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Genome-wide association study of the backfat thickness trait in two pig populations

Dandan ZHU,Xiaolei LIU,Rothschild MAX,Zhiwu ZHANG,Shuhong ZHAO,Bin FAN

《农业科学与工程前沿（英文）》 2014年 第1卷 第2期   页码 91-95 doi: 10.15302/J-FASE-2014005

摘要： Backfat thickness is a good predictor of carcass lean content, an economically important trait, and a main breeding target in pig improvement. In this study, the candidate genes and genomic regions associated with the tenth rib backfat thickness trait were identified in two independent pig populations, using a genome-wide association study of porcine 60K SNP genotype data applying the compressed mixed linear model (CMLM) statistical method. For each population, 30 most significant single-nucleotide polymorphisms (SNPs) were selected and SNP annotation implemented using Build 10.2. In the first population, 25 significant SNPs were distributed on seven chromosomes, and SNPs on SSC1 and SSC7 showed great significance for fat deposition. The most significant SNP (ALGA0006623) was located on SSC1, upstream of the gene. In the second population, 27 significant SNPs were recognized by annotation, and 12 SNPs on SSC12 were related to fat deposition. Two haplotype blocks, M1GA0016251-MARC0075799 and ALGA0065251-MARC0014203-M1GA0016298-ALGA0065308, were detected in significant regions where the and genes were identified as contributing to fat metabolism. The results indicated that genetic mechanism regulating backfat thickness is complex, and that genome-wide associations can be affected by populations with different genetic backgrounds.

关键词： backfat thickness     SNP chip     genome-wide association study     compressed mixed linear model     pig    

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A post-GWAS replication study confirming the association of

Shaohua YANG,Chao QI,Yan XIE,Xiaogang CUI,Yahui GAO,Jianping JIANG,Li JIANG,Shengli ZHANG,Qin ZHANG,Dongxiao SUN

《农业科学与工程前沿（英文）》 2014年 第1卷 第4期   页码 321-330 doi: 10.15302/J-FASE-2014037

摘要： Genome-wide association studies with an Illumina Bovine50K chip have detected 105 SNPs associated with one or multiple milk production traits in the Chinese Holstein population. Of these, 38 significant SNPs detected with high confidence by both L1-TDT and MMRA methods were selected to further mine potential key genes affecting milk yield and milk composition. By blasting the flanking sequences of these 38 SNPs with the bovine genome sequence combined with comparative genomics analysis, 26 genes were found to contain or be near to such SNPs. Among them, the gene is merely 87 bp away from the significant SNP, Hapmap30383-BTC-005848. Hence, we report herein genotype-phenotype associations to further validate the genetic effects of the gene. By pooled DNA sequencing of 14 unrelated Holstein sires, a total of 18 with seven novel SNPs were identified. Among them, nine SNPs were in the 5′ regulatory region, one in exon 6 and the other in the 3′ UTR and 3′ regulatory region. A total of nine of these identified SNPs were successfully genotyped and analyzed by mass spectrometry for association with five milk production traits in an independent resource population. The results showed that these SNPs were statistically significant for more than two traits [ <(0.0001-0.0267)]. In addition, mRNA expression analyses revealed that was ubiquitous in eight different tissues, with a relatively higher expression level in the mammary gland than in other tissues. These findings, therefore, provide strong evidence for association of variants with milk yield and milk composition traits and may be applied in Chinese Holstein breeding programs.

关键词： GWAS     functional annotation     Chinese Holstein     milk production traits     C14H8orf33 gene     single nucleotide polymorphisms     association study    

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J-shaped association between dietary zinc intake and new-onset hypertension: a nationwide cohort study

《医学前沿（英文）》 2023年 第17卷 第1期   页码 156-164 doi: 10.1007/s11684-022-0932-3

摘要： We aimed to investigate the relationship of dietary zinc intake with new-onset hypertension among Chinese adults. A total of 12,177 participants who were free of hypertension at baseline from the China Health and Nutrition Survey were included. Dietary intake was assessed by three consecutive 24-h dietary recalls combined with a household food inventory. Participants with systolic blood pressure ≥ 140 mmHg or diastolic blood pressure ≥ 90 mmHg or diagnosed by a physician or under antihypertensive treatment during the follow-up were defined as having new-onset hypertension. During a median follow-up duration of 6.1 years, 4269 participants developed new-onset hypertension. Overall, the association between dietary zinc intake and new-onset hypertension followed a J-shape (P for non-linearity < 0.001). The risk of new-onset hypertension significantly decreased with the increment of dietary zinc intake (per mg/day: hazard ratio (HR) 0.93; 95% confidence interval (CI) 0.88–0.98) in participants with zinc intake < 10.9 mg/day, and increased with the increment of zinc intake (per mg/day: HR 1.14; 95% CI 1.11–1.16) in participants with zinc intake ≥ 10.9 mg/day. In conclusion, there was a J-shaped association between dietary zinc intake and new-onset hypertension in general Chinese adults, with an inflection point at about 10.9 mg/day.

关键词： dietary zinc intake     new-onset hypertension     general population     CHNS    

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U-shaped association between telomere length and esophageal squamous cell carcinoma risk: a case-controlstudy in Chinese population

null

《医学前沿（英文）》 2015年 第9卷 第4期   页码 478-486 doi: 10.1007/s11684-015-0420-0

摘要：

Telomeres play a critical role in biological ageing by maintaining chromosomal integrity and preventing chromosome ends fusion. Epidemiological studies have suggested that inter-individual differences of telomere length could affect predisposition to multiple cancers, but evidence regarding esophageal squamous cell carcinoma (ESCC) was still uncertain. Several telomere length-related single nucleotide polymorphisms (TL-SNPs) in Caucasians have been reported in genome-wide association studies. However, the effects of telomere length and TL-SNPs on ESCC development are unclear. Therefore, we conducted a case-control study (1045 ESCC cases and 1433 controls) to evaluate the associations between telomere length, TL-SNPs, and ESCC risk in Chinese population. As a result, ESCC cases showed overall shorter relative telomere length (RTL) (median: 1.34) than controls (median: 1.50, P<0.001). More interestingly, an evident nonlinear U-shaped association was observed between RTL and ESCC risk (P<0.001), with odds ratios (95% confidence interval) equal to 2.40 (1.84–3.14), 1.36 (1.03–1.79), 1.01 (0.76–1.35), and 1.37 (1.03–1.82) for individuals in the 1st (the shortest), 2nd, 3rd, and 5th (the longest) quintile, respectively, compared with those in the 4th quintile as reference group. No significant associations were observed between the eight reported TL-SNPs and ESCC susceptibility. These findings suggest that either short or extremely long telomeres may be risk factors for ESCC in the Chinese population.

关键词： esophageal squamous cell carcinoma     telomere length     genetic variants     susceptibility     genome-wide association study    

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A genome-wide association study of five meat quality traits in Yorkshire pigs

Qian DONG,Huiying LIU,Xinyun LI,Wei WEI,Shuhong ZHAO,Jianhua CAO

《农业科学与工程前沿（英文）》 2014年 第1卷 第2期   页码 137-143 doi: 10.15302/J-FASE-2014014

摘要： Meat quality is an important trait in the pig industry. To identify genomic regions and haplotype blocks responsible for meat quality traits in pigs, a genome-wide association study was conducted for five traits including intramuscular fat content, pH at 45 min and 24 h, drip loss within 24 h and water-holding capacity in 231 Yorkshire barrows using illumina porcine 60k SNP chips. The results showed that a total of 344 single nucleotide polymorphisms (SNP) were significantly associated with five meat quality traits ( <1×10 ). Moreover, 323 SNPs were within the reported QTL regions, of which 21 were novel. Also, 158 SNPs fell into the proximal region of meat quality related genes. In addition, 25 haplotype blocks based on 116 SNPs were revealed with SNP combination patterns for five traits. Our study added new SNP information for identification of meat quality traits in pigs and will help elucidate the mechanisms of meat quality in pigs.

关键词： Pig     GWAS     meat quality trait     SNP    

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Association of maternal depression with dietary intake, growth, and development of preterm infants: acohort study in Beijing, China

Han Wang, Hong Zhou, Yan Zhang, Yan Wang, Jing Sun

《医学前沿（英文）》 2018年 第12卷 第5期   页码 533-541 doi: 10.1007/s11684-017-0591-y

摘要：

This study aimed to explore the association of maternal depression with nutrient intake, growth, and development of preterm infants. A cohort study of 201 infants was conducted in Beijing. Based on the gestational age of an infant and status of the mother, the infants were divided into four groups: non-depression-fullterm (64), non-depression-preterm (70), depression-fullterm (36), and depression-preterm (31). Data on sociodemographic characteristics, nutritional intake, growth, and developmental status of children at 8 months (corrected ages) were collected using a quantitative questionnaire, a 24-Hour Dietary Recall, anthropometric measurements, and the Bayley-III scale. A multivariate analysis was used to evaluate the effects of maternal depression and preterm birth on infant growth and development. The energy, protein, and carbohydrate intake in the depression group was lower than the recommended amounts. The depression preterm groups indicated the lowest Z-scores for length and weight and the lowest Bayley-III scores. Preterm infants of depressed mothers are at high risks of poor growth and development delay.

关键词： maternal depression     preterm     infant     nutrition     growth     development    

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Advancement in genetic variants conferring obesity susceptibility from genome-wide association studies

null

《医学前沿（英文）》 2015年 第9卷 第2期   页码 146-161 doi: 10.1007/s11684-014-0373-8

摘要：

Obesity prevalence has increased in recent years. Lifestyle change fuels obesity, but genetic factors cause more than 50% of average variations in obesity. The advent of genome-wide association studies (GWAS) has hastened the progress of polygenic obesity research. As of this writing, more than 73 obesity susceptibility loci have been identified in ethnic groups through GWAS. The identified loci explain only 2% to 4% of obesity heritability, thereby indicating that a large proportion of loci remain undiscovered. Thus, the next step is to identify and confirm novel loci, which may exhibit smaller effects and lower allele frequencies than established loci. However, achieving these tasks has been difficult for researchers. GWAS help researchers discover the causal loci. Moreover, numerous biological studies have been performed on the polygenic effects on obesity, such as studies on fat mass- and obesity-associated gene (FTO), but the role of these polygenic effects in the mechanism of obesity remains unclear. Thus, obesity-causing variations should be identified, and insights into the biology of polygenic effects on obesity are needed.

关键词： obesity     genetics     genome-wide association studies     body mass index     fat mass- and obesity-associated gene    

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Genome-wide association studies: inherent limitations and future challenges

null

《医学前沿（英文）》 2012年 第6卷 第4期   页码 444-450 doi: 10.1007/s11684-012-0225-3

摘要：

Genome-wide association studies (GWAS) have achieved great success in identifying genetic variants related to complex human diseases such as cancer and have provided valuable insights into their genetic architecture. Recently, GWAS is quite the fashion in China. However, there are issues related to its nature. Enormous work needs to be done in the post-GWAS era. Deep sequencing followed by functional studies will be needed to elucidate the underpinning biological mechanisms and further translate GWAS findings into medical practice. Along with pharmacogenomics, the success of GWAS in identifying genetic risk factors and genetic differences in drug response has been gradually enabling personalized medicine. In this article, we used hepatocellular carcinoma (HCC) as an example to demonstrate some of the inherent limitations and summarized future challenges of GWAS.

关键词： genome-wide association studies (GWAS)     genetic variant     cancer     limitation     challenge    

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Genetics of ischemic and hemorrhagic stroke in Chinese population

Wei-Li ZHANG MD, PhD, Ru-Tai HUI MD, PhD,

《医学前沿（英文）》 2010年 第4卷 第1期   页码 21-28 doi: 10.1007/s11684-010-0013-x

摘要： Stroke is a major cause of adult death and disability worldwide. Epidemiological and animal studies have provided strong evidence that the pathogenesis of stroke is multi-factorial and induced by a combination of environmental and genetic risk factors, but the identification of individual causative variants remains little known. Genetic influences are likely to be polygenic with small effect sizes, and stroke itself consists of a number of different subtypes which may each have different genetic profiles. In addition, various ethnic populations may have different stroke risk, such as Asian race. The reasons for high risk of stroke among the Chinese, especially hemorrhagic stroke, remain unknown. Most human studies have taken a candidate gene approach using case-control methodology. To be reliably detected, small relative risks require large sample sizes, probably 1000 patients or more. Genome-wide association (GWA) study is an unbiased and comprehensive approach to identify common risk alleles for complex diseases. Recently, a multistage GWA study has identified three loci on chromosomes 2q, 8q and 9p to be associated with intracranial aneurysm in European and Japanese populations. Another GWA finding is the identification of risk variants for cardioembolic stroke on chromosome 4q25 in European populations. In this review, we mainly focus on the results from case-control association studies on genetic factors that play a role in the risk of ischemic and hemorrhagic stroke in Chinese population. The combined effects of multiple susceptibility genes for stroke risk are also summarized.

关键词： genetics     ischemic stroke     hemorrhagic stroke     association study    

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DQB1*060101 may contribute to susceptibility to immunoglobulin A nephropathy in southern Han Chinese

null

《医学前沿（英文）》 2016年 第10卷 第4期   页码 507-516 doi: 10.1007/s11684-016-0475-6

摘要：

Immunoglobulin A nephropathy (IgAN) is a common form of chronic glomerulonephritis with unknown pathogenesis. Accumulating evidences have shown the ethnic-specific association between certain human leukocyte antigen (HLA) alleles and IgAN susceptibility. This study was designed to explore the relationship between HLA-DQB1 alleles and disease susceptibility and clinical manifestations of patients with IgAN in southern Han Chinese. A PCR sequence-based typing technique was used to detect HLA-DQB1 alleles in 217 IgAN patients and 229 healthy subjects. Clinical data were collected from each patient at the time of renal biopsy. Twenty HLA-DQB1 alleles were detected in IgAN patients and healthy subjects. High frequency of HLA-DQB1*060101 and low frequency of HLA-DQB1*030101 were observed in IgAN patients compared with healthy controls. Further stratification analysis revealed that the frequency of DQB1*060101 was significantly higher in patients with urine protein≥1.0 g/24 h than in patients with urine protein<1.0 g/24 h. In combination with our previous DRB1 results, we also analyzed the association of DRB1-DQB1 haplotypes with IgAN. We found that the frequency of haplotype DRB1*090102-DQB1*060101 was significantly higher [odds ratio (OR) = 4.409, Pc = 0.016], whereas that of HLA-DRB1*070101-DQB1*020101 was significantly lower (OR= 0.194, Pc = 0.016) compared with healthy controls. Our study indicated that HLA-DQB1*060101 alleles may be a potential predictor of high-risk IgAN susceptibility in Chinese Han population.

关键词： DQB1     human leukocyte antigen (HLA)     IgA nephropathy     haplotype     association study    

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关联规则挖掘算法综述

毕建欣,张岐山

《中国工程科学》 2005年 第7卷 第4期   页码 88-94

摘要：

介绍了关联规则挖掘算法的基本原理，并按照挖掘中涉及到的变量数目（维数）、数据的抽象层次和处理变量的类别（布尔型和数值型），依次对关联规则挖掘算法的研究进行综述，并对一些典型的算法进行分析和比较，最后展望了关联规则挖掘算法的研究方向。

关键词： 数据挖掘     关联规则     算法     综述    

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Obesity and overweight prevalence and its association with undiagnosed hypertension in Shanghai population

null

《医学前沿（英文）》 2012年 第6卷 第3期   页码 322-328 doi: 10.1007/s11684-012-0204-8

摘要：

The aim of this study was to determine the prevalence of overweight and obese subjects in the Shanghai population of China and its association with undiagnosed hypertension, by taking age, gender and place of residence (urban or suburban) into account. A cross-sectional population-based survey was conducted in 2007. The sample included 13 359 participants aged 15–69 years. Weight, height, and blood pressure were recorded, and information about gender, age and place of residence was obtained. Overweight and obesity prevalence were calculated by the body mass index (BMI) definition recommended by Working Group on Obesity in China (normal weight, 18.5–23.9 kg/m2; overweight, 24–27.9 kg/m2; obesity,≥28 kg/m2). Undiagnosed hypertension was defined by China criteria in accord with that of WHO-ISH (subjects with systolic pressure≥140 mmHg, and/or diastolic pressure≥90 mmHg). Multiple logistic regression analyses were used to assess the association of overweight or obesity with undiagnosed hypertension by adjusting for age, gender and place of residence. The overall overweight, obesity, and undiagnosed hypertension prevalence were 27.6% (95% CI: 26.8–28.4), 6.6% (95% CI: 6.2–7.0), and 15.5% (95% CI: 14.9–16.1), respectively. Compared to normal weight subjects, the odds ratios (OR) for subjects who were overweight and had hypertension was 2.33 (95% CI: 2.10–2.59); that for obesity and hypertension was 4.27 (95% CI: 3.66–4.99). These data suggest that overweight and obesity prevalence and their association with undiagnosed hypertension are high in our study population.

关键词： overweight     obesity     undiagnosed hypertension     prevalence     association    

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Association study on GNB3 gene polymorphism with essential hypertension in Xinjiang Uygur group

JING Jianying, WANG Dan, WANG Xiaofeng, JIN Jianzhong, JIN Li, JIAO Yi, WEN Hao, LIN Renyong

《医学前沿（英文）》 2007年 第1卷 第2期   页码 230-233 doi: 10.1007/s11684-007-0045-z

摘要： The relationship between the tenth exon C825T of G-protein β3 subunit (GNB) genetic polymorphism and hypertension in the Uygur population of China was investigated. A nested case-control study ( = 738) was carried out. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) technique was used to genotype GNB C825T polymorphism in 354 hypertensive (HT) and 384 normotensive (NT) Uygur subjects. The distributions of GNB C825T genotypes were CC (27.2%), TT (42.9%), and CT (29.9%) in the hypertensive subjects and CC (27.7%), TT (42.4%), CT (29.9%) in the normotensive subjects. There were no significant differences in the genotype distributions between the two groups ( = 0.0262 P = 0.99). The T allele was 51.4% in hypertensive subjects and 51.2% in normotensive subjects, which, between the two groups, was not a significant difference ( = 0.0016 P = 0.97). Further analysis shows that there is no association between C825T genotypes and age, body mass index (BMI), Glucose (GLU), Triglyceride (TG), Cholesterol (CHO), systolic blood pressure (SBP) and diastolic blood pressure (DBP). No evidence was found to suggest an association between GNB C825T polymorphism and hypertension in the Uygur population of China.

关键词： case-control     significant difference     reaction-restriction fragment     C825T polymorphism     evidence    

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Genetic Study Identifies CBLN4 as a Novel Susceptibility Gene for Accident Proneness

Shu-lin Zhang,Hui-qing Jin,Yang Song,Wan-sheng Yu,Liang-dan Sun

《工程管理前沿（英文）》 2016年 第3卷 第1期   页码 30-38 doi: 10.15302/J-FEM-2016008

摘要： Frequent traffic accidents constitute a major danger to human beings. The accident-prone driver who has the stable physiological, psychological, and behavioral characteristics is one of the most prominent causes of traffic accidents. The internal link between the individual characteristics and the accident proneness has been a difficult point in the accident prevention research. The authors selected accident-prone drivers as cases and safe drivers as controls (case-control group) from 18,360 drivers who were enrolled from three public transportation incorporations of China using area stratified sampling method. The case-control groups were 1:1 matched. The authors performed genome-wide association study (GWAS) by 179 cases and 179 controls using the U.S. Affymetrix Genome-Wide Human Mapping SNP 6.0 Array. The authors observed that the gene frequencies of 34 single-nucleotide polymorphisms (SNPs) in three regions of cases were higher than those in the control ( <10 ). The authors then tested two independent replication sets for strong association 6 SNPs in 349 pairs of case-control drivers using the U.S. ABI 3730 sequencing method. The results indicated that SNP rs6069499 within linked CBLN4 gene are strongly associated with accident proneness ( =6.37×10 ). According to CBLN4 gene mainly involved in adrenal development and the regulation of secretion, the authors performed 12 biochemical parameters of the blood using radioimmunoassay. The levels of dopamine (DA) and adrenocorticotropic (ACTH) hormone showed significant differences between accident-prone drivers and safe drivers ( =0.03, =0.01). It is suggested that the accident-prone drivers may have the idiosyncrasy of susceptibility.

关键词： accident proneness     genome-wide association study (GWAS)     dopamine (DA)     ACTH     susceptibility gene     traffic accident epidemiology     accident prevention     traffic safety     three-dimensional model    

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Abiotic association of phthalic acid esters with humic acid of a sludge landfill

Xiaoli CHAI, Yongxia HAO, Xin ZHAO, Guixiang LIU, Ying ZHU, Rong JI, Jun WU, Huanhuan TONG, Youcai ZHAO

《环境科学与工程前沿（英文）》 2012年 第6卷 第6期   页码 778-783 doi: 10.1007/s11783-012-0434-7

摘要： The abiotic association between phthalic acid esters (PAEs) and humic substances (HS) in sludge landfill plays an important role in the fate and stability of PAEs. An equilibrium dialysis combined with C-labeling was used to study the abiotic association of two abundant PAEs (diethyl phthalate and di- -butyl phthalate) with humic acid (HA) isolated from a sludge landfill with different stabilization times and different molecular weights. Elemental analysis and Fourier Transform Infrared Spectrophotometer (FTIR) suggested that high value of HA was related to the high aromatic content and large molecular weight of HA. The results indicated that the association strength of PAEs with HA depended on both the properties of the PAEs and the characteristics of HA. The values of the association were strongly dependent on solution pH, and decreased dramatically as the pH was increased from 3.0 to 9.0. The results suggested that non-specific hydrophobic interaction between PAEs and HA was the main contributor to the association of the PAEs with HA. The interactive hydrogen-bonds between the HA and the PAEs molecules may also be involved in the association.

关键词： abiotic association     phthalic acid esters (PAEs)     humic acid     sludge     landfill    

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标题 作者 时间 类型 操作

Genome-wide association study of the backfat thickness trait in two pig populations

Dandan ZHU,Xiaolei LIU,Rothschild MAX,Zhiwu ZHANG,Shuhong ZHAO,Bin FAN

期刊论文

A post-GWAS replication study confirming the association of

Shaohua YANG,Chao QI,Yan XIE,Xiaogang CUI,Yahui GAO,Jianping JIANG,Li JIANG,Shengli ZHANG,Qin ZHANG,Dongxiao SUN

期刊论文

J-shaped association between dietary zinc intake and new-onset hypertension: a nationwide cohort study

期刊论文

U-shaped association between telomere length and esophageal squamous cell carcinoma risk: a case-controlstudy in Chinese population

null

期刊论文

A genome-wide association study of five meat quality traits in Yorkshire pigs

Qian DONG,Huiying LIU,Xinyun LI,Wei WEI,Shuhong ZHAO,Jianhua CAO

期刊论文

Association of maternal depression with dietary intake, growth, and development of preterm infants: acohort study in Beijing, China

Han Wang, Hong Zhou, Yan Zhang, Yan Wang, Jing Sun

期刊论文

Advancement in genetic variants conferring obesity susceptibility from genome-wide association studies

null

期刊论文

Genome-wide association studies: inherent limitations and future challenges

null

期刊论文

Genetics of ischemic and hemorrhagic stroke in Chinese population

Wei-Li ZHANG MD, PhD, Ru-Tai HUI MD, PhD,

期刊论文

DQB1*060101 may contribute to susceptibility to immunoglobulin A nephropathy in southern Han Chinese

null

期刊论文

关联规则挖掘算法综述

毕建欣,张岐山

期刊论文

Obesity and overweight prevalence and its association with undiagnosed hypertension in Shanghai population

null

期刊论文

Association study on GNB3 gene polymorphism with essential hypertension in Xinjiang Uygur group

JING Jianying, WANG Dan, WANG Xiaofeng, JIN Jianzhong, JIN Li, JIAO Yi, WEN Hao, LIN Renyong

期刊论文

Genetic Study Identifies CBLN4 as a Novel Susceptibility Gene for Accident Proneness

Shu-lin Zhang,Hui-qing Jin,Yang Song,Wan-sheng Yu,Liang-dan Sun

期刊论文

Abiotic association of phthalic acid esters with humic acid of a sludge landfill

Xiaoli CHAI, Yongxia HAO, Xin ZHAO, Guixiang LIU, Ying ZHU, Rong JI, Jun WU, Huanhuan TONG, Youcai ZHAO

期刊论文