Digital Commons Network^™

Assessment Of In-Frame Indel Variants In An Unsolved Cohort Of Inherited Retinal Diseases Using Machine Learning, David E Rauch, Meng Wang, Muhammad Jafar Hussain Hafiz, Daniel C Brock, Yumei Li, Molly Marra, Mark E Pennesi, Paul Yang, Everett Lesley, Irma Lopez, Robert Koenekoop, Edward Ryan Collantes, Joanne Bolinao, Rui Chen

Faculty, Staff and Students Publications

The standard for in silico pathogenicity prediction of in-frame insertions and deletions (indels) is less established compared to other types of variations. We aimed to systematically assess the performance of in silico machine learning (ML) tools on a patient cohort with inherited retinal diseases (IRDs). The performance of four ML tools (CADD, FATHMM-indel, VEST4, and MetaRNN-indel) was compared. Among them, MetaRNN-indel showed the best overall results. MetaRNN-indel was then applied to 1013 unsolved IRD patients, identifying two likely pathogenic causal variants in two unrelated IRD patients by confirming clinical phenotypes. Hence, our findings indicate that reliable prediction of the pathogenicity …

Sewers To Solutions: A Guide To Wastewater Pathogen Monitoring, Justin R Clark, Anthony W Maresso

Faculty, Staff and Students Publications

Wastewater-based epidemiology (WBE) is the analysis of wastewater to detect pathogen levels or activity for public health awareness or action. Pioneered in the 1940s, WBE underwent a resurgence during the COVID-19 pandemic, providing important information about number of cases, outbreaks, and seasonal impact. With advancements in detection technologies and growing interest in environmental surveillance, WBE is poised to become a standard practice in public health monitoring. Here, we provide an overview of the current state of the art of pathogen WBE, including methods of molecular detection, analysis of wastewater data, real-world applications and programs, public health interventions, and benefits and …

Amino Acids And Lean Mass Accretion In Preterm Neonates, Antonio C Ramos Dos Santos, Marta L Fiorotto, Teresa A Davis

Faculty, Staff and Students Publications

Purpose of review: This review evaluates recent evidence on how total protein and energy intake, amino acid composition, and nutrient delivery modality influence protein synthesis in preterm neonates, with the goal of informing nutritional strategies to support optimal lean mass accretion and growth.

Recent findings: Preterm neonates exhibit anabolic resistance to feeding due to impaired insulin and amino acid signaling in skeletal muscle. Enteral nutrition, especially fortified human milk, supports better lean mass accretion and neurodevelopment than parenteral nutrition. Intermittent bolus feeding and pulsatile leucine supplementation during continuous feeding further enhance mTORC1-dependent translation initiation signaling and protein synthesis efficiency in …

Unraveling Posttranslational Modification Complexity: Advances In Quantitative Histone Proteoform Mass Spectrometry, Karl F Poncha, Alyssa T Paparella, Nicolas L Young

Faculty, Staff and Students Publications

Histone proteins and their posttranslational modifications are central to chromatin structure and function. These modifications often occur in combinations, generating a diverse array of histone proteoforms that contribute to the dynamic regulation of chromatin architecture. Advancements in mass spectrometry-based proteomics, particularly top-down and middle-down approaches, have significantly enhanced our ability to characterize these proteoforms and elucidate PTM crosstalk. This review provides an analysis of the epigenetic machinery involved in the addition, recognition, and removal of histone PTMs, emphasizing the complexity introduced by histone variants and combinatorial PTM patterns. We examine the challenges and limitations of traditional antibody-based methods for PTM …

Faik Tagirov And Tatar Constructivism: The Making Of A New Tatar Book, Miriam Akhmetshin

Scripps Senior Theses

Working in the style of constructivism, Faik Tagirov primarily designed book covers for Tatar agitational literature in the 1920s. Studying at VKhUTEMAS and working for numerous publishing houses, Tagirov participated in several domestic and international exhibitions with well-known artists like Aleksandr Rodchenko and El Lissitzky. Tagirov utilized photomontage, geometricism, and unique typographical designs to create potent materials for a Tatar population. Current scholarship fails to adequately acknowledge the diverse influences impacting the work of non-Russian artists such as Tagirov. Using visual and iconographic analysis, I argue for an approach that recognizes Tagirov's work as syncretic in nature, utilizing both indigenous …

Between Trends And Truths: Tiktok Therapy-Speak And Mental Health, Zoe Stephens

Scripps Senior Theses

The rise of therapy-speak on social media has introduced mental health terminology into everyday discourse among young adults, yet its psychological impacts remain unclear (Chevalier, 2024; Jain et al., 2025). The present study investigated the effects of TikTok videos containing therapy-speak on stigma toward mental illness, mental health awareness, and mental health literacy. Using a between-groups experimental design, 95 U.S. college students aged 18 to 24 were randomly assigned to view either therapy-speak TikTok content or neutral TikTok content. Participants subsequently completed three post-exposure measures: the Mental Health Literacy Scale (MHLS; O’Connor & Casey, 2015), a self-constructed Mental Health Awareness …

Fashioning The Body Politic: Explorations Of The Political Semiotics Of Fashion In France And England During The French Revolution, Annika F. Gauthier

Scripps Senior Theses

In the midst of the French Revolution, women’s fashion underwent a complete revolution, moving from the multi-layered elaborate gowns of the ancien regime, to light, form-fitting dresses. These gowns reveal the way clothing reflects the political positions of women and the ways the French and the British used clothing to construct national identity and politics. Following research on the political symbolism and role of clothing across France and Britain, this thesis reviews fashion’s overarching connection to politics, revealing its role in the early French Revolution’s conception of women and patriotism, women’s responses to political exclusions, and rival nations’ adaptations of …

End-To-End Development And Experimental Validation Of A 1/10-Scale Autonomous Vehicle, Rikkin Pankaj Panchal

Electrical Engineering Theses

Autonomous vehicle development demands vast resources, making scaled down platforms a critical alternative for solving core algorithmic challenges. The primary contribution of this thesis is the end to end development and validation of a complete real time autonomous driving pipeline deployed on a one tenth scale vehicle. To streamline platform development, an AI assisted annotation framework automates dataset generation, significantly reducing manual labor while improving training data quality. The system perception stack features a reinforcement learning guided online multi camera calibration framework that enables adaptive surround view stitching without the need for offline recalibration. This is paired with robust lane …

Correction: Establishing Standardized Transthoracic Echocardiography Reference Ranges For Mouse Models: Insights Into The Impact Of Anesthesia, Sex, And Age, Manuela A Oestereicher, Christopher S Ward, Elida Schneltzer, Susan Marschall, Helmut Fuchs, Valerie Gailus-Durner, Ghina Bou About, Mohammed Selloum, Hamid Meziane, Michelle Stewart, Lydia Teboul, Clare Norris, Dale Pimm, Marina Kan, Federico López Gómez, Robert Wilson, Mayra Monroy, Sheraz Pasha, Eva Zabrodska, Jan Prochazka, David Pajuelo Reguera, Zuzana Nichtova, Yann Herault, Sara Wells, Helen Parkinson, Jason D Heaney, Radislav Sedlacek, Xiang Gao, Martin Hrabe De Angelis, Nadine Spielmann

Faculty, Staff and Students Publications

This corrects the article "Establishing standardized transthoracic echocardiography reference ranges for mouse models: insights into the impact of anesthesia, sex, and age" in volume 12, 1695034.

Highly Variable Expressivity Of A Cnv Deletion Involving Tbx4 In Three Deceased Siblings With Lung Developmental Disorder And Their Mildly Affected Mother And Grandfather, Przemyslaw Szafranski, Tomasz Gambin, Michal Kadlof, Michał Denkiewicz, Dariusz Plewczynski, Hyun Jeong Kim, Gail Deutsch, Nahir Cortes-Santiago, Salmo Raskin, Paweł Stankiewicz

Faculty, Staff and Students Publications

Single nucleotide variants (SNVs) and copy-number variant (CNV) deletions involving TBX4 have been associated with pulmonary arterial hypertension, ischiocoxopodopatellar syndrome, and lethal lung developmental disorders (LLDDs). Thus far, all large CNV deletions encompassing entire TBX4 have been found to have arisen de novo. Here, we present a three-generation family with three neonate siblings who died within 35-66 days due to histopathologically diagnosed LLDD. Whole-genome sequencing identified an ~108-kb CNV deletion encompassing TBX4 in all three infants. The deletion was also found in their mother with a history of pneumonia and persistent thick upper airway secretions and in the maternal grandfather …

Senolytic-Resistant Senescent Cells Have A Distinct Sasp Profile And Functional Impact: The Path To Developing Senosensitizers, Utkarsh Tripathi, Masayoshi Suda, Vagisha Kulshreshtha, Bryan T Piatkowski, Allyson K Palmer, Nino Giorgadze, Christina Inman, Nathan Gasek, Ming Xu, Kurt O Johnson, Tamar Pirtskhalava, Selim Chaib, Larissa P G Langhi Prata, Yi Zhu, Renuka Kandhaya-Pillai, Stefan G Tullius, Saranya P Wyles, Rambabu Majji, Hari Krishna Yalamanchili, David B Allison, Tamar Tchkonia, James L Kirkland

Faculty, Staff and Students Publications

The senescent cell (SC) fate is linked to aging, multiple disorders and diseases, and physical dysfunction. Senolytics, agents that selectively eliminate 30%-70% of SCs, act by transiently disabling the senescent cell antiapoptotic pathways (SCAPs), which defend those SCs that are proapoptotic and pro-inflammatory from their own senescence-associated secretory phenotype (SASP). Consistent with this, a JAK/STAT inhibitor, Ruxolitinib, which attenuates the pro-inflammatory SASP of senescent human preadipocytes, caused them to become "senolytic-resistant". Administering senolytics to obese mice selectively decreased the abundance of the subset of SCs that is pro-inflammatory. In cell cultures, the 30%-70% of human senescent preadipocytes or human umbilical …

Emptiness Is Enlightenment: Two Interpretations Of Nāgārjuna's Middle Way As Buddhist Soteriology, Isabella R. Sullivan

Scripps Senior Theses

This thesis investigates the soteriological implications of Nāgārjuna’s doctrine of emptiness (śūnyatā) as presented in the Mūlamadhyamakakārikā (MMK), or Root Verses of the Middle Way. While Nāgārjuna’s radical denial of intrinsic existence (svabhāva) is widely recognized as a masterful critique of metaphysics, modern scholarship remains divided on whether this "right view" can sufficiently ground the Buddhist Path to Liberation. This project centers on a comparative analysis of two prominent modern interpretations: Jay Garfield’s semantic anti-dualism and Giuseppe Ferraro’s anti-metaphysical realism.

The inquiry evaluates these perspectives against the doctrinal frameworks of the Four Noble Truths, dependent …

From South Korea To South Central: The 1992 Los Angeles Uprising And The "Rooftop Korean", Mina Althea Lamson Jung

Scripps Senior Theses

This thesis examines the historical formation of the "rooftop Korean," the racial figure of the armed Korean American shopkeeper that emerged during the 1992 Los Angeles Uprising and has since been mobilized repeatedly in service of anti-Black counterinsurgency. Drawing on the framework of racial capitalism, this thesis argues that the rooftop Korean was not a spontaneous product of the Korean-Black conflict in South Central Los Angeles but the culmination of decades of U.S.-Korea relations, South Korean militarization, and the racial geography of capitalist development on both sides of the Pacific.

Tracing a transnational arc from the Korean War through the …

Shrines On Asphalt Shoulders: Documenting Roadside Memorials In Western U.S. Roadscapes, Isabella R. Sullivan

Scripps Senior Theses

This thesis analyses the practice of documenting and uploading roadside memorials in the Western United States as a socially transformative process facilitated between two distinct kinds of noticing. Drawing on (auto)ethnographies of roadside memorial sites in Colorado and California, interviews with photographers and cartographers working primarily in the American Southwest, and Google Street View media, this research examines how recognition of the social negotiations involving memory and mortality that are already present in the physical shrines evolves when documenters capture and transpose them online. First, these documenters have developed the “eyes to see” roadside memorials for various significant reasons in …

The Politics Of Fatness And The Demand For Our Collective Joy, Sky Caldwell

Scripps Senior Theses

The Politics of Fatness and the Demand for Our Collective Joy aims to assess the political-economic reasonings behind the return of overt anti-fatness and its coincidence with the re-normalization of the far right. My research looks at the sudden mass marketing of GLP-1 drugs and the use of the body as a spatial fix during recession-era economic conditions. First, this interdisciplinary project asks why the body positivity movement has not been successful in the greater fight against anti-fatness. Then, through archival research, discourse analysis, ethnographic interviews, and photography, my project explores various case studies of successful spaces and collectives working …

The Demand For Attention: Notification Technology And The Restructuring Of Communication, Sabrina Feld

Scripps Senior Theses

This thesis argues that notifications are not merely features of digital devices but infrastructural forces that quietly reorganize the conditions under which communication is perceived, enacted, and understood. Drawing on Science, Technology, and Society (STS) frameworks, specifically Actor-Network Theory and Langdon Winner's concept of Forms of Life, the first chapter traces how notifications produce a Form of Life organized around continuous responsiveness, in which incoming information appears as a pending demand, silence carries new moral weight, and the capacity for self-determined availability is structurally foreclosed. Understood this way, notifications become a case study for a broader pattern in which technological …

Viral Misunderstandings: Reddit Posts And The Covid-19 Infodemic, Julia C. Knutson

Scripps Senior Theses

Information epidemics or “infodemics” became the center of misinformation conversations, due to a global increase in information spread surrounding the COVID-19 pandemic. While many academic scholars and institutions, such as the World Health Organization (WHO) attribute the cause of infodemics to anti-science attitudes and the public’s lack of scientific literacy, scholars in Science, Technology, and Society argue that analyzing misinformation within these isolated bounds limits our understanding of its underlying social and historical contexts. Using the COVID-19 pandemic as a case study for misinformation analysis reveals a gap in our current understanding of how people who resonate with or spread …

(Dis)Orientations: Finding Rhythm Within Queer Nightlife In Los Angeles, Frances Bright Currie

Scripps Senior Theses

This thesis examines how queer individuals in Los Angeles perceive, inhabit, and reshape their experiences in queer cultural spaces. Through this project, I trace the evolution of queer nightlife in Los Angeles (from early gay counterspaces, through the collectivist politics of the Queer Nation, to post-gay assimilation and contemporary “inclusive” queer nightlife) in order to examine how queer space has been shaped and reshaped by a recurring tension between the utopian promise of universality and inclusion and the material realities of exclusion. Drawing on ethnographic fieldwork, queer theory, and approaches to memory and the archive, I argue that queer nightlife …

The Judicial Containment Of Adivasi Rights Across India's Mineral Belt, Sajni S. Sheth-Voss

Scripps Senior Theses

This thesis examines how Adivasi resistance to mining-induced dispossession across India’s mineral belt is increasingly channeled into the judiciary, arguing that this shift functions as a mechanism of containment rather than a pathway to justice. Despite a robust legal framework designed to protect Adivasi land and consent rights, systematic non-enforcement and political closure have hollowed out policy and electoral channels, pushing communities into litigation as a last resort. Drawing on scholarship in political economy, legal studies, and political ecology, alongside primary sources including court documents and activist statements, this study follows how disputes move across institutions and are ultimately reshaped …

The Effect Of The Affordable Care Act Medicaid Expansion On The Risk Of Hospital Closure And Adolescent Hpv Immunization In Rural Counties, Juliette Des Rosiers

Scripps Senior Theses

From 2005 to 2025, over 200 rural hospitals shut their doors, often citing increased operational costs, staffing shortages, low patient volume, regulatory barriers, financial challenges exacerbated by the COVID-19 pandemic, and uncompensated care as common contributors to the closures. Rural patients are often referred by their primary care physician to a hospital for regular immunizations, since smaller clinics have less capacity to provide immunizations due to a shortage of pediatricians and limited vaccine stock. A crucial vaccine that is not required by schools and underutilized in rural areas is that against human papillomavirus (HPV), a virus that infects cutaneous and …

Beyond Ssris: Omega-3 Fatty Acids And The Neurobiology Of Impulsivity In Borderline Personality Disorder, Sujean Doo

Scripps Senior Theses

Impulsivity is a central and clinically significant dimension of Borderline Personality Disorder (BPD), and is strongly associated with self-harm, aggression, and suicide risk. Despite its prognostic importance, pharmacologic management of impulsivity in BPD remains inconsistent. Selective serotonin reuptake inhibitors (SSRIs) are frequently prescribed; however, randomized controlled trials demonstrate limited efficacy for impulsive-aggression, and some patients experience a paradoxical behavioral activation. Meta-analytic and systematic reviews further suggest that mood stabilizers and second-generation antipsychotics may outperform antidepressants, yet no specific medication is indicated to target impulsive behavioral dyscontrol.

This thesis synthesizes findings from systematic reviews, randomized trials, and neuroimaging research to evaluate …

Remembering Choices: Feedback, Memory Accuracy, And Context-Dependent Preference Shifts, Cameryn K A Okamura

Scripps Senior Theses

Preferences are often assumed to be stable across time and context, yet research on cognition and behavioral economics suggests otherwise. The present study examined whether false reminders of prior choices amplify susceptibility to the asymmetric dominance effect, commonly known as the decoy effect, and secondly, whether working memory capacity moderates this relationship. Twenty-one participants completed an online experiment in which they first chose between pairs of everyday consumer products or services before receiving accurate, inaccurate, or no reminders of their earlier selections. They then made new choices from triplet sets containing a target (T), competitor (C), and asymmetrically dominated decoy …

Recipes And Resources: Food As A Decolonial Tool For The 1.5 Generation, Reyna Guadalupe Silva Carrillo

Scripps Senior Theses

Food is more than just nourishment for the 1.5-generation, people who come to the United States as children and now navigate between cultures; it is a language of memory, resistance, and survival across borders. This project raises an important question: how do 1.5-generation students navigate identity, belonging, and survival through food, and how can a zine serve as a medium for sharing community knowledge? My project argues that food is an important way 1.5-generation students use language to remember, resist, and survive across borders. Using pláticas, an informal conversation-based approach, this project focuses on the experience of 1.5-generation students at …

A Strategy To Identify Biliary Atresia Efficiently: A Perspective From A Texas Center, Sanjiv Harpavat, Tebyan A Rabbani, Ashley M Upton, Sridevi Devaraj, Jose A Hernandez, Benjamin L Shneider

Faculty, Staff and Students Publications

Infants with biliary atresia are often diagnosed after 60 days of life because the disease is difficult to detect in its early stages. However, infants treated before 30-45 days of life have the best long-term outcomes. To help accelerate the biliary atresia diagnosis, we have developed a streamlined strategy that involves two sequential tests: (1) direct or conjugated bilirubin measurements and (2) a feeding abdominal ultrasound exam. In this review, the strategy is shared to encourage others to provide feedback as well as to consider incorporating portions into their own clinical workflows.

What It Takes To "Become" Another: An Account Of Immersive Character Imagining, Ariana G. Didomenico

Scripps Senior Theses

Often, when one engages with fiction, one imaginatively portrays the mental states of the characters within said fiction. Typically, when one does this, one relates to the character as separate from oneself, and is consciously aware that what they are imagining is fictional. However, this is not always the case: when one engages in what I will call ‘immersive c-imagining’, one feels roughly as though a character’s thoughts and feelings are one’s own. Furthermore, there is a special subtype of immersive c-imagining, ‘inferential immersive c-imagining’, which occurs when one immersively c-imagines while, at the same time, efficiently and accurately inferring …

Integrating Non-Binary Morphology Into Spanish Grammatical Gender: A Study On Native And Second-Language Speakers, Abigail H. Gustafson

Scripps Senior Theses

This study investigates how native (L1) and second-language (L2) Spanish speakers process non-binary gender morphology, focusing on the pronoun ‘elle’ and the adjective/noun ending ‘-e’. Prior studies show that native speakers outperform L2 speakers in processing traditional masculine–feminine agreement, non-binary forms and their emergence in a binary grammatical system are understudied. To address this gap, I conducted an online reaction-time experiment with bilingual speakers from the Claremont Colleges, who judged the grammaticality of Spanish sentences containing either grammatical gender or social gender (él/ella/elle) agreement and disagreement. Survey data also captured participants’ familiarity with and attitudes toward the pronoun ‘elle’. The …

Madison, Wisconsin As A Climate Haven: Infrastructure, Environmental Justice, And Community Voice, Sophia N. Heffner

Scripps Senior Theses

As climate change accelerates internal migration within the United States, the concept of “climate havens” has emerged as a way to identify communities that may become receiving zones for displaced populations. Madison, Wisconsin has increasingly been positioned within academic, policy, and media discourse as a potential climate haven due to its geographic advantages, strong public infrastructure, and proactive climate policy environment. This paper evaluates Madison’s readiness for this role through an equity-centered, participatory planning lens. Drawing on planning documents, climate data, municipal policies, and interdisciplinary scholarship, it argues that Madison’s long-term success as a sustainable and inclusive climate haven depends …

Astrocytic Sox9 Overexpression In Alzheimer’S Disease Mouse Models Promotes Aβ Plaque Phagocytosis And Preserves Cognitive Function, Dong-Joo Choi, Sanjana Murali, Wookbong Kwon, Junsung Woo, Eun-Ah Christine Song, Yeunjung Ko, Debosmita Sardar, Brittney Lozzi, Yi-Ting Cheng, Michael R Williamson, Teng-Wei Huang, Kaitlyn Sanchez, Joanna Jankowsky, Benjamin Deneen

Faculty, Staff and Students Publications

Astrocytes play essential roles in the brain, and their dysfunction is associated with nearly every form of neurological disease. Despite their ubiquity, knowledge of how astrocytes contribute to disease pathogenesis is incomplete; accordingly, harnessing their biology toward therapeutics remains a major challenge. Here we show that the transcription factor Sox9 plays a context-specific role in maintaining astrocyte function and circuit activity in the aging hippocampus and Alzheimer's disease (AD) models. We found that Sox9 overexpression in astrocytes in AD models clears existing amyloid beta (Aβ) plaques and preserves cognitive function. Mechanistically, Sox9 promotes the phagocytosis of Aβ plaques by astrocytes …

Mapping The Structural Connections Between The Anterior Cingulate Cortex And The Insula/Ventrolateral Prefrontal Cortex.Mapping The Structural Connections Between The Anterior Cingulate Cortex And The Insula/Ventrolateral Prefrontal Cortex, Wei Tang, Javier Guaje, Shreyas Fadnavis, Sarah R Heilbronner, Eleftherios Garyfallidis

Faculty, Staff and Students Publications

The anterior cingulate cortex (ACC) is functionally closely related with the insula and the ventral lateral prefrontal cortex (vlPFC). The ACC and insula are the main hubs of the salience network, a set of functionally related brain regions involved in detecting salient stimuli and coordinating inter-network communication, while communication between ACC and vlPFC is closely linked to inhibitory control. However, despite strong indirect evidence from nonhuman primate (NHP) tract tracing, the structural connections between the ACC and the insula/vlPFC remain poorly understood in the human brain, in part because standard approaches fail to capture this projection. In this study, we …

Age-Related Variations Of The Hemodynamic Response Function Spatially Resolved Across Human Cerebral Cortex, Nooshin J Fesharaki, Amanda Taylor, David Ress

Faculty, Staff and Students Publications

Normal aging leads to regional vascular and neural alterations. Age-related impairments in neurovascular coupling (NVC) affect the blood-oxygen-level-dependent (BOLD) hemodynamic response function (HRF) measured with functional magnetic resonance imaging, causing changes in both amplitude and temporal dynamics. Previously, global, systematic age-related changes in HRF characteristics were demonstrated, consistent with known microvascular aging effects. In this follow-up study, a standard space was used to compare spatially resolved cortical HRF dynamics between sex-balanced groups of young and older adults. The results showed substantial age-related differences in both HRF amplitude and timing across distinct cortical regions. Nearly twice as much cortical area exhibited …