• Study, Evaluation, and Applications of MRI Contrast Agents that Work Based on CEST and T2-EX Mechanisms

      Daryaei, Iman (The University of Arizona., 2017)
      MRI is a powerful imaging method that offers several advantages including non-ionizing radiation, significant depth of penetration, and great spatial resolution. Current demand for precision medicine and the movement toward personalized medicine have encouraged researchers in the field of medical imaging to develop MRI-based techniques. Various techniques are now available for molecular imaging by MRI. MRI started by utilizing T1 relaxation properties of molecules but soon after other relaxation mechanisms such as T2 and recently Chemical Exchange Saturation Transfer (CEST) were developed. Each of those MRI techniques offers advantages and disadvantages such as differences in experimental procedures, complexity of the method, selectivity and specificity of signals, and translation into clinical applications. We have been developing MRI techniques and responsive contrast agents for CEST MRI in the Pagel laboratory (Contrast Agent and Molecular Imaging Laboratory, also called CAMEL) for the past decade. We have mainly utilized MRI techniques and responsive contrast agents to detect and measure cancer biomarkers. Detection of the activity of enzymes and measurement of pH have been our main focus, and we have developed catalyCEST MRI probes and techniques for the detection of the activity of enzymes and acidoCEST for the measurement of pH. My research started with investigation on paramagnetic agents as potential CEST MRI probes (paraCEST) and continued with an investigation on diamagnetic agents (diaCEST). I completed several projects in which I prepared and evaluated paraCEST and diaCEST contrast agents for the detection of DT-diaphorase, and alkaline phosphatase enzymes, respectively. Although CEST MRI was my main activity in CAMEL, I started a new direction in CAMEL after encountering a series of observations that were unexplainable with CEST MRI. Through my research, I introduced a new class of responsive contrast agents based on the T2-Exchange (T2-Ex) relaxation mechanism. I employed the T2-Ex mechanism to evaluate responsive contrast agents for the detection of nitric oxide biomolecule and nitroreductase enzyme. My research activities in the CAMEL group resulted in one review paper, one book chapter, two published research articles, and two submitted research manuscripts at the time of preparing my PhD dissertation. In addition to my projects, I was involved in another project that focused on nanocapsule drug delivery, which resulted in a second author publication.
    • Generalizability of Universal Screening Measures for Behavioral and Emotional Risk

      Tanner, Nicholas Andrew (The University of Arizona., 2017)
      Data derived from universal screening procedures are increasingly utilized by schools to identify and provide additional supports to students at-risk of behavioral and emotional concerns. As screening has the potential to be resource intensive, effort has been placed on the development of efficient screening procedures, namely brief behavior rating scales. This study utilized classical test theory and generalizability theory to examine the extent to which differences among students, raters, occasions, and screening measures affect the meaningfulness of data derived from universal screening procedures. Teacher pairs from three middle school classrooms completed two brief behavior rating scales during fall and spring screening administrations for all students in their respective classrooms. Correlation coefficients examining interrater reliability, test-retest reliability, and concurrent validity were generally strong. Generalizability analyses indicated that the majority of variance in teacher ratings were attributable to student differences across all score comparisons, but differences between teacher ratings for particular students accounted for relatively large percentages of error variance among student behavior ratings. Although decision studies showed that increasing the number of screening occasions resulted in more generalizable data, the impact of increasing the number of raters resulted in more efficient screening procedures.
    • Chemical Transformations Supported by the [Re₆(μ₃-Se)₈]²⁺ Cluster Core

      Corbin, William C. (The University of Arizona., 2015)
      Hexanuclear transition metal clusters are a distinct class of chemical compounds that have some very interesting chemical and physical properties. Of recent interest in this field has been the [Re₆(μ₃-Se)₈]²⁺ cluster core. This Lewis acidic cluster core contains six substitutable coordination sites, and site differentiation can be accessed through protecting group ligands. The Lewis acidity has been shown to activate unsaturated cluster-bound ligands, and the expanded atom-like structure and high symmetry of the cluster core has potential use in synthesizing some fascinating and novel hybrid materials. Little work has been performed in establishing the scope of these chemical transformations. The work herein describes the efforts and successes of such work. Chapter 1 provides the essential background required for understanding the [Re₆(μ₃-Se)₈]²⁺ cluster core's synthesis, properties, and currently known research directions and successes. This chapter first introduces hexanuclear clusters in a general format, then focuses on the established catalytic and material capabilities that have been determined using this specific cluster core. Chapter 2 discusses the synthesis, characterization, and hydrogen-bonded assemblies formed from [Re₆(μ₃-Se)₈]²⁺ cluster-isonicotinic acid cluster complexes. These complexes have potential uses as hybrid inorganic/organic linkers for the generation of luminescent Lewis acidic metal-organic frameworks (MOFs). Prospective applications of such materials include catalysis, separations, and gas storage. Chapter 3 focuses on the novel chemistry of [Re₆(μ₃-Se)₈]²⁺ cluster-activated CH₃CN with N-based nucleophiles to form acetamidines. These ligands are of interest due to their use in medicinal chemistry, CO₂/CS₂ sequestration, and the formation of synthetically-relevant species. Quantitative yields are obtained and single-crystal XRD analyses reveal specific stereochemical outcomes. Trifluoroacetic acid (TFA) in a cluster-amidine CH₃CN solution removes the ligand as the acetamidinium TFA salt, and the starting cluster solvate is reproduced making a recyclable catalyst. Chapter 4 expands on a project similar to that of chapter 3, except that O-based nucleophiles are utilized for specific cluster isomers. The newly formed ligands, imino esters, are of interest in organic synthesis as valuable starting materials for the generation of β-lactams and heterocycles. ³¹P NMR and single–crystal XRD reveal Z stereochemistry is preferred in the cis isomer, but conflicting results for the hexasubstituted isomer leave stereochemical analyses unresolved. Chapter 5 attempts to incorporate the chemistry established in chapters 2-4 to provide some fresh and interesting research outlooks possible with the [Re₆(μ₃-Se)₈]²⁺ cluster core. Incorporation of the cluster into MOFs is discussed, and the possibility of post-synthetic modifications for metal sequestration, catalysis, and sensing is explained. Appendix A provides all the NMR data obtained for synthesized materials with peak picks and integrations provided. Appendix B entails all crystallographic information for structures determined after syntheses. Appendix C provide high-resolution mass spectra.
    • A Computational Framework to Determine the Mechanical Properties of Ocular Tissues and a Parametric Study on their Effects on the Biomechanical Response of Lamina Cribrosa

      Ayyalasomayajula, Avinash (The University of Arizona., 2015)
      As is the case with many ocular neuropathies, primary open-angle glaucoma (POAG) leads to an irreversible damage to the visual field. Loss of visual field first occurs in the peripheral vision and slowly propagates towards the middle. Although there are differences in its rate of incidence, glaucoma is projected to be the leading cause of blindness, second only to cataract, affecting significant percentage of populations across different age, race/ethnic groups. A hallmark of POAG is the dysfunction of retinal ganglion cells (RGCs) which connect to the axons which, in turn, relay the visual information from the eye to the brain. Previous research has shown that axonal density in the optic nerve head (ONH) is greatly reduced due to chronically elevated intraocular pressure (IOP). IOP-lowering treatment has been shown to reduce the visual field loss, and continues to be the dominant treatment methodology for glaucoma. Previous research has shown that the biomechanics of the lamina cribrosa (LC) - a highly porous tissue through which the axons carrying the visual information exit the eye, is important in influencing the viability of the RGCs. In a normal eye, the LC is primarily made up of collagen of types I, III, and IV which encompass (specifically, arranged circularly) the axon shafts and the blood vessels (1). In addition to elevated IOP, changes in the material properties of ocular tissues in and around the ONH region, which include peripapillary sclera and LC, could affect its biomechanics, which could be a result of changing microstructure and morphology of these tissues, and may contribute to POAG. The current work is aimed at creating computational models to incorporate the complex nature of ocular tissues, and develop computational techniques to characterize the variation in the material properties of ocular tissues (which include the tissue moduli, fiber orientation, permeability etc.), and study the effects they have on the biomechanical response of the LC region.
    • Developing Content for an Online Virtual Interactive Simulation Case for Cultural Competency of Nursing Students in Caring for Puerto Ricans in New York City: A Community Based Participatory Research Approach

      Mathew, Lilly (The University of Arizona., 2015)
      With growing cultural diversity in the United States (U.S.), health disparities continue to exist among many ethnic minority populations impacting the U.S. economy. Health disparities are health differences that are noted in a particular cultural group in respect to higher rates of diseases and deaths in comparison to others. These cultural groups have common attributes and can be based on race, ethnicity, disability, sexual orientation, income, residential location and many others. One such example is individuals of Puerto Rican heritage, the second largest Hispanic group living in the U.S. mainland. Puerto Ricans are identified to have multiple health disparities in comparison to other Hispanic and non-Hispanic population groups living in the U.S. Among other factors, common cultural health care beliefs and practices of individuals impact health outcomes. Healthcare professionals like nurses are expected to provide culturally competent care to vulnerable populations with known health disparities. Culturally competent care refers to delivering care congruent with patients' cultural beliefs and practices. Therefore, it is important to educate health professionals regarding caring for vulnerable populations. The purpose of this community-based participatory research (CBPR) study was to develop content for an educational tool, an online virtual interactive simulation (OVIS) case for developing cultural competency of nursing students in caring for the Puerto Rican population of New York City (NYC). The content development for OVIS was guided by the framework for Cultural Competency Simulation Experiences (CCSE), which was developed as a part of this dissertation. The CCSE framework guided the content development of OVIS using a CBPR approach. A community advisory board was developed which consisted of cultural, clinical and educational experts, residing in New York and Puerto Rico.
    • Causes and Consequences of Plant Responses to Environmental Change over Physiological, Ecological, and Evolutionary Time

      Sloat, Lindsey Leigh (The University of Arizona., 2015)
      Assessing how environmental change affects plants is increasingly important as terrestrial ecologists attempt to predict future patterns from current processes. However, this challenge is complicated because plant communities can respond to environmental variation at different, but overlapping scales. Additionally, both patterns and the processes that drive them are sensitive to the methods that scientists use to study them. Consequently, a variety of experimental and theoretical approaches are necessary to improve our understanding of how organisms, communities, and ecosystems will respond to future change. Collectively, the studies in this thesis employ a diverse array of approaches to test important ecological theories, including long-term observational studies, manipulative experiments, and analyses that leverage both local and global datasets. The Enquist lab has been measuring subalpine meadow carbon fluxes and climate variables at the Rocky Mountain Biological Laboratory (RMBL), for over 13 years at the time of this writing. Examining correlations between climate and carbon flux over this time has led to the identification of interesting patterns between snowmelt, precipitation events, and rates of carbon exchange. Despite the longer growing season, early snowmelt dates ultimately result in lower productivity in these systems. Pairing this study with the results of a soil moisture manipulation experiment aided in the discovery that the strength and duration of the foresummer drought was directly related to rates of carbon exchange and biomass accumulation in these systems. Thus, integrating long-term observational work with an experimental manipulation served to link pattern and process in a way that was not possible with either study alone. The studies in this thesis range in scale from sub-organismal (chapter 3), to community ecosystem (chapters 1 and 2), to continental (chapter 4). Across all scales afunctional trait ecology approach contributes a holistic view of how these changes may impact organismal, ecosystem, and evolutionary responses to environmental variation. Plants are frequently faced with fundamental performance tradeoffs, which arise due to physical, chemical, genetic/evolutionary, and/or ecological constraints. As a result, functional trait measurements can reflect ecological strategies or resource acquisition strategies. Functional ecology offers a promising approach to linking the attributes of individuals to and communities to ecosystem processes. Understanding how individuals, communities, and ecosystems will respond to environmental change is a fundamental question in ecology. I address this topic using a variety of novel experimental methods and statistical techniques. I use a functional ecology approach by considering not only the species in a community, but also the distribution of functional traits that those species represent. It is in this way that I test ecological hypotheses regarding plant responses to environmental change over physiological, ecological, and evolutionary time scales.
    • A Study to Examine the Feasibility of an Integrative Approach to Interventions in Reducing Anxiety

      Parmar, Rajni (The University of Arizona., 2015)
      Background: Magnetic resonance imaging (MRI) related anxiety is a multidimensional phenomenon with symptoms that include claustrophobia, fear of being hurt, fear of the unknown, and fear about results, and often causes patients to move during their MRI examination resulting in motion artifacts leading to the need for repeat scans and translating into poor quality of care, increasing costs, and declining workflow efficiency. Although most facilities performing MRIs use various techniques in an attempt to reduce anxiety, new interventions are needed to improve patient support. Objective: The purpose of this feasibility study in patients undergoing MRI was to (1) determine recruitment rates; (2) determine adherence to touch and foot massage interventions; (3) determine provider and participant's acceptability of physical presence, human touch or foot massage interventions; and (4) examine the effects of touch or foot massage interventions as compared to physical presence during MRI on anxiety. Methods: A quasi-experimental design was used for this feasibility study where the interventions were foot massage and touch. For the control group, the researcher remained in the room with the patient. Recruitment of the sample (N=60) was done from the Center for Neurosciences (CNS). In addition to measuring provider and participant acceptability, anxiety was assessed using a single item verbally administered anxiety rating (VAR) scale. Results: Recruitment of participants from the CNS generated a recruitment rate of 78.2%. There were no barriers to the application of the intervention protocol. The overall mean value of effectiveness was 8.53, SD = 2.4. There was a significant difference among the three groups in terms of effectiveness of the intervention F=15.19(2, 57), p < .001. The MRI technologist felt that these interventions were helpful to the participants in keeping them calm and they did not disrupt the workflow or increase or decrease the length of the scan. Multilevel Modeling analysis revealed that the foot massage intervention had a significant contribution in the model (β= -1.35, SE=.63, p < 0.01). Effect of the touch intervention was not significant. Conclusion: The use of foot massage or touch is feasible in the MRI setting. Patients' comments indicate acceptability of an integrative approach to interventions.
    • AdaptiSPECT: a Preclinical Imaging System

      Chaix, Cécile (The University of Arizona., 2015)
      This dissertation addresses the design, development, calibration and performance evaluation of a pre-clinical imaging system called AdaptiSPECT. Single-Photon Emission Computed Tomography (SPECT) systems are powerful tools for multiple applications in small-animal research, ranging from drug discovery to fundamental biology. Traditionally, pinhole SPECT systems are designed with fixed imaging characteristics in terms of sensitivity, resolution and size of the field of view, that are dictated by the hardware configuration of the system. The SPECT system described in this dissertation can change its hardware configuration in response to the subject data it is acquiring in order to improve the imaging performance. We employed 16 modular gamma-ray detectors, each of which consists of a NaI:Tl scintillation crystal, a fused silica lightguide, and an array of 9 PMTs. The camera is designed to work with maximum-likelihood position estimation methods. These detectors are arranged into 2 rings of 8 detectors around an adjustable pinhole aperture. The aperture itself comprises three cylinders of different diameters, each with pinholes of different diameters. The three aperture cylinders are stacked together along the imager axis, and selection of the appropriate ring of pinholes is carried out by translating the entire aperture assembly. In addition, some sections of the aperture are fitted with shutters to open or close additional pinholes that increase sensitivity. We reviewed the method used to calibrate AdaptiSPECT, and proposed a new interpolation scheme specific to adaptive SPECT imaging systems where the detectors can move to multiple locations, that yields system matrices for any configuration employed during adaptive imaging. We evaluated the performances of AdaptiSPECT for various configurations. The magnification of the system ranges from 1.2 to 11.1. The corresponding resolution ranges from 3.2 mm to 0.6 mm, and the corresponding transaxial field-of-view ranges from 84 mm to 10 mm. The sensitivity of the system varies from 220 cps/MBq to 340 cps/MBq for various configurations. Imaging of a mouse injected with a bone radiotracer revealed the finer structures that can be acquired at higher magnifications, and illustrated the ability to conveniently image with a variety of magnifications during the same study. In summary, we have brought the concept of an adaptive SPECT imaging system as it was originally described by Barrett et al. in 2008 to life. We have engineered a system that can switch configurations with speed, precision, and repeatability suitable to carry out adaptive imaging studies on small animals, thus opening the door to a new research and medical imaging paradigm in which the imager hardware is adjusted on the fly to maximize task-performance for a specific patient, not, as currently, an ensemble of patients.
    • Engineering Equality: The Organization of Education Labor Markets and the Distribution of Teacher Quality in Japan

      Seebruck, Ryan (The University of Arizona., 2015)
      This research is an organizational comparative analysis of how the structure of education labor markets affects educational equality. Extant literature on teacher distribution is centered on the U.S. and rarely assesses the influence of organizational structure. My research here addresses these gaps by studying a unique facet of Japan's public education system: jinji idou, a mandatory teacher rotation system governed by the prefectural board of education in which teachers are systematically transferred to other schools in the prefecture throughout their careers. Because jinji idou is absent in private schools, a comparison of the distribution of teacher quality among schools in the private sector with schools in the public sector produces a comparative design that increases my ability to credit jinji idou as a causal condition affecting teacher distribution. My research is motivated by four claims. First, teacher quality is one of the predominant causal variables affecting student performance, outweighing variables such as class size, student background, or spending. Second, there is an unequal distribution of quality teachers in the U.S. that disfavors poor students. Third, this unequal distribution is structurally based—caused by policies that encourage quality teachers to gravitate to affluent schools while less qualified teachers remain at poor schools. Fourth, Japan's public education system is more egalitarian than its U.S. counterpart as determined by the fact that Japanese students have more equal access to quality teachers than U.S. students. Following that, I investigate the organizational structure of education labor markets in Japan: how the careers of educators are managed and the effects this has on teacher distribution. I utilize a mixed-method approach, gathering original quantitative and qualitative data in both public and private schools. Qualitative data provide a detailed breakdown of the formal and informal policies governing this teacher rotation system, and quantitative data examine how this rotation system affects the distribution of teachers both cross and within schools. By examining the more centrally controlled public school sector with more locally controlled private schools in Japan, I am able to explicate how the different organizational structures of the labor markets in these sectors affect access to quality teachers. Results indicate that, for the most part, the public sector distributes teachers more equitably across schools. Furthermore, the public sector has, on average, higher mean levels of teacher quality and higher levels of school performance. This intimates that education labor markets can be structured in ways that simultaneously maximize performance while minimizing variation between schools, findings which should be of interest to scholars interested in structural inequality or educational egalitarianism. In addition to teacher quality distribution, I also analyze the relationship between individual teacher quality traits and school performance, showing that not every teacher quality measure is significantly associated with school performance—information that should be germane to policy makers deciding how to best allocate school-level resources in order to maximize educational egalitarianism. In short, my findings provide an empirical basis for policy makers to consider how the governance of teachers' careers affects educational egalitarianism, and I believe these results not only complement the sociology of education literature but also help refine organizational theory, which is often based on for-profit organizations rather than public institutions such as schools.
    • How do Amazonian Tropical Forest Systems Photosynthesize under Seasonal Climatic Variability: Insights from Tropical Phenology

      Wu, Jin (The University of Arizona., 2015)
      Amazonian evergreen forests are of broad interest, attributable to their ecological, economic, aesthetic, and cultural importance. However, their fate under climate change remains uncertain, largely due to unclear mechanisms in regulating tropical photosynthetic metabolism. Understanding mechanistic controls on these dynamics across time scales (e.g. hours to years) is essential and a prerequisite for realistically predicting tropical forest responses to inter-annual and longer-term climate variation and change. Tropical forest photosynthesis can be conceptualized as being driven by two interacting causes: variation due to changes in environmental drivers (e.g. solar radiation, diffuse light fraction, and vapor pressure deficit) interacting with model parameters that govern photosynthetic behavior, and variation in photosynthetic capacity (PC) due to changes in the parameters themselves. In this thesis, I aim to reveal photosynthetic controls by addressing three fundamental but complementary questions: (1) What are the mechanisms by which the subtle tropical phenology exert controls on tropical photosynthetic seasonality? (2) How do the extrinsic and intrinsic controls regulate the photosynthesis processes at hourly to interannual time scales in an Amazonian evergreen forest? (3) Are there sufficiently consistent relations among leaf traits, ages, and spectra that allow a single model predict the leaf aging process of Amazonian evergreen trees? To address question 1, I firstly show that seasonal change in ecosystem-scale photosynthetic capacity (PC), rather than environmental drivers, is the primary driver of seasonality of gross primary productivity (GPP) at four Amazonian evergreen forests spanning gradients in rainfall seasonality, forest composition, and flux seasonality. Using novel near-surface camera-detected leaf phenology to drive a simple leaf-cohort canopy model at two of these sites, I further show that leaf ontogeny and demography explain the changes in ecosystem photosynthetic capacity. The coordination of new leaf growth and old leaf divestment (litterfall) during the dry season shifts canopy composition towards younger leaves with higher photosynthetic capacity, driving large seasonal increases (~27%) in ecosystem photosynthetic capacity. To address question 2, I used the 7-year eddy covariance (EC) measurements in an Amazonian tropical evergreen forest. I used a statistical model to partition the variability of 7-year EC-derived GPP into two main causes: variation due to changes in extrinsic environmental drivers and variation in intrinsic PC. The fitted model well predicts variability in EC-derived GPP at hourly (R²=0.71) to interannaul (R²=0.81) timescales. Attributing model predictions to causal factors at different timescales, I find that ~92% of the variability in modeled hourly GPP could be attributed to environmental driver variability, and ~5% to variability in PC. When aggregating the modeled GPP into the annual time-step, the attribution is reversed (only ~4% to environment and ~91% to PC). These results challenge conventional approaches for modeling evergreen forests, which neglect intrinsic controls on PC and assume that the primary photosynthetic control at both long and short timescales is due to changes in the hourly-to-diurnal environment on the physiological phenotype. This work thus highlights the importance of accounting for differential regulation of different components of GPP at different timescales, and of identifying the underlying feedbacks and adaptive mechanisms which regulate them. To address question 3, I explored the potential for a general spectrally based leaf age model across tropical sites and within the vertical canopy profiles using a phenological dataset of 1831 leaves collected at two lowland Amazonian forests in Peru (12 species) and Brazil (11 species). This work shows that a simple model (parameterized using only Peruvian canopy leaves) successfully predicts ages of canopy leaves from both Peru (R²=0.83) and Brazil (R²=0.77), but ages for Brazilian understory leaves with significantly different growth environment and leaf trait values have lower prediction accuracy (R²=0.48). Prediction accuracy for all Brazilian samples is improved when information on growth environment and leaf traits were added into the model (5% R² increase; R²=0.69), or when leaves from the full range of trait values are used to parameterize the model (15% R² increase; R²=0.79). This work shows that fundamental ecophysiological rules constrain leaf traits and spectra to develop consistently across species and growth environment, providing a basis for a general model associating leaf age with spectra in tropical forests. In sum, in this thesis, I (1) conceptualize photosynthesis as being driven by two interacting dynamics, extrinsic and intrinsic, (2) propose and validate a model for biological mechanisms that mediate seasonal dynamics of tropical forest photosynthesis, (3) assess and quantify the factors controlling tropical forest photosynthesis on timescales from hourly to interannual, and (4) develop a general model for monitoring leaf aging processes of tropical trees across sites and growth environments. The revealed mechanisms (and proposed models) in this thesis greatly improve our mechanistic understanding of the photosynthetic and phenological processes in tropical evergreen forests. Strategic incorporation of these mechanisms will improve ecological, evolutionary and earth system theories describing tropical forests structure and function, allowing more accurate representation of forest dynamics and feedbacks to climate in earth system models.
    • Controversy in Seventeenth-Century English Coffeehouses: Transcultural Interactions with an Oriental Import

      Pierce, Mary Lynn (The University of Arizona., 2015)
      By analyzing and contextualizing the polarized discourses on coffee and coffeehouses in post-1652 England, this dissertation argues that the divisive worldviews of the English population at this critical historical juncture shaped the contentious reception of coffee. Countless scholarly efforts dealing with seventeenth-century coffeehouses, those of London in particular, have helped explaining the rapid growing popularity of coffee and the establishments in which it was consumed, the coffeehouse. Building upon exiting literature, this work advances a new approach to shed light the interconnection between social and cultural anxieties, paradoxes and contradictions in seventeenth-century English society, and the contradictory discourses surrounding the rise of coffee in England. My project demonstrates that pervasive anxieties about the rise of religious heterodoxy, the ambiguous dispositions of the English people towards the Ottoman Turks, and the ever-present concerns surrounding the tenuous state of patriarchal manhood collectively helped to both encourage and discourage interactions with the Islamic practice of coffee drinking in coffeehouses. Coffee and coffeehouses came from the Ottoman Empire, the land of the presumed Turks. One sector of society, the optimists, embraced the exotic novelty from the Islamic world and participated enthusiastically in a custom shared with their Turkish, Arab and Persian counterparts since the early sixteenth century. Conversely, the pessimists vilified the adoption of cultural and dietary practices from a non-Christian society; they condemned the enthusiasts' cosmopolitanism as a sign of disloyalty that would only deepen discord in the nation. Indeed, they proclaimed the craze for the Turkish-imported habit as a sign of degeneration, threatening not just Englishmen's religiosity, but also their manliness. Coffee and coffeehouse came from the Ottoman Empire, the land of the presumed effeminate Turks at that. Intimate intermingling with this imported novelty thus compromised England's identity and even sovereignty. By relying upon a borderlands approach that is inspired by gender analysis, this dissertation seeks an alternative theoretical path to explain the controversy and contention swirling around a new drink and novel spaces of sociability among a populace dislocated by years of religious, political and cultural turmoil.
    • Characterizing the Star Forming Properties of Herschel-Detected Gravitationally Lensed Galaxies

      Walth, Gregory Lee (The University of Arizona., 2015)
      Dusty star forming galaxies (DSFGs), characterized by their far-infrared (far-IR) emission, undergo the largest starbursts in the Universe, contributing to the majority of the cosmic star formation rate density at z = 1−4. The Herschel Space Observatory for the first time was able observe the full far-IR dust emission for a large population of high-redshift DSFGs, thereby accurately measuring their star formation rates. With gravitational lensing, we are able to surpass the Herschel confusion limit and probe intrinsically less luminous and therefore more normal star-forming galaxies. With this goal in mind, we have conducted a large Herschel survey, the Herschel Lensing Survey, of the cores of almost 600 massive galaxy clusters, where the effects of gravitational lensing are the strongest. In this thesis, I present follow-up studies of gravitationally lensed Herschel-detected DSFGs by utilizing multi-wavelength data from optical to radio. Specifically, I characterize the star forming properties of gravitationally lensed DSFGs by using these three subsamples: (1) A gravitationally lensed DSFG galaxy at z = 0.6 in one of the most massive galaxy clusters, Abell S1063 (at z = 0.3), (2) One of the brightest sources in HLS, which is a system of two strongly gravitationally lensed galaxies, one at z = 2.0 (optically faint gravitational arc) and the other at z = 4.7 (triply-imaged galaxy), (3) A sample of the brightest sources in HLS at z = 1−4, in which we detect rest-frame optical nebular emission lines (e.g. Hα, Hβ, [OIII]λλ4959,5007) by utilizing near-IR spectroscopy. The main results from these studies are as follows: (1) In the cluster-lensed DSFG at z = 0.6, discovered in the core of Abell S1063, we identify a luminous (SFR = 10 M⊙/yr) giant (D~1 kpc) HII region similar to those typically found at higher redshift (z~2). We show that the HII region is embedded in a rotating disk and likely formed in isolation, rather than through galaxy interaction, which is observed in local galaxies. We can use this source as a nearby laboratory for star forming regions at z ~ 2, in which more detailed follow-up of this source can help us to understand their origin/properties. (2) We discovered that one of the brightest sources in HLS is a blend of two cluster-lensed DSFGs, one at z = 2.0 (an optically faint arc) and the other at z = 4.7 (triply-imaged galaxy), implying that a sample of bright Herschel sources may have such multiplicity. In the z = 2.0 arc, the sub-arcsecond clumps detected in the SMA image surprisingly do not correspond to the clumps in the JVLA CO(1-0) image. When investigating the CO(1-0) velocity structure, there is a substantial amount of molecular gas (likely a molecular wind/outflow) we find that we find is not associated with star formation. This suggests that the CO morphology in DSFGs could be strongly influenced by molecular outflows resulting in the over-prediction of the amount of the molecular gas available for star formation. In the z = 2.0 arc, we also constrain αCO~4. While this value is normal for galaxies like the Milky Way, it is quite unusual for ULIRGs. This hints that the physical conditions may be much different in the arc from other ULIRGs, which usually have αCO ≈ 0.8.(3) We successfully detect rest-frame optical emission lines in 8 gravitationally lensed DSFGs at z = 1−4 using ground-based near-IR spectroscopy with Keck, LBT and Magellan. The luminosities of these lines are substantially less than what the far-IR derived star formation rates predict, suggesting that these DSFGs have large dust attenuations. The difference in the star formation rates is a factor of 30 x (AV= 4), which is larger than previously reported for DSFGs at z > 1. One galaxy (z = 1.5) in the sample showed the largest suppression with a factor of 550x (AV = 7), which is similar to local ULIRGs. Future prospects: Herschel provided a glimpse into the star formation of DSFGs, but only the brightest at z > 2 could be studied in detail without gravitational lensing. ALMA will revolutionize the study of DSFGs with its high spatial resolution submm/mm imaging of their dust continuum and molecular gas, and it will begin to unravel their physical properties. In order to detect nebular emission lines in fainter higher redshift sources, 20-30 meter class telescopes, with next generation near-IR spectrographs, will be necessary. JWST will play a significant role as it will target rest-frame optical nebular emission lines in DSFGs unobtainable from the ground as well as weaker Hydrogen series lines (such as Paschen and Brackett series) to better understand their instantaneous star formation and dust attenuation.
    • Methods for Measuring Tamarisk (Tamarix spp.) Water Use on Two Sub-Watersheds in The Western United States as Impacted by The Tamarisk Leaf Beetle (Diorhabda spp.)

      Pearlstein, Susanna Lee (The University of Arizona., 2015)
      The Dolores River in Utah and the Virgin River in Nevada are ecosystems under pressure from increased groundwater withdrawal due to growing human populations, climate change and introduced species such as Tamarix spp. (tamarisk). Tamarisk is reputed to take excessive water from its environment. Controlling tamarisk is of concern in the western United States where plants grow quickly in already fragile and diminishing riparian areas. For this reason, biologic control beetles Chrysomelidae: Diorhabda carinulata were released to weaken the tamarisk population, thus reducing its water use. The studies for this dissertation were conducted between 2010 and 2011. We quantified tamarisk water use over multiple cycles of annual defoliation using sap flow measurements, leaf area index (LAI), well data, allometry and satellite imagery from EOS-1 Moderate Resolution Imaging Spectrometer (MODIS) sensor. Study objectives for the Virgin River were to measure evapotranspiration (ET) before beetles ever arrived and to examine the effects on tamarisk ET in the year after beetle arrival. This site showed plant ET from sap flow averaged about 4.3 mm m⁻² leaf day⁻¹ in 2010. In 2011, ET from sap flow averaged 6.4 mm m⁻² leaf area day⁻¹ pre beetle arrival, but dropped to 3-4 mm m⁻² leaf area day⁻¹ after beetle arrival. Stand level ET measured by MODIS was 2.2 mm d⁻¹ in 2010 and approximately 1.5 mm day⁻¹ when beetle arrival was measured in 2011. Significant visual change was apparent as the trees senesced. Results showed the first year of beetle arrival resulted in reduced ET but did not result in significant water savings. We also compared the reaction of the newly defoliated (in 2011) Virgin River site to the long-term defoliated (since 2007) Dolores River site to explore if all beetle invasions were created equal. This paper views the two sites as fairly extreme examples of tamarisk stand reaction to the beetle. While no mortality was reported at the Dolores River site, the site is much older, less photosynthetically active and covers far less ground when compared to the younger tamarisk monoculture on the Virgin River. Pre-beetle arrival Normalized Difference Vegetation Index (NDVI) values were higher on the Virgin River than on the Dolores River. Beetle arrival at each site was captured with Landsat NDVI and a reduced NDVI signal (13% drop in NDVI at Dolores River, 5% drop at Virgin River) was seen after beetle arrival.
    • Chemical Tools for the Selective Control of Proteins: Protein Kinases and Acetyl Transferases

      Restituyo Rosario, Elizabeth (The University of Arizona., 2015)
      Post-translational modifications (PTMs) of proteins are now known to increase the complexity of biological signaling networks. The ability to selectively control the activity of individual proteins and enzymes involved in PTMs enables studies of biological systems and in designing therapeutic agents. The phosphorylation of serine, threonine, and tyrosine catalyzed by protein kinases play an important role in signaling and when deregulated are involved in different types of cancer amongst other diseases. Therefore, selective regulation of kinase activity by inhibition could provide a means to understand signaling and also aid in developing therapies. The design of specific kinase inhibitors is challenging because most inhibitors target the common ATP-binding site, leading to several off-target hits with adverse effects. With this in mind, a fragment-based bivalent strategy was developed to potentially increase affinity and selectivity. Our approach seeks to target the ATP-binding site with a small molecule while simultaneously targeting any available site on the kinase with a cyclic peptide that potentially increases selectivity and affinity. The bivalent approach has produced effective and selective inhibitors for cAMP-dependent protein kinase (PKA). Herein, we extended this approach to Aurora kinase (Aurora A), RSK1 and MSK1. Using our optimized selection conditions, we have successfully selected several cyclic peptide ligands to later generate bivalent ligands for these kinases. This strategy may prove a robust method to discover new allosteric sites on kinases as well as other proteins, furthermore it also has the potential to provide insight towards the design of new ATP targeted approaches. A second area of research focuses on PTMs involved in the acetylation of lysine residues by enzymes dubbed histone acetyl transferases (HATs) or lysine acetyl transferases (KATs). Recent studies have shown that a large fraction of the proteome may be modifies by KATs but it is challenging to develop uniquely selective inhibitors as the KATs like Kinases have similar active sites. Towards the goal of developing a method to control a single KAT in the presence of other KATs, we designed ligand-gated split-proteins based on a sequence dissimilarity based approach. Potential fragmentation sites were identified by insertion of a 25-residue loop insertion. Successful loop insertion mutants provided guidance for the dissection of KATs into fragments tethered to FKBP and FRB that cannot spontaneously assemble, but that do upon the addition of a ligand, rapamycin to generate catalytically active. The method was successfully applied to design the very first split-KAT, GCN5,which only showed activity in the presence of an added small molecule. The method was shown to be potentially general by application to a second KAT, PCAF. The above studies provide potentially new approaches for selectively targeting and studying PTMs catalyzed by kinases and lysine acetyl transferase.
    • Local Probe Spectroscopy of Two-Dimensional van der Waals Heterostructures

      Yankowitz, Matthew Abraham (The University of Arizona., 2015)
      A large family of materials, collectively known as "van der Waals materials," have attracted enormous research attention over the past decade following the realization that they could be isolated into individual crystalline monolayers, with charge carriers behaving effectively two-dimensionally. More recently, an even larger class of composite materials has been realized, made possible by combining the isolated atomic layers of different materials into "van der Waals heterostructures," which can exhibit electronic and optical behaviors not observed in the parent materials alone. This thesis describes efforts to characterize the atomic-scale structural and electronic properties of these van der Waals materials and heterostructures through scanning tunneling microscopy measurements. The majority of this work addresses the properties of monolayer and few-layer graphene, whose charge carriers are described by massless and massive chiral Dirac Hamiltonians, respectively. In heterostructures with hexagonal boron nitride, an insulating isomorph of graphene, we observe electronic interference patterns between the two materials which depend on their relative rotation. As a result, replica Dirac cones are formed in the valence and conduction bands of graphene, with their energy tuned by the rotation. Further, we are able to dynamically drag the graphene lattice in these heterostructures, owing to an interaction between the scanning probe tip and the domain walls formed by the electronic interference pattern. Similar dragging is observed in domain walls of trilayer graphene, whose electronic properties are found to depend on the stacking configuration of the three layers. Scanning tunneling spectroscopy provides a direct method for visualizing the scattering pathways of electrons in these materials. By analyzing the scattering, we can directly infer properties of the band structures and local environments of these heterostructures. In bilayer graphene, we map the electrically field-tunable band gap and extract electronic hopping parameters. In WSe₂, a semiconducting transition metal dichalcogenide, we observe spin and layer polarizations of the charge carriers, representing a coupling of the spin, valley and layer degrees of freedom.
    • The environment of Miami Wash, Gila County, Arizona, A. D. 1100 to 1400

      Lytle-Webb, Jamie (The University of Arizona., 1978)

      Kotecha, Ashok-Kumar Hiralalji, 1944- (The University of Arizona., 1977)

      James, Gail Lynne (The University of Arizona., 1979)

      Hall, Alene Winifred Brown (The University of Arizona., 1979)
    • Mitigating Sniping in Internet Auctions

      Nagy, Lindsey Danielle (The University of Arizona., 2013)
      My dissertation discusses a mechanism that thwarts sniping and improves efficiency in ascending Internet auctions with fixed ending times, specifically eBay. The first research chapter proposes a design of the bidding mechanism and the second chapter tests the effectiveness of the mechanism in a controlled environment. In addition, it presents an innovative theoretical representation of the eBay bidding environment. The first chapter investigates theoretically whether sellers can improve their profits in eBay-like auctions via the implementation of bidder credits. The analysis predicts that providing a credit, similar to a coupon or discount, for early bidding can thwart sniping and increase seller profit. The paper formulates and analyzes a multi-stage auction model with independently and identically distributed private values, where bidders place proxy bids. I show that sniping can emerge as a Bayesian-Nash equilibrium strategy so long as late bids run the risk of not being successfully received by the auctioneer; extending the prior work of Ockenfels and Roth. This equilibrium is inefficient and yields the worst outcome for sellers. The proposed credit mechanism awards a single early bidder a reduction, equal to the value of the credit, in the final price if he wins the auction. The optimal credit satisfies two necessary conditions; first, it increases seller ex-ante profit and second, it incentivizes bidders to deviate from the sniping equilibrium. Relative to the surplus generated by the sniping equilibrium, implementing the credit increases seller surplus and improves welfare. The second chapter experimentally investigates the effectiveness of the credit mechanism. In particular, it compares bidding strategies, seller profit, and overall efficiency in auction environments similar to eBay with and without credit incentives. I observe a significant decline in the frequency of sniping when subjects have the opportunity to receive the credit. The credit also improves auction efficiency primary because subjects overbid in auctions with the credit regardless of which subject has the credit. A within-subjects design allows me to directly compare differences across treatments conditional on the subjects being snipers. Auctions with snipers yield significantly lower profits to sellers because non-sniping rivals are bidding less aggressively when competing against a sniper.