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55 papers found.
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Human Papillomavirus Testing for Cervical Cancer Screening: Results From a 6-Year Prospective Study in Rural China

/Hospital, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, Peoples Republic of China (Ju-Fang Shi, Fang-Hui Zhao, Jing Li, Feng Chen, Wang Xiang, You-Lin Qiao); Department of

Rare variant discovery and calling by sequencing pooled samples with overlaps

Motivation: For many complex traits/diseases, it is believed that rare variants account for some of the missing heritability that cannot be explained by common variants. Sequencing a large number of samples through DNA pooling is a cost-effective strategy to discover rare variants and to investigate their associations with phenotypes. Overlapping pool designs provide further...

Detecting genome-wide epistases based on the clustering of relatively frequent items

Motivation: In genome-wide association studies (GWAS), up to millions of single nucleotide polymorphisms (SNPs) are genotyped for thousands of individuals. However, conventional single locus-based approaches are usually unable to detect gene–gene interactions underlying complex diseases. Due to the huge search space for complicated high order interactions, many existing multi...

Detecting epistatic effects in association studies at a genomic level based on an ensemble approach

Motivation: Most complex diseases involve multiple genes and their interactions. Although genome-wide association studies (GWAS) have shown some success for identifying genetic variants underlying complex diseases, most existing studies are based on limited single-locus approaches, which detect single nucleotide polymorphisms (SNPs) essentially based on their marginal...

Efficient identification of identical-by-descent status in pedigrees with many untyped individuals

Motivation: Inference of identical-by-descent (IBD) probabilities is the key in family-based linkage analysis. Using high-density single nucleotide polymorphism (SNP) markers, one can almost always infer haplotype configurations of each member in a family given all individuals being typed. Consequently, the IBD status can be obtained directly from haplotype configurations...

MAVEN: a tool for visualization and functional analysis of genome-wide association results

Kanchana Narayanan 0 Jing Li 0 Associate Editor: Alex Bateman 0 Department of Electrical Engineering and Computer Science, Case Western Reserve University Cleveland , OH, USA Summary: We describe

Haplotype-based linkage disequilibrium mapping via direct data mining

Motivation: With the availability of large-scale, high-density single-nucleotide polymorphism markers and information on haplotype structures and frequencies, a great challenge is how to take advantage of haplotype information in the association mapping of complex diseases in case–control studies. Results: We present a novel approach for association mapping based on directly...

Deregulation of Wnt/β-catenin signaling through genetic or epigenetic alterations in human neuroendocrine tumors

Carcinoid tumors are rare neuroendocrine tumors (NETs) that are increasing in incidence. Mutation and altered expression of Wnt/β-catenin signaling components have been described in many tumors but have not been well-studied in NETs. Here, we observed accumulation of β-catenin in the cytoplasm and/or nucleus in 25% of clinical NET tissues. By mutational analysis, the mutations of...

Human RIF1 encodes an anti-apoptotic factor required for DNA repair

Human Rap1-interacting protein 1 (RIF1) contributes to the ataxia telangiectasia, mutated-mediated DNA damage response against the dexterous effect of DNA lesions and plays a critical role in the S-phase checkpoint. However, the molecular mechanisms by which human RIF1 conquers DNA aberrations remain largely unknown. We here showed that inhibition of RIF1 expression by small...

SysPTM 2.0: an updated systematic resource for post-translational modification

motivated us to upgrade the database. We also acknowledge Dr Jing Li from Shanghai Jiaotong University for her suggestion on PTMCluster improvement.

Association of conventional haemostasis and coagulation tests with the risk of acute upper gastrointestinal bleeding in liver cirrhosis: a retrospective study

the thrombosed portal vein, prevent the development of portal vein thrombosis, and even improve liver function [18, 19]. Author contributions Jing Li reviewed the literature, wrote the protocol

Polysialylation promotes neural cell adhesion molecule-mediated cell migration in a fibroblast growth factor receptor-dependent manner, but independent of adhesion capability

Polysialic acid (PSA), a carbohydrate polymer mainly present in the neural cell adhesion molecule (NCAM), promotes neural plasticity; however, its mode of action in tumor malignancy remains largely unknown. In this study, we investigated the influence of polysialylation on cell migration. PSA consistently promoted cell migration on different extracellular matrices (ECMs) but...

Multiple and multivalent interactions of novel anti-AIDS drug candidates, sulfated polymannuronate (SPMG)-derived oligosaccharides, with gp120 and their anti-HIV activities

Sulfated polymannuronate (SPMG), a novel anti-AIDS drug candidate, combats HIV-1 infection mainly by binding to gp120 protein with high affinity. To explore the structural basis of this anti-HIV-1 action, size-defined oligosaccharides were prepared by semi-synthesis or separated from native SPMG. In this study, a series of homogeneously sized SPMG fragments are evaluated for...

Genotypic variants at 2q33 and risk of esophageal squamous cell carcinoma in China: a meta-analysis of genome-wide association studies

Genome-wide association studies have identified susceptibility loci for esophageal squamous cell carcinoma (ESCC). We conducted a meta-analysis of all single-nucleotide polymorphisms (SNPs) that showed nominally significant P-values in two previously published genome-wide scans that included a total of 2961 ESCC cases and 3400 controls. The meta-analysis revealed five SNPs at...

Global patterns of genetic diversity and signals of natural selection for human ADME genes

Genetic polymorphisms in many genes related to drug absorption, distribution, metabolism and excretion (ADME genes) contribute to the high heterogeneity of drug responses in humans. However, the extent to which genetic variation in ADME genes may contribute to differences among human populations in drug responses has not been studied. In this work, we investigate the global...

Shwachman-Bodian Diamond syndrome is a multi-functional protein implicated in cellular stress responses

Shwachman-Diamond syndrome (SDS; OMIM 260400) results from loss-of-function mutations in the Shwachman-Bodian Diamond syndrome (SBDS) gene. It is a multi-system disorder with clinical features of exocrine pancreatic dysfunction, skeletal abnormalities, bone marrow failure and predisposition to leukemic transformation. Although the cellular functions of SBDS are still unclear, its...

Regulation of IL-8 and IL-1β expression in Crohn's disease associated NOD2/CARD15 mutations

Crohn's disease (CD) is a chronic inflammation affecting the gastrointestinal tract. Three mutations (Arg702Trp, Gly908Arg and Leu1007fsinsC) within the NOD2/CARD15 gene increase CD susceptibility. Here, we define cytokine regulation in primary human mononuclear cells, with muramyl dipeptide (MDP), the minimal NOD2/CARD15 activating component of peptidoglycan. By microarray, MDP...

Calcineurin subunit B activates dendritic cells and acts as a cancer vaccine adjuvant

Safe and potent adjuvants are required to establish effective vaccines. In the present work, we show that calcineurin subunit B promotes the secretion of pro-inflammatory cytokines, such as tumor necrosis factor-α, interleukin-12p70 (IL-12 p70), IL-6 and the chemokine IL-8. It also up-regulates transcript levels of chemokines in bone marrow-derived dendritic cells. In an animal...

Novel design and simulation of a hybrid solar electricity system with organic Rankine cycle and PV cells

The proposed system mainly consists of flat-plate compound parabolic concentrators (CPCs) integrated with photovoltaic (PV) cells and organic Rankine cycle (ORC). The technologies of CPC, PV cell and ORC are analyzed, and feasibility of the hybrid solar electricity system is demonstrated. Novel configuration for the hybrid electricity generation is carefully designed to react to...

Effects of the Trace Amine Associated Receptor 1 Agonist RO5263397 on Abuse-Related Behavioral Indices of Methamphetamine in Rats

Methamphetamine is a major drug of abuse with no effective pharmacotherapy available. Trace amine associated receptor 1 is implicated in cocaine addiction and represents a potential therapeutic target. However, the effects of trace amine associated receptor 1 agonists on addiction-related behavioral effects of methamphetamine are unknown.