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Potential malignant transformation in the gastric mucosa of immunodeficient mice with persistent Mycoplasma penetrans infection

curation: Shuyan Cao, Yuxue Wang. Formal analysis: Shuyan Cao, Liping Zhou, Yuxue Wang. Funding acquisition: Shuyan Cao, Yuxue Wang. Investigation: Shuyan Cao, Dandan Shen, Yadong Wang, Linxi Li ... . Methodology: Shuyan Cao, Dandan Shen, Yadong Wang, Linxi Li. Project administration: Shuyan Cao, Dandan Shen, Yadong Wang, Linxi Li. Resources: Shuyan Cao, Liping Zhou, Yuxue Wang. 11 / 13 Software: Liping Zhou

Effects of hemoperfusion and continuous renal replacement therapy on patient survival following paraquat poisoning

analyses had been finished by all authors, and the results's review and the paper had been completed by Yadong Wang, Guangliang Hong and Zhongqiu Lu. Treatments Conventional treatments. Gastrolavage with ... S1 File. STROBE_checklist_v4_combined_PlosMedicine. (DOCX) S2 File. STROBE statement list answers. (DOC) Author Contributions Conceptualization: Yadong Wang, Guangju Zhao, Guangliang Hong, Zhongqiu

regSNPs-splicing: a tool for prioritizing synonymous single-nucleotide substitution

While synonymous single-nucleotide variants (sSNVs) have largely been unstudied, since they do not alter protein sequence, mounting evidence suggests that they may affect RNA conformation, splicing, and the stability of nascent-mRNAs to promote various diseases. Accurately prioritizing deleterious sSNVs from a pool of neutral ones can significantly improve our ability of...

InteGO2: a web tool for measuring and visualizing gene semantic similarities using Gene Ontology

Background The Gene Ontology (GO) has been used in high-throughput omics research as a major bioinformatics resource. The hierarchical structure of GO provides users a convenient platform for biological information abstraction and hypothesis testing. Computational methods have been developed to identify functionally similar genes. However, none of the existing measurements take...

Association between tooth loss and risk of oesophageal cancer: a dose–response meta-analysis

Many epidemiological studies have found that tooth loss is associated with susceptibility to oesophageal cancer. However, a definitive answer is yet to be discovered, and the findings are inconclusive. We performed a meta-analysis to assess the relationship between tooth loss and oesophageal cancer risk. We searched PubMed and Embase databases to screen eligible studies up to...

The association between methylenetetrahydrofolate reductase gene C677T polymorphisms and breast cancer risk in Chinese population

With great interest, we read the recent article entitled “Methylenetetrahydrofolate reductase polymorphisms and breast cancer risk in Chinese population: a meta-analysis of 22 case-control studies” published online in Tumor Biology, 2014, 35: 1695–1701. This article suggests that methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism was significantly associated with...

Note of clarification of data in the paper entitled association between BRIP1 (BACH1) polymorphisms and breast cancer risk

cases and 782 controls, respectively. The & Yadong Wang authors found that the association was lacking between the Pro919Ser polymorphisms and breast cancer risk in overall analysis [odds ratio (OR

Improving alignment accuracy on homopolymer regions for semiconductor-based sequencing technologies

Background Ion Torrent and Ion Proton are semiconductor-based sequencing technologies that feature rapid sequencing speed and low upfront and operating costs, thanks to the avoidance of modified nucleotides and optical measurements. Despite of these advantages, however, Ion semiconductor sequencing technologies suffer much reduced sequencing accuracy at the genomic loci with...

IRcall and IRclassifier: two methods for flexible detection of intron retention events from RNA-Seq data

Background The emergence of next-generation RNA sequencing (RNA-Seq) provides tremendous opportunities for researchers to analyze alternative splicing on a genome-wide scale. However, accurate detection of intron retention (IR) events from RNA-Seq data has remained an unresolved challenge in next-generation sequencing (NGS) studies. Results We propose two new methods: IRcall and...

A novel method based on two cameras for accurate estimation of arterial oxygen saturation

Background Photoplethysmographic imaging (PPGi) that is based on camera allows acquiring photoplethysmogram and measuring physiological parameters such as pulse rate, respiration rate and perfusion level. It has also shown potential for estimation of arterial oxygen saturation (SaO2). However, there are some technical limitations such as optical shunting, different camera...

The association between LEPR Q223R polymorphisms and breast cancer risk

Recently, we have read with great interest the article entitled “The association between polymorphisms in the leptin receptor (LEPR) gene and risk of breast cancer: a systematic review and pooled analysis” published online by Wang et al. (Breast Cancer Res Treat 136:231–239, 2012). This article suggests that the A allele of LEPR gene rs1137101 variant was low-penetrant risk...

Note of clarification of data in the paper titled X-ray repair cross-complementing group 1 codon 399 polymorphism and lung cancer risk: an updated meta-analysis

We read with great interest the paper titled “X-ray repair cross-complementing group 1 codon 399 polymorphism and lung cancer risk: an updated meta-analysis” published by Wang et al in Tumor Biology, 2014, 35:411–418. Their results suggest that codon 399 polymorphism of XRCC1 gene might contribute to individual’s susceptibility to lung cancer in Asian population and especially in...

Note of clarification of data in the paper entitled no association between XRCC1 gene Arg194Trp polymorphism and risk of lung cancer: evidence based on an updated cumulative meta-analysis

Yang Fuye Shao Haiyu Wang Yadong Wang 0 ) Department of Toxicology, Henan Center for Disease Control and Prevention , No.105 of South Nongye Road, Zhengzhou 450016 , People's Republic of China Lung

An integrative approach for measuring semantic similarities using gene ontology

Background Gene Ontology (GO) provides rich information and a convenient way to study gene functional similarity, which has been successfully used in various applications. However, the existing GO based similarity measurements have limited functions for only a subset of GO information is considered in each measure. An appropriate integration of the existing measures to take into...

Controlled Delivery of Sonic Hedgehog Morphogen and Its Potential for Cardiac Repair

The morphogen Sonic hedgehog (Shh) holds great promise for repair or regeneration of tissues suffering ischemic injury, however clinical translation is limited by its short half-life in the body. Here, we describe a coacervate delivery system which incorporates Shh, protects it from degradation, and sustains its release for at least 3 weeks. Shh released from the coacervate...

Towards integrative gene functional similarity measurement

Background In Gene Ontology, the "Molecular Function" (MF) categorization is a widely used knowledge framework for gene function comparison and prediction. Its structure and annotation provide a convenient way to compare gene functional similarities at the molecular level. The existing gene similarity measures, however, solely rely on one or few aspects of MF without utilizing...

Transcriptional regulation prediction of antiestrogen resistance in breast cancer based on RNA polymerase II binding data

Denan Zhang 0 Guohua Wang 0 Yadong Wang 0 0 Center for Bioinformatics, School of Computer Science and Technology, Harbin Institute of Technology , Harbin, 150001 , China Background: Although