Digital Commons Network^™

From Graph Theory For Robust Deep Networks To Graph Learning For Multimodal Cancer Analysis, Asim Waqas

USF Tampa Graduate Theses and Dissertations

This dissertation explores the intersection of graph theory and deep learning, focusing on enhancing the robustness of deep neural networks (DNNs) and applying these advancements to complex problems like cancer diagnosis and treatment. We investigate the structural properties of graphs and their influence on neural network performance, particularly in multimodal learning. The work delves into the design space of DNN architectures using graph-theoretic measures, transforming graphs into DNN architectures for various tasks, and examining their robustness against noise and adversarial attacks. The study extends to medical imaging, highlighting advanced DNN architectures like U-Net for brain tumor segmentation. It addresses the …

Porphyrin Overdrive In Cancer: Unraveling The Mechanisms And Therapeutic Potential, Pravin D. Meshram

USF Tampa Graduate Theses and Dissertations

The increased understanding of cancer cell metabolism has shown options for novel treatment strategies. This thesis looks at the role of heme metabolism, specifically "porphyrin overdrive," in cancer progression and treatment. Cancer cells are hypermetabolic and rely on heme synthesis. When treated with δ-aminolevulinic acid (ALA), they abnormally accumulate heme intermediates. This metabolic weakness presents an opportunity to exploit heme synthesis in targeted cancer therapy. In this study, we suggest a "Bait and Kill" technique that uses exogenous ALA to induce protoporphyrin IX (PpIX) buildup in cancer cells, making them more susceptible to oxidative stress. We investigate the possibility of …

Gender Role Depictions In Arabic Children’S Picture Books, Aljawharah A. Almuqbil

USF Tampa Graduate Theses and Dissertations

This study aimed to explore gender role depictions in children's Arabic picture books. The importance of this study emerged from its focus on young children, where the concept of gender begins to be constructed. This study provided insight into the nature of gender roles in children’s picture books, especially under the remarkable changes that Saudi society is witnessing and the lack of Arab studies in this area. Social cognitive theory, gender schema theory, and critical literacy pedagogy guided the study. A sample of 26 picture books was selected from the Child Book Club at King Abdulaziz Public Library and analyzed …

Mathematical Modeling Of Tumor Response Dynamics To Predict Progression-Free Survival In Patients With Recurrent High-Grade Glioma, Daniel James Glazar

USF Tampa Graduate Theses and Dissertations

In this dissertation, I aim to develop a mathematical model describing tumor volume response dynamics to perform individual dynamic predictions of progression-free survival (PFS) on patients with recurrent high-grade glioma (rHGG).

Patients with rHGG have a dismal prognosis with median overall survival (OS) of <12 months and median PFS of <7 months. However, there is a wide heterogeneity in treatment responses. Therefore, to aid clinicians with making decisions to alter therapeutic protocol, I would like to predict patient-specific PFS.

To perform individual dynamic predictions, I employ the Claret tumor growth inhibition (TGI) model. I further develop this model by coupling it with two different survival models. Inter-patient heterogeneity is also taken into account through mixed effects, including covariate effects. Model PFS predictions were evaluated using receiver operating characteristic (ROC) curve analysis as well as Brier …

Modeling Pelagic Feeding In The Gulf Of Mexico With Implications For Ecosystem-Based Fisheries Management, Rebecca L. Scott

USF Tampa Graduate Theses and Dissertations

The focus of this dissertation was simulating trophic dynamics in the pelagic Gulf of Mexico (GOM) with an emphasis on ecosystem-based fishery management (EBFM) strategies for large pelagic species. Fisheries management in the United States largely utilizes single-species assessments, although managers are increasingly interested in EBFM approaches to better account for ecosystem effects on stocks such as predator/prey dynamics. Production in the surface layer of the pelagic zone is variable with environmental conditions and prey is often concentrated in patches by hydrodynamic features. Production is also transported vertically via diel vertical migration, during which deep-sea species provide potentially key forage …

Black Holes In Time: The Effect Of Grid Radiation On The Tumor Immune Microenvironment, Rebecca A. Bekker

USF Tampa Graduate Theses and Dissertations

Tumor-immune interactions shape a developing tumor and its tumor immune microenvironment (TIME) resulting in either well-infiltrated, immunologically inflamed ‘hot’ tumor beds, or ‘cold’ immune deserts with low levels of infiltration. The pre-treatment immune state of the TIME is associated with treatment outcome; immunologically hot tumors generally exhibit better responses to radio- and immunotherapy than cold tumors. However, radiotherapy is known to induce opposing immunological consequences, resulting in both immunostimulatory and inhibitory responses. In fact, it is thought that the radiation induced tumoricidal immune response is curtailed by subsequent applications of radiation. Thus, I hypothesize that spatially fractionated radiotherapy (SFRT), administered …

‘The Overheated World’: Crisis Politics And Neoliberal Inertia, Shomik Chakrabarti

USF Tampa Graduate Theses and Dissertations

At the onset of the COVID-19 pandemic, policymakers were forced to balance the maintenance of ongoing economic activity alongside the measures advised by epidemiologists and other public health officials to contain the viral spread. The magnitude of the pandemic forced major conduits of the global economy to come to a sudden halt through incidents such as border closures, supply chain disruptions, lockdowns and calls for individuals to distance themselves from one another. Like the 2008 Global Financial Crisis, COVID-19 was thought to signal an inflection point for neoliberal political economy where a possible post-neoliberal era would develop in the aftermath …

Modeling The Development Of Borderline Personality Disorder: A Formal Theory Approach, Alexandria M. Choate

USF Tampa Graduate Theses and Dissertations

Borderline personality disorder (BPD) is a complex disorder characterized by instabilities in emotion regulation, impulse control, and interpersonal relationships. BPD affects adolescent and adult populations at similar rates, with traits often detectable in late childhood or early adolescence. Despite some progress in the understanding of BPD and its development, contemporary theories have yet to address several important questions in the literature. The present study suggests that many limitations associated with current theoretical models of BPD may be attributable to an overdependence on verbally specified, or weak theories. In most cases, weak theories are constructed using vague or imprecisely defined hypotheses …

Anonymized Identity Recognition And Classification Using Privacy Preserving Facial Encoding, Manas Sanjay Pakalapati

USF Tampa Graduate Theses and Dissertations

The need for sharing large-scale datasets to train deep neural network models, particularly in healthcare, raises significant data security and privacy concerns. To address these issues, methods such as data encryption or encoding are utilized. These techniques can encrypt the data and make it unreadable to humans, while still retaining its usefulness for training models.

In this study, we investigate various image encoding techniques designed to protect privacy by making images unrecognizable while still retaining their usefulness for model training. Our investigation utilized publicly available facial databases and focused on evaluating the trade-offs inherent in image encoding techniques, with a …

Comparing The Genomes Of Multidrug And Vancomycin-Resistant Enterococcus Faecium From A Florida Wastewater Treatment Plant, Eleanor Brodrick

USF Tampa Graduate Theses and Dissertations

Vancomycin-resistant Enterococcus (VRE) are a serious health threat, causing 50,000 infections and 5,000 deaths each year in the United States (CDC, 2019). Multidrug-resistant VRE are becoming more prevalent, and treatment options for infections caused by these organisms are limited (Arias et al., 2010; CDC, 2019). Multidrug resistant VRE have been previously isolated from wastewater in Brazil, Canada, and Portugal (Araújo et al., 2010; de_Farias et al., 2022; Sanderson et al., 2019). Thirteen vancomycin-resistant Enterococcus faecium isolated from three stages of a Florida wastewater treatment plant were fully resistant to the following antibiotics: vancomycin, ampicillin, ciprofloxacin, erythromycin, tetracycline, and nitrofurantoin, and …

Immunogenicity Of A Plasmodium Vivax Circumsporozoite Protein Vaccine, Eric Cruz Murphy

USF Tampa Graduate Theses and Dissertations

Malaria is a disease of global public health importance. Improving treatment methods focus on novel antimalarial drugs to combat parasite resistance and the development of vaccines with effective adjuvants. The current vaccine RTS,S/AS01 is moderately effective only against Plasmodium falciparum. There is no vaccine for Plasmodium vivax to date. The development and implementation of a vaccine against P. vivax would inhibit sporozoite infection of hepatocytes, block development into the blood stage and confer future immune protection. The circumsporozoite protein (CSP) is the most abundant on the surface of sporozoites and protein variants VK210 and VK247 are leading vaccine candidates for …

Cues And Identity: Assessing Substance Use Cues, Life Experience, And Context, Katelynn Carlsen

USF Tampa Graduate Theses and Dissertations

This project employs Ecological Momentary Assessment (EMA) methods alongside semi-structured interviews to examine substance use cues, or “triggers”, in the everyday context. This includes repeated assessment of participants’ behaviors and thoughts over time. EMA allows researchers to sample phenomena the moment they occur within the context. These methods are most used in psychology and clinical science. Current research on substance use relies on lab-based assessments to understand cues and their relationship to consumption (Carter and Tiffany 1999, Conklin and Tiffany 2003, Witteman et al. 2015). This analysis uses data collected by the Cues in the Everyday (CITED) Team. The CITED …

A Comparison Of Video Feedback And Video Self-Evaluation To Improve Tap Skills, Ellie Warmund

USF Tampa Graduate Theses and Dissertations

Within the research on behavioral interventions in sports, researchers have evaluated various feedback-based interventions to enhance performance of skills. Research has demonstrated the effectiveness of video feedback (VF) to improve performance across a variety of sports. Video self-evaluation (VSE), though less studied, is another feedback-based intervention that has been proven to improve sports skills. By using a multiple baseline across participants with an embedded alternating treatments design, this study compared VF to VSE to improve the performance of tap skills. We evaluated three skills for each dancer; one skill received VF, one received VSE, and one did not receive an …

An Analysis Of (Hu)Manid Using The Usf Donated Skeletal Collection: Estimating Sex And Ancestry For Edentulous Individuals, Natalie S. Wise

USF Tampa Graduate Theses and Dissertations

The Human Mandible Identification program, (hu)MANid©, enables anthropologists to estimate the sex and ancestry of unidentified skeletal remains from metric and morphoscopic variables from the mandible. The program is suitable for a variety of anthropological contexts, including forensic casework and bioarchaeological or paleoanthropological analyses. The purpose of this research project is to test the accuracy and applicability of the (hu)MANid program on edentulous mandibles. While the authors of (hu)MANid warn against data collection for edentulous mandibles, there are many circumstances in applied forensic casework where the unidentified person is edentulous. Edentulous individuals experience alveolar resorption, which is the loss of …

Patrol Car Swab Sampling For Biological Agents, Haylie Corcho

USF Tampa Graduate Theses and Dissertations

Law enforcement personnel have a variety of responsibilities and subsequently, a variety of different exposures. Biological agents are common in the environment and therefore, these exposures are a concern in the profession. There is a gap in research into biological agent exposures in this profession, particularly how it relates to surface contamination and within the officers’ vehicles. There is also a lack of standardized decontamination procedures for patrol vehicles, allowing for the potential persistence of these agents. The purpose of this study is to understand which biological agents are most common in patrol cars, which areas within the vehicles have …

Maturing Out Of Crime: A Test Of The Integrated Maturation Theory Of Desistance, Kelly E. Kortright

USF Tampa Graduate Theses and Dissertations

This dissertation partially tested a newer integrated theory, the Integrated Maturation Theory (IMT) of desistance. IMT argues that as maturation increases across five maturation domains (social role, civic, identity, psychosocial, and neurocognitive) the likelihood of offending decreases. Using a sample of serious justice-involved juveniles spanning ages 14-24 from the Pathways to Desistance Study, the individual and simultaneous maturation domain development of the social role, civic, identity, and psychosocial maturation domains, were explored for heterogeneity. Using a group-based trajectory modeling approach, including multi-trajectory modeling, this study advanced the understanding of maturation development by identifying sub-groups following declining trajectories of maturation and …

Cornus Officinalis Extract Activates The Keap1/Nrf2 Pathway And Delays T1d Onset In The Nod Mouse, Justin D. Fletcher

USF Tampa Graduate Theses and Dissertations

Type 1 diabetes (T1D) is an autoimmune disorder that results in the destruction of the insulin producing pancreatic β cells. The only therapeutic option following T1D clinical onset is exogenous insulin supplementation. At present, there is no cure for T1D and attempted interventional therapy has been focused on modulating the immune system. Few attempts have been pursued at preserving β cell function and survival. Here we provide a novel approach using extract from the fruit of the Cornus officinalis (CO) tree to preserve β cell function through the prevention of β cell stress. CO has been used in traditional Chinese …

The Relationship Between Rejection Sensitivity And Higher Order Cognitive Functions, Rachel Gaynor

USF Tampa Graduate Theses and Dissertations

Rejection sensitivity indexes individual differences in the expectation of, reaction to, and interpretation of possible rejection. Research on mechanisms underlying these individual differences have identified a reduction in top-down emotion regulatory processes in those exhibiting heightened rejection sensitivity. Most of these studies utilize rejection-specific affective stimuli. This study examined the relationship between rejection sensitivity score, calculated from the 18-question RSQ, and the recruitment of higher level inhibition resources, as indexed by the conflict N2, on three novel Flanker tasks. In order to further examine previously identified patterns in affective inhibition across differing levels of rejection sensitivity, and to determine whether …

Investigation Of Self-Assembly Of Hen Egg White Lysozyme Fibrils, Nabila Bushra

USF Tampa Graduate Theses and Dissertations

Amyloid proteins are a large group of proteins that tend to aggregate and form insoluble fibrils with a characteristic cross-β sheet structure. Intriguingly, this process of “amyloid formation” has been simultaneously linked to devastating human diseases called amyloidoses, ranging from Alzheimer’s Disease, cardiac amyloidoses to type II diabetes, as well as functional biological responses such as hormone storage and sperm quality control. Amyloid fibrils have also attracted significant attention for their unique mechanical, chemical, and optical characteristics, establishing them as promising tough biomaterials. The urgent need to find treatments for Alzheimer’s disease, and the demand for safe and renewable biomaterials …

Use Of Nanoparticle Additives To Achieve Desirable Properties In Fluorine-Free Firefighting Foams, Annelise Kathleen Curtin

USF Tampa Graduate Theses and Dissertations

Class B Firefighting foams play a crucial role in protecting equipment and people fromliquid fuel fires but concerns regarding the impacts of per- and poly-fluoroalkyl substances (PFAS) have resulted in bans on the use of aqueous film forming foam (AFFF). Fluorine-free replacements are yet to achieve the same level of performance. Nanoparticles including silica and clay have been used to improve foam stability, especially in environments where hydrocarbon fuels are present. These materials have also been used in solid composites to improve fire resistance. The stability of aqueous foams containing silica and Laponite RD nanoparticles along with surfactants of different …

High-Performance Computing In Next-Generation Sequencing Read Alignment, Minh H. Pham

USF Tampa Graduate Theses and Dissertations

Advancements in Next-Generation Sequencing (NGS) have dramatically reduced the cost and increased the speed of DNA sequencing. However, this rapid influx of data necessitates efficient and robust analysis tools, particularly for the complex task of aligning short NGS reads to reference genomes such as the human genome. We explore groundbreaking computational strategies and hardware acceleration to optimize this critical alignment process. This dissertation is structured around three innovative studies. First, we introduce a novel approach to dynamic memory allocation tailored for massively parallel systems, particularly Graphical Processing Units (GPUs), to support NGS alignment and other applications. Unlike traditional memory allocators …

Quantification And Diversity Of A Ubiquitous Ssdna Phage Group (Gokushovirinae) In The Red Sea Through The Polony Technique, Natalie A. Sawaya

USF Tampa Graduate Theses and Dissertations

With average concentrations of 107 virus-like particles per milliliter of seawater, viruses comprise the second largest biomass in the ocean, where they are a driving force of microbial evolution and constitute important roles in Earth’s biogeochemical cycles. Bacteriophage (phage), viruses that infect bacteria, are of particular importance in the marine ecosystem as they impact the efficiency of the microbial loop, which recycles carbon in surface waters, counteracting vertical export through the biological pump. Although double-stranded DNA phage have been researched extensively, single-stranded DNA (ssDNA) phage remain understudied, mostly due to methodological limitations.

The incorporation of rolling circle amplification (RCA) into …

Sars-Cov-2 Neurotropism: Understanding Effects At The Blood-Brain Barrier And Hematogenous Neuroinvasiveness, Taylor E. Martinez

USF Tampa Graduate Theses and Dissertations

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus responsible for COVID-19, has provisional counts of over 110 million documented cases and 1.218 million deaths (as of February 2024) in the United States since January 2020. SARS-CoV-2 is an airborne respiratory virus that primarily infects the lungs via the ACE2 receptor but has well-documented secondary target organs including the kidneys, the gastrointestinal tract, the heart, and the skin. SARS-CoV-2 also infects the brain, but the hematogenous route of viral entry to brain is still not fully characterized. Understanding how SARS-CoV-2 traverses the blood-brain barrier (BBB) as well as how it …

The Polyaneuploid Cancer Cell State And Therapeutic Resistance: Eco-Evolutionary Dynamics In Structured Populations, Anuraag Bukkuri

USF Tampa Graduate Theses and Dissertations

In this dissertation, I develop and apply eco-evolutionary modeling techniques to understand how the polyaneuploid cancer cell (PACC) state, entered when aneuploid cells exit the cell cycle after S phase and undergo a whole genome duplication, contributes to therapeutic resistance. Since resistance remains one of the primary causes of treatment failure in cancer patients, it is critical to understand how such demographic state transitions allow for acclimatization of cancer cells to therapeutic stressors and how they interact with evolutionary processes to promote irreversible resistance.

In Chapters Two and Three, I lay the foundation for this work. In Chapter Two, I …

Emergent Magnetism And Hyperthermia In Phase- And Size-Tunable Iron Oxide Nanostructures, K Mudiyanselage Tharindu Supun Bandara Attanayake

USF Tampa Graduate Theses and Dissertations

Iron oxide nanoparticles (IONPs) hold immense potential across diverse fields, from spintronics, magnetic hyperthermia to drug delivery, biodetection, and magnetic resonance imaging. Unlocking these applications hinges on our ability to tailor the magnetic properties of IONPs, and this dissertation presents novel and powerful approaches for enhancing magnetic and hyperthermic responses of multiphase iron oxide nanostructures. This is achieved by manipulating their phase volume fraction, size, and shape with a focus on the magnetic tunability of nanostructures via strategic control over structural and environmental parameters. The aforementioned has been achieved by the following three key approaches: (i) phase-tunability of iron oxide …

Predicting Ph At In-Situ Temperature For Aquatic Environments, Sarah E. Bartoloni

USF Tampa Graduate Theses and Dissertations

pH is typically measured at a constant temperature and, as needed, converted to in-situ temperature using a system of thermodynamic equations. Using this equilibrium approach, adjustment of pH to in situ conditions requires two measured CO2 system parameters (pH, total alkalinity, dissolved inorganic carbon, or CO2 fugacity). Currently, when pH is the only measured CO2 system parameter, linear models are used to adjust the pH to in-situ temperature. Although many studies have attempted to optimize CO2 equilibrium constants (K1 and K2) for the CO2 system over a range of conditions, very little prior work has experimentally examined which CO2 system …

Macrophage-Driven Car T Cell Resistance In B Cell Lymphoma, Sae Bom Lee

USF Tampa Graduate Theses and Dissertations

Chimeric antigen receptor (CAR) T-cell therapy has revolutionized the treatment of patients with relapsed/ refractory large B cell lymphoma (LBCL). Despite its promising efficacy, a subset of patients experiences primary resistance or relapse. In Chapter 2, we explore the tumor microenvironment (TME)-induced resistance mechanisms in patients with LBCL. Analysis of the intratumoral immune infiltrates in pre-infusion tumor biopsies revealed that the levels of immunoregulatory macrophages were elevated in patients who responded poorly to axicabtagene ciloleucel (axi-cel). Using preclinical mouse B cell tumor models, we found that the CAR T-cell-produced interferon-gamma (IFN-γ) enhanced the expression of inducible nitric oxide synthase (iNOS, …

Exploring The Dynamics Of September Fish Spawning On The West Florida Shelf Through The Dna Barcoding Of Fish Eggs, Keith G. Keel

USF Tampa Graduate Theses and Dissertations

Identifying spawning areas for economically and ecologically important fishes is critical for fisheries conservation and ecosystem-based management. Additionally, monitoring the spawning dynamics of fishes is increasingly important as temperatures and oceanic conditions change. I used genetic barcoding to identify fish eggs collected across the West Florida Shelf (WFS) during September of 2013, 2014, and 2019. Fish eggs were collected on National Oceanic and Atmospheric Administration (NOAA) Southeast Area Monitoring and Assessment Program (SEAMAP) ichthyoplankton cruises using a Continuous Underway Fish Egg Sampler (CUFES). Analysis of 4,400 fish eggs from the three years resulted in the identification of 83 unique species …

Quality Of Life Factors In Children With Dual Diagnosis Stuttering And Autism Spectrum Disorder, Kristen N. Rollins

USF Tampa Graduate Theses and Dissertations

Addressing quality of life is a critical part of speech-language pathology. Understanding quality of life deficits and challenges in our patients’ lives allows us to provide well-rounded treatment. Quality of life in children who stutter and children with autism spectrum disorder has been heavily researched (children with autism spectrum disorder to a lesser extent). However, despite approximately 1 in 1000 children being dually diagnosed with stuttering and autism spectrum disorder (Briley & Ellis, 2018), quality of life in this population has never been researched. This thesis aims to determine whether children diagnosed with both conditions experience similar quality of life …

Tetr Family Regulator, Farr, Influences Rot-Mediated Control Of Virulence Factor Expression In Staphylococcus Aureus, Julia C. Schumacher

USF Tampa Graduate Theses and Dissertations

Point-mutation variants of the TetR family regulator, FarR, have emerged across Staphylococcus aureus sequence types as conferring antibiotic and fatty acid resistance, particularly in Hospital-Associated Methicillin Resistant S. aureus (HA-MRSA) strains. FarR also exhibits an additional largely uncharacterized relationship to virulence factor production, seemingly through the global repressor of toxins—Rot, which functions to regulate S. aureus’ ability to colonize and persist in the host via a complex cascade of signaling. While Rot protein is post-transcriptionally regulated by the highly characterized Agr system, there is little known about its transcriptional regulation. Herein, we explored these dynamics by initially characterizing virulence phenotypes …