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  Amplification of Enterocytozoon hepatopenaei in Penaeus vannamei Hepatopancreas Primary Culture and Immunofluorescence Assay for Detection of Enterocytozoon hepatopenaei

  Viswanathan, V.K.; Cho, Sungman; Dhar, Arun K.; Riggs, Michael; McCarthy, Fiona W.; Fitzsimmons, Kevin M. (The University of Arizona., 2022)

  Hepatopancreatic microsporidiosis (HPM) disease leads to retarded growth in shrimp resulting in a major loss for the shrimp industry worldwide. The causative agent of HPM is a microsporidian known as Enterocytozoon hepatopenaei (EHP). It is little understood how EHP infects its host and hijacks its cellular machinery to replicate more organisms. Lack of an immortal cell line is a bottleneck in studying the cellular and molecular basis of EHP infection in shrimp. For this reason, EHP cannot be propagated in in vitro culture and must be propagated in live shrimp. The use of live EHP-infected shrimp remains the only way to study EHP infectivity. It was hypothesized that supplementing EHP with fresh host cells will aid the propagation of EHP in vitro. Further research must be done but with the data collected at this point, this hypothesis is rejected. In addition to the challenges in amplifying EHP in in vitro culture, there is no antibody-based detection method for EHP. EHP infection in a shrimp is examined by Hematoxylin and Eosin (H&E) histology and real-time polymerase chain reaction based detection methods. Monoclonal antibodies that were previously characterized by Riggs and colleagues to detect Cryptosporidium parvum (C. parvum), successfully detected other parasites. Based on this, it was hypothesized that monoclonal antibodies against C. parvum may also detect EHP.
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  Numerical Investigations of Receptivity, Stability and Transition for High-Speed Boundary Layers

  Fasel, Hermann F.; Haas, Anthony Paul; Craig, Alex; Hanquist, Kyle; Wernz, Stefan H.; Brio, Moysey (The University of Arizona., 2022)

  Numerical tools for receptivity and stability investigations in high-speed boundary layers were developed: A local Linear Stability Theory (LST) solver applicable for axisymmetric geometries as well as linear and nonlinear disturbance flow formulation solvers suitable for complex geometries. Explicit, implicit and time-spectral time-integration schemes were considered. Although explicit methods are comparatively simpler to implement for disturbance flow formulation solvers, the allowable time-step for stability reasons can be much smaller than that required by accuracy considerations. This is especially the case for receptivity problems involving sharp nose geometries, such as cones or wedges, because the resolution requirements in the nose region can lead to severe restrictions of the time-step for explicit schemes. The new solvers were verified and validated for a variety of flow conditions, geometries, and instabilities. Three investigations are presented. First, the effects of (small) leading edge bluntness on the linear stability of flat-plate boundary layers was investigated. For the conditions investigated, it was found that very small nose radii had already a significant effect on the stability characteristics. Second, the receptivity of a Mach 10 boundary layer on a 7 degree half-angle cone to freestream acoustic disturbances was considered. A detailed analysis as well as comparisons with LST are provided. For the case considered, slow acoustic waves converted rather naturally into the unstable mode S, while fast acoustic waves followed the trend of mode F until a specific downstream location where a switch occurred. Finally, linear and nonlinear cross-flow instability computations are presented for an infinite span swept wing with biconvex airfoil at Mach 2. The stability characteristics as well as flow structures associated with the linear, secondary instability and nonlinear regimes are presented and discussed.
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  Germination Response of Twelve Accessions of Bouteloua curtipendula (Michx.) Torr. (Poaceae) to a Simulated Winter Temperature Regime

  Fehmi, Jeffrey S.; Philabaum, Wyatt Thomas; Smith, Steven E.; Gornish, Elise S. (The University of Arizona., 2022)

  Twelve accessions of Bouteloua curtipendula were tested in a laboratory growth chamber to examine the effect of simulated winter temperature on the germination response of the selected accessions of B. curtipendula var. curtipendula (Michx.) Torr. and B. curtipendula var. caespitosa Gould & Kapadia, two botanical varieties of disparate origin. Accessions of the variety curtipendula had significantly higher total germination percentages compared to accessions whose variety was var. caespitosa under the winter treatment. Latitude was also significant with accessions whose origin was farther north exhibiting higher relative germination percentages under the winter treatment. Mean total germination percentage was significantly higher for accessions whose grains were from NPGS seed production facilities under the winter treatment compared to the mean of accessions from wild-collected populations. Mean seed (grain) mass was highly correlated (rs = 0.774) with relative germination percentages, suggesting seed vigor may be an important explanatory factor in germination under stressful conditions.
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  A Drosophila Model of Frontotemporal Dementia (FTD) Based on C9ORF72 Hexanucleotide Repeat Expansion

  Zarnescu, Daniela; Williams, Christi; Tax, Frans; Sutphin, George (The University of Arizona., 2022)

  Frontotemporal dementia (FTD) is a neurodegenerative disorder characterized by a spectrum of symptoms such as loss of intellectual functions, including memory problems, impaired reasoning, abstract thinking, executive function, that can severely impact daily living activities. Frontotemporal lobar degeneration (FTDL) leads to a diverse group of conditions that are hallmarked by atrophy in the prefrontal and anterior temporal cortices. FTD is substantially less common than Alzheimer’s disease, but still greatly impacts individual lives leading to high socioeconomic costs to treat. This specialized level of care is valued at $244 billion, but its costs extend to the family caregivers’ who have an increased risk for emotional distress and negative physical and mental outcomes. Additionally, the overall incidence of cases of FTD is expected to increase, as our aging population is expected to grow by 2030 to include 1 in 5 Americans 65 years old and over. Approximately, 43% of FTD patients have a family history related to dementia or associated neurodegenerative diseases, with up to 27% of individuals carrying an autosomal dominant mutation. When examining the subsets of familial FTD cases, mutations in three genes, microtubule-associated protein tau (MAPT), progranulin (GRN), and C9orf72, are prominent. The overarching hypothesis for this project is that overexpression of C9orf72 hexanucleotide repeat expansions (HREs) in RNA and/or dipeptide repeats (DPRs) in the encoded proteins in mushroom body neurons cause FTD like phenotypes in Drosophila. The present findings in this study show that overexpression of C9orf72 hexanucleotide repeat expansions (HREs) and DPRs in Drosophila MBs causes FTD like phenotypes. Sleep studies revealed that young flies expressing RNA only HREs exhibited greater sleepiness, while polyGR DPR flies displayed sleep changes later in their lifespan. Old (60 day) RNA only HRE expressing males showed sleep fragmentation while female flies exhibited greater sleepiness. Y-Maze assays uncovered that both RNA only HREs and polyGR DPRs caused increased locomotion rather than working memory deficits, as expected. This finding indicates possible hyperactivity in C9orf72 hexanucleotide repeat expansion flies through an increase in movement at both young and old age points. Morphological studies showed a profound, age dependent axonal thinning. In summary, this study shows that both C9orf72 HRE and DPR expressing flies exhibit sleep dysregulation, hyperactivity, and MB lobe thinning changes that could be examined closer to determine the underlying mechanisms of disease and provide further information on the genetic pathways and cellular mechanisms behind C9orf72 induced FTD.
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  Bandages and Plasters as Wound Care In Greco-Roman Antiquity: A Review of The Ancient Evidence and Experimental Analysis

  Hasaki, Eleni; Blanck, Allyson; Groves, Robert; Soren, David; Watson, James T. (The University of Arizona., 2022)

  This thesis project encompasses a comprehensive overview of visual, literary, and archaeological evidence concerning wound care in the ancient Greco-Roman world. Analysis of this evidence will explore medical themes such as the different types of medical responses to wounds available in antiquity, preparation of treatments, and the importance of instructionally minded prose in medical writing. I have approached wound care from an interdisciplinary perspective in order to develop a more nuanced understanding of treatment types associated with injury during these periods. The scope of this project is diachronic and considers the development of wound care (specifically the use of bandages and plasters) from the 5th century BCE to the 2nd century CE. Wound care can involve a range of treatments, but for this project I focus on bandages and plasters as the essential core of material technology which was used by Greco-Roman physicians to encourage wound healing. Currently, there are zero comprehensive studies of plaster as a unique classification of medical treatment. So, this thesis aims to begin approaching the topic in a comprehensive manner, placing it in association with wound care generally, and in contrast with the more well-known linen bandage. The second chapter begins this exploration by discussing visual evidence of bandages and injury as found in Greek and Roman art, to understand non-medical perspectives of wound care. Here, I argue that bandages can be used as a visual attribute for survival when representing important figures such as Patroclus, and, conversely, the lack of visable treatment represents a figure who will likely perish soon, or has already passed away. In the third chapter, I turn to the medical texts and explore how wound care treatments and recipes exist as instructional materials within the literature. Overall, this chapter further contributes to scholarly understanding of the instructional values, as described through the carefully crafted prose which encourages the dissemination of treatment methods and recipes to the reader. These chapters also explore how the Greco-Roman tradition of wound care expands from a much longer and generally Mediterranean medical tradition, derived in part from early Egyptian practices which directly inform the use of medical technology in the Greco-Roman world. This in turn has fundamentally structured our own modern approaches to injury and still informs the basic tenets of the wound care treatments we use every day. The remaining chapters are dedicated to exploring the logistics of ancient wound care using experimental archaeology techniques. Experimental analysis from these chapters explore how various versions of plaster treatments as described within the Hippocratic corpus, Celsus’ De Medicina, and other sources were created. This approach also shows how treatments written as recipes could be effectively recreated by the reader alone in most cases, and what types of common-sense knowledge might be required of the reader to do so successfully. I describe the sources and methodology used to re-create a few chosen plaster recipes known from antiquity, and present the results of each experiment in detail. These experiments were also undertaken in order to fully clarify what the ancient physician considered a plaster to be as a material product, and through this process I have developed a working definition for plaster treatments specifically. By forming these plaster type treatments in the modern day, it is possible to learn more about the limitations of their use, as well as how the treatments were categorized within medical thought. Discussion studies the variety of these treatments, as well as the common qualities and ingredients. Altogether, this approach confirms without a doubt that the medical treatises of Greco-Roman antiquity do have direct instructional value. The dissemination of knowledge through both medical and non-medical literature, as well as through art thus reflects the strength of these sources, and the relative importance they held in antiquity.
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  Optomechanics as a Probe for New Physics: From Dark Matter to Spontaneous Wave Function Collapse

  Wilson, Dalziel J.; Pandurangi, Utkal; Mansuripur, Masud; Wright, Ewan M. (The University of Arizona., 2022)

  Optomechanical systems can be used to probe weak forces arising from fundamental physical phenomena. Here, we analyze experimental efforts to search for ultralight dark matter and test spontaneous wave function collapse models, using ultra-low-loss micromechanical resonators based on silicon nitride membranes. We predict that constraints can be drawn in room temperature, table-top experiments that are competitive with the contemporary bounds set by large-scale experiments such as the Laser Interferometer Gravitational-Wave Observatory. In the future, we envision setting more stringent bounds by operating experiments in a cryostat.
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  Demonstration of Curvature Polynomials for Determining the Zernike Coefficients from Wavefront Curvature Data

  Kim, Daewook; Guruprasad, Divya; Mahajan, Virendra N.; Acosta, Eva; Chalifoux, Brandon D. (The University of Arizona., 2022)

  We describe numerical simulations to demonstrate the use of curvature polynomials introduced by Mahajan and Acosta in their paper “Zernike coefficients from wavefront curvature data” for determining the Zernike coefficients from wavefront curvature data. The wavefront curvature data was determined by evaluating the irradiance distributions in two planes that were symmetric about the focal plane. The irradiance distributions were calculated using the Zemax OpticStudio software program.For the aberration function, the wavefront curvature data was generated from the irradiance distributions. This data consists of the Laplacian of the wavefront across the pupil and its outward normal slope at its circular boundary. The inner products of the curvature polynomials and Laplacian of the wavefront are used to calculate the m ≠ n (i.e., non-harmonic) Zernike aberration coefficients, and the inner product of the boundary slope and curvature polynomials are required to calculate the m = n (i.e., harmonic) Zernike aberration coefficients. We explain the process of obtaining the Laplacian and slope of the wavefront from the two irradiance distributions. Independent case studies of different simulations are performed and explained in detail. The results obtained and limitations of the software are also presented.
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  Control of the Laminar Separation Bubble on a Plunging Airfoil using Plasma Actuators

  Little, Jesse; Pande, Arth; Craig, Alex; Fasel, Hermann (The University of Arizona., 2022)

  The laminar separation bubble on an X-56A wing section is studied experimentally for static and heaving/plunging conditions at α=12° with Re=200,000 (U_∞=11 m/s), and compared with numerical simulations. Heaving/plunging motion perpendicular to the airfoil chord with k=0.70, and h=0.48% is applied. Bubble shedding dynamics from previous studies dictated these parameters. Active flow control (AFC) in the form of ac-DBD plasma actuation is employed in experiments for both static and plunging wing conditions to influence the laminar separation bubble. Flat-plate PIV data was used to characterize the actuator performance in quiescent conditions. The experimental data is compared to 2D slot blowing/suction in CFD. In both cases, the AFC is applied for 75% of the plunging cycle from 90°<φ<360° with St_c=52 (1600 Hz). The simulations used a blowing ratio B=5% while the experiments used B≈1%, resulting in estimates of C_μ=0.000580% and C_μ=0.000534%, respectively. AFC in dimensional frequencies of St_c=26,C_μ=0.000368% (800 Hz) and St_c=104,C_μ=0.000662% (3200 Hz) is also applied to characterize its effect. AFC eliminates the LSB and prevents “bursting” which occurs in the unforced oscillating case. AFC at St_c=52 (1600 Hz) is found to be the most effective, as predicted by CFD simulations. The efficacy of the AFC mechanism arises from the excitation of the primary shear layer instability over the bubble. This produces spanwise 2-dimensional coherent structures in experiments (St_c=52) for both static and plunging conditions. CFD simulations suggest that forcing at the primary shear layer instability can delay transition downstream of reattachment. Similar control authority is observed in experiments, but quantitative evidence for transition delay remains elusive.
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  Environmental Health Catalyst: Visualizing Soil Contamination and Bioavailability of Metal(Loid)S for Action with Communities

  Ramírez-Andreotta, Mónica; Trahan, Alexandra Stewart; Chief, Karletta; Root, Robert (The University of Arizona., 2022)

  Mining poses ecological and human health risks. The state of Arizona has naturally occurring metal(loid)s that can be concentrated and transported during mining activities. These activities can increase human exposure to the mined and processed metal(loid)s. Exposure to metal(loid)s such as arsenic (As), lead (Pb), manganese (Mn), and copper (Cu) are associated with cancer and noncancer outcomes. This work outlines a co-created community science process with the rural town of Superior, AZ, where the community is subject to potential environmental hazards from legacy, active, and proposed extraction activities. Gardenroots, a co-created community science environmental health project started in Superior, AZ in 2018. Community scientists and university researchers determined metal(loid) concentrations in drinking water, soil, and dust. After extensive data sharing efforts, participants began to question past remediation efforts and pose new research questions, e.g.: (1) What sites were remediated?; (2) What determined a site’s eligibility for remediation?; and (3) How can we protect families that are unknowingly moving into homes that may have contaminated soil?. Thus, to answer the community questions, Gardenroots efforts evolved and responded by: (a) maintaining community engagement, (b) identifying and consolidating past monitoring and remediation efforts in the area, (c) creating an interactive soil map that visualized As, Pb, Mn, and Cu concentrations in soil; and (c) determining site-specific Pb and As gastric bioavailability. The soil visualizations include soil data from pre- (126 property values) and post-smelter (17 property values) demolition. To determine the bioaccessible fraction (BAF) of Pb and As, In-Vitro Bioaccessibility Assays EPA Method 1340 was conducted using the Gardenroots residential soils. Our assay calculations indicate bioaccessible fraction for As (12%-53%) and Pb (3%-79%). To provide additional soil sampling and prompt further soil remediation efforts, we worked with local, state, and federal agencies to organize and hosted a Center for Disease Control – Agency for Toxic Substances and Disease Registry soilSHOP on June 4, 2022. At this soilSHOP, we provided soil screening and health education to the Superior, AZ region. Based on community reporting and media tracking, Gardenroots and the soilSHOP prompted further action by Broken Hill Proprietary (BHP) Copper, to continue with their Voluntary Remediation Program (VRP) being overseen by the Arizona Department of Environmental Quality. The VRP is designed to provide environmental monitoring and remediation in town. It is anticipated that the recent actions taken by BHP Copper and Resolution Copper are a result of the co-created community science and soilSHOP, both of which are designed to reduce information disparities and increase environmental health literacy.
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  (Im)possibilities: Exhibition Curation at the National Museum of the American Indian and the Decolonizing Agenda

  Montgomery, Lindsay; Dawson, Charlotte Grace; Austin, Diane; John, Kelsey (The University of Arizona., 2022)

  In its 18 years of operation, the National Museum of the American Indian in Washington, D.C. has continued to attract the attention of researchers and non-specialist audiences alike. Researchers have characterized the museum as a grand experiment in “New Indian Museology” on a national stage, some even suggesting that the institution represents a decolonizing museum (Shannon 2014, Smith 2005). In this thesis, I describe how the NMAI has articulated their “New Indian Museology” and engaged with decolonial praxes through an analysis of their object-oriented displays. In focusing on the physical collections on display for public consumption, this research contributes to decolonial studies of the museum which did not systematically analyze material collections themselves which, “are in fact at the core of the NMAI in profoundly contradictory ways” (Ronan 2014:133). I situate the institution’s strategic goals, mission statements, and methodologies in the context of the actual work that they produce (the exhibitions themselves) to assess how the exhibitions do or do not meet the goals of the institution and the aims of decolonization. Through qualitative content analysis of object display labels and associated texts, I argue that while museum staff activate some elements of decolonial museology (e.g., including narratives of Indigenous persistence and resistance, allowing for Indigenous self-representation, thematic exhibitions), they are unevenly distributed across displays and embedded within colonial modes of knowledge production that are continually upheld in museum displays and the institutional structure. Though the museum continues to rework its curatorial ambitions and strategies, its very status as an institution created and funded by the settler nation-state to manage an enormous colonial object collection inhibits its ability to fully engage with decolonial praxes to create a “Native Place” (NMAI 2004 Strategic Plan).
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  "A Little Jest That Maybe We Could Try" — Playing with Myth in Supergiant Games' Hades (2020)

  Groves, Robert; Waddell, Philip; Morgan, Ian; McAllister, Ken (The University of Arizona., 2022)

  Supergiant Games’ video game Hades (2020) tells the story of Zagreus, son of Hades and Persephone, as he repeatedly struggles to escape his father’s Underworld and, for the first time in his life, meet his mother upon the surface of Greece. While brief, this synopsis immediately speaks to some of the many ways in which Hades is a particularly fascinating work of classical reception. In this thesis, I will conduct case studies of certain “micro-receptions,” so to speak, within the game. I will begin with consideration of Zagreus, exploring what little is known about this mythological figure, and how Supergiant Games at once rejects and embraces contradictions in his extant myths. I will then devote a significant portion of time to considering the Infernal Arms, the weapons which Zagreus uses during his attempts to escape the Underworld. First, I will consider what the Arms tell us about the history of Hades’ storyworld. Second, I will elucidate how the Arms provide crucial context for the relationship between the Hades’ Greece and the rest of its storyworld. Third, examinations of each Arm individually will reveal yet more about Hades’ storyworld, while also speaking to the characters of some of the Arms’ wielders. Finally, I will show how the Infernal Arms are a gateway to understanding how Supergiant Games situated Hades within our world, focusing on its status as a product of gaming history, of the year 2020, and of the United States of America. Indeed, Supergiant Games navigates these contexts with thought and grace, producing an accessible, fun work of classical reception which, as a result, has effectively immersed its players in the classics, introducing newcomers to ancient Greece while setting the stage for countless classical receptions yet to come.
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  Off-Grid Solar-Powered Nanofiltration Pilot Study Relevant to The Navajo Nation

  Karanikola, Vasiliki; Brizo, Ailyn Torres; Hickenbottom, Kerri; Achilli, Andrea (The University of Arizona., 2022)

  Rural communities that are not connected to the electric or water grid often face challenges with access to affordable and safe potable water. Photovoltaic-powered membrane processes are being explored as an option to meet this need for cost-effective, safe drinking water in rural communities. In particular, the lower power requirements and palatable product water make nanofiltration an attractive option. The suitability of nanofiltration depends on many factors such as water quality, operating conditions, and maintenance. Commercially produced nanofiltration membranes are generally assumed to be operated near-continuously, but the nature of the solar power means that photovoltaic water filtration systems are operated intermittently, which may increase fouling and increase likelihood of microbial growth.Water quality analyses was conducted on at 17 sites on the Navajo Nation to determine the need for water treatment and the suitability of nanofiltration. Exceedances of water quality standards for arsenic and/or uranium were found at five sites and exceedances for total dissolved solids were found at 12 water sources, indicating the need for water treatment. Intermittent operation was tested on a pilot-scale nanofiltration prototype for two months with a salt solution with a total dissolved solids concentration of 1350 mg/L containing Mg2+, SO42+, Cl-, and Ca2+. There was little to no change in performance over the two months. Operation with a solution including ferric sulfate caused membrane fouling within 3 days. The system was also tested with a solution containing humic acid alone and a solution containing humic acid and Mg2+, SO42+, Cl-, and Ca2+ with a TDS of 1350 mg/L. The addition of salts decreased flux by about 30% when pH was maintained above 7.5 and about 12% when pH was not controlled. Finally, the membrane fouled by ferric iron was subjected to an autopsy. The results suggest the foulant layer consists primarily of amorphous, colloidal iron.
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  Development of 1000 L Pilot Scale Biodigester for Assessment of Biogas Production and Quality in Biodigestion of Organic Substrates

  Cuello, Joel L.; Pryor, Barry M.; Ramos, Jorge Juan; Orchard, Samantha (The University of Arizona., 2022)

  Anaerobic digestion or biodigestion shows potential to become a cost-effective waste management strategy whereby industrial solid or semi-solid waste is upcycled into an alternative source of energy in the form of biogas. Biogas is a mixture of organic and inorganic gases composed primarily of methane (CH4), carbon dioxide (CO2), hydrogen sulfide (H2S) and trace gases. The general aim of this study was to test organic substrates with differing nitrogen contents for biogas production through biodigestion, which initially included the use of spent-mushroom-substrate (SMS), that is, the leftover straw/cotton seed substrate (70%/30%, respectively) following specialty mushroom production at the University of Arizona. The specific aim of this study was to investigate how three ratios of the substrate combination of oak wood pellets and soybean hull pellets, namely 1:3, 1:1, and 3:1 (oak:soy), using a 1000-L batch and stand-alone biodigester with horse manure providing the needed bacterial inocula, impacted biogas production and biogas composition. The results showed that the 1:3 treatment’s mean biogas yield of 2,854 L significantly exceeded that of the 1:1 treatment of 2,003 L (P<0.05), which in turn significantly exceeded that of the 3:1 treatment of 393 L (P<0.05). The biogas methane contents of the three treatments were statistically indistinguishable from one another (P<0.05); namely, 51% for the 1:3 treatment, 44% for the 1:1 ratio, and 48% for the 3:1 treatment. Similarly, the biogas CO2 contents of the three treatments were statistically indistinguishable (P<0.05); namely, 39% for the 1:3 treatment, 33% for the 1:1 ratio, and 36% for the 3:1 treatment. Thus, the 1:3 oak:soy treatment constituted the optimal treatment among the three treatments tested. This study is arguably the first or one of the first to investigate the use of oak wood and soybean hull as organic substrates for biogas production using biodigesters in the scale of 1000 L.
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  Species Sensitivity to Hydrologic Whiplash in the Tree-Ring Record of the High Sierra Nevada

  Hu, Jia; Winitsky, Anabel Galceran; Meko, David M.; Woodhouse, Connie A. (The University of Arizona., 2022)

  Year-to-year variability of precipitation and temperature has significant consequences for water management decision-making. “Whiplash” is a term which describes this variability at its most severe, referring to events at various timescales in which the hydroclimate switches between extremes. Tree-rings in the Truckee-Carson River Basin (California/Nevada watersheds with headwaters in the Sierra Nevada) and similar basins in semi-arid environments can provide proxy records of hydroclimate as their annual growth is tied directly to limitations in water-year rainfall and temperature, but traditional metrics of reporting explained variance do not distinguish a reconstruction’s sensitivity to whiplash events. In this study, a pool of total ring width indices from five conifer species (Abies magnifica, Juniperus occidentalis, Pinus ponderosa, Pinus jeffreyi, Tsuga mertensiana) in the Sierra Nevada were used to develop a series of standardized reconstructions of water-year regional precipitation using stepwise linear regression on lagged chronologies. A nonparametric analysis approach was then used to classify positive and negative whiplash events in observed and reconstructed regional precipitation. The statistical significance of matching events in regional precipitation by tree-ring reconstructions was assessed using a hypergeometric test. Results suggest that reconstructions from individual species and single sites of those species are often able to track whiplash events. Negative events (wet to dry) are generally tracked more consistently than positive events (dry to wet), although tracking sensitivity differs among species and especially strong tracking of positive events is exhibited by Tsuga. Tracking ability does not exhibit a linear relationship with the explained variance of a reconstruction and has little apparent relationship to the magnitude of whiplash events or the monthly distribution of annual precipitation during those whiplash years.
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  Sea Surface Temperature Variability in the Gulf of California Over the Last 1300 Years

  Anchukaitis, Kevin; Harris, Kira Danielle; Tierney, Jessica; Woodhouse, Connie (The University of Arizona., 2022)

  The North American Monsoon is a crucial component of the ecology and hydrology of the southwestern United States and northwestern Mexico. Sea surface temperatures in the Gulf of California (GoC) are linked to the strength of the monsoon and therefore understanding their variability in this region is essential. However, there are limited instrumental observations and a persistent lack of high resolution paleoclimate records from the core monsoon region. This prevents a better understanding of the behaviors and drivers of this system on time scales from decades to millennia and limits the accuracy of local paleo-temperature estimates. Here we generate a new record of warm season SST using the alkenone-based, UK′37 paleotemperature proxy from sediments cores spanning 695 to 1980 CE. Spectral analyses of our reconstruction show a prominent bicentennial oscillation and multidecadal variability throughout the record. There is a slight cooling trend over the entire reconstruction, but the record lacks a clearly delineated Medieval Climate Anomaly or Little Ice Age. Colder periods in our record appear to be associated with reduced solar forcing and periods of increased volcanism, similar to Northern Hemisphere temperature reconstructions. Multidecadal SST variability in the GoC is likely linked to broader patterns of unforced variability in the Pacific. Our SST record provides novel temperature information that can be used to investigate the link between marine conditions and regional terrestrial precipitation during the Common Era.
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  Exploring Writing Interventions for College Students

  Smith, Eric D.; Struyk, Melinda Willett; Cheng, Katherine C.; Pope, Elisabeth J. (The University of Arizona., 2022)

  Prior literature suggests that reflective writing is a beneficial tool in various measures of mental and physical well-being. This thesis explored whether reflective writing could also be used to intervene on empathy. Empathy is correlated with prosocial behavior, which is said to improve coping strategies, improve relationships, and even result in less physical ailments (Batson & Ahmad, 2009; Cohen et al., 1997, 2003; Decety & Jackson, 2004; Eisenberg & Miller, 1987; Helliwell et al., 2017; Konrath et al., 2011; Kremer & Dietzen, 1991; Medalie et al., 1976). Strategically designed writing prompts that manipulated pronoun usage were given to participants (N = 112) at a university in the southwest United States. Participants (18 – 21 years of age), took an empathy test measure two subscales of empathy (empathic concern and perspective taking) before the writing prompt. They were then asked to write about an interpersonal conflict using first-person pronouns for 7.5 minutes. Following the 7.5-minute writing phase, participants were randomly assigned to one of three conditions: the control, first-person self to other, or third-person omniscient condition. The control condition asked participants to continue writing about the same story in first-person. The first-person self to other condition asked participants to write from another person’s perspective in the story, also using first-person pronouns. Participants assigned to the third-person omniscient condition were asked to write about their story using third-person pronouns. Participants again took the empathy test measuring empathic concern and perspective taking after writing. Results revealed that lower scores on empathic concern predict more change in empathic concern scores following the writing prompt. This was also found to be true for perspective taking in the first-person self to other and third-person conditions, however, these results did reach statistical significance. Further studies should explore the benefit of writing interventions for individuals with lower empathy scores.
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  The Richtmyer-Meshkov Instability in Reshock in a Dual Driver Vertical Shock Tube

  Jacobs, Jeffrey W.; Ferguson, Kevin; Little, Jesse; Craig, Stuart A.; Brio, Moysey (The University of Arizona., 2022)

  We present experiments on the Richtmyer-Meshkov Instability (RMI) in reshock, conducted in a Dual-Driver Vertical Shock Tube (DDVST). The DDVST is a new shock tube that was designed, optimized, constructed, and utilized as part of this work. The DDVST, in effect, consists of two traditional single driver shock tubes, each consisting of a single driver and driven section, oriented vertically opposed on opposite sides of a test section. This new configuration permits a controllable time between the arrival of the first shock that initiates the RMI and the second shock that initiates the reshock regime. Additionally, the dual driver configuration also permits the strength of the first and second shocks to be individually controlled so as to allow for a prescribed post-reshock bulk interface velocity. This capability allows for the post-reshock bulk interface motion to be halted which in turn allows for the cameras used for imaging to be brought closer to the test section, increasing imaging resolution while maintaining a long temporal window in which the RMI may be observed. The DDVST was designed with the goal of achieving the longest post-reshock growth period possible within the physical and practical constraints of the laboratory setting in which the tube resides. The design process was assisted by coupling a numerical solver for 1D compressible flow within a shock tube to a genetic optimization routine with the aim of finding the combination of shock tube section lengths that produce the longest window in which the RMI in reshock may be observed. Different optimal designs corresponding to different light shock Mach numbers were calculated to examine whether a longer effective period of RMI evolution could be obtained for a given light shock Mach number. A single design was selected from these candidate designs based on its performance over a range of expected experimental parameters, which was then constructed and used for this work. The DDVST uses the method of Jones and Jacobs (Phys. Fluids \textbf{9} (10), October 1997) to generate the initial interface between the two test fluids without the use of a membrane which may influence the flow. This method forms the initial interface between two gases of differing density by flowing the more dense gas into to the tube from below a set of holes drilled at the desired interface location while simultaneously flowing a less dense gas from above the same holes. These two gas streams meet at the set of holes and flow out of the tube, forming a stable, stratified, and slightly diffuse interface. Multimode, three-dimensional, random initial perturbations are then imposed on the interface using a pair of voice coil actuators. The test gases for all experiments are Air and Sulfur Hexafluoride (SF$_6$) which yields an Atwood number of 0.67. The experiments presented as part of this work have a nominal light gas shock wave Mach number $M_L = 1.17~(\sigma = 0.007)$ and heavy gas shock wave Mach number $M_H = 1.18~(\sigma = 0.004)$ for all experiments, where $\sigma$ is the standard deviation. This results in the bulk interface motion being halted following the passage of the second shock. The experiments presented examine the influence of changing the length of time between shock and reshock on the behavior of the RMI in reshock for a range of shock to reshock times. Also examined is the influence on the order of arrival of the two shock waves, with both the traditional (light shock first) and reversed (Heavy shock first) configurations considered. The shock to reshock times examined are between -4.0 (Heavy shock first) and +3.8 (Light shock first) ms. The growth exponent, $\theta$, extracted from a fit of $h(t) = a t^\theta$ to the width of the mixing layer versus time for each experiment, appears to be insensitive to changes in the shock-to-reshock time or order of arrival of the two shocks, with an average value of $\theta_{H,W} = 0.365 \pm 0.018$ (95\%) and $\theta_{L,W} = 0.381 \pm 0.02$ (95\%) for heavy shock first and light shock first experiments, respectively, where (95\%) denotes the 95\% confidence interval of the result. The rate of decay of TKE appears to be affected by the order of arrival of the two shock waves, using a fit of $TKE(t) = a t^p$ to the total amount of TKE in the mixing layer for each experiment, yielding an average value of $p_H = -0.823 \pm 0.06$ (95\%) and $p_L = -1.061 \pm 0.032$ (95\%) for the heavy and light shock first experiments, respectively. The method of Thornber, Drikakis, Youngs, et al. (J. Fluid Mech. \textbf{654}, 2010) is used to extract a value of the growth exponent from these rate of decay of TKE measurements, yielding values of $\theta_{H,TKE} = 0.392 \pm 0.02$ (95\%) and $\theta_{L,TKE} = 0.312 \pm 0.011$ (95\%) for the heavy and light shock first experiments, respectively. Analysis of the anisotropy of the mixing layer over time is performed by examining the Reynolds anisotropy tensor in addition to the anisotropy ratio. An early time trend towards isotropy following reshock is found, with experiments with longer shock-to-reshock times demonstrating a more rapid trend towards isotropy than those with a shorter shock-to-reshock time. The anisotropy ratio of the mixing layer approaches an average minimum value of $A \approx 1.2$ for the longest shock-to-reshock times, and $A \approx 1.3$ for shorter shock to reshock times. The mixing layer becomes increasingly anisotropic over the remainder of the experiment, with no notable difference in the degree of anisotropy versus shock-to-reshock time or order of arrival of the two shock waves. The analysis of the spectrum of anisotropy shows that the largest scales of the flow have a trend towards anisotropy, but those at smaller scales tend to be isotropic. The Reynolds number, defined as $Re = h \dot{h} / \nu_{avg}$, is analyzed versus shock-to-reshock time. For shock-to-reshock times $\gtrapprox$ 1 ms, the Reynolds number is found to approach $Re \approx 1 \times 10^5$ for both heavy shock first and light shock first experiments. This is excess of the $Re > 1 \times 10^4$ proposed by Dimotakis (J. Fluid Mech. \textbf{409}, 2000) for a transition to turbulent mixing, though it does not meet the suggested critical value of $Re > 1.6 \times 10^5$ suggested by Zhou (Phys. Plasmas, \textbf{14} (8), 2007). Analysis of these experiments using the time-dependent turbulent length scales and associated turbulent transition criteria of Zhou, Robey, and Buckingham (Phys. Reveiw E, \textbf{67} (5), 2003) suggests that these experiments are beginning to transition to a fully turbulent state.
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  Actin Regulation of the Morphology, Dynamics, and Development of Dendritic Filopodia

  Mouneimne, Ghassan; Ly, Kenneth Tran; Charest, Pascale; Yao, Guang (The University of Arizona., 2022)

  Dendritic filopodia (DF) are thin, highly dynamic structures that project from neuronal dendrites. Once a DF finds and latches onto an axon from another neuron, the DF develops into the postsynaptic portion of a mature synapse. Synapses and their development from DF form the foundation of learning and memory and are implicated in many neurological diseases. The dynamics, morphology, and development of DF are heavily dependent on the actin reorganization within them. Because DF are composed of branched actin filaments, DF are distinct from conventional filopodia, which are composed of parallel, straight actin filaments. Thus, the actin regulation of DF is unique. This thesis will consider some of the proteins reported in the literature to be involved in actin regulation in DF, such as profilin, formins, the enabled (Ena)/vasodilator-stimulated phosphoprotein (VASP) homology proteins, the actin-related protein 2/3 (Arp2/3) complex, metastasis suppressor 1 (MTSS1)/missing-in-metastasis (MIM), and actin-depolymerizing factor (ADF)/cofilin, and synthesize the information to propose a comprehensive model of DF development. A deeper understanding of the regulation of DF can open the door for future research into the mechanisms of many diseases and new interventions and therapeutics for them.
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  Subgenome Fractionation in a Homoploid and Allopolyploid Hybrid Complex

  Barker, Michael S.; Vizzerra, Andres D.; Dlugosch, Katrina M.; McMahon, Michelle N. (The University of Arizona., 2022)

  Hybridization and polyploidization are common evolutionary processes in vascular plants. Both processes contribute to the evolution of allopolyploid species, but the unique contributions of hybridization versus polyploidy to these species is not clear. This is partly due to the absence of homoploid hybrid species and allopolyploid species from the same parental diploids. Here, I use a unique species complex in Selaginella to explore the impacts of hybridization and polyploidization on genome evolution. Selaginella is one of the largest genera of lycophytes, despite having one of the smallest nuclear genomes found in vascular plants. The southwestern US and mainland Mexico are a center of functional and taxonomic diversity in Selaginella. Here, in the transition zone between the Lower Colorado River Valley and Arizona Upland subdivisions, diploid hybrids, and allopolyploids of S. arizonica ✕ S. eremophila thrive. Both hybrid taxa have distinct levels of desiccation tolerance and occupy more extreme environments than either of the parents. Using a combination of transcriptome and genome data, I assembled and annotated five reference Selaginella genomes, including the two homoploid and allopolyploid taxa. I investigate the relative contributions of each parent to the genomes of the hybrids and compare the impact of hybridization and polyploidy on genome evolution. A genome content analysis using reciprocal best blast hits (RBH) found strong patterns of biased fractionation in the hybrid complex, each biasing between 12-16% towards one parent. Interestingly, this was a reciprocal pattern, the homoploid and allotetraploid each retained more genomic content from the opposite parent. We determined the maternal origin of the plastid organelles through de novo chloroplast genome assembly, alignment, and phylogenetic inference, which further revealed that more genomic content was retained from the maternal parent. In summary, we believe this is one of the only cases of reciprocal biased fractionation in a hybrid complex.
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  Head and Neck Dynamics: Prediction of Sports Related Head Impact Characteristics

  Laksari, Kaveh; Frantz, Callie; Missoum, Samy; Li, Zong-Ming (The University of Arizona., 2022)

  Brain injuries sustained during an impact to the head during sport and recreation related activities are a common occurrence. They can cause adverse effects in injured participants, some of which are identifiable immediately following contact, while others may not manifest for years. The study of concussive and sub-concussive impacts of sport and recreation activities is important in understanding the mechanism of impact, resultant brain response, and how injury manifests to improve risk of injury assessments, game-play decisions, and protective equipment. This study aims to relate the kinematic motion experienced by the head during impact, to the characteristics, magnitude, direction, and location, of the force applied to the head during contact. To investigate this relationship, a pendulum impact device was designed to replicate on-field impacts of contact sports, kinematic data was collected from an anthropomorphic test device during an applied impact, and the resultant kinematics were related to applied generalized force through Euler-Lagrange dynamics of a simplified rigid link model. Through this system of dynamic equations, the characteristics of applied force were predicted within reasonable bounds; the results of this study could lead to better on-field injury assessments and improved protective equipment.

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