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  • 1
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    Robust optimal control of switched autonomous systems (2016)
    Oxford University Press
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    Publication Date: 2016-07-06
    Description: This paper considers the robustness issue on switching time of switched systems, in which each switching point has perturbation for a small variation. Our goal is to find optimal switching instants such that the system's performance being resistant against perturbations. By using the integral averaging technique and combining with optimal control theory, the derivatives of the cost function with respect to the original switching times are derived. We focus on the fixed switching mode sequences and use a gradient-descent algorithm to find the optimal switching instants. The efficacy of the proposed method is illustrated via numerical examples.
    Print ISSN: 0265-0754
    Electronic ISSN: 1471-6887
    Topics: Mathematics
    Published by Oxford University Press
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  • 2
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    Differences in the physiological processes of Calanus sinicus inside and outside the Yellow Sea Cold Water Mass (2016)
    Oxford University Press
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    Publication Date: 2016-06-04
    Description: Calanus sinicus , the key zooplankton species in the Yellow Sea, China, over-summers in the Yellow Sea Cold Water Mass (YSCWM). Here, we compared the metabolic rates, morphological characteristics and relative expressions of seven genes associated with molting, gonad development, lipid catabolism and stress tolerance of C. sinicus captured both inside and outside the YSCWM in summer. With a large oil sac, low metabolic rate and suppressed molting development, the C5-stage copepods inside the YSCWM were probably quiescent. The gene expressions revealed differences in physiology between quiescent and active copepods in the two regions. When quiescent, the gene associated with molting [ecdysteroid receptor (EcR)] was down-regulated, while genes related to lipid catabolism (Hydroxyacyl CoA dehydrogenase) and stress tolerance (ferritin) were up-regulated. C5s at the margin of the YSCWM up-regulated EcR expression and this could be in response to the elevated Chl a concentration, suggesting that elevated food condition may serve as a trigger that terminated the over-summering of C. sinicus in the Yellow Sea. In conclusion, this study revealed the physiological processes of quiescent and active C. sinicus via morphological, physiological and molecular methods simultaneously, providing a foundation for future investigations of the mechanisms involved in over-summering in YSCWM.
    Print ISSN: 0142-7873
    Electronic ISSN: 1464-3774
    Topics: Biology
    Published by Oxford University Press
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  • 3
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    FALCON@home: a high-throughput protein structure prediction server based on remote homologue recognition (2016)
    Oxford University Press
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    Publication Date: 2016-02-02
    Description: : The protein structure prediction approaches can be categorized into template-based modeling (including homology modeling and threading) and free modeling. However, the existing threading tools perform poorly on remote homologous proteins. Thus, improving fold recognition for remote homologous proteins remains a challenge. Besides, the proteome-wide structure prediction poses another challenge of increasing prediction throughput. In this study, we presented FALCON@home as a protein structure prediction server focusing on remote homologue identification. The design of FALCON@home is based on the observation that a structural template, especially for remote homologous proteins, consists of conserved regions interweaved with highly variable regions. The highly variable regions lead to vague alignments in threading approaches. Thus, FALCON@home first extracts conserved regions from each template and then aligns a query protein with conserved regions only rather than the full-length template directly. This helps avoid the vague alignments rooted in highly variable regions, improving remote homologue identification. We implemented FALCON@home using the Berkeley Open Infrastructure of Network Computing (BOINC) volunteer computing protocol. With computation power donated from over 20 000 volunteer CPUs, FALCON@home shows a throughput as high as processing of over 1000 proteins per day. In the Critical Assessment of protein Structure Prediction (CASP11), the FALCON@home-based prediction was ranked the 12th in the template-based modeling category. As an application, the structures of 880 mouse mitochondria proteins were predicted, which revealed the significant correlation between protein half-lives and protein structural factors. Availability and implementation: FALCON@home is freely available at http://protein.ict.ac.cn/FALCON/ . Contact: shuaicli@cityu.edu.hk , dbu@ict.ac.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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  • 4
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    Multiple alignment-free sequence comparison (2013)
    Oxford University Press
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    Publication Date: 2013-10-19
    Description: Motivation: Recently, a range of new statistics have become available for the alignment-free comparison of two sequences based on k -tuple word content. Here, we extend these statistics to the simultaneous comparison of more than two sequences. Our suite of statistics contains, first, and , extensions of statistics for pairwise comparison of the joint k -tuple content of all the sequences, and second, , and , averages of sums of pairwise comparison statistics. The two tasks we consider are, first, to identify sequences that are similar to a set of target sequences, and, second, to measure the similarity within a set of sequences. Results: Our investigation uses both simulated data as well as cis -regulatory module data where the task is to identify cis -regulatory modules with similar transcription factor binding sites. We find that although for real data, all of our statistics show a similar performance, on simulated data the Shepp-type statistics are in some instances outperformed by star-type statistics. The multiple alignment-free statistics are more sensitive to contamination in the data than the pairwise average statistics. Availability: Our implementation of the five statistics is available as R package named ‘multiAlignFree’ at be http://www-rcf.usc.edu/~fsun/Programs/multiAlignFree/multiAlignFreemain.html . Contact: reinert@stats.ox.ac.uk 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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  • 5
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    Genetic factors affecting gene transcription and catalytic activity of UDP-glucuronosyltransferases in human liver (2014)
    Oxford University Press
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    Publication Date: 2014-09-20
    Description: The aim of this study was to discover cis - and trans -acting factors significantly affecting mRNA expression and catalytic activity of human hepatic UDP-glucuronosyltransferases (UGTs). Transcription levels of five major hepatic UGT1A ( UGT1A1, UGT1A3, UGT1A4, UGT1A6 and UGT1A9 ) and five UGT2B ( UGT2B4, UGT2B7, UGT2B10, UGT2B15 and UGT2B17 ) genes were quantified in human liver tissue samples ( n = 125) using real-time PCR. Glucuronidation activities of 14 substrates were measured in 47 livers. We genotyped 167 tagSNPs (single-nucleotide polymorphisms) in UGT1A ( n = 43) and UGT2B ( n = 124), as well as the known functional UGT1A1*28 and UGT2B17 CNV (copy number variation) polymorphisms. Transcription levels of 15 transcription factors (TFs) known to regulate these UGTs were quantified. We found that UGT expression and activity were highly variable among the livers (median and range of coefficient of variations: 135%, 74–217% and 52%, 39–105%, respectively). CAR, PXR and ESR1 were found to be the most important trans -regulators of UGT transcription (median and range of correlation coefficients: 46%, 6–58%; 47%, 9–58%; and 52%, 24–75%, respectively). Hepatic UGT activities were mainly determined by UGT gene transcription levels. Twenty-one polymorphisms were significantly (FDR-adjusted P 〈 0.05) associated with mRNA expression and/or activities of UGT1A1 , UGT1A3 and UGT2B17 . We found novel SNPs in the UGT2B17 CNV region accounting for variability in UGT2B17 gene transcription and testosterone glucuronidation rate, in addition to that attributable to the UGT2B17 CNV. Our study discovered novel pharmacogenetic markers and provided detailed insight into the genetic network regulating hepatic UGTs.
    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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    Multiple pathogenic proteins implicated in neuronopathic Gaucher disease mice (2014)
    Oxford University Press
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    Publication Date: 2014-07-05
    Description: Gaucher disease, a prevalent lysosomal storage disease (LSD), is caused by insufficient activity of acid β-glucosidase (GCase) and the resultant glucosylceramide (GC)/glucosylsphingosine (GS) accumulation in visceral organs (Type 1) and the central nervous system (Types 2 and 3). Recent clinical and genetic studies implicate a pathogenic link between Gaucher and neurodegenerative diseases. The aggregation and inclusion bodies of α-synuclein with ubiquitin are present in the brains of Gaucher disease patients and mouse models. Indirect evidence of β-amyloid pathology promoting α-synuclein fibrillation supports these pathogenic proteins as a common feature in neurodegenerative diseases. Here, multiple proteins are implicated in the pathogenesis of chronic neuronopathic Gaucher disease (nGD). Immunohistochemical and biochemical analyses showed significant amounts of β-amyloid and amyloid precursor protein (APP) aggregates in the cortex, hippocampus, stratum and substantia nigra of the nGD mice. APP aggregates were in neuronal cells and colocalized with α-synuclein signals. A majority of APP co-localized with the mitochondrial markers TOM40 and Cox IV; a small portion co-localized with the autophagy proteins, P62/LC3, and the lysosomal marker, LAMP1. In cultured wild-type brain cortical neural cells, the GCase-irreversible inhibitor, conduritol B epoxide (CBE), reproduced the APP/α-synuclein aggregation and the accumulation of GC/GS. Ultrastructural studies showed numerous larger-sized and electron-dense mitochondria in nGD cerebral cortical neural cells. Significant reductions of mitochondrial adenosine triphosphate production and oxygen consumption (28–40%) were detected in nGD brains and in CBE-treated neural cells. These studies implicate defective GCase function and GC/GS accumulation as risk factors for mitochondrial dysfunction and the multi-proteinopathies (α-synuclein-, APP- and Aβ-aggregates) in nGD.
    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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    Nucleosomes affect local transformation efficiency (2012)
    Oxford University Press
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    Publication Date: 2012-10-24
    Description: Genetic transformation is a natural process during which foreign DNA enters a cell and integrates into the genome. Apart from its relevance for horizontal gene transfer in nature, transformation is also the cornerstone of today's recombinant gene technology. Despite its importance, relatively little is known about the factors that determine transformation efficiency. We hypothesize that differences in DNA accessibility associated with nucleosome positioning may affect local transformation efficiency. We investigated the landscape of transformation efficiency at various positions in the Saccharomyces cerevisiae genome and correlated these measurements with nucleosome positioning. We find that transformation efficiency shows a highly significant inverse correlation with relative nucleosome density. This correlation was lost when the nucleosome pattern, but not the underlying sequence was changed. Together, our results demonstrate a novel role for nucleosomes and also allow researchers to predict transformation efficiency of a target region and select spots in the genome that are likely to yield higher transformation efficiency.
    Print ISSN: 0305-1048
    Electronic ISSN: 1362-4962
    Topics: Biology
    Published by Oxford University Press
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  • 8
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    Optimal expansion of a heated ideal gas with time-dependent heat conductance (2013)
    Oxford University Press
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    Publication Date: 2013-11-10
    Description: The optimal configuration of the expansion process of a heated ideal gas inside a cylinder for maximum work output with a movable piston and time-dependent heat conductance is determined in this paper. The heat conductance of cylinder walls is not a constant, but depends on the time-dependent heat transfer surface area of the walls in contact with gas. Euler-Lagrange formalism is applied to obtain the optimal process that maximizes the work output of the working fluid with fixed initial energy, initial volume, final volume and total time allowed for the expansion. The method of exhaustion is applied to determine the optimal initial value of internal energy of the Euler-Lagrange arc. Numerical examples for the optimal configurations with time-dependent heat conductance are provided, and the obtained results are compared with those obtained with constant heat conductance. The results show that the optimal initial value of internal energy of the Euler-Lagrange arc, the time corresponding to the maximum optimal internal energy and the time spent on the compression process with time-dependent heat conductance are quite different from those obtained with constant heat conductance. In addition, the volume and internal energy along Euler-Lagrange arc obtained with time-dependent heat conductance are much sharper compared with those obtained with constant heat conductance.
    Print ISSN: 1748-1317
    Electronic ISSN: 1748-1325
    Topics: Energy, Environment Protection, Nuclear Power Engineering , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Published by Oxford University Press
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  • 9
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    The Impact of Rural Pensions in China on Labor Migration (2018)
    Oxford University Press
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    Publication Date: 2018-03-06
    Description: We study the impact of China’s new rural pension program on promoting migration of labor by applying a regression discontinuity analysis to this new pension program. The results reveal a perceptible difference in labor migration among adult children whose parents are just above and below the age of pension eligibility: The adult children with a parent just attaining the pension-eligible age are more likely to be labor migrants compared with those with a parent just below the pension-eligible age. We also find that with a pension-eligible parent, the adult children are more likely to have off-farm jobs. These abrupt changes in household behavior at the cutoff suggest that these households are credit constrained. In addition, we find that the pension’s effect on migration is greater among adult children with a parent in poor health; pension-eligible elderly report that they are more likely to use inpatient services when needed and less likely to rely on adult children for care when they are ill. These results suggest that (expectations regarding) providing care for elderly parents has constrained labor migration from China's rural areas to some extent, and that the new rural pension program has helped to relax this constraint.
    Print ISSN: 0258-6770
    Electronic ISSN: 1564-698X
    Topics: Economics
    Published by Oxford University Press
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  • 10
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    Hexagonal Phase Intergrown with the Tetragonal Weyl Semimetal TaAs (2017)
    American Chemical Society (ACS)
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    Publication Date: 2017-03-25
    Description: Crystal Growth & Design DOI: 10.1021/acs.cgd.6b01743
    Print ISSN: 1528-7483
    Electronic ISSN: 1528-7505
    Topics: Chemistry and Pharmacology , Geosciences , Physics
    Published by American Chemical Society (ACS)
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