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Investigating Evolution Through the Lens of AI-driven Protein Exploration and Phylogenetic Modeling
No full textRecent advances in computational biology, artificial intelligence, and sequencing technologies have enabled new perspectives for addressing longstanding questions in evolutionary biology. Increased computational power has made large-scale simulations feasible for investigating diverse aspects of evolutionary and phylogenetic modeling. Similarly, deep learning algorithms now allow for the prediction of reasonably accurate tertiary protein structures, unlocking the potential for investigating diversity and evolution of protein structure across a broad range of organisms. This thesis presents two studies that target different aspects of evolutionary inference from unique perspectives. Yet, the share an overarching goal of presenting new perspectives on the evolutionary basis of biodiversity from comparative analyses of protein and trait evolution.
Viewing molecular evolution through the lens of protein structural diversity, the second chapter leverages deep learning models to examine olfactory receptor (OR) evolution in long-horn beetles. That is, we sought to investigate the diversity and structure of proteins encoded within recently-sequenced insect genomes using machine learning. Using two recently developed deep learning models, RoseTTAFold and AlphaFold, we predicted the tertiary structure of OR proteins in two Cerambycid species. We then investigated diversity among these OR proteins and analyzed the relationship between structural and sequence-level evolutionary distances. These findings highlight the promise of deep learning models for gaining meaningful biological insights, particularly in systems where experimental resources are limited.
The third chapter addresses evolutionary biology at a broader comparative scale, evaluating how phylogenetic assumptions influence evolutionary conclusions using statistical regression approaches. Here, we focused on a core question of comparative biology: understanding how phylogenetic modeling choices influence statistical conclusions about trait evolution. Through large-scale simulation studies and analysis of an empirical dataset containing traits associated with longevity, we assessed the sensitivity of phylogenetic regression to tree choice. Across these analyses, tree selection emerged as an important factor influencing the behavior of phylogenetic regression. The results show that an incorrect tree choice, that does not accurately represent the evolutionary history of a trait, can lead to significantly elevated false positive rates. This holds particularly true as the amount of data (species and traits) included in the analysis increases. These findings underscore the importance of thoughtful tree selection across studies in comparative biology. Together, these chapters highlight the diversity of questions and scales encompassed by evolutionary biology and contribute to a broader understanding of the field
Application of Ordinal Regression Models to Acquired Stress Resistance in Wild Strains of\u3ci\u3e Saccharomyces cerevisiae\u3c/i\u3e
Get PDFThis thesis explores the application of ordinal regression to the analysis of semi-quantitative growth assays often used when comparing fitness for different strains of the model yeast Saccharomyces cerevisiae. For stress survival assays, yeast stress resistance is measured using an ordered survival score that ranges from 0 (no growth) to 4 (confluent growth). Traditional approaches to analyze this type of data either treats data as a nominal categorical variable or as a continuous numerical variable. These approaches risk loss of information or violation of testing assumptions. In contrast, cumulative logit ordinal regression uses the information contained in the order of the data scores without requiring equal spacing between scores. This work also compares censored Poisson regression for colony count data while accounting for overlapping colonies.
Through simulation and example datasets, the performance of ordinal regression is compared to nominal-based tests (chi-sq, fisher’s exact) and summary approaches (t- test of score sums) for identifying differences in effect of treatment according to genotype. Results show ordinal modeling is a powerful technique that is manages to control Type I (false positive) error. Additionally, proposed here is a biologically intuitive summary statistic, minimum inhibitory concentration (MIC), derived from ordinal model estimates to quantify the lowest dose of stress that prevents survival.
Application of ordinal regression to example datasets further demonstrates advantages of ordinal regression for quantifying stress resistance. In one dataset, the effect deleting CTT1, a key gene for stress protection, is quantitatively assessed across different conditions. A second dataset evaluates hybrid yeast strains crossed from stress- sensitive and stress-resistant parents, allowing for quantification of resistance profiles across genetically diverse isolates. This thesis highlights the merits of ordinal regression for analyzing semi-quantitative survival data. By utilizing model-based estimation of effects with interpretable metrics, this thesis supports wider adoption of ordinal regression in cell and molecular biology research
Mechanical Properties and Microstructural Characteristics of Hydrated BCSA Cement at Extreme Temperatures
Get PDFBelitic Calcium Sulfoaluminate (BCSA) cement is an alternative binder known for its rapid setting and high early strength, making it ideal for applications such as fast-track construction and repair. This study presents a comprehensive investigation into the behavior of BCSA cement under a wide range of curing temperatures, with emphasis on early-age strength development, admixture effects, and the use of the maturity method for strength prediction.
The research evaluates BCSA cement performance in both hot and cold environments, ranging from approximately -28.9 °C (-20°F) to 49 °C (120°F). In warm climates, citric acid was used as a set retarder to improve workability and manage setting time, though careful dosage control was needed to avoid delays in strength gain. In cold climates, combinations of aluminum sulfate and chemical salts such as calcium chloride, calcium nitrate, and sodium chloride, were used to enhance early hydration. These chemical strategies proved effective in mitigating temperature-related performance issues and optimizing the strength of BCSA cement mixtures in challenging environments.
In addition to admixture optimization, the maturity method was applied to BCSA concrete mixtures to estimate in-place strength based on the cumulative effects of time and temperature. Datum temperatures and activation energies were determined experimentally, and maturity equations were developed. The results suggest that, when properly calibrated, the maturity method provides reliable strength predictions at 1 day of age ang later and can serve as a valuable tool in the quality control of BCSA concrete. Extremely early age strengths proved challenging to predict accurately.
Altogether, this investigation highlights the versatility of BCSA cement and provides practical recommendations for its use across a broad range of environmental conditions. By addressing both the chemical and thermal aspects of hydration, this research supports the continued development and implementation of BCSA-based systems in modern construction
Indigenous Materials Characterization for Additive Construction Applications
No full textAdvantages of concrete additive construction (AC) include the ability to print an object at the point of need with less waste, the geometric flexibility for novel shapes, and the reduction in the amount of hard physical labor required by construction workers. To date, most AC structures are designed and built using select high-quality materials, however, the implementation of indigenous, locally sourced soils and aggregates has started to grow as a feasible alternative, especially in remote locations in which the acquisition of conventional or select materials is unattainable. The potential to use indigenous materials reduces the logistical burdens associated with most concrete construction, and it improves the sustainability aspects, making the technology even more attractive.
To evaluate the suitability of indigenous materials sourced on-site to create AC concrete mixes, a full suite of characterization tests was conducted on a variety of indigenous materials sourced from around the world. The properties of the materials were determined, and then concrete mixes were evaluated to better understand the influence of various properties on the printability and strength of the AC concrete. Printability in this study refers to the pumpability and buildability of a mix, meaning the fresh material could be pumped through a progressive cavity pump, and then extruded beads could be stacked consecutively without excessive slump or collapse. The selection of the appropriate set of tests for a future testing protocol was guided by the most influential soil characteristics for AC concrete mix performance: the fines content, plasticity, gradation, and specific gravity in conjunction with absorption. These properties provided the relevant information needed to assess the suitability of indigenous materials for AC concrete mixes and identify cases when further processing is required in the field.
The amount of fines present was shown to influence workability and the water demand, and higher fines contents tended to improve the pumpability and buildability of a mix. The plasticity of the indigenous soils also strongly influenced the fresh and hardened properties of AC concrete mixes. Increased plasticity enhanced the pumpability and buildability of mixes; however, these mixes tended to have higher shrinkage cracking and lower strength. The gradation of indigenous materials provided information regarding maximum particle size and the coarseness of an aggregate, delimiting AC equipment and printing parameters. Gradation also likely helps identify the potential for a mix to pack within the rotor-stator; however, more research is needed to confirm the observations in this study. Specific gravity and absorption are important properties in the mix design proportions and having these values can help precisely control total water demand to ensure pumpability, avoid segregation, and enhance adhesion between layers.
The Methylene Blue Value (MBV) test was proposed as a field-applicable test method to determine the clay content of soils. MBV presented challenges regarding the variation of results from each soil analyzed. MBV denoted a directly proportioned linear function with clay content values, however, each soil analyzed resulted in a unique range of MBV. Because of this, the MBV was not able to uniquely identify the clay content or plasticity of a given indigenous soil
Sonic Subversion: An Intersectional Analysis of South African Punk, 1976-Present
Get PDFThe 1970s in South Africa were plagued by systematic racial segregation, widespread political violence, and fervent censorship under the apartheid regime. Political tensions were rising precipitously in the final years of the decade, stoked by the brutal police response to the Soweto Uprising (1976) and the murder of Black Consciousness leader Steve Biko (1977). It was amidst this atmosphere of profound oppression and increasing political unrest that punk made its South African debut. Apartheid South Africa served as a fertile breeding ground for punk’s inherent culture of defiance and anti-authoritarianism. Remarkably, punk has demonstrated the power to transcend sociodemographic boundaries such as race, class, language, and gender, even in the context of apartheid. This phenomenon is exemplified by bands such as National Wake, the country’s first multiracial punk band, Leopard, an all-female punk band to emerge in Durban in the late 1970s, and the Voëlvry tour in which young Afrikaners appropriated their mother tongue in a defiant act against the apartheid regime in its final years. This study examines the evolution of South African punk over the past five decades, considering how the subculture has shaped and been shaped by shifting political, social, and sonic landscapes during the apartheid years and in the decades following democratization. Through an analysis of DIY culture, fanzines, and independent record labels, this study highlights how grassroots networks fostered political solidarity and cultural identity. By considering South African punk through an intersectional framework, this work examines how overlapping identity factors have influenced individual experiences within the punk subculture to emphasize racial, ethnic, linguistic, and gendered diversity in the history of South African punk. In so doing, this work builds off of previous studies on South African punk that have focused predominantly on White male participants, specific locations, or narrow timeframes in an effort to provide a more nuanced understanding of the history of South African punk. This study is part of a growing body of research on punk in the Global South, which has long been eclipsed by scholarly examinations of punk in Europe and the United States. By drawing from a range of archival sources and newly conducted oral histories, this project will contribute to future research on punk and other subcultures in previously underexamined locales
Perceiving School Success: A Phenomenological Study of Asian Indian Parents
Get PDFThis phenomenological qualitative study aimed to explore how Asian Indian parents at East Ridge Elementary School perceived student success. The research sought to understand their experiences, their views on student success, and the factors they perceived as supports or barriers to achieving that success. Interviews with 14 Asian Indian families revealed four major themes: Positive School Experiences, Academic Programming, Holistic View of Education, and Parental Engagement. While communication emerged as a central element, it was not categorized as a theme but rather as a supporting factor. The study found that parents expressed satisfaction with the school’s cultural inclusivity and sense of community, though they identified areas for improvement in academic programming, particularly in curriculum clarity and opportunities for parental engagement. A secondary objective of the study was to explore differences among families with children receiving English Language services. The findings indicated that although academic success was a common priority, families in this subgroup faced distinct challenges, particularly related to language acquisition. Based on these findings, several practical recommendations were made, such as improving communication about the curriculum, expanding extracurricular opportunities, and strengthening parental involvement. The study also highlighted the importance of measuring student success beyond traditional academic assessments and suggested avenues for future research on effective communication strategies and cultural integration efforts. These recommendations have the potential to strengthen school-family partnerships and improve the educational experience for Asian Indian students and their families
Lawyers, Trauma, and Professional Well-Being: How the Legal Community Takes Back its Mental Health
Get PDFAccompanying a notable shift in the legal academy to being more attentive to our students’ mental health, there must be an equal (or even greater) shift to focusing on trauma, mental health, and well-being in the broader profession. Significantly, trauma and its effects are compounded when combined with the challenges faced by underrepresented populations within the profession. To date, these challenges have been greeted by an ad hoc, piecemeal reaction to stress and trauma,10 which only inhibits wellness in the profession. Part I explores the current literature in both the humanities and the legal profession, beginning with a brief discussion about trauma to explain what it is and its impacts on the legal profession. Part II then takes a didactic look at the legal profession and what makes it so vulnerable to trauma, discussing some of the societal and economic drivers that make trauma so prevalent in the profession, especially amongst minoritized populations. Next, in Part III, this Article discusses the legal profession’s current siloed efforts to understand trauma in the profession and to improve well-being, and its need to better strategize a solution that ensures more effective results. Finally, in Part IV, lies the bedrock of my thesis—that though trauma cannot be avoided in this profession (or anywhere), the best course of conduct is to embrace the new conversations about “human behavio[]r (including biases) and emotions” and how they affect the law
Negotiating Food Security
Get PDFIn the United States and worldwide, nutrition and food emerge as both high-profile public policy targets and as fundamental aspects of the right to self-determination. This Article examines how national security impacts food security in the United States. It explores conflicts and synergies between municipal, state, and federal law developments related to the right to food and investigates recent developments in how those commitments have been negotiated. The challenge and nebulous justiciability of the right to food can be in part attributed to existing global and national systems, which include supply chains, welfare programs, and foreign investment in the U.S. In lieu of the current critique of the status quo, U.S. lawmakers will soon be confronted with the need to reexamine and renegotiate existing national and international commitments, including those relative to food system restructuring, which will require collaboration between private and governmental actors. Such collaborations will be dictated by legal norms, soft laws, customary law, business practices, and the geopolitical makeup of the world. This Article makes the unique contribution of addressing how federal, state, and local decision-making processes factor into increasing food security and sustainable development. It also considers how these factors will determine whether the United States will have a competitive advantage in the global agro-economy, successfully securing food production for its citizens
Empowering Through Technology: An Internship Report on Augmentative and Alternative Communication Devices
Get PDFAugmentative and Alternative Communication (AAC) devices play a crucial role in supporting individuals with communication challenges, particularly children with developmental disabilities such as Autism Spectrum Disorder (ASD). This paper provides a comprehensive review of the literature on AAC and offers a detailed report of an internship experience at the University of Arkansas WE CARE Summer Camp. During the internship, firsthand experiences provided valuable insights into how AAC technologies can be applied to enhance communication, foster social connections, and support behavioral regulation.
The literature review explores the different types of AAC systems, including both aided and unaided options, and discusses the benefits and challenges of implementing these technologies. The internship report reflects on the day-to-day experiences of working with children who use AAC, highlighting the practical applications of the devices in a supportive camp environment. Observations from the internship illustrate the importance of individualized communication strategies and the impact of AAC on a child\u27s confidence and overall quality of life.
By combining academic research with real-world experiences, this report offers a well-rounded perspective on the role of AAC in the lives of children with developmental disabilities. It highlights the importance of continued education, caregiver and educator training, and collaborative support to maximize the benefits of AAC in various settings
NUTMEG: Separating Signal From Noise in Annotator Disagreement
No full textNLP (natural language processing) models often rely on human-labeled data for training and evaluation. Many approaches crowdsource this data from a large number of annotators with varying skills, backgrounds, and motivations, resulting in conflicting annotations. These conflicts have traditionally been resolved by aggregation methods that assume disagreements are errors. Recent work has argued that for many tasks annotators may have genuine disagreements and that variation should be treated as signal rather than noise. However, limited work has combined the two frameworks to separate signal from noise in human-labeled data. In this work, we introduce NUTMEG, a new Bayesian model that incorporates information about annotator backgrounds to remove noisy annotations from human-labeled training data while preserving systematic disagreements. We then use a synthetic data evaluation framework to show that NUTMEG is more effective at recovering ground-truth from annotations with systematic disagreement than traditional aggregation methods. We provide further analysis characterizing how differences in subpopulation sizes, rates of disagreement, and rates of spam affect the performance of our model. Finally, we demonstrate that downstream models trained on data aggregated by NUTMEG significantly outperform both models trained on traditionally aggregated data and models trained on the full set of disaggregated annotations. Our results highlight the importance of accounting for both annotator competence and systematic disagreements when training on human-labeled data