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  • Engineered Control Over Enzyme Activity

    Ghosh, Indraneel; Bienick, Matthew S.; Charest, Pascale; Cordes, Matthew; Montfort, William (The University of Arizona., 2019)
    Selectively modulating the activity of a desired enzyme in cells is a major goal in protein design and can aid in the development of methods for understanding and rewiring cell-signaling pathways. Traditional approaches such as small molecule inhibitors may be difficult to design for selectively targeting a particular enzyme, while gene knockdown methods often lead to compensatory cellular mechanisms thus obscuring true cell signaling. To overcome these issues, several methods have been developed for the specific control of protein activity for both understanding cell signaling as well as generating a portfolio of tunable proteins for a variety of applications. Herein, we demonstrate the design and validation of a potentially general allosteric approach for gating protein kinase and protein phosphatase activity. We have utilized the Bcl‐2 protein family and their small molecule inhibitors to design a system where specific BH3 domains are inserted into a kinase at predetermined, non-homologous positions. BH3 domains are unstructured but adopt an α-helical conformation upon interaction with a protein binding partner, such as Bcl-xL. Thus, in our system Bcl-xL acts as a poison and allosterically inhibits the function of BH3-inserted-enzymes. Subsequently, the addition of a small molecule inhibitor, ABT-737 or A-155463, binds to and displaces Bcl-xL, acting as an antidote, thus restoring enzymatic activity. We show that this method allows for controlling the activity of several protein tyrosine kinases and phosphatases with a small molecule in a dose-dependent fashion both in vitro and in mammalian cells. While our first-generation approach for engineering allostery within enzymes was successful, the protein-protein interactions (PPI) used for controlling the enzymes, Bcl-xL and Bad, are both known to interact with other endogenous proteins. In order to develop a biologically silent PPI we utilized a previously identified selective mutant of Bcl-xL, Bcl-xL R139A, and employed phage display to select for a mutant Bad peptide, MB_IW2, that specifically interacts with Bcl-xL R139A. This selected PPI successfully displayed selectivity in the context of our allosterically regulated kinases in mammalian cells over other known wild type protein binding partners. This design and evolution approach further expands the toolkit for selective enzyme control. In another project, we used sequence alignment methods coupled with structure-guided mutagenesis to design a new split-luciferase for monitoring PPIs. Simple strategies to monitor PPIs in cells allows for biophysical characterization of the proteome in its native environment while providing convenient assays for developing inhibitors for PPIs. In this study we describe the design and characterization of a new split-firefly luciferase (split-Fluc) that can be used for measuring PPIs. We show that our sequence dissimilarity (SD) based design results in several new first-generation split-Fluc with signal to background of > 20-fold. Importantly, second-generation split-Fluc PPI sensors designed through structure-guided mutagenesis of the fragmented enzyme interface resulted in multiple sensors with signal to background of > 200. We demonstrate that these new split-Fluc sensors can be readily used to monitor PPIs and their inhibition in mammalian cells. Taken together, our efforts have expanded the toolbox for exerting specific user-defined control over protein function and for monitoring protein interactions. These new tools will potentially contribute to the understanding of cell signaling mechanisms and in the development of new therapeutics.
  • Synthesis of Electrocatalytic [2Fe-2S]-Metallopolymers and Organic/Inorganic Hybrid Materials

    Pyun, Jeffrey; Karayilan, Metin; Glass, Richard S.; Lichtenberger, Dennis L.; Armstrong, Neal R.; Loy, Douglas A.; Monti, Oliver (The University of Arizona., 2019)
    This dissertation is composed of five chapters, detailing advances within the area of synthesis, characterization, and electrochemical analysis of polymer-supported [FeFe]-hydrogenase enzyme’s active site mimics, highlights the releavance of the work to the fields of polymer science, electrochemistry, and energy storage that are enabled through the development of novel [2Fe-2S] complexes and metallopolymers as discussed in the following chapters. The first chapter is a review summarizing the development of novel polymer-supported [2Fe-2S] catalyst systems and briefly highlighting non-polymeric supports for electrocatalytic and photocatalytic hydrogen evolution reactions. [FeFe]-hydrogenases are the best known naturally occurring metalloenzymes for hydrogen generation, and small molecule [2Fe-2S]-containing mimetics of the active site (H-cluster) of these metalloenzymes have been synthesized for years. These small [2Fe-2S] complexes have not reached the same capacity of the enzymes for hydrogen production thus far. Recently, modern polymer chemistry has been utilized to construct an outer coordination sphere around the [2Fe-2S] clusters to provide site isolation, water solubility, and improved catalytic activity. In this chapter, we survey the various macromolecular motifs and the catalytic properties of these supported [2Fe-2S] materials. The most recent catalysts that incorporate a single [2Fe-2S] complex, termed single-site [2Fe-2S] metallopolymers, exhibit superior activity for H2 production. The second chapter focuses on incorporation of a [2Fe-2S] catalytic site into metallopolymers using atom transfer radical polymerization (ATRP). Electrocatalytic [FeFe]-hydrogenase mimics for the hydrogen evolution reaction (HER) generally suffer from low activity, high overpotential, aggregation, oxygen sensitivity, and low solubility in water. Using ATRP, we have prepared a new class of [FeFe]-metallopolymers with precise molar mass, composition, and low polydispersity. The synthetic methodology introduced here allows for facile variation of polymer composition to optimize the [FeFe] solubility, activity, and long-term chemical and aerobic stability. We find that water-soluble functional metallopolymers perform electrocatalytic hydrogen production in neutral water with loadings as low as 2 ppm and operate at rates one order of magnitude faster than hydrogenases (ca. 250,000 s-1) and with low overpotential requirement. Furthermore, unlike the hydrogenases, these systems are insensitive to oxygen during catalysis with turnover numbers on the order of 40,000 under both anaerobic and aerobic conditions. The third chapter expands upon the methodology for the tunability of [2Fe-2S] metallopolymers by changing the monomer type and their compositions. Small-molecule catalysts inspired by the active sites of [FeFe]-hydrogenase enzymes have long struggled to achieve fast rates of hydrogen evolution, long-term stability, water solubility, and oxygen compatibility. We profoundly improved on these deficiencies by grafting polymers from a metalloinitiator containing a [2Fe-2S] moiety to form water soluble poly(2-dimethylamino)ethyl methacrylate) metallopolymers (PDMAEMA-g-[2Fe-2S]) using ATRP. This study illustrates the critical role of the polymer composition on enhancing hydrogen evolution and aerobic stability by comparing the catalytic activity of PDMAEMA-g-[2Fe-2S] with a non-ionic water-soluble metallopolymer based on poly(oligo(ethylene glycol) methacrylate) prepared via ATRP (POEGMA-g-[2Fe-2S]) with the same [2Fe-2S] metalloinitiator. Additionally, the tunability of catalyst activity is demonstrated by the synthesis of metallocopolymers incorporating the 2-(dimethylamino)ethyl methacrylate (DMAEMA) and oligo(ethylene glycol) methacrylate (OEGMA) monomers. Electrochemical investigations into these metallo(co)polymers show that PDMAEMA-g-[2Fe-2S] retains complete aerobic stability with catalytic current densities in excess of 20 mA/cm2, while POEGMA-g-[2Fe-2S] fails to reach 1.0 mA/cm2 current density even with the application of high overpotentials (η > 0.8 V) and loses all activity in the presence of oxygen. Random copolymers of the two monomers polymerized with the same [2Fe-2S] initiator showed intermediate activity in terms of current density, overpotential, and aerobic stability. The fourth chapter focuses on another [2Fe-2S] metalloinitiator with an aliphatic bridgehead and single initiator site for polymerization. Small molecule biomimetics inspired by the active site of the [FeFe]-hydrogenase enzymes have shown promising electrocatalytic activity for hydrogen (H2) generation. However, most of the active site mimics based on [2Fe-2S] clusters are not water soluble which hence limits the use of these electrocatalysts to organic media. Polymer-supported [2Fe-2S] systems, in particular, single-site metallopolymer catalysts, have shown drastic improvements for electrocatalytic H2 generation in aqueous milieu. [2Fe-2S] complexes functionalized within well-defined macromolecular supports via covalent bonding have demonstrated water solubility, enhanced site-isolation, and improved chemical stability during catalysis. In this chapter, we demonstrate the synthesis of a new propanedithiolate (pdt)-[2Fe-2S] complex bearing a single α-bromoester moiety for the use in ATRP as a novel metalloinitiator to prepare water-soluble poly(2-(dimethylamino)ethyl methacrylate) grafted (PDMAEMA-g-[2Fe-2S]) metallopolymers. Using this approach, metallopolymers with controllable molecular weights (Mn = 5-40 kg/mol) and low polydispersity (Mw/Mn = 1.09-1.36) were prepared, which allowed for the first-time observation of the effect of the metallopolymers' chain length on the electrocatalytic activity. The ability to control the composition and molecular weight of these metallopolymers enabled macromolecular engineering via ATRP of these materials to determine optimal structural features of metallopolymer catalysts for H2 production. The fifth chapter starts with the comparison between free-radical and controlled radical polymerizations and then details the synthesis and characterization of a new [2Fe-2S] complex for polymer-growth via reversible addition-fragmentation chain-transfer (RAFT) polymerization. Although ATRP allows polymerization of many commecially available monomers, RAFT polymerization can give easy access to direct polymerization of different monomers such as (meth)acrylic acid, 2-carboxyethyl acrylate, acryl amides, 1-glycerol methacrylate and eliminate any metal contamination in contrast to Cu-cataylzed polymerization. A new [2Fe-2S]-based RAFT metallo-agent was synthesized for the first-time to design metallopolymers for electrocatalytic hydrogen evolution reaction (HER). In this chapter, [2Fe-2S]-metallopolymers synthesized via RAFT polymerization and studied for electrochemical H2 evolution are discussed.
  • Bone-Specific Metabolism and Mechanism of Action of Curcuminoids in Blocking Osteolysis in Breast Cancer and Other Resorptive Bone Diseases

    Funk, Janet L.; Kunihiro, Andrew; Doetschman, Thomas C.; Limesand, Kirsten H.; Romagnolo, Donato F. (The University of Arizona., 2019)
    Osteoclast-mediated bone resorptive disorders, including post-menopausal osteoporosis, age-related bone loss, rheumatoid arthritis, and osteolytic bone metastases, affect over 55 million Americans each year. Breast cancer bone metastases, the model of bone resorptive disorders to be used here, causes osteolysis through a “vicious cycle”, whereby osteoclasts release growth factors (e.g., TGFβ) stored in the bone, which can cause bone-metastatic tumor cells to secrete pro-osteolytic factors (e.g., PTHrP), resulting in more osteoclast-mediated bone resorption. Curcuminoids, dietary polyphenols derived from the turmeric rhizome, inhibit progression of osteolytic bone metastases and other resorptive diseases by targeting osteoclasts and – in the case of bone metastases, also blocking tumoral TGFβ signaling – despite circulating as a glucuronide conjugate that is posited to lack bioactivity. These studies demonstrated that curcumin-glucuronide did not inhibit tumoral TGFβ signaling, with confirmation in multiple breast cancer cell lines that form TGFβ-dependent osteolytic lesions, nor did it inhibit osteoclastogenesis, with both TGFβ signaling and osteoclastogenesis being central to this osteolytic feed-forward loop. However, mouse bone marrow β-glucuronidase (GUSB) deconjugated curcumin-glucuronide to the active aglycone, which was maintained across sexual and skeletal development and with bone resorptive disorders, with evidence that human bone marrow also has deconjugation activity. Other bone-protective dietary polyphenols (e.g., quercetin and resveratrol) were also deconjugated by bone marrow, a GUSB-mediated effect that was required for bone-protective bioactivity, suggesting that GUSB-mediated deconjugation of abundantly glucuronidated dietary polyphenols may be a universal requirement to derive benefits. Finally, curcuminoids inhibited tumoral TGFβ signaling by reducing protein levels of TGFβR2 (receptor that binds TGFβ) and Smad2 (phosphorylated by TGFβR1 following activation of TGFβR2 to stimulate genes promoting bone metastasis progression) primarily through effects on gene expression that depended, in part, on oxidative metabolism. In toto, these novel findings answer a long-standing question about curcumin’s apparent lack of bioavailability, with implications for the bioactivity of other dietary polyphenols, and provide a framework for future studies to explore how interindividual GUSB expression in the population may impact both curcumin’s bone-protective bioactivity and its side effects as well as to further provide insight into cellular targets underlying curcumin’s inhibition of signaling pathways important in bone resorption.
  • Caregiving Abuelas: Mexican American Grandmothers’ Self-Management of T2DM while Caring for Grandchildren

    McEwen, Marylyn M.; Rascón, Aliria Muñoz; Crist, Janice D.; Reed, Pamela G. (The University of Arizona., 2019)
    Purpose: The purpose of this study was to describe the perceptions of Mexican American grandmothers managing type 2 diabetes (T2DM) while caring for a grandchild. The author explored these women’s behaviors, barriers, facilitators, and perceived resources necessary when managing T2DM. With the T2DM crisis becoming increasingly prevalent in the Mexican American population, a clear understanding of experiences of caregiving grandmothers managing T2DM as traditional family nurturers is critically important. Background: Mexican Americans are more likely to be diagnosed with, suffer complications from, and die from T2DM than Non-Hispanic Whites. Older Mexican American women, often seen as the family nurturer, are likely to be managing this disease in the context of caring for a grandchild. Women in this role often report self-sacrificing behaviors, fatigue, and stress- but also fulfillment and a sense of purpose in the caregiving role. Methods: Eight Mexican American women managing T2DM for at least one year while regularly caring for grandchildren were interviewed in English and Spanish for this qualitative description study. Interviews were transcribed verbatim and analyzed using qualitative content analysis. Results: Three domains emerged under the overarching theme of T2DM Self-Management in the Context of Caring for Grandchildren: 1) T2DM Attitudes, Beliefs and Perceptions, 2) T2DM Self-Management Behaviors, and 3) T2DM Self-Management in the Family System. Grandmothers consistently reported feeling a personal responsibility for their T2DM self-management as well as for the health and wellbeing of their families, including their grandchildren. Conclusions: Mexican American grandmothers saw themselves as family caregivers while emphasizing personal ownership for their T2DM self-management. Fundamental motivators for T2DM self-management included grandchildren and other family members. This also extended into descriptions of behaviors reflecting a responsibility to prevent diabetes and promote health across generations. These grandmother’s descriptions of barriers, facilitators, perceived necessary resources, and the impact of grandchild caregiving on T2DM self-management fills a previous knowledge gap and the new valuable insights will guide tailoring T2DM self-management interventions for Mexican American grandfamilies.
  • Geographic and Racial Disparities in Mortality of Dialysis Patients

    Calhoun, Elizabeth A.; Mohan, Prashanthinie; Roy-Chaudhury, Prabir; Barraza, Leila Fs; Gilliland, Stephen (The University of Arizona., 2020)
    BACKGROUND: The incidence rate and hospitalization rate for patients with End Stage Renal Disease (ESRD) vary across different counties in the U.S. Little information is available on how geography can impact patient mortality through county health status and gaps in supply and demand for hemodialysis services. METHODS: This is a retrospective cohort study where adult patients who initiated in-center hemodialysis between 2007 and 2016 and recorded in the United States Renal Data System (USRDS) were assessed for survival time and mortality rate. The primary exposure variable in Aim 1 was the overall county health status (Most Healthy vs Least Healthy) based on the health factor ranks published by County Health Rankings & Roadmap (CHR&R). The primary exposure variable for Aim 2 was the supply-demand gap for hemodialysis services as measured by the patient-station ratio for each county. The primary exposure variable for Aim 3 was the change in the number of dialysis stations between 2011 and 2016 for each county. Kaplan-Meier estimate used to compute the median survival time and Cox regression analysis was used to compute the hazard rate (HR) for mortality after adjusting for various confounders. RESULTS: Most Healthy counties in the U.S. are likely to be larger urban counties with predominantly white and older patients. On the contrary, Least Healthy counties are comparatively more rural and smaller counties with a higher percentage of African American population, more unemployed and Medicaid patients. Patients residing in Most Healthy counties (HR = 0.899, 95% CI 0.825,0.979) had a lower hazard rate (HR) for mortality compared to patients living in Least Healthy Counties (p value = 0.0143). In Aim 2, counties in Category 1 (counties with no hemodialysis stations), Category 2.1 (underutilized HD stations with population <50,000) and Category 2.2 (underutilized HD stations with population 50,000) had higher HR compared to the reference Category 3. However, when stratified by age and race, the HR was statistically significant for Blacks only for Category 2.2 for all age groups (HR = 1.11, 95% CI 1.06,1.16) and for Whites for Category 1 (aged 40 – 79; HR=1.1) and Category 2.2 (aged 65 – 79; HR=1.11). In Aim 3, counties with No Change had a marginally higher hazard rate (HR=1.04, 95% CI 1.02, 1.07) compared to counties with an increase in dialysis stations. Race was a significant confounder but not an effect modifier to this association (p-value 0.2942). CONCLUSION: County health status and lack of hemodialysis facilities affects survival of ESRD patients. Additionally, patients residing in some suburban counties or smaller metros had a higher hazard rate for mortality despite excess supply of dialysis stations. It is important for care providers and local health officials to understand the health factor profile and spatial distribution of dialysis stations in their county to help ESRD patients navigate barriers to care, reduce rates of dialysis withdrawal, and improve mortality outcomes.
  • Optical and Opto-Mechanical Design of an F/2.5 Broadband Infrared Objective Lens Using Multiple Cold Stops and Cooled Detectors

    Kim, Daewook; Deacon, C. Elizabeth; Liang, Rongguang; Sasián, José (The University of Arizona., 2019)
    This paper discusses the design and production of a f/2.5, 25mm focal length lens that images portions of the SWIR and MWIR spectrums from 1 – 5.5µm. Challenges associated with imaging in such a wide spectrum are discussed, including the need to correct for chromatic errors when a limited number of materials are available. The lens is designed to be used on three different cryogenically cooled detectors, each with differing stop locations relative to the lens. The paper discusses the effect that a varied stop has upon the third-order aberrations and covers specifics of an opto-mechanical design which meets the performance requirements for each detector. Cooled detectors require additional analysis to ensure that narcissus effects will not dominate the image. A method for analyzing the narcissus effects is highlighted. The evolution of the design as the lens is transitioned from theory into prototype is discussed. Images captured with the lens assembly are presented along with performance data to compare theoretical to measured performance.
  • A Framework for Secure Data Management in Medical Devices

    Rozenblit, Jersy W.; Almazyad, Ibrahim; Adegbija, Tosiron; Ditzler, Gregory (The University of Arizona., 2019)
    Data is considered as a valuable currency that our modern world thrives upon today. Individuals, groups and even nations work hand in hand to protect private data. When it comes to medical data, its protection is considerably more apparent and significant with guidelines such as HIPAA and FDA regulations in place. Data breaches on medical devices are known to have a significant impact on a patient’s wellbeing. Most of these data breach attacks occur during the transit state. With these attacks in mind, there is still a need for continuous feedback between a patient and a doctor based on data that is collected from such devices. In this thesis, we propose a methodology that develops an autonomous secure communication channel between doctors and patients. Through examining the data life cycle of software built within medical devices, we address various security measures. We propose Adaptive Mode Selection (AMS) to investigate threats amongst system functions. By leveraging this technique, we obtain access to a lifetime assessment for risk mitigation and communication mode selection within medical devices. A Priority-Queue Based (PQB) process is established to improve data management and data isolation within life-critical systems. Further, we propose Adaptive Protocol Selection (APS) to enhance data transmission over the most appropriate communication protocol based on risk values identified by AMS. These protocols include Wi-Fi, Bluetooth, Radio Frequency or more. The combination of AMS, PQB and APS contributes towards delivering better health services with continuous secured data feeds and reduction in time of medical intervention.
  • Activation and Deactivation of Semiconductor Surfaces

    Muscat, Anthony J.; Hinckley, Adam; Shadman, Farhang; Gervasio, Dominic; Raghavan, Srini (The University of Arizona., 2019)
    The development of surface modification techniques is an integral part of advancing semiconductor device fabrication beyond subtractive methods. Chemically altering surfaces to be more or less reactive can eliminate steps in production to form devices quicker and with less material waste. This doctoral dissertation presents a series of work dedicated to improving our understanding of various techniques of surface modification and developing processes that enhance the utility of existing methods. Self-assembled monolayers (SAMs) made from octadecyltrichlorosilane (OTS) are implemented for surface deactivation and defects are studied. Defective areas in SAMs limit their utility in device production and are notoriously difficult to eliminate. However, the addition of intermediate cleaning steps are shown to prevent defects to deactivate the growth of 10 nm TiO2 films by atomic layer deposition (ALD). Spectroscopic ellipsometry, goniometry, and x-ray photoelectron spectroscopy (XPS) are used to examine SAMs deposited using different cleaning steps and assess their ability to act as an ALD resist. Polar and non-polar agglomerates adsorbed to the SAM are removed by solvent extraction and aqueous cleaning in series, and defect free layers are deposited by a second liquid phase immersion. Atomic force microscopy (AFM) confirmed the removal of agglomerates so that OTS coated SiO2 surfaces were as smooth as clean SiO2, producing deactivated surfaces suitable for prototype devices. Intermediate cleaning steps were applied to OTS deposition to reduce immersion times from 24 h to 1 h and SAMs were analyzed with XPS. Peaks shown in O 1s regions indicating the presence of surface hydroxyls showed that immersion in SC-1 (NH4OH:H2O2:H2O) doubled hydroxyl concentration on the substrate while OTS surface coverage was left relatively unchanged. In addition to the removal of polar agglomerates from the SAM surface, SC-1 hydroxylates pinhole defects in the SAM to re-activate the underlying substrate for additional deposition. A second OTS deposition improved surface coverage to cover nearly every active site on the substrate to form defect-free layers. Exposure to 200 cycles of TiO2 ALD using TiCl4 and H2O confirmed that no defects were present, as afterwards Ti was not detected on the surface by XPS. Layers were patterned with conductive mode AFM to form open trenches approximately 160 nm wide within the SAM for area selective deposition. Approximately 8 nm of TiO2 was selectively deposited within trenches while no significant deposition was noted outside trenches to demonstrate an area-selective ALD process. Indirect surface modification is also demonstrated by altering ALD precursors and implementing in-situ cleaning steps. Aluminum oxide was grown using both water and peroxide as oxidants and resulting films were analyzed and compared using XPS. Peaks in the O 1s and Al 2p regions monitored the formation of the Al-O bond and found that film nucleation occurred quicker with a higher coverage of Al when using peroxide as an oxidant. Ellipsometry, however, showed no change in growth rate. The improvement of Al coverage with no increase in thickness indicates that surfaces exposed to peroxide ALD are more reactive during each growth cycle and can form denser films. Using XeF2 in-situ to clean Si wafers could also act as a surface deactivator during ALD. Heated XeF2 exposure removed native SiO2 either directly or by surface disruption for lift off with an additional heating step. Controllable oxide removal was achieved by introducing an Al-O bond on the surface to slow down native oxide etching. Hence, indirect methods of both surface activation and deactivation are possible by altering process chemistries.
  • Portable Optical Biosensors for the Rapid Classification of Clinical and Field Samples

    Yoon, Jeong-Yeol; Bills, Matthew; Wong, Raymond; Su, Judith; Konhilas, John (The University of Arizona., 2019)
    Three novel biosensor platforms will be discussed in this dissertation. The first sensor aims to reduce the cost and complexity typically associated with obtaining an accurate white blood cell and differential count. For our biosensor, a drop of blood is obtained via fingerpick from a subject. The sample is diluted, and the white blood cells are separated and fluorescent stained while flowing through a custom paper microfluidic chip. We than obtain a partial-differential and total WBC count using a using a smartphone and smartphone microscope attachment. This rapid classification could see use in resource poor settings as well as in modern settings where cost is a contributing factor. The second sensor uses an angular photodiode array to capture Mie scatter to rapidly diagnose cancer from a tissue surface. This is achieved by illuminating a tissue sample at several different angles and measuring the scattered light intensity from several discrete angles that is attenuated and amplified based on the variation in the size, abundance, and refractive indices of several cellular and tissue structural elements. Small changes in these parameters result in observable variation in optical scattering from a tissue sample. We predict and model Mie scatter from several different structural elements. The observed optical scattering obtained from rat and human tissue sets is consistent with our simulated findings, supporting our premise and encouraging further exploration. A device such as this could be a useful aid for clinicians diagnosing cancer by using it to detect cancer earlier. Our third device aims to meet the need of the South Korean coast guard to rapidly identify ocean oil spill samples in order to identify culpable parties, and inform clean-up efforts. We were tasked with designing a portable, lightweight, easy to use device to identify and classify oil spill samples. We designed a Raspberry-Pi based UV-Fluorometer to measure fluorescence from three UVA light sources (365nm, 375nm, and 385nm). The device is capable of accurately (95% correct classification) classifying samples into one of 4 broad categories (crude oil, heavy fuel oil (consisting of Bunker-C fuel oil and Marine Fuel Oil (MFO)), light fuel oil (consisting of all other fuel oils ranging from gasoline to Bunker-B), and lubricant oil) as well as provide an estimation of the samples’ physio-chemical makeup in the form of the sample’s percent saturate, aromatic, resin, and asphaltene contents.
  • Planum Temporale: Morphologic Taxonomy of the Superior Temporal Plane

    Musiek, Frank; Wong, Bryan M.; Fuglevand, Andrew; Cone, Barbara; Kielar, Aneta (The University of Arizona., 2019)
    Background: Planum Temporale (PT) is a crucial neuroauditory structure located in the dorsal superior temporal plane (STP) posterior to Heschl’s gyrus (HG). The PT has been implicated in complex auditory function and is well known for its preponderance of leftward asymmetry in normal brains and classic “pie- shaped” morphology. While a majority of cases have easily identifiable PT and HG, there exist some cases in which distinguishability of these two structures is difficult due to morphological variation. The goal of this study is to create a taxonomy of PT morphological features in order to improve the sometimes difficult identification and differentiation of PT from surrounding structures. Methods: A total of 50 (100 hemispheres) healthy intact, high-resolution T1- weighted brain MRIs were obtained from Open Access Series of Imaging Studies (OASIS) and included in this retrospective study. There were 28 women and 22 men, all right-handed. Ages ranged from 18-57 (mean=26.44) years. A 3D cortical surface mesh (grey matter) for each brain was generated using FreeSurfer and manipulated to view the STP using BrainVISA Anatomist neuroimaging software. The PT was isolated from surrounding structures based on pre-defined anatomical criteria and subsequent surface area measurements, linear measurements and qualitative measures were made. Results: A total of four PT configurations were identified: (1) Pie-shaped [45%], (2) Trapezoid-shaped [27%], (3) Rectangular-shaped [19%], and (4) None [9%]. Mean surface areas of measurable PT configurations were: 511.96 mm2 for “Pie-shaped” (n=45), 517.36 mm2 for “Trapezoid-shaped” (n=27) and 472.12mm2 for “Rectangular-shaped” (n=19). The fourth category, “None” (n=9), was not calculable. There were significantly more “Trapezoid-shaped” PTs in females (p<.05). The “None” category occurred significantly more in males (p<.05) and in the right hemisphere (p<.05). Furthermore, the left hemisphere demonstrated significantly greater surface area for “Pie-shaped” PTs (p<.05). Conclusion: We believe that the proposed classifications is the first step in creating a comprehensive taxonomy of the STP. This will aid neuroanatomists, clinicians and students in terms of differentiation of sometimes complex topography of the STP.
  • Optimized State Estimation Method for Structural Health Monitoring Using Heterogeneous Measurements Under Uncertainty

    Jo, Hongki; Saleem, Muhammad Mazhar; Kundu, Tribikram; Tharp, Hal; Zhang, Lianyang (The University of Arizona., 2019)
    An optimized state estimation method that can effectively incorporate uncertainties associated with structural models and measurements is proposed for structural health monitoring. Heterogeneous structural measurements consisting of strain and acceleration time-histories are fused through a state space framework to obtain good quality state estimates over a broader range of frequencies. The unknown states are estimated through an augmented Kalman filter (AKF) which can identify all the states including structural response as well as excitations while effectively incorporating model error and measurement noise. Genetic algorithm-based optimization strategies are adopted to address the uncertainty issues and improve the efficacy of the state estimation process. Optimization is performed at two stages. First, sensor configuration is optimized; second, error covariance values on model, structural measurements and excitations, involved in the Kalman filter process, are optimized. Four studies are carried out for the development and validation of the proposed method. The first two studies are related to optimization of sensor configuration and error covariance values while the other two are focused on the performance validation of the proposed method through case studies, especially related to input force identification. In the first study, sensor numbers, locations and types are optimized using a genetic algorithm with a single objective function whereas in the second study, sensor configuration is optimized for spatially-varying dynamic loading of bridges using a multi-objective genetic algorithm. The third study pertains to spatiotemporal identification of impact force and corresponding structural responses. The concept of redundant sensors is utilized to locate the impact force, and then exact time-histories of force and structural responses are generated by optimizing the error covariance values. The fourth study is about the identification of traffic induced structural excitations. The study shows that once the state estimation method is optimized by selecting suitable error covariance values it remains stable against any traffic regime. A truss bridge example is utilized to demonstrate the effectiveness of the proposed method on identifying the traffic induced structural excitations. The results from all the studies show that the proposed method can effectively identify the structural response and excitations while successfully dealing with the uncertainties in structural models and measurements. Hence, it has a great potential for practical application to real-life structures.
  • Subversive Survival Through Critical Creativity in Community-Based Adult Second Language Contexts

    Warner, Chantelle; Shufflebarger, Amanda Marie; Gramling, David; Ecke, Peter; Nicholas, Sheilah (The University of Arizona., 2019)
    Community-based second language classes for adults with immigrant/refugee backgrounds often draw upon “survival English” frameworks; these approaches aim to equip language learners with the basic language they need to accomplish instrumental goals but do not align with current research in second language pedagogy (Auerbach, 1985). This dissertation draws upon theories of meaning-making (Kress & Selander, 2012; New London Group, 1996) and strengths-based paradigms (e.g. Gorski, 2016) to explore how adult second language learners and teachers can revise “survival” ideologies to make space for critically reflective, creative, and humanizing language encounters in community-based adult second language classes. The dissertation proposes critical creativity, which combines tenets of critical pedagogy with approaches to teaching that prioritize learner agency and creativity, as a framework which makes space for these goals. Through ethnographic approaches as well as artifact analysis, interviews, and surveys, the dissertation begins by characterizing community-based adult ESL classes and learning materials in the United States, examining how “survival” has become the default organizational thread of these contexts. It explores how learners, teachers, stances, and classroom activities facilitate meaning-making opportunities. Finally, drawing closely on work with students and teachers, the dissertation explores how teachers and students subvert “survival” as the ideological crux of their language teaching/learning activities through critical creative approaches. The dissertation ends with a multi-modal set of voices offered by students from community-based adult second language classrooms at all levels. Together, the chapters characterize a pedagogical context that is prolific yet underrepresented in second language acquisition and applied linguistics research—community-based adult second-language courses—and illuminate the work of learners and teachers in this context through a lens of resilience, creativity, and agentive meaning-making.
  • The CCAP: A New Physical Unclonable Function (PUF) for Protecting Internet of Things (IoT) and Other FPGA-Based Embedded Systems

    Hariri, Salim; Josiah, Jeff G.; Akoglu, Ali; Bruyere, Donald; Li, Ming (The University of Arizona., 2020)
    The importance of cybersecurity has grown exponentially over the years due to our highly interconnected world and the evolution of computer threats. These threats – once as simple as annoying computer viruses – are now destructive malware, ransomware, and advanced persistent threats (APT) sponsored by nation states used to steal military secrets, wage industrial espionage, and weaponize the Cyberspace into the 5th domain of future military conflict right behind Land, Sea, Air, and Space. Every device that interfaces with the Internet is a potential target. For instance, the attack surface for Internet of Things (IoT) is expected to expand with an estimated 14.2 billion connected “things” projected to be in use this year alone. These “things” are diverse and include rugged-industrial sensors, personal wearables, in-home appliances, and even some of the vehicles on the road today. Many IoT devices are beginning to utilize Field Programmable Gate Arrays (FPGAs) for their processing subsystem due to design flexibility and because FPGAs, as a design element, enable product lifecycle support through aftermarket upgradability of both the computer software (CSCI) and firmware/hardware (FWCI) configuration items. This allows manufacturers to enhance product functionality through over-the-Internet (OTI) or over-the-air (OTA) upgrades. Unfortunately, the increasing use of FPGAs has also brought a major concern of intellectual property (IP) theft and product counterfeiting. To help thwart IP theft, FPGA vendors such as Xilinx and Intel PSG (formerly Altera) provide end-users with the ability to encrypt design bitstreams at rest with a cryptographic key. This encryption key is typically stored in EEPROM, Battery-Backed RAM, or within dedicated Anti-Fuses within the device; however, numerous non-invasive, semi-invasive, and invasive attacks exist that can retrieve the encryption key and compromise the design bitstream. Physical (sometimes referred to as physically) unclonable functions (PUFs) have been proposed as a countermeasure to eliminate the need for cryptographic key storage. PUFs have been widely researched for nearly two decades. An efficient implementation for FPGAs has remained elusive and is an area of much needed research focus. The goal of this research was to deliver a new, innovative PUF design targeted specifically for FPGA implementation. We propose the CCAP which is an efficient, scalable hardware security primitive supporting today’s most advanced FPGAs. It requires no hard macros or interactive design floorplanning and is portable to any UltraScale+-based FPGA. Experimental results on several Avnet Ultra96 boards have shown excellent PUF performance in terms of PUF inter-device uniqueness, acceptable performance for PUF intra-device uniqueness, and good overall PUF output stability at the targeted operating temperatures. Additionally, the randomness of several CCAP “raw” signatures at various FPGA die locations have been tested and deemed random according to the NIST Randomness Test Suite, and chi-square “Goodness of Fit” test calculations. In the un-redacted portions of this dissertation, we discuss the motivation for this work, cover several of the prior PUF architectures in open literature and their shortcomings for FPGA implementation, examine our testing methodologies, provide some test results and analyses, propose a few real-world applications for the CCAP primitive, before ending with conclusion and possible future work. NOTE: The CCAP architecture and details pertaining to it are not publicly disclosed at this time.
  • The Architecture of the Deep Critical Zone: The Role of Lithology and Geologic Texture in Regolith Formation, Hydrologic Flowpath Development, and Weathering Dynamics

    Chorover, Jon D.; Moravec, Bryan; McIntosh, Jennifer C.; Rasmussen, Craig; Pelletier, Jon D.; Ferre, P.A. Ty (The University of Arizona., 2019)
    The critical zone (CZ) represents the living skin of the Earth’s surface, which extends from the bottom of freely circulating groundwater to the top of the vegetative canopy. CZ biogeochemistry includes abiotic and biotic weathering processes that occur within pores and fractures, which aggregate (or average) along the myriad of hydrologic flowpaths that make up the shallow and deep CZ. Landscapes evolve as a function of the both bottom-up controls, dependent on the initial geologic template and past weathering/geologic forcing (e.g. tectonics, sedimentary reworking, etc.), and top-down forcing driven by climate. As such, the dynamic interaction between top-down forcing and bottom-up controls is evident in the architectural framework of the CZ, exhibited by weathering profiles in the subsurface, and contemporary biogeochemical processes visible as exported solutes in surface, soil, and groundwater. Within this framework, point measurements collected along flowpaths, coupled with bulk solid sampling are traditionally used to identify weathering reactions occurring in the subsurface. Much of the foundational CZ science has been conducted in relatively simple, monolithic geologic settings, whereby spatial variability in mineral and geochemical compositions are explained by ongoing weathering front propagation and contemporary fluid/rock interactions. However, within the CZ literature, little attention has been paid to complex geologic settings, where past weathering processes may impart significant mineral and geochemical overprints not related to ongoing, contemporary CZ processes. Yet, CZ processes in these settings are dependent on past geologic processes as they alter both geologic texture (e.g. pore size and distribution) and mineral composition, especially at the fluid/surface interface, compared to fresh, unaltered protoliths. This framework provides the underpinning for the present study, where resolving weathering profiles in the complex geologic setting of the Jemez River Basin Critical Zone Observatory, located in the Valles Caldera National Preserve, northern New Mexico, required characterization of the CZ architecture as a function of both geologic legacy and contemporary CZ processes. The CZ architecture (to 50 m) in a small zero-order basin (ZOB, area approximately 16 ha) located in the JRB-CZO was characterized by an array of complementary approaches, analogous to needing as many equations as there are unknowns. In the summer of 2015, surface geophysical surveys were conducted in the ZOB, which included surface seismic and electrical resistivity surveys along two transects (one roughly north-south, the other roughly east-west). These surveys identified a slow p-wave velocity zone that extended 4 to 6 m deep that mantled the ZOB, coinciding with a highly weathered surface. Weathering decreased with depth (as shown with increasing p-wave velocities), with competent bedrock (p-wave velocities approximately 4,000 m s-1) present at a depth of approximately 50 m. Electrical resistivity profiles showed that the eastern portion of the ZOB had less water and/or clay than the western portion of the ZOB. Using these geophysical data, the depth of the weathering profile was estimated to extend to 50 m in depth. Informed by the geophysics, a drilling campaign was undertaken in the summer of 2016, excavating continuous cores down to approximately 46 m (eastern and western slopes) and 20 m (catchment convergent zone) at three locations in the ZOB, which reflected contrasting geologies and landscape positions (i.e. eastern drill location: Bandelier Tuff; western drill location: volcanic breccia; central drill location: convergent zone with mixed lithology). Core sample analysis, collected as subsamples approximately every 40 to 60 cm, revealed that the upper 15 to 18 m of the western and eastern borehole locations consisted of matrix dominated morphology, transitioning to fracture dominated morphology below ca. 15 m. The eastern borehole was composed of welded to sub-welded tuff with a mineral composition that included quartz, alkali and plagioclase feldspar, smectite, zeolites, and amorphous minerals in the upper 15 m, showing evidence of prior interaction with alkaline hydrothermal fluids. Below 15 m, the fractured welded tuff was comprised mostly of primary minerals (quartz, alkali and plagioclase feldspar, cristobalite, and volcanic glass), exhibiting relatively little weathering within the bulk. However, fracture surfaces were coated with oxidized Fe and Mn. The western borehole was composed of rounded to subrounded quartz, frayed biotite and calcite nodules in the upper 15 m, with a significant amount of illite and smectite present. At 14 m, the lithology changed to vesicular tuff, with significant zeolitization in the first 10 m coinciding with stratified ash deposits. The convergent zone was a mixture of smectite and oxidized Fe and Mn with weathering feldspar. Traditional, sigmoidal weathering front propagation was not visible in geochemical mass transfer coefficients (i.e. tau), likely as a result of incomplete weathering of rock fragments in the upper profile. However, trends in mass transfer calculations coincided with changes in mineral composition and geophysical data (e.g. magnetic susceptibility, seismic velocities, and electrical conductivity) as a function of depth. Multivariate statistical analysis of the complementary data sets, using linear discriminant analysis (LDA), identified zones within the weathering profiles, which was used to develop a conceptual framework of the deep CZ architecture and weathering profiles in the ZOB. A key finding from the deep CZ characterization study was the depth distribution and character of hydrothermally altered secondary mineral assemblages and overall secondary mineral phases in the contrasting geologies in the ZOB. It was hypothesized that these secondary mineral coatings likely played a significant role in aqueous geochemistry evolution along flowpaths due to fluid/surface interactions. Surface coatings included smectite and zeolites in the hydrothermally altered tuff on the eastern portion of the watershed down to 15 m, which transitioned to fracture surfaces coated with oxidized Fe and Mn. At all portions of the borehole at this location, larger primary mineral grains, such as alkali and plagioclase feldspars, were largely unweathered with some surface weathering occurring where smectite and zeolite precipitates on the surfaces. It was hypothesized that zeolites were precipitated as a result of glass weathering, and the smectites likely precipitated as a result of both zeolite and feldspar weathering. Enrichment of Sr and Ba, compared to Ca was observed in zeolitic zones. Enrichment of rare earth elements and Y (REY) was observed at depths where smectite content increased, indicating sorption of REY on clay surfaces. In addition, oxidized Fe and Mn on fracture surfaces appeared to shield bulk rocks from weathering. Reactions at the fluid/surface interface, whose surface composition and characteristics appear to be a result of both past and contemporary weathering processes, was hypothesized to control aqueous solution chemistry in the subsurface. Experimental weathering reactions of core materials were performed at increasing time steps, up to 1 year, to pinpoint geochemical reactions and mineral weathering rates occurring in the subsurface. Experimental weathering showed that colloidal dispersion released zeolites to solution, which were subsequently weathered to smectite. Calcite dissolution/precipitation reactions appeared to regulate solution chemistry in the volcanic breccia. Deep core samples, representing the fractured portion of the deep CZ, had experimental solution chemistry that did not match the groundwater signatures collected from deep monitoring wells in the ZOB. However, experimental solution chemistry from altered tuff samples appeared to closely match deep groundwater chemistry collected from monitoring wells, indicating deep groundwater chemistry in the ZOB derived most of its solution chemistry from reactions in the shallow CZ (e.g. <14 m) rather than at depth. The findings of this study suggest that contemporary CZ processes greatly rely on the geologic architecture and past geologic legacy in addition to climatic forcing. This is particularly true in complex volcaniclastic terrains, such as the Valles caldera. In addition, complementary analysis, including geophysics, drilling, mineralogy, geochemistry, and experimentation provide an in-depth view into spatial as well as temporal controls on deep CZ processes.
  • Exploring Parent Experiences with Early Palliative Care Practices in the Neonatal Intensive Care Unit

    Gephart, Sheila M.; Quinn, Megan; Crist, Janice; Shea, Kimberly (The University of Arizona., 2019)
    The anxiety and uncertain outcome of an admission of a seriously ill infant to the neonatal intensive care unit (NICU) can cause great stress for parents. This stress can lead to decreased quality of life and poor mental health outcomes including anxiety, depression, and posttraumatic stress disorder (PTSD), which NICU parents suffer from at higher rates than parents of well infants. Palliative care (PC) is an approach to care that aims to maintain the quality of life for a person and their loved ones by emphasizing value-based decision-making, management of distressing symptoms, and family-centered care. Early implementation of PC emphasizes shared decision-making, care planning, and support for coping with distress. Evidence from pediatric, adult, and perinatal literature supports the use of early PC, but barriers to implementation exist, and NICU PC literature focuses exclusively on end-of-life. Evidence is needed about these three early PC practices from NICU parents in order to develop a parent-centered program of early PC. The purpose of this study was to explore parent experiences with shared decision-making, care planning, and coping with distress during their child’s NICU admission. Qualitative descriptive methodology was used, and strategies of reflexive journaling, peer debriefing, and data audits were used to enhance trustworthiness. Participants were recruited online through email and social media sites of a parent organization. Sixteen individuals participated in semi-structured interviews using videoconferencing technology. Participants also completed an online survey to supply demographic information and describe relevant characteristics of their infants to contextualize the qualitative data and describe the sample. Qualitative data was analyzed with a conventional content analysis approach by coding important phrases and abstracting these to overarching themes. Parents’ descriptions of shared decision-making contained three key aspects of their experience: gathering information to make a decision, the emotional impact of the decision, and influences on their decision-making. In experiences with care planning parents described learning to advocate, having a spectator versus participant role, and experiencing care planning as communication. The key themes expressed regarding parental coping were exposure to trauma, survival mode, and a changing support network. These findings provide practicing clinicians with key areas for improvement: providing more support and collaboration in decision-making, true engagement of parents in care planning, and supporting peer support and interaction in the NICU environment. Implications for research include exploring parent experiences with early PC practices with a more ethnically and culturally diverse sample. Researchers may also further this research by developing and evaluating programs of PC emphasizing early intervention not limited to infants with a terminal diagnosis. Parents’ use of social media should be studied further due to its emerging use as a tool for peer connection and support in the NICU. Limitations of this study include a lack of diversity in sample race or ethnicity and marital status. This study provides a beginning foundation for the work of implementing early PC in the NICU from a parent-centered perspective, emphasizing communication and the building of relationships between parents and clinicians, and parents and researchers to achieve this goal.
  • Chalcogenide Hybrid Inorganic/Organic Polymers (CHIPs): Plastics for Infrared Imaging and Photonics

    Pyun, Jeffrey; Kleine, Tristan; Norwood, Robert A.; Glass, Richard S.; Njardarson, Jon T. (The University of Arizona., 2019)
    This dissertation contains five chapters describing recent advances in the use of a new class of polymeric materials (Chalcogenide Hybrid Inorganic/Organic Polymers (CHIPs)) for infrared imaging and photonics. Plastics are generally not used for these applications given their typically high optical losses at these wavelengths and low refractive indices. CHIPs are a revolutionary class of materials that are composed of a high loading of chalcogen moieties that are copolymerized with organic monomers into the backbone of the polymer. The large chalcogen content in CHIPs enables IR transparency and high refractive indices (n), whereas the organic comonomers afford solution and melt processablility making these materials highly attractive for use in the aforementioned applications. The last chapter focuses on the development of a novel photopolymer for use in photonic interconnects operating at telecommunication wavelengths. This chapter lays the groundwork for using this photopolymer in “smart print” technologies for optical communications. The first chapter is a review on the fundamentals and applications of infrared imaging, the current materials used as optical elements in those systems, and examples of polymeric materials that have been developed for the same purpose. IR imaging has numerous applications ranging from medical diagnostics to autonomous vehicle technologies, and is used frequently in the military for night vision. There is a growing consumer market for IR cameras as well, now that the cost of certain components has been reduced. However, expensive semiconductor materials are still used as the optical components. Consequently, there is a desire to replace semiconductors with cheaper, easier to work with plastics. CHIPs address this need as they are more IR transparent than conventional plastics and are amenable to conventional thermoplastic reforming techniques. These unique features of CHIPs are a result of the chemistry termed “inverse vulcanization” used to prepare them. The inverse vulcanization process uses elemental sulfur as a comonomer and reaction medium. At high temperatures, elemental sulfur is homolytically ring opened, resulting in a high concentration of sulfur radicals which then react with other chalcogens/organic vinylic comonomers. The resulting polymeric material contains a high content of IR transparent polysulfur bonds which is the basis for IR transparency in CHIPs. The second chapter describes the synthesis of a new organic comonomer for inverse vulcanization designed to improve the thermomechanical properties of CHIPs. Early CHIPs materials prepared using 1,3-di-isopropenylbenzene (DIB) suffered from low glass transition temperatures resulting in a narrow use range. To address this issue 1,3,5-tri-isopropenyl benzene (TIB) was synthesized and used in inverse vulcanization reactions. The higher favg (number of crosslinkable moieties per monomer unit) associated with TIB afforded a more densely crosslinked material according to dynamic rheological experiments. As expected, this increased crosslink density resulted in CHIPs with dramatically improved glass transition temperatures (approximately twice that of their DIB based analogues) exceeding Tg > 100 °C. Despite being highly crosslinked, this new material still exhibited the self-healing properties previously demonstrated for DIB based CHIPs. Most importantly, this new CHIPs material was similarly transparent in the mid wave IR to DIB based CHIPs. This work demonstrated that the thermomechanical properties of CHIPs could be adjusted to fit the demands of practical applications without sacrificing desirable optical properties. The third chapter explores the method used to further increase the refractive index of CHIPs materials. Refractive index is a volume averaged bulk property, thus higher loadings of sulfur result in higher refractive indices for CHIPs. However, the maximum refractive index possible is limited by the amount (~85 wt%) of sulfur that can be efficiently incorporated into CHIPs. Therefore, a higher refractive index chalcogen must be used to realize higher n. Tellurium is mildly toxic and exceedingly expensive, so selenium was chosen instead. The enabling discovery was that elemental selenium reacts with ring opened sulfur species, generating a reactive mixed chalcogen in situ, that copolymerizes with organic crosslinkers. This enabled preparation of CHIPs materials with n ≤ 2.1 demonstrating a marked increase over previously synthesized CHIPs materials. The expected mid wave IR transparency was observed and evaluated by IR imaging experiments as well. Most significantly, certain compositions were found to be solution processable. Access to soluble CHIPs with high refractive indices is critical for the solution-based fabrication of various photonic devices. Only one such device will be discussed in this dissertation, but other examples are currently under development. The preparation and characterization of 1D photonic crystals (1D PhCs) utilizing selenium containing CHIPs is the topic of the fourth chapter. 1D PhCs are dielectric devices assembled with alternating layers of high and low refractive index material. Layer thickness determines the λmax of the photonic bandgap while the difference in refractive index (Δn) between layers affects the magnitude of reflection. In this design, larger Δn values facilitate highly reflective mirrors assembled with only a few layers. Consequently, various combinations of metal oxides are often used to achieve large Δn. However, entirely inorganic 1D PhCs are brittle, limiting their use in certain applications, and why wholly polymeric 1D PhCs are of great interest as an alternative design. Fabrication of such devices is complicated by the need to generate a large number of layers to offset the typically small Δn values observed in polymeric 1D PhCs. This issue is addressed by employing ultra-high refractive index CHIPs as one of the layers. 1D PhCs were prepared by spin coating alternating layers of selenium containing CHIPs (high refractive index layer) and cellulose acetate (low refractive index layer). Devices fabricated in this manner were shown to possess >90% reflection with just 11 bilayers, and whose band gap was tuned across the near-infrared (1000-2000 nm). The fifth chapter is devoted to the preparation of long wave IR (LWIR) transparent CHIPs. Imaging in the LWIR is significantly cheaper than in the mid wave IR, and thus attractive for a variety of consumer applications. CHIPs are transparent in the mid wave IR as a result of low C-H bond content, but this does not necessarily translate to LWIR transparency. This is because the LWIR overlaps with the fingerprint region of the infrared spectrum which encompasses a broader range of vibrational absorption modes. Consequently, even the small amount of organic comonomer present in CHIPs results in opaque materials at longer wavelengths. Interestingly, some organic polymers, like polyethylene, are remarkably transparent over much of the LWIR. Polyethylene itself is not suited towards use as a broadband IR optic due to its polycrystallinity, but indicated polymeric materials could in principle be designed with adequate transparency in this region. To this end, simulated FTIR spectra of various model compounds representative of the corresponding polymeric repeat unit were used to guide the design of LWIR transparent CHIPs. Ultimately, a dimer based on the [2+2] cycloaddition of 2,5-norbornadiene (resulting in the monomer termed NBD2) emerged as a monomer amenable to inverse vulcanization chemistry and expected to possess improved LWIR transparency. Melt cast windows of CHIPs containing NBD2 or DIB as the organic crosslinker were then prepared with the same thickness and compared in LWIR imaging experiments. The DIB based CHIPs material was opaque at these wavelengths, while the new NBD2 based CHIPs material afforded significantly improved transparency. In the future, this methodology will be expanded to develop more CHIP materials that are suitable for LWIR imaging applications. The sixth chapter represents a departure from an emphasis on mid-IR transparent materials. Instead, the focus is development of materials for photonics applications at wavelengths relevant to the telecommunications industry (1310 and 1550 nm). In this work, a novel photopolymer (poly(SBOC)) was prepared and demonstrated as a material for fabrication of photonic interconnects. These devices require a high refractive index medium through which light propagates to be surrounded by lower refractive index material. Such patterning is typically achieved through photolithography and a number of solvent development/etching steps. Poly(SBOC) simplifies this process since permanent refractive index changes with high resolution are generated by direct laser writing in dry polymer films. Optical power attenuation through the device (propagation loss) is an important metric of photonic interconnects. To assess this for poly(SBOC), waveguides were fabricated and characterized by the cut back method. The propagation losses observed were ~2 dB/cm and commensurate to values typically observed for hydrocarbon based waveguides. The promising results from this project have resulted in a collaboration with the AIM Photonics program in the College of Optical Sciences at The University of Arizona to develop “smart write” photonic interconnects.
  • The Origins of Biodiversity Patterns in Vertebrates: New Insights Into Old Questions

    Wiens, John J.; Miller, Elizabeth Christina; Sanderson, Michael; Ferriere, Regis; Flessa, Karl (The University of Arizona., 2019)
    Species richness varies greatly among habitats, geography, and groups of organisms. What factors are responsible for these differences, and how did these differences arise over time? Within a clade, species are added through speciation and removed through extinction. Within a region or habitat, species can also be added through colonization. Organismal traits or environmental factors may influence richness indirectly by affecting speciation, extinction, or colonization. The goal of this dissertation is to investigate how these three processes have varied over time to form the species richness patterns observed today. To do this, I take advantage of four recent developments in evolutionary biology: (1) the collection of DNA sequence data across many taxa; (2) the time-calibration of molecular phylogenies; (3) the increased complexity of models of diversification and ancestral reconstruction; and (4) the aggregation of taxonomic, geographic, paleontological and trait data into public databases. In Appendix A, we investigate the disparity in amniote species richness between marine and nonmarine habitats. We found that, surprisingly, there was no systematic difference in rates associated with habitats. However, there was a strong relationship between species richness and the timing of habitat transition. Many marine transitions went extinct, and as a consequence almost all living marine lineages are Cenozoic in age. In contrast, amniotes have occupied land uninterrupted for over 300 million years. We concluded that extinction and time interact to produce the richness disparity between marine and nonmarine habitats. In Appendix B, we investigated the causes of the peak in marine richness at the Central Indo-Pacific (CIP) hotspot using percomorph fishes as a focal clade. We found that diversification rates were similar among warm oceans, and highest in cold oceans. The high diversity of the CIP is due to many lineages that colonized from 34–5.3 million years ago and then diversified in-situ. Other oceans have fewer colonizing lineages and/or more recent colonization leaving limited time for in-situ diversification. In Appendix C, we investigated the causes of the latitudinal diversity gradient on continents, using freshwater ray-finned fishes as a model clade. Colonization time explained 2–5 times more of the variation in species richness than diversification rates among 3,000+ freshwater drainage basins. The Neotropics is species-rich because it has supported steady diversification for ~100 million years, while other tropical regions have had periods of low diversification. While high-latitude lineages that are dominant today did not arrive until the Cenozoic, they diversified at a comparable or higher rate than tropical lineages. Finally, in Appendix D we tested the longstanding hypothesis that sexual dichromatism increases diversification rates. We tested this hypothesis at three phylogenetic scales: across all ray-finned fishes, within individual clades, and within nested subclades of the largest clades. We found no difference in rates between monochromatic and dichromatic fishes at the scale of all fishes. Only a few clades showed a relationship with dichromatism and diversification. Surprisingly, these clades did not include the subjects of classic population-level studies (e.g. cichlids). Support for such a relationship increased in most smaller subclades examined. We concluded that when sexual dichromatism influences diversification, its effects will be localized to small phylogenetic scales. Overall, the works in this dissertation yield new insights into longstanding problems in evolution and ecology.
  • The Spectrum of Asian Monsoon Variability: An Investigation of Low-Frequency Variability in Paleoclimate Proxies and Climate Models

    Overpeck, Jonathan T.; Thompson, Diane M.; Loope, Garrison; Quade, Jay; Meko, David M.; Yin, Jianjun (The University of Arizona., 2019)
    In this work we investigate the low-frequency (decadal-centennial) variability of the climate system in Monsoon Asia using a combination of instrumental, paleoclimate proxy, and climate model data. Understanding this critical component of the climate system is essential for accurately assessing the risk of low-probability extreme events such as megadroughts that may arise from the interaction of anthropogenic climate forcing and natural internal variability (Ault et al., 2014). In Appendix A, we use a network of hydroclimate proxies from Monsoon Asia as a case study to compare low-frequency variability in paleo-data to climate model simulations. We take a proxy system modeling approach, using climate output variables from isotope-enabled runs of iCESM, isoGSM, and iCAM5, to simulate synthetic proxy records, which creates a common ground for the comparison. We find that the pseudoproxies based on iCESM do not accurately capture the relative strength of multidecadal-century scale variability in the paleoclimate data. We find that the pseudoproxies based on isoGSM and iCAM5, which are constrained by instrumental observations, appear to match the scaling pattern of variability found in the proxy records. Our results indicate that state-of-the-art, fully coupled climate models are not able to generate a sufficient amount of multidecadal-century scale variability in hydroclimate. We find that one major source of multidecadal scale variability found in the proxies but not in the models comes from the combined interactions among the monsoon, El Niño-Southern Oscillation (ENSO), and the Indian Ocean sea-surface temperature variability. In Appendix B, we investigate the low-frequency variability found in multiproxy ENSO reconstructions, with the goal of understanding how this dominant source of hydroclimate variability on interannual scales may impact teleconnected regions on decadal-centennial time scales. Previous multiproxy reconstructions of ENSO have found a large amount of low-frequency variability but the time series of this low-frequency variability rarely matches between studies. We investigate potential biases in reconstructions of ENSO from the number and geographical distribution of sites, age model uncertainty, and sources of noise present in the individual proxy records. We conduct a series of sensitivity experiments using pseudoproxies to demonstrate that these factors have the potential to bias the spectrum of reconstructions causing them to overestimate the relative amount of decadal-century scale variability in the tropical Pacific. This could help explain why multiproxy ENSO reconstructions show greater multidecadal-century scale variability than is found in observations or climate model simulations. In Appendix C, we introduce a new paleo-monsoon proxy covering the last 2600 years based on grain size variability in a sediment core from Pale Daha, a small lake in western Nepal. We demonstrate that variability in grain size distribution over the last century matches with low-frequency precipitation variability found in 20th Century Reanalysis data (Compo et al., 2011). We identify a major pluvial from 950-1300 CE that matches with a similar pluvial in nearby Sahiya Cave (Sinha et al., 2015), and with increased monsoon circulation over the northern Arabian Sea (Anderson et al., 2002; Gupta et al., 2005). We find evidence that the monsoon precipitation at the site over the last 150 years has been particularly strong as compared to relatively weak monsoon rains from 1300-1800 CE. We then compare the trends found in paleo-monsoon proxies over the last 150 years and find that much of the apparently contradictory trends may be explained by the projected circulation and precipitation responses to anthropogenic forcing. This new interpretation is based on a simulated northward shift in circulation that may increase the relative fraction of precipitation at proxy sites received from the Arabian Sea and decrease the fraction from the Bay of Bengal. This shift in circulation could produce the trend in precipitation stable isotopes found in isotope based paleo-monsoon proxies. If true, these findings indicate that the South Asian Monsoon may already be experiencing the effects of anthropogenic climate change to a degree not yet fully appreciated, and that these changes are likely to continue into the future.
  • Environmental Fate and Toxicity of III-V Engineered Nanoparticles in Semiconductor Manufacturing

    Sierra-Alvarez, Reyes; Field, James A.; Nguyen, Chi Huynh; Farrell, James; Curry, Joan E. (The University of Arizona., 2019)
    Engineered nanoparticles (NPs) have many unique electronic, chemical, and optical properties. Gallium arsenide (GaAs) NPs and indium arsenide (InAs) NPs are being considered in different semiconductors and electronic devices due to their favorable properties such as high electron mobility with wide and adjustable band gaps and their reduced power consumption. Polishing of thin films in a process known as chemical and mechanical planarization (CMP) could lead potentially to the release of byproducts from GaAs and InAs, such as soluble III-V materials (Ga, In, and arsenic (As) species) and particulate III-V materials (GaAs NPs, InAs NPs, gallium oxide (Ga2O3), indium oxide (In2O3)) into the wastewater stream. Furthermore, the CMP process utilizes cerium oxide (CeO2), silica (SiO2), and alumina (Al2O3) as abrasive particles in slurries to polish and create flat surfaces. As a result, CeO2, SiO2, and Al2O3 NPs will also be present in the waste streams of the semiconductor industry. Additionally, some NPs can promote the transport of toxic chemicals into cells through the “Trojan Horse” effect, which can potentially alter the toxicity of the NPs via adsorbed chemicals. Among the soluble III-V ions, arsenic is a concern for the Trojan Horse effect because it is a highly toxic and carcinogenic element with soluble species that can become adsorbed onto NP surfaces. Although the toxicity of soluble arsenic species is well established, little is known about the potential toxicity of other soluble III-V materials and III-V NPs. Therefore, it is important to study and understand the environmental fate and toxicity of these materials. The objectives of this work are to investigate the potential toxicity and environmental fate of III-V nanomaterials and byproducts that could be formed in CMP slurries of semiconductor manufacturing effluents as well as to study the impact of CeO2 NPs on the sorption and toxicity of As species. The acute toxicity of GaAs, InAs, Ga2O3, and In2O3 particulates was investigated using two microbial assays targeting methanogenic archaea and the marine bacterium, Allivibrio fischeri. The results showed that GaAs and InAs NPs were acutely toxic towards these microorganisms while Ga2O3 and In2O3 NPs were not. The release of soluble arsenic species from arsenide NPs was shown to play a key role in the toxic effect of the arsenide NPs. Their toxicity increased with decreasing particle size and with increasing time because of the progressive corrosion of the NPs in the aqueous bioassay medium. In summary, the toxicity exerted by the arsenide NPs under environmental conditions will vary depending upon the particle size, dissolution time, and aqueous chemistry. In addition to microbial toxicity, these materials could cause toxic effects to human health. The toxic effects of Ga-based and In-based NPs (GaAs, InAs, Ga2O3, and In2O3) as well as soluble III-V salts (AsIII, AsV, GaIII, and InIII) on human bronchial epithelial cells (16HBE14o-) were evaluated using an impedance-based real time cell analyzing (RTCA) system. The results showed that only dissolved arsenic (AsIII and AsV) and arsenide particulate compounds caused significant inhibition at low concentrations (IC50 values after 16 h of exposure (16 h-IC50): 2.4 mg AsIII/L, 4.5 mg AsV/L, 6.2 mg GaAs NPs/L, and 68 mg InAs NPs/L). Similar to the case with the microbial toxicity, the cytotoxicity of the arsenide NPs to 16HBE14o- cells was mainly caused by dissolution of toxic As species (mostly AsIII). On the other hand, the soluble salt, GaIII-citrate, and Ga2O3 NPs caused mild inhibition while InIII-citrate and In2O3 NPs were not toxic at the concentrations tested (16 h-IC50 value: 260 mg Ga2O3 NPs/L), while InIII-citrate and In2O3 NPs were not toxic at the concentration tested (16 h-IC50 value: > 300 mg In2O3 NPs/L). In conclusion, GaAs NPs and, to a lesser extent InAs NPs, display toxicity to human lung cells and the adverse effects are expected to increase with increasing NP dissolution. Besides Ga- and In-based NPs, abrasive NPs used in CMP slurries (i.e. CeO2, Al2O3, colloidal SiO2 (c-SiO2), and fumed SiO2 (f-SiO2)) will be present in semiconductor effluents and they could potentially be toxic to microbial communities and human health. The toxic effects of well-characterized model CMP slurries on the marine bacterium A. fischeri and human bronchial epithelial cells 16HBE14o- cells were investigated. The results showed that f-SiO2 and CeO2 slurries did not cause acute toxicity on A. fischeri at concentrations as high as 1136 and 909 mg/L, respectively. In contrast, c-SiO2 and Al2O3 caused about 30% inhibition on microbial activity after 30 min of exposure at relatively high concentration (1364 mg c-SiO2/L and 1364 mg Al2O3/L). Lung cells were more sensitive to exposure to some of these inorganic oxide NPs. High concentrations (250 and 500 mg/L) of c-SiO2 and f-SiO2 slurries led to lung cell death in the RTCA assay. On the other hand, CeO2 and Al2O3 slurries were either not inhibitory or only showed limited inhibitory effect on 16HBE14o- cells after 24 h of exposure. As a whole, the results indicate that the abrasive NPs used in CMP are not likely to cause acute environmental and health risks at the low concentrations expected in surface water (< 1 mg/L). The presence of CMP NPs together with III-V soluble species can lead to emerging environmental and health problems. This study showed that CeO2 NPs effectively decreased the concentration of available AsIII in the culture medium through adsorption; hence showing the effect completely opposite of the “Trojan Horse” effect. Additionally, this work showed that internalization of CeO2 NPs by human lung cells was observed in vesicles (most likely lysosomes). Taken as a whole, this dissertation demonstrates that GaAs NPs, and to a lesser extent InAs NPs, cause acute toxicity to the studied microbial targets and to human lung cells due to the corrosion of the nanomaterials in the aqueous environment, and the ensuing release of toxic AsIII. Other nanomaterials anticipated in CMP effluents (i.e. Ga2O3 NPs and In2O3 NPs) were relatively non-toxic. Abrasive NPs like CeO2, Al2O3, c-SiO2, and f-SiO2 used in CMP slurries caused certain toxic effects to human bronchial epithelial cells at relatively high concentrations. The existence of CeO2 NPs along with soluble AsIII in waste effluent led to adsorption of AsIII onto CeO2 NPs that, as a result, decreased the toxicity of AsIII dramatically.
  • Chaperone Limitations in Prion Curing

    Capaldi, Andrew P.; Ge, Xuezhen; Serio, Tricia R.; Buchan, Ross J.; Chapman, Eli; Dieckmann, Carol L. (The University of Arizona., 2019)
    Amyloid promotes a dramatic transition in protein conformation that perpetuates, giving rise to a broad variety of distinct phenotypes, ranging from pathological disorders to dynamic heritable traits. Amyloid has long been thought to be resistant to clearance by the proteostasis network, but increasing evidence is challenging this view. For example, heat shock disassembles yeast prion amyloids, revealing in vivo solubilization of these aggregates. However, the exact proteostatic niche that promotes amyloid clearance is largely unknown. We identified several environmental stresses leading to prion curing via the same mechanism as heat shock and further showed that a shared characteristic was the activation of the transcription factor heat shock factor 1 (Hsf1). Strikingly, artificial Hsf1 activation interfered with heat shock-mediated prion curing, presumably due to overexpression of a nucleotide exchange factor Sse1. Limiting Sse1, which decelerates the Hsp70 cycle, promoted chaperone loading on prion aggregates and enabled artificial Hsf1 activation to resolve prion aggregates; in contrast, it impaired resolution of stress-induced aggregates and cell growth at elevated temperature. Thus, our study demonstrates that the proteostasis network, fine-tuned for optimal dissolution of non-amyloid aggregates, can be reconfigured for solubilization of amyloid by modulating the Hsp70 cycle.

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