3,955 results match your criteria Computers in Biology and Medicine [Journal]


Smeared multiscale finite element model for electrophysiology and ionic transport in biological tissue.

Comput Biol Med 2019 Mar 26;108:288-304. Epub 2019 Mar 26.

Houston Methodist Research Institute, The Department of Nanomedicine, 6670 Bertner Ave., R7-117, Houston, TX, 77030, USA.

Basic functions of living organisms are governed by the nervous system through bidirectional signals transmitted from the brain to neural networks. These signals are similar to electrical waves. In electrophysiology the goal is to study the electrical properties of biological cells and tissues, and the transmission of signals. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.023DOI Listing

Far-field contributions in multi-electrodes atrial recordings blur distinction between anatomical and functional reentries and may cause imaginary phase singularities - A computational study.

Comput Biol Med 2019 Mar 14;108:276-287. Epub 2019 Mar 14.

Center for Arrhythmia Research, University of Michigan, Ann Arbor, MI, USA.

Background: Atrial fibrillation (AF) is the most common cardiac arrhythmia and the most important cause of embolic stroke, requiring new technologies for its better understanding and therapies. Recent approaches to map the electrical activity during AF with multi-electrode systems aim at localizing patient-specific ablation targets of reentrant patterns. However, there is a critical need to determine the accuracy of those mapping systems. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.022DOI Listing

Characterizing the clinical implementation of a novel activation-repolarization metric to identify targets for catheter ablation of ventricular tachycardias using computational models.

Comput Biol Med 2019 Mar 23;108:263-275. Epub 2019 Mar 23.

School of Biomedical Engineering and Imaging Sciences, King's College London, London, United Kingdom. Electronic address: https://kclpure.kcl.ac.uk/portal/martin.bishop.html.

Identification of targets for catheter ablation of ventricular tachycardias (VTs) remains a significant challenge. VTs are often driven by re-entrant circuits resulting from a complex interaction between the front (activation) and tail (repolarization) of the electrical wavefront. Most mapping techniques do not take into account the tissue repolarization which may hinder the detection of ablation targets. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.018DOI Listing
March 2019
1 Read

Dynamic coherence factor based on the standard deviation for coherent plane-wave compounding.

Comput Biol Med 2019 Mar 28;108:249-262. Epub 2019 Mar 28.

Department of Biomedical Engineering, Hefei University of Technology, Hefei, 230009, China.

The ultrafast imaging technique based on plane wave transmission has been a commonly investigated imaging mode in medical ultrasound imaging. Coherent plane-wave compounding (CPWC) was proposed to improve the quality of plane-wave imaging (PWI), which obtained a high-quality image by summing the low-quality images formed by transmitting plane waves at different steering angles. Coherence factor (CF) weighting algorithms can effectively improve image contrast with low computational complexity. Read More

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March 2019
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Rapid automatic identification of parameters of the Bergman Minimal Model in Sprague-Dawley rats with experimental diabetes for adaptive insulin delivery.

Comput Biol Med 2019 Apr 8;108:242-248. Epub 2019 Apr 8.

IEEE Engineering in Medicine and Biology, Mexico City, Mexico. Electronic address:

Glucose-Insulin regulation models can be used to individualize insulin therapy. However, the experimental techniques currently used to identify the appropriate parameter sets of an individual are expensive, time consuming, and very unpleasant for the patient. Since there is a wide range of intrapersonal parameter variability, the identified parameters in a laboratory setting (at rest) are not optimal for dynamic conditions of daily activities. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.028DOI Listing

Spatial remodelling of calcium release units may impair cardiac electro-mechanical function: A simulation study.

Comput Biol Med 2019 Apr 13;108:234-241. Epub 2019 Apr 13.

School of Biomedical Engineering, Wenzhou Medical University, University Town, Chashan, Wenzhou, 325035, PR China. Electronic address:

Excitation-contraction coupling (E-C coupling) is thought to be based on elementary calcium release units (CRUs) in which clusters of ryanodine receptors (RyRs) localized on the sarcoplasmic reticulum (SR) are in close apposition to L-type Ca channels (LCCs) on the transverse tubules (TTs). However, a fraction of LCC-RyR structure may be uncoupled due to the remodelling of TTs, which would tend to destroy the E-C coupling in the failing heart. Here we proposed a multiscale model of the ventricular myocyte to investigate the relationship between LCC-RyR structure and cardiac electro-mechanical function. Read More

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April 2019
1 Read

Binary tree-like network with two-path Fusion Attention Feature for cervical cell nucleus segmentation.

Comput Biol Med 2019 Mar 29;108:223-233. Epub 2019 Mar 29.

School of Computer Science and Engineering, South China University of Technology, China. Electronic address:

Early detection of cervical lesion is of great significance in reducing mortality from cervical cancer, and segmentation of cervical cell nuclei plays an important role in screening for cervical lesion. Compared with traditional algorithms, several deep learning methods can improve the segmentation; however, due to blurred boundaries and complex gradients of medical images, the segmentation remains unsatisfactory. In addition, the existing datasets used by cervical cell nucleus segmentation research are lacking in terms of both quantity and diversity, so methods based on those datasets cannot effectively cope with challenging cases. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.011DOI Listing

A state-of-the-art review on badminton lunge attributes.

Comput Biol Med 2019 Apr 6;108:213-222. Epub 2019 Apr 6.

School of Mechanical Engineering, Engineering Campus, Universiti Sains Malaysia, 14300, Nibong Tebal, Penang, Malaysia. Electronic address:

Good badminton lunge skills have been quantitatively described using biomechanical attributes at both static and dynamic phases. The measurement of badminton lunge attributes has often been complicated by various experimental protocols used. No review article has considered or critically reviewed the attributes that align with badminton lunge performance. Read More

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April 2019
3 Reads

Multiscale modeling of the cardiovascular system for infants, children, and adolescents: Age-related alterations in cardiovascular parameters and hemodynamics.

Comput Biol Med 2019 Mar 23;108:200-212. Epub 2019 Mar 23.

Graduate School of Engineering, Chiba University, Inage, Chiba, Japan; Shanghai Jiao Tong University and Chiba University International Cooperative Research Center (SJTU-CU ICRC), Minhang District, Shanghai, China. Electronic address:

While zero- and one-dimensional multiscale modeling of the adult cardiovascular system (CVS) has been recognized as a useful tool in cardiovascular research and clinical applications, there are still not any generic cardiovascular models for a broad range of age groups. To study age-related alterations in cardiovascular parameters and hemodynamics, we here presented a versatile multiscale cardiovascular model considering the cardiovascular growth and development during aging. An adult cardiovascular model was first established by utilizing population-averaged physiological data. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.021DOI Listing
March 2019
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Ranking of stroke and cardiovascular risk factors for an optimal risk calculator design: Logistic regression approach.

Comput Biol Med 2019 Mar 25;108:182-195. Epub 2019 Mar 25.

Stroke Monitoring and Diagnostic Division, AtheroPoint™, Roseville, CA, USA. Electronic address:

Purpose: Conventional cardiovascular risk factors (CCVRFs) and carotid ultrasound image-based phenotypes (CUSIP) are independently associated with long-term risk of cardiovascular (CV) disease. In this study, 26 cardiovascular risk (CVR) factors which consisted of a combination of CCVRFs and CUSIP together were ranked. Further, an optimal risk calculator using AtheroEdge composite risk score (AECRS1. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.020DOI Listing
March 2019
1.240 Impact Factor

A two-step risk assessment method for radiofrequency ablations of spine metastases.

Comput Biol Med 2019 Mar 16;108:174-181. Epub 2019 Mar 16.

Otto-von-Guericke University, Department of Simulation and Graphics, Universitätsplatz 2, D-39106, Magdeburg, Germany; Research Campus STIMULATE, Sandtorstraße 23, D-39106, Magdeburg, Germany. Electronic address:

Background: Spine metastases (MTS) can be treated via Radiofrequency Ablation (RFA) electrodes. To bring these electrodes into vertebral MTS, pathways have to be created. This can be done via transpedicular hammering or drilling. Read More

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March 2019
1 Read

A multi-scale data fusion framework for bone age assessment with convolutional neural networks.

Comput Biol Med 2019 Mar 19;108:161-173. Epub 2019 Mar 19.

Department of Electrical and Computer Engineering, University of British Columbia, Vancouver, BC, Canada.

Bone age assessment (BAA) has various clinical applications such as diagnosis of endocrine disorders and prediction of final adult height for adolescents. Recent studies indicate that deep learning techniques have great potential in developing automated BAA methods with significant advantages over the conventional methods based on handcrafted features. In this paper, we propose a multi-scale data fusion framework for bone age assessment with X-ray images based on non-subsampled contourlet transform (NSCT) and convolutional neural networks (CNNs). Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.015DOI Listing
March 2019
1.240 Impact Factor

A novel end-to-end brain tumor segmentation method using improved fully convolutional networks.

Comput Biol Med 2019 Mar 18;108:150-160. Epub 2019 Mar 18.

School of Information Science and Technology, and Centers for Biomedical Engineering, University of Science and Technology of China, Hefei, AH 230027, China.

Accurate brain magnetic resonance imaging (MRI) tumor segmentation continues to be an active research topic in medical image analysis since it provides doctors with meaningful and reliable quantitative information in diagnosing and monitoring neurological diseases. Successful deep learning-based proposals have been designed, and most of them are built upon image patches. In this paper, a novel end-to-end brain tumor segmentation method is developed using an improved fully convolutional network by modifying the U-Net architecture. Read More

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March 2019
4 Reads

Genetic effects of welding fumes on the development of respiratory system diseases.

Comput Biol Med 2019 Apr 8;108:142-149. Epub 2019 Apr 8.

Bone Biology Division, Garvan Institute of Medical Research, Darlinghurst, NSW, Australia; Discipline of Pathology, School of Medical Sciences, Faculty of Medicine and Health, The University of Sydney, Australia. Electronic address:

Background: The welding process releases potentially hazardous gases and fumes, mainly composed of metallic oxides, fluorides and silicates. Long term welding fume (WF) inhalation is a recognized health issue that carries a risk of developing chronic health problems, particularly respiratory system diseases (RSDs). Aside from general airway irritation, WF exposure may drive direct cellular responses in the respiratory system which increase risk of RSD, but these are not well understood. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.04.004DOI Listing
April 2019
2 Reads

Learn to segment single cells with deep distance estimator and deep cell detector.

Comput Biol Med 2019 Apr 8;108:133-141. Epub 2019 Apr 8.

Department of Computational and System Biology, University of Pittsburgh, Pittsburgh, PA, 15260, USA; UPMC-Hillman Cancer Center, University of Pittsburgh, Pittsburgh, 15232, PA, USA. Electronic address:

Single cell segmentation is a critical and challenging step in cell imaging analysis. Traditional processing methods require time and labor to manually fine-tune parameters and lack parameter transferability between different situations. Recently, deep convolutional neural networks (CNN) treat segmentation as a pixel-wise classification problem and have become a general and efficient method for image segmentation. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.04.006DOI Listing
April 2019
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Augmented and virtual reality in dental medicine: A systematic review.

Comput Biol Med 2019 Mar 15;108:93-100. Epub 2019 Mar 15.

Department of Reconstructive Dentistry, University Center for Dental Medicine Basel, University of Basel, Switzerland, Hebelstr. 3, CH-4056, Basel, Switzerland.

Background: The aim of this systematic review was to provide an update on the contemporary knowledge and scientific development of augmented reality (AR) and virtual reality (VR) in dental medicine, and to identify future research needs to accomplish its clinical translation.

Method: A modified PICO-strategy was performed using an electronic (MEDLINE, EMBASE, CENTRAL) plus manual search up to 12/2018 exploring AR/VR in dentistry in the last 5 years. Inclusion criteria were limited to human studies focusing on the clinical application of AR/VR and associated field of interest in dental medicine. Read More

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March 2019
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PSO optimized 1-D CNN-SVM architecture for real-time detection and classification applications.

Comput Biol Med 2019 Mar 24;108:85-92. Epub 2019 Mar 24.

School of Electronics Engineering, VIT University, Chennai Campus, India. Electronic address:

In this paper, we propose a novel Particle Swarm Optimized (PSO) One-Dimensional Convolutional Neural Network with Support Vector Machine (1-D CNN-SVM) architecture for real-time detection and classification of diseases. The performance of the proposed architecture is validated with a novel hardware model for detecting Chronic Kidney Disease (CKD) from saliva samples. For detecting CKD, the urea concentration in the saliva sample is monitored by converting it into ammonia. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.017DOI Listing
March 2019
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Bone and soft tissue changes associated with a removable partial denture. A novel method with a fusion of CBCT and optical 3D images.

Comput Biol Med 2019 Mar 28;108:78-84. Epub 2019 Mar 28.

Department of Endodontics and Operative Dentistry, Faculty of Medicine, University of Ljubljana, Slovenia; Department of Restorative Dentistry and Endodontics, University Medical Centre Ljubljana, Slovenia. Electronic address:

Background: The purpose of this study was to propose a novel method for 3D evaluation of bone and mucosal changes in removable partial denture (RPD) foundation area using a fusion of cone beam computed tomography (CBCT) and optical 3D images.

Method: Two CBCT scans and three impressions, taken at insertion and after ten months of wearing the RPD, were acquired from five patients. 3D models of bone and surface were created from CBCT images and gypsum casts, respectively, spatially aligned and saved in Standard Tessellation Language file format. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.024DOI Listing
March 2019
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Directional fast-marching and multi-model strategy to extract coronary artery centerlines.

Comput Biol Med 2019 Apr 5;108:67-77. Epub 2019 Apr 5.

School of Data Science, Fudan University, Shanghai, China. Electronic address:

Background: Computed tomography angiography (CTA) is a non-invasive technique to image coronary arteries and evaluate coronary artery diseases (CAD). The diagnosis of CAD requires modeling anatomical structures and analyzing the function and pathology of the coronary arteries. Therefore, a robust and automated method for extracting reliable coronary artery centerlines is valuable in clinical practice. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.029DOI Listing
April 2019
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Video-oculography eye tracking towards clinical applications: A review.

Comput Biol Med 2019 Mar 30;108:57-66. Epub 2019 Mar 30.

Research Institute for Signals, Systems and Computational Intelligence, Sinc(i), FICH-UNL/CONICET, Ruta Nac. No 168, Km 472.4 (3000), Santa Fe, Argentina.

Most neurological diseases are usually accompanied by a broad spectrum of oculomotor alterations. Being able to record and analyze these different types of eye movements would be a valuable tool to understand the functional integrity of brain structures. Nowadays, video-oculography is the most widely used eye-movements assessing method. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.025DOI Listing
March 2019
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DeepClas4Bio: Connecting bioimaging tools with deep learning frameworks for image classification.

Comput Biol Med 2019 Apr 6;108:49-56. Epub 2019 Apr 6.

Department of Mathematics and Computer Science of University of La Rioja, Spain. Electronic address:

Background And Objective: Deep learning techniques have been successfully applied to tackle several image classification problems in bioimaging. However, the models created from deep learning frameworks cannot be easily accessed from bioimaging tools such as ImageJ or Icy; this means that life scientists are not able to take advantage of the results obtained with those models from their usual tools. In this paper, we aim to facilitate the interoperability of bioimaging tools with deep learning frameworks. Read More

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April 2019
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Independent component analysis based algorithms for high-density electromyogram decomposition: Experimental evaluation of upper extremity muscles.

Comput Biol Med 2019 Mar 13;108:42-48. Epub 2019 Mar 13.

Joint Department of Biomedical Engineering, University of North Carolina at Chapel Hill, North Carolina State University, United States. Electronic address:

Motor unit firing activities can provide critical information regarding neural control of skeletal muscles. Extracting motor unit activities reliably from surface electromyogram (EMG) is still a challenge in signal processing. We quantified the performance of three different independent component analysis (ICA)-based decomposition algorithms (Infomax, FastICA and RobustICA) on high-density EMG signals, obtained from arm muscles (biceps brachii and extensor digitorum communis) at different contraction levels. Read More

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March 2019
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Design of porous titanium scaffold for complete mandibular reconstruction: The influence of pore architecture parameters.

Comput Biol Med 2019 Mar 12;108:31-41. Epub 2019 Mar 12.

Department of Mechanical Engineering, Indian Institute of Technology Kharagpur, Kharagpur, 721 302, West Bengal, India. Electronic address:

Patients having a medical history of oral cancer, infectious diseases or trauma are often advised surgical intervention with customized complete mandibular constructs (CMC) made of Titanium (Ti) scaffolds. A numerical framework based on a homogenization technique was developed to investigate the influence of pore architecture parameters on homogenized orthotropic material properties of the scaffolds. A comparative 3D Finite Element (FE) analysis of six CMC models, having homogenized orthotropic material properties, under a mastication cycle, was undertaken to pre-clinically determine the optimal CMC for a patient. Read More

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March 2019
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Automated detection of sleep apnea using sparse residual entropy features with various dictionaries extracted from heart rate and EDR signals.

Comput Biol Med 2019 Mar 26;108:20-30. Epub 2019 Mar 26.

Department of Electronic & Computer Engineering, Ngee Ann Polytechnic, Singapore; Department of Biomedical Engineering, School of Science and Technology, SIM University, Singapore; Department of Biomedical Imaging, Faculty of Medicine, University of Malaya, Kuala Lumpur, Malaysia.

Sleep is a prominent physiological activity in our daily life. Sleep apnea is the category of sleep disorder during which the breathing of the person diminishes causing the alternation in the upper airway resistance. The electrocardiogram derived respiration (EDR) and heart rate (RR-time-series) signals are normally used for the detection of sleep apnea as these two signals capture cardio-pulmonary activity information. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.016DOI Listing
March 2019
2 Reads

Document-level attention-based BiLSTM-CRF incorporating disease dictionary for disease named entity recognition.

Comput Biol Med 2019 Apr 7;108:122-132. Epub 2019 Apr 7.

Department of Computer Science, Guangdong University of Technology, Guangzhou, China. Electronic address:

Background: Disease named entity recognition (NER) plays an important role in biomedical research. There are a significant number of challenging issues to be addressed; among these, the identification of rare diseases and complex disease names and the problem of tagging inconsistency (i.e. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.04.002DOI Listing
April 2019
6 Reads

Development of an innovative technology to segment luminal borders of intravascular ultrasound image sequences in a fully automated manner.

Comput Biol Med 2019 Mar 14;108:111-121. Epub 2019 Mar 14.

Faculty of Medicine and Health Sciences, Macquarie University, Sydney, NSW, 2109, Australia; School of Exercise, Biomedical and Health Sciences, Edith Cowan University, Perth, Australia.

Although intravascular ultrasound (IVUS) is the commonest intravascular imaging modality, it still is inefficient for clinical use as it requires laborious manual analysis. This study demonstrates the feasibility of a near real-time fully automated technology for accurate identification, detection, and quantification of luminal borders in intravascular images. This technology uses a combination of the novel approaches of a self-tuning engine, dynamic and static masking systems, radar-wise scan, and contour correction cycle method. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.008DOI Listing
March 2019
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Symmetrical cruciate-retaining versus medial pivot prostheses: The effect of intercondylar sagittal conformity on knee kinematics and contact mechanics.

Comput Biol Med 2019 Mar 10;108:101-110. Epub 2019 Mar 10.

Department of Mechanical Engineering, School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan.

Background: A total knee arthroplasty should restore the mechanical function of the knee and enable patients to perform desired daily activities. The joint kinematics and contact mechanics performance are important determinants of the success of total knee arthroplasty devices. The purpose of this study was to determine the effect of intercondylar sagittal conformity on kinematics and contact mechanics. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.005DOI Listing

The trauma severity model: An ensemble machine learning approach to risk prediction.

Comput Biol Med 2019 Mar 6;108:9-19. Epub 2019 Mar 6.

Department of Surgery, University of Rochester Medical Center, Rochester, NY, 14642, USA.

Statistical theory indicates that a flexible model can attain a lower generalization error than an inflexible model, provided that the setting is appropriate. This is highly relevant for mortality risk prediction with trauma patients, as researchers have focused exclusively on the use of generalized linear models for trauma risk prediction, and generalized linear models may be too inflexible to capture the potentially complex relationships in trauma data. To improve trauma risk prediction, we propose a machine learning model, the Trauma Severity Model (TSM). Read More

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March 2019
6 Reads

Three-dimensional optical coherence tomography image denoising through multi-input fully-convolutional networks.

Comput Biol Med 2019 Jan 19;108:1-8. Epub 2019 Jan 19.

College of Computer Science, Sichuan University, Chengdu, China.

In recent years, there has been a growing interest in applying convolutional neural networks (CNNs) to low-level vision tasks such as denoising and super-resolution. Due to the coherent nature of the image formation process, the optical coherence tomography (OCT) images are inevitably affected by noise. This paper proposes a new method named the multi-input fully-convolutional networks (MIFCN) for denoising of OCT images. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.01.010DOI Listing
January 2019
1.240 Impact Factor

Effect of whole-body vibration and sitting configurations on lumbar spinal loads of vehicle occupants.

Comput Biol Med 2019 Apr 25;107:292-301. Epub 2019 Feb 25.

Department of Mechanical Engineering, Sharif University of Technology, Tehran, Iran. Electronic address:

Whole-body vibration (WBV) has been identified as one of the serious risk factors leading to spinal disorders, particularly in professional drivers. Although the influential factors in this area have been investigated epidemiologically, finite element (FE) modeling can efficiently help us better understand the problem. In this study, a modified HYBRID III dummy FE model which was enhanced by detailed viscoelastic discs in the lumbar region was utilized to simulate the effect of WBV on lumbar spine loads. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.019DOI Listing
April 2019
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A compact matrix model for atrial electrograms for tissue conductivity estimation.

Comput Biol Med 2019 Apr 21;107:284-291. Epub 2019 Feb 21.

Department of Cardiology, Erasmus University Medical Center, the Netherlands.

Finding the hidden parameters of the cardiac electrophysiological model would help to gain more insight on the mechanisms underlying atrial fibrillation, and subsequently, facilitate the diagnosis and treatment of the disease in later stages. In this work, we aim to estimate tissue conductivity from recorded electrograms as an indication of tissue (mal)functioning. To do so, we first develop a simple but effective forward model to replace the computationally intensive reaction-diffusion equations governing the electrical propagation in tissue. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.012DOI Listing
April 2019
6 Reads

Medical data quality assessment: On the development of an automated framework for medical data curation.

Comput Biol Med 2019 Apr 7;107:270-283. Epub 2019 Mar 7.

Unit of Medical Technology and Intelligent Information Systems, Department of Materials Science and Engineering, University of Ioannina, Ioannina, GR45110, Greece; Department of Biomedical Research, FORTH-IMBB, Ioannina, GR45110, Greece. Electronic address:

Data quality assessment has gained attention in the recent years since more and more companies and medical centers are highlighting the importance of an automated framework to effectively manage the quality of their big data. Data cleaning, also known as data curation, lies in the heart of the data quality assessment and is a key aspect prior to the development of any data analytics services. In this work, we present the objectives, functionalities and methodological advances of an automated framework for data curation from a medical perspective. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.03.001DOI Listing
April 2019
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Muscle fibre morphology and microarchitecture in cerebral palsy patients obtained by 3D synchrotron X-ray computed tomography.

Comput Biol Med 2019 Apr 14;107:265-269. Epub 2019 Feb 14.

Department of Neuroscience, University of Copenhagen, Denmark.

Background: Synchrotron X-ray computed tomography (SXCT) allows for three-dimensional imaging of objects at a very high resolution and in large field-of-view.

Purpose: The aim of this study was to use SXCT imaging for morphological analysis of muscle tissue, in order to investigate whether the analysis reveals complementary information to two-dimensional microscopy.

Methods: Three-dimensional SXCT images of muscle biopsies were taken from participants with cerebral palsy and from healthy controls. Read More

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April 2019
3 Reads

Mathematical modelling of bone remodelling cycles including the NFκB signalling pathway.

Comput Biol Med 2019 Apr 8;107:257-264. Epub 2019 Mar 8.

Department of Breast and Thyroid Surgery, Shandong Provincial Hospital Affiliated to Shandong University, Jinan, 250021, PR China. Electronic address:

RANKL can promote the differentiation of osteoclast precursors into mature osteoclasts by binding to RANK expressed on the surfaces of osteoclast progenitor cells during bone remodelling. The NF-κB signalling pathway is downstream of RANKL and transmits the RANKL signal to nuclear promoter-bound protein complexes from cell surface receptors, which then regulates target gene expression to facilitate osteoclastogenesis. However, this important role of the NF-κB signalling pathway is usually ignored in published mathematical models of bone remodelling. Read More

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Portable brain-computer interface based on novel convolutional neural network.

Comput Biol Med 2019 Apr 4;107:248-256. Epub 2019 Mar 4.

Department of Electronic Science and Engineering, Southeast University, Nanjing, 210096, China. Electronic address:

Electroencephalography (EEG) is a powerful, noninvasive tool that provides a high temporal resolution to directly reflect brain activities. Conventional electrodes require skin preparation and the use of conductive gels, while subjects must wear uncomfortable EEG hats. These procedures usually create a challenge for subjects. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.023DOI Listing
April 2019
9 Reads

Layout-aware information extraction from semi-structured medical images.

Comput Biol Med 2019 Apr 25;107:235-247. Epub 2019 Feb 25.

AstraZeneca China, 199 Liangjing Road, Shanghai, 201203, PR China.

Textual information embedded in the medical image contains rich structured information about the medical condition of a patient. This paper aims at extracting structured textual information from semi-structured medical images. Given the recognized text spans of an image preprocessed by optical character recognition (OCR), due to the spatial discontinuity of texts spans as well as potential errors brought by OCR, the structured information extraction becomes more challenging. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.016DOI Listing

ColocalizR: An open-source application for cell-based high-throughput colocalization analysis.

Comput Biol Med 2019 Apr 2;107:227-234. Epub 2019 Mar 2.

Université Paris Descartes, Sorbonne Paris Cité, Paris, France; Equipe 11 Labellisée Ligue Nationale Contre le Cancer, Centre de Recherche des Cordeliers, Paris, France; Institut National de la Santé et de la Recherche Médicale, U1138, Paris, France; Université Pierre et Marie Curie, Paris, France; Metabolomics and Cell Biology Platforms, Gustave Roussy Cancer Campus, Villejuif, France; Faculty of Medicine, University of Paris Sud, Kremlin-Bicêtre, France; Pôle de Biologie, Hôpital Européen Georges Pompidou, AP-HP, Paris, France; Department of Women's and Children's Health, Karolinska University Hospital, Stockholm, Sweden. Electronic address:

The microscopic assessment of the colocalization of fluorescent signals has been widely used in cell biology. Although imaging techniques have drastically improved over the past decades, the quantification of colocalization by measures such as the Pearson correlation coefficient or Manders overlap coefficient, has not changed. Here, we report the development of an R-based application that allows to (i) automatically segment cells and subcellular compartments, (ii) measure morphology and texture features, and (iii) calculate the degree of colocalization within each cell. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.024DOI Listing

Application of agent-based modelling to assess single-molecule transport across the cell envelope of E. coli.

Comput Biol Med 2019 Apr 2;107:218-226. Epub 2019 Mar 2.

LEPABE - Dep. of Chemical Engineering, Faculty of Engineering, University of Porto, Rua Dr. Roberto Frias, 4200-465, Porto, Portugal. Electronic address:

Motivation: Single cells often show stochastic behaviour and variations in the physiological state of individual cells affect the behaviour observed in cell populations. This may be partially explained by variations in the concentration and spatial location of molecules within and in the vicinity of each cell.

Methods: This paper introduces an agent-based model that represents single-molecule transport through the cellular envelope of Escherichia coli at the micrometre scale. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.020DOI Listing
April 2019
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An idealized geometry that mimics average nasal spray deposition in adults: A computational study.

Comput Biol Med 2019 Apr 26;107:206-217. Epub 2019 Feb 26.

Department of Mechanical Engineering, University of Alberta, Edmonton, Canada. Electronic address:

This work describes the development of an idealized geometry that mimics average regional deposition of nasal sprays within realistic adult nasal geometries. Previous simulation results in seven realistic nasal airways (Kiaee et al. Int. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.013DOI Listing
April 2019
1.240 Impact Factor

DEWE: A novel tool for executing differential expression RNA-Seq workflows in biomedical research.

Comput Biol Med 2019 Apr 27;107:197-205. Epub 2019 Feb 27.

ESEI: Escuela Superior de Ingeniería Informática, University of Vigo, Edificio Politécnico, Campus Universitario As Lagoas s/n, 32004, Ourense, Spain; CINBIO - Centro de Investigaciones Biomédicas, University of Vigo, Campus Universitario Lagoas-Marcosende, 36310, Vigo, Spain; SING Research Group, Galicia Sur Health Research Institute (IIS Galicia Sur), SERGAS-UVIGO, Hospital Álvaro Cunqueiro, 36312, Vigo, Spain; CEB - Centre of Biological Engineering, University of Minho, Campus de Gualtar, 4710-057, Braga, Portugal. Electronic address:

Background: Transcriptomics profiling aims to identify and quantify all transcripts present within a cell type or tissue at a particular state, and thus provide information on the genes expressed in specific experimental settings, differentiation or disease conditions. RNA-Seq technology is becoming the standard approach for such studies, but available analysis tools are often hard to install, configure and use by users without advanced bioinformatics skills.

Methods: Within reason, DEWE aims to make RNA-Seq analysis as easy for non-proficient users as for experienced bioinformaticians. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.021DOI Listing
April 2019
1 Read

Human stress classification using EEG signals in response to music tracks.

Comput Biol Med 2019 Apr 25;107:182-196. Epub 2019 Feb 25.

Department of Software Engineering, University of Engineering and Technology, Taxila, 47050, Pakistan.

Stress is inevitably experienced by almost every person at some stage of their life. A reliable and accurate measurement of stress can give an estimate of an individual's stress burden. It is necessary to take essential steps to relieve the burden and regain control for better health. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.015DOI Listing
April 2019
5 Reads

AMAP: Hierarchical multi-label prediction of biologically active and antimicrobial peptides.

Comput Biol Med 2019 Apr 25;107:172-181. Epub 2019 Feb 25.

Biomedical Informatics Research Laboratory, Department of Computer and Information Sciences (DCIS), Pakistan Institute of Engineering and Applied Sciences (PIEAS), Nilore, Islamabad, Pakistan. Electronic address:

Due to increase in antibiotic resistance in recent years, development of efficient and accurate techniques for discovery and design of biologically active peptides such as antimicrobial peptides (AMPs) has become essential. The screening of natural and synthetic AMPs in the wet lab is a challenge due to time and cost involved in such experiments. Bioinformatics methods can be used to speed up discovery and design of antimicrobial peptides by limiting the wet-lab search to promising peptide sequences. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00104825193006
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http://dx.doi.org/10.1016/j.compbiomed.2019.02.018DOI Listing
April 2019
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Understanding the structure-function relationship of HPRT1 missense mutations in association with Lesch-Nyhan disease and HPRT1-related gout by in silico mutational analysis.

Comput Biol Med 2019 Apr 23;107:161-171. Epub 2019 Feb 23.

Department of Biomedical Sciences, College of Health and Sciences, Qatar University, Doha, Qatar. Electronic address:

The nucleotide salvage pathway is used to recycle degraded nucleotides (purines and pyrimidines); one of the enzymes that helps to recycle purines is hypoxanthine guanine phosphoribosyl transferase 1 (HGPRT1). Therefore, defects in this enzyme lead to the accumulation of DNA and nucleotide lesions and hence replication errors and genetic disorders. Missense mutations in hypoxanthine phosphoribosyl transferase 1 (HPRT1) are associated with deficiencies such as Lesch-Nyhan disease and chronic gout, which have manifestations such as arthritis, neurodegeneration, and cognitive disorders. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.014DOI Listing
April 2019
3 Reads
1.240 Impact Factor

Application of adaptive-network-based fuzzy inference systems to the parameter optimization of a biochemical rule-based model.

Authors:
Brittany R Hoard

Comput Biol Med 2019 Apr 14;107:153-160. Epub 2019 Feb 14.

University of New Mexico, 1 University of New Mexico, Albuquerque, NM, 87131, United States. Electronic address:

In this study, the binding of allergens to antibody-receptor complexes was investigated. This process is important in understanding the allergic response. A BioNetGen model that simulates this process, combined with a novel method for encoding steric effects via the optimization of the cutoff distance and the rule binding rate, was previously developed. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.01.021DOI Listing
April 2019
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Outcome prediction with serial neuron-specific enolase and machine learning in anoxic-ischaemic disorders of consciousness.

Comput Biol Med 2019 Apr 16;107:145-152. Epub 2019 Feb 16.

Department of Neurology, Therapiezentrum Burgau, Burgau, Germany.

Background: The continuation of life-sustaining therapy in critical care patients with anoxic-ischemic disorders of consciousness (AI-DOC) depends on prognostic tests such as serum neuron-specific enolase (NSE) concentration levels.

Objectives: To apply predictive models using machine learning methods to examine, one year after onset, the prognostic power of serial measurements of NSE in patients with AI-DOC. To compare the discriminative accuracy of this method to both standard single-day, absolute, and difference-between-days, relative NSE levels. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.006DOI Listing
April 2019
2 Reads

Spatially guided functional correlation tensor: A new method to associate body mass index and white matter neuroimaging.

Comput Biol Med 2019 Apr 19;107:137-144. Epub 2019 Feb 19.

Center for Neuroscience Imaging Research, Institute for Basic Science, Suwon, South Korea; School of Electronic and Electrical Engineering, Sungkyunkwan University, Suwon, South Korea. Electronic address:

Obesity causes critical health problems including cardiovascular disease, diabetes, and stroke. Various neuroimaging methods including diffusion tensor imaging (DTI) are used to explore white matter (WM) alterations in obesity. The functional correlation tensor (FCT) is a method to simulate DTI in WM using resting-state functional magnetic resonance imaging (rs-fMRI). Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.010DOI Listing

Heat Strain Decision Aid (HSDA) accurately predicts individual-based core body temperature rise while wearing chemical protective clothing.

Comput Biol Med 2019 Apr 16;107:131-136. Epub 2019 Feb 16.

Biophysics and Biomedical Modeling Division, U.S. Army Research Institute of Environmental Medicine, 10 General Greene Avenue, Bldg 42, Natick, MA 01760, USA. Electronic address:

Purpose: We examined the accuracy of the Heat Strain Decision Aid (HSDA) as a predictor of core body temperature in healthy individuals wearing chemical protective clothing during laboratory and field exercises in hot and humid conditions.

Methods: The laboratory experiment examined three chemical protective clothing ensembles in eight male volunteers (age 24 ± 6 years; height 178 ± 5 cm; body mass 76.6 ± 8. Read More

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https://linkinghub.elsevier.com/retrieve/pii/S00104825193005
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http://dx.doi.org/10.1016/j.compbiomed.2019.02.004DOI Listing
April 2019
6 Reads

AntiVPP 1.0: A portable tool for prediction of antiviral peptides.

Comput Biol Med 2019 Apr 19;107:127-130. Epub 2019 Feb 19.

Universidad de La Frontera, Department of Chemical Engineering, Faculty of Engineering and Science, Temuco, Chile. Electronic address:

Viruses are worldwide pathogens with a high impact on the human population. Despite the constant efforts to fight viral infections, there is a need to discover and design new drug candidates. Antiviral peptides are molecules with confirmed activity and constitute excellent alternatives for the treatment of viral infections. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.011DOI Listing
April 2019
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Feature selection using regularized neighbourhood component analysis to enhance the classification performance of motor imagery signals.

Comput Biol Med 2019 Apr 19;107:118-126. Epub 2019 Feb 19.

School of Biomedical Engineering, Indian Institute of Technology, Banaras Hindu University, Varanasi, India. Electronic address:

In motor imagery (MI) based brain-computer interface (BCI) signal analysis, mu and beta rhythms of electroencephalograms (EEGs) are widely investigated due to their high temporal resolution and capability to define the different movement-related mental tasks separately. However, due to the high dimensions and subject-specific behaviour of EEG features, there is a need for a suitable feature selection algorithm that can select the optimal features to give the best classification performance along with increased computational efficiency. The present study proposes a feature selection algorithm based on neighbourhood component analysis (NCA) with modification of the regularization parameter. Read More

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http://dx.doi.org/10.1016/j.compbiomed.2019.02.009DOI Listing
April 2019
1 Read
1.240 Impact Factor