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Analysis of the Maternal and Child Health Care Status in Suizhou City, Hubei Province, China, from 2005 to 2011

BackgroundImproving the health and well-being of women and children has long been a common goal throughout the world. From 2005 to 2011, Suizhou City had an annual average of 22,405 pregnant and parturient women (1.04% of the population) and 98,811 children under 5 years old (4.57% of the population). Understanding the status of maternal and child health care in Suizhou City...

Accurate HLA type inference using a weighted similarity graph

Background The human leukocyte antigen system (HLA) contains many highly variable genes. HLA genes play an important role in the human immune system, and HLA gene matching is crucial for the success of human organ transplantations. Numerous studies have demonstrated that variation in HLA genes is associated with many autoimmune, inflammatory and infectious diseases. However...

Recognition and processing of double-stranded DNA by ExoX, a distributive 3′–5′ exonuclease

Members of the DnaQ superfamily are major 3′–5′ exonucleases that degrade either only single-stranded DNA (ssDNA) or both ssDNA and double-stranded DNA (dsDNA). However, the mechanism by which dsDNA is recognized and digested remains unclear. Exonuclease X (ExoX) is a distributive DnaQ exonuclease that cleaves both ssDNA and dsDNA substrates. Here, we report the crystal...

Isolation and characterization of dengue virus serotype 2 from the large dengue outbreak in Guangdong, China in 2014

Dengue has been well recognized as a global public health threat, but only sporadic epidemics and imported cases were reported in recent decades in China. Since July 2014, an unexpected large dengue outbreak has occurred in Guangdong province, China, resulting in more than 40000 patients including six deaths. To clarify and characterize the causative agent of this outbreak, the...

SOCS3 Promoter Hypermethylation Is a Favorable Prognosticator and a Novel Indicator for G-CIMP-Positive GBM Patients

Background Hypermethylation of the suppressor of cytokine signaling 3(SOCS3) promoter has been reported to predict a poor prognosis in several cancers including glioblstoma multiforme (GBM). We explored the function of SOCS3 promoter hypermethylation in GBM cohorts, including analysis of the CpG island methylator phenotype (CIMP), when a large number of gene loci are...

Genetic Characterization of Human-Derived Hydatid Cysts of Echinococcus granulosus Sensu Lato in Heilongjiang Province and the First Report of G7 Genotype of E. canadensis in Humans in China

Cystic echinococcosis (CE) caused by the larval stage of Echinococcus granulosus sensu lato (s.l.) is one of the most important zoonotic parasitic diseases worldwide and 10 genotypes (G1–G10) have been reported. In China, almost all the epidemiological and genotyping studies of E. granulosus s.l. are from the west and northwest pasturing areas. However, in Heilongjiang Province...

Genetic polymorphisms of DNA double-strand break repair pathway genes and glioma susceptibility

Background Genetic variations in DNA double-strand break repair genes can influence the ability of a cell to repair damaged DNA and alter an individual’s susceptibility to cancer. We studied whether polymorphisms in DNA double-strand break repair genes are associated with an increased risk of glioma development. Methods We genotyped 10 potentially functional single nucleotide...

N-methylnicotinamide and nicotinamide N-methyltransferase are associated with microRNA-1291-altered pancreatic carcinoma cell metabolome and suppressed tumorigenesis

The cell metabolome comprises abundant information that may be predictive of cell functions in response to epigenetic or genetic changes at different stages of cell proliferation and metastasis. An unbiased ultra-performance liquid chromatography–mass spectrometry-based metabolomics study revealed a significantly altered metabolome for human pancreatic carcinoma PANC-1 cells with...

Nrf2 Pathway Regulates Multidrug-Resistance-Associated Protein 1 in Small Cell Lung Cancer

Although multidrug-resistance-associated protein-1 (MRP1) is a major contributor to multi-drug resistance (MDR), the regulatory mechanism of Mrp1 still remains unclear. Nrf2 is a transcription factor that regulates cellular defense response through antioxidant response elements (AREs) in normal tissues. Recently, Nrf2 has emerged as an important contributor to chemo-resistance in...

BMP4, a strong better prognosis predictor, has a subtype preference and cell development association in gliomas

Background The bone morphogenetic family proteins (BMP) are phytogenetically conserved proteins, which are essential for embryonic development. The key regulatory subunit, the bone morphogenetic protein 4 (BMP4), is overexpressed and associated with tumor metastasis in a variety of cancers. However, the prognostic and molecular features of gliomas with BMP4 expression is still...

Determination of the Crystal Structure and Active Residues of FabV, the Enoyl-ACP Reductase from Xanthomonas oryzae

Background Enoyl-ACP reductase (ENR) catalyses the last reduction reaction in the fatty acid elongation cycle in bacteria and is a good antimicrobial target candidate. FabV is the most recently discovered class of ENR, but we lack information about the atomic structure and the key residues involved in reductase activity except for the known conserved tyrosine and lysine residues...

Identification of a 6-Cytokine Prognostic Signature in Patients with Primary Glioblastoma Harboring M2 Microglia/Macrophage Phenotype Relevance

Background Glioblastomas (GBM) are comprised of a heterogeneous population of tumor cells, immune cells, and extracellular matrix. Interactions among these different cell types and pro-/anti-inflammatory cytokines may promote tumor development and progression. Aims The objective of this study was to develop a cytokine-related gene signature to improve outcome prediction for...

Improving probe set selection for microbial community analysis by leveraging taxonomic information of training sequences

Background Population levels of microbial phylotypes can be examined using a hybridization-based method that utilizes a small set of computationally-designed DNA probes targeted to a gene common to all. Our previous algorithm attempts to select a set of probes such that each training sequence manifests a unique theoretical hybridization pattern (a binary fingerprint) to a probe...

High-performance single-chip exon capture allows accurate whole exome sequencing using the Illumina Genome Analyzer

Here we present an adaptation of NimbleGen 2.1M-probe array sequence capture for whole exome sequencing using the Illumina Genome Analyzer (GA) platform. The protocol involves two-stage library construction. The specificity of exome enrichment was approximately 80% with 95.6% even coverage of the 34 Mb target region at an average sequencing depth of 33-fold. Comparison of our...

Structural Characterization of the Self-Association of the Death Domain of p75NTR

Zusen Fan 0 Tao Jiang 0 Wenqing Xu, University of Washington, United States of America 0 1 National Key Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences , Beijing

Presep: Predicting the Propensity of a Protein Being Secreted into the Supernatant when Expressed in Pichia pastoris

Pichia pastoris is commonly used for the production of recombinant proteins due to its preferential secretion of recombinant proteins, resulting in lower production costs and increased yields of target proteins. However, not all recombinant proteins can be successfully secreted in P. pastoris. A computational method that predicts the likelihood of a protein being secreted into...

Expression of hypoxia-related markers in inflammatory myofibroblastic tumors of the head and neck

Background The etiology of inflammatory myofibroblastic tumors (IMTs) is controversial and the prognosis is unpredictable. Previous studies have not investigated the expression of hypoxia-related markers in IMTs. Methods Between 2002 and 2012, 12 consecutive patients with histologically proven IMTs were enrolled in the study. Immunohistochemistry was used to detect GLUT-1, HIF-1...

SEED: efficient clustering of next-generation sequences

Motivation: Similarity clustering of next-generation sequences (NGS) is an important computational problem to study the population sizes of DNA/RNA molecules and to reduce the redundancies in NGS data. Currently, most sequence clustering algorithms are limited by their speed and scalability, and thus cannot handle data with tens of millions of reads. Results: Here, we introduce...

Accelerated similarity searching and clustering of large compound sets by geometric embedding and locality sensitive hashing

Motivation: Similarity searching and clustering of chemical compounds by structural similarities are important computational approaches for identifying drug-like small molecules. Most algorithms available for these tasks are limited by their speed and scalability, and cannot handle today's large compound databases with several million entries. Results: In this article, we...