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Tools For Biomolecular Modeling And Simulation, Xin Yang

Mathematics Theses and Dissertations

Electrostatic interactions play a pivotal role in understanding biomolecular systems, influencing their structural stability and functional dynamics. The Poisson-Boltzmann (PB) equation, a prevalent implicit solvent model that treats the solvent as a continuum while describes the mobile ions using the Boltzmann distribution, has become a standard tool for detailed investigations into biomolecular electrostatics. There are two primary methodologies: grid-based finite difference or finite element methods and body-fitted boundary element methods. This dissertation focuses on developing fast and accurate PB solvers, leveraging both methodologies, to meet diverse scientific needs and overcome various obstacles in the field.

“Return To Play”: The Impact Of, And Changes To, Ontario Children’S Physical Activity During Covid-19, Monika B. Szpunar Ms.

Electronic Thesis and Dissertation Repository

This dissertation explored parents’ and their children’s perspectives of returning to play/sport during the COVID-19 pandemic in Ontario, Canada, and assessed how children’s physical activity levels changed during COVID-19. To understand the initial impact of the pandemic, Study 1 (August 2020) explored the influence of family sociodemographic factors (e.g., housing type) and risk tolerance (using the validated Tolerance of Risk in Play Scale) on parents’ return to play/sport attitudes. Via interviews with parents (n = 9) and children (n = 12), Study 2 (December 2020 – January 2021) gathered participants’ experiences of getting active …

Does Acute Maximal Exercise Or Chronic Physical Activity Affect Circulating Angiotensin (1-9) Concentrations?, Kyle R. Weiman

Electronic Thesis and Dissertation Repository

Introduction: Epidemiological evidence suggests physical inactivity can increase the likelihood of hospitalization from the SARS-COV-2 virus. Further, some data indicate a greater ratio of angiotensin 1-9 to angiotensin I helps prevent severe outcomes during infection. Moreover, related hormones can enhance potentially both physical activity and health. The purpose of this study was to determine whether plasma concentrations of angiotensin (1-9) are modified after a single exhaustive exercise bout and whether sex or chronic physical activity is associated with greater plasma concentrations.

Methods: Participants (n=14) performed a graded exercise test on a cycle ergometer. Antecubital area venipunctures were performed before, immediately …

Development Of Recombinant Varicella-Zoster Virus Vaccines Expressing Sars-Cov-2 Antigens, Cody Wilson

Honors Theses

The COVID-19 pandemic caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) continues to cause infections and deaths around the globe. Since its emergence, scientists have worked diligently to discover and produce vaccines to battle the virus. While they successfully created and distributed vaccines, the vaccines are not without flaw. These vaccines do not grant long term immunity, require multiple booster shots, and have not prevented the emergence of viral variants. In this study, the SARS-CoV-2 receptor binding domain (RBD), which is a key part of the spike protein (S), and nucleocapsid (N) genetic sequences were inserted into the live varicella …

Human Milk: From Covid-19 Immunity To Breast Cancer Risk Assessment, Vignesh Narayanaswamy

Doctoral Dissertations

Breastmilk is a complex biological fluid containing macromolecules including lipids, oligosaccharides, proteins as well as several types of cells. Several studies have reported in detail of these components. My focus is studying the protein component of breastmilk, specifically antibodies, cytokines, and other secreted factors in the setting of different pathogenicity in women. Studies have demonstrated that the levels of numerous cytokines as well as the levels of pathogen-specific antibodies are altered in milk upon either maternal or infant infections. Additionally, there are reports that the levels of certain inflammatory markers are altered in milk among women with breast cancer or …

Three Essays On The U.S. Beef Supply Chain: Production, Marketing, And Price Dynamics, Erdal Erol

Theses and Dissertations--Agricultural Economics

This dissertation contains three essays on select economic components of the U.S. beef industry. The first and second essays concentrate on the different economic problems in beef cattle production. The third essay evaluates the price dynamics and the impact of COVID-19 along the beef supply chain.

The first essay explores the economics of culling decisions in cow-calf operations in the U.S. with a novel application of a dynamic mathematical programming model. The results provide an optimal culling strategy under the base model and a range of optimal strategies that vary with respect to different components such as fertility probabilities, market …

The Covid-19 Pandemic And Its Influence On The Human Immune System, Nicole L. Riha

Undergraduate Honors Theses

COVID-19 rapidly infected the world, and scientists continue to research how the disease spread and killed as many as it did by analyzing how it affects the human immune system and referring to past pandemics. Since the pandemic is ongoing, scientists do not fully understand how the virus works and if lockdowns were effective. Nevertheless, a discussion on what is known about COVID-19's influence on the human immune system is needed. With an understanding of the COVID-19 pandemic, scientists can make more effective treatments for COVID-19 and learn how to manage future pandemics.

Bioanalytical Studies Of Disease Protein Profiles: Maldi-Tof Ms, Prajkta Satish Chivte

Graduate Research Theses & Dissertations

Coronavirus disease-2019 (COVID-19), which is caused by a novel coronavirus named severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), has ravaged the world for the past 3 years. Even today, there still exists a need for rapid, accurate, economical and non-invasive diagnostic testing platforms that yield high specificity and sensitivity towards the constantly mutating SARS-CoV-2. Research has consistently indicated saliva to be a more amenable specimen type for early detection of SARS-CoV-2, compared to the oral and nasopharyngeal swabs. Considering the limitations and high demand of the existing COVID-19 testing platforms, this dissertation work studies used MALDI-ToF MS (matrix-assisted laser desorption/ionization-time of …

Optimizing Sample Collection And Data Interpretation For Effective Wastewater-Based Epidemiology In Combined Sewer Systems, Christopher Allen Anderson

Graduate Theses, Dissertations, and Problem Reports

COVID-19 has spurred growth in the science surrounding wastewater-based epidemiology (WBE) pertaining to the detection of severe acute respiratory virus 2 (SARS-CoV-2) in waste streams as an early warning signal for public health. However, the highly variable wastewater environment has made it difficult to standardize an approach for sampling and analysis, especially in locations using combined sewer infrastructure. This study addresses knowledge gaps of WBE via three specific aims: (1) to compare diurnal fluctuations of SARS-CoV-2 and the human fecal indicator, pepper mild mottle virus (PMMoV) in wastewater treatment plant (WWTP) influent samples collected during dry versus wet weather conditions; …

Impact Of The Washington State Covid-19 Lockdown On 5-10-Year-Ol School-Aged Children Residing In Kitties County, Peyton Rondeau

All Master's Theses

Background: The Washington State COVID-19 lockdown and subsequent school closures brought increased dependency on parents to provide nutritious meals and opportunities for physical activity for their children.

Purpose: The aim of this study was to describe the impacts of the Washington State COVID-19 lockdown on the dietary, physical activity, and screen time habits of children ages 5-10-years-old residing in Kittitas County.

Methods: A researcher-developed Qualtrics survey was created and validated via the Index of Item Objective Congruence. The survey was administered to parents via Facebook, using local Kittitas County Facebook groups.

Results: Most parents identified that the Washington lockdown negatively …

Role Of Tetraspanins In Sars-Cov-2 Fusion And Entry, Marcos Saul Santiago Figueroa

Master's Theses

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is responsible for the pandemic the world has been facing in recent years. Even as new countermeasures are developed, there is still much we don’t know in terms of its entry into host cells. Tetraspanins are transmembrane proteins that are near ubiquitous amongst cell types. They fulfill numerous roles, including that of a viral co-receptor. Here, we considered whether tetraspanins, specifically CD9, CD63, and CD81 influence SARS-CoV-2 fusion and entry. Using ACE2-LgBit and tetraspanin overexpressing EVs and HeLa cells, we find that the presence of excess tetraspanins inhibit fusion and entry. However, we …

From The Headlines: A Textual Analysis Of Social Polarization And Discord In Times Of Pandemic Across A Century In The United States, Alexa Demarco

Undergraduate Honors Theses

Within the past century, three major pandemics have affected the United States – the Spanish Flu, AIDS, and COVID-19. Each of these pandemics has tested the capabilities of the public health sector and the social resilience of the population. Scientists have studied the viruses and implemented public health measures to limit viral transmission, but the social responses to these preventative measures proved to be difficult to predict and control. The dissonance and polarization between the public health initiatives and the response of the general public in the most recent pandemic was apparent. Was this a pattern in other pandemics? Was …

The Impacts Of The Covid-19 Pandemic On The Food Security Of Mississippians, Hannah Noel Irwin

Theses and Dissertations

Mississippi leads the United States in food insecurity, with 15.3% of Mississippians experiencing food insecurity in a given year. To determine the impacts of the COVID-19 pandemic on the food insecurity of Mississippians, a survey containing the USDA Household Food Security Questionnaire was distributed to adult Mississippi residents. By employing the USDA Household Food Security Scale and the Foster-Greer-Thorbecke Methodology, this study finds that the food insecurity rate, food insecurity gap, and squared food insecurity gap have worsened in Mississippi since the beginning of the COVID-19 pandemic. Additionally, this study finds that households which were food insecure prior to March …

Sequencing The Guts Out Of Covid-19; The Evolution Behind The Covid-19 Pandemic, Madelyn Purnell

Undergraduate Honors Theses

The global COVID-19 pandemic has led to an urgent need for scalable methods for clinical diagnostics and tracking of virus variants. In this paper, we attempted a novel method of sequencing using Large Reverse Transcriptase-based cloning (LRTC). Although our methodology ended up not working due to high amount and fast degradation of RNA, we were able to sequence multiple variants of COVID-19 Positive samples from the BYU Student Health Center and 4 sewage samples to check for variant outbreaks in corresponding times. We were able to find several corresponding variants and track the progression of mutation in our local population.

Regulation Of Mhc Ii Trafficking And Expression By Host And Viral Factors, Alex Lac

Electronic Thesis and Dissertation Repository

Antigen presentation by major histocompatibility complex class II (MHC II) to the adaptive immune system is crucial for mounting sterilizing immune responses. This central role has made antigen presentation a target for antagonism by many pathogens. Notably, infections with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) decrease MHC II expression in several immune cells. The mechanisms responsible for this suppression are unknown but involves either redirecting MHC II molecules away from the cell surface or inhibiting MHC II expression. To understand how pathogens manipulate intracellular MHC II trafficking, we first investigated the role of the Golgi trafficking regulator, ERC1, in …

Examining The Association Between Brain Mri Measures At 7 Tesla And Cognition Following Covid-19 Infection, Helma Heidari

Electronic Thesis and Dissertation Repository

The long-term neuropsychological, cognitive, and neurobiological effects of the severe acute respiratory syndrome (SARS-CoV-2) in survivors with milder symptoms are still poorly understood. In this thesis we evaluated cognitive and psychological changes approximately five weeks after a wide range of symptoms in COVID-19 illness and determined whether advanced diffusion magnetic resonance imaging measures within subcortical brain structures of the limbic system were related to neurological, respiratory, psychiatric, and gastric symptoms experienced during the acute phase of illness. Cognitive and neuropsychological evaluations were performed in 45 participants who experienced neurological symptoms during the acute phase of COVID-19 illness. Participants also underwent …

Assessing Structural And Functional Brain Alterations And Work-Related Fatigue In Non-Hyposmic And Hyposmic Covid-19 Survivors, Rakibul Hafiz

Dissertations

In the year 2019, life began to change at the advent of a global pandemic caused by the novel coronavirus. Mask mandates and mass vaccinations have mitigated the effects significantly, yet cases keep rising with new variants, especially, in densely populated countries, like India. Recent neuroimaging evidence shows the virus can attack the central nervous system (CNS). However, exactly which brain regions undergo structural and functional changes remain largely unknown. Many patients experience 'loss of/reduced sense of smell' (i.e., hyposmic) and an alarming number of survivors develop persistent symptoms ('long-COVID') for several months after initial infection. Fatigue is the most …

Cellular Automata: The Mathematical Theory Behind The Spread Of Covid-19 And Prediction Of Future Spread, Alison Drumheller

Undergraduate Theses and Capstone Projects

This thesis seeks to analyze the spread of the original COVID-19 strain and develop a mathematical model to predict the chances of being infected by this disease using a number of variables. This model is based on the mathematical theory of cellular automata, otherwise known as the theory of spread. The research uses real world data of COVID-19 which includes infection rate, death rate, vaccination rate, use of masks, and transmission rates. By using cellular automata, we predict that the more preventative measures an individual puts in place for themselves, the less likely they are to be infected by the …

The Effects Of Wearing A Sports Mask Compared To A Standard Surgical Face Mask During The Forestry 5 Minute Submaximal Step Test, Christian Kumar

Undergraduate Theses and Capstone Projects

The existence of the COVID-19 global pandemic has forced the introduction of wearing face masks when in public spaces or in near proximity to others. Therefore, the purpose of this study was to determine the physiological effects and perceptions of wearing a sports mask compared to a standard surgical face mask during exercise. Nineteen subjects, 10 male and 9 female subjects ranging between 19-25 years of age completed the 5-minute Forestry Step Test randomized to wear either an Under Armour sports mask, a standard surgical mask, or wearing no mask. Resting and post-exercise heart rate, RPE, and metabolic data was …

The Impact Of Virtual Learning Modalities On The Academic Success Of Students In One Arkansas School District, Diane F. Richards

ATU Theses and Dissertations 2021 - Present

The COVID-19 pandemic changed the way Arkansas public schools’ offered students an education. While moving through this pandemic, many Arkansas schools implemented optional methods of delivery for their students. Some schools tried to maintain face-to-face classes, while others offered completely online classes. Still, others offered a hybrid format where students attended some face-to-face classes and online classes. One Arkansas school district offered all three options. School districts need guidance as to which teaching methods worked well. The long-term effects of the educational impact of COVID-19 are not known at this time. Schools could benefit from a guide with useful strategies …

The Use Of Nebulizer Medications As A Possible Treatment For Covid-19, Jacob Kaufman

Honors College Theses

For the past few years, the COVID-19 pandemic has been the focal point in healthcare and research. This disease has permanently changed daily life and left a historic impact on the world. Most people have felt the effects of this pandemic either directly, via infection, or indirectly, via change in workflow, financial impact, etc. The main question for this virus still remains today; how do we treat this illness effectively? While many ideas are being tested and suggested, a definite answer has yet to be procured. Vaccine rates are climbing on a daily basis, serving as the first and most …

Design And Development Of The Urban Population Health Observatory To Improve Disease Surveillance And Response, Whitney Brakefield

Doctoral Dissertations

Chronic and infectious diseases have a profound impact on the quality and length of life of populations that suffer from these conditions. Scientists, physicians, and health officials are seeking innovative approaches to decrease the morbidity and mortality of deadly diseases. Incorporating artificial intelligence and data science techniques across the health science domain could improve disease surveillance, intervention planning, and policymaking. In this dissertation, we describe the design and development of the Urban Population Health Observatory (UPHO), an explainable knowledge-based multimodal big data analytics platform. A common challenge for conducting multimodal big data analytics is integrating multidimensional heterogeneous data sources, which …

Developing And Applying Computational Algorithms To Reveal Health-Related Biomolecular Interactions, Yixin Xie

Open Access Theses & Dissertations

Computational biology is an interdisciplinary area that applies computational approaches in biological big data, including protein amino acid sequences, genetic sequences, etc., which is widely used to analyze protein-protein interactions, make predictions in drug discovery, develop vaccines, etc. Popular methods include mathematical modeling, molecular dynamics simulations, data science mythology, etc. With the help of computational algorithms and applications, drug development is much faster than traditional processes, as it reduces risks early on in a drug discovery process and helps researchers select target candidates that have the highest potential for success. In my doctoral research, I applied multi-scale computational approaches to …

Pandemics And Animal Welfare: How The Covid-19 Pandemic Has Affected The Companion Animal Industry In Northwest Arkansas, Sabrina Cox

Animal Science Undergraduate Honors Theses

The first cases of coronavirus reported in the United States came in January 2020 (World Health Organization, 2020). In the two years since then, countries around the world have been affected by COVID-19 and the subsequent social, economic, and mental health issues. Previous research shows that the animal healthcare field is already overrun with burnout, substance abuse, depression, and increased levels of stress (Gardner & Hini, 2006), and the pandemic has only compounded these issues (Mair et al., 2020). Observing a lack of meaningful reporting on the issues affecting veterinary staff led the researchers to investigate staff members’ practices, day- …

Nutritional Status In Critical Care Of Covid-19 Patients, Dolph Lewis Davis Iii

Theses and Dissertations--Nutrition and Food Systems

Critical care nutrition is a poorly researched, and such a sudden pandemic event requiring manipulation of nutritional status via propofol-induced sedation for mechanical ventilation is potentially impactful on patient outcomes. This paper seeks to provide context to the impact of critical care protocols on the nutritional status of obese patients suffering from COVID-19.

Development Of Balanced Budget Bites And Feasibility Evaluation, Holly Hansen, Kendra Kattelmann, Kathryn Morrison, Becky Jensen, Hailey Millner, Addison Reimer, Jen Sip, Brittany Canfield, Cydney Chamberlain

Health and Nutritional Sciences Graduate Students Plan B Capstone Projects

Objective: Balanced Budget Bites was created to educate individuals of Feeding Brookings about different cooking techniques, food safety, meal planning, budgeting, and financial resources in the Brookings, SD area while highlighting lower-cost food items. Participants and Recruitment: The target audience of Balanced Budget Bites were individuals that participated in Feeding Brookings that were recruited for four weeks via a flyer and a posting of the flyer on Feeding Brookings’ Facebook page. Method and Implementation: Participants of Feeding Brookings completed a pre-survey before taking Balanced Budget Bites to assess their skills, confidence, and knowledge related to nutrition and finance. The online …

A Study Of Mutations In Sars-Cov-2 Genomes, Michael Andrew Welford

Graduate Research Theses & Dissertations

The COVID-19 pandemic caused by the SARS-Cov-2 virus has affected the lives of everyone around the world. There has been a rapid appearance of new variants. As the variants affected the efficacy of vaccines, it is important to study the mutations of the variants. A pipeline of tools, SARS-CoV-2 Analyzer, was created to study the mutations in the most mutated S-gene of SARS-Cov-2. Two batches of data were used in this study: all samples available at The National Center for Biotechnology Information (NCBI) were downloaded in September 2021 (before the emergence of the first omicron variant) and December 2021 (after …

Effects Of Covid-19 Mandates On Student Engagement And Management Of Collegiate Equestrian Teams, Travis Fortune

Murray State Theses and Dissertations

Events like a global pandemic can negatively impact how organizations and groups function. From a collegiate perspective, this could include limiting or eliminating participation in co-curricular activities that have positive impacts on student experiences. Students use these events to make new friends, socialize and generate a sense of belonging, and gain interactions outside the classroom. In March 2020, a number of mandated restrictions were put into place in the United States in response to COVID-19, and collegiate equestrian teams' ability to practice and show were negatively impacted. Even though some restrictions were beginning to ease as of Fall 2021, many …

Flashbulb Memories Among College Students During Covid-19, Sabah Qureshi

Honors Undergraduate Theses

Flashbulb memories are formed through widely shared events that have affected the culture and community. The “flash” in flashbulb memories refers to the specific details that individuals have developed in their memories. The presented research focuses on the specific event of college students at the University of Central Florida (UCF) hearing about university closure due to the COVID-19 pandemic. This research study sought to identify the variables that have affected the accuracy of flashbulb memories formation regarding the event of college students hearing about university closure because of the pandemic. The variables of the students’ relevance to the university, location, …

A Comparison Of Chimpanzee Wound Rates Before And During Covid-19 Zoo Closures, Robin Elana Salak

All Master's Theses

Visitor effect studies have had inconsistent impacts on animals, due in part to the inability to control for all confounding variables such as time of day, seasonal weather patterns, and so forth. This study represents the first instance where chimpanzee (Pan troglodytes) wounding frequencies were investigated across extensive time periods in the presence and complete absence of visitors, thus eliminating many visitor-related variables. Additional variables were eliminated through the zoo selection process, based on institutional responses to a 29-question survey, providing a novel approach to the question of visitor effects. The aim of this study was to determine …