Using Ontology Fingerprints to disambiguate gene name entities in the biomedical literature.

Ambiguous gene names in the biomedical literature are a barrier to accurate information extraction. To overcome this hurdle, we generated Ontology Fingerprints for selected genes that are relevant for personalized cancer therapy. These Ontology Fingerprints were used to evaluate the association between genes and biomedical literature to disambiguate gene names.

The role of allopregnanolone in the anxiolytic-like effect of free and easy wanderer plus (FEWP), a polyherbal preparation.

Anxiety disorders are the serious and burdensome psychiatric illnesses, which are closely correlated with allopregnanolone. The down-regulation of allopregnanolone biosynthesis has been implicated as the possible contributor to the aetiology of anxiety disorders. Free and easy wanderer plus (FEWP) is a well-known traditional Chinese medicine that had been shown to be effective in various mood disorders.

Adapting a natural language processing tool to facilitate clinical trial curation for personalized cancer therapy.

The design of personalized cancer therapy based upon patients' molecular profile requires an enormous amount of effort to review, analyze and integrate molecular, pharmacological, clinical and patient-specific information. The vast size, rapid expansion and non-standardized formats of the relevant information sources make it difficult for oncologists to gather pertinent information that can support routine personalized treatment. In this paper, we introduce informatics tools that assist the retrieval and curation of cancer-related clinical trials involving targeted therapies.

Adsorption and transport of charged vs. neutral hydrophobic molecules at the membrane of murine erythroleukemia (MEL) cells.

The adsorption and transport of hydrophobic molecules at the membrane surface of pre- and post-DMSO induced differentiated murine erythroleukemia (MEL) cells were examined by time- and wavelength-resolved second harmonic light scattering. Two medium (<600 Da) hydrophobic molecules, cationic malachite green (MG) and neutral bromocresol purple (BCP), were investigated. While it was observed that the MG cation adsorbs onto the surface of the MEL cell, neutral BCP does not.

Enantioselective inhibition of carprofen towards UDP-glucuronosyltransferase (UGT) 2B7.

UDP-glucuronosyltransferases (UGTs)-catalyzed glucuronidation conjugation reaction plays an important role in the elimination of many important clinical drugs and endogenous substances. The present study aims to investigate the enantioselective inhibition of carprofen towards UGT isoforms. In vitro a recombinant UGT isoforms-catalyzed 4-methylumbelliferone (4-MU) glucuronidation incubation mixture was used to screen the inhibition potential of (R)-carprofen and (S)-carprofen towards multiple UGT isoforms.

Effects of exogenous nutrients on polyketide biosynthesis in Escherichia coli.

Heterologous hosts are important platforms for engineering natural product biosynthesis. Escherichia coli is such a host widely used for expression of various biosynthetic enzymes. While numerous studies have been focused on optimizing the expression conditions for desired functional proteins, this work describes how supplement of exogenous nutrients into the fermentation broth influences the formation of natural products in E.

Specific modifications of histone tails, but not DNA methylation, mirror the temporal variation of mammalian recombination hotspots.

Recombination clusters nonuniformly across mammalian genomes at discrete genomic loci referred to as recombination hotspots. Despite their ubiquitous presence, individual hotspots rapidly lose their activities, and the molecular and evolutionary mechanisms underlying such frequent hotspot turnovers (the so-called "recombination hotspot paradox") remain unresolved. Even though some sequence motifs are significantly associated with hotspots, multiple lines of evidence indicate that factors other than underlying sequences, such as epigenetic modifications, may affect the evolution of recombination hotspots.

Regulation profile of phosphatidylcholines (PCs) and lysophosphatidylcholines (LPCs) components towards UDP-glucuronosyltransferases (UGTs) isoforms.

1.Endogenous compounds have been reported to be the regulators of UDP-glucuronosyltransferases (UGTs) isoforms. This study aims to investigate the regulatory effects of the activity of UGT isoforms by two important lipid components phosphatidylcholine (PC) and lysophosphatidylcholines (LPC) using in vitro incubation system.

Evaluating predictive performance of network biomarkers with network structures.

Network is a powerful structure which reveals valuable characteristics of the underlying data. However, previous work on evaluating the predictive performance of network-based biomarkers does not take nodal connectedness into account. We argue that it is necessary to maximize the benefit from the network structure by employing appropriate techniques.

A minimally invasive method for retrieving single adherent cells of different types from cultures.

The field of single-cell analysis has gained a significant momentum over the last decade. Separation and isolation of individual cells is an indispensable step in almost all currently available single-cell analysis technologies. However, stress levels introduced by such manipulations remain largely unstudied.

A movable microelectrode array for chronic basal ganglia single-unit electrocorticogram co-recording in freely behaving rats.

The basal ganglia-cortical circuits are important for information process to brain function. However, chronic recording of single-unit activities in the basal ganglia nucleus has not yet been well established. We present a movable bundled microwire array for chronic subthalamic nucleus (STN) single-unit electrocorticogram co-recording.

Implementation of biomarker-driven cancer therapy: existing tools and remaining gaps.

There has been growing interest in biomarker-driven personalized cancer therapy, also known as precision medicine. Recently, dozens of molecular tests, including next generation sequencing, have been developed to detect biomarkers that have the potential to predict response of cancers to particular targeted therapies. However, detection of cancer-related biomarkers is only the first step in the battle.

Fundamental diversity of human CpG islands at multiple biological levels.

CpG islands (CGIs) are commonly used as genomic markers to study the patterns and regulatory consequences of DNA methylation. Interestingly, recent studies reveal a substantial diversity among CGIs: long and short CGIs, for example, exhibit contrasting patterns of gene expression complexity and nucleosome occupancy. Evolutionary origins of CGIs are also highly heterogeneous.

Arbidol exhibits strong inhibition towards UDP-glucuronosyltransferase (UGT) 1A9 and 2B7.

The aim of the present study was to investigate arbidol's inhibition towards UDP-glucuronosyltransferase (UGT) 1A9 and 2B7. The nonspecific probe substrate 4-methylumbelliferone (4-MU) and recombinant UGT enzymes (UGT1A9, UGT2B7) were firstly used to evaluate the inhibition of arbidol towards UGT1A9 and UGT2B7. Furthermore, specific substrates of UGT1A9 and UGT2B7 propofol and zidovudine (AZT) were used to determine the inhibition of arbidol towards UGT1A9 and UGT2B7.

Modified logistic regression models using gene coexpression and clinical features to predict prostate cancer progression.

Predicting disease progression is one of the most challenging problems in prostate cancer research. Adding gene expression data to prediction models that are based on clinical features has been proposed to improve accuracy. In the current study, we applied a logistic regression (LR) model combining clinical features and gene co-expression data to improve the accuracy of the prediction of prostate cancer progression.

MCF: a tool to find multi-scale community profiles in biological networks.

Recent developments of complex graph clustering methods have implicated the practical applications with biological networks in different settings. Multi-scale Community Finder (MCF) is a tool to profile network communities (i.e.

The Sophora flavescens flavonoid compound trifolirhizin inhibits acetylcholine induced airway smooth muscle contraction.

Asthma is a serious health problem worldwide, particularly in industrialized countries. Despite a better understanding of the pathophysiology of asthma, there are still considerable gaps in knowledge as well as a need for classes of drugs. ASHMI™ (Anti-asthma Herbal Medicine Intervention) is an aqueous extract of Ganoderma lucidum (Fr.

Design and application of an in vivo reporter assay for phenylalanine ammonia-lyase.

Phenylalanine ammonia-lyase (PAL) is an important enzyme that links primary metabolism to secondary metabolism. Its efficiency is often a critical factor that affects the overall flux of a related metabolic pathway, the titer of the final products, and the efficacy of PAL-based therapies. Thus, PAL is a common target for metabolic engineering, and it is of significant interest to screen efficient PALs for industrial and medical applications.

Efficient Semisupervised MEDLINE Document Clustering With MeSH-Semantic and Global-Content Constraints.

For clustering biomedical documents, we can consider three different types of information: the local-content (LC) information from documents, the global-content (GC) information from the whole MEDLINE collections, and the medical subject heading (MeSH)-semantic (MS) information. Previous methods for clustering biomedical documents are not necessarily effective for integrating different types of information, by which only one or two types of information have been used. Recently, the performance of MEDLINE document clustering has been enhanced by linearly combining both the LC and MS information.

Assessment of the association between XRCC1 Arg399Gln polymorphism and lung cancer in Chinese.

X-ray repair cross-complementing group 1 (XRCC1) is one of the major DNA repair proteins involved in the base excision repair and plays an important role in the maintenance of genomic integrity. Polymorphisms in XRCC1 may alter the function and repair capacity of XRCC1 protein which further results in the genetic instability and lung carcinogenesis. Previous studies investigating the relationship between XRCC1 Arg399Gln polymorphism and lung cancer risk in Chinese yielded contradictory results.

Low expression of dendritic cell-specific intercellular adhesion molecule-grabbing nonintegrin-related protein in non-Hodgkin lymphoma and significant correlations with lactic acid dehydrogenase and β2-microglobulin.

Dendritic cell-specific intercellular adhesion molecule-grabbing nonintegrin-related protein (DC-SIGNR), a type II integral membrane protein and a member of the C-type lectins, has been reported to bind various strains of HIV-1, HIV-2, and simian immunodeficiency virus. Serum DC-SIGNR is not currently available for the detection of non-Hodgkin lymphoma (NHL). Using an enzyme-linked immunosorbent assay (ELISA), we assessed the serum levels of DC-SIGNR in 70 cancer patients and 100 healthy controls.

DNA methylation and transcriptional noise.

Background: DNA methylation is one of the most phylogenetically widespread epigenetic modifications of genomic DNA. In particular, DNA methylation of transcription units ('gene bodies') is highly conserved across diverse taxa. However, the functional role of gene body methylation is not yet fully understood.

Engineered production of fungal anticancer cyclooligomer depsipeptides in Saccharomyces cerevisiae.

Two fungal cyclooligomer depsipeptide synthetases(CODSs), BbBEAS (352 kDa) and BbBSLS (348 kDa) from Beauveria bassiana ATCC7159, were reconstituted in Saccharomyces cerevisiae BJ5464-NpgA, leading to the production of the corresponding anticancer natural products, beauvericins and bassianolide, respectively. The titers of beauvericins (33.8 ± 1.

Learning topic models by belief propagation.

Latent Dirichlet allocation (LDA) is an important hierarchical Bayesian model for probabilistic topic modeling, which attracts worldwide interest and touches on many important applications in text mining, computer vision and computational biology. This paper represents the collapsed LDA as a factor graph, which enables the classic loopy belief propagation (BP) algorithm for approximate inference and parameter estimation. Although two commonly used approximate inference methods, such as variational Bayes (VB) and collapsed Gibbs sampling (GS), have gained great success in learning LDA, the proposed BP is competitive in both speed and accuracy, as validated by encouraging experimental results on four large-scale document datasets.

Rational reprogramming of fungal polyketide first-ring cyclization.

Resorcylic acid lactones and dihydroxyphenylacetic acid lactones represent important pharmacophores with heat shock response and immune system modulatory activities. The biosynthesis of these fungal polyketides involves a pair of collaborating iterative polyketide synthases (iPKSs): a highly reducing iPKS with product that is further elaborated by a nonreducing iPKS (nrPKS) to yield a 1,3-benzenediol moiety bridged by a macrolactone. Biosynthesis of unreduced polyketides requires the sequestration and programmed cyclization of highly reactive poly-β-ketoacyl intermediates to channel these uncommitted, pluripotent substrates to defined subsets of the polyketide structural space.