Biomedical Engineering and Bioengineering Commons^™

Study Of Iron Ion Transit Through Three-Fold Channel Of Ferritin Cage, Shah Alam Limon

Graduate Theses/Dissertations

Ferritin is an iron-storage globular protein with an ability to uptake, mineralize and release iron ions in a controllable manner. The globular hollow shell allows storage of mineralized iron, with several channels responsible for the transit of ions into the shell and out of it. Understanding of the detailed molecular functioning of ferritin is required for rational design of biomimetic conjugate nano-biosystems containing ferritin-like constituents. In this work, ferritin was investigated both numerically by all-atom molecular dynamics (MD) simulations, and experimentally by Raman spectroscopy. Molecular dynamic simulations of a model system comprising iron ions (Fe2+) and a ferritin trimer expressing …

Open Source Software For Automatic Detection Of Cone Photoreceptors In Adaptive Optics Ophthalmoscopy Using Convolutional Neural Networks, David Cunefare, Leyuan Fang, Robert F. Cooper, Alfredo Dubra, Joseph Carroll, Sina Farsiu

Biomedical Engineering Faculty Research and Publications

Imaging with an adaptive optics scanning light ophthalmoscope (AOSLO) enables direct visualization of the cone photoreceptor mosaic in the living human retina. Quantitative analysis of AOSLO images typically requires manual grading, which is time consuming, and subjective; thus, automated algorithms are highly desirable. Previously developed automated methods are often reliant on ad hoc rules that may not be transferable between different imaging modalities or retinal locations. In this work, we present a convolutional neural network (CNN) based method for cone detection that learns features of interest directly from training data. This cone-identifying algorithm was trained and validated on separate data …

A Brief Review Of Opt101 Sensor Application In Near-Infrared Spectroscopy Instrumentation For Intensive Care Unit Clinics, Ting Li, Fulin Zhong, Boan Pan, Zebin Li, Chong Huang, Zishan Deng

Biomedical Engineering Faculty Publications

The optoelectronic sensor OPT101 have merits in advanced optoelectronic response characteristics at wavelength range for medical near-infrared spectroscopy and small-size chip design with build-in trans-impedance amplifier. Our lab is devoted to developing a series of portable near-infrared spectroscopy (NIRS) devices embedded with OPT101 for applications in intensive care unit clinics, based on NIRS principle. Here we review the characteristics and advantages of OPT101 relative to clinical NIRS instrumentation, and the most recent achievements, including early-diagnosis and therapeutic effect evaluation of thrombus, noninvasive monitoring of patients' shock severity, and fatigue evaluation. The future prospect on OPT101 improvements in noninvasive clinical applications …

Chelator-Free Radiolabeling Of Serrs Nanoparticles For Whole-Body Pet And Intraoperative Raman Imaging, Matthew A. Wall, Travis Shaffer, Stefan Harmsen, Darjus-Felix Tschaharganeh, Chun-Hao Huang, Scott W. Lowe, Charles Michael Drain, Moritz F. Kircher

Publications and Research

A single contrast agent that offers whole-body non-invasive imaging along with the superior sensitivity and spatial resolution of surface-enhanced resonance Raman scattering (SERRS) imaging would allow both pre-operative mapping and intraoperative imaging and thus be highly desirable. We hypothesized that labeling our recently reported ultrabright SERRS nanoparticles with a suitable radiotracer would enable pre-operative identification of regions of interest with whole body imaging that can be rapidly corroborated with a Raman imaging device or handheld Raman scanner in order to provide high precision guidance during surgical procedures. Here we present a straightforward new method that produces radiolabeled SERRS nanoparticles for …

High Throughput Analysis Of The Penetration Of Iron Oxide/Polyethylene Glycol Nanoparticles Into Multicellular Breast Cancer Tumor Spheroids, Jonathan Robert Gabriel

Theses and Dissertations

The purpose of this study was to design and optimize a system for the high-throughput analysis of multicellular tumor spheroids (MCTS), and validate the system through the study of a complex biological model. The system was successfully created and optimized, allowing the histological recovery of MCTS at rates up to 90% for microarrays of 24-spheroids. Arrays of 96-spheroids were recovered at rates up to 86%. The system was used to study the penetration of 5k Da-polyethylene coated superparamagnetic iron-oxide nanoparticles (5k-PEG SPIONs) into HTB-126 breast cancer spheroids cultured to a mean diameter of 486 micrometer (± 25.2 micrometer). Results were …

Biomechanics Of Snoring And Sleep Apnea, Charles F. Babbs

Weldon School of Biomedical Engineering Faculty Working Papers

To understand the mechanisms of snoring and sleep apnea a first-principles biomechanical analysis was done for airflow through branched parallel channels, separated by a freely movable soft palate, and converging to a common channel at the base of the tongue in a “Y-shaped” configuration. Branches of the Y describe slit-like passages on the nasal and oral sides of the soft palate, when the palate is pushed by backward movement of the tongue to form a wedge between the tongue surface and the posterior pharyngeal wall. The common channel of the Y describes the oropharyngeal passage between the base of the …

Application Of Advanced Biomechanical Methods In Studying Low Back Pain – Recent Development In Estimation Of Lower Back Loads And Large-Array Surface Electromyography And Findings, Babak Bazrgari, Ting Xia

Biomedical Engineering Faculty Publications

Low back pain (LBP) is a major public health problem and the leading disabling musculoskeletal disorder globally. A number of biomechanical methods using kinematic, kinetic and/or neuromuscular approaches have been used to study LBP. In this narrative review, we report recent developments in two biomechanical methods: estimation of lower back loads and large-array surface electromyography (LA-SEMG) and the findings associated with LBP. The ability to estimate lower back loads is very important for the prevention and the management of work-related low back injuries based on the mechanical loading model as one category of LBP classification. The methods used for estimation …

Modeling De Novo Granulation Of Anaerobic Sludge, Anna Doloman, Honey Varghese, Charles D. Miller, Nicholas Flann

Computer Science Faculty and Staff Publications

Background: A unique combination of mechanical, physiochemical and biological forces influences granulation during processes of anaerobic digestion. Understanding this process requires a systems biology approach due to the need to consider not just single-cell metabolic processes, but also the multicellular organization and development of the granule.

Results: In this computational experiment, we address the role that physiochemical and biological processes play in granulation and provide a literature-validated working model of anaerobic granule de novo formation. The agent-based model developed in a cDynoMiCs simulation environment successfully demonstrated a de novo granulation in a glucose fed system, with the average specific methanogenic …

Physical Disruption Of Cell-Cell Contact Induces Vegf Expression In Rpe Cells, Fahrad Farjood, Elizabeth Vargis

Biological Engineering Faculty Publications

PURPOSE: To investigate the role of RPE cell-cell contact in vascular endothelial growth factor (VEGF) protein expression in cultures of primary human RPE (hRPE) cells and a human RPE cell line (ARPE-19). METHODS: Two in vitro methods, scratching and micropatterning, were used to control the physical dissociation of RPE cell-cell junctions. Scratching was performed by scoring monolayers of RPE cells with a cell scraper. Micropatterning was achieved by using a stencil patterning method. Extracellular VEGF expression was assessed by using an enzyme-linked immunosorbent assay (ELISA) kit. Immunocytochemistry (ICC) was performed to visualize the expression and localization of VEGF and intercellular …

A Multiscale Modeling Study Of The Mammary Gland, Joseph D. Butner

Biomedical Engineering ETDs

Multiscale, hybrid computer modeling has emerged as a valuable tool in the fields of computational systems biology and mathematical oncology. In this work, we present an overview of the motivations for, and development and implementation of, three hybrid multiscale models of the mammary gland system and early stage ductal carcinoma in situ (DCIS) in the gland. Pubertal mammary gland development was described first using a two-dimensional, lattice-based hybrid agent-based model description of the mammary terminal end bud (TEB), and then with a three-dimensional lattice-free TEB model. Both models implement a discrete, agent-based description of the cell scale, and a continuum, …

Bisphosphonate Functionalized Gold Nanoparticles For The Study And Treatment Of Osteoporotic Disease, Christopher Conners

USF Tampa Graduate Theses and Dissertations

The use of nanoparticles for disease treatment is an increasingly popular area of research. The potential for multi-functionality allows nanoparticles to be used as transport and delivery vehicles for drugs and as diagnostic aides, among other applications, to address the unmet needs of many disease treatments. One such class of disease is osteoporosis including severe disorders, like Paget’s disease, Osteogenesis Imperfecta and Legg Calve Perthes disease. In this dissertation, we discuss a nanoparticle system consisting of gold nanoparticles surface functionalized with primary amine bisphosphonates, which is a classification of pharmaceuticals that is common in the treatment of osteoporosis. Functionalized nanoparticles …

Understanding The Surface Fouling Mechanism Of Ultrananocrystalline Diamond Microelectrodes Using Microfluidics For Neurochemical Detection, An-Yi Chang

Doctoral Dissertations

Electrochemical methods are widely used for chronic neurochemical sensing, but thus far, the organic solution redox reactions fouled the electrodes' surface. It caused the reduction of sensitivity and the electrodes' lifetime.

Here, we present the boron-doped nanocrystalline diamond microelectrodes (BDUNCD) as the next generation electrode material for neurochemical sensor development. To aid in long-term chronic monitoring of neurochemicals, they have a wide window of electrochemical potential, extremely low background current, and excellent chemical inertness. The main research goal is to reduce the rate of electrode fouling due to the reaction by-products, and significantly extend their useful lifetime.

We systematically characterize …

Inter-Joint Coordination Deficits Revealed In The Decomposition Of Endpoint Jerk During Goal-Directed Arm Movement After Stroke, Jozsef Laczko, Robert A. Scheidt, Lucia Simo, Davide Piovesan

Biomedical Engineering Faculty Research and Publications

It is well documented that neurological deficits after stroke can disrupt motor control processes that affect the smoothness of reaching movements. The smoothness of hand trajectories during multi-joint reaching depends on shoulder and elbow joint angular velocities and their successive derivatives as well as on the instantaneous arm configuration and its rate of change. Right-handed survivors of unilateral hemiparetic stroke and neurologically-intact control participants held the handle of a two-joint robot and made horizontal planar reaching movements. We decomposed endpoint jerk into components related to shoulder and elbow joint angular velocity, acceleration, and jerk. We observed an abnormal decomposition pattern …

Markerless Kinematics Of Pediatric Manual Wheelchair Mobility, Jacob Robert Rammer

Dissertations (1934 -)

Pediatric manual wheelchair users face substantial risk of orthopaedic injury to the upper extremities, particularly the shoulders, during transition to wheelchair use and during growth and development. Propulsion strategy can influence mobility efficiency, activity participation, and quality of life. The current forefront of wheelchair biomechanics research includes translating findings from adult to pediatric populations, improving the quality and efficiency of care under constrained clinical funding, and understanding injury mechanisms and risk factors. Typically, clinicians evaluate wheelchair mobility using marker-based motion capture and instrumentation systems that are precise and accurate but also time-consuming, inconvenient, and expensive for repeated assessments. There is …

Nanosecond Electric Pulses Differentially Affect Inward And Outward Currents In Patch Clamped Adrenal Chromaffin Cells, Lisha Yang, Gale L. Craviso, P. Thomas Vernier, Indira Chatterjee, Normand Leblanc

Bioelectrics Publications

This study examined the effect of 5 ns electric pulses on macroscopic ionic currents in whole-cell voltage-clamped adrenal chromaffin cells. Current-voltage (I-V) relationships first established that the early peak inward current was primarily composed of a fast voltage-dependent Na⁺ current (I_Na), whereas the late outward current was composed of at least three ionic currents: a voltage-gated Ca²⁺ current (I_Ca), a Ca²⁺-activated K⁺ current (I_K(Ca)), and a sustained voltage-dependent delayed rectifier K⁺ current (I_KV). A constant-voltage step protocol was next used to monitor peak inward and late …

Evaluating Wall Shear Stress Indices To Uncover Stimuli For Restenosis And Malapposition In Stented Coronary Arteries, Ali A. Aleiou

Master's Theses (2009 -)

The cause of coronary artery neointimal thickening leading to restenosis in ~10% of drug-eluting stents is unknown. Although research suggests adverse values of traditional wall shear stress (WSS) indices may contribute, studies to date have not accounted for stent geometry, which dictates local WSS patterns influencing drug concentration. Recently proposed WSS indices such as WSS variability and WSS exposure time (WSSET) may shed further light on restenosis or, the opposite effect, resorption. The objective of this investigation was to locally evaluate traditional and recently proposed post-stenting metrics and their respective impact on restenosis or resorption. This study used de-identified data …

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

Computational Modeling & 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 …

The Use Of Audio Stimulation To Affect Sensorimotor Learning, Gregory Nicholas Ranky

Dissertations

Sensorimotor learning for the hand and fingers can be conducted using both hardware and software components, but the training regime is also important. Using repetitive sequence tapping allows measurement of defined metrics in a controlled, safe environment, and therefore statistical indications for subject improvement.

The process of entrainment, when a subject’s own movements synchronize to an external signal, has been tested in prior studies for memorization and recognition, but has not been investigated for correlation with sensorimotor learning.

This is tested with selected custom isochronic audio tones, combined with sequential finger tapping on a standard computer keyboard.

Whilst there were …

Effect Of Tannic Acid Crosslinking On The Mechanical Properties Of Collagen Scaffolds And Melanoma Cell Proliferation, Christopher J. Bridgeman

Theses and Dissertations

Metastatic melanoma is responsible for nearly 10,000 deaths in the United States each year. While the prognosis for patients with localized early stage melanoma cancer is good, the chances of survival for patients with late stage metastatic melanoma are only 16%. Matrix stiffness has been shown to have a profound effect on tumor metastasis for breast cancer, but little is known about its role on melanoma metastasis and progression. Similarly, the therapeutic effect of tannic acid (TA) has been extensively characterized for soft breast and leukemia cancers, but not for melanoma. The goal of the current study was to investigate …

The Specific Vulnerabilities Of Cancer Cells To The Cold Atmospheric Plasma-Stimulated Solutions., Dayun Yan, Haitao Cui, Wei Zhu, Niki Nourmohammadi, Julian Milberg, Lijie G Zhang, Jonathan H Sherman, Michael Keidar

Neurological Surgery Faculty Publications

Cold atmospheric plasma (CAP), a novel promising anti-cancer modality, has shown its selective anti-cancer capacity on dozens of cancer cell lines in vitro and on subcutaneous xenograft tumors in mice. Over the past five years, the CAP-stimulated solutions (PSS) have also shown their selective anti-cancer effect over different cancers in vitro and in vivo. The solutions used to make PSS include several bio-adaptable solutions, mainly cell culture medium and simple buffered solutions. Both the CAP-stimulated medium (PSM) and the CAP-stimulated buffered solution (PSB) are able to significantly kill cancer cells in vitro. In this study, we systematically compared the anti-cancer …

Quantitative Optical Measurement Of Mitochondrial Superoxide Dynamics In Pulmonary Artery Endothelial Cells, Zahra Ghanian, Girija G. Konduri, Said H. Audi, Amadou K.S. Camara, Mahsa Ranji

Biomedical Engineering Faculty Research and Publications

No abstract provided.

Characterization Of Surface Charges And Compensating Charges For Gene Delivery To Tissue, Ravi Shanmugha Preethi Vangapattu

USF Tampa Graduate Theses and Dissertations

Ever since the discovery of DNA, there has been many pathologies identified effecting mankind. With the development in technology, there are many methods to alleviate these pathologies. One such is gene therapy or gene delivery. It is a process of introducing some foreign material into the body to correct the effected cells. In principle, it is a modern method to cure cells or a method to transfer nucleic acid into a cell to treat specific cells in the body. The process of delivering a genetic material is carried out using vectors, namely, viral vectors and non-viral vectors. In viral vectors, …

Impaired Right Ventricular Contractile Function In Childhood Obesity And Its Association With Right And Left Ventricular Changes: A Cine Dense Cardiac Magnetic Resonance Study, Linyuan Jing, Arichanah Pulenthiran, Christopher D. Nevius, Abba Mejia-Spiegeler, Jonathan D. Suever, Gregory J. Wehner, H. Lester Kirchner, Christopher M. Haggerty, Brandon K. Fornwalt

Biomedical Engineering Faculty Publications

Background: Pediatric obesity is a growing public health problem, which is associated with increased risk of cardiovascular disease and premature death. Left ventricular (LV) remodeling (increased myocardial mass and thickness) and contractile dysfunction (impaired longitudinal strain) have been documented in obese children, but little attention has been paid to the right ventricle (RV). We hypothesized that obese/overweight children would have evidence of RV remodeling and contractile dysfunction.

Methods: One hundred and three children, ages 8–18 years, were prospectively recruited and underwent cardiovascular magnetic resonance (CMR), including both standard cine imaging and displacement encoding with stimulated echoes (DENSE) imaging, which allowed …

Effects Of Short Term Hypoxia-Preconditioning On Glial Phenotype Induction Of Human Mesenchymal Stem Cells, Zichen Qian, Qi Xing, Corey Fase, Kyle Jansen, Feng Zhao

Michigan Tech Publications, Part 1

Development of successful clinical treatments for peripheral nerve injury is limited due to the complications behind neural physiology. Human mesenchymal stem cells (hMSCs) have the ability to directly promote tissue repair and protect cells at the injury site. Studies have shown that hMSCs can be transplanted to improve nerve regeneration. Hypoxic culture condition has been proven to maintain the stemness of hMSCs for later differentiation. In this study, we investigated the effects of low oxygen (O₂) (2% and 5% O₂) pre-treatment and initial seeding density (500, 1000, and 2000 cells/cm²) on glial protein expression …

A Wood-Powered Lawn Mower: Separating The Rules Of Thumb From Engineering Design, William White

Mahurin Honors College Capstone Experience/Thesis Projects

Biomass gasification, the thermal process of exracting combustible gasses from organic matter, is an established procedure that has been used for many years to provide fuel in various applications. It is a potential source of renewable fuel and has proven useful as a crisis energy source. This thesis investigates the primary engineering science principles involved in gasifier-engine system design. It arises from and supplements a WKU mechanical engineering senior project. The senior project has developed a wood gasification system designed to power a riding lawn mower. The thesis reiews theory-based design and separates it from informal hit and miss approaches—rule …

Redox-Responsive Polysulfide-Based Biodegradable Organosilica Nanoparticles For Delivery Of Bioactive Agents, Seyyed Pouya Hadipour Moghaddam, Jiban Saikia, Mostafa Yazdimamaghani, Hamidreza Ghandehari

Chemical and Biochemical Engineering Faculty Research & Creative Works

Design and development of silica nanoparticles (SiO2 NPs) with a controlled degradation profile promises effective drug delivery with a predetermined carrier elimination profile. In this research, we fabricated a series of redox-responsive polysulfide-based biodegradable SiO2 NPs with low polydispersity and with variations in size (average diameters of 58 ± 7, 108 ± 11, 110 ± 9, 124 ± 9, and 332 ± 6 nm), porosity, and composition (disulfide vs tetra sulfide bonds). The degradation kinetics of the nanoparticles was analyzed in the presence of 8 mM glutathione (GSH), mimicking the intracellular reducing condition. Results indicate that porosity and core composition …

Morphometric Analysis Of The Talus On The Cohort Of Healthy And Arthritic Patient Population:, Tia Arvaneh

USF Tampa Graduate Theses and Dissertations

Prevalence of osteoarthritis (OA) is less common in the ankle compared to other joints; however, deformation brought on by degeneration causes pain, loss of function, and overall decreased quality of life. Current surgical interventions for end-stage ankle OA are not as reliable as surgical treatments for other joints. Ankle arthroplasty currently has high failure rates, and there are lack of substantial data from long-term outcome studies. By understanding the morphometric changes that occur during the different stages of OA, we are able to identify early signs of the disease with the intention to apply treatment earlier in order to preclude …

The Arm Movement Detection (Amd) Test: A Fast Robotic Test Of Proprioceptive Acuity In The Arm, Leigh A. Mrotek, Maria Bengtson, Tina M. Stoeckmann, Lior Botzer, Claude Ghez, John Mcguire, Robert A. Scheidt

Biomedical Engineering Faculty Research and Publications

Background

We examined the validity and reliability of a short robotic test of upper limb proprioception, the Arm Movement Detection (AMD) test, which yields a ratio-scaled, objective outcome measure to be used for evaluating the impact of sensory deficits on impairments of motor control, motor adaptation and functional recovery in stroke survivors.

Methods

Subjects grasped the handle of a horizontal planar robot, with their arm and the robot hidden from view. The robot applied graded force perturbations, which produced small displacements of the handle. The AMD test required subjects to respond verbally to queries regarding whether or not they detected …

Detection Of Structural Bolt Detorquing Using Direct Stethoscope Measurement, Joe Guarino, Robert Hamilton

Mechanical and Biomedical Engineering Faculty Publications and Presentations

A method for detecting loosened bolts in a structural joint based upon open-loop acoustic measurement is presented. The acoustic measurement is taken directly on the bolt head. The response of the bolt to a proximal hammer impact is evaluated and characterized using wavelet decomposition of the signal measured from the bolt head. Data were also taken from an accelerometer mounted longitudinally and transversely on the bolt head. Results from the stethoscope and the accelerometer are presented from a set of structural bolts in several conditions of preload and looseness. A stethoscope applied to the loose bolt and a proximal bolt …

The Effect Of Antigen Polymorphisms On Serological Antibody Detection Assays Based Upon The, Kristi M. Miley

USF Tampa Graduate Theses and Dissertations

Onchocerca volvulus is a filarial parasite transmitted to humans by female Simulium spp. black flies. Infection with this parasite can cause blindness and severe skin disease among humans in Africa and the Americas. Enzyme-linked Immunosorbent Assay serological testing of OV-16 antigen is a diagnostic tool for determining effective elimination of the parasite. Programs typically rely on OV–16 ELISA to evaluate the progress towards interruption and/or elimination of disease by mass drug distribution of ivermectin and vector larvicidal control efforts. As elimination grows closer, monoclonal antibody positive controls for OV-16 ELISA become important to develop for Onchocerca testing due to the …