The R implementation of the CRAN package PATHChange, a tool to study genetic pathway alterations in transcriptomic data
Tools that extract phenotype alterations from transcriptomic data are important to improve the interpretation of biological studies. PATHChange is a statistical CRAN package designed to work with data downloaded from the Gene Expression Omnibus database (GEO) to determine differential pathway expression in comparative studies including control samples. In this paper we present details of the structure, implementation and an example of use of the package. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 14, 2016 Category: Bioinformatics Authors: Carla A.R.S. Fontoura, Gastone Castellani, Jos é C.M. Mombach Source Type: research
Influence of gray level and space discretization on brain tumor heterogeneity measures obtained from magnetic resonance images
Tumor heterogeneity in medical imaging is a current research trend due to its potential relationship with tumor malignancy. The aim of this study is to analyze the effect of dynamic range and matrix size changes on the results of different heterogeneity measures. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 14, 2016 Category: Bioinformatics Authors: David Molina, Juli án Pérez-Beteta, Alicia Martínez-González, Juan Martino, Carlos Velasquez, Estanislao Arana, Víctor M. Pérez-García Source Type: research
Multi-window Detection for P-wave in Electrocardiograms Based on Bilateral Accumulative Area
P-wave detection is one of the most challenging aspects in electrocardiograms (ECGs) due to its low amplitude, low frequency, and variable waveforms. This work introduces a novel multi-window detection method for P-wave delineation based on the bilateral accumulative area. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 14, 2016 Category: Bioinformatics Authors: Riqing Chen, Yingsong Huang, Jian Wu Source Type: research
Endoscope Analysis on Peristaltic Blood Flow of Sisko Fluid with Titanium Magneto-Nanoparticles
In this article, endoscope analysis on peristaltic blood flow of Sisko fluid having Titanium magneto-nanoparticles through a uniform tube has been analyzed. The governing flow problem consists of continuity, linear momentum and thermal energy equations. The effect of magnetic field is also taken into account with the help of ohm's law. With the help of long wavelength and zero Reynolds number approximation, the governing equations are simplified. The reduced resulting nonlinear coupled equations are solved analytically with the help of Homotopy perturbation method (HPM). (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 12, 2016 Category: Bioinformatics Authors: M.M. Bhatti, A. Zeeshan, R. Ellahi Source Type: research
DRPPP: A machine learning based tool for prediction of disease resistance proteins in plants
Plant disease outbreak is increasing rapidly around the globe and is a major cause for crop loss worldwide. Plants, in turn, have developed diverse defense mechanisms to identify and evade different pathogenic microorganisms. Early identification of plant disease resistance genes (R genes) can be exploited for crop improvement programs. The present prediction methods are either based on sequence similarity/domain-based methods or electronically annotated sequences, which might miss existing unrecognized proteins or low similarity proteins. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 12, 2016 Category: Bioinformatics Authors: Tarun Pal, Varun Jaiswal, Rajinder S. Chauhan Source Type: research
Security and Privacy Preserving Approaches in the eHealth Clouds with Disaster Recovery Plan
Cloud computing was introduced as an alternative storage and computing model in the health sector as well as other sectors to handle large amounts of data. Many healthcare companies have moved their electronic data to the cloud in order to reduce in-house storage, IT development and maintenance costs. However, storing the healthcare records in a third-party server may cause serious storage, security and privacy issues. Therefore, many approaches have been proposed to preserve security as well as privacy in cloud computing projects. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 11, 2016 Category: Bioinformatics Authors: Aqeel Sahi, David Lai, Yan Li Source Type: research
Observer performance in characterization of carotid plaque texture and surface characteristics with 3D versus 2D ultrasound
To determine the reproducibility of three-dimensional (3D) ultrasound (US) over two-dimensional (2D) US in characterizing atherosclerotic carotid plaques using inter- and intra-observer agreement metrics. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 11, 2016 Category: Bioinformatics Authors: Sook Sam Leong, Anushya Vijayananthan, Nur Adura Yaakup, Nazri Shah, Kwan Hoong Ng, U. Rajendra Acharya, Mehmet Bilgen Source Type: research
Evaluation of Haptic Interfaces for Simulation of Drill Vibration in Virtual Temporal Bone Surgery
Surgical training is evolving from an observership model towards a new paradigm that includes virtual-reality (VR) simulation. In otolaryngology, temporal bone dissection has become intimately linked with VR simulation as the complexity of anatomy demands a high level of surgeon aptitude and confidence. While an adequate 3D visualization of the surgical site is available in current simulators, the force feedback rendered during haptic interaction does not convey vibrations. This lack of vibration rendering limits the simulation fidelity of a surgical drill such as that used in temporal bone dissection. (Source: Computers i...
Source: Computers in Biology and Medicine - September 11, 2016 Category: Bioinformatics Authors: Ahmad Ghasemloonia, Shalese Baxandall, Kourosh Zareinia, Justin T. Lui, Joseph C. Dort, Garnette R. Sutherland, Sonny Chan Source Type: research
Computation of Breast Ptosis from 3D Surface Scans of the Female Torso
This study presents a novel algorithm that utilizes three-dimensional (3D) features such as surface curvature and orientation for the assessment of breast ptosis from 3D scans of the female torso. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 7, 2016 Category: Bioinformatics Authors: Danni Li, Audrey Cheong, Gregory P. Reece, Melissa A. Crosby, Michelle C. Fingeret, Fatima A. Merchant Source Type: research
Quadratic Adaptive Algorithm for Solving Cardiac Action Potential Models
An adaptive integration method is proposed for computing cardiac action potential models accurately and efficiently. Time steps are adaptively chosen by solving a quadratic formula involving the first and second derivatives of the membrane action potential. To improve the numerical accuracy, we devise an extremum-locator (el) function to predict the local extremum when approaching the peak amplitude of the action potential. In addition, the time step restriction (tsr) technique is designed to limit the increase in time steps, and thus prevent the membrane potential from changing abruptly. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 4, 2016 Category: Bioinformatics Authors: Min-Hung Chen, Po-Yuan Chen, Ching-Hsing Luo Source Type: research
Phenomenological modelling and simulation of cell clusters in 3D cultures
Cell clustering and aggregation are fundamental processes in the development of several tissues and the progression of many diseases. The formation of these aggregates also has a direct impact on the oxygen concentration in their surroundings due to cellular respiration and poor oxygen diffusion through clusters. In this work, we propose a mathematical model that is capable of simulating cell cluster formation in 3D cultures through combining a particle-based and a finite element approach to recreate complex experimental conditions. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - September 1, 2016 Category: Bioinformatics Authors: I. Gonz ález-Valverde, C. Semino, J.M. García-Aznar Source Type: research
Biologically inspired survival analysis based on integrating gene expression as mediator with genomic variants
Accurately linking cancer molecular profiling with survival can lead to improvements in the clinical management of cancer. However, existing survival analysis relies on statistical evidence from a single level of data, without paying much attention to the integration of interacting multi-level data and the underlying biology. Advances in genomic techniques provide unprecedented power of characterizing the cancer tissue in a more complete manner than before, offering the opportunity to design biologically informed and integrative approaches for survival data analysis. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - August 30, 2016 Category: Bioinformatics Authors: Ibrahim Youssef, Robert Clarke, Ie-Ming Shih, Yue Wang, Guoqiang Yu Source Type: research
Realistic Texture Synthesis for Point-based Fruitage Phenotype
Although current 3D scanner technology can acquire textural images from a point model, visible seams in the image, inconvenient data acquisition and occupancy of a large space during use are points of concern for outdoor fruit models. In this paper, an SPSDW (simplification and perception based subdivision followed by down-sampling weighted average) method is proposed to balance memory usage and texture synthesis quality using a crop fruit, such as apples, as a research subject for a point-based fruit model. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - August 28, 2016 Category: Bioinformatics Authors: HuiJun Yang, Jian Chang, Dongjian He, Nan Geng, Meili Wang, JianJun Zhang, Xu Jing, Ehtzaz Chaudhry Source Type: research
Hidden Discriminative Features Extraction for Supervised High-order Time Series Modeling
In this paper, an orthogonal Tucker-decomposition-based extraction of high-order discriminative subspaces from a tensor-based time series data structure is presented, named as Tensor Discriminative Feature Extraction (TDFE). TDFE relies on the employment of category information for the maximization of the between-class scatter and the minimization of the within-class scatter to extract optimal hidden discriminative feature subspaces that are simultaneously spanned by every modality for supervised tensor modeling. (Source: Computers in Biology and Medicine)
Source: Computers in Biology and Medicine - August 26, 2016 Category: Bioinformatics Authors: Ngoc Anh Nguyen Thi, Hyung-Jeong Yang, Sunhee Kim Source Type: research
Mining balance disorders' data for the development of diagnostic decision support systems
In this work we present the methodology for the development of the EMBalance diagnostic Decision Support System (DSS) for balance disorders. Medical data from patients with balance disorders have been analysed using data mining techniques for the development of the diagnostic DSS. The proposed methodology uses various data, ranging from demographic characteristics to clinical examination, auditory and vestibular tests, in order to provide an accurate diagnosis. The system aims to provide decision support for general practitioners (GPs) and experts in the diagnosis of balance disorders as well as to provide recommendations ...
Source: Computers in Biology and Medicine - August 23, 2016 Category: Bioinformatics Authors: T.P. Exarchos, G. Rigas, A. Bibas, D. Kikidis, C. Nikitas, F.L. Wuyts, B. Ihtijarevic, L. Maes, M. Cenciarini, C. Maurer, N. Macdonald, D.-E. Bamiou, L. Luxon, M. Prasinos, G. Spanoudakis, D.D. Koutsouris, D.I. Fotiadis Source Type: research
