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This page shows you the most recent publications within this specialty of the MedWorm directory.

Incorporating time-delays in S-System model for reverse engineering genetic networks
Conclusion: The four well-known performance measures applied to the experimental studies on synthetic networks with various time-delayed regulations clearly demonstrate that the proposed method can capture both instantaneous and delayed interactions correctly with high precision. The experiments carried out on two well-known real-life networks, namely IRMA and SOS DNA repair network in Escherichia coli show a significant improvement compared with other state-of-the-art approaches for GRN modeling. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - June 18, 2013 Category: Bioinformatics Authors: Ahsan ChowdhuryMadhu ChettyNguyen Vinh Source Type: research

Quantifying single nucleotide variant detection sensitivity in exome sequencing
Conclusions: Non-reference alleles in the heterozygote state have a high chance of being missed when commonly applied read coverage thresholds are used despite the widely held assumption that there is good polymorphism detection at these coverage levels. Such alleles are likely to be of functional importance in population based studies of rare diseases, somatic mutations in cancer and explaining the "missing heritability" of quantitative traits. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - June 18, 2013 Category: Bioinformatics Authors: Alison MeynertLouise BicknellMatthew HurlesAndrew JacksonMartin Taylor Source Type: research

Heat stress--induced response of the proteomes of leaves from Salvia splendens Vista and King
Conclusions: Most of the identified proteins are involved in photosynthesis, metabolism, protein processing, or stress response, indicating that many different processes work together to establish a new cellular homeostasis in response to heat stress. (Source: Proteome Science)
Source: Proteome Science - June 18, 2013 Category: Bioinformatics Authors: Hui LiuGuozheng ShenXianping FangQiaojuan FuKangkang HuangYi ChenHong YuYun ZhaoLe ZhangLiang JinSonglin Ruan Source Type: research

The Aquaporin Channel Repertoire of the Tardigrade Milnesium tardigradum.
Abstract Limno-terrestrial tardigrades are small invertebrates that are subjected to periodic drought of their micro-environment. They have evolved to cope with these unfavorable conditions by anhydrobiosis, an ametabolic state of low cellular water. During drying and rehydration, tardigrades go through drastic changes in cellular water content. By our transcriptome sequencing effort of the limno-terrestrial tardigrade Milnesium tardigradum and by a combination of cloning and targeted sequence assembly, we identified transcripts encoding eleven putative aquaporins. Analysis of these sequences proposed 2 classical a...
Source: Bioinformatics and Biology Insights - June 15, 2013 Category: Bioinformatics Authors: Grohme MA, Mali B, Wełnicz W, Michel S, Schill RO, Frohme M Tags: Bioinform Biol Insights Source Type: research

Association between a multi-locus genetic risk score and inflammatory bowel disease.
Abstract To date, the utility of single genetic markers to improve disease risk assessment still explains only a small proportion of genetic variance for many complex diseases. This missing heritability may be explained by additional variants with weak effects. To discover and incorporate these additional genetic factors, statistical and computational methods must be evaluated and developed. We develop a multi-locus genetic risk score (GRS) based approach to analyze genes in NADPH oxidase complex which may result in susceptibility to development of inflammatory bowel disease (IBD). We find the complex is highly ass...
Source: Bioinformatics and Biology Insights - June 15, 2013 Category: Bioinformatics Authors: Hu P, Muise AM, Xing X, Brumell JH, Silverberg MS, Xu W Tags: Bioinform Biol Insights Source Type: research

Aromatic-aromatic interactions: analysis of π-π interactions in interleukins and TNF proteins.
In this study we have analyzed the roles played by the π-π interactions in interleukins (ILs) and tumor necrosis factor (TNF) proteins. Majority of π-π interacting residues are conserved in ILs and TNF proteins. The accessible surface area calculations in these proteins reveal that these interactions might be important in stabilizing the inner core regions of these proteins. In addition to π-π interactions, the aromatic residues also form π-networks in ILs and TNF proteins. The results obtained in the present study indicate that π-π interactions and π-π networks play important roles in the structural stability o...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Sivasakthi V, Anitha P, Kumar KM, Bag S, Senthilvel P, Lavanya P, Swetha R, Anbarasu A, Ramaiah S Tags: Bioinformation Source Type: research

Binding mode prediction of biologically active compounds from plant Salvia Miltiorrhiza as integrase inhibitor.
Abstract Integrase (IN), an essential enzyme for HIV-1 replication, has been targeted in antiretroviral drug therapy. The emergence of HIV-1 variants clinically resistant to antiretroviral agents has lead to the development of alternative IN inhibitors. In the present work, binding modes of a high potent IN inhibitor, M522 and M532, within the catalytic binding site of wild type (WT) IN were determined using molecular docking calculation. Both M522 and M532 displayed similar modes of binding within the IN putative binding pocket and exhibited favorable interactions with the catalytic Mg(2+) ions, the nearby amino a...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Nunthaboot N, Lugsanangarm K, Kokpol S, Abd-Elazem IS Tags: Bioinformation Source Type: research

Isolation and characterization of ethanol tolerant yeast strains.
Abstract Yeast strains are commonly associated with sugar rich environments. Various fruit samples were selected as source for isolating yeast cells. The isolated cultures were identified at Genus level by colony morphology, biochemical characteristics and cell morphological characters. An attempt has been made to check the viability of yeast cells under different concentrations of ethanol. Ethanol tolerance of each strain was studied by allowing the yeast to grow in liquid YEPD (Yeast Extract Peptone Dextrose) medium having different concentrations of ethanol. A total of fifteen yeast strains isolated from differe...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Tikka C, Osuru HP, Atluri N, Raghavulu PC, Yellapu NK, Mannur IS, Prasad UV, Aluru S, K NV, Bhaskar M Tags: Bioinformation Source Type: research

Design of a set of probes with high potential for influenza virus epidemiological surveillance.
Abstract An Influenza Probe Set (IPS) consisting in 1,249 9-mer probes for genomic fingerprinting of closely and distantly related Influenza Virus strains was designed and tested in silico. The IPS was derived from alignments of Influenza genomes. The RNA segments of 5,133 influenza strains having diverse degree of relatedness were concatenated and aligned. After alignment, 9-mer sites having high Shannon entropy were searched. Additional criteria such as: G+C content between 35 to 65%, absence of dimer or trimer consecutive repeats, a minimum of 2 differences between 9mers and selecting only sequences with Tm valu...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Carreño-Durán LR, Larios-Serrato V, Jaimes-Díaz H, Pérez-Cervantes H, Zepeda-López H, Sánchez-Vallejo CJ, Olguín-Ruiz GE, Maldonado-Rodríguez R, Méndez-Tenorio A Tags: Bioinformation Source Type: research

Binding interactions of porphyrin derivatives with Ca(2+) ATPase of sarcoplasmic reticulum (SERCA1a).
Abstract The use of Porphyrin derivatives as photosensitizers in Photodynamic Therapy (PDT) was investigated by means of a molecular docking study. These molecules can bind to intracellular targets such as P-type CaCa(2+) ATPase of sarcoplasmic reticulum (SERCA1a). CAChe software was successfully employed for conducting the docking of Tetraphenylporphinesulfonate(TPPS), 5,10,15,20- Tetrakis (4-sulfonatophenyl) porphyrinato Iron(III) Chloride (FeTPPS) and 5,10,15,20-Tetrakis (4-sulfonatophenyl) porphyrinato Iron(III) nitrosyl Chloride (FeNOTPPS) with CaCa(2+) ATPase from sarcoplasmic reticulum of rabbit. The results...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Hai A, Kizilbash NA, Zaidi SH, Alruwaili J Tags: Bioinformation Source Type: research

Molecular signaling cascade of miRNAs in causing Diabetes Nephropathy.
Abstract Diabetic nephropathy (DN) is one of the major microvascular diseases and most common in diabetic patient, finally results in kidney failure. The main features of DN are basement membrane thickening, microalbuminuria, proteinuria, glomerular, mesangial hypertrophy and ECM protein accumulation. Recent discoveries have been shown that numerous pathways are activated during the development of DN in Diabetes mellitus. The small non-coding miRNA plays an important role in regulating the pathway which is involved in DN. In our study we consolidate different pathways which regulated by miRNAs in molecular signalin...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Padmashree DG, Swamy NR Tags: Bioinformation Source Type: research

PathAct: a novel method for pathway analysis using gene expression profiles.
Abstract We developed PathAct, a novel method for pathway analysis to investigate the biological and clinical implications of the gene expression profiles. The advantage of PathAct in comparison with the conventional pathway analysis methods is that it can estimate pathway activity levels for individual patient quantitatively in the form of a pathway-by-sample matrix. This matrix can be used for further analysis such as hierarchical clustering and other analysis methods. To evaluate the feasibility of PathAct, comparison with frequently used gene-enrichment analysis methods was conducted using two public microarray...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Mogushi K, Tanaka H Tags: Bioinformation Source Type: research

Preimplantation genetic diagnosis in Saudi Arabia.
In this study only 24% of the embryos were transferred and the remaining was not transferred because of the abnormalities or undesired sex of the embryos. The structural and numerical abnormalities were found to be 16.8%. PMID: 23750087 [PubMed] (Source: Bioinformation)
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Abotalib Z Tags: Bioinformation Source Type: research

Interaction of active compounds from Aegle marmelos CORREA with histamine-1 receptor.
CONCLUSIONS: Based on molecular docking, Amino acid residues involved in ligand protein interactions were Asp107, Lys179, Lys191, Asn198, and Trp428. PMID: 23750086 [PubMed] (Source: Bioinformation)
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Nugroho AE, Agistia DD, Tegar M, Purnomo H Tags: Bioinformation Source Type: research

Molecule of the month: miRNA and Parkinson's disease protein PARK2.
PMID: 23750085 [PubMed] (Source: Bioinformation)
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Shapshak P Tags: Bioinformation Source Type: research

InDiaMed: A Comprehensive Database of Indian Medicinal plants for Diabetes.
Abstract UNLABELLED: According to International Diabetes Federation (IDF), India has 62.4 million people with diabetes and by 2030 it is predicted that the number will rise to 100 million. Studies claim that there are around 410 experimentally proven Indian medicinal plants which have anti-diabetic activity, of which the mechanism of action of 109 plants has been elucidated or reported. So, the need of the hour is to explore the claims of Indian medicinal flora and open up the facets of many Indian plants which are being examined for their beneficial role in diabetes. So, we created a database (InDiaMed) of Indian ...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Tota K, Rayabarapu N, Moosa S, Talla V, Bhyravbhatla B, Rao S Tags: Bioinformation Source Type: research

Phyto diab care: Phytoremedial database for antidiabetics.
Abstract UNLABELLED: Diabetes, a chronic disease debilitating to normal healthy lifestyle, onsets due to insufficient amount of insulin production or ineffective utilization of the amount produced. Although, pharmaceutical research has brought up remedial drugs and numerous candidates in various phases of clinical trials, off-target effects and unwanted physiological actions are a constant source of concern and contra indicatory in case of diabetic patients. Here we present a phytoremedial database, Phyto Diab Care, broadly applicable to any known anti-diabetic medicinal plant and phytochemicals sourced from them. ...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Luhach S, Goel A, Taj G, Goyal P, Kumar A Tags: Bioinformation Source Type: research

An improved hypergeometric probability method for identification of functionally linked proteins using phylogenetic profiles.
Abstract Predicting functions of proteins and alternatively spliced isoforms encoded in a genome is one of the important applications of bioinformatics in the post-genome era. Due to the practical limitation of experimental characterization of all proteins encoded in a genome using biochemical studies, bioinformatics methods provide powerful tools for function annotation and prediction. These methods also help minimize the growing sequence-to-function gap. Phylogenetic profiling is a bioinformatics approach to identify the influence of a trait across species and can be employed to infer the evolutionary history of ...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Kotaru AR, Shameer K, Sundaramurthy P, Joshi RC Tags: Bioinformation Source Type: research

Constructing phylogenetic trees using interacting pathways.
Abstract Phylogenetic trees are used to represent evolutionary relationships among biological species or organisms. The construction of phylogenetic trees is based on the similarities or differences of their physical or genetic features. Traditional approaches of constructing phylogenetic trees mainly focus on physical features. The recent advancement of high-throughput technologies has led to accumulation of huge amounts of biological data, which in turn changed the way of biological studies in various aspects. In this paper, we report our approach of building phylogenetic trees using the information of interactin...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Wan P, Che D Tags: Bioinformation Source Type: research

Heparin-benzyl alcohol enhancement of biofilms formation and antifungal susceptibility of vaginal Candida species isolated from pregnant and nonpregnant Saudi women.
Abstract Biofilm formation by Candida species is a major contribute to their pathogenic potential.The aim of this study was to determine in vitro effects of EDTA, cycloheximide, and heparin-benzyl alcohol preservative on C. albicans (126) and non-albicans (31)vaginal yeast isolates biofilm formations and their susceptibility against three antifungal Etest strips. Results of the crystal violet-assay, indicated that biofilms formation were most commonly observed [100%] for C. kefyr, C. utilis, C. famata, and Rhodotorula mucilaginosa, followed by C. glabrata [70%], C. tropicalis [50%], C. albicans [29%], Saccharomyces...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Al-Akeel RA, El-Kersh TA, Al-Sheikh YA, Al-Ahmadey ZZ Tags: Bioinformation Source Type: research

Statistical analysis of pentose phosphate pathway genes from eubacteria and eukarya reveals translational selection as a major force in shaping codon usage pattern.
Abstract Comparative analysis of metabolic pathways among widely diverse species provides an excellent opportunity to extract information about the functional relation of organisms and pentose phosphate pathway exemplifies one such pathway. A comparative codon usage analysis of the pentose phosphate pathway genes of a diverse group of organisms representing different niches and the related factors affecting codon usage with special reference to the major forces influencing codon usage patterns was carried out. It was observed that organism specific codon usage bias percolates into vital metabolic pathway genes irre...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Pal A, Mukhopadhyay S, Bothra AK Tags: Bioinformation Source Type: research

Artificial signal peptide prediction by a hidden markov model to improve protein secretion via Lactococcus lactis bacteria.
Abstract A hidden Markov model (HMM) has been utilized to predict and generate artificial secretory signal peptide sequences. The strength of signal peptides of proteins from different subcellular locations via Lactococcus lactis bacteria correlated with their HMM bit scores in the model. The results show that the HMM bit score +12 are determined as the threshold for discriminating secreteory signal sequences from the others. The model is used to generate artificial signal peptides with different bit scores for secretory proteins. The signal peptide with the maximum bit score strongly directs proteins secretion. ...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Razmara J, Deris SB, Illias RB, Parvizpour S Tags: Bioinformation Source Type: research

In silico characterization of putative drug targets in Staphylococcus saprophyticus, causing bovine mastitis.
Abstract The bovine mastitis caused by coagulase negative staphylococci (CNS) has increased in many herds of urban and rural areas of India. Emergence of multi drug resistant bacteria has further made its management more complex and serious. Therefore, innovation of novel specific drug for the treatment of disease caused by particular organism remained to be a challenge. Hence, in the present study a bacterium was isolated from milk of the cow with bovine mastitis and was identified as S. saprophyticus, 44 pathways of S. saprophyticus retrieved (KEGG) from web server were found to be non homologous to the host Bos ...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Bhasme PC, Kurjogi MM, Sanakal RD, Kaliwal RB, Kaliwal BB Tags: Bioinformation Source Type: research

Docking studies of piperine - iron conjugate with human CYP450 3A4.
Abstract Piperine, a major constituent of Piper nigrum (Black pepper), is one of the well known components in many Ayurvedic formulations. Piperine is most studied bioenhancer because it inhibits drug metabolizing enzymes in rodents and increases plasma concentrations of several drugs, including P-glycoprotein substrates. However, there areno evidences on piperine-iron conjugate to inhibit human CYP450 3A4. We therefore investigated the influence of piperine-Fe conjugate to study the metabolism of iron with CYP450 3A4. Our in silico results showed that Piperine when conjugated with iron, inhibited activity of CYP45...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Alugolu V, Rentala S, Komarraju AL, Parimi UD Tags: Bioinformation Source Type: research

Chemo-informatic design of antibiotic geldenamycin analogs to target stress proteins HSP90 of pathogenic protozoan parasites.
Abstract Stress proteins HSP90 (Heat shock proteins) are essential molecular chaperones involved in signal transduction, cell cycle control, stress management, folding and degradation of proteins. HSP90 have been found in a variety of organisms including pathogens suggesting that they are ancient and conserved proteins. Here, using molecular modeling and docking protocols, antibiotic Geldenamycin and its analog are targeted to the HSP90 homolog proteins of pathogenic protozoans Plasmodium falciparum, Leishmania donovani, Trypanosoma brucei and Entamoeba Histolytica. The designed analogs of geldenamycin have shown d...
Source: Bioinformation - June 15, 2013 Category: Bioinformatics Authors: Singh C, Atri N Tags: Bioinformation Source Type: research

bioNerDS: exploring bioinformatics' database and software use through literature mining
Conclusions: We demonstrate the feasibility of automatically identifying resource names on a large-scale from the scientific literature and show that the generated data can be used for exploration of bioinformatics database and software usage. For example, our results help to investigate the rate of change in resource usage and corroborate the suspicion that a vast majority of resources are created, but rarely (if ever) used thereafter. bioNerDS is available at http://bionerds.sourceforge.net/. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - June 15, 2013 Category: Bioinformatics Authors: Geraint DuckGoran NenadicAndy BrassDavid RobertsonRobert Stevens Source Type: research

Boosting forward-time population genetic simulators through genotype compression
Conclusions: As evolutionary analyses are being increasingly performed on genomes, pathways, and networks, particularly in the era of systems biology, scaling population genetic simulators to handle large-scale simulations is crucial. We believe our method offers a significant step in that direction. Further, the techniques we provide are generic and can be integrated with existing population genetic simulators to boost their performance in terms of memory usage. (Source: BMC Bioinformatics - Latest articles)
Source: BMC Bioinformatics - Latest articles - June 14, 2013 Category: Bioinformatics Authors: Troy RuthsLuay Nakhleh Source Type: research

PrePrint: A Combination of Feature Extraction Methods with an Ensemble of Different Classifiers for Protein Structural Class Prediction Problem
In this study, we propose a novel feature extraction model which incorporates physicochemical and evolutionary-based information simultaneously. We also propose overlapped segmented distribution and autocorrelation based feature extraction methods to provide more local and global discriminatory information. The proposed feature extraction methods are explored for 15 most promising attributes that are selected from a wide range of physicochemical-based attributes. Finally, by applying an ensemble of different classifiers namely, Adaboost.M1, LogitBoost, Naive Bayes, Multi-Layer Perceptron (MLP), and Support Vector Machine (...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - June 13, 2013 Category: Bioinformatics Source Type: research

PrePrint: Quantitative Analysis of Live-Cell Growth at the Shoot Apex of Arabidopsis thaliana: Algorithms for Feature Measurement and Temporal alignment.
Study of the molecular control of organ growth requires establishment of the causal relationship between gene expression and cell behaviors. We seek to understand this relationship at the shoot apical meristem (SAM) of model plant Arabidopsis thaliana. This requires the spatial mapping and temporal alignment of different functional domains into a single template. Live cell imaging techniques allow us to observe real time organ primordia growth and gene expression dynamics at cellular resolution. In this paper, we propose a framework for measurement of growth features at the 3D reconstructed surface of organ primordia, as w...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - June 13, 2013 Category: Bioinformatics Source Type: research

PrePrint: Informative SNPs Selection Based on Two-Locus and Multilocus Linkage Disequilibrium: Criteria of Max-Correlation and Min-Redundancy
In this study, we innovatively derive optimization criteria by combining two-locus and multilocus LD measure to obtain the criteria of Max-Correlation and Min-Redundancy (MCMR). Then, we use a greedy algorithm to select the candidate set of informative SNPs constrained by the criteria. Finally, we use backward scheme to refine the candidate subset. We separately use small and middle (>1,000 SNPs) datasets to evaluate MCMR in terms of the reconstuction accuracy, the time complexity and the compactness. Additionally, to demonstrate that MCMR is practical for large datasets, we design a parameter w to adapt to vari...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - June 13, 2013 Category: Bioinformatics Source Type: research

PrePrint: Multi-Label Learning via Random Label Selection for Protein Subcellular Multi-Locations Prediction
Prediction of protein subcellular localization is an important but challenging problem, particularly when proteins may simultaneously exist at, or move between, two or more different subcellular location sites. Most of the existing protein subcellular localization methods are only used to deal with the single-location proteins. In the past few years, only a few methods have been proposed to tackle proteins with multiple locations. However, they only adopt a simple strategy, that is, transforming the multi-location proteins to multiple proteins with single location, which doesn't take correlations among different subcellula...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - June 13, 2013 Category: Bioinformatics Source Type: research

PrePrint: Maximum Likelihood Inference of the Evolutionary History of a PPI Network from the Duplication History of its Proteins
Evolutionary history of protein-protein interaction (PPI) networks provides valuable insight into molecular mechanisms of network growth. In this paper, we study how to infer the evolutionary history of a PPI network from its protein duplication relationship. We show that for a plausible evolutionary history of a PPI network, its relative quality, measured by the so-called loss number, is independent of the growth parameters of the network and can be computed efficiently. This finding leads us to propose two fast maximum likelihood algorithms to infer the evolutionary history of a PPI network given the duplication history ...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - June 13, 2013 Category: Bioinformatics Source Type: research

Sparse maximum margin discriminant analysis for feature extraction and gene selection on gene expression data
Abstract: Dimensionality reduction is necessary for gene expression data classification. In this paper, we propose a new method for reducing the dimensionality of gene expression data. First, based on a sparse representation, we developed a new criterion for characterizing the margin, which is called sparse maximum margin discriminant analysis (SMMDA); this approach can be used to find an optimal transform matrix such that the sparse margin is maximal in the transformed space. Second, using SMMDA, we present a new feature extraction method for gene expression data. Third, based on SMMDA, we propose a new discriminant gene ...
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Yan Cui, Chun-Hou Zheng, Jian Yang, Wen Sha Source Type: research

Evaluating the sleep quality of obstructive sleep apnea patients after continuous positive airway pressure treatment
Abstract: Continuous positive airway pressure treatment (CPAP) is administered to treat the common disorder of obstructive sleep apnea. However, patients receiving CPAP treatment without a sleep assessment and clinical diagnosis often do not feel or understand the improvement in their condition, necessitating a sleep quality improvement index for physicians to analyze improvements in patient treatment rapidly. This work presents a novel sleep quality evaluation system that calculates the improvement value for sleep quality using electroencephalogram and electrocardiogram signal features, as well as fuzzy inferences. Experi...
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Chien-Chang Hsu, Jie-Han Wu, Hou-Chang Chiu, Chia-Mo Lin Source Type: research

Mesh quality oriented 3D geometric vascular modeling based on parallel transport frame
Abstract: While a number of methods have been proposed to reconstruct geometrically and topologically accurate 3D vascular models from medical images, little attention has been paid to constantly maintain high mesh quality of these models during the reconstruction procedure, which is essential for many subsequent applications such as simulation-based surgical training and planning. We propose a set of methods to bridge this gap based on parallel transport frame. An improved bifurcation modeling method and two novel trifurcation modeling methods are developed based on 3D Bézier curve segments in order to ensure the continu...
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Jixiang Guo, Shun Li, Yim Pan Chui, Jing Qin, Pheng Ann Heng Source Type: research

Keratin protein property based classification of mammals and non-mammals using machine learning techniques
Abstract: Keratin protein is ubiquitous in most vertebrates and invertebrates, and has several important cellular and extracellular functions that are related to survival and protection. Keratin function has played a significant role in the natural selection of an organism. Hence, it acts as a marker of evolution. Much information about an organism and its evolution can therefore be obtained by investigating this important protein. In the present study, Keratin sequences were extracted from public data repositories and various important sequential, structural and physicochemical properties were computed and used for prepar...
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Amit Kumar Banerjee, Vadlamani Ravi, U.S.N. Murty, Anirudh P. Shanbhag, V. Lakshmi Prasanna Source Type: research

The precision of resting blood pressure measurement
Abstract: By analysis of timed series of blood pressure(BP) measurements from a single individual, it was shown that data-averaging did not usually give a true value of resting systolic or diastolic pressure. Such measurements fitted a pattern of first order decay from an initial pressure towards a resting systolic or diastolic pressure, P. Using non-linear regression analysis it was possible to approach a standard error of 1mmHg/1mmHg for P values on a single day; the between-day dispersion, over a period of months, was found to be about 2mmHg/2mmHg. Computer analysis is required to give values of resting systolic and dia...
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Christopher J. Bailey Source Type: research

A general model for continuous noninvasive pulmonary artery pressure estimation
We present a machine learning model based on heart sounds that estimates pulmonary artery pressure with enough accuracy to exclude an invasive diagnostic operation, allowing for consistent monitoring of heart condition in suspect patients without the cost and risk of invasive monitoring. We conduct a greedy search through 38 possible features using a 109-patient cross-validation to find the most predictive features. Our best general model has a standard estimate of error (SEE) of 8.3mmHg, which outperforms the previous best performance in the literature on a general set of unseen patient data. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Robert Smith, Dan Ventura Source Type: research

Computerized analysis of respiratory sounds during COPD exacerbations
Abstract: Acute exacerbation of chronic obstructive pulmonary disease (AECOPD) is a major event in the natural course of the disease, and is associated with significant mortality and socioeconomic impact. Abnormal respiratory sounds are commonly present in patients with AECOPD. Computerized analysis of these sounds can assist in diagnosis and in evaluation during follow-up. Exploratory data analysis methods were applied to respiratory sounds in these patients when they were hospitalized because of exacerbation. Two different patterns of presentation and evolution of respiratory sounds in AECOPD were found and described fro...
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Daniel Sánchez Morillo, Sonia Astorga Moreno, Miguel Ángel Fernández Granero, Antonio León Jiménez Source Type: research

An ant colony optimization based algorithm for identifying gene regulatory elements
Abstract: It is one of the most important tasks in bioinformatics to identify the regulatory elements in gene sequences. Most of the existing algorithms for identifying regulatory elements are inclined to converge into a local optimum, and have high time complexity. Ant Colony Optimization (ACO) is a meta-heuristic method based on swarm intelligence and is derived from a model inspired by the collective foraging behavior of real ants. Taking advantage of the ACO in traits such as self-organization and robustness, this paper designs and implements an ACO based algorithm named ACRI (ant-colony-regulatory-identification) for ...
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Wei Liu, Hanwu Chen, Ling Chen Source Type: research

An ontology of cancer therapies supporting interoperability and data consistency in EPRs
Abstract: Ontologies can formally describe the semantics of the medical domain in an unambiguous and machine processable form, acting as a conceptual interface between different applications that must interoperate.In this paper we present an ontology of cancer therapies originally developed to bridge the gap between an oncologic Electronic Patient Record (EPR) and a guideline-based decision support system. We show an application of the ontology complemented by rules to classify therapies recorded in the EPR. The results show how such an ontology can be used also to discover possible problems of data consistency in the EPR....
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Claudio Eccher, Alessandro Scipioni, Alexis A. Miller, Antonella Ferro, Domenico M. Pisanelli Source Type: research

Automatic sleep staging from ventilator signals in non-invasive ventilation
Abstract: Non-invasive ventilation (NIV), a recognized treatment for chronic hypercapnic respiratory failure, is predominantly applied at night. Nevertheless, the quality of sleep is rarely evaluated due to the required technological complexity. A new technique for automatic sleep staging is here proposed for patients treated by NIV. This new technique only requires signals (airflow and hemoglobin oxygen saturation) available in domiciliary ventilators plus a photo-plethysmogram, a signal already managed by some ventilators. Consequently, electroencephalogram, electrooculogram, electromyogram, and electrocardiogram recordi...
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Cristina C.R. C.C.R. Sady, Ubiratan S. U.S. Freitas, Adriana Portmann, Jean-François Muir, Christophe Letellier, Luis A. L.A. Aguirre Source Type: research

A femur fracture reduction method based on anatomy of the contralateral side
In this report, we describe a method to rebuild the original femur based on the contralateral side as the reference after ascertaining the bilateral symmetry of the body. The method was tested on animals using the spine model and the experimental results are discussed briefly. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Lei Hu, Jie Zhang, Changsheng Li, Yun Wang, Yan Yang, Peifu Tang, Liming Fang, Lihai Zhang, Hailong Du, Liquan Wang Source Type: research

MREJ: MRE elasticity reconstruction on ImageJ
This study contributes an open-source platform – MREJ – for MRE image processing and elasticity reconstruction. It is established on the widespread image-processing program ImageJ. Two algorithms for elasticity reconstruction were implemented with spatiotemporal directional filtering. The usability of the method is shown through virtual palpation on different phantoms and patients. Based on the results, we conclude that MREJ offers the MRE community a convenient and well-functioning program for image processing and elasticity interpretation. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Kui Xiang, Xia Li Zhu, Chang Xin Wang, Bing Nan Li Source Type: research

Mathematica program: Its use to simulate metabolic irreversible pathways and inhibition of the first enzyme of a pathway by its end product as visualized with the reservoir model
Abstract: The main objective of this report is to show the usefulness and versatility of the Mathematica program to simulate enzyme linear pathways and to depict the effect of changing the Vmax and/or Km values of one or more enzymes on the course of the reaction. In addition, analysis of the different types of inhibition of the first enzyme of the pathway by its end product is viewed with the reservoir model for enzyme kinetics. All the data shown here are quantitatively related to the kinetic constants of the implicated enzymes. Particular attention has been paid to calculate the time needed to achieve half of the possib...
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Francisco López-Cánovas, Paula J.F. Gomes, Antonio Sillero Source Type: research

A feasibility study of diagnosing cardiovascular diseases based on blood/urine element analysis and consensus models
In conclusion, the combination of a consensus DTree classifier and elemental analysis of blood samples can serve as an aid for diagnosis of cardiovascular diseases, especially in routine physical examination. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Hui Chen, Chao Tan, Zan Lin, Tong Wu, Yuanbo Diao Source Type: research

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(Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Source Type: research

Feature extraction and recognition of ictal EEG using EMD and SVM
In this study we propose a novel method for feature extraction and pattern recognition of ictal EEG, based upon empirical mode decomposition (EMD) and support vector machine (SVM). First the EEG signal is decomposed into Intrinsic Mode Functions (IMFs) using EMD, and then the coefficient of variation and fluctuation index of IMFs are extracted as features. SVM is then used as the classifier for recognition of ictal EEG. The experimental results show that this algorithm can achieve the sensitivity of 97.00% and specificity of 96.25% for interictal and ictal EEGs, and the sensitivity of 98.00% and specificity of 99.40% for n...
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Shufang Li, Weidong Zhou, Qi Yuan, Shujuan Geng, Dongmei Cai Source Type: research

An insight into the molecular basis for convergent evolution in fish antifreeze Proteins
Abstract: Antifreeze proteins (AFPs) prevent the growth of ice-crystals in order to enable certain organisms to survive under sub-zero temperature surroundings. These AFPs have evolved from different types of proteins without having any significant structural and sequence similarities among them. However, all the AFPs perform the same function of anti-freeze activity and are a classical example of convergent evolution. We have analyzed fish AFPs at the sequence level, the residue level and the physicochemical property group composition to discover molecular basis for this convergent evolution. Our study on amino acid distr...
Source: Computers in Biology and Medicine - June 13, 2013 Category: Bioinformatics Authors: Abhigyan Nath, Radha Chaube, Karthikeyan Subbiah Source Type: research

PrePrint: Operon Prediction using Chaos Embedded Particle Swarm Optimization
Operons contain valuable information for drug design and determining protein functions. Genes within an operon are co-transcribed to a single-strand mRNA and must be co-regulated. The identification of operons is thus critical for a detailed understanding of the gene regulations. However, currently used experimental methods for operon detection are generally difficult to implement and time-consuming. In this paper, we propose a chaotic binary particle swarm optimization (CBPSO) to predict operons in bacterial genomes. The intergenic distance, participation in the same metabolic pathway and the cluster of orthologous groups...
Source: IEEE/ACM Transactions on Computational Biology and Bioinformatics - June 13, 2013 Category: Bioinformatics Source Type: research