Master's Theses (Plan A and Professional Engineering Design Projects)
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Item Comparative RNA-seq analysis of fetal/neonatal iron deficient and thyroid hormone deficient neonatal rat brain and liver(2024-12) Hanson, BenjaminThyroid hormone deficiency and iron deficiency are two prevalent nutritional disorders that significantly impact neonatal development, particularly in the context of brain. This study investigates the unique and overlapping effects of these deficiencies on gene expression in the context of neurodevelopment. Our findings reveal that TH deficiency leads to the downregulation of several key genes involved in peroxisomal lipid metabolism, particularly those associated with beta-oxidation. This downregulation compromises the liver's capacity to oxidize fatty acids, resulting in reduced ketone body production. Similarly, iron deficiency triggers a metabolic switch from fatty acid beta-oxidation to glycolytic dependence, with significant downregulation of genes involved in ketogenesis and upregulation of glycolytic genes. We also found that there is a compounded effect on myelination and extracellular matrix organization, essential for neuronal connectivity and function. Notably, the study highlights the role of insulin-like growth factor signaling, which is significantly perturbed in both deficiencies, linking liver function to neurodevelopmental outcomes. The implications of these findings underscore the necessity for early detection and intervention strategies in populations at risk for TH and iron deficiencies, particularly in neonates. Future research should focus on elucidating the molecular mechanisms underlying these interactions and their long-term impacts on cognitive and motor development.Item Managing dicamba volatility and drift: technological advances and regulatory strategies to minimize off-target movement(2024-12) Hammer, CalebDicamba herbicides are a critical tool for managing herbicide-resistant weeds, but their high volatility and potential for off-target movement have raised significant concerns about unintended damage to non-target crops and ecosystems. Despite reformulations aimed at reducing volatility, the persistence of dicamba-related drift continues to challenge growers and regulators. This research aimed to address these challenges using a measurement and modeling approach. The objectives of the research were to: 1) quantify dicamba concentrations in the atmosphere downwind of application sites; 2) measure dicamba loss and off-site transport using atmospheric sampling and Lagrangian transport modeling; 3) assess meteorological influences on dicamba volatilization and drift; 4) employ Geographic Information Systems (GIS) to analyze spatial and meteorological factors driving dicamba’s off-target movement; and 5) develop a risk-rating scale to guide counties in Minnesota on dicamba application risks.Field experiments conducted over multiple growing seasons combined air sampling with backward and forward Lagrangian stochastic models to estimate dicamba emissions and downwind transport. Results revealed that dicamba volatilization persisted for several days post-application, with peak emissions occurring within the first 24 hours. High temperatures, stable atmospheric conditions, and low wind speeds were identified as significant drivers of off-target movement, challenging the effectiveness of current label requirements and application guidelines. Geospatial analysis of dicamba damage across Minnesota from 2018 to 2022 highlighted southern and western counties as high-risk areas, driven by local meteorological conditions and soybean density. The analysis further identified critical meteorological thresholds, such as atmospheric stability, wind speed, and temperature, that exacerbate dicamba drift. By integrating experimental data with spatial and statistical analyses, this work provides a comprehensive evaluation of dicamba volatility and its impact on non-target crops. The findings emphasize the limitations of existing regulatory frameworks and underscore the need for stricter application guidelines that account for post-application volatilization and regional variability in risk. This work offers actionable insights for improving herbicide application practices, guiding regulatory strategies, and mitigating the environmental impact of dicamba in agricultural systems.Item Use of winter hybrid Rye in diets for organic growing-finshing pigs(2024-11) Cristina Veloso Lima, GabriellaThis study evaluated the effects of replacing 50% of corn with hybrid rye in growing-finishing pig diets on pig performance, carcass characteristics, and phosphorus concentrations in fecal and manure samples. A total of 500 pigs (initial body weight = 18.9 ± 2.94 kg) were assigned to either a Control or Rye treatment (50 pigs/pen; 5 pens/treatment) based on sex and body weight. Control pigs received a corn-soybean meal diet, while Rye pigs were fed a diet where hybrid rye replaced 50% of the corn. Pigs were housed in a hoop barn, with wheat straw bedding provided to Control pigs and rye straw for Rye pigs. Pig performance, including body weight (BW), average daily gain (ADG), average daily feed intake (ADFI), and feed efficiency (G:F) were recorded every 28 days. At the end of the trial, carcass traits such as final BW, hot carcass weight (HCW), backfat thickness (BF), and loin eye area (LEA) were measured. Feed samples from each dietary phase were analyzed for nutrient composition, including phosphorus and phytic acid concentrations. Fecal samples from 80 pigs (40 Rye and 40 Control) were collected and analyzed for phosphorus and phytic acid concentration. Manure and bedding samples were also collected before, at the start and end of the trial and during manure clean-out to assess composition. There were no differences in BW, ADG, ADFI, or G:F between Control and Rye fed pigs (P > 0.05). However, carcass yield and LEA were lower in Rye-fed pigs (P < 0.05). Mortality was lower in Rye-fed pigs (P < 0.05), while morbidity was not different between treatments (P > 0.05). Phosphorus concentrations in Rye diets were higher across most phases (P < 0.05), but there were no differences in phosphorus or phytic acid concentrations in the fecal samples between treatments. There were no differences between treatments for most manure traits collected during and after the trial and at manure clean out (P > 0.05). In conclusion, replacing 50% of corn with hybrid rye in growing-finishing pig diets did not affect growth performance but resulted in reduced some carcass traits, including carcass yield, back fat, and loin eye area.Item Bringing nature inside: improving the indoor experience(2024) Davidson, MaiaIn the modern world, United Stated people spend 90% of the day indoors, going against the innate desire all human beings possess to be connected with nature. Understanding how the connection to nature benefits individuals, and what this lost connection may be causing or negatively enhancing, is an important part of future design because improving the design of interior spaces will improve the health of those using it. Expanding and deepening the design toolkit to include tangible elements, such as using tall potted plants as a spatial divider, purposefully placed colorful plants as wayfinding elements, hanging plants as light diffusers, and many other design solutions, offers clear opportunity to add natural benefits, such as improved mental health, cleaner air, and expanded attention, to any project. This study reviewed the literature of nature-based benefits and major issues people are struggling with and determined that the disconnect between humans and the natural world is harming society, and that a change must occur. These findings were used to determine an equitable solution that could be incorporated into the design world. Realizing the issues affect those of all economic and social standing, an affordable, small-scale solution became the focus of this study. Offering opportunity for anyone to include potted plants in design makes this solution as attainable as it is effective. Encouraging design professionals and those who seek to do so on their own to incorporate plants into interior design is the first step towards a more impactful reconnection with nature.Item Development of proteomics-based approaches and theraputics to identify and target RET kinase protein in lethal prostate cancer(2024-12) Dinh, Quynh ChauNeuroendocrine prostate cancer (NEPC) is a subtype of metastatic castration resistant prostate cancer (mCRPC). It arises as a resistance mechanism to second generation androgen deprivation therapy (ADT). Platinum-based chemotherapy is often indicated as first-line treatment, however, they only provided minimal benefit. Therefore, there is a need to identify new therapeutic targets for NEPC and stratify patients for personalized medicine. Our lab has found that RET protein could serve as a potential therapeutic target for NEPC. RET is a receptor tyrosine kinase, which is often translocated or mutated in lung cancer and in different subsets of neuroendocrine tumors. We found that RET mRNA levels were elevated in mCRPC patients with a NEPC phenotype and in NEPC patient-derived xenografts (PDXs) compared to adenocarcinoma samples. There are two new FDA-approved RET inhibitors, and these therapies show efficacy in cancers such as papillary thyroid cancer and non-small cell lung cancer with RET fusions. We would like to expand the scope of these studies to prostate cancer and identify mCRPC patients that will potentially benefit from RET inhibition therapy. To do that, I propose using targeted mass spectrometry to identify patients with high abundance of RET protein in circulating tumor cells (CTCs). I hypothesize that liquid biopsy-based detection of RET kinase protein will aid in the stratification of patients with mCRPC. I have identified 10 candidate RET peptides that perform well on the mass spectrometer. Future studies will include evaluating these peptides for their ability to detect endogenous RET protein in pre-clinical and clinical samples. To identify new RET inhibitors, I also evaluated the effects of novel RET inhibitors on RET activity and its downstream signaling in NEPC cell line models. Novel RET inhibitors were able to reduce the activity of RET, AKT, and ERK phosphorylation. In addition, a mechanistic study also revealed the role of ASCL1 on RET in prostate cancer. These results are aimed to build the needed tools that support the hypothesis that RET is important for the survival of NEPC tumors and assessing RET expression will aid in the treatment of mCRPC/NEPC patients.Item Increasing the applicability of transplantation tolerance in solid organs by leveraging linked suppression(2022-11) Finn, SadeObjectives: To investigate differences in immune responsiveness of islet allograft recipients before and after ADL infusion-based tolerance protocol. To understand the implications of MHC-I and MHC-II matching on linked suppression.Methodology: Peripheral blood mononuclear cells were collected from a cohort of 5 nonhuman primates who underwent islet transplantation after two peritransplant infusions of apoptotic donor leukocytes under the cover of short-term immunotherapy with anti-CD40 antibody, rapamycin, soluble tumor necrosis factor receptor and anti-IL-6R antibody between posttransplant day 60 and 90. Recipient PBMCs were cocultured with irradiated donor PBMC from the tolerized islet donor DR matched to the recipient (Donor DR Match), unrelated class I MHC allele matched donor (3P Class I Match), unrelated class II MHC allele matched donor (3P Class II Match), and unrelated MHC complete mismatched donor (Complete Mismatch) in a 5-day mixed leukocyte reaction. Both flow cytometry and cytometry by time of flight were used for data acquisition. Results: When recipient PBMCs treated with ADL infusion and short course immunotherapy was challenged with third-party antigen matched at either MHC-I (3P Class I) or MHC-II (3P Class II) to Donor DR, we again observed a near 2-fold increase in the Treg and Tr1 populations, providing evidence of linked suppression. Both third-party MHC matched conditions were associated with an increase in regulatory CD4 cell subsets and decreased CD4 and CD8 effector T cells compared to challenge with complete mismatched antigen. Conclusion: For the first time, we demonstrate linked suppression in a large animal model. Our study pointed to a slight trend of class II MHC matching showing greater expansion of Treg population compared to class I MHC matching that was consistent with the literature.Item Passage secondary flow effects on turbine endwall discrete holes film cooling(2024-08) Chen, Ting-WeiIn this thesis, film cooling effectiveness measurement results representative of gas turbine endwall cooling are discussed with emphasis on describing the effects that features in the complex turbine passage flow have on them. Film cooling is when cool air from elsewhere in the turbine is supplied through walls of the turbine passage that require cooling providing a protective layer of cool air over the surface to partially isolate it from the hot mainstream. Complexity comes from secondary flows naturally occurring in the passage. Important, is their influence on film cooling effectiveness. Holes for film cooling injection are typically distributed over the upstream portion of the passage walls in an attempt to cover and protect the full passage. The present study documents separate and combined effects present in the passage by studying a single hole of various shapes, hole orientation angles with respect to the main flow, injection-to-main-flow velocity ratios, and passage flow with and without vortices generated upstream. Representative endwall surface wall shear fields are documented in the literature as are hole pattern designs. They establish the angle between the near-wall flow approaching a selected hole and the centerline direction of the corresponding hole. Often, shear field data are not available within the passage and approach flow directions to some holes cannot accurately be applied. Then, the flow approaching only holes that are upstream in the passage (particularly, upstream of any coolant injection) can be accurately described. Nevertheless, measurements showing migration of coolant on the endwall downstream of selected holes have been valuable to document how coolant is affected by features in the surrounding flow, features such as the momentum of injection, the passage main flow direction, and the effects of vortices in the vicinity of the hole. One example is the discrete hole located under a vortex created at the airfoil leading edge and residing near the passage entrance where ejected coolant is swept by the vortex away from the endwall, resulting in low local values of surface effectiveness. This leaves the upstream endwall regions near the pressure and suction surfaces difficult to provide coolant coverage by discrete hole injection. The measurements documented in the present study provide guidance for interpreting such downstream distributions of coolant. Cases discussed herein have low injection rates upstream of the passage. Studies with high injection rates upstream of the inlet (high ratios of passage inlet momentum flow near the endwall to passage average momentum flow) are fundamentally different and are not discussed herein. Such cases have strong injection along the endwall immediately upstream of the passage inlet (strong combustor wall cooling) and, thus, would have a different passage secondary flow pattern. Such a pattern is discussed in Nawathe, et al., 2023 as the “impingement vortex.” The measurements of the present study document the endwall coolant coverage and coolant distributions in the flow at several planes downstream of injection. Such data not only show the cooling effectiveness but track the coolant in the passage flow. Flow measurements describe profiles of mean velocity, describing the boundary layer growth and momentum deficit of streamwise momentum upstream and downstream of injection. Understanding the interaction of secondary flows with film cooling in the turbine is significant to gas turbine designers. Dominant flow features of secondary flow are convected vortices in the mainstream, endwall crossflow, and suction and pressure legs of the vortex formed at the passage leading edge.Item Design optimization of a diffuser augmented, dual-rotor hydrokinetic turbine utilizing 2D actuator disk theory(2024-12) Walz, AndrewAn estimated 58,400 ± 109 TWh/year of untapped energy exists in rivers across the globe.Installing renewable technology at this capacity would mean significant reductions in greenhouse gas emissions and a slowdown of global warming. Hydrokinetic turbines have gained attraction in recent years to fulfill this need as they offer competitive power production with minimized environmental impact when compared to conventional fully dammed hydropower. Even more recently, researchers and manufactures have investigated how diffuser-augmentation of a hydrokinetic turbine can positively increase the power coefficient of these devices. Several design optimizations of these diffusers have been completed and some generalizations of their suggested shape have been made. Often neglected; however, are the adverse outcomes of diffuser augmentation, such as increased structural loading, increased manufacturing costs, and a reduction in compactness for array installation. The present study has developed a robust methodology for quantifying and implementing these adverse effects into the design optimization process. A total of 40, two-dimensional CFD numerical simulations are conducted, testing a wide range of diffuser shapes from flange style to airfoil style. Additionally, the actuator disk method is utilized across all design cycles to replicate the presence of a turbine rotor, creating a more realistic flow field; a step often neglected in existing two-dimensional design optimizations. The output parameter of maximizing interest is efficiency; a metric calculated by how effectively a diffuser shape can accelerate fluid through at the rotor plane. The output parameters of minimizing interest are diffuser pressure, diffuser material volume, and wake deficit; all metrics significantly influencing manufacturing costs and deployment constraints. A maximum of 29.4% and near minimum 24.9% efficiency values are recorded by the sharp flange and airfoil diffusers, respectively. However, where the flange diffuser excelled in maximizing efficiency, it under-performed in reducing the adverse effects. The contrary can be stated for the airfoil diffuser. An ‘optimal’ design is identified that shares characteristics to both diffuser shapes. Discussion includes insight on why this optimal design (DC 16) is most effective at this and how a future economic analysis could reveal a new optimal design dependent on the turbine deployer’s needs and manufacturing costs.Item Soil health system impacts on soil hydraulic functions in southern Minnesota(2023-12) Tangen, BaileySoil health management systems use agricultural practices incorporating living roots, persistent surface cover, diverse crop rotations, and minimal soil disturbance. These systems are widely believed to improve soil hydraulic functions. However, intense rainfall can cause physical slaking of aggregates, loss of surface pores, and reduced hydraulic functions. Soil health management systems correlate with stable aggregates and large soil pores, but it is not clear how these properties change with rainfall in fine-textured soil profiles in southern Minnesota, United States. Therefore, quantifying the hydraulic function of these systems is important as climate change intensifies growing season rainfall. Here, we investigated soil health system’s volumetric soil water content and aggregates’ response to rainfall. During 2021 and 2022, we collected data from five tillage and cover crop treatments in replicated plots at the Southern Research and Outreach Center in Waseca, MN, and paired conventional and soil health systems at three long-term on-farm sites (≥5 years, clay loam and silt loam soils). We monitored volumetric soil water content and soil aggregates within 24 hours before and 24 and 72 hours after select rainfall events. Across all locations, drier conditions led to greater rainfall capture. Differences in response to rain were found between the paired farm treatments. Generally, conventional sites had 5-20% more small aggregates following rain than soil health sites, but this effect was inconsistent across all locations. Soil health systems generally retained 10-30% more large water-stable aggregates than conventional systems in response to rain. Based on soil water retention curves, soil health treatments trended 2.5-12.5% more macroporosity than conventional systems, likely contributing to the water capture. At the farms, greater microporosity and connectivity led to 0.25-2 cm/hr greater unsaturated hydraulic conductivity relative to soil health sites, validating the greater macroporosity results we found in the soil health sites. Despite long-term treatment history at SROC, there was no unsaturated hydraulic conductivity difference, though trends showed a positive relationship with increased disturbance, like rip/chisel. Soil health indicators were higher for the soil health system of one on-farm site, where soil health practices included 30 years of long-term no-till and cover crops compared to moldboard plowing. This research indicates the importance of holistically incorporating soil health practices into field systems for achieving soil functions.Item Assessing Raw 264.7 migration in a mechanically-tunable 3D collagen-hyaluronic acid co-gel for use in Borrelia Burgdorferi pathology study(2024-05) Tucker, JaredBorrelia Burgdorferi, the bacteria associated with Lyme Disease, has been a topic of much research in recent decades, but it continues to prove difficult to understand how the bacteria interacts with the immune system on a cellular level, specifically macrophages. To aid in this work, a 3D hydrogel for cell culture was formulated using collagen and hyaluronic acid (HA) to help provide a system for studying these dynamic cellular responses in a soft-tissue environment. A design of experiments was organized to study the effects of collagen concentration, HA fragment size, and Collagen:HA mass ratio on both the hydrogel properties and macrophage mobility and growth. Mechanical characterization of the gels was conducted using rheology and found that collagen concentration, but not HA content, directly modulated the hydrogel storage modulus. The hydrogels were shown to be suitable for cell culture, allowing for cellular proliferation, but exhibited limited chemotaxis.Item Balancing trade-offs: an investigation into the agroecological impacts of winter legume cover crops employed in organically managed high tunnels(2024-12) Walsh, HannahHigh tunnels (HTs) are semi-permanent structures used in temperate climates to increase vegetable production by leveraging shoulder seasons when open fields (OFs) may be inaccessible due to cold weather or spring flooding. They have become increasingly popular in the U.S. with the advent of cost-share programs through the NRCS and are often promoted as a conservation practice. However, as an intensive practice, HTs are associated with soil structure degradation, increased pest and disease incidence, nutrient buildup, and loss of organic matter. Planting winter legume cover crops in rotation with summer vegetables is an emerging strategy to mitigate some of these adverse effects. There is limited knowledge of how winter cover crops' planting and termination time affect soil health and cash crop yield. Productivity trade-offs are expected, as early fall cover crop planting and late spring termination may interfere with lucrative cash crop production windows. However, extending the growth period of the cover crop may increase its potential to provide soil-enhancing biomass. This research evaluates the degree to which fall planting and spring termination time of two winter cover crops, hairy vetch (Vicia villosa Roth) and Austrian winter pea (Pisum sativum L.), affects 1) cover crop biomass and biomass nitrogen, 2) pepper yield, 3) permanganate oxidizable carbon (PoxC) 4) potentially mineralizable nitrogen (PMN) and 5) microbial biomass carbon (MBC) and nitrogen (MBN) in organically managed HTs. Results indicated a 176% difference in biomass production between the longest and shortest cover crop growth periods, with the longest period accumulating the most biomass. However, there was an associated decline in mean annual cash crop yield when the cover crop season was extended. Soil health indicators had mixed results but showed potential to build nutrient reserves over time, with the longest cover crop growth period increasing PMN as much as 5 times from Y1 to Y2. Microbial activity appeared to be limited in the HT, suggesting research should focus on soil biological processes in HTs.Item Streamlined structural design optimization with interactive visualization for multi-objective design spaces(2024) Suliin, JacobA common task for design engineers is the balancing of conflicting design objectives through the application of design of experiment (DOE) based methods to explore a design space. Traditional approaches to this problem require modeling the geometry with graphical user interface (GUI) based modeling software to generate the DOE runs. Visualizing these design tradeoffs, particularly when there are more than two objectives, is also a challenging task that often needs to be done manually. This thesis provides a streamlined approach to structural design optimization with interactive plotting for multi-objective design spaces, enabling engineers to easily visualize the objective space and identify optimal solutions. Utilizing Python and its available libraries, in conjunction with the innovative Jupyter Notebook environment, parameterized geometry is generated using Python code, and a static structural analysis is performed through a DOE. The resulting dataset from the DOE features five output objectives and is used in an optimization process generating Pareto optimal solutions, and thus a Pareto front for given pairs of constraints is generated. An interactive 2D scatter plot is generated with the Pareto front data, allowing users to quickly investigate the relationships between the inputs and output objectives. Additionally, two approaches for visualizing the tradeoff between more than two objectives are presented, enabling an informed decision to be made when selecting a candidate solution when balancing more than two objectives. These approaches are demonstrated on two example structural design problems. Finally, the potential application of large language models (LLMs) to the code based approach used in this thesis is discussed.Item Effects of low pathogenicity avian influenza on turkey breeding flocks and immune evaluation of an H1N2 DNA vaccine(2024-11) Studniski, MarissaLow pathogenicity avian influenza (LPAI) viruses can have substantial negative effects on egg production in turkey breeding flocks. Despite vaccination, turkey breeding hens continue to face disease associated with LPAI. Additionally, detecting a measurable immune response post-vaccination using traditional IAV killed vaccines has been challenging. In the present study, a plasmid-based DNA vaccine expressing the HA gene of an H1N2 LPAI virus in addition with immunostimulatory genes was developed and evaluated in turkeys. Turkeys were challenged with an H1N2 virus to determine the protective efficacy of the vaccine. Virus was neither detected in the birds post challenge by RT-PCR of oropharyngeal swabs nor were antibodies detected by ELISA from their sera. In conclusion, our study suggests DNA vaccine technology may be a good alternative to the currently administered autogenous vaccine, but due to the lack of a challenge model we were unable to properly evaluate immune efficacy of the vaccine.Item In situ characterization of focused ultrasound neuromodulation bioeffects: a Kalman Filter based approach(2024-11) Singh, AmitiLow-intensity focused ultrasound (LIFU) induces biological effects, such as thermal and mechanical responses, which can have applications in neuromodulation and thus require careful characterization. These responses generate measurable displacements captured by ultrasound imaging, which are analyzed using thermography and elastography to quantify thermal and mechanical effects respectively. However, these measurements are often biased by the simultaneous presence of both effects as well as environmental noise. To address this challenge, the Kalman Filter and the Extended Kalman Filter (EKF), are utilized in this work to separate the thermal and mechanical effects in real-time while incorporating the physics underlying these systems. Additionally, parameter estimation is performed to identify unknown model parameters, enabling a more robust separation of these effects.Item Genetic exploration of exercise associated sudden death in racehorses(2024) Stock, JoyBackground: Exercise-associated sudden death (EASD) is a fatal collapse occurring during or within 2 hours of racing or training in an otherwise healthy individual. It represents a significant cause of mortality in racehorses, accounting for 25% of the approximately 500 annual racehorse fatalities in the United States. Beyond its negative impact on equine welfare, EASD poses risks to jockey safety and challenges the public perception of horse racing. Cardiac-related issues are the cause of approximately 50% of EASD cases. Cardiac arrhythmias are also thought to be an important contributor to the EASD cases without a diagnosis at necropsy. In human patients without a diagnosis at necropsy, ion channelopathies are found to be an important underlying cause. The genetics underlying EASD have been largely unexplored in horses.Hypothesis: Thoroughbred racehorses with variants in ion channels and other arrhythmogenic genes are predisposed to a higher risk of EASD. Specific Aim1: This study aimed to identify causative positional candidate regions for EASD in Thoroughbred racehorses. Methods: Whole-genome sequencing (target: 12X coverage) and a Genome-wide Efficient Mixed Model Association (GEMMA) univariate linear mixed model genome-wide association study (GWAS) were performed on 50 EASD cases and 48 controls. Results: We identified 8 significant regions linked to EASD. Although genes in these regions were not directly analogous to known human ion channelopathy genes, aquaporin 4 (AQP4) and potassium channel tetramerization domain containing 1 (KCTD1) on the region in chromosome 8, showed potential relevance to dysrhythmia development. Specific Aim 2: This study aimed to identify causative variants in arrhythmogenic candidate genes for EASD in Thoroughbred racehorses. Methods: Candidate genes were identified using a keyword-based query of four databases: Phenolyzer, ClinVar, Online Mendelian Inheritance of Man, and OpenTargets. From these, a narrow (genes identified in all four programs) and a broad (genes identified in two or three programs) candidate gene set were established. SnpSift CaseControl was used to identify significant differences between EASD cases and controls. Results: We identified a significant modifier variant in troponin T2-cardiac type (TNNT2) from the narrow gene set. The broad gene set analysis identified 39 significant variants across 21 genes, with notable findings in triadin (TRDN) and calcium voltage-gated channel subunit alpha1 D (CACNA1D), both of which are linked to cardiac arrhythmias in people and may contribute to equine EASD. Conclusions: We identified variants and genes that may be contributing to EASD in Thoroughbred racehorses. These variants and genes warrant further investigation for their roles in exercise-induced arrhythmias, sudden death, and EASD in Thoroughbred racehorses.Item Dynamic regulation of replication timing during cell lineage decisions(2023-12) Sadu Murari, Lakshana SruthiDuring embryogenesis, the fetal liver is one of the first organs to develop after the heart, relying heavily on signals from the adjacent cardiac mesoderm. As lineage specification proceeds during development and cells differentiate, genomic regions are segregated into early or late replicating domains, establishing a cell type-specific replication timing (RT) program. Decades of intensive research have uncovered a strong correlation between developmental changes in RT, genome organization, and the transcriptome. While global changes in RT have been identified during distinct differentiation pathways, lineage-specific changes during organ development remain unexplored. Identifying factors regulating changes in replication timing pertaining to cardiac and hepatic development would help better understand how replication timing is regulated during lineage decisions and help establish better models to study congenital defects. Here, we sought to study the developmental switches in RT, and the corresponding changes in the transcriptome, of hESC-derived hepatocyte-like cells and cardiomyocyte-like cells. We also developed a novel multi-omics approach for the parallel analysis of replication timing and gene expression (PARTAGE), as well as an optimized method for live single-cell subcloning of HepG2 cells to enable genome editing experiments and generation of mutant cell lines.Item The role of growth mindset in motivating novice persistence: how experts bounce back after failure(2022-12) Ristani, GinaExperts become experts partly because of their willingness to engage in thousands of hours of deliberate practice. What motivates this persistence despite constant failure? This question was addressed in a study replicated from Chase (2013) of experts in the domains of mathematics and English literature enrolled at a U.S. university (N = 40, 23 mathematics and 17 English experts). We investigated their persistence when tackling challenging tasks in their domain of expertise and the domain in which they were novices. Different patterns in experts’ verbalized failure attributions for their in-domain task and their out-domain task were explained by the implicit theory of intelligence individuals held. These findings indicate experts’ failure attributions and growth mindset may bolster persistence when tackling challenging problems in their domains. Future research might explore whether interventions encouraging a growth mindset may motivate novices to persist even after repeated failures on the path to expertise.Item Holographic air-quality monitor (HAM)(2023) Bravo-Frank, NicholasThis study introduces a holographic air-quality monitor (HAM) for real-time detection, sizing, and classification of airborne particulate matter. Integrated with Arduino and additional sensors, the HAM operates in a 10-500 μm size range at 26 liters per minute (LPM). Performance assessments involved comparisons with brightfield microscopy and an integrated reference PM sensor, accurately sizing 20μm silver-coated glass balls and 100μm PMMA clear microspheres. Practical demonstrations in a living room and kitchen setting further confirmed the HAM's sensitivity to varied particulate matter. However, challenges in handling transparent particles and high particle concentrations highlight future improvement areas, including optimizing machine learning models and enhancing segmentation techniques. This innovative approach promises significant contributions to air quality monitoring by offering precise and comprehensive data for large and irregular shaped particulate matter.Item Characterization of colloidal nanoparticles: a comparison study among light scattering and atomizing instruments(2024-11) Rahman, Md AtiqurControlling nanoparticle characteristics throughout the semiconductor manufacturing process is essential for reducing chip failure probability and enhancing production stability. To identify the properties of engineered nanoparticles, several advanced analytical tools—such as atomizers, scanning electron microscopy (SEM), dynamic light scattering (DLS), and nanoparticle tracking analysis (NTA)—have been utilized, each with its inherent limitations and boundary conditions. The manuscript highlights a newly developed methodology using ES-SMPS for characterizing colloidal nanoparticles and presents a detailed comparison of the aforementioned instruments, evaluating their relative advantages. In Chapter 1, we mainly present the development of a methodology for characterizing nanoparticles in low-concentration samples using the ES-SMPS, and then compare the performance of ES-SMPS with atomizer and NTA. To serve this purpose, we first conducted a parametric study to identify optimal conditions for separating the residue peak from the main particle peak. The findings indicate that to effectively separate the residue from the particle peak, the sample should have higher electrical conductivity and be pushed with a lower flow rate, while the system sheath flow rate should remain high. We then determined the range of detectable liquid concentrations measurable by the ES-SMPS, Atomizer, and NTA for comparison purposes. It was found that the operating range of the NTA (~10⁹ to ~10⁷ particles/mL) was narrower than that of the ES 3480 and Kanomax atomizer which can operate over a broader range of ~4 × 10¹² to ~10⁸ particles/mL and ~2 × 10¹² to ~10⁸ particles/mL respectively. Finally, we compared the sensitivity of precise particle counting across ES-SMPS models (ES 3480 and ES 3482), the Kanomax Atomizer, and NTA over a range of silica particle sizes from 23 to 200 nm. When it comes to particle size determination, atomizing instruments provide more accurate measurements than NTA. Unlike the NTA, which overestimated the particle concentration, the atomizing equipment provided a more accurate measurement. The findings of this research offer valuable insights for selecting suitable instruments for applications that require precise characterization of colloidal particles. In Chapter 2, we employed primarily three techniques electrospray-scanning mobility particle sizer (ES-SMPS), nanoparticle tracking analysis (NTA), and dynamic light scattering (DLS) to assess multimodal samples. In the case of monodisperse particles, both the ES-SMPS (all sizes) and NTA (particle size larger than 40 nm) accurately determined the mean size, while the DLS approach overestimated it. The ES-SMPS technique demonstrated precision in particle counting of multimodal samples with a standard deviation of around 2.5-4%. Conversely, the NTA's ability to count particles potentially leads to misinterpretation. The ES-SMPS approach could identify particle peaks in multimodal (bimodal, trimodal, and tetra-modal) samples, and show the relatively right position of the mode diameter. In contrast to ES-SMPS, DLS, and NTA have weaknesses in characterizing multimodal samples. While NTA’s performance depends on the optical properties of particles and it can’t measure silica particles smaller than 30-40 nm, ES-SMPS are independent of light scattering and can do the job even with a particle of ~13 nm. The ES-SMPS also excelled in separating particle peaks of bimodal sample with a size interval gap of 10 nm whereas NTA needs at least 20-50 nm depending on the particle type. To sum up, the ES-SMPS method performs better and gives an accurate measurement of characterizing multimodal samples as compared to NTA and DLS.Item Geometric properties of Springer fibers of type A over a division ring(2024-11) Park, ArianaWe define and study Springer fibers over a general division ring R over ℝ, rather than the usual algebraically closed field. We give examples of such Springer fibers and provide geometric properties, mostly about their irreducible components, that generalize properties known for Springer fibers over algebraically closed fields. In particular, when discussing the geometric properties of such Springer fibers, we focus on type A Springer fibers, that is, where the underlying Lie algebra is of type A.