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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

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
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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

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
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Description
As the complexity of robotic systems and applications grows rapidly, development of high-performance, easy to use, and fully integrated development environments for those systems is inevitable. Model-Based Design (MBD) of dynamic systems using engineering software such as Simulink® from MathWorks®, SciCos from Metalau team and SystemModeler® from Wolfram® is quite

As the complexity of robotic systems and applications grows rapidly, development of high-performance, easy to use, and fully integrated development environments for those systems is inevitable. Model-Based Design (MBD) of dynamic systems using engineering software such as Simulink® from MathWorks®, SciCos from Metalau team and SystemModeler® from Wolfram® is quite popular nowadays. They provide tools for modeling, simulation, verification and in some cases automatic code generation for desktop applications, embedded systems and robots. For real-world implementation of models on the actual hardware, those models should be converted into compilable machine code either manually or automatically. Due to the complexity of robotic systems, manual code translation from model to code is not a feasible optimal solution so we need to move towards automated code generation for such systems. MathWorks® offers code generation facilities called Coder® products for this purpose. However in order to fully exploit the power of model-based design and code generation tools for robotic applications, we need to enhance those software systems by adding and modifying toolboxes, files and other artifacts as well as developing guidelines and procedures. In this thesis, an effort has been made to propose a guideline as well as a Simulink® library, StateFlow® interface API and a C/C++ interface API to complete this toolchain for NAO humanoid robots. Thus the model of the hierarchical control architecture can be easily and properly converted to code and built for implementation.
ContributorsRaji Kermani, Ramtin (Author) / Fainekos, Georgios (Thesis advisor) / Lee, Yann-Hang (Committee member) / Sarjoughian, Hessam S. (Committee member) / Arizona State University (Publisher)
Created2013
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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

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
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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).

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
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Description
With increasing transistor volume and reducing feature size, it has become a major design constraint to reduce power consumption also. This has given rise to aggressive architectural changes for on-chip power management and rapid development to energy efficient hardware accelerators. Accordingly, the objective of this research work is to facilitate

With increasing transistor volume and reducing feature size, it has become a major design constraint to reduce power consumption also. This has given rise to aggressive architectural changes for on-chip power management and rapid development to energy efficient hardware accelerators. Accordingly, the objective of this research work is to facilitate software developers to leverage these hardware techniques and improve energy efficiency of the system. To achieve this, I propose two solutions for Linux kernel: Optimal use of these architectural enhancements to achieve greater energy efficiency requires accurate modeling of processor power consumption. Though there are many models available in literature to model processor power consumption, there is a lack of such models to capture power consumption at the task-level. Task-level energy models are a requirement for an operating system (OS) to perform real-time power management as OS time multiplexes tasks to enable sharing of hardware resources. I propose a detailed design methodology for constructing an architecture agnostic task-level power model and incorporating it into a modern operating system to build an online task-level power profiler. The profiler is implemented inside the latest Linux kernel and validated for Intel Sandy Bridge processor. It has a negligible overhead of less than 1\% hardware resource consumption. The profiler power prediction was demonstrated for various application benchmarks from SPEC to PARSEC with less than 4\% error. I also demonstrate the importance of the proposed profiler for emerging architectural techniques through use case scenarios, which include heterogeneous computing and fine grained per-core DVFS. Along with architectural enhancement in general purpose processors to improve energy efficiency, hardware accelerators like Coarse Grain reconfigurable architecture (CGRA) are gaining popularity. Unlike vector processors, which rely on data parallelism, CGRA can provide greater flexibility and compiler level control making it more suitable for present SoC environment. To provide streamline development environment for CGRA, I propose a flexible framework in Linux to do design space exploration for CGRA. With accurate and flexible hardware models, fine grained integration with accurate architectural simulator, and Linux memory management and DMA support, a user can carry out limitless experiments on CGRA in full system environment.
ContributorsDesai, Digant Pareshkumar (Author) / Vrudhula, Sarma (Thesis advisor) / Chakrabarti, Chaitali (Committee member) / Wu, Carole-Jean (Committee member) / Arizona State University (Publisher)
Created2013
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Description
Smart home system (SHS) is a kind of information system aiming at realizing home automation. The SHS can connect with almost any kind of electronic/electric device used in a home so that they can be controlled and monitored centrally. Today's technology also allows the home owners to control and monitor

Smart home system (SHS) is a kind of information system aiming at realizing home automation. The SHS can connect with almost any kind of electronic/electric device used in a home so that they can be controlled and monitored centrally. Today's technology also allows the home owners to control and monitor the SHS installed in their homes remotely. This is typically realized by giving the SHS network access ability. Although the SHS's network access ability brings a lot of conveniences to the home owners, it also makes the SHS facing more security threats than ever before. As a result, when designing a SHS, the security threats it might face should be given careful considerations. System security threats can be solved properly by understanding them and knowing the parts in the system that should be protected against them first. This leads to the idea of solving the security threats a SHS might face from the requirements engineering level. Following this idea, this paper proposes a systematic approach to generate the security requirements specifications for the SHS. It can be viewed as the first step toward the complete SHS security requirements engineering process.
ContributorsXu, Rongcao (Author) / Ghazarian, Arbi (Thesis advisor) / Bansal, Ajay (Committee member) / Lindquist, Timothy (Committee member) / Arizona State University (Publisher)
Created2013
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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

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
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Description
Motion capture using cost-effective sensing technology is challenging and the huge success of Microsoft Kinect has been attracting researchers to uncover the potential of using this technology into computer vision applications. In this thesis, an upper-body motion analysis in a home-based system for stroke rehabilitation using novel RGB-D camera -

Motion capture using cost-effective sensing technology is challenging and the huge success of Microsoft Kinect has been attracting researchers to uncover the potential of using this technology into computer vision applications. In this thesis, an upper-body motion analysis in a home-based system for stroke rehabilitation using novel RGB-D camera - Kinect is presented. We address this problem by first conducting a systematic analysis of the usability of Kinect for motion analysis in stroke rehabilitation. Then a hybrid upper body tracking approach is proposed which combines off-the-shelf skeleton tracking with a novel depth-fused mean shift tracking method. We proposed several kinematic features reliably extracted from the proposed inexpensive and portable motion capture system and classifiers that correlate torso movement to clinical measures of unimpaired and impaired. Experiment results show that the proposed sensing and analysis works reliably on measuring torso movement quality and is promising for end-point tracking. The system is currently being deployed for large-scale evaluations.
ContributorsDu, Tingfang (Author) / Turaga, Pavan (Thesis advisor) / Spanias, Andreas (Committee member) / Rikakis, Thanassis (Committee member) / Arizona State University (Publisher)
Created2012
Description
This thesis introduces the Model-Based Development of Multi-iRobot Toolbox (MBDMIRT), a Simulink-based toolbox designed to provide the means to acquire and practice the Model-Based Development (MBD) skills necessary to design real-time embedded system. The toolbox was developed in the Cyber-Physical System Laboratory at Arizona State University. The MBDMIRT toolbox runs

This thesis introduces the Model-Based Development of Multi-iRobot Toolbox (MBDMIRT), a Simulink-based toolbox designed to provide the means to acquire and practice the Model-Based Development (MBD) skills necessary to design real-time embedded system. The toolbox was developed in the Cyber-Physical System Laboratory at Arizona State University. The MBDMIRT toolbox runs under MATLAB/Simulink to simulate the movements of multiple iRobots and to control, after verification by simulation, multiple physical iRobots accordingly. It adopts the Simulink/Stateflow, which exemplifies an approach to MBD, to program the behaviors of the iRobots. The MBDMIRT toolbox reuses and augments the open-source MATLAB-Based Simulator for the iRobot Create from Cornell University to run the simulation. Regarding the mechanism of iRobot control, the MBDMIRT toolbox applies the MATLAB Toolbox for the iRobot Create (MTIC) from United States Naval Academy to command the physical iRobots. The MBDMIRT toolbox supports a timer in both the simulation and the control, which is based on the local clock of the PC running the toolbox. In addition to the build-in sensors of an iRobot, the toolbox can simulate four user-added sensors, which are overhead localization system (OLS), sonar sensors, a camera, and Light Detection And Ranging (LIDAR). While controlling a physical iRobot, the toolbox supports the StarGazer OLS manufactured by HAGISONIC, Inc.
ContributorsSu, Shih-Kai (Author) / Fainekos, Georgios E (Thesis advisor) / Sarjoughian, Hessam S. (Committee member) / Artemiadis, Panagiotis K (Committee member) / Arizona State University (Publisher)
Created2012