Physical Sciences and Mathematics Commons^™

The Application Of Multi-Isotope Analysis To Assist In Geoprofiling Unidentified Decedents Within Florida, Liotta D. Noche-Dowdy

USF Tampa Graduate Theses and Dissertations

The biochemistry of human tissues can provide information for geoprofiling (geographic birthplace or migration patterns) of an unidentified decedent. Utilizing isotope analyses (both stable and radiogenic) from teeth, bone, nails, and/or hair reveals specific isotopic information that correlates to diverse geographic regions reflecting an individual’s birthplace and migration patterns. Isotope analysis of enamel and bone has been employed in bioarchaeology for decades to reconstruct the diet, health, and migration patterns of past populations. Isotope ratios measured from enamel can then be compared to isotope ratios measured from bone of the individual to track patterns of migration. The enamel from the …

3d Organ-Scale Models Of Tumor Growth And Treatment, Rafael Ramon Bravo

USF Tampa Graduate Theses and Dissertations

To understand the dynamics of cancer, mathematical oncologists have developed models of tumor growth and treatment response. Some models are mechanistic and approach tumor growth at the cell-scale, focusing on the evolution of cancerous cells within the ecology of normal tissue, and are often simulated with agent-based modeling. Other models are more clinically motivated and model tumor growth operating at the organ-scale, using patient data to predict treatment response, and are often simulated with partial differential equations. We developed the Hybrid Automata Library which includes both agent-based modeling and partial differential equations for modeling at either of these scales. We …

Development Of Decision-Support Tools For Water Resources Management In Coupled Human-Natural Systems, Edgar J. Guerrón Orejuela

USF Tampa Graduate Theses and Dissertations

Water is an indispensable resource for all forms of life. Water is a cornerstone for economic development, public health, and social well-being. However, increasing water demand and challenges posed by climate change, pollution, population growth, and land use change underscore the urgent need for effective water management strategies. To address these complexities and ensure the sustainable use of water resources, it is imperative to adopt science-based decision-support tools. These tools leverage data, models, and analytical techniques to provide valuable insights and recommendations that guide decision-makers in formulating evidence-based policies and practices.

Effective water management requires a comprehensive understanding of the …

Local Seismic Investigations In Arizona: Analysis Of A Low-To-Moderate-Magnitude Aftershock Sequence And A Pilot Study Of Monsoon-Driven Flash Floods, Kathryn Margo Dorn

USF Tampa Graduate Theses and Dissertations

Arizona encompasses a strikingly diverse array of geological terranes and physiographic terrain and consequently experiences a wide range of tectonic and meteorological phenomena, many of which generate distinctive seismic signals. For much of the past century, however, the state has largely lacked the style of dense seismic networks now prevalent in some regions of neighboring California, allowing myriad low-magnitude earthquakes and other subtle seismic sources to elude detection and characterization. In this dissertation, I utilize the high-resolution data of two temporary local seismic networks to investigate two such sources – the primarily low-magnitude but prolific aftershock sequence of the 29 …

An Inference-Centric Approach To Natural Language Processing And Cognitive Modeling, Animesh Nighojkar

USF Tampa Graduate Theses and Dissertations

Reasoning over natural text is highly nuanced, and interpretations can vary widely depending on cultural background, financial status, age, gender, or even mood. This doctoral dissertation seeks to not only mimic human reasoning behaviors but also improve the task used in natural language processing (NLP) to capture naturalistic reasoning, known as the Natural Language Inference (NLI) task. NLI involves determining whether a hypothesis is true (entailment), false (contradiction), or indeterminate (neutral) based on a given premise. Initially, we will investigate the extent to which NLP systems designed to capture semantic equivalence actually measure meaning equivalence. After establishing that they do …

The Asymmetric Total Synthesis Of Membranolide And Efforts Towards The Oxeatamides, Sean Bradley

USF Tampa Graduate Theses and Dissertations

Total synthesis is a discipline within organic chemistry that is a constant force that propels the field forward. In our lab, we have immersed ourselves within the field of total synthesis to gain access to complex natural products, perform SAR studies, as well as highlight interesting methodology. Within these endeavors, we have completed the first asymmetric synthesis of membranolide. This has allowed us to explore potential biofilm eradication in our efforts to develop novel therapeutics to combat the ESKAPE pathogens and multi-drug resistance. We have also begun to pursue the first asymmetric total synthesis of the oxeatamides. By utilizing our …

Reimagining Web Design: Empowering Agency Of Specialized Audiences Through User-Centered Heuristics, Haley Jones

USF Tampa Graduate Theses and Dissertations

This research seeks to create an alternative model for website design that interrogates standardized, linear ways of knowing and being by placing the audience at the center of the web design process. This research contributed a reimagined approach to traditional and standardized web design heuristics by considering an audience-centric methodology that was practical and applicable for web design praxis to create equitable user experiences which can empower audiences to recall their own knowledge and experience to make meaning for themselves through a reimagining of knowledge-making processes in a network of digitized information. In perceiving the rhetorical choice in design of …

Resolving Antarctic Margin Paleoceanography For Two Different Timescales And Archives, Theresa M. King

USF Tampa Graduate Theses and Dissertations

Recent decades have seen increased rates of ice mass loss from Antarctic ice sheets, through thinning of many ice shelves around the periphery of the continent. The most vulnerable are the glacial systems that are marine-terminating and grounded below sea level, a characteristic that exposes these systems to sea level rise and warming oceans. Enhanced basal melting under the influence of warm ocean water masses can lead to thinning and retreat of glaciers, and ultimately to the acceleration of grounded ice loss. To contextualize current ice mass loss and contribute to accurate model projections for future retreat scenarios, it is …

Antarctic Atmosphere-Ocean-Ice Interactions During Past Warm Climates: An Ice-Proximal Perspective, Imogen Mireille Browne

USF Tampa Graduate Theses and Dissertations

Antarctica’s ice sheets contain 58 m of sea level equivalent ice and thus exert a fundamental control on global sea level on decadal to million-year timescales. Interactions between Antarctica’s ice sheets, regional atmospheric circulation, and the Southern Ocean influence ice sheet mass balance, sea ice formation, and deep water production, which regulate Earth’s climate. At present, Antarctica’s fringing ice shelves and outlet glaciers, particularly in West Antarctica, are losing mass as warm ocean waters move landward across the continental shelves, melting the underside of ice shelves and eroding glacial grounding lines. In East Antarctica, net ice mass gain is occurring …

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 …

Investigation Of The Use Of Recycled Concrete Aggregates In Porous Asphalt Mixture, Asad Elmagarhe

USF Tampa Graduate Theses and Dissertations

This study aims to address the national need for using recycled concrete in road pavements. This is especially important in the governmental and corporate sectors, where reducing the cost and carbon footprint of construction projects is a priority. The long-term goal is to meet the public demand for environmentally friendly infrastructure and minimize the harmful effects of waste disposal on humans and the environment.

The project focuses on using recycled concrete aggregate (RCA) in porous asphalt pavement to reduce stormwater runoff, a popular environmentally friendly road design. However, compared to regular dense asphalt mixtures, porous asphalt mixtures (PAM) are more …

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 …

Stochastic Analytical Predictive Models For Life Sciences And Crop Production Process, Erasmus Tetteh-Bator

USF Tampa Graduate Theses and Dissertations

Analytical predictive modeling uses algorithm-based mathematical, probabilistic and statistical methods to anticipate future events by identifying patterns in past data. It is a technique for predicting outcomes and a key application of statistical analysis in real-world scenarios. Real data-driven predictive models in various fields, such as life sciences, economics,or production industry, help individuals and institutions make data-driven informed decisions, which is essential for business success, providing companies with a competitive edge.

One of every five adult deaths is caused by heart disease and one person dies every 33 from cardiovascular disease in the United States according to the Center for …

Optimizing Cybersecurity Operations Using Data-Driven Intelligence, Jalal Ghadermazi

USF Tampa Graduate Theses and Dissertations

Cybersecurity operations centers (CSOCs) play a crucial role in safeguarding organizations from cyber threats. CSOC operations are divided into two main areas: Intrusion detection systems (IDS) and security response team (SRT) operations. Machine learning (ML) and deep learning (DL) advancements have significantly improved IDSs. IDS can be either flow-based, suitable for offline analysis, or packet-based, which analyze traffic in real-time. However, packet-based IDS often treat packets independently, ignoring the sequential nature of network communication. Additionally, recent ML/DL approaches also struggle with capturing global and structural information and novel attack detection due to their reliance on labeled data. The SRT within …

Transforming Organizational Cyber Security With Artificial Intelligence And Data-Driven Optimization, Soumyadeep Hore

USF Tampa Graduate Theses and Dissertations

This dissertation presents a comprehensive framework for enhancing organizational cybersecurity through data-driven intelligence. The research integrates multiple methodologies to tackle challenges in network intrusion detection and vulnerability management within cybersecurity operations centers (CSOCs). First, the research investigates vulnerability prioritization and mitigation techniques currently employed by CSOCs. To further streamline the vulnerability prioritization and mitigation process a machine learning (ML)-based Vulnerability Priority Scoring System (VPSS) is introduced, significantly improving the prioritization and mitigation of context-sensitive vulnerabilities. The VPSS outperforms traditional methods, reducing the cumulative vulnerability exposure score by up to 30% by considering both organizational context and vulnerability severity. Next, the …

A Robust Data-Driven Framework For Artificial Intelligent Systems, Quoc H. Nguyen

USF Tampa Graduate Theses and Dissertations

Artificial Intelligence (AI) systems have demonstrated remarkable performance across various domains. However, their robustness remains a critical concern, particularly in terms of data and model reliability. This dissertation aims to address the challenges associated with building robust AI systems by focusing on two key aspects: data robustness and model robustness. Data robustness poses significant challenges, including data shift, concept shifting, limited and imbalanced datasets, and interoperability issues in IoT systems for data collection. Existing methods fall short in handling dynamic business objectives and evolving data landscapes effectively. To bridge these gaps, we propose an IoT framework that ensures interoperability, seamless …

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 …

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 …

Optimal Selection Of Good Polynomials And Constructions Of Locally Recoverable Codes Via Galois Theory, Austin Dukes

USF Tampa Graduate Theses and Dissertations

To keep up with the ever-growing demand for reliable and efficient availability of data,locally recoverable codes (LRCs) have been the focus of much study due to their applications in cloud and distributed storage systems. A fundamental construction of LRCs was given in [36] based on polynomials which relied on the existence of r-good polynomials. In the same paper some constructions of good polynomials were given, but these constructions did not cover every configuration of parameters. Naturally this led to research into constructing good polynomials for what was not addressed in [36], but new ponderings were also posed, such as the …

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 …

Painting A New Perspective On Ordovician Echinoderm Diversity Patterns, Ohav Barak Harris

USF Tampa Graduate Theses and Dissertations

The Ordovician Period was a time of great biotic and environmental change, encompassing two important biotic events: the Great Ordovician Biodiversification Event (GOBE) and the Late Ordovician Mass Extinction (LOME). The GOBE occurred during the Middle Ordovician and was a period of rapid diversity increase for marine invertebrate groups, as lower-level taxonomic groups like families and genera came into the forefront. The Ordovician ends with the LOME, an extinction event that is thought to have occurred in two phases: an initial glaciation followed by a subsequent warming. Approximately 85% of marine species went extinct during the LOME, making it the …

Specification, Enforcement, And Measurement Of Integrity Policies, Kevin Dennis

USF Tampa Graduate Theses and Dissertations

The first step to improving an organization's security posture is to define the organization's security goals. At a technical level, these goals are expressed as security policies. Security policies are predicates over programs, that return true or false if the program adheres to the policy. Defining these policies correctly is thus essential to ensuring the overarching security goals are met, but it is often quite difficult to translate human-oriented goals into their technical policy counterparts. In addition, these policies must be specified so that they are enforceable while minimizing false positives and false negatives. Integrity policies, which specify how data …

Unveiling Ferroelectric And Multifunctional Insights In Hybrid Formate Perovskites, Abduljelili Popoola

USF Tampa Graduate Theses and Dissertations

Formate perovskites, denoted as AB(HCOO)3, represent a diverse group of hybrid organic-inorganic compounds, renowned for their numerous phase transitions and a wide array of properties. These properties encompass (anti)ferroelectricity, ferroelasticity, (anti)ferromagnetism, and multiferroism. Despite extensive research on these materials, a comprehensive examination of their properties across a substantial number of formate perovskites remains scarce. This scarcity stems from structural complexity of these materials, potential systematic errors arising from different measurement techniques or incomplete data. For instance, data for critical parameters like piezoelectricity, dielectricity, and elasticity tensors have been lacking.

In this study, we address these challenges by employing first-principles density …

Evaluation Of Reduced Graphene Oxide For Advanced Thermal Management In Microwave Electronics Packaging, Utkarsh Misra

USF Tampa Graduate Theses and Dissertations

The continuous push towards making electronic devices smaller and denser, largely driven by the demand for higher power capabilities, has led to a critical need for innovative and comprehensive methods for managing the heat these devices generate. Traditional cooling solutions for electronics often rely on methods such as copper-based layers or channels to distribute and dispel heat. However, these conventional methods and materials are becoming increasingly insufficient, especially for Radio Frequency (RF) and millimeter-wave electronics. These components are becoming ever more compact while requiring more power, thus presenting unique challenges for thermal management in their packaging.

In this thesis we …

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 …

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 …

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 …

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 …

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 …