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Knowledge-Driven Feature Selection and Engineering for Genotype Data with Large Language Models.
Get PDFPredicting phenotypes with complex genetic bases based on a small, interpretable set of variant features remains a challenging task. Conventionally, data-driven approaches are used for this task, yet the high dimensional nature of genotype data makes the analysis and prediction difficult. Motivated by the biomedical knowledge encoded in pre-trained LLMs and the emerging applications for genetics, we set to examine the ability of LLMs in feature selection and engineering for tabular genotype data, with a novel knowledge-driven framework. We develop FREEFORM, Free-flow Reasoning and Ensembling for Enhanced Feature Output and Robust Modeling, designed with chain-of-thought and ensembling principles, to select and engineer features with the intrinsic knowledge of LLMs. Evaluated on two distinct genotype-phenotype datasets, genetic ancestry and hereditary hearing loss, we find this framework outperforms several data-driven methods, particularly on low-data regimes. FREEFORM is available as open-source framework at GitHub: https://github.com/PennShenLab/FREEFORM
A covalent chemical probe for Chikungunya nsP2 cysteine protease with antialphaviral activity and proteome-wide selectivity
Get PDFChikungunya is a mosquito-borne viral disease that causes fever and severe joint pain for which there is no direct acting drug treatments. Vinyl sulfone SGC-NSP2PRO-1 (3) was identified as a potent inhibitor of the nsP2 cysteine protease (nsP2pro) that reduced viral titer against infectious isolates of Chikungunya and other alphaviruses. The covalent warhead in 3 captured the active site C478 and inactivated nsP2pro with a kinact/Ki ratio of 5950 M–1 s–1. The vinyl sulfone 3 was inactive across a panel of 23 other cysteine proteases and demonstrated remarkable proteome-wide selectivity by two chemoproteomic methods. A negative control analog SGC-NSP2PRO-1N (4) retained the isoxazole core and covalent warhead but demonstrated > 100-fold decrease in enzyme inhibition. Both 3 and 4 were stable across a wide range of pH in solution and upon prolonged storage as solids. Vinyl sulfone 3 and its negative control 4 will find utility as high-quality chemical probes to study the role of the nsP2pro in cellular studies of alphaviral replication and virulence
In-betweenness and Critical Disaster Studies in Sherri L. Smith’s Orleans: “We are here! We are still here!”
Get PDFYoung adult novelists and their readers have always been aware of the trajectory of history, politics, social problems, and the way these issues get located in literature. Through this understanding, they push back against popular notions that YA is “lesser than” supposedly serious adult fiction just because its target demographic is the young. In fact, YA, particularly YA dystopian novels, are often radical and are at the vanguard of grappling with complex and compounding issues. Orleans, for example, seems to be almost predictive when looked at from a modern standpoint. The future it imagined has come about: first published in 2013, the novel marks its virus—the Delta Fever—as having started in 2020, eerily similar to the onset of COVID-19. It was during this same year that the Black Lives Matter protests broke out, first in the United States and then around the world, mirroring issues of race in the novel and how that intersects with the virus. While many of these “prophetic” similarities between modern times and Orleans could be marked off as just a lucky guess on the author’s part, I argue that it instead shows just how aware YA readers and novelists, like Smith, are of history, politics, and social issues—and of how the future directly grows out of human choices in the past. With this heightened awareness that the genre lends itself to, comes the ability to notice patterns and imagine how they will play out in real life. In this thesis, I use Orleans as a case-study for how YA dystopian authors often simultaneously reflect, process, and project through the liminal spaces and symbols present in their novels. However, I also argue that these authors move beyond mere critique and instead suggest that we can begin to shape the world by having more beneficial beliefs.Bachelor of Art
Local Tastes, Global Pressures: Three Ethnographic Case Studies into the Promises and Limits of Alternative Food Networks
Get PDFAlternative Food Networks (AFNs), generally defined as systems of exchange operating outside industrial food systems while often emphasizing sustainability and cultural preservation, have been the focus of interdisciplinary scholarship since the 1990s (Michel-Villarreal et al. 2024). Scholars frequently analyze AFNs through Karl Polanyi’s theory of embeddedness, which critiques the notion of self-regulating markets and highlights the role of countermovements in mitigating the harms of industrial foodways. However, as AFNs gain mainstream attention, they are often framed within a false dichotomy of "alternative" and "conventional" systems. This research, through case studies of urban night markets in Taiwan, the La Rioja wine region of Spain, and a segment of the California almond industry, argues for a more nuanced understanding of AFNs. It demonstrates that these networks not only prioritize social and environmental sustainability but also engage with profit motives, challenging simplistic binaries and offering a more comprehensive view of contemporary food systems.Bachelor of Art
Partisan Dynamics and Penal Policy: A Cross-State Analysis of Political Influence on Mental Health Evaluations in the Juvenile Justice System
Get PDFThis study investigates whether mental health assessments in juvenile detention facilities are sufficiently prioritized and how political dynamics within states influence this prioritization. The central research question explores the role of partisanship by focusing on the control of state legislatures and governors. The research investigates how these political actors prioritize the implementation of mental health evaluations for incarcerated youth. Building on existing literature that highlights partisan differences in moral emphasis and policy preferences, I theorize that Republican-led states are less likely to prioritize early and comprehensive mental health assessments compared to Democratic-led or politically divided states. To test this theory, I employ a mixed methods approach, combining case studies with quantitative data from nearly all 50 states. The findings reveal that Democratic-controlled states tend to conduct speedier mental health evaluations, states with higher spending per incarcerated person correlate with faster assessment timelines, and privatized detention facilities show a slight delay in speedier evaluations. However, this effect appears minimal. These patterns suggest partisan and fiscal factors play significant roles in shaping juvenile mental health policy, though unmeasured variables may also contribute to the observed outcomes.Bachelor of Art
The Impact of Natural Gas Prices on Pipeline Leaks and Incidents
Get PDFThis paper examines two databases of pipeline reports, one for leaks and one for incidents reaching a certain severity threshold. It focuses on natural gas distribution pipelines, and uses variation in the city gate price of natural gas, an input cost, across regions to determine the impact of an increase in the price of a commodity flowing through a pipeline on rates of pipeline incidents, as well as the impacts of pipeline incidents. Economic theory predicts many possible motivations, which combine to indicate an unclear effect on price. There is very weak evidence that an increase in city gate price lowers the chance of a recorded incident, but much stronger evidence that an increase in city gate price increases the number of leaks repaired on mains, not supporting the theoretical model. The main finding is that a $1 increase in city gate price leads to 4.065 more leaks being repaired on the mains of a given pipeline operator in a given year, on average. An attempt to estimate this with synthetic difference-in-difference models struggles due to a policy change intended to introduce competition causing insufficient changes in price. All in all, this paper provides partial evidence that policies aimed at preventing leaks should take into account the effects of city gate prices.Bachelor of Scienc
The Business of Habit: How Sports Betting Legalization and Bet Designs Transformed the Industry
Get PDFFollowing the Supreme Court’s decision in Murphy v. National Collegiate Athletic Association (2018), which struck down the Professional and Amateur Sports Protection Act (PASPA), states gained the authority to regulate sports betting independently. Since then, the industry has expanded into a multi-billion-dollar market. This study examines the key drivers of this growth, the population groups it targets, and the strategies sports betting agencies employ to maximize profit and sustain engagement. Empirical analysis shows that state legalization leads to a significant increase in tax revenue, with online sports betting as the primary driver. Moreover, the extent of this growth varies by state characteristics, with higher revenue growth observed in states with higher socioeconomic status, greater emphasis on health, and a larger Democratic population. The theoretical model further explores how parlay bets and inducements exploit agents' false perceptions of odds and shape habit formation. Lastly, the research calls for a ban on sports betting commercials to prevent the exploitation of cognitive biases, reduce harm to problem gamblers, and promote a more ethical and transparent sports betting environment.Bachelor of Scienc
Don't Know Better
Get PDFThis collection explores memory. Remembering what it’s like to be a little girl. Remember the strange way that growing up affects the head and the heart. How it’s embarrassing and tough, and everyone has to do it. To remember the stories I was raised on in the Appalachian mountains. Stories about death and dying, birth, miracles. Stories about relatives with unusual names and princesses who ruled over fields and wind that talks when it has something to say. Pieces of those stories have found their way in here. They helped make me who I am, so of course they did. This collection begins with some of my youngest characters and builds to a story told from the perspective of a skeleton–the whole gamut of life. Also included are three poems written during my time in Advanced Poetry here at Carolina. Bachelor of Art
Associations Between Avoidant/Restrictive Food Intake Disorder Dimensions and Obsessive-Compulsive Symptomatology Stratified by Gender
Get PDFExisting literature suggests that restrictive eating disorders commonly co-occur and share similar characteristics with obsessive-compulsive disorder (OCD). Certain dimensions of avoidant/restrictive food intake disorder (ARFID) have been shown to be associated with anxiety disorders, however, research on the relationship between ARFID and OCD specifically is limited. Previous literature on the sex/gender differences in ARFID presentations and OCD symptomatology show mixed findings. This study investigated the associations between ARFID dimensions and OCD symptomatology, considering depression and anxiety across sex/gender groups.Bachelor of Scienc
Associations Between White Matter Microstructure and Symptoms of Anxiety
Get PDFAnxiety disorders are among the most prevalent psychiatric disorders and impact millions of individuals of all ages. As such, it is important to understand brain mechanisms that underlie symptoms of anxiety. The cingulum and uncinate fasciculus (UF) are two white matter tracts that are involved in downregulating negative emotions and have been studied in relation to anxiety disorders using diffusion tensor imaging (DTI). Although there is a lack of consistency in previous research, many earlier studies found negative associations between anxiety symptoms and fractional anisotropy (FA) values in these tracts. In this study, we examined the associations between symptoms of anxiety and white matter microstructure, specifically FA, of the bilateral cingulum and UF. The full sample included 235 children, ages 8 and 10, who underwent DTI scanning along with parent-reported anxiety symptoms using the Behavior Assessment System for Children (BASC). We ran partial correlations, including relevant covariates (child gender, maternal education, BASC version, and scanner/sequence type) in all analyses. We found significant positive partial correlations between anxiety scores and left cingulum FA at both 8 and 10 years of age. There were also significant positive partial correlations between 8-year anxiety and 10-year left cingulum FA and right UF FA. Lastly, there were significant positive partial correlations between 10-year anxiety and 8-year left and right cingulum FA. In all cases, higher symptoms of anxiety were associated with higher FA. Our findings, contrary to previous studies, contribute to a growing body of literature exploring the neural underpinnings of anxiety. Bachelor of Art