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The healthcare system in this country is currently unacceptable. New technologies may contribute to reducing cost and improving outcomes. Early diagnosis and treatment represents the least risky option for addressing this issue. Such a technology needs to be inexpensive, highly sensitive, highly specific, and amenable to adoption in a clinic. This thesis explores an immunodiagnostic technology based on highly scalable, non-natural sequence peptide microarrays designed to profile the humoral immune response and address the healthcare problem. The primary aim of this thesis is to explore the ability of these arrays to map continuous (linear) epitopes. I discovered that using a technique termed subsequence analysis where epitopes could be decisively mapped to an eliciting protein with high success rate. This led to the discovery of novel linear epitopes from Plasmodium falciparum (Malaria) and Treponema palladium (Syphilis), as well as validation of previously discovered epitopes in Dengue and monoclonal antibodies. Next, I developed and tested a classification scheme based on Support Vector Machines for development of a Dengue Fever diagnostic, achieving higher sensitivity and specificity than current FDA approved techniques. The software underlying this method is available for download under the BSD license. Following this, I developed a kinetic model for immunosignatures and tested it against existing data driven by previously unexplained phenomena. This model provides a framework and informs ways to optimize the platform for maximum stability and efficiency. I also explored the role of sequence composition in explaining an immunosignature binding profile, determining a strong role for charged residues that seems to have some predictive ability for disease. Finally, I developed a database, software and indexing strategy based on Apache Lucene for searching motif patterns (regular expressions) in large biological databases. These projects as a whole have advanced knowledge of how to approach high throughput immunodiagnostics and provide an example of how technology can be fused with biology in order to affect scientific and health outcomes.
ContributorsRicher, Joshua Amos (Author) / Johnston, Stephen A. (Thesis advisor) / Woodbury, Neal (Committee member) / Stafford, Phillip (Committee member) / Papandreou-Suppappola, Antonia (Committee member) / Arizona State University (Publisher)
Created2014
Description
As a developing nation, China is currently faced with the challenge of providing
safe, reliable and adequate energy resources to the county's growing urban areas as well as to its expanding rural populations. To meet this demand, the country has initiated massive construction projects to expand its national energy infrastructure, particularly in the form of natural gas pipeline. The most notable of these projects is the ongoing West-East Gas Pipeline Project. This project is currently in its third phase, which will supply clean and efficient natural gas to nearly sixty million users located in the densely populated Yangtze River Delta.
Trenchless Technologies, in particular the construction method of Horizontal
Directional Drilling (HDD), have played a critical role in executing this project by
providing economical, practical and environmentally responsible ways to install buried pipeline systems. HDD has proven to be the most popular method selected to overcome challenges along the path of the pipeline, which include mountainous terrain, extensive farmland and numerous bodies of water. The Yangtze River, among other large-scale water bodies, have proven to be the most difficult obstacle for the pipeline installation as it widens and changes course numerous times along its path to the East China Sea. The purpose of this study is to examine those practices being used in China in order to compare those to those long used practices in the North American in order to understand the advantages of Chinese advancements.
Developing countries would benefit from the Chinese advancements for large-scale HDD installation. In developed areas, such as North America, studying Chinese execution may allow for new ideas to help to improve long established methods. These factors combined further solidify China's role as the global leader in trenchless technology methods and provide the opportunity for Chinese HDD contractors to contribute to the world's knowledge for best practices of the Horizontal Directional Drilling method.
safe, reliable and adequate energy resources to the county's growing urban areas as well as to its expanding rural populations. To meet this demand, the country has initiated massive construction projects to expand its national energy infrastructure, particularly in the form of natural gas pipeline. The most notable of these projects is the ongoing West-East Gas Pipeline Project. This project is currently in its third phase, which will supply clean and efficient natural gas to nearly sixty million users located in the densely populated Yangtze River Delta.
Trenchless Technologies, in particular the construction method of Horizontal
Directional Drilling (HDD), have played a critical role in executing this project by
providing economical, practical and environmentally responsible ways to install buried pipeline systems. HDD has proven to be the most popular method selected to overcome challenges along the path of the pipeline, which include mountainous terrain, extensive farmland and numerous bodies of water. The Yangtze River, among other large-scale water bodies, have proven to be the most difficult obstacle for the pipeline installation as it widens and changes course numerous times along its path to the East China Sea. The purpose of this study is to examine those practices being used in China in order to compare those to those long used practices in the North American in order to understand the advantages of Chinese advancements.
Developing countries would benefit from the Chinese advancements for large-scale HDD installation. In developed areas, such as North America, studying Chinese execution may allow for new ideas to help to improve long established methods. These factors combined further solidify China's role as the global leader in trenchless technology methods and provide the opportunity for Chinese HDD contractors to contribute to the world's knowledge for best practices of the Horizontal Directional Drilling method.
ContributorsCarlin, Maureen Cassin (Author) / Ariaratnam, Samuel T (Thesis advisor) / Chong, Oswald (Committee member) / Bearup, Wylie (Committee member) / Arizona State University (Publisher)
Created2014
Description
The solar energy sector has been growing rapidly over the past decade. Growth in renewable electricity generation using photovoltaic (PV) systems is accompanied by an increased awareness of the fault conditions developing during the operational lifetime of these systems. While the annual energy losses caused by faults in PV systems could reach up to 18.9% of their total capacity, emerging technologies and models are driving for greater efficiency to assure the reliability of a product under its actual application. The objectives of this dissertation consist of (1) reviewing the state of the art and practice of prognostics and health management for the Direct Current (DC) side of photovoltaic systems; (2) assessing the corrosion of the driven posts supporting PV structures in utility scale plants; and (3) assessing the probabilistic risk associated with the failure of polymeric materials that are used in tracker and fixed tilt systems.
As photovoltaic systems age under relatively harsh and changing environmental conditions, several potential fault conditions can develop during the operational lifetime including corrosion of supporting structures and failures of polymeric materials. The ability to accurately predict the remaining useful life of photovoltaic systems is critical for plants ‘continuous operation. This research contributes to the body of knowledge of PV systems reliability by: (1) developing a meta-model of the expected service life of mounting structures; (2) creating decision frameworks and tools to support practitioners in mitigating risks; (3) and supporting material selection for fielded and future photovoltaic systems. The newly developed frameworks were validated by a global solar company.
As photovoltaic systems age under relatively harsh and changing environmental conditions, several potential fault conditions can develop during the operational lifetime including corrosion of supporting structures and failures of polymeric materials. The ability to accurately predict the remaining useful life of photovoltaic systems is critical for plants ‘continuous operation. This research contributes to the body of knowledge of PV systems reliability by: (1) developing a meta-model of the expected service life of mounting structures; (2) creating decision frameworks and tools to support practitioners in mitigating risks; (3) and supporting material selection for fielded and future photovoltaic systems. The newly developed frameworks were validated by a global solar company.
ContributorsChokor, Abbas (Author) / El Asmar, Mounir (Thesis advisor) / Chong, Oswald (Committee member) / Ernzen, James (Committee member) / Arizona State University (Publisher)
Created2017
Description
Civil infrastructures undergo frequent spatial changes such as deviations between as-designed model and as-is condition, rigid body motions of the structure, and deformations of individual elements of the structure, etc. These spatial changes can occur during the design phase, the construction phase, or during the service life of a structure. Inability to accurately detect and analyze the impact of such changes may miss opportunities for early detections of pending structural integrity and stability issues. Commercial Building Information Modeling (BIM) tools could hardly track differences between as-designed and as-built conditions as they mainly focus on design changes and rely on project managers to manually update and analyze the impact of field changes on the project performance. Structural engineers collect detailed onsite data of a civil infrastructure to perform manual updates of the model for structural analysis, but such approach tends to become tedious and complicated while handling large civil infrastructures.
Previous studies started collecting detailed geometric data generated by 3D laser scanners for defect detection and geometric change analysis of structures. However, previous studies have not yet systematically examined methods for exploring the correlation between the detected geometric changes and their relation to the behaviors of the structural system. Manually checking every possible loading combination leading to the observed geometric change is tedious and sometimes error-prone. The work presented in this dissertation develops a spatial change analysis framework that utilizes spatiotemporal data collected using 3D laser scanning technology and the as-designed models of the structures to automatically detect, classify, and correlate the spatial changes of a structure. The change detection part of the developed framework is computationally efficient and can automatically detect spatial changes between as-designed model and as-built data or between two sets of as-built data collected using 3D laser scanning technology. Then a spatial change classification algorithm automatically classifies the detected spatial changes as global (rigid body motion) and local deformations (tension, compression). Finally, a change correlation technique utilizes a qualitative shape-based reasoning approach for identifying correlated deformations of structure elements connected at joints that contradicts the joint equilibrium. Those contradicting deformations can help to eliminate improbable loading combinations therefore guiding the loading path analysis of the structure.
Previous studies started collecting detailed geometric data generated by 3D laser scanners for defect detection and geometric change analysis of structures. However, previous studies have not yet systematically examined methods for exploring the correlation between the detected geometric changes and their relation to the behaviors of the structural system. Manually checking every possible loading combination leading to the observed geometric change is tedious and sometimes error-prone. The work presented in this dissertation develops a spatial change analysis framework that utilizes spatiotemporal data collected using 3D laser scanning technology and the as-designed models of the structures to automatically detect, classify, and correlate the spatial changes of a structure. The change detection part of the developed framework is computationally efficient and can automatically detect spatial changes between as-designed model and as-built data or between two sets of as-built data collected using 3D laser scanning technology. Then a spatial change classification algorithm automatically classifies the detected spatial changes as global (rigid body motion) and local deformations (tension, compression). Finally, a change correlation technique utilizes a qualitative shape-based reasoning approach for identifying correlated deformations of structure elements connected at joints that contradicts the joint equilibrium. Those contradicting deformations can help to eliminate improbable loading combinations therefore guiding the loading path analysis of the structure.
ContributorsKalasapudi, Vamsi Sai (Author) / Tang, Pingbo (Thesis advisor) / Chong, Oswald (Committee member) / Hjelmstad, Keith (Committee member) / Arizona State University (Publisher)
Created2017
Description
The performance of the Alpha Sprayed Polyurethane Foam (SPF) roofing system is perceived as not an economical option when compared to a 20-year modified bitumen roofing system. Today, the majority of roofs are being replaced, rather than newly installed. The coating manufacturer, Neogard, implemented the Alpha roofing program to identify the best contractors in the industry and to measure their roof performance. The Alpha roof system has shown consistent high performance on over 230 million square feet of surveyed roof. The author proposes to identify if the Alpha roof system is renewable, has proven performance that competes with the traditional modified roofing system, and is a more economical option by evaluating an Alpha roof system installation and the performance of a 29-year-old Alpha roof system. The Dallas Independent School District utilized the Alpha program for William Lipscomb Elementary School in 2016. Dallas Fort Worth Urethane installed the Alpha SPF roof system with high customer satisfaction ratings. This roofing installation showed the value of the Alpha roof system by saving over 20% on costs for the installation and will save approximately 69% of costs on the recoating of the roof in 20 years. The Casa View Elementary School roof system was installed with a Neogard Permathane roof system in 1987. This roof was hail tested with ten drops from 17 feet 9 inches of 1-3/4-inch steel ball (9 out of 10 passed) and four drops from 17 feet 9 inches with a 3-inch diameter steel ball (2 out of 4 passed). The analysis of the passing and failing core samples show that the thickness of the top and base Alpha SPF coating is one of the major differences in a roof passing or failing the FM-SH hail test. Over the 40-year service life, the main difference of purchasing a 61,000 square feet Alpha SPF roof versus modified bitumen roof are savings of approximately $1,067,500. Past hail tests on Alpha SPF roof systems show its cost effectiveness with high customer satisfaction (9.8 out of 10), an over 40-year service life after a $6.00/SF recoat and savings of over $1M for DISD.
ContributorsZulanas, Charles J., IV (Author) / Kashiwagi, Dean T. (Thesis advisor) / Kashiwagi, Jacob S (Thesis advisor) / Chong, Oswald (Committee member) / Arizona State University (Publisher)
Created2017
Description
Commercial buildings in the United States account for 19% of the total energy consumption annually. Commercial Building Energy Consumption Survey (CBECS), which serves as the benchmark for all the commercial buildings provides critical input for EnergyStar models. Smart energy management technologies, sensors, innovative demand response programs, and updated versions of certification programs elevate the opportunity to mitigate energy-related problems (blackouts and overproduction) and guides energy managers to optimize the consumption characteristics. With increasing advancements in technologies relying on the ‘Big Data,' codes and certification programs such as the American Society of Heating, Refrigerating and Air-Conditioning Engineers (ASHRAE), and the Leadership in Energy and Environmental Design (LEED) evaluates during the pre-construction phase. It is mostly carried out with the assumed quantitative and qualitative values calculated from energy models such as Energy Plus and E-quest. However, the energy consumption analysis through Knowledge Discovery in Databases (KDD) is not commonly used by energy managers to perform complete implementation, causing the need for better energy analytic framework.
The dissertation utilizes Interval Data (ID) and establishes three different frameworks to identify electricity losses, predict electricity consumption and detect anomalies using data mining, deep learning, and mathematical models. The process of energy analytics integrates with the computational science and contributes to several objectives which are to
1. Develop a framework to identify both technical and non-technical losses using clustering and semi-supervised learning techniques.
2. Develop an integrated framework to predict electricity consumption using wavelet based data transformation model and deep learning algorithms.
3. Develop a framework to detect anomalies using ensemble empirical mode decomposition and isolation forest algorithms.
With a thorough research background, the first phase details on performing data analytics on the demand-supply database to determine the potential energy loss reduction potentials. Data preprocessing and electricity prediction framework in the second phase integrates mathematical models and deep learning algorithms to accurately predict consumption. The third phase employs data decomposition model and data mining techniques to detect the anomalies of institutional buildings.
The dissertation utilizes Interval Data (ID) and establishes three different frameworks to identify electricity losses, predict electricity consumption and detect anomalies using data mining, deep learning, and mathematical models. The process of energy analytics integrates with the computational science and contributes to several objectives which are to
1. Develop a framework to identify both technical and non-technical losses using clustering and semi-supervised learning techniques.
2. Develop an integrated framework to predict electricity consumption using wavelet based data transformation model and deep learning algorithms.
3. Develop a framework to detect anomalies using ensemble empirical mode decomposition and isolation forest algorithms.
With a thorough research background, the first phase details on performing data analytics on the demand-supply database to determine the potential energy loss reduction potentials. Data preprocessing and electricity prediction framework in the second phase integrates mathematical models and deep learning algorithms to accurately predict consumption. The third phase employs data decomposition model and data mining techniques to detect the anomalies of institutional buildings.
ContributorsNaganathan, Hariharan (Author) / Chong, Oswald W (Thesis advisor) / Ariaratnam, Samuel T (Committee member) / Parrish, Kristen (Committee member) / Arizona State University (Publisher)
Created2017
Description
Trees serve as a natural umbrella to mitigate insolation absorbed by features of the urban environment, especially building structures and pavements. For a desert community, trees are a particularly valuable asset because they contribute to energy conservation efforts, improve home values, allow for cost savings, and promote enhanced health and well-being. The main obstacle in creating a sustainable urban community in a desert city with trees is the scarceness and cost of irrigation water. Thus, strategically located and arranged desert trees with the fewest tree numbers possible potentially translate into significant energy, water and long-term cost savings as well as conservation, economic, and health benefits. The objective of this dissertation is to achieve this research goal with integrated methods from both theoretical and empirical perspectives.
This dissertation includes three main parts. The first part proposes a spatial optimization method to optimize the tree locations with the objective to maximize shade coverage on building facades and open structures and minimize shade coverage on building rooftops in a 3-dimensional environment. Second, an outdoor urban physical scale model with field measurement is presented to understand the cooling and locational benefits of tree shade. The third part implements a microclimate numerical simulation model to analyze how the specific tree locations and arrangements influence outdoor microclimates and improve human thermal comfort. These three parts of the dissertation attempt to fill the research gap of how to strategically locate trees at the building to neighborhood scale, and quantifying the impact of such arrangements.
Results highlight the significance of arranging residential shade trees across different geographical scales. In both the building and neighborhood scales, research results recommend that trees should be arranged in the central part of the building south front yard. More cooling benefits are provided to the building structures and outdoor microclimates with a cluster tree arrangement without canopy overlap; however, if residents are interested in creating a better outdoor thermal environment, open space between trees is needed to enhance the wind environment for better human thermal comfort. Considering the rapid urbanization process, limited water resources supply, and the severe heat stress in the urban areas, judicious design and planning of trees is of increasing importance for improving the life quality and sustaining the urban environment.
ContributorsZhao, Qunshan (Author) / Wentz, Elizabeth (Thesis advisor) / Sailor, David (Committee member) / Wang, Zhi-Hua (Committee member) / Arizona State University (Publisher)
Created2017
Description
Immunosignature is a technology that retrieves information from the immune system. The technology is based on microarrays with peptides chosen from random sequence space. My thesis focuses on improving the Immunosignature platform and using Immunosignatures to improve diagnosis for diseases. I first contributed to the optimization of the immunosignature platform by introducing scoring metrics to select optimal parameters, considering performance as well as practicality. Next, I primarily worked on identifying a signature shared across various pathogens that can distinguish them from the healthy population. I further retrieved consensus epitopes from the disease common signature and proposed that most pathogens could share the signature by studying the enrichment of the common signature in the pathogen proteomes. Following this, I worked on studying cancer samples from different stages and correlated the immune response with whether the epitope presented by tumor is similar to the pathogen proteome. An effective immune response is defined as an antibody titer increasing followed by decrease, suggesting elimination of the epitope. I found that an effective immune response usually correlates with epitopes that are more similar to pathogens. This suggests that the immune system might occupy a limited space and can be effective against only certain epitopes that have similarity with pathogens. I then participated in the attempt to solve the antibiotic resistance problem by developing a classification algorithm that can distinguish bacterial versus viral infection. This algorithm outperforms other currently available classification methods. Finally, I worked on the concept of deriving a single number to represent all the data on the immunosignature platform. This is in resemblance to the concept of temperature, which is an approximate measurement of whether an individual is healthy. The measure of Immune Entropy was found to work best as a single measurement to describe the immune system information derived from the immunosignature. Entropy is relatively invariant in healthy population, but shows significant differences when comparing healthy donors with patients either infected with a pathogen or have cancer.
ContributorsWang, Lu (Author) / Johnston, Stephen (Thesis advisor) / Stafford, Phillip (Committee member) / Buetow, Kenneth (Committee member) / McFadden, Grant (Committee member) / Arizona State University (Publisher)
Created2018
Description
Immunotherapy has been revitalized with the advent of immune checkpoint blockade
treatments, and neo-antigens are the targets of immune system in cancer patients who
respond to the treatments. The cancer vaccine field is focused on using neo-antigens from
unique point mutations of genomic sequence in the cancer patient for making
personalized cancer vaccines. However, we choose a different path to find frameshift
neo-antigens at the mRNA level and develop broadly effective cancer vaccines based on
frameshift antigens.
In this dissertation, I have summarized and characterized all the potential frameshift
antigens from microsatellite regions in human, dog and mouse. A list of frameshift
antigens was validated by PCR in tumor samples and the mutation rate was calculated for
one candidate – SEC62. I develop a method to screen the antibody response against
frameshift antigens in human and dog cancer patients by using frameshift peptide arrays.
Frameshift antigens selected by positive antibody response in cancer patients or by MHC
predictions show protection in different mouse tumor models. A dog version of the
cancer vaccine based on frameshift antigens was developed and tested in a small safety
trial. The results demonstrate that the vaccine is safe and it can induce strong B and T cell
immune responses. Further, I built the human exon junction frameshift database which
includes all possible frameshift antigens from mis-splicing events in exon junctions, and I
develop a method to find potential frameshift antigens from large cancer
immunosignature dataset with these databases. In addition, I test the idea of ‘early cancer
diagnosis, early treatment’ in a transgenic mouse cancer model. The results show that
ii
early treatment gives significantly better protection than late treatment and the correct
time point for treatment is crucial to give the best clinical benefit. A model for early
treatment is developed with these results.
Frameshift neo-antigens from microsatellite regions and mis-splicing events are
abundant at mRNA level and they are better antigens than neo-antigens from point
mutations in the genomic sequences of cancer patients in terms of high immunogenicity,
low probability to cause autoimmune diseases and low cost to develop a broadly effective
vaccine. This dissertation demonstrates the feasibility of using frameshift antigens for
cancer vaccine development.
treatments, and neo-antigens are the targets of immune system in cancer patients who
respond to the treatments. The cancer vaccine field is focused on using neo-antigens from
unique point mutations of genomic sequence in the cancer patient for making
personalized cancer vaccines. However, we choose a different path to find frameshift
neo-antigens at the mRNA level and develop broadly effective cancer vaccines based on
frameshift antigens.
In this dissertation, I have summarized and characterized all the potential frameshift
antigens from microsatellite regions in human, dog and mouse. A list of frameshift
antigens was validated by PCR in tumor samples and the mutation rate was calculated for
one candidate – SEC62. I develop a method to screen the antibody response against
frameshift antigens in human and dog cancer patients by using frameshift peptide arrays.
Frameshift antigens selected by positive antibody response in cancer patients or by MHC
predictions show protection in different mouse tumor models. A dog version of the
cancer vaccine based on frameshift antigens was developed and tested in a small safety
trial. The results demonstrate that the vaccine is safe and it can induce strong B and T cell
immune responses. Further, I built the human exon junction frameshift database which
includes all possible frameshift antigens from mis-splicing events in exon junctions, and I
develop a method to find potential frameshift antigens from large cancer
immunosignature dataset with these databases. In addition, I test the idea of ‘early cancer
diagnosis, early treatment’ in a transgenic mouse cancer model. The results show that
ii
early treatment gives significantly better protection than late treatment and the correct
time point for treatment is crucial to give the best clinical benefit. A model for early
treatment is developed with these results.
Frameshift neo-antigens from microsatellite regions and mis-splicing events are
abundant at mRNA level and they are better antigens than neo-antigens from point
mutations in the genomic sequences of cancer patients in terms of high immunogenicity,
low probability to cause autoimmune diseases and low cost to develop a broadly effective
vaccine. This dissertation demonstrates the feasibility of using frameshift antigens for
cancer vaccine development.
ContributorsZhang, Jian (Author) / Johnston, Stephen Albert (Thesis advisor) / Chang, Yung (Committee member) / Stafford, Phillip (Committee member) / Chen, Qiang (Committee member) / Arizona State University (Publisher)
Created2018
Description
Regulatory agencies, such as the Occupational Safety and Health Administration (OSHA), and the National Institute of Occupational Safety and Health (NIOSH), recognize that decisions regarding occupational health are often economically driven, with worker health only a secondary concern (Ruttenberg, 2014). To investigate the four National Occupational Research Agenda (NORA) long-standing health concerns—welding fumes, crystalline silica, noise, and musculoskeletal disorders—a mixed methods research is conducted. Fourfold structuration, a holistic communication process with roots in indigenous/ancient knowledge, is used to organize data and facilitate making tangible relationships of health to productivity and profits that are abstract and often stated by industries, such as construction, as difficult to quantify. From both construction trade worker and occupational health and safety expert interviews data/codes are developed. For the qualitative method, the codes are organized into a constructivist grounded theory depicting the construction industry with regard to its foundation – profits. A theoretical exercise translating the qualitative codes into potential productivity losses is presented as a way for quantifying the abstract relationships of health to productivity. For the quantitative study, the data/codes are used to develop a comprehensive list of practices, barriers to, and catalysts for addressing health in construction. A significant quantitative finding is that occupational health and safety (OSH) experts are not traditionally involved at the highest levels of the OSHA Hierarchy of Controls, where the greatest opportunity to prevent exposure to health hazards is possible. Organized via a holistic framework, this research emphasizes our primary responsibility to each other as highlighted in recent NIOSH worker health agendas.
ContributorsTello, Linda Marguerite (Author) / Grau, David (Thesis advisor) / Koro-Ljungberg, Mirka (Committee member) / Hanemann, Michael (Committee member) / Chong, Oswald (Committee member) / Arizona State University (Publisher)
Created2017