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- Genre: Masters Thesis
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Description
Coccidioidomycosis, also known as Valley Fever, is a disease caused by the dimorphic soil-dwelling fungus, Coccidioides sp. Coccidioidomycosis is difficult to diagnose because symptoms are similar to community-acquired pneumonia. Current diagnostic tests rely on antibody responses, but immune responses can be delayed and aberrant, resulting in false negative diagnoses. Unlike serology, detection of coccidioidal proteins or other fungal components in blood could distinguish valley fever from other pulmonary infections and provide a definitive diagnosis. Using mass spectrometry (LC-MS/MS) we examined the plasma peptidome from patients with serologically confirmed coccidioidomycosis. Mass spectra were searched using the protein database from the Coccidioides species, generated and annotated by the Broad Institute. 15 of 20 patients with serologically confirmed coccidioidomycosis demonstrated the presence of a peptide in plasma, "PGLDSKSLACTFSQV" (PGLD). The peptide is derived from an open reading frame from a "conserved hypothetical protein" annotated with 2 exons, and to date, found only in the C. posadasii strain Silviera RMSCC 3488 genomic sequence. In this thesis work, cDNA sequence analysis from polyadenylated RNA confirms the peptide sequence and genomic location of the peptide, but does not indicate that the intron in the gene prediction of C. posadasii strain Silviera RMSCC 3488 is present. A monoclonal antibody generated against the peptide bound to a 16kDa protein in T27K coccidioidal lysate. Detecting components of the fungus plasma could be a useful diagnostic tool, especially when serology does not provide a definitive diagnosis.
ContributorsDuffy, Stacy Leigh (Author) / Lake, Douglas (Thesis advisor) / Magee, Dewey Mitch (Committee member) / Antwi, Kwasi (Committee member) / Arizona State University (Publisher)
Created2013
Description
Modified and artificial water sources can be used as a management tool for game and non-game wildlife species. State, federal, and private agencies allocate significant resources to install and maintain artificial water sources (AWS) annually. Capture mark recapture methods were used to sample small mammal communities in the vicinity of five AWS and five paired control sites (treatments) in the surrounding Sonoran desert from October 2011 to May 2012. I measured plant species richness, density, and percent cover in the spring of 2012. A Multi-response Permutation Procedure was used to identify differences in small mammal community abundance, biomass, and species richness by season and treatment. I used Principle Component Analysis to reduce 11 habitat characteristics to five habitat factors. I related rodent occurrence to habitat characteristics using multiple and logistic regression. A total of 370 individual mammals representing three genera and eight species of rodents were captured across 4800 trap nights. Desert pocket mouse (Chaetodipus penicillatus) was the most common species in both seasons and treatments. Whereas rodent community abundance, biomass, and richness were similar between seasons, community variables of AWS were greater than CS. Rodent diversity was similar between treatments. Desert pocket mouse abundance and biomass were twice as high at AWS when compared to controls. Biomass of white-throated woodrat (Neotoma albigula) was five times greater at AWS. Habitat characteristics were similar between treatments. Neither presence of water nor distance to water explained substantial habitat variation. Occurrence of rodent species was associated with habitat characteristics. Desert rodent communities are adapted for arid environments (i.e. Heteromyids) and are not dependent on "free water". Higher abundances of desert pocket mouse at AWS were most likely related to increased disturbance and debris and not the presence of water. The results of this study and previous studies suggest that more investigation is needed and that short term studies may not be able to detect interactions (if any) between AWS and desert small mammal communities.
ContributorsSwitalski, Aaron (Author) / Bateman, Heather L (Thesis advisor) / Miller, William (Committee member) / Alford, Eddie (Committee member) / Arizona State University (Publisher)
Created2013
Description
For CFD validation, hypersonic flow fields are simulated and compared with experimental data specifically designed to recreate conditions found by hypersonic vehicles. Simulated flow fields on a cone-ogive with flare at Mach 7.2 are compared with experimental data from NASA Ames Research Center 3.5" hypersonic wind tunnel. A parametric study of turbulence models is presented and concludes that the k-kl-omega transition and SST transition turbulence model have the best correlation. Downstream of the flare's shockwave, good correlation is found for all boundary layer profiles, with some slight discrepancies of the static temperature near the surface. Simulated flow fields on a blunt cone with flare above Mach 10 are compared with experimental data from CUBRC LENS hypervelocity shock tunnel. Lack of vibrational non-equilibrium calculations causes discrepancies in heat flux near the leading edge. Temperature profiles, where non-equilibrium effects are dominant, are compared with the dissociation of molecules to show the effects of dissociation on static temperature. Following the validation studies is a parametric analysis of a hypersonic inlet from Mach 6 to 20. Compressor performance is investigated for numerous cowl leading edge locations up to speeds of Mach 10. The variable cowl study showed positive trends in compressor performance parameters for a range of Mach numbers that arise from maximizing the intake of compressed flow. An interesting phenomenon due to the change in shock wave formation for different Mach numbers developed inside the cowl that had a negative influence on the total pressure recovery. Investigation of the hypersonic inlet at different altitudes is performed to study the effects of Reynolds number, and consequently, turbulent viscous effects on compressor performance. Turbulent boundary layer separation was noted as the cause for a change in compressor performance parameters due to a change in Reynolds number. This effect would not be noticeable if laminar flow was assumed. Mach numbers up to 20 are investigated to study the effects of vibrational and chemical non-equilibrium on compressor performance. A direct impact on the trends on the kinetic energy efficiency and compressor efficiency was found due to dissociation.
ContributorsOliden, Daniel (Author) / Lee, Tae-Woo (Thesis advisor) / Peet, Yulia (Committee member) / Huang, Huei-Ping (Committee member) / Arizona State University (Publisher)
Created2013
Description
ABSTRACT 1. Aposematic signals advertise prey distastefulness or metabolic unprofitability to potential predators and have evolved independently in many prey groups over the course of evolutionary history as a means of protection from predation. Most aposematic signals investigated to date exhibit highly chromatic patterning; however, relatives in these toxic groups with patterns of very low chroma have been largely overlooked. 2. We propose that bright displays with low chroma arose in toxic prey species because they were more effective at deterring predation than were their chromatic counterparts, especially when viewed in relatively low light environments such as forest understories. 3. We analyzed the reflectance and radiance of color patches on the wings of 90 tropical butterfly species that belong to groups with documented toxicity that vary in their habitat preferences to test this prediction: Warning signal chroma and perceived chromaticity are expected to be higher and brightness lower in species that fly in open environments when compared to those that fly in forested environments. 4. Analyses of the reflectance and radiance of warning color patches and predator visual modeling support this prediction. Moreover, phylogenetic tests, which correct for statistical non-independence due to phylogenetic relatedness of test species, also support the hypothesis of an evolutionary correlation between perceived chromaticity of aposematic signals and the flight habits of the butterflies that exhibit these signals.
ContributorsDouglas, Jonathan Marion (Author) / Rutowski, Ronald L (Thesis advisor) / Gadau, Juergen (Committee member) / McGraw, Kevin J. (Committee member) / Arizona State University (Publisher)
Created2013
Description
Derived from the necessity to increase testing capabilities of hybrid rocket motor (HRM) propulsion systems for Daedalus Astronautics at Arizona State University, a small-scale motor and test stand were designed and developed to characterize all components of the system. The motor is designed for simple integration and setup, such that both the forward-end enclosure and end cap can be easily removed for rapid integration of components during testing. Each of the components of the motor is removable allowing for a broad range of testing capabilities. While examining injectors and their potential it is thought ideal to obtain the highest regression rates and overall motor performance possible. The oxidizer and fuel are N2O and hydroxyl-terminated polybutadiene (HTPB), respectively, due to previous experience and simplicity. The injector designs, selected for the same reasons, are designed such that they vary only in the swirl angle. This system provides the platform for characterizing the effects of varying said swirl angle on HRM performance.
ContributorsSummers, Matt H (Author) / Lee, Taewoo (Thesis advisor) / Chen, Kangping (Committee member) / Wells, Valana (Committee member) / Arizona State University (Publisher)
Created2013
Description
A new theoretical model was developed utilizing energy conservation methods in order to determine the fully-atomized cross-sectional Sauter mean diameters of pressure-swirl atomizers. A detailed boundary-layer assessment led to the development of a new viscous dissipation model for droplets in the spray. Integral momentum methods were also used to determine the complete velocity history of the droplets and entrained gas in the spray. The model was extensively validated through comparison with experiment and it was found that the model could predict the correct droplet size with high accuracy for a wide range of operating conditions. Based on detailed analysis, it was found that the energy model has a tendency to overestimate the droplet diameters for very low injection velocities, Weber numbers, and cone angles. A full parametric study was also performed in order to unveil some underlying behavior of pressure-swirl atomizers. It was found that at high injection velocities, the kinetic energy in the spray is significantly larger than the surface tension energy, therefore, efforts into improving atomization quality by changing the liquid's surface tension may not be the most productive. From the parametric studies it was also shown how the Sauter mean diameter and entrained velocities vary with increasing ambient gas density. Overall, the present energy model has the potential to provide quick and reasonably accurate solutions for a wide range of operating conditions enabling the user to determine how different injection parameters affect the spray quality.
ContributorsMoradi, Ali (Author) / Lee, Taewoo (Thesis advisor) / Herrmann, Marcus (Committee member) / Huang, Huei-Ping (Committee member) / Arizona State University (Publisher)
Created2013
Description
Random peptide microarrays are a powerful tool for both the treatment and diagnostics of infectious diseases. On the treatment side, selected random peptides on the microarray have either binding or lytic potency against certain pathogens cells, thus they can be synthesized into new antimicrobial agents, denoted as synbodies (synthetic antibodies). On the diagnostic side, serum containing specific infection-related antibodies create unique and distinct "pathogen-immunosignatures" on the random peptide microarray distinct from the healthy control serum, and this different mode of binding can be used as a more precise measurement than traditional ELISA tests. My thesis project is separated into these two parts: the first part falls into the treatment side and the second one focuses on the diagnostic side. My first chapter shows that a substitution amino acid peptide library helps to improve the activity of a recently reported synthetic antimicrobial peptide selected by the random peptide microarray. By substituting one or two amino acids of the original lead peptide, the new substitutes show changed hemolytic effects against mouse red blood cells and changed potency against two pathogens: Staphylococcus aureus and Pseudomonas aeruginosa. Two new substitutes are then combined together to form the synbody, which shows a significantly antimicrobial potency against Staphylococcus aureus (<0.5uM). In the second chapter, I explore the possibility of using the 10K Ver.2 random peptide microarray to monitor the humoral immune response of dengue. Over 2.5 billion people (40% of the world's population) live in dengue transmitting areas. However, currently there is no efficient dengue treatment or vaccine. Here, with limited dengue patient serum samples, we show that the immunosignature has the potential to not only distinguish the dengue infection from non-infected people, but also the primary dengue infection from the secondary dengue infections, dengue infection from West Nile Virus (WNV) infection, and even between different dengue serotypes. By further bioinformatic analysis, we demonstrate that the significant peptides selected to distinguish dengue infected and normal samples may indicate the epitopes responsible for the immune response.
ContributorsWang, Xiao (Author) / Johnston, Stephen Albert (Thesis advisor) / Blattman, Joseph (Committee member) / Arntzen, Charles (Committee member) / Arizona State University (Publisher)
Created2013
Description
This research examines the current challenges of using Lamb wave interrogation methods to localize fatigue crack damage in a complex metallic structural component subjected to unknown temperatures. The goal of this work is to improve damage localization results for a structural component interrogated at an unknown temperature, by developing a probabilistic and reference-free framework for estimating Lamb wave velocities and the damage location. The methodology for damage localization at unknown temperatures includes the following key elements: i) a model that can describe the change in Lamb wave velocities with temperature; ii) the extension of an advanced time-frequency based signal processing technique for enhanced time-of-flight feature extraction from a dispersive signal; iii) the development of a Bayesian damage localization framework incorporating data association and sensor fusion. The technique requires no additional transducers to be installed on a structure, and allows for the estimation of both the temperature and the wave velocity in the component. Additionally, the framework of the algorithm allows it to function completely in an unsupervised manner by probabilistically accounting for all measurement origin uncertainty. The novel algorithm was experimentally validated using an aluminum lug joint with a growing fatigue crack. The lug joint was interrogated using piezoelectric transducers at multiple fatigue crack lengths, and at temperatures between 20°C and 80°C. The results showed that the algorithm could accurately predict the temperature and wave speed of the lug joint. The localization results for the fatigue damage were found to correlate well with the true locations at long crack lengths, but loss of accuracy was observed in localizing small cracks due to time-of-flight measurement errors. To validate the algorithm across a wider range of temperatures the electromechanically coupled LISA/SIM model was used to simulate the effects of temperatures. The numerical results showed that this approach would be capable of experimentally estimating the temperature and velocity in the lug joint for temperatures from -60°C to 150°C. The velocity estimation algorithm was found to significantly increase the accuracy of localization at temperatures above 120°C when error due to incorrect velocity selection begins to outweigh the error due to time-of-flight measurements.
ContributorsHensberry, Kevin (Author) / Chattopadhyay, Aditi (Thesis advisor) / Liu, Yongming (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Arizona State University (Publisher)
Created2013
Description
Gas turbines have become widely used in the generation of power for cities. They are used all over the world and must operate under a wide variety of ambient conditions. Every turbine has a temperature at which it operates at peak capacity. In order to attain this temperature in the hotter months various cooling methods are used such as refrigeration inlet cooling systems, evaporative methods, and thermal energy storage systems. One of the more widely used is the evaporative systems because it is one of the safest and easiest to utilize method. However, the behavior of water droplets within the inlet to the turbine has not been extensively studied or documented. It is important to understand how the droplets behave within the inlet so that water droplets above a critical diameter will not enter the compressor and cause damage to the compressor blades. In order to do this a FLUENT simulation was constructed in order to determine the behavior of the water droplets and if any droplets remain at the exit of the inlet, along with their size. In order to do this several engineering drawings were obtained from SRP and studies in order to obtain the correct dimensions. Then the simulation was set up using data obtained from SRP and Parker-Hannifin, the maker of the spray nozzles. Then several sets of simulations were run in order to see how the water droplets behaved under various conditions. These results were then analyzed and quantified so that they could be easily understood. The results showed that the possible damage to the compressor increased with increasing temperature at a constant relative humidity. This is due in part to the fact that in order to keep a constant relative humidity at varying temperatures the mass fraction of water vapor in the air must be changed. As temperature increases the water vapor mass fraction must increase in order to maintain a constant relative humidity. This in turn makes it slightly increases the evaporation time of the water droplets. This will then lead to more droplets exiting the inlet and at larger diameters.
ContributorsHargrave, Kevin (Author) / Lee, Taewoo (Thesis advisor) / Huang, Huei-Ping (Committee member) / Chen, Kaangping (Committee member) / Arizona State University (Publisher)
Created2013
Description
Biological diversity is threatened by increasing anthropogenic modification of natural environments and increasing demands on natural resources. Sonoran desert tortoises (Gopherus morafkai) currently have Candidate status under the Endangered Species Act (ESA) based on health and habitat threats. To ensure this animal persists in the midst of multiple threats requires an understanding of the life history and ecology of each population. I looked at one physiological and one behavioral aspect of a population of tortoises at the Sugarloaf Mountain (SL) study site in central Arizona, USA. I used 21 years of capture-recapture records to estimate growth parameters of the entire population. I investigated habitat selection of juvenile tortoises by selecting 117 locations of 11 tortoises that had been tracked by radio-telemetry one to three times weekly for two years, selecting locations from both summer active season and during winter hibernation. I compared 22 microhabitat variables of tortoise locations to random SL locations to determine habitat use and availability. Male tortoises at SL reach a greater asymptotic length than females, and males and females appear to grow at the same rate. Juvenile tortoises at the SL site use steep rocky hillsides with high proportions of sand and annual vegetation, few succulents, and enclosed shelters in summer. They use enclosed shelters on steep slopes for winter hibernation. An understanding of these features can allow managers to quantify Sonoran desert tortoise habitat needs and life history characteristics and to understand the impact of land use policies.
ContributorsBridges, Andrew (Author) / Bateman, Heather L (Thesis advisor) / Miller, William (Committee member) / Ulrich, Jon (Committee member) / Arizona State University (Publisher)
Created2012