MedWorm: Bioinformatics Top 20

Explication of interactions between HMGCR isoform 2 and various statins through In silico modeling and docking

Computers in Biology and Medicine — Sun, 22 Jan 2012 03:06:38 +0100

This study was designed to understand the mode of interactions of HMGCR isoform 2 with other statins. Hence, ligands such as Atorvastatin (DB01076), Lovastatin (DB00227), Fluvastatin (DB01095), Simvastatin (DB00641), Pravastatin (DB00175), Rosuvastatin (DB01098) and Cerivastatin (DB00439) were docked with enzymes HMGCR isoform 1 (pdb: 1DQ8) and modeled HMGCR isoform 2 (gi|196049380). Our homology modeling results were further processed to model the structure of human HMGCR isoform 2 and its accuracy was confirmed through RMS Z-scores (1.249). These interactions revealed that binding residues such as Arg515, Asp516, Tyr517 and Asn518 are found to be conserved in HMGCR isoform 2 with various statins. Our studies further concluded that Atorvastatin is most efficient inhibitor against both the...

MedWorm Message: Get the very latest Swine Flu news via the MedWorm Swine Flu RSS news feed - updated hourly from thousands of authoritative health and news sources.

Improved modeling of clinical data with kernel methods

Artificial Intelligence in Medicine — Sun, 22 Jan 2012 03:06:39 +0100

Conclusion: For clinical data consisting of variables of different types, the proposed kernel function – which takes into account the type and range of each variable – has shown to be a better alternative for linear and non-linear classification problems. (Source: Artificial Intelligence in Medicine)

A simple statistical test to infer the causality of target/phenotype correlation from small molecule phenotypic screens

Bioinformatics — Mon, 30 Jan 2012 05:00:00 +0100

This study indicates that, empowered by appropriate statistical adjustment, small molecule inhibitor perturbation remains a powerful tool to pin down the relevant biomarker for drug safety and efficacy research. Contact: xin.wei@roche.com Supplementary information: Supplementary data are available at Bioinformatics online. (Source: Bioinformatics)

Machine learning algorithms and forced oscillation measurements applied to the automatic identification of chronic obstructive pulmonary disease

Computer Methods and Programs in Biomedicine — Wed, 25 Jan 2012 04:50:49 +0100

In conclusion, the results of this study indicate that the proposed classifiers may contribute to easy the diagnostic of COPD by using forced oscillation measurements. (Source: Computer Methods and Programs in Biomedicine)

Passive fetal monitoring by adaptive wavelet denoising method

Computers in Biology and Medicine — Sun, 22 Jan 2012 03:06:38 +0100

Abstract: Fetal Heart Rate (FHR) monitoring is one of the most important fetal well being tests. Existing FHR monitoring methods are based on Doppler ultrasound technique, which has several disadvantages. Passive fetal monitoring by phonocardiography is an appropriate alternative; however, its implementation is a challenging task due to low energy of fetal heart sounds and multiple interference signals presence. In this paper, an advanced signal processing method for passive fetal monitoring based on adaptive wavelet denoising is presented. The method's performance is compared with Doppler ultrasound monitor. The results show 94–97.5% accuracy, including highly disturbed cases. (Source: Computers in Biology and Medicine)

Editorial Board & Publication information

Computers in Biology and Medicine — Sun, 22 Jan 2012 03:06:38 +0100

(Source: Computers in Biology and Medicine)

MedWorm Message: Get the very latest Swine Flu news via the MedWorm Swine Flu RSS news feed - updated hourly from thousands of authoritative health and news sources.

Spectral analysis of heart rate variability with the autoregressive method: What model order to choose?

Computers in Biology and Medicine — Sun, 22 Jan 2012 03:06:38 +0100

Abstract: This work assessed the influence of the autoregressive model order (ARMO) on the spectral analysis of the heart rate variability (HRV). A sample of 68 R–R series obtained from digital ECG records of young healthy adults in the supine position was used. Normalized spectral indexes for each ARMO were compared by Friedman test followed by the Dunn's procedure and statistical significance was set at P (Source: Computers in Biology and Medicine)

Modeling porous scaffold microstructure by a reaction–diffusion system and its degradation by hydrolysis

Computers in Biology and Medicine — Sun, 22 Jan 2012 03:06:38 +0100

Abstract: One of the most important areas of Tissue Engineering is the research about bone regeneration and the replacement of its function. To meet this requirement, scaffolds have been developed to allow the cell migration, the growth of bone tissue, the transport of growth factors and nutrients and the renovation of the mechanical properties of bone. Scaffolds are made of different biomaterials and manufactured using various techniques that, in some cases, do not allow full control over the size and orientation of the pores that characterize the scaffold microstructure. From this perspective, we propose a novel hypothesis that a reaction–diffusion system can be used to design the geometrical specifications of the bone matrix. The validation of this hypothesis is performed by simulatio...

Factors Affecting Intention among Students to Be Vaccinated against A/H1N1 Influenza: A Health Belief Model Approach

EURASIP Journal on Bioinformatics and Systems Biology — Tue, 20 Dec 2011 15:07:57 +0100

This study examined the factors affecting the intention to be vaccinated against the swine flu among students in Israel. Questionnaires were distributed in December 2009 among 387 students at higher-education institutions. The research questionnaire included sociodemographic characteristics and Health Belief Model principles. The results show that the factors positively affecting the intention to take the swine flu vaccine were past experience with seasonal flu shot and three HBM categories: higher levels of perceived susceptibility for catching the illness, perceived seriousness of illness, and lower levels of barriers. We conclude that offering the vaccine at workplaces may raise the intention to take the vaccine among young people in Israel. (Source: EURASIP Journal on Bioinformatics an...

Computational model for analyzing the evolutionary patterns of the neuraminidase gene of influenza A/H1N1.

Computational Biology and Chemistry — Fri, 30 Dec 2011 05:00:00 +0100

In this study, we performed computer simulations to evaluate the changes of selection potentials of codons in influenza A/H1N1 from 1999 to 2009. We artificially generated the sequences by using the transition matrices of positively selected codons over time, and their similarities against the database of influenzavirus A genus were determined by BLAST search. This is the first approach to predict the evolutionary direction of influenza A virus (H1N1) by simulating the codon substitutions over time. We observed that the BLAST results showed the high similarities with pandemic influenza A/H1N1 in 2009, suggesting that the classical human-origin influenza A/H1N1 isolated before 2009 might contain some selection potentials of swine-origin viruses. Computer simulations using the time series co...

Single stage and multistage classification models for the prediction of liver fibrosis degree in patients with chronic hepatitis C infection

Computer Methods and Programs in Biomedicine — Wed, 25 Jan 2012 04:50:49 +0100

Abstract: Predicting significant fibrosis or cirrhosis in patients with hepatitis C virus has persistently preoccupied the research agenda of many specialized research centers. Many studies have been conducted to evaluate the use of readily available laboratory tests to predict significant fibrosis or cirrhosis with the purpose to substantially reduce the number of biopsies performed. Although many of them reported significant predictive values of several serum markers for the diagnosis of cirrhosis, none of these diagnostic techniques was successful in accurately predicting early stages of liver fibrosis. Therefore, in this study a single stage classification model and a multistage stepwise classification model based on Neural Network, Decision Tree, Logistic Regression, and Nearest Neigh...

MedWorm Message: Get the very latest Swine Flu news via the MedWorm Swine Flu RSS news feed - updated hourly from thousands of authoritative health and news sources.

Using partial decision trees to predict Parkinson’s symptoms: A new approach for diagnosis and therapy in patients suffering from Parkinson’s disease

Computers in Biology and Medicine — Sun, 22 Jan 2012 03:06:38 +0100

Abstract: In this work we present a method based on partial decision trees and association rules for the prediction of Parkinson's disease (PD) symptoms. The proposed method is part of the PERFORM system. PERFORM is used for the treatment of PD patients and even advocate specific combinations of medications. The approach presented in this paper is included in the data miner module of PERFORM. A patient performs some initial examinations and the module predicts the future occurrence of the symptoms based on the initial examinations and medications taken. Using the method, the expert can prescribe specific medications that will not cause, or postpone the appearance of specific symptoms to the patient. The approach employed is able to provide interpretation for the predictions made, by provid...

Propagating semantic information in biochemical network models

BMC Bioinformatics - Latest articles — Mon, 30 Jan 2012 05:00:00 +0100

Conclusions: Semantic propagation and model alignment are included in the open-source library semanticSBML, available on sourceforge. Online services for model alignment and for annotation prediction can be used at http://www.semanticsbml.org. (Source: BMC Bioinformatics - Latest articles)

Improving the medical scale predictability by the pairwise comparisons method: Evidence from a clinical data study

Computer Methods and Programs in Biomedicine — Wed, 25 Jan 2012 04:50:49 +0100

Abstract: In the clinical practice of psychiatry, presence or absence of particular symptoms is based on the subjective interpretation, by the clinician, of mental and behavioural descriptions offered by the patient. However, this subjectivity that characterizes the diagnostic decision making process may limit the reliability of diagnosis. In this current study, the pairwise comparisons (PC) method is used to investigate whether the psychometric properties of a medical screening questionnaire can be improved. The pilot data described herein did indeed demonstrate that modest improvements in diagnostic accuracy could be achieved using PC, and provides early evidence that the inconsistency produced by subjective clinical ratings can be reduced using this method, thus providing impetus for fu...

PrePrint: GSGS: A Computational Approach to Reconstruct Signaling Pathway Structures from Gene Sets

IEEE/ACM Transactions on Computational Biology and Bioinformatics — Sat, 07 Jan 2012 10:32:40 +0100

Reconstruction of signaling pathway structures is essential to decipher complex regulatory relationships in living cells. Existing approaches often rely on unrealistic biological assumptions and do not explicitly consider signal transduction mechanisms. Signal transduction events refer to linear cascades of reactions from cell surface to nucleus and characterize a signaling pathway. We propose a novel approach, Gene Set Gibbs Sampling, to reverse engineer signaling pathway structures from gene sets related to pathways. We hypothesize that signaling pathways are structurally an ensemble of overlapping linear signal transduction events which we encode as Information Flows (IFs). We infer signaling pathway structures from gene sets, referred to as Information Flow Gene Sets (IFGSs), correspon...

DMAN: a Java tool for analysis of multi-well differential scanning fluorimetry experiments

Bioinformatics — Mon, 30 Jan 2012 05:00:00 +0100

Summary: Differential scanning fluorimetry (DSF) is a rapid technique that can be used in structural biology to study protein–ligand interactions. We have developed DMAN, a novel tool to analyse multi-well plate data obtained in DSF experiments. DMAN is easy to install and provides a user-friendly interface. Multi-well plate layouts can be designed by the user and experimental data can be annotated and analysed by DMAN according to the specified plate layout. Statistical tests for significance are performed automatically, and graphical tools are also provided to assist in data analysis. The modular concept of this software will allow easy development of other multi-well plate analysis applications in the future. Availability and implementation: DMAN is implemented in Java to provide ...

MedWorm Message: Get the very latest Swine Flu news via the MedWorm Swine Flu RSS news feed - updated hourly from thousands of authoritative health and news sources.

Construction and completion of flux balance models from pathway databases

Bioinformatics — Mon, 30 Jan 2012 05:00:00 +0100

We present a multiple gap-filling method to accelerate the development of FBA models using a new tool, called MetaFlux, based on mixed integer linear programming (MILP). The method suggests corrections to the sets of reactions, biomass metabolites, nutrients and secretions. The method generates FBA models directly from Pathway/Genome Databases. Thus, FBA models developed in this framework are easily queried and visualized using the Pathway Tools software. Predicted fluxes are more easily comprehended by visualizing them on diagrams of individual metabolic pathways or of metabolic maps. MetaFlux can also remove redundant high-flux loops, solve FBA models once they are generated and model the effects of gene knockouts. MetaFlux has been validated through construction of FBA models for Escher...

Minimal cut sets in a metabolic network are elementary modes in a dual network

Bioinformatics — Mon, 30 Jan 2012 05:00:00 +0100

Motivation: Elementary modes (EMs) and minimal cut sets (MCSs) provide important techniques for metabolic network modeling. Whereas EMs describe minimal subnetworks that can function in steady state, MCSs are sets of reactions whose removal will disable certain network functions. Effective algorithms were developed for EM computation while calculation of MCSs is typically addressed by indirect methods requiring the computation of EMs as initial step. Results: In this contribution, we provide a method that determines MCSs directly without calculating the EMs. We introduce a duality framework for metabolic networks where the enumeration of MCSs in the original network is reduced to identifying the EMs in a dual network. As a further extension, we propose a generalization of MCSs in metabolic...

Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data

Bioinformatics — Mon, 30 Jan 2012 05:00:00 +0100

We describe a new, substantially redesigned version of our tool Metscape that allows users to enter experimental data for metabolites, genes and pathways and display them in the context of relevant metabolic networks. Metscape 2 uses an internal relational database that integrates data from KEGG and EHMN databases. The new version of the tool allows users to identify enriched pathways from expression profiling data, build and analyze the networks of genes and metabolites, and visualize changes in the gene/metabolite data. We demonstrate the applications of Metscape to annotate molecular pathways for human and mouse metabolites implicated in the pathogenesis of sepsis-induced acute lung injury, for the analysis of gene expression and metabolite data from pancreatic ductal adenocarcinoma, an...

PathVar: analysis of gene and protein expression variance in cellular pathways using microarray data

Bioinformatics — Mon, 30 Jan 2012 05:00:00 +0100

Summary: Finding significant differences between the expression levels of genes or proteins across diverse biological conditions is one of the primary goals in the analysis of functional genomics data. However, existing methods for identifying differentially expressed genes or sets of genes by comparing measures of the average expression across predefined sample groups do not detect differential variance in the expression levels across genes in cellular pathways. Since corresponding pathway deregulations occur frequently in microarray gene or protein expression data, we present a new dedicated web application, PathVar, to analyze these data sources. The software ranks pathway-representing gene/protein sets in terms of the differences of the variance in the within-pathway expression levels ...