• Liberation: The Story of a French Daily

      Herrera Cruz, Ignacio (The University of Arizona., Not availa)
    • A Comparative Study of Broadcast and Print Coverage in Three Criminal Cases

      Hudson, Lisa Rae (The University of Arizona., Not availa)
    • HCMV Manipulation of Host Cholesteryl Ester Metabolism

      Dahlmann, Elizabeth Alan (The University of Arizona., 2019)
      Human cytomegalovirus (HCMV) is a β-herpesvirus that infects over 50% of people above the age of 40. Once infected, HCMV establishes a lifelong latent infection with periodic reactivation. Most infections are asymptomatic. However, infection in immunocompromised patients may result in fatal HCMV-related complications. Further, congenitally-acquired HCMV infection is the leading cause of birth defects in the United States. The HCMV virion contains a large double-stranded DNA genome encapsidated by a protein shell that is surrounded by a lipid membrane. Like all enveloped viruses, HCMV steals host lipids to generate its envelope membrane. While previous studies demonstrate that HCMV replication requires lipid metabolism, the details of virally-induced lipid changes remain poorly defined. We performed an untargeted lipidomic screen using liquid chromatography high resolution tandem mass spectrometry to identify and quantitatively measure how infection alters the lipidome of cells. We found that HCMV increases cholesteryl esters (CE) by 24 hours post infection. CE lipids are synthesized by sterol O-acyltransferase 1 (SOAT1) attaching a fatty acyl-CoA to a cholesterol molecule. I hypothesized that early stages of HCMV replication induce CE biosynthesis and that CE are required for viral replication. In support of our hypothesis, we found HCMV induces SOAT1 gene expression. Further, HCMV immediate early pUL37x1 is partially responsible for virally-induced CE accumulation. We found that treating infected cells with a SOAT1 inhibitor blocked CE production and infection. Overall, our findings suggest that HCMV induces CE synthesis that can be targeted to block infection.
    • Tobacco Residue On Archaeological Pipes: Analysis Via Solid-Phase Microextraction Gas Chromatography – Mass Spectrometry

      Lindsey, Wendy (The University of Arizona., 2019)
      Current methods of residue analysis in the fields of archaeological science and cultural heritage science mostly rely on destructive sampling methods that often damage objects of cultural heritage. Tobacco residues found on an archaeological object may contain insights into the object’s use in antiquity, even impacting its legal status under the Native American Graves Repatriation and Protection Act. However, museum or legal limitations on destructive sampling often prevent curators and conservators from carrying out any analysis. In addition, contamination is a concern for any residue analysis, especially for items that have been in a museum for decades or centuries. By conducting a series of experimental analyses that included documented archaeological collections from the Arizona State Museum, we have developed a non-destructive method for the detection of tobacco residue. Solid-phase microextraction (SPME) in combination with widely-available gas chromatography – mass spectrometry (GCMS), was used to successfully detect nicotine as a biomarker in tobacco residues from three of the museum pipes.
    • Stress in Augmented Reality Human Computer Interfaces

      Elbishari, Yunes M Y (The University of Arizona., 2019)
      The ability of a user to control their attention within an Augmented Reality (AR) Human Computer Interaction (HCI) is an unreliable quality for the design of an AR system. An alternative design approach is to adopt adaptive HCIs that adapt to specific user needs. One user need is to manage stress levels. Stress is an issue because it affects user performance. Often users are not aware of their stress levels, therefore a User Interface (UI) that independently identifies stress and automatically adapts to it would be very beneficial. The present study examines the research questions: how would a UI adapt to stress and what would be the utility of such be? The study included both descriptive and experimental elements. The descriptive element reasons from fundamental neuroscience and psychology that stress is an important factor in user performance and that a UI that reduced excessive stress would have utility, namely it would enable improved user performance. The experimental element proved a means to measure stress via a proxy. The experiment utilized a situation demanding an AR UI, that is both real world and computer created data were required to complete the required tasks: one “performance” task for which user performance mattered and a “distraction” task to ensure the user’s cognitive engagement was saturated. The experiment demonstrated that stress (measured by proxy) is directly correlated to stimuli complexity of the AR UI and that user performance in an AR UI is inversely correlated to stress. These facts together provide a strong indication that an AR UI that adapts to the stress proxy would provide significant value to the user.
    • The Status and Vitality of Moroccan Tamazight and Darija

      Graybill, Aaron James (The University of Arizona., 2019)
      Various social and political factors determine language status and vitality. These factors are fluid and change over time, making status harder to measure. However, through an overview of the recent political and educational history, and current events in Morocco, I chart the status changes of Darija (Moroccan Arabic) and Tamazight (Berber) using the UNESCO language vitality framework. The results show that Tamazight is shifting in its respective status and vitality. In contrast, Darija, while maintaining linguistic vitality demographically and historically, lacks institutional support. This lack of institutional support has implications for key vitality factors and stems from its subordinate place in relation to Standard Arabic. Tamazight, after the recent history of marginalization, is beginning to enjoy increased institutional support. The result is an increase in Tamazight broadcasting and textbooks as well as the appointment of an Amazigh Prime Minister. However, despite this support, Tamazight is still in a demographic decline, and it remains to be seen whether government interventions will slow or reverse this language shift.
    • Reverse Engineering of Ancient Ceramic Technologies from Southeast Asia and South China

      Kivi, Nicholas (The University of Arizona., 2019)
      Ceramic technologies of Myanmar and South China were analyzed in order to determine characteristic traits and technological origins. Given Myanmar’s geographically strategic position between China and Southwest Asia, its ceramic history needs to be reevaluated among the distinct traditions of Southeast Asia. The ceramics of Myanmar show evidence of imitation China and Southwest/Central Asia using locally sourced materials, giving support to Dr. Myo Thant Tyn’s theory of the convergence of the Chinese and Southwest/Central Asian ceramic traditions in Myanmar. Seven ceramic technologies of Myanmar were analyzed: celadons, black-glazed jars (lead-barium and lead-iron-manganese glazes), brown ash glaze ware, green and opaque white-painted glaze ware and turquoise-glazed, coarse-bodied white earthenware. Celadon glazes and brown glazes were made with ash, similar to the Chinese celadon tradition. Green-and-white opaque ware utilized copper-green colorant glaze decoration with tin and lead oxides as opacifying agents on low-fired oxidized bodies. Both these traditions are probably derived from Southwest Asian ceramic and glass traditions. High-soda, copper-turquoise glazes on coarse white earthenware bodies are influenced by Southwest and Central Asian low-fire ceramic and glass traditions. Black-glazed, “Martaban”-style storage jars were variable in body and glaze technology and are still of indeterminable technological origin. A phase-separated glaze was analyzed that had a similar phase-separated appearance to northern Chinese Jun ware. Additionally, two black-glazed ware types from South China with vertical streaking phase separation were analyzed: Xiba kiln of Sichuan and Jianyang kilns of Fujian. The recently discovered and excavated Xiba kiln made experimental and striking stoneware bowls similar to Jianyang “hare’s fur” ware. Reverse engineering the manufacture of Xiba kiln ware determined that Xiba was an innovative site that imitated Jianyang ware aesthetically but not technologically. Xiba and Jianyang do not have any connection to the six Burmese glaze styles, however, future analyses of Southeast Asian ceramics can use the data for comparison and variability research.
    • An 8 Channel Imager/Polarimeter for Astronomical Observations

      Taylor, Brian William (The University of Arizona., 2019)
      Discussion of optical designs and instrument polarization for an Eight Channel Imager/Po- larimeter are presented. The designs will cover the optical and Near Infrared(NIR) wavelengths from 330nm to 2400nm in a simultaneous acquisition mode for eight distinct broad bands. The simultaneous acquisition provides capabilities to study unique events such as supernovae, Gamma Ray Bursts(GRBs), and occultations. It also increases the efficiency of long term monitoring pro- grams such as the study of blazars. The selection of the wavelength bands were specifically chosen to match the Sloan Digital Sky Survey(u′, g′, r′, i′,z′) and the 2MASS(J,H,K) catalogs.
    • CC16 Depletion in the Lung Due to Early Life Biomass Exposures

      Calderon, Stephanie Marie (The University of Arizona., 2019)
      Millions of people across the globe are affected by respiratory diseases that include chronic obstructive pulmonary disease (COPD), asthma, emphysema, as well as cancer. COPD is the third leading cause of death worldwide due to the increase in global air pollution and smoking. Currently, there is no treatment that can change the outcome of the disease. The clinical manifestations of COPD are lung function decline and recurrent episodes of exacerbations (Knabe, 2015). Many pollutants that can lead to COPD come from sources such as wood and coal burning, cigarette smoke, and industrial air pollution. Many people across the world rely on the combustion of biomass for fuel as energy for heating and cooking. Biomass smoke exposures are recognized as a significant public health issue due to respiratory health implications. This paper will provide a review and synthesis of human and mice studies of lung insults that cause inflammatory diseases such as COPD and explore the role of club cell protein 16 in the development of disease following exposure to biomass smoke.
    • Upstream Regulators of TORC1 Signaling Pathway in Saccharomyces cerevisiae

      Vaishampayan, Prajakta (The University of Arizona., 2019)
      Many nutrients including glucose, phosphate and amino acids regulate TORC1 activity and when the cells are in stress or starvation conditions, TORC1 activity is inhibited. It remains unclear how this happens. So, we are interested in mapping the signaling system that talks to TORC1 to ultimately understand how the complex integrates signals to control growth in stress conditions. In this project, the response of TORC1 under nitrogen, glucose and phosphate starvation conditions was checked in strains lacking one or more stress signaling pathway proteins to identify the mechanism which leads to inhibition of TORC1 in stress conditions.
    • Matrix Matters: Biomarker Potentials of Phagocytes, Exosomes, and Cytokines

      Buckley, Maverick J. (The University of Arizona., 2019)
      Overview: The Applied Biosciences Professional Science Masters (ABS-PSM) program at the University of Arizona prepares students in the fields of biological science to enter areas of business and scientific competition. This interdisciplinary course of study involves the completion of an internship wherein students demonstrate scientific inquiry in the context of the goals and economic pursuits of the hosting agency. Students are required to convey how their projects contribute to the ambitions of the company or academic institution as well as to the larger scientific field. In this report, two internship projects completed to fulfill this requirement for the ABS-PSM degree will be described. Biomedical research and diagnostics rely heavily on the use of biomarkers for drug discovery and disease management. Biomarkers are “characteristics that are objectively measured and evaluated as indicators of normal biological processes, pathogenic processes, or pharmacologic responses to therapeutic interventions,” as defined by the National Institutes of Health Biomarkers Definitions Working Group (2001). Drug development and many facets of clinical diagnostics involve the measurement of a combination of biomarkers to evaluate the status of disease in an individual or their physiological changes following some treatment. In contrast to symptoms, biomarkers are not perceived by the patient but rather are observed from outside the patient (Strimbu & Tavel, 2010). The most well-studied biomarkers, such as troponin for the assessment of cardiac injury (Babuin & Jaffe, 2005), are applied regularly in predicting the incidence or outcome of a disease. This use of biomarkers as clinically meaningful surrogate endpoints is entirely justifiable, but only when such a characteristic has extensively and repeatedly proven predictive of outcome (Strimbu & Tavel, 2010). Additionally, the most logical biomarkers are those directly involved in the pathophysiology of a certain pathway, enabling more accurate interpretations of an individual’s disease status to be made. The evaluation of a biomarker’s potential is challenged by the way in which it is measured. Biological samples are wide in variety, and, aside from ensuring the marker is present in the medium at all, determining what sample type is most compatible with existing instruments and what is most associated with a disease or anatomic site is a complex task. Cardiac troponin, for example, is measured in a peripheral blood sample to assess heart damage. The correlation of this enzyme’s concentration in the blood with heart muscle damage makes it a valuable disease indicator because the enzyme is produced in cardiac tissue and immediately released into the circulation (Antman et al., 1996). Neurodegenerative disease markers are markedly complicated because their presence in conventional fluid samples may not be accurately representative of concentrations in the brain. MSDx, Inc. (Tucson, AZ), a company that develops diagnostic solutions for neurodegenerative diseases, has identified phagocytes as a suitable source of biomarkers for this purpose. These cells naturally concentrate and carry remnants of disease pathology through phagocytosis, thereby preserving intact markers of neurodegeneration from the potentially degradative extracellular environment that can be quantified in a blood sample. In comparing this approach to conventional fluid analyses, the first chapter in this report describes a literature review performed on various potential neurodegenerative disease biomarkers and their alterations relative to controls by sample matrix. A second aspect of this project that will be discussed was an exploration of entities involved in the research of exosomes, a type of extracellular microvesicle capable of carrying proteins between cells. Cytokine concentrations in the blood also change during various disease processes such as inflammation, making them attractive potential biomarkers. Their use, though, is hindered by variation in normal levels from person to person and an uncertainty as to the optimal sample matrix in which to quantify them. For biomarkers to be identified among cytokines, it is essential to first determine what constitutes “normal” levels of a selection of pathologically relevant cytokines, whether serum or plasma samples should be used, and what collection and processing practices such as anticoagulant should be employed. This is the overarching goal of a group at the University of Arizona BIO5 Institute whose small pilot study will be the focus of the second chapter of this report. The study involved recruiting a cohort of self-identified healthy adult volunteers at specific time intervals and obtaining blood samples for quantifying their cytokines using a commercial multiplex Luminex-based assay. An abbreviated preliminary analysis of the results was then conducted, which concerned the levels of cytokines obtained at different time points and in different sample matrices, supporting a brief evaluation of the benefits and drawbacks of using certain anticoagulants and preparation strategies over others. Both projects produced exciting findings related to biomarker discovery and measurement. Based on my review, phagocytes seem to be largely ignored in neurodegeneration research, yet represent a promising medium in that they avoid many of the drawbacks associated with measuring central nervous system components outside the brain; as well, they did not appear to be studied elsewhere beyond MSDx nor their potential to carry important biomarkers dismissed. On the other hand, exosomes have been shown to be increasingly studied in neurology with broad potential, but important challenges mostly related to their small size remain. Cytokines, in contrast to such biomarker cargo carriers, are information couriers that may also have biomarker potential. These intercellular messengers mediate inflammatory processes but are in constant production at different degrees depending on one’s immunologic and overall health status. Determining what is normal must first be established and is a major challenge since cytokine levels vary by individual, even in an uninfected state. To advance this process, plasma collected with EDTA as an anticoagulant may be optimal, though serum is attractive due to its widespread use and would help make comparisons with the majority of other cytokine studies possible. Despite its invaluable capability to simultaneously measure multiple cytokines in a single sample, the bead-based assay also has its weaknesses that may be related to the matrix type or antibodies being used. Thus, determining the most appropriate method for sample retrieval, reliable measurement of the marker of interest, and establishment of reference values for novel biomarkers appear to be the most pressing challenges associated with the goals described here.
    • Forensic Rockfall Dating at Kartchner Caverns

      Bates, Melissa Elizabeth (The University of Arizona., 2018)
      This study discusses the time dependent nature of geomechanics and explores low-impact methods for dating rockfalls in the cave environment. Kartchner Caverns provides a unique environment to perform this study because of its high humidity, absence of sunlight, gently fluctuating temperature, and seclusion from the above ground surface which causes the cave to be inhabited by specific types microorganisms. High precision microscopy and microbial DNA extraction were used in order to better understand the changes that rock surfaces undergo when they are exposed to the cave environment. Spectral data collection was done in order to research the applicability of remote sensing technology to assess the degree of weathering of rock surfaces at the project site. It was concluded that microbiology and chemical processes may play an important role in weathering in the cave environment and spectral imaging has the potential to be an effective data collection method.
    • How Connected Is Connected? Structural Measures to Estimate Effective Conductivity

      Klakovich, Jeffrey Vincent (The University of Arizona., 2018)
      Connectivity has been a target of investigation for subsurface hydrology for decades. We apply seven new and existing connectivity measures to 2-D, binary hydraulic conductivity (K) grids that include a range of percent high K mixtures. Effective conductivity (Keff) for 1-D flow through the domain is calculated from the results of flow simulation (MODFLOW) and compared with connectivity measures. In addition, characteristics of the percolating network (connected high K bodies that span entire domain) are investigated. Results indicate that most of the range of Keff (80%-90%) for approximately 1 million randomly generated grids over a range of percent high K mixtures only exists among percolating grids. We demonstrate that the number of unique percolating paths (NPP) is the most important structural feature for predicting Keff. We show that NPP can explain to a large degree the mean behavior of Keff as a function of percent high K material. It may also explain the variance of Keff as a function of percent high K, however this has not been shown conclusively. Most connectivity measures were not found to correlate with Keff. In general, it seems connectivity is only important for Keff when high and low K values are similar (one order of magnitude different). Therefore, the overall impact of connectivity is relatively small. The dependence of Keff on the continuity of high K paths suggests that methods that return volume-averaged properties (e.g. electrical resistivity tomography) may have limited ability to predict Keff. High resolution imagery or water isotopic tracer tests to infer structure may be necessary for accurate estimation of Keff.
    • Predicting the Size and Location of a Cavity in a Solid Half-Space from the Scattered Ultrasonic Fields Using Genetic Algorithms

      Alnuaimi, Hamad (The University of Arizona., 2018)
      Genetic algorithms are used to predict the size and location of an elliptical cavity within a solid half-space. The scattering of ultrasonic waves in the solid half-space with a cavity is modeled using Distributed Point Source Method (DPSM). DPSM which is a semi-analytical technique that utilizes Green’s function is used for modeling because this technique is more efficient than popular but not so efficient Finite Element Method (FEM). FEM is very inefficient for modeling ultrasonic wave propagation problems at high frequencies and for solving an inverse problem one needs an algorithm that can solve the forward problem efficiently. The inverse problem is solved by applying a genetic algorithm to the forward problem to determine the optimum solution. The optimum population size and number of generations are determined. Results and analysis are performed for 3 cases of unknown variables.
    • Effects of Lactobacillus Reuteri Supplementation on Serum Cholesterol and Cardiac Damage

      Koppinger, Matthew P. (The University of Arizona., 2018)
      Dysbiosis of the gut microbiota has been implicated in the progression and severity of a number of disorders, including cardiovascular disease. Probiotics offer a means to positively manipulate the gut microbiota and can improve cardiovascular risk factors, like hypertension and hypercholesterolemia. Research investigating the effects of probiotic supplementation in the context of cardiac injury is limited. Furthermore, the mechanism by which probiotics impart benefits and where these benefits are incurred in the GI tract is not well elucidated. The aims of this thesis were to investigate the effects of probiotic supplementation in the context of cardiac injury and better understand probiotic localization following administration. In the first study, LDLr KO and wild-type mice were administered Lactobacillus reuteri for 5-6 weeks before initiation of an ischemia/reperfusion protocol. In the second study, transit and localization of the probiotic, Bifidobacterium animalis subspecies lactis 420 (B420), were monitored in the GI tract following single and consecutive administrations. Results of the first study show that supplementation with L. reuteri significantly attenuates cardiac damage following myocardial infarction. The second study found that B420 presence in the GI tract was lost rapidly following cessation of treatment. Together, these results show that probiotic supplementation may offer an alternative therapy for improving cardiac health and that continuous treatment is necessary for probiotics to impart their beneficial effects.
    • Mapping Saguaro Cacti Using Digital Aerial Imagery in Saguaro National Park

      Carter, Forest (The University of Arizona., 2018)
      The saguaro cactus has been the subject of extensive ecological research since the establishment of Saguaro National Monument in 1933. Saguaro mapping and monitoring has always been limited in extent due to inherent restrictions of in situ field methods. This research developed a method for automated mapping of mature saguaros over large extents using fine spatial resolution digital aerial imagery. Saguaro shadow signatures were identified using a novel contrasting custom search kernel method. The shadows detected were used as proxies for mature saguaro locations. This research focused on (1) the development of a method of automatically identifying saguaros using their shadows in aerial imagery, (2) applying the method to aerial imagery of Saguaro National Park (SNP) to conduct a large extent saguaro census, (3) validation of the saguaro distributions against in situ field measurements, (4) investigating causes of shadow omissions, (5) estimating total saguaro densities and populations in SNP. The shadow method developed identified 446,092 saguaros across 231 square kilometers in Saguaro National Park. These results were found to be highly correlated (R2 value of 0.966) with saguaro locations recorded by SNP staff in 11 field plots in 2011. This study demonstrates that mature saguaros can be reliably mapped automatically using digital aerial imagery. The method developed will facilitate saguaro monitoring and ecological resource management in SNP and throughout the range of the saguaro cactus.
    • Liquefaction of the Brain Following Stroke Shares Multiple Characteristics with Atherosclerosis and Mediates Secondary Neurodegeneration in an Osteopontin-Dependent Mechanism

      Chung, Amanda (The University of Arizona., 2018)
      The response to ischemic injury in the brain is different to the response to ischemic injury in other organs and tissues. Almost exclusive to the brain, and for unknown reasons, dead tissue liquefies in response to ischemia by the process of liquefactive necrosis. However, the data we present here indicate that at the macroscopic, microscopic, and molecular level, liquefactive necrosis strongly resembles atherosclerosis. We show that chronic stroke infarcts contain foamy macrophages, cholesterol crystals, high levels of osteopontin and matrix metalloproteases, and a similar cytokine profile to atherosclerosis. Crystalline cholesterol is a principal driver of atherosclerosis, and because cholesterol is an important structural component of myelin, we propose that liquefactive necrosis in response to stroke is caused by an inflammatory response to myelin debris, and is exacerbated by the formation of cholesterol crystals within macrophages. We propose that this leads to the chronic production of high levels of proteases, which in a partially osteopontin-dependent mechanism, causes secondary neurodegeneration and encephalomalacia of the surrounding tissue. In support of this, we show that genetically ablating osteopontin substantially reduces the production of degradative enzymes following stroke, reduces secondary neurodegeneration, and improves recovery. These findings suggest that treatments that prevent or target the regression of atherosclerosis may also be useful for mitigating the harmful effects of liquefactive necrosis following stroke.
    • Linking Net Assimilation with Multispectral Vegetation Classification to Understand Mesquite-Grass Response to Fire

      Sutter, Leland Frederic (The University of Arizona., 2018)
      Understanding vegetation dynamics across space and time has been a grand challenge in Earth sciences, but the induction of remote sensing products has made large-scale mapping of vegetation possible. We initially used Landsat satellites (30 m; eight-day return interval) to assess the Sawmill Fire of 2017 within the Santa Rita Experimental Range. Because of the spatial and temporal decoupling associated with this remote sensing product, important, but smaller-scale disturbances may not be properly captured; this prompted the use of finer scaled data. As such, we used an unmanned aerial vehicle (UAV) equipped with a five band Micasense RedEdge camera for derived land classification and scaling. Additionally, we measured leaf level net assimilated photosynthesis (ANET) to quantify plant function. We repeated the measurements at three points in time at a control and burned site. Spectrally, changes in the Relative Normalized Burn Ratio (RNBR) using Landsat images from directly before the fire and then after the growing season showed minimal evidence of the fire because of its spatial scale, though there were significant impacts from the fire on vegetative physiognomy and ecosystem function. Classifications built from the multispectral camera showed an overall accuracy of 0.89. This study shows the need for fine-resolution data from newly available UAV systems for practical land management practices. Low altitude, fine resolution data, combined with ecophysiological datasets, can be used to quantify and follow tractable land cover changes not captured by our traditional, lower resolution remote sensing sensors and derived products.
    • The Pathophysiology of Chronic Stroke Infarcts: What Happens After Brain Tissue Dies?

      Likens, Jacob Andrew (The University of Arizona., 2018)
      A stroke can occur when blood flow to a specific area of the brain is interrupted. There has been extensive research in both animal models and humans that has characterized the pathophysiology of the first few weeks following stroke. However, there has been far less research into the chronic stage of infarction. This is an important area for research because more than 10 million individuals worldwide suffer a stroke each year. Approximately one-third of these survivors develop dementia in the first year after their stroke. The cause behind this dementia is currently unclear, and there are no neuro-protective drugs that can improve recovery and provide cognitive protection in the chronic time period. Therefore, the chronic stage of stroke recovery is a promising target for future therapeutics for stroke-related dementia and, as will be shown later in the paper, Alzheimer’s disease as there are likely to be neurodegenerative processes that proceed for months following stroke. The goal of this thesis is to provide a review of what is currently known about the pathophysiology of chronic stroke infarcts (an area of brain tissue that has necrotized due to a blockage in an artery in the brain causing a lack of oxygen), explain why so little is known, and how we can learn more, and provide potential mechanistic links between the response to dead brain tissue and the development of dementia.