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Computers in Biology and Medicine

A Alexiadis, K Stamatopoulos, W Wen, H K Batchelor, S Bakalis, M Barigou, M J H Simmons
We developed a mathematical model that describes the motion of viscous fluids in the partially-filled colon caused by the periodic contractions of flexible walls (peristalsis). In-vitro data are used to validate the model. The model is then used to identify two fundamental mechanisms of mass transport: the surfing mode and the pouring mode. The first mechanism is faster, but only involves the surface of the liquid. The second mechanism causes deeper mixing, and appears to be the main transport mechanism. Based on the gained understanding, we propose a series of measures that can improve the reliability of in-vitro models...
January 9, 2017: Computers in Biology and Medicine
Sun Zheng, Yuan Yuan, Han Duoduo
Intravascular photoacoustic (IVPA) is a newly developed catheter-based imaging technique for the diagnosis of arterial atherosclerosis. A framework of simulating IVPA transversal images from a cross-sectional vessel model with given optical and acoustic parameters was presented. The light illumination and transportation in multi-layered wall and atherosclerotic plaque tissues were modeled through Monte Carlo (MC) simulation. The generation and transmission of photoacoustic (PA) waves in the acoustically homogeneous medium were modeled through the PA wave equation, which is solved explicitly with a finite difference time domain (FDTD) algorithm in polar coordinates...
January 6, 2017: Computers in Biology and Medicine
Fahime Khozeimeh, Roohallah Alizadehsani, Mohamad Roshanzamir, Abbas Khosravi, Pouran Layegh, Saeid Nahavandi
As benign tumors, warts are made through the mediation of Human Papillomavirus (HPV) and may grow on all parts of body, especially hands and feet. There are several treatment methods for this illness. However, none of them can heal all patients. Consequently, physicians are looking for more effective and customized treatments for each patient. They are endeavoring to discover which treatments have better impacts on a particular patient. The aim of this study is to identify the appropriate treatment for two common types of warts (plantar and common) and to predict the responses of two of the best methods (immunotherapy and cryotherapy) to the treatment...
January 6, 2017: Computers in Biology and Medicine
Andrius Sološenko, Andrius Petrėnas, Vaidotas Marozas, Leif Sörnmo
A phenomenological model for simulating the photoplethysmogram (PPG) during atrial fibrillation (AF) is proposed. The simulated PPG is solely based on RR interval information, and, therefore, any annotated ECG database can be used to model sinus rhythm, AF, or rhythms with premature beats. A PPG pulse is modeled by a linear combination of a log-normal and two Gaussian waveforms. The model PPG is obtained by placing individual pulses according to the RR intervals so that a connected signal is created. The model is evaluated on synchronously recorded ECG and PPG signals from the MIMIC and the University of Queensland Vital Signs Dataset databases...
December 28, 2016: Computers in Biology and Medicine
Yuqian Li, Xin Liu, Feng Wei, Diana M Sima, Sofie Van Cauter, Uwe Himmelreich, Yiming Pi, Guang Hu, Yi Yao, Sabine Van Huffel
Proton Magnetic Resonance Spectroscopic Imaging ((1)H MRSI) has shown great potential in tumor diagnosis since it provides localized biochemical information discriminating different tissue types, though it typically has low spatial resolution. Magnetic Resonance Imaging (MRI) is widely used in tumor diagnosis as an in vivo tool due to its high resolution and excellent soft tissue discrimination. This paper presents an advanced data fusion scheme for brain tumor diagnosis using both MRSI and MRI data to improve the tumor differentiation accuracy of MRSI alone...
December 27, 2016: Computers in Biology and Medicine
Islam Reda, Ahmed Shalaby, Mohammed Elmogy, Ahmed Abou Elfotouh, Fahmi Khalifa, Mohamed Abou El-Ghar, Ehsan Hosseini-Asl, Georgy Gimel'farb, Naoufel Werghi, Ayman El-Baz
Early detection of prostate cancer increases chances of patients' survival. Our automated non-invasive system for computer-aided diagnosis (CAD) of prostate cancer segments the prostate on diffusion-weighted magnetic resonance images (DW-MRI) acquired at different b-values, estimates its apparent diffusion coefficients (ADC), and classifies their descriptors - empirical cumulative distribution functions (CDF) - with a trained deep learning network. To segment the prostate, an evolving geometric (level-set-based) deformable model is guided by a speed function depending on intensity attributes extracted from the DW-MRI with nonnegative matrix factorization (NMF)...
December 23, 2016: Computers in Biology and Medicine
Shiwen Shen, Simon X Han, Panayiotis Petousis, Robert E Weiss, Frank Meng, Alex A T Bui, William Hsu
A growing number of individuals who are considered at high risk of cancer are now routinely undergoing population screening. However, noted harms such as radiation exposure, overdiagnosis, and overtreatment underscore the need for better temporal models that predict who should be screened and at what frequency. The mean sojourn time (MST), an average duration period when a tumor can be detected by imaging but with no observable clinical symptoms, is a critical variable for formulating screening policy. Estimation of MST has been long studied using continuous Markov model (CMM) with Maximum likelihood estimation (MLE)...
December 22, 2016: Computers in Biology and Medicine
Nastaran Dehghan Khalilabad, Hamid Hassanpour
Microarray technology is a powerful genomic tool for simultaneously studying and analyzing the behavior of thousands of genes. The analysis of images obtained from this technology plays a critical role in the detection and treatment of diseases. The aim of the current study is to develop an automated system for analyzing data from microarray images in order to detect cancerous cases. The proposed system consists of three main phases, namely image processing, data mining, and the detection of the disease. The image processing phase performs operations such as refining image rotation, gridding (locating genes) and extracting raw data from images the data mining includes normalizing the extracted data and selecting the more effective genes...
December 21, 2016: Computers in Biology and Medicine
Jair Trapé Goulart, Rosana Almada Bassani, José Wilson Magalhães Bassani
BACKGROUND AND OBJECTIVE: The isolated cardiomyocyte preparation is amenable to several experimental approaches not suitable to the myocardial tissue, which has allowed the gain of important information on the pathophysiology of the cardiac muscle. Thus, the development of techniques for functional studies in this preparation is important. The goal of the present study was to develop a computer program to extract contraction traces generated by cyclic cell shortening from cardiomyocyte video image files...
December 21, 2016: Computers in Biology and Medicine
Adam G Polak, Janusz Mroczka, Dariusz Wysoczański
Since computed tomography (CT) was developed over 35 years ago, new mathematical ideas and computational algorithms have been continuingly elaborated to improve the quality of reconstructed images. In recent years, a considerable effort can be noticed to apply the sparse solution of underdetermined system theory to the reconstruction of CT images from undersampled data. Its significance stems from the possibility of obtaining good quality CT images from low dose projections. Among diverse approaches, total variation (TV) minimizing 2D gradients of an image, seems to be the most popular method...
December 21, 2016: Computers in Biology and Medicine
Ramalingaswamy Cheruku, Damodar Reddy Edla, Venkatanareshbabu Kuppili
Diabetes is a major health challenge around the world. Existing rule-based classification systems have been widely used for diabetes diagnosis, even though they must overcome the challenge of producing a comprehensive optimal ruleset while balancing accuracy, sensitivity and specificity values. To resolve this drawback, in this paper, a Spider Monkey Optimization-based rule miner (SM-RuleMiner) has been proposed for diabetes classification. A novel fitness function has also been incorporated into SM-RuleMiner to generate a comprehensive optimal ruleset while balancing accuracy, sensitivity and specificity...
December 19, 2016: Computers in Biology and Medicine
Satishkumar S Chavan, Abhishek Mahajan, Sanjay N Talbar, Subhash Desai, Meenakshi Thakur, Anil D'cruz
Neurocysticercosis (NCC) is a parasite infection caused by the tapeworm Taenia solium in its larvae stage which affects the central nervous system of the human body (a definite host). It results in the formation of multiple lesions in the brain at different locations during its various stages. During diagnosis of such symptomatic patients, these lesions can be better visualized using a feature based fusion of Computed Tomography (CT) and Magnetic Resonance Imaging (MRI). This paper presents a novel approach to Multimodality Medical Image Fusion (MMIF) used for the analysis of the lesions for the diagnostic purpose and post treatment review of NCC...
December 18, 2016: Computers in Biology and Medicine
Akshay Kota Aswath Kumar, Angelina Drahi, Vincent Jacquemet
BACKGROUND: Repolarization gradients contribute to arrhythmogenicity. In reaction-diffusion models of cardiac tissue, heterogeneities in action potential duration (APD) can be created by locally modifying an intrinsic membrane kinetics parameter. Electrotonic coupling, however, acts as a confounding factor that modulates APD dispersion. METHOD: We developed an algorithm based on a quasi-Newton method that iteratively adjusts the spatial distribution of a membrane parameter to reproduce a pre-defined target APD map in a coupled tissue...
December 18, 2016: Computers in Biology and Medicine
Elodie Puybareau, Diane Genest, Emilie Barbeau, Marc Léonard, Hugues Talbot
Studies on fish embryo models are widely developed in research. They are used in several research fields including drug discovery or environmental toxicology. In this article, we propose an entirely automated assay to detect cardiac arrest in Medaka (Oryzias latipes) based on image analysis. We propose a multi-scale pipeline based on mathematical morphology. Starting from video sequences of entire wells in 24-well plates, we focus on the embryo, detect its heart, and ascertain whether or not the heart is beating based on intensity variation analysis...
December 15, 2016: Computers in Biology and Medicine
Joao B Florindo, Odemir M Bruno, Gabriel Landini
The Odontogenic keratocyst (OKC) is a cystic lesion of the jaws, which has high growth and recurrence rates compared to other cysts of the jaws (for instance, radicular cyst, which is the most common jaw cyst type). For this reason OKCs are considered by some to be benign neoplasms. There exist two sub-types of OKCs (sporadic and syndromic) and the ability to discriminate between these sub-types, as well as other jaw cysts, is an important task in terms of disease diagnosis and prognosis. With the development of digital pathology, computational algorithms have become central to addressing this type of problem...
December 8, 2016: Computers in Biology and Medicine
Christina Orphanidou
A new method for extracting the respiratory rate from ECG and PPG obtained via wearable sensors is presented. The proposed technique employs Ensemble Empirical Mode Decomposition in order to identify the respiration "mode" from the noise-corrupted Heart Rate Variability/Pulse Rate Variability and Amplitude Modulation signals extracted from ECG and PPG signals. The technique was validated with respect to a Respiratory Impedance Pneumography (RIP) signal using the mean absolute and the average relative errors for a group ambulatory hospital patients...
December 7, 2016: Computers in Biology and Medicine
Mirna Moukhtar, Wafi Chaar, Ziad Abdel-Razzak, Mohamad Khalil, Samir Taha, Hala Chamieh
PURPOSE: Superfamily 1 and Superfamily 2 helicases, two of the largest helicase protein families, play vital roles in many biological processes including replication, transcription and translation. Study of helicase proteins in the model microorganisms of archaea have largely contributed to the understanding of their function, architecture and assembly. Based on a large phylogenomics approach, we have identified and classified all SF1 and SF2 protein families in ninety five sequenced archaea genomes...
December 6, 2016: Computers in Biology and Medicine
V Urovi, O Jimenez-Del-Toro, F Dubosson, A Ruiz Torres, M I Schumacher
This paper describes a novel temporal logic-based framework for reasoning with continuous data collected from wearable sensors. The work is motivated by the Metabolic Syndrome, a cluster of conditions which are linked to obesity and unhealthy lifestyle. We assume that, by interpreting the physiological parameters of continuous monitoring, we can identify which patients have a higher risk of Metabolic Syndrome. We define temporal patterns for reasoning with continuous data and specify the coordination mechanisms for combining different sets of clinical guidelines that relate to this condition...
December 5, 2016: Computers in Biology and Medicine
Aiguo Wang, Ning An, Jing Yang, Guilin Chen, Lian Li, Gil Alterovitz
Gene selection seeks to find a small subset of discriminant genes from the gene expression profiles. Current gene selection methods such as wrapper-based models mainly address the issue of obtaining high-quality gene subsets. However, they are considerably time consuming, due to the existence of irrelevant and redundant genes. In this study, we present an improved wrapper-based gene selection method by introducing the Markov blanket technique to reduce the required wrapper evaluation time. In addition, our method can identify targeting genes while eliminating redundant ones in an efficient way...
December 5, 2016: Computers in Biology and Medicine
Maristella Borges Silva, Andrei Nakagawa Silva, Eduardo Lázaro Martins Naves, Evanisi Teresa Palomari, Alcimar Barbosa Soares
We propose a new method for detecting the onset of the stretch reflex response for assessment of spasticity based on the Tonic Stretch Reflex Threshold (TSRT). Our strategy relies on a three-stage approach to detect the onset of the reflex EMG activity: (i) Reduction of baseline activity by means of Empirical Mode Decomposition; (ii) Extraction of the complex envelope of the EMG signal by means of Hilbert Transform (HT) and; iii) A double threshold decision rule. Simulated and real EMG data were used to evaluate and compare our method (TSRT-EHD) against three other popular methods described in the literature to assess TSRT ('Kim', 'Ferreira' and 'Blanchette')...
December 2, 2016: Computers in Biology and Medicine
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