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Search Results: 1 - 10 of 36539 matches for " Yen-Feng Chiu "
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A Novel Support Vector Machine-Based Approach for Rare Variant Detection
Yao-Hwei Fang, Yen-Feng Chiu
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0071114
Abstract: Advances in next-generation sequencing technologies have enabled the identification of multiple rare single nucleotide polymorphisms involved in diseases or traits. Several strategies for identifying rare variants that contribute to disease susceptibility have recently been proposed. An important feature of many of these statistical methods is the pooling or collapsing of multiple rare single nucleotide variants to achieve a reasonably high frequency and effect. However, if the pooled rare variants are associated with the trait in different directions, then the pooling may weaken the signal, thereby reducing its statistical power. In the present paper, we propose a backward support vector machine (BSVM)-based variant selection procedure to identify informative disease-associated rare variants. In the selection procedure, the rare variants are weighted and collapsed according to their positive or negative associations with the disease, which may be associated with common variants and rare variants with protective, deleterious, or neutral effects. This nonparametric variant selection procedure is able to account for confounding factors and can also be adopted in other regression frameworks. The results of a simulation study and a data example show that the proposed BSVM approach is more powerful than four other approaches under the considered scenarios, while maintaining valid type I errors.
Incorporation of covariates in simultaneous localization of two linked loci using affected relative pairs
Yen-Feng Chiu, Jeng-Min Chiou, Kung-Yee Liang, Chun-Yi Lee
BMC Genetics , 2010, DOI: 10.1186/1471-2156-11-67
Abstract: We showed that the efficiency was enhanced by incorporating a quantitative covariate parametrically or non-parametrically while localizing two disease loci using ARPs. In addition to its help in identifying factors associated with the disease and in improving the efficiency in estimating disease loci, this extension also allows investigators to account for heterogeneity in risk-ratios for different ARPs. Data released from the collaborative study on the genetics of alcoholism (COGA) for Genetic Analysis Workshop 14 (GAW 14) were used to illustrate the application of this extended method.The simulation studies and example illustrated that the efficiency in estimating disease loci was demonstratively enhanced by incorporating a quantitative covariate and by using all relative pairs while mapping two linked loci simultaneously.With the advance of genotyping techniques, genome-wide association analysis has become the mainstream technique in genetic mapping. However, studies have shown that using information from linkage scans can improve the power of association mapping in genome scans [1]. In addition, linkage analysis could be more powerful than association analysis for some genetic mechanisms; family data can also help to estimate familial risks [2]. Hence, linkage analysis remains a useful and supplemental tool to map genes for complex diseases. As complex diseases often involve quantitative biomarkers or environmental factors, incorporating these quantitative factors into linkage mapping can improve the power to detect disease loci [3] or the efficiency of estimating disease loci. Efficiency is defined as the inverse of the variance estimate for the disease locus estimate. Thus, smaller variance estimates have higher efficiencies. Moreover, the incorporation of covariates provides information that can be used to characterize disease loci, which is important for understanding disease etiologies and mechanisms and for identifying population subgroups that may have pa
Common ALDH2 genetic variants predict development of hypertension in the SAPPHIRe prospective cohort: Gene-environmental interaction with alcohol consumption
Chang Yi-Cheng,Chiu Yen-Feng,Lee I-Te,Ho Low-Tone
BMC Cardiovascular Disorders , 2012, DOI: 10.1186/1471-2261-12-58
Abstract: Background Genetic variants near/within the ALDH2 gene encoding the mitochondrial aldehyde dehydrogenase 2 have been associated with blood pressure and hypertension in several case–control association studies in East Asian populations. Methods Three common tag single nucleotide polymorphisms (tagSNP) in the ALDH2 gene were genotyped in 1,134 subjects of Chinese origin from the Stanford Asia-Pacific Program for Hypertension and Insulin Resistance (SAPPHIRe) family cohort. We examined whether the ALDH2 SNP genotypes predicted the development of hypertension in the prospective SAPPHIRe cohort. Results Over an average follow-up period of 5.7 years, carriers homozygous for the rs2238152 T allele in the ALDH2 gene were more likely to progress to hypertension than were non-carriers (hazard ratio [HR], 2.88, 95% confidence interval [CI], 1.06-7.84, P = 0.03), corresponding to a population attributable risk of ~7.1%. The risk associated with the rs2238152 T allele were strongest in heavy/moderate alcohol drinkers and was reduced in non-drinkers, indicating an interaction between ALDH2 genetic variants and alcohol intake on the risk of hypertension (P for interaction = 0.04). The risk allele was associated with significantly lower ALDH2 gene expression levels in human adipose tissue. Conclusion ALDH2 genetic variants were associated with progression to hypertension in a prospective Chinese cohort. The association was modified by alcohol consumption.
Bronchiolitis Obliterans Organizing Pneumonia in Swine Associated with Porcine Circovirus Type 2 Infection
Ching-Chang Cheng,Yen-Feng Lee,Nai-Nu Lin,Chieh-Liang Wu,Kwong-Chung Tung,Yung-Tsung Chiu
Journal of Biomedicine and Biotechnology , 2011, DOI: 10.1155/2011/245728
Abstract: Bronchiolitis obliterans organizing pneumonia (BOOP) is a chronic respiratory disease. Although the pathogenesis of BOOP is still incompletely understood, BOOP is responsive to steroids and has a good prognosis. In our five pigs with chronic postweaning multisystemic wasting syndrome (PMWS), typical BOOP lesions were revealed. All five porcine lungs showed typical intraluminal plugs, and porcine circovirus type 2 (PCV2) was identified. They also exhibited similar pathologic findings such as proliferation of type II pneumocytes and myofibroblasts (MFBs), extracellular collagen matrix (ECM) deposition, and fragmentation of elastic fibers. MFBs migration correlative molecules, for instance, gelatinase A, B and osteopontin, appeared strongly in the progressing marginal area of polypoid intraluminal plugs of fibrotic lesion. These molecules colocalized with the active MFBs. Both gelatinase activity and intercellular level of active MFBs were significantly increased (<.05). Porcine chronic bronchopneumonia leads to BOOP and it is associated with PCV2 persistent infection. Swine BOOP demonstrates similar cellular constituents with human BOOP. Perhaps their molecular mechanisms of pathogenesis operate in a similar way. Thus we infer that the swine BOOP can be considered as a potential animal model for human BOOP associated with natural viral infection. Moreover, it is more convenient to obtain samples.
Taiwanese Vegetarians and Omnivores: Dietary Composition, Prevalence of Diabetes and IFG
Tina H. T. Chiu, Hui-Ya Huang, Yen-Feng Chiu, Wen-Harn Pan, Hui-Yi Kao, Jason P. C. Chiu, Ming-Nan Lin, Chin-Lon Lin
PLOS ONE , 2014, DOI: 10.1371/journal.pone.0088547
Abstract: Introduction Vegetarian diets have been shown to improve glucose metabolism and reduce risk for diabetes in Westerners but whether Chinese vegetarian diets have the same benefits is unknown. Methods We evaluated the association between diet and diabetes/impaired fasting glucose (IFG) among 4384 Taiwanese Buddhist volunteers and identified diabetes/IFG cases from a comprehensive review of medical history and fasting plasma glucose. Results Vegetarians had higher intakes of carbohydrates, fiber, calcium, magnesium, total and non-heme iron, folate, vitamin A, and lower intakes of saturated fat, cholesterol, and vitamin B12. Besides avoiding meat and fish, vegetarians had higher intakes of soy products, vegetables, whole grains, but similar intakes of dairy and fruits, compared with omnivores. The crude prevalence of diabetes in vegetarians versus omnivores is 0.6% versus 2.3% in pre-menopausal women, 2.8% versus 10% in menopausal women, and 4.3% versus 8.1% in men. Polytomous logistic regression adjusting for age, body mass index, family history of diabetes, education, leisure time physical activity, smoking and alcohol, showed that this vegetarian diet was negatively associated with diabetes and IFG in men (OR for diabetes: 0.49, 95% CI: 0.28–0.89; OR for IFG: 0.66, 95% CI: 0.46–0.95); in pre-menopausal women (OR for diabetes: 0.26, 95% CI: 0.06–1.21; OR for IFG: 0.60, 95% CI: 0.35–1.04); and in menopausal women (OR for diabetes: 0.25, 95% CI: 0.15–0.42; OR for IFG: 0.73, 95% CI: 0.56–0.95). Conclusion We found a strong protective association between Taiwanese vegetarian diet and diabetes/IFG, after controlling for various potential confounders and risk factors.
Central obesity is important but not essential component of the metabolic syndrome for predicting diabetes mellitus in a hypertensive family-based cohort. Results from the Stanford Asia-pacific program for hypertension and insulin resistance (SAPPHIRe) Taiwan follow-up study
I-Te Lee, Yen-Feng Chiu, Chii-Min Hwu, Chih-Tsueng He, Fu-Tien Chiang, Yu-Chun Lin, Themistocles Assimes, J Curb, Wayne H-H Sheu
Cardiovascular Diabetology , 2012, DOI: 10.1186/1475-2840-11-43
Abstract: Non-diabetic Chinese were enrolled and MetS components were assessed to establish baseline data in a hypertensive family-based cohort study. Based on medical records and glucose tolerance test (OGTT), the cumulative incidence of diabetes was analyzed in this five-year study by Cox regression models. Contribution of central obesity to development of new-onset diabetes was assessed in subjects with the same number of positive MetS components.Among the total of 595 subjects who completed the assessment, 125 (21.0%) developed diabetes. Incidence of diabetes increased in direct proportion to the number of positive MetS components (P???0.001). Although subjects with central obesity had a higher incidence of diabetes than those without (55.7 vs. 30.0 events/1000 person-years, P???0.001), the difference became non-significant after adjusting of the number of positive MetS components (hazard ratio?=?0.72, 95%CI: 0.45-1.13). Furthermore, in all participants with three positive MetS components, there was no difference in the incidence of diabetes between subjects with and without central obesity (hazard ratio?=?1.04, 95%CI: 0.50-2.16).In Chinese hypertensive families, the incidence of diabetes in subjects without central obesity was similar to that in subjects with central obesity when they also had the same number of positive MetS components. We suggest that central obesity is very important, but not the essential component of the metabolic syndrome for predicting of new-onset diabetes. (Trial registration: NCT00260910, ClinicalTrials.gov).It is well known that insulin resistance is associated with hypertension [1]. Within hypertensive families, interestingly, subjects without hypertension also have high insulin resistance, which is similar in degree to that of subjects with present hypertension [2]. On the other hand, obesity imposes an additional impact on insulin resistance in the members of a hypertensive family, regardless of whether they have hypertension or not [3,4].
SLC2A10 genetic polymorphism predicts development of peripheral arterial disease in patients with type 2 diabetes. SLC2A10 and PAD in type 2 diabetes
Yi-Der Jiang, Yi-Cheng Chang, Yen-Feng Chiu, Tien-Jyun Chang, Hung-Yuan Li, Wen-Hsing Lin, Hsiang-Yu Yuan, Yuan-Tsong Chen, Lee-Ming Chuang
BMC Medical Genetics , 2010, DOI: 10.1186/1471-2350-11-126
Abstract: We genotyped 10 single nucleotide polymorphisms and one microsatellite spanning 34 kb across the SLC2A10 gene in a prospective cohort of 372 diabetic patients. Their association with the development of peripheral arterial disease (PAD) in type 2 diabetic patients was analyzed.At baseline, several common SNPs of SLC2A10 gene were associated with PAD in type 2 diabetic patients. A common haplotype was associated with higher risk of PAD in type 2 diabetic patients (haplotype frequency: 6.3%, P = 0.03; odds ratio [OR]: 14.5; 95% confidence interval [CI]: 1.3- 160.7) at baseline. Over an average follow-up period of 5.7 years, carriers with the risk-conferring haplotype were more likely to develop PAD (P = 0.007; hazard ratio: 6.78; 95% CI: 1.66- 27.6) than were non-carriers. These associations remained significant after adjustment for other risk factors of PAD.Our data demonstrate that genetic polymorphism of the SLC2A10 gene is an independent risk factor for PAD in type 2 diabetes.Peripheral arterial disease (PAD), defined as lower extremity arterial atherosclerosis, is one of most common diseases of the arteries and is a major complication of type 2 diabetes [1]. Conventional cardiovascular risk factors such as aging, smoking, hyperglycemia, hypertension and dyslipidemia have been shown to be associated with PAD [1]. However, the increased risk for atherosclerotic diseases in diabetic patients can be only partially explained by the conventional risk factors [2]. In fact, a high heritability for ankle-brachial blood pressure index (ABI), an index of PAD, has been obtained in Twin studies in Caucasians [3], indicating that additional genetic factors might be involved in the pathogenesis of PAD. In this respect, the search for genetic causes of PAD remains limited [4].Recently, a genetic form of arterial tortuosity syndrome (ATS; OMIM 208050) was reported to be caused by loss-of-function mutations in the SLC2A10 gene encoding the facilitative glucose transporter GLUT10. A
Genetic Variation in the NOC Gene Is Associated with Body Mass Index in Chinese Subjects
Yi-Cheng Chang, Yen-Feng Chiu, Pi-Hua Liu, Siow Wei Hee, Tien-Jyun Chang, Yi-Der Jiang, Wei-Jei Lee, Po-Chu Lee, Hui-Yi Kao, Juey-Jen Hwang, Lee-Ming Chuang
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0069622
Abstract: Circadian clock genes are critical regulators of energy homeostasis and metabolism. However, whether variation in the circadian genes is associated with metabolic phenotypes in humans remains to be explored. In this study, we systemically genotyped 20 tag single nucleotide polymorphisms (SNPs) in 8 candidate genes involved in circadian clock, including CLOCK, BMAL1(ARNTL), PER1, PER2, CRY1, CRY2, CSNK1E,, and NOC(CCRN4L) in 1,510 non-diabetic Chinese subjects in Taipei and Yunlin populations in Taiwan. Their associations with metabolic phenotypes were analyzed. We found that genetic variation in the NOC gene, rs9684900 was associated with body mass index (BMI) (P = 0.0016, Bonferroni corrected P = 0.032). Another variant, rs135764 in the CSNK1E gene was associated with fasting glucose (P = 0.0023, Bonferroni corrected P = 0.046). These associations were consistent in both Taipei and Yunlin populations. Significant epistatic and joint effects between SNPs on BMI and related phenotypes were observed. Furthermore, NOC mRNA levels in human abdominal adipose tissue were significantly increased in obese subjects compared to non-obese controls. Conclusion Genetic variation in the NOC gene is associated with BMI in Chinese subjects.
Association between Dietary Fiber Intake and Physical Performance in Older Adults: A Nationwide Study in Taiwan
I-Chien Wu, Hsing-Yi Chang, Chih-Cheng Hsu, Yen-Feng Chiu, Shu-Han Yu, Yi-Fen Tsai, Shi-Chen Shen, Ken N. Kuo, Ching-Yu Chen, Kiang Liu, Marion M. Lee, Chao A. Hsiung
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0080209
Abstract: Background Physical performance is a major determinant of health in older adults, and is related to lifestyle factors. Dietary fiber has multiple health benefits. It remains unclear whether fiber intake is independently linked to superior physical performance. We aimed to assess the association between dietary fiber and physical performance in older adults. Methods This was a cross-sectional study conducted with community-dwelling adults aged 55 years and older (n=2680) from the ongoing Healthy Aging Longitudinal Study (HALST) in Taiwan 2008-2010. Daily dietary fiber intake was assessed using a validated food frequency questionnaire. Physical performance was determined objectively by measuring gait speed, 6-minute walk distance, timed “up and go” (TUG), summary performance score, hand grip strength. Results Adjusting for all potential confounders, participants with higher fiber intake had significantly faster gait speed, longer 6-minute walk distance, faster TUG, higher summary performance score, and higher hand grip strength (all P <.05). Comparing with the highest quartile of fiber intake, the lowest quartile of fiber intake was significantly associated with the lowest sex-specific quartile of gait speed (adjusted OR, 2.18 in men [95% CI, 1.33-3.55] and 3.65 in women [95% CI, 2.20-6.05]), 6-minute walk distance (OR, 2.40 in men [95% CI, 1.38-4.17] and 4.32 in women [95% CI, 2.37-7.89]), TUG (OR, 2.42 in men [95% CI, 1.43-4.12] and 3.27 in women [95% CI, 1.94-5.52]), summary performance score (OR, 2.12 in men [95% CI, 1.19-3.78] and 5.47 in women [95% CI, 3.20-9.35]), and hand grip strength (OR, 2.64 in men [95% CI, 1.61-4.32] and 4.43 in women [95% CI, 2.62-7.50]). Conclusions Dietary fiber intake was independently associated with better physical performance.
Effect of preozonation on improvement of settleability of solid in highly concentrated organic wastewater of Japanese wheat and sweet potato spirit-distillery
Masafumi Tateda,Masanori Fujita,Michihiko Ike,QUI Yen-feng,Satoru Kokubo,
Masafumi Tate
,Masanori Fujit,Michihiko Ike,QUI Yen-feng,Satoru Kokubo

环境科学学报(英文版) , 2004,
Abstract: Solid-liquid separation of the wastewater is very difficult because of high viscosity and high SS concentration. In this study, the effectiveness of preozonation on improving the settleability of the solids in wheat and sweet potato wastewaters was investigated using a bench-scale system and pilot treatment system respectively. Results showed that solid-liquid separation in the wheat wastewater was greatly improved by the decanter in the system(SS reduction from 24100 mg/L to 100 mg/L). However, preozonation practice did not show a significant effect on solid-liquid separation of the sweet potato wastewater. Effect of preozonation on solid-liquid separation between wheat and sweet potato wastewater showed different.
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