Digital Commons Network^™

Dnabert Reveals Tf Motifs Information In Dna With Attention, Zetong Zhao

Public Health Theses

Traditional motif discovery tools often do not capture cooperative interactions between transcription factors (TFs). This study employs DNABERT, a transformer-based deep learning model, to analyze TF binding sites (TFBS) using attention mechanisms and k-mer tokenization. Fine-tuned on ENCODE ChIP-seq data, DNABERT achieved high predictive accuracy and could identify co-binders such as FOS and JUND through motif enrichment analysis. The model inferred position weight matrices (PWMs) aligning with JASPAR motifs and highlighted the regulatory importance of sequences near gene start regions. Comparisons with BPNet showed strong correlations, which validated DNABERT’s ability to capture TF-specific patterns. While constrained by dataset biases and …

Period Poverty And The Politics Of Refusal: Building Menstrual Equity Beyond The State Through Mutual Aid, Alanah Armstead

Public Health Theses

This thesis examines period poverty as a consequence of systemic neglect, disproportionately affecting those made vulnerable by intersecting structures of racial, gendered, and economic injustice. Situating menstruation as a public health crisis shaped by policy failure, social stigma, and institutional disregard, this research critiques dominant legal and policy frameworks that approach menstrual equity through a limited scope that overlooks deeper structural inequalities rooted in race and class. This thesis explores how marginalized populations experience legal and welfare systems as sites of surveillance and moral judgment in the context of menstrual equity. Through seven semi-structured interviews with menstrual justice organizers, this …

The Village Determinants Of Self-Rated Health And Mental Health: A Multilevel Analysis Of Environments In Rural Honduran Villages, Marnen Elizabeth Decker

Public Health Theses

I investigated the associations of village structural, behavioral, and social environments with self-rated health and mental health among adults residing in remote rural villages in the mountainous Copán region of Honduras. I estimated nested multilevel logistic models with 17,318 adults in 174 villages. All models controlled for individual characteristics to distill true village-level effects, and nested structure was employed to facilitate direct comparison across models. Both poor self-rated health and mental health were inversely associated with village size and positively associated with coffee cultivation. Poor self-rated health was also positively associated with friend/adversary tie ratio, and poor self-rated mental health …

Association Between Primary Covid-19 Vaccine Type And Booster Uptake Among Incarcerated People In Connecticut: A Retrospective Cohort Study, Michael Condon Elhardt

Public Health Theses

Importance: Booster doses of the COVID-19 vaccine are critical for maintaining protection against SARS-CoV-2, especially in high-risk settings such as correctional facilities. Understanding how initial vaccine type influences booster uptake can inform vaccination strategies in these and other underserved populations.Objective: To assess whether the type of COVID-19 vaccine received for the primary series—either viral vector (Janssen/Jcovden) or mRNA (Moderna/Spikevax or Pfizer-BioNTech/Comirnaty)—was associated with timing or likelihood of booster completion among incarcerated individuals. Design: Retrospective cohort study using survival analysis methods. The study period spanned from February 2, 2021, to May 31, 2023. Setting: Connecticut Department of Correction (DOC) facilities, including …

Empowering Mothers In New Haven: Evaluating The Impact Of A Maternal Health Program For New And Expecting Black And Brown Mothers, Ethelia Holt

Public Health Theses

The U.S. maternal mortality rate has surpassed that of other high-income countries, with mental health conditions now among the leading causes of perinatal death. These challenges disproportionately affect Black and Brown women, who are less likely to receive adequate follow-up care. The Maternal Health Program for New & Expectant Black and Brown Mothers aimed to improve maternal mental health through psychoeducation, skill-building, financial literacy, and connection to local resources.

A mixed-methods evaluation was conducted using pre- and post-program survey data (N = 7) to assess changes in mental health symptoms, knowledge, self-care, and financial habits. Descriptive statistics were the primary …

Empowering Mothers In New Haven: Evaluating The Impact Of A Maternal Health Program For New And Expecting Black And Brown Mothers, Ethelia Holt

Public Health Theses

The U.S. maternal mortality rate has surpassed that of other high-income countries, with mental health conditions now among the leading causes of perinatal death. These challenges disproportionately affect Black and Brown women, who are less likely to receive adequate follow-up care. The Maternal Health Program for New & Expectant Black and Brown Mothers aimed to improve maternal mental health through psychoeducation, skill-building, financial literacy, and connection to local resources.

A mixed-methods evaluation was conducted using pre- and post-program survey data (N = 7) to assess changes in mental health symptoms, knowledge, self-care, and financial habits. Descriptive statistics were the primary …

Environmental Justice Dimensions Of Orphaned Oil And Gas Wells In The United States, Grace Marie Hauser

Public Health Theses

Orphaned oil and gas (O&G) wells can leak methane and other hazardous pollutants,contributing to air and water contamination that threatens public health while also imposing financial burdens on local governments and taxpayers for remediation. However, the environmental and public health impacts remain understudied, in part due to limited understanding of the number and location of orphaned O&G wells. In this thesis we aimed to (1) create a national orphaned wells dataset covering years through 2024, (2) estimate the count and distribution of orphaned wells in the United States through 2024, and (3) evaluate the association between community environmental justice (EJ) …

Comparative Effectiveness Of Digital Breast Tomosynthesis And Digital Mammography In Detecting Invasive Lobular Carcinoma And Smaller Tumors Among Older Women, Sida Huang

Public Health Theses

AbstractBackground: Digital breast tomosynthesis (DBT) has demonstrated improved cancer detection and reduced false-positive and recall rates compared with digital mammography (DM) alone in trials of women aged over 50. However, its benefits for older women remain uncertain. We hypothesized that among women aged 67+, breast cancer detected via DBT are more likely to be invasive lobular carcinoma (ILC) and present at a smaller size at diagnosis, and this association persists among women aged 75+. Additionally, we hypothesized that DBT detects ILC at a smaller tumor size. Methods: We conducted a retrospective cohort study of women aged 67+ with screen-detected ER+/HER2- …

Assessing The Cross-Species Vaccine Potential Of Pfripr Using Transgenic Chimeric Plasmodium Knowlesi Models, Peiqi Li

Public Health Theses

Malaria remains a major global health burden, with an estimated 263 million cases and597,000 deaths reported in 83 countries in 2023 (1). While P. falciparum is responsible for the most severe cases, non-falciparum species such as P. vivax, P. ovale curtisi, P. ovale wallikeri, P. malariae, and P. knowlesi also pose significant public health risks, particularly in co-endemic regions. Current malaria vaccine efforts mainly focus on P. falciparum which is reasonable because over 90% of the global malaria-related morbidity and mortality are caused by P. falciparum (2). However, laying emphasis on targeting P. falciparum leaves a critical gap in cross- …

Universal School Meal Programs At The State-Level: Assessing The Next Iteration Of Child Nutrition Policy For A New Generation Of Students, Grace V. Manes

Public Health Theses

BackgroundEight states have passed legislation to codify universal school meal programs (USMPs) for public and nonprofit schools. These programs provide free school breakfasts and lunches to all students with no exclusions. A strong link exists between health, education, and social outcomes and the presence of subsidized school meal programs, and these outcomes are often used to advocate for such programs. This study assesses the prevalence of other state policies passed to address health, education and social outcomes (Medicaid expansion, universal pre-k, and state child tax credits) among states which have also passed USMP policies. We hypothesized that USMP passage would …

Exploring The Chemistry Of Wildfire Smoke: Leveraging High-Resolution Mass Spectrometry Approaches To Detect Chemical Signatures, Aline Grace Friesen Maybank

Public Health Theses

Background: Wildfire smoke is an increasingly important public health concern. While regulatory monitoring emphasizes fine particulate matter (PM2.5), wildfire smoke is composed of complex mixtures of volatile and semi-volatile organic compounds (VOCs and SVOCs), many of which are harmful to human health but are understudied.

Methods: Fresh Air Clips, passive chemical samplers, were deployed in Kamloops and Kelowna from March to September 2024 to measure VOC and SVOC concentrations before, during, and after the wildfire season. Chemical samples were analyzed using high-resolution mass spectrometry. PM2.5 concentrations, wildfire perimeters, wind direction and speed data, and HYSPLIT back-trajectories were integrated to classify …

Respirable Crystalline Silica In Stone Countertop Fabrication, Caitlin Mcgowan

Public Health Theses

Background: Artificial stone, a synthetic product that typically contains >90% silica mixed with resins and dyes, has become highly popular for kitchen and bathroom countertops. Meanwhile, silicosis outbreaks in workers who fabricate and install artificial stone countertops are increasingly being reported worldwide and in the US. Our objective is to better characterize work processes and exposures to respirable crystalline silica (RCS) among these workers in the United States. Methods: In collaboration with the Natural Stone Institute and the International Surface Fabricators Association, both trade organizations that represent the stone industry, an online survey was administered to stone countertop fabrication shops …

Life Satisfaction In Justice-Involved Opioid Users, Cassandra Michel

Public Health Theses

Life satisfaction—an individual’s overall evaluation of their life, including their feelings and attitudes toward it—has been linked to a range of psychological and physical health outcomes. While numerous studies have examined the factors associated with life satisfaction across various populations, such as healthy young and older adults, limited research has focused on individuals with substance use disorders or those involved in the criminal justice system. This study explored the relationship between psychosocial and structural factors and life satisfaction among justice-involved individuals with a history of opioid use disorder. Using cross-sectional survey data from a sample of 372 participants, I conducted …

Insights Into Medical Surveillance Among Engineered Stone Countertop Workers In The United States Of America, Tony Huy Nguyen

Public Health Theses

Background: An alarming rise in the number of cases of silicosis, a progressive and incurable lung disease, among engineered stone (ES) workers has prompted concern about the extent of the problem in the U.S. and whether ES can be used safely. Overexposure to high levels of respirable crystalline silica (RCS) during fabrication or installation of ES can increase the risk of developing a more severe case of silicosis. Medical surveillance studies on US ES workers are limited.Aim: The overall objective of this study was to better understand the state of medical surveillance for ES workers using employer surveys and employee …

Stage-Specific Disruption Of Cancer Cell Metabolism By Pfas: Connecting “Forever Chemicals” To The Growing Public Health Challenge Of Colorectal Cancer, Hannah O'Halloran

Public Health Theses

Per and polyfluoroalkyl substances (PFAS), termed “forever chemicals” for their persistence in the environment, are under investigation for their carcinogenic effects, but their specific impacts on colorectal cancer (CRC) progression remain largely unexplored. This study uses untargeted metabolomics to examine the effects of PFAS exposure on cells of CRC stages 2, 3, and 4, and identify state-specific alterations in important metabolic pathways. Later stage cells exhibit a greater response than early stage cells, suggesting increased susceptibility to PFAS effects in cells of more advanced cancer. PFOS had a greater effect on the metabolism of the cell lines compared to PFOA, …

From Success To Setbacks: A Case Study Of The Sex Wrap And The Impact Of Instagram's Evolving Policies On Sexual Health Education, Megan Piller

Public Health Theses

Due to the inconsistent and noncomprehensive nature of sexual health education across the United States, many adolescents and emerging adults are turning to digital platforms, specifically social media, for necessary information. The Sex Wrap (TSW), a podcast and Instagram-focused intervention, was established to fill critical knowledge gaps among these populations and empower them in their sexual decision-making. To serve as a case study, engagement metrics from TSW’s Instagram account between October 2020 and September 2021 were analyzed to determine which post types, tones, and thematic categories resonated most with users across the platform. However, Instagram, once a highly effective tool …

Global Comparison Of Children’S Exposomes, Inumidun Oyebode

Public Health Theses

Environmental influences impact health, often with enhanced susceptibility for theyoung. Understanding the sources of these environmental factors is critical for mitigating exposures. Globally, children are exposed to many sources that differ by policy, urbanization, and socioeconomic conditions. Specifically, urbanization creates variation in exposure sources that differ in rural (refuse combustion, cooking biomass combustion, indoor residual spray) and urban areas (vehicle combustion, industrial activity). Differences in policy further shape these exposure patterns by regulating pollution sources, chemical use, and environmental protections across countries. This thesis evaluated environmental exposures of children living in United States, South Africa, and Singapore contributing to a …

A Pilot Rct Of Mhealth & Chw Intervention For Art Adherence, Shivesh Shourya

Public Health Theses

Despite the availability of antiretroviral therapy (ART), only 66% of people with HIV in the U.S. achieve viral suppression, often due to suboptimal ART adherence. Barriers such as limited access to care and forgetfulness impact adherence, which must be ≥95% to prevent viral rebound. Combining community health worker (CHW) support with mobile health (mHealth) technologies may help address these barriers and improve outcomes. This pilot study evaluated the feasibility, acceptability, and preliminary efficacy of the remotely delivered Community Health Worker and mHealth to Improve Viral Suppression (CHAMPS) intervention, which combines the WiseApp, CHW support, and the CleverCap smart pill bottle. …

Epidemiological Changes In Shiga Toxin-Producing Escherichia Coli (Stec) Pre- And Post-Covid In Connecticut, 2018–2019 And 2023–2024, Brooke Thanh-Hang Tran

Public Health Theses

Background: Shiga toxin-producing Escherichia coli (STEC) causes over 265,000 infections, 3,600 hospitalizations, and 30 deaths annually in the U.S.. While STEC O157 is the most common serotype, the increased use of culture-independent diagnostic tests (CIDT) led to a rise in non-O157 serotypes detected. Nationally, STEC incidence declined during the COVID-19 pandemic but has since surpassed pre-pandemic levels. An analysis was conducted to determine the changes that occurred in STEC infections in Connecticut from pre-pandemic to post-pandemic and to identify differences between culture-confirmed cases and CIDT-only/untyped cases.Methods: A descriptive analysis using STEC surveillance data collected in Connecticut was performed to identify …

Integrating Rare Variant Association Studies With Embedding-Based Methods: Simiskato, Changheng Wang

Public Health Theses

Understanding the genetic basis of rare diseases remains a central challenge in human genomics, especially when conventional methods rely on case-control labels that may oversimplify complex clinical variation. In this thesis, we introduce SimiSKATO, a novel approach that integrates phenotype embeddings with rare variant association testing. Using PERADIGM-generated similarity scores to represent clinical resemblance between individuals, SimiSKATO treats these scores as continuous traits within the SKAT-O framework. By applying this method to rare diseases in the UK Biobank, we demonstrate that SimiSKATO not only replicates known gene-disease associations but also identifies biologically plausible novel candidates missed by other methods. This …

Expanding The Trypanosoma Brucei Parasite Detection Limit Through Tb177 Gene Detection In Qpcr, Yi Yan

Public Health Theses

Trypanosomiasis, caused by protozoan parasites of the Trypanosoma genus, remains a significant health and veterinary burden in sub-Saharan Africa, with Human African Trypanosomiasis (HAT) and Animal African Trypanosomiasis (AAT) posing ongoing threats to underserved populations. Despite advances in therapeutics, the lack of sensitive and scalable diagnostic tools continues to limit early detection, effective disease management, and evaluation of emerging vaccine candidates. Current diagnostic methods such as light microscopy and serological tests frequently fail to detect low levels of parasitemia during the early stages of infection, thereby delaying intervention and increasing the risk of disease progression and transmission.

Our study mainly …

Temporal Analysis In Connectivity Structure Of Human Disease Co-Occurance Network, Jingxuan Xu

Public Health Theses

Recent research on human disease networks (HDNs) has revealed the importance of jointly analyzing multiple diseasesand their interconnections, yet many existing approaches focus on molecular-based data and do not fully capture non-molecular relationships. Building on the concept of the phenotypical HDN, we leverage Medicare inpatient claims data to construct a comprehensive disease co-occurrence network. In our framework, two diseases are deemed interconnected if their observed probability of co-occurrence significantly deviates from that expected under independence. We adopt the weighted gene co-expression network analysis (WGCNA) framework to build our network, using a ϕ-correlation measure and a hard threshold to ensure a …

Probing Non-Perturbative Qcd With Jet Substructure Measurements At Star, Youqi Song

Yale Graduate School of Arts and Sciences Dissertations

In high-energy particle collisions, when incoming quarks and gluons (partons) exchange a large momentum during scattering, the outgoing partons undergo parton showers by primarily radiating off gluons successively. Hadrons are formed when the parton energies are sufficiently low. The collimated sprays of particles created through this process are called jets. Studies of the internal structure of jets, known as jet substructure, can provide insight into Quantum Chromodynamics (QCD), the theory that governs the interaction between partons and their formation into hadrons. In this thesis, I present two sets of measurements of jet substructure observables that are sensitive to the theoretically …

Data-Driven Functional Connectivity Investigations Into Neural Correlates Of Lateral Preferences, Link Tejavibulya

Yale Graduate School of Arts and Sciences Dissertations

Lateral preferences are ubiquitously present throughout the body despite its oversimplifications towards handedness. Studies on lateral preferences have therefore been simplified and binarized based on handedness preferences despite incongruencies and reduced proportions of right-preference as other limbs and measures are taken into consideration. In spite of this, studies on brain-laterality preferences that have been simplified and confined towards brain-handedness studies have demonstrated that handedness greatly affects how the brain is functionally organized and that these preferences are linked to high concurrences with other behavioral traits, both normative and psychiatric. For instance, males are more likely to be left-handed than females …

Security And Privacy Of Quantum Computers, Chuanqi Xu

Yale Graduate School of Arts and Sciences Dissertations

Quantum computing promises to revolutionize the way we solve computationally intractable problems by harnessing quantum phenomena such as superposition, interference, and entanglement. Over the past two decades, the field has witnessed a dramatic evolution—from early devices with one or two qubits to modern machines featuring over a thousand qubits, with projections now foretelling error-corrected systems with millions of qubits and capable of executing millions of gates. Moreover, quantum computing is no longer a theoretical or experimental concept. Quantum computers have become widely accessible via cloud-based platforms with companies such as IBM, Amazon, and Microsoft. These services not only democratize access …

Reducing Opioid Use Following Posterior Spinal Fusion Procedures: A Pilot Project, Kevin Matthew Cornett

Yale School of Nursing Digital Theses

Importance: Opioid misuse and mortality remain a prevalent problem in the United States and there is a high rate of chronic opioid-use after spinal fusions. Current guidelines recommend the optimization of non-opioid analgesics as a primary pain control strategy with opioids acting as a secondary agent. Objective: To pilot an analgesic decision tree (ADT) featuring non-opioid analgesics to reduce postoperative pain, opioid consumption, and the incidence of adverse events during the first 48 hours after patients undergo a posterior spinal fusion. Methods: A literature review of opioid-sparing analgesics was conducted and a protocol developed as an interdisciplinary collaboration. The ADT …

Readmission Reduction Of 1st Year Transplant Recipients, Kristin Freed

Yale School of Nursing Digital Theses

Abstract Readmission Reduction of 1st Year Transplant Recipients Clear communication with patients at their health-literacy level improves patient outcomes, fosters trust, and is associated with readmission reduction. Readmission of transplant recipients are correlated with morbidity, medical errors, higher healthcare economic costs, and indicative of decreased survival post- transplant. Literature suggests that up to 72% of transplant recipients may have low health literacy increasing risk of readmission. The Agency of Healthcare Research and Quality created the REALM-SF assessment as a tool for medical providers to evaluate a patient’s health literacy status in a timely manner. This Doctor of Nursing Practice (DNP) …

A (Great) Many Of Many Constructions, Jim Wood, Squid Tamar-Mattis

Yale Working Papers in Grammatical Diversity

In this paper, we discuss a series of constructions across various English dialects involving the word many, drawing examples from the Dictionary of American Regional English (DARE) and web searches. The constructions include both standard and colloquial forms, including formally singular and plural constructions, as well as those employing a lot of and a great many. We connect these constructions to existing linguistic analyses, particularly those proposed by Kayne (2002, 2006, 2007a,b, 2017).

Mapping The ‘Alternative One’ Construction In American English, Guilherme M. C. Pereira

Yale Working Papers in Grammatical Diversity

Alternative one is an understudied construction accepted by speakers of some American English dialects in sentences like (i), where the word one appears immediately after a disjunction.

(i) I need to talk to John or Malcolm, one.
'I need to talk to John or Malcolm, one or the other.'

(Montgomery 2006:152)

In this paper, I present maps of acceptability judgments of this construction in the U.S., using data from a survey administered by the Yale Grammatical Diversity Project in 2020 and 2021. The maps confirm the geographical distribution claimed for alternative one in the Dictionary of American Regional English (Cassidy …

I Have A Survey On Lonely Transitives! Do You Want?, Linda Do

Yale Working Papers in Grammatical Diversity

In this paper, I describe a recently observed grammatical construction that the YGDP has termed "lonely transitives" (LonTs). Used by some speakers of English in informal contexts, the construction consists of a traditionally transitive verb used without an object. LonTs can only be used if there is sufficient prior linguistic or situational context to recover the null object and if the sentence retains the same meaning as the verb used with an overt object. Using the results of a survey I conducted, I discuss the syntactic distribution of LonTs and suggest that it may be much wider than previously established …