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221 papers found.
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bmo-miR-0001 and bmo-miR-0015 down-regulate expression of Bombyx mori fibroin light chain gene in vitro

mechanisms of silk protein biosynthesis. Compliance with ethics guidelines Chen CHEN, Yang-yang FAN, Xin WANG, Fei SONG, Tao JIANG, Ping QIAN, Shun-ming TANG, and Xing-jia SHEN declare that they have no

Phylogeny-based classification of microbial communities

Motivation: Next-generation sequencing coupled with metagenomics has led to the rapid growth of sequence databases and enabled a new branch of microbiology called comparative metagenomics. Comparative metagenomic analysis studies compositional patterns within and between different environments providing a deep insight into the structure and function of complex microbial...

TIMP1 is a prognostic marker for the progression and metastasis of colon cancer through FAK-PI3K/AKT and MAPK pathway

Background Tissue inhibitor matrix metalloproteinase 1 (TIMP1) plays a vital role in carcinogenesis, yet its precise functional roles and regulation remain unclear. In this study, we aim to investigate its biological function and clinical significance in human colon cancer. Methods We analyzed the expression of TIMP1 in both public database (Oncomine and TCGA) and 94 cases of...

Development of an immunochromatographic strip for the serodiagnosis of Theileria infection in sheep

Background Theileria uilenbergi and T. luwenshuni are tick-borne protozoan parasites, transmitted by Haemaphysalis qinghaiensis and H. longicornis, respectively. They are the main causative agents of theileriosis in small ruminants in China. The disease has resulted in severe economic losses and hindered the development of sheep and goat husbandry industry in the endemic regions...

Release of Si from Silicon, a Ferrosilicon (FeSi) Alloy and a Synthetic Silicate Mineral in Simulated Biological Media

Unique quantitative bioaccessibility data has been generated, and the influence of surface/material and test media characteristics on the elemental release process were assessed for silicon containing materials in specific synthetic body fluids at certain time periods at a fixed loading. The metal release test protocol, elaborated by the KTH team, has previously been used for...

Detection of Homologous Recombination Events in Bacterial Genomes

We study the detection of mutations, sequencing errors, and homologous recombination events (HREs) in a set of closely related microbial genomes. We base the model on single nucleotide polymorphisms (SNPs) and break the genomes into blocks to handle the rearrangement problem. Then we apply a dynamic programming algorithm to model whether changes within each block are likely a...

Comparison of Retrograde Balloon Dilatation and Laparoscopic Pyeloplasty for Treatment of Ureteropelvic Junction Obstruction: Results of a 2-Year Follow-Up

Objective To evaluate the efficacy of laparoscopic pyeloplasty relative to retrograde balloon dilatation for the treatment of ureteropelvic junction obstruction (UPJO). Methods This retrospective study enrolled UPJO patients with stricture length < 2 cm who had been treated with laparoscopic pyeloplasty (LP; 44 cases) or balloon dilatation (BD; 38 cases) from Jan 2010 to Jan 2012...

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...

A single aspergillus fumigatus intracranial abscess in an immunocompetent patient with parietal lobe tumorectomy

Aspergillosis of the central nervous system is a rare fungal infection that is mainly reported in patients with immune deficiency, such as AIDS patients and organ transplant patients treated with immunosuppressive agents, and is uncommon among patients with intact immune function. We report here a rare case of intracranial aspergillosis in a patient who had previously undergone a...

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...

Tumor Detection at 3 Tesla with an Activatable Cell Penetrating Peptide Dendrimer (ACPPD-Gd), a T1 Magnetic Resonance (MR) Molecular Imaging Agent

Purpose The ability to detect small malignant lesions with magnetic resonance imaging (MRI) is limited by inadequate accumulations of Gd with standard chelate agents. To date, no T1-targeted agents have proven superiority to Gd chelates in their ability to detect small tumors at clinically relevant field strengths. Activatable cell-penetrating peptides and their Gd-loaded...

Diagnostic Value of SFRP1 as a Favorable Predictive and Prognostic Biomarker in Patients with Prostate Cancer

Growing genetic and molecular biological evidence suggests that the disruption of balance between Secreted Frizzled-Related Protein-1 (SFRP1) and β-catenin plays an important role in the initiation and development of multiple cancers. The aim of this study was to examine whether the expression of SFRP1 and β-catenin is associated with the clinical-pathologic features of patients...

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...

Accurate inference of isoforms from multiple sample RNA-Seq data

Background RNA-Seq based transcriptome assembly has become a fundamental technique for studying expressed mRNAs (i.e., transcripts or isoforms) in a cell using high-throughput sequencing technologies, and is serving as a basis to analyze the structural and quantitative differences of expressed isoforms between samples. However, the current transcriptome assembly algorithms are...

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...

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...

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...

Revealing an outward-facing open conformational state in a CLC Cl-/H+ exchange transporter

CLC secondary active transporters exchange Cl- for H+. Crystal structures have suggested that the conformational change from occluded to outward-facing states is unusually simple, involving only the rotation of a conserved glutamate (Gluex) upon its protonation. Using 19F NMR, we show that as [H+] is increased to protonate Gluex and enrich the outward-facing state, a residue ~20...