ABOUT THE COLLECTIONS

The graduate and undergraduate research collections share, archive and preserve research from University of Arizona students. Collections include honors theses, master's theses, and dissertations, in addition to capstone and other specialized research and presentation topics.


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If you have questions about items in these collections, or are a faculty member who would like to provide students in your program an opportunity to showcase their research, please contact the Office of Digital Innovation & Stewardship at repository@u.library.arizona.edu with your request. We look forward to working with you.

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Recent Submissions

  • Geology and ore deposits of the Richmond Basin area, Gila county, Arizona

    Butler, B.S.; Bishop, O.M. (Ottey Manley), 1905- (The University of Arizona., 1935)
  • Tomorrow's Garden: Uniting Tradition Technology Community

    Kindler, Brad (The University of Arizona., 2019)
    Today challenges of climate change, population growth, biodiversity loss, and water scarcity, lead farmers to ask new questions about how to grow food in a changing environment. Additionally, innovative technology and public food preferences present challenges and opportunities for farmers to consider before planting. Honoring Tucson’s diverse community and unique history, this study proposes the design of Tomorrow’s Garden. This garden seeks to punctuate Mission Garden’s historic timeline with a demonstration of sustainable and innovative agricultural practices. Outcomes of this proposal include the design of a garden that has the capacity to adapt to changing climate, as well as build community through design process and project implementation.
  • El Rio Preserve riparian rehabilitation & community recreation

    Stoicof, Alexandra (The University of Arizona., 2017)
    The Sonoran Desert is a unique biodiverse landscape of approximately 100,000 square miles in Southwestern United States. It is characterized by seasonal monsoon rains in both the summer and winter that sustain some 2,000 different plant species, making it a comparatively lush desert. Because of the Sonoran Desert’s geographic location and seasonal precipitation patterns, a variety of biomes can be found in the region, including tundra, coniferous forest, temperate deciduous forest, grassland, chaparral, desert, thornscrub, and tropical forest (Arizona-Sonora Desert Museum, 2017). Within these biomes are corridors of riparian communities, which are areas of watercourses that create unique habitats. In the Southwest, many of these riparian watercourses are currently ephemeral and only fl ow temporarily throughout the year. These xeroriparian habitats (dry riparian) are largely and increasingly ephemeral because of human disturbances. Watercourses that once were perennial, such as the Santa Cruz River, now flow primarily only during the monsoon rains. Riparian communities are critical components in the network of biomes and habitats in the Sonoran Desert. They provide corridors for the movements of plants and animals, and sustain unique species in the desert that require more water. These communities are also beautiful, lush landscapes that are often enjoyed by humans for their oasis-like qualities; trails, camping and picnicking spots, and scenic points-of-view are often found along watercourses. The El Rio Preserve in Marana, Arizona is such a riparian community tucked along the banks of the Santa Cruz River. It is part of a chain of other regionally-significant habitats, and presents opportunities for both habitat and human recreation. Many species of plants and animals have found refuge at El Rio, including invasive species. Its origins as a former borrow pit, however, make it a disturbed xeroriparian landscape that could benefit from rehabilitation strategies. The following Master’s Report presents a process and design for El Rio. A majority of the work was done in collaboration with the Town of Marana. Public participation was a large component of the project, which informed many design decisions. A comprehensive literature and case review, and ongoing site assessments also contributed to the final design and rehabilitation strategies.
  • MULTI[FUNCTIONAL] an approach to maximize use of remnant urban space

    Hatch, Andrew (The University of Arizona., 2016)
    The urbanization boom this country experienced in the twentieth century set the foundation for the urban fabric we live in today. The urban fabric functions as a result of the many and varied systems modern society has built in hopes of taming the forces of nature. An important example of one of these networks, though seldom seen and rarely celebrated, is the urban drainage system. Creeks and wetlands covered significant portions of coastal southern California until urbanization arrived in the early twentieth century. Typically small in scale but rich in biodiversity, these creeks came roaring to life following winter rains, draining the basin to the sea, all while feeding the wetlands that protected the coastal land. However, in an attempt to eliminate flooding risk and provide stable land on which to build, the majority of the coastal creeks were entombed in concrete, some above ground, and others below. What sounded like a good idea at the time has become a relic of the past. The experiment has demonstrated what happens when an ecological resource is misinterpreted as a liability in the urban fabric. That is, with research and observation, it is now becoming clear that these resources are assets to the communities and regions in their vicinities. Additionally, these potential resources have been walled off and shut away from the public, creating corridors that act as barriers within the urban fabric. A new attitude has emerged toward urban drainage infrastructure as the potential ecological and social benefits of green infrastructure become clearer in the public’s mind. Research along with many successful infrastructure projects from around the globe demonstrate the potential multiple benefits green infrastructure strategies can provide. These projects offer examples of strategies and elements that combine to create successful multi-functional spaces centered on urban infrastructure. A desire to synthesize these new strategies and traditional landscape architectural methods informed the development of a master plan for remnant urban space straddling a channelized coastal waterway in Oxnard, CA. This project demonstrates one approach to re-imagining coastal infrastructure as a multifunctional asset that provides habitat and recreational and social opportunities for the local community.
  • CORONADO AIRPORT A Project in Flight

    Gamboa, Malerie (The University of Arizona., 2019)
    Located at the junction of different urban tracts in Albuquerque, New Mexico, the abandoned Coronado Airport was once a popular small aircraft airport. Operational from 1961 to 2001, the Coronado Airport was ultimately closed due to safety concerns, a fate shared by other small aircraft facilities around the U.S. Currently the 268 acre abandoned site contains only the two runways and several large concrete foundations where the airport buildings and hangars were once located. Although in a state of disrepair and left with only remnants of its former use, the site has the opportunity to become an effective and iconic space for the City of Albuquerque and surrounding communities. The Coronado Airport redevelopment project could also provide design and reuse concepts applicable to other equivalent sites within urban areas around the country. Through visual observations and site research this is a prime location to develop multi-purpose functions including a large natural park in an urban setting, alternative forms of active and passive recreation, while acting as a landmark for the city. The Coronado Airport redevelopment project explores the challenges of creating a destination for both locals and visitors through the reuse of an abandoned site while showcasing its transformation over time and acknowledging its former use. Moreover, the design incorporates elements of this diverse landscape context, its past use as an airport, the significant role of flight in the region, and new physical and metaphorical connections that can be enhanced and created.
  • Transcription Profiling of Angiogensis using DNA Microarrays

    Hoying, James; Budoff, Adam; Williams, Stuart; Galbraith, David (The University of Arizona., 2000)
    Angiogenesis is the process by which new blood vessels form from an existing vasculature. The degree of angiogenesis and the character of the resulting microvascular beds vary between different healing environments such as wound healing and tumor angiogenesis. These differences are due, in part, to qualitative and quantitative differences in the molecular function within the tissue undergoing angiogenesis. For this study, these two types of angiogenic environments were created in mice and characterized on a gene expression level by utilizing cDNA microarrays. A DNA microarray containing 58 mouse genes from many different molecular classes relevant to angiogenesis was manufactured and tested. Optimal conditions and protocols for the use of microarray technology were designed and implemented. Results show that a polymerinduced angiogenic wound healing response differs greatly in its transcription profile from a tumor, suggesting that different types of angiogenesis occur in different environments.
  • A Novel Pathology Device for the Improvement of Intraoperative Breast-Cancer Tissue Gross Examination

    Arabyan, Ara; Kachur, Xenia; (The University of Arizona., 2011)
    The aim of this study was to design and test key aspects of a novel device, consisting of a polymer referencing enclosure (hardware) and a gel component, for the standardization of intraoperative gross pathology examination of excised breast cancer tissue. The proposed device improves the current practice of tissue preparation for radiographic and pathological examination without changing the existing process and without imposing retraining requirements on professional staff involved in the current process. To identify the optimal composition of the gel component to be used, 32 gel formulations were tested to determine setting times and maximum temperature reached during setting. The radiographic properties of 12 gel formulations and 15 plastic materials for potential use in the hardware were also tested. A negative correlation was found to exist between setting time and maximum temperature reached, narrowing down gel selections to those setting in <10 minutes with a temperature peak of <54 °C. The radiographic properties of the tested and downselected gels and plastics were found to be such that these materials are unlikely to interfere with lesion identification in radiological examinations. A completed tissue study for examination of gel effects on tissue properties revealed no effects, thereby clearing this device for potential clinical applications.
  • Closure of Loop-Mediated Isothermal Amplification Chamber on Lab-On-Chip Using Thermal-Responsive Valve

    Szivek, John; Love, Christopher J.; (The University of Arizona., 2012)
    Point-of-care tests for nucleic acids are important for the diagnosis and management of infectious and genetic diseases, biowarfare agents, and for drug research. Recent integration of loop-mediated isothermal amplification (LAMP) onto a lab-on-chip (LOC) platform allows sensitive and specific, detection of target DNA or RNA sequences for point-of-care (POC) applications. However, because of the high risk of contamination to LAMP products, robust and simple methods of hermetically sealing the reaction chamber are essential. In addition, having a method for isolation of nucleic acids at the level of the chip is more effective for POC applications because a laboratory setting is not required to complete the analysis. This report describes an integrated, polymer-based cassette which was designed for detection of DNA/RNA target-sequences by using LAMP and a solid-state nucleic acid purification membrane. The LAMP chamber seals using a self-actuated thermalresponsive valve made from expandable microspheres suspended in Polydimethylsiloxane (PDMS). A flow-through, Flinders Technology Associates membrane (Whatman FT A®) was installed on the cassette with the expectation of providing isolation and purification of nucleic acids. The cassette was designed, fabricated and the efficacy of the valve to seal the LAMP chamber was investigated. The valve underwent expansion and held pressures of233 +/- 5.0 kPa without signs of leakage. A portable, battery-powered, polyimide-based thin film heater, placed outside the cassette, provided thermal control. In addition, a LAMP primer set was designed for the serotonin receptor 5HTRIA promoter gene using Primer Explorer V 4 software (http:/ /primerexplorer.jp/elamp4.0.0/index.html) for LAMP detection of neurotransmitter serotonin. The integrated, portable LAMP cassette will be attractive in global health-care challenges, mainly in resource-poor locations, where the availability of laboratory equipment and/or trained personal is restricted.
  • Immunoassay-Based Microsensing

    Hoying, James; Jabbour, Maurice Elie; Deymier, Pierre; Guzman, Roberto; Barnaby, Hugh; Cuello, Joel (The University of Arizona., 2005)
    Immunoassay systems are recognized as superior modalities for detecting biological substances. Immunoassay sensing offers the advantages of selectivity and sensitivity. Development of a portable micro-immunoassay system is quite desirable for fieldwork applications. The basis of such portable sensing approach would combine molecular printing techniques with solid-state devices. In this work, I report on advances in attaching and patterning antibodies on Si02 substrates with the aim of retaining their biological functionality. The integration of functional antibodies with conventional photodetectors through direct printing onto the oxide layer of the detector will result in a device with on-chip readout. To that effect, monoclonal IgG antibody was printed onto chemically modified and thermally oxidized silicon substrates. Using a generic immunoassay, I was able to validate the activity of the antibody adsorbed on epoxyterminated silane surface coatings. An assay based on Mouse anti-biotin - Biotin conjugated to horseradish peroxidase interaction was used to show the activity of printed antibody, specifically the molecular orientation of the antibody, on the silane-coated surface. In addition, avalanche photodiodes were used as solid-state detector for light detection. Avalanche photodiodes were able to detect the chemiluminescence, an indication of the sensitivity of the sensor for the immunoassay. Furthermore, there were clear differences between 'control' measurements obtained using a saline buffer solution compared to actual measurements obtained from antibody attachment to the surface of the sensor. This difference in signals is an indication that protein-protein interaction 10 occurred. To that effect, on-chip readout, namely in situ measurement of light detection without the aid of additional detector, was shown. In summary, I present, as a proof of concept, one example of immunoassay-based microsensing through the integration of antibody with avalanche photodiodes. This may have potential application in designing commercial, low cost, and portable biosensors.
  • Maximal Oxygen Consumption Rates in One-Leg and Two-Leg Exercise: A Theoretical Model

    Secomb, Timothy; Patel, Deepa Praful; Cohen, Zoe; Granzier, Henk; Konhilas, John (The University of Arizona., 2011)
    The goal of this project was to create a theoretical model to predict maximal oxygen consumption rates in one-leg and two-leg exercise. A MATLAB code was developed to simulate both capillary-level oxygen transport (in the legs) and systemic oxygen transport. Predicted values for oxygen consumption closely matched experimental data. The model was used to explain the trend of a lower maximal oxygen consumption rate in two-leg exercise compared to one-leg exercise. As activity increases from rest to one-leg exercise to two-leg exercise, the oxygen demand of the active components, the cardiac output, and the blood flow rate also increase. However, the fraction of cardiac output to the active leg(s) decreases when the second leg is activated. At the capillary level, the oxygen extraction is increased at the arteriolar end of each capillary, resulting in regions of hypoxic tissue towards the venous end. Venous oxygen saturation is decreased, leading to lower venous P02 returning to the lungs. The increased cardiac output decreases the time that the deoxygenated blood has in contact with the alveoli. As a result, arterial P 02 for blood exiting the lungs is lower. This decreases the pressure gradient between the tissue and the capillary and limits diffusive transport. In summary, the reduction of oxygen consumption rate per unit muscle mass in two-leg exercise relative to one-leg exercise is accounted for quantitatively by the model and shown to result from the combined effects of reduced flow and reduced oxygen saturation of blood to each leg in two-leg exercise.
  • Modifying Aqueous Humor Dynamics for the Treatment of Glaucoma

    Snyder, Robert; Khatri, Chandra Michelle; Stamer, Dan; Matsunaga, Terry; Pagel, Marty (The University of Arizona., 2011)
    Glaucoma is one of the leading causes of irreversible blindness in the world, and the leading cause in many developing countries. It is a progressive loss of optic nerve tissue typically caused by increased intraocular pressure and treated by lowering the pressure. In developing nations where the disease is most common medications are not affordable and surgery is expensive and unstable. A new surgical approach and drainage device material that could lead to a cost effective, permanent solution were studied. A tube connected to an e-PTFE reservoir shunts fluid from inside the eye to the subconjunctival reservoir. E-PTFE was chosen because it is biocompatible and porous, while promoting angiogenesis and lymphangiogenesis on its surface. The surrounding vessels can carry the fluid back into the systemic circulation. A tangential surgical approach was evaluated because it could spare and protect lymphatic vessels. Recent studies have shown that lymphatics are important in aqueous outflow. Preliminary results showed that theePTFE device could sufficiently lower IOP and that the lymphatics are potentially involved in aqueous outflow after surgery. These results indicate the importance of further evaluating a new surgical approach that addresses the role of lymphatics in fluid outflow from a glaucoma drainage device.
  • Predictive Variables of Counter-Shock During Resuscitation in a Swine Model

    Indik, Julia; Allen, Daniel N.; (The University of Arizona., 2010)
    The purpose of this study was to examine parameters with potential to predict the outcome of counter-shocks during resuscitation. Out-of-hospital discharge rates decline 8-10% per minute of untreated cardiac arrest (3 ,4 ), therefore time wasted during resuscitation for unsuccessful counter-shocks can be reduced if scrutiny is given toward additional variables of predictive ability. Our experiment was designed to find the predictive ability of amplitude spectral area (AMSA), slope, end-tidal carbon dioxide, coronary perfusion pressure, the condition of acute myocardial infarction (MI), and the duration of ventricular fibrillation (VF) induced cardiac arrest preceding resuscitation in a swine model. Variables were tested by logistic regression (a= 0.1). Groups were set up in a 2x2 design: MI versus control; 2 minute vs 8 minute VF. We found AMSA, slope, MI and duration of VF significant predictors of countershock. We also found AMSA, slope, and duration of VF as independent predictors of counter-shock.
  • Formulation of Perfluorocarbon-Filled Droplets for Ultrasound-Mediated Applications

    Matsunaga, Terry; Wong, Vincent; (The University of Arizona., 2011)
    Microbubbles and nanodroplets are tools used in medicine for diagnosis and therapy. Probubbles are initially submicrometer droplets that become microbubbles in tumors as a result of ultrasonic force. The aim of this investigation was to determine vaporization thresholds of perfluorocarbon (PFC) droplets as a function of PFC boiling point and droplet size. PFC droplets with boiling points -1. 7 to 56.6°C were formulated followed by acoustic droplet vaporization (ADV) and stability testing. Under ultrasound acoustic outputs used, perfluorohexane (PFH) droplets did not vaporize while perfluoro(-2- methyl-3-pentanone) (PFMP), perfluoropentane (PFP), and perfluorobutane (PFB) droplets did vaporize. The acoustic output required to vaporize droplets decreased with decreasing boiling point. Vaporization threshold is a function of size with larger diameter droplets requiring less ultrasound output to vaporize. PFH, PFMP, and PFP droplets remained stable after 16 weeks in 4°C and 23°C environments, but PFMP and PFP evaporated entirely in a 40°C oven after 12 weeks.
  • The Functional Role of the N2B Region Within the Elastic Sarcomeric Protein Titin

    Granzier, Henk; Nedrud, Joshua James; (The University of Arizona., 2011)
    Utilizing a N2B knockout (KO) mouse model in which the exon that encodes the cardiac-specific N2B unique sequence (N2B-Us) spring element (exon 49) has been deleted, I investigated the mechanical role of the N2B-Us, one of the three extensible regions of cardiac titin. I was able to show that the extensibility provided by the N2B-Us limits energy loss during stretch and shortening cycles of the heart (i.e., during diastole and systole). In a range of conditions, KO mice showed significant increases in hysteresis, a measure of energy loss determined from the area between the stretch and release force-sarcomere length curves, over wild type (WT) mice. Most prominently, hysteresis increased significantly from 320±46 pJ/mm2 /sarcomere in WT tissue to 650±94 pJ/mm2 /sarcomere in KO tissue that had been preconditioned with a physiological stretch-release protocol (p < 0.005). To complement this KO model, oxidative stress was used to mechanically inactivate portions of the N2B-Us of WT titin through cysteine crosslinking. This inactivation displayed a greater increase in hysteresis response in WT compared to KO tissue, (32.3±5% vs. 12.9±2.2%, p-value < 0.05). The results of this study support the concept that the mechanical function of the N2B-Us of titin is to reduce hysteresis and increase the efficiency of the cardiac cycle.
  • Rapid Detection of Malaria Antigen in Human Whole Blood using a Handheld Lab-On-Chip Device

    Yoon, Jeong-Yeol; Stemple, Charles Christopher; (The University of Arizona., 2011)
    Malaria is a human infectious disease that affects around 250 million people each year. Primarily found in regions of Africa, Asia, and South America, malaria is typically caused by the protozoa Plasmodium falciparum, and results in symptoms ranging from high fever to death. The most common detection methods currently consist of ELISA, PCR, and blood film smears; however, each of these methods requires a full laboratory environment for proper utilization, with assay times ranging from 2-8 hours. In this study, a novel handheld detection device based on the properties of immunoagglutination will be modified to detect malaria in human whole blood through histidine-rich protein 2 (HRP-2), an antigen expressed only by P. falciparum. HRP-2 antibodies are covalently attached to 920 ?m carboxylated polystyrene nanoparticles, which are mixed with the target human whole blood in a lab-on-chip testing environment. Using a 640 nm LED and avalanche photodiode pair, the sample is illuminated and forward light scatter caused by immunoagglutination of the HRP-2 antigen to the antibodies present on the nanoparticles is measured. The final device is compact, battery powered, low-cost, and capable of detecting HRP-2 antigens in human whole blood with a detection limit of 1 pg/ml and an assay time of approximately 8 minutes. The device represents a significant improvement in assay time over current malaria detection methods at a relatively low cost.
  • Adhesion of Myoblasts to RGD-Alginate

    Calvert, Paul; Tanooryan, Mansooreh; (The University of Arizona., 2003)
    Several types of alginate have been developed, but none of them alone are able to interact with mammalian cells. Alginate does not provide anchorage points that are essential for cell growth and proliferation. As this hydrogel meets many requirements for tissue engineering, modification of alginate was proposed in order to stimulate cell adhesion. After recognition of RGD binding site in ECM proteins, synthetic RGD peptides were coupled with alginate via aqueous carbodiimide chemistry. I applied this conjugation and optimized it in terms of various parameters of the coupling reaction. Mouse skeletal Myoblasts were cultured on the surface of the modified alginate. They were attached, spread and differentiated to form myotubes. This showed that an RGD containing peptide has the ability to mimic ECM molecule binding sites and stimulate adhesion to materials that are otherwise unable to interact with cells. I also demonstrated that RGD density enhanced proliferation and spreading. Increasing crosslinker density made stiffer gels and controlled cell differentiation. Including free Ca2+ improved swelling properties of alginate gel, enforced cell attachment and enhanced conversion of myoblasts to myotubes.
  • Sub-Cytotoxic Nanoparticle Exposure to Airway Epithelial Cells Causes Alterations in Cellular Signaling

    Boitano, Scott; McCorkel, Mia; Sierra-Alvarez, Reyes; Pagel, Marty; Lynch, Ron (The University of Arizona., 2011)
    There are strong correlations between ultrafine particle deposition in the lung and chronic respiratory illness. The growing prevalence of engineered nanoparticles (ENPs) in society presents a new lung toxicant exposure that has the potential to cause adverse affects in the lung, and specifically, on lung innate immune function. We examined the cytotoxicity of hafnium oxide (HfO2), cerium oxide (CeO2), and silicon oxide (SiO2) ENPs, and their micron-sized equivalents, to cultured human airway epithelial cells (16HBE14o-) in terms of cell death and reduction in paracrine ATP signaling as a measure of one aspect of innate immune function in lung epithelium. We used high-throughput real time cell analysis (RTCA) assays and fluorescent-based Live/Dead assays to evaluate cell death to establish cytotoxic levels of ENPs to airway epithelium. We used RTCA with digital imaging video microscopy to evaluate changes in ATP-induced cell signaling following exposure to low, non-cytotoxic doses of ENPs (10 - 50 mg/L). ENP induced cytotoxicity occurred only at high exposures, whereas acute (24 hr) incubations with ENPs resulted in altered ATP-induced cellular signaling at low doses of ENPs. We conclude that sub-cytotoxic exposures to ENPs can alter a basic innate immune function in lung epithelial cells that could contribute to respiratory disease. Such measurements of toxicity may be better indicators of potential health hazards of ENPs than simple cell death assays.
  • Synthesis of Upconverting Nanoparticles for Temperature Sensing Applications

    Romanowski, Marek; Joshua, Gihan Sumith; Pagel, Marty; Matsunaga, Terry; Yoon, Jeong-Jeol (The University of Arizona., 2012)
    Lanthanide-doped nanoparticles have been increasingly gaining attention as possible contrast agents due to their unique upconversion luminescence properties. The luminescence of certain emission bands from NaYF4 :Er3+/Yb3+ nanoparticles are also temperature dependent, and can be used as a ratiometric temperature sensor by monitoring the green-to-red emission ratio. The objective of this study was to reproducibly synthesize NaYF4:Er3 +/Yb3+ nanoparticles, use them to create a thin film on a glass surface, and visualize temperature changes on this coated surface. Nanoparticles were prepared via thermal decomposition at 300° C, underwent an acid treatment process to remove the oleate ligands from their surfaces, and were introduced to glass slides that had been functionalized with carboxyl groups. The temperature of the coated glass slide was varied, and images taken using a CCD camera were used to construct the green-tared emission ratio, which showed a linear trend with respect to increasing temperature.

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