Now showing items 21-40 of 102817

    • Detection and Isolation of Salivary Biomarkers Using a Novel Hybrid Size Exclusion - Immobilized Metal Affinity Chromatography Matrix

      Guzman, Roberto; Rodriguez, Christopher; Savagatrup, Suchol; Saez, Eduardo (The University of Arizona., 2023)
      Biomarkers are a vital tool used in the diagnosis of multiple different diseases, from the presence of creatine kinase in blood indicating muscle damage, to the presence of glucose in urine signaling high blood sugar and possibly diabetes. One major limitation for biomarkers comes in the difficulty of isolating them from biological fluids (such as blood, urine, saliva, etc.). Another big problem is that biomarkers are usually found in low concentrations together with large amounts of proteins that makes the isolation of target biomarkers quite difficult. Isolating a desired biomarker from a patient sample requires multiple steps and these steps can vary depending on the bodily fluid being sampled.This work deals with novel separations of small molecular size compounds from large molecules. This technology combines, in the same separation medium, the characteristics and advantages of size exclusion and affinity adsorptive protein separations methods. The novel features involve the covalent attachment of permeation polymers to a matrix so that after modification preferentially "rejects" biomolecules of a certain size (large proteins, for example), and allows only compounds of appropriate size (small biomarkers, for example) to penetrate the "rejection" zone, thus allowing them to interact with affinity groups previously attached on the surface of the matrix. The main objective of this work was to develop a method to isolate specific biomarkers directly from saliva, a quite relevant biological fluid. The hybrid chromatographic matrix in this case consisted of size exclusion chromatographic matrices functionalized with specific affinity ligands (Iminodiacetic acid (IDA) and Dipicolylamine (DPA) as chelators) and polymers (polyethylene glycol, PEG). In this approach, PEG acts as a blocking polymer that acts as a permeating barrier that allows only small proteins to permeate and interact with the chelator on the surface, larger proteins cannot penetrate permeating barrier. The method was used to isolate the small biomarkers, creatinine, spermine, choline and isethionate and the small protein myoglobin from synthetic saliva preparations. Myoglobin has been linked as a salivary biomarker for myocardial necrosis, creatinine has been linked to chronic kidney disease and spermine, choline and isethionate have been shown to be promising salivary biomarkers for breast cancer. The novel approach was effective at isolating and almost completely recovering most of the target biomarkers from the other components of the synthetic saliva used in the research.
    • Investigation of the Electronic Structure of 2D Materials Using X-Ray and UV Photoemission Techniques

      Monti, Oliver; Zachritz, Sara; Schwartz, Steven; Huxter, Vanessa; Bredas, Jean-Luc (The University of Arizona., 2023)
      The limitations of current day electronics have created a tremendous drive to find new materials for more advanced electronic devices. However, without a fundamental understanding of key interfacial processes, such as electron transfer or charge carrier dynamics, developing practical devices becomes an impossible task. It therefore is of vital importance to comprehend the fundamental physics that governs these interfacial processes to fulfill the practical need for more advanced electronic devices. In this dissertation, I mainly focus on the class of inorganic 2D materials called transition metal dichalcogenides that present a wide range of electronic properties based on their composition. I begin by exploring the ultrafast charge carrier dynamics at the interface between an organic and inorganic semiconductor (C60/WSe2). The interfacial charge transfer, which results in an interfacial electric field, reveals new opportunities to control the different spin degrees of freedom inherent to the inorganic semiconductor (WSe2) and provides a novel mechanism to create spin-polarization in a nonmagnetic heterostructure. Next, I investigate the temperature-induced electronic phase transition between the semimetallic 1T’-phase of MoTe2 and the topological Weyl semimetal Td-MoTe2. The platform provided by this phase transition constitutes a new opportunity for systematic control of the electronic structure. As a result of the more exotic electronic properties of Td-MoTe2, new scattering pathways are available and I demonstrate how the electronic structure influences the ultrafast charge-carrier dynamics in the two phases. Finally, I demonstrate the importance of the electronic structure and its influence on the luminescent properties of two types of lanthanide-doped metalorganic complexes. The energy level alignment between the ligands and the rare earth centers in the complexes determines not only the efficiency of the material’s luminescent capabilities but also its influence on the emissive color properties. Overall, the case studies presented in this dissertation highlight how the electronic structure governs the ultrafast charge carrier dynamics and electron transfer properties, presenting new opportunities towards advanced electronic devices.
    • Improving PL Approximations of Harmonic Maps and a Penalty-Function Approach to Harmonic Maps

      Glickenstein, David; Banks, Robert; Venkataramani, Shankar C.; Sethuraman, Sunder; Izosimov, Anton (The University of Arizona., 2023)
      In this dissertation, we consider two problems in the approximation of harmonic maps between empirically-known manifolds embedded in Euclidean spaces. First, we suppose that the domain manifold $\mathcal{M}$ is known by a point cloud $M_s$ and that $M_s$ has been used to reconstruct a $PL$ surface $\tau$ approximating $\mathcal{M}$. Then, assuming that we have a $PL$ map $f^\tau: \tau\to \mathbb{R}^k_\mathcal{N}$ that approximates a harmonic map $\mathcal{M}\to \mathcal{N}$, we ask how we can improve the approximation by using finer triangulations. In particular, we ask where we should add a single vertex to the domain triangulation $\tau$ given a single added vertex in the image triangulation $\mathscr{T}=f^\tau(\tau)$. We prove that a unique optimal solution exists when $\mathcal{M}\subset\mathbb{R}^2$. We find this optimal solution explicitly for several special cases and constrain it in general via an inverse problem. We then consider the problem of how to approximate a harmonic map $\mathcal{M}\to \mathcal{N}$ when the target manifold $\mathcal{N}\subset \mathbb{R}^k$ is known only by the point cloud $N_t$. We explicitly construct a $\mathscr{C}^1$ penalty functional $\mathscr{P}_t$ which is determined by $N_t$ and such that, if $f: \mathcal{M}\to \mathbb{R}^k$ and $f(\mathcal{M})$ is near $\mathcal{N}$, then $\mathscr{P}_t(f)$ is small. We then investigate how approximate harmonic maps can be found by locally minimizing functionals of the form $\mathscr{G}_t(\lambda, f)=\mathscr{E}(f)+\lambda\mathscr{P}_t(f)$ where $\mathscr{E}$ is the Dirichlet energy and $\lambda$ is a positive parameter. This work provides a foundation for extending the methods of \cite{ChenStruwe1989} to sampled manifolds.
    • An Informal Online Community in the Digital Wilds: Possibilities for Language Learning

      Castek, Jill; Oguilve, Veronica; Dupuy, Beatrice; Hellmich, Emily (The University of Arizona., 2023)
      This study explores the establishment and evolution of an informal online community, tracing how it developed and evolved. More specifically, the study analyzed the characteristics of the online space, as well as how members engaged within the community, including participation patterns, preferences, and opinions and identity construction. The community members were made up of multilingual and global participants; the space was creativity-driven, free, and open to all. Free navigation mirrors how informal communities work in the digital wilds where interaction is voluntary and interest-driven. Using descriptive methods, this research looked at language learning as the product of social interaction as participation varied across asynchronous posting, responding, and engagement in live conversations. One hundred eighty-eight participants came from different ethnic, linguistic, and geographical backgrounds, and explored their shared and individual interests and learning opportunities within the virtual space. All online activities were situated in a dynamic system of interactions that developed over time in response to participation patterns and preferences. Four participation profiles were developed by calculating members’ weighted activities which included post clicks, cheers, messages, comments, and participation in live Zoom events. Analysis revealed characteristics and preferences of the Power, the Motivated, the Curious, and the Attentive member. Findings from this study suggest expanding opportunities for self-directed and collaborative work in member-driven online communities that encourage incidental language learning and the exploration of different perspectives and cultures. Implications address the importance of incidental language learning, which should be carried over into formal language learning environments. In informal spaces where language learning is not explicit, learners can make their own decisions, explore the world on their own terms and make their own conclusions on what is valuable or meaningful for themselves as they interact with others. Keywords: online community, informal learning, incidental language learning, Ecological Approach, Critical Relationality, global interaction, communication, multimodality, creativity.
    • When Political Precarity Meets Climate Vulnerability: A Case of Tibetan Refugee Pastoralists from Ladakh, Northern India

      Myadar, Orhon; Yangkey, Tenzin; Curley, Andrew; Smith, Sara; Gergan, Mabel (The University of Arizona., 2023)
      Herding in the Ladakh region is a common yet dwindling practice as Ladakh faces changing political and socio-economic conditions. In the Changthang region of Ladakh, Changpa (Ladakhi) and Tibetan refugee pastoralists continue to practice herding and support their livelihood. However, in the last few decades, they are facing compound challenges to sustaining their traditional herding livelihoods due to urbanization, youth migration, and generational change. In this study, I look at how Tibetan refugee pastoralists in Changthang Samed (out of nine different locations) perceive climate change and its impact on their livelihood. Tibetan refugee pastoralists relocated to the region in the 1960s following the Chinese occupation of Tibet. By studying Tibetan pastoralists’ coping strategies that they use to meet the changing physical environment (as a constitution of political, and socioeconomic change in the background), I will explore how their political status affects their ability to employ specific coping strategies. Drawing from critical social science, political ecology of climate adaptation, and political geography literature, I situate the experience of Tibetan refugee pastoralists and their plight in the global climate conversation as well as the regional climate change dialogue. I do so by exploring the intersection of climate vulnerability and political precarity.
    • Postcolonial Theory and Native American Literature

      Fatzinger, Amy S.; Sun, Xiaochen; Jenkins, Jennifer L.; Fox, Mary J. (The University of Arizona., 2023)
      Studying Native American literature through the lens of postcolonial theory has been controversial both in the field of Native American studies and postcolonial studies. However, this historical study of the evolution of thought among of scholars of Native American literature regarding the main research question of whether postcolonial theory can be meaningfully applied to Native American literature leads to the discovery that literary nationalists and cosmopolitans—supporters and opponents of postcolonial theory in the field of Native American studies—are actually working toward the same direction, revealing the impact of colonial discourses upon Native American people and striving to deconstruct such colonial influences. Eight postcolonial terms, including Antonio Gramsci's hegemony, Bill Ashcroft's appropriation, Gayatri Chakravorty Spivak's strategic essentialism, Homi Bhabha’s mimicry, liminality and vernacular cosmopolitanism, Frantz Fanon's critical nationalism and the idea of center and margin in Bill Ashcroft, Careth Griffiths, and Helen Tiffin’s The Empire Writes Back, are systematically selected and applied to four Native American texts—D’Arcy McNickle’s The Surrounded (1986), James Welch’s Fools Crow (1936), Louise Erdrich’s Tracks (1988), and Frances Washburn’s The Sacred White Turkey (2010)—both to examine if they can illuminate the influences of colonization upon Native American people, and to address the concerns of postcolonial scholars and scholars in the field of Native American literature.
    • A Modeled Demonstration of Hydromechanical Coupling in an Active Open Pit Mine

      Ferré, P.A. Ty; Noonan, Gillian Erin; Yeh, Tian-Chyi Jim; Lorig, Loren (The University of Arizona., 2023)
      Understanding the interaction of rock and water under stress is often a key factor in assessing slope stability in open-pit mining. Mining activity can increase or decrease the total stress acting on a rock mass, affecting the properties and behavior of the rock and water in the subsurface. In this research project, numerical modeling is used to demonstrate the concept of hydromechanical coupling based on an open-pit mining case study where coupled behavior due to slope excavation is observed in a piezometer monitoring sensor. The theory behind hydromechanical coupling and the physical parameters contributing to this behavior are discussed. Site monitoring data are analyzed, and their behavior are reproduced using the 2D numerical modeling software FLAC and a simplified coupled modeling process to produce mechanical- and flow-induced changes to a starting model developed based on the mine site conditions and mining activity. The work then assesses the sensitivity of contributing material parameters to modeled pore pressure responses and examines the range of important parameter values. This research aims to promote the understanding of hydrologic monitoring data behavior in pit slopes by producing a modeled hydromechanical explanation to provide improved knowledge for mine practitioners to use when planning mining activity, monitoring programs, and slope design. This work helps hydrogeologists interpret piezometer data and therefore make better decisions and models.
    • Mineralogical Controls on Cobalt Leaching From Mixed-Oxide Ore

      Barton, Isabel; Tillotson, Nicholas Lane; Wessman, Andrew; Zhang, Jinhong (The University of Arizona., 2023)
      In recent years, demand for cobalt—largely driven by demand for rechargeable lithium-ion batteries for electric vehicles and personal electronics—has grown faster than global cobalt production, necessitating a new look at the world’s cobalt resources and cobalt processing technologies. Oxide and oxyhydroxide ores constitute an important cobalt resource worldwide, and, if polymetallic seafloor nodules and crusts are included, make up the majority of global cobalt resources. The chief Co ore minerals in oxide ores are heterogenite (CoOOH or HCoO2) in stratiform sediment-hosted (SSH) Cu-Co ores, asbolane ((Ni, Co)xMn(O,OH)4∙nH2O) in Ni-Co laterite ores and some SSH deposits, and manganese oxide minerals such as vernadite (MnO2) in seafloor oxides, which are often also rich in Ni and Cu. Acid leaching is the cheapest and lowest-impact way to recover Co from oxide ores, but the precise mechanisms of cobalt-oxide leaching are not well characterized. In order to define major mineralogical factors in cobalt-oxide leaching performance, we leached Congolese SSH Cu-Co oxide ores and Pacific Ocean seafloor nodules in acid, then performed a comparative mineralogical study of leached and unleached samples using SEM-EDS and EPMA analyses. Both ores leached best under heat in a reducing environment, with maximum Co recoveries of 7% from our seafloor nodules and 99% from our SSH Cu-Co oxide ores. Recoveries of Ni and Cu from our seafloor nodules were as high as 40% and 33%, with a clear leaching gradient across our roughly 1 cm samples indicating that leaching was primarily limited by lixiviant access rather than by mineral leachability. We attribute the difference in Co recovery to the solubility of the host mineral’s lattice. Cobalt in SSH Cu-Co ores occurs in the relatively soluble Co-oxide lattice of heterogenite whereas Co in seafloor nodules substitutes for Mn in the relatively insoluble Mn-oxide lattice of vernadite, and consequently cannot be extracted with high recoveries without considerable, possibly prohibitive expense. Generalized to other ore types, the solubility of the mineral that hosts Co, as defined by the main structural metal, can be used as a broad guide to the leachability of Co in different oxide ores.
    • Investigation of Active Control of Boundary Layer Transition in Laminar Separation Bubbles

      Little, Jesse C.; Borgmann, David; Fasel, Hermann F.; Craig, Stuart A. (The University of Arizona., 2023)
      The presented research addresses the dynamics of the transition process in laminar separation bubbles (LSBs). Two major objectives will be discussed in this work: an investigation of the natural transition process in an LSB forming in the flow along a flat plate when subjected to an adverse pressure gradient (APG) and active flow control (AFC) exploiting the inherent instabilities in the LSB shear layer to control and delay laminar to turbulent transition.Extensive characterization of the boundary conditions in the experiment indicate a low turbulence environment necessary for stability and transition research. Prior to characterization of the LSB, the boundary layer along the flat plate model is investigated in the absence of the APG. Development of Tollmien Schlichting (T-S) waves in the laminar boundary layer along the flat plate show linear growth for several tested amplitudes and frequencies. Comparison to linear stability theory (LST) calculations and accompanying direct numerical simulations (DNS) show reasonable agreement in disturbance profiles and downstream amplitude development. Differences to the numerical results increase with downstream distance and are attributed to a slight favorable pressure gradient and the onset of non-linear behavior around the first maximum in the disturbance amplitude profiles in the experiment. Results confirm adequate quality of the free-stream turbulence (FST) (Tu ≤ 0.035%) and velocity spectra in the Arizona Low Speed Wind Tunnel (ALSWT) for the subsequent LSB transition study. The flow around the displacement body, used to impose the favorable to adverse pressure gradient to the flat plate model, is investigated and flow control measures are installed to ensure smooth, attached flow along the surface of the NACA 643−618 airfoil. The resulting baseline matches the time-averaged LSB from DNS with low levels of random disturbances (Tu = 0.02%). Two major unsteady features are found in the experiment. Low frequency (6 Hz, St = 0.02) content in the shear layer is connected to a large scale ’flapping’ motion, leading to significant periodic change in the reattachment location, causing an expansion/ contraction of downstream half of the LSB. High frequency content is related to the inviscid Kelvin-Helmholtz instability, causing disturbance amplification along the separated shear layer. Finite disturbance growth leads to formation of two-dimensional vortical structures, followed by rapid breakdown to turbulence upstream of mean reattachment. The dominant frequency in the shear layer (centered at 250 Hz, St = 0.88) is found higher than in the DNS (185 Hz, St = 0.671). Linear stability calculations on the matching baseline show a broad peak of unstable frequencies, similar in shape to the experimental results, centered between the peak values found in experiment and DNS. AFC is applied upstream of laminar separation. Initial forcing further upstream in the favorable pressure gradient shows significant strengthening of the two-dimensional roller structures leading to significant reduction in bubble size. All tested AFC in the experiment was successful in suppressing the large scale, low frequency ’flapping’ in the LSB and led to a change in transition dynamics. Notable damping due to the reminder of the favorable pressure, reduces disturbance amplitudes far below the critical amplitude (Acr) suggested by secondary instability analysis (SIA) and rapid breakdown to turbulence similar to the baseline case is observed for all forcing amplitudes. Moving the actuator close to the onset of the adverse pressure gradient increases separation control authority and pressure data suggests the LSB is suppressed at high forcing amplitudes. Time resolved PIV data identifies significant amplitudes of two-dimensional roller structures, especially at low and intermediate amplitudes. Increased forcing amplitudes leads to three-dimensionality in the mean flow causing a peak valley formation predominantly in the streamwise velocity component. Spanwise periodic structures with a wavelength of λz = 1 and a frequency of half of the forced frequency, are observed in all tested cases, with decreasing amplitude at higher forcing amplitudes. Fourier amplitude development suggest an optimal set of forcing parameters at (6 kVpp). Results show a delay in secondary mode amplitude growth and signs of delay of transition in the experiment. This case is compared to numerical results and matches the wavelength of the primary and secondary instability with predictions from LST, SIA and DNS, confirming the same transition dynamics present in the experiment and numerical simulations. Addition of FST in the DNS significantly reduces the delay in transition found in the numerical simulations without FST, explaining the observed differences to the experiment.
    • Dynamic Supervised Principal Component Analysis for Classification

      Zhang, Hao Helen; Ouyang, Wenbo; Hao, Ning; Niu, Yue; An, Lingling (The University of Arizona., 2023)
      Contemporary research places great importance on high-dimensional classification, with dynamic classification problems being of particular interest. Such problems involve situations where the distributions of both classes are not static and change with time or other index variables. This paper proposes a new framework in the context of linear discriminant analysis (LDA) for learning classification decision rules that can adapt to changes with respect to the index variable. Furthermore, many existing works on high-dimensional classification problems make the sparsity assumption about the original feature space, which may not hold in practice. Our framework relaxes this assumption by learning the hidden sparse structure of the data through data rotation. In this work, we propose a new dimension reduction method in the context of dynamic problems. The new method employs a kernel smoothing procedure to determine the suitable direction for dimension reduction. Numerical simulations and real data examples are illustrated to demonstrate the performance of the new approach in terms of both classification accuracy and computational efficiency. One extension to solve non-normal data problems is also included.
    • Improving Nursing Confidence in the Management of Behavioral Health Patients in the Emergency Department

      Reel, Sally; Zimmerman, Jennifer Ann; Edmund, Sara; Velo, Jamie (The University of Arizona., 2023)
      Purpose: Improve nursing confidence in providing care to behavioral health behavioral healthpatients in the emergency department through education and implementation of the Safe Structure template, which addresses identified nursing barriers. Background and Significance: There is substantial growth in the number of behavioral health patients presenting to the emergency department. Evidence shows there are four primary barriers to nursing care of behavioral health patients in the emergency department: physical environment, time constraints, resources, and the overall impact on the process of triage within their role. Nursing learned behaviors, stigma, and attitudes contribute to frustration and fear of caring for the behavioral health population. Nurses report lack of confidence and education in their ability to care for the behavioral health population. Methods: Descriptive quantitative study design using a retrospective post then pre-surveys to measuring nursing confidence levels post education on nursing barriers to care for behavioral health patients and the use of the safe structure template using a five-point Likert scale. Results: Post-the-pre surveys (n=28) were completed. Although findings were not clinically significant (p >.05), there was a slight overall increase in mean confidence levels post education. Pre-education, the nurses who completed the survey reported on average most confident in their ability to provide safe limitations consistent with environment and policies for behavioral health patients (M = 3.21±1.287) and least confident in their ability to create a daily routine for behavioral health patients (M=2.93 ±1.303) Confidence scores from nurses post-education were similar to the pre-confidence results with a slight rise in confidence their ability to provide safe limitations consistent with environment and policies for behavioral health patients 11 (M=3.71±0.854). Paired t test of nursing confidence levels did not reveal statistically significant findings in confidence levels (p >.05). Conclusion: Nurses continue to experience gaps and lack confidence in their ability to care for behavioral health patients in the emergency department. The limited findings of this project support the need for ongoing education, training, and support. The need for streamline education and time to complete is education based on nursing feedback.
    • Surface Metrology Methods for X-ray Telescope Mirrors, Freeforms, and Heliostats

      Chalifoux, Brandon D.; Wisniewski, Hayden James; Kim, Daewook; Schattenburg, Mark L. (The University of Arizona., 2023)
      Modern optical systems require or greatly benefit from freeform or non-rotationally symmetric optics. Increasingly stringent system performance requirements demand high accuracy surface shapes, which drives the need for surface metrology beyond state-of-the-art. This dissertation discusses three projects aimed at filling the need for more accurate or more flexible metrology methods to enable the construction of next generation systems. First is axial shift mapping, a self-referencing metrology technique to measure spaced based X-ray telescope mirrors. X-ray telescopes are composed of nested off-axis parabolic and hyperbolic surfaces, which are difficult to characterize due to their acylindrical shape. I present a shifting Fizeau interferometry technique that decouples contributions from the surface under test in the interferogram from the contributions due to the reference surface. I will present experimental results from using axial shift mapping to characterize a cylindrical mirror. This technique will allow better characterization of X-ray telescope mirrors on the path to a diffraction limited X-ray telescope. Second is the Virtual Ball Probe, an optical profiler being developed at Apre Instruments, Inc. Typically, optical profilers require the probe tip to be normal to the surface. This requires complicated stage geometry and can block certain areas of optics such as steep concave surfaces. The Virtual Ball Probe is designed to measure optical freeforms with surface slopes up to 50 degrees without the need for tilting of the probe tip to be normal with the surface. This allows for simple stage geometry and can accurately measure steep internal optical surfaces. I will discuss the system design and show current system performance. This system fills the need for an accurate yet flexible metrology system for modern freeform optics. Third is Grating Embedded Mirrors for single shot heliostat optical metrology. Commercial concentrated solar power plants are required to accurately monitor the surface slope error and canting error of thousands of heliostats to maintain plant efficiency. We have fabricated test Grating Embedded Mirrors (GEMs), which are float glass mirrors with phase gratings written into the bulk glass using an ultra-fast laser. We use these gratings to direct light to non-specular directions. I placed these grating embedded mirrors in front of a metrology system dubbed Diffractive Auto-Stigmatic Hartmann Camera (DASHCam) to measure the mirror surface slope error. I will compare the results gathered by DASHCam to the surface slope error as measured by a Fizeau Interferometer. GEM’s flexibility of design and ease of measurement is aimed at providing a compact, accurate, and high-speed heliostat slope error metrology system that is robust to harsh environmental conditions for the next generation of concentrated solar power plants. Together, these metrology systems advance the state-of-the-art by increasing flexibility while lowering uncertainty to meet the increasingly stringent requirements of next generation systems.
    • Crop Remix? Farmer's Crop Choice in Response to Covid-19 Evidence from Burkina Faso

      Josephson, Anna L.; Michler, Jeffrey D.; Rudin-Rush, Lorin Isaac; Bloem, Jeffrey R. (The University of Arizona., 2023)
      Half a billion households around the world are smallholder agricultural households. These households are at a unique risk to unexpected shocks like the COVID-19 pandemic. This paper looks at how planting behavior changes from before the outbreak of the COVID-19 pandemic. We leverage household panel data from Burkina Faso where information on planting behavior was collected before the outbreak of the virus. Our main findings are that households who had the opportunity to change crops for the 2020 and 2021 growing seasons indeed changed crops. Additionally, households grew more cereal crops (especially maize) after the pandemic than before, while household use of agricultural inputs did not meaningfully change Further examination is needed to understand if the households resist changing crops due to effects from the pandemic or due to unrelated factors.
    • Examination of the Cop Operon Repressor and the Effects of Copper and Zinc in Streptococcus pneumoniae

      So, Magdalene Y.; O'Brien, Henrik Y.; Viswanathan, V.K.; Van Doorslaer, Koenraad M.; Johnson, Michael D. L. (The University of Arizona., 2023)
      Streptococcus pneumoniae is a Gram-positive opportunistic pathogen that typically lives asymptomatically in the human nasopharynx but can cause pneumoniae, meningitis, otitis media, and sepsis. As with any organism living within a host, S. pneumoniae must acquire all its nutrients from the host. One group of essential nutrients is metals. Metals are vital to many cellular processes where they serve as structural components or catalytic cofactors of proteins. While metals are essential for life, they can also become toxic if their concentration is not tightly regulated. Bombardment of bacteria with toxic metals is one of the strategies of the mammalian innate immune system. Two metals that are known for their antimicrobial activity are copper and zinc. The metal environment will change as the bacteria move to different host tissues or experience the host immune response. In order to overcome stresses imposed by excess metal, bacteria encode metal efflux proteins. A notable example is the cop operon, a dedicated copper export system under the control of CopY. CopY is a metal-sensitive repressor that binds more tightly to DNA in a zinc-bound state and releases from DNA upon copper binding. Due to the role of these two metals in CopY regulation and their use as antimicrobials, we studied how changes in their concentrations impact S. pneumoniae. This dissertation explores the transcriptional and metabolic profile under a range of zinc and copper concentrations. In addition, we focused on CopY as we had predicted its regulon would likely expand beyond the cop operon. However, this was not the case, and we now propose an updated consensus operator sequence for CopY. Lastly, we look at how dysregulation of the cop operon affects the cell and we present the early stages of work to predict the CopY regulon across bacteria for which a full annotated genome is available.
    • Into the Mire: A Floristic and Ecology Informed Field Guide of Stordalen Mire

      Saleska, Scott; Szetela, Jessica; Arnold, Betsy; Ferrierre, Regis (The University of Arizona., 2023)
      Plant communities are often used as a basis for ecosystem studies, as they both greatly impact, and are greatly impacted by environmental interactions. Vegetation in the Arctic is particularly sensitive to disruptions in temperature and water regimes, altering vegetation and thus species diversity, composition, productivity, structure, and biomass. Species have differential responses to regime shifts due to unique tissue types, nutrient composition, plasticity, and production and growth strategies. Accounting for these traits and processes in vegetation may aid in understanding ecosystem level problems, especially when such studies are conducted in a cross-disciplinary framework. Stordalen Mire in Abisko, Sweden is impacted by climate-mediated permafrost thaw, driving shifts in soil moisture, nutrient availability, and the composition of plant and microbial communities. Due to the topographical and hydrological heterogeneity of Stordalen, the distribution of the species is influenced by patch dynamics creating a mosaic of ecological subsections across the landscape -- each with a differing composition of plants and their traits. This guide is motivated by the value brought by knowledge of individual plant taxa and their traits, and the ways their reactions to change will affect both vegetation and broader processes in ecosystem functioning. Additionally, it provides a resource for scientists conducting studies related to plants by including a species list compiled through the literature, and identification information for some of the most common and influential species on Stordalen Mire. Of the 43 species recorded at Stordalen Mire, 26 are vascular plants and 17 are bryophyte species. These species are members of 26 genera, representing 21 families. Recent studies have called for examining immediate, subsequent, and long-term effects of climate on vegetation shifts – both on individual species and species assemblages. Literature reviews of these species have revealed patterns in phenology, physiology, competition, nutrient cycling, carbon fluxes, microbiome interactions, etc., providing a plethora of future directions of research.
    • The RNA Helicase Ded1 Interacts with Cell Cycle Components and Other Key Proteins During Cellular Stress

      Bolger, Timothy; Carey, Sara Brooke; Buchan, Ross; Capaldi, Andrew; Sutphin, George (The University of Arizona., 2023)
      DEAD-box RNA helicases regulate each stage of the RNA life-cycle during gene expression. Ded1 is an essential yeast DEAD-box protein that regulates translation initiation through its effects on mRNA secondary structure and formation of pre-initiation complexes. Ded1 binding to mRNA is not sequence specific, and therefore, it relies on interaction partners for its specificity and regulatory activities during initiation. Stress conditions require large-scale changes in translation that upregulate certain stress response genes but repress most other nonstress-related genes. The target-of-rapamycin (TOR) pathway is a major regulator of these changes, and we have found that Ded1 is a critical mediator of this stress response. Interestingly, in contrast to its role in promoting translation initiation in pro-growth conditions, Ded1 plays an active role in repressing translation upon TOR inactivation. My work focuses on further characterizing the currently unknown interactions critical for Ded1’s repressive function during cellular stress. My results support a physical interaction between Ded1 and Cdc28 in stress conditions that is absent in normal growth conditions, and follow-up results suggest that this interaction may help to coordinate the cell cycle and translation during stress. Along with this clear connection to Cdc28, I conducted a large-scale screen that also shows connections of Ded1 with ATP transport, stress granule formation, cellular localization, cellular trafficking, and mitochondrial translation. All of these could play a key role in understanding how Ded1 fits into the larger picture of translational regulation during TOR inactivation and each subset seen in the annotated GO terms could be an individual area of study for future understanding of stress responses and translation.
    • Dwarf Galaxies as Probes of Galaxy Evolution

      Juneau, Stephanie; Dey, Arjun; Pucha, Ragadeepika; Hainline, Kevin; Fan, Xiaohui (The University of Arizona., 2023)
      Low-mass "dwarf" galaxies (stellar mass, M* <= 3 x 10^9 Msun), being ubiquitous in the universe, are excellent laboratories for testing critical components of galaxy evolution. The current and future photometric and spectroscopic surveys, including the Sloan Digital Sky Survey (SDSS), the Dark Energy Survey (DES), the Dark Energy Spectroscopic Instrument (DESI) survey, and the Legacy Survey of Space and Time (LSST) are facilitating the study of these galaxies in great detail. In this dissertation, I probe three different aspects of galaxy evolution using dwarf galaxies. Firstly, by conducting the widest (1.5 deg diameter field of view) and the deepest (down to g ~ 26.5 mag) survey of resolved stars in a Local Group dwarf galaxy, IC 1613, I found evidence of hierarchical accretion in the galaxy. This is an important first step in understanding structure formation in dwarf galaxies. Secondly, I demonstrated that the compact morphologies of Lyman-Alpha Emitters (LAEs), i.e., low-mass, high-redshift galaxies, are key to Ly-alpha escape, a process that is crucial for understanding the epoch of reionization. Finally, using an unprecedented spectroscopic sample of ~190,000 low-mass galaxies from the DESI survey, I identified >2,500 active galactic nuclei (AGNs) out to z ~ 0.45, more than tripling the existing census of optical dwarf AGN candidates. Compared to previous systematic searches, I have extended the discovery space of such candidates to lower galaxy masses and to higher redshifts. Additionally, I extended the black hole (BH) mass - galaxy stellar mass (M_BH - M*) scaling relation down to log (M*/Msun) ~ 8.4. This statistical sample of AGN in low-mass galaxies will have important implications for the study of galaxy-BH co-evolution at the low-mass end of the galaxy mass function. Furthermore, I created four publicly available Jupyter Notebooks that show how to access and analyze photometric and spectroscopic data for the scientific analysis of galaxies.
    • Effects of Flow Restoration, Vegetation Structure, and Bridges on Birds of the Lower Santa Cruz River

      Bogan, Michael T.; Rocha, Erasmo Pablo; Zylstra, Erin; Steidl, Robert (The University of Arizona., 2023)
      Riparian areas in the arid Southwest are important refuges for many taxa that rely onthem for foraging, breeding, as corridors, and as a source of water. These areas are also disappearing though, and urbanization plays a major part in the degradation of these areas. As cities grow, natural vegetation is replaced with impermeable surfaces, resources are depleted, and aquifers are often drawn to support city growth. However, urbanization also has the potential to restore riparian areas. In this study, we focused on the use of effluent (treated wastewater) to restore riparian areas along the Santa Cruz River in Tucson, Arizona and how flow restoration affected bird assemblages. We identified and counted birds weekly at nine plots in each of four study reaches from February to April 2022. We measured environmental characteristics at each plot, including average flow of surface water, density of shrubs, amount of canopy cover, and distance to the nearest road bridge. Using these data, we set out to answer the following question: how do changes in stream flow, vegetation structure, and proximity to bridges affect bird communities overall and the population densities of individual species in an urban riparian system? We found that flow had a positive relationship with bird species richness, but no other measured environmental factor had a strong relationship with richness. Bird communities within each reach generally were distinct from one another, and changes in assemblage composition were correlated with flow, the density of shrubs, and canopy cover. Densities of five focal bird species varied among plots. Densities of two species were positively associated with stream flow while density of a third species was negatively associated with flow. Densities of other species varied with shrub density and canopy cover. Our results showcase how restoration of riparian areas using effluent has the potential to support unique species and assemblages of birds, and that a mosaic of different riparian areas support the highest diversity at a regional scale. We believe that collaborations between urban planners and ecologists when undertaking this type of project have the potential for significant positive impacts on riparian birds.
    • Removing Structural Stigma Barriers in Substance Use Disorders: Dast-10-R Introduction and Feasibility of Use

      Bouchard, Lindsay A.; Young, Janay R.; Crowley, Lisa; Skinner, Harvey A. (The University of Arizona., 2023)
      Purpose: This quality improvement project aimed to foster transformative learning (TL) and increase knowledge regarding the use of non-stigmatizing terminology use in substance use disorder (SUD), introduce the drug abuse screening test-10-revised (DAST-10-R), and measure its feasibility for use in screening, brief intervention, and referral to treatment (SBIRT) protocols at a federally qualified health clinic (FQHC). Background: SUD is a chronic, treatable condition. People with SUD must first be identified as having the problem; then, effective treatment can be provided. There is a call to action for removing stigma barriers to effectively identify and treat the growing number of people with SUD, as the US faces the highest number of opioid related overdose deaths in history. Methods: This DNP project used a pre-post survey design as a method for measuring attitudes in TL, knowledge gained on non-stigmatizing terminology use in SUD, and feasibility of using the DAST-10-R screening tool in practice. Pre/post-intervention groups were compared on Likert and knowledge-based survey items. Likert items measured attitude; knowledge-based items measured knowledge gains. Groups were compared on Likert-type ratings using Mann-Whitney U tests for median and interquartile ranges and compared on their respective proportions of correct answers for each knowledge question using either Chi-square analysis or Fisher’s Exact Test for frequency and percentiles. Significance was assumed at an alpha value of 0.05, and analyses were performed using SPSS Version 29. Results: There were 14 behavioral health leadership team participants from the FQHC. All participants completed the pre-survey, and 10 completed the post-survey. There was evidence for transformative learning and knowledge gains on recommended terms to use in SUD. The DAST-10-R scored high rates for the feasibility of use in clinical practice. Conclusions: Education is effective for fostering transformative learning to remove structural stigma terminology in SUD realms, and the DAST-10-R is feasible for use in clinical behavioral health SBIRT protocols.
    • Li Zi-Li and His Viola Concerto: Musical Analysis and a Study of Performance Interpretation

      Gebrian, Molly MAG; Wei, Ziyun; Alejo, Philip PHA; Kantor, Timothy TAK; Traut, Don DGT (The University of Arizona., 2023)
      This research document intends to examine the Viola Concerto No. 1 by Li Zi-Li in depth and offers musical analysis as well as interpretations and suggestions for how to perform this work. Compared to Western viola repertoire, Chinese viola repertoire is much less studied and performed by violists. Currently, Chinese-born composers who write music for Western musical instruments are very few, but they are pioneers who have established the foundation of Chinese viola music. They combine Chinese folk style and Western compositional techniques to help promote Chinese folk styles to audiences around the world. Li, for example, incorporates Chinese musical and stylistic elements into this work using Western musical conventions as a unique way for violists to promote the main genres and styles of Inner Mongolian music. With the help of Li’s viola concerto, violists can widen audiences for Chinese viola music, and encourage Chinese composers to compose more viola works in this genre and style.