Digital Commons Network^™

From Mechanisms To Management: Implications Of Biogeochemical Controllers And Land Management For Soil Carbon Cycling And Storage, Savannah R. Adkins

All Graduate Theses and Dissertations, Fall 2023 to Present

Climate change and its cascading effects are driven by increases in atmospheric carbon dioxide (CO₂). Many climate solutions exists to remove this excess carbon (C) from the atmosphere, and soils, in particular, represent one of the few win-win solutions. Soils play a vital role in the global C cycle because they store more C than plants and the atmosphere combined, however, they also release more CO₂ annually than fossil fuel combustion (a major contributor to accelerating climate change). Therefore, preventing CO₂ loss from soil could help slow the progression of climate change, and increasing overall soil …

Integrating Manager Perspectives Into The Evaluation Of Wetland Revegetation Strategies, Loren F. Taylor

All Graduate Theses and Dissertations, Fall 2023 to Present

Ecological restoration is the process of assisting the recovery of an ecosystem that has been degraded and is dependent on complex and context-specific decisions. The decision-making process influencing restoration is rarely examined alongside ecological processes. There is a need for research that incorporates the social, economic, institutional, and logistical considerations that shape real-world practices, as well as ecological processes. Decisions made by restoration practitioners and land managers (hereon “manager”) are challenged by the lack of information shared regarding the practical constraints (e.g., cost, labor, specialized equipment) they face. Revegetation, particularly in wetlands, poses challenges due to site conditions and degradation …

Biocontrol Of Canada Thistle (Cirsium Arvense) With The Rust Fungus, Puccinia Punctiformis In The Intermountain West: Integrated Weed Management Compatibility And Characterization Of Microbiome Associations, Caitlin Henderson

All Graduate Theses and Dissertations, Fall 2023 to Present

Canada thistle (Cirsium arvense) is an invasive weed of major concern in both agricultural and native areas. It competes against native plants, reduces crop production and quality, and causes significant costs in management and damages. Canada thistle can survive and spread through seeds, but primarily does so through its extensive root system, which causes the greatest management difficulties. There are several control methods for this invasive weed, herbicides are perhaps the most common and effective, however, they have limitations and negative consequences. Herbicide use near waterways is restricted and there are growing concerns of the development of herbicide …

Assessing The Human Health Impacts Of Nutrient-Dense Diets: Clinical Trials On Regenerative Agriculture And Protein Source, Jennifer Jensen-Cloward

All Graduate Theses and Dissertations, Fall 2023 to Present

Increasing consumer demand for sustainable, animal-friendly food options has sparked discussion about farming production practices. As more people prioritize their food choices, questions have circulated about how farming practices might impact not just the environment, but also human health. Regenerative agriculture is a farming method that has gained popularity for its potential to improve both food quality and environmental outcomes. It focuses on restoring ecosystem function, ultimately impacting the resulting nutrients in food products, and includes foods like grass-fed meat and organic produce. However, it is still unclear whether these practices make a difference in human health. This dissertation informs …

Investigating Pyrethroid Insecticide Resistance In The Alfalfa Pest Insects Hypera Postica (Alfalfa Weevil) And Lygus Spp. (Lygus Bugs) In Utah Alfalfa Fields, Rosalie Sepesy

All Graduate Theses and Dissertations, Fall 2023 to Present

Chemical insecticides are commonly used to manage the damage to crops caused by agricultural pest insects. Reliance on insecticides for pest management has resulted in insecticide resistance in many insect species worldwide. Alfalfa weevils (Hypera postica) and lygus bugs (species within the genus, Lygus), are major pests to alfalfa hay and seed respectively and cause significant economic damage. The goal of this dissertation was screen Utah alfalfa fields for resistant alfalfa weevil and lygus bug populations, investigate genetic mutations that can influence resistance in alfalfa weevils, and establish which species of lygus bugs are present in Utah …

The Effects Of Lactoferrin And Iron-Enriched Whey On Iron Status Of Collegiate Females, Connor Kemp

All Graduate Theses and Dissertations, Fall 2023 to Present

Iron deficiency has remained a global issue even in developed countries despite food fortification and increased nutritional literacy, biological women of child baring age are at particular risk due to menstruation and reduced dietary intake of iron containing foods compared to men. This issue is of particular concern in athletics due to the critical role of iron in oxygen transport and energy metabolism. With nearly half of female athletes presenting low iron status iron supplementation is often necessary. With iron supplementation often resulting in gastrointestinal symptoms that could negatively impact sport performance itself there is a need to explore other …

Development Of Novel Small Molecule Therapeutics For Myotonic Dystrophy, Xhesika Azis

Biological Sciences

Myotonic Dystrophy type 1 (DM1) results from expanded CUG repeat RNA that sequesters MBNL proteins and disrupts alternative splicing. Small molecules that bind toxic repeat RNA and release MBNL proteins represent a promising therapeutic strategy. This thesis examines newly synthesized modified polycyclic compounds (MPCs) engineered to target CUG RNA with enhanced specificity and efficacy. Through Suzuki–Miyaura coupling and benzoquinone-mediated cyclization, MPC03 was synthesized and characterized by NMR and LC–MS.

The biological activity of these compounds was assessed in DM1 patient-derived myotubes and fibroblasts. MPC03 consistently produced dose-dependent rescue of multiple MBNL-regulated exons, restoring splicing patterns toward those observed in healthy …

Fungal Biodiversity, Microbial Communities, And Ecosystem Function In Non-Perennial Streams, Charles T. Bond

Dissertations

A global majority of steams are non-perennial, drying at some point in time and space. Despite the vital roles that fungi and other microbes play in stream ecosystems, most research on stream microbiomes comes from perennial (continuously flowing) streams. The present series of studies addresses this research gap by examining microbial community composition and function in non-perennial streams, with an emphasis on fungi. Chapter I reviews existing scientific literature on the ecological processes that shape microbiome structure and function in non-perennial streams and outlines the varieties of fungi that may live there. Chapter II uses rDNA metabarcoding to survey fungal …

The Genetic And Environmental Determinants Of Stress Resilience Across Model Systems, Carson Len Stacy

Graduate Theses and Dissertations

Survival in fluctuating environments demands that organisms effectively anticipate and respond to future challenges. This capacity is shaped by both genetic background and environmental context. In this dissertation, I apply a population aware lens to explore how genetic diversity and environmental conditions intersect to shape stress survival. Integrating functional genomics and transcriptomics in Saccharomyces cerevisiae (brewer’s yeast) and a vertebrate (common canary) system, I dissect gene-by-environment (GE) interactions that underpin resilience. First, I move beyond a single reference genome by using a pan-genomic CRISPR knockout screen to assess osmotic stress survival across diverse S. cerevisiae isolates. This analysis reveals a …

Why The Long Face? The Distribution And Niche Of The Imperiled Narrow-Faced Kangaroo Rat (Dipodomys Venustus), Garrett L. Gimbel

Master's Theses

Distribution models provide a practical use case of connecting ecological niche theory with species’ occurrence and assemblages. By explicitly linking Hutchinson’s “niche space” with geographic space researchers can gain valuable information on a species’ niche characteristics and interactions, thereby informing conservation and management practices. The narrow-faced kangaroo rat (Dipodomys venustus) is a highly understudied kangaroo rat species endemic to the central coast of California and is an ideal species to explore niche theory in distribution modeling. Three subspecies are currently recognized: The Santa Cruz kangaroo rat (D. v. venustus), the elephant-eared kangaroo rat (D. v. …

Skeleton Weed Program 2024-25: Annual Report To Grain Growers, Department Of Primary Industries And Regional Development, Western Australia

Biosecurity published reports

Skeleton weed is a major pest of grain crops and can significantly reduce grain crop yields by competing for moisture and nutrients (mainly nitrogen), due to its deep perennial root system.

Skeleton weed is a declared plant in WA under section 22 of the Biosecurity and Agriculture Management Act (2007) and is assigned to control category 2 (Eradication) for the whole of the State, except in the Narembeen and Yilgarn Shires, where it is category 3 (Management).

Modelling indicates that under a nil management scenario, the cost to WA broadacre agriculture will be approximately $19.2 million per year after twenty …

Analyzing The Impact Of Diet On Dusky Gopher Frog (Lithobates Sevosus) Development In Head Start Programs, Mckalyn Nelson

Honors Theses

Species are constantly impacted by human activity, directly or indirectly. One critically endangered species under investigation is the dusky gopher frog (Lithobates sevosus), which is an endemic species of frog found in the southeastern United States. Historically found from Louisiana to Alabama, a drought in 2002 narrowed the dusky gopher frog range even further. Head start programs have been shown to be effective in increasing population numbers; however, there is not much published data on the effectiveness of captive rearing diets for these programs. The dusky gopher frog head start program at the University of Southern Mississippi’s Lake …

Near-Infrared-Spectroscopy-Derived Oxygen Desaturation Rates During Post-Exercise Circulatory Occlusion As Predictors Of Cardiorespiratory Fitness Markers, Carstell Lee

Honors Theses

Cardiorespiratory fitness, measured as maximal oxygen consumption (VO₂max) is a critical predictor of all-cause mortality and overall cardiovascular health. Metabolic carts are the current gold standard for evaluation of VO₂max, but are inaccessible to most facilities and individuals, and are expensive ($20,000+). Near-Infrared spectroscopy (NIRS) has emerged as an accessible and affordable ($5,000-$10,000) alternative for evaluating skeletal muscle oxygenation kinetics and mitochondrial oxidative capacity. However, there is limited research in examining whether NIRS-derived oxygen desaturation rates can be a predictor of cardiorespiratory fitness markers (such as VO₂max and peak power output [PPO]), and whether these measurements show a superior predictive …

Expression, Purification And Characterization Of Full Length Tdp-43, Danya Abouzaid

Honors Theses

TAR DNA-binding protein 43 (TDP-43) is a 43 kDa RNA-binding protein linked to several neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS), frontotemporal dementia (FTD), and Alzheimer’s disease. 5-7,28,30,33 Studying full-length TDP-43 has been difficult because of its intrinsic instability and tendency to aggregate.19,25,28,33,36 In this study, we focused on overcoming the difficulties to express full-length TDP-43 in E. coli recombinantly. We focused on expressing full-length TDP-43 as a fusion construct with a maltose-binding protein (MBP) to improve solubility and stability. Our strategy was to purify TDP-43-MBP fusion and make biomolecular condensates with RNA before cleaving the tag with thrombin protease. …

Blood-Based Clinical Markers For Early Dementia Detection: Insights From Ad-Detect-Cohort, Benard Aliwa, Jasmit Shah, Olivera Nesic Taylor,, Samuel Nguku, Juzar Hooker, Dilraj Sokhi, Sylvia Mbugua, Litha Musili, Rachel Maina, Harrison Kaleli, Levi Muyela, Anne Njoki Gitere, Anne Nyambura, Zul Merali, Karen Blackmon, Chinedu Momoh

Brain and Mind Institute

Background: Over 55 million people worldwide live with dementia, with more than60% residing in low- and middle-income countries. Alzheimer’s disease, the mostcommon form of dementia, accounts for 60–70% of cases. Early and accurate diagnosisremains a global challenge, necessitating novel approaches to mitigate the diseaseburden. Biomarkers hold significant promise in improving diagnostic accuracy andpredicting disease progression. Validated biomarkers for the preclinical stages ofdementia are crucial for advancing diagnosis and therapeutic strategies. We aimedto identify potential clinical markers for early dementia detection and assess theirpredictive accuracy in identifying high-risk individuals.

Method: We analyzed blood samples from dementia cases (n = 30) and …

Tracing The Journey Of Dissolved Organic Matter: From Leaf Litter Photodegradation To Microbial Processing In Tropical Streams, Samantha Nicole Sullivan

Chemistry & Biochemistry Theses & Dissertations

Dissolved organic matter (DOM) is a major reservoir of organic carbon in aquatic ecosystems and plays a central role in global carbon cycling through its transformation and remineralization to carbon dioxide (CO₂). As DOM moves from terrestrial environments into streams and rivers, its chemical composition is altered by a combination of microbial and photochemical oxidation processes that regulate both its reactivity and its persistence during transport. However, the molecular mechanisms governing these oxidative transitions, particularly in tropical ecosystems characterized by strong hydrologic seasonality and substantial inputs of plant-derived material, remain insufficiently resolved. This dissertation integrates ultrahigh-resolution mass spectrometry, optical characterization, …

Large Language Models (Llms) For Clinical Note Generation: International Classification Of Disease (Icd) Code, Knowledge Graph (Kg) And Prompt Evaluation, Ivan P. Makohon

Computer Science Theses & Dissertations

In the past decade, a surge in the amount of electronic health record (EHR) data in the United States occurred, driven by a favorable policy environment created by the Health Information Technology for Economic and Clinical Health (HITECH) Act of 2009 and the 21st Century Cures Act of 2016. Clinical notes for patients’ assessments, diagnoses, and treatments are captured in these EHRs in free-form text by physicians, who spend a considerable amount of time entering them. Manually writing these notes is time-consuming, increasing patient waiting times and potentially delaying diagnoses. Large language models (LLMs), such as GPT-4o, possess the ability …

National-Scale Open Cattle Feedlot Detection Using Deep Learning And High-Resolution Aerial Images: Spatial Distribution And Animal Welfare Analysis, Uilson Ricardo Venancio Aires, Vitor Souza Martins, Dakota Hester, Thainara Lima, Lucas Borges Ferreira

Research Data

Open cattle feedlots are a major form of beef production infrastructure in the United States, characterized by outdoor confinement, high animal densities, and regulated feeding practices. Despite their economic importance, a comprehensive and spatially consistent national database of these facilities remains limited. This dataset provides labeled training data, trained deep learning models, and geospatial detection outputs developed to support automated identification of open cattle feedlots from aerial imagery. The dataset includes a manually curated shapefile of 11,746 open cattle feedlot facilities identified through visual interpretation of high-resolution aerial imagery in highly productive counties of Nebraska, Kansas, and Texas. These labels …

Effects Of Injectable Trace Mineral Timing On Calf Performance And Health Indicators, Marie E. Goulais

Graduate Theses and Dissertations

One hundred and fourteen calves (average BW= 224kg ± 89kg) were utilized to evaluate the effects of injectable trace mineral (ITM) administration on calf performance and health when administered pre-weaning and at weaning. Calves were blocked by sex, stratified by age, and randomly assigned to one of the following treatment groups: 1) no ITM injection (CON), 2) ITM administered 28 d before weaning (PW), or 3) ITM administration at weaning (WEAN). Calves were vaccinated against respiratory pathogens on D-28 and D0. At weaning, cattle were transported to a local auction market, held overnight and returned the following morning. Body weight …

Hyperspectral Indicators And Characterization Of Glyphosate-Induced Stress In Common Lambsquarters (Chenopodium Album L.), Mario Andrés Soto Valencia

Graduate Theses and Dissertations

Hyperspectral sensing enables detection of herbicide stress in weeds, but practical use requires strategies for redundancy control, rating variability management, and evaluator bias mitigation. This thesis evaluates common lambsquarters (Chenopodium album) under glyphosate exposure, aiming to identify key wavelengths, construct vegetation indices, and improve injury modeling. Greenhouse experiments used dimensionality reduction methods (principal component analysis, Relief F, Bayesian discriminant analysis) to isolate 34 unique wavelengths from about 3,200 bands. Calibration data were collected 14 days after treatment (DAT) to support wavelength selection and model development, while data from 27 DAT were used for independent validation. Class comparisons across six statistically …

Novel Approaches To Disinfecting Poultry Processing Wastewater For Reuse, Seth Olorunmijuwonlo Adesope

Graduate Theses and Dissertations

Water is an essential resource used in poultry processing, generating large volumes of foodborne pathogen-rich wastewater posing treats to public health. Treating poultry processing wastewater (PPW) is crucial for safe water reuse and sustainable development. Conventional disinfection methods like aerobic digestion and chlorination, although effective, impose considerable operational cost and generate harmful by-products. Integrated recycling systems such as advanced oxidation processes (AOPs) which destroy micro-organisms through the generation of reactive oxygen species (ROS) present a promising opportunity for enhancing resources and sustainability. This study investigated the use of photo-electrochemical (PEC), specifically by combining electrochemical (EC) and photochemical (PC; Photosensitizer and …

Transcriptomic And Contractile Adaptations In Skeletal Muscle In A Rodent Model Of Anorexia Nervosa, Oscar Armando Vicen

Graduate Theses and Dissertations

BACKGROUND: Anorexia Nervosa (AN) is a psychiatric disorder marked by severe chronic caloric restriction and is primarily diagnosed through psychological and behavioral symptoms. AN has the highest mortality of any psychiatric disorder with an increased risk of all-cause mortality. Many individuals with a history of AN experience incomplete recovery despite intervention treatment. Skeletal muscle molecular mechanisms under chronic energy deprivation remain poorly understood. PURPOSE: To investigate transcriptomic profiles of the gastrocnemius muscle following one month of a rodent model of AN. This study analyzed whether the molecular changes correlate with collected muscular force data to provide a comprehensive understanding of …

Effect Of Peracetic Acid Dip Frequency On The Quality And Functional Properties Of Non-Marinated And Marinated Broiler Tenderloins, Joaquin Jose Esquivel Vergara

Graduate Theses and Dissertations

The poultry industry continues to balance the need for effective antimicrobial interventions with the preservation of meat quality. Among the most widely used antimicrobial agents, peracetic acid (PAA) has proven effective for reducing foodborne pathogens in poultry products. However, excessive or repeated exposure to PAA can influence meat functionality by altering protein structure, color, and water-holding capacity. Therefore, the broad objective of this study was to evaluate the effect of PAA dip frequency and post-treatment marination timing on the physicochemical and functional quality of broiler tenderloins (Pectoralis minor), in order to provide processing insights that optimize both microbial safety and …

Multiple Aspects Of Environmental Temperature Have Complex Interactions With Avian Parental Behavior To Influence Offspring Outcomes, William H. Kirkpatrick

Graduate Theses and Dissertations

Anthropogenic climate change is projected to shift not only average temperatures across the globe, but also the amount of thermal variation experienced in the natural environment. Exposure to shifts in averages and a wider range of thermal experiences will cause shifts in wildlife behavior. In avian species, behaviors exhibited during reproduction have implications for the well-being of their offspring. Here, I explore specific incubation behaviors in four species: Scaled Quail (Callipepla squamata), Northern Bobwhite Quail (Colinus virginianus), Tree Swallows (Tachycineta bicolor), and Eastern Bluebirds (Sialia sialis). I examined constancy, or the percentage of time on the nest, and off-bout duration, …

Broiler Responsiveness To Dietary Amino Acid Density In A Commercial Setting, Virginia Slick

Graduate Theses and Dissertations

The majority of research assessing the amino acid responsiveness in broilers has been conducted in experimental designs utilizing pens that contain 12 to 25 birds with high replication. While this trial design is beneficial as a way to perform high replications with multiple treatments in a way that is both economically and spatially feasible, it may not accurately translate to a rearing environment more similar to that of commercial open floor housing. This research was conducted to determine if the effects of lysine driven amino acid density diets that have been found in the traditional floor pen setting correlate to …

Hormonal Control Of Seawater Acclimation In The Intestine Of The Atlantic Killifish (Fundulus Heteroclitus), Karma Je Hine

Graduate Theses and Dissertations

The Atlantic killifish (Fundulus Heteroclitus) is a teleost found in brackish water estuaries, which are subject to large fluctuations in salinity, that handles osmotic stress by triggering compensatory actions across their osmoregulatory organs. As the external salinity increases, the killifish intestine exhibits a high degree of phenotypic plasticity, as the protein composition of the gut epithelium can be modified to absorb desalinated water (H2O) from ingested seawater (SW). Three osmoregulatory hormones, prolactin (P), growth hormone (GH), and cortisol (F), have been observed to be crucial for these transitions to occur in many species of teleosts, including killifish. This research sought …

Mitochondria-Mediated Epigenetic Transfer Between Chondrosarcoma And Wild-Type Cells, Caleb C. J. Wyckoff

Biomedical Sciences Theses & Dissertations

Glioblastoma (GB), acute myeloid leukemia (AML), chronic lymphocytic leukemia (CLL), cholangiocarcinoma, and chondrosarcoma (CS) cancers all contain mutations in the gene isocitrate dehydrogenase 2 (IDH2). The mutant IDH2 enzyme exhibits transformation of alpha-ketoglutarate (αKG) into the oncometabolite D-2-hydroxyglutarate (D2HG) in the mitochondria of these cancers. Mitochondrial-mediated transfer between cancer cells and recipient cells is a significant event that impacts the physiology of the receiving cell, specifically the epigenetic landscape. Previous experiments indicating increased DNA methylation in mesenchymal stem cells exposed to IDH1 or IDH2 conditioned medium underscore the potential role of D2HG to alter methylation states. Additionally, the presence of …

Evaluation Of Ocean Lidar Enhancement Through Miniaturization And Gated Pmt-Based Range Extension, Chandler Austin Slater

OES Theses and Dissertations

Oceanographic lidar systems remotely characterize the vertical structure of the upper ocean by recording the light backscattered from a laser pulse as it propagates through the water column. Historically these systems have been constrained by limited detection ranges, often capturing only a portion of the illuminated water column, typically fading to noise around the 10% isolume. A primary constraint has been the limited dynamic range of digitizers, which inhibits the ability to resolve both intense near-field and faint far-field backscatter signals within a single acquisition. To address this, we developed a novel optical lidar system incorporating gated photomultiplier tubes (PMTs) …

Margalefidinium Polykrikoides Group Iii Va, Usa Strain Growth And Sac-Like Pellicle Cyst Dynamics, Eduardo Pérez Vega

OES Theses and Dissertations

Margalefidinium polykrikoides is a harmful cosmopolitan dinoflagellate that blooms in coastal waters. The effect of temperature and salinity on the growth of M. polykrikoides VA strain was examined using microscopy and growth models. M. polykrikoides Group III VA strain grew better at warmer temperatures and lower salinities than M. polykrikoides Group III NY strain, Group I Korea strain, and Japan strain (unknown group). Modelers need to use the temperature and salinity growth responses from M. polykrikoides Group III VA strain to better simulate and predict M. polykrikoides blooms in the Chesapeake Bay.

Dinoflagellates produce cysts as a strategy to withstand …

(R2135) System Dynamical Analysis For Ann-Based Numerical Solutions Of A Compartmental Model: A Bio-Mathematical Model Of Drug Diffusion Through The Compartments Of Blood And Tissue, Rakesh Kumar, Sudarshan Dhua

Applications and Applied Mathematics: An International Journal (AAM)

This paper provides a considerably efficient numerical approach to acquire the solutions of a biomathematical model administrating oral and intravenous distribution of pharmaceuticals in the human body. The proposed numerical approach based on an artificial neural network is employed to extract numerical solutions for a detailed set of ordinary differential equations and analyze the change in concentration of drug diffusion via the compartments of blood and tissue medium. We primarily focus on analyzing three different models established on the diffusion process, exercising laws of mass action and Fick’s principle. In this work, the existing model is reformulated as an optimization …