The graduate and undergraduate research collections share, archive and preserve research from University of Arizona students. Collections include honors theses, master's theses, and dissertations, in addition to capstone and other specialized research and presentation topics.


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  • Characterizing Large-Scale Resting State Effective Connectivity Patterns with Functionally Constrained Priors in Individuals with a History of Major Depressive Disorder

    Allen, John J.A.; Ding, Yaohui; Chen, Nan-kuei N.C.; Andrews-Hanna, Jessica J.A.; Wilson, Robert R.W. (The University of Arizona., 2021)
    Major depressive disorder (MDD) is a common mental health condition (Kessler & Bromet, 2013) and the 3rd leading cause of disability worldwide (James et al., 2018). MDD history is a significant risk factor for relapse and recurrence of depression (Buckman et al., 2018; Burcusa & Iacono, 2007). The current study investigated resting state effective connectivity among 13 brain regions from three resting state networks (i.e., default, salience, and central executive), which had been implicated in the pathophysiology of MDD from previous studies (Kaiser et al., 2015; Mulders et al., 2015). In the current study, both within- and between-networks effective connectivity were found to be different in those with a MDD history (N=29) compared to the healthy controls (N=28), through spectral dynamic causal modeling (Friston, Kahan, Biswal, et al., 2014), Bayesian model reduction (Friston et al., 2016), and parametric empirical Bayes (Zeidman, Jafarian, Seghier, et al., 2019) analyses. Of particular interest is the finding that there is more negative effective connectivity from right anterior insula to left dorsolateral prefrontal cortex and left inferior parietal lobe in MDD history. Previous studies have found less causal influence from anterior insula to prefrontal cortex in currently depressed individuals (Hyett et al., 2015; Iwabuchi et al., 2014; Kandilarova et al., 2018). Given the importance of anterior insular in interoception and subjective feelings (Craig & Craig, 2009), the current study provides some preliminary evidence that altered effective connectivity between anterior insula and prefrontal cortex may be related to MDD history as well.
  • Trapping Sets of Iterative Decoders for Quantum and Classical Low-Density Parity-Check Codes

    Vasic, Bane; Guha, Saikat; Raveendran, Nithin; Lazos, Loukas; Tandon, Ravi; Lux, Klaus (The University of Arizona., 2021)
    Protecting logical information in the form of a classical bit or a quantum bit (qubit) is an essential step in ensuring fault-tolerant classical or quantum computation. Error correction codes and their decoders perform this step by adding redundant information that aids the decoder to recover or protect the logical information even in the presence of noise. Low-density parity-check (LDPC) codes have been one of the most popular error correction candidates in modern communication and data storage systems. Similarly, their quantum analogues, quantum LDPC codes are being actively pursued as excellent prospects for error correction in future fault-tolerant quantum systems due to their asymptotically non-zero rates, sparse parity check matrices, and efficient iterative decoding algorithms. This dissertation deals with failure configurations, known as \emph{trapping sets} of classical and quantum LDPC codes when decoded with iterative message passing decoding algorithms, and the \emph{error floor phenomenon} - the degradation of logical error rate performance at low physical noise regime. The study of quantum trapping sets will enable the construction of better quantum LDPC codes and also help in modifying iterative quantum decoders to achieve higher fault-tolerant thresholds and lower error floors. Towards this goal, the dissertation also presents iterative decoders for classical and quantum LDPC codes using the \emph{deep neural network framework}, novel iterative decoding algorithms, and a decoder-aware \emph{expansion-contraction method} for error floor estimation. In this dissertation, we first establish a systematic methodology by which one can identify and classify \emph{quantum trapping sets} (QTSs) according to their topological structure and decoder used. For this purpose, we leverage the known harmful configurations in the Tanner graph, called \emph{trapping sets} (TSs), from the classical error correction world. The conventional definition of a trapping set of classical LDPC codes is generalized to address the syndrome decoding scenario for quantum LDPC codes. Furthermore, we show that the knowledge of QTSs can be used to design better quantum LDPC codes and decoders. In the context of the development of novel decoders, we extend the stochastic resonance based decoders to quantum LDPC codes, propose iteration-varying message passing decoders with their message update rules learned by neural networks tuned for low logical error rate, and present a syndrome based generalized belief propagation algorithm for tackling convergence failure of iterative decoders due to the presence of short cycles. Our analysis of TSs of a layered decoding architecture clearly reveals the dependence of the harmfulness of TSs (classical or quantum) on the iterative decoder, and thus on the error floor estimates. We present a computationally efficient method for estimating error floors of LDPC codes over the binary symmetric channel without any prior knowledge of its trapping sets. The sub-graph expansion-contraction method is a general procedure for TS characterization, which lists all harmful error patterns up to a given weight for the LDPC code and decoder. Based on this decoder-aware trapping set characterization for LDPC codes, we propose a model-driven deep neural network (DNN) framework that unfolds the decoding iterations, to design the \emph{decoder diversity of finite alphabet iterative decoders (FAIDs)}. Our decoder diversity DNN-FAID delivers excellent waterfall performance along with a low error floor.
  • Low-Cost Chromatic Confocal Endomicroscope for the Diagnosis of Cervical Precancer

    Kang, Dongkyun; Kulkarni, Nachiket; Gmitro, Arthur; Barton, Jennifer (The University of Arizona., 2021)
    Cervical cancer is one of the major cancers in women living in low- and middle-income countries (LMICs). The resources needed to conduct the gold standard histopathological diagnosis, such as a trained personnel and lab equipment, are scarce in LMICs. Hence, low-cost approaches such as visual inspection with acetic acid (VIA) are used to diagnose cervical cancer. VIA and other low-cost approaches, however, often lead to overdiagnosis and overtreatment of the patient due to their low specificity. There is an unmet need for a low-cost tool that can provide both high sensitivity and specificity.This dissertation discusses the design and development of a chromatic confocal endomicroscope (CCE) that can examine the cervical tissue in vivo with a goal of aiding the diagnosis of cervical malignancy. The novelty of this device is to use longitudinal chromatic aberration to acquire cross-sectional images of the tissue without any scanning mechanisms. A custom hyperchromatic objective lens was optimally designed to focus different wavelengths of the illumination light into different depths: 500-700 nm was focused over a depth range of 110 µm. Slit apertures were used for illumination and detection, which eliminated the need for beam scanning along the slit length direction and enabled cross-sectional, two-dimensional imaging without any mechanical scanners. A custom miniature spectrometer was used to analyze the spectrum of light scattered back from the tissue and generate confocal images. The manufactured CCE device had a small form factor with an overall device diameter and length of 9 mm and 70 mm, respectively. The material cost was less than $1,500. The measured lateral and axial resolution was 2 µm and 4 µm over an axial depth of 100 µm. The CCE device was able to visualize cellular structures of human tissue, in vivo at different axial depths. Cellular nuclei of the lower lip epithelium were clearly visualized from the CCE images, which might indicate that other epithelial tissues such as the cervical epithelium can also be visualized with CCE. This might merit clinical evaluation of CCE for the diagnosis of cervical malignancy.
  • Prospective Teachers’ Narrative Sense-Making of Equity

    Wood, Marcy B.; Neihaus, Aubrey; McGraw, Rebecca; Clift, Renee; Gunckel, Kristin (The University of Arizona., 2021)
    Equity has been a persistent focus of research in education and in particular teacher education. While numerous studies have investigated instructional interventions aimed at supporting teachers’ learning about equity, few studies have investigated teachers’ learning of equity. In this study, I used narrative inquiry as a lens through which to investigate how prospective elementary teachers make sense of equity. From eight participants’ stories, I developed ten categories of types of experiences that are drawn on in these equity narratives. I also documented eleven narrative techniques used in the stories that make equity sense-making visible. I delve into how two of these techniques (explicit re-narration and visual metaphors) make sense-making visible to researchers and teacher educators. These findings have implications for future research on teacher education research in equity as well as teacher education practice.
  • Examining Protective and At-Risk Factors on Children’s Social and Emotional Development and School Readiness

    Cimetta, Adriana D.; Medina, Margaret Ariana; Cheng, Katherine; Smith, Eric D. (The University of Arizona., 2021)
    Early childhood is critical for a child’s healthy development. Such development can affect children throughout the lifespan. In particular, social emotional development has been used as a predictor for school readiness, delinquency, career outcomes and earnings, and overall quality of life (Denham et al., 2009). This study examined the relationships of protective factors and at-risk factors on 3,988 children between the ages of two to six years on children’s social emotional development and if these variables are also predictive of a child’s social emotional development. Additionally, this study assessed if children’s social emotional development is predictive of children's literacy and math school readiness. This study intended to investigate a strength-based model by examining moderating effects of poverty on a child’s social emotional development in determining methods for assisting children living in poverty. Pearson’s R correlations and stepwise linear regression models were run. Results indicated that protective factors have statistically significant relationships and predict higher social emotional development scores and at-risk factors have statistically significant relationships and predict lower social emotional development scores. Lastly, implications, limitations, and future directions for research are also discussed.Keywords: social emotional development, school readiness, protective factors, at-risk factors
  • Elevated Fibroblast Growth Factor 23 Mediates Cardiac Fibrosis in the Setting of Chronic Kidney Disease

    Wilson, Jean M.; Crawford, Monique; Streicher, John; Runyan, Raymond (The University of Arizona., 2021)
    Background: CKD (chronic kidney disease) is a progressive disease with a global prevalence of 11-13% (Hill et al., 2016). CKD disrupts homeostasis resulting in large majority of patients with CKD also suffering from CVD (cardiovascular disease), with over 90% of CKD patients having cardiac fibrosis (Graham-Brown et al., 2017). FGF23, a phosphaturic hormone derived from bone, has been found to be elevated in patients with CKD and is associated with increased mortality in this patient population. Elevated serum FGF23 levels lead to LVH (left ventricular hypertrophy) and cardiac fibrosis, however, the mechanism by which fibrosis develops is unknown. We hypothesize that FGF23 mediates cardiac fibrosis by activation of the RAAS (renin-angiotensin-aldosterone-system), TGF-β (transforming growth factor-β), and wnt/β-catenin pathways in cardiac myocytes and fibroblasts. Methods:A literature review was conducted to identify the current literature on FGF23, CKD, cardiac fibrosis, RAAS, TGF-β, wnt/β-catenin and the molecular mechanisms leading to pathology. Search engines used were PubMed, Elsevier, NCBI (National Center for Biotechnology Information), University of Arizona Library, Google, and Wikipedia. Keywords included: CKD prevalence and mortality, bone and mineral metabolism, FGF23 mortality, angiotensin II (ANGII) and cardiac fibrosis, and phosphate homeostasis. Conclusion: In a series of steps, systemic FGF23 mediates cardiac fibrosis via non-conical signaling pathways by first activating the RAAS in cardiac myocytes. RAAS activation in cardiac myocytes increases ANGII expression. ANGII crosstalk with cardiac fibroblasts leads to activation of fibroblasts and TGF-β pathways. TGF-β and 5wnt3a/β-catenin in cardiac fibroblasts activate pro-fibrotic gene expression. TGFβ and wnt3a/β-catenin from cardiac fibroblasts crosstalk with cardiac myocytes to induce pro-fibrotic gene expression and augment RAAS signaling pathway, respectively.
  • Development of New Anionic Cascades and Analysis of US FDA Drug Architectures

    Njardarson, Jon T.; Delost, Michael D.; Wondrak, Georg; Hulme, Christopher; Sun, Daekyu; Jewett, John (The University of Arizona., 2021)
    This dissertation is divided into five chapters, encompassing innovative synthetic contributions in the area of Darzens annulations, anionic-amino-Cope cascades, structural analysis of FDA-approved pharmaceuticals as well as book chapter contributions in highlighting synthetic contributions in oxirane and aziridine chemistry. Chapter 1 presents two-book chapter contributions made which highlight synthetic contributions made with oxiranes and aziridines. Part 1: focuses on synthetic contributions made with oxiranes (epoxides) from 2008-2018. Part II focuses on homologation approaches to access oxiranes and aziridines from carbonyl and imines. Chapter II presents two-published perspectives, published in the Journal of Medical Chemistry. Part I analyzes oxygen-heterocycles seen in FDA-approved pharmaceuticals. Part II analyzes the structural diversity in FDA-approved combination drugs. Chapter III: presents novel contributions made in the arena of anionic-amino-Cope rearrangements (Part I) and applications (Part II). Chapter IV presents novel contributions made with vinylogous (Aza)-Darzens annulations. Part I discusses an asymmetric-vinylogous Aza-Darzens protocol with a bromo-butenolide nucleophile. Part II describes phenyl sulfone-containing vinylogous (Aza)-Darzens routes. Chapter V describe mild protocols to obtain trisubstituted trifluoromethylthiolated (SCF3) aziridines and cyclopropanes.
  • Re-membering Jalal Al-E Ahmad and His Intimate Circle: The Possibility of Rupture and Reinforcement in the Hegemonic Masculinity of the Pahlavi Era

    Darling, Linda; Ghoreishian, Ana; Darling, Linda; Ortiz, David; Pieper Mooney, Jadwiga; Talattof, Kamran (The University of Arizona., 2021)
    My research examines the impacts of Jalal Al-e Ahmad, Simin Daneshvar and a selection of theirintimate intellectual circle on the hegemonic masculinity of their era as it approached the “unthinkable” Iranian Revolution of 1979. Given that Al-e Ahmad became so profoundly influential as it relates to the emergence of the post-revolutionary Perso-Islamic identity, my dissertation focuses primarily on Al-e Ahmad’s life, letters and literary work. More specifically, I am interested in examining the gender practices among this selection of Pahlavi-era Iranian intellectuals in their personal lives and their literary works. Since the reconfiguration of gender practice is influenced by multiple actors in both state and civil society, my analysis utilizes a Gramscian framework of cultural change which carefully explores the significant role that intellectuals can play in the continuous renegotiations of gender practices. After establishing a working structure of Iranian hegemonic masculinity in the Pahlavi Era, Ioffer six areas of inquiry. Chapter 1 gives a brief overview of the 19th-20th century intellectuals in modern Iran and locates Al-e Ahmad in that context. Chapter 2 establishes the framework for hegemonic masculinity during the Pahlavi Era by examining the driving forces of Iran’s reconfigurations of hegemonic masculinity including the state and religious patriarchy as well as the Iranian women’s rights movement. Chapter 3 focuses on how Al-e Ahmad's relationship to Daneshvar challenged and reinforced hegemonic masculinity. Chapter 4 explores a selection of Al-e Ahmad’s short stories in the context of violence and injustice under religious and state patriarchy. Chapter 5 delves into Al-e Ahmad’s Westoxification as it relates to hegemonic masculinity and silence. Chapter 6 examines Al-e Ahmad, sex, sexuality and gendered renegotiations in the context of religiosity, secularism, and the unfulfilled rupture of sexual taboos. This research concludes by noting that while Al-e Ahmad and his intimate circle reinforced hegemonic masculinity, if we are to look at gendered performativity as something that needs repeated performance, these disruptions - however unintentional or fleeting - bring us one step closer toward a sustainable rupture of hegemonic masculinities.
  • The Wikipedia Global Consciousness Index: A Measurement of the Awareness and Meaning of the World-as-a-Whole

    Mitchneck, Beth; Jones, J.P.; Stieve, Thomas; Ortiz, David; Surdeanu, Mihai (The University of Arizona., 2021)
    To supplement current globalization indexes, I propose a new index, the Wikipedia Global Consciousness Index (WikiGCI). Available indexes that measure globalization rely on network definitions for their theoretical frameworks and count objects crossing borders. The WikiGCI, defined as a measure of awareness and meaning of the world-as-a-whole, is founded on Robertson’s (1992, 2009, 2011) suggestion of global consciousness. The first research objective is to construct the new index as an empirical assessment of global consciousness by applying the top 100 global articles as the empirical units. Global articles are the Wikipedia articles edited in the most countries, identified by geolocating the IP address edits. Furthermore, I discursively analyze how these Wikipedia articles express global consciousness by statements of global wholeness in their narratives. I also apply Steger and James’ (2013, 2019) analysis of global social meaning to the global articles to identify how editors express ideology, imaginaries, and categories of the being-in-the-world. The second research objective is to discursively analyze regional patterns in Wikipedia’s global and local articles. I performed a mixed method, multilingual discursive analysis to examine how four globalizing discourses (references to the countries in the world’s economic core, the use of English in citations, references to international media institutions, and the monetization of commodities) can distinguish place representations between two groups of articles. One group of articles edited only in Peru, Russia and the U.S. were local articles with local representations. The other group consisted of the global articles edited in those three countries as well as the rest of the world that contained the widest, shared representation of the world. This discourse analysis reveals that the representation of the world is not strictly determined by the core. While the socio-economic power in the core creates the globalizing discourses, non-core editors engage with the discourses to depict the world based on the socio-historic conditions of their countries.
  • College, Chronic Illness, and COVID-19: It’s Complicated

    Rhoades, Gary; Mohr, Whitney C.; Kraus, Amanda; Lee, Jenny (The University of Arizona., 2021)
    This dissertation explores literature related to disability, university communication, andinequality regimes to understand the conceptualization of the ideal college student and how COVID-19 disrupted and enforced the systemic ideals of who belongs at and in the rhetoric of institutions of higher education. This study investigated how university leadership, public briefings, and email communication during the COVID-19 era were (or were not) inclusive of students with chronic illness and/or immunodeficiencies. A qualitative case study and qualitative methodologies were used to explore the communication of one university to and about the chronically ill population for 1 year as it reacted and responded to the Coronavirus (COVID-19) pandemic. My analysis found that university leadership communicated in a way that excluded students with chronic illness from the college experience, and when this population was included, the rhetoric was problematic, blaming, and shaming. University communications, media, and marketing are focused on the “ideal” college student and the “ideal” college experience. Higher education institutions need to reconceptualize their perception of who and what is ideal. Inclusive communications and marketing are key in reflecting the college’s commitment to the chronically ill. It was through this dissertation, the related research and recommendations, and my own lived experiences that I began to reconceptualize the idea of being immunocompromised in college and begin to understand it as being immunocomplicated.
  • Maturing Engineered Heart Tissues for Titin-Based Disease Modeling

    Granzier, Hendrikus L.; Keschrumrus, Vic P.; Tardiff, Jil C.; Konhilas, John P.; Colson, Brett A. (The University of Arizona., 2021)
    Engineered heart tissues (EHTs) are three-dimensional, fibrin-based heart muscle constructs developed as an advanced disease modeling tool for therapeutic development and personalized medicine, but at a fraction of the time and cost of traditional animal models. EHT maturity can be evaluated by identifying the isoforms of titin, a giant filamentous protein that regulates sarcomere organization and provides passive stiffness to cardiomyocytes, and has been implicated in cardiomyopathies. For example, dilated cardiomyopathy (DCM) patients have been shown to undergo eccentric remodeling with a switch from a stiffer N2B isoform to a more compliant N2BA isoform. Current neonatal rat EHTs express immature titin isoform expression patterns and require additional maturation to improve clinical relevancy. This dissertation examines different approaches to maturing titin isoform expression in EHTs using angiotensin II and triiodothyronine supplementation, chronic electrical stimulation, and extracellular matrix (ECM) modifications. Angiotensin II supplementation at 20 µM significantly increased mature N2B titin isoform expression while triiodothyronine supplementation had no significant effect. Chronic electrical stimulation at 0.5 Hz significantly enhanced the force production, fractional shortening, and contraction velocity in EHTs. However, paced EHTs exhibited a negative force-frequency relationship indicating other factors like calcium handling should also be considered for maturation. Surprisingly only N2BA titin isoform expression was significantly increased in paced EHTs. Sarcomere width and ECM, myofiber, mitochondria, and void fractional area were also significantly increase in paced EHTs while significant reduction was observed in Z-disk width, sarcomere length, collagen fibril width, and cytoplasm, cardiomyocyte, and empty fractional area. Decreasing the fibrinogen concentration lowered the Young’s Modulus of the initial fibrin gel used for generating EHTs. This change in extracellular matrix stiffness enhanced contraction kinetics during development and significantly increased the mature N2B titin isoform expression. Finally, EHTs generated from human induced pluripotent stem cells differentiated into cardiomyocytes were examined for maturity level. Contraction kinetics reveal significantly lower values in comparison to neonatal rat EHTs and only fetal cardiac titin isoform was detected in titin analysis. Overall, these findings have only scratched the surface of the intricate overlap of biological, mechanical, and electrical cues necessary to fully mature EHTs.
  • Patterns of Parental Involvement and Influences on Elementary School Student STEM Efficacy and Interests

    Perfect, Michelle; Ochoa, Estrella; Silva Torres, Graciela E.; Vega, Desiree (The University of Arizona., 2021)
    Science, Technology, Engineering, and Math (STEM) is widely acknowledged as a critical component to a healthy economy and global competitiveness. In the last decade, researchers have stressed the need for the development and implementation of instructional components to effectively engage students in STEM learning as early as possible. Previous research has suggested that parental involvement can improve academic outcomes for students. The purpose of this study was to examine the potential connection between increased levels of parental involvement and increased student STEM efficacy. The study closely followed the Hoover-Dempsey Model of Parental Involvement Processes (Hoover- Dempsey et al., 2001) that indicated that parental involvement methods are the mechanisms through which parent-level factors including parental self-efficacy predict student academic outcomes including student self-efficacy. In addition, parental efficacy, and the effects of immersion classes on parental involvement were examined. After transforming the data to correct for parental involvement measures not being normally distributed, canonical correlation analysis revealed significant correlations between the variate for the four parental involvement variables and the variate for the three student efficacy variables when run as sets. Hayes Process Macro for SPSS (Hayes, 2018) found significant direct effects of parent efficacy on student efficacy in math, but not for student efficacy in science or technology/engineering. There were no significant mediational relationships between the variables, however parental efficacy was significantly related to the three parental involvement mediators: Encouragement, Instruction, and Modeling, and Reinforcement was significantly related to student efficacy for math. Based on the results, data support that parental involvement and parent efficacy does influence STEM efficacy among students enrolled in a middle class to affluent school district. Future research needs to examine additional aspects of the Hoover-Dempsey Model in the context of STEM outcomes including how student STEM efficacy translates into student achievement outcomes accounting for the sociocultural context such as nuances of SES, age, gender, disability, and race/ethnicity. Finally, strategies such as inclusive outreach programs and SES conscious engagement opportunities are discussed along with future research to test if those approaches are effective in facilitating the strengthening of STEM outcomes in American school students.
  • Monitoring and Assessment of Heat Stress and Heat Strain in Hot Arizona Mines

    Momayez, Moe M.; Cordova Rubina, Veronica Amanda; Lutz, Eric E.; Waqas, Muhammad M.; Lee, Jaeheon J.; Reed, Rustin R. (The University of Arizona., 2021)
    Occupational heat stress is one of the main causes of health-related risks in the mining industry. Heat stress can cause heat strokes, heat exhaustion, hyperthermia and sometimes even death. Therefore, the importance of monitoring heat stress and using cooling technologies in a mine is critical to mitigating these occupational health risks. Heat stress is conventionally monitored using stress indices. The estimation of stress indices requires measuring dynamically changing parameters, which imposes a challenge to monitoring stress. Core body temperature (CBT) has proven to be a relevant proxy for heat stress. However, measuring CBT is an invasive technique that may not always be feasible. In the first part of this study, we identify two easily and non-invasively measurable physiological parameters: heart rate (BPM) and urine-specific gravity (USG). Further, we relate these parameters to CBT. We also investigate the dependence of these parameters on miners' physiological parameters, such as use of energy drinks and the body mass indices (BMI). Our findings show a strong correlation between CBT and heart rate (Pearson Correlation >0.4), rendering the latter as a useful tool to monitor heat stress. The intake of energy drinks shows causation to increase dehydration (p value=0.049). Furthermore, in the second part of this study, we investigate how to reduce the risk of heat stress in mine operators. In order to evaluate limiting factors, we examine the amount of heat absorbed by hardhats of different colors, where our findings are that white hardhats are best at absorbing minimal energy (15F less than black hardhats). Additionally, we study the performance of three commercial cooling vests and a combination set (i.e., evaporative cooling cap and sleeves) in reducing perceptual heat strain (23% of improvement in Physical Strain Alleviation wearing evaporative vest). We find that the overall perceived heat stress index of mine operators is considerably less with cooling devices.
  • Molecular Phylogeny and Revision of Species Groups of Nearctic Bombardier Beetles (Carabidae: Brachininae: Brachinus)

    Moore, Wendy; Ikagawa, Raine; McMahon, Michelle; Bogan, Michael (The University of Arizona., 2021)
    Bombardier beetles of the genus Brachinus Weber are notorious for their explosive defensive chemistry; when threatened, they aim a 100°C cloud of benzoquinones directly at an enemy. Despite ongoing research on their defensive chemistry and ecology, the group lacks a robust molecular phylogeny. In this study, three loci from both the mitochondrial and nuclear genome (COI, CAD, 28S) were used to reconstruct the phylogeny of Nearctic Brachinus and to test hypothesized relationships based on a previous study based upon morphological characters (Erwin, 1970). All molecular phylogenetic analyses recovered all species groups proposed by Erwin as monophyletic except for the fumans species group. We find that Erwin’s fumans species group is polyphyletic. In its place, we erect the following five species groups: cinctipennis, fumans (revised), galactoderus, phaeocerus, and quadripennis. External morphological characters were traced on the molecular phylogeny to identify potential diagnostic characters. Apomorphic characters were identified for two new species groups, the fumans (revised) and phaeocerus groups. We also expand the cordicollis group to include B. medius and the americanus group.
  • Enhanced Delivery of Antibody Therapy Using Focused Ultrasound in a Mouse Model of Parkinson’s Disease

    Trouard, Theodore P.; Murphy, Devin Patrick; Chen, Nan-kuei; Hutchinson, Elizabeth B. (The University of Arizona., 2021)
    Parkinson’s Disease (PD) is the second-most prevalent neurodegenerative disorder after Alzheimer’s Disease and affects 680,000 US adults over the age of 45 as of 2010 [Marras et al. 2018]. This disease results in a loss of dopaminergic neurons, specifically in the substantia nigra. PD has also been associated with the accumulation of toxic oligomeric variants of alpha-synuclein (-syn). Although there are several medications that can help manage symptoms for PD, there is no cure. We have successfully created antibody reagents that selectively target toxic -syn variants without binding to non-oligomeric forms of normal alpha-synuclein. However, the blood-brain barrier (BBB) is a major obstacle for drug delivery and treatment of PD due to its low permeability to foreign objects. Due to the size of the monoclonal antibody, it is unable to cross the BBB without transporter proteins or temporary disruption of the BBB. This antibody therapy is delivered using novel magnetic resonance guided focused ultrasound (MRgFUS) treatment, which transiently disrupts tight junctions between epithelial cells in the BBB, resulting in gaps large enough for the antibody therapy to cross the BBB. Results indicate that the BBB was successfully opened over multiple timepoints, and the procedure does not cause extensive tissue damage. The results also show that the targeted antibody selectively binds to toxic -syn in regions of the brain where the BBB has been temporarily disrupted. Future work includes longitudinal studies to determine if this treatment combination can delay disease progression or improve quality of life in murine models of Parkinson’s Disease.
  • Toward Ameliorating Multiracial Experiences in Higher Education: Elevating Student Voices and Critiquing Multiracially-Exclusive Policy & Practice

    López, Francesca; Labistre Champion, Angela; Koyama, Jill; Henry, Kevin (The University of Arizona., 2021)
    Focus on multiracially-identified college students has continued to gain momentum in contemporary educational research, along with public and academic awareness of this burgeoning population—which has given needed voice to the unique and nuanced experiences and needs central to multiracial students’ lives. However, most recent scholarship has begun to more critically examine higher education institutions’ continued exclusion of multiracial students in various areas of policy and practice—much of which includes (but is not necessarily limited to) examination of student affairs organizations designed to support college students who hold minoritized racial/ethnic identities. Centering interviews with multiracial graduate and undergraduate students at Eastern University, Central Coast University, and Southwestern University and drawing from two critical multiracial frameworks (in particular, MultiCrit and the Contextualizing Multiraciality in Campus Climate Model (CMCC)), this study sought to not only examine and highlight multiracial exclusion in student affairs education, but also extend beyond that to include facets of higher education not widely encompassed in extant scholarship: curriculum and mentorship. Additional and equally important aims of this study included a comparative investigation of institutional policies and practices which contribute to the erasure of multiracial student identity (across the three different institutions), as well as exploration of emergent similarities in peer interactions and identity processes shared across multiracial college students’ experiences.
  • Characterization of U(-V) Deposits in the La Sal District, UT and CO and their Relationship to Paradox Basin Fluid Flow

    Barton, Mark D.; Bos Orent, Eytan; Barton, Isabel F.; Hughes, Amanda N.; Hall, Susan M. (The University of Arizona., 2021)
    The tabular sandstone-hosted uranium (U) and vanadium (V) deposits of the La Sal district form a 1-3 km wide, 30-km long belt spanning the Utah-Colorado border. They exemplify one of the principal types of U(-V) mineralization of the Paradox Basin and encompassing Colorado Plateau. Building on previous work, new field, petrographic and geochemical data provide the framework for an updated district synthesis of La Sal and its place in the broader geological context. Ore is hosted in the uppermost fluvial sandstones of the Salt Wash Member of the Jurassic Morrison Formation and forms elongate orebodies up to 180 m long, 90 m wide, and 1 m thick. Sparse organic material, mainly in the form of coalified plant fragments, is present in the sandstones which are interbedded with finer-grained silty, muddy and calcareous units. Principal changes in the rocks include bleaching by removal or reaction of early diagenetic hematite, a feature that is coextensive with quartz overgrowths . Later formed were compositionally distinct carbonate cements, and reaction of feldspars to kaolinitic clays. Bleaching was prior to or contemporaneous with (or both) mineralization, which is restricted to bleached rocks. Petrography shows that ore minerals (uraninite, coffinite, and montroseite) at least in part predate growth of authigenic quartz cements, and were in turn followed by the formation of V-rich sheet silicates (which may reflect reaction of montroseite with quartz and other minerals), carbonates, and clay cements. Depositional features control where mineral growth occurred and include sedimentary structures (e.g., crossbedding), primary porosity, and the distribution of lithofacies in trends like the La Sal channel system. The thin section to district-scale observations suggest that mineralization reflects mixing of two fluids, as has been suggested in other Plateau deposits, or, alternatively as a reaction of oxidized fluids with a preceding exogenous reduced component caused by bleaching. Increasing evidence in this area and elsewhere in the Paradox Basin suggests a complex fluid history including a major role for hydrocarbon-bearing fluids in bleaching and localization of metals beginning at least as early as the Late Triassic.
  • Consensus Control of Multi-Agent Rigid Body Systems using Rotation Matrices and Exponential Coordinates

    Butcher, Eric; Maadani, Mohammad; Enikov, Eniko; Reverdy, Paul; Tharp, Hal; Phillips, Sean (The University of Arizona., 2021)
    This dissertation addresses the 6-DOF consensus control problem of multi-agent rigid body systems. The consensus protocols are designed using two different attitude representations: rotation matrices and principal rotation vectors (exponential coordinates). The control objective is stabilizing the system of rigid bodies to a configuration where all the rigid bodies have a common attitude and prescribed relative positions with velocity synchronization. In this work, for the most part, a fixed and undirected communication topology is considered for the consensus control design and analysis. However, the stability of consensus in multi-agent systems with periodically switched communication topology is also studied using Floquet theory. In addition, the application of Floquet theory in analyzing cases such as switched systems with joint connectivity, unstable subsystems (antagonistic interactions), and nonlinear systems is also studied. As the first methodology for consensus control of multi-agent rigid body systems, the configurations of the rigid bodies are described in terms of the exponential coordinates associated with the Lie groups SO(3) and SE(3). Moreover, the stability of the consensus in multi-agent rigid body systems with periodically switched communication topology is studied using Floquet theory and linearizing the closed-loop systems. The second type of protocols for consensus control of a multi-agent system of $N$ heterogeneous rigid bodies are proposed in the framework of the tangent bundles TSO(3) and TSE(3) associated with Lie groups SO(3) and SE(3), respectively. The feedback control design uses the rotation matrix as opposed to various attitude parameterizations. Almost global asymptotic stability of the consensus subspace is demonstrated using an extension of the Morse-Lyapunov (M-L) approach. Also, the presence of unstable non-consensus equilibria in the closed-loop dynamics is discussed and shown in illustrative examples. A new strategy for full pose and velocity consensus control of multi-agent rigid body systems in the presence of communication delays is presented in this dissertation. Specifically, consensus protocols are proposed on the Banach manifold associated with the tangent bundle TSE(3)^N. The stability argument is strengthened from that used in prior studies by using an extension of Morse-Lyapunov-Krasovskii (M-L-K) approach, and sufficient conditions are derived to achieve almost global asymptotic stability of the consensus subspace. This work also investigates the finite-time pose consensus control of multi-agent rigid body systems using Morse-Lyapunov analysis in the framework of the tangent bundle TSE(3) associated with SE(3). Almost global finite-time stability of the consensus subspace in the nonlinear state space is demonstrated. As another finite-time consensus control problem, the prescribed-time consensus of multi-agent rigid body systems using exponential coordinates is also studied. Specifically, the control objective is to stabilize the relative pose configurations with velocity synchronization of a multi-agent rigid body system in a user-defined convergence time. In this dissertation, the consensus control of multi-agent rigid body spacecraft in orbital relative motion is explored using two approaches. In the first approach, a proportional-derivative (PD) consensus control method, an extension of the Morse-Lyapunov analysis in the framework of the tangent bundle TSE(3) associated with Lie group SE(3) is used. In the second approach, a proportional-integral-derivative (PID) consensus control protocol is introduced where the configurations of the rigid bodies are described in terms of the exponential coordinates associated with the Lie group SE(3). In general, the rigid-body attitude control problems are formulated in terms of full attitude configurations. However, in cases involving control objectives stated in terms of pointing the rigid body, reduced-attitude configurations defined in S^2 are exploited. In this dissertation, distributed control algorithms are proposed for asymptotically stable synchronization and balancing of a multi-agent rigid body reduced-attitude system using Lyapunov analysis. The control objective in the balancing problem is the maximization of the minimum relative angular distance between each pair of rigid body reduced attitudes.
  • Modeling and Emulation of Optical Networks for SDN Control

    Kilper, Daniel; Quraishy, Aamir Nasir; Pau, Stanley; Norwood, Robert; Fan, Linran (The University of Arizona., 2021)
    Today's telecommunications networks are facing increasing internet traffic demands for a variety of high data-rate applications including virtual reality (VR), video-conferencing, and high-definition (HD) video streaming. Optical networks are more efficient than wired and copper networks over long distances and high speeds, and thus have been a large contributor for increasing data capacities over the past several decades. Developments in optical fiber technologies have allowed optical networks to be manufactured at steadily lower cost per bit. However networks do not just need to handle larger traffic volumes, they also need to work with existing network architectures and accommodate traffic requests with different requirements. One method for addressing this challenge is Software Defined Networking (SDN). SDN separates the control and data-plane so the data management and control decisions are made by a central controller that direct information as need be. However, developing SDN systems for optical networks at scale is difficult because optical networks need to consider signal quality and nonlinear fiber impairment. Mininet-Optical is an optical network emulator designed to emulate a multi-layer optical network so network designers can develop SDN control algorithms. Mininet is an open-source tool for studying SDN but does not support optical networks. We developed an optical layer simulator that is integrated into Mininet Optical. We evaluated this approach using the open-source planning tool GNPy and showed strong agreement. We also developed an SDN control algorithm for provisioning optical networks with bandwidth variable transceivers (BVTs) and examined how the SDN controller responds to diurnal traffic. BVT technology has received attention from the SDN community because of its ability to change modulation formats to optimize network capacity and their performance depends on the quality of transmission. This adds an extra element of control that SDN controllers can use to respond to varying traffic conditions such as diurnal traffic patterns and respond to different traffic needs. In this thesis we discuss SDN control, BVTs, Diurnal traffic modeling, optical fiber transmission physics, and the mininet optical system. From this, we will examine SDN control for a network with BVTs handling requests from metro networks in residential and office areas with diurnal traffic. This work shows how BVTs operate in an SDN controlled network while responding to time-varying traffic, and show non-linear impairment induced switching for heavily-loaded traffic.
  • They See Me Different…Like an Immigrant Cause of How I Sound: Perceived Difference, Limitations, & Co-Naturalizations of Race and Language

    Lopez, Francesca A.; Richardson, Casey; Combs, Mary Carol; Koyama, Jill P.; Wildner Bassett, Mary (The University of Arizona., 2021)
    Latinx English language learners (ELLs) have long been the intended targets of U.S. language planning and policy efforts that seek to manage both the use of Spanish and its speakers. Since 2000, Arizona has adopted some of the most restrictive educational policies that shape the schooling of its ELLs (e.g., Proposition 203 and House Bill 2064). Like other bilingual education policies, Arizona’s frame Latinx ELLs as needing linguistic remediation in order for ELLs to develop proficiency in academic English for them to be successful in the modern, global economy (Flores, 2016). Yet academic/home language distinctions have been shown to position multilinguals’ language practices as deficient compared to an unmarked norm even when ELLs ostensibly model language practices that are validated when produced by non-racialized individuals (Flores & Rosa, 2015; Rosa, 2016). What is not well-known is if/how multilinguals reconstruct raciolinguistic ideologies. This descriptive qualitative study is guided by the research question: In what ways do Latinx multilingual students reproduce raciolinguistic ideologies? To better understand the pervasiveness of raciolinguistic ideologies, I interviewed ten Latinx multilinguals from two high schools in southern Arizona and thematically analyzed the data (Braun & Clarke, 2006). The findings showed Latinx multilingual students reproducing raciolinguistic ideologies, particularly in relation to co-naturalizations of race and language, perceived linguistic limitations, and raciolinguistic difference. These findings suggest that multilinguals sometimes adopt the stances of white perceiving subjects that re/construct multilingual language practices as inferior (Flores & Rosa, 2015; Inoue, 2003; Rosa & Flores, 2017), and deviating from an idealized monolingual norm (Flores, 2013). I conclude that there is a need for practitioners to advance efforts to dismantle raciolinguistic ideologies, and that the interventions most needed by multilinguals are ones that challenge the ubiquity of raciolinguistic ideologies and contribute to their denaturalization.

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