Digital Commons Network^™

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 …

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 …

An Investigation Of Quaternary Metal Chalcogenide Semiconductors Possessing Intrinsically Low Thermal Conductivity, Oluwagbemiga P. Ojo

USF Tampa Graduate Theses and Dissertations

Inorganic materials with unique physical properties are vital components of modern technology, from electronic devices to energy storage and conversion systems. Recent advancements in materials research and development have garnered significant interest, particularly in the realm of sustainable energy applications like thermoelectrics and photovoltaics. The development of novel materials with enhanced electronic and thermal properties has emerged as a focal point in advancing these critical applications. Furthermore, low thermal conductivity materials are sought after for technologically significant applications such as thermal barrier coatings, rewriteable data storage utilizing phase change materials and thermoelectrics. However, the current efficiency levels of materials used …

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 …

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 …

Classifying Traumatic Brain Injury: Associations With Executive Functioning And Externalizing Behavior, Lauren F. Fournier

USF Tampa Graduate Theses and Dissertations

Traumatic brain injury (TBI) involves a head injury that is, for some individuals, associated with long-term behavioral difficulties, including externalizing behaviors. The literature on TBI and its links to externalizing is limited in several important ways. First, there is evidence that current classification system of mild, moderate, or severe is imprecise and contains important variation within TBI categories. Second, TBI and externalizing are understudied among high functioning individuals, such as undergraduate students, despite rates of TBI among this population that are similar to those of the general population. Third, while it is theorized that executive functioning deficits explain the association …

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 …

Subtropical Estuarine Ecosystems Display Both Long-Term Stability And Change, Garrett L. Miller

USF Tampa Graduate Theses and Dissertations

Subtropical estuaries often support abundant and diverse faunal assemblages, but it is unclear how these productive ecosystems are responding to climate change. In the eastern Gulf of Mexico, estuarine faunal assemblages have been sampled for decades as part of a fisheries-independent long-term monitoring program. I assessed trends in submerged aquatic vegetation, water temperature, and the abundance, richness, and structure of faunal assemblages over more than two decades in four estuarine systems using this dataset. I used both univariate and multivariate analyses to quantify and describe the dynamics of these habitat and faunal variables. Further, I separated my analyses for summer …

Internalized Binegativity, Alcohol Consumption, And Expectancies Following An Experience Of Binegativity: An Experimental Study, Alexander P. Rivera

USF Tampa Graduate Theses and Dissertations

Individuals who identify as bisexual have repeatedly been found to consume alcohol at higherrates than individuals who identify as heterosexual or homosexual and are at greater risk for developing AUD. Per the Minority Stress Model, this heightened risk for bisexuals’ poor alcohol outcomes may be attributed to experiences of bisexual-specific stressors (i.e., experienced binegativity) and beliefs about their own bisexual identity., which have previously been associated with increased alcohol use. To date, however, no studies have examined if experiences of binegativity are associated with changes in internalized binegativity and alcohol outcomes in an experimental design. The current study aimed to …

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 …

The Joint Effects Of Sleep And Pain, And Moderations By Work Characteristics, Christina Xuong Mu

USF Tampa Graduate Theses and Dissertations

Reactivity describes interindividual differences in the physiological or emotional responses following an antecedent stressor. For instance, higher stressor reactivity to shorter sleep (i.e., those who report greater stressor severity following shorter-than-usual sleep) and higher negative affective reactivity to stressors (i.e., those who report more negative affect following a stressful event) have worse mental and physical health. Pain reactivity to shorter sleep is a novel concept that describes differences in pain responses following a night of shorter-than-usual sleep. Higher pain reactivity to shorter sleep means that individuals report more pain locations or higher pain severity following shorter-than-usual sleep the previous night, …

Sargassum In The Florida Keys: Assessment Using High Resolution Remote Sensing, Sarah “Sully” Sullivan

USF Tampa Graduate Theses and Dissertations

Pelagic Sargassum in the Atlantic Ocean, one type of floating macroalgae, has increased in biomass and extent since 2011, bringing environmental, health, and economic issues to coastal communities. The introduction of large quantities of Sargassum to the Florida Keys, a tourism hub renowned for coral reef and marine diversity, poses a potentially devastating threat. Currently, Sargassum mats are widely monitored using medium resolution satellite imagery such as those collected by the Moderate Resolution Imaging Spectroradiometer (MODIS, 1km) and spectral band difference algorithms such as the Alternative Floating Algae Index (AFAI), but the resulting maps lack the detail and nearshore certainty …

Navigating Shrinking Cities: Towards Coordinated Urban Development From The Perspective Of Flow And Network, Yuzhou Chen

USF Tampa Graduate Theses and Dissertations

As cities worldwide undergo rapid but uneven changes, proposing smart and sustainable urban development strategies has been a popular interdisciplinary research in the 21st century. In particular, the phenomenon of shrinking cities characterized by economic recession and population decline is becoming increasingly severe in developed countries and even developing countries. In the real world, research focusing on individual shrinking cities often neglects the interconnectedness between cities within the network formed by flows. Therefore, coordinating the development strategies for multiple closely connected cities, especially for shrinking cities, is a step up from focusing on individual cities.

This dissertation aims to propose …

Did I Do That?: Lived Experience And Media Representation Of The Awkward Black Girl, Kendra Williams

USF Tampa Graduate Theses and Dissertations

For my thesis project I will introduce the Awkward Black Girl as a new race gender script. Though there are minor nuances of the Awkward Black Girl within television, Issa Rae’s performance of the Awkward Black Girl in Misadventures of Awkward Black Girl and the HBO hit series Insecure remains prevalent to contemporary media representations. Though there is limited scholarship within the field of Communication available about the Awkward Black Girl, most of the scholarship consists of analysis and discourse centering Rae’s portrayal in her web series and television show. I explore Quinta Brunson’s portrayal of the Awkward Black Girl …

Confronting Sexism On Tiktok: Is Sarcastic Humor Effective?, Rebecca A. Upton

USF Tampa Graduate Theses and Dissertations

Confronting sexism is important but can be difficult because of the social backlash that is associated with it. However, many individuals have begun to call out sexism online. For example, the social media platform TikTok is an increasingly popular space for women to confront misogyny. In one current trend, creators target individuals who create sexist content by using sarcasm to humorously mock their original video. In this study, I examined the effectiveness of this trend in persuading observers and how the use of sarcastic and mocking humor influences perceptions of a woman confronting sexism. 492 participants were randomly assigned to …

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 …

Modeling And Optimization Of Time Delay Unit Network Architectures For Reducing Complexity Of Ultra- Wideband Phased Antenna Arrays, Daniel A. Ramirez

USF Tampa Graduate Theses and Dissertations

This dissertation presents a systematic technique for modeling and optimization of the hierarchical time delay unit (TDU) architectures of ultra-wideband (UWB) phased antenna arrays (PAAs). The first major contribution of this dissertation is the optimization of a linear PAA by casting the problem in the standard form of integer linear programming (ILP) optimization with an objective function that targets minimizing the total number of TDUs within the RF feed network fanout while maintaining phase error and manufacturability constraints. This optimization can significantly reduce the cost, power, and complexity of UWB PAAs in contrast to prior methods that iteratively converge on …

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 …

Effects Of Intercultural Interactions In 3d Virtual World On Efl Students’ Intercultural Communicative Competence, Foreign Language Anxiety, And Motivation, Umi H. Saidah

USF Tampa Graduate Theses and Dissertations

Virtual worlds (VWs) as emerging technologies have been perceived as positive by students for foreign language (FL) learning. VW affordances of presence and immersion have enabled FL researchers and practitioners to design and develop classroom-like environments in virtual settings, allowing authentic intercultural interactions from different geographical locations, in a variety of languages. This study conducted mixed methods research to deliver English lessons via an immersive 3D VW for avatar-context-avatar interactions via voice chat with a view to improving ICC necessary for effective intercultural interaction. The avatar-avatar interactions were between a native English-speaking instructor and English as a foreign language (EFL) …

Developing Cultural Humility Through The Arts: Evaluating An Arts Intervention For Healthcare Provider Leaders, Katie L. Nickel

USF Tampa Graduate Theses and Dissertations

At all levels of healthcare, providers are experiencing rising levels of professional burnout. For healthcare provider leaders, burnout is particularly critical since leaders must maintain healthy and trusting relationships with patients and their teams of healthcare professionals. This utilization-focused evaluation study explores an arts intervention program designed to promote cultural humility among healthcare providers. Increased cultural humility may provide coping tools for healthcare providers to ward off burnout. The arts intervention took place over three sessions: one at a museum, one virtual, and one at a hospital. Four types of data were collected including a quantitative pre- and post-survey, observation …

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 …

A Phase-1 Trial Of Intensive Hybrid Stuttering Modification/Fluency Shaping Therapy, Jessica Smith

USF Tampa Graduate Theses and Dissertations

Purpose: The purpose of this study was to analyze changes in frequency stuttering behaviors, speech rate, and feelings/attitudes following the University of South Florida Program for Advanced Treatment of Stuttering (USF-PATS), a hybrid stuttering modification/fluency shaping program intended for teenagers and adults who stutter moderately to very severely.

Method: Baseline and post-treatment speech samples for participants (N = 3) were analyzed for speech rate and presence of stuttering behaviors (repeated movements, fixed postures, and superfluous behaviors) across conditions (monologue and reading). An abbreviated thematic analysis was completed to analyze feelings/attitudes post-treatment.

Results: Results revealed a decrease to zero and near-zero …

Uprooted, Displaced, Resilient: Kosovar Women’S Narratives Of Organizing For Survival During The Kosovo War, Erjona Gashi

USF Tampa Graduate Theses and Dissertations

The goal of this dissertation is to foreground Kosovar women’s narratives and organizing properties during the Kosovo War. I examine the overlooked gendered roles and day-to-day lived experiences of Kosovar women, survivors of the Serb genocide, political violence, and oppression, and investigate their organizing properties during the Kosovo War (1998-1999). In acknowledging women’s plurality of experiences and perspectives, I challenge the currently pervasive and monolithic narrative of women as passive victims of war present in scholarship in organizational communication and instead make overt the narrative of women as critical organizational actors that sustain lives during and after the war. Using …

Organizing Queer Civil Rights Movements: Pride Parades And Communicative Dilemmas, David J. Dooling

USF Tampa Graduate Theses and Dissertations

Pride parades (“Pride”) are sites of communicative tension for the queer community. While the political origins of queer civil rights practiced widespread resistance to institutional heteronormativity and homophobia, Pride is a space where business owners, community stakeholders, and activists debate the political utility of queerness. This dissertation employs queer and sociomaterial theoretical traditions, and autoethnographic methodological approaches to explore the communicative strategies of Pride organizers—individuals who create, coordinate, and conceptualize the display of sexuality and gender in the public sphere. I draw on tension-centered approaches to organizational communication, feminist dilemmatic theorizing, and co-sexuality to investigate power-laden structures and decision-making in …

Abundance, Distribution, And Diversity Of The Paralarval Cephalopod Community In The Northern Gulf Of Mexico, Shannon Leah Riley

USF Tampa Graduate Theses and Dissertations

The abundance, distribution, and diversity of cephalopod paralarvae from the upper water column (0-130 meters) in the northern Gulf of Mexico (GOM) was studied using samples collected during six ichthyoplankton surveys between 2009 and 2012. A total of 2240 cephalopod paralarvae belonging to 21 families were examined. Octopodidae, Enoploteuthidae, and Ommastrephidae were the most abundant taxa collected in the time series. Five taxa had significantly different abundances between some sampling periods, while no significant differences in abundance occurred between any GOM regions (northwest GOM shelf, north-central GOM shelf, West Florida Shelf, GOM slope, and GOM basin). The majority of taxa …

Differences In Speech Patterns Produced By Spanish-English Language Learners During Single-Language And Mixed-Language Remote Academic Vocabulary Instruction, Ester Garcia

USF Tampa Graduate Theses and Dissertations

Individuals with lower proficiency in a second language tend to produce more disfluent speech patterns in the second language. Speech disfluencies refer to interruptions in the forward flow of speech and are distinct from the colloquial use of “fluency,” to characterize knowledge of a language. Prior research indicates that some speech disfluency patterns may be more common among Spanish-English bilingual children, who tend to produce more mazes (fragments of an utterance) and syllable repetitions than their monolingual peers. These patterns have been attributed to 1) acquiring a new language; 2) the influence of Spanish as a first language (L1) on …

Spectral Properties Of Wetlands In Michigan Using Remote Sensing To Identify And Classify Wetlands In Roscommon County, Michigan, Kolin Williamson

USF Tampa Graduate Theses and Dissertations

Biological, geological, and physical. These are only a handful of the many environmental aspects that wetlands functions maintain and protect. Unfortunately, wetlands within the United States have been razed at an alarming rate. The State of Michigan has not gone through this unscathed either, loosing over 1000 acres of wetland a year. One of the most important tools to prevent this destruction are the maps and programs that show where these essential ecosystems are located. The current, federally-created maps and imaging software in use by environmental consultants and contractors may not be up to date which can pose challenges for …

Public-Private Partnerships In Student Housing: A Qualitative Content Analysis Of Acuho-I Publications, Ana Mercé Mcdermott Hernandez

USF Tampa Graduate Theses and Dissertations

This study examines public-private partnerships (P3s) as represented in the Association of College and University Housing Officers – International (ACUHO-I) publications from 1951-2023 and shares themes and patterns found. P3s have been used for on-campus student housing since the 1960s, yet the method is not well represented in the discourse of the student housing profession. The purpose of this qualitative content analysis is to serve as a resource for higher education administrators to support the evaluation of the P3 methodology for future student housing projects.

Less than 2% of the 12,264 ACUHO-I publication entries reviewed were related to on-campus student …

The Effect Of Fixed Time Delays On The Synchronization Phase Transition, Shaizat Bakhytzhan

USF Tampa Graduate Theses and Dissertations

Nature is full of synchronization phenomena, which are essential to many scientific fields like biology, chemistry, physics, and neuroscience. The Kuramoto model is a well-known theoretical model that helps explain the fundamental ideas behind synchronization dynamics [6]. Nevertheless, in practical situations, systems frequently display intrinsic latency, which can greatly impact their behavior during synchronization. This insight inspired our work, which looks at the results of adding temporal delays to the Kuramoto model. In particular, we investigate how the system’s synchronization dynamics are affected by delays. We shed light on the mechanisms underpinning synchronization in the face of temporal delays and …

Modeling The Human Learning Process Using An Industrial Steam Boiler Analogy To Design A Psychophysiological-Based Hypermedia Adaptive Automation System, Liliana María Villavicencio López

USF Tampa Graduate Theses and Dissertations

This dissertation aims to address the existing gap in the integration of various dimensions within the student learning system, encompassing cognitive, emotional, and physical variables. The primary objective is to construct a Personalized Learning Adaptive Automation model using Electroencephalography (EEG) technology.

To provide deeper insight into the intricate nature of the Human Learning Process, this study introduces a novel analogy with an Industrial Steam Boiler. This analogy serves as a distinctive contribution to research in the field.

The research methodology involved the collection of brainwaves data from engineering students while they undertook educational tasks of varying levels of difficulty, categorized …