A periodic spatio-spectral filter for event-related potentials
With respect to single trial detection of event-related potentials (ERPs), spatial and spectral filters are two of the most commonly used pre-processing techniques for signal enhancement. Spatial filters reduce the dimensionality of the data while suppressing the noise contribution and spectral filters attenuate frequency components that most likely belong to noise subspace. However, the frequency spectrum of ERPs overlap with that of the ongoing electroencephalogram (EEG) and different types of artifacts. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - October 5, 2016 Category: Bioinformatics Authors: Foad Ghaderi, Su Kyoung Kim, Elsa Andrea Kirchner Source Type: research
A graph-based approach for spatio-temporal segmentation of coronary arteries in X-ray angiographic sequences
The segmentation and tracking of coronary arteries (CAs) are critical steps for the computation of biophysical measurements in pediatric interventional cardiology. In the literature, most methods are focused on either segmenting the vessel lumen or on tracking the vessel centerline. However, they do not simultaneously combine the segmentation and tracking of a specific CA. This paper introduces a novel algorithm for CA segmentation and tracking from 2D X-ray angiography sequences. The proposed algorithm is based on the Temporal Vessel Walker (TVW) segmentation method, which combines graph-based formulation and temporal pri...
Source: Computers in Biology and Medicine - October 3, 2016 Category: Bioinformatics Authors: Faten M'hiri, Luc Duong, Christian Desrosiers, Mohamed Leye, Joaquim Mir ó, Mohamed Cheriet Source Type: research
Rapid Reconstruction of Quantitative Susceptibility Mapping via Improved ℓ0 Norm approximation
Quantitative susceptibility mapping (QSM) reconstruction is a well-known ill-posed problem. Various regularization techniques have been proposed for solving this problem. In this paper, a rapid method is proposed that uses ℓ0 norm minimization in a gradient domain. Because ℓ0 minimization is an NP-hard problem, a special alternating optimization strategy is employed to simplify the reconstruction algorithm. The proposed algorithm uses only simple point-wise multiplications and thresholding operations, and signific antly speeds up the calculation. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - October 3, 2016 Category: Bioinformatics Authors: Congbo Cai, Xi Chen, Weijun Liu, Shuhui Cai, Delu Zeng, Xinghao Ding Source Type: research
Computational identification of non-synonymous polymorphisms within regions corresponding to protein interaction sites
Protein-protein interactions (PPI) play an important role in function of all organisms and enable understanding of underlying metabolic processes. Computational predictions of PPIs are an important aspect in proteomics, as experimental methods may result in high degree of false positive results and are more expensive. Although there are many databases collecting predicted PPIs, exploration of genetics information underlying PPI interactions has not been investigated thoroughly. The aim of the present study was to identify genomic locations corresponding to regions involved in predicted PPIs and to collect non-synonymous po...
Source: Computers in Biology and Medicine - October 3, 2016 Category: Bioinformatics Authors: Blaz Skrlj, Tanja Kunej Source Type: research
T2-adjusted computed diffusion-weighted imaging: A novel method to enhance tumour visualisation
To introduce T2-adjusted computed DWI (T2-cDWI), a method that provides synthetic images at arbitrary b-values and echo times (TEs) that improve tissue contrast by removing or increasing T2 contrast in diffusion-weighted images. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 30, 2016 Category: Bioinformatics Authors: Lin Cheng, Matthew D. Blackledge, David J. Collins, Matthew R. Orton, Neil P. Jerome, Thorsten Feiweier, Mihaela Rata, Veronica Morgan, Nina Tunariu, Martin O. Leach, Dow-Mu Koh Source Type: research
ECG segmentation and fiducial point extraction using multi hidden Markov model
In this paper, we propose a novel method for extracting fiducial points (FPs) of electrocardiogram (ECG) signals. We propose the use of multi hidden Markov model (MultiHMM) as opposed to the traditional use of Classic HMM. In the MultiHMM method, each segment of an ECG beat is represented by a separate ergodic continuous density HMM. Each HMM has different state number and is trained separately. In the test step, the log-likelihood of two consecutive HMMs is compared and a path is estimated, which shows the correspondence of each part of the ECG signal to the HMM with the maximum log-likelihood. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 27, 2016 Category: Bioinformatics Authors: Mahsa Akhbari, Mohammad B. Shamsollahi, Omid Sayadi, Antonis A. Armoundas, Christian Jutten Source Type: research
Self-organizing Visualization and Pattern Matching of Vectorcardiographic QRS Waveforms
QRS morphology is commonly used in the electrocardiographic diagnosis of ventricular depolarization such as left bundle branch block (LBBB) and ventricular septal infarction. We investigated whether pattern matching of QRS loops in the 3-dimensional vectorcardiogram (VCG) will improve the grouping of patients whose space-time electrical activity akin to each other, thereby assisting in clinical decision making. First, pattern dissimilarity of VCG QRS loops is qualitatively measured and characterized among patients, resulting in a 93 ×93 distance matrix of patient-to-patient dissimilarity. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 26, 2016 Category: Bioinformatics Authors: Hui Yang, Fabio Leonelli Source Type: research
Automated retina identification based on multiscale elastic registration
In this work we propose a novel method for identifying individuals based on retinal fundus image matching. The method is based on the image registration of retina blood vessels, since it is known that the retina vasculature of an individual is a signature, i.e., a distinctive pattern of the individual. The proposed image registration consists of a multiscale affine registration followed by a multiscale elastic registration. The major advantage of this particular two-step image registration procedure is that it is able to account for both rigid and non-rigid deformations either inherent to the retina tissues or as a result ...
Source: Computers in Biology and Medicine - September 25, 2016 Category: Bioinformatics Authors: Isabel N. Figueiredo, Susana Moura, J úlio S. Neves, Luís Pinto, Sunil Kumar, Carlos M. Oliveira, João D. Ramos Source Type: research
Improving Information Retrieval in Functional Analysis
Transcriptome analysis is essential to understand the mechanisms regulating key biological processes and functions. The first step usually consists of identifying candidate genes; to find out which pathways are affected by those genes, however, functional analysis (FA) is mandatory. The most frequently used strategies for this purpose are Gene Set and Singular Enrichment Analysis (GSEA and SEA) over Gene Ontology. Several statistical methods have been developed and compared in terms of computational efficiency and/or statistical appropriateness. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 23, 2016 Category: Bioinformatics Authors: Juan C Rodriguez, Germ án A González, Cristóbal Fresno, Andrea S Llera, Elmer A Fernández Source Type: research
A method of REM-NREM sleep distinction using ECG signal for unobtrusive personal monitoring
Computers are used extensively in sleep labs for polysomnography and for assistance in sleep staging. However, the test is highly inconvenient to the patient and requires availability of specially equipped sleep labs. Alternative approaches that enable unobtrusive in-home sleep staging with ECG or other signals are highly desirable. In this paper we describe a method that can be used for distinction of REM and NREM sleep stages using spectral and non-linear features of ECG derived RR interval series. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 22, 2016 Category: Bioinformatics Authors: Jaspal Singh, R.K. Sharma, A.K. Gupta Source Type: research
A Computational Model for Investigating the Effects of Changes in Bioavailability of Insulin-Like Growth Factor-1 on the Homeostasis of the Intervertebral Disc
Insulin-like growth factor-1 (IGF-1) is well-known for upregulating cell proliferation and biosynthesis of the extracellular matrix in the intervertebral disc (IVD). Pathological conditions, such as obesity or chronic kidney disease cause IGF-1 deficiency in plasma. How this deficiency impacts disc homeostasis remains unknown. Pro-anabolic approaches for the treatment of disc degeneration based on enhancing IGF-1 bioavailability to tissue-cells are considered, but knowledge of their effectiveness in enhancing cellular anabolism of a degenerated disc is limited. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 21, 2016 Category: Bioinformatics Authors: Shady Elmasry, Shihab Asfour, Juan Pablo de Rivero Vaccari, Francesco Travascio Source Type: research
Lung Motion Estimation by Robust Point Matching and Spatiotemporal Tracking for 4D CT
We propose a deformable registration approach to estimate patient-specific lung motion during free breathing for four-dimensional (4D) computed tomography (CT) based on point matching and tracking between images in different phases. First, a robust point matching (RPM) algorithm coarsely aligns the source phase image onto all other target phase images of 4D CT. Scale-invariant feature transform (SIFT) is introduced into the cost function in order to accelerate and stabilize the convergence of the point matching. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 18, 2016 Category: Bioinformatics Authors: Jianbing Yi, Hao Yang, Xuan Yang, Guoliang Chen Source Type: research
Computer-Aided Detection (CADx) for Plastic Deformation Fractures in Pediatric Forearm
Bowing fractures are incomplete fractures of tubular long bones, often observed in pediatric patients, where plain radiographic film is the non-invasive imaging modality of choice in routine radiological workflow. Due to weak association between bent bone and distinct cortex disruption, bowing fractures may not be diagnosed properly while reading plain radiography. Missed fractures and dislocations are common in accidents and emergency practice, particularly in children. These missed injuries can result in more complicated treatment or even long-term disability. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 16, 2016 Category: Bioinformatics Authors: Yuwei Zhou, Uygar Teomete, Ozgur Dandin, Onur Osman, Taner Dandinoglu, Ulas Bagci, Weizhao Zhao Source Type: research
Application of multiphysics models to efficient design of experiments of solute transport across articular cartilage
In this study, we used a combination of micro-computed tomography experiments and biphasic-solute finite element models to study the effects of three parameters of the overlying bath on the diffusion of neutral solutes across cartilage zones. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 16, 2016 Category: Bioinformatics Authors: Behdad Pouran, Vahid Arbabi, Harrie Weinans, Amir A. Zadpoor Source Type: research
Extraction and Processing of Videocapsule Data to Detect and Measure the Presence of Villous Atrophy in Celiac Disease Patients
Videocapsule endoscopy is a relative new method to analyze the gastrointestinal tract for the presence of pathologic features. It is of relevance to detect villous atrophy in the small bowel, which is a defining symptom of celiac disease. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 15, 2016 Category: Bioinformatics Authors: Edward J. Ciaccio, Govind Bhagat, Suzanne K. Lewis, Peter H. Green Source Type: research
