Matching Items (587)
Description
Genomic structural variation (SV) is defined as gross alterations in the genome broadly classified as insertions/duplications, deletions inversions and translocations. DNA sequencing ushered structural variant discovery beyond laboratory detection techniques to high resolution informatics approaches. Bioinformatics tools for computational discovery of SVs however are still missing variants in the complex cancer genome. This study aimed to define genomic context leading to tool failure and design novel algorithm addressing this context. Methods: The study tested the widely held but unproven hypothesis that tools fail to detect variants which lie in repeat regions. Publicly available 1000-Genomes dataset with experimentally validated variants was tested with SVDetect-tool for presence of true positives (TP) SVs versus false negative (FN) SVs, expecting that FNs would be overrepresented in repeat regions. Further, the novel algorithm designed to informatically capture the biological etiology of translocations (non-allelic homologous recombination and 3&ndashD; placement of chromosomes in cells –context) was tested using simulated dataset. Translocations were created in known translocation hotspots and the novel&ndashalgorithm; tool compared with SVDetect and BreakDancer. Results: 53% of false negative (FN) deletions were within repeat structure compared to 81% true positive (TP) deletions. Similarly, 33% FN insertions versus 42% TP, 26% FN duplication versus 57% TP and 54% FN novel sequences versus 62% TP were within repeats. Repeat structure was not driving the tool's inability to detect variants and could not be used as context. The novel algorithm with a redefined context, when tested against SVDetect and BreakDancer was able to detect 10/10 simulated translocations with 30X coverage dataset and 100% allele frequency, while SVDetect captured 4/10 and BreakDancer detected 6/10. For 15X coverage dataset with 100% allele frequency, novel algorithm was able to detect all ten translocations albeit with fewer reads supporting the same. BreakDancer detected 4/10 and SVDetect detected 2/10 Conclusion: This study showed that presence of repetitive elements in general within a structural variant did not influence the tool's ability to capture it. This context-based algorithm proved better than current tools even with half the genome coverage than accepted protocol and provides an important first step for novel translocation discovery in cancer genome.
ContributorsShetty, Sheetal (Author) / Dinu, Valentin (Thesis advisor) / Bussey, Kimberly (Committee member) / Scotch, Matthew (Committee member) / Wallstrom, Garrick (Committee member) / Arizona State University (Publisher)
Created2014
Description
The processes of a human somatic cell are very complex with various genetic mechanisms governing its fate. Such cells undergo various genetic mutations, which translate to the genetic aberrations that we see in cancer. There are more than 100 types of cancer, each having many more subtypes with aberrations being unique to each. In the past two decades, the widespread application of high-throughput genomic technologies, such as micro-arrays and next-generation sequencing, has led to the revelation of many such aberrations. Known types and subtypes can be readily identified using gene-expression profiling and more importantly, high-throughput genomic datasets have helped identify novel sub-types with distinct signatures. Recent studies showing usage of gene-expression profiling in clinical decision making in breast cancer patients underscore the utility of high-throughput datasets. Beyond prognosis, understanding the underlying cellular processes is essential for effective cancer treatment. Various high-throughput techniques are now available to look at a particular aspect of a genetic mechanism in cancer tissue. To look at these mechanisms individually is akin to looking at a broken watch; taking apart each of its parts, looking at them individually and finally making a list of all the faulty ones. Integrative approaches are needed to transform one-dimensional cancer signatures into multi-dimensional interaction and regulatory networks, consequently bettering our understanding of cellular processes in cancer. Here, I attempt to (i) address ways to effectively identify high quality variants when multiple assays on the same sample samples are available through two novel tools, snpSniffer and NGSPE; (ii) glean new biological insight into multiple myeloma through two novel integrative analysis approaches making use of disparate high-throughput datasets. While these methods focus on multiple myeloma datasets, the informatics approaches are applicable to all cancer datasets and will thus help advance cancer genomics.
ContributorsYellapantula, Venkata (Author) / Dinu, Valentin (Thesis advisor) / Scotch, Matthew (Committee member) / Wallstrom, Garrick (Committee member) / Keats, Jonathan (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
No two cancers are alike. Cancer is a dynamic and heterogeneous disease, such heterogeneity arise among patients with the same cancer type, among cancer cells within the same individual’s tumor and even among cells within the same sub-clone over time. The recent application of next-generation sequencing and precision medicine techniques is the driving force to uncover the complexity of cancer and the best clinical practice. The core concept of precision medicine is to move away from crowd-based, best-for-most treatment and take individual variability into account when optimizing the prevention and treatment strategies. Next-generation sequencing is the method to sift through the entire 3 billion letters of each patient’s DNA genetic code in a massively parallel fashion.
The deluge of next-generation sequencing data nowadays has shifted the bottleneck of cancer research from multiple “-omics” data collection to integrative analysis and data interpretation. In this dissertation, I attempt to address two distinct, but dependent, challenges. The first is to design specific computational algorithms and tools that can process and extract useful information from the raw data in an efficient, robust, and reproducible manner. The second challenge is to develop high-level computational methods and data frameworks for integrating and interpreting these data. Specifically, Chapter 2 presents a tool called Snipea (SNv Integration, Prioritization, Ensemble, and Annotation) to further identify, prioritize and annotate somatic SNVs (Single Nucleotide Variant) called from multiple variant callers. Chapter 3 describes a novel alignment-based algorithm to accurately and losslessly classify sequencing reads from xenograft models. Chapter 4 describes a direct and biologically motivated framework and associated methods for identification of putative aberrations causing survival difference in GBM patients by integrating whole-genome sequencing, exome sequencing, RNA-Sequencing, methylation array and clinical data. Lastly, chapter 5 explores longitudinal and intratumor heterogeneity studies to reveal the temporal and spatial context of tumor evolution. The long-term goal is to help patients with cancer, particularly those who are in front of us today. Genome-based analysis of the patient tumor can identify genomic alterations unique to each patient’s tumor that are candidate therapeutic targets to decrease therapy resistance and improve clinical outcome.
The deluge of next-generation sequencing data nowadays has shifted the bottleneck of cancer research from multiple “-omics” data collection to integrative analysis and data interpretation. In this dissertation, I attempt to address two distinct, but dependent, challenges. The first is to design specific computational algorithms and tools that can process and extract useful information from the raw data in an efficient, robust, and reproducible manner. The second challenge is to develop high-level computational methods and data frameworks for integrating and interpreting these data. Specifically, Chapter 2 presents a tool called Snipea (SNv Integration, Prioritization, Ensemble, and Annotation) to further identify, prioritize and annotate somatic SNVs (Single Nucleotide Variant) called from multiple variant callers. Chapter 3 describes a novel alignment-based algorithm to accurately and losslessly classify sequencing reads from xenograft models. Chapter 4 describes a direct and biologically motivated framework and associated methods for identification of putative aberrations causing survival difference in GBM patients by integrating whole-genome sequencing, exome sequencing, RNA-Sequencing, methylation array and clinical data. Lastly, chapter 5 explores longitudinal and intratumor heterogeneity studies to reveal the temporal and spatial context of tumor evolution. The long-term goal is to help patients with cancer, particularly those who are in front of us today. Genome-based analysis of the patient tumor can identify genomic alterations unique to each patient’s tumor that are candidate therapeutic targets to decrease therapy resistance and improve clinical outcome.
ContributorsPeng, Sen (Author) / Dinu, Valentin (Thesis advisor) / Scotch, Matthew (Committee member) / Wallstrom, Garrick (Committee member) / Arizona State University (Publisher)
Created2015
Description
Given the importance of buildings as major consumers of resources worldwide, several organizations are working avidly to ensure the negative impacts of buildings are minimized. The U.S. Green Building Council's (USGBC) Leadership in Energy and Environmental Design (LEED) rating system is one such effort to recognize buildings that are designed to achieve a superior performance in several areas including energy consumption and indoor environmental quality (IEQ). The primary objectives of this study are to investigate the performance of LEED certified facilities in terms of energy consumption and occupant satisfaction with IEQ, and introduce a framework to assess the performance of LEED certified buildings.
This thesis attempts to achieve the research objectives by examining the LEED certified buildings on the Arizona State University (ASU) campus in Tempe, AZ, from two complementary perspectives: the Macro-level and the Micro-level. Heating, cooling, and electricity data were collected from the LEED-certified buildings on campus, and their energy use intensity was calculated in order to investigate the buildings' actual energy performance. Additionally, IEQ occupant satisfaction surveys were used to investigate users' satisfaction with the space layout, space furniture, thermal comfort, indoor air quality, lighting level, acoustic quality, water efficiency, cleanliness and maintenance of the facilities they occupy.
From a Macro-level perspective, the results suggest ASU LEED buildings consume less energy than regional counterparts, and exhibit higher occupant satisfaction than national counterparts. The occupant satisfaction results are in line with the literature on LEED buildings, whereas the energy results contribute to the inconclusive body of knowledge on energy performance improvements linked to LEED certification. From a Micro-level perspective, data analysis suggest an inconsistency between the LEED points earned for the Energy & Atmosphere and IEQ categories, on one hand, and the respective levels of energy consumption and occupant satisfaction on the other hand. Accordingly, this study showcases the variation in the performance results when approached from different perspectives. This contribution highlights the need to consider the Macro-level and Micro-level assessments in tandem, and assess LEED building performance from these two distinct but complementary perspectives in order to develop a more comprehensive understanding of the actual building performance.
This thesis attempts to achieve the research objectives by examining the LEED certified buildings on the Arizona State University (ASU) campus in Tempe, AZ, from two complementary perspectives: the Macro-level and the Micro-level. Heating, cooling, and electricity data were collected from the LEED-certified buildings on campus, and their energy use intensity was calculated in order to investigate the buildings' actual energy performance. Additionally, IEQ occupant satisfaction surveys were used to investigate users' satisfaction with the space layout, space furniture, thermal comfort, indoor air quality, lighting level, acoustic quality, water efficiency, cleanliness and maintenance of the facilities they occupy.
From a Macro-level perspective, the results suggest ASU LEED buildings consume less energy than regional counterparts, and exhibit higher occupant satisfaction than national counterparts. The occupant satisfaction results are in line with the literature on LEED buildings, whereas the energy results contribute to the inconclusive body of knowledge on energy performance improvements linked to LEED certification. From a Micro-level perspective, data analysis suggest an inconsistency between the LEED points earned for the Energy & Atmosphere and IEQ categories, on one hand, and the respective levels of energy consumption and occupant satisfaction on the other hand. Accordingly, this study showcases the variation in the performance results when approached from different perspectives. This contribution highlights the need to consider the Macro-level and Micro-level assessments in tandem, and assess LEED building performance from these two distinct but complementary perspectives in order to develop a more comprehensive understanding of the actual building performance.
ContributorsChokor, Abbas (Author) / El Asmar, Mounir (Thesis advisor) / Chong, Oswald (Committee member) / Parrish, Kristen (Committee member) / Arizona State University (Publisher)
Created2015
Description
Today, we use resources faster than they can be replaced. Construction consumes more resources than any other industry and has one of the largest waste streams. Resource consumption and waste generation are expected to grow as the global population increases. The circular economy (CE) is based on the concept of a closed-loop cycle (CLC) and proposes a solution that, in theory, can eliminate the environmental impacts caused by construction and demolition (C&D) waste and increase the efficiency of resources’ use. In a CLC, building materials are reused, remanufactured, recycled, and reintegrated into other buildings (or into other sectors) without creating any waste.
Designing out waste is the core principle of the CE. Design for disassembly or design for deconstruction (DfD) is the practice of planning the future deconstruction of a building and the reuse of its materials. Concepts like DfD, CE, and product-service systems (PSS) can work together to promote CLC in the built environment. PSS are business models based on stewardship instead of ownership. CE combines DfD, PSS, materials’ durability, and materials’ reuse in multiple life cycles to promote a low-carbon, regenerative economy. CE prioritizes reuse over recycling. Dealing with resource scarcity demands us to think beyond the incremental changes from recycling waste; it demands an urgent, systemic, and radical change in the way we design, build, and procure construction materials.
This dissertation aims to answer three research questions: 1) How can researchers estimate the environmental benefits of reusing building components, 2) What variables are susceptible to affect the environmental impact assessment of reuse, and 3) What are the barriers and opportunities for DfD and materials’ reuse in the current design practice in the United States.
The first part of this study investigated how different life cycle assessment (LCA) methods (i.e., hybrid LCA and process-based LCA), assumptions (e.g., reuse rates, transportation distances, number of reuses), and LCA timelines can affect the results of a closed-loop LCA. The second part of this study built on interviews with architects in the United States to understand why DfD is not part of the current design practice in the country.
Designing out waste is the core principle of the CE. Design for disassembly or design for deconstruction (DfD) is the practice of planning the future deconstruction of a building and the reuse of its materials. Concepts like DfD, CE, and product-service systems (PSS) can work together to promote CLC in the built environment. PSS are business models based on stewardship instead of ownership. CE combines DfD, PSS, materials’ durability, and materials’ reuse in multiple life cycles to promote a low-carbon, regenerative economy. CE prioritizes reuse over recycling. Dealing with resource scarcity demands us to think beyond the incremental changes from recycling waste; it demands an urgent, systemic, and radical change in the way we design, build, and procure construction materials.
This dissertation aims to answer three research questions: 1) How can researchers estimate the environmental benefits of reusing building components, 2) What variables are susceptible to affect the environmental impact assessment of reuse, and 3) What are the barriers and opportunities for DfD and materials’ reuse in the current design practice in the United States.
The first part of this study investigated how different life cycle assessment (LCA) methods (i.e., hybrid LCA and process-based LCA), assumptions (e.g., reuse rates, transportation distances, number of reuses), and LCA timelines can affect the results of a closed-loop LCA. The second part of this study built on interviews with architects in the United States to understand why DfD is not part of the current design practice in the country.
ContributorsCruz Rios, Fernanda (Author) / Grau, David (Committee member) / Chong, Oswald (Committee member) / Parrish, Kristen (Committee member) / Arizona State University (Publisher)
Created2018
Description
The United States building sector was the most significant carbon emission contributor (over 40%). The United States government is trying to decrease carbon emissions by enacting policies, but emissions increased by approximately 7 percent in the U.S. between 1990 and 2013. To reduce emissions, investigating the factors affecting carbon emissions should be a priority. Therefore, in this dissertation, this research examine the relationship between carbon emissions and the factors affecting them from macro and micro perspectives. From a macroscopic perspective, the relationship between carbon dioxide, energy resource consumption, energy prices, GDP (gross domestic product), waste generation, and recycling waste generation in the building and waste sectors has been verified. From a microscopic perspective, the impact of non-permanent electric appliances and stationary and non-stationary occupancy has been investigated. To verify the relationships, various kinds of statistical and data mining techniques were applied, such as the Granger causality test, linear and logarithmic correlation, and regression method. The results show that natural gas and electricity prices are higher than others, as coal impacts their consumption, and electricity and coal consumption were found to cause significant carbon emissions. Also, waste generation and recycling significantly increase and decrease emissions from the waste sector, respectively. Moreover, non-permanent appliances such as desktop computers and monitors consume a lot of electricity, and significant energy saving potential has been shown. Lastly, a linear relationship exists between buildings’ electricity use and total occupancy, but no significant relationship exists between occupancy and thermal loads, such as cooling and heating loads. These findings will potentially provide policymakers with a better understanding of and insights into carbon emission manipulation in the building sector.
ContributorsLee, Seungtaek (Author) / Chong, Oswald (Thesis advisor) / Sullivan, Kenneth (Committee member) / Tang, Pingbo (Committee member) / Arizona State University (Publisher)
Created2018
Description
High childhood obesity rates have resulted in many interventions to attempt to lower these rates. Interventions such as day camps, residential camps, therapy-based interventions and family-based interventions lead to changes in weight and self-esteem but family-based intervention leads to the longest-term success for children ages nine to 17. Analysis of the interventions was measured using tools such as BMI, BMI-percentiles, and weight. Psychological measures such as self-esteem, happiness, and quality of life analysis was preferred, however were not measured in all studies. While most interventions resulted in weight loss and increased self-esteem, results were often not long-term. Studies provided evidence that family-based therapy has potential to last long-term, however there is a lack of research. To determine the most effective childhood nutrition intervention research must conduct follow-ups for many years after the initial intervention to ensure they provide long-term results.
ContributorsAnderson, Megan Lee (Author) / McCoy, Maureen (Thesis director) / Kniskern, Megan (Committee member) / College of Health Solutions (Contributor) / Barrett, The Honors College (Contributor)
Created2020-05
Description
This paper describes the research done to quantify the relationship between external air temperature and energy consumption and internal air temperature and energy consumption. The study was conducted on a LEED Gold certified building, College Avenue Commons, located on Arizona State University's Tempe campus. It includes information on the background of previous studies in the area, some that agree with the research hypotheses and some that take a different path. Real-time data was collected hourly for energy consumption and external air temperature. Intermittent internal air temperature was collected by undergraduate researcher, Charles Banke. Regression analysis was used to prove two research hypotheses. The authors found no correlation between external air temperature and energy consumption, nor did they find a relationship between internal air temperature and energy consumption. This paper also includes recommendations for future work to improve the study.
ContributorsBanke, Charles Michael (Author) / Chong, Oswald (Thesis director) / Parrish, Kristen (Committee member) / Mechanical and Aerospace Engineering Program (Contributor) / Barrett, The Honors College (Contributor)
Created2018-05
Description
Building construction, design and maintenance is a sector of engineering where improved efficiency will have immense impacts on resource consumption and environmental health. This research closely examines the Leadership in Environment and Energy Design (LEED) rating system and the International Green Construction Code (IgCC). The IgCC is a model code, written with the same structure as many building codes. It is a standard that can be enforced if a city's government decides to adopt it. When IgCC is enforced, the buildings either meet all of the requirements set forth in the document or it fails to meet the code standards. The LEED Rating System, on the other hand, is not a building code. LEED certified buildings are built according to the standards of their local jurisdiction and in addition to that, building owners can chose to pursue a LEED certification. This is a rating system that awards points based on the sustainable measures achieved by a building. A comparison of these green building systems highlights their accomplishments in terms of reduced electricity usage, usage of low-impact materials, indoor environmental quality and other innovative features. It was determined that in general IgCC is more holistic, stringent approach to green building. At the same time the LEED rating system a wider variety of green building options. In addition, building data from LEED certified buildings was complied and analyzed to understand important trends. Both of these methods are progressing towards low-impact, efficient infrastructure and a side-by-side comparison, as done in this research, shed light on the strengths and weaknesses of each method, allowing for future improvements.
ContributorsCampbell, Kaleigh Ruth (Author) / Chong, Oswald (Thesis director) / Parrish, Kristen (Committee member) / Civil, Environmental and Sustainable Engineering Programs (Contributor) / Barrett, The Honors College (Contributor)
Created2016-05