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  • 1
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    Similar simulation study on the characteristics of the electric potential response to coal mining (2017)
    Oxford University Press
    Details
    Publication Date: 2017-12-19
    Print ISSN: 1742-2132
    Electronic ISSN: 1742-2140
    Topics: Geosciences
    Published by Oxford University Press on behalf of Sinopec Geophysical Research Institute.
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  • 2
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    ChIP-seq reveals the global regulator AlgR mediating cyclic di-GMP synthesis in Pseudomonas aeruginosa (2015)
    Oxford University Press
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    Publication Date: 2015-09-30
    Description: AlgR is a key transcriptional regulator required for the expression of multiple virulence factors, including type IV pili and alginate in Pseudomonas aeruginosa . However, the regulon and molecular regulatory mechanism of AlgR have yet to be fully elucidated. Here, among 157 loci that were identified by a ChIP-seq assay, we characterized a gene, mucR , which encodes an enzyme that synthesizes the intracellular second messenger cyclic diguanylate (c-di-GMP). A algR strain produced lesser biofilm than did the wild-type strain, which is consistent with a phenotype controlled by c-di-GMP. AlgR positively regulates mucR via direct binding to its promoter. A algR mucR double mutant produced lesser biofilm than did the single algR mutant, demonstrating that c-di-GMP is a positive regulator of biofilm formation. AlgR controls the levels of c-di-GMP synthesis via direct regulation of mucR . In addition, the cognate sensor of AlgR, FimS/AlgZ, also plays an important role in P. aeruginosa virulence. Taken together, this study provides new insights into the AlgR regulon and reveals the involvement of c-di-GMP in the mechanism underlying AlgR regulation.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Resource-Efficient Data Gathering in Sensor Networks for Environment Reconstruction (2015)
    Oxford University Press
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    Publication Date: 2015-06-02
    Description: Environment reconstruction is to rebuild the physical environment in the cyberspace using the sensory data collected by sensor networks, which is a fundamental method for human to understand the physical world in depth. A lot of basic scientific work such as nature discovery and organic evolution heavily relies on the environment reconstruction. However, gathering large amount of environmental data costs huge energy and storage space. The shortage of energy and storage resources has become a major problem in sensor networks for environment reconstruction applications. Motivated by exploiting the inherent feature of environmental data, in this paper, we design a novel data gathering protocol based on compressive sensing theory and time series analysis to further improve the resource efficiency. This protocol adapts the duty cycle and sensing probability of every sensor node according to the dynamic environment, which cannot only guarantee the reconstruction accuracy, but also save energy and storage resources. We implement the proposed protocol on a 51-node testbed and conduct the simulations based on three real datasets from Intel Indoor, GreenOrbs and Ocean Sense projects. Both the experiment and simulation performances demonstrate that our method significantly outperforms the conventional methods in terms of resource efficiency and reconstruction accuracy.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 4
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    A possible 55-d X-ray period of the ultraluminous accreting pulsar M82 X-2 (2016)
    Oxford University Press
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    Publication Date: 2016-07-30
    Description: We report on the possible detection of a 55-d X-ray modulation for the ultraluminous accreting pulsar M82 X–2 from archival Chandra observations. Because M82 X–2 is known to have a 2.5-d orbital period, if the 55-d period is real, then it will be the superorbital period of the system. We also investigated variabilities of three other nearby ultraluminous X-ray sources in the central region of M82 with the Chandra data, and we did not find any evidence of periodicities. Furthermore, we re-examined the previously reported 62-d periodicity near the central region of M82 by performing a systematic timing study with all the archival Rossi X-Ray Timing Explorer and Swift data. Using various dynamic timing analysis methods, we have confirmed that the 62-d period is not stable, suggesting that it is not the orbital period of M82 X–1; this is in agreement with previous work.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 5
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    Nonsense-mediated decay regulates key components of homologous recombination (2016)
    Oxford University Press
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    Publication Date: 2016-06-21
    Description: Cells frequently experience DNA damage that requires repair by homologous recombination (HR). Proteins involved in HR are carefully coordinated to ensure proper and efficient repair without interfering with normal cellular processes. In Saccharomyces cerevisiae , Rad55 functions in the early steps of HR and is regulated in response to DNA damage through phosphorylation by the Mec1 and Rad53 kinases of the DNA damage response. To further identify regulatory processes that target HR, we performed a high-throughput genetic interaction screen with RAD55 phosphorylation site mutants. Genes involved in the mRNA quality control process, nonsense-mediated decay (NMD), were found to genetically interact with rad55 phospho-site mutants. Further characterization revealed that RAD55 transcript and protein levels are regulated by NMD. Regulation of HR by NMD extends to multiple targets beyond RAD55 , including RAD51, RAD54 and RAD57 . Finally, we demonstrate that loss of NMD results in an increase in recombination rates and resistance to the DNA damaging agent methyl methanesulfonate, suggesting this pathway negatively regulates HR under normal growth conditions.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 6
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    QTLMiner: QTL database curation by mining tables in literature (2015)
    Oxford University Press
    Details
    Publication Date: 2015-05-12
    Description: Motivation: Figures and tables in biomedical literature record vast amounts of important experiment results. In scientific papers, for example, quantitative trait locus (QTL) information is usually presented in tables. However, most of the popular text-mining methods focus on extracting knowledge from unstructured free text. As far as we know, there are no published works on mining tables in biomedical literature. In this article, we propose a method to extract QTL information from tables and plain text found in literature. Heterogeneous and complex tables were converted into a structured database, combined with information extracted from plain text. Our method could greatly reduce labor burdens involved with database curation. Results: We applied our method on a soybean QTL database curation, from which 2278 records were extracted from 228 papers with a precision rate of 96.9% and a recall rate of 83.3%, F value for the method is 89.6%. Availability and implementation: QTLMiner is available at www.soyomics.com/qtlminer/ . Contact: yuanxh@iga.ac.cn
    Print ISSN: 1367-4803
    Electronic ISSN: 1460-2059
    Topics: Biology , Computer Science , Medicine
    Published by Oxford University Press
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  • 7
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    Revisiting the ultraluminous supersoft source in M 101: an optically thick outflow model (2015)
    Oxford University Press
    Details
    Publication Date: 2015-12-26
    Description: The M 101 galaxy contains the best-known example of an ultraluminous supersoft source (ULS), dominated by a thermal component at kT 0.1 keV. The origin of the thermal component and the relation between ULSs and standard (broad-band spectrum) ultraluminous X-ray sources are still controversial. We re-examined the X-ray spectral and timing properties of the M 101 ULS using archival Chandra and XMM–Newton observations. We show that the X-ray time-variability and spectral properties are inconsistent with standard-disc emission. The characteristic radius R bb of the thermal emitter varies from epoch to epoch between 10 000 and 100 000 km; the colour temperature kT bb varies between 50 and 140 eV and the two quantities scale approximately as $R_{\rm bb} \propto T_{\rm bb}^{-2}$ . In addition to the smooth continuum, we also find (at some epochs) spectral residuals well fitted with thermal-plasma models and absorption edges: we interpret this as evidence that we are looking at a clumpy, multitemperature outflow. We suggest that at sufficiently high accretion rates and inclination angles, the supercritical, radiatively driven outflow becomes effectively optically thick and completely thermalizes the harder X-ray photons from the inner part of the inflow, removing the hard spectral tail. We develop a simple, spherically symmetric outflow model and show that it is consistent with the observed temperatures, radii and luminosities. A larger, cooler photosphere shifts the emission peak into the far-UV and makes the source dimmer in X-rays but possibly ultraluminous in the UV. We compare our results and interpretation with those of Liu et al.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 8
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    Widespread deuteration across the IRDC G035.39-00.33 (2016)
    Oxford University Press
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    Publication Date: 2016-03-23
    Description: Infrared Dark Clouds (IRDCs) are cold, dense regions that are usually found within Giant Molecular Clouds. Ongoing star formation within IRDCs is typically still deeply embedded within the surrounding molecular gas. Characterizing the properties of relatively quiescent IRDCs may therefore help us to understand the earliest phases of the star formation process. Studies of local molecular clouds have revealed that deuterated species are enhanced in the earliest phases of star formation. In this paper, we test this towards IRDC G035.39–00.33. We present an 80 arcsec by 140 arcsec map of the J = 2 -〉 1 transition of N 2 D + , obtained with the Institut de Radioastronomie Millimétrique 30 m telescope telescope. We find that N 2 D + is widespread throughout G035.39–00.33. Complementary observations of N 2 H + (1 – 0) are used to estimate the deuterium fraction, D $_\mathrm{frac}^\mathrm{N_2H^+}$    N (N 2 D + )/ N (N 2 H + ). We report a mean D $_\mathrm{frac}^\mathrm{N_2H^+}$  = 0.04 ± 0.01, with a maximum of D $_\mathrm{frac}^\mathrm{N_2H^+}$  = 0.09 ± 0.02. The mean deuterium fraction is ~3 orders of magnitude greater than the interstellar [D]/[H] ratio. High angular resolution observations are required to exclude beam dilution effects of compact deuterated cores. Using chemical modelling, we find that the average observed values of D $_\mathrm{frac}^\mathrm{N_2H^+}$ are in agreement with an equilibrium deuterium fraction, given the general properties of the cloud. This implies that the IRDC is at least ~3 Myr old, which is ~8 times longer than the mean free-fall time of the observed deuterated region.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    Pathogenesis of Candida albicans biofilm (2016)
    Oxford University Press
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    Publication Date: 2016-04-07
    Description: Candida albicans is the most common human fungal pathogen causing diseases ranging from mucosal to systemic infections. As a commensal, C. albicans asymptomatically colonizes mucosal surfaces; however, any disruption in the host environment or under conditions of immune dysfunction, C. albicans can proliferate and invade virtually any site in the host. The ability of this highly adaptable fungal species to transition from commensal to pathogen is due to a repertoire of virulence factors. Specifically, the ability to switch morphology and form biofilms are properties central to C. albicans pathogenesis. In fact, the majority of C. albicans infections are associated with biofilm formation on host or abiotic surfaces such as indwelling medical devices, which carry high morbidity and mortality. Significantly, biofilms formed by C. albicans are inherently tolerant to antimicrobial therapy and therefore, the susceptibility of Candida biofilms to the current therapeutic agents remains low. The aim of this review is to provide an overview of C. albicans highlighting some of the diverse biofilm-associated diseases caused by this opportunistic pathogen and the animal models available to study them. Further, the classes of antifungal agents used to combat these resilient infections are discussed along with mechanisms of drug resistance.
    Print ISSN: 0928-8244
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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    Accuracy of the moment-tensor inversion of far-field P waves (2019)
    Oxford University Press
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    Publication Date: 2019
    Description: 〈span〉〈div〉Summary〈/div〉The far-field assumption is widely used and suitable for the moment-tensor inversion, in which the source-receiver distance is quite long. However, the description of far field is uncertain and an explicit far-field range is missing. In this study, the explicit far-field range is determined and the errors of moment-tensor solutions produced by the far-field approximation are analyzed. The distance, for which the far-field assumption is satisfied and the effect of the near-field term can be ignored, is directionally dependent. For the shear dislocation, in the directions near the nodal lines of the far-field P waves, the far-field distance is heavily dependent on the displacement component used to invert moment tensors. The radial component of displacement, which is parallel to the wave propagation direction, is recommended for the inversion and the corresponding far-field distance is quite short. In the directions far from the nodal lines, the selection of displacement components has little influence on the far-field distance. The maximum far-field distance appears in the directions of the pressure and tensile axes of the source and the value is about 30 wavelengths of radiated waves. Using more receivers (〉6) in the moment-tensor inversion can shorten the far-field distance. The effect of the near-field term on the moment-tensor inversion for tensile dislocations and isotropic sources (explosion or implosion) can be ignored. The conclusions obtained in this study are helpful for determining the positions of receivers and evaluating the accuracy of moment-tensor solutions, with far-field assumption being applied in the inversion.〈/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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