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. Wed, 17 Mar 2010 16:48:09 +0100 http://www.medworm.com/index.php?rid=3342211&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482510000168%2Fabstract%3Frss%3Dyes Abstract: Atrial fibrillation is the most common type of arrhythmia to affect humans. One of the treatment modalities for atrial fibrillation is an electrical cardioversion. Electrical cardioversion can result in one of three outcomes: an immediate termination of arrhythmic activity, a delayed termination or unsuccessful termination. The mechanism of delayed termination is unknown. Here we present a model of an atrial fibrillation as a coexistence of several spiral waves pinned to the inhomogeneities in active media. We show that in inhomogeneous system delayed termination can be explained as the unpinning of a spiral wave from inhomogeneities and its termination after collision with the edge of the system. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342211 Mon, 01 Mar 2010 00:00:00 +0100 3342211 http://www.medworm.com/index.php?rid=3342210&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482510000090%2Fabstract%3Frss%3Dyes Abstract: Quantum physics and molecular biology are two disciplines that have evolved relatively independently. However, recently a wealth of evidence has demonstrated the importance of quantum mechanics for biological systems and thus a new field of quantum biology is emerging. There are many claims that quantum mechanics plays a key role in the origin and/or operation of biological organisms. We consider the nucleonic acid of virus as a quantum system in this paper and discuss virus life cycle from the view-point of quantum and simulate it using quantum gates for the first time. The maximally entangled states show infected cell can change to entire cell, the virus can switch from the lysogenic to the lytic and the prophages can remain latent in the bacterial chromosome for many generatio... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342210 Mon, 01 Mar 2010 00:00:00 +0100 3342210 http://www.medworm.com/index.php?rid=3342209&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482510000089%2Fabstract%3Frss%3Dyes Abstract: The distinctiveness of clinical environments demands specific solutions in the design of both usable and practical user interfaces for 3D medical imaging. In this work, a novel user interface to provide a direct interaction in 3D space by off-the-shelf input devices is proposed. The interface, which has been implemented and integrated into an open-source medical image viewer, features a depth-enhanced mouse pointer and a novel rotation technique that uses the object's geometry as the rotation handle. The usability of the proposed approach is evaluated to show its effectiveness for use in professional 3D imaging applications. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342209 Mon, 01 Mar 2010 00:00:00 +0100 3342209 http://www.medworm.com/index.php?rid=3342208&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482510000077%2Fabstract%3Frss%3Dyes Abstract: Metabolic pathway diagrams provide a wealth of information on how reactions combine to perform biological functions. While pathway diagrams are arranged in a way that allows a specific area of metabolism to be visualised, the inherent complexity of each pathway makes it difficult to identify the sets of reactions linking groups of compounds; a common task for researchers attempting to explain observed correlations or looking for further compounds of potential interest to use in validation work. Here we introduce Linked Metabolites, a tool that identifies sets of reactions linking groups of compounds in the context of the KEGG pathway diagrams. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342208 Mon, 01 Mar 2010 00:00:00 +0100 3342208 http://www.medworm.com/index.php?rid=3342207&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482510000065%2Fabstract%3Frss%3Dyes Abstract: Midline shift is one of the most important quantitative features clinicians use to evaluate the severity of brain compression by various pathologies. It can be recognized by modeling brain deformation according to the estimated biomechanical properties of the brain and the cerebrospinal fluid spaces. This paper proposes a novel method to identify the deformed midline according to the above hypothesis. In this model, the deformed midline is decomposed into three segments: the upper and the lower straight segments representing parts of the tough dura mater separating two brain hemispheres, and the central curved segment formed by a quadratic Bezier curve, representing the intervening soft brain tissue. The deformed midline is obtained by minimizing the summed square of the differen... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342207 Mon, 01 Mar 2010 00:00:00 +0100 3342207 http://www.medworm.com/index.php?rid=3342206&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482510000053%2Fabstract%3Frss%3Dyes Abstract: Single clustering methods have often been used to elucidate clusters in high dimensional medical data, even though reliance on a single algorithm is known to be problematic. In this paper, we present a methodology to determine a set of ‘core classes’ by using a range of techniques to reach consensus across several different clustering algorithms, and to ascertain the key characteristics of these classes. We apply the methodology to immunohistochemical data from breast cancer patients. In doing so, we identify six core classes, of which several may be novel sub-groups not previously emphasised in literature. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342206 Mon, 01 Mar 2010 00:00:00 +0100 3342206 http://www.medworm.com/index.php?rid=3342205&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS001048251000003X%2Fabstract%3Frss%3Dyes This study applied a knowledge-driven data integration framework for the inference of protein–protein interactions (PPI). Evidence from diverse genomic features is integrated using a knowledge-driven Bayesian network (KD-BN). Receiver operating characteristic (ROC) curves may not be the optimal assessment method to evaluate a classifier's performance in PPI prediction as the majority of the area under the curve (AUC) may not represent biologically meaningful results. It may be of benefit to interpret the AUC of a partial ROC curve whereby biologically interesting results are represented. Therefore, the novel application of the assessment method referred to as the partial ROC has been employed in this study to assess predictive performance of PPI predictions along with calculating the Tru... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342205 Mon, 01 Mar 2010 00:00:00 +0100 3342205 http://www.medworm.com/index.php?rid=3342204&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482510000028%2Fabstract%3Frss%3Dyes Abstract: A protein function pair approach, based on protein–protein interaction (PPI) data, is proposed to predict protein functions. Randomization tests are performed on the PPI dataset, which resulted in a protein function correlation scoring value which is used to rank the relative importance of a function pair. It has been found that certain classes of protein functions tend to be correlated together. Scoring values of these correlation pairs allow us to predict the functionality of a protein given that it interacts with proteins having well-defined function annotations.The jackknife test is used to validate the function pair method. The protein function pair approach achieves a prediction sensitivity comparable to an approach using more sophisticated method. The main advantages of ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342204 Mon, 01 Mar 2010 00:00:00 +0100 3342204 http://www.medworm.com/index.php?rid=3342203&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002212%2Fabstract%3Frss%3Dyes Abstract: A relabeling algorithm for retrieval of noisy instances with binary outcomes is presented. The relabeling algorithm iteratively retrieves, selects, and re-labels data instances (i.e., transforms a decision space) to improve prediction quality. It emphasizes knowledge generalization and confidence rather than classification accuracy. A confidence index incorporating classification accuracy, prediction error, impurities in the relabeled dataset, and cluster purities was designed. The proposed approach is illustrated with a binary outcome dataset and was successfully tested on the standard benchmark four UCI repository dataset as well as bladder cancer immunotherapy data. A subset of the most stable instances (i.e., 7% to 51% of the sample) with high confidence (i.e., between 64%–... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342203 Mon, 01 Mar 2010 00:00:00 +0100 3342203 http://www.medworm.com/index.php?rid=3342202&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002194%2Fabstract%3Frss%3Dyes In this study, an efficient, semi-automated and cost-effective solution for the analysis of fMRI images acquired in a clinical setting is presented relying heavily on open source software. The core of the pipeline is the software Analysis of Functional NeuroImages (AFNI, National Institute of Mental Health (NIMH)) combined with K-PACS and ImageJ. Its application is illustrated with clinical fMRI exams and with a research study involving comparing subjects diagnosed with Parkinson's disease and age-matched controls. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342202 Mon, 01 Mar 2010 00:00:00 +0100 3342202 http://www.medworm.com/index.php?rid=3342201&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002182%2Fabstract%3Frss%3Dyes Abstract: An abdominal aortic aneurysm (AAA) is the area of a localized widening of the abdominal aorta, with a frequent presence of thrombus. Segmentation and quantitative analysis of the thrombus in AAA are of paramount importance for diagnosis, risk assessment and determination of treatment options. The proposed thrombus segmentation method utilizes the power and flexibility of the 3-D graph search approach based on a triangular mesh. The method was tested in 9 3-D MDCT angiography data sets (9 patients with AAA, 1300 image slices), and the mean unsigned errors for the luminal and thrombotic surfaces were and . To achieve these results, control points needed to be interactively entered on image slices per 3-D CTA data set. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342201 Mon, 01 Mar 2010 00:00:00 +0100 3342201 http://www.medworm.com/index.php?rid=3342200&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002170%2Fabstract%3Frss%3Dyes Abstract: Using one of the well known mathematical models for immunotherapy of tumor–immune interactions, in this paper an algorithm is developed to optimize the immunotherapy in cancer treatment. The optimal control strategy is defined to maximize the effector cells and interleukin-2 concentration, while minimizing the tumor cells. The performance index is developed to stop the growth of tumor cells even at the end of the treatment. The maximum principle approach is the optimal control strategy in this paper. Analyzing the results and comparing them with very recent researches, it is shown that the amount of tumor cells with the proposed control algorithm is less then the others, both during and after the completion of the treatment. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342200 Mon, 01 Mar 2010 00:00:00 +0100 3342200 http://www.medworm.com/index.php?rid=3342199&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002169%2Fabstract%3Frss%3Dyes Abstract: A diving algorithm is a safe combination of model and data to efficiently stage diver ascents following arbitrary underwater exposures. To that end, we detail a modern one, the LANL reduced gradient bubble model (RGBM), dynamical principles, and correlations with the LANL Data Bank data. Table, profile, and meter fit and risk parameters are obtained in statistical likelihood analysis from decompression exposure data. The RGBM algorithm enjoys extensive and utilitarian application in mixed gas diving, both in recreational and technical sectors, and forms the bases for released tables, software, and decompression meters used by scientific, commercial, and research divers. The LANL Data Bank is described, and the methods used to deduce risk are detailed. Risk functions for dissolved... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342199 Mon, 01 Mar 2010 00:00:00 +0100 3342199 http://www.medworm.com/index.php?rid=3342198&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS001048250900198X%2Fabstract%3Frss%3Dyes Abstract: This paper presents an ensemble of feature selection and classification technique for classifying two types of breast lesion, benign and malignant. Features are selected based on their area under the ROC curves (AUC) which are then classified using a hybrid hidden Markov model (HMM)-fuzzy approach. HMM generated log-likelihood values are used to generate minimized fuzzy rules which are further optimized using gradient descent algorithms in order to enhance classification performance. The developed model is applied to Wisconsin breast cancer dataset to test its performance. The results indicate that a combination of selected features and the HMM-fuzzy approach can classify effectively the lesion types using only two fuzzy rules. Our experimental results also indicate that the prop... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342198 Mon, 01 Mar 2010 00:00:00 +0100 3342198 http://www.medworm.com/index.php?rid=3342197&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002200%2Fabstract%3Frss%3Dyes As Computers in Biology and Medicine begins is fortieth year of publication, its Founding Editor, Robert Ledley, steps down as Editor-in-Chief. Pausing to consider this remarkable man and his accomplished career illuminates the histories of both the discipline of biomedical computing and of this journal, and may well provide insights into the forces that will shape both in future. The following comments are heavily indebted to the work of Joseph November, whose Ph.D. thesis for Princeton's Program in History of Science is serving as the basis of a new book about the early history of computers in biomedicine . November's work is a compelling (and fun) read for anyone working in this field, and documents the fragility of a new discipline and the careers of the people creating it—and the ma... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342197 Mon, 01 Mar 2010 00:00:00 +0100 3342197 http://www.medworm.com/index.php?rid=3342196&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482510000223%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3342196 Mon, 01 Mar 2010 00:00:00 +0100 3342196 http://www.medworm.com/index.php?rid=3262385&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002157%2Fabstract%3Frss%3Dyes Abstract: Fast bone segmentation is often important in computer-aided medical systems. Thresholding-based techniques have been widely used to identify the object of interest (bone) against dark backgrounds. However, the darker areas that are often present in bone tissue may adversely affect the results obtained using existing thresholding-based segmentation methods. We propose an automatic, fast, robust and accurate method for the segmentation of bone using 3D adaptive thresholding. An initial segmentation is first performed to partition the image into bone and non-bone classes, followed by an iterative process of 3D correlation to update voxel classification. This iterative process significantly improves the thresholding performance. A post-processing step of 3D region growing is used to ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262385 Mon, 01 Feb 2010 00:00:00 +0100 3262385 http://www.medworm.com/index.php?rid=3262384&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002145%2Fabstract%3Frss%3Dyes Abstract: The uterine electromyogram or electrohysterogram (EHG) is one of the most promising biophysical markers of preterm labor. At this time no recording parameter standard exists for EHG recordings which can be a problem for the establishment of international multicentric trials. In this paper, we present a management and processing system dedicated to storing and processing EHG signals. This system can process EHG signals recorded in different experimental conditions i.e. different sampling frequencies. The signal management is performed using an easy to use graphical user interface. Other available functions include visualization, preprocessing and analysis of EHG signals. The proposed processing functions provide temporal, spectral and time-scale parameters obtained from the EHG bi... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262384 Mon, 01 Feb 2010 00:00:00 +0100 3262384 http://www.medworm.com/index.php?rid=3262383&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002133%2Fabstract%3Frss%3Dyes Abstract: This paper employs the energy minimum to enhance drug docking efficiency in a computer aided drug design (CADD) system. The energy minimum application is used to enhance CADD docking performance. The proposed method is discussed in three aspects, adaptive genetic algorithms (AGA), Lyapunov stability theorem and molecular force field. As in previous researches, docking is the crucial component in drug development. The number of docking sites affects the drug docking speed. Reducing the scope of the geometric search is the key task. This paper proposes AGA to improve geometric molecular docking search efficiency. The Lyapunov stability theorem forwards the stability state identification. Protein folding intention generally finds the most appropriate stability state when the thermod... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262383 Mon, 01 Feb 2010 00:00:00 +0100 3262383 http://www.medworm.com/index.php?rid=3262382&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002121%2Fabstract%3Frss%3Dyes Abstract: Computer models and simulations of X-ray imaging systems are becoming a very precious tool during the development and evaluation of new X-ray imaging techniques. To provide, however, a faithful simulation of a system, all components must be accurately modelled and tested, followed by verification through experimental measurements. This paper presents a validation study of the XRayImagingSimulator, an in-house developed X-ray imaging simulator, which is extensively used as a basic tool in carrying out complex breast imaging simulations. The approach followed compares results obtained via an experimental setup for breast phantom (CIRS 011A) imaging, using synchrotron radiation (SYRMEP beamline at ELETTRA), with those from its simulated setup under the same conditions. The study dem... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262382 Mon, 01 Feb 2010 00:00:00 +0100 3262382 http://www.medworm.com/index.php?rid=3262381&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS001048250900211X%2Fabstract%3Frss%3Dyes Abstract: The need to share gait analysis data to improve clinical decision support has been recognised since the early 1990s. GaitaBase has been established to provide a web-accessible repository system of gait analysis data to improve the sharing of data across local and international clinical and research community. It is used by several clinical and research groups across the world providing cross-group access permissions to retrieve and analyse the data. The system is useful for bench-marking and quality assurance, clinical consultation, and collaborative research. It has the capacity to increase the population sample size and improve the quality of ‘normative’ gait data. In addition the accumulated stored data may facilitate clinicians in comparing their own gait data with others... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262381 Mon, 01 Feb 2010 00:00:00 +0100 3262381 http://www.medworm.com/index.php?rid=3262380&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002108%2Fabstract%3Frss%3Dyes Abstract: The paper describes the design and training of a fuzzy neural network used for early diagnosis of a patient through an FPGA based implementation of a smart instrument. The system employs a fuzzy interface cascaded with a feed-forward neural network. In order to obtain an optimum decision regarding the future pathophysiological state of a patient, the optimal weights of the synapses between the neurons have been determined by using inverse delayed function model of neurons. The neurons that are considered in the proposed network are devoid of self connections instead of commonly used self connected neurons. The current work also find out the optimal number of neurons in the hidden layer for accurate diagnosis as against the available number of CLB in the FPGA. The system has been ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262380 Mon, 01 Feb 2010 00:00:00 +0100 3262380 http://www.medworm.com/index.php?rid=3262379&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002091%2Fabstract%3Frss%3Dyes Abstract: Since Golub applied gene expression profiles (GEP) to the molecular classification of tumor subtypes for more accurately and reliably clinical diagnosis, a number of studies on GEP-based tumor classification have been done. However, the challenges from high dimension and small sample size of tumor dataset still exist. This paper presents a new tumor classification approach based on an ensemble of probabilistic neural network (PNN) and neighborhood rough set model based gene reduction. Informative genes were initially selected by gene ranking based on an iterative search margin algorithm and then were further refined by gene reduction to select many minimum gene subsets. Finally, the candidate base PNN classifiers trained by each of the selected gene subsets were integrated by maj... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262379 Mon, 01 Feb 2010 00:00:00 +0100 3262379 http://www.medworm.com/index.php?rid=3262378&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS001048250900208X%2Fabstract%3Frss%3Dyes Abstract: In this paper, we describe a framework for multiclass cell detection in composite images consisting of images obtained with three different contrast methods for transmitted light illumination (referred to as multicontrast composite images). Compared to previous multiclass cell detection results , the use of multicontrast composite images was found to improve the detection accuracy by introducing more discriminatory information into the system. Preprocessing multicontrast composite images with Kernel PCA was found to be superior to traditional linear PCA preprocessing, especially in difficult classification scenarios where high-order nonlinear correlations are expected to be important. Systematic study of our approach under different overlap conditions suggests that it possesses s... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262378 Mon, 01 Feb 2010 00:00:00 +0100 3262378 http://www.medworm.com/index.php?rid=3262377&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002078%2Fabstract%3Frss%3Dyes Abstract: The aberrant hypermethylation of CpG islands in promoter regions of genes plays an important role in the onset and progression of Breast cancer. Meanwhile, it is highly associated with human genomic features. Two feature selection algorithms: t-test and CfsSubsetEval were used to obtain efficient feature subsets. We discovered 14 significant feature subsets by CfsSubsetEval, which can distinguish hypermethylated genes from control genes. As a result, 393 unconfirmed hypermethylated genes in Breast cancer were prioritized. These genes were assigned the hypermethylated scores and were supported by literature and Gene Ontology enrichment. This paper suggests that the feature subsets could be served as discriminating genomic markers to infer novel hypermethylated genes in cancer pote... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262377 Mon, 01 Feb 2010 00:00:00 +0100 3262377 http://www.medworm.com/index.php?rid=3262376&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002066%2Fabstract%3Frss%3Dyes Abstract: Although short interfering RNA (siRNA) has been widely used for studying gene functions in mammalian cells, its gene silencing efficacy varies markedly and there are only a few consistencies among the recently reported design rules/guidelines for selecting siRNA sequences effective for mammalian genes. Another shortcoming of the previously reported methods is that they cannot estimate the probability that a candidate sequence will silence the target gene. This paper first reviewed the recently reported siRNA design guidelines and clarified the problems concerning the guidelines. It then proposed two prediction methods—Radial Basis Function (RBF) network and decision tree learning—and their combined method for selecting effective siRNA target sequences from many possible candi... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262376 Mon, 01 Feb 2010 00:00:00 +0100 3262376 http://www.medworm.com/index.php?rid=3262375&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002054%2Fabstract%3Frss%3Dyes In this study, this is achieved by using an indexing scheme designated as three-level indexing hierarchy (TIH) to search for the appropriate cut-in point in the session and to identify the commands which should be applied to restore the current image contents to their original condition at the cut-in point. In the proposed indexing scheme, the performance of the cut-in point determination process and the content restoration procedure is enhanced by maintaining a link between all the changes which take place in the image contents over the duration of the session and the commands which induce these changes. The evaluation results confirm that TIH outperforms existing scene-based retrieval systems in terms of both an improved computational efficiency and a lower storage requirement. (Source: ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262375 Mon, 01 Feb 2010 00:00:00 +0100 3262375 http://www.medworm.com/index.php?rid=3262374&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002042%2Fabstract%3Frss%3Dyes Abstract: The identification of some important retinal anatomical regions is a prerequisite for the computer aided diagnosis of several retinal diseases. In this paper, we propose a new adaptive method for the automatic segmentation of the optic disk in digital color fundus images, using mathematical morphology. The proposed method has been designed to be robust under varying illumination and image acquisition conditions, common in eye fundus imaging. Our experimental results based on two publicly available eye fundus image databases are encouraging, and indicate that our approach potentially can achieve a better performance than other known methods proposed in the literature. Using the DRIVE database (which consists of 40 retinal images), our method achieves a success rate of 100% in the ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262374 Mon, 01 Feb 2010 00:00:00 +0100 3262374 http://www.medworm.com/index.php?rid=3262373&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002030%2Fabstract%3Frss%3Dyes Abstract: This paper describes a modeling method of the tissue temperature evolution over time in hyper or hypothermia. The tissue temperature evolution over time is classically described by Pennes’ bioheat transfer equation which is generally solved by a finite difference method. In this paper we will present a method where the bioheat transfer equation can be algebraically solved after a Fourier transformation over the space coordinates. As an example, we implemented this method for the simulation of a percutaneous high intensity ultrasound hepatocellular carcinoma curative treatment and compared it with the finite difference method and experimental data. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262373 Mon, 01 Feb 2010 00:00:00 +0100 3262373 http://www.medworm.com/index.php?rid=3262372&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482510000119%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3262372 Mon, 01 Feb 2010 00:00:00 +0100 3262372 http://www.medworm.com/index.php?rid=3181918&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002029%2Fabstract%3Frss%3Dyes Abstract: A new iterative center weighted median filter (ICWMF) for ring artifact reduction from the micro-computed tomographic () image is proposed in this paper. The center weight of the median filter is computed based on the characteristic of the ring artifact in the mean curve of the projection data. The filter operates on the deviation of the mean curve to smooth the ring generating peaks and troughs iteratively while preserving the details due to image. A convergence criterion for the iterative algorithm is determined from the distribution of the local deviation computed from the mean curve deviation. The estimate of the mean curve obtained using the ICWMF is used to correct the ring corrupted projection data from which reconstruction gives the ring artifact suppressed image. Test re... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3181918 Fri, 01 Jan 2010 00:00:00 +0100 3181918 http://www.medworm.com/index.php?rid=3181917&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002017%2Fabstract%3Frss%3Dyes Abstract: Approximately 30% of individuals with epilepsy have refractory seizures that cannot be controlled by current pharmacological treatment measures. For such patients, responsive neurostimulation prior to a seizure may lead to greater efficacy when compared with current treatments. In this paper, we present a real-time adaptive Wiener prediction algorithm implemented on a digital signal processor to be used with local field potential (LFP) recordings. The hardware implementation of the algorithm enables it to be a miniaturized portable system that could be used in a hand-held device. The adaptive nature of the algorithm allows the seizure data to be compared with baseline data occurring in the recent past rather than a preset value. This enhances the sensitivity of the algorithm by a... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3181917 Fri, 01 Jan 2010 00:00:00 +0100 3181917 http://www.medworm.com/index.php?rid=3181916&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002005%2Fabstract%3Frss%3Dyes Abstract: In this paper, the continuous time wavelet entropy (CTWE) of auditory evoked potentials (AEP) has been characterized by evaluating the relative wavelet energies (RWE) in specified EEG frequency bands. Thus, the rapid variations of CTWE due to the auditory stimulation could be detected in post-stimulus time interval. This approach removes the probability of missing the information hidden in short time intervals. The discrete time and continuous time wavelet based wavelet entropy variations were compared on non-target and target AEP data. It was observed that CTWE can also be an alternative method to analyze entropy as a function of time. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3181916 Fri, 01 Jan 2010 00:00:00 +0100 3181916 http://www.medworm.com/index.php?rid=3181915&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001991%2Fabstract%3Frss%3Dyes Abstract: The use of vascular intersection aberration as one of the signs when monitoring and diagnosing diabetic retinopathy from retina fundus images (FIs) has been widely reported in the literature. In this paper, a new hybrid approach called the combined cross-point number (CCN) method able to detect the vascular bifurcation and intersection points in FIs is proposed. The CCN method makes use of two vascular intersection detection techniques, namely the modified cross-point number (MCN) method and the simple cross-point number (SCN) method. Our proposed approach was tested on images obtained from two different and publicly available fundus image databases. The results show a very high precision, accuracy, sensitivity and low false rate in detecting both bifurcation and crossover points... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3181915 Fri, 01 Jan 2010 00:00:00 +0100 3181915 http://www.medworm.com/index.php?rid=3181914&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001978%2Fabstract%3Frss%3Dyes Conclusion: Measurement of the recovery coefficient provides an assessment of tomographic spatial resolution, particularly in clinical studies conditions. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3181914 Fri, 01 Jan 2010 00:00:00 +0100 3181914 http://www.medworm.com/index.php?rid=3181913&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001966%2Fabstract%3Frss%3Dyes Abstract: MRI has become an effective tool for anatomical mice studies. Currently, embryologists study the development of mouse embryos in order to understand the mechanisms of human development. The aim of the research presented in this paper, is to develop a semi-automatic image segmentation framework based 3D deformable models to identify cardiac malformations which are a major cause of death in children. The segmentation systems have been used to segment 3D mouse embryos heart structures. Results on the ventricles and on the heart muscle are presented and compared with manually segmented models. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3181913 Fri, 01 Jan 2010 00:00:00 +0100 3181913 http://www.medworm.com/index.php?rid=3181912&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001954%2Fabstract%3Frss%3Dyes Abstract: Acoustic analysis of voice features can complete the invasive observation-based methods for the diagnosis of vocal fold pathologies. Selection of an appropriate feature extraction method from the voice can significantly improve the diagnostic results for patients with vocal disorders. In this paper, the performance of nonlinear dynamics and acoustical perturbation features is evaluated in order to distinguish patients with vocal fold disorder and other normal cases. As a matter of fact, vocal fold pathology is one of the major causes of voice quality reduction or feature variation in patients with dysphonic voices. Due to the devastating impact of vocal folds dysfunction on the complex dynamical structure of the speech signals, spectral analysis methods are not suitable for chara... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3181912 Fri, 01 Jan 2010 00:00:00 +0100 3181912 http://www.medworm.com/index.php?rid=3181911&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001942%2Fabstract%3Frss%3Dyes Abstract: We have developed and tested a new simple computerized finite element method (FEM) approach to MR-to-PET nonrigid breast-image registration. The method requires five–nine fiducial skin markers (FSMs) visible in MRI and PET that need to be located in the same spots on the breast and two on the flanks during both scans. Patients need to be similarly positioned prone during MRI and PET scans. This is accomplished by means of a low gamma-ray attenuation breast coil replica used as the breast support during the PET scan. We demonstrate that, under such conditions, the observed FSM displacement vectors between MR and PET images, distributed piecewise linearly over the breast volume, produce a deformed FEM mesh that reasonably approximates nonrigid deformation of the breast tissue bet... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3181911 Fri, 01 Jan 2010 00:00:00 +0100 3181911 http://www.medworm.com/index.php?rid=3181910&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001851%2Fabstract%3Frss%3Dyes Abstract: Anticholinesterase poisoning is an important health problem in our country, and a complete understanding of its underlying mechanisms is essential for the emergency physician. So, this study focused on two purposes. First one was aimed to investigate the biochemical analysis to determine the tissue levels of malondialdehyde (MDA), glutathione and nitric oxide (NO). Secondly, it was planned to model and formulate the effects of some drugs on cardiac tissues levels of NO, MDA and glutathione in acute organophosphate poisoning in rats by the application of neural network based on experimental results. It has been planned to determine whether artificial neural network (ANN) is appropriate tool to analyze and formulate it. As a result, it has been considered that ANN can be effectivel... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3181910 Fri, 01 Jan 2010 00:00:00 +0100 3181910 http://www.medworm.com/index.php?rid=3181909&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001802%2Fabstract%3Frss%3Dyes Abstract: In this paper a variational framework for joint segmentation and motion estimation is employed for inspecting heart in Cine MRI sequences. A functional including Mumford–Shah segmentation and optical flow based dense motion estimation is approximated using the phase-field technique. The minimizer of the functional provides an optimum motion field and edge set by considering both spatial and temporal discontinuities. Exploiting calculus of variation principles, multiple partial differential equations associated with the Euler–Lagrange equations of the functional are extracted, first. Next, the finite element method is used to discretize the resulting PDEs for numerical solution. Several simulation runs are used to test the convergence and the parameter sensitivity of the metho... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3181909 Fri, 01 Jan 2010 00:00:00 +0100 3181909 http://www.medworm.com/index.php?rid=3181908&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001796%2Fabstract%3Frss%3Dyes Abstract: In this paper, a novel cardiac sound spectral analysis method using the normalized autoregressive power spectral density (NAR-PSD) curve with the support vector machine (SVM) technique is proposed for classifying the cardiac sound murmurs. The 489 cardiac sound signals with 196 normal and 293 abnormal sound cases acquired from six healthy volunteers and 34 patients were tested. Normal sound signals were recorded by our self-produced wireless electric stethoscope system where the subjects are selected who have no the history of other heart complications. Abnormal sound signals were grouped into six heart valvular disorders such as the atrial fibrillation, aortic insufficiency, aortic stenosis, mitral regurgitation, mitral stenosis and split sounds. These abnormal subjects were als... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3181908 Fri, 01 Jan 2010 00:00:00 +0100 3181908 http://www.medworm.com/index.php?rid=3181907&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001784%2Fabstract%3Frss%3Dyes Abstract: The registration of multi-modal medical image data is important in the fields of image guided surgery and computer aided medical diagnosis. Registration accuracy is of utmost importance in both fields, however in the former, the speed of registration is equally important. In this paper, we present a point-based ‘fast’ non-rigid registration algorithm which exhibits significant speedups as compared to the non-optimised equivalent algorithm. Additionally, we make use of the parallel nature of the graphics processing unit (GPU) of the video adapter card of a standard PC to gain further speedups. The algorithm achieved sub-second performance when tested on the registration of MR with CT image data of size . (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3181907 Fri, 01 Jan 2010 00:00:00 +0100 3181907 http://www.medworm.com/index.php?rid=3181906&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509002236%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=3181906 Fri, 01 Jan 2010 00:00:00 +0100 3181906 http://www.medworm.com/index.php?rid=2995509&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS001048250900184X%2Fabstract%3Frss%3Dyes 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 with the whole data set at once, utilizing the context information and correcting several slices simultaneously. Proposed heuristic editing support and automatic visual hig... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2995509 Mon, 16 Nov 2009 16:28:45 +0100 2995509 http://www.medworm.com/index.php?rid=2995508&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001826%2Fabstract%3Frss%3Dyes 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) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2995508 Mon, 16 Nov 2009 16:28:45 +0100 2995508 http://www.medworm.com/index.php?rid=2995507&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001814%2Fabstract%3Frss%3Dyes 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 used to evaluate the neural classifier performance. The system performance variability due to different ground truth agreement levels is discussed. In particular, the poo... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2995507 Mon, 16 Nov 2009 16:28:45 +0100 2995507 http://www.medworm.com/index.php?rid=2995506&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001772%2Fabstract%3Frss%3Dyes 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 screening after the 28th week of gestation. By these means low-risk population may also be fully tested for cardiac malfunctions. (Source: Computers in Biology and Medic... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2995506 Mon, 16 Nov 2009 16:28:45 +0100 2995506 http://www.medworm.com/index.php?rid=2995505&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001760%2Fabstract%3Frss%3Dyes 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 occurrence prediction. Alternative optimization and homogeneous parallel processing techniques yielded faster model optimization times. (Source: Computers in Biology and... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2995505 Mon, 16 Nov 2009 16:28:45 +0100 2995505 http://www.medworm.com/index.php?rid=2995504&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS001048250900167X%2Fabstract%3Frss%3Dyes 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 interventions, pharmacodynamic therapies, ischemia detection, and/or in assessment of the time course of electrical activation. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2995504 Mon, 16 Nov 2009 16:28:44 +0100 2995504 http://www.medworm.com/index.php?rid=2995503&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001668%2Fabstract%3Frss%3Dyes 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 very precisely in a quantitative manner and unveils the opportunity to understand OSF related changes in cell population having definite geometric properties. The paper p... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2995503 Mon, 16 Nov 2009 16:28:44 +0100 2995503 http://www.medworm.com/index.php?rid=2995502&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001656%2Fabstract%3Frss%3Dyes 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 effectiveness of the selected structural features. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2995502 Mon, 16 Nov 2009 16:28:44 +0100 2995502 http://www.medworm.com/index.php?rid=2995501&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001644%2Fabstract%3Frss%3Dyes 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 joint moment was evaluated by comparing the model output with the moment computed using inverse dynamics. The model did predict the ankle moment with acceptable accuracy,... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2995501 Mon, 16 Nov 2009 16:28:44 +0100 2995501 http://www.medworm.com/index.php?rid=2995500&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001632%2Fabstract%3Frss%3Dyes 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 this work includes of introducing new types of indicators base upon some nonlinear features besides of proposing a new feature of point distribution in phase space. Our ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2995500 Mon, 16 Nov 2009 16:28:44 +0100 2995500 http://www.medworm.com/index.php?rid=2995499&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001620%2Fabstract%3Frss%3Dyes 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 be very promising, since we obtained an accuracy of 96.04% and Az ROC of 0.946 with Geary's coefficient and an accuracy of 99.39% and Az ROC of 1 with Moran's index to d... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2995499 Mon, 16 Nov 2009 16:28:44 +0100 2995499 http://www.medworm.com/index.php?rid=2995498&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001875%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2995498 Mon, 16 Nov 2009 16:28:43 +0100 2995498 http://www.medworm.com/index.php?rid=2868698&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001619%2Fabstract%3Frss%3Dyes 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 evaluated in the light of experimental studies on animal models or clinical trials. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868698 Wed, 07 Oct 2009 16:31:47 +0100 2868698 http://www.medworm.com/index.php?rid=2868697&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001607%2Fabstract%3Frss%3Dyes 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 window length of 3s. This early estimate of VF may be useful in emergency cases where defibrillators are to be applied. Comparative results with the existing methods in te... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868697 Wed, 07 Oct 2009 16:31:47 +0100 2868697 http://www.medworm.com/index.php?rid=2868696&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001590%2Fabstract%3Frss%3Dyes 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 blocked while respiratory efforts continue. During CSA the airway is open, however, there are no respiratory efforts. In this paper we aim to classify sleep apnea in one of thr... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868696 Wed, 07 Oct 2009 16:31:44 +0100 2868696 http://www.medworm.com/index.php?rid=2868695&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001589%2Fabstract%3Frss%3Dyes 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 an important role in interactions with DNA or signaling proteins. Additionally, unique primary sequence repeats were found in all three proteins. (Source: Computers in Bio... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868695 Wed, 07 Oct 2009 16:31:44 +0100 2868695 http://www.medworm.com/index.php?rid=2868694&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001577%2Fabstract%3Frss%3Dyes 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 approximately maintained at 96% for IPPV and 93% for SPONT, with false positive rates of 0.4% for each category and 4.3% ‘Uncertain’ inferences. (Source: Computers in Bio... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868694 Wed, 07 Oct 2009 16:31:43 +0100 2868694 http://www.medworm.com/index.php?rid=2868693&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001504%2Fabstract%3Frss%3Dyes 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 proposed virtual-reality system has the potential to serve as an alternative training tool to supplement conventional cataract surgery education. (Source: Computers in Biology... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868693 Wed, 07 Oct 2009 16:31:43 +0100 2868693 http://www.medworm.com/index.php?rid=2868692&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001498%2Fabstract%3Frss%3Dyes 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. The information of about protein secondary structure is used to increase the protein domain boundaries signal. Lastly, support vector machines (SVM) are used to classify ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868692 Wed, 07 Oct 2009 16:31:43 +0100 2868692 http://www.medworm.com/index.php?rid=2868691&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001486%2Fabstract%3Frss%3Dyes 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 waveforms have to be carefully interpreted. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868691 Wed, 07 Oct 2009 16:31:43 +0100 2868691 http://www.medworm.com/index.php?rid=2868690&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001474%2Fabstract%3Frss%3Dyes 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 or as tools for analysing sleep disordered breathing. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868690 Wed, 07 Oct 2009 16:31:43 +0100 2868690 http://www.medworm.com/index.php?rid=2868689&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001462%2Fabstract%3Frss%3Dyes 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 experimental medical greyscale images from different modalities and different body districts and results are reported. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868689 Wed, 07 Oct 2009 16:31:43 +0100 2868689 http://www.medworm.com/index.php?rid=2868688&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001450%2Fabstract%3Frss%3Dyes 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 four medium power ones. This implies that selection of about 100 genetic markers, differing in capacity to distinguish between the disease and control groups by (say) 10%, w... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868688 Wed, 07 Oct 2009 16:31:43 +0100 2868688 http://www.medworm.com/index.php?rid=2868687&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001449%2Fabstract%3Frss%3Dyes 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 comparative evaluation among LORETA, FOCUSS and GIA was conducted for both isolated point sources and distributed sources, the results demonstrate that GIA is more flexible and ef... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868687 Wed, 07 Oct 2009 16:31:43 +0100 2868687 http://www.medworm.com/index.php?rid=2868686&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001358%2Fabstract%3Frss%3Dyes 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 two images during optimization of transformation parameters, but also brings a more robust registration with less computational cost. Experimental results on clinical data... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868686 Wed, 07 Oct 2009 16:31:43 +0100 2868686 http://www.medworm.com/index.php?rid=2868685&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001322%2Fabstract%3Frss%3Dyes 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. To show the validity of the proposed method, we apply it to classify three DNA microarray data sets involving various human normal and tumor tissue samples. The experiment... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868685 Wed, 07 Oct 2009 16:31:43 +0100 2868685 http://www.medworm.com/index.php?rid=2868684&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001061%2Fabstract%3Frss%3Dyes 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: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868684 Wed, 07 Oct 2009 16:31:43 +0100 2868684 http://www.medworm.com/index.php?rid=2868683&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001693%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2868683 Wed, 07 Oct 2009 16:31:42 +0100 2868683 http://www.medworm.com/index.php?rid=2737413&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001371%2Fabstract%3Frss%3Dyes 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 feature from a stabilogram signal, which well describes the differences between young and elderly people's swaying processes. When our feature is applied to the K nearest neig... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2737413 Thu, 27 Aug 2009 13:37:01 +0100 2737413 http://www.medworm.com/index.php?rid=2737412&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS001048250900136X%2Fabstract%3Frss%3Dyes 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) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2737412 Thu, 27 Aug 2009 13:37:01 +0100 2737412 http://www.medworm.com/index.php?rid=2737411&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001346%2Fabstract%3Frss%3Dyes 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 evaluated using two completely independent data sets. Results for a test set, evaluated with free-response receiver operating characteristic (FROC) analysis, yielded a s... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2737411 Thu, 27 Aug 2009 13:37:01 +0100 2737411 http://www.medworm.com/index.php?rid=2737410&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001334%2Fabstract%3Frss%3Dyes 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 computer to another using windows hyper-terminal and XBee RF transceiver module. Automated analysis algorithm can be further developed. (Source: Computers in Biology and Medicin... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2737410 Thu, 27 Aug 2009 13:37:01 +0100 2737410 http://www.medworm.com/index.php?rid=2737409&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001310%2Fabstract%3Frss%3Dyes 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 architecture based on the {E,H,L} alphabet instead of the DSSP secondary structure alphabet. In the second step secondary structure information (predicted or true) is addit... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2737409 Thu, 27 Aug 2009 13:37:01 +0100 2737409 http://www.medworm.com/index.php?rid=2737408&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001309%2Fabstract%3Frss%3Dyes 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 equation quantitatively and to observe the flow separation. The results obtained show that the flow separates mostly towards the downstream of the multi-stenoses. However, ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2737408 Thu, 27 Aug 2009 13:37:01 +0100 2737408 http://www.medworm.com/index.php?rid=2737407&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001292%2Fabstract%3Frss%3Dyes 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 Alegre. The validation was performed using Ground Truth images, generated by experts, and has shown promising results. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2737407 Thu, 27 Aug 2009 13:37:01 +0100 2737407 http://www.medworm.com/index.php?rid=2737406&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001279%2Fabstract%3Frss%3Dyes 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) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2737406 Thu, 27 Aug 2009 13:37:01 +0100 2737406 http://www.medworm.com/index.php?rid=2737405&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001231%2Fabstract%3Frss%3Dyes 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 repeated for every subsequent slice in the CT set without further user input, as the segmented region from the previous slice is used as the ROI for the current slice. This cre... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2737405 Thu, 27 Aug 2009 13:37:01 +0100 2737405 http://www.medworm.com/index.php?rid=2737404&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS001048250900122X%2Fabstract%3Frss%3Dyes 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 (GA) with the fitness functions of support vector machine's (SVM) and k-nearest neighbor's (KNN) recognition rates. Finally, obtained feature vectors have been passed on to... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2737404 Thu, 27 Aug 2009 13:37:00 +0100 2737404 http://www.medworm.com/index.php?rid=2737403&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000948%2Fabstract%3Frss%3Dyes 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 adult life cycle. This classification is also important to understanding the biology of the ontogenetic development of common marmosets, providing new insights for the manage... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2737403 Thu, 27 Aug 2009 13:37:00 +0100 2737403 http://www.medworm.com/index.php?rid=2737402&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001528%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2737402 Thu, 27 Aug 2009 13:37:00 +0100 2737402 http://www.medworm.com/index.php?rid=2674049&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001280%2Fabstract%3Frss%3Dyes 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 algebra operations. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2674049 Thu, 06 Aug 2009 12:27:16 +0100 2674049 http://www.medworm.com/index.php?rid=2674048&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001267%2Fabstract%3Frss%3Dyes 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 filter is employed to considerably improve the classification accuracy. Experimental results show that our approach based on MFCC coefficients combined to GMM is well adapte... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2674048 Thu, 06 Aug 2009 12:27:16 +0100 2674048 http://www.medworm.com/index.php?rid=2674047&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001255%2Fabstract%3Frss%3Dyes 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 the best performance of other kinds of classification models, is achieved. Experimental results show that the wavelet detail coefficients are efficient way to characteri... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2674047 Thu, 06 Aug 2009 12:27:16 +0100 2674047 http://www.medworm.com/index.php?rid=2674046&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001243%2Fabstract%3Frss%3Dyes 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 for choosing appropriate laser treatment parameters in medical praxis. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2674046 Thu, 06 Aug 2009 12:27:16 +0100 2674046 http://www.medworm.com/index.php?rid=2674045&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001218%2Fabstract%3Frss%3Dyes 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-synaptic influence. The fast (alternating) component (AC) of the mechanical–electrical transduction signal controls the motor protein prestin and fast changes in axial length ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2674045 Thu, 06 Aug 2009 12:27:16 +0100 2674045 http://www.medworm.com/index.php?rid=2674044&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001140%2Fabstract%3Frss%3Dyes 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 inguinal hernia. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2674044 Thu, 06 Aug 2009 12:27:16 +0100 2674044 http://www.medworm.com/index.php?rid=2674043&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001139%2Fabstract%3Frss%3Dyes 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 obtained using a support vector machine (SVM) classifier, based on a cell descriptor constructed from the shape and edge strength of the cells’ contour. In addition we pr... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2674043 Thu, 06 Aug 2009 12:27:15 +0100 2674043 http://www.medworm.com/index.php?rid=2674042&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001127%2Fabstract%3Frss%3Dyes 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% and specificity of 59%. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2674042 Thu, 06 Aug 2009 12:27:15 +0100 2674042 http://www.medworm.com/index.php?rid=2674041&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001115%2Fabstract%3Frss%3Dyes 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 method is tested for various types of RS recordings and found effective by yielding an overall maximum spectral difference of for a frequency range below 800Hz. (Source: C... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2674041 Thu, 06 Aug 2009 12:27:15 +0100 2674041 http://www.medworm.com/index.php?rid=2674040&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001103%2Fabstract%3Frss%3Dyes 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 show that it is possible to identify frequency-dependent changes in the correlation structure between channels which may be indicative of seizure activity.The technique i... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2674040 Thu, 06 Aug 2009 12:27:15 +0100 2674040 http://www.medworm.com/index.php?rid=2674039&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001097%2Fabstract%3Frss%3Dyes In conclusion, new numerical techniques should be proposed in order to achieve accurate simulations of the problem involved in cemented hip replacements. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2674039 Thu, 06 Aug 2009 12:27:15 +0100 2674039 http://www.medworm.com/index.php?rid=2674038&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001085%2Fabstract%3Frss%3Dyes In this study, we propose a method to preserve the privacy and security of patients’ portable medical records in portable storage media to avoid any inappropriate or unintentional disclosure. Following HIPAA guidelines, the method is designed to protect, recover and verify patient's identifiers in portable EHRs. The results of this study show that our methods are effective in ensuring both information security and privacy preservation for patients through portable storage medium. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2674038 Thu, 06 Aug 2009 12:27:15 +0100 2674038 http://www.medworm.com/index.php?rid=2674037&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001395%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2674037 Thu, 06 Aug 2009 12:27:15 +0100 2674037 http://www.medworm.com/index.php?rid=2583903&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001073%2Fabstract%3Frss%3Dyes Abstract: This paper presented the usage of statistics over the set of the features representing the electroencephalogram (EEG) signals. Since classification is more accurate when the pattern is simplified through representation by important features, feature extraction and selection play an important role in classifying systems such as neural networks. Multilayer perceptron neural network (MLPNN) architectures were formulated and used as basis for detection of electroencephalographic changes. Three types of EEG signals (EEG signals recorded from healthy volunteers with eyes open, epilepsy patients in the epileptogenic zone during a seizure-free interval, and epilepsy patients during epileptic seizures) were classified. The selected Lyapunov exponents, wavelet coefficients and the power le... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2583903 Thu, 09 Jul 2009 12:15:05 +0100 2583903 http://www.medworm.com/index.php?rid=2583902&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000985%2Fabstract%3Frss%3Dyes Abstract: This paper proposes an ontology-based approach of modeling clinical pathway workflows at the semantic level for facilitating computerized clinical pathway implementation and efficient delivery of high-quality healthcare services. A clinical pathway ontology (CPO) is formally defined in OWL web ontology language (OWL) to provide common semantic foundation for meaningful representation and exchange of pathway-related knowledge. A CPO-based semantic modeling method is then presented to describe clinical pathways as interconnected hierarchical models including the top-level outcome flow and intervention workflow level along a care timeline. Furthermore, relevant temporal knowledge can be fully represented by combing temporal entities in CPO and temporal rules based on semantic web ru... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2583902 Thu, 09 Jul 2009 12:15:05 +0100 2583902 http://www.medworm.com/index.php?rid=2583901&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000973%2Fabstract%3Frss%3Dyes In this study, wavelet networks have been used to parameterize and quantify pulmonary crackles with an aim to depict the waveform with a small set of meaningful parameters. Complex Morlet wavelets are used at the nodes of both single and double-node networks to model the waveforms with the double-node rendering smaller modeling error. The features extracted from the model parameters have been compared with the conventional time domain features in a two-class clustering experiment with nearly 90% matching between the clusters of different parameter sets and with the model parameters forming clusters more closely distributed around their means and better separated from each other. Moreover, using simulated crackles embedded on real respiratory sounds, features extracted from wavelet networks... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2583901 Thu, 09 Jul 2009 12:15:05 +0100 2583901 http://www.medworm.com/index.php?rid=2583900&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000961%2Fabstract%3Frss%3Dyes Abstract: A computer simulation has been performed to study the influence of the pulse pressure variation on the arterial compliance readings in regard to different calculation techniques and arterial wall elastic properties. We applied the derivative- and amplitude-based (delta-based) calculation techniques to the model of the pressure vs. arterial lumen area relationship of different arteries. The simulated pulse pressure increase resulted in an essential reduction of the delta-based compliance in its near maximum region, and in an increase or no change outside this region. In the case of the relationship of a lower steepness the alterations were smaller. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2583900 Thu, 09 Jul 2009 12:15:04 +0100 2583900 http://www.medworm.com/index.php?rid=2583899&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS001048250900095X%2Fabstract%3Frss%3Dyes Abstract: The aim of this work is to predict non-invasively if an AF episode terminates spontaneously or not by analyzing the increase of atrial activity organization prior to paroxysmal atrial fibrillation (PAF) termination. Sample entropy was selected as non-linear organization index. Synthetic PAF signals were used to evaluate the notable impact of noise in AA organization estimation. Three strategies to reduce noise, ventricular residues and enhance the atrial activity main features were proposed. The best prediction results were obtained through main atrial wave (MAW) organization estimation. The MAW can be considered as the fundamental waveform associated to the AA. The 92% of the terminating and non-terminating analyzed PAF episodes were correctly classified. Thereby, it can be conc... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2583899 Thu, 09 Jul 2009 12:15:04 +0100 2583899 http://www.medworm.com/index.php?rid=2583898&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000936%2Fabstract%3Frss%3Dyes Abstract: Mitochondrial proteins associated with a wide spectrum of human diseases and currently large amounts of tissue or organ specific human mitochondrial proteome datasets are generated. However, high-throughput comparative proteomic methods have yet to be applied to extract subtle differences among mitochondria from different tissues or muscle types. The aim of this work was to provide an integrated way to identify and compare huge mitochondrial protein or peptide mass spectral data sets acquired from expert mitochondrial proteome or biomarker discovery community. Proteome comparison of human mitochondria (PCHM) is a web-based analysis environment for manual or automatic analysis of individual peptide mass fingerprints alongside a database of proteins and peptides identified in vario... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2583898 Thu, 09 Jul 2009 12:15:04 +0100 2583898 http://www.medworm.com/index.php?rid=2583897&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000924%2Fabstract%3Frss%3Dyes Abstract: In this paper, four new features for the analysis of breast masses are presented. These features were designed to be insensitive to the exact shape of the contour of the masses, so that an approximate contour, such as the one extracted via an automated segmentation algorithm, can be employed in their computation. Two of the features, and , measure the degree of spiculation of a mass and its likelihood of being spiculated. One of these features, , is a measure of the relative gradient orientation of pixels that correspond to possible spicules. The other feature, , is based on a comparison of mutual information measures between selected components of the mammographic images. The last two features, and , measure the local fuzziness of the mass margins based on points defined automat... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2583897 Thu, 09 Jul 2009 12:15:04 +0100 2583897 http://www.medworm.com/index.php?rid=2583896&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000821%2Fabstract%3Frss%3Dyes Abstract: A three-dimensional boundary element model of the human eye is developed to investigate the thermal effects of eye tumor on the ocular temperature distribution. The human eye is modeled as comprising several regions which have different thermal properties. The tumor is one of these regions. The thermal effects of the tumor are simulated by taking it to have a very high metabolic heat generation and blood perfusion rate. Inside the tumor, the steady state temperature is governed by the Pennes bioheat equation. Elsewhere, in normal tissues of the eye, the temperature satisfies the Laplace's equation. To compute the temperature on the corneal surface, the surface boundary of each region is divided into triangular elements. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2583896 Thu, 09 Jul 2009 12:15:04 +0100 2583896 http://www.medworm.com/index.php?rid=2583895&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000791%2Fabstract%3Frss%3Dyes Abstract: Recent advances in graphics processing unit (GPU) have enabled direct volume rendering at interactive rates. However, although perspective volume rendering for opaque isosurface is rapidly performed using conventional GPU-based method, perspective volume rendering for non-opaque volume such as translucency rendering is still slow. In this paper, we propose an efficient GPU-based acceleration technique of fast perspective volume ray casting for translucency rendering in computed tomography (CT) colonography. The empty space searching step is separated from the shading and compositing steps, and they are divided into separate processing passes in the GPU. Using this multi-pass acceleration, empty space leaping is performed exactly at the voxel level rather than at the block level, ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2583895 Thu, 09 Jul 2009 12:15:04 +0100 2583895 http://www.medworm.com/index.php?rid=2583894&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001164%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2583894 Thu, 09 Jul 2009 12:15:04 +0100 2583894 http://www.medworm.com/index.php?rid=2506241&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000912%2Fabstract%3Frss%3Dyes In this study, a modified active contour (also called snake) segmentation method based on a faster gradient-vector-flow (GVF) calculation algorithm is proposed. The accelerated method was tested on multiple organs, including lung, right ventricle, kidney and prostate. Compared to the original algorithm, the improved one reduced GVF calculation times to one-half or less without compromising contour accuracy. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2506241 Thu, 25 Jun 2009 08:57:42 +0100 2506241 http://www.medworm.com/index.php?rid=2506240&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000833%2Fabstract%3Frss%3Dyes Abstract: Gene expression datasets is a means to classify and predict the diagnostic categories of a patient. Informative genes and representative samples selection are two important aspects for reducing gene expression data. Identifying and pruning redundant genes and samples simultaneously can improve the performance of classification and circumvent the local optima problem. In the present paper, the modified particle swarm optimization was applied to selecting optimal genes and samples simultaneously and support vector machine was used as an objective function to determine the optimum set of genes and samples. To evaluate the performance of the new proposed method, it was applied to three publicly available microarray datasets. It has been demonstrated that the proposed method for gene ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2506240 Thu, 25 Jun 2009 08:57:42 +0100 2506240 http://www.medworm.com/index.php?rid=2506239&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS001048250900081X%2Fabstract%3Frss%3Dyes Abstract: In this paper, a generalized application of Kohonen Network for automatic point correspondence of unimodal medical images is presented. Given a pair of two-dimensional medical images of the same anatomical region and a set of interest points in one of the images, the algorithm detects effectively the set of corresponding points in the second image, by exploiting the properties of the Kohonen self organizing maps (SOMs) and embedding them in a stochastic optimization framework. The correspondences are established by determining the parameters of local transformations that map the interest points of the first image to their corresponding points in the second image. The parameters of each transformation are computed in an iterative way, using a modification of the competitive learni... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2506239 Thu, 25 Jun 2009 08:57:42 +0100 2506239 http://www.medworm.com/index.php?rid=2506238&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000808%2Fabstract%3Frss%3Dyes Abstract: During ambulatory monitoring, it is often required to record the electroencephalogram (EEG) and the electrocardiogram (ECG) simultaneously. It would be ideal if both EEG and ECG can be obtained with one measurement. We introduce an algorithm combining the wavelet shrinkage and signal averaging techniques to extract the EEG and ECG components from an EEG lead signal to a noncephalic reference (NCR). The evaluation using simulation data and measured data showed that the normalized power spectrum unvaried in all frequency bands for the EEG components, and the sensitivity and specificity of R-wave detection for the ECG component were nearly 100%. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2506238 Thu, 25 Jun 2009 08:57:42 +0100 2506238 http://www.medworm.com/index.php?rid=2506237&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS001048250900078X%2Fabstract%3Frss%3Dyes Abstract: In this paper, an algorithm for detection of reference spheres from digital panoramic radiographic images is presented. The proposed algorithm was tested on a database of 107 digital panoramic radiographic images which were used for dental diagnostics. Results show that the proposed method exhibits for detection of reference spheres, a sensitivity of 97.33% and specificity of 93.85%. Performance time differed between 0.55 and 2.36s depending on image size. The aim of this work was to provide a fast ellipse detection algorithm to reduce measuring time on preoperative implant planning by lowering the computational cost. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2506237 Thu, 25 Jun 2009 08:57:42 +0100 2506237 http://www.medworm.com/index.php?rid=2506236&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000766%2Fabstract%3Frss%3Dyes This study provides a performance evaluation of the correlation sum in terms of accuracy, sensitivity, and specificity in its ability to classify seizure files from non-seizure files. The main thrust of the study is whether computable properties (“metrics”) of EEG tracings over time allow a seizure to be detected. This study evaluates raw intracranial EEG (iEEG) recordings with the intent to detect a seizure and classify different EEG epoch files. One hundred twenty-six iEEG files from eleven sequential patients are processed and the correlation sum is extracted from non-overlapping scrolling windows of 1-s duration.The novelty of this research is in defining a generalized nonlinear approach to classify EEG seizure segments by introducing nonlinear decision functions with the flexibili... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2506236 Thu, 25 Jun 2009 08:57:42 +0100 2506236 http://www.medworm.com/index.php?rid=2506235&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000675%2Fabstract%3Frss%3Dyes Abstract: The purpose of this study is to establish an optimal module of breast configuration, under normal seating state, for postoperative evaluation of a female breast implant surgery. The analytical parameters of breast configuration, such as the breast position, size and shape, can be derived from a three-dimensional (3D), full-sized image process under non-radiation condition. This optimal module converts the breast position, size and shape to the breast configuration indicator consisting of three components or indices—the breast position, volume and breast congruence rate. In conjunction with the continuity analysis, the breast configuration indicator would allow a surgeon to practically grasp the progress during the postsurgery revisits. In addition, the module derived from the p... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2506235 Thu, 25 Jun 2009 08:57:42 +0100 2506235 http://www.medworm.com/index.php?rid=2506234&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000663%2Fabstract%3Frss%3Dyes Abstract: We developed a database compiling in vivo doses of compounds for various activities in certain animal species. The related database covers almost 100 years of experiments. The conceptual scheme of the database was created using concepts of the entity-relationship modeling principles. Using published references, dosages and their effects on laboratory animals were entered as data. As the next stage of our work, we have started to examine the available literature to information about the experimental dosages of various drugs used in other studies.The database provides various interfaces, including graphical-user interfaces and interfaces for Internet access. The database will be useful as a knowledge infrastructure for researchers who have to perform dose-scan experiments for a spe... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2506234 Thu, 25 Jun 2009 08:57:42 +0100 2506234 http://www.medworm.com/index.php?rid=2506233&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482508001820%2Fabstract%3Frss%3Dyes Abstract: This work is based on the premise that fingertip temperature variation during arterial occlusion and subsequent reperfusion can be used as an indirect measurement of vascular reactivity, commonly assessed by directly measuring flow and its temporal alterations in response to arterial occlusion. Temperature of the fingers depends on blood perfusion and environmental factors. The temperature change experienced during hyperemia or high blood flow after occlusion depend on the capacity of the occluded arteries to restore normal circulation or vascular reactivity.This work uses two mathematical models of heat transfer to show the relationship between blood flow and changes in fingertip temperature experienced during vascular occlusion and reperfusion. The models consider different lev... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2506233 Thu, 25 Jun 2009 08:57:42 +0100 2506233 http://www.medworm.com/index.php?rid=2506232&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509001012%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2506232 Thu, 25 Jun 2009 08:57:42 +0100 2506232 http://www.medworm.com/index.php?rid=2436684&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000778%2Fabstract%3Frss%3Dyes Abstract: A series of discrete models were developed to study the development of cyclic reprocessing buildup (CRB) on medical devices, and to explore the effect of cleaning efficacy and type of disinfection on the removal of this CRB. A cellular automata (CA) model was used to simulate the development of CRB, including microbial replication and production of extracellular matrix (EM). The process of disinfection (microbes being killed, EM being cross-linked or oxidized, etc.) was also described in the CA model. Next, a stochastic model, Ising's model combined with Monte Carlo methods was used to simulate the removal of CRB from a surface by cleaning. These models were developed to simulate the persistent residual CRB that occurs on reused medical devices such as flexible endoscopes, to det... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2436684 Wed, 27 May 2009 14:11:57 +0100 2436684 http://www.medworm.com/index.php?rid=2436683&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000651%2Fabstract%3Frss%3Dyes This study demonstrates the performance of the event-synchronous interference canceller (ESC) in mECG removal from ADS data, recorded during pregnancy and labor. Its advantage as a compensation method for extended ADS processing is discussed. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2436683 Wed, 27 May 2009 14:11:55 +0100 2436683 http://www.medworm.com/index.php?rid=2436682&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS001048250900064X%2Fabstract%3Frss%3Dyes We present here a mathematical model of chondrocytes hypertrophy, regulated by molecular factors, able to predict the onset of secondary ossification centres during long bones development. From the results obtained, we can conclude that the chemical feedback between two reactive molecular factors through a reaction–diffusion mechanism could explain the stable spatial pattern found in the origination of secondary ossification centres, as well as the dependency of such a pattern on the size and shape of the bone head, in line with what has been observed in different animals. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2436682 Wed, 27 May 2009 14:11:54 +0100 2436682 http://www.medworm.com/index.php?rid=2436681&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000638%2Fabstract%3Frss%3Dyes Abstract: Spatial alignment of image data is a common task in computer vision and medical imaging. This should preferentially be done with minimal intervention of an operator. Similarity measures with origin in the information theory such as mutual information (MI) have proven to be robust registration criteria for this purpose. Intra-oral radiographs can be considered images of piecewise rigid objects. Teeth and jaws are rigid but can be displaced with respect to each other. Therefore MI criteria combined with affine deformations tend to fail, when teeth and jaws move with respect to each other between image acquisitions. In this paper, we consider a focused weighing of pixels in the reference image. The resulting criterion, focused mutual information (FMI) is an adequate tool for the reg... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2436681 Wed, 27 May 2009 14:11:52 +0100 2436681 http://www.medworm.com/index.php?rid=2436680&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000614%2Fabstract%3Frss%3Dyes Abstract: The aim of this paper is to propose a new Markov random field (MRF) model for the backscattered ultrasonic echo in order to get information about backscatter characteristics, such as the scatterer density, amplitude and spacing. The model combines the Nakagami distribution that describes the envelope of backscattered echo with spatial interaction using MRF. In this paper, the parameters of the model and the estimation parameter method are introduced. Computer simulation using ultrasound radio-frequency (RF) simulator and experiments on choroidal malignant melanoma have been undertaken to test the validity of the model. The relationship between the parameters of MRF model and the backscatter characteristics has been established. Furthermore, the ability of the model to distinguish... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2436680 Wed, 27 May 2009 14:11:48 +0100 2436680 http://www.medworm.com/index.php?rid=2436679&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000602%2Fabstract%3Frss%3Dyes Abstract: In protein fold recognition, the main disadvantage of hidden Markov models (HMMs) is the employment of large-scale model architectures which require large data sets and high computational resources for training. Also, HMMs must consider sequential information about secondary structures of proteins, to improve prediction performance and reduce model parameters. Therefore, we propose a novel method for protein fold recognition based on a hidden Markov model, called a 9-state HMM. The method can (i) reduce the number of states using secondary structure information about proteins for each fold and (ii) recognize protein folds more accurately than other HMMs. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2436679 Wed, 27 May 2009 14:11:47 +0100 2436679 http://www.medworm.com/index.php?rid=2436678&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000596%2Fabstract%3Frss%3Dyes Abstract: This paper presents a new proposal of a very low cost and highly efficient interference canceller to be applied to biomedical signals. The power line reference is obtained from analog to digital conversion while higher harmonics are mathematically estimated by means of trigonometric relations. These signals are processed by an adaptive algorithm in order to suppress harmonic interference. Biomedical acquisition systems that incorporate a conventional adaptive canceller, whose reference signal is sampled from power line, can be easily modified to improve interference suppression without hardware modifications. Real application examples are supplied in order to demonstrate its usefulness in electroencephalographic, electrocardiographic and auditory evoked potential signals. (Source... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2436678 Wed, 27 May 2009 14:11:45 +0100 2436678 http://www.medworm.com/index.php?rid=2436677&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000584%2Fabstract%3Frss%3Dyes Abstract: In this paper, new quantitative linear (HLF ratio: high frequency/low frequency spectral power ratio) and non-linear parameters (ZC: zero crossing and FD: fractal dimension) which can assist the physician in real-time decision whether a shunt is required or not during intra-operative EEG monitoring of carotid endarterectomy are presented. The results obtained with the new parameters are compared with those achieved by other indexes proposed in the literature. The HLF ratio and ZC parameters yielded the best results with a 100% of correct identification of both shunt and no-shunt situations. The ZC can be also easily implemented in the real-time monitoring of EEG. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2436677 Wed, 27 May 2009 14:11:44 +0100 2436677 http://www.medworm.com/index.php?rid=2436676&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000572%2Fabstract%3Frss%3Dyes Abstract: An in-silico model, of the glucocorticoid regulated glutamate release, in rat hippocampal tissue, is constructed. The model permits the pseudo-steady state estimation of various fluxes, experimentally impossible to measure, from a set of measured rates. Estimates of the astrocytic pyruvate carboxylase reaction and the neuronal TCA cycle rates are correlated with different dexamethasone concentrations, in order to extrapolate explicit kinetic equations. The model suggests that the observed effects of glucocorticoids can be attributed to the inhibitory actions of dexamethasone on two competing pathways, that of the neuronal TCA cycle and the biosynthetic pathway of neurotransmitter glutamate. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2436676 Wed, 27 May 2009 14:11:43 +0100 2436676 http://www.medworm.com/index.php?rid=2436675&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000444%2Fabstract%3Frss%3Dyes Abstract: Although many deformable models have been proposed in medical applications for segmenting isolated structures in the human anatomy, not much of such work had been done on tubular structures such as the vasculature. In this paper, we propose a statistical assembled model for tubular structures (SAMTUS) to segment entire tubular structure from three-dimensional (3D) volumetric data. To our knowledge, there is no literature about the statistical deformable model for entire tubular structures. Specifically, the statistical tubular model is composed of a statistical axis model (SAM) and a statistical surface model (SSM). Both of them are assembled from a set of branch segments through the control points. Instead of searching for fuzzy correspondence along tubular axes or surfaces, we ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2436675 Wed, 27 May 2009 14:11:39 +0100 2436675 http://www.medworm.com/index.php?rid=2436674&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000857%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2436674 Wed, 27 May 2009 14:11:38 +0100 2436674 http://www.medworm.com/index.php?rid=2387574&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000560%2Fabstract%3Frss%3Dyes We describe the algorithm we have developed based on the technique of determinant inequalities and the concept of minimization of mutual information to process the covariance matrix element by element to minimize the noise caused by systematic uncertainty in the SPECT imaging of 113mIn and its utility to experimentalists to design and improve their process of measurement and instrumentation. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2387574 Fri, 01 May 2009 04:00:00 +0100 2387574 http://www.medworm.com/index.php?rid=2387573&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000559%2Fabstract%3Frss%3Dyes Abstract: By using an equivalent electronic circuit either mitral or aortic regurgitation was simulated. Simulation allowed not only a measurement of various pressures within the cardiovascular system and cardiac output, but also mitral and aortic flow.In normal conditions mitral and aortic flows were monophasic, anterograde. In valve regurgitation mitral and aortic flows were, as expected, biphasic.In mitral regurgitation, during systole and diastole the valve flow was retrograde and anterograde, respectively.In aortic regurgitation, during systole and diastole the valve flow was anterograde and retrograde, respectively.The magnitude of the regurgitant valve flow was measured by time-integration and compared to the net flow, i.e. cardiac output. Valve flow was determined not only by the m... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2387573 Fri, 01 May 2009 04:00:00 +0100 2387573 http://www.medworm.com/index.php?rid=2387572&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000523%2Fabstract%3Frss%3Dyes Abstract: We have developed an integrated tool for statistical analysis of large-scale LC-MS profiles of complex protein mixtures comprising a set of procedures for data processing, selection of biomarkers used in early diagnostic and classification of patients based on their peptide mass fingerprints.Here, a novel boosting technique is proposed, which is embedded in our framework for MS data analysis. Our boosting scheme is based on Hannan-consistent game playing strategies. We analyze boosting from a game-theoretic perspective and define a new class of boosting algorithms called H-boosting methods.In the experimental part of this work we apply the new classifier together with classical and state-of-the-art algorithms to classify ovarian cancer and cystic fibrosis patients based on peptid... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2387572 Fri, 01 May 2009 04:00:00 +0100 2387572 http://www.medworm.com/index.php?rid=2387571&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000511%2Fabstract%3Frss%3Dyes In conclusion, this paper proposes a novel viewpoint to observe how the heart distributes blood into arterial system under normal and abnormal situations in spectral domain. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2387571 Fri, 01 May 2009 04:00:00 +0100 2387571 http://www.medworm.com/index.php?rid=2387570&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000432%2Fabstract%3Frss%3Dyes Abstract: The ultimate aim for classifying elbow versus shoulder torque intentions is to develop robust brain–computer interface (BCI) devices for patients who suffer from movement disorders following brain injury such as stroke. In this paper, we investigate the advanced classification approach classifier-enhanced time–frequency synthesized spatial pattern algorithm (classifier-enhanced TFSP) in classifying a subject's intent of generating an isometric shoulder abduction (SABD) or elbow flexion (EF) torque using signals obtained from 163 scalp electroencephalographic (EEG) electrodes. Two classifiers, the support vector classifier (SVC) and the classification and regression tree (CART), are integrated in the TFSP algorithm that decomposes the signal into a weighted time, frequency and... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2387570 Fri, 01 May 2009 04:00:00 +0100 2387570 http://www.medworm.com/index.php?rid=2387569&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000420%2Fabstract%3Frss%3Dyes In this study, we investigated time domain, time–frequency domain and combination of these as a compound representation of sEMG signal's features to access required signal information. In order to implement pattern recognition of sEMG signals for various hand movements, two intelligent classifiers, namely artificial neural network (ANN) and fuzzy inference system (FIS), were utilized. The results indicate that our approach of using compound features with principle component analysis (PCA) as dimensionality reduction technique, and FIS as the classifier, provides the best performance for sEMG pattern recognition system. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2387569 Fri, 01 May 2009 04:00:00 +0100 2387569 http://www.medworm.com/index.php?rid=2387568&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000419%2Fabstract%3Frss%3Dyes Abstract: Most classifiers output predictions for new instances without indicating how reliable they could be. Transductive confidence machine (TCM) is a novel framework that provides hedged prediction coupled with valid confidence. Many popular machine learning algorithms can be transformed into the framework of TCM, and therefore be used for producing hedged predictions. This paper incorporates random forest (RF) to propose a method named TCM-RF for classification of chronic gastritis data. Our method benefits from TCM-RF's high performance when features are noisy, highly correlated and of mixed types. The experimental results show that TCM-RF produces informative as well as effective predictions. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2387568 Fri, 01 May 2009 04:00:00 +0100 2387568 http://www.medworm.com/index.php?rid=2387567&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000390%2Fabstract%3Frss%3Dyes We presented an application of the Lattice Boltzmann method (LBM) to study the dynamics of Min proteins oscillations in Escherichia coli. The oscillations involve MinC, MinD and MinE proteins, which are required for proper placement of the division septum in the middle of a bacterial cell. Here, the LBM is applied to a set of the deterministic reaction diffusion equations which describes the dynamics of the Min proteins. This determines the midcell division plane at the cellular level. We specifically use the LBM to study the dynamic pole-to-pole oscillations of the Min proteins in two dimensions. We observed that Min proteins’ pattern formation depends on the cell's shape. The LBM numerical results are in good agreement with previous findings, using other methods and agree qualitatively... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2387567 Fri, 01 May 2009 04:00:00 +0100 2387567 http://www.medworm.com/index.php?rid=2387566&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000298%2Fabstract%3Frss%3Dyes Abstract: Spiral pair creation and dynamics is a widely occurring phenomenon in nature. It can appear in the heart tissue, causing severe arrhythmia, known as a figure-eight reentry. We consider the appearance of a spiral pair source, its minimal strength for survival, and the possible results of its interaction with a plane wave. In particular, its ability to outlast such an encounter is of interest. We also consider the question of exposing the source to a train of pulses, in terms of the frequency and angle of encounter. Results show different regimes of behavior, e.g. source annihilation, motion of the source away from, or towards the origin of the plane waves, its breaking and multiplication. Relevance of these results to heart arrhythmia and their possible cancellation by external pa... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2387566 Fri, 01 May 2009 04:00:00 +0100 2387566 http://www.medworm.com/index.php?rid=2387565&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000699%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2387565 Fri, 01 May 2009 04:00:00 +0100 2387565 http://www.medworm.com/index.php?rid=2346949&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000328%2Fabstract%3Frss%3Dyes Abstract: Searching biomedical information in a large collection of medical data is a complex task. The use of tools and biomedical resources could ease the retrieval of the information desired. In this paper, we use the medical ontology MeSH to improve a Multimodal Information Retrieval System by expanding the user's query with medical terms. In order to accomplish our experiments, we have used the dataset provided by ImageCLEFmed task organizers for years 2005 and 2006. This dataset is composed of a multimodal collection (images and text) of clinical cases, a list of queries for each year, and a list of relevance judgments for each query to evaluate the results. The results from the experiments show that the use of a medical ontology to expand the queries greatly improves the results. (S... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2346949 Wed, 01 Apr 2009 04:00:00 +0100 2346949 http://www.medworm.com/index.php?rid=2346948&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000316%2Fabstract%3Frss%3Dyes In this study, a novel sliding window strategy is proposed on the basis of power spectrum analysis for the accurate location of eukaryotic protein coding regions. The proposed sliding window strategy is very simple and the sliding step of window is changeable. Our tests show that the average location error for the novel method is 12 bases. Compared with the previous location error of 54 bases using the fixed sliding step, the novel sliding window strategy increased the location accuracy greatly. Further, the consumed CPU time to run the novel strategy is much shorter than the strategy of the fixed length sliding step. So, the computational complexity for the novel method is decreased greatly. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2346948 Wed, 01 Apr 2009 04:00:00 +0100 2346948 http://www.medworm.com/index.php?rid=2346947&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000304%2Fabstract%3Frss%3Dyes Abstract: Based on digital signal method, we propose a new representation of DNA primary sequence. The representation can completely avoid loss of information in the transfer of data from a DNA sequence to its mathematical representation. Afterwards, we suggest one such approach to reach quantification of similarities based on digital signal similarity theory. The examination of similarities/dissimilarities among the coding sequences of the first exon of β-globin gene of 11 species shows the utility of the scheme. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2346947 Wed, 01 Apr 2009 04:00:00 +0100 2346947 http://www.medworm.com/index.php?rid=2346946&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000286%2Fabstract%3Frss%3Dyes Abstract: The interpretation of the complex molecular descriptions generated by high-throughput gene expression technologies is still challenging. The development of new tools to identify common regulatory mechanisms involved in the control of the expression of a set of co-expressed genes, might enhance our capacity to extract functional information from genomic data sets. Here we present FactorY, a website that allows identification of enriched transcription factor binding sites (TFBSs) in the proximal promoter of a cluster of genes, as well as functional interpretation, and intuitive visualization of the results. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2346946 Wed, 01 Apr 2009 04:00:00 +0100 2346946 http://www.medworm.com/index.php?rid=2346945&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000274%2Fabstract%3Frss%3Dyes Abstract: Cancer chemotherapy complexity ranges from the routes that the drug must follow before reaching the tumor site (pharmacokinetics), to the drug effects on tumor depletion (pharmacodynamics). Previous researchers, in their majority, have focused either on the pharmacokinetics (PK) or on the pharmacodynamics (PD) aspects of chemotherapy. Moreover, models that account for the molecular mechanisms of cancer development have limited scope in addressing the protein signals involved in tumor progression. For instance, the recently developed models for the p53 network, for which a number of mutations have been reported, must be integrated for further understanding of the disease. Here, we propose an integrated model that is composed of a compartmental PK/PD representation for drug therapy... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2346945 Wed, 01 Apr 2009 04:00:00 +0100 2346945 http://www.medworm.com/index.php?rid=2346944&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000195%2Fabstract%3Frss%3Dyes Abstract: Various ECG instruments have addressed a wide variety of clinical and technical issues. However, there is still scope for improvement in them particularly in the area of their susceptibility to noise, lack of universal connectivity and off-line processing. A prototype system has been developed that caters to these limitations. It includes an analog system and a FM transceiver pair interfaced through sound port of the computer. The real time acquired data is viewed and filtered using MATLAB software. The ECG system described captures the bio-signal faithfully in real time wireless mode with minimum noise and has universal connectivity. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2346944 Wed, 01 Apr 2009 04:00:00 +0100 2346944 http://www.medworm.com/index.php?rid=2346943&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000183%2Fabstract%3Frss%3Dyes Abstract: We studied the Influence of Mg2+ ions on binding modes of HIV-1 integrase (IN) with thiazolothiazepine (THI) inhibitor by molecular simulation. The results in this work show that the binding process of THI and IN can be divided into two phases, the docking phase and the molecular dynamics (MD) phase. Docking results show that Mg2+ ions, the cofactors of HIV-1 IN in vivo, can remarkably affect THI binding on IN. In each chain of HIV-1 IN, two Mg2+ ions take part in the docking phase. Each of the two chains of HIV-1 IN dimer contains two Mg2+ ions. The Mg2+ ion, which binds with ASP64 and ASP116, can result in lower docking energy but higher binding specificity. Another Mg2+ ion, which binds with ASP64 and GLU152, is harmful for the THI binding on IN. The synergetic actions of thes... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2346943 Wed, 01 Apr 2009 04:00:00 +0100 2346943 http://www.medworm.com/index.php?rid=2346942&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000171%2Fabstract%3Frss%3Dyes Abstract: We introduce a framework for mining event related dynamics based on conditional FCM (CFCM). For a given set of responses, the variation in the data is summarized by means of a small set of meaningful prototypes accompanied with a low-dimensional graph capturing their relative relationships. CFCM enables prototyping in a principled manner. User-defined constraints, which are imposed by the nature of experimental data and/or dictated by the neuroscientist's intuition, direct the process of knowledge extraction and can robustify single-trial analysis. The method is introduced using simulated data and demonstrated using actual encephalographic data. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2346942 Wed, 01 Apr 2009 04:00:00 +0100 2346942 http://www.medworm.com/index.php?rid=2346941&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS001048250900016X%2Fabstract%3Frss%3Dyes Abstract: Most of dendrites in the central nervous system are now known to have active channels. These active dendrites play important roles not only in signal summation but also in computation. For the simulation of these important active dendrites, the compartment model based on the finite volume or finite difference discretization was mainly adopted. In this paper, we employ the Chebychev pseudo-spectral method well developed in computational physics, and demonstrate that it can achieve a higher precision with the same number of equations than the compartment model. Moreover, it is also shown that the Chebychev pseudo-spectral method converges faster to attain a given precision. Hence, for the simulations of active dendrites, the Chebychev pseudo-spectral method can be an attractive alt... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2346941 Wed, 01 Apr 2009 04:00:00 +0100 2346941 http://www.medworm.com/index.php?rid=2346940&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000158%2Fabstract%3Frss%3Dyes Abstract: Regarding the fact that the protein structure is principally encoded in its sequence, investigating the bonding state of cysteine has gained a great deal of attention due to its significance in the formation of protein structure. Due to lack of evident influence of free cysteines on the protein structure, it may be expected that only half-cystines convey encoded information. The results obtained from the analysis of amino acid distribution in proximity of both states of cysteines explicitly indicated that perquisite information for inducing cysteine bonding state is present even in the flanking amino acid sequences of free cysteines. (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2346940 Wed, 01 Apr 2009 04:00:00 +0100 2346940 http://www.medworm.com/index.php?rid=2346939&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482508001832%2Fabstract%3Frss%3Dyes Abstract: A quantitative summary of computer models in diving applications is presented, underscoring dual phase dynamics and quantifying metrics in tissue and blood. Algorithms covered include the multitissue, diffusion, split phase gradient, linear-exponential, asymmetric tissue, thermodynamic, varying permeability, reduced gradient bubble, tissue bubble diffusion, and linear-exponential phase models. Defining relationships are listed, and diver staging regimens are underscored. Implementations, diving sectors, and correlations are indicated for models with a history of widespread acceptance, utilization, and safe application across recreational, scientific, military, research, and technical communities. Presently, all models are incomplete, but many (included above) are useful, having r... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2346939 Wed, 01 Apr 2009 04:00:00 +0100 2346939 http://www.medworm.com/index.php?rid=2346938&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.journals.elsevierhealth.com%2Fperiodicals%2Fcbm%2Farticle%2FPIIS0010482509000468%2Fabstract%3Frss%3Dyes (Source: Computers in Biology and Medicine) Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2346938 Wed, 01 Apr 2009 04:00:00 +0100 2346938 http://www.medworm.com/index.php?rid=2297432&cid=s_34417_79_f&fid=34417&url=http%3A%2F%2Fwww.ncbi.nlm.nih.gov%2Fentrez%2Fquery.fcgi%3Ftmpl%3DNoSidebarfile%26db%3DPubMed%26cmd%3DRetrieve%26list_uids%3D19303070%26dopt%3DAbstract Authors: Rabinovitch A, Biton Y, Gutman M, Aviram I Spiral pair creation and dynamics is a widely occurring phenomenon in nature. It can appear in the heart tissue, causing severe arrhythmia, known as a figure-eight reentry. We consider the appearance of a spiral pair source, its minimal strength for survival, and the possible results of its interaction with a plane wave. In particular, its ability to outlast such an encounter is of interest. We also consider the question of exposing the source to a train of pulses, in terms of the frequency and angle of encounter. Results show different regimes of behavior, e.g. source annihilation, motion of the source away from, or towards the origin of the plane waves, its breaking and multiplication. Relevance of these results to heart arrhythmia ... Computers in Biology and Medicine journals http://www.medworm.com/rss/comments.php?id=2297432 Wed, 18 Mar 2009 04:00:00 +0100 2297432