• Protein Engineering Methods to Understand Kinase Signaling and Protein-Protein Interactions

  Ghosh, Indraneel; Amofah, Bismark; Charest, Pascale; Marty, Michael; Montfort, William R. (The University of Arizona., 2022)

  Tyrosine phosphorylation is one of the key covalent post-translational modifications through which multicellular organisms communicate. Phosphorylation of tyrosine residues on proteins can modulate enzymatic activity and can create binding sites for the recruitment of downstream signaling proteins. Conservation of enzyme structure across the human kinome makes it difficult to design small molecules to selectively modulate kinase activity, which can help elucidate their roles in signaling pathways and in diseases. To circumvent this limitation, we have developed a split-protein method to control the activity of individual kinases by utilizing chemical inducer of dimerization (CID) proteins. The split-protein approach relies on the identification of viable fragmentation sites in a protein that can be used to generate ligand-gated control of protein activity. The major focus of this dissertation is the identification of new kinase and firefly luciferase fragmentation sites for temporal control of a specific kinase and for the study of protein-protein interactions, respectively. With a sequence dissimilarity-based approach and structure-guided analysis, we successfully identified new split-Src sites, the first split-Syk site, the first split-Abl-1aFL, and new firefly luciferase fragmentation sites utilizing the CIDs of rapamycin and/or abscisic acid. Temporal control of split-Abl-1a coupled with quantitative phosphoproteomics analysis aided in the understanding of Abl-1 cellular signaling. Both known and novel substrates were identified, and validation of novel phosphotyrosine targets like AFDN, AMOT, DDX3X, NCAPH present opportunities for studying and understanding unanticipated functions of Abl-1. In summary, this work describes the split-protein approach to selectively control and dissect the complex signaling processes of specific protein tyrosine kinases (PTKs) and for monitoring PPIs. The new tools developed could potentially be used to rewire signaling pathways and aid in the development of novel therapeutic targets.
• The Honey Bee Superorganism: Social Insect Life History and the Microbiome

  Duca, Frank A.; Copeland, Duan; Anderson, Kirk E.; McCarthy, Fiona M.; Schlenke, Todd A.; Stock, Patricia (The University of Arizona., 2022)

  Honey bee colonies are a complex society of individuals functioning to serve the collective group, colloquially known as a ‘superorganism.’ Their life history is intimately linked with their ability to separate reproduction, resource provisioning, defense, and offspring across thousands of individuals. Similarly, their gut microbiota also greatly influences their physiology and health. Here we explore the honey bee gut microbiota at pivotal moments during the honey bee life history. First we explore gut microbial succession and gene expression in freshly mated queens placed in colonies (high metabolic demand) or queen banks (low metabolic demand). We found differences in gut microbiota abundance between the two environments; colony queens were less diverse, while queen bank queens had microbiota similar to older queens who produce less eggs. We also found gene expression was similar between the two environments, suggesting post-mating had a stronger effect on gut gene expression. Our findings suggest that the queen gut microbiota experiences an extended period of microbial succession associated with post-mating development and colony assimilation. Next, we looked at the gut microbiota’s role in precocious forager midguts and ileums by determining if aging of the microbiota precedes or succeeds physiological aging. We found that social structure greatly influenced the absolute and relative abundance of midgut and ileum microbiota. We also performed immune and oxidative stress gene expression and found genes were explained by an interaction of both age and behavioral task. Our findings suggest that the physiological cost of early foraging is early senescence to the individual which can progress to population dwindling at the colony level. Finally, we conducted the first metaanalysis of the honey bee gut microbiota. We resolve the core microbiota and rare biosphere from over 3000 16S rRNA gene sequence libraries. We also highlight strain diversity and niche partitioning of the core microbiota. Collectively, we present the honey bee microbiota as a functional component of honey bee health from the novel perspectives of nascent queens, precocious foragers, and through a macro lens meta-analysis.
• Precipitation Patterns Influence on Greenland Ice Sheet Regrowth During the Last Interglacial Period: CESM2 Simulation

  Lofverstrom, Marcus; Berry, Allison Renee; Tierney, Jessica; Yin, Jianjun (The University of Arizona., 2022)

  The Greenland Ice Sheet (GrIS) is highly vulnerable to climate warming. Most obvious are the threats of sea-level rise due to GrIS melting, but there are also far-reaching climate effects through complex interactions with atmospheric and oceanic circulation that control the hydroclimate in the North Atlantic. To better understand how the GrIS regrows following an extreme deglaciation event during warmer climates, we analyze a unique, transient simulation of the Last Interglacial warm period (LIG; 127 to 119 ka; thousand years before present) with the Community Earth System Model Version 2 (CESM2) that includes an interactive ice-sheet component. Although the LIG warmth is primarily attributed to high summer insolation and is therefore not a perfect analog for greenhouse gas dominated anthropogenic global warming. The lowest values of surface mass balance occur at 122 ka, when the GrIS has separated into a large northern dome and a smaller southern dome. By 120 ka, the two domes are reconnected as the ice sheet begins to regrow as the summer climate continues to cool. In the modern climate, Greenland receives most precipitation during winter months along the southeastern coast. However, in the LIG simulation, winter precipitation is reduced in this region, while summer precipitation is more abundant. This is contradictory to modern climate, as precipitation during summer months tends to be most abundant in western Greenland. Understanding the dynamics of this response is not only key for interpreting proxy-data signals in past climates but may also be important for improving predictions of storm track dynamics and water resources availability in the face of climate variability and change.
• Wavefront Control Techniques for the Direct Imaging of Exoplanets

  Males, Jared R.; Rodack, Alexander Thomas; Kim, Daewook; Guyon, Olivier; Frazin, Richard A. (The University of Arizona., 2022)

  Over two decades ago, the first planet around a star other than the Sun was discovered. With each passing year, more and more such exoplanets are discovered as new technologies and methods of discovery are developed and enhanced. As these techniques continue to mature, humanity gets closer to finally being able to answer the question: are we alone in the universe? Improvements to Adaptive Optics (AO) have enabled ground-based observation to expand to including high-contrast imaging instruments called coronagraphs that are meant to make the direct imaging of exoplanet light possible.Direct imaging is a method of observation that gives astronomers the ability to determine if a planet exhibits signatures of life via spectroscopic analysis for biomarkers. This is a difficult task for three major reasons: the planet orbits very close to its host star if it is located in the so-called habitable zone, the planet light is up to 10^-10 times fainter than the host star light, and static and quasi-static aberration being present during the observation degrades both coronagraph performance and post-processing technique efficacy. In this dissertation, I explore two methods for estimating non-common path aberration (NCPA) in the science instrument of AO enabled, ground-based telescopes. The first is a method called the Differential Optical Transfer Function (dOTF), which is a simple, non-iterative, non-interferometric technique to estimate the complex amplitude field in the exit pupil of an optical system exploiting the properties of the functional derivative of the Optical Transfer Function. dOTF is demonstrated in both simulation and lab based experiments, showing several possible applications, including AO system self calibration, segment cophasing, and estimating systematic NCPA using an off-axis light source. The second method is known as Frazin's algorithm, which is a statistical regression framework that uses wavefront sensor (WFS) and science camera (SC) telemetry with advanced computational models of optical systems to estimate any NCPA and any present exoplanet signals. I develop the history of the method starting from its inception in 2013 and its extension to potential real-time use in 2018, followed by the conception of an improved version that is fully realizable. Three separate estimators are presented within the framework, and then are demonstrated via comprehensive end-to-end simulation of an AO system running at 1kHz frame rate with a Lyot Coronagraph in the science arm. Finally, preliminary future extensions of the work done on Frazin's algorithm are presented to guide future steps to evolve the method to improve the current limits of ground-based direct imaging of exoplanets.
• Hydrogeochemical Evolution of Basinal Fluids in the Paradox Basin: Implications for Sources, Paleofluid Flow, Residence Time, and Water-Rock-Gas-Microbe Interactions

  McIntosh, Jennifer; Kim, Jihyun; Meixner, Thomas; Guo, Bo; Ferguson, Grant (The University of Arizona., 2022)

  Understanding evolution of paleofluid flow through the Earth’s shallow crust is important for water, mineral, and energy resource management, including extraction of subsurface resources and storage of alternative energy and waste products. The migration of water, gas, and life between surface and deep subsurface systems and its consequence by water-rock-gas-microbe interactions can be evaluated by characterizing hydrogeochemical features of fluids (e.g., formation water and natural gas) in sedimentary basins. This study focuses on the Paradox Basin in the Colorado Plateau, which has iconic manifestations of multiple episodes of paleofluid flow, including widespread sandstone bleaching, ore mineralization (e.g., Cu; U; Fe; Mn), and hydrocarbons, CO2, and He accumulation. Based on molecular and isotopic signatures in formation water and natural gas samples, the origin, types, composition, distribution, and residence time of remnant fluids in the Paradox Basin have been evaluated to constrain the hydrochemical and geological histories responsible for paleofluid flow and solute transport. Highly evaporated paleo-seawater derived brines (i.e., connate brines), associated with the Pennsylvanian Paradox Formation evaporites, migrated into adjacent under- and/or over-lying formations through faults by compaction. These H2S- and hydrocarbon-bearing reduced, saline fluids were responsible for much of the sandstone bleaching in overlying Triassic-Cretaceous shallow sediments, forming reduced traps for later Cu and U deposition. Natural gas throughout the basin is primarily thermogenic in origin recording different thermal maturities of gas generation. Microbial methanogenesis may have been inhibited by the deep burial history of the Paradox Basin and abundance of sulfate. Salt dissolution above and below the evaporites, by topographically-driven meteoric recharge, provided a source of more oxic, sulfate-rich shallow brines. Deep meteoric circulation (up to 3 km depth in the last 1.1 Ma, based on 81Kr dating), in response to the recent denudation of the Colorado Plateau (<4-10 Ma), contributed to flushing of residual brines in aquifers above and below the evaporites and biodegradation of hydrocarbons in shallow reservoirs (based on molecular and isotopic signatures of hydrocarbon in natural gas, including clumped isotopes of methane). The origin, types, and distribution of existing fluids in the Paradox Basin provide important constraints to understand the evolution of paleofluid flow and subsequent water-rock-gas-microbe interactions recorded in sedimentary rocks over geological time.
• Food and Resources Expanded to Support Health and Type 2 Diabetes for Food Insecure Individuals

  Hingle, Melanie; Short, Eliza; Taren, Douglas; Thompson, Deborah; Roe, Denise; da Silva, Vanessa (The University of Arizona., 2022)

  Diabetes mellitus is a growing public health concern affecting 34.2 million people in the United States, with type 2 diabetes mellitus (T2DM) accounting for 90-95% of diabetes cases. Food insecurity greatly affects the management and long-term consequences of this diet-related disease. There are few food-based diabetes self-management education and support (DSMES) interventions for food insecure individuals with T2DM, and existing interventions have shown limited success in improving indicators of T2DM self-management. To address gaps in prior food -based DSMES interventions, we conducted the Food and Resources Expanded to Support Health (FRESH) Study, a collaboration between a regional food bank, a federally qualified health center (FQHC), and a research university in Southern Arizona. The purpose of this study was to develop and test the feasibility and acceptability of a food-based DSMES intervention to improve management of T2DM for food insecure community members. This study was conducted in three phases. Phase I characterized food bank client diet quality in 197 participants using 24-hour dietary recalls and the Healthy Eating Index-2015 to identify targets for intervention. Phase II explored food bank clients’ perception and utilization of the current food assistance, and whether additional resources were needed to support T2DM management. Findings from Phase I and Phase II produced a therapeutic food assistance package (consisting of food + educational resources) tailored to food bank client social and cultural contexts and T2DM nutrition therapy guidelines. In Phase III, we evaluated the feasibility and acceptability of our therapeutic food assistance package in combination with registered dietitian visits in 21 food insecure patients with T2DM recruited from our FQHC partner (El Rio Community Health Center). Across the three phases, we observed: Phase I: low diet quality of food bank clients in comparison to national food secure samples; food pantry visits within 1-4 days (compared to >5 days) were associated with higher diet quality in non-Hispanic participants, but not Hispanic participants. Hybrid thematic analysis of Phase II qualitative data revealed that food assistance use was influenced by individual and household preferences, and identified multiple foods and resources desired by clients. Participants reported challenges affecting their ability to manage T2DM, yet expressed resilience and interest in improving T2DM management. Analysis of Phase III findings revealed a priori feasibility benchmarks were met, including adherence to the intervention and retention rates. Qualitative findings suggested that the intervention was acceptable to participants, and they had many ideas for strengthening the program; food bank and health clinic personnel interview data suggested staff were overall positive about the intervention, and they provided recommendations on how to refine the intervention to increase sustainability and integration within each organizational structure. Next steps should prioritize participant and staff feedback for future intervention delivery, including expanding strategies to recruit participants at El Rio, developing a standard operating procedure for program delivery at the food bank, and tailoring the intervention to the diverse needs of participants. A randomized controlled trial is needed to determine the efficacy of the refined food-based DSMES intervention for food insecure individuals with T2DM, and to evaluate the long-term sustainability of the program in this setting.
• Queer Debt: Affective Politics of Security and Intimacy in Kurdish Turkey

  Silverstein, Brian; Plemons, Eric; Karakus, Emrah; Stryker, Susan; Korkman, Zeynep; Marston, Sallie (The University of Arizona., 2022)

  The conflict between the Turkish state and Kurdistan Worker’s Party (PKK) that began in 1984 entered a cease-fire in 2010 but returned to re-intensified militarized conflict in 2015. This has led to massive infrastructural and human destruction in Southeast Turkey, accompanied by intensified surveillance and urban counterinsurgency against Kurds. As with many aspects of Kurdish identity politics in Turkey, the ways in which Kurdish queer folks are articulating, debating, and living identities are intimately and increasingly interwoven with institutions, discourses, and practices of securitization. This dissertation shows how queer and trans Kurds adopt, adapt, and use surveillance to constitute moral worlds, craft ethical subjectivities by negotiating the value of life and work with one another, the broader community, and the state. These negotiations involve vocabularies, strategies, and affective attachments derived from the longstanding militarized conflict and surveillance. Key to this dynamic is the notion of bedel, the feelings of indebtedness, loss, and obligation among Kurds to struggle for the cause of Kurdish rights. Drawing on 24-months of field research in several key sites and locations, including Kurdish LGBTI organizations and apartments rented by sex workers and “partyers” in Istanbul and Diyarbakır, the project demonstrates how securitization is affectively experienced through belonging, difference, loyalty, and betrayal. Through bedel, queer and trans Kurds in Kurdish Turkey police boundaries for their security and livelihoods, constitute moral value, respectability, belonging, and honor in the Kurdish society, craft “chameleon subjectivities” for disorienting racial and sexual violence, and collectivize an ethical politics of face to solve disputes within their community, shifting the meanings of bedel in the process.
• Normalization and Imputation in Microbial Studies

  An, Lingling; Luo, Qianwen; Hu, Chengcheng; Li, Haiquan; Slack, Donald C. (The University of Arizona., 2022)

  The microbiome is the genetic material of all the microbes and is involved in many biological functions. Microbes are found on our skin, in our mouth, gut, and genitals. The human microbiome makes an essential contribution to the normal functioning of our bodies and our health. With the increased interest and the reduction of the cost of sequencing, there are more data available and call for statistical analysis methods. This dissertation focus on two preprocessing steps for microbial studies: normalization and imputation. Metagenomic time-series studies provide insights to investigate the dynamics of microbial systems. Normalization is the first critical step in microbial count data analysis used to account for variable library sizes. However, there is no method to normalize the microbial count data for a time-series study appropriately. Here we propose TimeNorm when both the within and across time point structures are considered. Under various settings through simulation studies TimeNorm is shown surpass the existing normalization methods developed for static data. The second project focus on solving the sparsity issues. Microbiome data analysis is challenging because of the existence of a large number of non-biological zeros, which hinders downstream analysis. We propose two imputation methods, PhyImpute and UniFracImpute, for microbial count data to identify and impute the non-biological zeros by borrowing information from similar samples to address this challenge. The proposed work directly involves the probability of non-biological and phylogenetic trees to account for sample-to-sample similarity estimation. The proposed imputation methods have demonstrated better performance than the existing methods through comprehensive simulation studies and real data analyses.
• How Loving Allyship and Caring Accountability Design Access and Inclusion in the Writing Classroom

  Troutman Robbins, Stephanie; Kutcher, Cheryl; Mapes, Aimee C.; Shivers McNair, Ann; Bose, Dev (The University of Arizona., 2022)

  Written during COVID-19, this dissertation takes the form of a three-article exploration of different ways that the first-year writing classroom can facilitate connection through purposeful design of self and classroom structures. In considering how we can make the classroom a more accessible and inclusive space, each article explores scholars in disability studies, black feminism, and activism work, who imagine and shape their communities through love, accountable allyship, care, and solidarity. Article 1, “Love and Accountable Allyship in the Classroom: An Intervention,” argues that the collapsed inner and outer spaces (home and work/education) revealed the importance of embracing a person-first pedagogy, valuing connection and humanization while being mindful of systems inside and outside the classroom. Article 2, “Rhetoric of Care: A Critical Pedagogy Framework for Solidarity in the Classroom,” argues that the Rhetoric and Composition canonized frameworks for care are missing crucial elements that are preventing truly caring relationships within classrooms, like addressing white supremacy, and it concludes that forming intimacy across difference can sustain all of us. Finally, in article 3, “Designing Love and Care in the Classroom,” I begin to examine how the intricacies of theory within the field of design can be applied to university structures (teaching persona, pedagogy, syllabi, course policies, course materials, curriculum, assessment) and start to reflect on how I have begun to think about rebuilding a healthier self and classroom system, specifically by simultaneously holding destruction of whiteness and space for equity. Overall, this dissertation contributes to the conversation around the re-humanization of those working within academic institutions.
• Design, Fabrication, and Characterization of Novel Polymers Based Integrated Photonic Devices

  Norwood, Robert; Nishant, Abhinav; Kieu, Khanh; Pyun, Jeffrey (The University of Arizona., 2022)

  The field of integrated photonics is a key technological area that is rapidly gaining interest from the academic and industrial community. The first wave of innovation in this area was fueled by the demand created by the optical data communications industry, with products such as optical transceivers. The impact of this technology continues to grow with newer applications building up in areas such as next-generation consumer devices, medical instruments, space technologies, and defense-related interests. Further advances in photonic materials and devices are required to keep up with the demand while maintaining stringent cost margins and advancing performance milestones. Optical polymers provide a path to achieve these cost targets while offering diverse opportunities for innovation. In this dissertation, we demonstrate the application of three new optical polymers, each offering a solution to a unique set of problems being faced by the scientific research community. First, we will discuss the applications of chalcogenide hybrid inorganic/organic polymers (CHIPs), developed in collaboration with the Pyun group in the Department of Chemistry and Biochemistry at The University of Arizona. CHIPs are first-of-their-kind, high refractive index optical polymers with high transparency in the infrared regime. We will discuss the processing techniques of this polymer in order to create high-quality thin films and then introduce several photonic devices that were fabricated in this material platform and designed to operate at short-wave infrared wavelengths (SWIR). This family of polymers was also used to demonstrate other photonic devices targeting mid-infrared (MWIR) and long-wave infrared (LWIR) wavelengths. Next, we will introduce devices made from a novel optical polymers that we call refractive index contrast (RIC) polymers. The clever chemistry behind these polymers allows for a dry film fabrication approach to fabricate photonic devices such as optical waveguides and grayscale index tapers. This polymer's key advantage is highlighted by fabricating optical interconnects on flexible substrates that were used to transfer light between two spatially separated ion-exchange waveguide samples. Finally, we will discuss our work using electro-optic polymers to fabricate low-loss, high bandwidth electro-optic phase modulators with state-of-the-art performance
• Policy and Power in Public Health: The Impact of Policy Expansions and Exclusions on Farmworkers’ Health Insurance Coverage

  Barraza, Leila; Rosales, Cecilia; Koch, Bryna; Armin, Julie; Ellingson, Kate; Sabo, Samantha (The University of Arizona., 2022)

  Problem Statement: The majority of the two to three million migrant and seasonal farmworkers (MSFW) in the United States are foreign-born, and 47% are unauthorized immigrants. Farmworkers have a markedly lower rate of health insurance coverage compared to the general population. Aims: The quantitative aims for this project are to identify the effects of the 1) Affordable Care Act (ACA) and 2) the Deficit Reduction Act (DRA) and Personal Responsibility and Work Opportunity Reconciliation Act (PRWORA) on farmworker and their families’ odds of health insurance coverage. Both aims include a sub-aim: to identify if citizenship and immigration status moderates the effects of these policies on the odds of coverage. The third aim of the research is to explore the state level political environment in Arizona around public health policy expansion. Aim 1 and 2 Outcome Measures: There are three outcome measures in the quantitative research: farmworker health insurance coverage, child health insurance coverage, and household Medicaid use in the prior two years. Methods: For the quantitative aims, logistic regression analyses were conducted with pooled data (1993-2018) of National Agricultural Workers Survey (NAWS) (1993-2018) (N=42,611) to assess the odds of health insurance coverage post-policy implementation. Results: Farmworkers’ odds of coverage were higher post-ACA compared to pre-ACA (OR, 2.92; 95% CI, 2.67-3.19) as were the odds of reporting child coverage (OR, 4.16; 95% CI, 3.39-5.11). The odds of household Medicaid use were higher post-ACA compared to pre-ACA (OR, 1.50; 95% CI, 1.37-1.64). Post-ACA, greater percentages of farmworkers in Medicaid expansion states reported coverage and stratification of the regression models by Medicaid expansion state showed expansion was an important factor. While immigrant farmworkers have lower odds of coverage, the moderation model did not identify a negative effect of immigration status. However, a negative moderation effect for unauthorized farmworkers was observed in Medicaid expansion states. An unanticipated positive moderation effect was observed for authorized immigrant farmworkers in the ACA period. There was no change in odds of household Medicaid use post-PRWORA compared to pre-PRWORA but post-DRA odds were higher than pre-DRA odds of household Medicaid use (OR, 2.19; 95% CI, 2.00-2.40). Aim 3Methods: For the qualitative aim I conducted key informant interviews (N=3). To contribute additional information to the interviews and triangulate information from the interviews, I also compiled secondary sources including newspaper articles (N=298) and recordings of legislative proceedings (N=4). I used a grounded approach to content analysis and implemented both inductive and deductive coding. Results: The analysis provides a description of the health policy environment in Arizona, using Medicaid expansion as a critical event. Salient categories included the role of the economic environment, budget, relationships, personal experience, worldview, and constituency groups. This qualitative aim will explore the perspectives of health policy stakeholders including their attitudes, knowledge, and beliefs about the intent and outcomes of exclusions and inclusions and how these policies operate within a public health framework of creating the conditions (opportunity) for people to be healthy. Conclusion: The health insurance policy expansions implemented by the ACA have benefited farmworkers and their families. However, the rate of coverage for farmworkers remains low and disparities by citizenship and immigration status remain; however, there were mixed results on how the immigration status of farmworkers effects the relationship between policy and coverage. Results indicate that state decisions such as Medicaid expansion and pathways to coverage outside of Medicaid expansion may play an important role for authorized immigrant farmworkers. The qualitative results provide additional insights for public health and health advocacy groups as they embark on future efforts to expand health coverage in Arizona.
• Design and Synthesis of Controllers for Societal-Scale Cyber-Physical Systems

  Sprinkle, Jonathan; Bhadani, Rahul Kumar; Djordjevic, Ivan; Head, Larry; Ditzler, Gregory (The University of Arizona., 2022)

  In this dissertation, a unifying framework for controller design, synthesis, and validation for societal-scale Cyber-Physical Systems (CPS) is proposed. We use vehicular CPS as a case study of societal-scale CPS. These systems require large-scale simulation to reduce the need for physical tests or field experiments. Such large-scale simulations demand reproducibility and repeatability of results---or else the use of simulation provides no insights into the overall system's dynamics. Many current simulation tools for CPS lack the properties of reproducibility and repeatability. Our proposed approach for \Rahul{scalability} and repeatability of existing simulation tools includes offloading dynamics of systems using federated models, message handling and synchronization to operate a simulator at slower than real-time, or synchronously with another system. The approaches do not require rewriting those simulation tools, thus permitting assembly of tools at their interfaces. With such simulation tools, it is now possible to use model-based design and code-generation techniques to deploy the same implementation in simulation that would be deployed in an experiment. Such approaches may be inaccessible for simulation tools that do not support real-time behavior. Our approach permits the validation of novel controllers and algorithms not only through software-in-the-loop (SWIL) or hardware-in-the-loop (HWIL) simulation but also transfer seamlessly for real-world testing. In this way, both model and simulator can be improved iteratively by feeding data from the physical environment. Large-scale CPS are producing a massive amount of data in real-time which is being used for decision-making and control that engage with infrastructure and humans. For Vehicular CPS, data comes in the form of multiple modalities such as CAN bus, GPS, dashcam, LiDAR, etc. We further propose a generic timeseries tool to work with such vehicular data that allows researchers to gain novel insights about driving behavior, discover rare events, and facilitate data-driven applications for vehicular CPS. We present three case studies: (i) Followerstopper, (ii) deployment of a reinforcement learning controller, and (iii) dual-ring-barrier traffic signal controller. The first two case studies are related to Lagrangian control of an autonomous vehicle (AV) in mixed urban traffic consisting of some highly automated vehicles among mostly human-driven vehicles. The third case study presents a co-simulation of an infrastructure controller using SUMO and ROS whose development takes an approach of model-based design. These use cases provide an engineering solution to improving a controller candidate for societal-scale CPS through a data-driven approach, deterministic and repeatable simulation, and their deployment in the real world.
• Characterization of Remotely Sensed, Modeled, and In-Situ Derived Ambient Aerosol Properties

  Sorooshian, Armin; Schlosser, Joseph Simon; Arellano, Avelino; Farrell, James; Karanikola, Vasiliki (The University of Arizona., 2022)

  Ambient atmospheric aerosol particles impact human health, visibility, Earth’s radiation balance, and cloud formation. To better constrain the impacts of ambient aerosol particles, weather and climate forecast and reanalysis models require accurate and robust measurements from spaceborne remote sensing platforms. Prior to being utilized on spaceborne platforms, suborbital field campaigns (e.g., aircraft platforms) are being leveraged to design and validate the accuracy of aerosol particle properties that are retrieved from remote sensing instruments. Direct (i.e., in-situ) measurements of intrinsic and extrinsic aerosol particle properties serve as the primary method to validate the remote sensing retrievals and improve the assumptions that are used within weather and climate models. This work utilizes data from three intensive research campaigns to characterize the horizontal and vertical distribution and composition of several important natural and anthropogenic ambient aerosol types. The first study presented in this work utilizes in-situ aerosol concentration and meteorological data gathered from MONterey Aerosol Research Campaign (MONARC), which was carried out in May–June 2019 and featured 14 repeated identical flights off the California coast over the open ocean at the same time each flight day. This study identified four meteorological regimes during MONARC with each corresponding to different characteristic vertical and horizontal distributions of supermicrometer sea salt aerosol number and volume concentration (N>1 and V>1, respectively). Furthermore, machine learning analysis was used to show that the relative predictive strength of various marine boundary layer properties varied depending on predicting N>1 or V>1. Marine boundary layer depth was more highly ranked for predicting N>1 but turbulent kinetic energy was higher for predicting V>1. The second study presented in this work focuses on analyzing the presence and evolution primary and secondary anthropogenic aerosol species in Incheon and Seoul, South Korea. This work examines measurements of size-resolved aerosol composition at a ground site in Incheon along with other aerosol characteristics for contrast between Incheon (coastal) and Seoul (inland), South Korea, during a transboundary pollution event during the early part of an intensive sampling period between 4 and 11 March 2019. Select findings resulting from this analysis are (i) secondarily produced inorganic and organic acids exhibited significant mass concentrations above 0.94 μm during the pollution event and (ii) a high correlation (r = 0.95) between oxalate and sulfate was identified, which a marker of secondary aqueous production of oxalate. The final study presented in this work proposes a simple method to derive verticallyresolved aerosol particle number concentration (Na) using combined polarimetric and lidar remote sensing observations and validates it using collocated in-situ measurements taken in the first two Aerosol Cloud meTeorology Interactions oVer the western ATlantic Experiment (ACTIVATE) deployments. In this study, the lidar+polarimeter Na was found to agree to within 105% for 90% of the collocated in-situ Na data. This method provides a simple and direct approach to corroborate the results from such complex retrievals, particularly for simpler cases of single or two-layer aerosol systems.
• Timely Signals of Systematic Audit Quality from Market Participants: Evidence from Activist Short-Seller Campaigns

  Michas, Paul N.; Sunder, Shyam V.; Zhao, Meiling; Cheng, Mei; Cheng, Lin (The University of Arizona., 2022)

  Extant studies generally focus on signals of systematic audit quality from regulatory oversight of auditors, which can take up to several years to be revealed. Using a sample of firms targeted by activist short sellers (activists) for financial misreporting, I examine whether capital market participants provide credible and timely signals of systematic audit quality at the auditor office level. I find that activists provide timely signals of systematic audit failures at auditor offices of targeted firms (targeted offices) that exist across audits of concurrent non-targeted firms, and that these signals persist for three years on average. I also find that activist signals are more informative when the activists are more credible. Further, I document that non-targeted clients dismiss targeted offices following activist campaigns, but only when the activists are relatively credible, suggesting that clients recognize the variation in the quality of activist signals and respond accordingly. Finally, I find that audit failures revealed by activists are less persistent than those not revealed by activists, indicating that activists facilitate auditor offices’ remediation of systematic audit quality problems. Overall, my study highlights activist short-seller campaigns as a credible and timely channel through which systematic audit quality of auditor offices is signaled by market participants.
• Doing Time: Incarceration and the Novel Form

  Zwinger, Lynda; Sims, Rachel; Lempert, Manya; Lucey, Colleen (The University of Arizona., 2022)

  Long considered a formal paradox, a formal antinomy, the form of the novel has its genesis in the conditions of incarceration and solitary confinement. Traversing distinctions of national canon, period, or era, the novel form includes a great number of novelists who have done time in prison. In Don Quixote, one of the great progenitors of the novel, Miguel de Cervantes discusses the prison as the birthplace of the novel form. From this declaration of the novel’s incarcerated origins, this study engages with novels written by novelists who have also done time. Through a consideration of John Bunyan’s The Pilgrim’s Progress (1678), Charles Dickens’s Little Dorrit (1855-1857), Fyodor Dostoevsky’s Notes from a Dead House (1860-1862), and Jean-Paul Sartre’s Nausea (1938), this study investigates the formal, life-saving properties of the novel through the lens of incarceration and isolation. Specifically, I argue that the novel is a structural hinge—another type of antimony as a form that both anchors and moves. The novel’s hinged structure, I claim, was born out of isolation and at times the solitary confinement of novelists who have been incarcerated. Through a phenomenological and formal analysis bolstered by the works of Lisa Guenther, Maurice Merleau-Ponty, Caroline Levine, Margaret Doody, and Stuart Grassian among other phenomenologists and formalist critics, I demonstrate that built into the novel’s formal genetics is a subjectivity-preserving, world-providing joint—a joint denied humans and novelists alike in solitary confinement. That the multiplicity and mutability of the novel form has, in part, come from conditions of deprivation, rigidity, and monotony is due to the disintegration incarceration and isolation have on an existent’s relationship with as well as access to the self, other intersubjects, and the world. In conditions of confined isolation, the self becomes unhinged without a worldly anchor and without hinged movement and relationality with another subjectivity. Through this deprivation and through these conditions of absence, I argue, the abundance, dexterity, and bounty of the novel form was born.
• Mission-Oriented System Architecture and Optimal Aerial Terrain Guarding for a Collaborative Team of UAVs

  Son, Young-Jun; Na, Hoyoung; Liu, Jian; Lin, Wei (The University of Arizona., 2022)

  Thanks to rapid technological development, multi-Unmanned Aerial Vehicle (UAV) systems have been actively adopted in the military to accomplish various missions, including intelligence, surveillance, and reconnaissance (ISR), target acquisition, and border patrol. Although multi-UAV systems have the potential to increase the efficiency of military operations, the majority of current military system architectures that utilize multiple UAVs are not well suited for tactical-level operations because most of the current military systems have been designed in an ad-hoc manner to achieve specific purposes. In addition, the developments have only focused on behaviors of individual UAVs without mission-level perspectives as a primary engineering factor. Consequently, existing ad-hoc systems are limited in their reusability across missions unless the human operators have specialized engineering skills.Given this reality, this dissertation aims to formalize the systems engineering process of military multi-UAV systems by incorporating mission-oriented features that enhance architecture reusability and composability. The proposed systems engineering approach, called mission-oriented iterative systems engineering process, is a top-down, mission-centric methodology that consists of four main steps: 1) specification of mission requirements, 2) creation of normative models, 3) simulation of models, and 4) real implementation. Based on model-based systems engineering (MBSE) and mission engineering (ME) foundations, the outputs of each step are formalized in SysML language to facilitate understanding of the system. Military doctrines, such as Mission Command and Operations Process, are regarded as primary factors for engineering the system. Throughout this dissertation, the search and attack mission, a military offensive operation used to establish or regain contact with the enemy, is utilized as the target mission to demonstrate the details of the engineering process proposed. In the search and attack operation using UAVs, it is critical to determine how to maximize the visible regions on the terrain surface by deploying multiple UAVs. Therefore, terrain visibility from the aerial observation points and related constraints are deeply examined in this research. Based on the examination, a new optimization problem, the Aerial Terrain Guarding Problem with Visibility Constraints (ATGP-VC), and its solution approach are presented to determine an optimal set of aerial points to maximize the collective visibility on terrain surface. A task assignment problem to assign aerial points to UAVs is also discussed. The developed system with the proposed engineering process is tested and validated using a hardware-in-the-loop (HITL) simulation testbed, which involves various hardware components (i.e., a real UAV equipped with onboard computational units and sensors) and software components (i.e., flight dynamics simulator and hardware interfaces). Detailed architectures of each component are designed and presented.
• PMTCT Implementation and Early Infant Diagnosis of HIV Infection in Lagos, Nigeria: The Mix, Missed and the Muffed

  Ehiri, John; Pettygrove, Sydney; Okusanya, Babasola Oluwatomi; Gerald, Lynn; Taren, Douglas (The University of Arizona., 2022)

  Background: Nigeria has a large population of people living with HIV infection, with Lagos state as one of the six priority states for national HIV prevention interventions because of its high HIV prevalence. In Lagos state, the primary health care system is the most proximal to the populace, including pregnant women infected with HIV. National and state efforts to prevent new pediatric HIV infection using prevention of mother-to-child transmission (PMTCT) strategies, including early infant diagnosis (EID) of HIV infection have evolved and has been scaled since 2002 when PMTCT interventions commenced in Nigeria. With suboptimal uptake of PMTCT strategies and EID of HIV in Lagos, the dissertation research assessed the contemporary evidence on interventions to increase EID uptake and health systems barriers to a seamless implementation of PMTCT intervention at the primary health care level of Lagos state, Nigeria. Objectives: This dissertation comprises four studies. A systematic review and meta-analysis, a quantitative survey of service providers’ knowledge of the Nigerian PMTCT guidelines recommendations, mixed-method research, and a qualitative study. The studies’ aims were to achieve the following 1). Synthesize and provide the evidence quality of interventions to increase uptake of early infant diagnosis of HIV at 4-8 weeks of life for an HIV-exposed infant. 2). Assess the knowledge of PMTCT service providers of the Nigerian PMTCT treatment guidelines. 3). Assess the uptake and challenges of early infant diagnosis of HIV at the primary health level in Lagos state. 4). Assess the barriers encountered by service providers in the routine provision of PMTCT services at the primary health care level in Lagos state, Nigeria. Methods: A systematic review and meta-analysis were conducted between May and December 2020 to identify and critically appraise the evidence quality of interventions to increase uptake of early infant diagnosis of HIV infection at 4-8 weeks of life. Five databases (PUBMED, CINAHL, EMBASE, PsycINFO and Web of Science) were searched for eligible studies. Search output and data extraction were performed using Covidence® by two researchers independently. GRADE (Grading of recommendations, assessment, development, and evaluations) was used to present the quality of evidence of interventions. Data collection for the dissertation research involved quantitative and qualitative data collection. The quantitative data collection was both primary survey of health workers knowledge of the Nigerian PMTCT guidelines and secondary data collection using PMTCT program registers of the facilities. The qualitative research was in-depth interviews of service providers. The dissertation research was conducted in 23 primary health centers across all five administrative districts of Lagos state from July to September 2021. For the quantitative survey to assess knowledge of service providers and secondary data collection, REDCap® was used for data collection and statistical analysis was conducted with R. Responses of in-depth interviews were recorded on electronic voice recorders and transcription done verbatim before analysis with MAXQDA®. Inductive and deductive themes were created from the transcripts. The dissertation research was approved by the Human Research Ethics Committee of Lagos University Teaching Hospital, Lagos, Nigeria and given an Ethical deferral by the University of Arizona Institutional Review Board. Results: The systematic review and meta-analysis included 16 eligible studies involving 13,956 HIV-exposed infants. Included studies were published between 2014 and 2019 from sub-Saharan Africa and India. Nine experimental and seven observational studies included had low to moderate risk of bias and evaluated eHealth services, service improvement projects, service integration programs, behavioral interventions, and male partner involvement, compared to usual care.There was no evidence that eHealth, health systems improvements, integration of EID, conditional cash transfer, mother-to-mother support, or partner (male) involvement interventions increased uptake of EID at 4-8 weeks of age. There was also no evidence that any intervention was effective in increasing HIV-infected infants’ identification at 4–8 weeks of age. Aim 2: One hundred and thirteen (113) respondents participated in the survey. Most respondents knew that HIV screening at the first prenatal clinic was an entry point to PMTCT services (97%) and that posttest counseling of HIV-negative women was necessary (82%). Similarly, most respondents (89%) knew that early infant diagnosis (EID) of HIV should occur at 6-8 weeks of life (89%). However, only four (3.5%) respondents knew the group counseling and opt-out screening recommendation of the guidelines; 63% did not know that hematocrit check should be at every antenatal clinic visit. Forty-eight (42.5%) service providers had good knowledge scores. Knowledge score was not influenced by health worker cadre (p=0.436), training(P=0.537) and professional qualification of  5years (P=0.43) Aim 3: Twenty-two Lagos state primary health centres participated in the research. Fifteen (68.2%) PHCs had both PMTCT HIV counseling and Infant follow-up registers. The documentation of DBS sample collection was observed in 12 (54.6%) PHCs, while both DBS sample collection and EID results documentation was observed in only 9 (40.9%) PHCs. There were both maternal and health systems’ challenges to early infant diagnosis of HIV infection. The denial of HIV status was the only maternal factor reported to militate against the utilization of EID services. Health systems challenges include unavailability of IED services, uncertainty of service providers about the provision of EID services in the facility in which they work, referral to secondary health facilities (with potential to loss to follow-up) for EID services and delayed availability of EID results in the facility. For aim 4: Twenty-two service providers participated in the in-depth interviews, comprising 18 nurses/midwives and four physicians. Patient-level barriers to PMTCT services encountered by service providers included non-disclosure of HIV status to husband, denial of HIV infection, non-compliance with combined antiretroviral therapy (cART), non-compliance with referral, sense of guilt and shame, loss to follow-up, difficulty in identifying HIV-infected women when they come in labour, mixed infant feeding and formular feeding challenges, non-compliance with infant prophylaxis with nevirapine and financial constraints. Health systems related barriers are unavailability of PMTCT services (PMTCT deserts), challenges with HIV counseling and testing, including inadequate test kits, challenges with repeat prenatal HIV screening for women with previous HIV-negative results, stigma and discrimination, lack of treatment guidelines, and manpower shortage. Conclusion: There was no evidence that common interventions increased uptake of EID at 4-8 weeks of age. Hence, further research is required to identify interventions that increase early infant diagnosis of HIV at 4-8 weeks of age.Service providers’ knowledge of PMTCT guidelines recommendations varied, with poor knowledge of group counseling and opt out screening recommendation. Also, the low uptake and constraints of EID uptake as well as the patient-level and health systems barriers to optimal PMTCT service provision require re-training of service providers on timing and documentation of EID and proper counseling of newly diagnosed HIV-infected pregnant women to ameliorate both individual and health systems barriers to a reducing new pediatric HIV infection in Lagos, Nigeria.
• Women's Unspeakable Desire in British and German Modernism

  Lempert, Manya; Hansen, Sovay Muriel; Kosta, Barbara; Skibsrud, Johanna (The University of Arizona., 2022)

  This dissertation, “Women’s Unspeakable Desire in British and German Modernism,” argues that the Weimar Republic’s modernism should condition our understanding of literary modernism in Britain. My project contributes to the growing field of new modernist studies and argues for expanding the boundaries of British modernism to consider the ways in which the modernisms of other parts of the world ought to inform the field. My project asks and responds to the query: How is women’s unspeakable desire for more from life represented and externalized in British and German fiction produced during and after the First World War? “Unspeakable” is meant here in its double sense: that there is no adequate language with which to discuss this desire and that this desire, were it expressed, would be considered appalling and indecent. I claim that in these texts female characters’ desire is expressed by way of metonymy: that is, their desire is conveyed by way of objects adjacent to them in the narrative, so that they and their authors may avoid directly discussing taboo subjects and still communicate desire that eludes language. The field of modernist studies has long been dominated by an understanding of modernism as an artistic and literary movement that originated and flourished in Britain with canonical giants such as James Joyce, Ezra Pound, T.S. Eliot, and Virginia Woolf (as of the 1970s), all of whom still certainly epitomize literary modernism. However, many leading British modernists found second homes in Berlin of the 1920s, where they were able to live queer and more openly desirous lives in public. In the cases of Virginia Woolf, W.H. Auden, Christopher Isherwood, Katherine Mansfield, and others, their artistic work and particularly their discussions of desire, are often inflected by their time spent in Germany during the early twentieth century. The more permissive social and legal ethos of the Weimar Republic undeniably introduced new ways of understanding desire across the western world. Each of my dissertation chapters focuses on one such modernist and the way in which she uniquely uses metonymy to sidestep a lack of adequate language for her female characters’ aspirations. Chapter 1 argues that the fiction of Irmgard Keun reveals how fashion plays a crucial role in understanding female desire in modernism. Chapter 2 argues that Virginia Woolf uses both objects in the natural world and fashion in her fictional narratives to register female characters’ desires to make their secret, core selves visible. Chapter 3 examines the way Katherine Mansfield’s fiction employs objects to obliquely address taboo subjects such as queerness, hatred of motherhood, and deep loneliness, all relevant to women’s desire for different lives. Chapter 4 argues that May Sinclair’s novel Mary Olivier (1919) constructs a protagonist who finds the material word inadequate to answer to her desires and she therefore resorts to abstract metonyms that her metaphysical Idealist philosophy constructs. Characters in Keun, Woolf, and Mansfield connect these transgressive yearnings to items in their proximity; Sinclair’s heroine rejects the material world for the spiritual, and her epiphany is that nothing in this world can fulfill her desires. That characters’ dreams of liberation accrue metonymically to a fur coat (Keun), to a lighthouse (Woolf), to an aloe plant (Mansfield), or to an immaterial realm (Sinclair) is a literary expression of these authors’ feminism. Their fiction registers the repression and demonization of female desire, yet it foregrounds metonyms for life beyond the status quo.
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  Using ArcGIS Dashboards To Monitor Scheduled Python Geoprocessing Scripts

  Sanchez Trigueros, Fernando; Montes, Celso (The University of Arizona., 2022-05)

  There is a need in Pima County’s Information Technology Department, Geographic Information Systems Division for visualizing the status of GIS scheduled Python jobs that run on various servers throughout the day and night. Most scheduled job owners get notified if there is a problem with the script. However, end users of the data may not necessarily be notified that the data they are viewing did not update. This leads to the end users being perplexed on why their edits made the day before are not visible. The solution was to create a Python module called PC_Monitor that the script owner imports into the beginning of an existing or new script that is executed at the end of the script in either its own try, except statement or at the end of a finally statement. Parameters need to be passed into one of the module’s functions to successfully update the database table. The database table is then used for visualizing the status of the script using ArcGIS Dashboards widgets. The module captures various information programmatically using user inputs. Most importantly, the module captures and records the status of the script (Success, Finished with Warnings, or Failed) and the first 255 characters of the status message for Finished with Warnings and Failed. The module has been successful in various test situations on multiple servers. The PC_Monitor module alongside the ArcGIS Dashboard will help our organization’s GIS users to visually monitor the status of Python scripts, keep track of Python scripts, and the effect those scripts have on data sets.
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  Adapting Green Roofs for Desert Climates

  Deitering, Sydney; College of Architecture, Planning and Landscape Architecture; Iuliano, Joey; Wong, Kenny (The University of Arizona., 2022-04-21)

  The following paper is an in-depth assessment of the challenges and benefits of implementing green roofs (a layer of vegetation planted over a waterproofing system that is installed on top of a flat or slightly–sloped roof) in hot and arid climates. (NPS) Green roofs provide a variety of benefits that would be helpful in the creation and upkeep of sustainable, green buildings-but they also bring about costs and a need for resources in an area where these resources are not abundant. Through an analysis of several different groups of vegetation, structures, and watering methods a discussion of the costs and benefits will help reimagine the traditional green roof to be better suited for the dry, drought-ridden desert climate of Tucson, Arizona.

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