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  • 11
    Publication Date: 2019
    Description: 〈span〉〈div〉ABSTRACT〈/div〉The Paleogene shale of the Dongying depression, a continental basin in eastern China, is taken as the study subject to examine the microscopic features of lacustrine shale reservoirs in the oil window. This study shows that shale pores in this evolutionary stage are present at the micrometer to nanometer scale, but fractures commonly have extension distances at the millimeter scale. Pores and fractures can be divided into three types, namely, primary pores, secondary pores, and cracks. Primary pores commonly have good connectivity at shallow burial depth. With the increase of burial depth, primary porosity is reduced because of compaction and cementation. Secondary pores are important in shale, including dissolved pores inside grains and at grain edge, and dissolution pores inside the hybrid of organic matter (OM) and clay minerals, and evaporite minerals, including carbonates or sulfates. Types of cracks were observed: bedding fissures, dissolution fractures, and structural fractures. The development of bedding fissures is related to the deposition of shale laminae. The formation of dissolution fractures is related to acidic fluids, such as organic acids and hydrogen sulfide, whereas the formation of structural fractures is jointly controlled by fault development, fluid overpressure, and lithofacies. The pores and fractures in the oil window of lacustrine shale can store and channel oil and gas. The hybrid OM–clay–carbonate (sulfate) and the pores inside are important through the oil window. Moreover, the development of the pores depends not only on hydrocarbon generation but also on the interaction of hydrocarbons and organic acid dissolution. This finding has important significance in the accumulation of oil and gas in continental shales.〈/span〉
    Print ISSN: 0149-1423
    Electronic ISSN: 1943-2674
    Topics: Geosciences
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  • 12
    Publication Date: 2016-08-28
    Description: Chlamydial species are common intracellular parasites that cause various diseases, mainly characterized by persistent infection, which lead to inflammatory responses modulated by pattern recognition receptors (PRRs). The best understood PRRs are the extracellular Toll-like receptors, but recent significant advances have focused on two important proteins, NOD1 and NOD2, which are members of the intracellular nucleotide-binding oligomerization domain receptor family and are capable of triggering the host innate immune signaling pathways. This results in the production of pro-inflammatory cytokines, which is vital for an adequate host defense against intracellular chlamydial infection. NOD1/2 ligands are known to derive from peptidoglycan, and the latest research has resolved the paradox of whether chlamydial species possess this bacterial cell wall component; this finding is likely to promote in-depth investigations into the interaction between the NOD proteins and chlamydial pathogens. In this review, we summarize the basic characteristics and signal transduction functions of NOD1 and NOD2 and highlight the new research on the roles of NOD1 and NOD2 in the host defense against chlamydial infection.
    Keywords: Pathogens & Pathogenicity
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
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  • 13
    Publication Date: 2016-01-16
    Description: The oxygen vacancy model has been used to explain the magnetic and electrical transport properties of dilute magnetic semiconductors and resistive switching. In particular, some authors have claimed that they found a symmetric peak corresponding to the oxygen vacancies in O1s photoelectron spectra. In this paper, using X-ray photoelectron spectra with argon ion etching, it is shown that this symmetric peak may also be interpreted as being related to O 1− anions, rather than to oxygen vacancies.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
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  • 14
    Publication Date: 2015-12-10
    Description: : Demultiplexing is used after high-throughput sequencing to in silico assign reads to the samples of origin based on the sequenced reads of the indices. Existing demultiplexing tools based on the similarity between the read index and the reference index sequences may fail to provide satisfactory results on low-quality datasets. We developed Bayexer, a Bayesian demultiplexing algorithm for Illumina sequencers. Bayexer uses the information extracted directly from the contaminant sequences of the targeting reads as the training dataset for a naïve Bayes classifier to assign reads. According to our evaluation, Bayexer provides higher capability, accuracy and speed on various real datasets than other tools. Availability and implementation : Bayexer is implemented in Perl and freely available at https://github.com/HaisiYi/Bayexer . Contact: litao@ihb.ac.cn or lizhe@ibcas.ac.cn 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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  • 15
    Publication Date: 2011-04-06
    Description: Contemporary physical science studies rely on the effective analyses of geographically dispersed spatial data and simulations of physical phenomena. Single computers and generic high-end computing are not sufficient to process the data for complex physical science analysis and simulations, which can be successfully supported only through distributed computing, best optimized through the application of spatial principles. Spatial computing, the computing aspect of a spatial cyberinfrastructure, refers to a computing paradigm that utilizes spatial principles to optimize distributed computers to catalyze advancements in the physical sciences. Spatial principles govern the interactions between scientific parameters across space and time by providing the spatial connections and constraints to drive the progression of the phenomena. Therefore, spatial computing studies could better position us to leverage spatial principles in simulating physical phenomena and, by extension, advance the physical sciences. Using geospatial science as an example, this paper illustrates through three research examples how spatial computing could (i) enable data intensive science with efficient data/services search, access, and utilization, (ii) facilitate physical science studies with enabling high-performance computing capabilities, and (iii) empower scientists with multidimensional visualization tools to understand observations and simulations. The research examples demonstrate that spatial computing is of critical importance to design computing methods to catalyze physical science studies with better data access, phenomena simulation, and analytical visualization. We envision that spatial computing will become a core technology that drives fundamental physical science advancements in the 21st century.
    Keywords: Spatial Cyberinfrastructure
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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  • 16
    Publication Date: 2019
    Description: 〈p〉The ruminants are one of the most successful mammalian lineages, exhibiting morphological and habitat diversity and containing several key livestock species. To better understand their evolution, we generated and analyzed de novo assembled genomes of 44 ruminant species, representing all six Ruminantia families. We used these genomes to create a time-calibrated phylogeny to resolve topological controversies, overcoming the challenges of incomplete lineage sorting. Population dynamic analyses show that population declines commenced between 100,000 and 50,000 years ago, which is concomitant with expansion in human populations. We also reveal genes and regulatory elements that possibly contribute to the evolution of the digestive system, cranial appendages, immune system, metabolism, body size, cursorial locomotion, and dentition of the ruminants.〈/p〉
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
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  • 17
    Publication Date: 2019
    Description: 〈span〉〈div〉SUMMARY〈/div〉Finite-difference (FD) methods are widely used for numerical solution of acoustic and elastic wave equations. Temporal high-order FD methods exhibit better accuracy and stability than the methods with second-order differencing in time. Also, the implicit calculation of spatial derivatives can bring significant improvement in accuracy. The present implicit FD methods with high-order accuracy in time are based on centred grids. In this paper, we propose an implicit staggered-grid FD (SFD) scheme with a combined stencil, which is the combination of rhombus/pyramid and cross stencils in 2-D/3-D case, for modelling scalar wave propagation. Our scheme computes the temporal and spatial derivatives using high-order temporal and implicit spatial FD operators based on the combined stencil and the conventional stencil, respectively. We derive the dispersion relations of the FD scheme for 2-D and 3-D scalar wave equations and estimate temporal and implicit spatial FD coefficients by Taylor series expansion (TE) and least squares (LS). According to the kinds of FD coefficients, we formulate four implicit SFD operators: TE–TE, TE–LS, LS–TE and LS–LS operators. We carry out the comparison between our scheme and several existing SFD schemes: the conventional explicit and implicit, optimal explicit and implicit and explicit temporal high-order schemes. 2-D and 3-D dispersion analysis, stability analysis and modelling examples reveal that our implicit scheme has greater accuracy than other schemes and requires slightly stricter stability condition than the explicit temporal high-order SFD schemes. Owing to higher accuracy, our implicit SFD scheme with LS-LS operators allows for shorter FD operators and larger grid spacing, which can increase the computational efficiency.〈/span〉
    Print ISSN: 2051-1965
    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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  • 18
    Publication Date: 2014-01-16
    Description: We investigated the spectral and timing properties of the type B quasi-periodic oscillations (QPOs) showing up in the transient black hole binary GX 339-4 during its four outbursts observed by Rossi X-ray Timing Explorer (RXTE)/PCA and HEXTE in 2002, 2004, 2007 and 2010. We find that, the dependence on variability of the accretion flow turns out to be similar for the type B QPOs occurring in these four outbursts. We therefore take the results from the 2010 outburst for presentation. Our spectral results obtained from both the energy and time domains show that, the occurrence of the type B QPO is accompanied with sudden increase of hard component flux, relatively smaller inner disk radius, stable disk but variable corona. The latter may be understood in a scenario of variable input of seed photons for Comptonization in the corona. Further clues to probing the possible origination of the type B QPO come from our analysis of time lag and its energy dependence. The energy dependence of type B QPO amplitude suggests that the hard component dominate the variability and the time lag spectral analysis results suggests the type B QPO could be related to inverse Compton scattering. The time lag between hard and soft energy band is about 10 ms and found to depend on frequency in a form of –0.7 for type B QPOs in the rising phase. Finally we put these results in a context of a blob mechanism at work.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
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  • 19
    Publication Date: 2013-10-12
    Description: A series of CuO/Ce 0.6 Zr 0.4 O 2 catalysts doped with rare earth (Y, La) oxides and transition metal (Fe, Co, Ni) promoters were synthesized by the coprecipitation method. The effects of the additive type and content on the structure, redox properties, and water-gas shift (WGS) catalytic activity were investigated in detail by X-ray diffraction, N 2 physisorption, scanning electron microscopy, energy-dispersive X-ray spectroscopy, H 2 temperature-programmed reduction, and Raman spectroscopy. The catalytic activity was tested in terms of CO in H 2 -rich coal-derived synthesis gas, which simulated the actual gas composition of an integrated gasification combined cycle system. The experimental results revealed the beneficial role of doping with 3 wt % Fe in enhancing the catalytic performance by increasing the oxygen storage and mobility capacity, the reducibility, and the synergistic interaction between copper oxide and ceria-zirconia. The metal-support interactions within ceria-based catalysts are important in WGS reactions. Microporous catalysts were therefore doped with rare earth oxides or transition metal promoters and catalytic activity was tested. Both additive type and content can influence the catalytic activity by affecting oxygen vacancies, reducibility, and the interaction between copper oxide and support.
    Print ISSN: 0930-7516
    Electronic ISSN: 1521-4125
    Topics: Chemistry and Pharmacology , Process Engineering, Biotechnology, Nutrition Technology
    Published by Wiley
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  • 20
    Publication Date: 2013-10-16
    Description: The postdomestication adaptation of maize to longer days required reduced photoperiod sensitivity to optimize flowering time. We performed a genome-wide association study and confirmed that ZmCCT, encoding a CCT domain-containing protein, is associated with the photoperiod response. In early-flowering maize we detected a CACTA-like transposable element (TE) within the ZmCCT...
    Print ISSN: 0027-8424
    Electronic ISSN: 1091-6490
    Topics: Biology , Medicine , Natural Sciences in General
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