MedWorm.com provides a medical RSS filtering service. Over 6000 RSS medical sources are combined and output via different filters. This feed contains the latest items from the 'Computers in Biology and Medicine' source. Thu, 09 Feb 2012 22:12:27 +0100 http://www.medworm.com/index.php?rid=5617674&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002368%2Fabstract%3Frss%3Dyes We present a software (ETHOWATCHER®) developed to support ethography, object tracking and extraction of kinematic variables from digital video files of laboratory animals. The tracking module allows controlled segmentation of the target from the background, extracting image attributes used to calculate the distance traveled, orientation, length, area and a path graph of the experimental animal. The ethography module allows recording of catalog-based behaviors from environment or from video files continuously or frame-by-frame. The output reports duration, frequency and latency of each behavior and the sequence of events in a time-segmented format, set by the user. Validation tests were conducted on kinematic measurements and on the detection of known behavioral effects of drugs. This soft... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617674 Sun, 22 Jan 2012 03:06:38 +0100 5617674 http://www.medworm.com/index.php?rid=5617673&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002344%2Fabstract%3Frss%3Dyes Abstract: Biclustering is becoming a popular technique for the study of gene expression data. This is mainly due to the capability of biclustering to address the data using various dimensions simultaneously, as opposed to clustering, which can use only one dimension at the time. Different heuristics have been proposed in order to discover interesting biclusters in data. Such heuristics have one common characteristic: they are guided by a measure that determines the quality of biclusters. It follows that defining such a measure is probably the most important aspect. One of the popular quality measure is the mean squared residue (MSR). However, it has been proven that MSR fails at identifying some kind of patterns. This motivates us to introduce a novel measure, called virtual error (VE), th... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617673 Sun, 22 Jan 2012 03:06:38 +0100 5617673 http://www.medworm.com/index.php?rid=5617672&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002320%2Fabstract%3Frss%3Dyes Abstract: Many high cognitive applications, such as vision processing and representation and understanding of images, often need to analyse in detail how an ongoing visual search was performed in a representative subset of the image, which may be arranged into sequences of loci, called regions of interest (ROIs). We used the Trial Making Test (TMT) in which subjects are asked to fixate a sequence of letters and numbers in a logical alphanumeric order. The main characteristic of TMT is to force the subject to perform a default and well-known path. The comparison of the expected scan-path with the observed scan-path provides a valuable method to investigate how a task force the subject to maintain a top-down internal representation of execution and how bottom-up influences the performance. W... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617672 Sun, 22 Jan 2012 03:06:38 +0100 5617672 http://www.medworm.com/index.php?rid=5617671&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002319%2Fabstract%3Frss%3Dyes Abstract: A number of recent studies have shown that loop-design is more efficient than reference control design. Data analysis for loop-design microarray experiments is commonly undertaken using linear models and statistical tests. These techniques require specialized knowledge in statistical programming. However, limited loop-design web-based tools are available. We have developed the THEME (Tsing Hua Engine of Microarray Experiment) that exploits all necessary data analysis tools for loop-design microarray studies. THEME allows users to construct linear models and to apply multiple user-defined statistical tests of hypotheses for detection of DEG (differentially expressed genes). Users can modify entries of design matrix for experimental design as well as that of contrast matrix for sta... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617671 Sun, 22 Jan 2012 03:06:38 +0100 5617671 http://www.medworm.com/index.php?rid=5617670&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002307%2Fabstract%3Frss%3Dyes Abstract: Analysis of gene expression profiles needs a complete matrix of gene array values; consequently, imputation methods have been suggested. In this paper, an algorithm that is based on conjugate gradient (CG) method is proposed to estimate missing values. k-nearest neighbors of the missed entry are first selected based on absolute values of their Pearson correlation coefficient. Then a subset of genes among the k-nearest neighbors is labeled as the best similar ones. CG algorithm with this subset as its input is then used to estimate the missing values.Our proposed CG based algorithm (CGimpute) is evaluated on different data sets. The results are compared with sequential local least squares (SLLSimpute), Bayesian principle component analysis (BPCAimpute), local least squares imputat... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617670 Sun, 22 Jan 2012 03:06:38 +0100 5617670 http://www.medworm.com/index.php?rid=5617669&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002290%2Fabstract%3Frss%3Dyes Abstract: Identifying patients in a Target Customer Segment (TCS) is important to determine the demand for, and to appropriately allocate resources for, health care services. The purpose of this study is to propose a two-stage clustering-classification model through (1) initially integrating the RFM attribute and K-means algorithm for clustering the TCS patients and (2) then integrating the global discretization method and the rough set theory for classifying hospitalized departments and optimizing health care services. To assess the performance of the proposed model, a dataset was used from a representative hospital (termed Hospital-A) that was extracted from a database from an empirical study in Taiwan comprised of 183,947 samples that were characterized by 44 attributes during 2008. The... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617669 Sun, 22 Jan 2012 03:06:38 +0100 5617669 http://www.medworm.com/index.php?rid=5617668&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002289%2Fabstract%3Frss%3Dyes Abstract: We evaluated whether frequency analysis could detect the development of interstitial fibrosis in rats. SHR/Izm and age-matched WKY/Izm were used. Limb lead II electrocardiograms were recorded. Continuous wavelet transform (CWT) was applied for the time–frequency analysis. The integrated time–frequency power (ITFP) between QRS complexes was measured and compared between groups. The ITFP at low-frequency bands (≤125Hz) was significantly higher in SHR/Izm. The percent change of ITFP showed the different patterns between groups. Prominent interstitial fibrosis with an increase in TIMP-1 mRNA expression was also observed in SHR/Izm. These results were partly reproduced in a computer simulation. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617668 Sun, 22 Jan 2012 03:06:38 +0100 5617668 http://www.medworm.com/index.php?rid=5617667&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002277%2Fabstract%3Frss%3Dyes 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... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617667 Sun, 22 Jan 2012 03:06:38 +0100 5617667 http://www.medworm.com/index.php?rid=5617666&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002265%2Fabstract%3Frss%3Dyes Abstract: Set enrichment analysis (SEA) is used to identify enriched biological categories/terms within high-throughput differential expression experiments. This is done by evaluating the proportion of differentially expressed genes against a background reference (BR). However, the choice of the “appropriate” BR is a perplexing problem and results will depend on it.Here, a visualization procedure that integrates results from several BRs and a stability analysis of enriched terms is presented as a tool to aid SEA. The multi-reference contrast method (MRCM) combines results from multiple BRs in a unique picture. The application of the proposed method was illustrated in one proteomic and three microarray experiments. The MRCM facilitates the exploration task involved in ontology analysis ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617666 Sun, 22 Jan 2012 03:06:38 +0100 5617666 http://www.medworm.com/index.php?rid=5617665&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002253%2Fabstract%3Frss%3Dyes Abstract: Knowing the subcellular localization of proteins within the cell is an important step in elucidating its role in biological processes, its function and its potential as a drug target for disease diagnosis. As the number of complete genomes rapidly increases, accurate and efficient methods that automatically predict the subcellular localizations become more urgent. In the current paper, we developed a novel method that coupled the discrete wavelet transform with support vector machine based on the amino acid polarity to predict the subcellular localizations of prokaryotic and eukaryotic proteins. The results obtained by the jackknife test were quite promising, and indicated that the proposed method remarkably improved the prediction accuracy of subcellular locations, and could be ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617665 Sun, 22 Jan 2012 03:06:38 +0100 5617665 http://www.medworm.com/index.php?rid=5617664&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002241%2Fabstract%3Frss%3Dyes 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) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617664 Sun, 22 Jan 2012 03:06:38 +0100 5617664 http://www.medworm.com/index.php?rid=5617663&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS001048251100223X%2Fabstract%3Frss%3Dyes 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) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617663 Sun, 22 Jan 2012 03:06:38 +0100 5617663 http://www.medworm.com/index.php?rid=5617662&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002228%2Fabstract%3Frss%3Dyes 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... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617662 Sun, 22 Jan 2012 03:06:38 +0100 5617662 http://www.medworm.com/index.php?rid=5617661&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002216%2Fabstract%3Frss%3Dyes 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... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617661 Sun, 22 Jan 2012 03:06:38 +0100 5617661 http://www.medworm.com/index.php?rid=5617660&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482512000054%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5617660 Sun, 22 Jan 2012 03:06:38 +0100 5617660 http://www.medworm.com/index.php?rid=5521026&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002149%2Fabstract%3Frss%3Dyes Abstract: Strabismus is a pathology that affects about 4% of the population, causing aesthetic problems, reversible at any age; however, problems that can also cause irreversible muscular alterations, and alter the vision mechanism. The Hirschberg test is one of the exams used to detect this pathology. The application of high technology resources to help diagnose and treat ophthalmological conditions is, lamentably, not commonly found in the sub-specialty of strabismus. This work presents a methodology for automatic detection of strabismus in digital images through the Hirschberg test. For such, the work was organized into four stages: (1) finding the region of the eyes; (2) determining the precise location of the eyes; (3) locating the limbus and brightness; and (4) identifying strabismus... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521026 Tue, 20 Dec 2011 15:07:45 +0100 5521026 http://www.medworm.com/index.php?rid=5521025&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002137%2Fabstract%3Frss%3Dyes Abstract: Epileptogenesis is a dynamic process producing increased seizure susceptibility. Electroencephalography (EEG) data provides information critical in understanding the evolution of epileptiform changes throughout epileptic foci. We designed an algorithm to facilitate efficient large-scale EEG analysis via linked automation of multiple data processing steps. Using EEG recordings obtained from electrical stimulation studies, the following steps of EEG analysis were automated: (1) alignment and isolation of pre- and post-stimulation intervals, (2) generation of user-defined band frequency waveforms, (3) spike-sorting, (4) quantification of spike and burst data and (5) power spectral density analysis. This algorithm allows for quicker, more efficient EEG analysis. (Source: Computers in... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521025 Tue, 20 Dec 2011 15:07:45 +0100 5521025 http://www.medworm.com/index.php?rid=5521024&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002125%2Fabstract%3Frss%3Dyes Abstract: This paper presents a method for breast cancer diagnosis in digital mammogram images. Multiresolution representations, wavelet or curvelet, are used to transform the mammogram images into a long vector of coefficients. A matrix is constructed by putting wavelet or curvelet coefficients of each image in row vector, where the number of rows is the number of images, and the number of columns is the number of coefficients. A feature extraction method is developed based on the statistical t-test method. The method is ranking the features (columns) according to its capability to differentiate the classes. Then, a dynamic threshold is applied to optimize the number of features, which can achieve the maximum classification accuracy rate. The method depends on extracting the features that... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521024 Tue, 20 Dec 2011 15:07:45 +0100 5521024 http://www.medworm.com/index.php?rid=5521023&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002113%2Fabstract%3Frss%3Dyes Abstract: Current computational predictions of splice sites largely depend on the sequence patterns of known intronic sequence features (ISFs) described in the classical intron definition model (IDM). The computation-oriented IDM (CO-IDM) clearly provides more specific and concrete information for describing intron flanks of splice sites (IFSSs). In the paper, we proposed a novel approach of fuzzy decision trees (FDTs) which utilize (1) weighted ISFs of twelve uni-frame patterns (UFPs) and forty-five multi-frame patterns (MFPs) and (2) gain ratios to improve the performances in identifying an intron. First, we fuzzified extracted features from genomic sequences using membership functions with an unsupervised self-organizing map (SOM) technique. Then, we brought in different viewpoints of g... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521023 Tue, 20 Dec 2011 15:07:45 +0100 5521023 http://www.medworm.com/index.php?rid=5521022&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002101%2Fabstract%3Frss%3Dyes Abstract: The present study reports the development of a template for the active binding site of Cdk5 for structure-based drug design. The developed template of Cdk5 was validated by redocking with ligands I (PBD code 1UNG), II (PBD code 1UNL) and III (PBD code 1UNH). The results demonstrate a good match of the docked and the crystallographic binding orientations with RMSD less than 2.0Å. The validation results show that the constructed Cdk5 template is a good model system for predicting ligand binding orientations and binding affinities. Furthermore, the developed template was applied to predict binding mode and binding affinity of thirty-six known Cdk5 inhibitors. The results showed that the binding energy of almost Cdk5 inhibitors related to their biological evaluation. (Source: Comput... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521022 Tue, 20 Dec 2011 15:07:45 +0100 5521022 http://www.medworm.com/index.php?rid=5521021&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002095%2Fabstract%3Frss%3Dyes This study proposes a general framework for structural motif discovery. The framework is based on a modular design in which the system components can be modified or replaced independently to increase its applicability to various studies. It is a two-stage approach that first converts protein 3D structures into structural alphabet sequences, and then applies a sequence motif-finding tool to these sequences to detect conserved motifs. We named the structural motif database we built the SA-Motifbase, which provides the structural information conserved at different hierarchical levels in SCOP. For each motif, SA-Motifbase presents its 3D view; alphabet letter preference; alphabet letter frequency distribution; and the significance. SA-Motifbase is available at http://bioinfo.cis.nctu.edu.tw/sa... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521021 Tue, 20 Dec 2011 15:07:45 +0100 5521021 http://www.medworm.com/index.php?rid=5521020&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002083%2Fabstract%3Frss%3Dyes Abstract: In this paper an Empirical Mode Decomposition (EMD) based ECG signal enhancement and QRS detection algorithm is proposed. Being a non-invasive measurement, ECG is prone to various high and low frequency noises causing baseline wander and power line interference, which act as a source of error in QRS and other feature extraction. EMD is a fully adaptive signal decomposition technique that generates Intrinsic Mode Functions (IMF) as decomposition output. Here, first baseline wander is corrected by selective reconstruction based slope minimization technique from IMFs and then high frequency noise is removed by eliminating a noisy set of lower order IMFs with a statistical peak correction as high frequency noise elimination is accompanied by peak deformation of sharp characteristic w... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521020 Tue, 20 Dec 2011 15:07:45 +0100 5521020 http://www.medworm.com/index.php?rid=5521019&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002071%2Fabstract%3Frss%3Dyes In this study, we propose a fully automated segmentation method. Noise on the acquired mammogram is reduced by median filtering; multidirectional scanning is then applied to the resultant image using a moving window 15×1 in size. The border pixels are detected using the intensity value and maximum gradient value of the window. The breast boundary is identified from the detected pixels filtered using an averaging filter. The segmentation accuracy on a dataset of 84 mammograms from the MIAS database is 99%. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521019 Tue, 20 Dec 2011 15:07:45 +0100 5521019 http://www.medworm.com/index.php?rid=5521018&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS001048251100206X%2Fabstract%3Frss%3Dyes Abstract: Differential operators can detect significant changes in signals. This has been utilized to enhance the contrast of the seizure signatures in depth EEG or ECoG. We have actually taken normalized exponential of absolute value of single or double derivative of epileptic ECoG. This in short we call differential filtering. Windowed variance operation has been performed to automatically detect seizure onset on differentially filtered signal. A novel method for determining the duration of seizure has also been proposed. Since all operations take only linear time, the whole method is extremely fast. Seven empirical parameters have been introduced whose patient specific thresholding brings down the rate of false detection to a bare minimum. Results of implementation of the methods on the... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521018 Tue, 20 Dec 2011 15:07:45 +0100 5521018 http://www.medworm.com/index.php?rid=5521017&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002058%2Fabstract%3Frss%3Dyes Abstract: The prediction of the translation initiation site in an mRNA or cDNA sequence is an essential step in gene prediction and an open research problem in bioinformatics. Although recent approaches perform well, more effective and reliable methodologies are solicited. We developed an adaptable data mining method, called StackTIS, which is modular and consists of three prediction components that are combined into a meta-classification system, using stacked generalization, in a highly effective framework. We performed extensive experiments on sequences of two diverse eukaryotic organisms (Homo sapiens and Oryza sativa), indicating that StackTIS achieves statistically significant improvement in performance. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521017 Tue, 20 Dec 2011 15:07:45 +0100 5521017 http://www.medworm.com/index.php?rid=5521016&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002046%2Fabstract%3Frss%3Dyes Abstract: Recently, automated segmentation of retinal vessels in optic fundus images has been an important focus of much research. In this paper, we propose a multi-scale method to segment retinal vessels based on a weighted two-dimensional (2D) medialness function. The results of the medialness function are first multiplied by the eigenvalues of the Hessian matrix. Next, centerlines of vessels are extracted using noise reduction and reconnection procedures. Finally, vessel radii are estimated and retinal vessels are segmented. The proposed method is evaluated and compared with several recent methods using images from the DRIVE and STARE databases. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521016 Tue, 20 Dec 2011 15:07:45 +0100 5521016 http://www.medworm.com/index.php?rid=5521015&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002010%2Fabstract%3Frss%3Dyes Abstract: A computational model was developed for studying the flow field and particle deposition in a human upper airway system, including: nasal cavity, nasopharynx, oropharynx, larynx and trachea. A series of coronal CT scan images of a 24 year old woman was used to construct the 3D model. The Lagrangian and Eulerian approaches were used, respectively, to find the trajectories of micro-particles and concentration of nano-particles. The total and regional deposition fractions of micro/nanoparticles were evaluated and the major hot spots for the deposition of inhaled particles were found. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521015 Tue, 20 Dec 2011 15:07:45 +0100 5521015 http://www.medworm.com/index.php?rid=5521014&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002009%2Fabstract%3Frss%3Dyes Abstract: This paper presented a new ant colony optimization (ACO) feature selection method to classify hand motion surface electromyography (sEMG) signals. The multiple channels of sEMG recordings make the dimensionality of sEMG feature grow dramatically. It is known that the informative feature subset with small size is a precondition for the accurate and computationally efficient classification strategy. Therefore, this study proposed an ACO based feature selection scheme using the heuristic information measured by the minimum redundancy maximum relevance criterion (ACO-mRMR). The experiments were conducted on ten subjects with eight upper limb motions. Two feature sets, i.e., time domain features combined with autoregressive model coefficients (TDAR) and wavelet transform (WT) features... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521014 Tue, 20 Dec 2011 15:07:45 +0100 5521014 http://www.medworm.com/index.php?rid=5521013&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001995%2Fabstract%3Frss%3Dyes Abstract: In this work, two novel background correction (BC) methods, along with several commonly used ones, are evaluated regarding noise reduction in eleven two-channel self-versus-self (SVS) hybridizations. The evaluation of each BC method is investigated under the use of four statistical criteria combined into a single measure, the polygon area measure. Overall, our proposed BC approaches perform very well in terms of the proposed measure for most of the cases and provide an improved effect regarding technical noise reduction. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521013 Tue, 20 Dec 2011 15:07:45 +0100 5521013 http://www.medworm.com/index.php?rid=5521012&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001922%2Fabstract%3Frss%3Dyes Abstract: Respiratory motion results in significant motion blur in thoracic and abdomen PET imaging. The extent of respiratory motion blur is mainly correlated with breathing amplitude, tumor size and location. In this paper we introduce a statistical study to quantitatively show the factors influencing the extent of respiratory motion blur in thoracic PET images. The study is centered on two regression models, one is linked with motion blur induced loss of mean intensity(LMI), tumor motion magnitude and tumor size, and another is to investigate the influence of tumor location, patient gender and patient height on tumor motion magnitude. We use the blur identification and image restoration technique to estimate the tumor motion and compute the LMI. The regression model was validated by sim... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521012 Tue, 20 Dec 2011 15:07:45 +0100 5521012 http://www.medworm.com/index.php?rid=5521011&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001910%2Fabstract%3Frss%3Dyes Abstract: There are two main mechanisms of miRNA-mediated gene silencing: either mRNA degradation or translational repression. However, the precise mechanism of target mRNAs regulated by miRNA remains unclear. As a complementary approach to experiment, a computational method was proposed to recognize the mechanism of miRNA-mediated gene silencing in human. We have analyzed extensive features correlated with miRNA-mediated silencing mechanism of mRNA. It is found that, the duplex structure, the number of binding sites and the structural accessibility of target site region are effective factors in determining whether a target mRNA is cleaved or only translationally inhibited. An SVM-based classifier was constructed to predict the regulation mode of miRNA based on these informative features. ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521011 Tue, 20 Dec 2011 15:07:45 +0100 5521011 http://www.medworm.com/index.php?rid=5521010&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002411%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5521010 Tue, 20 Dec 2011 15:07:45 +0100 5521010 http://www.medworm.com/index.php?rid=5437841&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000941%2Fabstract%3Frss%3Dyes Abstract: Schizophrenia is often considered as a dysconnection syndrome in which, abnormal interactions between large-scale functional brain networks result in cognitive and perceptual deficits. In this article we apply the graph theoretic measures to brain functional networks based on the resting EEGs of fourteen schizophrenic patients in comparison with those of fourteen matched control subjects. The networks were extracted from common-average-referenced EEG time-series through partial and unpartial cross-correlation methods. Unpartial correlation detects functional connectivity based on direct and/or indirect links, while partial correlation allows one to ignore indirect links. We quantified the network properties with the graph metrics, including mall-worldness, vulnerability, modulari... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437841 Wed, 23 Nov 2011 15:24:56 +0100 5437841 http://www.medworm.com/index.php?rid=5437840&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000758%2Fabstract%3Frss%3Dyes Abstract: The present study is a preliminary attempt to use graph theory for deriving distinct features of resting-state functional networks in young adults with autism spectrum disorder (ASD). Networks modeled neuromagnetic signal interactions between sensors using three alternative interdependence measures: (a) a non-linear measure of generalized synchronization (robust interdependence measure [RIM]), (b) mutual information (MI), and (c) partial directed coherence (PDC). To summarize the information contained in each network model we employed well-established global graph measures (average strength, assortativity, clustering, and efficiency) as well as graph measures (average strength of edges) tailored to specific hypotheses concerning the spatial distribution of abnormalities in connec... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437840 Wed, 23 Nov 2011 15:24:56 +0100 5437840 http://www.medworm.com/index.php?rid=5437839&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000825%2Fabstract%3Frss%3Dyes Abstract: Estimation of effective connectivity, a measure of the influence among brain regions, can potentially reveal valuable information about organization of brain networks. Effective connectivity is usually evaluated from the functional data of a single modality. In this paper we show why that may lead to incorrect conclusions about effective connectivity. In this paper we use Bayesian networks to estimate connectivity on two different modalities. We analyze structures of estimated effective connectivity networks using aggregate statistics from the field of complex networks. Our study is conducted on functional MRI and magnetoencephalography data collected from the same subjects under identical paradigms. Results showed some similarities but also revealed some striking differences in ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437839 Wed, 23 Nov 2011 15:24:56 +0100 5437839 http://www.medworm.com/index.php?rid=5437838&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001892%2Fabstract%3Frss%3Dyes We present the two models in detail and discuss their applicability to FMRI data, and their interpretational limits. We also propose a unified approach that models both lagged and contemporaneous effects. The unifying model, structural vector autoregression (SVAR), may improve statistical and explanatory power, and avoid some prevalent pitfalls that can occur when VAR and SEM are utilized separately. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437838 Wed, 23 Nov 2011 15:24:56 +0100 5437838 http://www.medworm.com/index.php?rid=5437837&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001272%2Fabstract%3Frss%3Dyes Abstract: During the past several years a variety of methods have been developed to estimate the effective connectivity of neural networks from measurements of brain activity in an attempt to study causal interactions among distinct brain areas. Understanding the relative strengths and weaknesses of these methods, the assumptions they rely on, the accuracy they provide, and the computation time they require is of paramount importance in selecting the optimal method for a particular experimental task and for interpreting the results obtained. In this paper, the accuracy of the six most commonly used techniques for calculating effective connectivity are compared, namely directed transfer function, partial directed coherence, squared partial directed coherence, full frequency directed transfe... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437837 Wed, 23 Nov 2011 15:24:56 +0100 5437837 http://www.medworm.com/index.php?rid=5437836&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000837%2Fabstract%3Frss%3Dyes Abstract: The most common method for calculating Granger causality requires the fitting of a system of autoregressive equations to multiple interrelated signals. Historically, the Levinson, Wiggins, Robinson (LWR) algorithm and the least-squares linear regression (LSLR) approach are the most widely used methods for fitting these autoregressive equations. In this manuscript we compare these algorithms head-to-head. LSLR, as implemented using the Dynamic Autoregressive Neuromagnetic Causal Imaging (DANCI) method, was faster, and produced better residual error, normality, independence, and autocorrelation functions when analyzing real magnetoencephalography signals. Simulations demonstrated that the accuracy of LSLR was much higher than the LWR method and that the LSLR method, at least as imp... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437836 Wed, 23 Nov 2011 15:24:56 +0100 5437836 http://www.medworm.com/index.php?rid=5437835&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001405%2Fabstract%3Frss%3Dyes Abstract: Brain connectivity can be modeled and quantified with a large number of techniques. The main objective of this paper is to present the most modern and widely established mathematical methods for calculating connectivity that is commonly applied to functional high resolution multichannel neurophysiological signals, including electroencephalographic (EEG) and magnetoencephalographic (MEG) signals. A historical timeline of each technique is outlined along with some illustrative applications. The most crucial underlying assumptions of the presented methodologies are discussed in order to help the reader understand where each technique fits into the bigger picture of measuring brain connectivity. In this endeavor, linear, nonlinear, causality-assessing and information-based techniques... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437835 Wed, 23 Nov 2011 15:24:56 +0100 5437835 http://www.medworm.com/index.php?rid=5437834&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001569%2Fabstract%3Frss%3Dyes Abstract: Here we present a novel multimodal analysis of network connectivity in the language system. We assessed connectivity of Broca's area using tractography with diffusion tensor imaging (DTI), and with cortico-cortical evoked potentials (CCEPs) to measure the spread of artificial currents applied directly to human cortex. We found that both the amplitude and latency of CCEP currents significantly correlates (r2=0.41, p (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437834 Wed, 23 Nov 2011 15:24:56 +0100 5437834 http://www.medworm.com/index.php?rid=5437833&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482510001617%2Fabstract%3Frss%3Dyes Abstract: Electrocorticography (ECoG) allows for measurement of task-related local field potentials directly from cortex in neurosurgical patients. Diffusion tensor imaging (DTI) tractography is an MRI technique that allows for reconstruction of brain white matter tracts, which can be used to infer structural connectivity. This paper reports a novel merger of these two modalities. A processing stream is described in which fiber tracts near intracranial macroelectrodes showing task-related functional responses are isolated to explore structural networks related to working memory maintenance. Results show that ECoG-constrained tractography is useful for revealing structural connectivity patterns related to spatially- and temporally-specific functional responses. (Source: Computers in Biology... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437833 Wed, 23 Nov 2011 15:24:56 +0100 5437833 http://www.medworm.com/index.php?rid=5437832&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000965%2Fabstract%3Frss%3Dyes Abstract: White matter (WM) microstructure can be evaluated by diffusion tensor imaging (DTI). Tract-based spatial statistical (TBSS) analysis provides a means of assessing alterations in WM tracts. In this paper, both voxel-based morphometry (VBM) and TBSS are examined using DTI data of temporal lobe epilepsy (TLE) patients and nonepileptic subjects. In addition to fractional anisotropy (FA), ellipsoidal area ratio (EAR) is used in this study. Significant reductions of FA and EAR are identified by TBSS in the parahippocampal white matter. Because of methodological differences, TBSS detects more localized abnormalities than VBM, while the EAR is more sensitive to WM alteration than FA. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437832 Wed, 23 Nov 2011 15:24:56 +0100 5437832 http://www.medworm.com/index.php?rid=5437831&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482510001484%2Fabstract%3Frss%3Dyes Abstract: In this work, we present a framework to fuse and quantify tissue microstructural attributes (e.g. diffusion, functional, relaxation and perfusion MRI) using high spatial resolution T1-weighted volumetric measurements. The proposed computational procedures can be implemented by utilizing advanced, image segmentation, registration and diffusion tensor image processing software. Feasibility of the framework is also demonstrated using in-house developed software and freely available software such as FreeSurfer for regional tissue segmentation, Advanced Normalization Tools (ANTs) for registration and DTIStudio for fiber tracking and diffusion tensor data processing. We also demonstrate the application of these methods in the provision of quality control measures to assess the fidelity... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437831 Wed, 23 Nov 2011 15:24:56 +0100 5437831 http://www.medworm.com/index.php?rid=5437830&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482510001472%2Fabstract%3Frss%3Dyes Abstract: In this work we provide an up-to-date short review of computational magnetic resonance imaging (MRI) and software tools that are widely used to process and analyze diffusion-weighted MRI data. A review of different methods used to acquire, model and analyze diffusion-weighted imaging data (DWI) is first provided with focus on diffusion tensor imaging (DTI). The major preprocessing, processing and post-processing procedures applied to DTI data are discussed. A list of freely available software packages to analyze diffusion MRI data is also provided. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437830 Wed, 23 Nov 2011 15:24:56 +0100 5437830 http://www.medworm.com/index.php?rid=5437829&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002022%2Fabstract%3Frss%3Dyes Cognitive neuroscience could be said to have been born in August 1868, when the French physician/anatomist Paul Broca presented work to the British Association demonstrating the localization of speech to a specific area of the brain . The notion of the importance of the connection of specialized areas of the brain fell in and out of favor for nearly a century before Norman Geschwind's 1965 landmark work, “Disconnection syndromes in animals and man” . Since then we have continued to learn more about the brain's architecture and how different areas of the brain interact to process information. We have discovered that large-scale circuits process ‘what’ and ‘where’ information in parallel , that language areas reorganize to process both spoken and written language and that low-lev... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437829 Wed, 23 Nov 2011 15:24:56 +0100 5437829 http://www.medworm.com/index.php?rid=5437828&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002034%2Fabstract%3Frss%3Dyes When Robert Ledley founded this journal in 1970, the number of international peer-reviewed scholarly journals for workers in biomedical computation could be comfortably counted on the fingers of one hand. Over the past 40 years, this field has evolved and grown considerably, alongside closely allied disciplines such as Information Science, Cognitive Science, Applied Mathematics and Statistics, Psychology/Sociology, Medical Decision-Making, and of course Computer Science, which has itself benefitted from advances in software design as well improvements in hardware speed, capacity, and communications ability that now enable computations to be performed in a mobile phone that would have been unthinkably demanding (if possible at all) for any facility existing in 1970. These advances have proc... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437828 Wed, 23 Nov 2011 15:24:56 +0100 5437828 http://www.medworm.com/index.php?rid=5437827&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511002162%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5437827 Wed, 23 Nov 2011 15:24:56 +0100 5437827 http://www.medworm.com/index.php?rid=5356111&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001909%2Fabstract%3Frss%3Dyes Conclusion: We successfully predicted the 6-year incidence of MetS using an ANN system based on clinical data, including HOMA-IR and serum adiponectin, in Japanese male subjects. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5356111 Fri, 28 Oct 2011 08:22:11 +0100 5356111 http://www.medworm.com/index.php?rid=5356110&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001880%2Fabstract%3Frss%3Dyes Abstract: Uncovering the transcriptional modules with context-specific cellular activities or functions is important for understanding biological network, deciphering regulatory mechanisms and identifying biomarkers. In this paper, we propose to use the penalized matrix decomposition (PMD) to discover the transcriptional modules from microarray data. With the sparsity constraint on the decomposition factors, metagenes can be extracted from the gene expression data and they can well capture the intrinsic patterns of genes with the similar functions. Meanwhile, the PMD factors of each gene are good indicators of the cluster it belongs to. Compared with traditional methods, our method can cluster genes of similar functions but without similar expression profiles. It can also assign a gene int... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5356110 Fri, 28 Oct 2011 08:22:11 +0100 5356110 http://www.medworm.com/index.php?rid=5356109&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001879%2Fabstract%3Frss%3Dyes Abstract: Selecting a subset of genes with strong discriminative power is a very important step in classification problems based on gene expression data. Lasso and Dantzig selector are known to have automatic variable selection ability in linear regression analysis. This paper applies Lasso and Dantzig selector to select the most informative genes for representing the probability of an example being positive as a linear function of the gene expression data. The selected genes are further used to fit different classifiers for cancer classification. Comparative experiments were conducted on six publicly available cancer datasets, and the detailed comparison results show that in general, Lasso is more capable than Dantzig selector at selecting informative genes for cancer classification. (Sou... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5356109 Fri, 28 Oct 2011 08:22:11 +0100 5356109 http://www.medworm.com/index.php?rid=5356108&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001867%2Fabstract%3Frss%3Dyes Conclusion: All four novel methods deliver powerful tools for the diagnosis of hypovolemic patients. The degree of the hypovolemic state of each patient can be estimated with a hitherto unattained degree of reliability. Using ROC analysis and GA the estimation can be improved further. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5356108 Fri, 28 Oct 2011 08:22:11 +0100 5356108 http://www.medworm.com/index.php?rid=5356107&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001764%2Fabstract%3Frss%3Dyes Abstract: Studies showed that vascular diseases were prone to occur in curved arteries. In this paper, biomechanical behaviors of curved artery with flexible wall subjected to physiological flow were presented. Fluid–structure interaction effect was considered. The Von Mises stress variation and distribution patterns, the influence of artery curvature and flexibility on peak wall Von Mises stress, diameter change and cross sectional shape variation of the curved artery in the cardiac cycle were studied in detail. We believe that the findings may provide important implications for individualized treatment for patients with cardiovascular disease. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5356107 Fri, 28 Oct 2011 08:22:11 +0100 5356107 http://www.medworm.com/index.php?rid=5356106&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001752%2Fabstract%3Frss%3Dyes In this study, a prediction model of the substrates and non-substrates of BCRP was developed using a modified support vector machine (SVM) method, namely GA–CG–SVM. The overall prediction accuracy of the established GA–CG–SVM model is 91.3% for the training set and 85.0% for an independent validation set. For comparison, two other machine learning methods, namely, C4.5 DT and k-NN, were also adopted to build prediction models. The results show that the GA–CG–SVM model is significantly superior to C4.5 DT and k-NN models in terms of the prediction accuracy. To sum up, the prediction model of BCRP substrates and non-substrates generated by the GA–CG–SVM method is sufficiently good and could be used as a screening tool for identifying the substrates and non-substrates of BCRP.... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5356106 Fri, 28 Oct 2011 08:22:11 +0100 5356106 http://www.medworm.com/index.php?rid=5356105&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001387%2Fabstract%3Frss%3Dyes Abstract: In this paper we describe epiModel, a code developed in Mathematica that facilitates the building of systems of differential equations corresponding to type-epidemiological linear or quadratic models whose characteristics are defined in text files following an easy syntax. It includes the possibility of obtaining the equations of models involving age and/or sex groups. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5356105 Fri, 28 Oct 2011 08:22:11 +0100 5356105 http://www.medworm.com/index.php?rid=5356104&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001946%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5356104 Fri, 28 Oct 2011 08:22:11 +0100 5356104 http://www.medworm.com/index.php?rid=5234401&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001740%2Fabstract%3Frss%3Dyes This study presents a novel algorithm to measure joint space widths (JSWs) in patients with rheumatoid arthritis (RA) using radiographic hand images. Radiographic images were first preprocessed, and then phalangeal regions corresponding to the bone structures of each finger were extracted using step-wedge functions. Phalangeal branch paths were also extracted. Each of the five extracted phalangeal branch paths matched the bone structures of each finger exactly and ran through the center of each finger. The algorithm automatically detected 14 joints, which were identified as sharp changes in gray scale intensity along phalangeal branch paths through the profile plot. The regions of interest corresponding to the 14 joints were subsequently extracted. A total of 35 radiographic images from th... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234401 Tue, 20 Sep 2011 06:05:30 +0100 5234401 http://www.medworm.com/index.php?rid=5234400&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001739%2Fabstract%3Frss%3Dyes Abstract: Microarrays technology has been expanding remarkably since its launch about 15 years ago. With its advancement along with the increase of popularity, the technology affords the luxury that gene expressions can be measured in any of its multiple platforms. However, the generated results from the microarray platforms remain incomparable. In this direction, we earlier developed and tested an approach to address the incomparability of the expression measures of Affymetrix®- and cDNA-platforms. The method was an exploit involving transformation of Affymetrix data, which brought the gene expressions of both cDNA and Affymetrix platforms to a common and comparable level. The encouraging outcome of that investigation has subsequently acted as a motivator to focus attention on examining ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234400 Tue, 20 Sep 2011 06:05:30 +0100 5234400 http://www.medworm.com/index.php?rid=5234399&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001727%2Fabstract%3Frss%3Dyes Abstract: Temperature changes in the resting proximal human forearm have been studied non-invasively, using computer simulation. A procedure for spatial model generation, based on digitized slice data, has been applied. A mathematical model and a 3-D computer simulation program have been implemented. Heat transfer in the non-homogenous tissue was modeled with a well known bio-heat equation. The heat production by tissue metabolism was modeled using the Q10 rule, while the heat exchange between the blood and tissue was modeled as a function of local temperature and regional blood flow. The stability and accuracy of the method was confirmed by varying the simulation parameters, the initial and boundary values, and the model dimensions, with subsequent analysis of the results.We have explaine... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234399 Tue, 20 Sep 2011 06:05:30 +0100 5234399 http://www.medworm.com/index.php?rid=5234398&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001715%2Fabstract%3Frss%3Dyes Abstract: Colposcopy is a well-established method to detect and diagnose intraepithelial lesions and uterine cervical cancer in early stages. During the exam color and texture changes are induced by the application of a contrast agent (e.g.3–5% acetic acid solution or iodine). Our aim is to densely quantify the change in the acetowhite decay level for a sequence of images captured during a colposcopy exam to help the physician in his diagnosis providing new tools that overcome subjectivity and improve reproducibility. As the change in acetowhite decay level must be calculated from the same tissue point in all images, we present an elastic image registration scheme able to compensate patient, camera and tissue movement robustly in cervical images. The image registration is based on a nove... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234398 Tue, 20 Sep 2011 06:05:30 +0100 5234398 http://www.medworm.com/index.php?rid=5234397&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001703%2Fabstract%3Frss%3Dyes Abstract: Methods for predicting protein secondary structures provide information that is useful both in ab initio structure prediction and as additional restraints for fold recognition algorithms. Secondary structure predictions may also be used to guide the design of site directed mutagenesis studies, and to locate potential functionally important residues. In this article, we propose a multi-modal back propagation neural network (MMBP) method for predicting protein secondary structures. Using a Knowledge Discovery Theory based on Inner Cognitive Mechanism (KDTICM) method, we have constructed a compound pyramid model (CPM), which is composed of three layers of intelligent interface that integrate multi-modal back propagation neural network (MMBP), mixed-modal SVM (MMS), modified Knowledg... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234397 Tue, 20 Sep 2011 06:05:30 +0100 5234397 http://www.medworm.com/index.php?rid=5234396&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001697%2Fabstract%3Frss%3Dyes Abstract: To determine the impact of mechanical heterogeneity on the distribution of regional flows and pressures in the injured lung, we developed an anatomic model of the canine lung comprised of an asymmetric branching airway network, which can be stored as binary tree data structure. The entire tree can be traversed using a recursive flow divider algorithm, allowing for efficient computation of acinar flow and pressure distributions in a mechanically heterogeneous lung. These distributions were found to be highly dependent on ventilation frequency and the heterogeneity of tissue elastances, reflecting the preferential distribution of ventilation to areas of lower regional impedance. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234396 Tue, 20 Sep 2011 06:05:30 +0100 5234396 http://www.medworm.com/index.php?rid=5234395&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001685%2Fabstract%3Frss%3Dyes Abstract: Tumor growth models subject to virotherapy treatment are analyzed and compared in this paper. Tumor growth conditions are obtained for each model type based on the virus infection rate and immune suppressive drug delivery. Equilibrium conditions resulted into quadratic functions for which the tumor radius remained constant during virotherapy. An irrigation tumor model for virotherapy treatment was also proposed. This model consists of irrigation layers distributed radially along the tumor and attached to a common blood circulation compartment. The irrigation model has similar dynamic and steady state characteristics to the diffusion model, which has been supported by experimental results. The irrigation model considers the immune system cell generation and consumption outside the... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234395 Tue, 20 Sep 2011 06:05:30 +0100 5234395 http://www.medworm.com/index.php?rid=5234394&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001594%2Fabstract%3Frss%3Dyes Abstract: The temporal behavior of segmentation clock oscillations shows phase synchrony via mean field like coupling of delta protein restricting to nearest neighbors only, in a configuration of cells arranged in a regular three dimensional array. We found the increase of amplitudes of oscillating dynamical variables of the cells as the activation rate of delta-notch signaling is increased, however, the frequencies of oscillations are decreased correspondingly. Our results show the phase transition from desynchronized to synchronized behavior by identifying three regimes, namely, desynchronized, transition and synchronized regimes supported by various qualitative and quantitative measurements. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234394 Tue, 20 Sep 2011 06:05:30 +0100 5234394 http://www.medworm.com/index.php?rid=5234393&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001582%2Fabstract%3Frss%3Dyes Abstract: We propose a method to quantify superior–inferior (SI) motion of a rigid target using the 3D contour from free-breathing CT (FBCT). The technique utilizes similarity between 2D contours (Jaccard Index) and a population based density function for probability of motion amplitude, and is applicable both when the static target shape is and is not known beforehand. Simulations and phantom measurements showed that motion reconstruction is often feasible, with decreasing accuracy as discrepancy is introduced between assumed and actual static shape. When no static shape is used the analysis is most robust for slow scanning speeds relative to the motion period. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234393 Tue, 20 Sep 2011 06:05:30 +0100 5234393 http://www.medworm.com/index.php?rid=5234392&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001570%2Fabstract%3Frss%3Dyes Abstract: Doctors applying mechanical ventilation need to find the best balance between benefit and risk for the patient. Mathematical models simulating patient's reactions to alterations in the ventilation regime may be employed. A framework is introduced that is able to dynamically combine mathematical models from different model families to form a complex interacting model system. Each of these families consists of submodels differing in complexity of dynamics formulation or anatomical/geometrical resolution. The interaction of model systems reveals qualitatively varying results depending on the complexity of the involved models. Realistic overlaying of respiratory and cardiovascular rhythms can be detected in blood gas concentrations. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234392 Tue, 20 Sep 2011 06:05:29 +0100 5234392 http://www.medworm.com/index.php?rid=5234391&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001557%2Fabstract%3Frss%3Dyes Abstract: MicroRNAs are small non-coding RNAs that regulate gene expression at multiple levels. The discovery of virally encoded miRNAs attracted immense attention towards their role in viral replication and pathogenesis. Kaposi's-sarcoma-associated herpes virus encodes miRNA that functions as an orthologue of human cellular miRNA, i.e., hsa-miR-155. Keeping the same view we extended the miRNA-homology search between the miRNAs of humans and Epstein–Barr virus. The In silico analyses shows that EBV encoded miR-BART-5 has a significant ‘seed’ sequence homology to hsa-miR-18 of humans. Further, the mRNA transcripts of the human genes involved in cellular growth could potentially be targeted by both viral as well as human miRNAs. The known etiological role of hsa-miR-18 as an oncomiR su... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234391 Tue, 20 Sep 2011 06:05:29 +0100 5234391 http://www.medworm.com/index.php?rid=5234390&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001545%2Fabstract%3Frss%3Dyes Abstract: This work proposes the application of neural network multi-models to the prediction of adverse acute hypotensive episodes (AHE) occurring in intensive care units (ICU). A generic methodology consisting of two phases is considered. In the first phase, a correlation analysis between the current blood pressure time signal and a collection of historical blood pressure templates is carried out. From this procedure the most similar signals are determined and the respective prediction neural models, previously trained, selected. Then, in a second phase, the multi-model structure is employed to predict the future evolution of current blood pressure signal, enabling to detect the occurrence of an AHE.The effectiveness of the methodology was validated in the context of the 10th PhysioNet/C... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234390 Tue, 20 Sep 2011 06:05:29 +0100 5234390 http://www.medworm.com/index.php?rid=5234389&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001533%2Fabstract%3Frss%3Dyes Abstract: Abdominal aortic aneurysm (AAA) is a condition where the weakening of the aortic wall leads to its widening and the generation of a thrombus. To prevent a possible rupture of the aortic wall, AAA can be treated non-invasively by means of the endovascular aneurysm repair technique (EVAR), consisting of placing a stent-graft inside the aorta by a cateter to exclude the aneurysm sac from the blood circulation. A major complication is the presence of liquid blood turbulences, called endoleaks, in the thrombus formed in the space between the aortic wall and the stent-graft. In this paper we propose an automatic method for the detection of type II endoleaks in computer tomography angiography (CTA) images. The lumen and thrombus in the aneurysm area are first segmented using a radial mo... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234389 Tue, 20 Sep 2011 06:05:29 +0100 5234389 http://www.medworm.com/index.php?rid=5234388&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS001048251100179X%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5234388 Tue, 20 Sep 2011 06:05:29 +0100 5234388 http://www.medworm.com/index.php?rid=5138093&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001521%2Fabstract%3Frss%3Dyes Abstract: Although MHC–peptide binding is the most selective event in epitope presentation process, the protein fragments generated by proteasomal cleavage require to be recognized by transporter associated with antigen processing (TAP) and translocated from cytosol to endoplasmic reticulum before they can be loaded into the ligand-binding groove of MHC. In this article, we report the use of a new and powerful machine learning tool called Gaussian process (GP) to model the linear and nonlinear relationships between the sequence pattern and binding affinity of peptide to TAP, and to explain the physicochemical properties and structural implications underlying the specific recognition and association of peptide with TAP. The resulting statistics are compared systematically with those obtai... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138093 Wed, 17 Aug 2011 18:46:38 +0100 5138093 http://www.medworm.com/index.php?rid=5138092&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS001048251100151X%2Fabstract%3Frss%3Dyes Abstract: Monitoring glaucoma patients and ensuring optimal treatment requires accurate and precise detection of progression. Many glaucomatous progression detection strategies may be formulated for Scanning Laser Polarimetry (SLP) data of the local nerve fiber thickness. In this paper, several strategies, all based on repeated GDx VCC SLP measurements, are tested to identify the optimal one for clinical use. The parameters of the methods were adapted to yield a set specificity of 97.5% on real image series. For a fixed sensitivity of 90%, the minimally detectable loss was subsequently determined for both localized and diffuse loss. Due to the large size of the required data set, a previously described simulation method was used for assessing the minimally detectable loss. The optimal stra... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138092 Wed, 17 Aug 2011 18:46:35 +0100 5138092 http://www.medworm.com/index.php?rid=5138091&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001442%2Fabstract%3Frss%3Dyes Abstract: This paper proposes an efficient compression scheme for compressing time-varying medical volumetric data. The scheme uses 3-D motion estimation to create a homogenous preprocessed data to be compressed by a 3-D image compression algorithm using hierarchical vector quantization. A new block distortion measure, called variance of residual (VOR), and three 3-D fast block matching algorithms are used to improve the motion estimation process in term of speed and data fidelity. The 3-D image compression process involves the application of two different encoding techniques based on the homogeneity of input data. Our method can achieve a higher fidelity and faster decompression time compared to other lossy compression methods producing similar compression ratios. The combination of 3-D m... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138091 Wed, 17 Aug 2011 18:46:32 +0100 5138091 http://www.medworm.com/index.php?rid=5138090&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001429%2Fabstract%3Frss%3Dyes Abstract: State-transition models are employed to project future prevalence rates of risk factors and diseases within populations. Sensitivity analysis should be performed to assess the reliability of the results but often the number of inputs of the model is so huge, and running the model is so time-consuming, that not all methods of sensitivity analysis are practically available.Screening methods detect which inputs have a major influence on the outputs. We briefly review the available screening methods, and discuss one in particular, Morris' OAT Design. We applied the method under different assumptions to a module of the RIVM Chronic Diseases Model, where we projected the rates of never smokers, former smokers and current smokers in time up to the year 2050, based on smoking rates, star... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138090 Wed, 17 Aug 2011 18:46:27 +0100 5138090 http://www.medworm.com/index.php?rid=5138089&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001417%2Fabstract%3Frss%3Dyes Abstract: We aimed testing feasibility of identification of regional left ventricular (LV) endocardial motion abnormalities in mice undergoing coronary ligation (MI), using cine magnetic resonance with retrospective gating and computation of regional fractional area change (RFAC), by comparison with histological “gold standard” evaluation. ROC analysis determined the optimal RFAC cut-off values for detecting regional ischemic injury. This approach was tested on 18 MI and 10 sham mice. Automated regional LV motion interpretation and bull's eye display allowed non-invasive localization of the induced infarction. Possible applications to future studies assessing the effectiveness of pharmacological treatments or regenerative medicine are expected. (Source: Computers in Biology and Medicin... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138089 Wed, 17 Aug 2011 18:46:22 +0100 5138089 http://www.medworm.com/index.php?rid=5138088&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001399%2Fabstract%3Frss%3Dyes Abstract: The presence of abnormalities in the vocal system affects the quality of the voice and changes its characteristics. Digital analysis of pathological voices can be an effective and non-invasive tool for the detection of such alterations. This paper proposes a wavelet-based method to distinguish between normal and disordered voices. Wavelet filter banks are used in conjunction with support vector machines, as feature extractors and classifiers, respectively. Orthogonal filter banks are implemented using a highly efficient structure known as “lattice” that parameterizes filter banks and produces a few parameters. The overall problem is to find these parameters such that perfect classification is achieved. To search for such parameters, a genetic algorithm with a fitness function... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138088 Wed, 17 Aug 2011 18:46:13 +0100 5138088 http://www.medworm.com/index.php?rid=5138087&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001375%2Fabstract%3Frss%3Dyes Abstract: It is well-established that blood viscosity plays a significant role in the determination of the health of the individual. It has been reported that many cardiovascular diseases are associated with blood viscosity. In this paper, the dynamic behaviors of aortic aneurysm subject to physiological blood flow with normal and high viscosities are presented. Fluid–structure interaction (FSI) method was used in the computational simulation. The influence of blood viscosity on flow dynamics within the aneurysm sac, aneurismal diameter, cross sectional shape, wall axial displacement and wall shear stress (WSS) was studied in detail. This investigation uncovered the correlations between blood viscosity and the dynamic behaviors of aortic aneurysm, which have rarely been found in existing... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138087 Wed, 17 Aug 2011 18:46:06 +0100 5138087 http://www.medworm.com/index.php?rid=5138086&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001363%2Fabstract%3Frss%3Dyes Abstract: Heart murmurs are pathological sounds produced by turbulent blood flow due to certain cardiac defects such as valves disorders. Detection of murmurs via auscultation is a task that depends on the proficiency of physician. There are many cases in which the accuracy of detection is questionable. The purpose of this study is development of a new mathematical model of systolic murmurs to extract their crucial features for identifying the heart diseases. A high resolution algorithm, multivariate matching pursuit, was used to model the murmurs by decomposing them into a series of parametric time–frequency atoms. Then, a novel model-based feature extraction method which uses the model parameters was performed to identify the cardiac sound signals. The proposed framework was applied to... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138086 Wed, 17 Aug 2011 18:46:01 +0100 5138086 http://www.medworm.com/index.php?rid=5138085&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001351%2Fabstract%3Frss%3Dyes This study presents a straightforward approach to computer-aided polyp detection and explores its advantages and future potential. A straightforward computer-aided polyp detection (CAD) scheme was developed that consisted of colon wall segmentation, a polyp-specific volumetric filter, and the counting and thresholding of cluster volume sizes. 65 patients had undergone the bowel cleaning scheme without fecal tagging and the optical colonoscopy (OC) and CT colonography (CTC) were performed. The polyp sizes determined by OC were used as reference measurements. The CTC dataset with 103 polyps were divided into training and test datasets. After tuning for the optimal parameter settings, the per-polyp sensitivities of the developed CAD scheme for clinically relevant polyps (≥6mm) were 100% at ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138085 Wed, 17 Aug 2011 18:45:57 +0100 5138085 http://www.medworm.com/index.php?rid=5138084&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS001048251100134X%2Fabstract%3Frss%3Dyes Abstract: Central-chest lymph nodes play a vital role in lung-cancer staging. The definition of lymph nodes from three-dimensional (3D) multidetector computed-tomography (MDCT) images, however, remains an open problem. We propose two methods for computer-based segmentation of the central-chest lymph nodes from a 3D MDCT scan: the single-section live wire and the single-click live wire. For the single-section live wire, the user first applies the standard live wire to a single two-dimensional (2D) section after which automated analysis completes the segmentation process. The single-click live wire is similar but is almost completely automatic. Ground-truth studies involving human 3D MDCT scans demonstrate the robustness, efficiency, and intra-observer and inter-observer reproducibility of t... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138084 Wed, 17 Aug 2011 18:45:55 +0100 5138084 http://www.medworm.com/index.php?rid=5138083&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001338%2Fabstract%3Frss%3Dyes Abstract: Tumor-site-specific delivery of anti-cancer drugs remains one of the most prevailing problems in cancer treatment. While conventional means of chemo-delivery invariably leave different degrees of side-effects on healthy tissues, in recent times, intelligent chemical designs have been exploited to reduce the cross-consequences. In particular, the strategies involving superparamaganetic nanoparticles with surface assembled oligonucleotides as therapeutic carrier have raised affirmative promises. Process is designed in such a way that the therapeutic molecules are released preferentially at target site as the complementary oligonucleotide chains dissociate over the heat generated by the nanoparticles under the excitation of low frequency electromagnetic energy. In spite of the preli... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138083 Wed, 17 Aug 2011 18:45:48 +0100 5138083 http://www.medworm.com/index.php?rid=5138082&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001326%2Fabstract%3Frss%3Dyes Abstract: Bayesian network (BN) has been successfully used to infer the regulatory relationships of genes from microarray dataset. However, one major limitation of BN approach is the computational cost because the calculation time grows more than exponentially with the dimension of the dataset. In this paper, we propose a sub-space greedy search method for efficient Bayesian Network inference. Particularly, this method limits the greedy search space by only selecting gene pairs with higher partial correlation coefficients. Using both synthetic and real data, we demonstrate that the proposed method achieved comparable results with standard greedy search method yet saved ∼50% of the computational time. We believe that sub-space search method can be widely used for efficient BN inference in... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138082 Wed, 17 Aug 2011 18:45:46 +0100 5138082 http://www.medworm.com/index.php?rid=5138081&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001314%2Fabstract%3Frss%3Dyes Abstract: Midline shift (MLS) is an important quantitative feature clinicians use to evaluate the severity of brain compression by various pathologies. The midline consists of many anatomical structures including the septum pellucidum (SP), a thin membrane between the frontal horns (FH) of the lateral ventricles. We proposed a procedure that can measure MLS by recognizing the SP within the given CT study. The FH region is selected from all ventricular regions by expert rules and the multiresolution binary level set method. The SP is recognized using Hough transform, weighted by repeated morphological erosion. Our system is tested on images from 80 patients admitted to the neurosurgical intensive care unit. The results are evaluated by human experts. The mean difference between automatic an... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138081 Wed, 17 Aug 2011 18:45:43 +0100 5138081 http://www.medworm.com/index.php?rid=5138080&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001302%2Fabstract%3Frss%3Dyes Abstract: In this paper an automated dermatological tool for the parameterization of melanomas is presented. The system is based on the standard ABCD Rule and dermatological Pattern Recognition protocols. On the one hand, a complete stack of algorithms for the asymmetry, border, color, and diameter parameterization were developed. On the other hand, three automatic algorithms for digital image processing have been developed in order to detect the appropriate patterns. These allow one to calculate certain quantitative features based on the aspect and inner patterns of the melanoma using simple-operation algorithms, in order to minimize response time. The database used consists of 160 500×500-pixel RGB images (20 images per pattern) cataloged by dermatologists, and the results have turned o... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138080 Wed, 17 Aug 2011 18:45:39 +0100 5138080 http://www.medworm.com/index.php?rid=5138079&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001144%2Fabstract%3Frss%3Dyes Abstract: The main objective of this research is to develop a fuzzy-based framework for diagnosis of different acid–base disorders. There are several acid–base disorders that cause many clinical complications and their proper diagnosis is the only way for their efficient treatment. The common disorders are metabolic acidosis, metabolic alkalosis, non-anion gap acidosis, anion-gap acidosis, acute respiratory alkalosis and chronic respiratory alkalosis. The proposed fuzzy-based framework was used to diagnose all of these disorders using four parameters directly measured in blood: hydrogen-ion concentration (pH), arterial blood carbon dioxide partial pressure (paCO2), sodium ions concentration (Na+) and chloride ions concentration (Cl−) along with 12 features extracted from the directly... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138079 Wed, 17 Aug 2011 18:45:37 +0100 5138079 http://www.medworm.com/index.php?rid=5138078&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001612%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5138078 Wed, 17 Aug 2011 18:45:36 +0100 5138078 http://www.medworm.com/index.php?rid=5061706&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001296%2Fabstract%3Frss%3Dyes Abstract: In mammography diagnosis systems, high False Negative Rate (FNR) has always been a significant problem since a false negative answer may lead to a patient's death. This paper is directed towards the development of a novel Computer-aided Diagnosis (CADx) system for the diagnosis of breast masses. It aims at intensifying the performance of CADx algorithms as well as reducing the FNR by utilizing Zernike moments as descriptors of shape and margin characteristics. The input Regions of Interest (ROIs) are segmented manually and further subjected to a number of preprocessing stages. The outcomes of preprocessing stage are two processed images containing co-scaled translated masses. Besides, one of these images represents the shape characteristics of the mass, while the other describes ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061706 Mon, 25 Jul 2011 20:14:02 +0100 5061706 http://www.medworm.com/index.php?rid=5061705&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001284%2Fabstract%3Frss%3Dyes Abstract: In this work we propose two brain extraction methods (BEM) that solely depend on the brain anatomy and its intensity characteristics. Our methods are simple, unsupervised and knowledge based. Using an adaptive intensity thresholding method on the magnetic resonance images of head scans, a binary image is obtained. The binary image is labeled using the anatomical facts that the scalp is the boundary between head and background, and the skull is the boundary separating brain and scalp. A run length scheme is applied on the labeled image to get a rough brain mask. Morphological operations are then performed to obtain the fine brain on the assumption that brain is the largest connected component (LCC). But the LCC concept failed to work on some slices where brain is composed of more ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061705 Mon, 25 Jul 2011 20:14:02 +0100 5061705 http://www.medworm.com/index.php?rid=5061704&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001260%2Fabstract%3Frss%3Dyes Abstract: A new way to implement the Simulated Annealing (SA) algorithm was developed and tested that improves computation performance by using shorter Markov chain length (inner iterations) and repeating the entire SA process until the final function value meets the solution criterion. The new approach coupled with the adaptive neighborhood method was tested on the Rosenbrock function in 4 and 13 dimensions. This implementation significantly improved the computation speed without degrading solution quality. The proposed implementation was used to characterize pulmonary architecture from micro CT image data demonstrating the algorithm's effectiveness especially for problems with high computational demand and when the solution quality requirement can be pre-specified. Using this implementat... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061704 Mon, 25 Jul 2011 20:14:02 +0100 5061704 http://www.medworm.com/index.php?rid=5061703&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001259%2Fabstract%3Frss%3Dyes We examined 138 saliva samples for the presence or absence of the blood antigens ABH using haemagglutination inhibition methodology. The outcomes of the tests were scanned and examined by special software, which used the HSV colour model, allowed setting the parameters in a way that enabled differentiation of agglutination clusters from suspensions of erythrocytes and subsequently calculated the area of agglutination clusters. The size of the area was (inversely) related to the presence of ABH substances in saliva. Both the secretor phenotypes and the intensity of secretion into saliva were statistically analysed in relation to gender, blood type, blood group genotype frequencies and secretor genotype frequencies. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061703 Mon, 25 Jul 2011 20:14:02 +0100 5061703 http://www.medworm.com/index.php?rid=5061702&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001247%2Fabstract%3Frss%3Dyes We present a comprehensive method based on two-layer classifiers. The 1st layer is used to detect up to superfamily and family in SCOP hierarchy using optimized binary SVM classification rules. It used the kernel function known as the Bio-kernel, which incorporates the biological information in the classification process. The 2nd layer uses discriminative SVM algorithm with string kernel that will detect up to protein fold level in SCOP hierarchy. The results obtained were evaluated using mean ROC and mean MRFP and the significance of the result produced with pairwise t-test was tested. Experimental results show that our approaches significantly improve the performance of remote protein homology detection and fold recognition for all three different version SCOP datasets (1.53, 1.67 and 1.... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061702 Mon, 25 Jul 2011 20:14:02 +0100 5061702 http://www.medworm.com/index.php?rid=5061701&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001235%2Fabstract%3Frss%3Dyes This study employed a time–frequency filtering technique to improve click evoked otoacoustic emission (CEOAE) detection at lower frequency bands, and hence to reduce the number of referral cases in neonatal OAE screening. Using this approach the detectability of CEOAEs, in terms of lower frequency SNRs and whole wave reproducibility, was significantly improved. Evaluations of screening outcomes demonstrated this method significantly reduced the overall referral rate, by 2.5 percentage points in initial CEOAE hearing screening. This approach may have potential application in OAE technology and in neonatal hearing screening programmes. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061701 Mon, 25 Jul 2011 20:14:02 +0100 5061701 http://www.medworm.com/index.php?rid=5061700&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001168%2Fabstract%3Frss%3Dyes In this study, five novel herbal extracts in combination with doxorubicin and cisplatin have been used to sensitize ACHN and A2780/cp cells. These herbal extracts have been selected on the basis of novel cheminformatics methodology and assayed for the first time. The findings confirmed predicted outcomes from the in silico research and the results introduced may bring to use the effects of these herbs in reversing of multidrug resistance (MDR) phenomenon.Highlights: ► These herbal extracts have been selected on the basis of novel cheminformatics methodology and assayed for the first time. ► Results introduce selectivity effect of extract in inducing cytotoxicity on cancerous cell lines with synergistic effect. ► The findings confirmed that in silico predictions can bring to use the e... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061700 Mon, 25 Jul 2011 20:14:02 +0100 5061700 http://www.medworm.com/index.php?rid=5061699&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001132%2Fabstract%3Frss%3Dyes Abstract: Breast cancer occurs with high frequency among the world's population and its effects impact the patients' perception of their own sexuality and their very personal image. This work presents a computational methodology that helps specialists detect breast masses in mammogram images. The first stage of the methodology aims to improve the mammogram image. This stage consists in removing objects outside the breast, reducing noise and highlighting the internal structures of the breast. Next, cellular neural networks are used to segment the regions that might contain masses. These regions have their shapes analyzed through shape descriptors (eccentricity, circularity, density, circular disproportion and circular density) and their textures analyzed through geostatistic functions (Ripl... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061699 Mon, 25 Jul 2011 20:14:01 +0100 5061699 http://www.medworm.com/index.php?rid=5061698&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001120%2Fabstract%3Frss%3Dyes Abstract: Automated prediction of protein subcellular localization is an important tool for genome annotation and drug discovery, and Support Vector Machines (SVMs) can effectively solve this problem in a supervised manner. However, the datasets obtained from real experiments are likely to contain outliers or noises, which can lead to poor generalization ability and classification accuracy. To explore this problem, we adopt strategies to lower the effect of outliers. First we design a method based on Weighted SVMs, different weights are assigned to different data points, so the training algorithm will learn the decision boundary according to the relative importance of the data points. Second we analyse the influence of Principal Component Analysis (PCA) on WSVM classification, propose a hy... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061698 Mon, 25 Jul 2011 20:14:01 +0100 5061698 http://www.medworm.com/index.php?rid=5061697&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001119%2Fabstract%3Frss%3Dyes In this study, a simple, fast and powerful method is presented for protein remote homology detection, which combines support vector machine with auto-cross covariance transformation. The PSSMs are converted into a series of fixed-length vectors by auto-cross covariance transformation and these vectors are then input to a support vector machine classifier for remote homology detection. The sequence-order effects can be effectively captured by this scheme. Experiments are performed on well-established datasets, and the remote homology is simulated at the superfamily and the fold level, respectively. The results show that the proposed method, referred to as ACCRe, is comparable or even better than the state-of-the-art methods in terms of detection performance, and its time complexity is super... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061697 Mon, 25 Jul 2011 20:14:01 +0100 5061697 http://www.medworm.com/index.php?rid=5061696&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001107%2Fabstract%3Frss%3Dyes In this study, an adaptive electroencephalogram (EEG) analysis system is proposed for a two-session, single-trial classification of motor imagery (MI) data. Applying event-related brain potential (ERP) data acquired from the sensorimotor cortices, the adaptive linear discriminant analysis (LDA) is used for classification of left- and right-hand MI data and for simultaneous and continuous update of its parameters. In addition to the original use of continuous wavelet transform (CWT) and Student's two-sample t-statistics, the 2D anisotropic Gaussian filter is proposed to further refine the selection of active segments. The multiresolution fractal features are then extracted from wavelet data by means of modified fractal dimension. The classification in session 2 is performed by adaptive LDA,... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061696 Mon, 25 Jul 2011 20:14:01 +0100 5061696 http://www.medworm.com/index.php?rid=5061695&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001090%2Fabstract%3Frss%3Dyes Abstract: In this paper a novel automatic approach to identify brain structures in magnetic resonance imaging (MRI) is presented for volumetric measurements. The method is based on the idea of active contour models and support vector machine (SVM) classifiers. The main contributions of the presented method are effective modifications on brain images for active contour model and extracting simple and beneficial features for the SVM classifier. The segmentation process starts with a new generation of active contour models, i.e., vector field convolution (VFC) on modified brain images. VFC results are brain images with the least non-brain regions which are passed on to the SVM classification. The SVM features are selected according to the structure of brain tissues, gray matter (GM), white ma... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061695 Mon, 25 Jul 2011 20:14:00 +0100 5061695 http://www.medworm.com/index.php?rid=5061694&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001077%2Fabstract%3Frss%3Dyes Abstract: Instabilities in the electro-chemical resting state of the heart can generate ectopic waves that in turn can initiate arrhythmias. We derive methods for computing the resting state for mathematical models of the electro-chemical process underpinning a heartbeat, and we estimate the stability of the resting state by invoking the largest real part of the eigenvalues of a linearized model. The implementation of the methods is described and a number of numerical experiments illustrate the feasibility of the methods. In particular, we test the methods for problems where we can compare the solutions with analytical results, and problems where we have solutions computed by independent software. The software is also tested for a fairly realistic 3D model. (Source: Computers in Biology an... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061694 Mon, 25 Jul 2011 20:14:00 +0100 5061694 http://www.medworm.com/index.php?rid=5061693&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001065%2Fabstract%3Frss%3Dyes Abstract: Dementia is a growing concern due to the aging process of the western societies. Non-invasive detection is therefore a high priority research endeavor. In this paper we report results of classification systems applied to the feature vectors obtained by a feature extraction method computed on structural magnetic resonance imaging (sMRI) volumes for the detection of two neurological disorders with cognitive impairment: myotonic dystrophy of type 1 (MD1) and Alzheimer disease (AD). The feature extraction process is based on the voxel clusters detected by voxel-based morphometry (VBM) analysis of sMRI upon a set of patient and control subjects. This feature extraction process is specific for each kind of disease and is grounded on the findings obtained by medical experts. The 10-fold... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061693 Mon, 25 Jul 2011 20:14:00 +0100 5061693 http://www.medworm.com/index.php?rid=5061692&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000916%2Fabstract%3Frss%3Dyes This study presents a novel method, called DIAMOND, to induce classification rules from datasets containing non-linear interactions between the input data and the classes to be predicted. Given a set of objects with some classes, DIAMOND separates the objects into different cubes, and assigns each cube to a class. Via the unions of these cubes, DIAMOND uses mixed-integer programs to induce classification rules with better rates of accuracy, support and compact. This study uses three practical datasets (Iris flower, HSV patients, and breast cancer patients) to illustrate the advantages of DIAMOND over some current methods. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061692 Mon, 25 Jul 2011 20:13:59 +0100 5061692 http://www.medworm.com/index.php?rid=5061691&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000850%2Fabstract%3Frss%3Dyes We present a system that achieves an integrated approach with online management of complex datasets for clinical trials within care records using a specific study as an example to show functionality in practice; illustrating how this system provides an ideal resource to meet the needs of both clinicians and researchers.Highlights: ► We present the first use of an integrated database for clinical and clinical research purposes. ► Technical aspects of this new application are detailed. ► Practical use of the integrated database in a clinical study is described. ► The development and use of this new database meets UK aspirations for best practice. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061691 Mon, 25 Jul 2011 20:13:59 +0100 5061691 http://www.medworm.com/index.php?rid=5061690&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001466%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=5061690 Mon, 25 Jul 2011 20:13:59 +0100 5061690 http://www.medworm.com/index.php?rid=4951772&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001053%2Fabstract%3Frss%3Dyes Abstract: A mathematical model is presented that describes the health-endangering interaction of fibrous particles deposited in the human alveoli with alveolar fluids, cells, and tissues. As suggested by the theoretical approach, short fibers (diameter: 0.5μm, length: 2–10μm) are preferably ingested by alveolar macrophages and removed from the alveolar surface 10–15 days after exposure. Long (diameter: 0.5μm, length: 10–50μm) biopersistent fibers are not effectively cleared from the alveoli due to the repeated process of frustrated phagocytosis. Long biosoluble fibers also undergo a frustrated phagocytosis, with processes of extensive lysis leading to their significant shortening. The decrease in length causes the initiation of those clearance mechanisms that are efficient for sh... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951772 Tue, 21 Jun 2011 18:02:19 +0100 4951772 http://www.medworm.com/index.php?rid=4951771&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000977%2Fabstract%3Frss%3Dyes Abstract: An automated method has been presented for the detection of epileptic spikes in the electroencephalogram (EEG) using a deterministic finite automata (DFA) and has been named as DFAspike. EEG data (sampled, 256Hz) files are the inputs to the DFAspike. The DFAspike was tested with different data files containing epileptic spikes. The obtained recognition rate of epileptic spike was 99.13% on an average. This system does not require any kind of prior training or human intrusion. The result shows that the designed system can be very effectively used for the detection of spikes present in the recorded EEG signals. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951771 Tue, 21 Jun 2011 18:02:18 +0100 4951771 http://www.medworm.com/index.php?rid=4951770&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000953%2Fabstract%3Frss%3Dyes We present a stochastic cellular automaton (CA) model to computationally study what could be an alternative treatment, namely Leukapheresis (LCAP), to remove HIV infected leukocytes in the lymphoid tissue. We base our investigations on Monte Carlo computer simulations. Our major objective is to investigate how the number of infected CD4+ T cells changes in response to LCAP during the short-time (weeks) and long-time (years) scales of HIV/AIDS progression in an infected individual. To achieve our goal, we analyze the time evolution of the CD4+ T cell population in the lymphoid tissue (i.e., the lymph node) for HIV dynamics in treatment situations with various starting times and frequencies and under a no treatment condition. Our findings suggest that the effectiveness of the treatment depen... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951770 Tue, 21 Jun 2011 18:02:18 +0100 4951770 http://www.medworm.com/index.php?rid=4951769&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000904%2Fabstract%3Frss%3Dyes Abstract: The D2 dopamine receptor (D2DR) is an important target for the treatment of some central nervous system disorders, such as Parkinson disease, schizophrenia and drug-dependence. In this work, we built 3-D models of the long form of human and rat D2DRs by considering data from the crystallized D3 dopamine receptor, β2 adrenoceptor and A2a adenosine receptor as templates. Then, docking was performed with ligand and protein residue flexibility. These results were used to analyze ligand recognition and estimate binding affinity. Our results show that the predicted ligand affinity correlates with experimental data, and binding modes are very similar between the D2DRs of these two species. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951769 Tue, 21 Jun 2011 18:02:18 +0100 4951769 http://www.medworm.com/index.php?rid=4951768&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000898%2Fabstract%3Frss%3Dyes We present a computer-aided detection (CAD) scheme for early detection of ischemic stroke with small lesions using image feature characteristics. A novel Circular Adaptive Region of Interest (CAROI) method is proposed to analyze the Computed Tomography (CT) images of the brain. Our result indicates that for the emergency physicians and radiology residents, there is a significant improvement in sensitivity and specificity when using CAD (P (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951768 Tue, 21 Jun 2011 18:02:18 +0100 4951768 http://www.medworm.com/index.php?rid=4951767&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000886%2Fabstract%3Frss%3Dyes Abstract: TNFα-mediated apoptosis is one of the complex and tightly regulated cellular processes as it involves the activation of both pro- and anti-apoptotic signaling pathways. Thus, it is important to elucidate the molecular players of this process and their dynamics in order to gain an in-depth understanding of the mechanisms underlying apoptosis. To this end, we proposed an integrated model of TNFα-mediated apoptosis pathway in Type I cells, formulated based on the principles of mass action kinetics. The model includes major apoptotic modules—the extrinsic and intrinsic pathways, the NFκB survival signaling and various regulatory mechanisms. We performed simulations and sensitivity analyses to study the role of NFκB pathway in regulating apoptosis, and identified IAP as one of t... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951767 Tue, 21 Jun 2011 18:02:18 +0100 4951767 http://www.medworm.com/index.php?rid=4951766&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000874%2Fabstract%3Frss%3Dyes Abstract: This paper presents grey structure activity relationship analysis for phenolic acid phenethyl esters from the bioactivity on oral cancer SAS, OEC-M1 and human breast cancer MCF-7. First of all, 14 compounds of phenolic acid phenethyl esters are synthesized, while the bioactivity (cytotoxicity) on the cancer cells SAS, OEC-M1, MCF-7 is tested. Next, the relationship weighting of functional groups of phenolic acid phenethyl esters is found by applying the grey GM(0, N) model on the measured data. Moreover, evident structure activity relationships are established to rule the biological effect of such compounds, e.g., the most important functional group affecting the cytotoxicity on the cancer cells is found. It is interesting that the analyzed result is consistent with the actual ci... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951766 Tue, 21 Jun 2011 18:02:18 +0100 4951766 http://www.medworm.com/index.php?rid=4951765&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000862%2Fabstract%3Frss%3Dyes Abstract: Cryosurgery is particularly suitable for the treatment of unresectable liver tumors. However, a major bottleneck is encountered during the treatment of large-sized irregularly shaped tumors. Large and complex liver tumors have varying degree of shape irregularity. Adopting a multiprobe freezing model, simulations for an irregularly shaped liver tumor were conducted. The model, validated with both in-vitro data from an experimental setup, showed good agreement of up to 5.8%. The chosen mathematical treatment and simulation technique permit the study of employing multiple cryoprobes to destroy cancer cells in irregularly shaped tumors. Results from our study indicated that multiple cryoprobes can be strategically positioned to form ice-fronts with various contours that adhere to th... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951765 Tue, 21 Jun 2011 18:02:18 +0100 4951765 http://www.medworm.com/index.php?rid=4951764&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000813%2Fabstract%3Frss%3Dyes Abstract: Uncontrollable and unlimited cell growth leads to tumor genesis in the brain. If brain tumors are not diagnosed early and cured properly, they could cause permanent brain damage or even death to patients. As in all methods of treatments, any information about tumor position and size is important for successful treatment; hence, finding an accurate and a fully automated method to give information to physicians is necessary.A fully automatic and accurate method for tumor region detection and segmentation in brain magnetic resonance (MR) images is suggested. The presented approach is an improved fuzzy connectedness (FC) algorithm based on a scale in which the seed point is selected automatically. This algorithm is independent of the tumor type in terms of its pixels intensity. Tumor... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951764 Tue, 21 Jun 2011 18:02:18 +0100 4951764 http://www.medworm.com/index.php?rid=4951763&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000801%2Fabstract%3Frss%3Dyes Abstract: This work deals with the assessment of different parameterization techniques for lung sounds (LS) acquired on the whole posterior thoracic surface for normal versus abnormal LS classification. Besides the conventional technique of power spectral density (PSD), the eigenvalues of the covariance matrix and both the univariate autoregressive (UAR) and the multivariate autoregressive models (MAR) were applied for constructing feature vectors as input to a supervised neural network (SNN). The results showed the effectiveness of the UAR modeling for multichannel LS parameterization, using new data, with classification accuracy of 75% and 93% for healthy subjects and patients, respectively. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951763 Tue, 21 Jun 2011 18:02:18 +0100 4951763 http://www.medworm.com/index.php?rid=4951762&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000795%2Fabstract%3Frss%3Dyes Abstract: Aquatic ecosystems are continuously threatened by a growing number of human induced changes. Macroinvertebrate biomonitoring is particularly efficient in pinpointing the cause–effect structure between slow and subtle changes and their detrimental consequences in aquatic ecosystems. The greatest obstacle to implementing efficient biomonitoring is currently the cost-intensive human expert taxonomic identification of samples. While there is evidence that automated recognition techniques can match human taxa identification accuracy at greatly reduced costs, so far the development of automated identification techniques for aquatic organisms has been minimal. In this paper, we focus on advancing classification and data retrieval that are instrumental when processing large macroinvert... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951762 Tue, 21 Jun 2011 18:02:17 +0100 4951762 http://www.medworm.com/index.php?rid=4951761&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000783%2Fabstract%3Frss%3Dyes Abstract: Scientific computing is a multidisciplinary field that goes beyond the use of computer as machine where researchers write simple texts, presentations or store analysis and results of their experiments. Because of the huge hardware/software resources invested in experiments and simulations, this new approach to scientific computing currently adopted by research groups is well represented by e-Science. This work aims to propose a new architecture based on intelligent agents to search, recover and compose simulation models, generated in the context of research projects related to biological domain. The SASAgent architecture is described as a multi-tier, comprising three main modules, where CelO ontology satisfies requirements put by e-science projects mainly represented by the seman... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951761 Tue, 21 Jun 2011 18:02:17 +0100 4951761 http://www.medworm.com/index.php?rid=4951760&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000771%2Fabstract%3Frss%3Dyes In this study we investigated whether p-BRS using phenylephrine injection can be predicted from non-pharmacological time and frequency domain indices computed from electrocardiogram (ECG) and blood pressure (BP) data acquired during deep breathing. In this scheme, ECG and BP data were recorded from 16 subjects in a two-phase experiment. In the first phase the subjects performed irregular deep breaths and in the second phase the subjects received phenylephrine injection. From the first phase of the experiment, a large pool of predictors describing the local characteristic of beat-to-beat interval tachogram (RR) and systolic blood pressure (SBP) were extracted in time and frequency domains. A subset of these indices was selected using twelve subjects with an exhaustive search fused with a le... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951760 Tue, 21 Jun 2011 18:02:17 +0100 4951760 http://www.medworm.com/index.php?rid=4951759&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS001048251100076X%2Fabstract%3Frss%3Dyes Abstract: Compared to backward feature selection (BFS) method in gene expression data analysis, forward feature selection (FFS) method can obtain an expected feature subset with less iteration. However, the number of FFS method is considerably less than that of BFS method. More efficient FFS methods need to be developed. In this paper, two FFS methods based on the pruning of the classifier ensembles generated by single attribute are proposed for gene selection. The main contributions are as follows: (1) a new loss function, p-insensitive loss function, is proposed to overcome the disadvantage of the margin Euclidean distance loss function in the pruning of classifier ensembles; (2) two FFS methods based on the margin Euclidean distance loss function and the p-insensitive loss function, nam... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951759 Tue, 21 Jun 2011 18:02:17 +0100 4951759 http://www.medworm.com/index.php?rid=4951758&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000722%2Fabstract%3Frss%3Dyes In this study, the different phases of pressure sore generation and healing are investigated through a combined analysis of high-frequency ultrasound (20MHz) images and digital color photographs. Pressure sores were artificially induced in guinea pigs, and the injured regions were monitored for 21 days (data were obtained on days 3, 7, 14, and 21). Several statistical features of the images were extracted, relating to both the altering pattern of tissue and its superficial appearance. The features were grouped into five independent categories, and each category was used to train a neural network whose outputs were the four days. The outputs of the five classifiers were then fused using a fuzzy integral to provide the final decision. We demonstrate that the suggested method provides a bette... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951758 Tue, 21 Jun 2011 18:02:17 +0100 4951758 http://www.medworm.com/index.php?rid=4951757&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS001048251100059X%2Fabstract%3Frss%3Dyes In this study, a new X-ray-based reconstruction method was proposed using the free form deformation method with two X-ray images and three CT images. The obtained femur model is closer to a CT-based 3D femur model in comparison with the reconstruction method using only X-ray images. This method will have benefits for many clinical and biomechanical applications. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951757 Tue, 21 Jun 2011 18:02:17 +0100 4951757 http://www.medworm.com/index.php?rid=4951756&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001181%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4951756 Tue, 21 Jun 2011 18:02:17 +0100 4951756 http://www.medworm.com/index.php?rid=4882933&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000746%2Fabstract%3Frss%3Dyes Abstract: Many methods for automatic heartbeat classification have been applied and reported in literature, but relatively few of them concerned with patient independent classification because of the less significant results compared to patient dependent ones. In this work, using phase space reconstruction in order to classify five heartbeat types can fill this gap to some extent. In the first and second method, Reconstructed phase space (RPS) is modeled by the Gaussian mixture model (GMM) and bins, respectively, and then classified by classic Bayesian classifier. In the third method, RPS is directly used to train predictor time-delayed neural networks (TDNN) and classified based on minimum prediction error. All three methods highly outperform the results reported before, for patient indep... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882933 Tue, 31 May 2011 23:00:00 +0100 4882933 http://www.medworm.com/index.php?rid=4882932&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000734%2Fabstract%3Frss%3Dyes Abstract: This paper presents a novel method of detecting and describing pathological changes that can be visualized on dynamic computer tomography brain maps (perfusion CT). The system was tested on a set of dynamic perfusion computer tomography maps. Each set consisted of two perfusion maps (CBF, CBV and TTP for testing the irregularity detection algorithm) and one CT brain scan (for the registration algorithm) from 8 different patients with suspected strokes. In 36 of the 84 brain maps, abnormal perfusion was diagnosed. The results of the algorithm were compared with the findings of a team of two radiologists. All of the CBF and CBV maps that did not show a diagnosed asymmetry were classified correctly (i.e. no asymmetry was detected). In four of the TTP maps the algorithm found asymmet... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882932 Tue, 31 May 2011 23:00:00 +0100 4882932 http://www.medworm.com/index.php?rid=4882931&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000709%2Fabstract%3Frss%3Dyes Abstract: High resolution tomographic images acquired with a digital X-ray detector are often degraded by the so called ring artifacts. In this paper, a detail analysis including the classification, detection and correction of these ring artifacts is presented. At first, a novel idea for classifying rings into two categories, namely type I and type II rings, is proposed based on their statistical characteristics. The defective detector elements and the dusty scintillator screens result in type I ring and the mis-calibrated detector elements lead to type II ring. Unlike conventional approaches, we emphasize here on the separate detection and correction schemes for each type of rings for their effective removal. For the detection of type I ring, the histogram of the responses of the detector... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882931 Tue, 31 May 2011 23:00:00 +0100 4882931 http://www.medworm.com/index.php?rid=4882930&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000606%2Fabstract%3Frss%3Dyes Abstract: An automatic sleep/wake stages classifier that deals with the presence of artifacts and that provides a confidence index with each decision is proposed. The decision system is composed of two stages: the first stage checks the 20s epoch of polysomnographic signals (EEG, EOG and EMG) for the presence of artifacts and selects the artifact-free signals. The second stage classifies the epoch using one classifier selected out of four, using feature inputs extracted from the artifact-free signals only. A confidence index is associated with each decision made, depending on the classifier used and on the class assigned, so that the user's confidence in the automatic decision is increased. The two-stage system was tested on a large database of 46 night recordings. It reached 85.5% of over... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882930 Tue, 31 May 2011 23:00:00 +0100 4882930 http://www.medworm.com/index.php?rid=4882929&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000588%2Fabstract%3Frss%3Dyes Abstract: Computerized Tomography (CT) images are High Dynamic Range (HDR) images of the X-ray attenuation coefficients of the body's tissues. The inability to see abnormalities in tissues with marked differences in their X-ray attenuation coefficients, in a single CT window, poses a significant clinical problem in radiology. In order to provide proper contrast, which reveals all the required clinical details within each specifically imaged tissue, a single CT slice must be viewed by a radiologist four times: the first viewing focuses on the lung window; the second viewing focuses on the soft tissues window; the third viewing focuses on the liver window; and the fourth viewing focuses on the bone window. In order to enhance the ability to perform a complete diagnosis, while decreasing diag... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882929 Tue, 31 May 2011 23:00:00 +0100 4882929 http://www.medworm.com/index.php?rid=4882928&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000576%2Fabstract%3Frss%3Dyes This study investigated the characteristics of a new computer-controlled sound source phantom for testing sensors. Results suggested that sensors with different sizes require special phantom requirements. The effectiveness of certain approaches on increasing the spatial and spectral uniformity of the phantom surface signal was studied. Non-uniformities >20dB were removable, which can be particularly helpful in comparing the characteristics of different size sensors more accurately. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882928 Tue, 31 May 2011 23:00:00 +0100 4882928 http://www.medworm.com/index.php?rid=4882927&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000564%2Fabstract%3Frss%3Dyes Abstract: Many trace elements (TE) occur naturally in marine environments and accomplish decisive functions in humans to maintain good health. Mytilus galloprovincialis (MG) is a rich source of TE, but since it is grown near industrial outfalls, they become polluted with elevated levels of TE concentration and serve as biomarkers of pollution. As bioremediation is increasingly reliant on machine learning data processing techniques, we propose the information theoretic concept of using MG for bioremediation. The in situ bioremediation in MG is accomplished by reduction in concentration of TE by the technique of determinant inequalities and the maximization of Mutual Information (MI) without adding any chemical element externally. We bring out the superiority of our technique of MI over that... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882927 Tue, 31 May 2011 23:00:00 +0100 4882927 http://www.medworm.com/index.php?rid=4882926&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000552%2Fabstract%3Frss%3Dyes Abstract: Diabetes is a chronic and complex endocrine disease with metabolic disorders caused by the imbalance between secreted and needed insulin levels. In the present study, all probabilities were examined considering ten (10) indications (210=1024 different cases) of diabetes using medical expert system (MES), and accordingly, a truth table was established. This table was simplified by the simplification method of logic functions. 15 main rules were obtained using minimization method for Boolean Functions (BFs). These rules established rules base of ES. Subsequently, the parameters of 768 patients were compared with this ES. Accuracy rate of the estimations of MES, created as a result these comparisons, was determined as 97.13% in diabetes patients, 97% in non-diabetes patients, 96.5% ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882926 Tue, 31 May 2011 23:00:00 +0100 4882926 http://www.medworm.com/index.php?rid=4882925&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000540%2Fabstract%3Frss%3Dyes Abstract: Development and integration of image registration methods become increasingly important for clinical workstations. Due to the complexity of such methods, prototyping, evaluation and workflow integration require in-depth knowledge foremostly available to registration developers. Rapid development and deployment is therefore often difficult, particularly for comprehensive software frameworks. In this article, we introduce a novel rapid prototyping framework for voxel-based registration. It is specifically designed to allow evaluation and adaption by developers with less knowledge on registration internals. Based on a unique “one-iteration” paradigm, it enables accelerated algorithm development. Furthermore, methods are interchangeable at runtime using an intuitive graphical plu... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882925 Tue, 31 May 2011 23:00:00 +0100 4882925 http://www.medworm.com/index.php?rid=4882924&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000539%2Fabstract%3Frss%3Dyes We describe the mathematical models, explain their numerical approximation and finally we present various possible practical applications on the images of zebrafish embryogenesis—computation of important quantitative characteristics, evaluation of the cell shape, detection of cell divisions and others. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882924 Tue, 31 May 2011 23:00:00 +0100 4882924 http://www.medworm.com/index.php?rid=4882923&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000527%2Fabstract%3Frss%3Dyes Abstract: Automated classification of duodenal texture patches with histological ground truth in case of pediatric celiac disease is proposed. The classical focus of classification in this context is a two-class problem: mucosa affected by celiac disease and unaffected duodenal tissue. We extend this focus and apply classification according to a modified Marsh scheme into four classes. In addition to other techniques used previously for classification of endoscopic imagery, we apply local binary pattern (LBP) operators and propose two new operator types, one of which adapts to the different properties of wavelet transform subbands. The achieved results are promising in that operators based on LBP turn out to achieve better results compared to many other texture classification techniques as... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882923 Tue, 31 May 2011 23:00:00 +0100 4882923 http://www.medworm.com/index.php?rid=4882922&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000515%2Fabstract%3Frss%3Dyes Abstract: Purpose of this study was to evaluate the reliability and validity of 4D rasterstereography under dynamic conditions. Therefore simulated anatomical fixed points on a wooden plate were measured during different movements. Seven different motion patterns in all three angles of space were evaluated. The simulated parameter trunk length was measured with an accuracy of 3.58mm (SD±3.29mm) and the dimple distance was detected with an accuracy of 0.88mm (SD±1.04mm). With this rasterstereographic prototype it is possible to examine dynamically the spinal posture with adequate accuracy. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882922 Tue, 31 May 2011 23:00:00 +0100 4882922 http://www.medworm.com/index.php?rid=4882921&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511001041%2Fabstract%3Frss%3Dyes In sadness, we note the recent death, in Scottsdale, Arizona, of Blaire Volman Mossman, who for many years served as Managing Editor of this journal, as well as three others created by our Founding Editor, Robert Ledley, while both served on the professional staff of the National Biomedical Research Foundation in Washington, DC. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882921 Tue, 31 May 2011 23:00:00 +0100 4882921 http://www.medworm.com/index.php?rid=4882920&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000990%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4882920 Tue, 31 May 2011 23:00:00 +0100 4882920 http://www.medworm.com/index.php?rid=4742114&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000503%2Fabstract%3Frss%3Dyes This study surveyed the older adult users of Taiwan as subjects. User perception of the telecare services was collected via face-to-face interview. The grey system theory was used to examine the model. The results showed that the overall living quality has the greatest effect on the perceived effects of the telecare on their quality of life, followed by the acquisition of information, accessibility of medical care services, and safety. This finding may serve as a reference to future studies and it also shows that the grey system theory is a feasible analysis method. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4742114 Sat, 23 Apr 2011 06:28:29 +0100 4742114 http://www.medworm.com/index.php?rid=4742113&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000497%2Fabstract%3Frss%3Dyes Abstract: In this paper, we present a novel active contour (AC) model for medical image segmentation that is based on a convex combination of two energy functionals to both minimize the inhomogeneity within an object and maximize the distance between the object and the background. This combination is necessary because objects in medical images, e.g., bones, are usually highly inhomogeneous while distinct organs should generate distinct image configurations. Compared with the conventional Chan–Vese AC, the proposed model yields similar performance in a set of CT images but performs better in an MRI data set, which is generally in lower contrast. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4742113 Sat, 23 Apr 2011 06:28:28 +0100 4742113 http://www.medworm.com/index.php?rid=4742112&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000436%2Fabstract%3Frss%3Dyes Abstract: An automated algorithm for detection of the acetabular rim was developed. Accuracy of the algorithm was validated in a sawbone study and compared against manually conducted digitization attempts, which were established as the ground truth. The latter proved to be reliable and reproducible, demonstrated by almost perfect intra- and interobserver reliability. Validation of the automated algorithm showed no significant difference compared to the manually acquired data in terms of detected version and inclination. Automated detection of the acetabular rim contour and the spatial orientation of the acetabular opening plane can be accurately achieved with this algorithm. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4742112 Sat, 23 Apr 2011 06:28:28 +0100 4742112 http://www.medworm.com/index.php?rid=4742111&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000369%2Fabstract%3Frss%3Dyes Abstract: This paper illustrates a method for time-plane feature extraction from digitized ECG sample using statistical approach. The algorithm detects the position and magnitude of the QRS complex, P and T wave for a single lead ECG dataset. The processing is broadly based on relative comparison of magnitude and slopes of ECG samples. Then the baseline modulation in the dataset is removed. The R-peak detection and baseline modulation is tested MIT-BIH arrhythmia database as well as 12-lead datasets in MIT-PTB database (PTBDB) and available under Physionet. The overall accuracy obtained is more than 99%. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4742111 Sat, 23 Apr 2011 06:28:28 +0100 4742111 http://www.medworm.com/index.php?rid=4742110&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000357%2Fabstract%3Frss%3Dyes Abstract: The mobile behavior of 1481 peptides in ion mobility spectrometry (IMS), which are generated by protease digestion of the Drosophila melanogaster proteome, is modeled and predicted based on two different types of characterization methods, i.e. sequence-based approach and structure-based approach. In this procedure, the sequence-based approach considers both the amino acid composition of a peptide and the local environment profile of each amino acid in the peptide; the structure-based approach is performed with the CODESSA protocol, which regards a peptide as a common organic compound and generates more than 200 statistically significant variables to characterize the whole structure profile of a peptide molecule. Subsequently, the nonlinear support vector machine (SVM) and Gaussia... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4742110 Sat, 23 Apr 2011 06:28:26 +0100 4742110 http://www.medworm.com/index.php?rid=4742109&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000345%2Fabstract%3Frss%3Dyes In this study, we present a resampling strategy based Random Forests (RF) ensemble classifier to improve diagnosis of cardiac arrhythmia. Random forests is an ensemble classifier that consists of many decision trees and outputs the class that is the mode of the class's output by individual trees. In this way, an RF ensemble classifier performs better than a single tree from classification performance point of view. In general, multiclass datasets having unbalanced distribution of sample sizes are difficult to analyze in terms of class discrimination. Cardiac arrhythmia is such a dataset that has multiple classes with small sample sizes and it is therefore adequate to test our resampling based training strategy. The dataset contains 452 samples in fourteen types of arrhythmias and eleven of... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4742109 Sat, 23 Apr 2011 06:28:26 +0100 4742109 http://www.medworm.com/index.php?rid=4742108&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000333%2Fabstract%3Frss%3Dyes Abstract: Noninvasive ventilation is a clinical procedure that enables patients with chronic respiratory failure to reduce the work of breathing and to improve blood oxygenation. In order to attain such goals, the ventilation support is expected to be phase synchronized with the patient spontaneous breathing. Unfortunately, asynchrony events are not rare. In order to provide more effective ventilation schemes, the patient–ventilator interactions should be better understood both during normal rhythm and asynchronism. This paper investigates this problem using data-driven modeling. Hence the estimation of input–output and autonomous models from pressure and airflow time series is discussed and illustrated. Issues concerning the nonlinearity of the interactions and modeling assumptions ar... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4742108 Sat, 23 Apr 2011 06:28:26 +0100 4742108 http://www.medworm.com/index.php?rid=4742107&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000321%2Fabstract%3Frss%3Dyes Abstract: This paper proposes a similarity matrix-based hybrid algorithm for the contact map overlap (CMO) problem in protein structure alignment. In this algorithm, Genetic Algorithm (GA) is used as a framework, in which the initial solutions are constructed with similarity matrix heuristic, and Extremal Optimization (EO) is embedded as a mutated operator. In this process, EO quickly approaches near-optimal solutions and GA generates improved global approximations. Five similarity measurements including ratio, inner product, cosine function, Jaccard index and Dice coefficient have been exploited to compute the similarity matrix between two contact maps. The simulations demonstrate that our algorithm is significantly faster and gets better results for most of the test sets. (Source: Comput... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4742107 Sat, 23 Apr 2011 06:28:25 +0100 4742107 http://www.medworm.com/index.php?rid=4742106&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000631%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4742106 Sat, 23 Apr 2011 06:28:25 +0100 4742106 http://www.medworm.com/index.php?rid=4663505&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000308%2Fabstract%3Frss%3Dyes Abstract: This paper presents an automatic tool capable to learn from a patients data set with 24 medical indicators characterizing each sample and to subsequently use the acquired knowledge to differentiate between five degrees of liver fibrosis. The indicators represent clinical observations and the liver stiffness provided by the new, non-invasive procedure of Fibroscan. The proposed technique combines a hill climbing algorithm that selects subsets of important attributes for an accurate classification and a core represented by a cooperative coevolutionary classifier that builds rules for establishing the diagnosis for every new patient. The results of the novel method proved to be superior as compared to the ones obtained by other important classification techniques from the literature... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4663505 Thu, 31 Mar 2011 23:00:00 +0100 4663505 http://www.medworm.com/index.php?rid=4663504&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS001048251100028X%2Fabstract%3Frss%3Dyes Abstract: Gene expression profiles, which represent the state of a cell at a molecular level, have great potential as a medical diagnosis tool. In cancer classification, available training data sets are generally of a fairly small sample size compared to the number of genes involved. Along with training data limitations, this constitutes a challenge to certain classification methods. Feature (gene) selection can be used to successfully extract those genes that directly influence classification accuracy and to eliminate genes which have no influence on it. This significantly improves calculation performance and classification accuracy. In this paper, correlation-based feature selection (CFS) and the Taguchi-genetic algorithm (TGA) method were combined into a hybrid method, and the K-nearest... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4663504 Thu, 31 Mar 2011 23:00:00 +0100 4663504 http://www.medworm.com/index.php?rid=4663503&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000217%2Fabstract%3Frss%3Dyes Abstract: In order to predict variations of drug concentration during a given period of time, numerical solutions of pharmacokinetic models need to be obtained efficiently. Analytical solutions of linear pharmacokinetic models are usually obtained using the Laplace transform and inverse Laplace tables. The derivations of solutions to complex nonlinear models are tedious, and such solution process may be difficult to implement as a robust software code. For nonlinear models, the fourth-order Runge–Kutta (RK4) is the most classical numerical method in obtaining approximate numerical solutions, which is impossible to be implemented in distributed computing environments without much modification. The reason is that numerical solutions obtained by using RK4 can only be computed in sequential ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4663503 Thu, 31 Mar 2011 23:00:00 +0100 4663503 http://www.medworm.com/index.php?rid=4663502&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000205%2Fabstract%3Frss%3Dyes Abstract: A mobile medical device, dubbed HeartSaver, is developed for real-time monitoring of a patient's electrocardiogram (ECG) and automatic detection of several cardiac pathologies, including atrial fibrillation, myocardial infarction and atrio-ventricular block. HeartSaver is based on adroit integration of four different modern technologies: electronics, wireless communication, computer, and information technologies in the service of medicine. The physical device consists of four modules: sensor and ECG processing unit, a microcontroller, a link between the microcontroller and the cell phone, and mobile software associated with the system. HeartSaver includes automated cardiac pathology detection algorithms. These algorithms are simple enough to be implemented on a low-cost, limited-... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4663502 Thu, 31 Mar 2011 23:00:00 +0100 4663502 http://www.medworm.com/index.php?rid=4663501&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000199%2Fabstract%3Frss%3Dyes In this study, we used an ionic model of canine ventricular myocytes (CVM) to investigate the effect of calcium release from the sacroplasm reticulum (SR), as well as the effect of L-type calcium current, on cardiac short-term memory. We calculated short-term memory response by testing the time to reach steady-state APD after an abrupt shortening of basic cycling length (BCL) in pacing protocol. Our results indicated that as the release of calcium from SR was gradually prevented, short-term memory response decreased, while the blockade of L-type calcium channel had little effect on short-term memory. Finally, we declared that the amount of intracellular calcium released from SR affected short-term memory of cardiac tissues more than that of L-type calcium channel. (Source: Computers in Bio... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4663501 Thu, 31 Mar 2011 23:00:00 +0100 4663501 http://www.medworm.com/index.php?rid=4663500&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000187%2Fabstract%3Frss%3Dyes Abstract: In divergent-beam computed tomography (CT), sparse angular sampling frequently leads to conspicuous streak artifacts. In this paper, we propose a novel non-local means (NL-means) based iterative-correction projection onto convex sets (POCS) algorithm, named as NLMIC-POCS, for effective and robust sparse angular CT reconstruction. The motivation for using NLMIC-POCS is that NL-means filtered image can produce an acceptable priori solution for sequential POCS iterative reconstruction. The NLMIC-POCS algorithm has been tested on simulated and real phantom data. The experimental results show that the presented NLMIC-POCS algorithm can significantly improve the image quality of the sparse angular CT reconstruction in suppressing streak artifacts and preserving the edges of the image. ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4663500 Thu, 31 Mar 2011 23:00:00 +0100 4663500 http://www.medworm.com/index.php?rid=4663499&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482511000291%2Fabstract%3Frss%3Dyes In this study, we applied the supervised machine-learning algorithms Conditional Random Fields (CRFs) to automatically parse a citation into its fields (e.g., Author, Title, Journal, and Year). With a subset of html format open-access PubMed Central articles, we report an overall 97.95% F1-score. The citation parser can be accessed at: http://www.cs.uwm.edu/∼qing/projects/cithit/index.html. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4663499 Thu, 31 Mar 2011 23:00:00 +0100 4663499 http://www.medworm.com/index.php?rid=4663498&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.computersinbiologyandmedicine.com%2Farticle%2FPIIS0010482510001216%2Fabstract%3Frss%3Dyes Abstract: A small scale documentation analysis was conducted to explore the medical and surgical nursing content of the patient record at a large teaching hospital affiliated with Partners Healthcare System (PHS), in preparation for a computerized documentation system. Through this study, we identified a number of problems associated with the paper record that require resolution in the new computerized system, including elimination of documentation redundancy, areas where more structure is needed to properly capture data on nursing practice, and various design considerations to support a more complete and accurate documentation of nursing care. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=4663498 Thu, 31 Mar 2011 23:00:00 +0100 4663498