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  • 1
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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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  • 2
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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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  • 3
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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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  • 4
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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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  • 5
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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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  • 6
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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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  • 7
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    Y-Chromosome Structural Diversity in the Bonobo and Chimpanzee Lineages (2016)
    Oxford University Press
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    Publication Date: 2016-08-05
    Description: The male-specific regions of primate Y-chromosomes (MSY) are enriched for multi-copy genes highly expressed in the testis. These genes are located in large repetitive sequences arranged as palindromes, inverted-, and tandem repeats termed amplicons. In humans, these genes have critical roles in male fertility and are essential for the production of sperm. The structure of human and chimpanzee amplicon sequences show remarkable difference relative to the remainder of the genome, a difference that may be the result of intense selective pressure on male fertility. Four subspecies of common chimpanzees have undergone extended periods of isolation and appear to be in the early process of subspeciation. A recent study found amplicons enriched for testis-expressed genes on the primate X-chromosome the target of hard selective sweeps, and male-fertility genes on the Y-chromosome may also be the targets of selection. However, little is understood about Y-chromosome amplicon diversity within and across chimpanzee populations. Here, we analyze nine common chimpanzee (representing three subspecies: Pan troglodytes schweinfurthii , Pan troglodytes ellioti , and Pan troglodytes verus ) and two bonobo ( Pan paniscus) male whole-genome sequences to assess Y ampliconic copy-number diversity across the Pan genus. We observe that the copy number of Y chromosome amplicons is variable among chimpanzees and bonobos, and identify several lineage-specific patterns, including variable copy number of azoospermia candidates RBMY and DAZ . We detect recurrent switchpoints of copy-number change along the ampliconic tracts across chimpanzee populations, which may be the result of localized genome instability or selective forces.
    Electronic ISSN: 1759-6653
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Experimental study of the types of cavitation by air seeding using light microscopy (2015)
    Oxford University Press
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    Publication Date: 2015-12-18
    Description: Recently, three types of cavitation: (i) expanding gradually; (ii) expanding—exploding, becoming a long-shaped bubble—lengthening by degrees; (iii) suddenly exploding and fully filling the conduit instantly, were proposed. Directed by this theory, experiments were performed using light microscopy to study the natural drying processes of xylem sections of Platycladus orientalis (L.) Franco. Three different phenomena of gas filling process in conduits were captured by replaying recorded videos. The first phenomenon is that a bubble emerging in a conduit expands and elongates gradually to fill the conduit. The second phenomenon is that a bubble emerging in a conduit expands gradually, and then suddenly becomes long-shaped, and extends continuously. The third phenomenon is that a bubble instantly fully fills a conduit. This paper suggests in these experiments that after losing the bulk water of a section, as the water stress of that section became more severe, the water pressures of different conduits of the section were not necessarily the same, and as time went on, the water pressures decreased constantly. Considering some practical factors, the three phenomena captured in our experiment are explained by our theory.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 9
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    Three types of cavitation caused by air seeding (2012)
    Oxford University Press
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    Publication Date: 2012-11-09
    Description: There are different opinions of the dynamics of an air bubble entering a xylem conduit. In this paper, we present a thorough mechanical analysis and conclude that there are three types of cavitation caused by air seeding. After an air seed enters a conduit at high xylem pressure , along with the drop of the water potential, it will expand gradually to a long-shaped bubble and extend continually. This is the first type of air seeding, or the type of expanding gradually. When the xylem pressure is moderate, right after an air seed enters a conduit, it will expand first. Then, as soon as the pressure reaches a threshold the bubble will blow up to form a bubble in long shape, accompanied by acoustic (or ultra-acoustic) emission. It will extend further as xylem pressure decreases continually. This is the second type of air seeding, or the type of expanding—exploding, becoming a long-shaped bubble—lengthening by degrees. In the range of ( is atmospheric pressure), soon after an air seed is sucked into a conduit it will explode immediately and the conduit will be full of the gas of the bubble instantly. This is the third type of air seeding, or the type of sudden exploding and filling conduit instantly. The third type is the frequent event in daily life of plant.
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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  • 10
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    Physical analysis of the process of cavitation in xylem sap (2002)
    Oxford University Press
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    Publication Date: 2002-06-01
    Print ISSN: 0829-318X
    Electronic ISSN: 1758-4469
    Topics: Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Published by Oxford University Press
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