Matching Items (121)
171888-Thumbnail Image.png
Description
Computational models have long been used to describe and predict the outcome of complex immunological processes. The dissertation work described here centers on the construction of multiscale computational immunology models that derives biological insights at the population, systems, and atomistic levels. First, SARS-CoV-2 mortality is investigated through the lens of

Computational models have long been used to describe and predict the outcome of complex immunological processes. The dissertation work described here centers on the construction of multiscale computational immunology models that derives biological insights at the population, systems, and atomistic levels. First, SARS-CoV-2 mortality is investigated through the lens of the predicted robustness of CD8+ T cell responses in 23 different populations. The robustness of CD8+ T cell responses in a given population was modeled by predicting the efficiency of endemic MHC-I protein variants to present peptides derived from SARS-CoV-2 proteins to circulating T cells. To accomplish this task, an algorithm, called EnsembleMHC, was developed to predict viral peptides with a high probability of being recognized by CD T cells. It was discovered that there was significant variation in the efficiency of different MHC-I protein variants to present SARS-CoV-2 derived peptides, and countries enriched with variants with high presentation efficiency had significantly lower mortality rates. Second, a biophysics-based MHC-I peptide prediction algorithm was developed. The MHC-I protein is the most polymorphic protein in the human genome with polymorphisms in the peptide binding causing striking changes in the amino acid compositions, or binding motifs, of peptide species capable of stable binding. A deep learning model, coined HLA-Inception, was trained to predict peptide binding using only biophysical properties, namely electrostatic potential. HLA-Inception was shown to be extremely accurate and efficient at predicting peptide binding motifs and was used to determine the peptide binding motifs of 5,821 MHC-I protein variants. Finally, the impact of stalk glycosylations on NL63 protein dynamics was investigated. Previous data has shown that coronavirus crown glycans play an important role in immune evasion and receptor binding, however, little is known about the role of the stalk glycans. Through the integration of computational biology, experimental data, and physics-based simulations, the stalk glycans were shown to heavily influence the bending angle of spike protein, with a particular emphasis on the glycan at position 1242. Further investigation revealed that removal of the N1242 glycan significantly reduced infectivity, highlighting a new potential therapeutic target. Overall, these investigations and associated innovations in integrative modeling.
ContributorsWilson, Eric Andrew (Author) / Anderson, Karen (Thesis advisor) / Singharoy, Abhishek (Thesis advisor) / Woodbury, Neal (Committee member) / Sulc, Petr (Committee member) / Arizona State University (Publisher)
Created2022
189328-Thumbnail Image.png
Description
Evolution is a key feature of undergraduate biology education: the AmericanAssociation for the Advancement of Science (AAAS) has identified evolution as one of the five core concepts of biology, and it is relevant to a wide array of biology-related careers. If biology instructors want students to use evolution to address scientific challenges post-graduation,

Evolution is a key feature of undergraduate biology education: the AmericanAssociation for the Advancement of Science (AAAS) has identified evolution as one of the five core concepts of biology, and it is relevant to a wide array of biology-related careers. If biology instructors want students to use evolution to address scientific challenges post-graduation, students need to be able to apply evolutionary principles to real-life situations, and accept that the theory of evolution is the best scientific explanation for the unity and diversity of life on Earth. In order to help students progress on both fronts, biology education researchers need surveys that measure evolution acceptance and assessments that measure students’ ability to apply evolutionary concepts. This dissertation improves the measurement of student understanding and acceptance of evolution by (1) developing a novel Evolutionary Medicine Assessment that measures students’ ability to apply the core principles of Evolutionary Medicine to a variety of health-related scenarios, (2) reevaluating existing measures of student evolution acceptance by using student interviews to assess response process validity, and (3) correcting the validity issues identified on the most widely-used measure of evolution acceptance - the Measure of Acceptance of the Theory of Evolution (MATE) - by developing and validating a revised version of this survey: the MATE 2.0.
ContributorsMisheva, Anastasia Taya (Author) / Brownell, Sara (Thesis advisor) / Barnes, Elizabeth (Committee member) / Collins, James (Committee member) / Cooper, Katelyn (Committee member) / Sterner, Beckett (Committee member) / Arizona State University (Publisher)
Created2023
171936-Thumbnail Image.png
Description
Although Saudi Arabia is moving towards a sustainable future, Existing residential buildings in the country are extremely unsustainable. Therefore, there is a necessity for greening the existing residential building. Mostadam green rating systems was developed by the Saudi ministry of housing in 2019 to address the long-term sustainability vision in

Although Saudi Arabia is moving towards a sustainable future, Existing residential buildings in the country are extremely unsustainable. Therefore, there is a necessity for greening the existing residential building. Mostadam green rating systems was developed by the Saudi ministry of housing in 2019 to address the long-term sustainability vision in residential buildings in the country. By setting Mostadam requirements as an objective of the retrofit process, it will ensure that the building achieve sustainability. However, Mostadam is new and there is a lack of knowledge of implementing its requirements on existing buildings. The aim of this research is to develop a framework to green existing residential buildings in Saudi Arabia to achieve Mostadam energy and water minimum requirements. The framework was developed based on an extensive keyword-based search and an analysis of 92 relevant research. The process starts with assessing the building against the minimum requirements of energy and water of Mostadam. After that, optimization phase is conducted. Building information modelling is used in the optimization phase. Energy and water efficiency optimization measures are identified from the analysed literature. Revit is used in the base model authoring and Green building studio cloud is used to simulate the energy and water efficiency measures. Then, payback period is calculated for all the efficiency measured to assess the decision making. A case study of a villa in Riyadh, Saudi Arabia is provided. result shows that the implemented efficiency measures led to an increment of 37.5% in annual energy savings and 26.1% in the annual water savings. Results shows that the application of the proposed framework supports evaluating energy and water efficiency measures to implement it on the buildings to achieve Mostadam minimum energy and water requirements. Recommendations were made for future work to bridge the knowledge gap.
ContributorsMohamed, Sara Murad (Author) / Sullivan, Kenneth (Thesis advisor) / Chong, Oswald (Committee member) / Hurtado, Kristen (Committee member) / Arizona State University (Publisher)
Created2022
168450-Thumbnail Image.png
Description
As the construction industry in Saudi Arabia was on its way to thriving again. Their growth was due to the unprecedented volume of planned projects such as large-scale and unique projects. Suddenly, the world was faced with one of the most disrupting events in the last century which had a

As the construction industry in Saudi Arabia was on its way to thriving again. Their growth was due to the unprecedented volume of planned projects such as large-scale and unique projects. Suddenly, the world was faced with one of the most disrupting events in the last century which had a devastating impact on the construction industry specifically. This paper explores mainly the impact of the COVID-19 pandemic on construction projects in Saudi Arabia. Particularly, this paper explores how the pandemic and its related events contributed to the projects' schedule disturbances. This is because most of the projects rely on manpower and supply chains which were heavily disrupted due to the protective measures. For that, a study was conducted to evaluate the impact on the construction projects in Saudi Arabia, to what extent the schedule projects were affected, and what were the main reasons for the schedule delays. The research relied on a field survey and schedule analysis for 12 projects which resulted in identifying several causes of delays and the delayed durations that the projects in Saudi Arabia were facing. This research allows those in construction fields to identify the main causes of delays in order to avoid or minimize the impact of these issues on future projects.
ContributorsObeid, Muhammad Hasan Hani (Author) / Ariaratnam, Samuel (Thesis advisor) / El Asmar, Mounir (Committee member) / Chong, Oswald (Committee member) / Arizona State University (Publisher)
Created2021
166198-Thumbnail Image.png
Description
People with disabilities are underrepresented in the Science, Technology, Engineering, and Math (STEM) workforce (NSF, 2016). One way to increase representation of people with disabilities in STEM fields is by supporting students with disabilities (SWDs) at the undergraduate level. In undergraduate education in the United States, SWDs represent approximately 19%

People with disabilities are underrepresented in the Science, Technology, Engineering, and Math (STEM) workforce (NSF, 2016). One way to increase representation of people with disabilities in STEM fields is by supporting students with disabilities (SWDs) at the undergraduate level. In undergraduate education in the United States, SWDs represent approximately 19% of the undergraduate community (U.S. Census Bureau, 2021). However, SWDs have lower graduation and retention rates. This is particularly true for STEM majors, where SWDs make up about 9% of the STEM community in higher education. The AAC&U has defined a list of High-Impact Practices (HIPs), which are active learning practices and experiences that encourage deep learning by promoting student engagement, and could ultimately support student retention (AAC&U). To date, student-centered disability research has not explored the extent to which SWDs participate in HIPs. We hypothesized that SWDs are less likely than students without disabilities to be involved in HIPs and that students who identify as having severe disabilities would participate in HIPs at lower rates. In this study, we conducted a national survey to examine involvement in HIPs for students with disabilities in STEM. We found that disability status significantly affects the probability of participation in undergraduate research, but is not a significant factor for participation in most other HIPs. We also found that self-reported severity of disability did not significantly impact participation in HIPs, though we observed trends that students reporting higher severity generally reported lower participation in HIPs. Our open-ended responses did indicate that SWDs still faced barriers to participation in HIPs.
ContributorsPais, Danielle (Author) / Brownell, Sara (Thesis director) / Cooper, Katelyn (Committee member) / Barrett, The Honors College (Contributor) / Historical, Philosophical & Religious Studies, Sch (Contributor) / School of Life Sciences (Contributor) / School of International Letters and Cultures (Contributor)
Created2022-05
165130-Thumbnail Image.png
Description

There is increasing interest in understanding how active learning affects students’ mental health as science courses transition from traditional lecture to active learning. Prior research has found that active learning can both alleviate and exacerbate undergraduate mental health problems. Existing studies have only examined the relationship between active learning and

There is increasing interest in understanding how active learning affects students’ mental health as science courses transition from traditional lecture to active learning. Prior research has found that active learning can both alleviate and exacerbate undergraduate mental health problems. Existing studies have only examined the relationship between active learning and anxiety. No studies have examined the relationship between active learning and undergraduate depression. To address this gap in the literature, we conducted hour-long exploratory interviews with 29 students with depression who had taken active learning science courses across six U.S. institutions. We probed what aspects of active learning practices exacerbate or alleviate depressive symptoms and how students’ depression affects their experiences in active learning. We found that aspects of active learning practices exacerbate and alleviate students’ depressive symptoms, and depression negatively impacts students’ experiences in active learning. The underlying aspects of active learning practices that impact students’ depression fall into four overarching categories: inherently social, inherently engaging, opportunities to compare selves to others, and opportunities to validate or invalidate intelligence. We hope that by better understanding the experiences of undergraduates with depression in active learning courses we can create more inclusive learning environments for these students.

ContributorsAraghi, Tala (Author) / Cooper, Katelyn (Thesis director) / Brownell, Sara (Committee member) / Busch, Carly (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor)
Created2022-05
165842-Thumbnail Image.png
Description
Mounting evidence suggests that gender biases favoring men and racial biases favoring whites and Asians contribute to the underrepresentation of women and underrepresented minorities (URM) in science, technology, engineering, and mathematics (STEM). Systemic issues caused by gender and racial biases create barriers that prevent women and URM from entering STEM

Mounting evidence suggests that gender biases favoring men and racial biases favoring whites and Asians contribute to the underrepresentation of women and underrepresented minorities (URM) in science, technology, engineering, and mathematics (STEM). Systemic issues caused by gender and racial biases create barriers that prevent women and URM from entering STEM from the structure of education to admission or promotions to higher-level positions. One of these barriers is unconscious biases that impact the quality of letters of recommendation for women and URM and their success in application processes to higher education. Though letters of recommendation provide a qualitative aspect to an application and can reveal the typical performance of the applicant, research has found that the unstructured nature of the traditional recommendation letter allows for gender and racial bias to impact the quality of letters of recommendation. Standardized letters of recommendation have been implemented in various fields and have been found to reduce the presence of bias in recommendation letters. This paper reviews the trends seen across the literature regarding equity in the use of letters of recommendation for undergraduates.
ContributorsKolath, Nina (Author) / Brownell, Sara (Thesis director) / Goodwin, Emma (Committee member) / Barrett, The Honors College (Contributor) / School of Criminology and Criminal Justice (Contributor) / School of Life Sciences (Contributor)
Created2022-05
191019-Thumbnail Image.png
Description
This work focuses on a novel approach to combine electrical current with cyanobacterial technology, called microbial electrophotosynthesis (MEPS). It involves using genetically modified PSII-less Synechocystis PCC 6803 cells to avoid photoinhibition, a problem that hinders green energy. In the work, a cathodic electron delivery system is employed for growth and

This work focuses on a novel approach to combine electrical current with cyanobacterial technology, called microbial electrophotosynthesis (MEPS). It involves using genetically modified PSII-less Synechocystis PCC 6803 cells to avoid photoinhibition, a problem that hinders green energy. In the work, a cathodic electron delivery system is employed for growth and synthesis. Photoinhibition leads to the dissipation energy and lower yield, and is a major obstacle to preventing green energy from competing with fossil fuels. However, the urgent need for alternative energy sources is driven by soaring energy consumption and rising atmospheric carbon dioxide levels. When developed, MEPS can contribute to a carbon capture technology while helping with energy demands. It is thought that if PSII electron flux can be replaced with an alternative source photosynthesis could be enhanced for more effective production. MEPS has the potential to address these challenges by serving as a carbon capture technology while meeting energy demands. The idea is to replace PSII electron flux with an alternative source, which can be enhanced for higher yields in light intensities not tolerated with PSII. This research specifically focuses on creating the initiation of electron flux between the cathode and the MEPS cells while controlling and measuring the system in real time. The successful proof-of-concept work shows that MEPS can indeed generate high-light-dependent current at intensities up to 2050 µmol photons m^‒2 s^‒1, delivering 113 µmol electrons h^‒1 mg-chl^‒1. The results were further developed to characterize redox tuning for electron delivery of flux to the photosynthetic electron transport chain and redox-based kinetic analysis to model the limitations of the MEPS system.
ContributorsLewis, Christine Michelle (Author) / Torres, César I (Thesis advisor) / Fromme, Petra (Thesis advisor) / Woodbury, Neal (Committee member) / Hayes, Mark (Committee member) / Arizona State University (Publisher)
Created2023
193014-Thumbnail Image.png
Description
The consequences of failures from large-diameter water pipelines can be severe. Results can include significant property damage, damage to adjacent infrastructure such as roads and bridges resulting in transportation delays or shutdowns, adjacent structural damage to buildings resulting in loss of business, service disruption to a significant number of

The consequences of failures from large-diameter water pipelines can be severe. Results can include significant property damage, damage to adjacent infrastructure such as roads and bridges resulting in transportation delays or shutdowns, adjacent structural damage to buildings resulting in loss of business, service disruption to a significant number of customers, loss of water, costly emergency repairs, and even loss of life. The American Water Works Association’s (AWWA) 2020 “State of the Water Industry” report states the top issue facing the water industry since 2016 is aging infrastructure, with the second being financing for improvements. The industry must find innovative ways to extend asset life and reduce maintenance expenditures. While are many different assets comprise the drinking water industry, pipelines are a major component and often neglected because they are typically buried. Reliability Centered Maintenance (RCM) is a process used to determine the most effective maintenance strategy for an asset, with the ultimate goal being to establish the required function of the asset with the required reliability at the lowest operations and maintenance costs. The RCM philosophy considers Preventive Maintenance, Predictive Maintenance, Condition Based Monitoring, Reactive Maintenance, and Proactive Maintenance techniques in an integrated manner to increase the probability an asset will perform its designed function throughout its design life with minimal maintenance. In addition to determining maintenance tasks, the timely performance of those tasks is crucial. If performed too late an asset may fail; if performed too early, resources that may be used better elsewhere are expended. Utility agencies can save time and money by using RCM analysis for their drinking water infrastructure. This dissertation reviews industries using RCM, discusses the benefits of an RCM analysis, and goes through a case study of an RCM at a large aqueduct in the United States. The dissertation further discusses the consequence of failure of large diameter water pipelines and proposes a regression model to help agencies determine the optimum time to perform maintenance tasks on large diameter prestressed concrete pipelines using RCM analysis.
ContributorsGeisbush, James R (Author) / Ariaratnam, Samuel T (Thesis advisor) / Grau, David (Committee member) / Chong, Oswald (Committee member) / Arizona State University (Publisher)
Created2024
Description

Mental health conditions can impact college students’ social and academic achievements. As such, students may disclose mental illnesses on medical school applications. Yet, no study has investigated to what extent disclosure of a mental health condition impacts medical school acceptance. We designed an audit study to address this gap. We

Mental health conditions can impact college students’ social and academic achievements. As such, students may disclose mental illnesses on medical school applications. Yet, no study has investigated to what extent disclosure of a mental health condition impacts medical school acceptance. We designed an audit study to address this gap. We surveyed 99 potential admissions committee members from at least 43 unique M.D.-granting schools in the U.S. Participants rated a fictitious portion of a medical school application on acceptability, competence, and likeability. They were randomly assigned to a condition: an application that explained a low semester GPA due to a mental health condition, an application that explained a low semester GPA due to a physical health condition, or an application that had a low semester GPA but did not describe any health condition. Using ANOVAs, multinomial regression, and open-coding, we found that committee members do not rate applications lower when a mental health condition is revealed. When asked about their concerns regarding the application, 27.0% of participants who received an application that revealed a mental health condition mentioned it as a concern; 14.7% of participants who received an application that revealed a physical health condition mentioned it as a concern. Committee members were also asked about when revealing a mental health condition would be beneficial and when it would be detrimental. This work indicates that medical school admissions committee members do not exhibit a bias towards mental health conditions and provides recommendations on how to discuss mental illness on medical school applications.

ContributorsAbraham, Anna (Author) / Brownell, Sara (Thesis director) / Cooper, Katelyn (Committee member) / Barrett, The Honors College (Contributor) / School of Life Sciences (Contributor) / Department of Psychology (Contributor) / School of Human Evolution & Social Change (Contributor)
Created2022-05