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  Quantum Network Protocols and Architectures

  Guha, Saikat; Patil, Ashlesha; Rengaswamy, Narayanan; Soh, Daniel; Gimeno-Segovia, Mercedes (The University of Arizona., 2025)

  Quantum networks promise to generate shared entanglement between distant users, which can support applications such as quantum key distribution, distributed quantum computing and distributed quantum sensing. A quantum network is made up of nodes known as quantum repeaters. A quantum repeater protects quantum information using error-corrected physical quantum memories or quantum error-correcting codes made up of photonic entangled states. This dissertation advances the state of the art for both varieties of quantum repeaters. It begins with an all-inclusive guidebook to the stabilizer formalism and linear optics---interspersed with new results and insights on graphical rules for arbitrary Clifford manipulations of stabilizer states---which is used extensively throughout the dissertation. In the first part of the dissertation, we present protocols for quantum-memory-based repeaters, the quantum logic and measurement capabilities of which govern the quantum operations performed at the repeater node. The two-qubit Bell state measurement (BSM) is the most commonly used operation by a quantum repeater to lengthen the reach of entanglement to more than one link connecting nearest network nodes. The entanglement generation rate of the protocols that utilize only BSMs decays exponentially with the distance between users. Our first protocol achieves an entanglement rate that does not scale with distance between end users. It uses multi-qubit joint projective measurements, such as projections onto maximally-entangled 3-qubit GHZ states. The second protocol we present performs BSMs and distills noisy Bell states using quantum error correcting codes, across optimized hop lengths, to generate entanglement along a repeater chain. We show that the choice of the code, and hence its distance properties and error correcting abilities, can enable trading between the entanglement rate versus the fidelity delivered to the end users.The second part of the dissertation investigates architectures for all-photonic quantum repeaters, which utilize a particular class of dual-rail photonic-qubit entangled states, known as the repeater graph state (RGS), as a quantum error correcting code to store quantum information. The RGS acts as a quantum memory by error correcting against photon loss on its locally-held photonic qubits (while photonic qubits entangled with the RGS fly to the neighboring nodes to seek nearest-neighbor entanglement). The same RGS also allows for multiplexed BSMs and GHZ projections only via single-qubit measurements on its photons, once the success-failure outcomes of the remote entanglement attempts to the neighboring nodes come back, using the principles of measurement based quantum computing. The quality of an RGS is therefore characterized by two factors: (1) the amount of error correction it can provide for a given RGS size, which translates into the end-to-end entanglement rate, and (2) the number of single photon sources required to prepare the RGS near-deterministically at every clock cycle, which turns into the major resource requirement for all-photonic repeaters. We dramatically improve both of the above by designing an RGS that achieves a higher entanglement rate compared with previously-known RGS geometries and associated protocols, but with fewer qubits in it, and can be prepared using fewer photon sources. By employing quantum emitters as single photon sources and allowing for simple quantum logic operations between emitters and photons that have been experimentally demonstrated, we devised three schemes to prepare photonic entangled states: (1) a linear-optics-based scheme that recycles graph states from failed fusion attempts, thereby reducing the number of quantum emitters needed by about a half, (2) a deterministic scheme using only a handful of emitters but with an increased qubit loss probability accrued in the generated photonic graph state, and (3) a hybrid scheme combining the benefits of the two schemes above. We evaluate the rate-vs.-distance performance of our all-photonic repeater protocol using our optimized emitter-based and the hybrid RGS-preparation schemes, and show orders of magnitude improvement in the number of emitters needed at each repeater node, compared with previously-known schemes.
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  Impact of Mindfulness Breathing Education on Nurses’ Stress in the Psychiatric Unit

  Velo, Jamie; Alpha, Augustine Joe; Velo, Jamie; Young, Janay; Bouchard, Lindsay (The University of Arizona., 2024)

  This Doctor of Nursing Practice (DNP) project aimed to train nurses and other healthcare professionals at the Tripler Army Medical Center (TAMC) psychiatric inpatient unit in mindfulness-based breathing techniques via brief educational intervention. The goal of the project was to enhance stress management and increase their intention to continue using the method in the future.This quality improvement project, employed a descriptive study design. Participation was voluntary, with nurses and healthcare workers providing informed consent. Data was collected through pretest and posttest surveys administered via Qualtrics software, which was also used for analysis. A total of 23 participants completed the pretest, and 26 completed the posttest survey. The results revealed a significant shift in participants' attitudes toward mindfulness-based interventions. Participants demonstrated a heightened interest in and willingness to engage in mindfulness practices, indicating a growing awareness of the benefits of these techniques in managing stress and promoting well-being among healthcare professionals. This positive shift in attitude highlighted an evolving perception of mindfulness programs within the healthcare community.
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  AI-Powered Portable Optical Biosensors for Environmental Toxicants and Biomarkers

  Yoon, Jeong-Yeol; Tang, Yisha; Witte, Russell; Reynolds, Kelly; Kim, Minkyu (The University of Arizona., 2025)

  Detecting environmental toxicants and biomarkers is vital for protecting ecosystems and public health, yet current methods often lack portability, speed, and precision for field and point- of-care applications. AI-powered portable optical biosensors address these challenges by combining molecular detection units with compact optical devices and advanced data analytics. These systems offer high sensitivity, specificity, portability, and rapid decision-making.This dissertation focuses on developing AI-powered biosensor platforms for environmental field testing and medical diagnostics. Four platforms were designed to detect microRNAs, protein biomarkers, micro/nanoplastics (MNPs), and per- and polyfluoroalkyl substances (PFAS). The detection relies on light scattering or intensity measurements captured by compact photodetectors or smartphone cameras, analyzed using AI frameworks like computer vision and machine learning for pattern recognition, contaminant level prediction, and scalability via cloud processing. Chapter 2 outlines the targets, detection methods, and data analysis techniques across the projects. Overall, this work highlights the transformative potential of AI-powered biosensors in advancing environmental monitoring, healthcare, and industry, with future research aiming to enhance detection capabilities and expand applications.
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  Enhancing the Detection of Contamination Events in Water Distribution Systems by Integrating Alternative Sources of Information in Real-Time

  Boccelli, Dominic L.; Salcedo, Camilo Andres; Lansey, Kevin; Duan, Jennifer; Morrison, Clayton (The University of Arizona., 2025)

  Water distribution systems (WDS) are one of the most vulnerable components of water infrastructure systems. After the events of 9/11, there was increased concern regarding the potential for the deliberate introduction of chemical agents that may affect public health. Later, these concerns moved towards accidental water quality incidents produced by, for example, cross-connections and low-pressure events. In either case, Surveillance Response Systems (SRS) were formulated to protect water quality by make prompt detection and confirmation of contamination events. The overall objective of this dissertation is to develop a decision framework capable of making a timely detection, confirmation and forecasting of a contamination event in WDS. The fulfilment of this objective relied on the use of confirmatory sampling locations (CSLs) as a way to overcome the limitations of traditional water quality monitoring, which includes the high cost of sensors and limited detection capabilities due to the lack of contaminant-specific sensors. Based on previous research that provided a foundation to identify the best individual CSL using an entropy metric derived from information theory, this dissertation proposed the Updating Greedy Algorithm (UGA) to identify a set of \emph{multiple} CSLs in real-time. The UGA used an approximation to the entropy metric and a greedy heuristic to identify the set of CSLs. When tested on a small network, the UGA results were almost identical to the solutions achieved by a Genetic Algorithm using an exact formulation of the entropy metric, but in orders of magnitude less time. As the number of CSLs increased, the placements were spatially very similar (similar hydraulic paths), which may lead to a potential overlap of information across the CSL. To enable the implementation of the UGA in real-sized networks, the UGA was extended into a cluster-based optimization approach in order to reduce the solution space. The clustering algorithm grouped the network nodes based upon similarities in hydraulic connectivity. Each cluster was then assigned a representative sampling unit within each cluster to be used as a potential CSL. Two types of sampling units were used: i) the centroids of the cluster and ii) the location within the cluster that maximized information gain. The use of the clusters and sampling units were proposed to reduce the computational burden of the algorithm while maintaining a similar set of spatially distributed potential CSL. Ultimately, this approach was tested on a large network, and was shown capable of generating optimal solutions within an amount of time consistent with real-time application (1 hour). Finally, the reduction of information overlap was investigated through the introduction of the Multi-Objective Updating Greedy Algorithm (MUGA). The MUGA incorporated D-optimality, a correlation metric, to increase the spatial distribution of CSLs across the network while maximizing the amount of information gained from the samples. The trade-off between Information Gain and D-Optimality showed that the information gain tended to place CSLs along similar hydraulic paths, reinforcing existing connections, whereas the maximization of D-Optimality placed CSLs in unexplored hydraulic paths, creating new connections. The MUGA was tested in a large network using the clustering approach previously developed. The MUGA approach was shown to be computational efficient, and able to achieve good results (relative to Genetic Algorithm solutions). Overall, the addition of the D-optimality was capable of spatially distribution the CSLs and, at lower weights, was able to help avoid some local minima when using the Information Gain as a single objective. Overall, the deployment of CSLs provides useful information to characterize a contamination event, that enhances detection, confirmation and forecasting capabilities of SRS. These methodologies must be efficient enough to provide good solutions in at a time frame useful for real-time application. This research developed an approximation to the exact solution for information gain, a clustering approach to reduce the solution space of large networks, a greedy heuristic placement algorithm, and a multi-objective placement algorithm that that were shown capable of generating good CSL solutions in less than an hour -- often in seconds for the single objective placement. Further research may explore the response of the proposed approaches under diverse characteristics of a contamination event (varying injection locations and times), as well as considering demand uncertainty. Finally, as some contaminants may remain undetected, the inclusion of alternate data sources (e.g., public health data) may be integrated to enhance detection capabilities of SRS.
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  Academic Trajectories and Professional Identities of Graduate Students in an MA TESL Program in the United States

  Kayi-Aydar, Hayriye; Custodio Ribeiro, Amable Daiane; Atkinson, Dwight; Panferov Reese, Suzanne; Dupuy, Beatrice (The University of Arizona., 2024)

  The ways that language teachers construct, enact, and negotiate their identities as part oftheir professional learning and growth have been largely explored in the literature (see Kayi-Aydar, 2019a, for a review). The processes of identity negotiation and enactment are shaped by a wide range of factors, such as past experiences or dreams about the future. Research has shown that MA students in Teaching English as a Second Language (TESL) undergo a complex and multilayered process of identity negotiation that not only influences but is also influenced by their perceptions (Canagarajah, 2012; Hamman et al., 2012; Yazan, 2014), agency (Tao & Gao, 2017), and teaching practices (Kanno & Stuart, 2011). My dissertation contributes to the existing literature on the professional identity construction and negotiation of multilingual and multicultural students in graduate programs in TESL. Furthermore, it sheds light on the impact of graduate students’ past experiences as L2 learners and current experiences as graduate students on their identity construction as teachers. A comprehensive investigation of how MA TESL students construct and negotiate their professional identities based on various personal and professional learning experiences can illustrate the complex ways in which they become who they are, how their beliefs and values evolve, how they perform and make decisions in their classrooms, and what kinds of expectations they hold for the future. Moreover, by analyzing the experiences and perspectives of a diverse group of MA students, and in some cases, longitudinally, this qualitative dissertation study, situated within poststructuralist perspectives of identity (e.g., Norton, 2014; Norton & Morgan, 2013; Pavlenko, 2002), demonstrates how students make sense of their institutional learning, how they theorize their practices, and how they understand and establish relationships within their professional contexts. Data for this study were collected through semi-structured interviews, journal entries, documents, and classroom observations. The primary approaches for data analysis involved both thematic (Braun & Clarke, 2006) and discourse analysis (Gee, 2011). This dissertation aims to answer the following research questions: 1. How do personal experiences of L2 learning influence MA TESL students professional identity enactment and negotiation? 2. How do students’ learning experiences in an MA TESL program contribute to or shape the construction of their professional and imagined identities? How do those experiences impact the enactment of their TESL teacher agency and sense of becoming a TESL practitioner? Findings indicate that biographic experiences at the personal and institutional levels shaped MA students construction of invested, agentive, and legitimate teacher identities. Specifically, participants were influenced by the relationships they established with their L2s in the past and the qualities of teaching they observed as L2 learners. Findings also indicate that as the participants engaged in the coursework and gained pedagogical and content knowledge in the MA TESL program, they struggled to construct a “disciplinary identity” (Pennington, 2015) due to dual (e.g., student-teacher) and conflicting identities (e.g., the native/nonnative speaker). Finally, the formal education that participants experienced and developed in the MA program seemed to nurture their critical awareness about linguistic diversity and multilingualism and promoted the enactment of agency toward meaningful changes in their classroom practice, curriculum, and adopted methodologies.
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  Positive Youth Development & Resilience among Youth with Disabilities in Foster Care during their Transition to Adulthood

  Walsh, Michele E.; Bell Farkas, Jacy Kamiko; Toomey, Russell B.; Armin, Julie S.; Tomasa, Lynne T. (The University of Arizona., 2024)

  This study utilizes Positive Youth Development (PYD) and resilience frameworks as a lens to examine the transition experiences for youth with disabilities who experience and exit foster care through secondary analysis of data collected from a statewide needs assessment, Fostering Positive Outcomes: Assessing transition needs and supports for youth with disabilities in foster care (FPO Project). Secondary analysis of data from the multi-mixed methods approach of the FPO project (group concept mapping, surveys, focus group and interview data) was conducted with application of Lerner et al (2015) Five C Model + Contribution (i.e., Six Cs) indicators of PYD – competence, confidence, character, connection, caring, and contribution. Utilizing a bioecological perspective, this study centers the voices of youth with lived experience to examine resiliency and positive development to answer the following research questions: 1) How are the Six Cs of positive youth development expressed in describing the foster care transition experiences of youth with disabilities? 2) How do multiple systems of support affect the Six Cs of positive youth development for youth with disabilities transitioning from foster care? Findings from this study highlight the complexities, challenges and opportunities for disabled youth experiencing foster care to thrive in adulthood. Each of the PYD indicators, the Six Cs, were described as primarily absent in this population’s transition experiences and may appear in different ways for this specific population. Potential new pathways for PYD were identified that encompass the unique experiences and developmental processes among youth with disabilities in foster care. Findings were translated to propose an adapted Six C model with expanded definitions to make each indicator more applicable and inclusive of this population, as well as help guide the development of interventions specific to this population for positive adaptation. One of the most notable findings based on interactions across the Six Cs is the emergence of self-determination as a major theme which may be a unique indicator of “thriving” among youth with disabilities in foster care. Moreover, youth at this intersection engage with multiple systems of support related to child welfare, disability, education, vocation, and health. Findings indicate gatekeeping, stigma and biases, and staffing and provider issues associated with policies and practices of these systems pose significant barriers to PYD. This study’s findings give rise to implications for the PYD model and resilience, and further scholarship needed in this area, as well as implications for practice and policy with recommendations for interventions through a multi-pronged ecological approach to improve outcomes for youth with disabilities who experience foster care. This study helps to address the gap in the scholarship regarding youth with disabilities who experience foster care and the explicit use of relational developmental frameworks through innovative methods with an under studied, marginalized, and hard to reach population.
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  The Immune Response to SARS-CoV-2 in the Context of Aging and Viral Evolution

  Wilson, Justin E.; Bradshaw, Christine Mason; Campos, Samuel K.; Bhattacharya, Deepta; Nikolich, Janko Ž. (The University of Arizona., 2024)

  Coronavirus disease 2019 (COVID-19) was declared a pandemic by the World Health Organization in March 2020. The rapid spread of the virus, SARS-CoV-2, necessitated prompt development of vaccines, therapeutics, and a more comprehensive understanding of the virus’ biology. To aid in the early investigation of SARS-CoV-2, we aimed to generate a new transgenic mouse model that better recapitulates features of SARS-CoV-2 infection in humans. We demonstrate that reducing the hACE2 transgene in the K18-hACE2 transgenic mouse alleviates neuroinvasion and reduces the mortality rate of SARS-CoV-2 infection. One year after the emergence of SARS-CoV-2, viral variants evolved that challenged the existing population immunity induced by natural infection and vaccination. Improving our understanding of how the immune system adapts to the evolution of SARS-CoV-2 is crucial for developing protective vaccines. This dissertation explores this topic from two perspectives: 1) Investigating whether the immunity generated by the ancestral SARS-CoV-2 vaccinations in older adults can provide effective immune responses against new viral variants and 2) understanding the contribution of each component of the memory immune response in immune imprinting induced by ancestral vaccination.
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  Understanding Sexual Victimization Among College Women: A Multivariate Analysis of Campus and Individual Level Factors

  Burross, Heidi L.; Ledezma, Priscila M.; Cimetta, Adriana; Koss, Mary P. (The University of Arizona., 2024)

  This dissertation examines the association between sexual victimization among college womenand individual- and campus-level factors using a nationally representative dataset. Specifically, it explores whether a higher proportion of same-sex and same-race peers provides a protective buffer against sexual victimization. The study controls for known risk factors, such as class standing, sexual orientation, and living situation, and investigates how institutional characteristics like enrollment size and student body composition influence the likelihood of victimization and formal reporting. Key findings reveal that first-year and sophomore students are less likely to report victimization than seniors, non-heterosexual women face a higher risk for attempted rape and sexual coercion, and students living in sorority housing or off-campus are more vulnerable to certain forms of sexual exploitation. Additionally, a higher percentage of same-race peers is associated with a lower likelihood of attempted sexual coercion. These findings contribute to the growing literature on sexual exploitation in higher education, highlighting the need for larger and more comprehensive datasets to fully capture the complexity of campus-level influences on sexual exploitation. Understanding these relationships is critical for developing more effective prevention strategies.
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  Effects of Creative Dance and Body Percussion for Older Adults at Risk for Dementia – a Mixed-Method Experimental Design

  Shirai, Yumi; Gubner, Jennie; Yang, Yunjia; Chen, Zhao; Dyke-Compton, Tamara (The University of Arizona., 2024)

  Mild cognitive impairment (MCI) is considered the transitional stage from healthy aging to Alzheimer's disease or related dementia (ADRD), and people with MCI are at high risk for ADRD. Interventions for people with MCI to prevent and delay the onset of ADRD are significant in public health. This mixed-methods study evaluated and compared the impact of Creative Dance (improvisational approach) and Body Percussion (choreographic approach) on the cognition and well-being of older adults with MCI. Methods: 20 participants with MCI were randomized into either the Creative Dance (CD) or Body Percussion (BP) group. Each group had two one-hour interventions per week for 10 weeks. Quantitative assessments on attention, memory, and creativity were done before and after the interventions in both groups. Participants completed the Positive Well-being survey before and after the 1st, 5th, 10th, 15th, and 20th classes. Qualitative methods, including focus group interviews, survey answers, and observations, were used to explore the potential mechanisms of specific dance approaches. Results: The CD group showed a significant improvement in creativity (p = .05), with greater gains compared to the BP group (p < .05). Both groups experienced a significant increase in short-term positive well-being after the 1-hour class (p < .001); however, only the BP group demonstrated significant long-term improvement over ten weeks (p < .05). Even though quantitative data did not show a statistically significant difference, mixed data showed the BP group presented a positive indication of improving attention/reaction time, visual-spatial short-term memory, physical benefits, and self-efficacy than the CD group. The CD group showed a positive indication of promoting social interaction and personal expression compared to the BP group. Qualitative results showed that self-efficacy, emotional engagement, expression, and social interactions contribute to Positive Well-being. Semi-structured improvisation in the CD group is the potential key factor to promote creativity. Remembering and repeating the movements with timing in the BP group are the potential key factors for improving attention, reaction time, and memory. A study diagram presents the mechanisms of how and why the intervention caused the primary outcomes.
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  Utilizing an Educational Intervention to Increase Psychiatric Staff Knowledge on Aggression Screening and Implementation

  Bouchard, Lindsay A.; Lopez, John Joseph; Williams, Deborah K.; Gallagher, Shawn P. (The University of Arizona., 2025)

  Purpose: The purpose of this Doctor of Nursing Practice (DNP) project was to assess the effectiveness of an educational intervention designed to enhance psychiatric staff knowledge and willingness to implement an evidence-based aggression screening tool, the Dynamic Appraisal of Situational Aggression (DASA), during patient admissions. The project also aimed to identify barriers and facilitators to the integration of structured aggression screening into clinical practice.Background: Aggression in psychiatric settings posed significant risks to patient and staff safety. Evidence-based tools like the DASA had been shown to improve the identification of aggression risk and promote proactive interventions. Despite these benefits, implementation was often hindered by knowledge gaps, resistance to change, and systemic barriers. Addressing these challenges through targeted educational initiatives improved staff preparedness and fostered safer environments. Methods: A single-group pretest-posttest design was utilized to evaluate the impact of the educational intervention on staff knowledge of the DASA tool. The intervention included a structured presentation emphasizing the operational use of the tool and the importance of mitigating personal bias. Due to limited staff availability, only the director of risk management participated in both the pretest and posttest. Quantitative data from knowledge assessments were analyzed, and qualitative feedback from the participant was thematically analyzed to identify implementation barriers and perceptions. Results: The participant demonstrated consistent pretest and posttest scores of 8/10, indicating a high baseline knowledge level but no measurable improvement. Qualitative data collected revealed key themes, including confusion regarding tool sequencing, corporate barriers to implementation, and the perceived feasibility of the DASA tool when adequately supported by leadership and training. These findings emphasized the need for systemic changes and enhanced educational efforts. Conclusions: This project highlighted the potential of targeted educational interventions to improve aggression screening practices in psychiatric settings. While limited by sample size, the findings underscored the importance of leadership engagement, ongoing training, and policy adjustments to facilitate the integration of structured tools like the DASA. Future efforts should focus on addressing systemic barriers, expanding training initiatives, and conducting multi-site evaluations to validate these findings and enhance scalability.
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  Leveraging Label-Free Multiphoton Microscopy for Diagnostic Applications: Probing Tissue Biology for Enhanced Disease Detection and Analysis

  Sawyer, Travis W.; Knapp, Thomas Graham; Gmitro, Arthur F.; Duan, Suzann; Kang, Dongkyun; Hutchinson, Elizabeth B. (The University of Arizona., 2024)

  Label-free optical imaging is a rapidly expanding field with growing diagnostic potential,fueled by advances in imaging technology and computational methods. This bioimaging method relies on light-tissue interactions to generate detectable contrast. These interactions can result in various physical phenomena, such as the emission of fluorescence from endogenous molecules and harmonic generation. The label-free contrast generated by these interactions is directly influenced by tissue state, where variations in the abundance and organization of contrast- producing molecules and structures lead to unique signatures. This is particularly relevant in cancer research and diagnostics, given the complexity of the disease. A model of this complexity can be found in gastroenteropancreatic neuroendocrine tumors (GEP-NETs), a highly heterogeneous cancer type that develops in the gastrointestinal tract. Optical imaging diagnostics have the potential to improve our ability to rapidly assess disease states and infer the biological characteristics of tumors, thus advancing personalized medicine (i.e., administering therapies tailored to specific tumor subtypes). This study explores the use of label-free optical imaging, particularly multiphoton microscopy (MPM), as a diagnostic tool using GEP-NETs as a disease model. In three key sections, we: 1) investigate the processing of MPM images to remove artifacts that hinder image analysis and feature extraction; 2) examine the use of MPM image features in fixed and fresh tissue to distinguish between normal and diseased tissue; and 3) combine advanced gene sequencing with MPM to validate existing and explore new image features that differentiate normal from diseased tissue and tumor subtypes. The results of Section 1 provide an open-source, easily implementable method for reducing tile artifacts in scanned MPM images, with suggestions for further improving this methodology. Section 2 shows that MPM image features in both fixed tissue and fresh tissue are qualitatively different between normal and cancerous tissue in GEP-NET cases, with quantitative analysis pending for fresh tissue. These features can be utilized in simple classifier algorithms to accurately distinguish tissue types, including tumor regions, suggesting potential future applications in computer-aided diagnostics. Finally, the study demonstrates that combining spatial gene sequencing with MPM imaging reveals correlations between known MPM features and regional changes in gene expression pathways. MPM and spatial gene features were also used to train deep-learning classifiers, which were able to classify MPM images into genetic clusters with high accuracy, indicating promising applications in optical genetic phenotyping.
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  Phenotypic Profiling of Colon Tumor Organoid Monolayers Characterizes a FOLFOX-Induced, AKT-Driven Subpopulation of Chemoresistant Cells

  Thorne, Curtis A.; Morris, Julia Michela; Scott, Aaron J.; Cress, Anne E.; Cusanovich, Darren A. (The University of Arizona., 2025)

  Colorectal cancer (CRC) is the third most commonly diagnosed cancer in the US as well as the third most common cause of cancer-related death. Standard treatment includes surgical resection and adjuvant chemotherapy with multidrug regimens such as FOLFOX (Folinic Acid, 5-Fluorouracil, Oxaliplatin). However, due to high heterogeneity in colon tumors, patient response is variable and tools to predict drug response are few. Additionally, resistance, which can lead to recurrence and metastasis, is not uncommon. As such, there is a need for improved treatment options, better methods for predicting drug response, and better understanding of resistance mechanisms in CRC. Here, we introduce a host of new methodologies to phenotypically characterize CRC with the long term goals of better understanding chemotherapy resistance and creating actionable clinical tools that can model and predict individual tumors’ drug response. We have curated a set of colon tumor organoids, titled the Heterogeneity Library, that represents a variety of CRC subtypes. We used our newly designed phenotypic profiling pipeline, which leverages DAPI, pAKT, CD44v9, and H2AX, to characterize a FOLFOX-induced, PI3K/AKT-driven survival signature originally identified in our transcriptomic data. Unbiased subpopulation analysis confirms a cohort of cells with high PI3K/AKT signaling, high DNA damage, and high levels of stem cell markers across organoids. We believe that cells increasingly upregulate survival signaling, including extracellular matrix components and growth factor receptors, which all activate AKT, which in turn leads to a protective, resistant phenotype. Ultimately, we posit the observed FOLFOX dose-dependent increases in the fraction of these resistant cells across tumor types is a combination of adaptation down this proposed Resistance Trajectory in combination with a selection process whereby susceptible cells are readily eliminated, leaving the increasingly mesenchymal progenitor- and stem-like cells to expand despite FOX exposure. Finally, we endeavored to target this resistant population by treating organoid monolayers with a combination of FOLFOX and Dactolisib, the PI3K/mTOR dual inhibitor, which exhibited significant synergy across organoids. Even the most FOLFOX-resistant organoid – made up almost entirely of the previously described highly damaged, AKT-driven, stem-like resistant cells – demonstrated increased FOLFOX efficacy when also treated with Dactolisib. We hope that with further validation, the novel contributions of this dissertation can be developed into actionable tools for use from bench to bedside.
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  Perspectives From White Outsider School Administrators in Latinx Communities Along the U.S./Mexico Border

  Bertrand, Melanie; Nguyen, Chi; McBeth, Kevin Andrew; Bertrand, Melanie; Nguyen, Chi; Arnold, Stephen (The University of Arizona., 2024)

  This study was designed to examine perspectives from White Outsider School Administrators (WOSAs) in K-12 rural and border school districts in the Southwestern United States along the U.S./Mexico border. The idea for this study stemmed from the disproportionate percentage of White school principals and administrators (56.4%-73.9% in Arizona, California, New Mexico and Texas) compared to the non-White, Hispanic demographic makeup of Southwestern states (NCES, 2023). Additionally, this correlates with the disparity in the teaching profession overall, which is overwhelmingly White (75%), compared with a student body that is 38% White, 45% Hispanic, 5% Black and 4% Native American (NCES, 2021). I therefore focused on school administrators who were not racially aligned with the populations they serve, and those who did not grow up in the communities where they work. The purpose of the study was to determine how externally recruited school administrators, racially different from the populations they were hired to serve in rural, borderland communities, met the needs of local, Latinx populations unlike themselves. It identified WOSAs’ motivations for moving to predominantly Latinx border school communities, the relationships they established when working in these environments, and the ways in which their perceptions of identity influenced their school practices. This firsthand, descriptive case study of WOSAs near the U.S./Mexico border confronted the issue of how Outsider school leaders navigate challenges unique to their settings, as well as the challenges that their identities and backgrounds present, particularly upon Latinx members. This qualitative research offered an in-depth analysis of WOSAs and their relationships with school and local communities. It shared empirical research from interviews of three primary WOSAs and 12 additional participants living and working in border communities. The study utilized a combination of Critical Race Theory and Latino Critical Theory lenses to examine perceptions of race, and offered a Community Equity Literacy lens to introduce perspectives based upon place-centered community relationships. Key findings from this research showed that WOSAs’ identities were important toward a shared sense of beliefs, values, and priorities, and that Outsider identities may create “gaps” that influence outcomes for Latinx members. I described opportunities for Outsider school leaders to employ self-reflective practices that offer learning opportunities for transformative and social justice leadership. I concluded the study by sharing the relevance and urgency of this work to reveal opportunities from which other rural educational leaders may move toward equitable, socially just practices.
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  High-Speed Quantum Communication Over Free-Space Optical Links and Mitigating Atmospheric Turbulence Effects

  Djordjevic, Ivan B.; Nafria, Vijay; Djordjevic, Ivan B.; Kostuk, Raymond; Ashok, Amit; Rengaswamy, Narayanan (The University of Arizona., 2025)

  Quantum communication in free-space optical (FSO) link is the primary focus of my research as explained in this dissertations. In particular, the research is concerned with the reliable and practical high-speed FSO communication systems in both quantum and classical communication domains. Exploring the possibilities of communicating under strong atmospheric turbulence regime in urban terrestrial environment was the main objective of various experiments that in future can potentially be extended to terrestrial-to-space, satellite, and inter-planetary optical communications. The superiority of the FSO communication system against the RF communication lies in its capacity for higher data rates, lower power overheads, reliability, range of wavelengths, and simplicity of installation. Although RF communication is effective when it comes to broadcast type links, the data rate capacity of laser communication are still far superior as we know from optical fiber communication. This research work is another step in advancing the possibilities of FSO communication systems. To accomplish these aforementioned goals, I have developed a 1.5 km long FSO link testbed between Department of Electrical and Computer Engineering (ECE) and Optical Sciences (OpSci) Meinel buildings at the University of Arizona campus for the practical demonstrations of FSO communication. The single most significant nemesis of an FSO communication system is the deterioration of link quality that arises due to atmospheric turbulence effects that severely limits its range, quality of transmission, and overall functioning. Typically, in most of the FSO experiments we start with phase modulation of a laser beam, ASE (amplified spontaneous emission) noise source, or signal photons from the entanglement pair (in case of quantum communication) imposing the phase-shift keying (PSK) signal. Now this information carrying beam traverses through the FSO link that is getting heated variably from the heat radiating from the surface below. These processes vary spatially, temporally, time of the day, and seasonally. Atmospheric turbulence effects exhibit as phase and wavefront distortion and scintillation at the receive side which leads to poor power reception, beam wandering, and ultimately loss of information. We characterize our FSO link’s operational quality in terms of bit-error rate and we treat it as a benchmark. To mitigate the losses incurred due to phase aberrations, we make use of adaptive optics (AO) techniques for azimuthal phase compensation. Our AO system is based on deformable mirror and a Shack-Hartmann wavefront sensor. I always strive to improve the data-rate and link efficiency with every new experiment, which I have demonstrated in many papers. The link currently operates at over 35% transmissivity, and the link is capable of performing experiments and research work with data rates up to 10 Gb/s and even 20 Gb/s. We demonstrated the first ever outdoor FSO based entanglement assisted communication and a radar system with quantum sensing features using entanglement. Our entanglement assisted systems outperform both the standard Shannon limit for communication and standard quantum limit for sensing applications. In classical communication we developed methods from basic FSO link that demonstrate BER improvements by application of AO. We developed a unique method to generate bright entangled photons by using only telecom devices that can survive strong atmospheric turbulence effects. To improve the FSO quantum system reliability we perform phase-conjugation on idler photons rather than signal photons that are affected by atmospheric turbulence effects. We developed a low probability of intercept (LPI) system that keeps communication covert and secure from an adversary. We also developed a unique method of information encoding-decoding called “wavelength-diversity” that shows significant improvement over conventional laser communication in FSO channel that matches improvements from AO at a fraction of its cost.
• The Spine Less Traveled: Navigating Mechanisms and Exploring Treatments for Pain in Alzheimer’s Disease

  Martin, Laurent; Ibrahim, Mohab; Korah, Hannah; Martin, Laurent; Ibrahim, Mohab; Vanderah, Todd; Anderson, Trent; Gurtner, Geoffrey (The University of Arizona., 2024)

  To contextualize the importance of my PhD work, the following chapters of this manuscript delve into the intersections of chronic pain and Alzheimer’s disease. This journey begins with a comprehensive review exploring shared pathological mechanisms between these conditions, highlighting the critical need to deepen our understanding of their interactions for more effective pain management strategies. Building on this foundation, the research section presents findings from a mouse model of Alzheimer’s disease, focusing on the neurobiological pathways of pain transmission and examining why common analgesics may not offer the same relief in this context. Finally, my work expands into innovative approaches, where surgical techniques have been refined in models of chronic pain, and a non-pharmacological therapy using green light photoneuromodulation is evaluated for its therapeutic potential. Together, these studies aim to advance both scientific understanding and patient care for those living with complex, interwoven conditions.
• Spectroscopic Tools for Studies of Voltage-Based Degradation of Organic Semiconductors: From Simple Films to Device-like Architectures

  Pemberton, Jeanne E.; Blackburn, Thomas; Monti, Oliver; Lichtenberger, Dennis; Heien, Leandro M. (The University of Arizona., 2025)

  Organic semiconductors (OSCs) have recently become of interest for inclusion in various organic electronics due to their advantageous properties. OSCs are the active elements in printable and flexible electronic devices such as thermoelectrics, light-emitting diodes, photovoltaics, and field-effect transistors. Despite the beneficial properties of OSCs, hurdles remain for widespread commercial adoption. Specifically, organic photovoltaics have historically had comparably lower power conversion efficiencies and stabilities than their inorganic counterparts. While recent progress has made significant strides in closing the power conversion efficiency gap, greater device lifetimes are still necessary to make them practical for commercial applications. The power conversion efficiency problem has been addressed by synthesizing semiconducting molecules that contains both electron-donating and accepting components, which leads to fine-tuned control of the electron density localization on the OSC, which affects the various electronic properties such as bandgap to better absorption properties. However, the instability issue is more complex, with both physical and chemical components that often coincide. This dissertation will show that spectroscopy and device-like conditions are critical in understanding the chemical degradation of active layer components in organic photovoltaics. To investigate the degradation of donor-acceptor active layer materials, poly[[4,8-bis[(2-ethylhexyl)oxy]benzo[1,2-b:4,5-b']dithiophene-2,6-diyl][3-fluoro-2-[(2- ethylhexyl)carbonyl]thieno[3,4-b]thiophenediyl ]] (PTB7) was used as a model system in studies with preogressively increasing device-like architectures. The initial investigation into the effect of applied voltage on the degradation of the donor materials was investigated with Fouriier transform infrared spectroscopy (FTIR), electrical characterization, and x-ray photoelectron spectroscopy (XPS) to understand the role of atmospheric exposure in degradation of PTB7 in the absence of light. FTIR and XPS results show clear evidence of degradation through the introduction of oxygen-containing functional groups into the polymer backbone. This degradation was explained through the formation of intermediate charge transfer complexes beginning with contact charge transfer, forming a charge transfer complex (CTC) that then leads to a full charge transfer (CT) that allows oxygen to be made into superoxide anion radical, O_2^(.-). This species is proposed as the active degradant due to limited formation pathways of other reactive oxygen species (ROS) without illumination. Similar degradation does not occur under identical conditions in an inert nitrogen environment for the same applied voltage. Superoxide-induced degradation also follows a distinct pathway, leading to the formation of unique degradation products that differ from those previously reported from photooxidation of PTB7. Over sufficiently long time periods, film degradation occurs in the dark under applied voltage, with the extent of degradation enhanced in the presence of water vapor in the degradation environment. To better understand the role of applied voltage in the degradation of PTB7, films were exposed simultanesously to both light and voltage. This exposure also leads to degradation, but the products exhibit contributions from both applied voltage and photooxidation. Despite differences in the degradation time scale, hours for illumination and hundreds of hours for applied voltage, when combined, the presence of both applied voltage and illumination alters the degradation pathway from that observed with illumination only. This is an interesting finding, as degradation for the voltage-only conditions relies on superoxide anion as the ROS, whereas singlet oxygen is thought to be the ROS under illumination. Based on the difference in degradation timescale, singlet oxygen is the ROS more likely to degrade the film. Despite having different predominat ROS active, applied voltage alters the degradation from photoillumination only and highlights the complex interplay of device operation and degradation. A final series of studies adopted a full device-like architecture to add relevant additional interfaces and structure to the model system. Changes in degradation relative to the simplistic model systems described above were observed, although similar degradation products are formed. This convergence to similar products highlights the complexity of performing simplified analysis of devices as standalone films. Also, it highlights the need for stability testing not to be performed at either the open circuit potential or in the absence of an electrical load that an organic photovoltaic will experience when operating. The additional interfaces and structure affect the degradation extent and products, thus providing an additional reason device degradation studies must account for more device-like architectures and operational conditions to understand the complex degradation chemistry of organic photovoltaics.
• Advancing LXR Modulation for Drug Discovery: Coregulator Profiling and the Development of Nonlipogenic ABCA1 Inducers

  Thatcher, Gregory; Laham, Megan S.; Jewett, John; Marty, Michael; Galligan, Jim (The University of Arizona., 2025)

  The liver X receptor (LXR) is a nuclear hormone receptor (NHR) that plays a key role in regulating cholesterol transport (e.g., apoE, ABCA1), insulin signaling, and inflammation, making it a promising drug target for various diseases. However, the development of LXR agonists is often hindered by the undesirable side effect of lipogenesis, driven by the activation of genes such as SREBP1c. To mitigate this, drug discovery efforts have focused on selectively targeting LXRβ, based on the premise that LXRα, predominantly expressed in the liver, is responsible for lipogenesis. Despite these efforts, LXRβ-selective agonists have not yielded successful clinical outcomes. This study presents the development of precision coregulator recruitment TR-FRET (pCRT) assays to classify LXR modulators. By evaluating both coactivator and corepressor recruitment, the pCRT assays generate distinct coregulator profiles for each LXR ligand. These profiles offer valuable insights into the lipogenic versus nonlipogenic properties of LXR ligands. The work expands the characterization of LXR ligands beyond simple binding assays, providing a more comprehensive understanding. Additionally, the profiling system was used to assess optimized nonlipogenic ABCA1 inducers (NLAIs), which showed improved ABCA1 expression. These NLAIs also demonstrated better solubility and metabolic stability compared to previously reported NLAIs.
• Scintillating Metal Organic Frameworks for Low-Energy Radioisotope Detection: Material Development and Applications

  Aspinwall, Craig; Ke, Chen-Yi; Armstrong, Neal; McGrath, Dominic; Miranda, Katrina (The University of Arizona., 2024)

  Metal-organic frameworks (MOFs), formed by the self-assembly of organic molecules andmetal components, represent a unique class of multifunctional materials. Their exceptional properties—such as modularity, high porosity, tunable emissions, and customizable crystalline structure and physical size—distinguish MOFs from other materials and have led to diverse applications across multidisciplinary fields. Notably, scintillating MOFs offer a novel approach to ionizing radiation detection. The well-ordered structure of MOFs enables precise atomic-level control over the arrangement of constituent molecules, enhancing scintillating properties. This precise control paves the way for developing next-generation scintillators with improved performance. This dissertation presents three innovative designs of scintillating MOFs for the direct detection of challenging low-energy beta-emitting radioisotopes in aqueous solutions, with applications also extending to biologically relevant fields. First, we synthesized scintillating MOFs by covalently coordinating scintillating molecules into MOF structures, demonstrating effective detection of tritium in its stable molecular form within aqueous solutions. Second, we developed fluorophore-doped MOFs for detecting low-energy beta-emitting radioisotopes. Here, the incorporated fluorophore molecules endow the MOFs with scintillating properties, presenting a straightforward method for producing scintillating MOFs with flexible design and optical tunability based on dopant fluorophores. Additionally, we introduce a MOF-based scintillation proximity assay (SPA). Initially, we fabricated the MOFs by coating them with polyethylenimine (PEI) for chemical derivatization, then conjugated them with 4-carboxyphenylboronic acid (4- CPBA) to enable selective binding to glucose via molecular recognition. Our results show that 4- CPBA-functionalized MOFs exhibit enhanced scintillation responses to radiolabeled glucose 20 through specific adsorption, demonstrating the potential of MOFs to enable molecular interaction detection—laying the groundwork for SPA applications. In summary, this dissertation highlights the effectiveness of MOFs as scintillating materials for analyzing low-energy beta-emitting radioisotopes and their potential utility and adaptability in advancing SPA methodologies.
• Harnessing the Spatial Degree of Freedom for Quantum Photonic Sensors

  Guha, Saikat; he, wenhua; Gagatsos, Christos; Wilson, Dalziel; Soh, Daniel (The University of Arizona., 2025)

  Quantum information and estimation theory provide a systematic framework for analyzing fundamental performance limits in optical sensing tasks and have proven helpful in the design of novel sensor systems. In this dissertation, we analyze a canonical imaging task, that of estimating the transverse displacement of an optical beam, while optimally using the rich spatial-mode degree of freedom, the quantum state(s) in which those modes are excited, and the design of novel receivers that may employ optical pre-processing of the target-return information-bearing light. We theoretically analyze this task using a free-space propagation channel with soft-Gaussian apertures at both the transmitter and the receiver sides, to allow for an analytical treatment of diffraction loss. Using a quantum Fisher information (QFI) analysis, we find the optimal spatial mode—to excite in either a coherent state (laser-light) or a displaced squeezed state—for a probe with a transmitted-energy constraint, when paired with their respective optimal receiver choices. We also report several alternatives of structured optimal receiver designs, i.e., those whose classical Fisher information (CFI) equals the QFI of the optimal classical or quantum probes. Furthermore, using a CFI analysis, we find the optimal spatial mode to excite a coherent state in, when the receiver employs a pixelated camera. We report preliminary experimental results for the above, wherein our setup is capable of exciting an arbitrary spatial mode in a coherent state with a phase-only spatial light modulator (SLM). Finally, we present the margins of improvement in precision attainable for beam-deflection sensing with the various aforementioned optimized classical and quantum strategies, including a conjecture on the optimal Gaussian spatially-entangled probe. We conclude this dissertation with thoughts on various future directions on theoretical and experimental investigations of quantum enhanced optomechanical sensing and beyond.
• The Production of Portuguese Mid-Vowels by English-Spanish Bilinguals

  Staples, Shelley; Centanin Bertho, Mariana; Carvalho, Ana; Simonet, Miquel; Picoral, Adriana; Wedel, Andrew (The University of Arizona., 2024)

  Portuguese is among the 15 languages other than English with higher enrollment rates in higher education institutions across the US (MLA, 2023). The majority of students taking Portuguese courses also speak Spanish, thus, they are English-Spanish bilinguals learning Portuguese as a third language. However, their experience with Spanish is not homogenous: some have learned Spanish as an L1 or heritage language, in a naturalistic environment, and others have learned Spanish as an L2, later in life, in an instructional setting. In this context, this study aims at investigating the acquisition of L3 Portuguese, more specifically the phonological aspect, by English-Spanish bilinguals, comparing L1 Spanish and L2 Spanish speakers and three course levels (first, second, and third consecutive semesters of a Portuguese language program). More specifically, this study provides an acoustic analysis of learners’ production of Portuguese mid-close and mid-open vowels, two phonemic contrasts that do not exist in Spanish phonology but pertain to the acoustic space of English vowels.Theoretical models in L3 acquisition have mainly investigated how learners’ linguistic repertoire affects their process of acquisition of the third (or more) languages, i.e. which language(s) are more likely to be the source of transfer and if transfer will happen exclusively from one language or on a property-by-property basis (Schwartz and Sprouse, 2021). The studies in L3 Portuguese have mainly focused on morphosyntax features (e.g. Giancasparo et al., 2015; Cabrelli Amaro et al., 2015) and show evidence of transfer from the most typologically similar language in learners’ linguistic repertoire, favoring the Typological Similar Model (Rothman, 2011; Rothman, 2014). Therefore, in the context of English-Spanish bilinguals learning L3 Portuguese it is expected that Spanish will be the main source of cross-linguistic transfer. However, this debate is not settled yet specially when it concerns L3 phonological acquisition (Cabrelli & Pichan, 2019). The student population of this dissertation – English-Spanish speakers, with different experiences in Spanish acquisition, learning L3 Portuguese – is an ideal context to test if the experience learning Spanish will affect the source of linguistic transfer to Portuguese. The studies in this field are hosted under formal linguistics and have followed an experimental approach, using grammaticality judgement tasks, perception tasks, discrimination tasks, and elicited production tasks. Meanwhile, spoken corpora studies, based on compilation of naturally occurring language, have the potential to contribute to the field as it reveals features of learners’ spontaneous or semi-spontaneous performance. For that reason, this study proposes the acoustic analysis of the oral production of English-Spanish speakers’ learners of L3 Portuguese compiled in the Multilingual Academic Corpus of Assignments – Writing and Speech (Staples et al. 2019-). The corpus subset analyzed in this dissertation includes the production of oral course assignments by 38 students enrolled in three course levels (first, second, and third semester), 21 who have acquired Spanish as L1/heritage languages and 17 who have learned Spanish as an L2 later in life in instructional settings. The goal is to determine if there is any significant difference in learners’ production comparing L1 Spanish and L2 Spanish speakers and across course levels. As the L3 theoretical models strongly suggest the English-Spanish bilinguals will draw from Spanish in the development of their Portuguese acquisition, I selected mid-open and mid-closed vowels as the target segments for learners’ production analysis. A frequency and functional load analysis was also carried out in a corpus representative of spontaneous spoken language in Brazilian Portuguese, the C-ORAL-Brasil-I (Raso & Mello, 2012). Based on the analysis of frequency of occurrence of English segments in Gilner and Morales (2010), the results indicated that mid-close and mid-open vowels (/e-ɛ/ and /o-ɔ/) have the potential to cause perception and production issues in Spanish speakers’ Portuguese production because open vowels are much less frequent than their closed counterparts. This difference in frequency may cause the less frequent item (the open vowels /ɛ, ɔ/) to be more obscure for learners to notice and distinct from their closed pairs (/e, o/), especially because such phonemic contrasts do not exist in Spanish. The Pillai score (Hall-Lew, 2010), a value from 0 to 1 that indicates how much two datapoint clusters overlap, was calculated for each participants’ production of /e-ɛ/ and /o-ɔ/. Results show no significant distinction between mid-front vowels and mid-back vowels in learners’ production. The Mann-Whitney statistical test was used to compare the Pillai scores between L1 and L2 Spanish groups and no significant difference between groups was observed. The Kruskal-Wallis statistical test was used to determine any significant difference across course levels. The only comparison that showed significant difference was in the production of /o-ɔ/ between second and third semester. Interestingly, second semester had a higher Pillai score mean (.37) than third semester (.14). Since the closer to 1 the more distinct the two vowels are, this finding suggests that learning experience does not necessarily affect the production of this phonemic contrast. The results also indicate that the experience learning Spanish was not a determinant factor in learners’ production. Euclidean distance was also calculated as another indicator of level of merge between /e-ɛ/ and /o-ɔ/. The Euclidean distance means of course level groups and linguistic profile showed similar results as the Pillai score analysis. There was no clear pattern of open/closed mid-vowels distinction across course levels. Linguistic profile was also not determinant to participants production. These findings may suggest that order of acquisition of Spanish is does not affect participants’ production, in supporting the Typological Similarity Model (Rothman, 2011). Nonetheless, this finding should be taken with cautious as unbalanced sample sizes may have affected the results as well as individual differences.

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