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Title: REACTIVE ION ENHANCED MAGNETRON SPUTTERING OF NITRIDE THIN FILMS
Creator: Talukder, Al-Ahsan
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Magnetron sputtering is a popular vacuum plasma coating technique used for depositing metals, dielectrics, semiconductors, alloys, and compounds onto a wide range of substrates. In this work, we present two popular types of magnetron sputtering, i.e., pulsed DC and RF magnetron sputtering, for depositing piezoelectric aluminum nitride (AlN) thin films with high Young’s modulus. The effects of important process parameters on the plasma I-V characteristics, deposition rate, and the properties...
Show moreMagnetron sputtering is a popular vacuum plasma coating technique used for depositing metals, dielectrics, semiconductors, alloys, and compounds onto a wide range of substrates. In this work, we present two popular types of magnetron sputtering, i.e., pulsed DC and RF magnetron sputtering, for depositing piezoelectric aluminum nitride (AlN) thin films with high Young’s modulus. The effects of important process parameters on the plasma I-V characteristics, deposition rate, and the properties of the deposited AlN films, are studied comprehensively. The effects of these process parameters on Young’s modulus of the deposited films are also presented. Scanning electron microscope imaging revealed a c-axis oriented columnar growth of AlN. Performance of surface acoustic devices, utilizing the AlN films deposited by magnetron sputtering, are also presented, which confirms the differences in qualities and microstructures of the pulsed DC and RF sputtered films. The RF sputtered AlN films showed a denser microstructure with smaller grains and a smoother surface than the pulsed DC sputtered films. However, the deposition rate of RF sputtering is about half of the pulsed DC sputtering process. We also present a novel ion source enhanced pulsed DC magnetron sputtering for depositing high-quality nitrogen-doped zinc telluride (ZnTe:N) thin films. This ion source enhanced magnetron sputtering provides an increased deposition rate, efficient N-doping, and improved electrical, structural, and optical properties than the traditional magnetron sputtering. Ion source enhanced deposition leads to ZnTe:N films with smaller lattice spacing and wider X-ray diffraction peak, which indicates denser films with smaller crystallites embedded in an amorphous matrix.
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Title: Towards Robust and Reliable Communication for Millimeter Wave Networks
Creator: Zarifneshat, Masoud
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The future generations of wireless networks benefit significantly from millimeter wave technology (mmW) with frequencies ranging from about 30 GHz to 300 GHz. Specifically, the fifth generation of wireless networks has already implemented the mmW technology and the capacity requirements defined in 6G will also benefit from the mmW spectrum. Despite the attractions of the mmW technology, the mmW spectrum has some inherent propagation properties that introduce challenges. The first is that free...
Show moreThe future generations of wireless networks benefit significantly from millimeter wave technology (mmW) with frequencies ranging from about 30 GHz to 300 GHz. Specifically, the fifth generation of wireless networks has already implemented the mmW technology and the capacity requirements defined in 6G will also benefit from the mmW spectrum. Despite the attractions of the mmW technology, the mmW spectrum has some inherent propagation properties that introduce challenges. The first is that free space pathloss in mmW is more severe than that in the sub 6 GHz band. To make the mmW signal travel farther, communication systems need to use phased array antennas to concentrate the signal power to a limited direction in space at each given time. Directional communication can incur high overhead on the system because it needs to probe the space for finding signal paths. To have efficient communication in the mmW spectrum, the transmitter and the receiver should align their beams on strong signal paths which is a high overhead task. The second is a low diffraction of the mmW spectrum. The low diffraction causes almost any object including the human body to easily block the mmW signal degrading the mmW link quality. Avoiding and recovering from the blockage in the mmW communications, especially in dynamic environments, is particularly challenging because of the fast changes of the mmW channel. Due to the unique characteristics of the mmW propagation, the traditional user association methods perform poorly in the mmW spectrum. Therefore, we propose user association methods that consider the inherent propagation characteristics of the mmW signal. We first propose a method that collects the history of blockage incidents throughout the network and exploits the historical blockage incidents to associate user equipment to the base station with lower blockage possibility. The simulation results show that our proposed algorithm performs better in terms of improving the quality of the links and blockage rate in the network. User association based only on one objective may deteriorate other objectives. Therefore, we formulate a biobjective optimization problem to consider two objectives of load balance and blockage possibility in the network. We conduct Lagrangian dual analysis to decrease time complexity. The results show that our solution to the biobjective optimization problem has a better outcome compared to optimizing each objective alone. After we investigate the user association problem, we further look into the problem of maintaining a robust link between a transmitter and a receiver. The directional propagation of the mmW signal creates the opportunity to exploit multipath for a robust link. The main reasons for the link quality degradation are blockage and link movement. We devise a learning-based prediction framework to classify link blockage and link movement efficiently and quickly using diffraction values for taking appropriate mitigating actions. The simulations show that the prediction framework can predict blockage with close to 90% accuracy. The prediction framework will eliminate the need for time-consuming methods to discriminate between link movement and link blockage. After detecting the reason for the link degradation, the system needs to do the beam alignment on the updated mmW signal paths. The beam alignment on the signal paths is a high overhead task. We propose using signaling in another frequency band to discover the paths surrounding a receiver working in the mmW spectrum. In this way, the receiver does not have to do an expensive beam scan in the mmW band. Our experiments with off-the-shelf devices show that we can use a non-mmW frequency band's paths to align the beams in mmW frequency. In this dissertation, we provide solutions to the fundamental problems in mmW communication. We propose a user association method that is designed for mmW networks considering challenges of mmW signal. A closed-form solution for a biobjective optimization problem to optimize both blockage and load balance of the network is also provided. Moreover, we show that we can efficiently use the out-of-band signal to exploit multipath created in mmW communication. The future research direction includes investigating the methods proposed in this dissertation to solve some of the classic problems in the wireless networks that exist in the mmW spectrum.
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Title: CLIMATIC VARIABILITY AND CHANGE IN THE MIDWESTERN UNITED STATES : IMPLICATIONS FOR NITROGEN LEACHING IN AGRICULTURAL SYSTEMS
Creator: Baule, William James
Date: 2022
Collection: Electronic Theses & Dissertations
Description: How has the background climate of the Midwestern United States changed over recent decades and how has this affected nitrate leaching? These are the core questions addressed in this dissertation, through three self-contained studies focused on different aspects of the climate-agriculture interface in the Midwestern United States. In Chapter 2, statistical methods are used to quantify the solar radiation biases present in a widely used reanalysis-based hydrometeorological dataset over space,...
Show moreHow has the background climate of the Midwestern United States changed over recent decades and how has this affected nitrate leaching? These are the core questions addressed in this dissertation, through three self-contained studies focused on different aspects of the climate-agriculture interface in the Midwestern United States. In Chapter 2, statistical methods are used to quantify the solar radiation biases present in a widely used reanalysis-based hydrometeorological dataset over space, implement statistical bias correction and interpolation to address the spatial nature of this bias, and quantify the impacts of the solar radiation bias and proposed correction on simulated maize yields and water stress. Correction of reanalysis solar radiation alone brought simulated yield and water usage more in line with simulations forced with in-situ solar radiation. Chapter 3 examines changes in precipitation, utilizing a unique approach to station screening during the period 1951-2019 over a region encompassing the Great Lakes and broader Midwestern regions, of the United States. A multiple tier procedure was utilized to identify high quality input data series from the Global Historical Climatology Network-Daily dataset. Temporal and spatial trends were analyzed for a broad range of related annual and seasonal indicators ranging from accumulated totals and frequency of threshold events to event duration and potential linkages with total precipitable water. Our analyses confirm the results of previous studies while providing unique insights to data quality and seasonality. The trends of the indicators in our study exhibited more cohesive spatial patterns and temporal similarities when compared with studies with different quality control criteria, illustrating the importance of quality control of observations in climatic studies and highlighting the complexity of the changing character of precipitation. In Chapter 4, System Approach to Land Use Sustainability, a process-based crop model was applied with gridded soil and meteorological data using a yield stability zone concept to simulate corn and soybean production in 14 Midwestern states at the sub-field scale during the 1989-2019 period. Five zones based on multi-year yield stability were simulated for each field at 30m x 30m resolution, with zones being relative to each individual field. Outputs were evaluated using a nitrogen balance approach to establish zone-specific statistical distributions of nitrate leaching across the 14 states, specifically highlighting periods with changing and highly variable precipitation. Results indicate that low stable, unstable hill tops, and unstable slope zones are associated with an outsized contribution to overall nitrate leaching and that unstable zones exhibit variable year-to-year response to weather tied to their position in the landscape. Spatial analysis of the results suggests leaching is tied to precipitation variability, water stress, and total precipitation amount. In aggregate, the chapters presented here highlight the interconnectedness of the soil-plant-atmosphere continuum to changes in hydrologic regime and sensitivity to the biases in the data used to conduct analyses, run models, and from which conclusions are drawn. The study findings shed light on the potential for improved management of agricultural fields and illustrate how process-based crop models can be useful for designing management practices to reduce environmental pollution and increase profits to producers.
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Title: EPIDEMIOLOGY, EVOLUTION, AND DIAGNOSTICS OF TUBERCULOSIS IN HUMANS AND ANIMALS
Creator: Hadi, Syeda Anum
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Tuberculosis control in animals and humans alike requires early detection of Mycobacterium tuberculosis complex as well as current knowledge about the transmission patterns of the disease in the respective populations. These two building blocks provide the foundation on which the disease control programs can build their policies to expediate control efforts. In this thesis we amalgamate molecular epidemiology, genomics, and proteomics. We studied the transmission pattern of M. tuberculosis...
Show moreTuberculosis control in animals and humans alike requires early detection of Mycobacterium tuberculosis complex as well as current knowledge about the transmission patterns of the disease in the respective populations. These two building blocks provide the foundation on which the disease control programs can build their policies to expediate control efforts. In this thesis we amalgamate molecular epidemiology, genomics, and proteomics. We studied the transmission pattern of M. tuberculosis and its evolution within a marginalized population. The patterns led to the identification of gaps in TB control policies in marginalized populations with little access to healthcare. Similarly, we studied the genomewide polymorphisms in a naturally attenuated strain - M. bovis strain Ravenel to elucidate possible mechanisms for its reduced virulence and pathogenicity. Insights gained from genome sequence analysis in conjunction with pathogenesis study for M. bovis Ravenel paved the pathway to defining the complex and multi-faceted reasons for attenuation of the oldest bacteria of the world. Next, pathogen-specific biomarkers were evaluated to assist in unambiguous disease detection across multiple host species. Discovery and validation of biomarkers work facilitated the field diagnostic applications for TB in animals and humans. This three-pronged approach developed in this study, understanding the genomic basis of attenuation, and enhanced field TB diagnostics in the animal-human interface.
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Title: CHARACTERIZATION OF MANUAL EXPLORATORY BEHAVIORS IN EARLY CHILDHOOD
Creator: Patel, Priya Prakashbhai
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Manual exploratory behaviors observed during early childhood have critical functional and clinical role in the motor development of a child (Lockman & Kahrs, 2017). This dissertation is aimed to (1) address the challenges faced in the quantitative analysis of these behaviors, (2) conduct quantitative analysis of two important manual exploratory behaviors, (3) extend the current knowledge on the effects of age and object properties on these behaviors beyond infancy by assessing them in...
Show moreManual exploratory behaviors observed during early childhood have critical functional and clinical role in the motor development of a child (Lockman & Kahrs, 2017). This dissertation is aimed to (1) address the challenges faced in the quantitative analysis of these behaviors, (2) conduct quantitative analysis of two important manual exploratory behaviors, (3) extend the current knowledge on the effects of age and object properties on these behaviors beyond infancy by assessing them in preschoolers. In Study 1, a machine learning (ML) -based automated classification system was developed as a proof-of-concept for the classification of manual exploratory behaviors that address the challenges encountered in the quantitative analysis of these behaviors. This system was developed using data from adult participants and it can currently classify three manual exploratory behaviors namely- rotation, throwing and fingering with substantially higher accuracy than chance level (average accuracy = 85.0 + 4.16%). Based on these findings, ML -based approach appears to be both- a feasible and a scalable alternative to conventional video coding for identifying the manual exploratory behaviors on time series; thereby, facilitating their quantitative assessment. In Study 2, quantitative assessment of two important manual exploratory behaviors- rotation and throwing was conducted along with the assessment of ML classifiers on data from children (3 – 5 years old). The ML classifiers showed substantial decrease in performance owing to differences in movements between children and adults as well as technical difficulties. Rotation behaviors became more variable and faster with increasing age while the characteristics of throwing behaviors were inconclusive of developmental differences across the three ages. In Study 3, the effects of age and three object properties (size, shape and texture) were assessed on the qualitative characteristics of manual exploratory behaviors in children (3 – 5 years old). Manual exploration of objects was driven at different levels by age and object properties in preschoolers. In terms of age, throwing behaviors were more common in the 3-year group while rotational behaviors in the 5-year group. In terms of the three object properties, object size and shape directed child’s hand preference in reaching objects while object size and texture influenced their manual exploratory behaviors. In addition, object texture was found to mainly influence child’s first interactions with the objects as the squeezing and fingering behaviors occurred more often during the first interactions with the objects. The findings suggest that the dynamic interplay between learning to perceive object properties and manually exploring them continues to develop and adapt beyond infancy. In summary, manual exploratory behaviors, similar to other motor behaviors, are influenced by different individual, task and environment factors. These effects continue beyond infancy and throughout early childhood. A thorough qualitative and quantitative assessment is required to fully understand their functional and clinical role in early childhood. For this, ML -based approach is recommended to address the challenges in their quantitative analysis and to facilitate the overall scope of investigating these behaviors.
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Title: Nucleon and pion gluon parton distribution function from lattice QCD calculation
Creator: Fan, Zhouyou
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Parton distribution functions (PDFs) are important to characterize the structure of the hadrons such as protons and neutrons. The contribution to the structure from quarks has been studied in detail during the past few decades. The structure in the gluon sector is also important but less studied. For high-energy hadrons, the gluon contribution dominates at small $x$, where $x$ is the momentum fraction carried by a quark or gluon. At large $x$, the uncertainty of the gluon PDF is large,...
Show moreParton distribution functions (PDFs) are important to characterize the structure of the hadrons such as protons and neutrons. The contribution to the structure from quarks has been studied in detail during the past few decades. The structure in the gluon sector is also important but less studied. For high-energy hadrons, the gluon contribution dominates at small $x$, where $x$ is the momentum fraction carried by a quark or gluon. At large $x$, the uncertainty of the gluon PDF is large, especially compared to that of the quark PDFs at large $x$. Gluon PDFs for nucleons and pions are mostly extracted from global analysis of experimental data using perturbation theory as a guide. Theoretically, lattice QCD provides an independent non-perturbative theoretical approach to calculate the gluon PDFs.We present the exploratory study of nucleon gluon PDFs from lattice QCD using the quasi-PDF approach. Using valence overlap fermions on the $2+1$-flavor domain-wall fermion gauge ensemble, the quasi-PDF matrix elements we obtain agree with the Fourier transform of the global-fit PDF within statistical uncertainty. We further study the $x$-dependent nucleon and pion gluon distributions via the pseudo-PDF approach on lattice ensembles with $2+1+1$ flavors of highly improved staggered quarks (HISQ) generated by the MILC Collaboration. Using clover fermions for the valence action, and adding momentum smearing, PDFs are found for pion boost momenta up to 2.56~GeV. Several lattice sizes and spacings ($a\approx 0.9, 0.12$ and 0.15~fm) were evaluated, resulting in three pion masses, $M_{\pi}\approx 220$, 310 and 690~MeV/$c^2$.
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Title: THE IMPACT OF THE AFFORDABLE CARE ACT ON UNINTENDED PREGNANCY
Creator: MacCallum-Bridges, Colleen Lynn
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Background & Objectives: Nearly half of all pregnancies in the United States (US) are unintended (i.e., mis-timed or unwanted), and roughly 5% of US women experience an unintended pregnancy each year, suggesting the population-level need for contraceptives is not being met. Further, these pregnancies are experienced disproportionately by women who are younger, women of color, and women of lower socioeconomic status – indicating these groups are particularly underserved. The Patient Protection...
Show moreBackground & Objectives: Nearly half of all pregnancies in the United States (US) are unintended (i.e., mis-timed or unwanted), and roughly 5% of US women experience an unintended pregnancy each year, suggesting the population-level need for contraceptives is not being met. Further, these pregnancies are experienced disproportionately by women who are younger, women of color, and women of lower socioeconomic status – indicating these groups are particularly underserved. The Patient Protection and Affordable Care Act (ACA) had the potential to improve our ability to meet this population-level need by increasing access to and affordability of contraceptive products and services. There is evidence that the ACA increased health insurance coverage and is associated with an increase in the use of highly effective long-acting reversible contraceptives, but it is unclear whether these effects translated into fewer unintended pregnancies. Further, it is unknown whether these effects were equitably distributed across race and ethnicity. Thus, the objectives of this dissertation are to: 1) estimate the overall impact of the ACA on unintended pregnancy, and if evidence of an impact exists, describe the timing of this impact, 2) explore three mechanisms of the ACA by investigating the impact of three major provisions (i.e., the dependent coverage provision, Marketplace subsidies, and ACA insurance expansions), and 3) assess the impact of the ACA on racial/ethnic disparities in unintended pregnancy. Methods: Data from multiple cross-sectional cycles of the National Survey of Family Growth (NSFG) were used. NSFG uses a multistage probabilistic sampling methodology to survey non-institutionalized civilian men and women regarding family planning, marriage, divorce, and both general and reproductive health. I included sexually active female respondents aged 18-44 interviewed between 2006 and 2019 (n=25,426). To address objectives (1) and (2) I used a difference-in-differences approach to compare trends in unintended pregnancy between women who were eligible to benefit from the intervention (the overall ACA or one of the listed components), to that of women who were ineligible to benefit. Eligibility was determined by respondent age and income. To address objective (3), I used a pre/post analysis to explore how racial/ethnic disparities in unintended pregnancy differed prior to and following enactment of the overall ACA and its components. Results: There was evidence that: 1) the overall ACA was associated with a 2.1 percentage point (ppt) decrease in unintended pregnancy among eligible women, and this decrease was fairly consistent during and following the ACA’s implementation period, 2) the dependent coverage provision was associated with a large (8.2 ppt) decrease in unintended pregnancy among lower income young women, and 3) the disparities in unintended pregnancy between Hispanic and non-Hispanic (NH) White women and between NH Black and NH White women decreased by 2.9 ppt and 4.1 ppt, respectively, among eligible women following full implementation of the ACA. There was insufficient evidence that the Marketplace subsidies or insurance expansions were associated with unintended pregnancy, or that the dependent coverage provision, Marketplace subsidies, or insurance expansions were associated with racial/ethnic disparities in unintended pregnancy. Conclusions: The overall ACA and the dependent coverage provision may be associated with reductions in unintended pregnancy, and the magnitude of these associations appear to differ across sociodemographic subgroups (i.e., income, race/ethnicity) – holding implications for health equity. These findings provide insight regarding how the ACA works to influence reproductive health, and for whom – which is critical information for both researchers and public policy makers who seek to improve reproductive health and health equity.
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Title: THE MEASUREMENT OF PHYSICAL ACTIVITY SELF-EFFICACY IN INTERVENTIONS THAT PROMOTE PHYSICAL ACTIVITY IN ADULTS
Creator: Bateman, Andre Godfrey
Date: 2022
Collection: Electronic Theses & Dissertations
Description: This dissertation comprises two studies focused on the measurement of self-efficacy associated with physical activity-promoting interventions in adults. Recent research indicates that most adults do not achieve sufficient daily physical activity for health. The research also shows that adults with obesity are even less likely to engage in sufficient physical activity for health. Physical inactivity is associated with negative health outcomes such as cardiovascular disease and is therefore a...
Show moreThis dissertation comprises two studies focused on the measurement of self-efficacy associated with physical activity-promoting interventions in adults. Recent research indicates that most adults do not achieve sufficient daily physical activity for health. The research also shows that adults with obesity are even less likely to engage in sufficient physical activity for health. Physical inactivity is associated with negative health outcomes such as cardiovascular disease and is therefore a major public health concern. There is however evidence that certain motivational constructs, such as self-efficacy are associated with increased physical activity in adults. As a result, behavioral interventions utilizing these constructs as modifiable mediators of physical activity behavior have been employed to increase physical activity in different populations.Study 1 is a systematic review focused on examining the theoretical and measurement quality of physical activity self-efficacy scales in physical activity-promoting interventions for adults. The search strategy was based on the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. One hundred sixteen studies were reviewed, from which the physical activity self-efficacy scales were identified and extracted. Of the scales identified, 14 were multi-item and five were single item scales. The systematic review uncovered that the identified scales had varying conceptual and measurement related properties despite having good administrative quality in general. The major issues identified with self-efficacy measurement were: (a) a lack of concordance between self-efficacy and physical activity measurement, (b) a lack of specified physical activity levels to which the self-efficacy measurements refer, (c) self-efficacy scales described with theoretically imprecise construct labels, (d) a lack of emphasis on essential conceptual properties of self-efficacy scales, (e) a lack of specification of the dimensionality of self-efficacy scales and (f) the use of single-item measures of self-efficacy. Essential conceptual and measurement related recommendations were made in response to these issues to improve the measurement of physical activity self-efficacy in physical activity-promoting interventions. Study 2 employed a latent variable approach to explore the dimensionality, temporal invariance, and external validity of responses to the self-efficacy to regulate physical activity scale (SERPA). The SERPA is a modified version of the barriers self-efficacy scale. This study analyzed data from the Well-Being and Physical Activity Study (WBPA; ClinicalTrials.gov, identifier: NCT03194854). The WBPA consisted of 461 participants at baseline which decreased to 427 participants at 30 days post baseline. The WBPA deployed the Fun For Wellness (FFW) intervention. One objective of the FFW intervention was to promote physical activity in adults with obesity. A two-dimensional factor structure explained responses to the SERPA at baseline. Factor 1 was conceptualized as self-efficacy to regulate barriers to physical activity participation based on social considerations. Factor 2 was conceptualized as self-efficacy to regulate internally perceived barriers to physical activity participation. There was strong evidence for the effectiveness of the FFW intervention to exert a direct effect on the proposed two-dimensional structure of latent self-efficacy to regulate physical activity in adults with obesity at 30 days post-baseline.
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Title: A PLACE OF PERSONAL AND CULTURAL RESISTANCE : USING BLACK FEMINIST VALUES, PERSPECTIVES, AND EMBODIED KNOWLEDGES TO (RE)EXAMINE INSTITUTIONAL LOGICS AND ETHICS IN DIGITAL RESEARCH
Creator: Haywood, Constance Monique
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Centering the experiences and practices of Black women scholars who engage research in areas of Black technological and digital engagement, this dissertation examines how Black women and Black feminist-identifying digital researchers’ personal, cultural, and professional identities inform methodological and ethical decision-making in their work. Building on the theoretical approaches of Black feminist thinkers like Patricia Hill Collins and the Combahee River Collective, this project...
Show moreCentering the experiences and practices of Black women scholars who engage research in areas of Black technological and digital engagement, this dissertation examines how Black women and Black feminist-identifying digital researchers’ personal, cultural, and professional identities inform methodological and ethical decision-making in their work. Building on the theoretical approaches of Black feminist thinkers like Patricia Hill Collins and the Combahee River Collective, this project addresses the complexities of digital ethics by 1) examining how Black women’s unique, lived experience(s) both inform and are impacted by their work and 2) uncovering the processes that support -- and sometimes create tensions with -- research aroundBlack digital publics, users, and spaces. This project places a special focus on the work of Black women and Black feminist-identifying scholars in writing studies-related fields, collecting and analyzing data from multiple qualitative interviews amongst five research participants.Ultimately, this dissertation highlights the growing work and practices of Black women digital researchers, using Black feminist theory as a means to uncover how Black women researchers reconsider, repurpose, and reapproach their research practices from embodied and critical standpoints. This project also adds to growing conversations around the development ofdigital methodologies in writing and communication-related fields, particularly those that place a greater priority on researchers’ ethical responsibilities to multiple-marginalized technology users and communities.
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Title: Regulation of Chlamydomonas reinhardtii cell cycle during synchronous growth
Creator: Lin, Yang-Tsung
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The regulation of the cell cycle in microalgae has long been a central topic in third-generation biofuel studies, as it relates to biomass accumulation and lipid production, the two determining factors of economically feasible biofuel production. The discovery of Compromised Hydrolysis of TAG 7 (CHT7) in the green alga Chlamydomonas reinhardtii has provided valuable insights into the metabolic status-dependent regulation of the cell cycle. CHT7 belongs to the CHC protein family, members of...
Show moreThe regulation of the cell cycle in microalgae has long been a central topic in third-generation biofuel studies, as it relates to biomass accumulation and lipid production, the two determining factors of economically feasible biofuel production. The discovery of Compromised Hydrolysis of TAG 7 (CHT7) in the green alga Chlamydomonas reinhardtii has provided valuable insights into the metabolic status-dependent regulation of the cell cycle. CHT7 belongs to the CHC protein family, members of which include transcriptional regulators programming the initiation of cell division. A similar role of CHT7 in mediating cell cycle progression has been suggested. However, the regulatory mechanism and specific processes regulated by CHT7 have yet to be determined. In this dissertation, I applied bioinformatics approaches to comprehensively study CHT7-mediated gene regulation during the cell cycle using cell cultures synchronously grown in bioreactors. I found that specific pathways such as DNA replication, chromosome condensation, and spindle assembly are affected by the absence of CHT7. Other affected pathways include cell-wall remodeling and previously uncharacterized putative kinase cascades. In addition, I discovered the presence of two potential cis-regulatory elements near the transcription start site of misregulated genes in cht7, which are potentially linked to homeodomain transcription factors. Moreover, I explored the potential relationship between the CHT7-mediated pathway and the gene network governed by the retinoblastoma protein complex. Lastly, I characterized the function of a novel CHC protein in cell cycle progression and compared it with the role of CHT7. Together, these studies facilitate a better understanding of the cell cycle regulation in microalgae.
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Title: Advancements in Applied Behavior Analysis Service Delivery, Supervision, and Feedback
Creator: Thomas, Emma
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Supervision is critical to the field of Applied Behavior Analysis (ABA) because it improves the quality of services provided to the recipients of behavioral services which in turn increases client protection and helps to portray the field of ABA as one that is committed to socially significant behavior change (Britton & Cicoria, 2019; Brodhead & Higbee, 2012; Hartley et al., 2016; LeBlanc & Luiselli, 2016; LeBlanc et al., 2020; Turner et al., 2016). Without effective supervision, the quality...
Show moreSupervision is critical to the field of Applied Behavior Analysis (ABA) because it improves the quality of services provided to the recipients of behavioral services which in turn increases client protection and helps to portray the field of ABA as one that is committed to socially significant behavior change (Britton & Cicoria, 2019; Brodhead & Higbee, 2012; Hartley et al., 2016; LeBlanc & Luiselli, 2016; LeBlanc et al., 2020; Turner et al., 2016). Without effective supervision, the quality of services may decrease and negatively impact treatment outcomes for the clients (Britton & Cicoria, 2019; Dixon et al., 2016; Eikeseth, 2009; LeBlanc & Luiselli, 2016; Shapiro & Kazemi, 2017). Given the rapid growth of the field of ABA, supervision will continue to play a critical role in training, fostering the growth and development of professionals and ensuring those professionals uphold the high standards of the profession (Hajiaghamohseni et al., 2020; Turner et al., 2016; Turner, 2017). The current dissertation addressed and evaluated supervision of behavior analytic services provided to individuals with autism spectrum disorder (ASD) in three different contexts: (1) supervision provided during the implementation of behavioral interventions, (2) supervision provided via Telehealth, specifically evaluating barriers and strategies used to address and/or mitigate those barriers, and (3) supervision provided via Telehealth in the form of email performance-based feedback. Collectively, these chapters sought to address gaps in the current behavior analytic supervision literature and identify additional areas of study. Chapter 1 provides an overall introduction connecting the three separate, but related chapters (Chapters 2-4) and includes a supervision logic model. Chapter 2 is a systematic literature review that evaluated the extent to which recently published articles included information regarding supervision and staff training of the individuals implementing behavioral interventions to young children with ASD. The results of Chapter 2 revealed that there is little to no consensus on reporting supervision and staff training characteristics in the current behavioral intervention literature. Research implications and reporting recommendations will be discussed. Chapter 3 is a survey study that evaluated the barriers Board Certified Behavior Analysts (BCBAs) experienced and the strategies BCBAs used to address and/or mitigate the barriers that arose when providing supervision via Telehealth. The results of Chapter 3 revealed that BCBAs that provide supervision via Telehealth are not exempt from experiencing barriers. Research and practical implications will be discussed. Chapter 4 is a single case research design study that evaluated the extent to which email performance-based feedback increased procedural fidelity of teacher candidates’ implementation of a multiple stimulus without replacement (MSWO) preference assessment. The results revealed that email performance-based feedback was effective in increasing procedural fidelity of MSWO preference assessment implementation. These results support previous literature suggesting that email performance-based feedback alone is effective in increasing target behavior(s). Research implications will be discussed. Finally, Chapter 5 provides an overall discussion about the findings of the three chapters (Chapters 2-4), recommendations for research and practice, and considerations for the future direction of supervision in the field of ABA.
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Title: DISCOURSES OF WELL-BEING OF ADOLESCENT GIRLS LIVING IN PATAGONIA, CHILE
Creator: Bilbao Nieva, Maria Isidora
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The term well-being entails material and subjective elements, and it is critical to promote it during adolescence. Access to opportunities and resources are key determinants to well-being, but not all adolescents have the same living conditions. In the specific case of adolescent girls living in Latin American countries, structural barriers to well-being are derived from gender and cultural factors that influence their everyday experiences. From a Community Psychology perspective, structural...
Show moreThe term well-being entails material and subjective elements, and it is critical to promote it during adolescence. Access to opportunities and resources are key determinants to well-being, but not all adolescents have the same living conditions. In the specific case of adolescent girls living in Latin American countries, structural barriers to well-being are derived from gender and cultural factors that influence their everyday experiences. From a Community Psychology perspective, structural factors are critical to well-being promotion and should be considered alongside individual-level factors.Using Feminist Critical Discourse Analysis, this study examined the discourses of well-being of ten adolescent girls from low-income families living in Coyhaique. The analysis was focused on how girls talk about what contributes to their well-being, with a specific focus on structural conditions that affect them. The results showed that while they spoke of individual-level factors contributing to their well-being, they also mentioned structural issues influenced by gender and culture. Those structural level factors were related to resources, support networks, and community environment. Implications for well-being promotion are discussed.
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Title: Variational Bayes inference of Ising models and their applications
Creator: Kim, Minwoo
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Ising models originated in statistical physics have been widely used in modeling spatialdata and computer vision problems. However, statistical inference of this model and its application to many practical fields remain challenging due to intractable nature of the normalizing constant in the likelihood. This dissertation consists of two main themes, (1) parameter estimation of Ising model and (2) structured variable selection based on the Ising model using variational Bayes (VB).In Chapter 1,...
Show moreIsing models originated in statistical physics have been widely used in modeling spatialdata and computer vision problems. However, statistical inference of this model and its application to many practical fields remain challenging due to intractable nature of the normalizing constant in the likelihood. This dissertation consists of two main themes, (1) parameter estimation of Ising model and (2) structured variable selection based on the Ising model using variational Bayes (VB).In Chapter 1, we review the background, research questions and development of Isingmodel, variational Bayes, and other statistical concepts. An Ising model basically deal with a binary random vector in which each component is dependent on its neighbors. There exist various versions of Ising model depending on parameterization and neighboring structure. In Chapter 2, with two-parameter Ising model, we describe a novel procedure for the pa- rameter estimation based on VB which is computationally efficient and accurate compared to existing methods. Traditional pseudo maximum likelihood estimate (PMLE) can pro- vide accurate results only for smaller number of neighbors. A Bayesian approach based on Markov chain Monte Carlo (MCMC) performs better even with a large number of neighbors. Computational costs of MCMC, however, are quite expensive in terms of time. Accordingly, we propose a VB method with two variational families, mean-field (MF) Gaussian family and bivariate normal (BN) family. Extensive simulation studies validate the efficacy of the families. Using our VB methods, computing times are remarkably decreased without dete- rioration in performance accuracy, or in some scenarios we get much more accurate output. In addition, we demonstrates theoretical properties of the proposed VB method under MF family. The main theoretical contribution of our work lies in establishing the consistency of the variational posterior for the Ising model with the true likelihood replaced by the pseudo- likelihood. Under certain conditions, we first derive the rates at which the true posterior based on the pseudo-likelihood concentrates around the εn- shrinking neighborhoods of the true parameters. With a suitable bound on the Kullback-Leibler distance between the true and the variational posterior, we next establish the rate of contraction for the variational pos- terior and demonstrate that the variational posterior also concentrates around εn-shrinking neighborhoods of the true parameter.In Chapter 3, we propose a Bayesian variable selection technique for a regression setupin which the regression coefficients hold structural dependency. We employ spike and slab priors on the regression coefficients as follows: (i) In order to capture the intrinsic structure, we first consider Ising prior on latent binary variables. If a latent variable takes one, the corresponding regression coefficient is active, otherwise, it is inactive. (ii) Employing spike and slab prior, we put Gaussian priors (slab) on the active coefficients and inactive coefficients will be zeros with probability one (spike).
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Title: WISDOM FROM A MENTOR IN A MATTER OF MINUTES : INVESTIGATING A PROPOSED MODEL OF FLASH MENTORSHIP IN STUDENT-ALUMNI INTERACTIONS
Creator: Wisner, Amy Marie
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Mentoring is an age-old practice that proves meaningful for protégés across contexts and program designs. Because both mentoring practice and mentoring research take place in a wide variety of domains and with seemingly limitless program details, it has become difficult to define or execute with any precision. Mentoring practitioners and researchers would benefit greatly from a mentorship model to inform their program designs and selection of mentoring type best-suited to the situation. In...
Show moreMentoring is an age-old practice that proves meaningful for protégés across contexts and program designs. Because both mentoring practice and mentoring research take place in a wide variety of domains and with seemingly limitless program details, it has become difficult to define or execute with any precision. Mentoring practitioners and researchers would benefit greatly from a mentorship model to inform their program designs and selection of mentoring type best-suited to the situation. In recent years, a type of mentoring that has gained popularity is flash mentorship. This short-term, one-time interaction is desirable because of the limited commitment required for everyone involved. However, little is known about the effectiveness of this type of mentorship. The current work sought to develop a model of effective flash mentorship with the broader goal of establishing best practices for pairing mentors with protégés in meaningful ways. A proposed model of flash mentorship posited that relationship quality and advice quality predicted protégé situational satisfaction. Antecedents of relationship quality were posited to include attraction and deep-level similarity. Antecedents of advice quality were posited to include message features and mentor expertise. Although all causal links posited by the model were of sufficient magnitude to be consistent with predictions, the fit of the model proved insufficient. Limitations of the findings and recommendations for future research are discussed.
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Title: Fast and Memory-Efficient Subspace Embeddings for Tensor Data with Applications
Creator: Zare, Ali
Date: 2022
Collection: Electronic Theses & Dissertations
Description: The widespread use of multisensor technology and the emergence of big data sets have brought the necessity to develop more versatile tools to represent higher-order data with multiple aspects and high dimensionality. Data in the form of multidimensional arrays, also referred to as tensors, arise in a variety of applications including chemometrics, physics, hyperspectral imaging, high-resolution videos, neuroimaging, biometrics, and social network analysis. Early multiway data analysis...
Show moreThe widespread use of multisensor technology and the emergence of big data sets have brought the necessity to develop more versatile tools to represent higher-order data with multiple aspects and high dimensionality. Data in the form of multidimensional arrays, also referred to as tensors, arise in a variety of applications including chemometrics, physics, hyperspectral imaging, high-resolution videos, neuroimaging, biometrics, and social network analysis. Early multiway data analysis approaches used to reformat such tensor data as large vectors or matrices and would then resort to dimensionality reduction methods developed for low-dimensional data. However, by vectorizing tensors, the inherent multiway structure of the data and the possible correlation between different dimensions will be lost, in some cases resulting in a degradation in the performance of vector-based methods. Moreover, in many cases, vectorizing tensors leads to vectors with extremely high dimensionality that might render most existing methods computationally impractical. In the case of dimension reduction, the enormous amount of memory needed to store the embedding matrix becomes the main obstacle. This highlights the need for approaches that are applied to tensor data in their multi-dimensional form. To reduce the dimension of an $n_1 \times n_2 \times \dots \times n_d$ tensor to $m_1 \times m_2 \times \dots \times m_d$ with $m_j \leq n_j$, MPCA\footnote{Multilinear Principal Component Analysis} would change the memory requirement from $\prod_{j=1}^d m_jn_j$ for vector PCA to $\sum_{j=1}^d m_jn_j$, which can be a considerable improvement.On the other hand, tensor dimension reduction methods such as MPCA need training samples for the projection matrices to be learned. This makes such methods time consuming and computationally less efficient than oblivious approaches such as the Johnson-Lindenstrauss embedding. The term \textit{oblivious} refers to the fact that one does not need any data samples beforehand to learn the embedding that projects a new data sample onto a lower-dimensional space.\\ In this thesis, first a review of tensor concepts and algebra as well as common tensor decompositions is presented. Next, a modewise JL approach is proposed for compressing tensors without reshaping them into potentially very large vectors. Theoretical guarantees for the norm and inner product approximation errors as well as theoretical bounds on the embedding dimension are presented for data with low CP rank, and the corresponding effects of basis coherence assumptions are addressed. Experiments are performed using various choices of embedding matrices. Results verify the validity of one- and two-stage modewise JL embeddings in preserving the norm of MRI and synthesized data constructed from both coherent and incoherent bases. Two novel applications of the proposed modewise JL method are discussed. (i) Approximate solutions to least squares problems as a computationally efficient way of fitting tensor decompositions: The proposed approach is incorporated as a stage in the fitting procedure, and is tested on relatively low-rank MRI data. Results show improvement in computational complexity at a slight cost in the accuracy of the solution in the Euclidean norm. (ii) Many-Body Perturbation Theory problems involving energy calculations: In large model spaces, the dimension sizes of tensors can grow fast, rendering the direct calculation of perturbative correction terms challenging. The second-order energy correction term as well as the one-body radius correction are formulated and modeled as inner products in such a way that modewise JL can be used to reduce the computational complexity of the calculations. Experiments are performed on data from various nuclei in different model space sizes, and show that in the case of large model spaces, very good compression can be achieved at the price of small errors in the estimated energy values.
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Title: The Impact of Social Class on Students’ Pre-College Perceptions of Co-Curricular Involvement
Creator: Rossman, Danielle
Date: 2022
Collection: Electronic Theses & Dissertations
Description: This dissertation uses a cross sectional quantitative design to investigate the relationship between first-year college students’ social class and their pre-college interest in engaging in co-curricular experiences during college, their motivations for engaging in co-curricular experiences, and their perceptions of whether co-curricular activities will teach them leadership and work ethic skills. The study also investigated multiple variables to address social class- including metrics of...
Show moreThis dissertation uses a cross sectional quantitative design to investigate the relationship between first-year college students’ social class and their pre-college interest in engaging in co-curricular experiences during college, their motivations for engaging in co-curricular experiences, and their perceptions of whether co-curricular activities will teach them leadership and work ethic skills. The study also investigated multiple variables to address social class- including metrics of subjective social status and socioeconomic status. The study used data from two surveys that were administered to a sample (N = 839) of first-year, first-time college students from a regional comprehensive university prior to their matriculation. The findings of this study indicate that students’ awareness of their socioeconomic status was the only significant predictor of their interest in getting involved in co-curricular activities during college. Students’ perceived family contribution to their college education significantly predicted their interest in working during college, while social class had no impact on a student’s interest in joining fraternity and sorority life or in student government association. There was a significant relationship between a student’s race, gender, and high school extracurricular experiences and their motivation for engagement. A student’s Expected Family Contribution was not a significant predictor of the student’s interest, motivation, or perception related to involvement. Students’ awareness of their socioeconomic status also impacted their perceptions that they could learn leadership skills and work ethic from co-curricular activities, while students with higher subjective social class were more likely to believe they could learn leadership skills from being a participant or member in co-curricular experiences. Implications of these findings for research, theory and practice are offered. More research is needed that explores the impact of social class, and incorporates multiple diverse metrics of social class, on students’ college experience. Studies that investigate the ability of on-campus employment to serve as a high impact proactive for students who may not otherwise have the ability to participate in co-curricular experiences on campus are also needed.
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Title: FATE OF SILVER NANOPARTICLES DURING SIMULATED COMMERCIAL PROCESSING OF FRESH-CUT LETTUCE
Creator: Gunathilaka, Gayathri Upeksha
Date: 2022
Collection: Electronic Theses & Dissertations
Description: ABSTRACTFATE OF SILVER NANOPARTICLES DURING SIMULATED COMMERCIAL PROCESSING OF FRESH-CUT LETTUCEByGayathri Upeksha GunathilakaThe use of silver nanoparticles (Ag NPs) in pesticides could lead to residual levels in food crops, thus raising both food safety and environmental concerns. The effectiveness of typical produce processing practices to remove Ag NPs from fresh produce is poorly understood. Further, little is known about the behavior of Ag NPs in wash water during commercial production...
Show moreABSTRACTFATE OF SILVER NANOPARTICLES DURING SIMULATED COMMERCIAL PROCESSING OF FRESH-CUT LETTUCEByGayathri Upeksha GunathilakaThe use of silver nanoparticles (Ag NPs) in pesticides could lead to residual levels in food crops, thus raising both food safety and environmental concerns. The effectiveness of typical produce processing practices to remove Ag NPs from fresh produce is poorly understood. Further, little is known about the behavior of Ag NPs in wash water during commercial production of fresh-cut produce, which limits our ability to design effective mitigation strategies.The first study evaluated the behavior of Ag NPs over time when exposed to commercially applicable chlorine concentrations (2–100 mg chlorine/L) in simulated lettuce wash water. Aggregation and dissolution of Ag NPs (5 mg/L) were evaluated in the presence and absence of dissolved lettuce extract (DLE, 0.1%). Aggregate size of Ag NPs increased faster in the presence of chlorine (49 to 431 nm) compared to the control (P < 0.05). Lower dissolved Ag concentrations and more negative zeta potentials were found in the presence of chlorine (0.01 to 0.03 mg/L and -39 to -95 mV) and DLE (0.01 to 0.14 mg/L and -28 to -32 mV), as compared to the control (0.54 to 0.8 mg/L and -10 to -20 mV) (P < 0.05). Transmission electron microscopy with energy dispersive spectroscopy confirmed the formation of composite AgCl-Ag NPs particles in the presence of chlorine. The increased aggregate size over time likely resulted from nucleation and crystal growth of AgCl. In the presence of DLE, Ag NPs and AgCl precipitates were embedded in and bound to the DLE matrix. These observations suggest that chlorine and plant-released organic matter could substantially change the fate of Ag NPs in wash water and subsequently their environmental impact. In the second study the removal of Ag NPs from Ag NP-contaminated lettuce leaves was investigated during batch and small-scale pilot processing. First, a batch-type system (4-L carboy jar) was used to evaluate the impact of commercial produce sanitizers and simulated leafy green processing water on the removal of Ag NPs from contaminated lettuce. Peroxyacetic acid (PAA; 80 mg/L) and chlorine (100 mg/L and pH 6.5) were used with/without 2.5% (w/v) organic load as washing treatments with deionized water serving as the control treatment. Treating lettuce with the organic load alone, organic load with chlorine, chlorine alone, 0% organic load and peroxyacetic acid removed about 2.7%–6.6% of Ag from the lettuce after 5 min of washing. Thereafter, the removal of Ag NPs from contaminated lettuce was assessed using a small-scale pilot processing line during 90 seconds of flume-washing followed by centrifugal drying (a typical washing practice in commercial produce processing). The Ag removal efficiency ranged between 0.3% to 3%, probably resulting from strong binding of Ag with plant organic materials. Significantly greater Ag concentrations were found in the centrifugal water than in flume water, suggesting that centrifugation removed additional Ag from lettuce. The low Ag removal observed in both the simulated batch-type and pilot-scale produce washing systems demonstrate that typical produce processing conditions may not be effective in removing Ag NPs from contaminated produce. Thus, it is necessary to further investigate and develop effective methods for the Ag NP removal from contaminated produce.
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Title: A POTENTIAL ROLE FOR EARLY GUT MICROBIAL COLONIZATION IN INFANT BEHAVIOR AND CHILD SLEEP DISORDERS
Creator: Ma, Tengfei
Date: 2022
Collection: Electronic Theses & Dissertations
Description: There is increasing evidence from pre-clinical and human studies implicating the microbiota–gut–brain axis in behavior and sleep physiology. Infancy is a critical time period for brain development and is vulnerable to the harmful effects of gut dysbiosis. Thus, it is crucial to understand how gut microbial colonization during this period may influence behavior and sleep physiology in the later stages of life.We analyzed data from 194 mother-infant pairs from the Michigan Archive for Research...
Show moreThere is increasing evidence from pre-clinical and human studies implicating the microbiota–gut–brain axis in behavior and sleep physiology. Infancy is a critical time period for brain development and is vulnerable to the harmful effects of gut dysbiosis. Thus, it is crucial to understand how gut microbial colonization during this period may influence behavior and sleep physiology in the later stages of life.We analyzed data from 194 mother-infant pairs from the Michigan Archive for Research on Child Health (MARCH) cohort Study. Clinical and demographic information was obtained from the birth certificate and interview during pregnancy and childhood. Fecal samples from infants at 3-9 months of age were sequenced at the V4 region of the 16S rRNA gene. In the first study, which examined whether feeding practices may affect early gut microbial colonization, we found that the gut microbiota of infants who were exclusively breastfed displayed a significantly lower Shannon diversity (p-adjust < 0.001) and a different gut microbiota composition than infants who were not breastfed (p-value = 0.001). Among the exclusively breastfed infants, recipients of supplemental vitamin D displayed a significantly lower Shannon diversity (p-adjust = 0.007) and different gut microbiota composition structure than non-supplemented, breastfed infants (p-value = 0.02). In addition, several individual taxa were identified to be associated with different feeding practices. In the second study, we examined whether gut microbiota in early infancy was associated with temperament in the nine-month-old infants. We identified that a microbial cluster characterized by a higher abundance of Bifidobacterium, Veillonella, and Escherichia-Shigella that was associated with lower emotionality scores (coefficient = -0.58, p-value = 0.02) compared to a cluster characterized by a higher abundance of Bacteroides. This association was especially prominent among infants who were not supplemented with vitamin D (coefficient = -1.01, p-value = 0.01), while no significant association was found among infants who were supplemented (coefficient = -0.43, p-value = 0.20). In the final aim, we assessed the association between gut microbiota in early infancy and the difficulty of initiating and maintaining sleep at age of two years. The gut microbiota of children who had difficulty maintaining sleep displayed significantly higher Shannon index (OR: 2.41, 95% CI= 1.23-4.93, p-adjust < 0.04) and Chao 1 index (OR: 1.01, 95% CI= 1.0-1.03, p-adjust < 0.008) after adjustment for covariates. We also observed that gut microbiota composition was significantly different between children with difficulty initiating (p-value= 0.043) and maintaining sleep (p-value= 0.004) by PERMANOVA based on the unweighted UniFrac distance metric. In conclusion, these results from analysis in a prospective cohort study suggest that early gut microbial colonization is shaped by breastfeeding status, vitamin D supplement, and maternal characteristics including gestational age, delivery mode and education level. Our findings suggested that the infant gut microbiome clusters may be associated with the temperament characteristic of negative emotionality in 9-month-old infants. We also demonstrated a significant association between infant gut microbiome composition and sleep problems in 2-year-old children. Thus, our results add to the evidence that early gut microbial colonization may be linked with brain outcomes with potential long-term effects.
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Title: Quantitative Analysis of New Key Factors of Immune Cells in Autoimmune Diseases
Creator: Bunn, Demarcus
Date: 2022
Collection: Electronic Theses & Dissertations
Description: AbstractExplorations of New Key Factors of Immune Cells in Autoimmune Diseases By Demarcus Bunn The work presented in this dissertation demonstrates an emerging role of immune cells in type one diabetes (T1D) and multiple sclerosis (MS). The immune cells that will be presented are neutrophils and T-cells. Presented work shows an altered cell metabolism in both disease states that leads to further secondary complications. An overview of the immunology, as well as each autoimmune disease, will...
Show moreAbstractExplorations of New Key Factors of Immune Cells in Autoimmune Diseases By Demarcus Bunn The work presented in this dissertation demonstrates an emerging role of immune cells in type one diabetes (T1D) and multiple sclerosis (MS). The immune cells that will be presented are neutrophils and T-cells. Presented work shows an altered cell metabolism in both disease states that leads to further secondary complications. An overview of the immunology, as well as each autoimmune disease, will be presented. Experimental efforts to increase or decrease cell metabolism in order to alleviate secondary complications will be shown. Furthermore, the use of 3D printed devices for in vitro models mimicking these disease states properties will be presented.Individuals T1D have a history of being more susceptible to infection. This section of the dissertation will demonstrate how a once forgotten pancreatic peptide, C-peptide, has a positive effect on raising immunity through improving immune cell energetics. Previous studies in the Spence lab have shown that C-peptide only binds to red blood cells (RBC) in the presence of albumin, but for the biological changes, Zn2+ is needed. Spence lab research has shown that the combination of C-peptide/Zn2+/albumin increases the metabolism of RBCs. This work shows novel data showing that C-peptide binds specifically to other cell types. Additionally, changes in cell metabolism will be investigated. This portion of the dissertation is important for alleviating reoccurring and persistent infections.MS is characterized by the destruction of the myelin sheath around the nerves. The cell type that does the damage is T lymphocytes. However, little research has been done investigating what makes the permeability of the blood-brain barrier increase. Here, we will introduce the potential role of NETosis, a form of programmed cell death, has on blood brain barrier permeability. There have been recent reports that exogenous adenosine triphosphate (ATP) increases the rate of NETosis production in vitro. Previous work in the Spence lab has shown that RBCs from individuals with MS secrete significantly more ATP than control red blood cells. Presented work will show that ATP derived directly from RBCs causes dysregulation of NETosis. The concluding section of the dissertation will be dedicated to 3D printing. An overview of the current state and future advancements of 3D printing will be presented. Presented work will show the use of 3D printing to provide more relevant conditions for in vitro experiments. Here, 3D printed models were used to investigate immune cell behaviors and changes in cell bioenergetics.
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Title: Molecular epidemiology, pangenomic diversity, and comparative genomics of Campylobacter jejuni
Creator: Rodrigues, Jose Alexandre
Date: 2022
Collection: Electronic Theses & Dissertations
Description: Campylobacter jejuni, the leading cause of bacterial gastroenteritis in the United States, is often resistant to commonly used antibiotics and has been classified as a serious threat to public health. Through this work, we sought to evaluate infection trends, quantify resistance frequencies, identify epidemiological factors associated with infection, and use whole-genome sequencing (WGS) as well as comparative phylogenomic and pangenomic approaches to understand circulating C. jejuni...
Show moreCampylobacter jejuni, the leading cause of bacterial gastroenteritis in the United States, is often resistant to commonly used antibiotics and has been classified as a serious threat to public health. Through this work, we sought to evaluate infection trends, quantify resistance frequencies, identify epidemiological factors associated with infection, and use whole-genome sequencing (WGS) as well as comparative phylogenomic and pangenomic approaches to understand circulating C. jejuni populations in Michigan. C. jejuni isolates (n=214) were collected from patients via an active surveillance system at four metropolitan hospitals in Michigan between 2011 and 2014. Among the 214 C. jejuni isolates, 135 (63.1%) were resistant to at least one antibiotic. Resistance was observed for all nine antibiotics tested yielding 11 distinct resistance phenotypes. Tetracycline resistance predominated (n=120; 56.1%) followed by resistance to ciprofloxacin (n= 49; 22.9%), which increased from 15.6% in 2011 to 25.0% in 2014. Notably, patients with ciprofloxacin resistant infections were more likely to report traveling in the past month (Odds Ratio (OR): 3.0; 95% confidence interval (CI): 1.37, 6.68) and international travel (OR: 9.8; 95% CI: 3.69, 26.09). To further characterize these strains, we used WGS to examine the pangenome and investigate the genomic epidemiology of this set of C. jejuni strains recovered from Michigan patients. Among the 214 strains evaluated, 83 unique multilocus sequence types (STs) were identified that were classified as belonging to 19 previously defined clonal complexes (CCs). Core-gene phylogenetic reconstruction based on 615 genes identified three clades, with Clade I comprising six subclades (IA-IF) and predominating (83.2%) among the strains. Because specific cattle-associated STs, such as ST-982, predominated among strains from Michigan patients, we also examined a collection of 72 C. jejuni strains from cattle recovered during an overlapping time period by WGS. Several phylogenetic analyses demonstrated that most cattle strains clustered separately within the phylogeny, but a subset clustered together with human strains. Hence, we used high quality single nucleotide polymorphism (hqSNP) profiling to more comprehensively examine those cattle and human strains that clustered together to evaluate the likelihood of interspecies transmission. Notably, this method distinguished highly related strains and identified clusters comprising strains from both humans and cattle. For instance, 88 SNPs separated a cattle and human strain that were previously classified as ST-8, while the human and cattle derived ST-982 strains differed by >200 SNP differences. These findings demonstrate that highly similar strains were circulating among Michigan patients and cattle during the same time period and highlight the potential for interspecies transmission and diversification within each host. In all, the data presented illustrate that WGS and pangenomic analyses are important tools for enhancing our understanding of the distribution, dissemination, and evolution of specific pathogen populations. Combined with more traditional phenotypic and genotypic approaches, these tools can guide the development of public health prevention and mitigation strategies for C. jejuni and other foodborne pathogens.
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