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  • 1
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    Quasi-monoenergetic ion beam acceleration by laser-driven shock and solitary waves in near-critical plasmas (2016)
    American Institute of Physics (AIP)
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    Publication Date: 2016-07-29
    Description: Ion acceleration in near-critical plasmas driven by intense laser pulses is investigated theoretically and numerically. A theoretical model has been given for clarification of the ion acceleration dynamics in relation to different laser and target parameters. Two distinct regimes have been identified, where ions are accelerated by, respectively, the laser-induced shock wave in the weakly driven regime (comparatively low laser intensity) and the nonlinear solitary wave in the strongly driven regime (comparatively high laser intensity). Two-dimensional particle-in-cell simulations show that quasi-monoenergetic proton beams with a peak energy of 94.6 MeV and an energy spread 15.8% are obtained by intense laser pulses at intensity I 0  = 3 × 10 20  W/cm 2 and pulse duration τ  = 0.5 ps in the strongly driven regime, which is more advantageous than that got in the weakly driven regime. In addition, 233 MeV proton beams with narrow spread can be produced by extending τ to 1.0 ps in the strongly driven regime.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 2
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    Incorporating organelle correlations into semi-supervised learning for protein subcellular localization prediction (2016)
    Oxford University Press
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    Publication Date: 2016-07-09
    Description: Motivation: Bioimages of subcellular protein distribution as a new data source have attracted much attention in the field of automated prediction of proteins subcellular localization. Performance of existing systems is significantly limited by the small number of high-quality images with explicit annotations, resulting in the small sample size learning problem. This limitation is more serious for the multi-location proteins that co-exist at two or more organelles, because it is difficult to accurately annotate those proteins by biological experiments or automated systems. Results: In this study, we designed a new protein subcellular localization prediction pipeline aiming to deal with the small sample size learning and multi-location proteins annotation problems. Five semi-supervised algorithms that can make use of lower-quality data were integrated, and a new multi-label classification approach by incorporating the correlations among different organelles in cells was proposed. The organelle correlations were modeled by the Bayesian network, and the topology of the correlation graph was used to guide the order of binary classifiers training in the multi-label classification to reflect the label dependence relationship. The proposed protocol was applied on both immunohistochemistry and immunofluorescence images, and our experimental results demonstrated its efficiency. Availability and implementation: The datasets and code are available at: www.csbio.sjtu.edu.cn/bioinf/CorrASemiB . Contact: hbshen@sjtu.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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  • 3
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    Collisionless shocks driven by 800 nm laser pulses generate high-energy carbon ions (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-01-31
    Description: We present experimental studies on ion acceleration from diamond-like carbon (DLC) foils irradiated by 800 nm, linearly polarized laser pulses with peak intensity of 1.7 × 10 19  W/cm 2 to 3.5 × 10 19  W/cm 2 at oblique incidence. Diamond-like carbon foils are heated by the prepulse of a high-contrast laser pulse and expand to form plasmas of near-critical density caused by thermal effect before the arrival of the main pulse. It is demonstrated that carbon ions are accelerated by a collisionless shock wave in slightly overdense plasma excited by forward-moving hot electrons generated by the main pulse.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 4
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    Cascaded proton acceleration by collisionless electrostatic shock (2015)
    American Institute of Physics (AIP)
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    Publication Date: 2015-07-07
    Description: A new scheme for proton acceleration by cascaded collisionless electrostatic shock (CES) is proposed. By irradiating a foil target with a moderate high-intensity laser beam, a stable CES field can be induced, which is employed as the accelerating field for the booster stage of proton acceleration. The mechanism is studied through simulations and theoretical analysis, showing that a 55 MeV seed proton beam can be further accelerated to 265 MeV while keeping a good energy spread. This scheme offers a feasible approach to produce proton beams with energy of hundreds of MeV by existing available high-intensity laser facilities.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 5
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    Now you see it, now you don't: the disappearing central engine of the quasar J1011+5442 (2015)
    Oxford University Press
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    Publication Date: 2015-11-20
    Description: We report the discovery of a new ‘changing-look' quasar, SDSS J101152.98+544206.4, through repeat spectroscopy from the Time Domain Spectroscopic Survey. This is an addition to a small but growing set of quasars whose blue continua and broad optical emission lines have been observed to decline by a large factor on a time-scale of approximately a decade. The 5100 Å monochromatic continuum luminosity of this quasar drops by a factor of 〉9.8 in a rest-frame time interval of 〈9.7 yr, while the broad Hα luminosity drops by a factor of 55 in the same amount of time. The width of the broad Hα line increases in the dim state such that the black hole mass derived from the appropriate single-epoch scaling relation agrees between the two epochs within a factor of 3. The fluxes of the narrow emission lines do not appear to change between epochs. The light curve obtained by the Catalina Sky Survey suggests that the transition occurs within a rest-frame time interval of approximately 500 d. We examine three possible mechanisms for this transition suggested in the recent literature. An abrupt change in the reddening towards the central engine is disfavoured by the substantial difference between the time-scale to obscure the central engine and the observed time-scale of the transition. A decaying tidal disruption flare is consistent with the decay rate of the light curve but not with the prolonged bright state preceding the decay; nor can this scenario provide the power required by the luminosities of the emission lines. An abrupt drop in the accretion rate on to the supermassive black hole appears to be the most plausible explanation for the rapid dimming.
    Print ISSN: 0035-8711
    Electronic ISSN: 1365-2966
    Topics: Physics
    Published by Oxford University Press
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  • 6
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    Target normal sheath acceleration of foil ions by laser-trapped hot electrons from a long subcritical-density preplasma (2014)
    American Institute of Physics (AIP)
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    Publication Date: 2014-12-11
    Description: In a long subcritical density plasma, an ultrashort ultraintense laser pulse can self-organize into a fast but sub-relativistic propagating structure consisting of the modulated laser light and a large number of trapped electrons from the plasma. Upon impact of the structure with a solid foil target placed in the latter, the remaining laser light is reflected, but the dense and hot trapped electrons pass through the foil, together with the impact-generated target-frontsurface electrons to form a dense hot electron cloud at the back of the target suitable for enhancing target normal sheath acceleration of the target-backsurface ions. The accelerated ions are well collimated and of high charge and energy densities, with peak energies a full order of magnitude higher than that from target normal sheath acceleration without the subcritical density plasma. In the latter case, the space-charge field accelerating the ions is limited since they are formed only by the target-frontsurface electrons during the very short instant of laser reflection.
    Print ISSN: 1070-664X
    Electronic ISSN: 1089-7674
    Topics: Physics
    Published by American Institute of Physics (AIP)
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  • 7
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    Systems mapping: how to map genes for biomass allocation toward an ideotype (2014)
    Oxford University Press
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    Publication Date: 2014-07-19
    Description: The recent availability of high-throughput genetic and genomic data allows the genetic architecture of complex traits to be systematically mapped. The application of these genetic results to design and breed new crop types can be made possible through systems mapping. Systems mapping is a computational model that dissects a complex phenotype into its underlying components, coordinates different components in terms of biological laws through mathematical equations and maps specific genes that mediate each component and its connection with other components. Here, we present a new direction of systems mapping by integrating this tool with carbon economy. With an optimal spatial distribution of carbon fluxes between sources and sinks, plants tend to maximize whole-plant growth and competitive ability under limited availability of resources. We argue that such an economical strategy for plant growth and development, once integrated with systems mapping, will not only provide mechanistic insights into plant biology, but also help to spark a renaissance of interest in ideotype breeding in crops and trees.
    Print ISSN: 1467-5463
    Electronic ISSN: 1477-4054
    Topics: Biology , Computer Science
    Published by Oxford University Press
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  • 8
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    An Orthogonal Genetic Algorithm for QoS-Aware Service Composition (2016)
    Oxford University Press
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    Publication Date: 2016-12-10
    Description: Service composition has been proven to be a convincing computing paradigm for rapidly constructing large-scale distributed applications within and across organizational boundaries. Quality of service (QoS)-aware service composition, i.e. selection of the optimal execution plan that maximizes the composition's end-to-end QoS properties, is an active area of research and development endeavors in service composition. In this article, we propose an orthogonal genetic algorithm (OGA) for QoS-aware service composition problem. Its significant feature is to incorporate an orthogonal design method into the initial population generation process and crossover operation. As a result, our algorithm is more robust and can search the solution space in a statistically sound manner. We have executed the OGA to solve 81 randomly generated service composition problems with different sizes and structures based on QWS data set including 2507 real Web services. The results indicate that our OGA can find near-optimal solutions within moderate numbers of generation and has the performance superiority in comparison with many existing optimization algorithms.
    Print ISSN: 0010-4620
    Electronic ISSN: 1460-2067
    Topics: Computer Science
    Published by Oxford University Press
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  • 9
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    A novel estrogen receptor-microRNA 190a-PAR-1-pathway regulates breast cancer progression, a finding initially suggested by genome-wide analysis of loci associated with lymph-node metastasis (2013)
    Oxford University Press
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    Publication Date: 2013-12-21
    Description: To identify microRNAs that are important in regulating breast cancer progression, the present study used data for the 199 961 single-nucleotide polymorphisms (SNPs) in 837 breast cancer patients genotyped in a recent genome-wide association study to identify loci associated with lymph node metastasis (LNM). SNPs tagging the 15q22.2 locus showed a significant association with LNM and miR-190a was found to be the only microRNA in this region. The role of miR-190a in LNM was supported by the findings that increased miR-190a expression inhibited cell migration and invasiveness and that the target of miR-190a was protease-activated-receptor 1 (PAR-1), which is a metastasis promoting protein in several cancers. In addition, the promoter region of miR-190a was defined and found to contain half of an estrogen response element, suggesting that miR-190a is regulated by estrogen receptor (ER) signaling. This was confirmed by the findings that miR-190a expression was activated by 17β-estradiol and that ERα bound directly to this promoter. The importance of this ERα-miR190a-PAR-1 link in breast tumorigenesis is suggested by the findings of (i) an association between genetic polymorphism of the miR-190a -containing region and LNM that is modified by SNPs of PAR-1 and is particularly significant in ERα-positive patients and (ii) a combined effect of ERα and miR-190a expression on tumor grade/cancer stage. More importantly, the level of miR-190a expression in primary breast carcinomas correlated with overall survival. These findings suggest a novel pathway in which ERα signaling regulates miR-190a expression, causing inhibition of PAR-1 expression, correlated with inhibition of cancer metastasis.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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  • 10
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    Identification of a novel FGFRL1 MicroRNA target site polymorphism for bone mineral density in meta-analyses of genome-wide association studies (2015)
    Oxford University Press
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    Publication Date: 2015-07-24
    Description: MicroRNAs (miRNAs) are critical post-transcriptional regulators. Based on a previous genome-wide association (GWA) scan, we conducted a polymorphism in microRNA target sites (poly-miRTS)- centric multistage meta-analysis for lumbar spine (LS)-, total hip (HIP)- and femoral neck (FN)-bone mineral density (BMD). In stage I, 41 102 poly-miRTSs were meta-analyzed in seven cohorts with a genome-wide significance (GWS) α = 0.05/41 102 = 1.22 x 10 –6 . By applying α = 5 x 10 –5 (suggestive significance), 11 poly-miRTSs were selected, with FGFRL1 rs4647940 and PRR5 rs3213550 as top signals for FN-BMD ( P = 7.67 x 10 –6 and 1.58 x 10 –5 ) in gender-combined sample. In stage II in silico replication (two cohorts), FGFRL1 rs4647940 was the only signal marginally replicated for FN-BMD ( P = 5.08 x 10 –3 ) at α = 0.10/11 = 9.09 x 10 -3 . PRR5 rs3213550 was also selected based on biological significance. In stage III de novo genotyping replication (two cohorts), FGFRL1 rs4647940 was the only signal significantly replicated for FN-BMD ( P = 7.55 x 10 –6 ) at α = 0.05/2 = 0.025 in gender-combined sample. Aggregating three stages, FGFRL1 rs4647940 was the single stage I-discovered and stages II- and III-replicated signal attaining GWS for FN-BMD ( P = 8.87 x 10 –12 ). Dual-luciferase reporter assays demonstrated that FGFRL1 3' untranslated region harboring rs4647940 appears to be hsa-miR-140-5p's target site. In a zebrafish microinjection experiment, dre-miR-140-5p is shown to exert a dramatic impact on craniofacial skeleton formation. Taken together, we provided functional evidence for a novel FGFRL1 poly-miRTS rs4647940 in a previously known 4p16.3 locus, and experimental and clinical genetics studies have shown both FGFRL1 and hsa-miR-140-5p are important for bone formation.
    Print ISSN: 0964-6906
    Electronic ISSN: 1460-2083
    Topics: Biology , Medicine
    Published by Oxford University Press
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