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Biomedical Engineering and Computational Biology

David Tes, Ahmed Aber, Mohsin Zafar, Luke Horton, Audrey Fotouhi, Qiuyun Xu, Ali Moiin, Andrew D Thompson, Tatiana Cristina Moraes Pinto Blumetti, Steven Daveluy, Wei Chen, Mohammadreza Nasiriavanaki
Background: Granular cell tumor (GCT) is a relatively uncommon tumor that may affect the skin. The tumor can develop anywhere on the body, although it is predominately seen in oral cavities and in the head and neck regions. Here, we present the results of optical coherence tomography (OCT) imaging of a large GCT located on the abdomen of a patient. We also present an analytical method to differentiate between healthy tissue and GCT tissues. Materials and methods: A multibeam, Fourier domain, swept source OCT was used for imaging...
2018: Biomedical Engineering and Computational Biology
Elsje Pienaar
Rare events such as genetic mutations or cell-cell interactions are important contributors to dynamics in complex biological systems, eg, in drug-resistant infections. Computational approaches can help analyze rare events that are difficult to study experimentally. However, analyzing the frequency and dynamics of rare events in computational models can also be challenging due to high computational resource demands, especially for high-fidelity stochastic computational models. To facilitate analysis of rare events in complex biological systems, we present a multifidelity analysis approach that uses medium-fidelity analysis (Monte Carlo simulations) and/or low-fidelity analysis (Markov chain models) to analyze high-fidelity stochastic model results...
2018: Biomedical Engineering and Computational Biology
David Tes, Karl Kratkiewicz, Ahmed Aber, Luke Horton, Mohsin Zafar, Nour Arafat, Afreen Fatima, Mohammad Rn Avanaki
Alzheimer disease is the most common form of dementia, affecting more than 5 million people in the United States. During the progression of Alzheimer disease, a particular protein begins to accumulate in the brain and also in extensions of the brain, ie, the retina. This protein, amyloid-β (Aβ), exhibits fluorescent properties. The purpose of this research article is to explore the implications of designing a fluorescent imaging system able to detect Aβ proteins in the retina. We designed and implemented a fluorescent imaging system with a range of applications that can be reconfigured on a fluorophore to fluorophore basis and tested its feasibility and capabilities using Cy5 and CRANAD-2 imaging probes...
2018: Biomedical Engineering and Computational Biology
Camden Cheek, Huiyong Zheng, Brian R Hallstrom, Richard E Hughes
Improving the quality of care for hip arthroplasty (replacement) patients requires the systematic evaluation of clinical performance of implants and the identification of "outlier" devices that have an especially high risk of reoperation ("revision"). Postmarket surveillance of arthroplasty implants, which rests on the analysis of large patient registries, has been effective in identifying outlier implants such as the ASR metal-on-metal hip resurfacing device that was recalled. Although identifying an implant as an outlier implies a causal relationship between the implant and revision risk, traditional signal detection methods use classical biostatistical methods...
2018: Biomedical Engineering and Computational Biology
Glen Atlas, John K-J Li, Shawn Amin, Robert G Hahn
A closed-form integro-differential equation (IDE) model of plasma dilution (PD) has been derived which represents both the intravenous (IV) infusion of crystalloid and the postinfusion period. Specifically, PD is mathematically represented using a combination of constant ratio, differential, and integral components. Furthermore, this model has successfully been applied to preexisting data, from a prior human study, in which crystalloid was infused for a period of 30 minutes at the beginning of thyroid surgery...
2017: Biomedical Engineering and Computational Biology
Yohannes Nigatie
Nowadays, kidney failure is a problem of many peoples in the world. We know that the main function of kidney is maintaining the chemical quality of blood particularly removing urea through urine. But when they malfunction, the pathologic state known as uremia results in a condition in which the urea is retained in the body. Failure of the kidney results in building up of harmful wastes and excess fluids in the body. Kidney diseases (failures) can be due to infections, high blood pressure (hypertension), diabetes, and/or extensive use of medication...
2017: Biomedical Engineering and Computational Biology
Saba Adabi, Zahra Turani, Emad Fatemizadeh, Anne Clayton, Mohammadreza Nasiriavanaki
Optical coherence tomography (OCT) delivers 3-dimensional images of tissue microstructures. Although OCT imaging offers a promising high-resolution method, OCT images experience some artifacts that lead to misapprehension of tissue structures. Speckle, intensity decay, and blurring are 3 major artifacts in OCT images. Speckle is due to the low coherent light source used in the configuration of OCT. Intensity decay is a deterioration of light with respect to depth, and blurring is the consequence of deficiencies of optical components...
2017: Biomedical Engineering and Computational Biology
Kavita Ganesan, Shane Lloyd, Vikren Sarkar
The ability to find highly related clinical concepts is essential for many applications such as for hypothesis generation, query expansion for medical literature search, search results filtering, ICD-10 code filtering and many other applications. While manually constructed medical terminologies such as SNOMED CT can surface certain related concepts, these terminologies are inadequate as they depend on expertise of several subject matter experts making the terminology curation process open to geographic and language bias...
2016: Biomedical Engineering and Computational Biology
Han Li, Kexin Lin, Danial Shahmirzadi
This study aims to quantify the effects of geometry and stiffness of aneurysms on the pulse wave velocity (PWV) and propagation in fluid-solid interaction (FSI) simulations of arterial pulsatile flow. Spatiotemporal maps of both the wall displacement and fluid velocity were generated in order to obtain the pulse wave propagation through fluid and solid media, and to examine the interactions between the two waves. The results indicate that the presence of abdominal aortic aneurysm (AAA) sac and variations in the sac modulus affect the propagation of the pulse waves both qualitatively (eg, patterns of change of forward and reflective waves) and quantitatively (eg, decreasing of PWV within the sac and its increase beyond the sac as the sac stiffness increases)...
2016: Biomedical Engineering and Computational Biology
Elie Zakhem, Sean V Murphy, Matthew L Davis, Shreya Raghavan, Mai T Lam
No abstract text is available yet for this article.
2016: Biomedical Engineering and Computational Biology
Etai Sapoznik, Guoguang Niu, Yu Zhou, Sean V Murphy, Shay Soker
Fluorescent protein imaging, a promising tool in biological research, incorporates numerous applications that can be of specific use in the field of regenerative medicine. To enhance tissue regeneration efforts, scientists have been developing new ways to monitor tissue development and maturation in vitro and in vivo. To that end, new imaging tools and novel fluorescent proteins have been developed for the purpose of performing deep-tissue high-resolution imaging. These new methods, such as intra-vital microscopy and Förster resonance energy transfer, are providing new insights into cellular behavior, including cell migration, morphology, and phenotypic changes in a dynamic environment...
2016: Biomedical Engineering and Computational Biology
Anna L Buczak, Benjamin Baugher, Erhan Guven, Linda Moniz, Steven M Babin, Jean-Paul Chretien
Influenza is a highly contagious disease that causes seasonal epidemics with significant morbidity and mortality. The ability to predict influenza peak several weeks in advance would allow for timely preventive public health planning and interventions to be used to mitigate these outbreaks. Because influenza may also impact the operational readiness of active duty personnel, the US military places a high priority on surveillance and preparedness for seasonal outbreaks. A method for creating models for predicting peak influenza visits per total health-care visits (ie, activity) weeks in advance has been developed using advanced data mining techniques on disparate epidemiological and environmental data...
2016: Biomedical Engineering and Computational Biology
Dipasri Konar, Mahesh Devarasetty, Didem V Yildiz, Anthony Atala, Sean V Murphy
Animal and two-dimensional cell culture models have had a profound impact on not only lung research but also medical research at large, despite inherent flaws and differences when compared with in vivo and clinical observations. Three-dimensional (3D) tissue models are a natural progression and extension of existing techniques that seek to plug the gaps and mitigate the drawbacks of two-dimensional and animal technologies. In this review, we describe the transition of historic models to contemporary 3D cell and organoid models, the varieties of current 3D cell and tissue culture modalities, the common methods for imaging these models, and finally, the applications of these models and imaging techniques to lung research...
2016: Biomedical Engineering and Computational Biology
Saurabh Chaubey, Shikha J Goodwin
Multiple sclerosis is a disease caused by demyelination of nerve fibers. In order to determine the loss of signal with the percentage of demyelination, we need to develop models that can simulate this effect. Existing time-based models does not provide a method to determine the influences of demyelination based on simulation results. Our goal is to develop a system identification approach to generate a transfer function in the frequency domain. The idea is to create a unified modeling approach for neural action potential propagation along the length of an axon containing number of Nodes of Ranvier (N)...
2016: Biomedical Engineering and Computational Biology
Abolfazl Razi, Fatemeh Afghah, Salendra Singh, Vinay Varadan
Identifying subsets of genes that jointly mediate cancer etiology, progression, or therapy response remains a challenging problem due to the complexity and heterogeneity in cancer biology, a problem further exacerbated by the relatively small number of cancer samples profiled as compared with the sheer number of potential molecular factors involved. Pure data-driven methods that merely rely on multiomics data have been successful in discovering potentially functional genes but suffer from high false-positive rates and tend to report subsets of genes whose biological interrelationships are unclear...
2016: Biomedical Engineering and Computational Biology
Saradwata Sarkar, Sudipta Das
Imaging is playing an increasingly important role in the detection of prostate cancer (PCa). This review summarizes the key imaging modalities-multiparametric ultrasound (US), multiparametric magnetic resonance imaging (MRI), MRI-US fusion imaging, and positron emission tomography (PET) imaging-used in the diagnosis and localization of PCa. Emphasis is laid on the biological and functional characteristics of tumors that rationalize the use of a specific imaging technique. Changes to anatomical architecture of tissue can be detected by anatomical grayscale US and T2-weighted MRI...
2016: Biomedical Engineering and Computational Biology
Abraham Pouliakis, Efrossyni Karakitsou, Niki Margari, Panagiotis Bountris, Maria Haritou, John Panayiotides, Dimitrios Koutsouris, Petros Karakitsos
OBJECTIVE: This study aims to analyze the role of artificial neural networks (ANNs) in cytopathology. More specifically, it aims to highlight the importance of employing ANNs in existing and future applications and in identifying unexplored or poorly explored research topics. STUDY DESIGN: A systematic search was conducted in scientific databases for articles related to cytopathology and ANNs with respect to anatomical places of the human body where cytopathology is performed...
2016: Biomedical Engineering and Computational Biology
Khalil N Bitar, Elie Zakhem
There are numerous available biodegradable materials that can be used as scaffolds in regenerative medicine. Currently, there is a huge emphasis on the designing phase of the scaffolds. Materials can be designed to have different properties in order to match the specific application. Modifying scaffolds enhances their bioactivity and improves the regeneration capacity. Modifications of the scaffolds can be later characterized using several tissue engineering tools. In addition to the material, cell source is an important component of the regeneration process...
2014: Biomedical Engineering and Computational Biology
Bernadette McCrory, Chad A LaGrange, Ms Hallbeck
Adverse events because of medical errors are a leading cause of death in the United States (US) exceeding the mortality rates of motor vehicle accidents, breast cancer, and AIDS. Improvements can and should be made to reduce the rates of preventable surgical errors because they account for nearly half of all adverse events within hospitals. Although minimally invasive surgery (MIS) has proven patient benefits such as reduced postoperative pain and hospital stay, its operative environment imposes substantial physical and cognitive strain on the surgeon increasing the risk of error...
2014: Biomedical Engineering and Computational Biology
John N Maina, Sikiru A Jimoh
Complete blood-gas barrier breaks (BGBBs) and epithelial-epithelial cells connections breaks (E-ECCBs) were enumerated in the lungs of free range chickens, Gallus gallus variant domesticus after vascular perfusion at different pressures. The E-ECCBs surpassed the BGBBs by a factor of ~2. This showed that the former parts of the gas exchange tissue were structurally weaker or more vulnerable to failure than the latter. The differences in the numbers of BGBBs and E-ECCBs in the different regions of the lung supplied with blood by the 4 main branches of the pulmonary artery (PA) corresponded with the diameters of the blood vessels, the angles at which they bifurcated from the PA, and the positions along the PA where they branched off...
2013: Biomedical Engineering and Computational Biology
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