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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
In recent years, an increase of environmental temperature in urban areas has raised many concerns. These areas are subjected to higher temperature compared to the rural surrounding areas. Modification of land surface and the use of materials such as concrete and/or asphalt are the main factors influencing the surface energy balance and therefore the environmental temperature in the urban areas. Engineered materials have relatively higher solar energy absorption and tend to trap a relatively higher incoming solar radiation. They also possess a higher heat storage capacity that allows them to retain heat during the day and then slowly release it back into the atmosphere as the sun goes down. This phenomenon is known as the Urban Heat Island (UHI) effect and causes an increase in the urban air temperature. Many researchers believe that albedo is the key pavement affecting the urban heat island. However, this research has shown that the problem is more complex and that solar reflectivity may not be the only important factor to evaluate the ability of a pavement to mitigate UHI. The main objective of this study was to analyze and research the influence of pavement materials on the near surface air temperature. In order to accomplish this effort, test sections consisting of Hot Mix Asphalt (HMA), Porous Hot Mix asphalt (PHMA), Portland Cement Concrete (PCC), Pervious Portland Cement Concrete (PPCC), artificial turf, and landscape gravels were constructed in the Phoenix, Arizona area. Air temperature, albedo, wind speed, solar radiation, and wind direction were recorded, analyzed and compared above each pavement material type. The results showed that there was no significant difference in the air temperature at 3-feet and above, regardless of the type of the pavement. Near surface pavement temperatures were also measured and modeled. The results indicated that for the UHI analysis, it is important to consider the interaction between pavement structure, material properties, and environmental factors. Overall, this study demonstrated the complexity of evaluating pavement structures for UHI mitigation; it provided great insight on the effects of material types and properties on surface temperatures and near surface air temperature.
ContributorsPourshams-Manzouri, Tina (Author) / Kaloush, Kamil (Thesis advisor) / Wang, Zhihua (Thesis advisor) / Zapata, Claudia E. (Committee member) / Mamlouk, Michael (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
The rapid escalation of technology and the widespread emergence of modern technological equipments have resulted in the generation of humongous amounts of digital data (in the form of images, videos and text). This has expanded the possibility of solving real world problems using computational learning frameworks. However, while gathering a large amount of data is cheap and easy, annotating them with class labels is an expensive process in terms of time, labor and human expertise. This has paved the way for research in the field of active learning. Such algorithms automatically select the salient and exemplar instances from large quantities of unlabeled data and are effective in reducing human labeling effort in inducing classification models. To utilize the possible presence of multiple labeling agents, there have been attempts towards a batch mode form of active learning, where a batch of data instances is selected simultaneously for manual annotation. This dissertation is aimed at the development of novel batch mode active learning algorithms to reduce manual effort in training classification models in real world multimedia pattern recognition applications. Four major contributions are proposed in this work: $(i)$ a framework for dynamic batch mode active learning, where the batch size and the specific data instances to be queried are selected adaptively through a single formulation, based on the complexity of the data stream in question, $(ii)$ a batch mode active learning strategy for fuzzy label classification problems, where there is an inherent imprecision and vagueness in the class label definitions, $(iii)$ batch mode active learning algorithms based on convex relaxations of an NP-hard integer quadratic programming (IQP) problem, with guaranteed bounds on the solution quality and $(iv)$ an active matrix completion algorithm and its application to solve several variants of the active learning problem (transductive active learning, multi-label active learning, active feature acquisition and active learning for regression). These contributions are validated on the face recognition and facial expression recognition problems (which are commonly encountered in real world applications like robotics, security and assistive technology for the blind and the visually impaired) and also on collaborative filtering applications like movie recommendation.
ContributorsChakraborty, Shayok (Author) / Panchanathan, Sethuraman (Thesis advisor) / Balasubramanian, Vineeth N. (Committee member) / Li, Baoxin (Committee member) / Mittelmann, Hans (Committee member) / Ye, Jieping (Committee member) / Arizona State University (Publisher)
Created2013
Description
The increasing popularity of Twitter renders improved trustworthiness and relevance assessment of tweets much more important for search. However, given the limitations on the size of tweets, it is hard to extract measures for ranking from the tweet's content alone. I propose a method of ranking tweets by generating a reputation score for each tweet that is based not just on content, but also additional information from the Twitter ecosystem that consists of users, tweets, and the web pages that tweets link to. This information is obtained by modeling the Twitter ecosystem as a three-layer graph. The reputation score is used to power two novel methods of ranking tweets by propagating the reputation over an agreement graph based on tweets' content similarity. Additionally, I show how the agreement graph helps counter tweet spam. An evaluation of my method on 16~million tweets from the TREC 2011 Microblog Dataset shows that it doubles the precision over baseline Twitter Search and achieves higher precision than current state of the art method. I present a detailed internal empirical evaluation of RAProp in comparison to several alternative approaches proposed by me, as well as external evaluation in comparison to the current state of the art method.
ContributorsRavikumar, Srijith (Author) / Kambhampati, Subbarao (Thesis advisor) / Davulcu, Hasan (Committee member) / Liu, Huan (Committee member) / Arizona State University (Publisher)
Created2013
Description
Vehicle type choice is a significant determinant of fuel consumption and energy sustainability; larger, heavier vehicles consume more fuel, and expel twice as many pollutants, than their smaller, lighter counterparts. Over the course of the past few decades, vehicle type choice has seen a vast shift, due to many households making more trips in larger vehicles with lower fuel economy. During the 1990s, SUVs were the fastest growing segment of the automotive industry, comprising 7% of the total light vehicle market in 1990, and 25% in 2005. More recently, due to rising oil prices, greater awareness to environmental sensitivity, the desire to reduce dependence on foreign oil, and the availability of new vehicle technologies, many households are considering the use of newer vehicles with better fuel economy, such as hybrids and electric vehicles, over the use of the SUV or low fuel economy vehicles they may already own. The goal of this research is to examine how vehicle miles traveled, fuel consumption and emissions may be reduced through shifts in vehicle type choice behavior. Using the 2009 National Household Travel Survey data it is possible to develop a model to estimate household travel demand and total fuel consumption. If given a vehicle choice shift scenario, using the model it would be possible to calculate the potential fuel consumption savings that would result from such a shift. In this way, it is possible to estimate fuel consumption reductions that would take place under a wide variety of scenarios.
ContributorsChristian, Keith (Author) / Pendyala, Ram M. (Thesis advisor) / Chester, Mikhail (Committee member) / Kaloush, Kamil (Committee member) / Ahn, Soyoung (Committee member) / Arizona State University (Publisher)
Created2013
Description
Manufacture of building materials requires significant energy, and as demand for these materials continues to increase, the energy requirement will as well. Offsetting this energy use will require increased focus on sustainable building materials. Further, the energy used in building, particularly in heating and air conditioning, accounts for 40 percent of a buildings energy use. Increasing the efficiency of building materials will reduce energy usage over the life time of the building. Current methods for maintaining the interior environment can be highly inefficient depending on the building materials selected. Materials such as concrete have low thermal efficiency and have a low heat capacity meaning it provides little insulation. Use of phase change materials (PCM) provides the opportunity to increase environmental efficiency of buildings by using the inherent latent heat storage as well as the increased heat capacity. Incorporating PCM into concrete via lightweight aggregates (LWA) by direct addition is seen as a viable option for increasing the thermal storage capabilities of concrete, thereby increasing building energy efficiency. As PCM change phase from solid to liquid, heat is absorbed from the surroundings, decreasing the demand on the air conditioning systems on a hot day or vice versa on a cold day. Further these materials provide an additional insulating capacity above the value of plain concrete. When the temperature drops outside the PCM turns back into a solid and releases the energy stored from the day. PCM is a hydrophobic material and causes reductions in compressive strength when incorporated directly into concrete, as shown in previous studies. A proposed method for mitigating this detrimental effect, while still incorporating PCM into concrete is to encapsulate the PCM in aggregate. This technique would, in theory, allow for the use of phase change materials directly in concrete, increasing the thermal efficiency of buildings, while negating the negative effect on compressive strength of the material.
ContributorsSharma, Breeann (Author) / Neithalath, Narayanan (Thesis advisor) / Mobasher, Barzin (Committee member) / Rajan, Subramaniam D. (Committee member) / Arizona State University (Publisher)
Created2013
Description
The history of outdoor water use in the Phoenix, Arizona metropolitan area has given rise to a general landscape aesthetic and pattern of residential irrigation that seem in discord with the natural desert environment. While xeric landscaping that incorporates native desert ecology has potential for reducing urban irrigation demand, there are societal and environmental factors that make mesic landscaping, including shade trees and grass lawns, a common choice for residential yards. In either case, there is potential for water savings through irrigation schedules based on fluxes affecting soil moisture in the active plant rooting zone. In this thesis, a point-scale model of soil moisture dynamics was applied to two urban sites in the Phoenix area: one with xeric landscaping, and one with mesic. The model was calibrated to observed soil moisture data from irrigated and non-irrigated sensors, with local daily precipitation and potential evapotranspiration records as model forcing. Simulations were then conducted to investigate effects of irrigation scheduling, plant stress parameters, and precipitation variability on soil moisture dynamics, water balance partitioning, and plant water stress. Results indicated a substantial difference in soil water storage capacity at the two sites, which affected sensitivity to irrigation scenarios. Seasonal variation was critical in avoiding unproductive water losses at the xeric site, and allowed for small water savings at the mesic site by maintaining mild levels of plant stress. The model was also used to determine minimum annual irrigation required to achieve specified levels of plant stress at each site using long-term meteorological records. While the xeric site showed greater potential for water savings, a bimodal schedule consisting of low winter and summer irrigation was identified as a means to conserve water at both sites, with moderate levels of plant water stress. For lower stress levels, potential water savings were found by fixing irrigation depth and seasonally varying the irrigation interval, consistent with municipal recommendations in the Phoenix metropolitan area. These results provide a deeper understanding of the ecohydrologic differences between the two types of landscape treatments, and can assist water and landscape managers in identifying opportunities for water savings in desert urban areas.
ContributorsVolo, Thomas J (Author) / Vivoni, Enrique R (Thesis advisor) / Ruddell, Benjamin L (Committee member) / Wang, Zhihua (Committee member) / Arizona State University (Publisher)
Created2013
Description
The academic literature on science communication widely acknowledges a problem: science communication between experts and lay audiences is important, but it is not done well. General audience popular science books, however, carry a reputation for clear science communication and are understudied in the academic literature. For this doctoral dissertation, I utilize Sam Harris's The Moral Landscape, a general audience science book on the particularly thorny topic of neuroscientific approaches to morality, as a case-study to explore the possibility of using general audience science books as models for science communication more broadly. I conduct a literary analysis of the text that delimits the scope of its project, its intended audience, and the domains of science to be communicated. I also identify seven literary aspects of the text: three positive aspects that facilitate clarity and four negative aspects that interfere with lay public engagement. I conclude that The Moral Landscape relies on an assumed knowledge base and intuitions of its audience that cannot reasonably be expected of lay audiences; therefore, it cannot properly be construed as popular science communication. It nevertheless contains normative lessons for the broader science project, both in literary aspects to be salvaged and literary aspects and concepts to consciously be avoided and combated. I note that The Moral Landscape's failings can also be taken as an indication that typical descriptions of science communication offer under-detailed taxonomies of both audiences for science communication and the varieties of science communication aimed at those audiences. Future directions of study include rethinking appropriate target audiences for science literacy projects and developing a more discriminating taxonomy of both science communication and lay publics.
ContributorsJohnson, Nathan W (Author) / Robert, Jason S (Thesis advisor) / Creath, Richard (Committee member) / Martinez, Jacqueline (Committee member) / Sylvester, Edward (Committee member) / Lynch, John (Committee member) / Arizona State University (Publisher)
Created2013
Description
Once perceived as an unimportant occurrence in living organisms, cell degeneration was reconfigured as an important biological phenomenon in development, aging, health, and diseases in the twentieth century. This dissertation tells a twentieth-century history of scientific investigations on cell degeneration, including cell death and aging. By describing four central developments in cell degeneration research with the four major chapters, I trace the emergence of the degenerating cell as a scientific object, describe the generations of a variety of concepts, interpretations and usages associated with cell death and aging, and analyze the transforming influences of the rising cell degeneration research. Particularly, the four chapters show how the changing scientific practices about cellular life in embryology, cell culture, aging research, and molecular biology of Caenorhabditis elegans shaped the interpretations about cell degeneration in the twentieth-century as life-shaping, limit-setting, complex, yet regulated. These events created and consolidated important concepts in life sciences such as programmed cell death, the Hayflick limit, apoptosis, and death genes. These cases also transformed the material and epistemic practices about the end of cellular life subsequently and led to the formations of new research communities. The four cases together show the ways cell degeneration became a shared subject between molecular cell biology, developmental biology, gerontology, oncology, and pathology of degenerative diseases. These practices and perspectives created a special kind of interconnectivity between different fields and led to a level of interdisciplinarity within cell degeneration research by the early 1990s.
ContributorsJiang, Lijing (Author) / Maienschein, Jane (Thesis advisor) / Laubichler, Manfred (Thesis advisor) / Hurlbut, James (Committee member) / Creath, Richard (Committee member) / White, Michael (Committee member) / Arizona State University (Publisher)
Created2013