• Eddavidite, a New Mineral Species, and the Murdochite (Cu12Pb2O15Cl2)-Eddavidite (Cu12Pb2O15Br2) Series

      Downs, Robert T.; Rosenblatt, Melli; Holliday, Vance; Thirumalai, Kaustubh (The University of Arizona., 2021)
      Eddavidite is a new mineral species (IMA2018-010) with ideal formula Cu12Pb2O15Br2. It has cubic Fm3m symmetry; a = 9.2407(9) Å; V = 789.1(2) Å3; Z = 2. Eddavidite is the bromide analog of murdochite, with which it forms a solid solution series. The type locality is the Southwest mine, Bisbee, Arizona, U.S.A. Eddavidite also occurs in the Ojuela mine, Mapimí, Durango, Mexico. Eddavidite forms zones within mixed murdochite-eddavidite crystals. Spot analyses of Bisbee samples show up to 67% eddavidite component while Ojuela samples show up to 62%. Eddavidite-murdochite crystals show forms {100} and {111}; the habit grades from simple cubic through cuboctahedral to unmodified octahedral. Eddavidite is black and opaque with submetallic luster, and visually indistinguishable from intergrown murdochite. Its Mohs’ hardness is 4. Eddavidite exhibits good cleavage on {111}. The empirical formula, normalized to 12 Cu apfu is Cu12(Pb1.92Fe0.06Si0.06) (O15.08F0.02) (Br0.99Cl0.89•0.12). dcalc. = 6.33 g/cm3. dmeas. = 6.45 g/cm3. The crystal structure consists of corner sharing square planar CuO4 units, arranged in Cu12O24 metal oxide clusters, which encapsulate Br atoms. PbO8 cubes share edges with Cu12O24 clusters in a continuous framework. Eddavidite is one of only 10 mineral species with essential Br. Eddavidite crystallizes from bromine enriched fluids leftover from desiccation of paleo-seawater at its two known localities.
    • Sensing and Arresting Corrosion of Haynes 230 Alloy in Molten Chloride Salts at 800°C

      Gervasio, Dominic; Sasaran, Vlad; Farrell, James; Guzman, Roberto (The University of Arizona., 2021)
      The corrosion of metal in molten chloride salt is studied and lowered using a power supply. A particular emphasis is on the ternary eutectic sodium chloride, potassium chloride and magnesium chloride (MgCl2-KCl-NaCl) salt with a melting point of 387°C, because it is the high temperature heat transfer fluid of choice in electrical power generators and Haynes 230 alloy (H230), because H230 is a ductile metal which retains its strength at high temperatures (800oC). A potential negative of the open circuit potential of H230 metal alloy in ternary eutectic MgCl2-KCl-NaCl is applied, the cathodic potential generates a negative (cathodic) current for the reduction any oxidants, such as metal ions, oxygen and water, in the molten salt. The magnitude of the cathodic current is a signal of the level of oxidants present in the salt. Applying the cathodic potential also arrests ionization of metal, that is, corrosion of the metal. The increasing level of oxidant impurities, (particularly water) in the molten chloride salts causes the open circuit potential (OCP) of H230 versus a silver and silver chloride reference electrode (SSE) to shift positive, which gives a warning that the molten chloride salt heat transfer fluid is corrosive to metal. The OCP is crudely measured by direct readings of H230 and SSE with a voltmeter and refined by potentiodynamic scans of current versus potential of H230 versus SSE, where the H230 potential is scanned 30 millivolts starting negative of to positive of the OCP found with the voltmeter. A linear rate equation, called the Stern-Geary method is used to find corrosion potentials and estimate corrosion rates (CR) of H230 alloy in molten salt at various relative humidity (RH) of Argon atmospheres equilibrated with the molten salt. In oxidant free ternary MgCl2-KCl-NaCl eutectic molten salt, the OCP of H230 vs SSE is -866±24 [mV] and CR of 85±9 [micron/year]. In ternary eutectic molten salt equilibrated with a 40% RH Argon flow the OCP of H230 vs SSE is -363±1 [mV] and CR of 4670±780 [micron/year]. When a negative potential, of -200mV from OCP in anaerobic salt, is applied to a H230 working electrode in eutectic molten salt at 800oC and 100% RH Argon flow is flowed over salt for 20h, it was found that this H230 working electrode (WE) was cathodically protected, because the WE (cathode) lost only 0.0552g while the counter H230 electrode (CE), a “sacrificial” anode, lost 0.4513g. This gives a preliminary assessment a cathodic potential is effective for arresting corrosion of H230 metal in oxidant-contaminated salt at temperatures up to 800oC.
    • The Origins and Evolution of an Early Microbial Rhodopsin Protein

      Kacar, Betul; Sephus, Cathryn Dawn; Gutenkunst, Ryan; Duhamel, Solange (The University of Arizona., 2021)
      The advent of cellular organisms took place sometime between the start of prebiotic chemosynthesis on Earth and the evolution of the last universal common ancestor. Cellularity is now a fundamental organizational principle shared by all life on Earth and represents a key transition in evolutionary history. The emergence of cellular organization necessitated organisms to evolve a means to permit and regulate the exchange of material between the intracellular compartment and the extracellular environment. This capability implies both the ability to embed proteins into their membranes and to translocate molecules across their membranes. Other factors integral to the progression of early cellular life were the maintenance of transmembrane potential and chemiosmotic coupling for generating and conserving energy, and pigments to absorb light energy for photosynthetic and phototrophic metabolisms. Microbial rhodopsins, a superfamily of photoactive membrane proteins, have been suggested to be the simplest and possibly most ancient form of a phototrophic metabolism, likely providing a mechanism for microbial energy capture in Earth’s early shallow marine ecosystems. The retinal-based photosystem (rhodopsin) is composed of one retinal chromophore and one opsin protein. In this system, light absorption directly drives a conformational change in the protein via the isomerization of the retinal moiety to carry out biological functions such as ion pumping and ATP synthesis. Here, computational approaches were used to investigate the evolutionary history of rhodopsin proteins, combining phylogenic reconstruction and ancestral sequence inferences. Additionally, protein structure modeling and biophysical predictions were used to reveal ancestral rhodopsin functionality. Together, these results may shed light on the evolution of pigment-based metabolisms and prove beneficial for understanding the characteristics of early cellular membranes.
    • Occupancy of Terrestrial Mammal Populations in U.S. National Parks of the Southwest

      Prudic, Kathleen L.; Buckisch, Alexander; Steidl, Robert J.; Hubbard, John A. (The University of Arizona., 2021)
      North American mammal populations face many novel and powerful threats that are changing quickly over space and time. To complicate management and conservation decisions further, few established monitoring programs that can reliably detect changes in multiple mammal populations across species exist. Knowledge about the persistent threats and long-term trends of mammal populations are of immense importance to the public, the scientific community, as well as federal and state agencies charged with managing and protecting natural resources. We used an existing camera-based protocol to estimate occupancy of several terrestrial mammal species in seven U.S. National Parks in the Sonoran Desert. We surveyed 241 sites for 365 days to evaluate the detection efficiency (detected vs expected species) in different park units, evaluate a set of environmental variables with the potential to influence occupancy (ψ) and detection (p) probabilities of terrestrial mammals, and to estimate statistical power of the protocol to detect changes in occupancy. On average, we detected 76% (95% CI: 64% – 88%) of medium-to-large sized, native, mammals known to be present in surveyed park units. Mean occupancy across all park units ranged from 0.79 (0.10 – 0.86) for coyote (Canis latrans) to 0.12 (0.04 – 0.28) for black bear (Ursus americanus). Mean detection probability was highest for black-tailed jackrabbit (Lepus californicus) (0.35, 0.27 – 0.45) and lowest for mountain lion (Puma concolor) (0.06, 0.02 – 0.19). For many species, occupancy decreased as elevation and slope increased, and detection probability increased as precipitation increased during the study period. In addition, statistical power to detect changes in occupancy between two surveys was influenced mostly by occupancy and the number of sites surveyed. Power to detect changes in occupancy only increased to around 35 survey occasions (deployment days) above which it was relatively insensitive to increases in the number of survey occasions. Similarly, species with a higher initial occupancy achieved power to detect a change in occupancy faster (fewer survey occasions) and with less survey effort (fewer sites) than species with lower initial occupancy, whereas power was insensitive to changes in detection probability above 0.40. The camera trapping protocol we evaluated is sufficient to detect changes in occupancy with high power for species that are common (ψ = 0.80 – 0.99) and relatively easy to detect (p = 0.20 – 0.99), but not for species that are rare (ψ = 0.10 – 0.50) or difficult to detect (p = 0.10 – 0.19). For rare species, we suggest increasing detection probability by using lures and baits, increasing the duration of the survey period and surveyed sites, or strategically placing cameras in known areas of high activity. We conclude that the camera trapping design is well suited for simultaneously and cost-effectively monitoring terrestrial mammal communities within and between park units over the long term. This monitoring protocol has potential to inform conservation and management of mammals within the NPS and many other areas of North America.
    • On Lieb-Robinson Bounds in Open Quantum Systems

      Sims, Robert; Roon, Eric Brandon; Ercolani, Nicholas; Keller, Christoph (The University of Arizona., 2021)
      In 1971, A. Kossakowski \cite{kossakowski} axiomatized the study of the dynamics associated to non-Hamiltonian systems of quantum particles. These have come to be known as Open Systems, and through the work of Lindblad \cite{Lindblad76}, a classification of the generators of the dynamics of such systems in the Heisenberg picture -- for bounded generators -- is known (this is not so for the unbounded case). Following the work of Gorini, Kossakowski, and Sudarshan: \cite{gks}; we prove this classification scheme in finite dimensions, where it is accessible by computational means as in \cite{alickifannes}. With this knowledge, we prove a Lieb-Robinson bound for the irreversible dynamics in the case of time-independent interactions on a countable (possibly infinite) collection of sites. Such a result was proven by \cite{Nachtergaele} for the time-dependent case, in 2011.
    • Remediation of Per-and Polyfluoroalkyl Contaminated Groundwater Using Cationic Hydrophobic Polymers as Ultra-High Affinity Sorbents

      Sierra-Alvarez, Reyes; Field, James A.; Gomeniuc, Anton; Chorover, Jon; Karanikola, Vasiliki (The University of Arizona., 2021)
      Per-and polyfluoroalkyl substances (PFAS) are a group of man-made chemicals which most known representatives are perfluoroctanoic acid (PFOA) and the perfluorooctane sulfonate (PFOS). These chemicals have been widely used in both industrial processes and consumer products and they are ubiquitous environmental contaminants. Many PFAS are toxic, bioaccumulative and very persistent in the environment. Due to the growing concern about the potential adverse effects of PFAS on human health, the U.S. Environmental Protection Agency has established a health advisory limit for drinking water for both PFOA and PFOS combined of 70 ng L-1. This very low advisory level together with the high resistance of PFAS to chemical and biological degradation make the removal of PFAS from aquatic bodies a complicated task, being the only currently feasible option the use of activated carbon or ionic exchange adsorption processes. These approaches are very costly due to the need for frequent bed replacement; thus, new treatment methods are required to efficiently remove PFAS from contaminated water. PFAS sulfonates and carboxylates contain a hydrophobic fluorocarbon chain and they are present as anionic species under environmental conditions. Based on these properties, this study proposed the synthesis and use of cationic hydrophobic polymers based on aniline and pyrrole as ultra-high affinity PFAS sorbents. These polymers were chosen because their positive charge and hydrophobic carbon backbone is expected to promote strong electrostatic and hydrophobic interactions with anionic PFAS. Polypyrrole (PPy) and six polymers based on aniline with different functional group substitutions were synthesized, namely, polyaniline (PANI), poly-o-toluidine (POT), poly-o-anisidine (POA), poly-o-ethylaniline (PEA), poly-sec-butylaniline (PSB), and polynaphthylamine (PNA). The impact of the different substitutions on the polymer properties as well as their effectiveness as PFAS adsorbents was evaluated. The use of precursors with different substituents had a major impact on the chemical composition of the polymers as shown by elemental analysis, as well as FTIR and XPS analysis. Likewise, the chemical structure of the precursors had a large impact on different physico-chemical properties of the polymers such as their specific surface area, zeta potential, isoelectric point, and acid-base behavior. From the seven synthesized polymers, PANI, POT, and POA presented the best PFAS adsorption characteristics. Individual isotherm experiments showed that POT, with a Freundlich coefficient of 78 (mg g-1)(mg L-1)-n, was the sorbent with the highest affinity for PFOA, followed by PANI and POA, with Freundlich coefficients of 46 and 30 (mg g-1)(mg L-1)-n, respectively. The Freundlich coefficient of PAC, 187 (mg g-1)(mg L-1)-n, was higher compared to that of POT. Nonetheless, at environmental relevant concentrations (ng L-1 to µg L-1), POT showed similar PFOA affinity and adsorption capacity as crushed granular activated carbon (PAC). Furthermore, evaluation of PFOA adsorption under increasing pH (pH range from 3 to 11) showed that the range of maximum sorption capacity varied depending on the polymers. This behavior suggests that the hydrophobic cationic polymers can be customized to enhance PFAS adsorption under different aqueous chemistry conditions. Contaminated groundwater often contains a mixture of PFAS, therefore, the adsorption of the fluorinated compounds listed in the EPA Third Unregulated Contaminant Monitoring Rule(i.e., perfluoroheptanoic acid (PFHpA), perfluorooctanoic acid (PFOA), perfluorononanoic acid (PFNA), perfluorobutane sulfonate (PFBS), perfluorohexane sulfonate (PFHxS), and PFOS) as well as the fluorotelomer FtS 6:2 using the most promising sorbents was evaluated. Single solute isotherms as well as isotherms determined using a multicomponent PFAS mixture showed that both, the ionic head group and chain length, had a strong impact on the adsorption of the different PFAS. Perfluoroalkyl sulfonates were more effectively adsorbed than their carboxylic analogues with the same chain length. Furthermore, the adsorption of PFAS with the same functional head group increased with increasing fluorocarbon chain length, suggesting the importance of hydrophobic interactions between the fluorinated compounds and the adsorbent. This behavior was observed in experiments with both POT and PAC. Adsorption process are generally very sensitive to the aqueous chemistry (e.g., pH, ionic strength, ionic composition) as well as the presence of co-contaminants, such as natural organic matter (NOM), that compete for active sites on the sorbent surface and decrease the adsorption of the targeted compounds. PFOA adsorption capacity of the polymers was found to decrease with increasing NOM concentration, but to a much lower extent compared to PAC. At the highest NOM concentration tested (2 mg L-1), the PFOA adsorption capacity of POT and PANI decreased by 40 and 60%, respectively, whereas PAC lost nearly all its adsorption capacity under the same conditions. This observation could be due to the involvement of both hydrophobic and electrostatic interactions on PFAS adsorption by the polymeric adsorbents, while PFAS adsorption by PAC only relies on hydrophobic interactions. On the other hand, increasing ionic strength had an important impact on the PFOA adsorption capacity of PANI and POA, which decreased by 93% when the ionic strength was as low as 5 mM NaCl. In contrast, POT only lost 20% of its initial PFOA adsorption capacity in the presence of very high NaCl levels (500 mM). The impact of tionic strength on the adsorption process was highly depended on the ionic species. In contrast with NaCl, divalent salts at ionic strength of 5 meq L-1 (CaCl2 and Na2SO4) caused a substantial increase in the affinity of the polymers for PFOA, up to six times in the case of POA at a salt concentration of 5 meq L-1. Under the same conditions, the divalent salts did not alter the PFOA adsorption capacity of PAC. The synthesized polymers had a relatively low specific surface area (1-26 m2g-1) compared to GAC, a widely used PFAS adsorbent (814 m2 g-1). The low specific surface area (SSA) of the polymers suggests that it may be possible to enhance significantly the PFAS adsorption capacity of these materials by increasing their SSA. Different approaches were explored to obtain polymers with high SSA such as the synthesis of nano-sized- and crosslinked polymers. The synthesis of nano-sized polymers led to a large increase in the fraction of small size pores (size < 1 nm), however this increase was not accompanied by an enhancement of the SSA and PFOA adsorption capacity of PANI. Crosslinking of PANI with paraformaldehyde led to a very high increase of the SSA of the polymer (up to 20-fold) as well as an increase in the fraction of small size pores (< 5 nm). However, a proportional increase in the PFOA adsorption capacity of the crosslinked polymer was not observed, and its Freundlich constant was just doubled. The results obtained also indicated that the increase in SSA was strongly dependent on the dose of crosslinker utilized. Due to the morphology of the synthesized polymers, which are fine powders, their use in packed-column adsorption processes would be complicated due to high pressure losses and polymer washout. Thus, synthesis of polymers grafted on a granular material was performed, using GAC and cellulose as supporting materials. Our results confirmed that the studied polymers could be grafted on GAC and that the synthesized composites presented high SSA and high affinity for PFAS compounds. The adsorption capacity of the composite materials was similar to that GAC and even higher when small amounts of PANI were grafted on the GAC surface. In contrast with the GAC/polymer composites, PANI grafted on microcrystalline showed a very low PFAS adsorption capacity. Predicting the rate at which adsorption takes place is important for adsorber design. Therefore, kinetic experiments were performed to characterize the rate of PFOA adsorption by the most promising materials. The kinetics of PFOA adsorption by the evaluated polymers were comparable to that of a leading PAC, except for crosslinked PANI that had a 70% higher second-order adsorption rate than PAC. Overall, these results indicate that the most effective hydrophobic cationic polymers (PANI, POT, and POA) offer great promise for the removal of PFAS from contaminated water. These sorbents display high PFAS adsorption affinity and capacity, rapid PFAS adsorption kinetics, and they can be grafted on a granular material to facilitate their use in continuous-flow absorbers. The involvement of electrostatic and hydrophobic adsorption mechanisms on PFAS adsorption by the new materials provides clear advantages for their application under variable aquatic chemistry conditions (e.g. presence of contaminants, NOM, ionic species) when compared to conventional adsorbents such as granular activated carbon.
    • Optimization and Design Strategies for Wireless Battery Free Implantable Electronics Using Deep-Learning-Based Markerless Tracking

      Gutruf, Philipp; Azami, Amirhossein; Yoon, Jeong-Yeol; Margolis, David (The University of Arizona., 2021)
      Wireless, battery-free neural interfaces enable the removal of large, bulky batteries and tethers required for conventional neural interfaces, which cause movement artifacts and impact the behavior of animal models. Allowing fully implanted neural and organ interfaces enables advanced insight into social interactions and expands studies towards subjects that move in 3D, such as birds. The free motion of subjects places an emphasis on mechanical, electromagnetic, and optical design approaches that accommodate operation in highly mobile areas and reduction of device impact on the motion of the subject. To enable designs highly tailored to the animal model, this thesis explores the utilization of Deep Neural Network (DNN) based markerless tracking of animals to inform designs of electromagnetics and mechanics design of wireless, battery-free electronics.To enable a high level of miniaturization, wireless and battery-free device architectures design of communication and energy harvesting antennas is critical to realize miniaturization, operational range, and data rates to allow for multimodal operation in subjects that move in 3D. This thesis explores informing the primary antenna design by extracting the animal's behavior using DNN tracking to shape intensity profiles optimized towards maximum energy transfer to miniaturized implants. Conversely, the thesis will also explore DNN tracking for the assessment of neural interface’s behavioral impact on the animal models to inform mechanical designs of subcutaneous structures to enable seamless organ interfaces such as the musculoskeletal system.
    • Role of Redox Shuttles in the Biotransformation of Insensitive Munition Compounds by Geobacter

      Sierra-Alvarez, Reyes; Field, James A.; Wong, Stanley; Brush, Adrianna (The University of Arizona., 2021)
      3-Nitro-1,2,4-triazol-5-one (NTO) is a nitroheterocyclic compound that is a component of insensitive explosives. Due to the lower risk of accidental detonation, insensitive munitions are being used more frequently in place of conventional explosives. Environmental contamination with insensitive munition compounds (IMCs) occurs from industrial wastewater discharge and undetonated material in soil. The toxicity of NTO is not fully understood and has created a need to remove it from the environment. Prior research has developed a highly enriched culture for NTO bioreduction. This culture, composed mainly of Geobacter anodireducens and Thauera species, reduces NTO to 3-amino-1,2,4-triazol-5-one (ATO) and oxidizes acetate to CO2. This study explores the possibility of using redox mediators to increase the rate of NTO reduction or to expand the range of compounds that could be reduced by the culture. The redox mediator chosen for these experiments is 9,10-anthraquinone-2,6-disulfonate (AQDS), a model compound for other humic substances present in soil. It was found that the addition of AQDS to the enrichment culture with NTO can increase the rate of NTO reduction. The AQDS was directly reduced to 9,10-anthrahydroquinone-2,6-disulfonate (AH2QDS) by the enrichment culture with acetate as an electron donor. The reduced quinone can chemically react with NTO and other nitro group containing compounds to reduce the nitro compounds while oxidizing back into AQDS. This study highlights the potential of increased NTO reduction rates with redox mediators and the potential to expand the substrate spectrum of what can be reduced by this enrichment culture.
    • Preferential Behaviors of Fluorinated Surface-Active Molecules at Liquid-Liquid Interfaces

      Savagatrup, Suchol; Trinh, Vivian; Karanikola, Vasiliki; Saéz, Avelino E. (The University of Arizona., 2021)
      Contamination of per- and polyfluoroalkyl substances (PFAS) in water supplies will continue to have serious health and environmental consequences. Despite the importance of detecting the presence of PFAS at potential sites of contamination and at treatment plants, there are few scalable techniques that provide the necessary selectivity to distinguish fluorinated surfactants (such as PFAS) from other surface-active components and the sensitivity to quantify the low concentration often present in real-world conditions. Existing gold standards—namely liquid chromatography electrospray tandem mass spectrometry (LC-MS/MS)—can provide ultra- low limits of detection and superb selectivity. However, such methods require well-equipped laboratory with well-trained specialists. Thus, these methods are cost-prohibitive for large scale efforts to fully map the presence of PFAS in water production wells or for regular monitoring of the effectiveness of treatment plans. This thesis explores an alternative method of detecting PFAS by evaluating their behaviors at multiple liquid-liquid interfaces. Chapter 1 provides an introduction to PFAS and their surface-active properties, as well as the current method of detection. It also introduces the techniques used to measure interfacial energy and their sensing applications. Chapter 2 characterizes the preferential interfacial behaviors of perfluorooctanoic acid (PFOA) and perfluorooctane sulfonate (PFOS) at the hydrocarbon oil-water (H/W) and fluorocarbon oil-water (F/W) interfaces. Sodium dodecyl sulfate (SDS) and Capstone FS-30 were used as model systems for hydrocarbon and fluorocarbon surfactants, respectively. The key highlights are (1) PFAS and fluorocarbon surfactants lower the interfacial tension at the F/W interface more readily than at the H/W interface and (2) by measuring the interfacial tensions at both F/W and H/W interfaces, it is possible to distinguish between fluorocarbon and hydrocarbon surfactants. Chapter 3 summarized experimental details and supporting information.
    • Titanite Petrochronology by LA-ICPMS: Method and Significance in Deciphering Igneous Processes

      Ducea, Mihai N.; Barla, Anca; Gehrels, George; Kapp, Paul A. (The University of Arizona., 2021)
      We describe an in situ method for simultaneous measurement of U-Th-Pb isotopes and complimentary trace and rare earth elements on titanite using a Thermo Element2 HR ICPMS coupled to Photon Machine Analyte G2 excimer laser. The ablation was carried out with a 25 μm spot size, a laser fluence of 5.56 J/cm2 and a laser repetition rate of 7 Hz. Four standard reference materials (BearLakeRoad titanite, Ecstall titanite, NIST612 and NIST614 glasses) were ablated systematically during the two analytical sessions to ensure data reliability and to correct for downhole elemental fractionation during ablation. Seven unknown granite and granodiorite samples were analyzed in this study to test the stability of the analytical parameters. After correcting for common Pb incorporation (where necessary), all seven samples yielded crystallization ages consistent with previously published data. Trace and rare earth elements determined during the ablation experiments were reduced using three separate reduction schemes in Iolite software. Results were further compared to trace element data measured in solution using a ThermoFisher X-Series II Quadrupole Inductively Coupled Plasma Mass Spectrometer (Q-ICP-MS). The comparison revealed the overall trace elements concentrations retrieved using BLR titanite as a primary reference material and 42Ca (19.8%) as the internal elemental standard (X_Trace_Elements_IS) are closer in value to the concentrations obtained by solution mode Q-ICPMS. We further discussed how temperatures calculated using zirconium concentrations in titanite coupled with total rare earth elements contents and specific elemental ratios can provide essential information about the igneous conditions titanites grew in.
    • Low-Cost and Portable Smartphone-Based Biosensors for Medical Diagnoses

      Yoon, Jeong-Yeol; Akarapipad, Patarajarin; Kim, Minkyu; Kang, Dongkyun (The University of Arizona., 2021)
      Rapid advances in technologies have enhanced healthcare devices and scientific tools to become more and more powerful, allowing observation in micro/nanoscale with high precision and accuracy. Nevertheless, one of the biggest issues is that not all people can easily afford or have access to these tools. Many healthcare devices or diagnostic equipment can be very expensive and time-consuming, requiring trained operators, a large space, and a complex laboratory setup. Clearly, it is not easy for the general public to access these kinds of tools and technologies, especially in limited-resource areas where people may have low income or an inadequate number of trained personnel. To overcome these limitations, my interest is to apply biosensing technologies to develop low-cost medical diagnostic devices that are easily accessible, portable, and easy to use. These can be achieved by utilizing inexpensive materials, implemented with available sensors on the smartphone, and improved using data processing. Two main projects that I have worked on are: 1. SARS-CoV-2 detection assays using (method 1) flow characteristics analysis and (method 2) smartphone-based fluorescence microscopic imaging device for particle counting, and 2. skin microbiome classification using multispectral light sources and autofluorescence imaging. In SARS-CoV-2 detection method 1, we indirectly detect the virus presence via the flow behavior of the antibody conjugated fluorescence particle solution on the sample preloaded paper-based microfluidic channel. For SARS-CoV-2 detection method 2, utilizing the same platform, we aimed to directly visualize the fluorescence signal from the immunoagglutination results on the paper-based microfluidic chip, which has the potential to be more sensitive than method 1, and in this method, I have focused on developing a low-cost and portable device to yield comparable results as the conventional microscope. For the last project, using a similar concept as in method 2, we developed a low-cost and non-invasive technique to classify bacterial species based on their autofluorescence by using multiple light sources and inexpensive color filter films, a smartphone camera, and a data processing algorithm.
    • Characterization of HIV-1 Accessory vpr Gene From Virologically Controlled HIV-Infected Older Patients on Long-Term Antiretroviral Therapy

      Ahmad, Nafees; Love, Maria Belen; Lybarger, Lonnie P.; Wertheimer, Anne M. (The University of Arizona., 2021)
      Human immunodeficiency virus type 1 (HIV) infected individuals are successfully treated by antiretroviral therapy (ART) which reduces the viral load to undetectable levels, improves CD4 T cell counts, reduces opportunistic infections and increases longevity of many people to older age. However, HIV still persists in reservoir cells such as resting T cells and monocytes/ macrophages and continues to cause a low level of inflammation with increased risk of morbidity and mortality. Therefore, genetic characterization of HIV latent viruses, may provide important information for curative strategies. Specifically, genetic characterization of the HIV vpr gene, which is essential for viral replication in resting T cells and monocytes/macrophages and viral persistence in infected individuals, may provide important information for curative strategies. Characterization of the HIV-1 vpr region from 14 HIV-infected older patients’ peripheral blood mononuclear cell (PBMC) DNA on long-term ART with controlled viremia, identified by undetectable viral load and improved CD4 T cell counts were performed by PCR amplification, cloning and sequencing of 182 quasispecies of HIV-1 followed by analysis of phylogenetic relationship, genetic variability, selective pressure and analyzing the biological and immunological domains. Phylogenetic analysis revealed that the vpr gene sequences of each patient formed distinct clusters that were well separated and discriminated from other patients’ sequences. There was a low degree of heterogeneity and lower estimates of genetic diversity in all 14 patients’ vpr sequences. Eight out of 14 patients’ vpr region sequences were found to be under positive selection pressure by showing a dN/dS ratio of >1. In the multiple alignment analysis of deduced Vpr sequences, most patients’ sequences had intact Vpr open reading frames, and some patients’ sequences had stop codons. Several patient-specific amino acid motifs and common amino acid motifs were found in deduced Vpr sequences. The functional domains required for Vpr activity, including virion incorporation, predicted alpha-helix formation, nuclear import of pre-integration complex and cell cycle arrest and differentiation were highly conserved in most of the Vpr sequences, and most of the substitutions were with conservative or compatible amino acids. Analysis of several previously characterized cytotoxic T-lymphocytes (CTL) epitopes within the Vpr showed substantial variation in the patients’ Vpr sequences, suggesting escape mutants. In conclusion, a low degree of genetic variability and maintenance of functional domains and conservative variations in CTL epitopes were the hallmarks of vpr sequences from the 14 virologically controlled HIV-infected older patients on long-term ART, which may provide important information to develop curative and preventive strategies.
    • Playing Japan: Japanese Culture and Folklore in Video Games of the Lost Decade and Beyond

      Miura, Takashi; Cockrell, Chance; Smith, Nathaniel M.; McAllister, Ken S. (The University of Arizona., 2021)
      This thesis explores images of Japanese folklore and culture in video games of the late twentieth and early twenty-first centuries, as well as ways in which game franchises of the period were localized as they were exported outside Japan. Following the introduction, which presents the central problem and scope of the work, the first chapter examines instances of pre-modern Japanese folklore as they appear across a range of video games. Specifically, this section looks at dogū, haniwa, magatama, kappa, tengu, tanuki, and kitsune, and it considers the ways in which appropriations of these images have changed over time in video games. The second chapter reverses this method of inquiry by taking particular game series as case studies to explore more instances of Japanese culture and compare strategies used in their global localization, or "glocalization." Specifically, this section discusses the history, cultural elements, globalization, and localization of the Mario, Kirby, and Pokémon series, ending with an analysis of the Pokémon franchise as representative of and reliant on trans-media storytelling, participatory culture, social capital, and global fantasy commodities. Finally, the conclusion summarizes ways in which Japanese culture has been presented, represented, and transmitted through video games.
    • Using Active Flow Control to Improve the Capabilities of a Tilt Wing Tilt Rotor Aircraft

      Wygnanski, Israel; Kay, Garrett A.; Little, Jesse; Tumin, Anatoli (The University of Arizona., 2021)
      This thesis covers wind tunnel experiments on a scale model of a V22 starboard wing. The wing had been used in previous experiments but was modified to incorporate a suction/blowing system at the leading edge. The model used a simple flap that was 3D printed with 28 sweeping jet actuators with a throat area of 0.025in2. Along with leading edge suction and blowing, the leading edge could be replaced with a 3D printed piece that had 30 actuators. Many experiments in the past looked at reducing the download on VTOL aircraft using multiple different active flow control techniques. The experiments covered in this thesis utilized different combinations of sweeping jet actuators over the flap and leading edge, leading edge steady blowing, leading edge suction, and a Krueger flap. Data was taken for an alpha range of -50˚ to -104˚ in 2˚ intervals and the range of flap deflections tested was 45˚ to 75˚ in 5˚ intervals. The experiments focused on the download, suck back force, and pitching moment acting on the wing. For the VTOL configuration, sweeping jet actuators operating with a Cμ of 1.50% delayed separation over the flap, allowing for larger flap deflections to be utilized during hover. This decreased the download by about 11% with the potential for larger download reductions with higher flap deflections and Cμ values. This configuration increased the nose down pitching moment and substantially increases the suck back force. Including leading edge suction with a flow rate comparable to that of the sweeping jet actuators reduced the download by about 21% compared to the VTOL baseline. This also decreased the nose down pitching moment by 8% while only increasing the suck back force by 14%. Adding a Krueger with sweeping jet actuators at the leading edge produced download results comparable to the configurations with sweeping jet actuators over the flap. The major difference was that it generated a suck forward instead of suck back force and decreased the nose down pitching moment by about 40% compared to the baseline. Changing this vehicle from a VTOL configuration to a STO configuration by tilting the rotors forward decreased the download by close to 17% without the need for any active flow control. Including active flow control at a Cμ of 1.50% reduced the download by 30% compared to the VTOL baseline configuration. One problem with the tilt rotor configuration is that there is a large increase in the nose down pitching moment. More experiments on a model of the full aircraft is needed to figure out how to compensate for the increased pitching moment.
    • The Hunt of the Unicorn Tapestry Set: A Recontextualization

      Romano, Irene B; Hogan, Ariel; Cuneo, Pia F.; Moore, Sarah J. (The University of Arizona., 2021)
      The original narrative and purpose of The Hunt of the Unicorn tapestries on display at The Cloisters of The Metropolitan Museum of Art in New York have been lost to time. Theories abound in an attempt to expound this lost narrative, including traditions of courtly love and the belief that the cycle represents the story of Christ’s Passion. While I offer my own insights as to why I do not fully agree with these interpretations, I argue that the narrative of the hunt is plain in this cycle and that there is much to learn in analyzing the human-canine relationship present in nearly every scene, rather than focus on what we can only hypothesize is there. In this research project my purpose is not to refute the main interpretations proposed in the past for The Hunt of the Unicorn tapestries; rather, I intend to redirect the dialogue about the tapestry set, focusing on the human-canine relationship depicted. Referencing various manuscripts of Gaston Phébus’ Livre de la Chasse, I connect the imagery within the illuminations to the scenes of the tapestry set, hoping to bring further attention to the importance of the relationship in the hopes that it serves as a starting point for museum visitors who may be interested in the tapestry set, but may be too intimidated by the vast scholarship surrounding the artworks. At the culmination of this research, I offer two hypothetical text panels I have written regarding 15th-century aristocratic hunting and the human-canine relationship required for the practice of venery, hunting with hounds, to further contextualize the intimidating tapestry set for the average museum visitor ofThe Cloisters.
    • Evaluation of Urban Heat Island Effect in Cybercity, New Delhi Using a 3D Urban Microclimate Model: Envi-Met

      Ida, Aletheia; Dhir, Kavya; Youssef, Omar; Sami, Ida (The University of Arizona., 2021)
      Cities will face many challenges in the future as the global population grows and atmospheric conditions change. Climate change can alter how we use urban outdoor spaces, posing a threat to the city's long-term viability, necessitating city adaptation strategies.Sudden increasing population makes urban areas more exposed to Urban Heat Island. As a result, cities tend to experience higher temperatures than its proximate neighboring rural or non-urban area. The capital city of India i.e., New Delhi is known for its inordinate heat conditions during summer months and dangerously high Air Quality Index during winter season. The purpose of this work is to study the formation of Urban Heat Island and its effects on the microclimate on a corporate park: Cyber City, Gurgaon (which has been termed as the “futuristic commercial hub”) carried out with the ENVI-met software. For this intent, three-dimensional urban microclimate simulations were carried out. The parameters used were the percentage of green cover surrounding the site, its proximity to a water body, speed of wind and other factors such as impervious surfaces, density, H/W ratios and anthropogenic conditions. Through a strong analysis of the theoretical subjects and the analysis from the base case results of Cyber city, vision and design strategies were developed. Green space and material strategies like façade greening, highly reflective materials, green roofs (extensive/intensive), heat protective glass et cetera were used. To minimize urban heat islands, future policy initiatives may concentrate on promoting strategies to change urban geometry and anthropogenic heat in cities. This research can be extended by ensuring that New Delhi delivers on the highest ambition of the Paris Agreement and gives an exemplary example of a carbon neutral city by the year of 2050.
    • A Dynamic Assessment of Indoor Air Quality Through Passive and Active Filtration Measures Applied to the Built Environment in a Residential Application

      Youssef, Omar; Heil, Robert Alan; Ida, Aletheia; Crosson, Courtney (The University of Arizona., 2021)
      This highly dedicated empirical research was initially conceptualized, implemented and contained in a living active laboratory environment primarily designed to inform the audience on the negative health effects of indoor ambient air quality and the overexposure of three primary point source pollutants known as particle matter 2.5, particle matter 10, carbon dioxide, and formaldehyde infiltrating the current built environment’s inadequate architectural features. Moreover, this research thesis is intended to modestly illustrate a limited combination of passive and active filtration strategies in conjunction with specific architectural ventilation recommendations that are designed to offset and reduce the direct and indirect exposure of harmful contaminant volumes of acute particle matter and hidden carcinogenic gaseous in multi-unit dwelling conditions demonstrated throughout this indoor air quality (IAQ) research. Furthermore, concealed in the title and facilitated throughout the research, the dynamics of IAQ is designed to demonstrate which complex adaptive passive and active filtration strategies are most effective limited to the disturbance in the dynamics of the amplitude of the logarithmic data scales and volume concentrations depicted with the use of the latest micro sensor technologies provided by Brwissen, Seesii and Temtop laboratories. Subsequently, from the empirical data IAQ analysis, a simplistic, precise, and quantified decision can then be assessed for which strategies are considerably the most appropriate and efficient for the current conditions that the filtration systems will be applied to in addition to placement recommendations for interior mechanical ventilation systems. Lastly, this research thesis was endorsed for the University of Arizona, as an informative piece calculated for the audience to make a professional proactive decision on how to maintain the volumes of ambient air molecules and improve the overall IAQ throughout the multi verse of living spaces obtainable at home.
    • Improving Mountain Snowfall Forecasts in the Southwestern US using Machine Learning Methods

      Castro, Christopher L.; Hoopes, Charles Andrew; Chang, Hsin-I; Ehsani, Reza; Behrangi, Ali (The University of Arizona., 2021)
      Snowfall forecasting has historically been an area of difficulty for operational meteorologists, particularly in the remote complex terrain of the Western US. Attempts at improving forecasts have been made, but skill is still poor, with snowfall routinely overpredicted. A major reason for this overprediction has been a failure to accurately predict snow-liquid ratios (SLR) ahead of major events. This research proposes, develops, and tests multiple machine learning methods for dynamic SLR prediction for the Sky Islands of southeast Arizona in the form of a simple feed-forward neural network, a support vector machine, and a k-nearest neighbor algorithm. Input parameters were chosen based on variables found by previous studies to have a regression-based relationship with SLR, with a focus on the lower-mid levels of the troposphere. These parameters were also used to construct a multiple linear regression model, and its performance was compared with the machine learning methods. Each of the machine learning methods showed significant improvement compared to the multiple linear regression. When tested on historical events, nearly 95% of the network-predicted SLR values fell within the margin of error of observed SLRs, calculated using verification data from Zeng et al (2018), with slightly higher accuracies for both the SVM and KNN algorithms. Each showed significant gain in skill compared to the multiple linear regression model. Current and future work is focusing on shifting to higher resolution data, as well as adjusting the model to look at a wider region within the mountainous Western US in order to achieve greater operational benefit.
    • Traces

      Vaden, Cerese; Steinert, Lauren Collins; Coleman, Aaron; Leslie, Kelly; Bradford, Carlton (The University of Arizona., 2021)
      Traces, presents real, traced, printed and projected marks, sourced from the communal printmaking studios at the University of Arizona. It is a combination of printmaking, glass, and light projection. The exhibition consists of three parts; 8 wall mounted, plastic drypoint plates, a series of 12 intaglio prints, and 3 intaglio wiped glass inking slabs mounted into tables. The work transforms unnoticed marks into transparent, excavated objects and explores history, memory, presence and absence. 
    • The Split Noun Phrase in Classical Latin

      Groves, Robert; Waddell, Philip; Feldcamp, Zachary Satoshi; Carnie, Andrew (The University of Arizona., 2021)
      In this thesis I investigate the syntax and prosody of discontinuous classical Latin noun phrases. I argue that they are the result of the interaction of Universal Grammar with syntactic and phonological parameters of language variation. Chapter 1 introduces the problems of discontinuous noun phrases for theories of grammar and surveys the history of research on the topic. Chapter 2 presents new evidence based on the distribution of syntactic punctuation in epigraphic texts, of negative polarity items, and of quantifiers that any theory of Latin syntax must involve hierarchical structure, recursion, and syntactic movement, both in the noun phrase, and in the clause. Chapter 3 argues based on the distribution of interpuncts in epigraphic and papyrus texts that second-position effects are the consequence of prosodic movement and are widespread throughout the lexicon. Chapter 4 summarizes the results of this thesis.