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221 papers found.
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-OMICS AND PROGNOSTIC MARKERS

BACKGROUND: Glioblastomas, the most common primary brain tumors in adults, still continue to have a predominantly fatal outcome. We previously cloned NPAS3 (neuronal PAS 3), a gene which is among the largest genes in the human genome and encodes a transcription factor. We recently discovered NPAS3 drives the progression of malignant astrocytomas as a tumor suppressor, by...

A Broadly Flavivirus Cross-Neutralizing Monoclonal Antibody that Recognizes a Novel Epitope within the Fusion Loop of E Protein

Flaviviruses are a group of human pathogenic, enveloped RNA viruses that includes dengue (DENV), yellow fever (YFV), West Nile (WNV), and Japanese encephalitis (JEV) viruses. Cross-reactive antibodies against Flavivirus have been described, but most of them are generally weakly neutralizing. In this study, a novel monoclonal antibody, designated mAb 2A10G6, was determined to have...

A Systems Biology-Based Gene Expression Classifier of Glioblastoma Predicts Survival with Solid Tumors

Accurate prediction of survival of cancer patients is still a key open problem in clinical research. Recently, many large-scale gene expression clusterings have identified sets of genes reportedly predictive of prognosis; however, those gene sets shared few genes in common and were poorly validated using independent data. We have developed a systems biology-based approach by...

A Truncation in the Aryl Hydrocarbon Receptor of the CRL:WI(Han) Rat Does Not Affect the Developmental Toxicity of TCDD

The aryl hydrocarbon receptor (AhR) is required for the toxicity of 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD), and so the AhR of CRL:WI and CRL:WI(Han) rats was characterized. Western blot showed AhR proteins of ∼110 and ∼97 kDa in individual rats from both strains. The AhR cDNA from a CRL:WI(Han) rat with the ∼110-kDa protein revealed a sequence that was identical to that of...

A comparative analysis of ESM-1 and vascular endothelial cell marker (CD34/CD105) expression on pituitary adenoma invasion

Objective Pituitary adenomas are benign neoplasms that display invasive behavior—a characteristic traditionally associated with malignancy—through an ill-defined mechanism. The role of angiogenesis-related molecules in this pathological condition remains perplexing. Our purpose is to assess the impact of endocan (endothelial cell specific molecule-1, ESM-1), CD34 and CD105 on...

A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus

A duplex real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay was improved for simultaneous detection of highly pathogenic H5N1 avian influenza virus and pandemic H1N1 (2009) influenza virus, which is suitable for early diagnosis of influenza-like patients and for epidemiological surveillance. The sensitivity of this duplex real-time RT-PCR assay was 0.02...

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...

A linear-time algorithm for reconstructing zero-recombinant haplotype configuration on a pedigree

Background When studying genetic diseases in which genetic variations are passed on to offspring, the ability to distinguish between paternal and maternal alleles is essential. Determining haplotypes from genotype data is called haplotype inference. Most existing computational algorithms for haplotype inference have been designed to use genotype data collected from individuals in...

A maximum common substructure-based algorithm for searching and predicting drug-like compounds

Motivation: The prediction of biologically active compounds is of great importance for high-throughput screening (HTS) approaches in drug discovery and chemical genomics. Many computational methods in this area focus on measuring the structural similarities between chemical structures. However, traditional similarity measures are often too rigid or consider only global...

A novel reporter system for neutralizing and enhancing antibody assay against dengue virus

Background Dengue virus (DENV) still poses a global public health threat, and no vaccine or antiviral therapy is currently available. Antibody plays distinct roles in controlling DENV infections. Neutralizing antibody is protective against DENV infection, whereas sub-neutralizing concentration of antibody can increase DENV infection, termed antibody-dependent enhancement (ADE...

A preliminary examination of the diagnostic value of deep learning in hip osteoarthritis

Chen 0 Tao Jiang 1 0 Infervision , Beijing , China 1 Department of Radiology, Beijing Chaoyang Hospital Affiliated to Capital Medical University , Beijing , China Hip Osteoarthritis (OA) is a common

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...

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...

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...

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...

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...

Adiponectin improves NF-κB-mediated inflammation and abates atherosclerosis progression in apolipoprotein E-deficient mice

Background Atherosclerosis is a common pathological basis of cardiovascular disease. Adiponectin (APN) has been shown to have an anti-atherosclerosis effect, and the underlying mechanisms, however, are largely unknown. Nuclear factor κB (NF-κB) has also been regarded as a proatherogenic factor, mainly because of its regulation of a variety of the proinflammatory genes linked to...

Age-period-cohort analysis for trends in body mass index in Ireland

Background Obesity is a growing problem worldwide and can often result in a variety of negative health outcomes. In this study we aim to apply partial least squares (PLS) methodology to estimate the separate effects of age, period and cohort on the trends in obesity as measured by body mass index (BMI). Methods Using PLS we will obtain gender specific linear effects of age...

AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references

Motivation: De novo assemblies of genomes remain one of the most challenging applications in next-generation sequencing. Usually, their results are incomplete and fragmented into hundreds of contigs. Repeats in genomes and sequencing errors are the main reasons for these complications. With the rapidly growing number of sequenced genomes, it is now feasible to improve assemblies...

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...