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Interactive surface-guided segmentation of brain MRI dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: MRI segmentation is a process of deriving semantic information from volume data. For brain MRI data, segmentation is initially performed at a voxel level and then continued at a brain surface level by generating its approximation. While successful most of the time, automated brain segmentation may leave errors which have to be removed interactively by editing individual 2D slices. We propose an approach for correcting these segmentation errors in 3D modeling space. We actively use the brain surface, which is estimated (potentially wrongly) in the automated FreeSurfer segmentation pipeline. It allows us to work wi...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Konstantin Levinski, Alexei Sourin, Vitali Zagorodnov Source Type: journals

Adaptive threshold method for the peak detection of photoplethysmographic waveformEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Photoplethysmography (PPG)-based temporal analyses have been widely used as a useful analytical method in physiological and cardiovascular diagnosis. Most of temporal approaches of PPG are based on detected peak points, peak and foot of PPG. The aim of presented study is the development of improved peak detection algorithm of PPG waveform. The present study demonstrates a promising approach to overcome respiration effect and to detect PPG peak. More extensive investigation is necessary to adapt for the cardiovascular diseases, whose PPG morphology has different form. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Hang Sik H.S. Shin, Chungkeun Lee, Myoungho Lee Source Type: journals

Pleural nodule identification in low-dose and thin-slice lung computed tomographyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: A completely automated system for the identification of pleural nodules in low-dose and thin-slice computed tomography (CT) of the lung has been developed. The directional-gradient concentration method has been applied to the pleura surface and combined with a morphological opening-based procedure to generate a list of nodule candidates. Each nodule candidate is characterized by 12 morphological and textural features, which are analyzed by a rule-based filter and a neural classifier. This detection system has been developed and validated on a dataset of 42 annotated CT scans. The k-fold cross validation has been ...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: A. Retico, M.E. M.E. Fantacci, I. Gori, P. Kasae, B. Golosio, A. Piccioli, P. Cerello, G. De Nunzio, S. Tangaro Source Type: journals

Computer method for perinatal screening of cardiac murmur using fetal phonocardiographyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: The main purpose of this paper is to demonstrate the capability of fetal phonocardiographic measurements to indicate some congenital heart defects. It deals with the results of investigations carried out during the last four years involving 820 pregnant women. During the investigations fetal cardiac murmurs presenting typical waveforms and incidences of acoustic signals were recorded. Causes of these murmurs are suggested based on comparison with the well-known waveforms of infants and children. A sophisticated signal processing method for murmur discovery is presented, that is also useful for automatic perinatal...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: F. Kovács, N. Kersner, K. Kádár, G. Hosszú Source Type: journals

A computationally advantageous system for fitting probabilistic decompression models to empirical dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: To investigate the nature and mechanisms of decompression sickness (DCS), we developed a system for evaluating the success of decompression models in predicting DCS probability from empirical data. Model parameters were estimated using maximum likelihood techniques. Exact integrals of risk functions and tissue kinetics transition times were derived. Agreement with previously published results was excellent including: (a) maximum likelihood values within one log-likelihood unit of previous results and improvements by re-optimization; (b) mean predicted DCS incidents within 1.4% of observed DCS; and (c) time of DCS...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Laurens E. L.E. Howle, Paul W. Weber, Richard D. Vann Source Type: journals

An interactive graphical user interface for comprehensive analysis of human and swine cardiac monophasic action potentialEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: This research describes a novel monophasic action potential (MAP) annotation algorithm coupled with an interactive graphical user interface (GUI). This algorithm incorporates a number of features to reduce error. Additionally, the GUI has several convenient features to view and manipulate the annotation visually. We analyzed data from swine and human hearts in normal sinus rhythm, during myocardial ischemia, and while eliciting high rates. Validation results indicate correlation >90% between human and computer measurements. This analysis system has several clinical applications in electrophysiological interventio...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Maneesh Shrivastav, Paul A. Iaizzo Source Type: journals

Automated classification of cells in sub-epithelial connective tissue of oral sub-mucous fibrosis—An SVM based approachEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study segmentation and classification of sub-epithelial connective tissue (SECT) cells except endothelial cells in oral mucosa of normal and OSF conditions has been reported. Segmentation has been carried out using multi-level thresholding and subsequently the cell population has been classified using support vector machine (SVM) based classifier. Moreover, the geometric features used here have been observed to be statistically significant, which enhance the statistical learning potential and classification accuracy of the classifier. Automated classification of SECT cells characterizes this precancerous condition ...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: M. Muthu Rama Krishnan, Mousumi Pal, Suneel K S.K. Bomminayuni, Chandan Chakraborty, Ranjan Rashmi R.R. Paul, Jyotirmoy Chatterjee, Ajoy K. A.K. Ray Source Type: journals

A combinatorial feature selection approach to describe the QSAR of dual site inhibitors of acetylcholinesteraseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Regarding the great potential of dual binding site inhibitors of acetylcholinesterase as the future potent drugs of Alzheimer's disease, this study was devoted to extraction of the most effective structural features of these inhibitors from among a large number of quantitative descriptors. To do this, we adopted a unique approach in quantitative structure–activity relationships. An efficient feature selection method was emphasized in such an approach, using the confirmative results of different routine and novel feature selection methods. The proposed methods generated quite consistent results ensuring the effe...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Ebrahim Barzegari E.B. Asadabadi, Parviz Abdolmaleki, Seyyed Mohsen Hosseini S.M.H. Barkooie, Samad Jahandideh, Mohammad Ali M.A. Rezaei Source Type: journals

An EMG-driven model to estimate muscle forces and joint moments in stroke patientsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Individuals following stroke exhibit altered muscle activation and movement patterns. Improving the efficiency of gait can be facilitated by knowing which muscles are affected and how they contribute to the pathological pattern. In this paper we present an electromyographically (EMG) driven musculoskeletal model to estimate muscle forces and joint moments. Subject specific EMG for the primary ankle plantar and dorsiflexor muscles, and joint kinematics during walking for four subjects following stroke were used as inputs to the model to predict ankle joint moments during stance. The model's ability to predict the ...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Qi Shao, Daniel N. D.N. Bassett, Kurt Manal, Thomas S. T.S. Buchanan Source Type: journals

On the discrimination of patho-physiological states in epilepsy by means of dynamical measuresEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: In the present paper a number of techniques were applied to determine the effects of epileptic seizure on spontaneous ongoing EEG. The idea is that seizure represents transitions of an epileptic brain from its normal (chaotic) state to an abnormal (more ordered) state. Some nonlinear measures including correlation dimension, maximum Lyapunov exponent and wavelet entropy and a graphical tool, named recurrence plot, as well as a novel technique that collects some statistics of the state space organization were used to characterize interictal, preictal and ictal states and derivate a phase transition. The novelty of...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Somayeh Raiesdana, Seyed Mohammad Reza Hashemi Golpayegani, Seyed Mohammad P Firoozabadi, Jafar Mehvari Habibabadi Source Type: journals

Classification of breast tissues using Moran's index and Geary's coefficient as texture signatures and SVMEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Female breast cancer is the major cause of cancer-related deaths in western countries. Efforts in computer vision have been made in order to help improving the diagnostic accuracy by radiologists. In this paper, we present a methodology that uses Moran's index and Geary's coefficient measures in breast tissues extracted from mammogram images. These measures are used as input features for a support vector machine classifier with the purpose of distinguishing tissues between normal and abnormal cases as well as classifying them into benign and malignant cancerous cases. The use of both proposed techniques showed to...
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Authors: Geraldo Braz Junior, Anselmo Cardoso de Paiva, Aristófanes Corrêa Silva, Alexandre Cesar Muniz de Oliveira Source Type: journals

Editorial Board & Publication informationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - November 16, 2009 Category: Bioinformatics Source Type: journals

Modeling schizophrenic-like neuronal patterns using nonlinear delayed differential equationsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We examined the simultaneous effect of altered dopamine and glutamate level on pyramidal cells using a mathematical model. The simulation results suggest that increased dopamine brings about irregular and aperiodic activity, interpreted as schizophrenic state. Hypoglutamatergic conditions have the same effect on the membrane potential of pyramidal cells. Increased glutamate level was able to neutralize the effects of the hyperdopamine state and normal periodic bursting behavior appeared. We suggest that glutamate receptor activation may have therapeutic results in schizophrenic patients. Surely, this hypothesis must be eva...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: Sareh Zendehrouh, Fatemeh Bakouie, Shahriar Gharibzadeh Source Type: journals

Detection of ventricular fibrillation using empirical mode decomposition and Bayes decision theoryEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Ventricular fibrillation (VF) is the most serious variety of arrhythmia which requires quick and accurate detection to save lives. In this paper, we propose an empirical mode decomposition (EMD) based algorithm for VF detection. The intrinsic mode functions (IMFs) of VF are orthogonal whereas the lower order IMFs of normal sinus rhythm (NSR) are not. The orthogonality indices derived from the first three consecutive intrinsic mode functions (IMFs) of NSR and VF are used for their discrimination. The proposed technique is applied to the MIT-BIH arrhythmia database. The accuracy of detection of VF is 99.70% for a w...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: Muhammad Abdullah Arafat, Jubair Sieed, Md. Kamrul Hasan Source Type: journals

Energy based feature extraction for classification of sleep apnea syndromeEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: In this paper it is aimed to classify sleep apnea syndrome (SAS) by using discrete wavelet transforms (DWT) and an artificial neural network (ANN). The abdominal and thoracic respiration signals are separated into spectral components by using multi-resolution DWT. Then the energy of these spectral components are applied to the inputs of the ANN. The neural network was configured to give three outputs to classify the SAS situation of the subject.The apnea can be mainly classified into three types: obstructive sleep apnea (OSA), central sleep apnea (CSA) and mixed sleep apnea (MSA). During OSA, the airway is blocke...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: Necmettin Sezgin, M. Emin Tagluk Source Type: journals

Comparative analysis of the Epstein-Barr virus encoded nuclear proteins of EBNA-3 familyEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: It is known that the EBNA-3 family proteins (EBNA-3, -4 and -6, alternative nomenclature EBNA-3A, B and C correspondingly) show a limited sequence similarity.We have analyzed EBNA-3 proteins both at the primary sequence and secondary structure levels. EBNA-3 and EBNA-4 were structurally more similar compared to other combinations with EBNA-6. We found “Stonin Homology Domain” profile in EBNA-4 and “Proline Rich Domain” in all EBNA-3 family of proteins. We have also found positive and negative charge clusters in all three proteins and mixed charge clusters in EBNA-3. Charged clusters are believed to play a...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: Surya Pavan S.P. Yenamandra, Ramakrishna Sompallae, George Klein, Elena Kashuba Source Type: journals

Determination of mode of ventilation using OSREEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study classifies the mode of ventilation using respiratory rate, inhaled and exhaled carbon dioxide concentrations in anaesthetised patients. Thirty seven patients were breathing spontaneously (SPONT) and 50 were on a ventilator (intermittent positive pressure ventilation, IPPV). A data-based methodology for rule inference from trained neural networks, orthogonal search-based rule extraction, identified two sets of low-order Boolean rules for differential identification of the mode of ventilation. Combining both models produced three possible outcomes; IPPV, SPONT and ‘Uncertain’. The true positive rates were appr...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: D. Faulke, T.A. Etchells, M.J. Harrison, P.J.G. Lisboa Source Type: journals

A virtual training simulator for learning cataract surgery with phacoemulsificationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: This paper presents the development of a low-cost cataract surgery simulator for trainees to practise phacoemulsification procedures with computer-generated models in virtual environments. It focuses on the training of cornea incision, capsulorrhexis and phaco-sculpting, which are simulated interactively with computationally efficient algorithms developed for tissue deformation, surface cutting and volume sculpting. Intuitive two-handed human–computer interactions are achieved with six degrees-of-freedom haptic devices. Performance of trainees on manual dexterity is recorded with quantifiable metrics. The propo...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: Kup-Sze K.-S. Choi, Sophia Soo, Fu-Lai F.-L. Chung Source Type: journals

SPlitSSI-SVM: An algorithm to reduce the misleading and increase the strength of domain signalEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
In this study, we proposed an algorithm named SplitSSI-SVM that works with the following steps. First, the training and testing datasets are generated to test the SplitSSI-SVM. Second, the protein sequence is split into subsequence based on order and disorder regions. The protein sequence that is more than 600 residues is split into subsequences to investigate the effectiveness of the protein domain prediction based on subsequence. Third, multiple sequence alignment is performed to predict the secondary structure using bidirectional recurrent neural networks (BRNN) where BRNN considers the interaction between amino acids. ...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: Hassan U. H.U. Kalsum, Zuraini A. Shah, Razib M. R.M. Othman, Rohayanti Hassan, Shafry M. Rahim, Hishammudin Asmuni, Jumail Taliba, Zalmiyah Zakaria Source Type: journals

A note on fractal dimensions of biomedical waveformsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: In this paper, we study performance of Katz method of computing fractal dimension of waveforms, and its estimation accuracy is compared with Higuchi's method. The study is performed on four synthetic parametric fractal waveforms for which true fractal dimensions can be calculated, and real sleep electroencephalogram. The dependence of Katz's fractal dimension on amplitude, frequency and sampling frequency of waveforms is noted. Even though the Higuchi's method has given more accurate estimation of fractal dimensions, the study suggests that the results of Katz's based fractal dimension analysis of biomedical wave...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: B.S. Raghavendra, D. Narayana Dutt Source Type: journals

Intelligent methods for identifying respiratory cycle phases from tracheal sound signal during sleepEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
We present two methods for identifying respiratory cycle phases from tracheal sound signal during sleep. The methods utilize the Hilbert transform in envelope extraction. They determine automatically a patient-specific amplitude threshold to be used in the detection. The core of one method is designed to be amplitude-independent whereas the other method uses solely the amplitude information. The methods provided average sensitivities of 98% and 99%, respectively, and positive prediction values of 100% on the total of 1434 respiratory cycles analysed from six different patients. The developed methods seem promising as such ...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: A. Kulkas, E. Huupponen, J. Virkkala, M. Tenhunen, A. Saastamoinen, E. Rauhala, S.-L. Himanen Source Type: journals

Adaptive compression algorithm from projections: Application on medical greyscale imagesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Image compression plays a crucial role in medical imaging, allowing efficient manipulation, storage, and transmission of binary, grey-scale, or colour images. Nevertheless, in medical applications the need to conserve the diagnostic validity of the image requires the use of lossless compression methods, producing low compression factors. In this paper, a novel near-lossless compression algorithm from projections, which almost eliminates both redundant information and noise from a greyscale image while retaining all relevant structures and producing high compression factors, is proposed. The algorithm is tested on...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: Giuseppe Placidi Source Type: journals

Statistical estimation of diagnosis with genetic markers based on decision tree analysis of complex diseaseEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: To explore combinations of genetic markers and to estimate their joint action, decision trees are built on the basis of marker frequencies in both disease and control groups. Youden's index (0.1–0.9 for a single marker) is calculated for genetic markers with different diagnostic capacities. When 23 single genetic markers with diagnostic power 0.10 are combined, the resulting diagnostic power is 0.5. Medium diagnostic power (Youden's index 0.7) can be obtained by combining four low effect diagnostic items. High diagnostic power (Youden's index 0.9) can be obtained by combining either eight low power items or fou...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: Liu Hui, Gai Liping Source Type: journals

Gaussian source model based iterative algorithm for EEG source imagingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Estimation of the neural active sources from the scalp electroencephalogram (EEG) is an ill-posed inverse problem. In this paper, we propose a new source model: Gaussian distributed Source Model (GSM), to model the activations in brain. GSM may imitate an Isolated Source Model (ISM) or a Distributed Source Model (DSM) by adopting different supporting range parameter of the Gaussian function. Using GSM, an iterative Gaussian source Imaging Algorithm (GIA) is developed to detect the EEG sources. As GIA dynamically reduces the solution space, the solution may gradually converge to a desired distribution. A comparati...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: Xu Lei, Peng Xu, Antao Chen, Dezhong Yao Source Type: journals

Robust and fast shell registration in PET and MR/CT brain imagesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: A robust and fast hybrid method using a shell volume that consists of high contrast voxels with their neighbors is proposed for registering PET and MR/CT brain images. Whereas conventional hybrid methods find the best matched pairs from several manually selected or automatically extracted local regions, our method automatically selects a shell volume in the PET image, and finds the best matched corresponding volume using normalized mutual information (NMI) in overlapping volumes while transforming the shell volume into an MR or CT image. A shell volume not only can reduce irrelevant corresponding voxels between t...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: Ho Lee, Jeongjin Lee, Namkug Kim, In Kyoon I.K. Lyoo, Yeong Gil Y.G. Shin Source Type: journals

Microarray data classification based on ensemble independent component selectionEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Independent component analysis (ICA) has been widely deployed to the analysis of microarray datasets. Although it was pointed out that after ICA transformation, different independent components (ICs) are of different biological significance, the IC selection problem is still far from fully explored. In this paper, we propose a genetic algorithm (GA) based ensemble independent component selection (EICS) system. In this system, GA is applied to select a set of optimal IC subsets, which are then used to build diverse and accurate base classifiers. Finally, all base classifiers are combined with majority vote rule. T...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: Kun-Hong K.-H. Liu, Bo Li, Qing-Qiang Q.-Q. Wu, Jun Zhang, Ji-Xiang J.-X. Du, Guo-Yan G.-Y. Liu Source Type: journals

Gray-scale edge detection for gastric tumor pathologic cell images by morphological analysisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: For the purpose of analyzing gastric tumor pathologic cell images, a novel method is developed with gray-scale edge detection of mathematical morphology in this study. In combination with texture features of the image under investigation, this paper works on edge detection with various structuring elements (SEs) and gray-scale values. The results of the experiment are presented, and we found several advantages by using the morphological edge detection scheme for the analysis of gastric tumor pathologic cell images. Meanwhile, the results of the binary morphological edge detection are given for comparison. (Source...
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Authors: Tian-gang T.-g. Li, Su-pin S.-p. Wang, Nan Zhao Source Type: journals

Editorial Board & Publication informationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - October 7, 2009 Category: Bioinformatics Source Type: journals

A method for the classification of corrective activity in context dependent postural controlling tasksEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Difficulties in maintaining postural stability are not common among young healthy people. However, with increasing age problems start to emerge. Deficits in the postural control system may also originate from a working environment where noise and solvents are present. Some diseases, for instance Menière's disease, can cause instability in walking and standing. Regardless of the origin of the problem in the balance system, it has to be detected in a meaningful, easily interpretable way. When detected, a suitable rehabilitation method can be proposed. In this paper we present a method which extracts a scalar featu...
Source: Computers in Biology and Medicine - August 27, 2009 Category: Bioinformatics Authors: Jyrki Rasku Source Type: journals

The utility of a marched absorbing layer boundary condition in the finite element analysis of diffuse photon density wave propagation in tissues relevant to breast imagingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Here we introduce a marched absorbing layer boundary condition for the finite element analysis of diffuse photon density wave propagation in tissues. We investigated and optimized the parameters required to set up a marched absorbing layer boundary for diffuse photon density wave propagation in media with different absorption and scattering coefficients. Comparing with using a breast model connected to a large substrate and a Robin boundary condition, using a marched absorbing layer boundary condition to replace part of the large base reduced the time for forward modeling by about 30%. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - August 27, 2009 Category: Bioinformatics Authors: Chengyu Li, M. Rex M.R. Cheung Source Type: journals

Application of the iris filter for automatic detection of pulmonary nodules on computed tomography imagesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: We have developed a computer-aided diagnosis (CAD) system to detect pulmonary nodules on thin-slice helical computed tomography (CT) images. We have also investigated the capability of an iris filter to discriminate between nodules and false-positive findings. Suspicious regions were characterized with features based on the iris filter output, gray level and morphological features, extracted from the CT images. Functions calculated by linear discriminant analysis (LDA) were used to reduce the number of false-positives.The system was evaluated on CT scans containing 77 pulmonary nodules. The system was trained and...
Source: Computers in Biology and Medicine - August 27, 2009 Category: Bioinformatics Authors: Jorge Juan J.J. Suárez-Cuenca, Pablo G. P.G. Tahoces, Miguel Souto, María J. M.J. Lado, Martine Remy-Jardin, Jacques Remy, Juan José Vidal Source Type: journals

Real time acquisition and PC to PC wireless transmission of human carotid pulse waveformEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Carotid pulse is an established physiological parameter used to deduce cardiac information. Technological advances allow non-invasive measurement of carotid waveform, but involve complex electronics. Simple and relatively inexpensive method is devised here to acquire the carotid pulse. Measurements were made non-invasively on human subjects in various postures using piezoelectric sensor. Transducer output is interfaced directly to a computer in real time and carotid wave is viewed successfully on virtual oscilloscope. Stored data is digitally filtered, visually analyzed and transferred wirelessly from one compute...
Source: Computers in Biology and Medicine - August 27, 2009 Category: Bioinformatics Authors: Dipali Bansal, Munna Khan, Ashok K. A.K. Salhan Source Type: journals

Improving the protein fold recognition accuracy of a reduced state-space hidden Markov modelEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Fold recognition is a challenging field strongly associated with protein function determination, which is crucial for biologists and the pharmaceutical industry. Hidden Markov models (HMMs) have been widely used for this purpose. In this paper we demonstrate how the fold recognition performance of a recently introduced HMM with a reduced state-space topology can be improved. Our method employs an efficient architecture and a low complexity training algorithm based on likelihood maximization. The fold recognition performance of the model is further improved in two steps. In the first step we use a smaller model ar...
Source: Computers in Biology and Medicine - August 27, 2009 Category: Bioinformatics Authors: Christos Lampros, Costas Papaloukas, Kostas Exarchos, Dimitrios I. D.I. Fotiadis, Dimitrios Tsalikakis Source Type: journals

Unsteady magnetohydrodynamic blood flow through irregular multi-stenosed arteriesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Flow of an electrically conducting fluid characterizing blood through the arteries having irregular shaped multi-stenoses in the environment of a uniform transverse magnetic-field is analysed. The flow is considered to be axisymmetric with an outline of the irregular stenoses obtained from a three-dimensional casting of a mild stenosed artery, so that the physical problem becomes more realistic from the physiological point of view. The marker and cell (MAC) and successive-over-relaxation (SOR) methods are respectively used to solve the governing unsteady magnetohydrodynamic (MHD) equations and pressure-Poisson eq...
Source: Computers in Biology and Medicine - August 27, 2009 Category: Bioinformatics Authors: Norzieha Mustapha, Norsarahaida Amin, Santabrata Chakravarty, Prashanta Kumar P.K. Mandal Source Type: journals

A computational method for the semi-automated quantitative analysis of tympanic membrane perforations and tympanosclerosisEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Tympanic membrane pathological findings such as perforations and tympanosclerotic plaques (along with conductive hearing loss and purulent drainage) are the most typical trademarks of either active or burned-out chronic otitis media. These findings are normally evaluated by an expert using visual subjective analysis. In this work, we present a computational semi-automated method to quantify these pathologies. We also present a validation study of the method using a subset of 39 cases randomly extracted from a set of more than 2000 cases (perforations and tympanosclerosis) of the Hospital de Clínicas de Porto Ale...
Source: Computers in Biology and Medicine - August 27, 2009 Category: Bioinformatics Authors: Eros Comunello, Aldo von Wangenheim, Vilson Heck Junior, Cristina Dornelles, Sady Selamen Costa Source Type: journals

Brain asymmetry measurement using EMISU (embedded interactive stimulation unit) in applied brain biophysicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: The basic motive to study the brain asymmetry using a dichotic paradigm, forced the authors to develop an interactive stimulus system, where not only the stimuli but also the responses could be interactively registered real time on to the EEG data. Therefore, an embedded interactive stimulation unit (EMISU) was constructed and applied in such a task, incorporating behavioral and evoked data from 20 volunteers (10 male, 10 female, 21.15 years). The results provided a significant factor of laterality in favor of right ear responses (p (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - August 27, 2009 Category: Bioinformatics Authors: Murat Ozgoren, Ugras Erdogan, Onur Bayazit, Serhat Taslica, Adile Oniz Source Type: journals

Three-dimensional segmentation of tumors from CT image data using an adaptive fuzzy systemEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: A new segmentation method using a fuzzy rule based system to segment tumors in a three-dimensional CT data was developed. To initialize the segmentation process, the user selects a region of interest (ROI) within the tumor in the first image of the CT study set. Using the ROI's spatial and intensity properties, fuzzy inputs are generated for use in the fuzzy rules inference system. With a set of predefined fuzzy rules, the system generates a defuzzified output for every pixel in terms of similarity to the object. Pixels with the highest similarity values are selected as tumor. This process is automatically repeat...
Source: Computers in Biology and Medicine - August 27, 2009 Category: Bioinformatics Authors: Jung Leng J.L. Foo, Go Miyano, Thom Lobe, Eliot Winer Source Type: journals

Optimal feature selection for the assessment of vocal fold disordersEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This article aims to distinguish these types of vocal diseases into four different classes for the purpose of automatic screening. Firstly, the reconstructed signal at each wavelet packet decomposition sub-band in five levels of decomposition with mother wavelet of (db10) is used to extract the nonlinear features of self-similarity and approximate entropy. Also, wavelet packet coefficients are used to measure energy and Shannon entropy features at different spectral sub-bands. Consequently, to find a discriminant feature vector, three different methods have been applied: Davies–Bouldin (DB) criteria, genetic algorithm (G...
Source: Computers in Biology and Medicine - August 27, 2009 Category: Bioinformatics Authors: Hossein Khadivi Heris, Babak Seyed Aghazadeh, Mansour Nikkhah-Bahrami Source Type: journals

New developmental stages for common marmosets (Callithrix jacchus) using mass and age variables obtained by K-means algorithm and self-organizing maps (SOM)Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study proposes new developmental stages for Callithrix jacchus, using K-Means algorithm and an artificial neural network–self-organising maps (SOM) as computational tools, based on weight and age. Eight developmental stages are proposed: Infant I, II and III, Juvenile I and II, Sub adult, Young adult and Older adult. This classification is consistent with the first appearance of several behavioural and physiological characteristics and thus may have generality in defining critical developmental periods. It also reveals differences in male and female development and establishes a stage for the onset of the final adul...
Source: Computers in Biology and Medicine - August 27, 2009 Category: Bioinformatics Authors: Adriano de Castro Leão, Adrião A. Duarte Dória Neto, Maria M.B.C. Bernardete Cordeiro de Sousa Source Type: journals

Editorial Board & Publication informationEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
(Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - August 27, 2009 Category: Bioinformatics Source Type: journals

A spreadsheet application for processing long-term EEG recordingsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
This study develops a Windows application for processing huge tabular text files. The tool has been especially designed for handling EEG files. As a consequence, tables with more than 65,536 rows and 256 columns, which is a limitation found in Microsoft's Excel, can be loaded, visualized and processed with no more restrictions than the ones imposed by the memory of the operating system.Beyond tabular visualization, additional tools are available for chart customization and spreadsheet like cell processing commands. Additionally, commands are included for signal processing, cluster analysis and computationally taxing matrix...
Source: Computers in Biology and Medicine - August 6, 2009 Category: Bioinformatics Authors: Melvin Ayala, Mercedes Cabrerizo, Maria Tito, Armando Barreto, Malek Adjouadi Source Type: journals

Pattern recognition methods applied to respiratory sounds classification into normal and wheeze classesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: In this paper, we present the pattern recognition methods proposed to classify respiratory sounds into normal and wheeze classes. We evaluate and compare the feature extraction techniques based on Fourier transform, linear predictive coding, wavelet transform and Mel-frequency cepstral coefficients (MFCC) in combination with the classification methods based on vector quantization, Gaussian mixture models (GMM) and artificial neural networks, using receiver operating characteristic curves. We propose the use of an optimized threshold to discriminate the wheezing class from the normal one. Also, post-processing fil...
Source: Computers in Biology and Medicine - August 6, 2009 Category: Bioinformatics Authors: Mohammed Bahoura Source Type: journals

Feature extraction and dimensionality reduction for mass spectrometry dataEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Mass spectrometry is being used to generate protein profiles from human serum, and proteomic data obtained from mass spectrometry have attracted great interest for the detection of early stage cancer. However, high dimensional mass spectrometry data cause considerable challenges. In this paper we propose a feature extraction algorithm based on wavelet analysis for high dimensional mass spectrometry data. A set of wavelet detail coefficients at different scale is used to detect the transient changes of mass spectrometry data. The experiments are performed on 2 datasets. A highly competitive accuracy, compared with...
Source: Computers in Biology and Medicine - August 6, 2009 Category: Bioinformatics Authors: Yihui Liu Source Type: journals

Efficient 3D numerical approach for temperature prediction in laser irradiated biological tissuesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Temperature prediction in biological tissues irradiated by an optical source is frequently required in some medical applications, like Thermotherapy, Hyperthermia or tissue ablation. In this work we propose a new numerical approach to solve the bio-heat equation. It is based on the two steps 3D modified Du Fort–Frankel algorithm, which allows a better convergence, more accuracy and a faster computation than previous numerical methods developed by other authors. The model also includes adaptive spatial mesh and time step refinement. These improved results for opto-thermal temperature distribution could be used f...
Source: Computers in Biology and Medicine - August 6, 2009 Category: Bioinformatics Authors: Félix Fanjul-Vélez, Oleg G. O.G. Romanov, José Luis Arce-Diego Source Type: journals

An adaptive model simulating the somatic motility and the active hair bundle motion of the OHCEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: The outer hair cells (OHC) of the mammalian inner ear change the sensitivity and frequency selectivity of the filtering system of the cochlea using two kinds of mechanical activity: the somatic motility and the active hair bundle motion. We designed a non-linear adaptive model of the OHC employing both mechanisms of the mechanical activity.The modeling results show that the high sensitivity and frequency selectivity of the filtering system of the cochlea depend on the somatic motility of the OHC. However, both mechanisms of mechanical activity are involved in the adaptation to sound intensity and efferent-synapti...
Source: Computers in Biology and Medicine - August 6, 2009 Category: Bioinformatics Authors: Antanas Stasiunas, Antanas Verikas, Rimvydas Miliauskas, Natalija Stasiuniene Source Type: journals

A simulation finite element model for the mechanics of the internal oblique muscle: A defense mechanism against inguinal hernia formation?Email this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: Simulation of the human muscular system has multiple applications in biomechanics, biomedicine and in the study of motion in general. Mechanical alterations of the normal functioning in the inguinal area (“inguinal shutter”) seems to be involved in the genesis of hernias in adults, but the role of this anatomical mechanisms is poorly understood. A finite element model for the mechanics of the internal oblique muscle allowed creating a dynamic model of the inguinal region applicable to the study of the shutter mechanism as a defence mechanism of contention of the abdominal viscera against development of an ing...
Source: Computers in Biology and Medicine - August 6, 2009 Category: Bioinformatics Authors: Gerard Fortuny, Javier Rodríguez-Navarro, Antonio Susín, Manuel Armengol-Carrasco, Manuel López-Cano Source Type: journals

Automated Arabidopsis plant root cell segmentation based on SVM classification and region mergingEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: To obtain development information of individual plant cells, it is necessary to perform in vivo imaging of the specimen under study, through time-lapse confocal microscopy. Automation of cell detection/marking process is important to provide research tools in order to ease the search for special events, such as cell division. In this paper we discuss an automatic cell detection approach for Arabidopsis thaliana based on segmentation, which selects the best cell candidates from a starting watershed-based image segmentation and improves the result by merging adjacent regions. The selection of individual cells is ob...
Source: Computers in Biology and Medicine - August 6, 2009 Category: Bioinformatics Authors: Monica Marcuzzo, Pedro Quelhas, Ana Campilho, Ana Maria Mendonça, Aurélio Campilho Source Type: journals

Aceto-white temporal pattern classification using k-NN to identify precancerous cervical lesion in colposcopic imagesEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: After Pap smear test, colposcopy is the most used technique to diagnose cervical cancer due to its higher sensitivity and specificity. One of the most promising approaches to improve the colposcopic test is the use of the aceto-white temporal patterns intrinsic to the color changes in digital images. However, there is not a complete understanding of how to use them to segment colposcopic images. In this work, we used the classification algorithm k-NN over the entire length of the aceto-white temporal pattern to automatically discriminate between normal and abnormal cervical tissue, reaching a sensitivity of 71% a...
Source: Computers in Biology and Medicine - August 6, 2009 Category: Bioinformatics Authors: Héctor-Gabriel H.G. Acosta-Mesa, Nicandro Cruz-Ramírez, Rodolfo Hernández-Jiménez Source Type: journals

A filter bank-based source extraction algorithm for heart sound removal in respiratory soundsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: In this paper, we consider the problem of heart sounds (HS) removal from respiratory sounds (RS), and a novel semi-blind single-channel source extraction algorithm is proposed. The proposed method is able to extract the underlying pure RS from the HS corrupted noisy input signals by incorporating the filter banks and template-based matching using FIR filters. For performance evaluation of the presented method, the average power spectral densities (PSD) of the input RS segments without HS have been compared with the PSD of the reconstructed signals over six selected frequency bands from 20 to 800Hz. The proposed m...
Source: Computers in Biology and Medicine - August 6, 2009 Category: Bioinformatics Authors: F. Jin, F. Sattar, D.Y.T. Goh Source Type: journals

Seizure characterisation using frequency-dependent multivariate dynamicsEmail this article to a colleague. Save this article to My Clippings. Discuss or comment on this article.
Abstract: The characterisation of epileptic seizures assists in the design of targeted pharmaceutical seizure prevention techniques and pre-surgical evaluations. In this paper, we expand on the recent use of multivariate techniques to study the cross-correlation dynamics between electroencephalographic (EEG) channels. The maximum overlap discrete wavelet transform (MODWT) is applied in order to separate the EEG channels into their underlying frequencies. The dynamics of the cross-correlation matrix between channels, at each frequency, are then analysed in terms of the eigenspectrum. By examination of the eigenspectrum, we ...
Source: Computers in Biology and Medicine - August 6, 2009 Category: Bioinformatics Authors: T. Conlon, H.J. H.J. Ruskin, M. Crane Source Type: journals