Engineering Commons^™

Knowledge Integration In Domain-Informed Machine Learning And Multi-Scale Modeling Of Nonlinear Dynamics In Complex Systems, Phat K. Huynh

USF Tampa Graduate Theses and Dissertations

Nonlinear dynamical systems have been extensively used to model various phenomena in the changing world around us, especially in science and engineering fields. Thanks to breakthrough advancements in sensing technologies, an increasingly high volume of multi-modal sensor data has been collected, which enables us gain better insights into complex systems dynamics and build sophisticated data-driven machine-learning-based dynamic models without having the access to the underlying governing equations. However, integrating domain-specific knowledge in machine learning algorithms remains pivotal for various reasons: it promises enhanced predictive accuracy, better model interpretability, and increased generalizability. This dissertation delves into three core research questions, each …

Evaluating Foot-Drop Interventions For Multiple Sclerosis Using A Multimodal System, Laura Marie Byrnes-Blanco

USF Tampa Graduate Theses and Dissertations

This dissertation explores how multimodal walking impacts quantitative and qualitative aspects of gait for persons with multiple sclerosis (pwMS) experiencing foot-drop. Foot-drop can dramatically impede mobility and clinicians routinely prescribe ankle-foot-orthosis (AFO) and functional electrical stimulation (FES) devices to alleviate its impacts on daily life. However, little is known about how these devices affect pwMS while traversing environments with real-world complexity. To explore this topic, an interventional, parallel assigned study was conducted. A realistic nature pathway containing changes in floor pitch, audiovisual stimulation, and during-trial tasks (for dual-tasking) was generated in an immersive virtual reality system called CAREN: Computer Assisted …

Development And Implementation Of Telemetry Devices To Identify And Characterize Sources Of Intraocular Pressure Variability In Rats, Christina M. Nicou

USF Tampa Graduate Theses and Dissertations

Eye health depends partially on intraocular pressure (IOP) as abnormal levels can lead to ocular tissue damage. Glaucoma is a neurodegenerative disease that affects nearly 80 million people worldwide [1]. It is associated with elevated IOP, which can lead to irreversible blindness. Relatively little is known about IOP dynamics and the physiological factors that affect it as IOP is typically monitored using tonometry. Tonometry is a common tool used by clinicians and researchers to measure IOP noninvasively. It provides a good estimate of IOP mean but not variance because data collection takes time. Readings can also be influenced by subject …

Human Spacesuit Interaction During Eva Of The Legs Using A Force Sensing System, Niraliben D. Patel

USF Tampa Graduate Theses and Dissertations

Astronauts perform a multitude of tasks in space, both in the spacecraft and outside of the spacecraft. Extravehicular Activity (EVA) refers to any activity that is completed outside of the spacecraft, whether it is work on the actual spacecraft, spacewalks, or conducting sample collections on other planets and moons. To do this safely, a pressurized Extravehicular Mobility Unit (EMU) or commonly known as the spacesuit is used. There have been multiple iterations of the United States EMU with advances to further optimize the astronaut safety and EVA tasks. However, there is still relatively little information on the movement of the …

Eeg Classifier Validation Methods For Neuroprosthetic Hand Development, Keigo Yamauchi

USF Tampa Graduate Theses and Dissertations

To date, many challenges have been reported in the development of neuroprosthetic hands using EEG and neural signals. In this study, we report the results of a literature review on Brain Computer Interface (BCI) technology, an investigation of estimation methods using applications in MATLAB, and the results of Electroencephalography (EEG) classification to assist in the development of neural prosthetic hands using biological signals such as EEG. Confusion Matrix was created using Motor Imagery (MI) data as the predictive value, and the average accuracy of more than 90% was obtained for the K-Nearest Neighbor (KNN) and decision tree method. The results …

Neroimaging Of Brain Activaion Using Diffuse Optical Tomography, Jingyu Huang

USF Tampa Graduate Theses and Dissertations

This research has two parts. The first part focuses on the use of non-invasive imaging technique, diffuse optical tomography (DOT), to study the brain activation during the stimulation in the clinical room. It further extends the application of DOT by using it to monitor the hemodynamic response during the TMS stimulation in different parameters. Diffuse optical tomography (DOT) is based on NIR light that exploits the relative transparency of biological tissue. The part two and three extends the application in the hospital for delirium patient study and arm muscle dystrophy by adding the sources and detectors to monitor the brain …

Aqueous Humor Dynamics And Compound Action Potentials In The Anesthetized And Conscious Freely Moving Rat, Youssef Mohamed

USF Tampa Graduate Theses and Dissertations

Vision is dependent on the proper functioning of many intricate components of the eye. Aqueous humor dynamics function to keep the eye inflated at the right pressures and nourish avascular tissue in the eye while properties of the corneoscleral shell dictate how dynamic changes in volume and pressure affect tissue at the optic nerve head. Retinal ganglion cells exit the globe at the optic nerve head and carry all of the visual information to the brain for perception of visual stimulus. In this dissertation, we aim to present a lumped parameter model of the eye that can accurately describe the …

A Protein-Based Therapeutic Combination For The Treatment Of Hard-To-Heal Wounds, Graham L. Strauss

USF Tampa Graduate Theses and Dissertations

Chronic wounds present many clinical challenges in relation to the successful treatment and closure of the damaged tissue. Most current treatment methods focused on one or two aspects to drive wound closure, while most chronic wounds are multifactorial environments with many of those dependencies relying on the termination of one another to effectively gain tissue construction, closure, and full skin thickness and composition. Natural wound healing processes allude to potential biologics that can impede the chronic breakdown of tissue, while restoring deposition of new tissue, and effectively leading to a healed wound. Proteases secreted by the body’s immune system lay …

Hybrid Rans-Les Hemolytic Power Law Modeling Of The Fda Blood Pump, Joseph Tarriela

USF Tampa Graduate Theses and Dissertations

This study applies the SBES and IDDES hybrid RANS-LES turbulence models along with the K-ω SST model to four flow conditions of the FDA blood pump. Validation of all three turbulence models show good agreement with experimental pressure and velocity fields. Evaluation of turbulent kinetic energy fields for the hybrid models show 80-90+% of kinetic energy is resolved in the rotor and diffuser regions of the pump. Hemolysis power law models were evaluated using the commonly used von Mises stress and additional energy dissipation stress (EDS). Results show viscous and Reynolds stresses computed with the K-ω SST under predict and …

Bayesian Network-Based Diagnostic Support Tool With Limited Point-Of-Care Ultrasound For Work-Related Elbow Injuries, Cristina Maria Franceschini Sánchez

USF Tampa Graduate Theses and Dissertations

The upper extremity is commonly injured at the workplace, frequently involving the elbow. Currently, there are not many diagnostic support tools for elbow injuries. Developing a clinical decision support tool would allow for narrowing differential diagnoses and guide management steps in a timely and cost-effective manner. In a descriptive retrospective cohort study, 85 non-contrast elbow MRIs were obtained from a large Workers Compensation insurer database. MRIs were either (a) greater than 2 weeks after first clinic visit, or (b) more than 6 weeks after injury, but (c) not more than 3 months after injury. A Bayesian network-based diagnostic support tool …

Assistive Technologies For Independent Navigation For People With Blindness, Howard Kaplan

USF Tampa Graduate Theses and Dissertations

The necessity for individuals to navigate from location to location is essential to daily life. The majority of humans use sight as the main source for determining how to move through their environment. However, there is a large population of people who are either blind or living with low vision. Based on a 2017 National Health Survey there are around 27 million adult Americans that have experienced vision loss (National Center for Health Statistics, 2017). According to the Eye Diseases Prevalence Research Group there are 3.4 million Americans 40 years and older that are legally blind or visually impaired (EDPRG, …

Multi-Material Hybrid Additive And Subtractive Manufacturing Of Photonic Devices, Roger Brandon Tipton

USF Tampa Graduate Theses and Dissertations

Optoelectronics focuses on the application of electronic devices that utilize forms of electromagnetic radiation including visible light and other wavelengths including ultraviolet and infrared. Optoelectronics typically include devices that emit light and detect light. Devices created using this technology include light-emitting diodes, laser diodes, photoresistors, photodiodes, solar cells, phototransistors, and fiber optics. Fiber optic interconnects are interesting devices in that they are used in conjunction with optoelectronic devices to transmit information between individual optoelectronic components.

Optoelectronics are typically produced by traditional lithography methods including etching, writing, and printing on rigid silicon substrates for fabricating devices. Other techniques like glass or …

Computer Simulation For Continuous Centrifugation Of High-Density Cell Cultures, Hironori Tomizawa

USF Tampa Graduate Theses and Dissertations

Perfusion bioreactors are used for cell production for cell therapies. The system uses cell separation devices such as centrifuge to facilitate cell growth by separating cells and spent media and allows constant media replacement. However, current cell separation technologies can increase shear stress, are generally not continuous processes, and are not as efficient as desired. These limit the amount of media replaced per unit time. Therefore, there is a need for a new system or a method that operates continuously to minimize cell damage, yield high cell concentration, and exchange media effectively. A set of research questions was formulated: (1) …

Mutational Analysis Of Latency Associated Peptide For Therapeutic Application, Johnny Will Stephens

USF Tampa Graduate Theses and Dissertations

TGF-β is an important protein for regulation of the immune system, and has been linked to promotion of tumor progression and cancer growth. Inhibiting TGF-β has been shown to be an effective therapeutic technique for fighting multiple cancer types. Engineering TGF-β’s natural inhibitor, Latency Associated Peptide (LAP), to improve its biophysical properties has potential to increase therapeutic efficacy.

Rosetta and FoldX can be used in concert to engineer stabilizing mutations of proteins. In accordance with this, PyRosetta and FoldX were used to predict stabilizing mutations of LAP. The most stabilizing mutations from each program were combined with mutually predicted mutations. …

Automated Wound Segmentation And Dimension Measurement Using Rgb-D Image, Chih-Yun Pai

USF Tampa Graduate Theses and Dissertations

Accurate pressure ulcer (PrU) measurement is critical in assessing the effectiveness of PrU treatment. The traditional measurement process is manual, subjective, and requires frequent contact with the wound. The manual measurement relies on human observation which makes the measurement inconsistent, and the frequent contact with the wound increases risk of contamination or infection. The purpose of this research was to develop an automatic Pressure Ulcer Monitoring System (PrUMS) using a depth camera to provide automated, non-contact wound measurement. In this dissertation, 1) a wound segmentation with traditional machine learning method, which combines the color classification using K-Nearest Neighbors and the …

Interrelation Of Thermal Stimulation With Haptic Perception, Emotion, And Memory, Mehdi Hojatmadani

USF Tampa Graduate Theses and Dissertations

Haptics is an interdisciplinary field of science that deals with how humans perceive and respond to different sensory cues perceived through touch. Thermal haptics as a branch deals with how humans perceive the temperature sensation and respond to that. The process in which thermal perception occurs is well known to researchers. What seems missing in the literature is how temperature interacts or sometimes intervenes in other physiological and psychological aspects of our lives. In this research, a series of studies are presented where the main focus was how temperature and brain interact with each other to impede or enhance our …

Development Of A Bipolar Radiofrequency Ablation Device For Renal Denervation, Noel Perez

USF Tampa Graduate Theses and Dissertations

The American Heart Association (AHA) reported in March 2020, hypertension (HT) is a major risk factor for cardiovascular diseases and heart stroke. Resistant hypertension (RH) is a subset of HT and affects 11-16% of hypertensive patients. RH is diagnosed when a patient cannot achieve blood pressure control despite taking three or more medications and is a serious clinical management challenge.

Renal denervation (RD) using radiofrequency (RF) ablation is an accepted form of RH therapy. RD devices are typically delivered through femoral access into the renal artery with the assistance of a standard guided sheath. In the European Union (EU), the …

Alternative Approaches To Protect Sensory Inner Ear Tissue Against Cisplatin-Induced Ototoxicity, Nicole K. Febles

USF Tampa Graduate Theses and Dissertations

Sensorineural hearing loss (SNHL) is a prevalent neurodegenerative disorder often involving permanent damage and loss to the inner ear’s mechano-sensory hair cells and spiral ganglion neuron fibers. Significant causes of SNHL are ototoxic drugs, environmental factors, loud noises, and continuous wear with age. A successful but ototoxic chemotherapeutic known as Cisplatin often damages auditory hair cells via mitochondria dysfunction, DNA fragmentation, and cellular death through apoptosis. Despite the high prevalence of SNHL, there currently is no FDA-approved prevention or cure. Thus, auditory and cancer researchers have investigated various individual otoprotective agent preventions with limited success. This dissertation used a novel …

Low-Cost Device For Laser Phacoemulsification: A Preliminary Study, Mitchell Harrah

USF Tampa Graduate Theses and Dissertations

The current gold standard of cataract removal surgery is phacoemulsification systems. These are divided based on the type of devices used; both are considered equal but with different delivery modes. These delivery methods are either acoustic or light-based. However, these devices pose two hurdles for impoverished areas: high costs and heavy resource usage. This thesis proposes a novel phacoemulsification system is based on the low-cost, off-shelf laser diodes that implement light-based phacoemulsification of cataracts. The system is tested for viability over two methods: finite element analysis and experimentation on various phantoms. Simulations on the device have occurred on the COMSOL …

The Feasibility Of 18f-Fdg Labeled Rbc And Pet/Ct Imaging Blood Perfusion And Vascular Dysfunction Measurements In Pre-Clinical Research, Shaowei Wang

USF Tampa Graduate Theses and Dissertations

Heart disease, dementia, and stroke are significant public health issues and leading causes of mortality and morbidity worldwide. Abnormalities in blood perfusion and vascular structures are seen in varieties of pathologies, including cerebrovascular diseases like stroke and dementia, hypertension, cardiovascular disease like atherosclerosis, diabetes, peripheral artery disease, and vasculitis, and tumor angiogenesis. Imaging perfusion/vascular abnormalities in these patients often plays a vital role in clinical diagnosis and treatment decisions.

Vascular diseases typically present as macrovascular or microvascular diseases. Microvascular disease (MVD) refers to vascular disease primarily affecting the arterioles, venules, and capillaries in various organs. Furthermore, MVD is widely found …

An Automated Framework For Connected Speech Evaluation Of Neurodegenerative Disease: A Case Study In Parkinson's Disease, Sai Bharadwaj Appakaya

USF Tampa Graduate Theses and Dissertations

Neurodegenerative diseases affect millions of people around the world. The progressive degeneration worsens the symptoms, heavily impacting the quality of life of the patients as well as the caregivers. Speech production is one of the physiological processes affected by neurodegenerative diseases like Alzheimer’s disease, amyotrophic lateral sclerosis (ALS) and Parkinson’s disease (PD). Speech is the most basic form of communication, and the effect of neurodegeneration degrades speech production, thereby reducing social interaction and mental well-being. PD is the second most common neurodegenerative disease affecting speech production in 90% of the diagnosed individuals. Speech analysis methods for PD in clinical methods …

An Investigation Of Cross-Links On Crystallization And Degradation In A Novel, Photocross-Linkable Poly (Lactic Acid) System, Nicholas Baksh

USF Tampa Graduate Theses and Dissertations

Polymeric molecular structure consists of repeating units bonded together. Mechanicalproperties can be altered without affecting chemical makeup by altering the number of these units. Small molecules can be introduced and/or polymers can be modified to form bonds between molecular chains. Cross-linking, as this is called, also introduces mechanical variation with minimal effects on chemical composition. Lastly, polymer chains reorient themselves in response to intermolecular forces. This temperature dependent response is known as crystallization. Although chemistry is unaltered, mechanical properties can depend highly on the percent of the sample that is crystallized.

Cross-linking is known to enhance the mechanical properties of …

Opto-Fluidic Manipulation Of Microparticles And Related Applications, Hao Wang

USF Tampa Graduate Theses and Dissertations

Contemporary biomedical technologies introduce many new instruments that are important for diagnosis and treatment of the patients. Instrument that can do rapid detection of bacterial infections, and further direct medical practitioner to prescribe optimal antibiotics is highly desirable. But unfortunately, this instrument is not available yet. Ideally, this instrument has to be portable to be used at point-of-care. This means it has to be small and inexpensive, but still highly accurate. Another critical requirement for the instrument is that the test results have to be available promptly. Because in case of such complications of bacterial infections as sepsis, each additional …

Convergence Of Auditory Nerve Fibers Onto Globular Bushy Cells, Matthew Kersting

USF Tampa Graduate Theses and Dissertations

Globular bushy cells (GBCs) of the cochlear nucleus are specialized neurons that encode the temporal features of sound. Multiple auditory nerve inputs are known to synapse onto a single GBC, but the exact number and sizes of these inputs have not been systematically investigated in adult mice. To gain a high-resolution and unbiased look at the auditory inputs contacting GBCs, our lab utilized Serial Block-Face Scanning Electron Microscopy. Specifically, 21 GBCs and all their large inputs were reconstructed at nanometer resolution. To produce the most precise results, we applied careful attention to the reconstruction and implemented cutting-edge meshing algorithms. We …

Protease Resistant Growth Factor Formulations For The Healing Of Chronic Wounds, Tabitha Boeringer

USF Tampa Graduate Theses and Dissertations

Chronic wounds are those wounds which are refractory to treatment, often taking years to heal. These wounds are complex and may present with elevated protease levels, resulting in rapid degradation of growth factors, both native and augmented via treatment. This study’s focus was the development of a system to protect growth factors from protease mediated degradation.

The protective system consisted of chimeric fusion proteins developed to contain both a growth factor or known protease inhibitory peptide and an Elastin-Like-Peptide (ELP)component. The unique phase transitioning abilities of the ELP component allowed for the self-assembly of these chimeric fusion proteins into a …

Spatial Heterogeneity Utilization In Ct Images For Lung Nodule Classication, Dmitrii Cherezov

USF Tampa Graduate Theses and Dissertations

Lung cancer (LC) is leading in the number of deaths among the other types of cancer. According to the American Cancer Society, 135,720 deaths during 2020 in the USA will be associated with LC. The patient 5-year survival rate of 16\% was reported in 1986 and 19% in 2019. One of the reasons why survival rate remains low is that the majority of patients diagnosed with cancer had stages III and IV. In contrast, a 5-year survival rate of 70% was reported for patients of stage IA after surgical resection in the National Lung Screening Trial.

CT screening detects a …

Active Deep Learning Method To Automate Unbiased Stereology Cell Counting, Saeed Alahmari

USF Tampa Graduate Theses and Dissertations

Cell quantification in histopathology images plays a significant role in understanding and diagnosing diseases such as cancer and Alzheimers. The gold-standard for quantifying cells in tissue sections is the unbiased stereology approach. Unfortunately, in unbiased stereology current practices rely on a well-trained human to manually count hundreds of cells in microscopy images. However, this human-based manual approach is time-consuming, labor-intensive, subject to human errors, recognition bias, fatigue, variable training, poor reproducibility, and inter-observer error. Thus, the lack of high-throughput technology for automating unbiased stereology analyses remains a major obstacle to further progress in a wide range of neuroscience and cancer …

Cancer Biomarker Detection In Human Plasma By Integrating Surface Acoustic Wave And Metal-Enhanced Fluorescence, Yuqi Huang

USF Tampa Graduate Theses and Dissertations

This thesis includes data and discussion about the technique of metal-enhanced fluorescence (MEF) to lower the detection limit of carcinoembryonic antigen (CEA). The detection limit goes down to 100pg/mL level when using MEF substrate made by rapid thermally annealed silver film covered by silica, which has great promise in diagnosing certain types of cancer that uses CEA as detection biomarker, such as pancreatic cancer and colon cancer. To further address the issue of background noises from non-specifically bound proteins (NSB) in complex media, such as plasma, serum, urine and blood, MEF is integrated with surface acoustic wave (SAW) streaming in …

Laser Micropatterning Effects On Corrosion Resistance Of Pure Magnesium Surfaces, Yahya Efe Yayoglu

USF Tampa Graduate Theses and Dissertations

Magnesium and its alloys are good candidates to manufacture medical implants. They have excellent biocompatibility and because they biodegrade secondary surgical operation to remove the implant could be eliminated. However, in aqueous environments, magnesium alloys rapidly corrode, resulting in premature degradation of the implant along with biologically intolerable hydrogen gas generation. In literature, there are multiple studies focused on creating water repelling hydrophobic magnesium surfaces in order to decrease corrosion rates. Hydrophobic properties can be achieved by creation of a roughness profile on an initially smooth surface combined with a treatment that reduces the free surface energy. In theory, hydrophobic …

Manipulation And Patterning Of Mammalian Cells Using Vibrations And Acoustic Forces, Joel Cooper

USF Tampa Graduate Theses and Dissertations

Recently, there has been a surge in researchers and scientists investigating different methods which move, manipulate, and pattern biological cells. Multiple different mechanisms can be used for cellular manipulation, microfluidics, biochemical queues, and even optics, just to name a few. However, all techniques have their downsides. A majority of these methods require expensive equipment or reagents and can only manipulate a small number of cells at a time.

Some of the most common cell manipulation devices utilize acoustic pressure waves to move the cells to desired locations. Currently, it is unknown what level of force from these types of devices …