Digital Commons Network^™

Identifying Quantitative Trait Loci Of Genetically Regulated Molecules To Reveal Biological Mechanisms In Complex Traits, Chen Lin

Yale Graduate School of Arts and Sciences Dissertations

Genome-wide association studies (GWAS) have identified thousands of genetic variants associated with complex traits and diseases, but most of these variants reside in non-coding regions, making their biological functions challenging to study and interpret. To investigate the potential roles of these variants, expression quantitative trait locus (eQTL) analyses associate genetic variants with gene expression, providing insights into their regulatory roles. Integrating eQTL results with GWAS summary statistics has motivated transcriptome-wide association studies (TWAS), which focus on testing associations between imputed genetically regulated gene expression (GReX) and complex traits, offering a powerful gene-level view of genetic contributions to disease. Despite substantial …

Exploration Of The Mechanisms Regulating Genomic Stability In Plants, Wenxin Yuan

Yale Graduate School of Arts and Sciences Dissertations

Genomic stability is a cornerstone of cellular integrity, with implications spanning genetic engineering, epigenetic regulation, and disease modeling. However, most studies rely on yeast or mammalian models, leaving significant gaps in our understanding of plant chromatin biology and genome stability mechanisms. Exploring the conserved and divergent processes regulating genome stability in plants has become increasingly important, especially as global climate change threatens crop yields and biodiversity. Furthermore, the developmental resilience of plants provides a unique opportunity to study genes essential in mammals, offering translational insights for agriculture and human health. This dissertation investigates the molecular and genetic mechanisms underpinning T-DNA …

Mechanistic Insights Into Respiratory Tract Susceptibility In Whim Syndrome, Yawen Jiang

Yale Graduate School of Arts and Sciences Dissertations

Warts, hypogammaglobulinemia, infections, and myelokathexis (WHIM) syndrome is a rare congenital immunodeficiency caused by gain-of-function (GOF) mutations in CXCR4. Although respiratory infections are common in WHIM patients, the underlying mechanisms of susceptibility remain unclear. Using a mouse model of WHIM syndrome, we show that myelokathexis does not impair lung immune surveillance under homeostatic conditions. During acute viral and bacterial respiratory infections, neutrophils and monocytes are efficiently recruited from circulation into the lung vasculature and parenchyma. However, these cells fail to reach the airways due to their retention in adventitial cuffs enriched with CXCL12-producing fibroblasts, where potentially function as niches typically …

Scalable Real-Time Decoding System For Quantum Error Correction, Namitha Godawatte Liyanage

Yale Graduate School of Arts and Sciences Dissertations

A real-time decoder capable of meeting the stringent requirements for accuracy, latency, and throughput is essential for fault-tolerant quantum computing. While prior work has demonstrated progress in decoding isolated logical qubits, scaling to interacting logical qubits introduces significantly greater challenges, as all logical qubits in the system must be decoded collectively. This thesis addresses these challenges through the design and implementation of DECOARC, a vertex-level parallel decoding architecture based on the decoding graph abstraction. DECOARC organizes parallel computing resources using a hybrid tree-grid topology. We instantiate DECOARC in this work through two complementary systems: HELIOS, for single logical qubits, and …

Development Of Quantum Machine Learning Methods Applied To Drug Discovery, Anthony Michael Smaldone

Yale Graduate School of Arts and Sciences Dissertations

At the intersection of quantum computing and machine learning, quantum machine learning (QML) has the potential to drive major breakthroughs in chemistry and drug discovery. This dissertation explores the development of quantum neural networks and their application within drug discovery tools, navigating a deliberate path from current methodologies towards quantum enhancement under progressively more practical assumptions. Initially, we present novel Quantum Convolutional Neural Network (QCNN) architectures for multi-channel supervised learning (Chapter 2), laying the groundwork for use in a wide variety of drug discovery tasks such as protein-ligand binding affinity and structure prediction. Despite state-of-the-art performance among QCNNs on benchmark, …

Investigating The Seasonal And Interannual Evolution Of Dissolved Oxygen In The Arctic Ocean’S Canada Basin, Ashley Arroyo

Yale Graduate School of Arts and Sciences Dissertations

This dissertation examines the evolution of dissolved oxygen in the waters of the Arctic Ocean's Canada Basin. Dissolved oxygen concentrations in the ocean are initially set at the surface through air-sea exchange and subsequently modified by physical and biogeochemical processes as waters circulate and mix. The variability of dissolved oxygen in the Arctic Ocean across seasonal and interannual timescales provides valuable insight into the broader evolution of water masses in the Arctic Ocean. As dissolved oxygen concentrations are gradually depleted in deeper waters via biological consumption, and only replenished when waters return to the surface, their distribution provides a valuable …

From Individuals To Ecosystems: The Role Of Intraspecific Variation And Phenotypic Plasticity In Ecosystem Function, Nathalie Rose Sommer

Yale Graduate School of Arts and Sciences Dissertations

Understanding how organisms shape ecosystems is a central goal of ecology, particularly in an era of rapid environmental change. While ecosystem models have traditionally emphasized species-level diversity and abiotic controls, this dissertation provides evidence that trait variation within species—driven by phenotypic plasticity and transgenerational effects—can have consequences for ecosystem structure and function. Intraspecific variation is increasingly recognized as a key component of biodiversity-ecosystem function relationships, yet its effects remain underrepresented in empirical studies and predictive frameworks. By integrating multigenerational field experiments, multi-trait assessments, and detailed ecosystem measurements in a long-term, well-characterized study system, this dissertation bridges evolutionary ecology and ecosystem …

Learning Randomized Reductions For Security, Privacy, And Side-Channel Resilience, Ferhat Erata

Yale Graduate School of Arts and Sciences Dissertations

Modern computing systems face multifaceted challenges in security, privacy, and leakage resilience. This dissertation makes four key contributions to addressing these challenges through novel combinations of symbolic reasoning, machine learning, and neurosymbolic techniques. First, it develops symbolic AI techniques for analyzing side-channel vulnerabilities in low-level code and quantum computers. I introduce novel symbolic register analyses to automatically detect power side-channel vulnerabilities in constant-time cryptographic implementations. Additionally, I demonstrate an algebraic reconstruction method using Mixed-Integer Linear Programming (MILP) optimization to reverse-engineer quantum circuits from power traces, enabling extraction of proprietary circuit information. Second, my research pioneers automated learning of randomized self-reductions …

Sermon Rhetoric And White Evangelical Support For The Republican Party, Stephan Paul Lendway

Yale Graduate School of Arts and Sciences Dissertations

One of the most notable political shifts in American politics over the past fifty years has been the sorting of political and religious elites to produce the partisan “God Gap.” Among religious voters, evangelicals, especially White evangelicals, support Republican presidential candidates at higher levels than other religious voters. I argue that may partly be because of evangelical sermon content. In particular, I posit that, relative to Catholic and mainline Protestant sermons,evangelical Protestant sermons are more likely to consist of cultural and elite threats and that these threats consist of more sin, politicization on the ideological right, and mobilizing rhetoric. First, …

Customer Management In Virtual Environments, Seung Yoon Lee

Yale Graduate School of Arts and Sciences Dissertations

The rapid expansion of digital and virtual environments has transformed customer management, providing firms with unprecedented opportunities to observe and influence consumer behavior in real-time. These self-contained worlds—ranging from gaming and education to health and the emerging metaverse—allow firms to not only track every consumer action but also dynamically modify the product and design the rules and incentives governing the very environments in which interactions take place. As a result, firms can optimize targeting strategies, personalize interventions, and design products and incentives in ways that were previously unattainable. My dissertation examines how firms can leverage these capabilities to manage customer …

Revising The Nation: Tribal Sovereignty And The American History Textbook, 1929-2002, Grace R. Ellis

Library Map Prize

This thesis examines Indigenous representation in twentieth-century American history textbooks. Chapter One contends that the most popular U.S. history textbook of the late twentieth century, The American Pageant, erased tribal nations from its narrative and its maps. Across twelve editions (1956-2002), The Pageant taught generations of students that “Indians” served only as barriers to building the modern American nation-state. While Indigenous erasure can be traced back to specific passages in The Pageant, erasure can better be understood as an iterative process, both textual and cartographic in nature. Beginning in 1983, The Pageant added new maps that depicted tribes …

Indigenous Technology Futurisms: Reclaiming Mackinac Island In Virtual Reality, Madeline A. Gupta

Library Map Prize

In Indigenous Technology Futurisms: Reclaiming Mackinac Island in Virtual Reality, Madeline A. Gupta introduces a place-based digital storytelling project that uses interactive mapping as the foundation for cultural reconnection and community wellness. Centered on Mackinac Island—ancestral land of the Anishinaabe people—the project features a custom-designed map by an Anishinaabe artist, allowing users to navigate a VR website by selecting specific locations across northern Michigan. Each map point opens into a spatial video experience paired with traditional audio content, including oral histories, poetry, and songs.

The project reframes digital cartography through an Indigenous lens, challenging Western colonial mapping practices that …

Cryo-Em Reveals The Mechanochemical Cycle Of Reactive Full-Length Human Dynein-1, Pengxin Chai

Yale Graduate School of Arts and Sciences Dissertations

Dynein is a microtubule-based motor protein complex that generates force and drives movement toward the minus ends of microtubules. Despite extensive structural, biochemical, and biophysical studies, key questions remain about how dynein achieves its unidirectional stepping and force-generating powerstroke through its ATP-dependent mechanochemical cycle. In this dissertation, I leverage recent advances in cryo-electron microscopy (cryo-EM) and develop novel cryo-EM image processing methods to elucidate the atomic-level details of the mechanochemical cycle of full-length cytoplasmic dynein-1. I directly visualize the conformational landscape of dynein both on and off microtubules, uncovering several novel and important reactive intermediates. These findings include the discovery …

A Commitment To Health For All: Reimagining Representation And Participation In The Who Beyond State-Centrism, Yen-Wen Liao

Public Health Theses

Despite its stated commitment to “health for all,” the World Health Organization (WHO) has long been subject to the influence of Member State politics. Specifically, the Organization’s state-based membership model and governance structure have continuously enabled powerful Member States to advance their political interests, leading to the exclusion and marginalization of populations based on the recognition or political status of their representatives. One such example is Taiwan, which has been repeatedly denied membership in the Organization despite the functional independence of its public health authority, leaving over 23 million people neglected amid two major health crises. These forms of exclusion …

Defining The Genetic Basis Of Autosomal Dominant Polycystic Liver Disease With Whole Exome Sequencing, Xinmiao Meng

Public Health Theses

Polycystic liver and kidney diseases are inherited disorders marked by progressive cyst formation in hepatic and renal tissues, leading to significant morbidity through organ enlargement, impaired function, and eventual kidney failure or painful hepatic enlargement. While several genes—including PKD1, PKD2, GANAB, and PRKCSH—are implicated, a substantial proportion of cases remain genetically unexplained, limiting diagnostic precision and therapeutic development. This thesis aims to refine the genetic understanding of polycystic liver diseases through whole exome sequencing of 292 individuals with liver and/or kidney cysts. We first identify pathogenic variants in known disease genes in 133 individuals (46%), confirming the recurrent involvement of …

The Immunological Pathogenesis Of Persistent Lyme Disease And Babesiosis, Evan Navori

Public Health Theses

Post-Treatment Lyme Disease Syndrome (PTLDS) and persistent babesiosis are late-stage manifestations of two tick-borne diseases. Both are characterized by protracted symptoms despite the use of standard antimicrobial treatment. PTLDS is thought to be associated with immune dysregulation rather than active infection, while persistent and relapsing babesiosis is due to long-lasting infection caused by host immunodeficiency, pathogen antimicrobial resistance, and immune evasion. This thesis examines the immunological host deficits underlying both conditions, one too strong and the other too weak, and explores the mechanisms that contribute to prolonged disease states. Numerous studies suggest that Borrelia burgdorferi, the causative bacteria of Lyme …

An Analysis Of The Impact Of Genetic Diversity In Pfsec13 And Pfendo Genes On Pre-Clinical Drug Response To Med6-189 Analogs: A Novel Potent Class Of Antimalarial Compounds, Don-Pedro Ume

Public Health Theses

Malaria is a deadly disease responsible for 263 million cases and 597,000 deaths in 2023, with the majority being from the WHO African Region. While resistance to chloroquine and sulfadoxine-pyrimethamine (SP) emerged decades ago, there have been records of partial resistance to artemisinin-based combination therapies (ACTs) in African countries like Rwanda, Uganda, and Ethiopia. Given that ACTs are the main malaria drug of choice in Africa, there is a need to develop novel antimalarial agents that target pathways not explored by the current antimalarial therapies. Mutations in coding genes (PfSec13 and Pfendoplasmin or PfEndo) have been previously associated with resistance …

One Move, Many Wins: Green Social Housing As A Solution For Housing Insecurity And Residential Energy Inefficiency In New Haven, Ct, Arinze Colin Agu

Public Health Theses

This thesis explores the dual challenges of housing insecurity and residential energy inefficiency in New Haven, Connecticut, and advances green social housing as a transformative policy response. Through a qualitative research design that integrates semi-structured interviews, document analysis, and policy review, the study uncovers the structural conditions that drive unaffordable, unhealthy, and energy-inefficient housing for low- and moderate-income residents. The findings reveal that high utility costs, poor building infrastructure, and disempowering tenant–landlord dynamics are not isolated issues but manifestations of deeper systemic inequities in housing and energy governance. Green social housing emerges as a strategic intervention that aligns sustainable building …

Measuring Sexual Citizenship: Health, Rights, And Pleasure In The Wake Of National Level Policy Changes – Considering Namibia, Sophia Emelia Deluca

Public Health Theses

While public health evidence and rhetoric is frequently leveraged in scholarship and policy advocacy related to changes in law/policy targeting LGBTQ+ individuals, the existing public health body of evidence surrounding punitive and progressive policy shifts does not fully account for the interconnectedness of the law’s impacts on health, rights, pleasure, and belonging. To address this and pave the way for more representative research, the triangle of sexual citizenship framework links pleasure, rights, health, and sexual citizenship as key, connected components of research in this field. To account for hesitancy and confusion on how to integrate components of the triangle of …

Selected Publications By William White, William White

Documents

No abstract provided.

A Systems Organizational Model Of Professional Role Development For New Apps: Building A Train The Trainer Program, Abigail H.B. Baugh

Yale School of Nursing Digital Theses

Most Advanced Practice Provider (APP) turnover occurs within the first year of practice. It is often linked to feelings of inadequacy caused by limited professional instruction and immediate expectations of full practice integration. These challenges are compounded further in systems with inconsistent onboarding processes and underprepared trainers, further exacerbating turnover rates. At East Carolina University (ECU) Health System, turnover rates for Physician Assistants and Nurse Practitioners reached 20% and 12%, respectively, surpassing national averages (ECU Health, 2024), highlighting the urgent need for a structured onboarding approach.A system-based Train-the-Trainer (TTT) program was developed to address these issues, focusing on essential areas …

Transgender And Gender Diverse People – Inclusive Healthcare System Access, Dakota Denielle Lawtum

Yale School of Nursing Digital Theses

Transgender and Gender Diverse People – Inclusive Healthcare System AccessPurpose: This DNP project implemented a dual strategy to increase system-wide access to care and awareness of the needs of transgender and gender diverse people. Background: The 2015 U.S. Transgender Survey is the most recent and largest survey of its kind in the United States comprising a total of 27,715 responses. (National Center for Transgender Equality, 2015, U.S. Transgender Survey). The results of this survey are as follows: 1) 26% of the total national respondents experienced insurance issues for gender affirming healthcare or being denied coverage for routine care; 2) 32% …

Increasing Professional Interpreter Use To Improve Patient Outcomes On The Inpatient Oncology Unit, Kimberly Medina

Yale School of Nursing Digital Theses

Language barriers in healthcare contribute to significant disparities including delays in diagnosis and treatment, patient confusion, and increased mortality (Kwan et al., 2023). Approximately 21.5% of the people in the United States speak a language other than English at home and 8.2% of that population subset report speaking English less than very well (U.S. Census Bureau, 2021). Furthermore, in 2023 8% of Medicare beneficiaries have limited English proficiency (LEP) speaking and 7% have LEP reading (Centers for Medicare &Medicaid, 2024). Ensuring meaningful language access to LEP patients is essential for improving clinical outcomes and maintaining compliance to federal anti-discrimination policies. …

Panel: Program For Advancing Nursing Excellence For Leaders, Christopher D. Tarquinio

Yale School of Nursing Digital Theses

Healthcare organizations strive for nursing excellence, evident through prestigious awards like Magnet® Recognition and the Beacon Award of Excellence®. Nurse leaders play a crucial role in fostering a culture of excellence, but many face challenges due to confidence levels. PANEL educates nurse leaders on the connections between nurse satisfaction, patient satisfaction, and nurse quality measures (NQMs). By applying PANEL principles and transformational leadership, healthcare systems can positively impact nurse satisfaction, patient satisfaction, and NQMs. The aims of this project were: to develop a nursing excellence program for nurse leaders within a community-based healthcare system with the goal of connecting the …

Beyond Vulnerability: Climate Change And The Moral Authority Of Youth, Amber Acquaye

Yale Medicine Thesis Digital Library

Young people worldwide demand a voice in climate governance, yet their perspectives remain largely excluded from the moral frameworks that shape climate policy. This exclusion not only marginalizes children’s lived experiences and ethical reasoning but also perpetuates paternalistic norms and dangerous marginalization. To counter this, this thesis study shows that youth are not just passive stakeholders but moral agents whose perspectives yield a more just and comprehensive understanding of climate responsibility. Recognizing their ethical insights is crucial for medicine, especially pediatrics and child psychiatry, given how climate change amplifies health risks like respiratory illnesses, heat-related conditions, and eco-anxiety. Understanding how …

Effect Of Constraining Underdilated Transjugular Intrahepatic Portosystemic Shunts, Ishan Ayyalasomayajula

Yale Medicine Thesis Digital Library

Transjugular intrahepatic portosystemic shunt (TIPS) placement remains a primary treatment option for managing the sequelae of portal hypertension. However, the degree of decompression must be balanced to avoid complications of overshunting, such as hepatic encephalopathy (HE), liver failure, and heart failure. Currently, the most utilized device for TIPS creation, the Viatorr endoprosthesis shunt can be dilated to between 8 and 10 mm. However, dilating to the minimal size can decrease the hepatic-venous pressure gradient (HVPG) below goal. However, shunts that were underdilated at placement can self-expand to their minimal diameter. Placing a constraining stent around the endograft theoretically precludes such …

Quantitative Assessment Of Facial Ptosis In Face Transplantation, Sam Boroumand

Yale Medicine Thesis Digital Library

As a transformative surgical procedure, face transplantation restores form and function to patients with severe facial disfigurements, yet the long-term aging dynamics of transplanted tissues remain poorly characterized. This study aimed to investigate the progression of facial ptosis in transplanted facial allografts over time, addressing a critical gap in the understanding of long-term outcomes following face transplantation. Specific aims include quantifying ptosis progression using cephalometric measurements, identifying regional variations in the degree of ptosis across the face, and comparing changes between face transplant recipients and a non-face transplanted control cohort to contextualize findings.

To assess these aims, standardized frontal headshots …

“A Double-Edged Sword”: Influence Of The 21st Century Cures Act On The Childhood Cancer Care Experience, Mona Clappier

Yale Medicine Thesis Digital Library

The 21st Century Cures Act yielded policy change that allows patients toimmediately access components of their electronic health record (EHR) via an online portal. For children, adolescents, and young adults (AYAs) with cancer and their families, this federal mandate has profound implications. We sought to explore how immediate EHR portal access influences the childhood cancer care experience. We conducted semi-structured interviews with key informants, including parents of children with cancer, AYAs with cancer, and pediatric oncology healthcare professionals, at three National Cancer Institute-designated comprehensive cancer centers. Interviews were recorded, transcribed, and thematically analyzed. Across 84 participants, 71% self-identified as women …

Effectiveness Of Interventions For Depressive Symptoms After Spinal Cord Injury: A Systematic Review, Robert Cotter

Yale Medicine Thesis Digital Library

Our aims were to summarize and evaluate evidence regarding the efficacy ofinterventions for depressive symptoms in adults living with spinal cord injury (SCI) and comorbid major depressive disorder or significant depressive symptoms to inform the development of clinical practice guidelines. Articles published since 2013 and available in Medline, The Cochrane Library, Embase, Scopus, CINAHL, or PsycINFO were evaluated. Databases were searched in June 2022 and updated November 2023. Inclusion criteria: age 18 years or older, traumatic SCI, and clinically significant depression (Population), mental health interventions including behavioral, pharmacological, and complementary and alternative medicine (Intervention), inclusion of a control group (Comparator), …

Prevalence, Management, And Outcomes Associated With Obstructive Sleep Apnea In The Medical Icu, Madeline Lilly Ehrenberg

Yale Medicine Thesis Digital Library

The prevalence of Obstructive Sleep Apnea (OSA) in the general adult population has been estimated to be between 9-17% in women and 25-30% in men. However, the prevalence of OSA among medical intensive care unit (MICU) patients is unknown. A 2015 systematic review by Knauert et al demonstrated the associations of OSA with many chronic diseases commonly seen in MICU patients (for instance, hypertension, type II diabetes mellitus, and congestive heart failure). This same review also shed light on the gaps in knowledge surrounding OSA, including underdiagnosis, undertreatment, and lack of research. Given the overall prevalence of OSA and the …