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Bacterial Chondronecrosis with Osteomyelitis in Broilers: Etiology and Selected Mitigation Measures
Full text linkBacterial chondronecrosis with osteomyelitis (BCO) is the predominant cause of lameness in broiler chickens. It mainly impacts broiler production and animal welfare, causing substantial financial losses accounting for 1- 2% due to bird condemnations at the marketing age. Remediating BCO lameness disease demands investigating its causes using appropriate models and evaluating preventive measures, such as enhancing epithelial tissue health and tight junction integrity in the digestive and respiratory tract, strengthening immune functions, and improving bone strength. Therefore, the objectives of this dissertation were to 1) study predisposing factors for BCO lameness by investigating the effects of deoxynivalenol (DON) and fumonisin (FUM) mycotoxins contamination on BCO lameness by exposing broilers reared on wire (W) and litter flooring (L) to diets contaminated with mycotoxins (MTX), 2) determine the efficacy of adding different combinations of 1,25-Dihydroxyvitamin D3-glycoside (G-1,25(OH)2D3) and phytogenic antioxidants on improving bone and gut health and the immune system 3) investigate the optimal timing for adding Availa® ZMC to broiler diets to mitigate BCO lameness, reduce feed additive costs, and effectively protect against BCO lameness. As a result, the findings in this dissertation include three main significant areas. First, increasing the incidence of BCO lameness using mycotoxins due to increasing intestinal permeability supports a correlation between intestinal barrier integrity and BCO lameness and suggests that DON and FUM mycotoxins are predisposing factors for increasing BCO. Second, no significant difference in protection against BCO when supplementing 1.0 µg G-1,25(OH)2D3 individually or in conjunction with polyherbal mixtures or Thyme oil. In addition, increasing the G-1,25(OH)2D3 dosage from 1.0 µg/kg to 10 µg/kg did not yield a lower lameness incidence beyond the low dosage. Finally, incorporating 0.15% Availa® ZMC supplementation into the broiler diet during the initial 28 days is considered ideal for the 0.15% Availa® ZMC dose compared to adding 0.15% Availa® ZMC for the entire production cycle. In conclusion, this collection of studies provides valuable insights into understanding the etiology of BCO lameness and finding possible ways to prevent and remediate its occurrences
Solving Real-World Optimization Problems using Near-Term Quantum Computing with Applications in Vehicle Routing and Drone Delivery
Full text linkQuantum computing (QC) stands at the cusp of revolutionizing computation, yet its near-term potential, constrained by Noisy Intermediate-Scale Quantum (NISQ) devices, remains underexplored. This dissertation investigates how hybrid quantum-classical algorithms can address combinatorial optimization challenges in logistics, focusing on vehicle routing and drone delivery—NP-hard problems with exponential solution spaces that defy classical exhaustive methods. Amidst NISQ limitations like limited qubits and high noise, we confront key challenges: encoding complex constraints, e.g., time windows, battery capacity, into quantum models, balancing quantum and classical components for scalability, and accessing scarce quantum resources. By integrating quantum annealing (QA) and the Quantum Approximate Optimization Algorithm (QAOA) with classical heuristics, this work demonstrates QC’s practical utility, advancing both optimization theory and real-world logistics applications.
The dissertation unfolds across four core contributions. First, the Hybrid Quantum Tabu Search (HQTS) optimally solves the 50-location Capacitated Vehicle Routing Problem (CVRP), achieving a 4.72% optimality gap. Secondly, we refine HQTS to reach a 2.15% gap with enhanced QA utilization, outperforming prior hybrids on standard datasets. Third, adapting HQTS for the CVRPTWwith D-Wave’s Constrained Quadratic Model solver yields a 3.85% gap on 100-location instances, leveraging a novel heuristic to ensure time-window feasibility where quantum outputs falter. Lastly, QUADRO, a pioneering framework for drone delivery, employs QAOA-driven routing and hybrid scheduling, minimizing transit time and makespan for fleets of 2–11 drones needing fewer than 100 qubits, rivaling classical benchmarks on adapted Augerat datasets. These advances, tested via D-Wave’s Advantage system and Qiskit simulations, showcase hybrid strategies that mitigate NISQ constraints, delivering scalable, feasible solutions to logistics challenges.
This work establishes near-term QC’s viability for combinatorial optimization, bridging theoretical promise with practical impact. Synthesizing quantum exploration with classical refinement achieves competitive performance, e.g., matching or surpassing Google ORTools in select CVRPTW cases, while illuminating NISQ limits, such as feasibility degradation beyond small scales. These hybrid strategies deliver scalable, feasible solutions, from a 2.15% optimality gap for CVRP to effective drone fleet management with fewer than 100 qubits, illuminating quantum computing’s potential despite its current constraints. Ultimately, this dissertation positions hybrid QC as a transformative tool for optimization challenges, offering a robust foundation for scaling quantum optimization into operational reality
Studies on the Economic Effects of Violence and Diversity
No full textThis dissertation uses econometric and experimental tools to study differential labor market outcomes, behavioral responses to mass violence, and team integration in the face of diversity.
The first chapter sheds light on the ongoing discussion of the gaps in labor market outcomes between natives and immigrants. Using both parametric and nonparametric estimation techniques on a rich dataset (the European Social Survey), I demonstrate that, even after accounting for selection into the labor force, immigrants are less likely to find employment than natives. A strong country-of-origin identity harms immigrants’ employment chances. The evidence suggests immigrants’ employment chances are also affected by the intensity of cultural differentials and by the attitudes of natives.
The second chapter documents changes in short-run economic activity after 42 mass shootings between 2018 and 2022 in the United States. Exploiting a large dataset of foot traffic to over 150 thousand points of interest (POIs), I use event study and Difference-in-Differences methodologies to evaluate the evolution in the number of visits to the places surrounding shooting sites. Results reveal that foot traffic patterns within a 5-mile radius from the shooting sites significantly change over time, resulting in a considerable relocation of economic activity.
The third chapter adds a level of depth to the study of teams – one that allows for the evaluation of team integration in the presence of diversity in a context where physical proximity to teammates is not a given. Using a lab experiment, I demonstrate that working in teams remotely does not affect cooperation, on average, and that the quality of a team and the identity of teammates plays a lesser role an individual’s cooperative behavior when the team does not interact in person.
Taken together, these chapters deepen our understanding of how diversity and violent social events affect economic outcomes, while opening interesting paths for future research
Atomic Level Characterization for the Transport Cycle Conformational Pathways of Multidrug Resistance Protein 1 (MRP1)
Full text linkThe multidrug resistance-associated protein 1 (MRP1/ABCC1) is an ATP-binding cassette (ABC) transporter that mediates the cellular efflux of endogenous and xenobiotic substrates, including therapeutic drugs. Its overexpression is a major contributor to multidrug resistance in cancer, which tends to result in negative clinical results. Even with considerable progress made in structural biology, the intricate details of how membrane lipid composition affects the conformational changes and functional switches of MRP1 still lack explanation.
This thesis employs long-timescale, all-atom molecular dynamics (MD) simulations to study the influence of various lipids on MRP1 lipid bilayer environments. Both inward-facing and outward-facing conformations of MRP1 were simulated using physiologically relevant POPC and POPE bilayers containing cholesterol. Attention was directed to key structural features, including domain movements, RMSD stability, salt bridge persistence, and hydrogen bonds.
The results demonstrate that bilayer composition strongly impacts the structural flexibility of MRP1. POPE-rich and cholesterol-containing bilayers have been demonstrated to strengthen stabilizing, electrostatic, and nucleotide-binding domain (NBD) compaction, such as ASP1453–LYS1332 and GLU1064–LYS1343, particularly in the inward-facing state. Conversely, POPC-rich membranes exhibit greater freedom of movement and weaker electrostatic interactions. In the post-hydrolysis outward-facing state, cholesterol destabilizes NBD by salt bridge severing and increasing inter-NBD distance, which aligns with reset-ready conformation. A salt bridge ASP749 and ARG1327 was found to undergo dissociation post ATP hydrolysis in all systems, acting as a structural switch onto the NBD opening.
These changes highlight the dynamic nature of the lateral pressure profile that the lipid environment exerts as an allosteric switch on MRP1 function. The results elucidate how specific lipids and membrane components dictate the function of the transporter, thus allowing for targeted approaches to modulate ABC transporter activity through membrane lipid manipulation. Such approaches may aid in formulating new therapeutic strategies to combat drug resistance in cancer and other diseases associated with proliferative ABC transporters
Bacterial Chondronecrosis with Osteomyelitis in Broiler Chickens: Experimental Lameness and Additive Probiotic Treatments
Full text linkWith the global population already surpassing 8.2 billion and expected to reach 9.7 billion by 2050, the poultry industry has seen a surge in demand due to its unmatched efficiency and affordability for consumers across the globe. Selective breeding and quality nutrition developments since the industry\u27s commercialization have allowed producers to grow broilers up to 7 pounds by market age. While this extraordinarily efficient process has allowed quality poultry products to be available worldwide, the modern-day broiler has developed a multitude of musculoskeletal issues. Due to the lack of integral skeletal development to match the rapid production of muscle tissue, producers are experiencing an assortment of lameness issues. Bacterial chondronecrosis with osteomyelitis (BCO) is currently the most prevalent lameness disease in modern broilers. BCO accounts for the majority of mortality and culls related to lameness in the commercial broiler. This bacterial disease is associated with a combination of poor gut integrity (“leaky gut”), aerosolized bacteria, poor skeletal integrity, and mechanical stress on the long bones of the leg. Opportunistic bacteria such as Staphylococcus spp., Enterococcus spp., and Escherichia coli hematogenously spread from the small intestine to microfractures in the growth plates of weight-bearing bones. Bacterial colonization leads to infection, inflammation, necrosis of bone tissue, and eventual death. In addition to the economic loss associated with lameness, BCO is considered a significant animal welfare issue as birds experience extreme discomfort and are often unable to access food and water properly.
In Chapter One, I reviewed the literature utilized in developing my understanding of BCO. The overview presented was established and improved through my experience in co-writing a review publication on the topic, as presented in Chapter 2. Chapter Two presents a complete literature review of current publications relating to BCO. In addition to the foundational knowledge built by Dr. Wideman and Dr. Alrubaye, findings since Dr. Wideman’s 2016 review have revealed more aspects related to BCO etiology, which are presented here.
In Chapter Three, we tested the efficacy of using a supplemental probiotic program alongside a multivalent electron beam (eBeam) vaccine in reducing the incidence of BCO in broiler chickens. At hatch, birds received an Enterococcus faecium spray (E. faecium 669, at 2 × 109CFU/bird), and, from day 1 to day 56, drinking water was treated with a triple-strain Bacillus-based product (B. subtilis 597, B. subtilis 600, and B. amyloliquefaciens 516 at 1 × 109 CFU/bird/day). Chicks were divided into five treatment groups under an aerosol transmission challenge model to simulate treatment effects in a commercial setting. The treatment groups included a positive control group on a wire-floor pen (T1), a negative control group (T2), a group receiving only the probiotic program (T3), a group receiving only the multivalent vaccine (T4), and a group receiving both programs (probiotic supplementation and multivalent vaccination). Broilers were assessed daily for clinical lameness from day 22 until trial completion at day 56. The data collected presented significantly reduced lameness in T3, T4, and T5 when compared to T1 and T2
Development of a Degradation Methodology for Introducing Thermal Performance Deterioration of TIMs to Quantify Reliability Metrics of Electronic Packages
No full textPower densities of electronic devices, specifically, integrated circuits (ICs) or chips, continue to rise significantly, generating considerable amounts of heat. These thermal load increases are detrimental to the performance and service life of chips within central processing units (CPUs) and graphics processing units (GPUs). These microprocessors are encompassed in electronic packages that provide several vital roles, most importantly heat removal. This is achieved by utilizing integrated heat spreaders and heat sinks that interact with various cooling architectures. However, surface deformities between components heavily limit the contact area for adequate heat transfer from the package. Thermal interface materials (TIMs) are incorporated into these high contact resistance regions, replacing non-conductive air gaps with conductive material that can conform to surface disparities. This improves the conduction thermal pathway and decreases abrupt temperature rises. However, TIMs experience extremely hostile conditions during their service life, deteriorating the thermal performance immensely and putting sensitive components at risk of failure. Numerous degradation trends have been observed in literature across a variety of TIMs, but only a handful of attempts at characterizing TIM degradation into predictive empirical models of thermal resistance. Furthermore, these predictive models were only subjected to thermal aging conditions or humidity stresses, with no models pertaining to stress conditions exhibited by processors. Additionally, the influence of TIM degradation on package reliability has not been explored in literature, potentially leading to overestimates of device lifetimes. In this thesis, a commercial TIM is subjected to power cycling conditions to replicate the thermo-mechanical stress conditions of a processor using a temperature difference (ΔT) of 75 °C and 85 °C, respectively. Quantifying the thermal resistance of the TIM was completed using a thermal circuit analysis and verified using steady-state thermal ANSYS simulations. Temperatures were measured using a thermocouple integrated into the heater placed on the TIM and an infrared camera that measured the temperature of the substrate underneath the TIM, with the substrate’s thermal resistance being accounted for in the thermal circuit analysis. The different stress conditions were plotted to analyze the degradation trends and develop a novel mathematical model to predict the thermal resistance of the TIM under power cycling conditions. Next, a methodology was established to examine the impacts of TIM degradation on the chip, specifically, its reliability, prognostics, and performance. The degradation models ascribed from literature were leveraged to emulate TIM degradation behaviors and applied to an electronic package frequently employed in server racks to develop critical relationships between electronic packages and TIM degradation
Rotation Errors Due to Field Quantization for Simultaneously Driven Atoms
Full text linkIf we want to physically implement qubits by using two level atoms within a cavity, then certain single-qubit gates (such as the X-gate) can be performed by bathing the atoms in an electromagnetic field from a laser. If the average photon count n̄ of the field greatly exceeds the number of N qubits, then the slight fluctuations of the field\u27s phase and amplitude are mostly negligible. However, such a strong field might require more energy than what is desirable for the setup. If a weaker field is used in which phase and amplitude fluctuations might be noticeable, then the gate implementation may be imperfect. This error means that the actual qubit state is different from what we would expect from a state created by a perfectly classical field. In this paper, we compare three different techniques to show how this error scales as 1/n̄ for any preferred system of X-gates or Rx(θ)-gates on N atoms. We use a semiclassical treatment of a fluctuating field in addition to the Tavis-Cummings model and second order perturbation. The second order perturbation gives excellent results for when the initial atomic state is in a Cat State or an average of all states. From this, we find equations for maximum and average gate errors, respectively. We show how this error can be reduced by squeezing the coherent source as well as adjusting the interaction time between the field and atoms to be different from what is classically expected
Male and Female Contributions to Sexual Dimorphism
Full text linkSince Darwin, the evolution of sexual dimorphism connects to different evolutionary mechanisms reflecting both natural selection and sexual selection. In primates, body size dimorphism has been attributed to multiple factors, including sexual selection, fecundity selection, ecological selection, and other factors. In contrast, canine tooth size dimorphism has been primarily associated with sexual selection in males with minor change in females, with other factors playing only a secondary role. This suggests that the degree to which body size dimorphism and canine size dimorphism covary, controlling for phylogeny, should reflect the strength of sexual selection. Conversely, the magnitude of divergence between the two dimorphism measures should indicate number of other factors that impact sexual size dimorphism. A key factor that is difficult to tease apart is how the measure of changes in either male or female canine tooth size or body size might impact the magnitude of sexual dimorphism. This study evaluates covariation in body mass dimorphism and canine height dimorphism, and the relative contribution of males and females to the evolution of sexual dimorphism. Tooth size and body mass data were gathered from the literature. The analysis includes PGLS-corrected linear regressions and independent contrasts, and linear parsimony reconstructions. The results of these analyses suggest that sexual selection through the mechanism of male competition is indeed the dominant factor underlying the evolution of both sexual size dimorphism and sexual canine dimorphism, but that other factors impact sexual size dimorphism disproportionately as compared to sexual canine dimorphism. Thus, the use of sexual size dimorphism as a proxy for sexual selection should be approached with caution
Physiological and Molecular Responses of Diverse Rice Genotypes under Drought Stress
Full text linkClimate change-induced drought stress is a significant constraint on global rice (Oryza sativa L.) production, threatening food security. This study evaluated the drought resilience of 15 diverse rice genotypes from the USDA mini-core collection under field, greenhouse, and osmotic stress conditions. Field trials assessed reproductive-stage drought tolerance based on panicle length (PL), number of spikelets per panicle (NSP), and spikelet sterility (SS). Greenhouse experiments examined moisture retention at the vegetative stage. Significant genotypic variation was observed, with genotypes 310724, 310779, 311181, 311603, 311793, and Vandana exhibiting drought tolerance through stable PL and SS. Additionally, genotypes 310100, 310428, 311255, N22, and Bengal demonstrated superior moisture retention. The study emphasizes selecting genotypes with stable performance to enhance drought tolerance, with 310779 and N22 standing out for their low spikelet sterility and strong drought resilience. In contrast, genotypes like 311111, 311140, 311180, and KB showed heightened sensitivity to drought, with reduced panicle length, fewer spikelets, and increased sterility, making them less suitable for drought-prone environments.
Under polyethylene glycol (PEG)-induced osmotic stress, Vandana, 301418, and 311140 exhibited strong tolerance, while 310428, 310724, 311111, 311180, 310779, and 311181 were sensitive. Drought-resistant genotypes exhibited increased root traits, including root length (RL), root-to-shoot ratio (RSR), total root number (TRN), and dry root weight (DRN). Further, drought-resistant genotypes Vandana, N22, 311255 and 311181 displayed an ABA-sensitive phenotype at early growth stages, with ABA-mediated signaling influencing osmotic stress tolerance. RT-qPCR analysis revealed increased ZIP gene expression in drought-tolerant genotypes following ABA application.
These findings underscore the importance of stress-specific evaluations in identifying drought-tolerant genotypes. However, genotypes such as Vandana, N22, and 311255 emerged as promising candidates for breeding programs aimed at improving drought resilience in rice. The study provides valuable insights for developing climate-resilient rice varieties, integrating physiological, morphological, and genetic approaches to enhance adaptation to water-limited conditions. Keywords: Drought tolerance, Oryza sativa, spikelet sterility, ABA signaling, ZIP gene, root phenotyping, PEG stress
