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Computers in Biology and Medicine

Naghmeh Mahmoodian, Anna Schaufler, Ali Pashazadeh, Axel Boese, Michael Friebe, Alfredo Illanes
Artery perforation during a vascular catheterization procedure is a potentially life threatening event. It is of particular importance for the surgeons to be aware of hidden or non-obvious events. To minimize the impact it is crucial for the surgeon to detect such a perforation very early. We propose a novel approach to identify perforations based on the acquisition and analysis of audio signals on the outside proximal end of a guide wire. The signals were acquired using a stethoscope equipped with a microphone and attached to the proximal end of the guide wire via a 3D printed adapter...
February 7, 2019: Computers in Biology and Medicine
Yiran Huang, Cheng Zhong
In this work, we study the list-colored graph motif problem, which was introduced to detect functional motifs in biological networks. Given a multi-set M of colors as the query motif and a list-colored graph G where each vertex in G is associated with a set of colors, the aim of this problem is to find a sub-graph of G whose vertex set is colored exactly as motif M. To solve this problem, we present a heuristic method to efficiently and accurately detect list-colored graph motifs in biological networks using branch-and-bound strategy...
February 2, 2019: Computers in Biology and Medicine
Stefan Pszczolkowski, Zhe K Law, Rebecca G Gallagher, Dewen Meng, David J Swienton, Paul S Morgan, Philip M Bath, Nikola Sprigg, Rob A Dineen
BACKGROUND: Spontaneous intracerebral haemorrhage (SICH) is a common condition with high morbidity and mortality. Segmentation of haematoma and perihaematoma oedema on medical images provides quantitative outcome measures for clinical trials and may provide important markers of prognosis in people with SICH. METHODS: We take advantage of improved contrast seen on magnetic resonance (MR) images of patients with acute and early subacute SICH and introduce an automated algorithm for haematoma and oedema segmentation from these images...
January 29, 2019: Computers in Biology and Medicine
Otilio Paulo da Silva Neto, José Denes Lima Araújo, Ana Gabriela Caldas Oliveira, Mara Cutrim, Aristófanes Corrêa Silva, Anselmo Cardoso Paiva, Marcelo Gattass
BACKGROUND: We propose a computational methodology capable of detecting and analyzing breast tumor habitats in images acquired by magnetic resonance imaging with dynamic contrast enhancement (DCE-MRI), based on the pathophysiological behavior of the contrast agent (CA). METHODS: The proposed methodology comprises three steps. In summary, the first step is the acquisition of images from the Quantitative Imaging Network Breast. In the second step, the segmentation of the breasts is performed to remove the background, noise, and other unwanted objects from the image...
January 26, 2019: Computers in Biology and Medicine
Chongyang Ye, Shahid Ali, Qing Sun, Mengmeng Guo, Yixuan Liu, Yan Gao, Bo Huo
Fluid flow in blood vessels or interstitial fluid flow within tissue cavities plays important roles in tissue regeneration. One of the fundamental issues for in vitro study of the effects of fluid shear stress (FSS) on cells is the development of a flow chamber that can provide a controlled FSS field. In this study, we developed a novel cone-and-plate flow chamber based on viscometry technology, in which the cone's shape was optimized to produce a uniform wall FSS field on the surface of a standard six-well cell culture plate...
January 25, 2019: Computers in Biology and Medicine
Kung-Jeng Wang, Jyun-Lin Chen, Kung-Min Wang
Lung cancer is one of the leading causes of mortality, and its medical expenditure has increased dramatically. Estimating the expenditure for this disease has become an urgent concern of the supporting families, medial institutes, and government. In this study, a conditional Gaussian Bayesian network (CGBN) model was developed to incorporate the comprehensive risk factors to estimate the medical expenditure of a lung cancer patient at different stages. A total of 961 patients were surveyed by the four severity stages of lung cancer...
January 24, 2019: Computers in Biology and Medicine
Bogdan Iancu, Usman Sanwal, Cristian Gratie, Ion Petre
The construction of large scale biological models is a laborious task, which is often addressed by adopting iterative routines for model augmentation, adding certain details to an initial high level abstraction of the biological phenomenon of interest. Refitting a model at every step of its development is time consuming and computationally intensive. The concept of model refinement brings about an effective alternative by providing adequate parameter values that ensure the preservation of its quantitative fit at every refinement step...
January 24, 2019: Computers in Biology and Medicine
Minoo Modaresnezhad, Ali Vahdati, Hamid Nemati, Ali Ardestani, Fereidoon Sadri
Utilization of existing clinical data for improving patient outcomes poses a number of challenging and complex problems involving lack of data integration, the absence of standardization across inhomogeneous data sources and computationally-demanding and time-consuming exploration of very large datasets. In this paper, we will present a robust semantic data integration, standardization and dimensionality reduction method to tackle and solve these problems. Our approach enables the integration of clinical data from diverse sources by resolving canonical inconsistencies and semantic heterogeneity as required by the National Library of Medicine's Unified Medical Language System (UMLS) to produce standardized medical data...
January 23, 2019: Computers in Biology and Medicine
Bahareh Kashani, Mansoor Hasani Bidgoli, Seyed Abolfazl Motahari, Nafiseh Sedaghat, Mohammad Hossein Modarressi
BACKGROUND: Nutrigenomic has revolutionized our understanding of nutrition. As plants make up a noticeable part of our diet, in the present study we chose microRNAs of edible plants and investigated if they can perfectly match human genes, indicating potential regulatory functionalities. METHODS: miRNAs were obtained using the PNRD database. Edible plants were separated and microRNAs in common in at least four of them entered our analysis. Using vmatchPattern, these 64 miRNAs went through four steps of refinement to improve target prediction: Alignment with the whole genome (2581 results), filtered for those in gene regions (1371 results), filtered for exon regions (66 results) and finally alignment with the human CDS (41 results)...
January 23, 2019: Computers in Biology and Medicine
Nicola Michielli, U Rajendra Acharya, Filippo Molinari
Automated evaluation of a subject's neurocognitive performance (NCP) is a relevant topic in neurological and clinical studies. NCP represents the mental/cognitive human capacity in performing a specific task. It is difficult to develop the study protocols as the subject's NCP changes in a known predictable way. Sleep is time-varying NCP and can be used to develop novel NCP techniques. Accurate analysis and interpretation of human sleep electroencephalographic (EEG) signals is needed for proper NCP assessment...
January 19, 2019: Computers in Biology and Medicine
Khalid M Saqr
No abstract text is available yet for this article.
January 18, 2019: Computers in Biology and Medicine
Boyang Su, Xikun Wang, Foad Kabinejadian, Calvin Chin, Thu Thao Le, Jun-Mei Zhang
With the aid of cardiac imaging techniques, recent numerical simulations of left ventricular flow can be patient-specific to better mimic physiological conditions. However, studies with a dynamic mitral valve (MV) remain extremely limited. Even so, the left atrium (LA) is usually simplified to be tubular regardless of its complex structure. Studies on the effect of this simplification are limited and observations are controversial. In this study, both tubular and generic atriums were incorporated in patient-specific simulations with and without the MV to qualitatively and quantitatively estimate the effects of the atrial model on downstream ventricular flow...
January 17, 2019: Computers in Biology and Medicine
Sayada Reemsha Kazmi, Ren Jun, Myeong-Sang Yu, Chanjin Jung, Dokyun Na
The fate of administered drugs is largely influenced by their metabolism. For example, endogenous enzyme-catalyzed conversion of drugs may result in therapeutic inactivation or activation or may transform the drugs into toxic chemical compounds. This highlights the importance of drug metabolism in drug discovery and development, and accounts for the wide variety of experimental technologies that provide insights into the fate of drugs. In view of the high cost of traditional drug development, a number of computational approaches have been developed for predicting the metabolic fate of drug candidates, allowing for screening of large numbers of chemical compounds and then identifying a small number of promising candidates...
January 16, 2019: Computers in Biology and Medicine
Yanxin Zhang, Ye Ma
Gait classification has been widely used for children with cerebral palsy (CP) to assist with clinical decision making and to evaluate different treatment outcomes. The aim of this study was to evaluate supervised machine learning algorithms in the classification of sagittal gait patterns for CP children with spastic diplegia. Gait parameters were extracted from gait data obtained from two hundred children with spastic diplegia CP, and were used to represent the key kinematic features of each individual's gait...
January 16, 2019: Computers in Biology and Medicine
Udaysankar Chockanathan, Adora M DSouza, Anas Z Abidin, Giovanni Schifitto, Axel Wismüller
HIV-associated neurocognitive disorders (HAND) represent an important source of neurologic complications in individuals with HIV. The dynamic, often subclinical, course of HAND has rendered diagnosis, which currently depends on neuropsychometric (NP) evaluation, a challenge for clinicians. Here, we present evidence that functional brain connectivity, derived by large-scale Granger causality (lsGC) analysis of resting-state functional MRI (rs-fMRI) time-series, represents a potential biomarker to address this critical diagnostic need...
January 15, 2019: Computers in Biology and Medicine
Jie Liu, Sheng Li, Faezeh Jahanmiri-Nezhad, William Zev Rymer, Ping Zhou
With the aim of developing a flexible and reliable procedure for superficial muscle innervation zone (IZ) localization, we proposed a method to estimate IZ location using surface electromyogram (EMG) based on robust linear regression. Regression lines were used to model the bidirectional propagation pattern of a single motor unit action potential (MUAP) and visualize the trajectory of the MUAP propagation. IZ localization was performed by identifying the origin of the bidirectional MUAP propagation. Robust linear regression and MUAP peak detection, combined with propagation phase reversal identification, may provide an efficient way to estimate IZ location...
January 14, 2019: Computers in Biology and Medicine
Ean H Ooi, Khiy W Lee, Shelley Yap, Mahmoud A Khattab, Iman Y Liao, Ean T Ooi, Ji J Foo, Shalini R Nair, Ahmad F Mohd Ali
Effects of different boundary conditions prescribed across the boundaries of radiofrequency ablation (RFA) models of liver cancer are investigated for the case where the tumour is at the liver boundary. Ground and Robin-type conditions (electrical field) and body temperature and thermal insulation (thermal field) conditions are examined. 3D models of the human liver based on publicly-available CT images of the liver are developed. An artificial tumour is placed inside the liver at the boundary. Simulations are carried out using the finite element method...
January 11, 2019: Computers in Biology and Medicine
Olufemi Emmanuel Kadri, Vishnu Deep Chandran, Migle Surblyte, Roman S Voronov
Ischemia which leads to heart attacks and strokes is one of the major causes of death in the world. Whether an occlusion occurs or not depends on the ability of a growing thrombus to resist flow forces exerted on its structure. This manuscript provides the first known in vivo measurement of how much stress a clot can withstand, before yielding to the surrounding blood flow. Namely, Lattice-Boltzmann Method flow simulations are performed based on 3D clot geometries, which are estimated from intravital microscopy images of laser-induced injuries in cremaster microvasculature of live mice...
January 11, 2019: Computers in Biology and Medicine
Andrew Chen, Jessele Vinluan, Claudia Retegan, Philip McCahy
OBJECTIVE: The Victorian Audit of Surgical Mortality (VASM) is part of the Australian and New Zealand Audit of Surgical Mortality, aiming to identify factors associated with surgical mortality. A quality assurance method was utilised to rectify system issues through error rate checks of VASM data points. This method ensured data collected and entered in the audit database were accurate. METHOD: Clinical data was collected using case record forms (CRFs), entered from paper forms by VASM staff or by the surgeon into an online interface...
January 8, 2019: Computers in Biology and Medicine
Narendra N Khanna, Ankush D Jamthikar, Deep Gupta, Andrew Nicolaides, Tadashi Araki, Luca Saba, Elisa Cuadrado-Godia, Aditya Sharma, Tomaz Omerzu, Harman S Suri, Ajay Gupta, Sophie Mavrogeni, Monika Turk, John R Laird, Athanasios Protogerou, Petros P Sfikakis, George D Kitas, Vijay Viswanathan, Jasjit S Suri
MOTIVATION: AtheroEdge Composite Risk Score (AECRS1.010yr ) is an integrated stroke/cardiovascular risk calculator that was recently developed and computes the 10-year risk of carotid image phenotypes by integrating conventional cardiovascular risk factors (CCVRFs). It is therefore important to understand how closely AECRS1.010yr is associated with the ten other currently available conventional cardiovascular risk calculators (CCVRCs). METHODS: The Institutional Review Board of Toho University approved the examination of the left/right common carotid arteries of 202 Japanese patients...
January 8, 2019: Computers in Biology and Medicine
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