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RNA’s Symphony: Harmonizing Splice Junctions and Exon Counts for a Novel Approach to Differential Splicing Analysis
No full textAlternative Splicing (AS) plays a critical role in transcriptome complexity and cell-type-specific gene regulation, yet its analysis remains methodologically fragmented, especially in the context of noisy and sparse single-cell RNA sequencing (scRNA-seq) data. This dissertation addresses key computational challenges in AS detection by evaluating existing tools, developing integrative frameworks, and proposing new strategies for improving analysis accuracy in both bulk and single-cell contexts. In chapter 1, I present a comprehensive literature review of computational tools designed for detecting and quantifying AS from bulk and scRNA-seq data. This review outlines major methodological paradigms, including exon-based and splice junction-based approaches, and evaluates their underlying statistical models, highlighting limitations in resolution, interpretability, and scalability. Chapter 2 introduces GrASE, a novel splicing graph-based method that unifies exon fragment-based and splice junction-based approaches. This unified framework not only facilitates cross-method benchmarking but also reveals AS events consistent across methods, and method-specific biases using short-read RNA-seq data. Lastly, chapter 3 presents a comprehensive benchmarking framework for differential AS detection in scRNA-seq data. Three count structures: exon counts, splice junction counts, and a newly proposed adjacent exon count, are evaluated in combination with three statistical models: negative binomial, beta-binomial, and mixed binomial. This chapter assesses performance across methods and highlights the trade-offs between statistical power and false discovery. A pseudo-bulking strategy is also explored to mitigate noise and enhance detection sensitivity in single-cell datasets. Collectively, this work advances the methodological landscape for AS analysis by providing a unified modeling framework, benchmarking strategies, and practical guidance for robust detection of splicing variation at single-cell resolution
Hot Spring Associated Infectious Diseases in the Great Basin and Southwest
No full textLike all bodies of freshwater, natural hot springs can harbor pathogenic microorganisms that carry the threat of infectious disease. The unique chemistry, increased temperature, and popularity for bathing may alter the risk profile of hot springs compared to other natural bodies of water. Despite this risk, the role of hot springs as a reservoir for infectious diseases remains understudied, particularly within the context of regional public health. Nevada and the Great Basin/Southwest have increasingly promoted hot springs for the purposes of tourism, and they share a strong link to the cultural heritage of the region. The unknown risk profile and the promotion of hot spring bathing could have unintended consequences for public health outcomes in the region and prompted this pilot study. This mixed-methods review investigated hot spring bathing hygiene within the Great Basin region and Southwest by examining hot spring site development, known pathogens, and disease outbreak response. Data for indicator bacteria for known hot spring bathing sites were gathered from public records, peer-reviewed articles, and local and federal water quality surveys which were evaluated against site development. Statistical analysis showed that most indicator bacteria declined as hot spring site development increased. Data for specific pathogens demonstrated general conformity to broader trends in hot springs associated infectious diseases, with a handful of regional outliers, such as Vibrio cholerae and red spider mites. Examination of outbreak responses showed that the most common response was posting warnings and/or guidance at the site itself or online. Remediation techniques, when applied, often consisted of draining or flushing the site to rid it of pathogen colonization. A major impediment to furthering hot spring hygiene seems to be that overlapping authorities and interests of various agencies can create gaps of responsibility and result in unchecked incidents. Final recommendations include increased signage at sites and development of other novel low-cost hygienic infrastructure along with increasing the mandate of environmental agencies to monitor and remediate hot springs in addition to other bodies of water
Understanding Ore Deposit Scale Controls On AU Enrichment in Carlin-Type AU Mineralization: A High-Resolution Study of The Rita K Deposit
No full textControls on the distribution of gold (Au) within the Rita K Carlin-type deposit are poorly understood. The primary Au-bearing carbonate unit Wispy, is a bioturbated muddy limestone with debris flow clasts that range in size but are typically \u3e5 cm occurring in the lower sections. The orebody is described as a syncline-anticline pair that hosts high-grade Au ore in the fold hinges. The spatial relationship between Au mineralization and fold hinges suggests that shortening due to folding is an important mechanism producing Au-enriched zones. However, the exact mechanism of Au enrichment and deposit-scale controls on Au distribution and fluid evolution through time remains unknown. The goal of this research is to investigate mechanisms causing variations in Au content throughout the Rita K deposit to inform future exploration and mining practices for Carlin-type deposits. Determining the relationship between structure, fluid flow, Au enrichment, and alteration is fundamental in building an ore deposit model at Rita K. For this study, we have selected two core holes based on the presence of debris flow deposits and vein networks to investigate fluid pathways at Rita K by utilizing a combination of bulk-rock geochemistry, reflected and transmitted light petrography, etching studies, micro-X-ray fluorescence mapping, and electron probe micro-analysis. Bulk-rock geochemistry data from our high-resolution study shows that debris flow samples are highly silicified, with an average of 86 wt.% (n=24, ±1σ, 1.34 wt.%) SiO2, when compared to vein network samples that average 39 wt.% (n=17, ±1σ, 10.0 wt.%) SiO2. The distribution of Si in micro-X-ray fluorescence element maps indicates that while vein networks facilitate fluid flow, debris flow deposits promote intergranular fluid flow enhancing wall rock interaction, sulfidation and Au deposition. Moreover, element mapping of pyrite grains challenges the well-established model that all arsenian pyrite rims on preexisting pyrite grains have a high Au content. Bulk rock geochemical data shows no correlation between Au and As in both debris flow samples (r2=0.002) and vein network samples (r2=0.12). The lack of correlation between Au and As suggests that intergranular fluid flow enhances fluid rock interaction leading to the formation of arsenian pyrite rims both with and without Au, and that pyrite rims are not necessarily required for the formation of Carlin-type Au deposits
The Speech-To-Song Illusion Across Development and the Effects of High-Level Expectations
No full textThe typical listener can readily categorize auditory stimuli as either speech or song even though these structures share many acoustic similarities. These musical and linguistic categories may nevertheless take time to develop as children acquire language- and music-specific knowledge. In the Speech-to-Song (STS) illusion, multiple repetitions of a natural spoken utterance can give rise to a perceptual switch wherein the stimulus begins to sound song-like to the listener. While the STS illusion has been well-researched in adult listeners, it had yet to be investigated in children. In our study, we examined whether children experience the STS illusion by presenting participants across age groups (4 – 5, 6 – 7, 8 – 11, 18+ years) with speech excerpts known to elicit the STS illusion and asking them to rate the degree to which each of 10 consecutive repetitions sounds song-like. We also asked whether they would better detect pitch changes to stimuli that violate versus conform to Western key structure, an advantage that has been observed in prior work with adults which implicates a role for musical schematic knowledge in the STS illusion. Participants robustly experienced the STS illusion similarly at all ages. Younger children required more repetitions than adults to experience the STS illusion, and unlike for adults, it remains unclear whether they recruited Western musical knowledge on our pitch detect task. Individual differences in performance on musical and linguistic perceptual tasks did not correlate with STS measures, suggesting that the repetition-induced musical processing mode characteristic of the STS illusion may reflect a more general auditory phenomenon that is less dependent on explicit musical and linguistic skills. Overall, our findings suggest that the ability to experience distinct, domain-specific modes of listening for speech and song are present early in development, but the nature of this experience may change with age as music-specific processing mechanisms develop and become more refined by listening experience
Relational Database Schema to Support Research Profiling Studies, Natural Language Processing, and Bibliometric Analysis
No full textIn this paper, a relational database schema is introduced that supports rapid prototyping, data preprocessing, and warehousing tasks associated with research profiling studies, natural language processing, and bibliometric analysis. Python scripts are leveraged for the seamless retrieval and processing of data from Semantic Scholar. This schema is tailored to efficiently analyze entities such as authors, their scientific papers, referenced papers, and cited papers. Adhering to the relational model, this schema offers a standardized approach to data storage and detailed information retrieval for scientific papers. Enhancing knowledge discovery in scientific databases, this schema provides researchers with a powerful platform for robust data management, retrieval, and analysis
Investing in Left Behind Places: Learning from Native American Tribal Communities
No full textAs part of the Brookings Scholar Lecture Series, Brookings Mountain West presents a lecture titled, Investing in \u27Left Behind\u27 Places: Learning from Native American Tribal Communities by Brookings fellow in Brookings Metro, Robert Maxim.
Over the past decade, U.S. political and economic discourse has centered on helping “left behind” places. The federal government joined this conversation, emphasizing everything from tariffs and trade protectionism to revitalize domestic industry, to landmark industrial policy bills aimed at pouring new federal investment into lagging places. Native American tribes can serve as an important case study for understanding how federal, state, and local policies can enhance place-based economic development in historically marginalized communities. There are perhaps no more “place-based” people than Indigenous people—the definition of Indigenous is rooted in a people’s connection to place, and tribal sovereignty is frequently defined in terms of legally prescribed boundaries. This lecture explores successes and barriers for Native American communities in engaging with recent federal, state, and other large-scale economic investments, and offers policy recommendations for supporting Tribes; other historically underinvested communities, including minority communities; as well as localities, metros, and regions
How Not to Teach With Technology: a Lighthearted Look at Educational Technology Pitfalls
No full textEducational technology can be both a catalyst for engagement and a source of unexpected chaos. The Do\u27s and Don\u27ts of Teaching with Technology: A Lighthearted Look at Educational Technology Pitfalls distills insights from IT support tickets, faculty consultations, and student feedback into practical (and lighthearted) DOs and DON’Ts. This poster highlights four key areas of tech use in higher education: Choosing the Right Tools, Setting Expectations, Avoiding Tech Overload, and Designing Intentionally, complete with comic-style illustrations and real-world wisdom. A companion guide, available via QR code, expands on these themes with additional examples, citations, and strategies for designing tech-enhanced learning that actually works.https://oasis.library.unlv.edu/btp_expo/1211/thumbnail.jp
The Importance of Recruitment of Low-Income Pregnant Persons in Interdisciplinary Research to Understand the Impact of Social and Environmental Determinants: Lessons Learned About Implementation and Recruitment
No full textBackground: Prior research indicates that enrolling underrepresented populations in clinical research is challenging. Although research has identified some barriers to participation and strategies to overcome them, studies have made little progress in being inclusive and representative. There remains a great need for including racial/ethnic minorities, low-income families, and pregnant women in research. The purpose of this article is to describe the implementation of enrollment strategies used in our study to understand the feasibility of building a maternal cohort and better understand the relationship between environmental and social impacts on maternal exposure and child outcomes.
Methods: Working across multiple academic units, our team implemented equity-focused team science strategies to recruit diverse populations into a research study. The phases included development, conceptualization, implementation, and translation.
Results: Our interdisciplinary team study used intentionality and commitment to deploy effective strategies including clearly defining the problem, selecting the correct team members to leverage expertise, clearly defining the study, establishing roles and responsibilities, representation, and clear and constant communication. A total of 100 pregnant women enrolled in our study using a team science interdisciplinary model.
Discussion: Building interdisciplinary teams can help us understand complex problems, increase innovation, and develop effective solutions in policy and practice. More specifically, interdisciplinary teams can advance our ability to recruit diverse populations into research. Future studies should consider how to harness the strengths of the different research team members to achieve more inclusive participation.
Health Equity Implications: This work has the potential to improve representation in research findings, enhance understanding of health disparities, and promote inclusive research practices
Long-Term Care Services and Support in the Mountain West, 2023
No full textThis fact sheet presents data from the American Association of Retired Persons (AARP) report, “Long-Term Services and Supports 2023 State Scorecard Report,” comparing Long-Term Services and Supports (LTSS) systems across multiple dimensions of performance for older adults, people with physical disabilities, and family caregivers for all 50 states. This fact sheet focuses on state-level LTSS system data for the Mountain West states of Arizona, Colorado, Nevada, New Mexico, and Utah
Federal Health Research Cuts in the Mountain West, 2025
No full textThis fact sheet presents data from the Science & Community Impacts Mapping Project (SCIMaP) report, “Impact of Federal Health Research Cuts,” which predicts economic and job losses resulting from proposed National Institutes of Health (NIH) funding/grants cuts for indirect research costs as of April 9, 2025. This fact sheet focuses on predicted economic and job loss for the Mountain West states of Arizona, Colorado, Nevada, New Mexico, and Utah, and county-level data for the State of Nevada