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  • Articles  (65)
  • Oxford University Press  (45)
  • American Institute of Physics (AIP)  (20)
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  • Articles  (65)
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  • 1
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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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  • 2
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    Effects of MreB paralogs on poly-{gamma}-glutamic acid synthesis and cell morphology in Bacillus amyloliquefaciens (2016)
    Oxford University Press
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    Publication Date: 2016-08-27
    Description: Actin-like MreB paralogs play important roles in cell shape maintenance, cell wall synthesis and the regulation of the D,L-endopeptidases, CwlO and LytE. The gram-positive bacteria, Bacillus amyloliquefaciens LL3, is a poly--glutamic acid (-PGA) producing strain that contains three MreB paralogs: MreB, Mbl and MreBH. In B. amyloliquefaciens , CwlO and LytE can degrade -PGA. In this study, we aimed to test the hypothesis that modulating transcript levels of MreB paralogs would alter the synthesis and degradation of -PGA. The results showed that overexpression or inhibition of MreB, Mbl or MreBH had distinct effects on cell morphology and the molecular weight of the -PGA products. In fermentation medium, cells of mreB inhibition mutant were 50.2% longer than LL3, and the -PGA titer increased by 55.7%. However, changing the expression level of mbl showed only slight effects on the morphology, -PGA molecular weight and titer. In the mreBH inhibition mutant, -PGA production and its molecular weight increased by 56.7% and 19.4%, respectively. These results confirmed our hypothesis that suppressing the expression of MreB paralogs might reduce -PGA degradation, and that improving the cell size could strengthen -PGA synthesis. This is the first report of enhanced -PGA production via suppression of actin-like MreB paralogs.
    Keywords: Biotechnology & Synthetic Biology
    Print ISSN: 0378-1097
    Electronic ISSN: 1574-6968
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    Metamorphic InAs1-xBix/In0.83Al0.17As quantum well structures on InP for mid-infrared emission (2016)
    American Institute of Physics (AIP)
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    Publication Date: 2016-09-21
    Description: This work reports on InP-based metamorphic quantum well structures with bismuth incorporation for mid-infrared applications. InAs 1-x Bi x quantum well structures have been grown on InP-based metamorphic In 0.83 Al 0.17 As buffers and photoluminescence beyond 3.1  μ m has been achieved at 300 K, which is longer than the referenced InAs quantum well. X-ray diffraction, cross-sectional transmission electron microscopy, and energy dispersive X-ray spectroscopy measurements reveal clear interfaces of InAsBi quantum well with low bismuth, while more defects and bismuth inhomogeneity were observed as more bismuth was incorporated.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    Nearly lattice-matched short-wave infrared InGaAsBi detectors on InP (2016)
    American Institute of Physics (AIP)
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    Publication Date: 2016-01-21
    Description: This work reports on the demonstration of a short-wave infrared detector nearly lattice matched to InP substrate using quaternary InGaAsBi as the absorption layer. The bismuth content of about 3.2% has red-shifted the 50% cut-off wavelength from about 1.6  μ m to 2.1  μ m at room temperature, indicating a bandgap reduction of about 180 meV due to bismuth incorporation. The detector shows an encouraging dark current density of 2.4 × 10 −4 A/cm 2 at bias voltage of −10 mV at 300 K. This work shows the promising potential of InP-based lattice-matched InGaAsBi detectors for short-wave infrared detection.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 5
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    Effect of bismuth surfactant on InP-based highly strained InAs/InGaAs triangular quantum wells (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-11-25
    Description: We report the effect of Bi surfactant on the properties of highly strained InAs/InGaAs triangular quantum wells grown on InP substrates. Reduced surface roughness, improved heterostructure interfaces and enhanced photoluminescence intensity at 2.2  μ m are observed by moderate Bi-mediated growth. The nonradiative processes are analysed based on temperature-dependent photoluminescence. It is confirmed that Bi incorporation is insignificant in the samples, whereas excessive Bi flux during the growth results in deteriorated performance. The surfactant effect of Bi is promising to improve InP-based highly strained structures while the excess of Bi flux needs to be avoided.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 6
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    InP-based type-I quantum well lasers up to 2.9 μm at 230 K in pulsed mode on a metamorphic buffer (2015)
    American Institute of Physics (AIP)
    Details
    Publication Date: 2015-03-24
    Description: This work reports on up to 2.9  μ m lasing at 230 K of InP-based type-I quantum well lasers. This record long wavelength lasing is achieved by applying InP-based Sb-free structures with eight periods of strain-compensated InAs quantum wells grown on metamorphic In 0.8 Al 0.2 As template layers. The continuous-wave threshold current density is 797 A/cm 2 and the idealized extrapolated threshold current density for infinite cavity length is as low as 58 A/cm 2 per quantum well at 120 K. This scheme is a promising pathway for extending the wavelength range of type-I quantum well lasers on InP substrates.
    Print ISSN: 0003-6951
    Electronic ISSN: 1077-3118
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 7
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    DiseaseMeth version 2.0: a major expansion and update of the human disease methylation database (2017)
    Oxford University Press
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    Publication Date: 2017-01-05
    Description: The human disease methylation database (DiseaseMeth,  http://bioinfo.hrbmu.edu.cn/diseasemeth/ ) is an interactive database that aims to present the most complete collection and annotation of aberrant DNA methylation in human diseases, especially various cancers. Recently, the high-throughput microarray and sequencing technologies have promoted the production of methylome data that contain comprehensive knowledge of human diseases. In this DiseaseMeth update, we have increased the number of samples from 3610 to 32 701, the number of diseases from 72 to 88 and the disease–gene associations from 216 201 to 679 602. DiseaseMeth version 2.0 provides an expanded comprehensive list of disease–gene associations based on manual curation from experimental studies and computational identification from high-throughput methylome data. Besides the data expansion, we also updated the search engine and visualization tools. In particular, we enhanced the differential analysis tools, which now enable online automated identification of DNA methylation abnormalities in human disease in a case-control or disease–disease manner. To facilitate further mining of the disease methylome, three new web tools were developed for cluster analysis, functional annotation and survival analysis. DiseaseMeth version 2.0 should be a useful resource platform for further understanding the molecular mechanisms of human diseases.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Insights into the location and dynamics of the coolest X-ray emitting gas in clusters of galaxies (2016)
    Oxford University Press
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    Publication Date: 2016-07-13
    Description: We extend our previous study of the cool gas responsible for the emission of O vii X-ray lines in the cores of clusters and groups of galaxies. This is the coolest X-ray emitting phase and connects the 10 000 K H α emitting gas to the million degree phase, providing a useful tool to understand cooling in these objects. We study the location of the O vii gas and its connection to the intermediate Fe xvii and hotter O viii phases. We use high-resolution X-ray grating spectra of elliptical galaxies with strong Fe xvii line emission and detect O vii in 11 of 24 objects. Comparing the O vii detection level and resonant scattering, which is sensitive to turbulence and temperature, suggests that O vii is preferably found in cooler objects, where the Fe xvii resonant line is suppressed due to resonant scattering, indicating subsonic turbulence. Although a larger sample of sources and further observations is needed to distinguish between effects from temperature and turbulence, our results are consistent with cooling being suppressed at high turbulence as predicted by models of active galactic nuclei feedback, gas sloshing and galactic mergers. In some objects, the O vii resonant-to-forbidden line ratio is decreased by either resonant scattering or charge exchange boosting the forbidden line, as we show for NGC 4636. Charge exchange indicates interaction between neutral and ionized gas phases. The Perseus cluster also shows a high Fe xvii forbidden-to-resonance line ratio, which can be explained with resonant scattering by low-turbulence cool gas in the line of sight.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 9
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    The first Doppler images of the eclipsing binary SZ Piscium (2015)
    Oxford University Press
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    Publication Date: 2015-12-16
    Description: We present the first Doppler images of the active eclipsing binary system SZ Psc, based on the high-resolution spectral data sets obtained in 2004 November and 2006 September–December. The least-squares deconvolution technique was applied to derive high signal-to-noise profiles from the observed spectra of SZ Psc. Absorption features contributed by a third component of the system were detected in the LSD profiles at all observed phases. We estimated the mass and period of the third component to be about 0.9 M and 1283 ± 10 d, respectively. After removing the contribution of the third body from the least-squares deconvolved profiles, we derived the surface maps of SZ Psc. The resulting Doppler images indicate significant star-spot activities on the surface of the K subgiant component. The distributions of star-spots are more complex than that revealed by previous photometric studies. The cooler K component exhibited pronounced high-latitude spots as well as numerous low- and intermediate-latitude spot groups during the entire observing seasons, but did not show any large, stable polar cap, different from many other active RS CVn-type binaries.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 10
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    ASDB: a resource for probing protein functions with small molecules (2016)
    Oxford University Press
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    Publication Date: 2016-06-01
    Description: : Identifying chemical probes or seeking scaffolds for a specific biological target is important for protein function studies. Therefore, we create the Annotated Scaffold Database (ASDB), a computer-readable and systematic target-annotated scaffold database, to serve such needs. The scaffolds in ASDB were derived from public databases including ChEMBL, DrugBank and TCMSP, with a scaffold-based classification approach. Each scaffold was assigned with an InChIKey as its unique identifier, energy-minimized 3D conformations, and other calculated properties. A scaffold is also associated with drugs, natural products, drug targets and medical indications. The database can be retrieved through text or structure query tools. ASDB collects 333 601 scaffolds, which are associated with 4368 targets. The scaffolds consist of 3032 scaffolds derived from drugs and 5163 scaffolds derived from natural products. For given scaffolds, scaffold-target networks can be generated from the database to demonstrate the relations of scaffolds and targets. Availability and implementation: ASDB is freely available at http://www.rcdd.org.cn/asdb/ with the major web browsers. Contact: junxu@biochemomes.com or xujun9@mail.sysu.edu.cn 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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