication Date: 2016-04-07
    Description: Aiming for a geophysical survey to around 1.5 km depth, we conduct a passive-source surface-wave survey along a 70-km-long line on the western side of the Junggar basin in northwest China. We use frequency–time analysis and spatial autocorrelation methods to extract surface-wave dispersion curves from ambient-noise data of station pairs, as well as ambient-noise multichannel analysis of surface waves from multistations. Dispersion curves corresponding to the same positions obtained by these three methods independently are comparable, which shows the validity of using these methods. After inverting more than 400 dispersion curves and aligning their results together, we construct a 2D shear S -wave velocity image around 1.5 km deep and 60 km long. A less than 6% difference between the inverted S -wave velocity profile and the borehole data in situ shows the relatively high accuracy of our method. The 2D S -wave velocity image clearly delineates the main geologic structures, including transition of landform, intrusion of rock mass, and shape of bedrock beneath the survey line.
    Print ISSN: 0037-1106
    Electronic ISSN: 1943-3573
    Topics: Geosciences , Physics
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  • 19
    Publication Date: 2018
    Description: 〈span〉〈div〉Abstract〈/div〉Recognizing and tracking weak reflections, which are characterized by low amplitude, low signal-to-noise ratio, and low degree of lateral continuity, is a long-time issue in 3D seismic interpretation and reservoir characterization. The problem is particularly acute with unconventional, fractured shale reservoirs, in which the impedance contrast is low and/or reservoir beds are below the tuning thickness. To improve the performance of interpreting weak reflections associated with shale reservoirs, we have developed a new workflow for weak-reflection tracking guided by a robust structural-orientation vector (SOV) estimation algorithm. The new SOV-guided auto-tracking workflow first uses the reflection orientation at the seed location as a constraint to project the most-likely locations in the neighboring traces, and then locally adjust them to maximally match the target reflection. We verify our workflow through application to a test seismic data set that is typical of routine 3D seismic surveys over shale oil and gas fields. The results demonstrate the improved quality of the resulting horizons compared with the traditional autotracking algorithms. We conclude that this new SOV-guided autotracking workflow can be used to enhance the performance and effectiveness of weak reflection mapping, which should have important implications for improved shale reservoirs visualization and characterization.〈/span〉
    Print ISSN: 2324-8858
    Electronic ISSN: 2324-8866
    Topics: Geosciences
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  • 20
    Publication Date: 2016-07-06
    Description: Evolview is an online visualization and management tool for customized and annotated phylogenetic trees. It allows users to visualize phylogenetic trees in various formats, customize the trees through built-in functions and user-supplied datasets and export the customization results to publication-ready figures. Its ‘dataset system’ contains not only the data to be visualized on the tree, but also ‘modifiers’ that control various aspects of the graphical annotation. Evolview is a single-page application (like Gmail); its carefully designed interface allows users to upload, visualize, manipulate and manage trees and datasets all in a single webpage. Developments since the last public release include a modern dataset editor with keyword highlighting functionality, seven newly added types of annotation datasets, collaboration support that allows users to share their trees and datasets and various improvements of the web interface and performance. In addition, we included eleven new ‘Demo’ trees to demonstrate the basic functionalities of Evolview, and five new ‘Showcase’ trees inspired by publications to showcase the power of Evolview in producing publication-ready figures. Evolview is freely available at: http://www.evolgenius.info/evolview/ .
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
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