More than 40,000 theses and dissertations produced at the University of Arizona are included in the UA Theses and Dissertations collections. These items are publicly available and full-text searchable. A small percentage of items are under embargo (restricted).

We have digitized the entire backfile of UA master's theses and doctoral dissertations that were held in the University of Arizona Libraries.

  • Submitting master's theses to the UA Libraries was optional for many decades; as a result, we do not have all master's theses that were written at the University of Arizona.
  • A small number of historical theses containing culturally sensitive material are not available online.
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Recent Submissions


    Wilson, Jean; Blum, Isabella Rosario (The University of Arizona., 2019)
    Differential membrane trafficking and modulation of lipid domains establishes and maintains cellular polarity in epithelial cells – these events are controlled largely by small GTPases. We have shown previously that Rab14 acts upstream of Arf6 in the establishment of the apical membrane, but how it interacts with other trafficking machinery is unknown. Rab22 has a polarized distribution in activated T-cells, but its role in epithelial polarity is not known. Here we report the colocalization of Rab14 with Rab22a in endosomes of Madin Darby canine kidney (MDCK) cells. Interestingly, Rab22 localizes to the cell:cell interface of polarizing cell pairs, and Rab14 and Rab22 colocalize in adjacent endosomes. Knockdown of Rab22 results in a multi-lumen phenotype in 3D culture, and overexpression of Rab22 in Rab14 knock down cells, results in the production of Rab22-positive extensions. Because of the relationship between Rab14, Rab22, and Arf6, we investigated the interaction of Rab22 with Arf6 GEFs and found that Rab22 co-immunoprecipitates with the Arf6 GEF EFA6. Furthermore, EFA6 is retained in intracellular puncta in Rab22 KD cells. These results suggest that Rab22 acts downstream of Rab14 to regulate Arf6 activity in the establishment of polarity.
  • Sertanejo Portuguese: Language Ideology & Creating Local Figures in the Sertão do Pajeú

    da Silva, Antônio José Bacelar; Suitts, Jacob; Bezerra, Katia; Brito, Dorothy (The University of Arizona., 2023)
    The Brazilian sertão occupies a unique position within the historical, cultural, and linguistic fabric of Brazilian society. Located in the hinterlands of Brazil’s Northeast, the sertão is home to an endemic culture, unique history and variety of Brazilian Portuguese (BP). Despite common knowledge that BP is variable and heterogeneous, standard and monolingual language ideologies circulate that do not reflect the linguistic reality of the country, yet still have profound effects on the ways that Brazilians perceive and understand language use. These ideologies play a role in the ongoing construction of ‘correct’ language use and the validity of nonstandard language varieties. With this research, I examine the language ideologies of residents of the sertão do Pajeú, and how they both reflect and contest notions of how Portuguese should be spoken and used according to standard language ideology. I argue that, while sertanejos reproduce nationally entrenched and prescriptive language ideologies, they also “subversively” assign positive value to the local vernacular as a meaningful component of regional identification and self-expression. Furthermore, I suggest that the reproduction and subversion of standard language ideology by residents of the sertão is not exempt from dominant ideologies, but rather is variable and informed by excluding ideologies itself.
  • Septage Reuse as Class A Biosolids – A Circular Bioeconomy

    Tamimi, Akrum A.; Boyd, Haley Anne; Farrell-Poe, Kitt K.; Waller, Peter P. (The University of Arizona., 2023)
    In the United States, the public uses 40 billion gallons of water daily (Moupin, 2015). Much of the water that is used domestically will remain in the centralized public water system and will require treatment at a wastewater treatment plant (WWTP). However, 20% of the US does not return the water directly to the centralized water system, instead utilizing onsite septic systems to treat and disperse their water (Septic Systems Fact Sheet, 2008). Disposal methods for septage, the waste pumped from the septic tanks, are more limited than wastewater disposal methods. Wastewater treatment plants often refuse septage haulers due to the variable and unknown nature of the septage contents. The septage accepted at WWTP faces the same disposal statistics as wastewater. Approximately half (45%) of wastewater is landfilled or incinerated and the other half (55%) is land applied (Shaddel et al., 2019). Each of these disposal methods poses a risk to the environment. Landfilling the septage decreases the life expectancy of the landfill site and increases the risk of polluting the soil and nearby water supplies. Incineration releases harmful gases and chemicals into the atmosphere, and land application increases the risk to human health via the movement of contamination and pollution.This study aimed to determine if treated septage is beneficial to crop growth and soil health when used as a fertilizer and irrigation source. Durum wheat was the crop that was chosen for this study. This crop was selected due to its dual-purpose uses. The seeds can be collected for seed production, and the rest of the crop can be used for fodder. Septage dispersal and treatment are regulated by the United States Environmental Protection Agency (EPA) under the same guidelines as sewage sludge and is referred to as biosolids when treated to reduce pathogen load. For this study, the septage was dewatered using a spiral filter press and then treated using a low-temperature dehumidification system to dry it to 90% total solids or higher to produce Class A septage that are then land applied. The dehumidification system operates at a temperature and time sufficient to result in Class A biosolids according to US Part 503 EPA Alternative 1 (EPA, 2018). The thermal treatment addresses the health concerns of direct land application. To reduce pathogen load, this experiment consisted of two parallel trials, each with eight treatments. Each trial included two different application rates of the Class A septage, one application of traditional chemical fertilizer, and a control that received no fertilizer treatment. These four treatments were the same across both trials. Trial 1 received canal water flood irrigation. The other half, trial 2, were flood irrigated with the filtrate removed during the dewatering stage that was aerated and treated using a bacterial blend specific to SludgeHammer, a water treatment company, and mixed with the condensate water collected during the thermal treatment process (SludgeHammer, 2023). The findings of the study show that Class A septage can be beneficially used as fertilizer to enhance plant growth and soil health. The application of the treated filtrate water, however, was found to improve plant growth but detrimentally impacted soil health. Due to elevated pathogen levels found in the soil after the experiment, using filtrate for irrigation is not recommended without further treatment. Further research is necessary to determine the optimal application rate of Class A septage and to assess the long-term effects of using septage-based fertilizers.
  • An Evaluation of the Grass-Cast Seasonal Rangeland Productivity Forecast for the Southwest U.S.

    Smith, William K.; Aguilar Cubilla, Emilio Daniel; Gornish, Elise; Moore, David (The University of Arizona., 2023)
    Increasing precipitation variability and extremes driven by climate change are already having significant impacts on semi-arid rangelands of the Southwest US, with critical consequences for livestock grazing and wildlife. Monitoring and forecasting the seasonal productivity of these vulnerable agroecosystems is needed to support effective resource management and conservation efforts. The United States Department of Agriculture (USDA) Grass-Cast rangeland productivity forecast tool was recently expanded to the Southwest U.S. (hereafter termed Grass-Cast Southwest) and provides short-term seasonal forecasts of rangeland productivity for Arizona and New Mexico starting two to three months in advance of the spring (April to June) and summer (June to October) growing season with the major objective of providing early decision support for rangeland managers. Here, we present an initial assessment of the 2020 to 2022 Grass-Cast Southwest rangeland forecasts for the spring and summer growing seasons. Importantly, this time period spans multiple anomalous wet and dry seasons and thus provides an opportunity to assess model performance during climatic extremes. We found that the Grass-Cast Southwest earliest spring forecasts produced in April were very accurate for all years evaluated (R = 0.6 to 0.9 ; RMSE = 106.6 to 5.5 lb/acre). Spring forecasts are accurate since in the Southwest rangeland productivity is driven by antecedent winter precipitation and relatively predictable increases in temperatures in the spring . By contrast, the earliest summer forecasts in produced in June were much less accurate (R = -0.5 to 0.7; RMSE = 81.3 to 315.7), since in the Southwest summer rangeland productivity depends on summer precipitation from the North America Monsoon (NAM), which is much more difficult to predict. As a next step we explore the relationship between Southwest rangeland productivity and the El Nino Southern Oscillation (ENSO) and we provide evidence that ENSO indices could improve Grass-cast forecasts the both the spring and summer growing season. We find a positive relationship between Southwest ANPP and ENSOJFM (January to March) for the spring season (R2 > 0.3; p < 0.001) and a negative linear relationship between ANPP and ENSOMAM (March to May) for the summer season (R2 > 0.1; p < 0.05). The ongoing improvement and advancement of ecological models, such as Grass-Cast, can play a crucial role in promoting the conservation and sustainable use of natural resources in the Southwest.
  • Women Professionals of Color at U.S. Medical Schools Navigating Emotional Labor

    Rhoades, Gary; Givens, Raquel Hernandez; Nicolazzo, Z; Cabrera, Nolan (The University of Arizona., 2023)
    This dissertation presents an ethnographic exploration of the experiences of nontrans women professionals of color employed at U.S. medical schools, focusing on the intersectionality of gender and race and its influence on emotional labor. By conducting qualitative interviews, this research seeks to elucidate the multifaceted nature of emotional labor within the context of medical school environments and shed light on the participants' perceptions of their roles. The study's objective is to comprehend how the convergence of gender and race shapes the emotional labor of women professionals of color in medical schools, examining the intricacies of their experiences and the impact of these experiences on the broader mission of diversity, equity, and inclusion within these institutions. Thirteen women professionals of color were interviewed, encompassing various organizational positions and racial/ethnic backgrounds, to capture a range of perspectives. The findings underscore the integral role that emotional labor plays in the daily tasks and responsibilities of the women professionals interviewed. The participants' contributions to advancing diversity, equity, and inclusion initiatives within their respective medical schools were intricately intertwined with their emotional labor. Moreover, the data analysis revealed nuances that cut across both organizational positions and racial/ethnic identities, offering a deeper understanding of the distinct challenges faced by these professionals. A significant divergence was identified between groups with Black and Middle Eastern participants, as they reported experiencing racialized emotions in their roles. This aligns with existing scholarship on racialized emotions and supports the notion that the emotional labor of women professionals of color cannot be detached from the racial dynamics within medical institutions (Wingfield; Bonilla-Silva). Furthermore, the study illuminates the participants' agency in managing emotional labor. They exhibited self-awareness and adeptly performed their gender and race roles to navigate through the gendered and racialized landscape of medicine. Additionally, the importance of finding community emerged as a vital coping strategy, as these professionals leveraged collective support to overcome the challenges inherent in their roles. In summary, this ethnographic study contributes to the growing body of knowledge on emotional labor, gender, and race within organizational contexts, with a specific focus on U.S. medical schools. The findings emphasize the intricate interplay of emotional labor and diversity initiatives, while also highlighting the agency of nontrans women professionals of color as they negotiate their roles in a complex and dynamic environment.
  • Modulators of Neuroimmune Interactions Induced by Toxoplasma gondii

    Koshy, Anita A.; Merritt, Emily Frances; Goodrum, Felicia D.; Kuhns, Michael S.; Bhattacharya, Martha RC (The University of Arizona., 2023)
    Toxoplasma gondii is a common, intracellular parasite that establishes a long-terminfection in neurons in the central nervous system (CNS). Infections are often asymptomatic; however, in individuals lacking a T cell response Toxoplasma infection can lead to uncontrolled neuroinflammation, and potentially death. A long-standing question in the field is how Toxoplasma survives long term within the host. One hypothesis suggests that long term persistence is enabled by parasites residing in neurons because neurons do not have the same cell-intrinsic immune capabilities to clear parasites as non-neuronal cells (i.e., neurons are thought to lack major histocompatibility complex as an immune receptor to interact with T cells and are considered unable to respond to cytokine). Another hypothesis is that Toxoplasma modifies neurons to allow persistence by manipulating neurons through injection of Toxoplasma effector proteins, known as ROPs and GRAs, which are secreted into host cells during infection and can alter host cell signaling. Given we know Toxoplasma modifies many signaling pathways through these effector proteins, we set out to identify novel pathways that may aid in parasite persistence by transcriptionally profiling neurons that have been injected with Toxoplasma proteins. We infected Cre reporter mice, which only express a green fluorescent protein (GFP) after Cre mediated recombination, with Toxoplasma strains that have Cre recombinase fused to an effector protein that is secreted into host cells prior to invasion. Therefore, in the brain we can detect Toxoplasma injected neurons (TINs). Laser capture microdissection allowed us to isolate these injected neurons from an infected brain and perform transcriptional analysis to compare the transcripts of these injected neurons to neighboring neurons that have not interacted with parasites (Bystander neurons). Pathway analysis indicated a high level of T cell transcripts within the TINs transcriptome compared to the Bystander neurons transcriptome. Analysis of immunofluorescently stained infected brain sections was consistent with T cells being in closer proximity to TINs compared to Bystander neurons. This extreme proximity suggested potential MHCI-T cell receptor interactions. To test this idea, we infected primary neuronal cultures with parasites expressing the model antigen, OVA, and cocultured antigen specific T cells with these infected cultures. We found T cells could be activated by the infected neuronal cultures, indicating neurons are capable of presenting peptide on MHCI to T cells. To explore the ability of neurons to clear parasites (a possible outcome of T cell-neuron interactions), we infected Cre reporter mice with a strain of Toxoplasma that only triggers Cre mediated recombination in host cells after a successful invasion (GCre). We generated 200μm thick brain sections from these mice, optically cleared the sections using PACT clearing, and generated 3D reconstructions of the GFP+ neurons to determine if they actively harbor parasites. Approximately 50% of rendered neurons did not harbor parasites, indicating that neurons are capable of clearing Toxoplasma in vivo. Lastly, within this dissertation, I explored the importance of a specific effector protein, GRA15, and how it contributes to parasite persistence. Analysis of the peripheral immune response and parasite burden in the brain indicates that GRA15—an effector that causes polarization to classically activated macrophages—is does not significantly influence parasite dissemination and persistence. Overall, this dissertation uses Toxoplasma as a tool to investigate the immune capacity of neurons. We find that neurons can interact with T cells and possess competence at clearing Toxoplasma. Future directions include describing how utilizing tools I generated will allow others to determine how T cell recognition of and activation by antigen generated at different life-stages of Toxoplasma contributes to parasite clearance vs persistence.
  • Using Response Generation Behaviors to Improve the Quality of Survey Data

    Valacich, Joseph; Kumar, Manasvi; Jenkins, Jeffrey; Hashim, Matthew; Chen, Wei; Brandimarte, Laura (The University of Arizona., 2023)
    Despite their prevalent use, online surveys are vulnerable to data quality problems that may be attributed to several factors, including respondent induced measurement errors that cause discrepancies between respondent attributes and their responses. This research explores how a respondent’s response generation data manifests in their human computer interaction (HCI) device usage; and how these fine-grained HCI data may be used to identify poor-quality responses in online surveys. The larger goal of this research is to establish a structured set of guidelines to address the presence, impact, and appropriate mitigation for poor-quality survey responses. To this end, this dissertation provides a framework that utilizes individual characteristics, survey characteristics, as well as other external factors to determine one's response generation process and consequently the usefulness of that response.This dissertation establishes the prevalence of poor-quality responses in survey research and examines how behavioral differences between respondents exhibiting previously known undesirable behaviors may be used to detect poor-quality responses. ‘Essay One’ examines the presence of poor quality data among professional survey respondents and how HCI based behavioral data can be used to identify them. ‘Essay Two’ examines the same problem among another common participant pool, university students. ‘Essay Three’ alleviates typical Type I concerns in ‘Essay One’ and ‘Essay Two’ by examining whether specific undesirable behaviors exhibited by respondents while answering a question may be captured using appropriate metrics. The overall results obtained suggest that behavioral differences during the response generation process may be captured through HCI devices to create appropriate metrics that identify poor quality responses.
  • Machine Learning Application in Sleep Disorder Analysis

    Roveda, Janet M.; Huo, Jiayan; Kuo, Phillip H.; Li, Ao; Toosizadeh, Nima (The University of Arizona., 2023)
    Sleep is a natural state of reduced consciousness and physical activity that is crucial for the body’s circadian rhythm and various physiological processes. Sleep disordered breathing events, such as sleep apnea, can cause cortical arousal during sleep, leading to sleep cycle breaking and sleep fragmentation. Inadequate sleep can jeopardize the immune system and pose a significant risk to health and life. Sleep disordered breathing (SDB) screening and understanding the coupling between cortical arousal and health burden are critical for sleep and health monitoring. Machine learning can be compatible of recognizing patterns in complex data and prediction on future unseen data, which not only can reduce the intensive labor for manual processing but also uncover the new knowledge that people may have not been awareof. In this dissertation, we developed a six-item questionnaire for obstructive sleep apnea (OSA) screening tool using a large general population database - Sleep Heart Health Study(SHHS). Two independent logistic regressions underlie the algorithm of OSA binary prediction by considering two phenotype groups. We evaluated the tool on the SHHS test set (n = 1237) and an independent set Wisconsin Sleep Cohort (WSC) (n = 1120). The model outperformed these questionnaires on both test sets regarding the area under the receiver operating characteristic (AUROC) and the area under the precision-recall curve (AUPRC). The model achieved AUROC (SHHS 1: 0.78, WSC: 0.76) and AUPRC (SHHS 1: 0.72, WSC: 0.74), respectively. A multi-task deep learning algorithm was investigated based on previous study for cortical arousal detection and sleep staging using the single-lead Electrocardiogram (ECG). The model was developed on Multi-Ethnic Study of Atherosclerosis (MESA) dataset of which 1069 full night PSG were included in this study. We analyzed the fairness of the model by comparing the performance between subgroups with different demographics factors including gender, age and ethnicity. The model achieved an AUROC of 0.947 and AUPRC of 0.61 regarding the arousal detection, and Conhen’s κ of 0.68 and overall accuracy of 0.79 for four stage sleep prediction-light(N1/N2), deep(N3/N4), REM and wake. Though numerical differences regarding the aforementioned metrics were observed between different subgroups, the differences were not statistical significant. We also analyzed the intermediate channel outputs that shared by both tasks to explore the features that model have learned from raw ECGs. The results showed that intermediate channel outputs have a strong correlation with instantaneous heart rate on at least 80% of the subjects in testing set. More complicated HRV features were also investigated, though less portion of subjects showed strong correlations. Lastly, we studied the instantaneous association between cortical arousal onsets and heart rate variability (HRV) with the help of deep learning model among the general population. We compared the HRV changes pre-, intra- and post- arousal occurrence using a 25-second window. We also examined the cardiac response difference between different genders (male and female) and different sleep stages(REM or NREM). Significant variations were observed in heart rate and HRVs due to arousal onsets. Most importantly, female showed a more intensive cardiac response to the arousal onsets compared to male subjects which can potentially result in heavier heart burdens and long-term cardiovascular morbidity. More intensive variations caused by arousal were observed in REM, implying the instantaneous elevation of the sympathetic tome which may stress the cardiac function and cause sudden cardiac death.
  • A Synergistic Approach to Radiation Shielding Design Through Computation-Informed Selection of Additively Manufacturable Composite Materials and Shield Configurations

    Potter, Barrett G.; Baumann, Nicholas; Simmons-Potter, Kelly; Muralidharan, Krishna; Pearson, Charlotte (The University of Arizona., 2023)
    Ionizing radiation is the collection of particles including photons, electrons, protons, andneutrons which have sufficient kinetic energy to remove bound electrons from an atomic nucleus. Thus, radiation effects can play a significant role in degrading the resiliency of technologies for a variety of applications, including those central to nuclear energy production and space travel. Radiation in these environments can be both acutely and chronically harmful to both humans and electronic and optical systems, hence the need for appropriate design of radiation protection measures and radiation resistance or hardness. In general, the three tenets of radiation protection are time, distance, and shielding. For many of these cutting-edge applications like space colonization and nuclear power generation via fission and fusion, the time within the radiation environment cannot be reduced nor the distance from the source increased, leaving radiation shielding as the primary method of exposure mitigation. The present work details and demonstrates a synergistic approach to radiation shielding design and implementation, focusing on the computation-based design of additively manufacturable composite radiation shielding materials. Monte Carlo simulations explore the shielding design space and inform optimization algorithms. The materials selected for these simulations are additively manufacturable via fused deposition modeling (FDM) into homogeneous and layered composite structures, the performance of which has been experimentally validated. Four publications are provided in the work (Chapters 4 – 7 respectively), in which the principles of this design approach have been demonstrated to address a range of radiation environments and shield design classes. The works are each presented with an assessment of their 16 contextual rationale and, when appropriate, a summary of subsequent follow-on efforts to extend the results and impact obtained beyond that of the original works. The first publication explored the effect of Cu loading on the radiation shielding performance of additively manufacturable homogeneous particle-loaded composites against monochromatic gamma and electron irradiation using GEANT4 Monte Carlo radiation transport code. Experimental validation of the GEANT4 simulations was performed for FDM printed Culoaded, Fe-loaded, and BaSO4-loaded composites. For gamma radiation between 0.1 and 15 MeV, shielding performance was essentially independent of composition because of the similarity of the mass attenuation coefficients of copper and PLA in that energy range and because the shield thicknesses investigated were less than the gamma mean free paths at each energy for each material. In contrast, for monochromatic electron radiation, the optimum composition was found to be dependent on both energy and shield areal density. This dependence was determined to correspond to the continuous slowing down approximation (CSDA) range for electrons, with pure Cu being optimal when the shield areal density is less than the CSDA range, and PLA with <10 wt.% Cu being optimal when the areal density is greater than the CSDA range. The second publication presented a material replacement case study. The total ionizing dose (TID) transmissivity of additively manufacturable homogeneous Cu-PLA composites was compared against 1 g/cm2 of aluminum (a prototypical radiation shielding for CubeSats in low earth orbit (LEO)) in the LEO trapped electron radiation environment. An optimization algorithm identified the required composite thickness to match the TID transmissivity of 1 g/cm2 of aluminum for each composite composition (increments of 10 wt.% Cu) and monoenergetic electron energy (0.1, 0.2, 0.5, 1, 2, 5 and 10 MeV). For all compositions except for pure PLA (0 17 wt.% Cu), there was at least a 60% shield mass reduction while achieving the same TID performance as 1 g/cm2 of aluminum, when the average mass reduction weighted by the LEO spectrum was calculated. A 10 wt.% Cu-loaded PLA homogeneous composite provided the same shielding effectiveness as 1 g/cm2 of Al while being 65% lighter and 24% thinner. Further volume reduction with similar mass improvements were achievable with higher Cu loaded compositions. The third publication demonstrated a simulation-based investigation of sensitive parameters for two-phase, multilayered radiation shielding against gamma and electron radiation. Similar to results of the first publication, gamma shielding is generally insensitive to number of layers, layer ordering, high-Z layer fraction, mean composition, and areal density compared to homogeneous compositions in the 0.1 to 10 MeV energy range. Experimental irradiation using a 60Co radioisotope source confirmed the gamma performance of the homogeneous composites and lack of improvement or reduction in performance from a layered composite shield. The sparce experimental results were used to reconstruct the most probable true center location of the gamma source. These results were used to determine the intrinsic mass attenuation coefficients of homogeneous composites at a mean gamma energy of 1.25 MeV. For monoenergetic electron radiation, an additively manufacturable hierarchical composite radiation shield provided the best TID reduction; 50 – 66% more than a homogeneous composite shield of identical composition. The optimum structure consisted of two layers, a PLA layer facing the incident radiation and an 83 wt.% Cu-loaded PLA layer behind, the latter being 0.3 of the entire shield thickness, resulting in a mean composition of 50 wt.% Cu. An areal density greater than or equal to 3x the CSDA range at the incident electron energy was required to observe significant performance enhancement with layered shielding. 18 The fourth and final publication was a culmination of all previous publications. It centered on simulation-based design of additively manufacturable radiation shielding consisting of 10 equal areal density layers of three possible materials, PLA, B4C-PLA, and CuPLA, for the deuteriumtritium fusion neutron (14 MeV) environment. An initial random search of the layer ordering– composition parameter space led to the selection of a compositional family with low yet largely varying TID transmissivity, depending on configuration. The TID transmissivity for every shield configuration within the compositional family consisting of 6 layers of PLA, 2 layers of B4C-PLA, and 2 layers of CuPLA (77.4 wt.% PLA, 16.6 wt.% Cu, and 6.0 wt.% B4C) was measured via simulation. A novel design parameter, Z-Grading Degree (?), which expresses how monotonically increasing (+) or decreasing (–) a shield configuration is, was found to correlate negatively with dose transmissivity. Further, position of the rear-most B4C-PLA layer was found to strongly correlate (in the negative sense) with dose transmissivity, i.e., the further back the B4C-PLA layer was within the shield, the more effective the shield was at reducing the transmitted total ionizing dose from 14 MeV neutron irradiation. These findings were confirmed with experimental irradiation testing using an uncollimated deuterium-tritium fusion neutron source. Anisotropies in the neutron flux data were used to confirm the spatial extent of the source and allowed for a novel reconstruction of its most probable true center location.
  • Coupling Data Science and Design Science to Solve Real-World Business and Healthcare Challenges

    Ram, Sudha; Li, Yuanxia; Brown, Susan; Leroy, Gondy (The University of Arizona., 2023)
    Big and heterogeneous data that have become increasingly available provide precious opportunities for addressing real-world challenges. Nevertheless, the 3Vs (volume, velocity and variety) of big data have created computational challenges. In addition, because big data are often not collected for the purpose of research, careful repurposing is needed in harnessing the power of data. Data science has provided powerful tools to address the 3Vs of big data, while design science offers a paradigm that guide the effective usage of tools and the repurpose of data. In this dissertation, three essays are included to demonstrate how data science and design science may be coupled to address real-world business and healthcare challenges. In the first essay, a theory-enhanced hierarchical neural network model with correction is proposed to provide fine-grained classification of social media users. The artifact is an important tool that helps the repurposing of social media data and is itself a demonstration of coupling data science tools (e.g., machine learning) with design science (e.g., theory-guided design). The second essay integrates and repurposes heterogenous data sources from the contact tracing process to evaluate multi-method contact tracing. It is another manifestation of using careful design with the help of analytical tools to obtain insights from data. The third essay investigates the use of theoretical lenses in startup success prediction. Specifically, the effect of social capital theory and knowledge spillover theory is experimented. It demonstrates how theories can guide the design choices and enhance predictive modeling that used to be data-centric. This dissertation has demonstrated how data science and design science can be integrated to address real-world business and healthcare challenges. It has great relevance to both the data science and designs science communities, and the artifacts and insights created also have great implications to researchers and practitioners in the field of social media analytics, contact tracing, and startup evaluating and investing.
  • Precision Identification and Targeting of Rod Microglia in Diffuse Brain-Injured Cortex

    Lifshitz, Jonathan; Giordano, Katherine R.; Stabenfeldt, Sarah; Morrison, Helena; Anderson, Trent; Van Keuren-Jensen, Kendall; Mastroeni, Diego (The University of Arizona., 2023)
    Diffuse traumatic brain injury (TBI) leads to complex pathophysiological processes that result in clinical symptoms. Neuroinflammation and associated microglia activation are hallmark pathophysiological processes of diffuse TBI and contribute significantly to both damage and ensuing repair. Microglia are the resident innate immune cells in the brain and microglia function is linked to cellular morphology. Inflammatory signaling after diffuse TBI initiates microglia activation where microglia go from a ramified morphology (small soma with long, highly branched processes) to an activated morphology (swollen soma with enlarged, retracted processes). We also report an abundance of rod microglia (elongated soma with polarized processes) in the cortex after diffuse TBI. Rod microglia were first described in the early 1900’s and have since been sporadically reported in neurological conditions such as chemical exposure, viral infection, Alzheimer’s disease, Lewy Body dementia, ischemia, and TBI. Despite their occurrence across injury and disease, very little is known about rod microglia. Investigations have been limited to post-mortem histology using general microglia markers. The objective of this dissertation was to identify markers and develop tools to differentiate rod microglia from other microglia morphologies and confirm rod microglia mechanisms after TBI with the central hypothesis that rod microglia have a unique molecular profile compared to other microglia morphologies. First, we applied phage display biopanning to isolate antigen-binding domains specific to rod microglia compared to other microglia morphologies. We modified a novel discovery pipeline to develop antibody-mimetics from antigen-binding domains that can be validated for rod microglia specificity and used for downstream applications such as immunohistochemistry. Next, we investigated gene expression of rod microglia pathology with single nucleus RNA sequencing to provide insight into rod microglia function. We identified three distinct subclusters of microglia within the somatosensory cortex and inferred that those with inflammatory and neurological disease pathways may represent rod microglia. Finally, we used diffusion magnetic resonance imaging (MRI) to refine a non-invasive imaging signature of rod microglia. Water restriction was visible by diffusion MRI in the somatosensory cortex and corresponding histology reported activated microglia in regions where water restriction was observed. While not a marker of rod microglia specifically, novel post-image processing was sensitive to detect changes in microglia. This dissertation is the first step in developing and validating tools to target rod microglia. Until rod microglia mechanisms can be investigated with new tools, their role in the evolution, progression, and resolution of diffuse TBI pathophysiology remains unknown.
  • Ecosystem Services on Shrub-Encroached Rangelands: Balancing Supply and Demand

    Archer, Steven R.; Jones, Scott Andrew; Fisher, Larry A.; Marsh, Stuart E.; Guertin, David P. (The University of Arizona., 2023)
    The encroachment of woody plants into grasslands and savannas has been a phenomenon widely reported across both the Southwestern US and globally. Once established, woody plants may be long-lived and highly persistent creating numerous challenges for resource managers. The upper limits of shrub cover are regionally dictated by mean annual precipitation, but topoedaphic features play a key role in determining these limits, which can vary widely at the local level. Grasslands and savannas are of high value to socioecological systems due to the diverse portfolio of ecosystem services they provide. However, the transition to shrublands and woodlands can alter both processes and functions ultimately disrupting the availability of these services. Although there is a significant body of research on woody plant encroachment, little is known about the upper limits of shrub cover for a given topoedaphic setting or how this conversion has altered important ecosystem services. Improving our understanding of these topics can enhance management of these systems and is therefore of broad geographic interest. The overarching goal of this dissertation was to explore the woody plant encroachment phenomenon through a holistic lens evaluating both the physical and social impacts of this landscape wide cover change. Within the following manuscript I will present research on the underlying topoedaphic drivers dictating rates and patterns of encroachment at the local level, the long term impacts of encroachment on key ecosystem services, as well as the social perceptions on which ecosystem services are valued highest across these systems. The first study used high spatial resolution imagery to classify cover of a model shrub (Prosopis velutina, velvet mesquite) proliferating in a Sonoran Desert grassland. The analysis also explored how the upper limits of shrub cover varies across ecological sites and topoedaphic settings. Upper limits were found to have a wide range variously dictated by elevation, slope inclination/aspect, soil texture, and rainfall re-distribution. Furthermore, this variation was not equal across ecological sites, especially between lowland and upland sites. For the second project I conducted a case study in southern Arizona and New Mexico to evaluate stakeholder perceptions of and preferences for various ecosystem services provided on semi-arid rangelands where shrub proliferation has impacted traditional livestock grazing. Perceptions of rangeland ecosystem services were elicited via a visually-based landscape interpretation while preferences were quantified using Best-Worst Scaling (BWS). Results suggest that stakeholders familiar with rangelands and their management generally perceive low shrub cover as providing a wider range of valued ecosystem services compared to rangelands with high shrub cover. Contrary to expectations, ecosystem service preferences in the context of shrub encroachment were generally uniform across all stakeholder groups surveyed (e.g. ranchers, state/federal governmental employees, non-governmental land managers, academicians, recreationists), with habitat for biodiversity and erosion control being identified as the most preferred. The third study built on the above case study by spatially modeling changes to the two highest valued ecosystem services (habitat for biodiversity and erosion control) following documented shrub encroachment across a semi-arid grassland in southern Arizona from 1936-2017. While overall shrub cover change was found to be low over this time (~5%) it was highly variable across the landscape. Changes to ecosystem services were also found to have high spatial variability with some services being increased in concert with encroachment while others were negatively impacted. Understanding where and to what extent these services have been altered will help improve planning efforts with respect to the location, type (e.g., prescribed fire), and timing of brush management.
  • Documenting Reawakening Languages: A Case Study of Tunica

    Henderson, Robert; Harvey, Megan Anna; Zepeda, Ofelia; de Lima Silva, Wilson (The University of Arizona., 2023)
    As more communities work to create new speakers of their languages we are seeing a new linguistic environment develop and, from that, particular styles of language use emerge. This dissertation adds to the growing literature on studying and supporting the process of language revitalization (e.g. Stebbins et al. 2017, Zuckerman 2021), by describing the process of documenting and analyzing Tunica (tun ISO 639-3), a reawakening language spoken in central Louisiana, USA. ‘Reawakening languages’ are languages whose usual transmission has been interrupted and the community is looking to learn them through existing documentation, meaning looking at their revitalization process has the potential to be both incredibly illuminating and in- credibly disruptive to language learners and language workers. With these concerns in mind, this dissertation presents a method for documenting languages as they are being revitalized that minimizes disruption and maximizes support by centering the documentation around language revitalization activities and output. The first chapter introduces key terms and situates current research in language revitalization. Chapter 2 provides background on Tunica, the revitalization efforts in the community, and the language structure. Chapter 3 provides general recommendations for documenting the process of languages being reclaimed and reawakened. Chapters 4 and 5 focus specifically on documenting Tunica, with Chapter 4 describing the process of documenting Tunica in the classroom, through the creation of podcasts, and with more traditional elicitation. Chapter 5 turns to the types of questions we can look at using documentation of reawakening languages by considering trends in three morphological and syntactic phenomena in the language: the use of gender-number-agreement clitics, the use of overt subjects, and the structure of questions. Chapter 6 ties this all together and looks towards future projects.
  • Metamorphism in IOCG Systems: Contact Metamorphism in the Candelaria-Punta del Cobre District, Chile

    Barton, Mark D.; Huggler, Sadie Meradyth Del; Rezeau, Herve; Mazdab, Frank (The University of Arizona., 2023)
    Near Copiapó, Chile, volcanic-dominated rocks of the Early Cretaceous Punta del Cobre Formation host Fe-oxide(-Cu-Au) (“IOCG”) mineralization with varied development of metamorphic mineral assemblages. Western occurrences, such as the Candelaria deposit, lie within the metamorphic aureole of the composite Copiapó batholith (110-120 Ma), while other, more easterly deposits in the district lack evidence of high-grade metamorphism. This allows comparison of features seen at Candelaria, but not at the other deposits, that may have resulted from contact metamorphism. Petrography and scanning electron microscopy of Candelaria samples reveal early penetrative, planar fabrics overprinted by texturally and mineralogically recrystallized assemblages. High-temperature metamorphism of iron-enriched protoliths led to the development of biotite, garnet, (Mg,Fe,Mn) amphiboles, and cordierite-bearing assemblages in the Punta del Cobre formation. Metamorphic silicates overgrowing and crosscutting deformed, recrystallized ore minerals suggests that shear-zone deformation and contact metamorphism occurred during and after mainstage Cu-sulfide and Fe-oxide deposition. Peak greenschist to amphibolite-facies contact metamorphism occurred at P<4 kbar and 730-815±50℃. New U-Pb geochronology of garnets spans 115.8±3.7 Ma to 87.5±3.7 Ma and broadly coincides with magmatism and later alteration in the district. The contact metamorphosed mineralization at Candelaria resembles nominally syn-metamorphic mineralization elsewhere in the world, supporting post-mineralization metamorphic interpretations at these other locations.
  • Methods for Simulating and Analyzing Quantum Turbulence of BECs in a Rotating Frame

    Anderson, Brian P.; Foshee, Daniel Kyle; Bradley, Ashton; Wright, Ewan M. (The University of Arizona., 2023)
    The relationships between turbulence and interesting fluid structures like those near the poles of Jupiter and Saturn are still an open research topic. A minimal model for understanding fundamental behaviors is desirable for isolating the relevant parameter space with predictive power. Minimal models in liquids inspire us to look for a more minimal model in 2D Bose-Einstein Condensates. We have created a framework for quickly simulating and analyzing 2D Bose-Einstein Condensates in a rotating reference frame to test a wide range of parameter space via the MATLAB parallel computing toolbox, the utilization of a graphics processing unit, and the high-powered computing cluster available to us through the University of Arizona. In the development of these methods, we find that our novel application of qualitative analysis shows evidence that differential rotation leads to the observation of counter-rotating eddies consistent with the development of characteristic structures from turbulent fluid flow. This work sets up a platform for researching quantum turbulence in 2D Bose-Einstein condensates evolving under differential rotation in a rotating frame and gives direction for research that may have connection to classical phenomena seen in the atmospheres of the gas giants of our solar system and in liquid models here on Earth.
  • The Estimation of High-contrast Spectra via Iterated Whitening

    Lin, Kevin K.; McBride, Jared Adam; Venkataramani, Shankar C.; Watkins, Joe (The University of Arizona., 2023)
    Power spectra are a fundamental tool in data analysis, signal processing, and linear prediction and control. Many who seek to estimate power spectrum are obliged to do so with very little theoretical information of the underlying process and prefer accurate estimates which require as little effort as possible. This work focuses on estimation of the power spectrum of time series data from dynamical systems and stochastic differential equations (SDEs) and attempts to satisfy the preferences above. The method, called iterated whitening (IW) spectral estimation, iteratively builds inexpensive filters that progressively ameliorate the data until the resulting modified data is suitable for accurate spectral estimation. This spectral estimate is then post-processed to return an accurate estimate of the original data. Time series from dynamical systems and SDEs often possess a very large dynamic spectral range which makes them difficult to estimate cheaply and accurately. IW provides a solution to this difficulty. In this dissertation, I discuss some of the issues that the Bartlett estimator has in approximating these ``high-contrast'' spectra by deriving expanded bias and variance formulas. I also showcase another technique for improving a spectral estimator using the method on control variates from Monte Carlo Markov chain theory. I apply these methods to some time series from a solution to the Kuramoto-Sivashinsky equation which is in spatiotemporal chaos.
  • Stress Analysis in Optical Systems

    Kupinski, Meredith K.; Parkinson, Jeremy Craig; Chalifoux, Brandon D.; Smith, Gregory A. (The University of Arizona., 2023)
    Structural failures can occur when loading conditions cause stress and strain within a material that exceeds the ultimate strength. Similarly, the performance of an optical system can be adversely affected by poorly characterized loading conditions and the resulting stress fields. Rigorous stress analysis is crucial to ensuring a specified performance can be achieved under varying environmental conditions. This work presents stress measurements and analysis for two projects: i) measurement of the stress-optic coefficient of N-Bk7, a glass commonly used for optical components, and ii) a payload design for a high-altitude ($\approx$ 30 [km]) balloon deployment of an Infrared Channeled Spectro-Polarimeter (IRCSP). The N-Bk7 stress analysis is functionally based on the relationship between stress and measured polarimetric response. Stress in optical systems induces birefringence, where the index of refraction is dependent on the polarization of the incident light. Measuring the retardance of a material can therefore help determine how the stress is affecting the index of refraction of the material. This effect is quantified by the stress optic coefficient. For this work, a Rotating Retarder Mueller Matrix Imaging Polarimeter (RRMIP) was used to measure the linear retardance of a diametrically loaded sample of N-Bk7 at a wavelength of 1550 [nm]. These retardance measurements were used to compute the N-Bk7 stress optic coefficient as compared to industry-reported values. Prior to the 2021 deployment of IRCSP on a high-altitude balloon, a fully autonomous system was developed to control the image acquisition, focal plane temperature, and humidity of the instrument. Operating this optical system at high altitudes required analysis of the varying environmental conditions to design an instrument enclosure that met both optical and safety specifications. Finite Element Analysis (FEA) was used to show efficacy of the mechanical design under expected flight loads to earn flight approval from Columbia Scientific Balloon Facility (CSBF). This enclosure has been apart of three successful balloon deployments of IRCSP. Additional work to design the electronics for a PID-controlled thermo-electric cooler in also included.
  • Detection and Isolation of Salivary Biomarkers Using a Novel Hybrid Size Exclusion - Immobilized Metal Affinity Chromatography Matrix

    Guzman, Roberto; Rodriguez, Christopher; Savagatrup, Suchol; Saez, Eduardo (The University of Arizona., 2023)
    Biomarkers are a vital tool used in the diagnosis of multiple different diseases, from the presence of creatine kinase in blood indicating muscle damage, to the presence of glucose in urine signaling high blood sugar and possibly diabetes. One major limitation for biomarkers comes in the difficulty of isolating them from biological fluids (such as blood, urine, saliva, etc.). Another big problem is that biomarkers are usually found in low concentrations together with large amounts of proteins that makes the isolation of target biomarkers quite difficult. Isolating a desired biomarker from a patient sample requires multiple steps and these steps can vary depending on the bodily fluid being sampled.This work deals with novel separations of small molecular size compounds from large molecules. This technology combines, in the same separation medium, the characteristics and advantages of size exclusion and affinity adsorptive protein separations methods. The novel features involve the covalent attachment of permeation polymers to a matrix so that after modification preferentially "rejects" biomolecules of a certain size (large proteins, for example), and allows only compounds of appropriate size (small biomarkers, for example) to penetrate the "rejection" zone, thus allowing them to interact with affinity groups previously attached on the surface of the matrix. The main objective of this work was to develop a method to isolate specific biomarkers directly from saliva, a quite relevant biological fluid. The hybrid chromatographic matrix in this case consisted of size exclusion chromatographic matrices functionalized with specific affinity ligands (Iminodiacetic acid (IDA) and Dipicolylamine (DPA) as chelators) and polymers (polyethylene glycol, PEG). In this approach, PEG acts as a blocking polymer that acts as a permeating barrier that allows only small proteins to permeate and interact with the chelator on the surface, larger proteins cannot penetrate permeating barrier. The method was used to isolate the small biomarkers, creatinine, spermine, choline and isethionate and the small protein myoglobin from synthetic saliva preparations. Myoglobin has been linked as a salivary biomarker for myocardial necrosis, creatinine has been linked to chronic kidney disease and spermine, choline and isethionate have been shown to be promising salivary biomarkers for breast cancer. The novel approach was effective at isolating and almost completely recovering most of the target biomarkers from the other components of the synthetic saliva used in the research.
  • Investigation of the Electronic Structure of 2D Materials Using X-Ray and UV Photoemission Techniques

    Monti, Oliver; Zachritz, Sara; Schwartz, Steven; Huxter, Vanessa; Bredas, Jean-Luc (The University of Arizona., 2023)
    The limitations of current day electronics have created a tremendous drive to find new materials for more advanced electronic devices. However, without a fundamental understanding of key interfacial processes, such as electron transfer or charge carrier dynamics, developing practical devices becomes an impossible task. It therefore is of vital importance to comprehend the fundamental physics that governs these interfacial processes to fulfill the practical need for more advanced electronic devices. In this dissertation, I mainly focus on the class of inorganic 2D materials called transition metal dichalcogenides that present a wide range of electronic properties based on their composition. I begin by exploring the ultrafast charge carrier dynamics at the interface between an organic and inorganic semiconductor (C60/WSe2). The interfacial charge transfer, which results in an interfacial electric field, reveals new opportunities to control the different spin degrees of freedom inherent to the inorganic semiconductor (WSe2) and provides a novel mechanism to create spin-polarization in a nonmagnetic heterostructure. Next, I investigate the temperature-induced electronic phase transition between the semimetallic 1T’-phase of MoTe2 and the topological Weyl semimetal Td-MoTe2. The platform provided by this phase transition constitutes a new opportunity for systematic control of the electronic structure. As a result of the more exotic electronic properties of Td-MoTe2, new scattering pathways are available and I demonstrate how the electronic structure influences the ultrafast charge-carrier dynamics in the two phases. Finally, I demonstrate the importance of the electronic structure and its influence on the luminescent properties of two types of lanthanide-doped metalorganic complexes. The energy level alignment between the ligands and the rare earth centers in the complexes determines not only the efficiency of the material’s luminescent capabilities but also its influence on the emissive color properties. Overall, the case studies presented in this dissertation highlight how the electronic structure governs the ultrafast charge carrier dynamics and electron transfer properties, presenting new opportunities towards advanced electronic devices.
  • Improving PL Approximations of Harmonic Maps and a Penalty-Function Approach to Harmonic Maps

    Glickenstein, David; Banks, Robert; Venkataramani, Shankar C.; Sethuraman, Sunder; Izosimov, Anton (The University of Arizona., 2023)
    In this dissertation, we consider two problems in the approximation of harmonic maps between empirically-known manifolds embedded in Euclidean spaces. First, we suppose that the domain manifold $\mathcal{M}$ is known by a point cloud $M_s$ and that $M_s$ has been used to reconstruct a $PL$ surface $\tau$ approximating $\mathcal{M}$. Then, assuming that we have a $PL$ map $f^\tau: \tau\to \mathbb{R}^k_\mathcal{N}$ that approximates a harmonic map $\mathcal{M}\to \mathcal{N}$, we ask how we can improve the approximation by using finer triangulations. In particular, we ask where we should add a single vertex to the domain triangulation $\tau$ given a single added vertex in the image triangulation $\mathscr{T}=f^\tau(\tau)$. We prove that a unique optimal solution exists when $\mathcal{M}\subset\mathbb{R}^2$. We find this optimal solution explicitly for several special cases and constrain it in general via an inverse problem. We then consider the problem of how to approximate a harmonic map $\mathcal{M}\to \mathcal{N}$ when the target manifold $\mathcal{N}\subset \mathbb{R}^k$ is known only by the point cloud $N_t$. We explicitly construct a $\mathscr{C}^1$ penalty functional $\mathscr{P}_t$ which is determined by $N_t$ and such that, if $f: \mathcal{M}\to \mathbb{R}^k$ and $f(\mathcal{M})$ is near $\mathcal{N}$, then $\mathscr{P}_t(f)$ is small. We then investigate how approximate harmonic maps can be found by locally minimizing functionals of the form $\mathscr{G}_t(\lambda, f)=\mathscr{E}(f)+\lambda\mathscr{P}_t(f)$ where $\mathscr{E}$ is the Dirichlet energy and $\lambda$ is a positive parameter. This work provides a foundation for extending the methods of \cite{ChenStruwe1989} to sampled manifolds.

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