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Modeling Dna Repair In Escherichia Coli Using A Boolean And Stochastic Framework, Gabrianne Ivey

All Theses

DNA can be damaged through both internal and external sources. Therefore, cells have created methods to repair DNA damage. In Escherichia coli, the system responsible for DNA repair is termed the SOS response. This system consists of more than 50 genes and contains three main repair pathways: nucleotide excision repair, translesion synthesis, and homologous recombination. The response is initiated when DNA lesions result in the accumulation of single-stranded DNA (ssDNA). The protein RecA is activated by binding to ssDNA and is then denoted RecA*. RecA* assists in the auto-cleavage of LexA which is the primary repressor protein involved in …

Development Of Novel Pharmaceutical For Optimization Of Opioid Overdose Treatment, Larae Kram

Celebrating Scholarship and Creativity Day (2018-)

Although opioids are highly effective drugs for pain management, their overuse and addictive nature has caused an opioid epidemic, resulting in many cases of opioid addiction and overdose. There are two current opioid overdose drugs that are FDA approved: naloxone and nalmefene. These drugs have a higher affinity to the active binding pocket on the opioid receptor than opioids do and displace the opioids, preventing any further binding of the opioid and halting the opioid’s effects. However, naloxone is not active long enough to outlast the duration of the opioid and nalmefene causes severe withdrawal symptoms. The development of more …

Glacial-Interglacial And Millennial-Scale Changes In Nitrous Oxide Emissions Pathways And Source Regions, J. A. Menking, J. E. Lee, E. J. Brook, J. Schmitt, L. Soussaintjean, H. Fischer, J. Kaiser, A. Rice

Physics Faculty Publications and Presentations

During the transition from the Last Glacial Maximum (LGM) to the Holocene, the atmospheric N2O mole fraction increased by 80 nmol mol−1. Using ice core measurements of N2O isotopomer ratios, we show that this increase was driven by increases in both nitrification and denitrification, with the relative partitioning between both production pathways depending on the assumed isotopic end‐member source signatures. Similarly, we also attribute a 35 nmol mol−1 N2O mole fraction increase during the Heinrich Stadial 4/Dansgaard Oeschger 8 (HS4/DO8) millennial‐scale event to increases in both N2O production pathways. In contrast, the 25 nmol mol−1 N2O mole fraction decrease during …

Monitoring The Qosh Tepa Canal Project: A Geospatial Timeline Of Taliban Water Diversion, Enerel L. Crosslin

Honors Thesis

The World Food Program states that “acute malnutrition in Afghanistan is above emergency thresholds in 25 out of 34 provinces and is expected to worsen”. Aiming to support agriculture, the Taliban began to build the 285 km “Qosh Tepa Canal” to divert 17% of the Amu Darya, which supports the livelihoods of millions of people in downstream Uzbekistan and Turkmenistan. The World Bank estimated that roughly 2.4 million Central Asians could become climate refugees by 2050. Our objectives are to create a timeline of satellite imagery of the canal’s construction. Our research questions are (1) Can we characterize water diversion …

Synthesis And Characterization Of 3,5 Trifluoromethyl Tpm With A Metal Carbonyl Complex, Emily P. Berkman

Undergraduate Honors Thesis Collection

Tris(pyrazolyl)methane (Tpm) ligands have a central carbon with 3 pyrazole rings attached. These were discovered in 1970 and have since been synthesized with many substituents on the rings. Based on the parent structure, my goal was to synthesize a fluorinated Tpm derivative. By adapting existing procedures, I have synthesized a Tpm derivative with trifluorinated methyl groups in the 3 and 5 positions of the pyrazole ring. The fluorinated ligand is expected to be electron withdrawing and exhibit interesting chemistry when bound to a metal center. Future directions of the project will be discussed.

Disulfide-Cleavable Linkers In Antibody-Drug Conjugates For Targeted Cancer Therapy, Emily Hwang

Undergraduate Honors Thesis Collection

This project aims to discover a way to improve the safety of and reduce adverse side effects of disulfide-linked antibody-drug conjugates. Disulfide-cleavable linkers for antibody-drug conjugates function by exploiting the differential concentrations of dominant thiol species in the blood plasma and in the cytosol of malignant cells. This project aimed to identify a relationship between the stability of disulfide cleavable linkers in the blood plasma and disulfide linker structure, to prevent premature release of the cytotoxic drug. Three disulfide linker analogs with varying carbon chain lengths were synthesized through reaction with 2,2’-dipyridyl disulfide. Each analog was conjugated to a fluorescent …

Cultural Health Benefits And Challenges Of Food Preparation And Consumption: A Comparative Study Of The United States, Italy, And Norway, Natalie G. Link

Undergraduate Honors Thesis Collection

This study aims to investigate the cultural health benefits and challenges associated with food preparation and consumption in the United States, Italy, and Norway, with a particular focus on citizens in lower socioeconomic levels. By examining the dietary habits, social structures, and health outcomes in these three countries, this research aims to uncover broader insights into the health status and well-being of their respective populations. The study will employ secondary data analysis approach examining existing research on cultural practices and social support systems. The findings of this research will contribute to a deeper understanding of the complex interplay between food …

Semiconductors In Space: Data Analysis Of Microgravity's Impact On Crystal Formation, Keegan Jo Jackson

Undergraduate Honors Thesis Collection

Comprehensive data analysis on crystal growth in microgravity is a requisite to inform understanding of prior work. Our research constructed and analyzed a database containing data gathered from research focusing on semiconductors grown in microgravity. Data curation spanned multiple decades, countries, and semiconductor materials. All relevant reported information was recorded in the database, notably data regarding the metrics used to determine the impact space had on crystal growth: size, structure, uniformity, and performance. After data cleaning and data processing, the database was organized and readied for analysis. Data analysis was performed using RStudio and SciKit-learn. RStudio was employed for data …

Linking The Past And The Future: Understanding How Pollutants Cause Corrosion During An Oddy Test, Kylie Blair Blake

Undergraduate Honors Thesis Collection

Artifacts and artwork continue to tell a story long after a time or culture has disappeared. Preventive art conservation science involves careful and responsible management of the objects entrusted in the care of the museum staff to ensure environmental and display conditions do not cause damage so future generations can observe and learn about past cultures. An accelerated metal corrosion test, the Oddy test, has been used to help determine the suitability of display and storage materials. The Oddy test is subjective, so newer methods are being developed involving the use of gas chromatography and mass spectrometry to identify specific …

A New Transition Metal Borate, Co6(B24O39(Oh)6(H2O) 6·2.21h2O, Synthesized Via A Mild Hydrothermal Synthesis, Alevtina Maksimova, Patrick Belt, Nilah Whitfield, Mark D. Smith, Gopabandhu Panigrahi, Gregory Morrison, Hans Conrad Zur Loye

Faculty Publications

A new transition metal borate hydrate, Co₆B₂₄O₃₉(OH)₆(H₂O)₆·2.21H₂O, was synthesized via a mild hydrothermal method using boric acid as the melt. The compound crystallizes in the trigonal space group P 3‾ with lattice parameters a = b = 13.17840(10) Å, c = 12.3287(2) Å, and a unit cell volume of 1854.27(4) ų (Z = 2). This borate hydrate crystallizes in a new structure type comprised of layers containing [BO3] trigonal planar units and [BO4] tetrahedra that are linked by CoO6 and Co(OH)2(H2O)4 octahedra via corner-sharing. The …

Biodegradable Active Packaging: Exploring The Antimicrobial Efficacy And Compostability Of Chitosan-Based Films, Rachel Mchugh

All Theses

The overarching purpose of this experiment is to create an active packaging component that has both antimicrobial and biodegradable properties specifically designed for poultry food products. For the scope of this study, the packaging component created would theoretically be used in conjunction with another material, such as a poultry tray which are commonly used for fresh poultry products. Based on the scope and purpose of this experiment, biopolymer films and coatings were considered after the initial literature review. Due to the goals of the packaging component, chitosan, a polysaccharide shown to have antimicrobial properties and an inherent ability to biodegrade, …

Kernel Density Estimation And Convolution, Nicholas Tenkorang

Open Access Theses & Dissertations

Kernel Density Estimation (KDE) is a widely used technique for estimating the probability density function of a random variable. In this study, we revisit KDE through the lens of convolution and extend this perspective to special cases such as positive, bounded and heavy tailed random variables. Building on this foundation, we propose a novel simulation-based density estimation method that generates new data by adding noise to observed values and then smoothing the resulting histogram using splines. A minor adjustment to natural cubic splines is required to ensure nonnegative estimates. The noise is drawn from a class of bounded polynomial kernel …

Electrochemically Precipitated Struvite Effects On Extractable Soil Nutrients, Owen Collins

Crop, Soil and Environmental Sciences Undergraduate Honors Theses

Struvite recovery from wastewater streams may provide an alternative to traditional fertilizer-phosphorus (P) sources, while also providing the benefit of reducing nitrogen and P loads in wastewater effluent and reducing effects of eutrophication in surface waters. Limited research has been conducted to assess the effects of struvite fertilization on concentrations of soil micronutrients and potassium (K) compared to other traditional fertilizer-P sources in historically agricultural soils. The objective of this study was to assess the effects of fertilizer-P source (i.e., synthetically produced electrochemically precipitated struvite [ECST], chemically precipitated struvite [CPST], monoammonium phosphate [MAP], diammonium phosphate [DAP], triple superphosphate [TSP], rock …

Reevaluating The Role Of Ruppia Maritima: Recruitment Dynamics And Habitat Use By Blue Crabs (Callinectes Sapidus) And Associated Benthic Fauna In A Mid-Atlantic Seagrass Community, Delaney St. Pierre

Theses, Dissertations and Culminating Projects

The value of seagrasses as essential fish habitat is well recognized, but limited data exist on the value of one particular species, Ruppia maritima (widgeon grass), as habitat for fish and invertebrates. During the summer of 2024, I evaluated R. maritima, Zostera marina (eelgrass) and mixed beds to assess their relative value as habitat in Barnegat Bay, New Jersey. Results from throw traps indicated significant monthly differences for pipefish, gobies, blue crabs, grass shrimp, and sand shrimp, driven by active recruitment events. When evaluating habitat type, we found no taxa that were significantly more abundant in Z. marina habitat as …

Thermal Biology Of The Eastern Treehole Mosquito Aedes Triseriatus (Diptera: Culcidae) And Other Vertivorous Dipterans, Kelly I. Zimmerman

Theses, Dissertations and Culminating Projects

Temperature plays a critical role in mosquito life cycle, behavior, and other ecological interactions. My dissertation analyzed how temperature affects egg hatch rates of the eastern treehole mosquito (Aedes triseriatus) and how amino acid substitutions in TRPA1 correlated with host finding through thermotaxis and the convergent evolution of vertebrate feeding/utilizing in Dipterans. As ectotherms, embryonic development and egg hatch rates are directly influenced by the water temperature mosquito eggs are oviposited into. Ae. triseriatus eggs do not hatch all at once, to avoid potentially high larval mortality rates due to their non-static oviposition sites. They engage in staggered egg hatching, …

Advancing Drug-Drug Interaction Prediction Using Multi-Modal Feature Integration With Graph Neural Networks, Ernest C. Chianumba

Theses, Dissertations and Culminating Projects

Pharmaceutical treatments are essential for managing medical conditions, but drug-drug interactions (DDIs) pose significant risks to patient safety and healthcare outcomes. This research integrates Knowledge Graphs and Graph Neural Networks to predict DDIs by exploring complex drug relationships. We construct a comprehensive knowledge graph using DrugBank data (1,000 drugs, 155,774 interactions) enriched with molecular features from PubChem. Our methodology introduces a novel multi-modal approach by integrating transformer-based embeddings (ChemBERTa, SPECTER, and SBERT) to create 1152-dimensional feature vectors that capture structural, biomedical literature, and semantic properties of drugs. Formulating DDI prediction as a link prediction task, we compare three Graph Neural …

Implementation Of Residual Tandem Neural Networks For Photonic Inverse Design, Ponthea A. Zahraii

Electrical Engineering and Computer Science (MS) Theses

Deep-learning approaches can greatly benefit the modeling and design of nanophotonic and optical structures. Traditional full-wave simulations are time and resource-intensive, which can act as a bottleneck in photonic design. On the other hand, deep-learning approaches for designing the response of nanophotonic geometries can be computationally inexpensive and produce accurate and efficient results. In this project, we specifically investigate the case of optical forces near meta-structures. We propose using an inverse design approach with residual blocks to account for the deep nature of this architecture and inherently address the non-uniqueness problem. A tandem approach, which consists of two interconnected models, …

Synthesis Of Single Chain Polymer Nanoparticle Networks By Reinitiating Raft Polymerization, Dallas Donovan

Honors Theses

Hydrogel materials, which are polymer networks comprised mostly of water, hold significant promise for biomedical applications due to their compatibility with biological systems. Conventional hydrogel materials are often brittle and weak, but most applications in biomedical systems require materials to be strong and tough. The topology of a polymer network dictates its mechanical properties. An important strategy for designing tougher hydrogels is the release of stored length, such as from the unfolding of polyprotein cross-linkers. Inspired by the success of the strategy, we report progress towards a fully synthetic design using single chain nanoparticles (SCNPs) into a hydrogel. SCNPs, which …

Compartmental Disaggregation: Bridging Simulation And Sampling Methods For Synthetic Population Data Generation, Dylan Mack

McKelvey School of Engineering Graduate Student Theses & Dissertations

As agent-based models (ABMs) grow increasingly widespread in public health, their associated challenges have become all the more significant. Lauded for their ability to capture population heterogeneity, nonlinear dynamics, and emergent behaviors, disease ABMs are also computationally expensive and often require detailed inputs that describe each agent at the individual-level, known as synthetic population data. Current approaches for synthetic population data generation generally fall into one of two categories: sampling or simulation. These methods are both feasible only under restricted conditions and suffer from challenges surrounding data availability and computing power. This thesis proposes compartmental disaggregation, an intermediate method for …

Novel Methods For Assessing And Prioritizing Road-Stream Crossings For Aquatic Organism Passage, Lesley E. Twiner

All Theses

Anthropogenic barriers such as dams and culverts have led to riverine habitat fragmentation and decreased fish diversity worldwide. Low-head structures such as culverts are far more abundant than large dams and may have a larger cumulative impact on river connectivity. Many efforts to inventory road crossing barriers and prioritize removal and restoration efforts do not consider temporal variation in flow. We used cameras to gain continuous water level monitoring data to quantify the relationship between precipitation events and outlet drop height. In the spring of 2024, we selected 25 culvert sites in upstate South Carolina and set up cameras to …

Antiproliferative Effects Of Salvia On Breast Cancers., Allison C. Portaro

College of Arts & Sciences Senior Theses

Breast cancer is the most common cancer diagnosed in female adults, with 2.3 million new cases worldwide in 2020. Plants have been used in traditional medicine and are a potential source of pharmaceuticals. One example is the large Lamiaceae (mint) family. The Salvia genus, commonly known as the sages, is the largest genus in Lamiaceae with almost 900 known species. Salvia lyrata (lyre-leaved sage) has a history of Native American medicinal use to treat cancers and other ailments resulting in this plant being referred to as ‘cancer weed.’ Extracts were produced from the leaves of S. lyrata, S. lyrata …

Shortage To Surge - Studying The Post-Covid-19 Guitar Retail Market, Jed H. Kim

Data Science Undergraduate Honors Theses

The COVID-19 pandemic was one of the most catalyzing events of the 21st century, leading to supply chain disruptions, lifestyle changes, and a massive shift towards digital technologies. During the COVID-19 lockdown, many people had more free time, and over 16 million individuals learned to play guitar in the first 2 years of the pandemic. According to a study by Fender, 62% of these new guitar learners cited the pandemic as their primary reason for learning the instrument. However, pandemic policies and supply chain disruptions meant that many guitar retailers were unable to satisfy demand, and backorders accumulated. After the …

Mitigating Nitrogen Losses: The Role Of Enhanced Efficiency Fertilizers In Sustainable Corn Production, Dipesh Giri

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Nitrogen (N) is essential for crop production, but its inefficient use often leads to environmental losses through nitrate leaching, ammonia volatilization, and nitrous oxide (N₂O) emissions. Enhanced efficiency fertilizers (EEFs), such as nitrification inhibitors (NIs) and urease inhibitors (UIs), have been developed to minimize these losses and improve nitrogen use efficiency (NUE). This research combined a multi-year field experiment and a controlled laboratory study to evaluate how dual-inhibitor fertilizers compare to conventional urea and single-inhibitor formulations in Nebraska cropping systems. The main objective was to understand how nitrogen inhibitors influence N availability, crop performance, and nitrogen losses across different environmental …

Extending Cover Crop Growing Window To Improve The Health Of Environmentally Sensitive Soils, Noshin Ara Tunazzina

Department of Agronomy and Horticulture: Dissertations, Theses, and Student Research

Sloping and sandy soils are highly susceptible to degradation. The health of these soils could be improved with cover crops (CCs). However, CC effectiveness in improving soil health mainly depends on CC biomass production, which is often low in temperate regions. The question is: how can we increase CC biomass production? Lengthening the CC growing window can be a potential strategy. This study assessed how 1) interseeded and terminated early (2-3 weeks before crop planting) CC, 2) interseeded and terminated late (at crop planting) CC, 3) drilled (after harvest) and terminated early CC, 4) drilled and terminated late CC, and …

Artificial Intelligence Through Young Eyes: A Study Of Students’ Perspectives And Experiences With Artificial Intelligence In Education, Chad Preston Salyer

Ed.D. Dissertations

Artificial intelligence was an emergent and powerful new force in education. The public release of ChatGPT 3.0 in 2022 transformed learning for many students. This phenomenological qualitative study sought to record and analyze student’s perspectives on the influence of artificial intelligence on their learning routines. This study collected data through surveys and interviews with undergraduate students, analyzing patterns of artificial intelligence usage, perceived benefits, and challenges. The findings revealed that most students used artificial intelligence as a primary learning tool and that those students viewed artificial intelligence as beneficial for personalized learning and skill development. However, concerns about over-reliance on …

A Study Of Knots And Quandles, Zhaoqi Wu

Math and Computer Science Honors Theses

We explore the mathematical theory of knots through the lens of algebraic structures known as kei and quandles. We begin by introducing classical knot invariants and then study the fundamental kei of a knot as a tool for distinguishing knot types. We generalize this approach using various kinds of quandles, including Alexander and dihedral quandles, and investigate their associated polynomial invariants. We also examine the connection between quandles and group theory, as well as their algebraic representations in quandle rings. Moreover, we analyze idempotent elements in quandle rings over finite fields, providing both general results and specific examples.

Yield Prediction Of Pv Solar Energy Systems And Its Application In The Energy Grid For Operational Efficiency, Pablo Bustamante

Open Access Theses & Dissertations

The generation of power from photovoltaic (PV) solar panels is influenced by a multitude of factors. These include the tilt and orientation of the solar panels, the latitude of their location, and the prevailing climate and weather conditions. Additionally, shading at specific locations, particularly if the panels are not part of a solar facility, can significantly impact their efficiency. The quality and efficiency of the panels themselves, along with the preventive maintenance of both the solar panels and associated components such as inverters and trackers, are also critical. Finally, the overall system design and installation play a vital role in …

Clinicogenomic Insights For Prostate Cancer Progression, Kelvin Ofori-Minta

Open Access Theses & Dissertations

Prostate cancer (PrCa) remains a critical challenge in precision oncology due to several reasons including its apparent heterogenous condition, recurrence following treatment and rapid progressive forms. Therefore, identifying patients at risk of progression is essential to fast-track therapeutic decisions and improve outcomes. Despite recent advances in genomic and molecular profiling, conventional PrCa risk assessment tools heavily rely on a few clinical parameters, neglecting the prognostic potential of genomic biomarkers in the presence of clinical biomarkers. This study presents a computational pipeline to harmonize and evaluate the prognostic value of clinicogenomic profiles of patients in modelling progression free survival (PFS). PFS, …

Multiscale Integration Of Receptor-Ligand Dynamics Into Discrete And Continuous Tumor Growth Models With Application To Tyrosine Kinase Inhibitor Treatment, Romasa Qasim

Open Access Theses & Dissertations

The epidermal growth factor (EGF) receptor cascade plays a crucial role in the survival and proliferation of tumor cells. Tyrosine kinase inhibitors (TKIs) are a class of drugs that inhibit epidermal growth factor receptors (EGFRs), thereby preventing the downstream signal transduction. Despite their importance, models that link spatial receptor dynamics to tumor growth remain scarce. Further, TKIs act through selective mechanisms, inhibiting active, inactive, or all receptor states, which poses a challenge to traditional modeling approaches.

We propose to numerically study two mathematical models incorporating receptor-dynamics into cancer models to describe the impact of EGFR overexpression and TKIs. The first …

Machine Learning And Protein Engineering Approaches To Understanding Kinesin-5 Activity, Jason Eden Sanchez

Open Access Theses & Dissertations

Cancer is a term describing a collection of diseases that result in uncontrolled cell growth. Cancer has manifold etiologies and underlying cancers are rouge biochemical pathways involving many different proteins. In the current work, two approaches are used to enhance knowledge of kinesin-5, a potential cancer target involved in cell division. Kinesin-5 promotes cell division by cross-linking and separating microtubules in dividing cells. The first approach uses machine learning (ML) to identify small molecule inhibitors for kinesin-5. Though decades of research have uncovered classes of small-molecules which inhibit kinesin-5 in vitro and in vivo, no candidates have reached phase III …