Biomedical Engineering and Bioengineering Commons^™

Genetic Code Expansion In Biochemical Investigations And Biomedical Applications, Nanxi Wang

Department of Chemistry: Dissertations, Theses, and Student Research

Genetic code expansion provides a powerful tool for site-specific incorporation of unnatural amino acids (unAAs) with novel biochemical and physiological properties into proteins in live cells and organisms. To achieve this, a nonsense codon suppression system, which consists of an orthogonal aminoacyl-tRNA synthetase (aaRS) and tRNA pair that specifically decodes a nonsense codon (e.g., amber codon and quadruplet codon) with an unAA but do not “cross talk” with their endogenous counterparts, was established. This Ph.D. thesis presents our efforts on evolution and application of nonsense codon suppression systems for biochemical and biomedical investigations.

In Chapter 1, a brief overview of …

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

Electrical & Computer Engineering Theses & Dissertations

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 …

Energy–Water Reduction And Wastewater Reclamation In A Fluid Milk Processing Facility, Carly Rain Adams, Yulie E. Meneses, Bing Wang, Curtis L. Weller

Department of Food Science and Technology: Dissertations, Theses, and Student Research

The energy-water nexus is the inseparable connection linking water and energy. We are faced with a unique opportunity to co-manage these resources, as conservation of one is directly linked to the conservation of its counterpart. Therefore, immediately facing this critical challenge, will lead to tangible impacts on the water and energy crisis our food system is faced with. Determining the role of water and energy in the food industry has proved to be the starting point for reducing the distance between process productivity and resource efficiency. Therefore, this research focuses on determining opportunities for water-energy optimization and wastewater reduction and …

Development Of An Atlas-Based Segmentation Of Cranial Nerves Using Shape-Aware Discrete Deformable Models For Neurosurgical Planning And Simulation, Sharmin Sultana

Computational Modeling & Simulation Engineering Theses & Dissertations

Twelve pairs of cranial nerves arise from the brain or brainstem and control our sensory functions such as vision, hearing, smell and taste as well as several motor functions to the head and neck including facial expressions and eye movement. Often, these cranial nerves are difficult to detect in MRI data, and thus represent problems in neurosurgery planning and simulation, due to their thin anatomical structure, in the face of low imaging resolution as well as image artifacts. As a result, they may be at risk in neurosurgical procedures around the skull base, which might have dire consequences such as …

Biotemplating Pores With Size And Shape Diversity For Li-Oxygen Battery Cathodes, Dahyun Oh, Cagla Ozgit-Akgun, Esin Akca, Leslie Thompson, Loza Tadesse, Ho-Cheol Kim, Gökhan Demirci, Robert Miller

Faculty Publications

Synthetic porogens provide an easy way to create porous structures, but their usage is limited due to synthetic difficulties, process complexities and prohibitive costs. Here we investigate the use of bacteria, sustainable and naturally abundant materials, as a pore template. The bacteria require no chemical synthesis, come in variable sizes and shapes, degrade easier and are approximately a million times cheaper than conventional porogens. We fabricate free standing porous multiwalled carbon nanotube (MWCNT) films using cultured, harmless bacteria as porogens, and demonstrate substantial Li-oxygen battery performance improvement by porosity control. Pore volume as well as shape in the cathodes were …

Chitosan Nanoparticle Modifications For Improved Gene Delivery In An Oral Dna Vaccine Application, Austin Helmink

Honors Program: Senior Projects (Public)

Vaccines represent one of the most significant medical innovations of the 20^th century, resulting in the eradication or near eradication of a handful of deadly diseases. However, many infectious diseases remain resistant to effective vaccination, largely due to a lack full immune activation by traditional protein-based vaccines. A promising alternative vaccination strategy is the emerging development of DNA vaccines, which rely upon the delivery of exogenous genetic material to host cells encoding for a viral or bacterial antigen in order to induce a robust immune response by closely mimicking live infection. The delivery of genetic material requires a carrier …

Computing Spatiotemporal Heat Maps Of Lipid Electropore Formation: A Statistical Approach, Willy Wriggers, Frederica Castellani, Julio A. Kovacs, P. Thomas Vernier

Mechanical & Aerospace Engineering Faculty Publications

We extend the multiscale spatiotemporal heat map strategies originally developed for interpreting molecular dynamics simulations of well-structured proteins to liquids such as lipid bilayers and solvents. Our analysis informs the experimental and theoretical investigation of electroporation, that is, the externally imposed breaching of the cell membrane under the influence of an electric field of sufficient magnitude. To understand the nanoscale architecture of electroporation, we transform time domain data of the coarse-grained interaction networks of lipids and solvents into spatial heat maps of the most relevant constituent molecules. The application takes advantage of our earlier graph-based activity functions by accounting for …

Developing An Imaging Biomarker To Detect Aberrant Brain Connectivity In Individual Patients, Esther Cox

Master's Theses (2009 -)

Resting state functional MRI (rsfMRI) has been proven to be a valuable tool in clinical applications such as pre-surgical mapping, but there is not yet a functional and usable algorithm that can be used by physicians in a clinical setting to evaluate an individual patient for diseases and aberrant brain connectivity. If a physician wants to evaluate a patient in this way, the rsfMRI data must be looked at “by hand,” i.e. the physician must manually evaluate the data and identify the functional ICN’s and whether they are normal or aberrant. An algorithm that would automate this process and supplement …

Rapid In Vivo Detection Of Rat Spinal Cord Injury With Double-Diffusion-Encoded Magnetic Resonance Spectroscopy, Nathan P. Skinner, Shekar N. Kurpad, Brian D. Schmit, L. Tugan Muftuler, Matthew D. Budde

Biomedical Engineering Faculty Research and Publications

Purpose

Diffusion-weighted imaging is a common experimental tool for evaluating spinal cord injury (SCI), yet it suffers from complications that decrease its clinical effectiveness. The most commonly used technique, diffusion tensor imaging (DTI), is often confounded by effects of edema accompanying acute SCI, limiting its sensitivity to the important functional status marker of axonal integrity. The purpose of this study is to introduce a novel diffusion-acquisition method with the goal of overcoming these limitations.

Methods

A double diffusion encoding (DDE) pulse sequence was implemented with a diffusion-weighted filter orthogonal to the spinal cord for suppressing nonneural signals prior to diffusion …

Computational And Performance Analysis Of A Continuous Magnetophoretic Bioseparation Chip With Alternating Magnetic Fields, Matin Golozar, Majid Molki, Jeff Darabi

SIUE Faculty Research, Scholarship, and Creative Activity

This paper presents the modeling and optimization of a magnetophoretic bioseparation chip for isolating cells, such as circulating tumor cells from the peripheral blood. The chip consists of a continuous-flow microfluidic platform that contains locally engineered magnetic field gradients. The high-gradient magnetic field produced by the magnets is spatially non-uniform and gives rise to an attractive force on magnetic particles flowing through a fluidic channel. Simulations of the particle–fluid transport and the magnetic force are performed to predict the trajectories and capture lengths of the particles within the fluidic channel. The computational model takes into account key forces, such as …

Plasmonic Stimulation Of Electrically Excitable Cells, Fnu Parveen

USF Tampa Graduate Theses and Dissertations

There is a compelling need for the development of new sensory and neural prosthetic devices which are capable of more precise point stimulation. Current prosthetic devices suffer from the limitation of low spatial resolution due to the non-specific stimulation characteristics of electrical stimulation, i.e., the spread of electric fields generated. We present a visible light stimulation method for modulating the firing patterns of electrically-excitable cells using surface plasmon resonance phenomena. In in-vitro studies using gold (Au) nanoparticle-coated nanoelectrodes, we show that this method (substrate coated with nanoparticles) has potential for incorporating the technology into neural stimulation prosthetics, such as cochlear …

Simulation Studies On Ecg Vector Dipole Extraction In Liquid Medium, Pratheek Michael

USF Tampa Graduate Theses and Dissertations

To circumvent some inherent problems in the conventional ECG, this research reinvestigates an ‘unassisted’ approach which enables ECG measurement without the placement of leads on the body. Employed in this research is a widely accepted assumption that the electrical activity of the heart may be represented, largely, by a 3-D time-varying current dipole (3D-CD). From the PhysioBank database, mECG and fECG data were obtained, and Singular Value Decomposition (SVD) was performed to estimate the time-varying Vector ECG dipole. To determine the sensing matrix responsible for transforming the activity of the 3D-CD into the potential distribution on the surface of the …

Polysaccharide Fabrication Platforms And Biocompatibility Assessment As Candidate Wound Dressing Materials, Donald C. Aduba Jr., Hu Yang

Chemical and Biochemical Engineering Faculty Research & Creative Works

Wound dressings are critical for wound care because they provide a physical barrier between the injury site and outside environment, preventing further damage or infection. Wound dressings also manage and even encourage the wound healing process for proper recovery. Polysaccharide biopolymers are slowly becoming popular as modern wound dressings materials because they are naturally derived, highly abundant, inexpensive, absorbent, non-toxic and non-immunogenic. Polysaccharide biopolymers have also been processed into biomimetic platforms that offer a bioactive component in wound dressings that aid the healing process. This review primarily focuses on the fabrication and biocompatibility assessment of polysaccharide materials. Specifically, fabrication platforms …

A Novel Hybrid Imaging System To Aid In Surgical Decision Making, Lawrence Yip, Madeleine Van De Kleut, Ivan Kosik, Astrid Chamson-Reig, Jeffrey Jl Carson

Western Research Forum

Background:

Breast cancer accounts for 25% of all cancer cases among women. In breast-conserving surgery, a common treatment, the tumour is excised with a healthy tissue margin. However, detection of the margin can be difficult. Current techniques to guide excision are often insufficient, and re-excision can occur up to 25% of the time.

Methods:

Photoacoustic imaging is a hybrid imaging modality that combines the advantages of optical imaging and ultrasound while using safe non-ionizing light. This project involves the development of a novel imaging system with a new scanner design to overcome common limitations and provide images to aid in …

Validation Of Postural Sway Measurements Using Wii Balance Board, Zachary Meade

UNO Student Research and Creative Activity Fair

Standing balance measurements, such as postural sway, are vital for determining functional ability, risk of falling and recovery of injuries. Often the need to collect data outside of the typical clinical or research setting arises. However, obtaining these measurements outside of a laboratory setting can be very difficult, as the mobility of a laboratory-grade force plate (FP) is minimal, and its cost can be upwards of $20,000. The purpose of this study is to create a cheaper alternative by validating the Wii Balance Board’s (WBB; Nintendo, Redmond, Washington, USA) ability to measure postural sway patterns. The WBB can be acquired …

On Utilizing Big Data To Assess Health Levels, Elham Rastegari

UNO Student Research and Creative Activity Fair

The general relationship between mobility/gait patterns and health conditions, has been established by many research studies. Gait patterns have been used in predicting fall incidents, assessing the movement of people with Parkinson disease and assessing gait characteristics of patients with major depression. However, not much has been reported in terms of how to utilize mobility data along with gait patterns to assess health levels and to identify early stages of certain diseases or conditions that impact mobility/gait patterns. In this project, we propose to develop a population analysis system based on recent Big Data technologies that relies on different types …

Peak Vertical Ground Reaction Force & Stance Phase Time To Assess Post-Tka Interlimb Asymmetry, Abderrahman Ouattas

UNO Student Research and Creative Activity Fair

In the US, more than 500,000 TKA surgeries are performed annually, to which 97% of those are led by OA¹. Although knee pain is diminished post-TKA, unilateral efficiency and walking asymmetry is still unresolved several years after the surgery². In fact, within a minimum of 10 years after the primary TKA, almost 50% of patients undergo a secondary TKA on the contralateral limb due to OA progression³. The purpose of this study was to determine if post-Total Knee Arthroplasty peak vertical ground reaction force (pVGRF) asymmetry could be identified using stance phase time differences …

Acl Reconstruction Results In Alterations For Force Control Variability During Multidirectional Force Production, Amelia S. Lanier

UNO Student Research and Creative Activity Fair

After anterior cruciate ligament (ACL) rupture most will undergo reconstructive surgery. Within the first year after surgery 25% of patients will re-tear their ACL. Most of those injured attempt to return to sports which include running and cutting. The ability to produce appropriate ground reaction forces may be crucial for the successful return to sports without re-injury. Understanding stability of multidirectional ground reaction force (mGRF) production in healthy and ACL reconstructed (ACL-r) patients can lend insight to the high instance of re-injury. Typically, stability has been measured using linear analyses, but these analyses cannot capture the subtle time varying changes …

The Effects Of Walking Speed On Gait Propulsion When Wearing An Ankle-Foot Orthosis, Alli Kalina

UNO Student Research and Creative Activity Fair

Peripheral artery disease (PAD) is a cardiovascular disease that results from blockage of one or more arteries in the lower extremity. Often, patients with PAD have reduced ability to push off with the foot at the end of the gait cycle. When walking, the ankle contributes the majority of the power to propel the body into the next step. An ankle-foot orthosis (AFO) is a device that aids in ankle propulsion by increasing the energy return, thus decreasing the ankle deficit in pathological individuals. The purpose is to investigate the effect of walking speed on ankle propulsion during walking. Subjects …

Biomechanics And Imaging, Jingfeng Jiang

TechTalks

From the perspective of biomechanics, my research is multidisciplinary, bridging the gap between physiology/biology and quantitative sciences. Currently, the applications are on cancer detection and differentiation, therapeutic monitoring, staging liver fibrosis, risk assessment of aneurysm rupture, and more.