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1.  A Rank-Based Test for Comparison of Multidimensional Outcomes 
For comparison of multiple outcomes commonly encountered in biomedical research, Huang et al. (2005) improved O’Brien’s (1984) rank-sum tests through the replacement of the ad hoc variance by the asymptotic variance of the test statistics. The improved tests control the Type I error rate at the desired level and gain power when the differences between the two comparison groups in each outcome variable fall into the same direction. However, they may lose power when the differences are in different directions (e.g., some are positive and some are negative). These tests and the popular Bonferroni correction failed to show important significant difference when applied to compare heart rates from a clinical trial to evaluate the effect of a procedure to remove the cardioprotective solution HTK. We propose an alternative test statistic, taking the maximum of the individual rank-sum statistics, which controls the type I error and maintains satisfactory power regardless of the directions of the differences. Simulation studies show the proposed test to be of higher power than other tests in certain alternative parameter space of interest. Furthermore, when used to analyze the heart rates data the proposed test yields more satisfactory results.
PMCID: PMC3102319  PMID: 21625372
Autism spectrum disorder; Behrens-Fisher problem; Cardioprotective solution; Case-control studies; Growth hormones; Multiple outcomes; Non-parametrics; Rank-sum statistics
2.  A Weighted Rank-Sum Procedure for Comparing Samples with Multiple Endpoints 
Statistics and its interface  2009;2(2):197-201.
For comparing the distribution of two samples with multiple endpoints, O’Brien (1984) proposed rank-sum-type test statistics. Huang et al. (2005) extended these statistics to the general nonparametric Behrens-Fisher hypothesis problem and obtained improved test statistics by replacing the ad hoc variance with the asymptotic variance of the rank-sum statistics. In this paper we generalize the work of O’Brien (1984) and Huang et al. (2005) and propose a weighted rank-sum statistic. We show that the weighted rank-sum statistic is asymptotically normally distributed, permitting the computation of power, p-values and confidence intervals. We further demonstrate via simulation that the weighted rank-sum statistic is efficient in controlling the type I error rate and under certain alternatives, is more powerful than the statistics of O’Brien (1984) and Huang et al.(2005).
PMCID: PMC2759535  PMID: 19823699
Asymptotic normality; Behrens-Fisher problem; Case-Control; Clinical trials; Multiple endpoints; Rank-sum statistics; Weights
3.  Nutrition Concerns of Insufficient and Excessive Intake of Dietary Minerals in Lactating Women: A Cross-Sectional Survey in Three Cities of China 
PLoS ONE  2016;11(1):e0146483.
Objectives of this study were 1) to investigate the mineral intake by Chinese lactating women, 2) to explore the dietary source of minerals, and 3) the ratios between different dietary minerals.
A total of 468 lactating women in 5–240 days post-partum participated in this study. Food intakes by participants were measured using one time of 24-hour dietary recall, and minerals from food were calculated based on the Chinese Food Composition Table, second edition.
In post-partum, women had inadequate food intake. 81.0% of women’s daily intake of dairy products was lower than 300g, and 97.1% of women’s daily intake of salt over 6g. For mineral intake, there were 81.8%, 59.0%, 47.6%, 45.7% and 66.8% of women’s calcium, magnesium, iron, zinc and selenium intake lower than the estimated average requirement, respectively, and 91.7% of women’s excessive intake of sodium. The calcium/phosphorus and sodium/potassium ratios were 0.41±0.26/1 and 3.13±2.89/1, respectively. Considering the dietary sources of minerals, 27.3%, 25.3% and 30.1% of iron, zinc and calcium were from animal-based food, respectively, and 60.3%, 66.1% and 58.0% of iron, zinc and calcium were from plant-based food, respectively. The phosphorus-protein ratio was 0.014±0.003/1. Lactation stage was associated with nutrient intake. Women within 30 days post-partum and the ones who live in Guangzhou had a significantly lower intake of certain minerals, while women with a high education experience had a high intake of calcium, potassium, iron and zinc. Productive age, whether obese or not, and delivery ways were not associated with mineral intakes (P all >0.05).
Chinese women in three studied cities had an inappropriate food intake and resulted in both insufficient and excessive intakes of certain minerals.
PMCID: PMC4701389  PMID: 26730592
4.  Gastrointestinal Adverse Events of Glucagon-Like Peptide-1 Receptor Agonists in Patients with Type 2 Diabetes: A Systematic Review and Network Meta-Analysis 
Introduction: Glucagon-like peptide-1 receptor agonists (GLP-1 RAs) are a new class of drugs used in the treatment of type 2 diabetes mellitus (T2DM). Gastrointestinal (GI) adverse events (AEs) are the most frequently reported treatment-related AEs for GLP-1 RAs. We aim to evaluate the effect of GLP-1 RAs on the incidence of GI AEs of T2DM.
Materials and Methods: The overview of the GI events of GLP-1 RAs has been performed on relevant publications through the literature search, such as MEDLINE, EMBASE, Cochrane Library, and The manufacturer was contacted regarding unpublished data. We analyzed direct and indirect comparisons of different treatments using Bayesian network meta-analysis.
Results: Taspoglutide 30 mg once weekly (TAS30QW) and lixisenatide 30 μg twice daily (LIX30BID) were ranked the top two drugs in terms of GI AEs versus placebo. The odds ratios of nausea and vomiting for TAS30QW were 11.8 (95% confidence interval [CI], 2.89, 46.9) and 51.7 (95% CI, 7.07, 415), respectively, and that of diarrhea was 4.93 (95% CI, 1.75, 14.7) for LIX30BID.
Conclusions: Our study found all GLP-1 RA dose regimens significantly increased the incidence of GI AEs, compared with placebo or conventional treatment. The occurrence of GI AEs was different with diverse dose regimens of GLP-1 RAs. TAS30QW had the maximum probability to occur nausea and vomiting, whereas LIX30BID had the maximum probability to cause development of diarrhea versus other treatments.
PMCID: PMC4290796  PMID: 25375397
5.  A robust association test for detecting genetic variants with heterogeneous effects 
One common strategy for detecting disease-associated genetic markers is to compare the genotype distributions between cases and controls, where cases have been diagnosed as having the disease condition. In a study of a complex disease with a heterogeneous etiology, the sampled case group most likely consists of people having different disease subtypes. If we conduct an association test by treating all cases as a single group, we maximize our chance of finding genetic risk factors with a homogeneous effect, regardless of the underlying disease etiology. However, this strategy might diminish the power for detecting risk factors whose effect size varies by disease subtype. We propose a robust statistical procedure to identify genetic risk factors that have either a uniform effect for all disease subtypes or heterogeneous effects across different subtypes, in situations where the subtypes are not predefined but can be characterized roughly by a set of clinical and/or pathologic markers. We demonstrate the advantage of the new procedure through numeric simulation studies and an application to a breast cancer study.
PMCID: PMC4263227  PMID: 25057183
Breast cancer; Etiology heterogeneity; Genetic association study; Multiple-comparison adjustment; Tree-based model
6.  Increased Risk of Dementia Among Sleep-Related Movement Disorders 
Medicine  2015;94(51):e2331.
Sleep-related movement disorders (SRMD) are sleep disorders. As poor sleep quality is associated with cognitive impairment, we hypothesized that SRMD patients were exposed to a great risk for developing dementia.
The present study was aimed to retrospectively examine the association of SRMD and dementia risk.
A retrospective longitudinal study was conducted using the data obtained from the Longitudinal Health Insurance Database (LHID) in Taiwan. The study cohort enrolled 604 patients with SRMD who were initially diagnosed and 2416 patients who were randomly selected and age/gender matched with the study group. SRMD, dementia, and other confounding factors were defined according to International Classification of Diseases Clinical Modification Codes. Cox proportional-hazards regressions were employed to examine adjusted hazard ratios (HR) after adjusting with confounding factors.
Our data revealed that patients with SRMD had a 3.952 times (95% CI = 1.124–4.767) higher risk to develop all-cause dementia compared with individuals without SRMD. The results showed that SRMD patients aged 45 to 64 exhibited highest risk of developing all-cause dementia (HR: 5.320, 95% CI = 1.770–5.991), followed by patients age ≥65 (HR: 4.123, 95% CI = 2.066–6.972) and <45 (HR: 3.170, 95% CI = 1.050–4.128), respectively. Females with SRMD were at greater risk to develop all-cause dementia (HR: 4.372, 95% CI = 1.175–5.624). The impact of SRMD on dementia risk was progressively increased by various follow-up time intervals (<1 year, 1–2 years, and ≥2 years).
The results suggest that SRMD is linked to an increased risk for dementia with gender-dependent and time-dependent characteristics.
PMCID: PMC4697990  PMID: 26705224
7.  Imputation and subset-based association analysis across different cancer types identifies multiple independent risk loci in the TERT-CLPTM1L region on chromosome 5p15.33 
Wang, Zhaoming | Zhu, Bin | Zhang, Mingfeng | Parikh, Hemang | Jia, Jinping | Chung, Charles C. | Sampson, Joshua N. | Hoskins, Jason W. | Hutchinson, Amy | Burdette, Laurie | Ibrahim, Abdisamad | Hautman, Christopher | Raj, Preethi S. | Abnet, Christian C. | Adjei, Andrew A. | Ahlbom, Anders | Albanes, Demetrius | Allen, Naomi E. | Ambrosone, Christine B. | Aldrich, Melinda | Amiano, Pilar | Amos, Christopher | Andersson, Ulrika | Andriole, Gerald | Andrulis, Irene L. | Arici, Cecilia | Arslan, Alan A. | Austin, Melissa A. | Baris, Dalsu | Barkauskas, Donald A. | Bassig, Bryan A. | Beane Freeman, Laura E. | Berg, Christine D. | Berndt, Sonja I. | Bertazzi, Pier Alberto | Biritwum, Richard B. | Black, Amanda | Blot, William | Boeing, Heiner | Boffetta, Paolo | Bolton, Kelly | Boutron-Ruault, Marie-Christine | Bracci, Paige M. | Brennan, Paul | Brinton, Louise A. | Brotzman, Michelle | Bueno-de-Mesquita, H. Bas | Buring, Julie E. | Butler, Mary Ann | Cai, Qiuyin | Cancel-Tassin, Geraldine | Canzian, Federico | Cao, Guangwen | Caporaso, Neil E. | Carrato, Alfredo | Carreon, Tania | Carta, Angela | Chang, Gee-Chen | Chang, I-Shou | Chang-Claude, Jenny | Che, Xu | Chen, Chien-Jen | Chen, Chih-Yi | Chen, Chung-Hsing | Chen, Constance | Chen, Kuan-Yu | Chen, Yuh-Min | Chokkalingam, Anand P. | Chu, Lisa W. | Clavel-Chapelon, Francoise | Colditz, Graham A. | Colt, Joanne S. | Conti, David | Cook, Michael B. | Cortessis, Victoria K. | Crawford, E. David | Cussenot, Olivier | Davis, Faith G. | De Vivo, Immaculata | Deng, Xiang | Ding, Ti | Dinney, Colin P. | Di Stefano, Anna Luisa | Diver, W. Ryan | Duell, Eric J. | Elena, Joanne W. | Fan, Jin-Hu | Feigelson, Heather Spencer | Feychting, Maria | Figueroa, Jonine D. | Flanagan, Adrienne M. | Fraumeni, Joseph F. | Freedman, Neal D. | Fridley, Brooke L. | Fuchs, Charles S. | Gago-Dominguez, Manuela | Gallinger, Steven | Gao, Yu-Tang | Gapstur, Susan M. | Garcia-Closas, Montserrat | Garcia-Closas, Reina | Gastier-Foster, Julie M. | Gaziano, J. Michael | Gerhard, Daniela S. | Giffen, Carol A. | Giles, Graham G. | Gillanders, Elizabeth M. | Giovannucci, Edward L. | Goggins, Michael | Gokgoz, Nalan | Goldstein, Alisa M. | Gonzalez, Carlos | Gorlick, Richard | Greene, Mark H. | Gross, Myron | Grossman, H. Barton | Grubb, Robert | Gu, Jian | Guan, Peng | Haiman, Christopher A. | Hallmans, Goran | Hankinson, Susan E. | Harris, Curtis C. | Hartge, Patricia | Hattinger, Claudia | Hayes, Richard B. | He, Qincheng | Helman, Lee | Henderson, Brian E. | Henriksson, Roger | Hoffman-Bolton, Judith | Hohensee, Chancellor | Holly, Elizabeth A. | Hong, Yun-Chul | Hoover, Robert N. | Hosgood, H. Dean | Hsiao, Chin-Fu | Hsing, Ann W. | Hsiung, Chao Agnes | Hu, Nan | Hu, Wei | Hu, Zhibin | Huang, Ming-Shyan | Hunter, David J. | Inskip, Peter D. | Ito, Hidemi | Jacobs, Eric J. | Jacobs, Kevin B. | Jenab, Mazda | Ji, Bu-Tian | Johansen, Christoffer | Johansson, Mattias | Johnson, Alison | Kaaks, Rudolf | Kamat, Ashish M. | Kamineni, Aruna | Karagas, Margaret | Khanna, Chand | Khaw, Kay-Tee | Kim, Christopher | Kim, In-Sam | Kim, Jin Hee | Kim, Yeul Hong | Kim, Young-Chul | Kim, Young Tae | Kang, Chang Hyun | Jung, Yoo Jin | Kitahara, Cari M. | Klein, Alison P. | Klein, Robert | Kogevinas, Manolis | Koh, Woon-Puay | Kohno, Takashi | Kolonel, Laurence N. | Kooperberg, Charles | Kratz, Christian P. | Krogh, Vittorio | Kunitoh, Hideo | Kurtz, Robert C. | Kurucu, Nilgun | Lan, Qing | Lathrop, Mark | Lau, Ching C. | Lecanda, Fernando | Lee, Kyoung-Mu | Lee, Maxwell P. | Le Marchand, Loic | Lerner, Seth P. | Li, Donghui | Liao, Linda M. | Lim, Wei-Yen | Lin, Dongxin | Lin, Jie | Lindstrom, Sara | Linet, Martha S. | Lissowska, Jolanta | Liu, Jianjun | Ljungberg, Börje | Lloreta, Josep | Lu, Daru | Ma, Jing | Malats, Nuria | Mannisto, Satu | Marina, Neyssa | Mastrangelo, Giuseppe | Matsuo, Keitaro | McGlynn, Katherine A. | McKean-Cowdin, Roberta | McNeill, Lorna H. | McWilliams, Robert R. | Melin, Beatrice S. | Meltzer, Paul S. | Mensah, James E. | Miao, Xiaoping | Michaud, Dominique S. | Mondul, Alison M. | Moore, Lee E. | Muir, Kenneth | Niwa, Shelley | Olson, Sara H. | Orr, Nick | Panico, Salvatore | Park, Jae Yong | Patel, Alpa V. | Patino-Garcia, Ana | Pavanello, Sofia | Peeters, Petra H. M. | Peplonska, Beata | Peters, Ulrike | Petersen, Gloria M. | Picci, Piero | Pike, Malcolm C. | Porru, Stefano | Prescott, Jennifer | Pu, Xia | Purdue, Mark P. | Qiao, You-Lin | Rajaraman, Preetha | Riboli, Elio | Risch, Harvey A. | Rodabough, Rebecca J. | Rothman, Nathaniel | Ruder, Avima M. | Ryu, Jeong-Seon | Sanson, Marc | Schned, Alan | Schumacher, Fredrick R. | Schwartz, Ann G. | Schwartz, Kendra L. | Schwenn, Molly | Scotlandi, Katia | Seow, Adeline | Serra, Consol | Serra, Massimo | Sesso, Howard D. | Severi, Gianluca | Shen, Hongbing | Shen, Min | Shete, Sanjay | Shiraishi, Kouya | Shu, Xiao-Ou | Siddiq, Afshan | Sierrasesumaga, Luis | Sierri, Sabina | Loon Sihoe, Alan Dart | Silverman, Debra T. | Simon, Matthias | Southey, Melissa C. | Spector, Logan | Spitz, Margaret | Stampfer, Meir | Stattin, Par | Stern, Mariana C. | Stevens, Victoria L. | Stolzenberg-Solomon, Rachael Z. | Stram, Daniel O. | Strom, Sara S. | Su, Wu-Chou | Sund, Malin | Sung, Sook Whan | Swerdlow, Anthony | Tan, Wen | Tanaka, Hideo | Tang, Wei | Tang, Ze-Zhang | Tardon, Adonina | Tay, Evelyn | Taylor, Philip R. | Tettey, Yao | Thomas, David M. | Tirabosco, Roberto | Tjonneland, Anne | Tobias, Geoffrey S. | Toro, Jorge R. | Travis, Ruth C. | Trichopoulos, Dimitrios | Troisi, Rebecca | Truelove, Ann | Tsai, Ying-Huang | Tucker, Margaret A. | Tumino, Rosario | Van Den Berg, David | Van Den Eeden, Stephen K. | Vermeulen, Roel | Vineis, Paolo | Visvanathan, Kala | Vogel, Ulla | Wang, Chaoyu | Wang, Chengfeng | Wang, Junwen | Wang, Sophia S. | Weiderpass, Elisabete | Weinstein, Stephanie J. | Wentzensen, Nicolas | Wheeler, William | White, Emily | Wiencke, John K. | Wolk, Alicja | Wolpin, Brian M. | Wong, Maria Pik | Wrensch, Margaret | Wu, Chen | Wu, Tangchun | Wu, Xifeng | Wu, Yi-Long | Wunder, Jay S. | Xiang, Yong-Bing | Xu, Jun | Yang, Hannah P. | Yang, Pan-Chyr | Yatabe, Yasushi | Ye, Yuanqing | Yeboah, Edward D. | Yin, Zhihua | Ying, Chen | Yu, Chong-Jen | Yu, Kai | Yuan, Jian-Min | Zanetti, Krista A. | Zeleniuch-Jacquotte, Anne | Zheng, Wei | Zhou, Baosen | Mirabello, Lisa | Savage, Sharon A. | Kraft, Peter | Chanock, Stephen J. | Yeager, Meredith | Landi, Maria Terese | Shi, Jianxin | Chatterjee, Nilanjan | Amundadottir, Laufey T.
Human Molecular Genetics  2014;23(24):6616-6633.
Genome-wide association studies (GWAS) have mapped risk alleles for at least 10 distinct cancers to a small region of 63 000 bp on chromosome 5p15.33. This region harbors the TERT and CLPTM1L genes; the former encodes the catalytic subunit of telomerase reverse transcriptase and the latter may play a role in apoptosis. To investigate further the genetic architecture of common susceptibility alleles in this region, we conducted an agnostic subset-based meta-analysis (association analysis based on subsets) across six distinct cancers in 34 248 cases and 45 036 controls. Based on sequential conditional analysis, we identified as many as six independent risk loci marked by common single-nucleotide polymorphisms: five in the TERT gene (Region 1: rs7726159, P = 2.10 × 10−39; Region 3: rs2853677, P = 3.30 × 10−36 and PConditional = 2.36 × 10−8; Region 4: rs2736098, P = 3.87 × 10−12 and PConditional = 5.19 × 10−6, Region 5: rs13172201, P = 0.041 and PConditional = 2.04 × 10−6; and Region 6: rs10069690, P = 7.49 × 10−15 and PConditional = 5.35 × 10−7) and one in the neighboring CLPTM1L gene (Region 2: rs451360; P = 1.90 × 10−18 and PConditional = 7.06 × 10−16). Between three and five cancers mapped to each independent locus with both risk-enhancing and protective effects. Allele-specific effects on DNA methylation were seen for a subset of risk loci, indicating that methylation and subsequent effects on gene expression may contribute to the biology of risk variants on 5p15.33. Our results provide strong support for extensive pleiotropy across this region of 5p15.33, to an extent not previously observed in other cancer susceptibility loci.
PMCID: PMC4240198  PMID: 25027329
8.  Two Susceptibility Loci Identified for Prostate Cancer Aggressiveness 
Nature communications  2015;6:6889.
Most men diagnosed with prostate cancer will experience indolent disease; hence discovering genetic variants that distinguish aggressive from non-aggressive prostate cancer is of critical clinical importance for disease prevention and treatment. In a multistage, case-only genome-wide association study of 12,518 prostate cancer cases, we identify two loci associated with Gleason score, a pathological measure of disease aggressiveness: rs35148638 at 5q14.3 (RASA1, P=6.49×10-9) and rs78943174 at 3q26.31 (NAALADL2, P=4.18×10-8). In a stratified case-control analysis, the SNP at 5q14.3 appears specific for aggressive prostate cancer (P=8.85×10-5) with no association for non-aggressive prostate cancer compared to controls (P=0.57). The proximity of these loci to genes involved in vascular disease suggests potential biological mechanisms worthy of further investigation.
PMCID: PMC4422072  PMID: 25939597
9.  Sex steroid hormone metabolism in relation to risk of aggressive prostate cancer 
The combined action of androgens and estrogens—specifically their balance—may play a role in prostate carcinogenesis but existing evidence is sparse and inconsistent. We investigated associations between serum sex steroid hormones, including estrogen metabolites, and risk of aggressive prostate cancer.
In a case-control study nested within the Prostate, Lung, Colorectal and Ovarian Cancer Screening Trial cohort we measured serum estrone, estradiol and 13 estrogen metabolites, in the 2-, 4, or 16-hydroxylation pathways, using a liquid chromatography-tandem mass spectrometry assay. Cases (n=195) were non-Hispanic white men aged 55–70 years when diagnosed with aggressive prostate cancer (stage III or IV and/or Gleason ≥7). Controls (n=195) were non-Hispanic white men without prostate cancer who were frequency-matched to cases by age and year at blood draw, time since baseline screen. Only men with serum testosterone and sex hormone-binding globulin measured previously were eligible. Logistic regression models were used to estimate odds ratios (OR) and 95% confidence intervals (95%CI).
Risk of aggressive prostate cancer was strongly inversely associated with estradiol:testosterone ratio (OR4th quartile vs. 1st =0.27, 95% CI 0.12–0.59, p trend=0.003) and positively associated with 2:16α-hydroxyestrone ratio (OR4th quartile vs. 1st =2.44, 95% CI 1.34–4.45, p trend=0.001). Estradiol, estrone and estrogen metabolites were unrelated to risk.
Our findings suggest that sex steroid hormones, specifically the estrogen-androgen balance, may be important in the development of aggressive prostate cancer.
Improved understanding of the hormonal etiology of prostate cancer is critical for prevention and therapeutic interventions.
PMCID: PMC4221438  PMID: 25178985
Prostate Cancer; Sex Steroid Hormones; Estrogen to Testosterone Ratio
10.  Ovarian granulocytic sarcoma as the primary manifestation of acute myelogenous leukemia 
Granulocytic sarcoma (GS) usually occurs concomitantly with or after the onset of acute myeloid leukemia (AML) or other myeloproliferative disorders, however, GS of the ovary as the primary manifestation of AML is exceedingly rare. To the best of our knowledge, eight cases of ovarian GS as the first sign of AML have been reported in the literature. Here, we report the ninth case: a 27-year-old female who presented with an ovarian mass without any underlying hematologic disorder. A high index of suspicion aided by immunohistochemistry established the correct diagnosis of undifferentiated GS that involved the ovary. Simultaneously, laboratory findings indicated that the blood counts continually increased after surgery. Five days after the surgery, bone marrow biopsy confirmed the presence of AML. After establishing the diagnosis, the patient was sent to the hematology department to receive cytosine arabinoside and idarubicin chemotherapy. This report outlines an exceedingly rare case of AML that initially manifested as an ovarian GS. Awareness of this entity will enable earlier diagnosis and appropriate treatment.
PMCID: PMC4680517  PMID: 26722572
Ovary neoplasm; granulocytic sarcoma; chloroma; acute myelogenous leukemia
11.  A population-based study on health-related quality of life among urban community residents in Shenyang, Northeast of China 
BMC Public Health  2015;15:921.
Due to the rising standard of living environment and advances in public health and medical care in China, it has been a tendency in recent years that health-related quality of life (HRQoL) has been increasingly acknowledged in community health management. However, large-scale population-based study on evaluating HQRoL in northeast of China was not conducted. This article aims to investigate the HRQoL in community residents in Northeast China and explore the associated factors.
Stratified multiple-stage sampling method was used in the cross-sectional survey to investigate HRQoL of community residents in northeast of China. Univariate analysis and multiple linear regressions were used to analyze the factors associated to HRQoL of the community residents.
The results were confirmed that HRQoL in general population was well performed for the first time in northeast of China in a large scale population. Community residents had better mental health than physical health. The factors influencing HRQoL included gender, age, educational level, marital status, ethnic group, chronic disease status, having breakfast frequency weekly and sleep quality. However, drinking and smoking habits did not affect residents’ HRQoL.
In this study, the result of the large-scale survey was satisfactory in northeast of China, providing HRQoL status of community residents. Policies on specific health management in community public health would emphasize on lifestyle behaviors especially eating habits in order to improving HRQoL.
PMCID: PMC4575423  PMID: 26386951
12.  Plant Functional Diversity Can Be Independent of Species Diversity: Observations Based on the Impact of 4-Yrs of Nitrogen and Phosphorus Additions in an Alpine Meadow 
PLoS ONE  2015;10(8):e0136040.
Past studies have widely documented the decrease in species diversity in response to addition of nutrients, however functional diversity is often independent from species diversity. In this study, we conducted a field experiment to examine the effect of nitrogen and phosphorus fertilization ((NH4)2 HPO4) at 0, 15, 30 and 60 g m-2 yr-1 (F0, F15, F30 and F60) after 4 years of continuous fertilization on functional diversity and species diversity, and its relationship with productivity in an alpine meadow community on the Tibetan Plateau. To this purpose, three community-weighted mean trait values (specific leaf area, SLA; mature plant height, MPH; and seed size, SS) for 30 common species in each fertilization level were determined; three components of functional diversity (functional richness, FRic; functional evenness, FEve; and Rao’s index of quadratic entropy, FRao) were quantified. Our results showed that: (i) species diversity sharply decreased, but functional diversity remained stable with fertilization; (ii) community-weighted mean traits (SLA and MPH) had a significant increase along the fertilization level; (iii) aboveground biomass was not correlated with functional diversity, but it was significantly correlated with species diversity and MPH. Our results suggest that decreases in species diversity due to fertilization do not result in corresponding changes in functional diversity. Functional identity of species may be more important than functional diversity in influencing aboveground productivity in this alpine meadow community, and our results also support the mass ratio hypothesis; that is, the traits of the dominant species influenced the community biomass production.
PMCID: PMC4546594  PMID: 26295345
13.  Niche and Neutral Processes Together Determine Diversity Loss in Response to Fertilization in an Alpine Meadow Community 
PLoS ONE  2015;10(8):e0134560.
Fertilization via nutrient deposition and agricultural inputs is one of the most important factors driving decreases in plant diversity. However, we still do not fully understand which processes (niche process or neutral process) are more important in leading to decreases in plant diversity caused by fertilization. A hypothesis-based approach was used to test the relative importance of niche versus neutral processes along a fertilization gradient in an alpine meadow community on the eastern Tibetan plateau, China. Niche overlap values were calculated for species biomass, and the null model was used to generate the values of niche overlap expected at random. A linear regression modeling was used to evaluate the relationship between functional traits (specific leaf area, leaf dry matter content, and leaf total nitrogen concentration) and species relative abundance. Our results demonstrated that observed niche overlap for species biomass was significantly higher than expected at lower fertilization gradients. Moreover, we also found a significantly negative correlation between species relative abundance and specific leaf area and leaf dry matter content, but a significantly positive correlation between relative abundance and leaf nitrogen concentration at lower fertilization gradients. However, these relationships were not significant at higher fertilization gradients. We concluded that community assembly is dynamic progression along the environmental gradients, and niche and neutral processes may together determine species diversity loss in response to fertilization.
PMCID: PMC4539233  PMID: 26280919
14.  A fast and powerful tree-based association test for detecting complex joint effects in case–control studies 
Bioinformatics  2014;30(15):2171-2178.
Motivation: Multivariate tests derived from the logistic regression model are widely used to assess the joint effect of multiple predictors on a disease outcome in case–control studies. These tests become less optimal if the joint effect cannot be approximated adequately by the additive model. The tree-structure model is an attractive alternative, as it is more apt to capture non-additive effects. However, the tree model is used most commonly for prediction and seldom for hypothesis testing, mainly because of the computational burden associated with the resampling-based procedure required for estimating the significance level.
Results: We designed a fast algorithm for building the tree-structure model and proposed a robust TREe-based Association Test (TREAT) that incorporates an adaptive model selection procedure to identify the optimal tree model representing the joint effect. We applied TREAT as a multilocus association test on >20 000 genes/regions in a study of esophageal squamous cell carcinoma (ESCC) and detected a highly significant novel association between the gene CDKN2B and ESCC (). We also demonstrated, through simulation studies, the power advantage of TREAT over other commonly used tests.
Availability and implementation: The package TREAT is freely available for download at, implemented in C++ and R and supported on 64-bit Linux and 64-bit MS Windows.
Supplementary information: Supplementary data are available at Bioinformatics online.
PMCID: PMC4103596  PMID: 24794927
15.  Efficient Sparse Signal Transmission over a Lossy Link Using Compressive Sensing 
Sensors (Basel, Switzerland)  2015;15(8):19880-19911.
Reliable data transmission over lossy communication link is expensive due to overheads for error protection. For signals that have inherent sparse structures, compressive sensing (CS) is applied to facilitate efficient sparse signal transmissions over lossy communication links without data compression or error protection. The natural packet loss in the lossy link is modeled as a random sampling process of the transmitted data, and the original signal will be reconstructed from the lossy transmission results using the CS-based reconstruction method at the receiving end. The impacts of packet lengths on transmission efficiency under different channel conditions have been discussed, and interleaving is incorporated to mitigate the impact of burst data loss. Extensive simulations and experiments have been conducted and compared to the traditional automatic repeat request (ARQ) interpolation technique, and very favorable results have been observed in terms of both accuracy of the reconstructed signals and the transmission energy consumption. Furthermore, the packet length effect provides useful insights for using compressed sensing for efficient sparse signal transmission via lossy links.
PMCID: PMC4570401  PMID: 26287195
lossy wireless link; compressive sensing; sparse signal transmission; packet length control
16.  Active suppression of intestinal CD4+TCRαβ+ T-lymphocyte maturation during the postnatal period 
Nature Communications  2015;6:7725.
Priming of the mucosal immune system during the postnatal period substantially influences host–microbial interaction and susceptibility to immune-mediated diseases in adult life. The underlying mechanisms are ill defined. Here we show that shortly after birth, CD4 T cells populate preformed lymphoid structures in the small intestine and quickly acquire a distinct transcriptional profile. T-cell recruitment is independent of microbial colonization and innate or adaptive immune stimulation but requires β7 integrin expression. Surprisingly, neonatal CD4 T cells remain immature throughout the postnatal period under homeostatic conditions but undergo maturation and gain effector function on barrier disruption. Maternal SIgA and regulatory T cells act in concert to prevent immune stimulation and maintain the immature phenotype of CD4 T cells in the postnatal intestine during homeostasis. Active suppression of CD4 T-cell maturation during the postnatal period might contribute to prevent auto-reactivity, sustain a broad TCR repertoire and establish life-long immune homeostasis.
The mechanisms governing the ontogeny and maturation of the mucosal immune system during the postnatal period are not well understood. Here the authors characterize the homing kinetic, anatomical distribution and maturation of early intestinal CD4 T cells and provide insights into active T-cell suppression during the postnatal period.
PMCID: PMC4518322  PMID: 26195040
17.  Cutting improves the productivity of lucerne-rich stands used in the revegetation of degraded arable land in a semi-arid environment 
Scientific Reports  2015;5:12130.
Understanding the relationships between vegetative and environmental variables is important for revegetation and ecosystem management on the Loess Plateau, China. Lucerne (Medicago sativa L.) has been widely used in the region to improve revegetation, soil and water conservation, and to enhance livestock production. However, there is little information on how environmental factors influence long-term succession in lucerne-rich vegetation. Our objective was to identify the main environmental variables controlling the succession process in lucerne-rich vegetation such that native species are not suppressed after sowing on the Loess Plateau. Vegetation and soil surveys were performed in 31 lucerne fields (three lucerne fields without any management from 2003–2013 and 28 fields containing 11-year-old lucerne with one cutting each year). Time after planting was the most important factor affecting plant species succession. Cutting significantly affected revegetation characteristics, such as aboveground biomass, plant density and diversity. Soil moisture content, soil organic carbon, soil available phosphorus and slope aspect were key environmental factors affecting plant species composition and aboveground biomass, density and diversity. Long-term cutting can cause self-thinning in lucerne, maintain the stability of lucerne production and slow its degradation. For effective management of lucerne fields, phosphate fertilizer should be applied and cutting performed.
PMCID: PMC4499809  PMID: 26166449
18.  ErbB4 regulation of a thalamic reticular nucleus circuit for sensory selection 
Nature neuroscience  2014;18(1):104-111.
Selective processing of behaviorally relevant sensory inputs against irrelevant ones is a fundamental cognitive function, impairments of which have been implicated in major psychiatric disorders. It is known that the thalamic reticular nucleus (TRN) gates sensory information en route to the cortex, however the underlying mechanisms remain unclear. Here we show in mice that deficiency of Erbb4 gene in somatostatin-expressing TRN neurons markedly altered behaviors dependent on sensory selection. Whereas performance in identifying targets from distractors was improved, the ability to switch attention between conflicting sensory cues was impaired. These behavioral changes were mediated by enhanced cortical drive onto TRN that promotes the TRN-mediated cortical feedback inhibition of thalamic neurons. Our results uncover a previously unknown role of ErbB4 in regulating cortico-TRN-thalamic circuit function. We propose that ErbB4 sets the sensitivity of TRN to cortical inputs at levels that can support sensory selection while allowing behavioral flexibility.
PMCID: PMC4281280  PMID: 25501036
19.  Characterization of SMAD3 Gene Variants for Possible Roles in Ventricular Septal Defects and Other Congenital Heart Diseases 
PLoS ONE  2015;10(6):e0131542.
Nodal/TGF signaling pathway has an important effect at early stages of differentiation of human embryonic stem cells in directing them to develop into different embryonic lineages. SMAD3 is a key intracellular messenger regulating factor in the Nodal/TGF signaling pathway, playing important roles in embryonic and, particularly, cardiovascular system development. The aim of this work was to find evidence on whether SMAD3 variations might be associated with ventricular septal defects (VSD) or other congenital heart diseases (CHD).
We sequenced the SMAD3 gene for 372 Chinese Han CHD patients including 176 VSD patients and evaluated SNP rs2289263, which is located before the 5’UTR sequence of the gene. The statistical analyses were conducted using Chi-Square Tests as implemented in SPSS (version 13.0). The Hardy-Weinberg equilibrium test of the population was carried out using the online software OEGE.
Three heterozygous variants in SMAD3 gene, rs2289263, rs35874463 and rs17228212, were identified. Statistical analyses showed that the rs2289263 variant located before the 5’UTR sequence of SMAD3 gene was associated with the risk of VSD (P value=0.013 <0.05).
The SNP rs2289263 in the SMAD3 gene is associated with VSD in Chinese Han populations.
PMCID: PMC4482402  PMID: 26110764
21.  Variants Associated with Susceptibility to Pancreatic Cancer and Melanoma Do Not Reciprocally Affect Risk 
Melanoma cases may exist in pancreatic cancer kindreds, while there is increased risk of pancreatic cancer in familial melanoma. The two cancers may share genetic susceptibility variants in common.
Three dbGaP-deposited GWAS datasets (MD Anderson melanoma, PanScan 1, and PanScan 2 for pancreatic cancer) were used. Thirty-seven melanoma susceptibility variants in 22 genomic regions from published GWAS, plus melanoma-related genes and pathways were examined for pancreatic cancer risk in the PanScan datasets. Conversely, nine known pancreatic cancer susceptibility variants were examined for melanoma risk in the MD Anderson dataset.
In the PanScan data, initial associations were found with melanoma susceptibility variants in NCOA6 (rs4911442) (OR=1.32, 95% CI 1.03–1.70, p=0.03), YWHAZP5 (rs17119461) (OR=2.62, 95% CI 1.08–6.35, p=0.03), and YWHAZP5 (rs17119490) (OR=2.62, 95% CI 1.08–6.34, p=0.03), TYRP1 (p=0.04), and IFNA13 (p=0.04). In the melanoma dataset, two pancreatic cancer susceptibility variants were associated: NR5A2 (rs12029406) (OR=1.39, 95% CI 1.01–1.92, p=0.04) and CLPTM1L-TERT (rs401681) (OR=1.16, 95% CI 1.01–1.34, p=0.04). None of these associations remained significant after correcting for multiple comparisons.
Reported variants of melanoma genes and pathways do not play a role in pancreatic cancer predisposition. Reciprocally, pancreatic cancer susceptibility variants are not associated with melanoma risk.
Known melanoma-related genes and pathways, as well as GWAS-derived susceptibility variants of melanoma and pancreatic cancer, do not explain the shared genetic etiology of these two cancers.
PMCID: PMC4120837  PMID: 24642353
Shared etiology; pancreatic cancer; melanoma; association analysis
22.  Sequential blood purification therapy for critical patients with hyperlipidemic severe acute pancreatitis 
AIM: To evaluate the efficacy of sequential blood purification therapy in the treatment of critical patients with hyperlipidemic severe acute pancreatitis.
METHODS: Thirty-one intensive care unit (ICU) patients with hyperlipidemic severe acute pancreatitis treated at the Second Affiliated Hospital of Harbin Medical University were divided into either a study group (n = 15; July 1, 2012 to June 30, 2014) or a control group (n = 16; July 1, 2010 to June 30, 2012) based on the implementation of sequential blood purification therapy. The control group received continuous venous-venous hemofiltration (CVVH) on the basis of conventional treatments, and the therapeutic dose of CVVH was 30 mL/kg per hour. The study group received sequential plasma exchange and CVVH on the basis of conventional treatments. The anticoagulation regimen of CVVH is the regional citrate anticoagulation. Mortality rate on day 28, rates of systemic and local complications, duration of ICU, and time to target serum lipid level, as well as physiologic and laboratory indices were compared between the two groups.
RESULTS: The mortality rate on day 28 was significantly lower in the study group than in the control group (13.33% vs 37.50%; P < 0.05). The duration of ICU stay was significantly shorter in the study group than in the control group (7.4 ± 1.35 d vs 9.19 ± 2.99 d, P < 0.05). The time to target serum lipid level was significantly shorter in the study group than in the control group (3.47 ± 0.52 d vs 7.90 ± 1.14 d, P < 0.01). There were no significant differences in the rates of systemic complications and local complications between the two groups (60% vs 50% and 80% vs 81%, respectively). In the comparisons of physiologic and laboratory indices, serum albumin and C-reactive protein were significantly better in the study group than in the control group after treatment (37.8 ± 4.6 g/L vs 38.9 ± 5.7 g/L, and 20.5 ± 6.4 mg/L vs 28.5 ± 7.1 mg/L, respectively, both P < 0.05). With the exception of plateletcrit, no other indices showed significant differences between the two groups.
CONCLUSION: Sequential blood purification therapy is effective in the treatment of ICU patients with hyperlipidemic severe acute pancreatitis and can improve patient prognosis.
PMCID: PMC4445108  PMID: 26034366
Continuous venous-venous hemofiltration; Hyperlipidemic severe acute pancreatitis; Sequential blood purification; Plasma exchange
23.  A genome-wide association study of prostate cancer in West African men 
Human genetics  2013;133(5):509-521.
Age-adjusted mortality rates for prostate cancer are higher for African American men compared with those of European ancestry. Recent data suggest that West African men also have elevated risk for prostate cancer relative to European men. Genetic susceptibility to prostate cancer could account for part of this difference.
We conducted a genome-wide association study (GWAS) of prostate cancer in West African men in the Ghana Prostate Study. Association testing was performed using multivariable logistic regression adjusted for age and genetic ancestry for 474 prostate cancer cases and 458 population-based controls on the Illumina HumanOmni-5 Quad BeadChip.
The most promising association was at 10p14 within an intron of a long non-coding RNA (lncRNA RP11-543F8.2) 360 kb centromeric of GATA3 (p=1.29E−7). In sub-analyses, SNPs at 5q31.3 were associated with high Gleason score (≥7) cancers, the strongest of which was a missense SNP in PCDHA1 (rs34575154, p=3.66E−8), and SNPs at Xq28 (rs985081, p=8.66E−9) and 6q21 (rs2185710, p=5.95E−8) were associated with low Gleason score (<7) cancers. We sought to validate our findings in silico in the African Ancestry Prostate Cancer GWAS Consortium, but only one SNP, at 10p14, replicated at p<0.05. Of the 90 prostate cancer loci reported from studies of men of European, Asian or African American ancestry, we were able to test 81 in the Ghana Prostate Study, and 10 of these replicated at p<0.05.
Further genetic studies of prostate cancer in West African men are needed to confirm our promising susceptibility loci.
PMCID: PMC3988225  PMID: 24185611
prostate cancer; Africa; GWAS; case-control
24.  A fast multilocus test with adaptive SNP selection for large-scale genetic-association studies 
As increasing evidence suggests that multiple correlated genetic variants could jointly influence the outcome, a multilocus test that aggregates association evidence across multiple genetic markers in a considered gene or a genomic region may be more powerful than a single-marker test for detecting susceptibility loci. We propose a multilocus test, AdaJoint, which adopts a variable selection procedure to identify a subset of genetic markers that jointly show the strongest association signal, and defines the test statistic based on the selected genetic markers. The P-value from the AdaJoint test is evaluated by a computationally efficient algorithm that effectively adjusts for multiple-comparison, and is hundreds of times faster than the standard permutation method. Simulation studies demonstrate that AdaJoint has the most robust performance among several commonly used multilocus tests. We perform multilocus analysis of over 26 000 genes/regions on two genome-wide association studies of pancreatic cancer. Compared with its competitors, AdaJoint identifies a much stronger association between the gene CLPTM1L and pancreatic cancer risk (6.0 × 10−8), with the signal optimally captured by two correlated single-nucleotide polymorphisms (SNPs). Finally, we show AdaJoint as a powerful tool for mapping cis-regulating methylation quantitative trait loci on normal breast tissues, and find many CpG sites whose methylation levels are jointly regulated by multiple SNPs nearby.
PMCID: PMC3992564  PMID: 24022295
genome-wide association study; cis-regulating meQTLs mapping; multilocus test; variable selection; multiple comparisons; pathway analysis
25.  A meta-analysis of 87,040 individuals identifies 23 new susceptibility loci for prostate cancer 
Al Olama, Ali Amin | Kote-Jarai, Zsofia | Berndt, Sonja I. | Conti, David V. | Schumacher, Fredrick | Han, Ying | Benlloch, Sara | Hazelett, Dennis J. | Wang, Zhaoming | Saunders, Ed | Leongamornlert, Daniel | Lindstrom, Sara | Jugurnauth-Little, Sara | Dadaev, Tokhir | Tymrakiewicz, Malgorzata | Stram, Daniel O. | Rand, Kristin | Wan, Peggy | Stram, Alex | Sheng, Xin | Pooler, Loreall C. | Park, Karen | Xia, Lucy | Tyrer, Jonathan | Kolonel, Laurence N. | Le Marchand, Loic | Hoover, Robert N. | Machiela, Mitchell J. | Yeager, Merideth | Burdette, Laurie | Chung, Charles C. | Hutchinson, Amy | Yu, Kai | Goh, Chee | Ahmed, Mahbubl | Govindasami, Koveela | Guy, Michelle | Tammela, Teuvo L.J. | Auvinen, Anssi | Wahlfors, Tiina | Schleutker, Johanna | Visakorpi, Tapio | Leinonen, Katri A. | Xu, Jianfeng | Aly, Markus | Donovan, Jenny | Travis, Ruth C. | Key, Tim J. | Siddiq, Afshan | Canzian, Federico | Khaw, Kay-Tee | Takahashi, Atsushi | Kubo, Michiaki | Pharoah, Paul | Pashayan, Nora | Weischer, Maren | Nordestgaard, Borge G. | Nielsen, Sune F. | Klarskov, Peter | Røder, Martin Andreas | Iversen, Peter | Thibodeau, Stephen N. | McDonnell, Shannon K | Schaid, Daniel J | Stanford, Janet L. | Kolb, Suzanne | Holt, Sarah | Knudsen, Beatrice | Coll, Antonio Hurtado | Gapstur, Susan M. | Diver, W. Ryan | Stevens, Victoria L. | Maier, Christiane | Luedeke, Manuel | Herkommer, Kathleen | Rinckleb, Antje E. | Strom, Sara S. | Pettaway, Curtis | Yeboah, Edward D. | Tettey, Yao | Biritwum, Richard B. | Adjei, Andrew A. | Tay, Evelyn | Truelove, Ann | Niwa, Shelley | Chokkalingam, Anand P. | Cannon-Albright, Lisa | Cybulski, Cezary | Wokołorczyk, Dominika | Kluźniak, Wojciech | Park, Jong | Sellers, Thomas | Lin, Hui-Yi | Isaacs, William B. | Partin, Alan W. | Brenner, Hermann | Dieffenbach, Aida Karina | Stegmaier, Christa | Chen, Constance | Giovannucci, Edward L. | Ma, Jing | Stampfer, Meir | Penney, Kathryn L. | Mucci, Lorelei | John, Esther M. | Ingles, Sue A. | Kittles, Rick A. | Murphy, Adam B. | Pandha, Hardev | Michael, Agnieszka | Kierzek, Andrzej M. | Blot, William | Signorello, Lisa B. | Zheng, Wei | Albanes, Demetrius | Virtamo, Jarmo | Weinstein, Stephanie | Nemesure, Barbara | Carpten, John | Leske, Cristina | Wu, Suh-Yuh | Hennis, Anselm | Kibel, Adam S. | Rybicki, Benjamin A. | Neslund-Dudas, Christine | Hsing, Ann W. | Chu, Lisa | Goodman, Phyllis J. | Klein, Eric A | Zheng, S. Lilly | Batra, Jyotsna | Clements, Judith | Spurdle, Amanda | Teixeira, Manuel R. | Paulo, Paula | Maia, Sofia | Slavov, Chavdar | Kaneva, Radka | Mitev, Vanio | Witte, John S. | Casey, Graham | Gillanders, Elizabeth M. | Seminara, Daniella | Riboli, Elio | Hamdy, Freddie C. | Coetzee, Gerhard A. | Li, Qiyuan | Freedman, Matthew L. | Hunter, David J. | Muir, Kenneth | Gronberg, Henrik | Neal, David E. | Southey, Melissa | Giles, Graham G. | Severi, Gianluca | Cook, Michael B. | Nakagawa, Hidewaki | Wiklund, Fredrik | Kraft, Peter | Chanock, Stephen J. | Henderson, Brian E. | Easton, Douglas F. | Eeles, Rosalind A. | Haiman, Christopher A.
Nature genetics  2014;46(10):1103-1109.
Genome-wide association studies (GWAS) have identified 76 variants associated with prostate cancer risk predominantly in populations of European ancestry. To identify additional susceptibility loci for this common cancer, we conducted a meta-analysis of >10 million SNPs in 43,303prostate cancer cases and 43,737 controls from studies in populations of European, African, Japanese and Latino ancestry. Twenty-three novel susceptibility loci were revealed at P<5×10-8; 15 variants were identified among men of European ancestry, 7 from multiethnic analyses and one was associated with early-onset prostate cancer. These 23 variants, in combination with the known prostate cancer risk variants, explain 33% of the familial risk of the disease in European ancestry populations. These findings provide new regions for investigation into the pathogenesis of prostate cancer and demonstrate the utility of combining ancestrally diverse populations to discover risk loci for disease.
PMCID: PMC4383163  PMID: 25217961

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