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The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

Barbacioru Vincent Bertholet Xiaoxi Megan Cao Tzu- Ming Chu Patrick J Collins Xiao-hui Fan Felix W Frueh James C Fuscoe Xu Guo Jing Han Damir Herman Huixiao Hong Ernest S Kawasaki Quan-Zhen Li Yuling

Association of ICAM3 Genetic Variant with Severe Acute Respiratory Syndrome

Genetic polymorphisms have been demonstrated to be associated with vulnerability to human infection. ICAM3, an intercellular adhesion molecule important for T cell activation, and FCER2 (CD23), an immune response gene, both located on chromosome 19p13.3 were investigated for host genetic susceptibility and association with clinical outcome. A case-control study based on 817...

Clinical and Molecular Epidemiological Features of Coronavirus HKU1–Associated Community-Acquired Pneumonia

BackgroundRecently, we described the discovery of a novel group 2 coronavirus, coronavirus HKU1 (CoV-HKU1), from a patient with pneumonia. However, the clinical and molecular epidemiological features of CoV-HKU1–associated pneumonia are unknown MethodsProspectively collected (during a 12-month period) nasopharyngeal aspirates (NPAs) from patients with community-acquired pneumonia...

Effect of Migration and Related Environmental Changes on Serum Lipid Levels in Southwestern Chinese Men

To determine migration-related differences in serum lipid levels and to estimate the contribution of environmental factors to these differences, the authors conducted a cross-sectional study among 1, 222 residents of southwestern China in 1988 and 1989: 521 Yi farmers living in a remote rural area, 340 Yi migrants to an urban setting, and 361 Han people living in the same urban...

Prospective Study of Hepatocellular Carcinoma and Liver Cirrhosis in Asymptomatic Chronic Hepatitis B Virus Carriers

The authors conducted a study to assess the importance of underlying liver cirihosis in the development of hepatocellular carcinoma (HCC) and the multifactorial etiology of liver cirrhosis in chronic carriers of hepatitis B virus (HBV). Between November 1980 and May 1990, all male hepatitis B surface antigen (HBsAg) carriers who routinely attended a clinic for asymptomatic HBV...

Polyadenylation of the mRNA of hepatitis delta virus is dependent on the structure of the nascent RNA and regulated by the small or large delta antigen

-Ying Yang 0 Jonathan T.Ou Chia-Ming Chu Yun-Fan Liaw Liver Unit Chang Gung Memorial Hospital Taipei Taiwan 0 Department of Microbiology and Immunology, Chang Gung College of Medicine and Technology

Comparison of RNA-seq and microarray-based models for clinical endpoint prediction

Background Gene expression profiling is being widely applied in cancer research to identify biomarkers for clinical endpoint prediction. Since RNA-seq provides a powerful tool for transcriptome-based applications beyond the limitations of microarrays, we sought to systematically evaluate the performance of RNA-seq-based and microarray-based classifiers in this MAQC-III/SEQC study...

Emergence of an S Gene Mutant during Thymosin α1 Therapy in a Patient with Chronic Hepatitis B

The presence of a hepatitis B virus S gene mutant was investigated in a patient being treated with thymosin α1. He was seropositive for hepatitis B e antigen throughout therapy but was intermittently seronegative for hepatitis B surface antigen (HBsAg) by an RIA. Sequence analysis revealed an S gene mutant in HBsAg-seronegative serum with two consecutive amino acid substitutions...

Tumor Necrosis Factor–α and Interleukin-10 Promoter Polymorphisms in Epstein-Barr Virus–Associated Gastric Carcinoma

To investigate whether genetic differences in cytokine promoter polymorphisms effect various outcomes after exposure to Epstein-Barr virus (EBV) infection, 30 patients with EBV-positive gastric carcinoma (GC), 120 patients with EBV-negative GC, and 220 control subjects were enrolled. Promoter polymorphisms of tumor necrosis factor (TNF)–α at positions −238 and −308 and of...

Altered expression patterns of lipid metabolism genes in an animal model of HCV core-related, nonobese, modest hepatic steatosis

Background Because the gene expression patterns of nonobese hepatic steatosis in affected patients remain unclear, we sought to explore these patterns using an animal model of nonobese hepatic steatosis. Methods We developed mice that conditionally express the hepatitis C virus (HCV) core protein regulated by the tetracycline transactivator (tTA). Microarray analyses and reverse...

Identification and characterization of a prevalent hepatitis B virus X protein mutant in Taiwanese patients with hepatocellular carcinoma

, Chang Gung Memorial Hospital, 199 Tung Hwa North Road, Taipei 105, TaiwanChau-Ting Yeh, Chien-Hong Shen, Dar-In Tai, Chia-Ming Chu & Yun-Fan LiawChang Gung University School of Medicine, Taipei 105 ... , TaiwanChau-Ting Yeh, Chien-Hong Shen, Dar-In Tai, Chia-Ming Chu & Yun-Fan Liaw AuthorsSearch for Chau-Ting Yeh in:Nature Research journals • PubMed • Google ScholarSearch for Chien-Hong Shen in:Nature Research

Palindromic sequences preceding the terminator increase polymerase III template activity

Four consecutive T residues in the sense strand are sufficient to terminate transcription by RNA polymerase III (pol III). Previously we observed that compared with this minimally sufficient terminator, five T residues immediately preceded by a palindromic sequence increases transcriptional expression both in vitro and in vivo, raising the question of whether a palindromic...

Prevention of Acute Myocardial Infarction and Stroke among Elderly Persons by Dual Pneumococcal and Influenza Vaccination: A Prospective Cohort Study

Background. DespiteWorld Health Organization recommendations, the rate of 23-valent pneumococcal (PPV) and influenza (TIV) vaccination among elderly persons in Hong Kong, China, is exceptionally low because of doubts about effectiveness of vaccination. The efficacy of dual vaccination remains unknown. Methods. From 3 December 2007 to 30 June 2008, we conducted a prospective...

Comparison of transcriptional responses in liver tissue and primary hepatocyte cell cultures after exposure to hexahydro-1, 3, 5-trinitro-1, 3, 5-triazine

Background Cell culture systems are useful in studying toxicological effects of chemicals such as Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), however little is known as to how accurately isolated cells reflect responses of intact organs. In this work, we compare transcriptional responses in livers of Sprague-Dawley rats and primary hepatocyte cells after exposure to RDX to...

Formation of 4′-carboxyl acid metabolite of imrecoxib by rat liver microsomes

Aim:Imrecoxib is a novel and moderately selective COX-2 inhibitor. The aim of the present in vitro investigation was to study the formation of the major metabolite 4′-carboxylic acid imrecoxib (M2) and identify the enzyme(s) involved in the reaction.Methods:The formation of M2 was studied in rat liver cytosol in the absence or presence of liver microsomes. The formed metabolite...

Role of rat liver cytochrome P450 3A and 2D in metabolism of imrecoxib

Aim:To investigate the in vitro metabolism of imrecoxib in rat liver microsomes and to identify the cytochrome P450 (CYP) forms involved in its metabolism.Methods:Liver microsomes of Wistar rats were prepared using an ultracentrifuge. The in vitro metabolism of imrecoxib was studied by incubation with rat liver microsomes. To characterize the CYP forms involved in the 4′-methyl...

Enhancement of radiosensitivity in human glioblastoma cells by the DNA N-mustard alkylating agent BO-1051 through augmented and sustained DNA damage response

Pei-Ming Chu 0 Shih-Hwa Chiou Tsann-Long Su Yi-Jang Lee Li-Hsin Chen Yi-Wei Chen Sang-Hue Yen Ming-Teh Chen Ming-Hsiung Chen Yang-Hsin Shih Pang-Hsien Tu Hsin-I Ma 0 0 Graduate Institutes of Life

Relative Impact of Incorporating Pharmacokinetics on Predicting In Vivo Hazard and Mode of Action from High-Throughput In Vitro Toxicity Assays

The use of high-throughput in vitro assays has been proposed to play a significant role in the future of toxicity testing. In this study, rat hepatic metabolic clearance and plasma protein binding were measured for 59 ToxCast phase I chemicals. Computational in vitro-to-in vivo extrapolation was used to estimate the daily dose in a rat, called the oral equivalent dose, which...