Theses and Dissertations
This collection includes both ASU Theses and Dissertations, submitted by graduate students, and the Barrett, Honors College theses submitted by undergraduate students.
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Description
Sparsity has become an important modeling tool in areas such as genetics, signal and audio processing, medical image processing, etc. Via the penalization of l-1 norm based regularization, the structured sparse learning algorithms can produce highly accurate models while imposing various predefined structures on the data, such as feature groups or graphs. In this thesis, I first propose to solve a sparse learning model with a general group structure, where the predefined groups may overlap with each other. Then, I present three real world applications which can benefit from the group structured sparse learning technique. In the first application, I study the Alzheimer's Disease diagnosis problem using multi-modality neuroimaging data. In this dataset, not every subject has all data sources available, exhibiting an unique and challenging block-wise missing pattern. In the second application, I study the automatic annotation and retrieval of fruit-fly gene expression pattern images. Combined with the spatial information, sparse learning techniques can be used to construct effective representation of the expression images. In the third application, I present a new computational approach to annotate developmental stage for Drosophila embryos in the gene expression images. In addition, it provides a stage score that enables one to more finely annotate each embryo so that they are divided into early and late periods of development within standard stage demarcations. Stage scores help us to illuminate global gene activities and changes much better, and more refined stage annotations improve our ability to better interpret results when expression pattern matches are discovered between genes.
ContributorsYuan, Lei (Author) / Ye, Jieping (Thesis advisor) / Wang, Yalin (Committee member) / Xue, Guoliang (Committee member) / Kumar, Sudhir (Committee member) / Arizona State University (Publisher)
Created2013
Description
Bully victimization has been associated with blunted cardiovascular responses to stress as well as elevated responses to stress. The difference between these altered physiological responses to stress is largely unknown. This study explored several possible moderators to the relationship between chronic stress and future cardiac output (an indicator of increased stress) in response to future stressors. These moderators include the difference between social and physical stressors and individual levels of loneliness. Participants were administered measures of loneliness and victimization history, and led to anticipate either a "social" (recorded speech) or "non-social" (pain tolerance test ) stressor, neither of which occurred. EKG and impedance cardiography were measured throughout the session. When anticipating both stressors, loneliness and victimization were associated with increased CO. A regression revealed a three-way interaction, with change in cardiac output depending on victimization history, loneliness, and condition in the physical stressor condition. Loneliness magnified the CO output levels of non-bullied individuals when facing a physical stressor. These results suggest that non- bullied participants high in loneliness are more stressed out when facing stressors, particularly stressors that are physically threatening in nature.
ContributorsHaneline, Magen (Author) / Newman, Matt (Thesis advisor) / Salerno, Jessica (Committee member) / Miller, Paul (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
Biological systems are complex in many dimensions as endless transportation and communication networks all function simultaneously. Our ability to intervene within both healthy and diseased systems is tied directly to our ability to understand and model core functionality. The progress in increasingly accurate and thorough high-throughput measurement technologies has provided a deluge of data from which we may attempt to infer a representation of the true genetic regulatory system. A gene regulatory network model, if accurate enough, may allow us to perform hypothesis testing in the form of computational experiments. Of great importance to modeling accuracy is the acknowledgment of biological contexts within the models -- i.e. recognizing the heterogeneous nature of the true biological system and the data it generates. This marriage of engineering, mathematics and computer science with systems biology creates a cycle of progress between computer simulation and lab experimentation, rapidly translating interventions and treatments for patients from the bench to the bedside. This dissertation will first discuss the landscape for modeling the biological system, explore the identification of targets for intervention in Boolean network models of biological interactions, and explore context specificity both in new graphical depictions of models embodying context-specific genomic regulation and in novel analysis approaches designed to reveal embedded contextual information. Overall, the dissertation will explore a spectrum of biological modeling with a goal towards therapeutic intervention, with both formal and informal notions of biological context, in such a way that will enable future work to have an even greater impact in terms of direct patient benefit on an individualized level.
ContributorsVerdicchio, Michael (Author) / Kim, Seungchan (Thesis advisor) / Baral, Chitta (Committee member) / Stolovitzky, Gustavo (Committee member) / Collofello, James (Committee member) / Arizona State University (Publisher)
Created2013
Description
Purpose: This study examines the role of social support on adjustment to widowhood. Past research has indicated that the role of social support on adjustment to widowhood remains inconclusive, and needs further examination. This study examines the varying coping trajectories of middle-aged and retired bereaved spouses. Additionally, this study examines how bereavement stage may also influence one's adaptation to widowhood. Methods: This study used in-depth and semi-structured interviews as a means of understanding the role of social support on adjustment to widowhood. Participants were recruited through two hospice services available in a major metropolitan area in the United States. Convenient and purposive samplings are used in this study; this study will execute a grounded theory approach in order to determine the inconclusive role of social support on adjustment to widowhood. This study is contrasting between two stages- life course stages (middle aged versus retirement aged people) and bereavement stages (a year or less time following the death of a spouse versus three or more years following the death of a spouse). As a means of reducing bias and subjectivity, all data collected during the interview will be transcribed immediately. Results: Middle-aged bereaved spouses reported higher levels of motivation for adjusting positively and quickly towards widowhood due to their concern for protecting the well-being of their surviving young children compared to retired bereaved spouses. Differences between middle-aged widows and widowers have been found in this study; middle-aged widowers have a higher linkage to negative health behaviors. Retired bereaved spouses may fare better depending upon their housing location. Living in a retirement center may lower negative effects of bereavement on retired spouses' health. Conclusions: Types of social support received and expected varied between middle-aged widows and widowers. Gender norms may influence the type of social support widows and widowers receive. Middle-aged widowers are less likely to receive emotional support which may explain their higher linkage to negative health behaviors. Bereavement stage and housing location may be the key factors that influence widowhood trajectories of retired bereaved spouses. Living in a retirement center may lower the negative effects of bereavement on overall health.
ContributorsRafieei, Noshin (Author) / Kronenfeld, Jennie (Thesis advisor) / Haas, Steven (Committee member) / Damgaard, Anni (Committee member) / Arizona State University (Publisher)
Created2013
Description
Research has demonstrated that temperature and relative humidity substantially influence overall perceptions of indoor air quality (Fang, Clausen, & Fanger, 1998). This finding places temperature quality as a high priority, especially for vulnerable adults over 60. Temperature extremes and fluctuation, as well as the perception of those conditions, affect physical performance, thermal comfort and health of older adults (Chatonnet & Cabanac, 1965, pp. 185-6; Fumiharu, Watanabe, Park, Shephard, & Aoyagi, 2005; Heijs & Stringer, 1988). The American Society of Heating, Refrigerating and Air-Conditioning Engineers (ASHRAE) and the International Organization for Standardization (ISO) have developed thermal-comfort standards for working-age, healthy individuals. None of these standards address the physiological and psychological needs of older adults (ASHRAE Standard 55, 2010; ISO-7730, 2005). This dissertation investigates the impacts of thermal conditions on self-reported health and perceived comfort for older adults, hypothesizing that warmer and more-table indoor thermal conditions will increase the health and perceived comfort of these adults. To this end, a new set of thermal comfort metrics was designed and tested to address the thermal preferences of older adults. The SENIOR COMFORT Metrics 2013 outlined new thresholds for optimal indoor high and low temperatures and set limits on thermal variability over time based on the ASHRAE-55 2010 model. This study was conducted at Sunnyslope Manor, a multi-unit, public-housing complex in the North Phoenix. Nearly 60% (76 of 118) of the residents (aged 62-82) were interviewed using a 110-question, self-reporting survey in 73 apartment units. A total of 40 questions and 20 sub-questions addressing perceptions of comfort, pain, sleep patterns, injuries, and mood were extracted from this larger health condition survey to assess health and thermal comfort. Indoor environmental thermal measurements included temperature in three locations: kitchen, living area, and bedroom and data were recorded every 15 minutes over 5 full days and 448 points. Study results start to indicate that older adults for Sunnyslope Manor preferred temperatures between 76 and 82.5 degrees Fahrenheit and that lower temperatures as outlined by ASHRAE-55 2010 increases the rate of injuries and mood changes in older adults among other findings.
ContributorsFonseca, Ernesto (Author) / Bryan, Harvey (Thesis advisor) / Ahrentzen, Sherry (Committee member) / Shea, Kimberly (Committee member) / Arizona State University (Publisher)
Created2013
Description
Vertebrate genomes demonstrate a remarkable range of sizes from 0.3 to 133 gigabase pairs. The proliferation of repeat elements are a major genomic expansion. In particular, long interspersed nuclear elements (LINES) are autonomous retrotransposons that have the ability to "cut and paste" themselves into a host genome through a mechanism called target-primed reverse transcription. LINES have been called "junk DNA," "viral DNA," and "selfish" DNA, and were once thought to be parasitic elements. However, LINES, which diversified before the emergence of many early vertebrates, has strongly shaped the evolution of eukaryotic genomes. This thesis will evaluate LINE abundance, diversity and activity in four anole lizards. An intrageneric analysis will be conducted using comparative phylogenetics and bioinformatics. Comparisons within the Anolis genus, which derives from a single lineage of an adaptive radiation, will be conducted to explore the relationship between LINE retrotransposon activity and causal changes in genomic size and composition.
ContributorsMay, Catherine (Author) / Kusumi, Kenro (Thesis advisor) / Gadau, Juergen (Committee member) / Rawls, Jeffery A (Committee member) / Arizona State University (Publisher)
Created2013
Description
In blindness research, the corpus callosum (CC) is the most frequently studied sub-cortical structure, due to its important involvement in visual processing. While most callosal analyses from brain structural magnetic resonance images (MRI) are limited to the 2D mid-sagittal slice, we propose a novel framework to capture a complete set of 3D morphological differences in the corpus callosum between two groups of subjects. The CCs are segmented from whole brain T1-weighted MRI and modeled as 3D tetrahedral meshes. The callosal surface is divided into superior and inferior patches on which we compute a volumetric harmonic field by solving the Laplace's equation with Dirichlet boundary conditions. We adopt a refined tetrahedral mesh to compute the Laplacian operator, so our computation can achieve sub-voxel accuracy. Thickness is estimated by tracing the streamlines in the harmonic field. We combine areal changes found using surface tensor-based morphometry and thickness information into a vector at each vertex to be used as a metric for the statistical analysis. Group differences are assessed on this combined measure through Hotelling's T2 test. The method is applied to statistically compare three groups consisting of: congenitally blind (CB), late blind (LB; onset > 8 years old) and sighted (SC) subjects. Our results reveal significant differences in several regions of the CC between both blind groups and the sighted groups; and to a lesser extent between the LB and CB groups. These results demonstrate the crucial role of visual deprivation during the developmental period in reshaping the structural architecture of the CC.
ContributorsXu, Liang (Author) / Wang, Yalin (Thesis advisor) / Maciejewski, Ross (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2013
Description
Surgery as a profession requires significant training to improve both clinical decision making and psychomotor proficiency. In the medical knowledge domain, tools have been developed, validated, and accepted for evaluation of surgeons' competencies. However, assessment of the psychomotor skills still relies on the Halstedian model of apprenticeship, wherein surgeons are observed during residency for judgment of their skills. Although the value of this method of skills assessment cannot be ignored, novel methodologies of objective skills assessment need to be designed, developed, and evaluated that augment the traditional approach. Several sensor-based systems have been developed to measure a user's skill quantitatively, but use of sensors could interfere with skill execution and thus limit the potential for evaluating real-life surgery. However, having a method to judge skills automatically in real-life conditions should be the ultimate goal, since only with such features that a system would be widely adopted. This research proposes a novel video-based approach for observing surgeons' hand and surgical tool movements in minimally invasive surgical training exercises as well as during laparoscopic surgery. Because our system does not require surgeons to wear special sensors, it has the distinct advantage over alternatives of offering skills assessment in both learning and real-life environments. The system automatically detects major skill-measuring features from surgical task videos using a computing system composed of a series of computer vision algorithms and provides on-screen real-time performance feedback for more efficient skill learning. Finally, the machine-learning approach is used to develop an observer-independent composite scoring model through objective and quantitative measurement of surgical skills. To increase effectiveness and usability of the developed system, it is integrated with a cloud-based tool, which automatically assesses surgical videos upload to the cloud.
ContributorsIslam, Gazi (Author) / Li, Baoxin (Thesis advisor) / Liang, Jianming (Thesis advisor) / Dinu, Valentin (Committee member) / Greenes, Robert (Committee member) / Smith, Marshall (Committee member) / Kahol, Kanav (Committee member) / Patel, Vimla L. (Committee member) / Arizona State University (Publisher)
Created2013
Description
In 1890, the State of Nevada built the Stewart Indian School on a parcel of land three miles south of Carson City, Nevada, and then sold the campus to the federal government. The Stewart Indian School operated as the only non-reservation Indian boarding school in Nevada until 1980 when the federal government closed the campus. Faced with the challenge of assimilating Native peoples into Anglo society after the conclusion of the Indian wars and the confinement of Indian nations on reservations, the federal government created boarding schools. Policymakers believed that in one generation they could completely eliminate Indian culture by removing children from their homes and educating them in boarding schools. The history of the Stewart Indian School from 1890 to 1940 is the story of a dynamic and changing institution. Only Washoe, Northern Paiute, and Western Shoshone students attended Stewart for the first decade, but over the next forty years, children from over sixty tribal groups enrolled at the school. They arrived from three dozen reservations and 335 different hometowns across the West. During this period, Stewart evolved from a repressive and exploitive institution, into a school that embodied the reform agenda of the Indian New Deal in the 1930s. This dissertation uses archival and ethnographic material to explain how the federal government's agenda failed. Rather than destroying Native culture, Stewart students and Nevada's Indian communities used the skills taught at the school to their advantage and became tribal leaders during the 1930s. This dissertation explores the individual and collective bodies of Stewart students. The body is a social construction constantly being fashioned by the intersectional forces of race, class, and gender. Each chapter explores the different ways the Stewart Indian School and the federal government tried to transform the students' bodies through their physical appearance, the built environment, health education, vocational training, and extracurricular activities such as band and sports.
ContributorsThompson, Bonnie (Author) / Iverson, Peter (Thesis advisor) / Gray, Susan (Thesis advisor) / Green, Monica (Committee member) / Arizona State University (Publisher)
Created2013