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- Genre: Academic theses
Description
High throughput transcriptome data analysis like Single-cell Ribonucleic Acid sequencing (scRNA-seq) and Circular Ribonucleic Acid (circRNA) data have made significant breakthroughs, especially in cancer genomics. Analysis of transcriptome time series data is core in identifying time point(s) where drastic changes in gene transcription are associated with homeostatic to non-homeostatic cellular transition (tipping points). In Chapter 2 of this dissertation, I present a novel cell-type specific and co-expression-based tipping point detection method to identify target gene (TG) versus transcription factor (TF) pairs whose differential co-expression across time points drive biological changes in different cell types and the time point when these changes are observed. This method was applied to scRNA-seq data sets from a SARS-CoV-2 study (18 time points), a human cerebellum development study (9 time points), and a lung injury study (18 time points). Similarly, leveraging transcriptome data across treatment time points, I developed methodologies to identify treatment-induced and cell-type specific differentially co-expressed pairs (DCEPs). In part one of Chapter 3, I presented a pipeline that used a series of statistical tests to detect DCEPs. This method was applied to scRNA-seq data of patients with non-small cell lung cancer (NSCLC) sequenced across cancer treatment times. However, this pipeline does not account for correlations among multiple single cells from the same sample and correlations among multiple samples from the same patient. In Part 2 of Chapter 3, I presented a solution to this problem using a mixed-effect model. In Chapter 4, I present a summary of my work that focused on the cross-species analysis of circRNA transcriptome time series data. I compared circRNA profiles in neonatal pig and mouse hearts, identified orthologous circRNAs, and discussed regulation mechanisms of cardiomyocyte proliferation and myocardial regeneration conserved between mouse and pig at different time points.
ContributorsNyarige, Verah Mocheche (Author) / Liu, Li (Thesis advisor) / Wang, Junwen (Thesis advisor) / Dinu, Valentin (Committee member) / Arizona State University (Publisher)
Created2022
Description
Beta-Amyloid(Aβ) plaques and tau protein tangles in the brain are now widely recognized as the defining hallmarks of Alzheimer’s disease (AD), followed by structural atrophy detectable on brain magnetic resonance imaging (MRI) scans. However, current methods to detect Aβ/tau pathology are either invasive (lumbar puncture) or quite costly and not widely available (positron emission tomography (PET)). And one of the particular neurodegenerative regions is the hippocampus to which the influence of Aβ/tau on has been one of the research projects focuses in the AD pathophysiological progress.
In this dissertation, I proposed three novel machine learning and statistical models to examine subtle aspects of the hippocampal morphometry from MRI that are associated with Aβ /tau burden in the brain, measured using PET images. The first model is a novel unsupervised feature reduction model to generate a low-dimensional representation of hippocampal morphometry for each individual subject, which has superior performance in predicting Aβ/tau burden in the brain. The second one is an efficient federated group lasso model to identify the hippocampal subregions where atrophy is strongly associated with abnormal Aβ/Tau. The last one is a federated model for imaging genetics, which can identify genetic and transcriptomic influences on hippocampal morphometry. Finally, I stated the results of these three models that have been published or submitted to peer-reviewed conferences and journals.
ContributorsWu, Jianfeng (Author) / Wang, Yalin (Thesis advisor) / Li, Baoxin (Committee member) / Liang, Jianming (Committee member) / Wang, Junwen (Committee member) / Wu, Teresa (Committee member) / Arizona State University (Publisher)
Created2022
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, 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
Description
Similar-identity role models, including instructors, can benefit science undergraduates by enhancing their self-efficacy and sense of belonging. However, for students to have similar-identity role models based on identities that can be hidden, instructors need to disclose their identities. For concealable stigmatized identities (CSIs) – identities that can be hidden and carry negative stereotypes – the impersonal and apolitical culture cultivated in many science disciplines likely makes instructor CSI disclosure unlikely. This dissertation comprises five studies I conducted to assess the presence of instructor role models with CSIs in undergraduate science classrooms and evaluate the impact on undergraduates of instructor CSI disclosure. I find that science instructors report CSIs at lower rates than undergraduates and typically keep these identities concealed. Additionally, I find that women instructors are more likely to disclose their CSIs to students compared to men. To assess the impact of instructor CSI disclosure on undergraduates, I report on findings from a descriptive exploratory study and a controlled field experiment in which an instructor reveals an LGBTQ+ identity. Undergraduates, especially those who also identify as LGBTQ+, benefit from instructor LGBTQ+ disclosure. Additionally, the majority of undergraduate participants agree that an instructor revealing an LGBTQ+ identity during class is appropriate. Together, the results presented in this dissertation highlight the current lack of instructor role models with CSIs and provide evidence of student benefits that may encourage instructors to reveal CSIs to undergraduates and subsequently provide much-needed role models. I hope this work can spark self-reflection among instructors to consider revealing CSIs to students and challenge the assumption that science environments should be devoid of personal identities.
ContributorsBusch, Carly Anne (Author) / Cooper, Katelyn (Thesis advisor) / Brownell, Sara (Thesis advisor) / Collins, James (Committee member) / Zheng, Yi (Committee member) / Arizona State University (Publisher)
Created2024
Description
Education through field exploration is fundamental in geoscience. But not all students enjoy equal access to field-based learning because of time, cost, distance, ability, and safety constraints. At the same time, technological advances afford ever more immersive, rich, and student-centered virtual field experiences. Virtual field trips may be the only practical options for most students to explore pedagogically rich but inaccessible places. A mixed-methods research project was conducted on an introductory and an advanced geology class to explore the implications of learning outcomes of in-person and virtual field-based instruction at Grand Canyon National Park. The study incorporated the Great Unconformity in the Grand Canyon, a 1.2 billion year break in the rock record; the Trail of Time, an interpretive walking timeline; and two immersive, interactive virtual field trips (iVFTs). The in-person field trip (ipFT) groups collectively explored the canyon and took an instructor-guided inquiry hike along the interpretive Trail of Time from rim level, while iVFT students individually explored the canyon and took a guided-inquiry virtual tour of Grand Canyon geology from river level. High-resolution 360° spherical images anchor the iVFTs and serve as a framework for programmed overlays that enable interactivity and allow the iVFT to provide feedback in response to student actions. Students in both modalities received pre- and post-trip Positive and Negative Affect Schedules (PANAS). The iVFT students recorded pre- to post-trip increases in positive affect (PA) scores and decreases in negative (NA) affect scores, representing an affective state conducive to learning. Pre- to post-trip mean scores on concept sketches used to assess visualization and geological knowledge increased for both classes and modalities. However, the iVFT pre- to post-trip increases were three times greater (statistically significant) than the ipFT gains. Both iVFT and ipFT students scored 92-98% on guided-inquiry worksheets completed during the trips, signifying both met learning outcomes. Virtual field trips do not trump traditional in-person field work, but they can meet and/or exceed similar learning objectives and may replace an inaccessible or impractical in-person field trip.
ContributorsRuberto, Thomas (Author) / Semken, Steve (Thesis advisor) / Anbar, Ariel (Committee member) / Brownell, Sara (Committee member) / Arizona State University (Publisher)
Created2018
Description
Evolution is the foundation of biology, yet it remains controversial even among college biology students. Acceptance of evolution is important for students if we want them to incorporate evolution into their scientific thinking. However, students’ religious beliefs are a consistent barrier to their acceptance of evolution due to a perceived conflict between religion and evolution. Using pre-post instructional surveys of students in introductory college biology, Study 1 establishes instructional strategies that can be effective for reducing students' perceived conflict between religion and evolution. Through interviews and qualitative analyses, Study 2 documents how instructors teaching evolution at public universities may be resistant towards implementing strategies that can reduce students' perceived conflict, perhaps because of their own lack of religious beliefs and lack of training and awareness about students' conflict with evolution. Interviews with religious students in Study 3 reveals that religious college biology students can perceive their instructors as unfriendly towards religion which can negatively impact these students' perceived conflict between religion and evolution. Study 4 explores how instructors at Christian universities, who share the same Christian backgrounds as their students, do not struggle with implementing strategies that reduce students' perceived conflict between religion and evolution. Cumulatively, these studies reveal a need for a new instructional framework for evolution education that takes into account the religious cultural difference between instructors who are teaching evolution and students who are learning evolution. As such, a new instructional framework is then described, Religious Cultural Competence in Evolution Education (ReCCEE), that can help instructors teach evolution in a way that can reduce students' perceived conflict between religion and evolution, increase student acceptance of evolution, and create more inclusive college biology classrooms for religious students.
ContributorsBarnes, Maryann Elizabeth (Author) / Brownell, Sara (Thesis advisor) / Nesse, Randolph (Committee member) / Collins, James (Committee member) / Husman, Jenefer (Committee member) / Maienschein, Jane (Committee member) / Arizona State University (Publisher)
Created2018
Description
This dissertation presents three novel algorithms with real-world applications to genomic oncology. While the methodologies presented here were all developed to overcome various challenges associated with the adoption of high throughput genomic data in clinical oncology, they can be used in other domains as well. First, a network informed feature ranking algorithm is presented, which shows a significant increase in ability to select true predictive features from simulated data sets when compared to other state of the art graphical feature ranking methods. The methodology also shows an increased ability to predict pathological complete response to preoperative chemotherapy from genomic sequencing data of breast cancer patients utilizing domain knowledge from protein-protein interaction networks.
Second, an algorithm that overcomes population biases inherent in the use of a human reference genome developed primarily from European populations is presented to classify microsatellite instability (MSI) status from next-generation-sequencing (NGS) data. The methodology significantly increases the accuracy of MSI status prediction in African and African American ancestries.
Finally, a single variable model is presented to capture the bimodality inherent in genomic data stemming from heterogeneous diseases. This model shows improvements over other parametric models in the measurements of receiver-operator characteristic (ROC) curves for bimodal data. The model is used to estimate ROC curves for heterogeneous biomarkers in a dataset containing breast cancer and cancer-free specimen.
ContributorsSaul, Michelle (Author) / Dinu, Valentin (Thesis advisor) / Liu, Li (Committee member) / Wang, Junwen (Committee member) / Arizona State University (Publisher)
Created2021
Description
Calls for changes in science education over the last several decades have contributed to a changing landscape of undergraduate life science education. As opposed to simply lecturing at students and expecting them to recite science facts, there has been a strong push to make systemic changes so that students not only know pertinent science content, but also walk away with critical science process skills. There have been suggestions to create environments that focus on goals such as evaluating scientific evidence and explanations, understanding the development of scientific knowledge, and participating in scientific practice and discourse. As a part of the call for increases in student participation in science practice, we’ve seen suggestions to increase student exposure to the tools, techniques, and published research within various science fields. The use of primary scientific literature in the classroom is documented as being a tool to introduce students to the nature of scientific reasoning, experimental design, and knowledge creation and transformation. Many of the current studies on primary scientific literature in undergraduate courses report on intensive course designs in which students interact with the material with very specific goals, as outlined by the authors and researchers. We know less about the practices that take place in typical undergraduate settings. This exploratory study looks at information provided by a national sample of faculty that alludes to what sort of practices are taking place and the reasoning for doing so. Through analysis of both closed-ended and open-ended survey questions we have found that faculty are engaging students with primary scientific literature for many reasons and in a variety of ways. We have also attempted to characterize the way in which faculty view the body of scientific literature, as members of the research community. We discuss the implications of faculty views on the utility and value of the body of scientific literature. We also argue that those perceptions inform how the material is used in the undergraduate classroom.
ContributorsWagoner, Nevada (Author) / Brownell, Sara (Thesis advisor) / Maienschein, Jane (Thesis advisor) / Ellison, Karin (Committee member) / Arizona State University (Publisher)
Created2016