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Molecular Understanding And Design Of Deep Eutectic Solvents And Proteins Using Computer Simulations And Machine Learning, Usman Lame Abbas

Theses and Dissertations--Chemical and Materials Engineering

Hydrophobic deep eutectic solvents (DESs) have emerged as excellent extractants. A major challenge is the lack of an efficient tool to discover DES candidates. Currently, the search relies heavily on the researchers’ intuition or a trial-and-error process, which leads to a low success rate or bypassing of promising candidates. DES performance depends on the heterogeneous hydrogen bond environment formed by multiple hydrogen bond donors and acceptors. Understanding this heterogeneous hydrogen bond environment can help develop principles for designing high performance DESs for extraction and other separation applications. This work investigates the structure and dynamics of hydrogen bonds in hydrophobic DESs …

Functional Analyses Of The Polycomb-Group Genes In Sea Lamprey Embryos Undergoing Programmed Dna Loss, Cody Saraceno

Theses and Dissertations--Biology

During early embryonic development, the sea lamprey (Petromyzon marinus) undergoes programmatic elimination of DNA from somatic progenitor cells in a process termed programmed genome rearrangement (PGR). Eliminated DNA eventually becomes condensed into micronuclei, which are then physically degraded and permanently lost from the cell. Previous studies indicated that many of the genes eliminated during PGR have mammalian homologs that are bound by polycomb repressive complex (PRC) in embryonic stem cells. To test whether PRC components play a role in the faithful elimination of germline-specific sequences, we used a combination of CRISPR/Cas9 and lightsheet microscopy to investigate the impact …

Language Models For Rare Disease Information Extraction: Empirical Insights And Model Comparisons, Shashank Gupta

Theses and Dissertations--Computer Science

End-to-end relation extraction (E2ERE) is a crucial task in natural language processing (NLP) that involves identifying and classifying semantic relationships between entities in text. This thesis compares three paradigms for end-to-end relation extraction (E2ERE) in biomedicine, focusing on rare diseases with discontinuous and nested entities. We evaluate Named Entity Recognition (NER) to Relation Extraction (RE) pipelines, sequence-to-sequence models, and generative pre-trained transformer (GPT) models using the RareDis information extraction dataset. Our findings indicate that pipeline models are the most effective, followed closely by sequence-to-sequence models. GPT models, despite having eight times as many parameters, perform worse than sequence-to-sequence models and …

Assessing Endophyte Frequency Distributions And The Effect Of Epichloë Brachyelytri In The Chemotypic And Genotypic Diversity Of Brachyelytrum Erectum, Rachel Ann Sneed

Theses and Dissertations--Plant Pathology

Seed-transmissible epichloid fungal endophytes are best known for their roles as defensive mutualists in cool-season grasses. Historically, the discovery of fungal endophytes was driven by investigations of plant toxicity to livestock, followed by extensive study of their alkaloids and protection against insects and nematodes. Epichloae can produce four classes of alkaloids: ergot alkaloids, lolines (saturated aminopyrrolizidines), indole–diterpenes, and peramine. It is increasingly evident that these hereditary symbionts have much more diverse chemical profiles both in individual populations and between them. To this end, differences in chemotypic profiles of these symbionts may translate to different evolutionary and environmental advantages across plant …

Strategic Nutritional Interventions With Probiotics And Their Relationship To Performance, Feeding Behavior, And Reticulorumen Environment In Cows And Calves Under Subacute Ruminal Acidosis Risk, Gustavo Mazon Correa Alves

Theses and Dissertations--Animal and Food Sciences

Subacute ruminal acidosis (SARA) is a digestive disorder in ruminants characterized by extended periods of low reticulorumen pH. This digestive disorder is commonly observed in ruminants fed diets with elevated proportions of non-fibrous carbohydrates. This disorder has been vastly studied in adult dairy cattle and has been associated with losses in milk production, changes in feeding behavior, damage to the gastrointestinal tract, and premature culling. Although vastly studied in adult cattle, there is limited research on the effects of SARA in calves. SARA might be prevented by modifying the reticulorumen environment with probiotic supplements containing lactateutilizing bacteria such as Megasphaera …

Improving Nutrition Screening Practice In The Hospitalized Heart Failure Patient Population, Amanda J. Bourgeois

DNP Projects

Background: Heart Failure is a disease known to affect nearly 6.5 million adults in the United States. Characterized by recurrent hospitalizations, heart failure significantly contributes to morbidity, mortality, and healthcare costs in the United States and worldwide. Because malnutrition is prevalent in the heart failure population, healthcare providers must perform nutritional assessments on admission to intervene in the case of malnutrition, prevent deterioration, and improve patient prognosis. Without intervention and early identification of malnutrition, heart failure hospitalizations will remain a significant problem.

Purpose: The purpose of this study is to evaluate the effect of an evidence-based educational program for cardiac …

Evaluation Of Boron Supplementation In Swine And Poultry, Tyler B. Chevalier

Theses and Dissertations--Animal and Food Sciences

The objectives of this dissertation were to evaluate dietary boron (B) supplementation as sodium borate in various swine models and broiler chicks through a series of experiments. The initial experiment evaluated supplemental B (0, 25, 50, and 100 ppm B) on serum insulin, glucose, and clinical chemistry panel of growing pigs. Serum insulin/glucose ratio tended to decrease linearly with increasing supplemental B in a fasting state (P = 0.08). These findings were more noticeable (linear effect, P = 0.02) in a postprandial state (~ 50 minutes following a meal). A series of follow-up studies further evaluating B supplementation (0, 5, …

The Effects Of Cannabidiol Cream On Soreness And Performance After Exercise In Untrained Individuals, Joseph Thomas Pastina

Theses and Dissertations--Kinesiology and Health Promotion

Background: Exercise-induced muscle damage (EIMD) results from unaccustomed exercise and can lead to delayed onset muscle soreness (DOMS). Impairments associated with EIMD and DOMS can result in moderate-to-severe discomfort and hindered performance. Recently, a compound derived from the cannabis plant, cannabidiol (CBD), has been used as a recovery tool for EIMD and DOMS. Despite the rising popularity of CBD products, their effectiveness in mitigating EIMD and DOMS is unknown. Purpose: The purpose of the present study was to investigate the effects of CBD cream on DOMS and performance after an intensive lower-body exercise protocol. In addition, the study sought to …

Rnai-Mediated Gene Silencing In The Exotic Redbay Ambrosia Beetle, Xyleborus Glabratus, And Insect-Fungal Interactions Within The Laurel Wilt Complex, Morgan Christine Knutsen

Theses and Dissertations--Entomology

Laurel wilt disease (LWD) is a lethal vascular disease impacting lauraceous hosts caused by Harringtonia lauricola, the fungal symbiont of the redbay ambrosia beetle (Xyleborus glabratus Eichoff) (RAB) (Coleoptera: Curculionidae). LWD has caused tree mortality throughout the southeastern United States and is continuing to spread into new regions. Current management methods have not been successful in preventing spread, warranting investigation into innovative techniques including RNA interference (RNAi).

Elongation factor-1 alpha (ef1a) and actin (act) were established as stably expressed reference genes after exposing beetles to different photoperiod, temperature, and dsRNA exposure. After RAB oral …

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 …

Use Of Molecular Genetics To Investigate Population Structure And Swayback In Horses, Navid Yousefimashouf

Theses and Dissertations--Veterinary Science

The present research incorporated molecular genetic methods to 1) investigate the genetic basis of Juvenile Onset Lordosis or Swayback in the American Saddlebred horses; and 2) conduct a population genetic study to compare the Persian Kurdish, Persian Arabian and American Thoroughbred horse populations.

Juvenile-onset lordosis, or swayback, is a condition in horses where the conformational topline back curvature drops significantly within the first two years of life. The trait has a higher prevalence in Saddlebreds (5%). Prior research on them quantified the trait using a Measurement of Back Contour (MBC), defining an MBC of >7.0 centimeters as swayback, and8.0) MBC …

Age- And Sex-Dependent Alterations In Primary Somatosensory Neuronal Calcium Network Dynamics During Locomotion, Sami L. Case

Theses and Dissertations--Pharmacology and Nutritional Sciences

Over the past 30 years, the calcium (Ca2+) hypothesis of brain aging has provided clear evidence that hippocampal neuronal Ca2+ dysregulation is a key biomarker of aging. Indeed, age-dependent Ca2+-mediated changes in intrinsic excitability, synaptic plasticity, and activity have helped identify some of the mechanisms engaged in memory and cognitive decline. However, much of this work has been done at the single-cell level, mostly in slice preparations, and in restricted structures of the brain. Recently, our lab identified age- and Ca2+-related neuronal network dysregulation in the cortex of the anesthetized animal. Still, investigations in the awake animal are needed to …

Increasing Efficiency Of Finishing Beef Production: Strategies To Optimize Starch Digestion, Improve Flake Quality, And Reduce Methane Emissions, Ronald J. Trotta

Theses and Dissertations--Animal and Food Sciences

To continue to meet the demands of increasing food production and environmental sustainability, new strategies are needed to enhance the efficiency of finishing cattle production. A review of the literature identified several nutritional and physiological constraints that limit the ability for cattle to digest starch and absorb glucose from the small intestine. Comparative sequencing analyses revealed a missing region of the sucrase-isomaltase protein which could affect the capacity for starch digestion in cattle. Post-flaking sampling and handling recommendations were generated based on a series of experiments to improve estimates of starch availability and flaking consistency for commercial feedlots and laboratories. …

Selenium Form-Induced Changes In The Early Luteal Phase Corpus Luteum, The Blood, And The Endometrium During Early Gestation In Beef Cows, Sarah Nancy Carr

Theses and Dissertations--Animal and Food Sciences

Selenium (Se) deficient soils and thus forages are widespread throughout the United States, necessitating supplementation of this trace mineral in the diet of grass-fed cattle to negate detrimental effects of a deficiency on immune function, growth, and fertility. Conventionally, Se is supplemented to cattle in a vitamin-mineral mix as an inorganic form (ISe) although the organic forms (OSe) are available when cattle consumer forage, and OSe has been shown to increase the bioavailability of Se in cattle. Previous research has demonstrated supplementation with 1:1 mixture (MIX) of ISe and OSe compared to ISe alone increases systemic concentrations of progesterone (P4) …

Linking Previous Experiences To Behavior And Health In The Honey Bee (Apis Mellifera), Rebecca R. Westwick

Theses and Dissertations--Entomology

An organism’s ability to respond to changing conditions can be vital to its success. Indeed, plasticity is a common feature of living organisms. Much of the research in this area, though, has focused on effects caused by environmental conditions. What has received relatively less attention is how social experiences and broader features of an organism’s social environment can lead to long-lasting changes in health and behavior. This knowledge gap exists despite the well-documented existence of health and behavioral effects after social interactions in certain taxa such as humans.

Social insects such as honey bees provide an excellent opportunity to better …

The Effects Of Extended Fructose Access On Relative Value And Demand For Fructose, Saccharin, And Ventral Tegmental Stimulation, Megan Halloran

Theses and Dissertations--Psychology

Globally, food addiction (FA) is a growing area of research and is largely attributed to the availability of foods that are both energy dense and high in fats and sugars. Further, it has been suggested, that sugar and fat, when consumed frequently, have properties similar to drugs of abuse. While the validity of FA is questioned, researchers have drawn parallels between substance use disorder (SUD) and FA. For example, sugar binge models emphasize craving, withdrawal and binging as primary components of FA, which are also hallmarks of SUD. Additionally, both natural rewards, like sugars, and drug rewards act on the …

Ecological Risk Assessment Of Transgenic Conditional Lethality Systems For Genetic Biocontrol Strategies, Fernan Rodrigo Perez-Galvez

Theses and Dissertations--Entomology

Genetic strategies of insect pest control are receiving increased interest due to recent advances in genetic engineering. By introducing alleles that make males functionally sterile, genetically modified (GM) insects can be used in area-wide pest management programs similar to the Sterile Insect Technique (SIT). Genetic control strategies carry several potential benefits, including improved efficacy and specificity, lower operation costs, and reduced dependence on chemical insecticides, but their use is still controversial despite extensive technical documentation indicating their innocuity to humans and the environment. This hesitation is likely due to the novel nature of the approach.

While the first field applications …

The Effect Of Physical Activity Courses On The Motivation For Physical Activity In College Students: A Scoping Review, Erica Fauste Waizenhofer Hill

Theses and Dissertations--Kinesiology and Health Promotion

The lack of physical activity and exercise participation has been an ongoing
problem for young adults aged 18-24. Universities and colleges worldwide offer a variety of required and elective physical activity courses for college credit to increase active participation in lifelong healthy lifestyles. This scoping review collected studies on college students’ motivation to participate in physical activity. The courses were taught using methods based on motivational theories. The authors of the studies collected information from the students before and after the classes to gather data on the theoretical framework’s effect on the students, if any. This review compiles this information, …

Management And Characterization Of Root-Knot Nematode (Meloidogyne Spp.) In Kentucky High Tunnels, Victoria Bajek

Theses and Dissertations--Plant and Soil Sciences

Kentucky is one of the most active adopters of high tunnels in the United States. Across the state, high tunnel growers have reaped the benefits of greater marketable yields, season extension, and protection from harsh weather. However, the high tunnel environment has increased soil temperatures and intensive crop production which has the potential to encourage root-knot nematode (RKN; Meloidogyne spp.) infestations. The extent and distribution of RKN in Kentucky were previously unknown. Two on-farm trials in infested high tunnels were conducted to determine whether grafting with RKN-resistant tomato rootstock is a viable management strategy. A statewide soil census to determine …

Building A Kentucky Baguette: Agronomic Traits, Bread Baking Quality Measurements, And Sensory Evaluation Of Modern And Landrace Wheat Cultivars Grown Under Conventional And Organic Nitrogen Management, Bryan Brady

Theses and Dissertations--Plant and Soil Sciences

The demand by artisan bread bakers across the United States for local wheat varieties has increased in recent years. The southeast is traditionally a soft winter wheat (SWW) region, producing low gluten flours more suitable for biscuits and cookies. Recently, hard winter wheat (HWW) varieties have been bred to produce acceptable yields in the high humidity environment of the southeastern United States. Artisan bread bakers in Kentucky would like to create a niche food value chain benefitting farmers, small-scale millers, bakers, consumers, and their local and regional food systems (LRFS). The increased demand and the availability of adapted hard wheat …

Exploring The Effects Of Environmental Factors On Rice Blast Disease, April Ellen Lamb

Theses and Dissertations--Plant Pathology

Rice blast disease, caused by the ascomycete fungus Magnaporthe oryzae, occurs in over 85 countries and results in an annual crop loss of 10-30%, a corresponding nutrient value of meals for 60 million people. As a result, it is listed as a critical plant disease by the United Nations. Understanding factors affecting disease severity is of critical concern for food security. M. oryzae has been used as a model system for studying effector-triggered immunity (ETI) by understanding that ETI is primarily a plant response. M. oryzae has been used as a model to study fungal pathogenicity, host specificity, genome …

Effects Of Fungicide Programs And Lower Leaf Removal On Wrapper Leaf Production In Connecticut Broadleaf Cigar Wrapper Tobacco, Caleb Haygan Perkins

Theses and Dissertations--Plant and Soil Sciences

In recent years, there has been increased demand for natural leaf cigar wrappers. Kentucky and Tennessee have been of recent interest as a new area for Connecticut Broadleaf production. Initial production experiences have shown that late-season frogeye leaf spot caused by the pathogen Cercospora nicotianae Ellis & Everh. may result in ‘green spot’ in cured leaf and cause a significant problem for producers of Connecticut Broadleaf cigar wrapper tobacco. Field trials were established in 2021 at Princeton, KY and 2022 in Mayfield, KY and Springfield, TN to evaluate effects of fungicide programs and lower leaf removal on wrapper production and …

Exploring The Molecular Basis Of Touch: A Comparative Analysis Of Gene Expression In Sensory Corpuscle-Rich And Corpuscle-Poor Skin Regions In The Duck, Thomas Hart

Theses and Dissertations--Biology

Cutaneous touch is facilitated by discrete cellular complexes composed of non-neuronal cells associated with mechanoreceptor neuron endings. The non-neuronal cells of these cutaneous end organ complexes (CEOCs) are believed to contribute to touch, but their role in touch sensation remains unclear. To better understand the function of CEOC cells, we sought to characterize the transcriptional profile of CEOC-rich tissue and identify genes expressed in CEOC cells. Bill skin of the tactile foraging Pekin duck (Anas platyrhynchos) is dense with CEOCs, specifically the avian analogs of mammalian Pacinian and Meissner corpuscles, while corpuscles in duck foot skin are scarce. Using RNA …

Costs And Benefits Of Integrating Poultry Into Cover Crop - Vegetable Rotations, Viktor Halmos

Theses and Dissertations--Entomology

Integrated livestock systems were once common leading up to the 20th century where livestock generated manure that was then used to fertilizer crop production in a closed- or semi-closed system. However, with the industrialization of agriculture in the mid to late 20th century, specialization drove simplified systems that segregated livestock from cropping systems. This segregation led to nutrient surpluses occurring in livestock operations, and nutrient demands in cropping systems creating a plethora of environmental issues. With the increased awareness of environmental issues, a renewed interest in integration has driven producers and researchers to experiment with integration again. For research, the …

Parental Effects On Offspring Reaction Norms: Consequences For Complex Phenotypes In Variable Environments, Alexandra G. Cones

Theses and Dissertations--Biology

Organismal traits all exhibit some degree of environmental sensitivity, and both the strength and direction of these phenotypically plastic responses to the environment can evolve in adaptive ways. For example, parents can use information about their own environment to precondition the traits of their offspring so that they thrive in their future environment. This transgenerational plasticity can also alter the plasticity of offspring, but explicit investigations of this specific phenomenon are rare. I begin with a review of the literature and provide a quantitative genetic framework to investigate this phenomenon, which I then explore empirically using avian embryos. The metabolic …

Effects Of Traumatic Brain Injury On The Intestinal Tract And Gut Microbiome, Anthony Desana

Theses and Dissertations--Physiology

Traumatic brain injury (TBI) initiates not only complex neurovascular and glial changes within the brain but also pathophysiological responses that extend beyond the central nervous system. The peripheral response to TBI has become an intensive area of research, as these systemic perturbations can induce dysfunction in multiple organ systems. As there are no approved therapeutics for TBI, it is imperative that we investigate the peripheral response to TBI to identify targets for future intervention. Of particular interest is the gastrointestinal (GI) system. Even in the absence of polytrauma, brain-injured individuals are at increased risk of suffering from GI-related morbidity and …

Evaluation Of Increasing Levels Of Mycotoxin-Containing Corn Fines On Diet Choice And Growth Performance Of Nursery Pigs, Duncan B. Paczosa

Theses and Dissertations--Animal and Food Sciences

Pigs fed mycotoxin contaminated diets at high concentrations will result in a detriment to health and performance. An initial study and a follow-up study were conducted to evaluate the effects of feeding increasing levels of mycotoxin-containing corn fines on growth performance, diet preference of pigs, and two possible mitigants.

The initial study was a 3 x 2 factorial containing three levels of fines (0, 10, and 20%, Diets 1-3, respectively) and either 0 ppm (Diets 1-3) or 40 ppm boron (Diets 4-6; Diets 4-6 were Diets 1-3, respectively, plus boron) as sodium tetraborate decahydrate as a possible mitigant. In this …

Utilizing Precision Technologies To Validate A Real-Time Location System For Dairy Cattle And Monitor Calf Behaviors During Heat Stress, Emily Rice

Theses and Dissertations--Animal and Food Sciences

With the increase in on-farm precision dairy technologies (PDT) utilization, large quantities of information are readily available to producers. A more recently available technology for use in livestock species is the real-time location system. These technologies offer dairy producers the opportunity to monitor and track real-time locations of cows, track locomotion patterns, and summarize specific area usage. However, the usefulness of these insights is heavily dependent on the performance of the technology. Therefore, the first objective of this dissertation was to assess the positioning recording performance and the usefulness of the data recorded of a real-time location system (Smartbow GmbH; …

Precision Livestock Farming And Personality As Tools To Understand Dairy Calf Individual Variation In Performance, Behavior, And Response To Stress, Megan Marie Woodrum Setser

Theses and Dissertations--Animal and Food Sciences

Individual differences impact animal responses to their environments and can be observed with animal personality (stable behavioral differences with populations) and food neophobia (avoidance of unfamiliar feeds). These individual differences can influence cattle performance and welfare. Precision technologies, such as automatic feeding systems (AFS) and accelerometers continuously measure feeding behaviors and activity and may allow us to relate individual differences to behaviors in the home environment. Therefore, the first objective was to determine if food neophobia was associated with feeding behaviors measured by AFS. Food neophobia was associated with rewarded visits to the AFS, but to no other feeding behaviors. …

Rewired Metabolism In Apoe4 Microglia: Implications For Inflammation And Neurodegeneration, Nicholas A. Devanney

Theses and Dissertations--Physiology

Among the earliest changes to occur in Alzheimer’s disease, metabolic dysfunction and chronic neuroinflammation are now known to be major driving forces in disease progression. The paradigm of ‘immunometabolism’ seeks to bridge these two facets, positing that metabolic transformations are indispensable in determining the response of immune cells, such as microglia – the brain’s resident immune population. Proinflammatory stimulation of microglia leads to a shift away from mitochondrial respiration towards a dramatic upregulation of the glycolysis pathway for energy production. This glycolytic burst provides microglia with a rapid supply of ATP, but comes at a cost, as utilizing glucose to …