Biomedical Engineering and Bioengineering Commons^™

Deep Brain Stimulation In Early-Stage Alzheimer's Disease: A Systematic Review Of Neuropsychological Outcomes, Nora Huey

Doctoral Dissertations

Alzheimer’s disease (AD) is a progressive neurodegenerative disorder characterized by cognitive decline, memory impairment, and disruption of neural networks involved in cognitive functioning. Although existing treatments may provide symptomatic benefit, there remains a need for interventions capable of slowing or stabilizing disease progression. Deep brain stimulation (DBS) has emerged as a potential neuromodulatory intervention for early-stage AD through stimulation of memory- and cognition-related neural circuitry. This dissertation employed a systematic review research methodology to examine teh neuropsychological and neurobiological outcomes associated with DBS targeting the fornix (DBS-f) and nucleus basalis of Meynert (DBS-NBM) in individuals with early-stage AD over 12–24 …

Comparative Performance Of Physiological Vital-Sign Forecasting Under Random And Patient-Wise Splitting Using Deep Learning, Lavanya Vasavi Chittem Reddy

Theses and Dissertations

Physiological vital-sign forecasting estimates future measurements based on recent temporal patterns and can support analysis of continuously recorded monitoring data. This study comparatively evaluated deep feedforward, recurrent, bidirectional recurrent, long short-term memory, and bidirectional long short-term memory architectures for one-step-ahead forecasting of peripheral oxygen saturation, heart rate, and pulse rate. Each model received consecutive observations of peripheral oxygen saturation, heart rate, pulse rate, respiratory rate, and age, while separate single-output models predicted the next value of the selected target.

Random and patient-wise data splitting were compared using identical input definitions, preprocessing procedures, model architectures, and training hyperparameters. The strongest architecture …

Isolating Human Monocytes And Characterizing Human Macrophage Polarization Through Flow Cytometry And Morphological Analysis, Arthur Peter Klujian

Biomedical Engineering

Peripheral Artery Occlusive Disease (PAOD) is a cardiovascular disease that affects more than 200 million people. It is characterized by atherosclerosis, a biologic process where peripheral arteries are restricted due to a buildup in cholesterol and fats. This eventually leads to ischemia, developing complications such as chronic inflammation and possible limb amputation. The current standard of care for patients includes surgical revascularization and exercise therapy. These treatment strategies have had limited success with alleviating symptoms and restoring perfusion, however, many patients still experience ischemia and do not fully restore blood flow. Further exploration in pursuit of treating these shortcomings led …

Motor Imagery Eeg Decoding For Brain-Computer Interfaces: Structured Representation, Transfer, And Drift, Yiming Shen

Graduate Doctoral Dissertations

Motor imagery EEG decoding is often summarized by the accuracy of a final classifier, but the classifier is only the last stage of the pipeline. Before classification, the signal has already been shaped by preprocessing, feature extraction, source-session organization, and adaptation. This dissertation studies how feature representation, source-session transfer, and drift shape reliable MI-EEG decoding for brain-computer interfaces.

It first studies within-session decoding on public MI-EEG datasets using nested validation that keeps preprocessing, feature fitting, and model selection inside the training folds. This analysis separates gains from feature representation from gains due to nonlinear classification, and relates both comparisons to …

Compact 1 Ghz Electron Paramagnetic Resonance Spectrometers For Preclinical Imaging Studies, Tanden A. Hovey

Electronic Theses and Dissertations

Magnetic resonance is one of the most generally useful scientific techniques. New horizons of understanding are revealed as technological advances make possible explorations of nuclear spins and electron spins at higher and lower magnetic fields and electromagnetic frequencies. While the greatest current effort is on ever higher magnetic fields and microwave frequencies, both in nuclear magnetic resonance (NMR) and electron paramagnetic resonance (EPR), the Eaton lab focusses on developing high signal-to-noise performance EPR at low microwave frequencies. EPR provides information about O2, pH, viscosity, glutathione concentrations, and reactive oxygen species in living organisms that MRI cannot. To yield clinically or …

A Longitudinal Study Of Achilles Tendon Adaptation In Ncaa Division I Female Gymnasts: Associations With Menstrual Status, Birth Control Use, Pain, Limb Dominance, And Training Exposure, Mattie Jane Hyde

Electronic Theses and Dissertations

This longitudinal study evaluated Achilles tendon (AT) thickness in 22 NCAA Division I (DI) female gymnasts across three consecutive seasons in relation to menstruation, birth control use, pain, limb dominance, training week, and year of collegiate competition. Weekly ultrasound and athlete survey data were analyzed using mixed-effects models for absolute AT thickness and change in thickness from baseline measurements. Associations were primarily characterized by interactions rather than uniform effects of individual predictors. A Pain × Limb Dominance × Week × Year interaction was associated with both thickness outcomes across season-specific and combined analyses, with relationship directions varying by limb, season …

An Investigation Of Pelvic Kinematics And Implications For Total Hip Arthroplasty, Kathryn Holland Colone

Electronic Theses and Dissertations

Total hip arthroplasty (THA) is one of the most commonly performed orthopaedic procedures, with approximately 500,000 surgeries performed annually in the United States alone. Although THA is widely regarded as highly successful, postoperative complications persist, highlighting the multifactorial nature of THA outcomes. Previous studies have demonstrated the importance of implant positioning and soft tissue mechanics, yet challenges remain in optimizing surgical decisions on a patient-specific basis. Recent advances in surgical planning tools have shifted the focus of preoperative planning toward optimizing patient-specific outcomes, highlighting the need to better understand how patient anatomy, surgical technique, and joint mechanics interact to influence …

Plasma-Generated Ozone For Odor Removal, Jordan Marot

Seton Hall University Dissertations and Theses (ETDs)

Ozone (O₃) is gaining popularity for its use in industrial and environmental applications, including water treatment, air purification, disinfection, and odor remediation. As a powerful oxidizing agent, ozone is highly effective in destroying harmful bacteria and degrading hazardous gas pollutants such as hydrogen sulfide (H₂S). Dielectric barrier discharge (DBD) reactors are widely used for commercial ozone production under atmospheric-pressure conditions. However, ozone yield and selectivity are strongly influenced by operating parameters, particularly gas flow rate, which affects residence time, energy transfer, and competing byproduct chemistry.

This study explores the influence of the air flow rate on …

Deciphering The Rules Of Odor-Driven Learning In The Fruit Fly Olfactory System, Cole B. Hanan

McKelvey School of Engineering Graduate Student Theses & Dissertations

Odorant identity is encoded by patterns of activity across olfactory receptor neurons (ORNs) and their corresponding glomeruli in the antennal lobe (AL). An odorant's valence can be modified by experience, allowing animals to associate previously neutral odors with appetitive or aversive outcomes. However, some odors appear resistant to such reassignment, and the factors determining whether an odor can acquire learned valence and whether that association generalizes to chemically related odors remain poorly understood. This thesis uses Drosophila melanogaster to address this question using a fully automated proboscis extension reflex (PER) conditioning assay. Odorants are presented via a computer-controlled olfactometer, reward …

A Functional Ultrasound Imaging (Fusi) Pipeline For Investigating Brain-Wide Hemodynamics During Torpor-Like Hypothermia, Owen J. Culver

McKelvey School of Engineering Graduate Student Theses & Dissertations

Torpor is a regulated state of reduced metabolic demand that enables animals to conserve energy under unfavorable environmental conditions. The controlled induction of a similar state, termed synthetic torpor, has potential applications in ischemic protection, organ preservation, cancer treatment, radiation protection, and long-term spaceflight. Although neuronal populations within the preoptic hypothalamus have been shown to initiate hypothermic and hypometabolic states, the distributed cerebral hemodynamic dynamics accompanying their induction and maintenance remain poorly understood. In this thesis, we developed an accessible functional ultrasound imaging (fUSI) acquisition and analysis pipeline and applied it to investigate cerebral hemodynamics during chemogenetic activation of the …

Isolation, Identification, And Enzymatic Screening Of Fungi From Utah Dryland Soils For Industrial And Waste Valorization Applications, Jessica Lorena Silva Cuero

All Graduate Reports and Creative Projects, Fall 2023 to Present

Agricultural waste accumulation presents environmental challenges but also opportunities for biological valorization into value-added products. Fungi are particularly well-suited for this purpose due to their capacity to produce extracellular enzymes involved in the degradation of complex organic substrates. Dryland ecosystems represent a promising source for bioprospecting microbes capable of producing such enzymes. Drylands harbor a high diversity of extremophilic microorganisms that can withstand harsh conditions, extreme heat, UV, and low nutrients using unique adaptations. This suggests that these microbes are resilient and capable of surviving under varying conditions and still produce enzymes for biotransformation. The objective of this study was …

Cadmium Biosorption By Fusarium Venenatum And Its Application In Functional Permeable Materials For Metal Removal, Bradley Lawson

All Graduate Theses and Dissertations, Fall 2023 to Present

Heavy metals are pollutants of increasing concern as continued industrialization and urbanization have escalated the discharge of these toxins into aquatic environments. Cadmium (Cd) is a metal of particular concern due to its acute toxicity and high mobility in aquatic ecosystems. Given these characteristics Cd poses significant health risks to both humans and aquatic ecosystems. The continued development of sustainable, low-cost remediation technology is imperative to manage metal pollution.

This research explores the use of fungal-based remediation systems to remove Cd from contaminated water. Living biomass of the filamentous fungus Fusarium venenatum was evaluated as a biosorbent material for Cd …

Multidimensional Determinants Of Gait, Balance, And Softball Performance In Female Youth: Biomechanics, Resource Access, And Psychosocial Factors, Allie G. Mcauliffe

Master's Theses

Movement quality is a fundamental indicator of healthy childhood development and supports physical, emotional, psychosocial, and cognitive well-being. Movement quality is influenced by multiple biomechanical, environmental, and psychosocial factors, yet the relationships among them remain poorly understood in underrepresented populations such as female youth, particularly in softball. Previous studies have largely examined biomechanics, resource access, and psychosocial experience independently, and few have investigated how these factors interact in female youth softball players. To address this gap, this study compared gait and balance characteristics between softball (N = 34) and non-softball (N = 7) female youth, examined associations between resource access, …

Evaluation Of Ostomy Pouching Change Practices Among Hospital-Based And Community-Based Nurses, Hannah Gerlach

All Theses

An estimated 725,000 to 1 million Americans are living with an ostomy and depend on ostomy pouching systems as part of their daily care. Effective ostomy management requires regular pouch changes and consistent skin care to prevent peristomal skin complications. Many individuals living with an ostomy face long-term challenges in managing their ostomy care, which can negatively affect their health-related quality of life. There is a need to understand how professional experience across different care environments, such as hospital-based and community-based settings, influences ostomy nursing care practices.

This study evaluates how nurses working in hospital-based settings and community-based settings perform …

A Surface-Bound Detection Architecture For Label-Free Evanescent-Wave Sensing Of Cobalt In Complex Fluids, Jeremiah W. Carpenter

All Dissertations

Cobalt exposure is a clinical concern in orthopedic implant surveillance, where cobalt-chromium wear debris can release ions detectable in blood and urine, and an environmental concern in mining-affected and industrial water systems. Reference laboratory methods, including inductively coupled plasma mass spectrometry, provide sensitive quantification but require centralized instrumentation, trained personnel, and controlled sample handling, which limits their availability for routine screening in decentralized clinical and environmental contexts. This dissertation develops a surface-bound detection architecture for label-free evanescent-wave sensing of cobalt in complex fluids. The architecture rests on a physical necessity argument grounded in interfacial optics: at physiologically and environmentally relevant …

Time-Frequency Analysis Of Arterial Pulse Signals Of Cardiovascular Disease Patients Measured By A Microfluidic-Based Tactile Sensor, Md Mahfuzur Rahman

Mechanical & Aerospace Engineering Theses & Dissertations

This dissertation presents a single-degree-of-freedom (SDOF) based time–frequency analysis framework that can simultaneously extract a comprehensive set of cardiovascular autonomic indices from arterial pulse wave recordings obtained at rest and post-exercise, supporting non-invasive monitoring of autonomic recovery during cardiac rehabilitation. The framework rests on three technical contributions.

First, an SDOF analytical model of motion artefacts quantifies two physically distinct distortion mechanisms: additive baseline drift and Time-Varying System Parameter (TVSP) generated distortion of the Tissue-Contact-Sensor (TCS) stack. Baseline drift is slowly varying and removable by filtering; TVSP distortion rides on all harmonics of the true pulse signal and cannot be removed …

Laponite Nanosilicate As A Platform For Antigen–Adjuvant Co-Delivery In Vaccination, Haoyu Qi

McKelvey School of Engineering Graduate Student Theses & Dissertations

Nanosilicates are two-dimensional, charged nanomaterials with tunable surface chemistry that enable electrostatic interactions with proteins and nucleic acids. These properties make Laponite nanosilicate a promising platform for vaccine delivery, where coordinated antigen–adjuvant presentation and lymph node delivery are important for shaping immune responses. This thesis investigated nanosilicates as scaffolds for lysozyme-based antigen delivery and co-delivery with CpG.

The preparation method reduced the apparent size of the NS–Lys–CpG complex at pH 10, although neutralization to pH 7 promoted larger aggregate formation. In vivo IVIS imaging after footpad injection showed persistent Cy7-associated fluorescence at the injection site for up to three weeks …

Computational And Ai Tools For Understanding Telomere-Associated Cancer Mechanisms, Eleni Adam

Computer Science Theses & Dissertations

Telomeres are the protective caps of the human chromosomes and are critical for genome stability. Dysfunctional telomeres caused by their erosion with age and cell proliferation as well as by defects in their maintenance is a major early event leading to genome changes and cancer. Subtelomeres possess the critical role of regulating adjacent telomeres. Due to their complex repeat structure and high variance from one person to another, these areas have not been analyzed in detail. We present a set of computational and machine learning tools to aid in the understanding of subtelomere structure and its rearrangements in cancer.

Initially, …

Mapping And Modeling Threat-Evoked Brain States After Early Life Adversity, Taylor W. Uselman

Biomedical Sciences ETDs

Early life adversity (ELA) increases lifelong neuropsychiatric vulnerability. Yet how ELA reorganizes brain-wide activity and circuit coordination across later experience remains unclear. This dissertation tests the hypothesis that ELA alters adult brain-wide activity and responses to threat through disrupted coordination among neural systems that regulate emotional experience, including prefrontal-limbic and monoaminergic systems. Longitudinal manganese-enhanced MRI of adult mice exposed to standard or fragmented early care, combined with computational processing and statistical modeling, quantified brain states before, during, and long after innate predator threat. These studies established that acute threat evokes large-scale, distributed brain activity that evolves over time. ELA potentiates …

Engineering Fsh-Cer T Cells To Enhance Response To Epithelial Ovarian Cancer, Nolan J. Beatty

USF Tampa Graduate Theses and Dissertations

Ovarian cancer remains a significant cause of cancer-related mortality, with epithelial ovarian cancer (EOC) being the most common subtype. Despite advances in treatment, the 5-year survival rate for late-stage EOC remains low due to factors such as tumor heterogeneity and an immunosuppressive tumor microenvironment (TME). This study investigates the therapeutic potential of chimeric endocrine receptor (CER) T cells engineered to express follicle stimulating hormone (FSH) in a syngeneic mouse model of EOC expressing follicle stimulating hormone receptor (ID8-FSHR). We compared two different co-stimulatory domains—CD28ζ and 4-1BBζ—in FSH-CER T cells and found that FSH-CD28ζ CER T cells exhibited enhanced cytotoxicity, proliferation, …

Design, Fabrication, And Testing Of A Pdms-Based Nanochannel Using Nano Embossing, Cooper James Haskamp

Graduate Theses and Dissertations

DNA sequencing has become increasingly important in the field of biomedical research and clinical applications. Currently, the most well-established sequencing technique is ‘Sequencing by Synthesis’ with accuracy in the range of 99.2% to 99.74% and sequencing lengths of only 300 base pairs. Sequencing by Synthesis is a lab-based method that requires expensive equipment and fast parallel computing. It is not suitable for portable, on-site applications. A new technique known as ‘nanopore’ was developed to meet these requirements. Nanopore is an electrical sequencing method that relies on the translocation of a DNA molecule through a nanoscale pore, where the blockage current …

A Portable Device To Elicit Sensory Trick And Monitor Forearm Muscle Activity In Pianists With Musician’S Dystonia, Josef Franczak

USF Tampa Graduate Theses and Dissertations

Musician’s Dystonia (MD) is a condition that can be acquired in professional musicians,causing involuntary contractions and the loss of fine motor control. The most common pharmaceutical treatment, botulinum toxin injections, has been shown to have side effects of muscle weakness and atrophy. The sensory trick, shown to temporarily relieve symptoms of dystonia, has potential to be used as an alternative or alongside current therapies, allowing patients with MD to return to playing music professionally. To systematically deploy the sensory trick and monitor forearm muscle activity, the first prototype of the Wearable Sensorimotor Integrator (wSMI) has been developed.

The wSMI is …

Sam-1: An Assistive Robot For Remote Patient Monitoring, Aana Farhana Ahsan

USF Tampa Graduate Theses and Dissertations

The global aging population has increased the demand for caregiving, while the availability of caregivers has not grown at the same pace. These trends have contributed to disparities in consistent and accessible care for older adults and increased caregiver burden. Geriatric care robots have emerged as a promising solution to support older adults and reduce caregiver burden. Existing systems have been developed for a wide range of applications, including rehabilitation, social support, assistance with activities of daily living, therapy, and caregiver telepresence. This thesis presents the development of SAM-1, an assistive robot designed to support remote monitoring of older adults …

Molecular Devolution For Gene Editing: Reverse Directed Evolution Of Cre Recombinase, Giovanna Esposito, Simran Sood, Katie Liu

Bioengineering Senior Theses

The principal objective of this paper is to provide a proof-of-concept of a novel protein engineering method called Molecular Devolution (MD). MD is an evolutionary protein engineering method that reduces the size of enzymes while retaining its functional properties. This paper outlines an MD protocol for Cre Recombinase. Cre Recombinase is an enzyme that is part of the Cre LoxP DNA Recombination System, which is a leading gene editing system widely used in genetic research. This paper outlines a MD approach that was used to miniaturize Cre Recombinase and remove unnecessary complexities, allowing for simpler and more e!cient use in …

A Point-Of-Care Hormone Monitoring Platform For Postpartum Health Assessment, Ava Mcdonald, Avary Torres, Frances Warneke

Bioengineering Senior Theses

Our point-of-care hormone monitoring device for postpartum health assessment uses paper-based microfluidics to provide an accessible and affordable hormone monitoring tool, tracking biomarkers correlated with postpartum depression (PPD). The device features a 3D-printed spring-box housing and platform containing chromatography paper testing sheets that are lined with polydimethulsiloxane (PDMS) and wax paper, embedded with specific reagents that generate colorimetric hormone readouts from saliva samples. This device was motivated by the need to address critical shortcomings in PPD care, where societal stigma surrounding mental health and reliance on self-reporting diagnostic methods prevent mothers from truthfully reporting symptoms and receiving timely support and …

Fluorescence Cryotomography For Preclinical Validation: Applications In Gene Therapy And Fluorescence-Guided Surgery, Caleb Y. J. Kwon

Dartmouth College Ph.D Dissertations

Fluorescence imaging has become a powerful tool in biomedical research and clinical practice, offering molecular specificity and high sensitivity for visualizing biological processes in real time, However, the successful translation of novel fluorescent probes or medicines from preclinical development to clinical applications requires rigorous validation of their biodistribution and target specificity. Traditional methods for assessing performance, such as bulk excised organ analysis or two-dimensional histology, provide limited information as they cannot capture the complete, organism-wide distribution of these probes or medicines. This thesis aims to improve this analysis pipeline through the application and optimization of fluorescence cryotomography for quantitative, high-resolution …

A Computational Micropatterning Approach To Study Caveolae And Protein Localization In Vascular Biology, Andrew B. Grespin

Electronic Theses and Dissertations

Caveolae are specialized, flask-shaped membrane invaginations highly expressed in endothelium and dysregulated in atherosclerosis. Caveolae play a central role in buffering membrane tension, yet the principles governing their spatial organization remain elusive. Thus, we sought to generate the most comprehensive and systematic analysis of blood vessel caveolar spatial organization. However, cell culturing, the backbone of human-focused biological research, does not standardly do well to model physiologically relevant cell behaviors such as migration or polarity-based tissue formation, particularly for punctate proteins and structures like caveolae. Micropatterns are cell-adhesive shapes that biophysically confine cell(s) to a user defined geometry which stereotype organelle …

Enhancing The Performance Of Brain-Computer Interfaces Via A Spatially-Aware Framework, Ahmed Ayman Eloraby

Theses and Dissertations

Electroencephalography (EEG)-based brain–computer interfaces (BCIs) provide a non-invasive pathway for communication, with the P300 speller being one of the most established paradigms. Despite its practicality, EEG signals present inherent challenges, including low signal-to-noise ratio, high dimensionality, and limited spatial resolution. These characteristics complicate the extraction of discriminative spatial patterns, which are critical for accurate P300 detection and character-level decoding.

This thesis addresses these challenges through the development of AttenPCA-Net, a deep learning framework that integrates spatially-aware processing with dimensionality reduction. Principal Component Analysis (PCA) is employed to reduce redundancy and noise while preserving the most informative components of the EEG …

Ai In Precision Medicine: Redefining Blindness Treatment Via Retinal Stem Cell Differentiation, Calissa Leong, Tiffany Nguyen

Interdisciplinary Design Senior Theses

Age Macular Degeneration (AMD) is currently the leading cause of blindness, driven by the degradation of Retinal Pigment Epithelial (RPE) cells. Stem-cell based therapies, particularly those involving induced pluripotent stem cells (iPSCs), typically consists of differentiating stem cells into RPE cells in vitro and transplanting them into the subretinal space. Our goal is to improve the accuracy of differentiation into RPE cells to better promote retinal regeneration. Traditional methods to alleviate symptoms of AMD is through therapeutic medications to slow disease progression, though stem cell therapy has emerged as a promising alternative. However, despite its potential, stem cell therapy presents …

Peridevice: A Packed Bed Reactor For Integrated Peritoneal Dialysis, Jake Wood, Gurtej Singh, Orion Cook, James Bell

Bioengineering Senior Theses

Chronic kidney disease affects approximately 800 million people worldwide, with more than 800,000 Americans living with end-stage kidney disease. Peritoneal dialysis provides patients with greater :flexibility and independence than traditional hemodialysis, but it is limited by the buildup of urea in the dialysate, which requires frequent fluid exchanges. Developing a system that continuously regenerates dialysate could help improve the efficacy of this treatment.

In this study, we developed the PeriDevice, a compact packed-bed reactor designed to remove urea from dialysate through enzymatic degradation. The 3D-printed device, using stereo lithography, filled with alginate microcapsules ( d = 1.5 mm) containing urease. …