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  • 1
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    MetPP: a computational platform for comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry-based metabolomics (2013)
    Oxford University Press
    Details
    Publication Date: 2013-07-06
    Description: Motivation: Due to the high complexity of metabolome, the comprehensive 2D gas chromatography time-of-flight mass spectrometry (GC x GC-TOF MS) is considered as a powerful analytical platform for metabolomics study. However, the applications of GC x GC-TOF MS in metabolomics are not popular owing to the lack of bioinformatics system for data analysis. Results: We developed a computational platform entitled metabolomics profiling pipeline (MetPP) for analysis of metabolomics data acquired on a GC x GC-TOF MS system. MetPP can process peak filtering and merging, retention index matching, peak list alignment, normalization, statistical significance tests and pattern recognition, using the peak lists deconvoluted from the instrument data as its input. The performance of MetPP software was tested with two sets of experimental data acquired in a spike-in experiment and a biomarker discovery experiment, respectively. MetPP not only correctly aligned the spiked-in metabolite standards from the experimental data, but also correctly recognized their concentration difference between sample groups. For analysis of the biomarker discovery data, 15 metabolites were recognized with significant concentration difference between the sample groups and these results agree with the literature results of histological analysis, demonstrating the effectiveness of applying MetPP software for disease biomarker discovery. Availability: The source code of MetPP is available at http://metaopen.sourceforge.net Contact: xiang.zhang@louisville.edu Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 2
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    Dicer interacts with SIRT7 and regulates H3K18 deacetylation in response to DNA damaging agents (2016)
    Oxford University Press
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    Publication Date: 2016-05-06
    Description: Dicer participates in heterochromatin formation in fission yeast and plants. However, whether it has a similar role in mammals remains controversial. Here we showed that the human Dicer protein interacts with SIRT7, an NAD + -dependent H3K18Ac (acetylated lysine 18 of histone H3) deacetylase, and holds a proportion of SIRT7 in the cytoplasm. Dicer knockdown led to an increase of chromatin-associated SIRT7 and simultaneously a decrease of cytoplasmic SIRT7, while its overexpression induced SIRT7 reduction in the chromatin-associated fraction and increment in the cytoplasm. Furthermore, DNA damaging agents promoted Dicer expression, leading to decreased level of chromatin-associated SIRT7 and increased level of H3K18Ac, which can be alleviated by Dicer knockdown. Taken together with that H3K18Ac was exclusively associated with the chromatin, our findings suggest that Dicer induction by DNA damaging treatments prevents H3K18Ac deacetylation, probably by trapping more SIRT7 in the cytoplasm.
    Keywords: Protein-protein interaction, Repair
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    A novel method for discovering local spatial clusters of genomic regions with functional relationships from DNA contact maps (2016)
    Oxford University Press
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    Publication Date: 2016-06-16
    Description: Motivation: The three-dimensional structure of genomes makes it possible for genomic regions not adjacent in the primary sequence to be spatially proximal. These DNA contacts have been found to be related to various molecular activities. Previous methods for analyzing DNA contact maps obtained from Hi-C experiments have largely focused on studying individual interactions, forming spatial clusters composed of contiguous blocks of genomic locations, or classifying these clusters into general categories based on some global properties of the contact maps. Results: Here, we describe a novel computational method that can flexibly identify small clusters of spatially proximal genomic regions based on their local contact patterns. Using simulated data that highly resemble Hi-C data obtained from real genome structures, we demonstrate that our method identifies spatial clusters that are more compact than methods previously used for clustering genomic regions based on DNA contact maps. The clusters identified by our method enable us to confirm functionally related genomic regions previously reported to be spatially proximal in different species. We further show that each genomic region can be assigned a numeric affinity value that indicates its degree of participation in each local cluster, and these affinity values correlate quantitatively with DNase I hypersensitivity, gene expression, super enhancer activities and replication timing in a cell type specific manner. We also show that these cluster affinity values can precisely define boundaries of reported topologically associating domains, and further define local sub-domains within each domain. Availability and implementation: The source code of BNMF and tutorials on how to use the software to extract local clusters from contact maps are available at http://yiplab.cse.cuhk.edu.hk/bnmf/ . Contact: kevinyip@cse.cuhk.edu.hk Supplementary information: Supplementary data are available at Bioinformatics online.
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 4
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    Advances in GPR data acquisition and analysis for archaeology (2015)
    Oxford University Press
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    Publication Date: 2015-04-24
    Description: The primary objective of this study is to evaluate the applicability and the effectiveness of ground-penetrating radar (GPR) to identify a thin burnt soil layer, buried more than 2 m below the topographic surface at the Liangzhu Site, in Southeastern China. The site was chosen for its relatively challenging conditions of GPR techniques due to electrical conductivity and to the presence of peach tree roots that produced scattering. We completed the data acquisition by using 100 and 200 MHz antennas in TE and TM broadside and cross-polarized configurations. In the data processing and interpretation phase, we used GPR attribute analysis, including instantaneous phase and geometrical attributes. Validation analysis ground-truthing performed after the geophysical surveys, validated the GPR imaging, confirmed the electrical conductivity and relative dielectric permittivity (RDP) measurements performed at different depths, and allowed a reliable quantitative correlation between GPR results and subsurface physical properties. The research demonstrates that multiple antenna configurations in GPR data acquisition combined with attribute analysis can enhance the ability to characterize prehistoric archaeological remains even in complex subsurface conditions.
    Keywords: Marine Geosciences and Applied Geophysics
    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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  • 5
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    Analysis on the variation characteristics of Wuguan River runoff in South Qinling Mountain (2018)
    Institute of Physics (IOP)
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    Publication Date: 2018-11-06
    Description: Aims at the hydrological analysis in the early stage of water conservancy project construction, studies the long series runoff and its variation law in Wuguan River, and analyzes the characteristics of annual and interannual changes in this paper, Provides basic support for the later reservoir construction. Based on the precipitation data (1959-2001) and the runoff data (1959-2014) from Wuguan hydrologic station, many methods such as statistical analysis, R/S, M-K trend test and mutation test were used to study the change rule of runoff. After that, influential factors of runoff were analyzed in the paper. Results show that the annual runoff of the Wuguan River is 1.53 million cubic meters, monthly runoff differs greatly in a year with clear period of concentration from Jul. to Oct.; Annual runoff showed a long-term decreasing trend and the mutation point appeared in 2010; Precipitation changes was the main cause of the decreasing runoff compared to human activities. Runoff fore...
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
    Published by Institute of Physics (IOP)
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  • 6
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    Doubly misspecified models (2012)
    Oxford University Press
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    Publication Date: 2012-05-22
    Description: Estimation bias arising from local model uncertainty and incomplete data has been studied by Copas & Eguchi (2005) under the assumption of a correctly specified marginal model. We extend the approach to allow additional local uncertainty in the assumed marginal model, arguing that this is almost unavoidable for nonlinear problems. We present a general bias analysis and sensitivity procedure for such doubly misspecified models and illustrate the breadth of application through three examples: logistic regression with a missing confounder, measurement error for binary responses and survival analysis with frailty. We show that a double-the-variance rule is not conservative under double misspecification. The ideas are brought together in a meta-analysis of studies of rehabilitation rates for juvenile offenders.
    Print ISSN: 0006-3444
    Electronic ISSN: 1464-3510
    Topics: Biology , Mathematics , Medicine
    Published by Oxford University Press
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  • 7
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    Crustal and uppermost mantle S-wave velocity structure beneath the Japanese islands from seismic ambient noise tomography (2013)
    Oxford University Press
    Details
    Publication Date: 2013-03-12
    Description: In this study, the crustal and uppermost mantle shear wave velocities beneath the Japanese islands have been determined by inversion from seismic ambient noise tomography using data recorded at 75 Full Range Seismograph Network of Japan broad-band seismic stations, which are uniformly distributed across the Japanese islands. By cross-correlating 2 yr of vertical component seismic ambient noise recordings, we are able to extract Rayleigh wave empirical Green's functions, which are subsequently used to measure phase velocity dispersion in the period band of 6–50 s. The dispersion data are then inverted to yield 2-D tomographic phase velocity maps and 3-D shear wave velocity models. Our results show that the velocity variations at short periods (~10 s), or in the uppermost crust, correlate well with the major known surface geological and tectonic features. In particular, the distribution of low-velocity anomalies shows good spatial correlation with active faults, volcanoes and terrains of sediment exposure, whereas the high-velocity anomalies are mainly associated with the mountain ranges. We also observe that large upper crustal earthquakes (5.0 ≤ M ≤ 8.0, depth ≤ 25 km) mainly occurred in low-velocity anomalies or along the boundary between low- and high-velocity anomalies, suggesting that large upper crustal earthquakes do not strike randomly or uniformly; rather they are inclined to nucleate within or adjacent to low-velocity areas.
    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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  • 8
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    Performance improvement of air source heat pump by using gas-injected rotary compressor (2017)
    Institute of Physics (IOP)
    Details
    Publication Date: 2017-09-06
    Description: Rotary compressor is most widely used in small capacity refrigeration and heat pump systems. For the air source heat pump, the heating capacity and the COP will be obviously degraded when it is utilized in low temperature ambient. Gas injection is an effective method to enhance its performance under those situations, which has been well applied in air source heat pump with scroll compressor. However, the development of the gas injection technology in rotary compressor is relatively slow due to limited performance improvement. In this research, the essential reason constraining the improvement of the gas injection on the rotary compressor and its heat pump system is identified. Two new injection structures for rotary compressors has been put forward to overcome the drawback of traditional injection structures. Based on a verified numerical model, the thermodynamic performance of air source heat pumps with the new gas-injected rotary compressor are investigated. The results indica...
    Print ISSN: 1757-8981
    Electronic ISSN: 1757-899X
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Institute of Physics (IOP)
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  • 9
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    Green Tunnel Construction Technology and Application (2018)
    Institute of Physics (IOP)
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    Publication Date: 2018-06-03
    Description: With the dramatic growth of urban tunnels in recent years, energy saving and environmental protection have received intensive attention in tunnel construction and operation. As reference to the concept of green buildings, this paper proposes the concept of green tunnels. Combining with the key issues of tunnel design, construction, operation and maintenance, the major aspects of green tunnels including prefabricated construction, noise control, ventilation & lighting energy saving, and digital intelligent maintenance are discussed and the future development of green tunnels is outlined with the economic and social benefits as indicators.
    Print ISSN: 1755-1307
    Electronic ISSN: 1755-1315
    Topics: Geography , Geosciences , Physics
    Published by Institute of Physics (IOP)
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  • 10
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    Anomalously large resistance at the charge neutrality point in a zero-gap InAs/GaSb bilayer (2018)
    Institute of Physics (IOP)
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    Publication Date: 2018-06-01
    Description: We report here our recent electron transport results in spatially separated two-dimensional electron and hole gases with nominally degenerate energy subbands, realized in an InAs(10 nm)/GaSb(5 nm) coupled quantum well. We observe a narrow and intense maximum (∼500 kΩ) in the four-terminal resistivity in the charge neutrality region, separating the electron-like and hole-like regimes, with a strong activated temperature dependence above T = 7 K and perfect stability against quantizing magnetic fields. We discuss several mechanisms for that unexpectedly large resistance in this zero-gap semi-metal system including the formation of an excitonic insulator state.
    Electronic ISSN: 1367-2630
    Topics: Physics
    Published by Institute of Physics (IOP)
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