Digital Commons Network^™

Constituent Partitioning Consensus Docking Models And Application In Drug Discovery, Rainer Metcalf

USF Tampa Graduate Theses and Dissertations

This work expounds on some of the current computational tools and programs available and the best practices associated with their use. A high-level introduction, intended for both novices and the semi-experienced, focusing on the more common programs used in scientific literature is the scope of this topic. Both classical and quantum techniques are described. Classical methodologies include Molecular Dynamics, Monte Carlo, energy minimization methods, molecular docking, low-mode, and homology modeling. Quantum chemistry techniques are also discussed encompassing Hartree-Fock, Post-Hartree-Fock theories, and Density Functional Theory along with associated basis sets.

Along with established methodologies, novel theoretical methods are introduced for furthering …

Development Of A Voxel-Based Monte Carlo Radiation Dosimetry Methodology For A Targeted Alpha Particle Therapy, Christopher John Tichacek

USF Tampa Graduate Theses and Dissertations

The use of targeted ligands to deliver radioisotopes directly to tumor cells is a promising therapeutic strategy. Because of the short path length and high LET of alpha particles, targeted alpha particles are ideal for treating metastatic disease while minimizing damage to non-targeted tissues. However, clinical methods for determining 3D radiation dosimetry in patients with multiple metastatic lesions are needed to support clinical translation of novel targeted alpha particle therapies for personalized treatment, especially in patients that have previously received radiotherapy. Recently interest in novel radiopharmaceutical development has grown significantly. However, compared to external beam radiation therapy, progress in customizing …

Ratios And Proportional Reasoning Representations In Open Educational Resources, Keisha L. Albritton

USF Tampa Graduate Theses and Dissertations

This study analyzed Open Educational Resource (OER) textbooks to determine similarities and differences between the resources in relation to the content addressing ratio and proportional reasoning standards. This study also analyzed whether the selected resources provided opportunities for students to engage with the Standards for Mathematical Practice. Data were collected from tasks within the 6th and 7th-grade textbooks from Engage NY, Open Up Resources and Utah Middle School Math Project. Each task was analyzed according to frameworks from Van de Walle (2007), Lamon (2012), Lesh et al. (1988) Tall and Vinner (1981), and Hunsader et al. (2014). The tasks were …

An Ecology Of Care: Training In Dependence And Caretaking In The Witcher 3: Wild Hunt, Elizabeth Rossbach

USF Tampa Graduate Theses and Dissertations

This project investigates the popular open-world fantasy RPG, The Witcher 3: Wild Hunt (CD Projekt RED 2015) and the ways in which the Witcher 3 brings questions of care and dependence to a digital medium so often thought of in terms of violence and/or mastery. Much of the previous discourse on video games, particularly role-playing games, has tended to center on violence and what this might mean for players behavior or the potential real world effects of this violence. Departing from a focus on violence I argue that the Witcher 3, reveals the potentials of open-world RPG video games to …

Development Of Α-Aa Peptides As Peptidomimetics For Antimicrobial Therapeutics And The Discovery Of Nanostructures, Sylvia E. Singh

USF Tampa Graduate Theses and Dissertations

For decades it has been convention to use antibiotics for the treatment of bacterial infections. Due to the overuse and misuse of these drugs, bacteria are becoming resistant to these treatments. This phenomenon has led to the search for alternative antibiotics, and in the study of Host Defense Peptides (HDPs). HDPs are the body’s innate immune response to infection. They are known to modulate immune system response and kills bacterial using various methods causing them to be less susceptible to bacterial resistance. The method by which we can mimic these biological peptides is called peptidomimetics. Various research shows the use …

The Role Of Secreted Proteases In Regulating Disease Progression In Staphylococcus Aureus, Brittney D. Gimza

USF Tampa Graduate Theses and Dissertations

Staphylococcus aureus is a highly successful pathogen capable of producing a wealth of virulence factors in the human host. Of note, ten extracellular proteases are produced alongside these virulence factors and play a multifaceted role during infection. They not only cleave host proteins to promote bacterial invasion, immune evasion and survival, but also control disease progression by modulating the stability of self-derived pathogenic determinants. The importance of the secreted proteases modulating virulence factor stability is evidenced by our groups previous finding that a protease-null strain has a substantially increased infectious capacity in a murine model of sepsis; resulting from the …

Education In The Settler Colony: Displacement, Inequality, And Disappearance Via Charter Schools, David R. Fisher

USF Tampa Graduate Theses and Dissertations

The encroachment of market-based practices on public education has resulted in the creation of vouchers, charter schools, virtual schools, home schools, and other forms of educational choice. While there has always been choice in education in the United States for the wealthy and White, the current conception of school choice, in theory, allows equal access to education for all. Undergirding the neoliberal practice of school choice is a connection to a troubling past of capitalist oppression and settler colonialism. Like settler colonialism, the practice of school choice has resulted in the displacement of educators, families, and students, inequality between different …

A Novel Cytokine Response Modulatory Function Of Mek Inhibitors Mediates Therapeutic Efficacy, Mengyu Xie

USF Tampa Graduate Theses and Dissertations

Despite the recent success of immune-checkpoint blockade therapy for late-stage non-small cell lung cancer (NSCLC), lung cancer is still the leading cause of cancer deaths worldwide. One of the most important characteristics of lung cancer in therapeutic decision-making are the targetable molecules, including EGFR, ALK, BRAF, and MEK. The excitement of immune-checkpoint blockade therapy has triggered concerted efforts that focus on exploring combinations of immune checkpoint therapy with other approved therapeutic regimens aiming at further augmenting positive outcomes and survival. However, the lack of understanding of underlying mechanisms and evidence-based clinical testing has hindered the progress to a cure. Hence, …

Cactus-Based Mucilage As A Natural Dispersant For Crude Oil Spills, Fei Guo

USF Tampa Graduate Theses and Dissertations

Oil spills are a critical threat to the marine environment, and the spilled oil as a source of pollution can have long-term adverse effects on the marine ecosystem. Traditional mechanical clean-up operations have apparent advantages for dealing with small and medium-scale oil spills. For large-scale oil spills, dispersants are a practical and minimally influential approach to the environment. As the dispersant components are iteratively updated, dispersants become more efficient and safer. However, the toxicity of the dispersants remains a significant impediment to their application. An efficient and non-toxic dispersant is increasingly becoming a requirement.

The cactus mucilage extracts studied in …

Exploration Of Gratitude In Cardiovascular Health: Mediators, Medication Adherence And Psychometrics, Lakeshia A. Cousin

USF Tampa Graduate Theses and Dissertations

The purpose of this dissertation was to explore the effect of gratitude on cardiovascular health outcomes using mediators, medication adherence, and psychometrics. The specific aims were to (1) establish the state of the science for gratitude and cardiovascular health outcomes via a state-of-the-science literature review, (2) explore mediators affecting gratitude and medication adherence using a structural equation model in patients with cardiovascular disease, and (3) analyze the psychometric properties of the Gratitude Questionnaire-6, a self-report questionnaire designed to assess individual differences to express dispositional gratitude, to provide evidence for the validity and reliability of the instrument in African Americans at …

(Re)Making Worlds Together: Rooster Teeth, Community, And Sites Of Engagement, Andrea M. M. Fortin

USF Tampa Graduate Theses and Dissertations

My research examines the communicative practices by which fans of the entertainment brand Rooster Teeth (RT)—with millions of members around the world engaged with one another through in-person meetups, as well as a variety of digital spaces — constitute community. I study these moments in communication in terms of sites of engagement, or real-time windows where actions occur through the intersection of people, mediational means, and social practices. My research is important for a contemporary understanding of communities, as well as being critical in considering how our online and offline practices are inextricably tied in ways we have only begun …

Epidemiological Analysis Of Malaria Decrease In El Salvador From 1955 Until 2017, Tatiana I. Gardellini Guevara

USF Tampa Graduate Theses and Dissertations

The disease of malaria is complex, with clinical presentation that ranges from severe and complicated to mild and uncomplicated or even to asymptomatic malaria. A recent effort made by several world organizations has shown important advances in the effort to control and eradicate malaria. Following the general ordinance established by the trans-border organizations, each country has tried to define, according to their local geopolitical scenario, individual ¨road maps¨ to succeed in reducing the morbidity and mortality caused by malaria. Moreover, it is now accepted universally that these road maps need to be revised and appropriated in order to correct actions …

"The Weak Are Meat, And The Strong Do Eat"; Representations Of The Slaughterhouse In Twentieth And Twenty-First Century Literature, Stephanie Lance

USF Tampa Graduate Theses and Dissertations

This dissertation explores how literary representations of the slaughterhouse predict the trajectory of human greed that is fueled by capitalist economic practices that shape environmental policies. I argue that literature brings attention to what is generally hidden from public view: the way humans and animals are erased in the production of food, which includes the inhumane treatment of humans and other animals in the slaughterhouse. The literature in this dissertation provides an avenue through which we can investigate the entangled oppression of humans and other animals in an effort to challenge perceptions that reduce animals, and marginalized humans, to objects. …

An Investigation Into The Heterogeneity Of Insect Arylalkylamine N-Acyltransferases, Brian G. O'Flynn

USF Tampa Graduate Theses and Dissertations

Arylalkylamine N-acyltransferases (AANATs) have in recent years been suggested as potential new insecticide targets. These promiscuous enzymes are involved in the N-acylation of biogenic amines to form N-acylamides. Mammalian AANAT is predominantly associated with circadian rhythm regulation, as it catalyzes the formation of N-acetylserotonin, the precursor of melatonin, from serotonin. In insects, this process is a key step in melanism, as well as hardening of the cuticle, removal of biogenic amines, and in the biosynthesis of fatty acid amides. The unique nature of each insect AANAT (iAANAT) isoform characterized indicates that while catalyzing similar reactions, each insect accommodates …

Assessing The Effects Of Observational Conditioning And Response-Contingent Pairing On Increasing Vocalizations In Children With Asd, Sydni Chance

USF Tampa Graduate Theses and Dissertations

Children with an Autism Spectrum Disorder (ASD) often display impairments in communication. More specifically, children with ASD may have difficulty developing language skills, for e.g., delay in verbal behavior, limited echoic skills, and/or lack of functional communication. A common way to combat this deficit is by increasing vocalizations in these children. Previous research has used various procedures to attempt to condition vocalizations as reinforcers, such as stimulus-stimulus pairing, response-contingent pairing (RCP), and operant discrimination training. Another procedure for conditioning stimuli is observational conditioning (OC), which is a type of observational learning. However, OC has not been assessed as a procedure …

Understanding The Influence Of The Cancer Microenvironment On Metabolism And Metastasis, Shonagh Russell

USF Tampa Graduate Theses and Dissertations

Cancer is a complex and heterogeneous disease. Not only is there considerable variability between different cancer types, but there is enormous variability between and within patients who have the same type of cancer. Within tumors, there are multiple cell types, including cancer cells, stromal cells, and immune cells. The tumor microenvironment often induces the healthy cells to become pro-tumorigenic. Cell metabolism is exquisitely sensitive to changes in the tumor microenvironment and can be measured to infer the aggressiveness of cancer and predict response to therapy. In this dissertation, we aim to understand how the microenvironment, specifically low pH, affects the …

Seeing King Solomon Through The Verses Of Hafez: A Critical Study Of Two Safavid Manuscript Paintings, Richard W. Ellis

USF Tampa Graduate Theses and Dissertations

This thesis is focused on a previously unpublished collage comprised of two manuscript fragments from Safavid Iran. One fragment contains a painting that depicts an enthronement scene featuring King Solomon, which, as I argue, was taken from a copy of the Majalis al-Ushshaq by Kamal al-Din Gazurgahi. The other fragment contains verses from the Divan of Hafez. The fragment from the Divan has been gutted and overlaps the painting of Solomon, effectively framing the image. Through visual and textual analysis, I argue that both fragments come from manuscripts that were produced in Shiraz. I further argue that the painting of …

Measurement Of Changes In Forest Fragmentation Caused By Road Construction Between 2000 And 2014 Using Gis In St. Johns County, Florida, Ahmet Karatas

USF Tampa Graduate Theses and Dissertations

Forests play a crucial role in maintaining the natural balance. They have essential features and structures used in the protection of flora and fauna. Human activities such as road construction disrupt ecosystems and negatively impact natural habitats. Roads cause forest fragmentation, and as a result of this, fragmentation has various negative effects on the natural habitat. These effects lead to loss of biological diversity, road mortality, habitat loss, fragmentation, and air pollution. The major goal of this study was to analyze changes in forest area, forest fragmentation, and forest road impacts using GIS for St. Johns County, Florida, between the …

Desertification Risk Analysis Based On Soils And Climate In Olive Cultivated Areas In Tulare County, California, Zehra Kavakli Karatas

USF Tampa Graduate Theses and Dissertations

Desertification is one of the most critical environmental problems caused by human activities and climate change. As a result of human activities, land degradation has been seen in many agricultural areas. Intense pressure on cultivated fields causes loss of soil fertility, which can then lead to desertification. Planting plant drought-resistant plants, such as olives, is one strategy for reducing desertification risk in cultivated areas. It is essential to find a way not only how to combat this process but also how to adapt or survive with desertification conditions. Defining desertification risks have a fundamental role in combating drought. The goal …

Life History Through The Eyes Of A Hogfish: Evidence Of Trophic Growth And Differential Juvenile Habitat Use, Meaghan E. Faletti

USF Tampa Graduate Theses and Dissertations

Understanding ontogenetic linkages among fish habitats is critical for conservation of fish populations and the ecosystems on which they rely. Natural tags such as stable isotopes are an effective tool commonly used to investigate ecological questions regarding fish movement and habitat use. Here, I analyzed stable isotopes from the sequentially deposited laminae of Hogfish (Lachnolaimus maximus) eye lenses from the eastern Gulf of Mexico (eGOM) to investigate trophic and geographic changes across individual life histories. I documented evidence of entire-life scale trophic growth through increases in δ15N. I also observed depth separation at the juvenile stage, evidenced by variation in …

Adaptations Of Ovid’S Metamorphoses In Late Medieval France: Material And Moral Recontextualization In The Tapestry Of Narcissus At The Fountain, Morgan J. Macey

USF Tampa Graduate Theses and Dissertations

As a result of Ovid’s prominence in Northern Europe from the twelfth through the sixteenth centuries, French adaptations of and commentaries on the Metamorphoses from the late medieval period abound. Here, I address the physical and moral transformation of the Narcissus myth in the tapestry of Narcissus at the Fountain. Specifically, I explore how the tapestry’s presentation of the youth transforms Ovid’s verse in a tantalizing yet moralizing image. To aid in this endeavour, I survey the intermediate sources which inspired said transformation. I argue the lavish clothing, lush garden, ornate fountain, and solemn reflection featured in the tapestry …

Evaluating The Effect Of Temperature On A Human Parasite And Its Intermediate Snail Host: Implications For A Changing Climate, Karena H. Nguyen

USF Tampa Graduate Theses and Dissertations

Global climate change is impacting the emergence, re-emergence, prevalence, and incidence of infectious diseases worldwide, including parasitic diseases of humans (Blum and Hotez 2018). Neglected tropical diseases, defined as a group of parasitic diseases affecting developing countries in the tropics (Hotez et al. 2007), are of particular concern because these diseases occur in areas that are also expected to experience rapid population growth and agricultural development in the coming decades. As human population and food demand increase, the greater the likelihood of humans encountering intermediate hosts that either inhabit agricultural areas or are impacted by agricultural development, which will influence …

Evaluating The Evidence Base For Evidence-Based Instructional Practices In Chemistry Through Meta-Analysis, Md Tawabur Rahman

USF Tampa Graduate Theses and Dissertations

Investigating the effectiveness of instructional practices provides an evidence base to inform instructional decisions. Synthesizing research studies on instructional effectiveness provides an estimate of the generalizability of effectiveness across settings, along with an exploration of factors that may moderate the impact, which cannot be achieved within individual studies. This study sought to provide a synthesis of evidence- based instructional practices (EBIPs) particular to chemistry through meta-analysis. 99 studies were analyzed comprising a broader view of chemistry specific studies than past meta-analyses. The results showed that EBIPs feature a demonstrably positive impact on students’ academic performance in chemistry, although assessment topic …

Chemolithotrophic Denitrification Of Nitrate Contaminated Groundwater Using Sulfur-Bearing Minerals, John Sutton

USF Tampa Graduate Theses and Dissertations

Nitrate contamination in groundwater resources poses a serious threat, not only to the health of those who would drink it, but also as a potential nutrient for eutrophication. Current methods of nitrate removal can efficiently remove nitrate below 10 mg/L as nitrogen, but may require resources unavailable to small community water systems (SCWS). Sulfur-oxidizing biological denitrification is a promising alternative that may be more suitable for SCWS. Sulfur-oxidizing denitrification has previously been shown to have a high nitrate removal efficiency; however, it produces water high in sulfate. Utilization of sulfide-bearing minerals, rather than elemental sulfur as an electron donor, may …

Fewer Wetlands More Connectivity: Implications Of Land Use-Land Cover Change In An Agricultural Landscape, Stephanie Lawlor

USF Tampa Graduate Theses and Dissertations

St. Lucie County (SLC) is a 1,782 km2 area in east-central Florida that drains to the Nationally Significant Indian River Lagoon (IRL). It is low lying and nearly level, with widespread non-floodplain wetlands (NFWs) and few natural channels. NFWs comprise the vast majority of SLC wetlands, both in terms of numbers and area. Since the early 20th century, SLC has undergone extensive land use-land cover (LULC) change and is now characterized by citrus farming in the interior and municipalities on its eastern coast on the Atlantic Ocean. This LULC change has been made possible by the construction of an extensive …

Sundaas Story: A Mixed-Methods Study Of Household Sanitation Provisioning In Urban Informal Housing In India, Sarita Vijay Panchang

USF Tampa Graduate Theses and Dissertations

The aims of this research were to examine sanitation insecurity in urban informal housing through the lens of the built environment, social disparities, and health implications. While the Millennium Development Goals for halving the global proportion of people without access to safe drinking water were met ahead of schedule, progress fell short for sanitation, creating new objectives for the Sustainable Development Goals to be met in 2030. Much research in the Global South is dedicated to community-level sanitation promotion, but often presumes a rural rather than urban setting. Urban informal housing settings constitute a unique challenge due to the range …

Autonomy, Suffering, And The Practice Of Medicine: A Relational Approach, Michael A. Stanfield

USF Tampa Graduate Theses and Dissertations

In this project, I argue that the conventional view of personal autonomy that is operational in contemporary American culture, bioethics and medical practice places undue emphasis on individualism and a limited range of personal qualities and attributes (such as self-sufficiency). Instead, I argue in favor of a relational approach to autonomy which recognizes that each person that exists has certain minimal connections or relations to others, and these connections/relations are identity-forming. Unfortunately, current medical practices have tended to overemphasize individuality and choice (consistent with the conventional view) while minimizing or excluding these relational aspects. As a result, informed consent and …

Design And Delivery Of Synthetic Mrna By A Peptide Nanoparticle, John H. Lockhart

USF Tampa Graduate Theses and Dissertations

The field of synthetic mRNA therapeutics is a rapidly expanding arm of gene therapies. The use of mRNA provides multiple benefits over viral or DNA vectors. synthetic mRNA vectors are immediately translated into protein after entering the cytoplasm of cells in contrast to DNA vectors that must first be transcribed to mRNA in the nucleus. This allows synthetic mRNA to produce a therapeutic protein in any cell type, including non-dividing cells. In addition, the non-replicative nature of mRNA means that insertional mutagenesis or generation of escape mutants is not a concern. However, the stimulation of innate immune responses by unmodified …

The Combined Effect Of Heat And Corona Charge On Molecular Delivery To A T-Cell Line In-Vitro, Molly A. Skinner

USF Tampa Graduate Theses and Dissertations

Gene therapy and immunotherapy are new up and coming fields in cancer treatment. In August of 2017, the first gene therapy was FDA approved called CAR-T cell therapy("FDA approval brings first gene therapy to the United States," 2017). This therapy uses the patient’s

own T-cells that are genetically modified to attack the cancerous cells. Currently, it takes 4-6 weeks to genetically modify these T-cells, which can be the difference between life and death for a cancer patient (Cheng, Jun, Jiang, & Xi, 2017). There is evidence that gene electrotransfer can help expedite the genetic modification process by having an easy …

Design And Implementation Of Degenerate Qpcr/Qrt-Pcr Primers To Detect Microbial Nitrogen Metabolism In Wastewater And Wastewater-Related Samples, Ryan F. Keeley

USF Tampa Graduate Theses and Dissertations

Nitrogen cycling processes can be tracked using quantitative Polymerase Chain Reaction (qPCR) to determine the presence and qReverse Transcriptase-PCR (qRT-PCR) to determine expression of key genes, or ‘biological markers’, for nitrogen metabolism. Nitrification is catalyzed in part, by two enzymes: ammonia monooxygenase (AMO; NH3 NH2OH) and nitrite oxidoreductase (NXR; NO2- NO3-). For denitrification, four enzymes act sequentially: nitrate reductase (NAR/NAP; NO3- NO2-), nitrite reductase (NIR; NO2- NO), nitric oxide reductase (NOR; NO  N2O), and nitrous oxide reductase (NOS; N2O  N2). A principle of wastewater treatment (WWT) is to remove excess nitrogen by taking advantage of natural nitrogen cycling …