• Flow Structure and Heat Transfer Characterization of a Blunt-Fin-Induced Shock-Wave/Laminar Boundary-Layer Interaction

      Little, Jesse C.; Castro Maldonado, Jorge Alberto; Craig, Stuart A.; Wernz, Stefan (The University of Arizona., 2021)
      An experimental investigation of a blunt-fin-induced shock-wave/laminar boundary-layer interaction (SBLI) has been conducted at a nominal Mach number of 4.The experimental data is supplemented by computational results from Reynolds-averaged Navier Stokes computations provided by Raytheon Missiles & Defense.Two blunt fins with a leading-edge diameter of 9.525 mm (3/8”) and sweep angles of 0 and 45 degrees were tested on a flat plate with unit Reynolds number 4.3×10^6 m−1 (Re_x= 2.7×10^5). The unswept fin produces significant separation extending x/D ≈ −5.5 upstream of the fin leading edge. Mach number contours indicate two horseshoe vortices wrapping around the unswept fin base. The swept fin SBLI features are subdued in comparison, but qualitatively similar, with evidence of horseshoe vortices also present. Temperature sensitive paint (TSP) was employed to investigate the near-wall flow structure and estimate surface heat flux. Prominent features include various reattachment lines associated with vortices in the separated region, as well as shock-shock interactions and shear-layer impingement on the fin leading edge. Increasing the sweep angle altered the flow topology considerably, including the location and magnitude of maximum heat flux. The surface distribution of Stanton numbers are derived, demonstrating complex interactions with a rich set of flow physics to be investigated in future work. Amongst other findings, the influence of sweep has a moderate impact on peak heat transfers, with Stanton numbers reaching 0.022 and 0.035 for the swept and unswept fins respectively.
    • Pedal the Old Pueblo: A Naturalistic Study on Bicycling in Tucson, AZ

      Woodhouse, Connie A.; Keith, Ladd; Iuliano, Joseph Edward; Plane, David (The University of Arizona., 2021)
      City investments in bicycle infrastructure can improve residents' health and wellness, lower pollution, fight climate change, and reduce congestion. While transportation geography and planning have long focused on looking at how vehicles, goods, and services move across a region, there is a growing body of research focused on the movement of people through a city. This dissertation uses both the City of Tucson and Pima County, Arizona–– a region of low-density development, traditionally focused on the car and now trying to improve cycling rates––to explore how cyclists interact with other road users and the built environment and how we can use that information for better bicycle infrastructure planning. The original research presented in this dissertation answers this question through three interconnected papers that explore the history of cycling planning and the opportunities and barriers to bicycle planning in the region (Appendix A), factors that influence route choice (Appendix B), and an analysis of the lived experiences of cycling in the region (Appendix C). This dissertation helps advance bicycle planning by expanding on how multiple types of riders––people who commute via bicycle, who ride for leisure, or who ride for sport––move through and interact with the built environment to design and plan better infrastructure. The dissertation highlights opportunities to continue to expand on the use of video to understand cyclist behavior and interactions in the built environment to identify gaps in the infrastructure. Additionally, the dissertation demonstrates opportunities for planning scholars and university outreach departments to collaborate with practitioners to put research into practice.
    • Dysregulation, Deficiency, and Virus Associated Pathologies Related to the Complement System

      Proffitt, James; Wilson, Justin; Buchanan, Dylon Cole; Ahmad, Nafees (The University of Arizona., 2021)
      The complement system is a frontline component of the immune response against invading pathogens. When functioning properly, it can help with the successful elimination of pathogens through opsonization, membrane attack complex formation, and cell signaling. When dysfunction or deficiency arises, these processes can be hindered and afflicted persons can be at increased risk of certain diseases due to the lack of complement protein production. These diseases can include systemic lupus erythematosus, glomerulonephritis, and increased risk of bacterial infections (de Cordoba et al., 2012). Several viruses have developed the capability of either evading or utilizing the complement system to their advantage. The emergence of SARS-CoV-2 has led to questions as to how this virus interacts with the complement system. While there is still much that is unknown, many of the pathologies caused by SARS-CoV-2 infection have a complement-induced component. For instance, patients diagnosed with severe COVID-19 disease have been noted to have elevated C3a and membrane attack complex components leading to lung, vasculature, and kidney damage (Java et al., 2020; Santiesteban-Lores et al., 2021). Additionally, the intracellular complement system, termed the complosome, is important for the regulation of immune cells by signaling homeostatic CD4+ T-cell survival through stimulating the mTOR pathway and for aiding in the immune response by activating the CD46 complement receptor (Liszewski et al., 2013; Arbore et al., 2017).
    • Doing Less with More: The Irrigation Efficiency Paradox and Water Conservation Policies in Western U.S. Agriculture

      Schlager, Edella; Pieper, Leah; Bakkensen, Laura; Baldwin, Elizabeth (The University of Arizona., 2021)
      This dissertation explores why water conservation occurs in agriculture in the Western U.S. under prior appropriation governing institutions and leads to changes in water usage patterns. The prior appropriation doctrine has long been criticized for failing to incentivize water conservation and efficiency in the application and allocation of water. Some states have attempted to correct this misfit between prior appropriation institutions and present needs for flexibility in water management by enacting conserved water statutes to further define and protect the water rights of those who implement conservation measures. However, an apparent side effect of one common form of water conservation, using more efficient irrigation technologies and techniques, is increased consumptive use of water in irrigated agriculture—what is referred to as the irrigation efficiency paradox (Grafton et al. 2018). I suggest that the “irrigation efficiency paradox” is not an unexpected result, especially in states with conserved water statutes, as increases in consumptive usage should be expected when property rights to water exist. I explore and analyze the motivations for enacting conserved water statutes, demonstrating that the lack of institutional incentives, the involvement of multiple types of stakeholders, and the degree of problem severity were critical factors in motivating consideration and adoption of a statute. I provide a direct empirical test of the effects of conserved water statutes on agricultural water usage, finding that conserved water statutes are associated in some cases with higher usage of efficient irrigation technology, but the statutes more often appear to have a negative effect on consumptive water usage, contrary to expectations from the irrigation efficiency paradox. I also analyze the role of conserved water statutes in encouraging conservation through participation in environmental water transactions, showing that while the financial incentives offered by the transactions was more likely to encourage participation, conserved water statutes did not make these effects more likely or contribute to water conservation and allocation goals. The overall findings of this dissertation indicate that conserved water statutes are likely not very effective or appropriate for incentivizing water conservation in agriculture, especially when the goals of policymakers and stakeholders are to increase allocative efficiency in water management, rather than simply increase technical efficiency for individual water users. This dissertation contributes to the literature on water management and common pool resource governance by offering a comprehensive examination of conserved water statutes and the impacts of the institutional incentive structure for water usage and conservation in irrigated agriculture in the West.
    • Essays in Platform and Network Economics

      Xiao, Mo; Liu, Xinyuan; Langer, Ashley; Galvao, Antonio (The University of Arizona., 2021)
      This dissertation studies competition, market structure and pricing mechanics in marketsthat feature network economics and platform economics. The first chapter studies the network structure of small cell deployment within a city, by estimating and comparing the network effect of a carrier’s existing small cells and the competition effect of rivals’ small cell network. Using a fixed-effects model as well as an IV model where cost instruments are used for a firm’s small cell deployment decision, the paper finds strong network effect outweighing the competition effect in carriers’ entry decisions, with network effect contributing to 70-90% of the variation in small cells. While small in magnitude, competition effect shapes the dominance of a carrier in a very local region, for example in the downtown area. Policy simulations based on the model estimates suggest a government subsidy targeted at the neighboring area of current network centers to be most effective in accelerating small cell deployment. Subsidy targeted at high cost low density areas do not lead to enough private investment to further deploy. In the second chapter, we document how online lenders exploit a flawed, new pricing mechanism in a peer-to-peer lending platform: Prosper.com. Switching from auctions to a posted-price mechanism in December 2010, Prosper assigned loan listings with different estimated loss rates into seven distinctive rating grades and adopted a single price for all listings with the same rating grade. We show that lenders adjusted their investment portfolios towards listings at the low end of the risk spectrum of each Prosper rating grade. We find heterogeneity in the speed of adjustment by lender experience, investment size, and diversification strategies. It took about 16 – 17 months for an average lender to take full advantage of the “cherry-picking” opportunity under the single-price regime, which is roughly when Prosper switched to a more flexible pricing mechanism. The third chapter is based on the observation that previous literature of consumer online rating has focused on information aggregation and the effect of ratings on own demand. The chapter seeks to find evidence on the demand effect of online ratings across local businesses. There are two competing mechanisms through which ratings of neighboring businesses could affect the performance of one local business. On one hand, the spillover effect predicts that a highly rated business would not only increase its own performance, but also the performance of surrounding businesses. On the other hand, the effect could be in the other direction: higher ratings drive more consumers to one business while lowering sales of neighboring businesses. This project is aimed at identifying these effects by exploiting the variation in neighborhood structure, geographic proximity of local businesses. The results show evidence on both competition effects and spillover effects of neighborhood business online reputation. Both these effects would decrease as I consider a neighborhood that is more distantly located from the center restaurant.
    • Lost in Translation: Variations in WNT Signaling and Other Translational Changes in a Drosophila Model of ALS

      Zarnescu, Daniela C.; Lehmkuhl, Erik; Bolger, Timothy A.; Capaldi, Andrew; Schwartz, Jacob (The University of Arizona., 2021)
      Amyotrophic lateral sclerosis (ALS) is a genetically heterogeneous neurodegenerative disease inwhich 97% of patients exhibit cytoplasmic aggregates containing the RNA binding protein TDP- 43, referred to as TDP-43 pathology. My project focused on understanding how TDP-43 pathology modifies translation. Using tagged ribosome affinity purifications in Drosophila models of TDP- 43 proteinopathy, we identified TDP-43 dependent translational alterations in motor neurons impacting the spliceosome, pentose phosphate and oxidative phosphorylation pathways. A subset of the mRNAs with altered translation are also enriched in TDP-43 complexes suggesting that they may be direct targets. Among these, dlp mRNA, which encodes the glypican Dally like protein (Dlp)/GPC6, a wingless (Wg/Wnt) signaling regulator is insolubilized both in flies and patient tissues with TDP-43 pathology. While Dlp/GPC6 forms puncta in the Drosophila neuropil and ALS spinal cords, it is reduced at the neuromuscular synapse in flies suggesting compartment specific effects of TDP-43 proteinopathy. These findings together with genetic interaction data show that Dlp/GPC6 is a novel, physiologically relevant target of TDP-43 proteinopathy. Recent further investigation suggests that Dlp puncta represent defunct endomembrane compartments and that TDP-43-Dlp dynamics persist outside of motor neurons.
    • Human Cytomegalovirus Infection in Endothelial Cells Induces the Secretory Autophagy Pathway for Egress

      Goodrum, Felicia; Molina, Belen; Wilson, Jean; Purdy, John; Campos, Samuel (The University of Arizona., 2021)
      Human cytomegalovirus (HCMV) is a β-herpesvirus that establishes a lifelong infectionwith the potential to infect multiple cell types, including vascular endothelial cells. While infection in fibroblasts is well-characterized, much remains to be understood about key differences in the infection of other cell types. Endothelial cells support a slow and chronic infection while contributing to the spread of the virus to distal organs. However, the cellular and molecular determinants of HCMV infection in endothelial cells remain poorly understood. Both infected endothelial cells and fibroblasts incorporate viral material, like virions and dense bodies, into a multivesicular body (MVB)-like vesicle. However, these vesicles have distinct biogenesis in each cell type. Virus-containing vesicles in fibroblasts are classical MVBs marked by CD63 and LBPA. However, characterization of the vesicles in endothelial cells showed that cis-Golgi (GM130), lysosomal-associated membrane protein- 1 (LAMP1) proteins are on the limiting membrane of the virus-induced vesicles, and autophagy maker LC3B is on the membranes of intraluminal vesicles. These markers are commonly associated with the secretory autophagy pathway. Moreover, the vesicles in endothelial cells lack CD63 and LBPA. These results suggest that the virus-containing vesicles in infected endothelial cells may traffic through the secretory autophagy pathway. Our findings support this suggestion in that we have found differences in protein levels of Rab8A and Rab8B, two proteins that distinguish degradative autophagy from secretory autophagy, in infected endothelial cells. These findings suggest that HCMV induces the secretory autophagy pathway in endothelial cells possibly for egress. Furthermore, HCMV has evolved mechanisms to co-opt host trafficking pathways for transport, virion maturation, and egress among other functions. The viral protein UL135 has been shown to have a role in the rearrangement of membrane trafficking, and incorporation of virus material into MVB-like vesicles. We investigated the role of UL135 in the biogenesis of the virus-induced vesicles and its involvement in the induction of the secretory autophagy pathway during infection using immunoblotting for both viral proteins and well-characterized markers of secretory and degradative autophagy. We found that, in the absence of pUL135, Rab8A, LC3B, and P62 are increased, suggesting that pUL135 is involved in the decrease of lysosomal activity thus the decrease in degradation. This may suggest that UL135 may be involved in the biogenesis of the LAMP-1, GM130, LC3B positive vesicles and possibly give preference to the secretory autophagy pathway when incorporating virus material into the vesicles for egress. This work provides novel insights into the diversity of mechanisms by which HCMV hijacks membrane trafficking in different cell types and will reveal cell type-dependent roles for secretory autophagy in HCMV infection.
    • The Creation and Application of Bioinformatic Techniques to Improve Therapeutic Options for Cancer Patients

      Padi, Megha; Grant, Adam; Ellis, Nathan; Gutenkunst, Ryan; Heimark, Ron; Romanoski, Casey (The University of Arizona., 2021)
      Tumors commonly exhibit high levels of both inter- and intra- heterogeneity. For this reason, the optimal therapeutic approach for cancer patients would ideally be a regimen that is catered toward their individual tumor. Unfortunately, rather than receiving a treatment based on the molecular profile of their tumor, most cancer patients receive a generalized therapeutic treatment based on the past performance of tumors at the same stage and location. These non-specific treatments often cause adverse side effects and may have only a slight impact on life expectancy of a patient. The limited treatment options for cancer patients are mainly because of the lack of knowledge of which prerequisites are required for a tumor to respond to an anti-cancer drug. Fortunately, with the advancement of next generation sequencing technologies, we can globally interrogate the molecular characteristics of individual tumors. Here, I present four ways to improve therapeutic options for cancer patients by utilizing and developing computational tools that analyze next generation sequencing data: 1) combining machine learning with Bayesian network structure learning to identify tissue specific mechanisms of drug response, 2) subtyping colorectal cancers to identify molecular mechanisms associated with early-onset colorectal cancer, 3) combining exome and RNA sequencing data to better identify influential tumor mutations, and 4) identifying breast cancer patients who are particularly susceptible to bone metastasis. The results from all four projects suggest that, although tumors from the same tissue typically exploit similar pathways to progress their tumor phenotype, the specific mechanisms they use to dysregulate the pathway often vary. Moreover, common genomic alterations that occur across multiple tumor types activate different tissue-specific mechanisms, which can dramatically alter the response of tumors to the same anti-cancer drug. Elucidating how tissue- and tumor-specific molecular dysregulation drives tumor phenotypes is an essential prerequisite to providing the optimal therapeutic for a cancer patient. By using the approaches and workflows I developed during my PhD, we can better suggest anti-cancer drugs that will elicit a response in cancer patients by identifying the biological pathways that are critical for tumor development in specific tissues and which molecular dysregulations may potentiate that pathway.
    • World Englishes and the Teaching of English as an International Language: Indonesian Teachers’ Perspectives and Professional Development Experiences

      Short, Kathy; Juwariyah, Siti; Kayi-Aydar, Hayriye; Reinhardt, Jonathon; Matsuda, Aya (The University of Arizona., 2021)
      This study examined teachers’ perspectives and professional development experiences about the teaching of English as an International language (TEIL) in relation to World Englishes (WE) at junior high school levels in Indonesia. Considering the growth of the number of English speakers around the world, it has been argued that WE-based TEIL is more realistic and relevant (Kachru & Nelson, 2006; Kirkpatrick, 2007; Matsuda, 2002, 2018). Accordingly, efforts have been done to challenge the standard English hegemony such as through teacher education programs. However, previous research focused primarily on pre-service teachers through teacher preparation programs at higher education levels. There were limited studies investigating in-service teachers’ professional development experiences, especially in relation to World Englishes and at junior high school levels in Indonesia. Meanwhile, professional development has been deemed important for in-service teachers as the content in pre-service education is usually limited and there are educational as well as pedagogical changes that in-service teachers need to constantly respond over time (Richards & Farrell, 2005). Considering how relevant and significant WE-based TEIL is, it is also crucial to update in-service teachers with such knowledge. Hence, this study was aimed at exploring and understanding teachers’ views on WE-based TEIL including their professional development experiences and use of social media in its implementation at Indonesian junior high schools. A mixed methods research design, in which both quantitative and qualitative data were collected in two phases of study (Creswell & Plano Clark, 2017), was used to answer three research questions: 1) What are teachers’ perspectives on incorporating World Englishes into the teaching of English as an international language at the junior high school level in Indonesia?, 2) How have teachers used social media as potential resources to incorporate World Englishes into the teaching of English as an international language at the junior high school level in Indonesia?, and 3) How have teachers experienced professional development in relation to English teaching in general and the incorporation of World Englishes in particular? 64 teachers joining a local English teacher forum participated in the online survey in the first phase, and 6 focal teachers were selected for the second phase, in which observations, focus group discussion, and interviews were used to collect the data. The quantitative data from the survey were analyzed using both descriptive and inferential statistics. The qualitative data from the survey, observations, focus group discussion, and interviews were triangulated and coded to identify themes and patterns in the data. The findings show that English language teaching at Indonesian junior high school levels was quite complex. While teachers acknowledged the importance of WE-based TEIL, they did not find it urgent to prioritize because they did not feel knowledgeable enough about WE and also because they were facing other problems as English teachers. In addition, even though teachers benefitted from using social media especially in locating WE materials, they could not really maximize it due to the insufficient institutional and technological support. Furthermore, the professional development that they have experienced has never focused on World Englishes. In fact, teachers’ professional development experiences did not address some of their problems and challenges in English teaching in general. Hence, the findings of this study generate some pedagogical implications and suggestions for future research in hopes to improve teacher professional development experiences about English teaching in general and in relation to WE in particular as well as to understand the issues in a broader scope in Indonesian contexts.
    • The Promise of Fantasy: Countering Heteronormative Storylines and Envisioning New(er) Latinx Imaginaries in Contemporary Media

      Bezerra, Katia; Carter, Bryan; Nazario, Claudia; Bolton, Jason C.; Hayward, Eva (The University of Arizona., 2021)
      Drawing from interdisciplinary ideologies, I discuss written, audio, and visual storylines that center women and/or queer Latinxs while challenging heteronormative and ethnocentric tenets in mainstream media. My analysis focuses on the ways the media represent intersectional Latinx identities; I pay special attention to the complex interplay of ethnicity, race, gender, and sexuality. The purpose of this study is to explore how critical storytelling combats ethnocentric, racist, sexist, and homophobic norms promoted in the media. To that end, I compare critical retellings against their traditional versions by closely reading the former to analyze how Latinx representation is impacted by the complex ways a person’s identity categories act upon each other. To demonstrate the ubiquity of racist, sexist, ethnocentric, and homophobic storytelling in both classical and critical narratives, this dissertation analyzes different media (i.e. children’s literature, Television programming, and music) by content creators from three geographic locations (i.e. Cuba, Brazil, and the U.S.) using English, Spanglish, Spanish and /or Portuguese. Chapter I provides an overview of the socializing functions of children’s literature, and a discussion of Había una vez a Spanish-language Cuban fairy tale series written with a multiethnic and feminist perspective. From my analysis, I determine that inserting marginalized individuals into dominant narratives results in stereotypical or prejudicial representations that justify dominant cultures and Eurocentric ideologies established during colonialism. Chapter II focuses on an examination of gender variance in Brazilian telenovelas and eletrofunk music that are broadcasted in Portuguese. The discussion in this chapter demonstrates that reworked storylines or retellings do not transcend biases in mainstream narratives when marginalized characters substitute standard or dominant protagonists. Instead, these types of substitutions communicate to audiences that power is attainable through assimilation to heteronormative and ethnocentric constructs—validating binary gender, compulsory heterosexuality, and European beauty standards. In Chapter III, I discuss the representation of U.S. Latinxs in U.S. media and focus on the five Latinx-focused television series of 2018, particularly on the show Vida’s ability to transcend ethnic and gender biases. I use Vida’s storytelling advances and limitations to delineate three praxes for critical storytelling designed to navigate narratives away from oppressive social norms and the type of storytelling they seek to challenge. I argue for critical storytelling to undertake all of the following three praxes: (1) have groups represented in numerical parity in all aspects of storytelling, (2) present narratives that deconstruct the social logic of oppressive norms, and (3) create new social imaginaries transcending oppressive storytelling and social norms. In other words, I argue for critical narratives written for, by, and about the groups being depicted to counter prejudices, homogenizing troupes, and stereotypes that are employed by traditional storytelling. Secondly, I propose that narratives directly challenge prejudicial ideologies and highlight power inequalities woven into dominant cultures and the media. Lastly, I argue that narratives provide new possible futures for marginalized groups by creating new imaginaries or looking to those of marginalized groups as viable alternatives. Thus, critical retellings can be realized by tapping into the promise of fantasy, an ever-present creative potential and the genre’s driving characteristic—creating the yet unknown.
    • Synthetically Diverse Triazabutadienes and Their Applications Towards Biological Systems

      Jewett, John; Wondrak, Georg; Shepard, Abigail J.; Hulme, Christopher; Sun, Daekyu (The University of Arizona., 2021)
      Small molecule tools for interrogating biological systems are important for studying the inner workings of the cell, from protein-protein interactions to understanding protein fluctuations and dynamics in different disease states. Aryl diazonium ions have been found to be a useful tool for studying proteins, capable of labeling tyrosine residues on a proteins surface. To prevent this electrophile from labeling everything in sight affording nonspecific reactions, a protecting group can be invoked. Once such example is the triazabutadiene, a nitrogen rich structural motif capable of falling apart upon protonation or in the presence of light. Previous studies have focused on characterizing deprotection kinetics at a physiological pH, and aryl diazonium ion adducts have been characterized on single proteins using a fluorophore conjugate. To further the understanding of the triazabutadiene system for both synthetic and biological applications, more complex probes must be designed, synthesized, and characterized to move towards in cellulo experiments. A triazabutadiene was designed bearing an alkyne handle on the sacrificial imidazole ring, which can be functionalized using copper-click chemistry to add on cell targeting moieties such as vitamins for active transport or small molecule signals for a specific organelle of interest. The development of such probes adds layers of synthetic complexity to the system as an acid and base sensitive functional group have been installed. Difficulties associated with methyl ester deprotection led to the explorative synthesis of less stable alkyl and silyl functional groups. While informative on general reactivity, all efforts were futile, either due to azide instability, triazabutadiene instability, or unsuccessful ester deprotection. Synthetic efforts for triazabutadiene functionalization have traditionally stayed away from the use of heat, due to the possibility of thermal intramolecular rearrangements, and metal catalysts, due to the chelating potential of the nitrogen rich scaffold. Previous findings have shown the triazabutadiene scaffold is compatible with copper-click chemistry conditions. These findings inspired the work of optimizing a Suzuki-coupling method for facile attachment of aryl rings to the triazabutadiene scaffold. Although there is a lack of support from literature, it was determined the scaffold is compatible with palladium-ferrocene complexes and can withstand temperatures of 95 °C for up to one hour. The biphenyl triazabutadienes, a novel synthetic class of compounds, are capable of deprotecting at physiological pH and labeling proteins, as determined using native mass spectrometry. An interesting nitrobenzoxadiazole triazabutadiene probe was discovered which displays a turn-on fluorescence profile upon protein labeling, with the intact triazabutadiene being non-fluorogenic. The aryl diazonium ion released upon deprotection was synthesized by an alternate route and tested on proteins to confirm these findings. A triazabutadiene containing a mitochondria targeting small molecule, a triphenylphosphonium ion, and a bromobenzene ring for mass spectrometry identification was synthesized and evaluated on proteins. The bromobenzene azo-adduct was found to label proteins, as confirmed using native mass spectrometry, and the adduct also remained intact during tandem mass spectrometry/mass spectrometry allowing for easy identification of labeled protein residues. The triazabutadiene was found to fall apart at pH 7 with the help of ultraviolet light, giving support for moving this system into a cellular setting for protein identification. In conclusion, this dissertation highlights the synthetic explorations of functionalizing triazabutadienes using novel synthetic plans, and the development of more complex probes with unexpected characteristics which will certainly find a use in the field of biological chemistry.
    • Derivation and Properties of a Modified Relativistic Klein-Gordon Equation for Late Time Evolution of Complex Scalar Fields in the Vicinity of Schwarzschild and Near-Extremal Reissner-Nordström Black Holes

      Brio, Moysey; Plackowski, Nikki; Venkataramani, Shankar; Imbert-Gérard, Lise-Marie (The University of Arizona., 2021)
      This dissertation has provided a framework for black hole perturbation theory, aimed at the study of the stability of black holes. We consider linear perturbations of the Einstein Field Equations and have derived a modified relativistic Klein-Gordon model in observable spacetime coordinates in the presence of Schwarzschild and Reissner-Nordström geometries. The second order partial differential equation for complex fields is dispersive hyperbolic, with its characteristics identical to the null geodesics of the standard ingoing Eddington-Finkelstein coordinates. The equation preserves several important features of the original system such as decaying tail and quasi-normal ringing in the presence of a nonlinear potential introduced due to self-interaction. The dispersion relation for the frozen coefficient equation further exhibits amplification/damping and the origin of the tail. Additionally, it displays convergence to the standard wave equation as waves move further away from the event horizon. The reversal of the sign in the group velocity, near the event horizon, explains the long tail present in the linear case. We have applied both finite differences and finite element methods (of arbitrary spatial polynomial order) to study effects of the charge for fully complex fields as well as effects of the nonlinear self-interaction. A transparent boundary condition was utilized with an experimentally determined advection velocity.We have validated the codes using the method of manufactured solutions and provided a rigorous framework for convergence in the finite element contents. Finally, we have developed an open-source body of code via the DEAL.II software package, which is released on Github at https://github.com/nholtzerresearch/SCRN_Code.
    • Mechanisms of Blood Brain Barrier Dysfunction in Stroke: A Therapeutic Opportunity

      Ronaldson, Patrick T.; Sami, Ayman; Vanderah, Todd W.; Lochhead, Jeffrey J. (The University of Arizona., 2021)
      Stroke is the 5th leading cause of death in the United States according to the 2019 CDC Mortality Data. There are ~795,000 new incidences of stroke each year, and this prevalence is increasing in correlation with the aging population of the United States [159]. At 4-6 hours post-stroke, there is breakdown of the blood brain barrier (BBB). The BBB is comprised of brain microvascular endothelial cells that line the cerebral microvasculature. Functionally, the BBB provides a physical and biochemical barrier between the brain and the systemic circulation. Barrier properties of the BBB are provided by tight junctions and transporters that control selective passage of substances into the brain. During stroke, tight junction integrity and transporter expression is considerably altered, leading to significant leakage of substances from the systemic circulation. Of particular significance, BBB dysfunction also results in edema and swelling in the brain. Following the leak is a generalized immune response that exacerbates the ischemic insult in the brain [236]. Neurons start to die because of the inflammation. If this edema is not controlled within the first 24 hours, cognitive damage is permanent, and death may result [160]. Thus, preservation of the BBB during ischemic injury is critical to maintaining the health of the individual and preventing BBB dysfunction. Due to the limited therapeutic options available, it is critical to discover novel strategies for treatment of stroke and preservation of BBB integrity. In this dissertation, stroke pathophysiology is reviewed with an emphasis on BBB dysfunction. Research methods that can be used to identify new stroke therapeutics that have vascular protective properties will also be highlighted. This discussion will focus on statins, a class of therapeutics that are commonly administered to stroke patients due to their known ability to improve post-stroke neurological outcomes.
    • Henri Dutilleux's Sonate pour piano, Op. 1 (1947–1948): External Influences on His Idiosyncratic Musical Style

      Woods, Rex; Pan, Shuo; Gibson, Tannis; Rosenblatt, Jay (The University of Arizona., 2021)
      The purpose of this study is to explain French composer Henri Dutilleux’s (1916-2013) idiosyncratic musical style through the analysis of form, melody, harmony, texture, rhythm, pianistic techniques, and other features of his transitional work Sonate pour piano Op. 1. Comparison of features of the Sonate proceed with salient excerpts from the Romantic era and from French impressionist composers — Claude Debussy (1862-1918), Maurice Ravel (1875-1937), and Gabriel Fauré (1845-1924) — illustrate Dutilleux’s assimilation of historical styles. Comparison with contemporaneous piano works by Olivier Messiaen (1908-1992), Maurice Ohana (1913-1992), Witold Lutoslawski (1913-1994), and György Ligeti (1923-2006), suggest that Dutilleux may have intentionally fused historical styles with contemporary musical elements into his personal musical discourse. The textural timbres inspired by carillon sonorities, Dutilleux’s preoccupation with the visual appearance of the music, and progressive thematic transformation inspired by French literature illustrate non-pianistic influences.
    • Deconstructing the Dangerous Dead: An Archaeothanatological Approach to Atypical Burial

      Watson, James; Stiner, Mary; Wilson, Jordan A.; Soren, David; Anderson, Bruce; Titelbaum, Anne (The University of Arizona., 2021)
      This dissertation explores the funerary taphonomy of non-normative burials across multiple contexts. Past research has demonstrated that mortuary contexts can offer specific insights into the social identity of the deceased, as well as the beliefs, hopes, and anxieties of the community that buried them. This insight is of special significance when an individual has not been provided the typical burial rites specific to their culture, including unique mortuary treatment or its complete absence. Such non-normative treatment can potentially indicate that the deceased held a special or unusual role in their society, that they had experienced marginalization during life, or that their death was perceived as untimely or unusual. These atypical or “deviant” burials have been documented as indicating periods of environmental stress, social upheaval, or a combination of these. This dissertation uses the archaeothanatological approach as a lens through which to consider how past intentional mortuary behavior can be separated from environmental alteration. As this dissertation demonstrates, the archaeothanatological method contains significant limitations, including a heavy reliance on experiments using nonhuman animal remains to construct the theory, a lack of studies exploring non-Western burial practices (such as exposure or excarnation), and limited consideration of how the approach may need to be modified based on local environmental conditions. Nevertheless, it can be a useful framework for bioarchaeologists to identify unusual treatment of the body and other ephemeral traces of mortuary ritual. The first study focuses on modern, unburied remains recovered from the Sonoran Desert and tests articulation relationships between joints in a specific environmental context. Results demonstrated that postmortem joint integrity is largely dependent not only on anatomical structure and function in life, but the impact of environmental factors such as weathering, temperature, ambient humidity, and most significantly, scavenger activity. The second study examines a burial population from the same geographic and environmental area (the Sonoran Desert) but dating to the Early Agricultural period (ca. 2100 BC to AD 50) and examines the non-normative burials of 21 individuals, with an emphasis on the burials of young females. These burials can be interpreted as a form of sexually antagonistic social signaling and may suggest the community was experiencing a period of significant stress involving resources scarcity, environmental change, or social transition. The final study examines a burial population of neonates and young children from a rural agricultural community in Late Antique (ca. 450 CE) Umbria, Italy. Results of my analysis suggest atypical mortuary treatment may be associated with necrophobia related to the untimely death of the infants, distress possibly heightened by a season of higher than usual infant mortality. More surprisingly, this analysis also indicates acts of mourning and a desire for remembrance, possibly enacted in secret, as such behavior would have been in conflict with cultural expectations regarding infant loss. My findings offer insight into a rural community’s shared stress surrounding sickness, child loss, and unique vernacular belief system in a time of significant cultural and social transition. The results of these studies demonstrate that the archaeothanatological method is limited in its applicability, as skeletal disarticulation, along with the effects of taphonomic processes, varies depending on the specific environmental conditions, and the degree to which the body is exposed to these. However, this research demonstrates how taphonomy can be used to better understand the application of social theory within bioarchaeology. Ultimately, this enables a more detailed analysis of individuals whose complex, reduced, or ambiguous social status—or potentially, the cause and manner of their death—may have precluded their access to normative and culturally appropriate funerary rites.
    • Assessment of Various Precipitation Products in Capturing Atmospheric Rivers and their Performance as a Function of Near-Surface Conditions

      Behrangi, Ali; Arabzadeh, Alireza; Dong, Xiquan; Gupta, Hoshin V. (The University of Arizona., 2021)
      Accurate estimation of precipitation is critical for hydrology, study of the Earth system, and various water-related applications. This study investigates the performance of various precipitation products in two challenging areas. First, their performance in capturing Atmospheric rivers (ARs) precipitation and extreme events related to ARs and, second, precipitation estimation over cold surfaces with snow and ice on the surface. The first chapter of our study comprises investigation of AR‐related precipitation using 18 years (2001–2018) of globally gridded AR locations. AR precipitation features are explored regionally and seasonally using remote sensing (Integrated Multi‐satellitE Retrievals for GPM version 6 [IMERG V6], daily Global Precipitation Climatology Project version 1.3 [GPCP V1.3], bias‐adjusted CPC Morphing Technique version 1 [CMORPH V1], Precipitation Estimation from Remotely Sensed Information using Artificial Neural Networks [PERSIANN‐CDR]), and reanalysis (MERRA‐2 and ECMWF Reanalysis 5th Generation [ERA5]) precipitation products. The second chapter includes assessment of IMERG’s various products (IMERG products include precipitation estimates from infrared (IR), combined PMW, and their combination) with respect to near-surface wet-bulb temperature (Tw), precipitation intensity, and surface type (i.e., with and without snow and ice on the surface) over the CONUS and using Stage-IV product as reference precipitation.The main results include: (1) Based on global AR-related precipitation analysis: most of the world (except the tropics) experience more intense precipitation from AR‐related events compared to non‐AR events. It was found that the degree of consistency between reanalysis and satellite‐based products is highly regionally dependent, partly due to the uneven distribution of in situ measurements. There is a better agreement among the products over the tropics than in higher latitudes. The largest inconsistencies occur over the Southern Ocean where IMERG shows the highest percentage of contribution of ARs to total precipitation and extreme events and consequently the highest deviation from other products used in this study. It is shown that, overall, pairs of IMERG/CMORPH and GPCP/PERSIANN‐CDR have higher spatial correlations globally, which is expected given the similarities in their retrieval methods. (2) Based on investigation of various products of IMERG for precipitation retrieval over surfaces with and without snow and ice cover: PMW products generally have higher skills than IR over snow- and ice-free surfaces. Over snow and ice surfaces (1) PMW products (except AMSR-2) show a higher correlation coefficient than IR, (2) IR and PMW precipitation products tend to overestimate precipitation, but at colder temperatures (e.g., Tw<-10oC) PMW products tend to underestimate and IR product continues to show large overestimations, and (3) PMW sensors show higher overall skill in detecting precipitation occurrence, but not necessarily at very cold Tw. The results suggest that the current approach of IMERG (i.e., replacing PMW with IR precipitation estimates over snow- and ice-surfaces) may need to be revised.
    • Network Analysis of Biomedical Data Using REACH Natural Language Processing

      Yao, Guang; Peri, Sateesh; Ellis, Nathan; Merchant, Nirav (The University of Arizona., 2021)
      One of the core features of scientific work is reading and researching literature. Facing an unknown disease, beginning a new research project, or writing a paper to present your own research data are all good examples of why someone would run a wide literature search. However, it is difficult to stay up to date with the cutting edge of scientific research. A more recent approach that exceeds the limits of traditional manual research lies in automated literature analysis using natural language processing (NLP), something which is particularly relevant in complex biomedical research. NLP permits more rapid access to the information contained in scientific databases and may help to drastically increase the reproducibility of literature searches, allowing researchers to process all documents for a definite result. Network analysis techniques can be used to analyze the information extracted from literature, which often comes in the form of relationships between various biomedical entities. We used the REACH NLP tool to read 1.2 million papers in PubMed to extract mentions of biologically-relevant molecules and their relationship/interaction with other molecules. We then created an application - Visualizing Entities and Relationships in Text (VERIT), that allows users to generate network visualizations by querying the database we generated, which contains relationships between chemicals, proteins, genes, and phenotypes that were extracted by running REACH.
    • Adaptive Multiscalar Design Approach for Urban Dust Storms

      Ida, Aletheia; Modrek, Anahita; Dickinson, Susannah; Dimond, Kirk (The University of Arizona., 2021)
      In the context of the 21st century, which identifies anthropocentrism as a dominant reason for environmental impacts, a consensus is emerging for thinking critically about adaptation and developing necessary actions in response to emerging socio-ecological realities. Continuous processes of urbanization are constantly impacting natural environments, which are deeply interrelated with the aggravation of cumulative environmental, economic, and social problems. This combination results in a profound ecosystem crisis, including climate change, at the epicenter of which are cities and, inevitably, architecture. The natural and urban environments are undergoing a systemic change driven primarily by the evolving processes in culture, science, industry, and commerce. As a result, the architecture discipline seeks to overcome its own preconceptions and adapt to these enhanced understandings of ecological relationships. Therefore, this research focuses on developing a design solution in response to air pollution in arid regions, specifically in Nogales, Mexico. Air pollution is a macro-scale problem that is caused mainly by human activities. If designers integrate human agency with architectural design strategies, we might begin to adapt positively to climate crises like air pollution while increasing our awareness about the impacts of human activities. This research proposes a wearable weather station on a scale of a human body equipped with climate sensors. The wearable weather station or human dust shelter will act like an urban element accessible to people when they face harmful air quality. The design process mainly focuses on environmental data like air movement pattern, the impact of sun and radiation on different surfaces, Sand and Dust Storm (SDS) behavior. The Plant and the adaptation systems in nature also play prominent role as a source of inspiration for learning the morphology and adaptation strategies. The evaluation of these natural systems for commonalities and differences through methodical and rigorous comparison of their flows and compositions reveals that adaptive systems have a strong relationship with context. Similar systems in varying contexts have different performance characteristics and different ways of responding because of the complex set of parameters within the context of evolutionary design. These adaptative systems in nature respond to a complex challenge, showing inherent traits that allow for adaptation to climate change, indicating that both material selection and design strategies need to be based on the specific ecological realities of a given context.
    • Deterministic Optimization for Short-Term Scheduling of Thin Seam Deposits With Autonomous Technologies

      Tenorio, Victor; Palomino, Orlando; Kemeny, John; Momayez, Moe; Vivas, Raul Ernesto (The University of Arizona., 2021)
      The extraction of thin seam mineral deposits requires to overcome several challenges due to the level of accuracy needed in order to cut layers of reduced thickness, which has a direct impact on the reserves, dilution control, and blending, therefore in the final economic results of the operation. This becomes more critical when seams are less than 40 cm. thick. A strategy based on the deployment of smart equipment, which includes autonomous Scrapers coupled with high precision Continuous Surfer Mining (CSM) machines, drones for surveying, and modern programming tools, provides a range of multiple scenarios of scheduled sequences, tailored to satisfying Processing Plant requirements. This proposed combination increases the reserve, diminishes the dilution, and improves the long-term present value of the mine. Case studies are presented with a test of the production system, a schedule algorithm, a short-term sequence code in Python, and the results for optimization using actual field data.
    • Wellness Among Diné Women Who Reside in a Navajo Nation Bordertown

      Kahn-John, Michelle; McEwen, Marylyn; Stuefen, Cristina; Gonzalez, Patrisia; Stauber, Leah (The University of Arizona., 2021)
      Purpose. This study engaged Diné women in describing wellness and how they maintain wellness utilizing a qualitative descriptive methodology and application of the culturally valued process of relational accountability. A Diné Cultural Advisory Committee provided guidance for analysis. Background. Indigenous peoples, including Diné, experience health inequities often addressed via deficit-based approaches. Wellness as a concept and strength-based mechanism to enhance health is pertinent for Indigenous Peoples. Post-colonial feminist theory, Indigenous feminisms, resilience theory, and historical trauma theory add relevant theoretical foundations for the robust description of wellness by Diné women residing in a Navajo Nation bordertown. Methods. The study design was qualitative descriptive. Semi-structured interviews were conducted with six Diné women via Zoom. The culturally relevant process of relational accountability was applied alongside the qualitative research process. Analysis was conducted in a culturally informed and inductive manner. Results. Discoveries on how Diné women perceive and maintain wellness resulted in an overarching theme of “It [Wellness] lays a foundation of who you are,” supported by four domains: “A concept of balance,” “I take this all with me no matter where I am,” “Things just became natural,” and “Diné Asdzání” (Navajo Woman). Domains 1 and 2 corresponded to research questions 1) “How is wellness described?” and 2) “How is wellness maintained?” and Domains 3 and 4 were unexpected and emergent, providing rich, relevant and critical contextual information. Findings support known data on Indigenous wellness: wellness as holistic, collective, inclusive of the living world, and specific to the Diné, inclusion of the concept of Hózhó as congruent to, or complementary to, wellness. Study findings reveal the integral aspect of relational wellness, and describe the diverse and complex manners in which Diné women maintain wellness, learn about wellness, and highlights personal attributes and values of these Diné women leaders. This study is an exemplar of the application of relational accountability when conducting research in Indigenous communities. Future research with Indigenous communities should integrate Indigenous methodologies and apply relational accountability. Further exploration of wellness with other Diné subpopulations is recommended as well as is inclusion of Indigenous feminisms as a theoretical foundation.