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Differential gene expression analysis using coexpression and RNA-Seq data

Motivation: RNA-Seq is increasingly being used for differential gene expression analysis, which was dominated by the microarray technology in the past decade. However, inferring differential gene expression based on the observed difference of RNA-Seq read counts has unique challenges that were not present in microarray-based analysis. The differential expression estimation may be...

BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences

Motivation: De novo transcriptome assemblies of RNA-Seq data are important for genomics applications of unsequenced organisms. Owing to the complexity and often incomplete representation of transcripts in sequencing libraries, the assembly of high-quality transcriptomes can be challenging. However, with the rapidly growing number of sequenced genomes, it is now feasible to...

Serum Uric Acid Increases Risk of Cancer Incidence and Mortality: A Systematic Review and Meta-Analysis

designed the experiments. Bin Wang, Wei Xu, Yuqing Liu, and Tao Jiang performed the experiments and collected data. Bin Wang and Xuan Wang analyzed the data. Changjiang Hua and Xuan Wang contributed reagents

Identifying the Association of Contrast Enhancement with Vascular Endothelia Growth Factor Expression in Anaplastic Gliomas: A Volumetric Magnetic Resonance Imaging Analysis

Contrast enhancement is a crucial radiologic feature of malignant brain tumors, which are associated with genetic changes of the tumor. The purpose of the current study was to investigate the potential relationship among tumor contrast enhancement with MR imaging, vascular endothelial growth factor (VEGF) expression, and survival outcome in anaplastic gliomas. MR images from 240...

Bufalin Induces Mitochondria-Dependent Apoptosis in Pancreatic and Oral Cancer Cells by Downregulating hTERT Expression via Activation of the JNK/p38 Pathway

 Shenyi Jiang,5 Chengguang Sui,1 Fandong Meng,1 Yan Li,1 Liye Fu,1 Tao Jiang,1 Yang Wang,1 Jia Su,1 and Youhong Jiang1 1Molecular Oncology Laboratory of Cancer Research Institute, The First Affiliated

A fast and accurate algorithm for single individual haplotyping

Background Due to the difficulty in separating two (paternal and maternal) copies of a chromosome, most published human genome sequences only provide genotype information, i.e., the mixed information of the underlying two haplotypes. However, phased haplotype information is needed to completely understand complex genetic polymorphisms and to increase the power of genome-wide...

Seasonal variation of size-fractionated phytoplankton in the Pearl River estuary

To investigate the dynamics of phytoplankton size structure in the Pearl River estuary, concentrations of size-fractionated chlorophyll a (Chl a) were determined during four cruises carried out in 2008 and 2010. The distribution of Chl a in this geographical location showed a high degree of temporal variation. Chl a concentrations were highest in autumn, approximately three times...

ALDH1A3: A Marker of Mesenchymal Phenotype in Gliomas Associated with Cell Invasion

Aldehyde dehydrogenases (ALDH) is a family of enzymes including 19 members. For now, ALDH activity had been wildly used as a marker of cancer stem cells (CSCs). But biological functions of relevant isoforms and their clinical applications are still controversial. Here, we investigate the clinical significance and potential function of ALDH1A3 in gliomas. By whole-genome...

Influence of bulking agents on CH4, N2O, and NH3 emissions during rapid composting of pig manure from the Chinese Ganqinfen system

small influence on the loss of total organic carbon, whereas it significantly influenced the loss of total nitrogen. Compliance with ethics guidelines Xiang-ping SUN, Peng LU, Tao JIANG, Frank

Is laparoscopic colorectal cancer surgery associated with an increased risk in obese patients? A retrospective study from China

Xiang Xia 0 Chen Huang 0 Tao Jiang Gang Cen Jun Cao Kejian Huang Zhengjun Qiu 0 Equal contributors Department of General Surgery, Shanghai Jiaotong University Affiliated First People's Hospital

Association of TLR2 and TLR4 Polymorphisms with Risk of Cancer: A Meta-Analysis

Backgrounds The activation of Toll-like receptors (TLRs) may be an important event in the immune evasion of tumor cell. Recently, numerous studies have investigated the associations between TLR2 −196 to −174 del and two SNPs of TLR4 (rs4986790 and rs4986791) and the susceptibility to different types of cancer; however, the results remain conflicting. The aim of this study was to...

Circulating microRNAs in cancer: origin, function and application

MicroRNAs (miRNAs) are a class of small non-coding RNAs that regulate gene expression at the posttranscriptional level. The dysregulation of miRNAs has been linked to a series of diseases, including various types of cancer. Since their discovery in the circulation of cancer patients, there has been a steady increase in the study of circulating miRNAs as stable, non-invasive...

Time-course changes in left ventricular myocardial deformation in STZ-induced rabbits on velocity vector imaging

Objectives To clarify the time-course changes in left ventricular myocardial deformation using velocity vector imaging and to provide insights into our understanding of the cardiac pathophysiology in diabetes mellitus. Methods Thirty New Zealand white rabbits were randomly divided into either the control group (n = 10) or the diabetes mellitus (DM) group (induced with STZ, n = 20...

Three isoforms of the Atg16L1 protein contribute different autophagic properties

The mammalian Atg16L1 protein consists of a coiled-coil domain and a tryptophan-aspartic acid (WD) repeat domain and is involved in the process of autophagy. However, the mechanisms underlying the effect of the Atg16L1 isoforms on autophagy remain to be elucidated in humans. In the present study, we successfully cloned three isoforms: Atg16L1-1, which contains the complete...

An Efficient Algorithm for Haplotype Inference on Pedigrees with a Small Number of Recombinants

Combinatorial (or rule-based) methods for inferring haplotypes from genotypes on a pedigree have been studied extensively in the recent literature. These methods generally try to reconstruct the haplotypes of each individual so that the total number of recombinants is minimized in the pedigree. The problem is NP-hard, although it is known that the number of recombinants in a...

Structural insights into the assembly of human translesion polymerase complexes

In addition to DNA repair pathways, cells utilize translesion DNA synthesis (TLS) to bypass DNA lesions during replication. During TLS, Y-family DNA polymerase (Polη, Polκ, Polı and Rev1) inserts specific nucleotide opposite preferred DNA lesions, and then Polζ consisting of two subunits, Rev3 and Rev7, carries out primer extension. Here, we report the complex structures of Rev3...

Novel core promoter elements in the oomycete pathogen Phytophthora infestans and their influence on expression detected by genome-wide analysis

Background The core promoter is the region flanking the transcription start site (TSS) that directs formation of the pre-initiation complex. Core promoters have been studied intensively in mammals and yeast, but not in more diverse eukaryotes. Here we investigate core promoters in oomycetes, a group within the Stramenopile kingdom that includes important plant and animal...

Isocitrate dehydrogenase 1 Gene Mutation Is Associated with Prognosis in Clinical Low-Grade Gliomas

Isocitrate dehydrogenase 1 gene mutations are found in most World Health Organization grade II and III gliomas and secondary glioblastomas. Isocitrate dehydrogenase 1 mutations are known to have prognostic value in high-grade gliomas. However, their prognostic significance in low-grade gliomas remains controversial. We determined the predictive and prognostic value of isocitrate...

Prognostic Significance of Complications after Laparoscopic Colectomy for Colon Cancer

, decision to publish, or preparation of the manuscript. Competing Interests: The co-author Tao Jiang is a PLOS ONE Editorial Board member. The authors confirm that this does not alter their adherence to PLOS