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Full-Text Articles in Biomedical Engineering and Bioengineering

Tracing Actin Filament Bundles In Three-Dimensional Electron Tomography Density Maps Of Hair Cell Stereocilia, Salim Sazzed, Junha Song, Julio Kovacs, Willi Wriggers, Manfred Auer, Jing He Apr 2018

Tracing Actin Filament Bundles In Three-Dimensional Electron Tomography Density Maps Of Hair Cell Stereocilia, Salim Sazzed, Junha Song, Julio Kovacs, Willi Wriggers, Manfred Auer, Jing He

Computer Science Faculty Publications

Cryo-electron tomography (cryo-ET) is a powerful method of visualizing the three-dimensional organization of supramolecular complexes, such as the cytoskeleton, in their native cell and tissue contexts. Due to its minimal electron dose and reconstruction artifacts arising from the missing wedge during data collection, cryo-ET typically results in noisy density maps that display anisotropic XY versus Z resolution. Molecular crowding further exacerbates the challenge of automatically detecting supramolecular complexes, such as the actin bundle in hair cell stereocilia. Stereocilia are pivotal to the mechanoelectrical transduction process in inner ear sensory epithelial hair cells. Given the complexity and dense arrangement of actin ...


Computational Modeling For Abnormal Brain Tissue Segmentation, Brain Tumor Tracking, And Grading, Syed Mohammad Shamin Reza Oct 2017

Computational Modeling For Abnormal Brain Tissue Segmentation, Brain Tumor Tracking, And Grading, Syed Mohammad Shamin Reza

Electrical & Computer Engineering Theses & Disssertations

This dissertation proposes novel texture feature-based computational models for quantitative analysis of abnormal tissues in two neurological disorders: brain tumor and stroke. Brain tumors are the cells with uncontrolled growth in the brain tissues and one of the major causes of death due to cancer. On the other hand, brain strokes occur due to the sudden interruption of the blood supply which damages the normal brain tissues and frequently causes death or persistent disability. Clinical management of these brain tumors and stroke lesions critically depends on robust quantitative analysis using different imaging modalities including Magnetic Resonance (MR) and Digital Pathology ...


Multi-Material Mesh Representation Of Anatomical Structures For Deep Brain Stimulation Planning, Tanweer Rashid Jul 2017

Multi-Material Mesh Representation Of Anatomical Structures For Deep Brain Stimulation Planning, Tanweer Rashid

Computational Modeling and Simulation Engineering Theses & Dissertations

The Dual Contouring algorithm (DC) is a grid-based process used to generate surface meshes from volumetric data. However, DC is unable to guarantee 2-manifold and watertight meshes due to the fact that it produces only one vertex for each grid cube. We present a modified Dual Contouring algorithm that is capable of overcoming this limitation. The proposed method decomposes an ambiguous grid cube into a set of tetrahedral cells and uses novel polygon generation rules that produce 2-manifold and watertight surface meshes with good-quality triangles. These meshes, being watertight and 2-manifold, are geometrically correct, and therefore can be used to ...


Low Temperature Plasma For The Treatment Of Epithelial Cancer Cells, Soheila Mohades Apr 2017

Low Temperature Plasma For The Treatment Of Epithelial Cancer Cells, Soheila Mohades

Electrical & Computer Engineering Theses & Disssertations

Biomedical applications of low temperature plasmas (LTP) may lead to a paradigm shift in treating various diseases by conducting fundamental research on the effects of LTP on cells, tissues, organisms (plants, insects, and microorganisms). This is a rapidly growing interdisciplinary research field that involves engineering, physics, life sciences, and chemistry to find novel solutions for urgent medical needs. Effects of different LTP sources have shown the anti-tumor properties of plasma exposure; however, there are still many unknowns about the interaction of plasma with eukaryotic cells which must be elucidated in order to evaluate the practical potential of plasma in cancer ...


Machine Learning Methods For Medical And Biological Image Computing, Rongjian Li Jul 2016

Machine Learning Methods For Medical And Biological Image Computing, Rongjian Li

Computer Science Theses & Dissertations

Medical and biological imaging technologies provide valuable visualization information of structure and function for an organ from the level of individual molecules to the whole object. Brain is the most complex organ in body, and it increasingly attracts intense research attentions with the rapid development of medical and bio-logical imaging technologies. A massive amount of high-dimensional brain imaging data being generated makes the design of computational methods for efficient analysis on those images highly demanded. The current study of computational methods using hand-crafted features does not scale with the increasing number of brain images, hindering the pace of scientific discoveries ...


A 'Tissue Model' To Study The Barrier Effects Of Living Tissues On The Reactive Species Generated By Surface Air Discharge, Tongtong He, Dingxin Liu, Han Xu, Zhichao Liu, Dehui Xu, Dong Li, Qiosong Li, Mingzhe Rong, Michael G. Kong May 2016

A 'Tissue Model' To Study The Barrier Effects Of Living Tissues On The Reactive Species Generated By Surface Air Discharge, Tongtong He, Dingxin Liu, Han Xu, Zhichao Liu, Dehui Xu, Dong Li, Qiosong Li, Mingzhe Rong, Michael G. Kong

Bioelectrics Publications

Gelatin gels are used as surrogates of human tissues to study their barrier effects on incoming reactive oxygen and nitrogen species (RONS) generated by surface air discharge. The penetration depth of nitrite into gelatin gel is measured in real time during plasma treatment, and the permeabilities of nitrite, nitrate, O3 and H2O2 through gelatin gel films are quantified by measuring their concentrations in the water underneath such films after plasma treatment. It is found that the penetration speed of nitrite increases linearly with the mass fraction of water in the gelatin gels, and the permeabilities of ...


Impairment Of Continuous Insulin Delivery Therapy And Analysis From Graeco-Latin Square Design Model, Norou Diawara, Ayodeji Demuren, Eric Gyuricsko Jan 2016

Impairment Of Continuous Insulin Delivery Therapy And Analysis From Graeco-Latin Square Design Model, Norou Diawara, Ayodeji Demuren, Eric Gyuricsko

Mathematics & Statistics Faculty Publications

The desire to deliver measured amount of insulin continuously to patients with type I diabetes, for glycemic control, has attracted a lot of attention. Continuous subcutaneous insulin infusion has seen some success in recent years. However, occlusion of insulin delivery may prevent the patient from receiving the prescribed dosage, with adverse consequence. An in vitro study of insulin delivery is performed, using different insulin pumps, insulin analogs and operating conditions. The aim is to identify incidences of occlusion due to bubble formation in the infusion line. A detailed statistical analysis was performed on the data collected to determine any significant ...


Evaluation Of The Effects Of A Plasma Activated Medium On Cancer Cells, S. Mohades, M. Laroussi, J. Sears, N. Barekzi, H. Razavi Jan 2015

Evaluation Of The Effects Of A Plasma Activated Medium On Cancer Cells, S. Mohades, M. Laroussi, J. Sears, N. Barekzi, H. Razavi

Electrical & Computer Engineering Faculty Publications

The interaction of low temperature plasma with liquids is a relevant topic of study to the field of plasma medicine. This is because cells and tissues are normally surrounded or covered by biological fluids. Therefore, the chemistry induced by the plasma in the aqueous state becomes crucial and usually dictates the biological outcomes. This process became even more important after the discovery that plasma activated media can be useful in killing various cancer cell lines. Here, we report on the measurements of concentrations of hydrogen peroxide, a species known to have strong biological effects, produced by application of plasma to ...


Killing Adherent And Nonadherent Cancer Cells With The Plasma Pencil, Mounir Laroussi, Soheila Mohades, Nazir Barekzi Jan 2015

Killing Adherent And Nonadherent Cancer Cells With The Plasma Pencil, Mounir Laroussi, Soheila Mohades, Nazir Barekzi

Electrical & Computer Engineering Faculty Publications

The application of low temperature plasmas in biology and medicine may lead to a paradigm shift in the way various diseases can be treated without serious side effects. Low temperature plasmas generated in gas mixtures that contain oxygen or air produce several chemically reactive species that have important biological implications when they interact with eukaryotic or prokaryotic cells. Here, a review of the effects of low temperature plasma generated by the plasma pencil on different cancerous cells is presented. Results indicate that plasma consistently shows a delayed killing effect that is dose dependent. In addition, there is some evidence that ...


Multi-Surface Simplex Spine Segmentation For Spine Surgery Simulation And Planning, Rabia Haq Jan 2015

Multi-Surface Simplex Spine Segmentation For Spine Surgery Simulation And Planning, Rabia Haq

Computational Modeling and Simulation Engineering Theses & Dissertations

This research proposes to develop a knowledge-based multi-surface simplex deformable model for segmentation of healthy as well as pathological lumbar spine data. It aims to provide a more accurate and robust segmentation scheme for identification of intervertebral disc pathologies to assist with spine surgery planning. A robust technique that combines multi-surface and shape statistics-aware variants of the deformable simplex model is presented. Statistical shape variation within the dataset has been captured by application of principal component analysis and incorporated during the segmentation process to refine results. In the case where shape statistics hinder detection of the pathological region, user-assistance is ...


A Nonrigid Registration Method For Correcting Brain Deformation Induced By Tumor Resection, Yixun Liu, Chengjun Yao, Fotis Drakopoulos, Jinsong Wu, Liangfu Zhou, Nikos Chrisochoides Jan 2014

A Nonrigid Registration Method For Correcting Brain Deformation Induced By Tumor Resection, Yixun Liu, Chengjun Yao, Fotis Drakopoulos, Jinsong Wu, Liangfu Zhou, Nikos Chrisochoides

Computer Science Faculty Publications

Purpose: This paper presents a nonrigid registration method to align preoperative MRI with intraoperative MRI to compensate for brain deformation during tumor resection. This method extends traditional point-based nonrigid registration in two aspects: (1) allow the input data to be incomplete and (2) simulate the underlying deformation with a heterogeneous biomechanical model.

Methods: The method formulates the registration as a three-variable (point correspondence, deformation field, and resection region) functional minimization problem, in which point correspondence is represented by a fuzzy assign matrix; Deformation field is represented by a piecewise linear function regularized by the strain energy of a heterogeneous biomechanical ...


Design And Study Of The Efflux Function Of The Egfp Fused Mexab-Oprm Membrane Transporter In Pseudomonas Aeruginosa Using Spectroscopy, Feng Ding, Kerry J. Lee, Ardeschir Vahedi-Faridi, Hiroshi Yoneyama, Christopher J. Osgood, Xiao-Hong Nancy Xu Jan 2014

Design And Study Of The Efflux Function Of The Egfp Fused Mexab-Oprm Membrane Transporter In Pseudomonas Aeruginosa Using Spectroscopy, Feng Ding, Kerry J. Lee, Ardeschir Vahedi-Faridi, Hiroshi Yoneyama, Christopher J. Osgood, Xiao-Hong Nancy Xu

Biological Sciences Faculty Publications

Multidrug membrane transporters (efflux pumps) can selectively extrude a variety of structurally and functionally diverse substrates (e.g., chemotoxics, antibiotics), leading to multidrug resistance (MDR) and ineffective treatment of a wide variety of diseases. In this study, we have designed and constructed a fusion gene (egfp-mexB) of N-terminal mexB with C-terminal egfp, inserted it into a plasmid vector (pMMB67EH), and successfully expressed it in the Δ MexB (MexB deletion) strain of Pseudomonas aeruginosato create a new strain that expresses MexA-(EGFP-MexB)-OprM. We characterized the fusion gene using gel electrophoresis and DNA sequencing, and determined its expression in live ...


Protein Loop Length Estimation From Medium Resolution Cryoem Images, Andrew R. Mcknight Jul 2013

Protein Loop Length Estimation From Medium Resolution Cryoem Images, Andrew R. Mcknight

Computer Science Theses & Dissertations

In the post-genomic era, proteomics research presents a new frontier in life science. Proteins play roles in virtually every biological process, and understanding their atomic structures is the key to unraveling how they carry out their work. Compared to the over half million protein sequences in UniProt, only around 25,000 unique sequences have been atomically modeled and deposited to PDB (Protein Databank). Cryoelectron Microscopy (cryoEM) is an important biophysical technique that produces 3D subnanometer resolution images of molecules not amenable to past approaches like x-ray crystallography or nuclear magnetic resonance. De novo modeling is becoming a promising approach to ...


Distal Placement Of An End-To-Side Bypass Graft Anastomosis: A 3d Computational Study, John Di Cicco, Ayodeji Demuren Jan 2013

Distal Placement Of An End-To-Side Bypass Graft Anastomosis: A 3d Computational Study, John Di Cicco, Ayodeji Demuren

Mechanical & Aerospace Engineering Faculty Publications

A three-dimensional (3D) computational fluid dynamics study of shear rates around distal end-to-side anastomoses has been conducted. Three 51% and three 75% cross-sectional area-reduced 6 mm cylinders were modeled each with a bypass cylinder attached at a 30-degree angle at different placements distal to the constriction. Steady, incompressible, Newtonian blood flow was assumed, and the full Reynolds-averaged Navier-Stokes equations, turbulent kinetic energy, and specific dissipation rate equations were solved on a locally structured multiblock mesh with hexahedral elements. Consequently, distal placement of an end-to-side bypass graft anastomosis was found to have an influence on the shear rate magnitudes. For the ...


Image-Guided Robotic Dental Implantation With Natural-Root-Formed Implants, Xiaoyan Sun Apr 2012

Image-Guided Robotic Dental Implantation With Natural-Root-Formed Implants, Xiaoyan Sun

Electrical & Computer Engineering Theses & Disssertations

Dental implantation is now recognized as the standard of the care for tooth replacement. Although many studies show high short term survival rates greater than 95%, long term studies (> 5 years) have shown success rates as low as 41.9%. Reasons affecting the long term success rates might include surgical factors such as limited accuracy of implant placement, lack of spacing controls, and overheating during the placement.

In this dissertation, a comprehensive solution for improving the outcome of current dental implantation is presented, which includes computer-aided preoperative planning for better visualization of patient-specific information and automated robotic site-preparation for superior ...


A Novel Pulsed Corona Discharge Reactor Based On Surface Streamers For No Conversion From N2-O2 Mixture Gases, M. A. Malik, Karl H. Schoenbach Mar 2011

A Novel Pulsed Corona Discharge Reactor Based On Surface Streamers For No Conversion From N2-O2 Mixture Gases, M. A. Malik, Karl H. Schoenbach

Bioelectrics Publications

A novel pulsed corona discharge reactor is described which utilizes surface-plasma along insulating surfaces. The electrodes are comprised of a stainless steel wire anode of 150 µm diameter stretched along the surface of a glass sheet and two parallel aluminum strips as cathodes. An eight-stage Marx bank, which provides 60 ns, 40-45 kV monopolar pulses, was used to produce the surface streamers in nitrogen-oxygen mixtures at atmospheric pressure. With increasing oxygen content, the energy efficiency for NO2 and O3 synthesis was found to increase. The energy efficiency is almost the same for the surface-plasma and volume-plasma. However, the surface-plasma was ...


Experimental Studies On The Plasma Bullet Propagation And Its Inhibition, Erdinc Karakas, Mounir Laroussi Jan 2010

Experimental Studies On The Plasma Bullet Propagation And Its Inhibition, Erdinc Karakas, Mounir Laroussi

Electrical & Computer Engineering Faculty Publications

Plasma bullets generated by atmospheric pressure low temperature plasma jets have recently been an active research topic due to their unique properties and their enhanced plasma chemistry. In this paper, experimental insights into the plasma bullet lifetime and its velocity are reported. Data obtained from intensified charge-coupled device camera and time-resolved optical emission spectroscopy (OES) elucidated the existence of a weakly ionized channel between the plasma bullet and its source (such as the plasma pencil). Factors responsible for the inhibition of the propagation of the bullet, such as low helium mole fraction, the magnitude of the applied voltage, and the ...


Destruction Of Α -Synuclein Based Amyloid Fibrils By A Low Temperature Plasma Jet, Erdinc Karakas, Agatha Munyanyi, Lesley Greene, Mounir Laroussi Jan 2010

Destruction Of Α -Synuclein Based Amyloid Fibrils By A Low Temperature Plasma Jet, Erdinc Karakas, Agatha Munyanyi, Lesley Greene, Mounir Laroussi

Electrical & Computer Engineering Faculty Publications

Amyloid fibrils are ordered beta-sheet aggregates that are associated with a number of neurodegenerative diseases such as Alzheimer and Parkinson. At present, there is no cure for these progressive and debilitating diseases. Here we report initial studies that indicate that low temperature atmospheric pressure plasma can break amyloid fibrils into smaller units in vitro. The plasma was generated by the plasma pencil, a device capable of emitting a long, low temperature plasma plume/jet. This avenue of research may facilitate the development of a plasma-based medical treatment.


Effects Of Non-Equilibrium Plasma On Eukaryotic Cells (Final Report: Grant Fa9550-06-1-0004), Mounir Laroussi, Fred C. Dobbs, Old Dominion University Aug 2009

Effects Of Non-Equilibrium Plasma On Eukaryotic Cells (Final Report: Grant Fa9550-06-1-0004), Mounir Laroussi, Fred C. Dobbs, Old Dominion University

Electrical & Computer Engineering Faculty Publications

This document is our final report describing the research activities carried out under AFOSR Grant FA9550-06-1-0004. First, descriptions of our cold plasma generation systems are presented. Two systems, developed with past and present AFOSR support, are available in our laboratory. The first is a pulsed device capable of emitting a cold plasma plume in room air. The second is an air plasma generator the core of which is a dielectric barrier discharge excited by a high AC voltage. Following these brief descriptions we first present the effects of an atmospheric pressure air plasma on four different types of eukaryotic microalgae ...


Real-Time Ultrasound Simulation For Medical Training And Standardized Patient Assessment, Bo Sun Apr 2008

Real-Time Ultrasound Simulation For Medical Training And Standardized Patient Assessment, Bo Sun

Computational Modeling and Simulation Engineering Theses & Dissertations

With the increasing role played by ultrasound in clinical diagnostics, ultrasound training in medical education has become more and more important. The clinical routine for ultrasound training is on real patients; therefore monitored and guided examinations involving medical students are quite time-constrained. Furthermore, standardized patients (SPs), who are increasingly used in medical school for teaching and assessing medical students, need to be augmented. These SPs are typically healthy individuals who can not accurately portray the variety of abnormalities that are needed for training especially when medical examinations involve instrument interactions. To augment SPs in a realistically effective way and also ...


Caffeine Model Identification For Vigilance Performance Prediction, Chun-Hui Huang Apr 2008

Caffeine Model Identification For Vigilance Performance Prediction, Chun-Hui Huang

Mechanical & Aerospace Engineering Theses & Dissertations

The pharmacodynamics and pharmacokinetics of caffeine have been well characterized. In this study, a caffeine dynamic model is developed to describe its pharmacodynamic effects on vigilance performance. Validated biomathematical models developed to address both individual and group fatigue and alertness in a non-laboratory setting represent a tremendous commercial opportunity. First, a test data set with caffeine effects isolated from circadian and homeostatic effects is created. Then a modeling approach for input and output effects is developed and different model structures for the caffeine effects are considered. Observer/Kalman filter Identification (OKID) algorithm is proposed and developed to identify the caffeine ...


Bactericidal Effects Of Cold Plasma Technology On Geobacillus Stearothermophilus And Bacillus Cereus Microorganisms, Angela D. Morris, Gayle B. Mccombs, Susan L. Tolle, Mounir Laroussi, Wayne L. Hynes Oct 2007

Bactericidal Effects Of Cold Plasma Technology On Geobacillus Stearothermophilus And Bacillus Cereus Microorganisms, Angela D. Morris, Gayle B. Mccombs, Susan L. Tolle, Mounir Laroussi, Wayne L. Hynes

Dental Hygiene Faculty Publications

Cold plasma is a state of matter that contains a large number of particles that are electrically charged. Plasmas generate chemically reactive species and ultraviolet radiation making them useful in decontamination applications (Kong & Laroussi, 2003). Research regarding the inactivation of gram-positive bacteria by cold plasma has been studied by Laroussi et al (2003); however, there is limited research regarding the germicidal effectiveness of cold plasma on Geobacillus stearothermophilus and Bacillus cereus microorganisms. The purpose of this study was to determine if cold plasma technology inactivates Geobacillus stearothermophilus and Bacillus cereus vegetative cells and spores. This study consisted of 981 samples; 762 experimental samples exposed to cold plasma at various times and 291 controls. Experimental samples were inoculated and exposed either ...


Room-Temperature Atmospheric Pressure Plasma For Biomedical Applications, Mounir Laroussi, Xinpei Lu Jan 2005

Room-Temperature Atmospheric Pressure Plasma For Biomedical Applications, Mounir Laroussi, Xinpei Lu

Electrical & Computer Engineering Faculty Publications

As low-temperature non-equilibrium plasmas come to play an increasing role in biomedical applications, reliable and user-friendly sources need to be developed. These plasma sources have to meet stringent requirements such as low temperature (at or near room temperature), no risk of arcing, operation at atmospheric pressure, preferably hand-held operation, low concentration of ozone generation, etc. In this letter, we present a device that meets exactly such requirements. This device is capable of generating a cold plasma plume several centimeters in length. It exhibits low power requirements as shown by its current-voltage characteristics. Using helium as a carrier gas, very little ...


Astronaut Eva Exposure Estimates From Cad Model Spacesuit Geometry, Giovanni De Angelis, Brooke M. Anderson, William Atwell, John E. Nealy, Gary D. Qualls, John W. Wilson Mar 2004

Astronaut Eva Exposure Estimates From Cad Model Spacesuit Geometry, Giovanni De Angelis, Brooke M. Anderson, William Atwell, John E. Nealy, Gary D. Qualls, John W. Wilson

Mathematics & Statistics Faculty Publications

Ongoing assembly and maintenance activities at the International Space Station (ISS) require much more extravehicular activity (EVA) than did the earlier U.S. Space Shuttle missions. It is thus desirable to determine and analyze, and possibly foresee, as accurately as possible what radiation exposures crew members involved in EVAs will experience in order to minimize risks and to establish exposure limits that must not to be exceeded. A detailed CAD model of the U.S. Space Shuttle EVA Spacesuit, developed at NASA Langley Research Center (LaRC), is used to represent the directional shielding of an astronaut; it has detailed helmet ...


Compact Supercell Method Based On Opposite Parity For Bragg Fibers, Wang Zhi, Ren Guobin, Lou Shuquin, Liang Weijun, Shangping Guo Jan 2003

Compact Supercell Method Based On Opposite Parity For Bragg Fibers, Wang Zhi, Ren Guobin, Lou Shuquin, Liang Weijun, Shangping Guo

Electrical & Computer Engineering Faculty Publications

The supercell- based orthonormal basis method is proposed to investigate the modal properties of the Bragg fibers. A square lattice is constructed by the whole Bragg fiber which is considered a supercell, and the periodical dielectric structure of the square lattice is decomposed using periodic functions (cosine). The modal electric field is expanded as the sum of the orthonormal set of Hermite-Gaussian basis functions based on the opposite parity of the transverse electric field. The propagation characteristics of Bragg fibers can be obtained after recasting the wave equation into an eigenvalue system. This method is implemented with very high efficiency ...