Browsing by Author "Zhao, Jin"

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    BMI, leisure-time physical activity, and physical fitness in adults in China: results from a series of national surveys, 2000–14
    (Elsevier, 2016-06) Tian, Ye; Jiang, Chongmin; Wang, Mei; Cai, Rui; Zhang, Yanfeng; He, Zihong; Wang, Huan; Wu, Dongming; Wang, Fubaihui; Tang, Qiang; Yang, Yang; Zhao, Jin; Lv, Shaojun; Zhou, Weihai; Yu, Bo; Lan, Jiang; Yang, Xinping; Zhang, Linxia; Tian, Hui; Gu, Zhuangzhuang; Song, Yiqing; Huang, Tianyi; McNaughton, Lars R.; Department of Epidemiology, Richard M. Fairbanks School of Public Health
    Background Obesity, physical inactivity, and reduced physical fitness contribute to the rising burden of chronic diseases in China. We investigated these factors in Chinese adults over a 14-year period (2000–14) using data from randomised national surveys. Methods We did four national surveys in 2000, 2005, 2010, and 2014 among Chinese adults aged 20–59 years. We used BMI to assess underweight (<18·5 kg/m2), overweight (≥23·0 to <27·5 kg/m2), and obesity (≥27·5 kg/m2). Central obesity was defined as a waist circumference greater than 90 cm in men and greater than 85 cm in women. We assessed leisure-time physical activity (LTPA) by whether or not participants had completed the recommended minimum 150 min of moderate or 75 min of vigorous exercise per week. Indices for assessment of physical fitness were forced vital capacity, resting heart rate, hand grip strength, sit and reach distance, and time standing on one leg. Findings 151 656 (78%) of 193 440 adults responded to the survey in 2000, 163 386 (84%) in 2005, 154 931 (80%) in 2010, and 146 703 (76%) in 2014. The prevalence of obesity increased from 8·6% in 2000, to 10·3% in 2005, 12·2% in 2010, and 12·9% in 2014 (estimated increase 0·32% per year, 95% CI 0·30–0·33; p<0·0001). The equivalent estimates were 37·4%, 39·2%, 40·7%, and 41·2% for overweight (estimated increase 0·27% per year, 95% CI 0·25–0·30; p<0·0001) and 13·9%, 18·3%, 22·1%, and 24·9% for central obesity (estimated increase 0·78% per year, 0·76–0·80; p<0·0001). The prevalence of overweight, obesity, and central obesity increased with age (all p<0·0001) and was higher in men than in women (all p<0·0001). We noted a simultaneous decrease in the prevalence of underweight (estimated decrease of 0·06% per year, 95% CI 0·04–0·07; p<0·0001). The proportion of adults meeting the minimum LTPA recommendation increased over time (17·2% in 2000, 18·1% in 2005, and 22·8% in 2014), with the estimated prevalence change per year being 0·33% (95% CI 0·24–0·42; p<0·0001) for underweight people, 0·50% (0·47–0·53; p<0·0001) for normal-weight people, 0·37% (0·34–0·40; p<0·0001) for overweight people, and 0·06% (0·00–0·13; p=0·044) for obese people. We noted deteriorations over time in all measures of physical fitness in normal-weight adults (all p<0·0001), apart from resting heart rate (p=0·69). Interpretation Despite increased participation in LTPA, we noted increases in overweight or obesity and a decrease in physical fitness in Chinese adults. Continued nationwide interventions are needed to promote physical activity and other healthy lifestyle behaviours in China.
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    IsoTree: A New Framework for De novo Transcriptome Assembly from RNA-seq Reads
    (IEEE, 2018-02) Zhao, Jin; Feng, Haodi; Zhu, Daming; Zhang, Chi; Xu, Ying; Medical and Molecular Genetics, School of Medicine
    High-throughput sequencing of mRNA has made the deep and efficient probing of transcriptome more affordable. However, the vast amounts of short RNA-seq reads make de novo transcriptome assembly an algorithmic challenge. In this work, we present IsoTree, a novel framework for transcripts reconstruction in the absence of reference genomes. Unlike most of de novo assembly methods that build de Bruijn graph or splicing graph by connecting $k-mers$ which are sets of overlapping substrings generated from reads, IsoTree constructs splicing graph by connecting reads directly. For each splicing graph, IsoTree applies an iterative scheme of mixed integer linear program to build a prefix tree, called isoform tree. Each path from the root node of the isoform tree to a leaf node represents a plausible transcript candidate which will be pruned based on the information of paired-end reads. Experiments showed that in most cases IsoTree performs better than other leading transcriptome assembly programs. IsoTree is available at https://github.com/Jane110111107/IsoTree.