Digital Commons Network^™

Hidden Workload In Emergency Medicine: Examining The Role Of Outside-Of-Shift Duties In Emergency Physician Fatigue, Sarah Meyer

All Theses

Emergency physicians (EPs) face high rates of burnout. In addition to well-known stressors, such as fatiguing shift work schedules and intense emotional and cognitive demands faced during clinical shifts, many EPs must also attend to certain outside-of-shift duties (OSDs)–extra-clinical role responsibilities that are expected but not always formally tracked or compensated. These duties often occur during times when EPs are expected to rest and recover from shift work. Despite concerns surrounding burnout in emergency medicine and beliefs among EPs that OSDs contribute to burnout, the effects of OSDs have rarely been studied. Using daily and weekly surveys across 28 days, …

Stochastic Universal Differential Equations For Epidemiological Modeling: Uncertainty Quantification In Disease Transmission Dynamics, Alice Menaya Armah-Bonney

Electronic Theses and Dissertations

Epidemic forecasting requires not only predictions of expected case counts, but also quantification of uncertainty, although existing surrogate modeling frameworks for agent-based models remain fundamentally deterministic. In this thesis a Stochastic Universal Differential Equation framework is presented that extends the deterministic Universal Differential Equation approach by incorporating a learnable stochastic diffusion term, enabling calibrated probabilistic forecasts while preserving the mechanistic interpretability and computational efficiency of the deterministic baseline. In doing so, a two-phase training algorithm is introduced to ensure stable convergence and the framework is validated against the ensemble output from ExaEpi, an exascale agent-based model of a COVID-19 outbreak …

Prevalence And Determinants Of Fully Vaccinated Status For Covid-19 Among Pregnant Women In Brazil, Ghana, Kenya, And Pakistan, Vaishnavi Mathur, Jessica Schue, Berhaun Fesshaye, Prachi Singh, Emily Miller, Caroline Badzi, Emefa Modey, Marleen Temmerman, Ferdinand Okwaro, Renato Souza

Centre of Excellence in Women and Child Health

Maternal immunization provides essential maternal and fetal protection for several infectious diseases. The variability in vaccination guidelines for pregnant women across countries and through the course of the COVID-19 pandemic influenced the perception of both the general public and broader health care systems towards COVID-19 vaccination in pregnancy and moreover shaped the accessibility and decision-making trajectory of pregnant women to become fully vaccinated. As part of a larger multi-country, mixed-methods study, the purpose of this cross-sectional analysis is to assess what factors are associated with pregnant women being fully vaccinated for COVID-19 in Brazil, Ghana, Kenya, and Pakistan. In each …

Pertussis, Children's Mercy Kansas City

Clinical Pathways

No abstract provided.

Agency Fact-Making, Haiyun Damon-Feng

Articles

Modern administrative-law scholarship, theory, and doctrine generally conceptualize agencies as engaging in three primary functions: rulemaking, enforcement, and adjudication. This understanding of agencies has informed deep debates surrounding the power, independence, and constitutional legitimacy of the administrative state. But the prevailing account is incomplete. It overlooks a fourth core function of the administrative state: its fact-making, or epistemic, function. Across the administrative state, agencies create and disseminate information in ways that are uniquely comprehensive and uniquely powerful. Agencies’ epistemic outputs include the census generated by the Census Bureau, repositories of public-health information maintained by the Centers for Disease Control and …

Arrest Rates And Police Presence In East Bay Area Counties Of Northern California, Christiana M. Tyler

Electronic Theses, Projects, and Dissertations

In this research study, we discuss the social phenomenon of mass incarceration in the United States. Previous research has evidenced clear racial disparities within this social issue, but has yet to make a connection between high incarceration rates and the sheer volume of police officers in many communities. This descriptive study sets out to discover whether there is a difference in incarceration rates based on the level of police presence in select counties in Northern California. The study will measure police presence by the number of police officers, using secondary data from U.S. government and nonprofit agencies. The researcher hypothesizes …

Sepsis As An Immune Continuum: Cytokine Storm To Lymphopenia And Pics, Chelsey King

Senior Honors Theses

Sepsis is a leading cause of morbidity and mortality worldwide, driven by a dynamic immune continuum that progresses from early hyperinflammation to profound immunosuppression. This review examines the three overlapping phases of sepsis: the inflammation-mediated cytokine storm driven by dysregulated PRR activation, NF-κB signaling, and NETosis; apoptosis-driven lymphopenia involving caspase-mediated lymphocyte death, dendritic cell dysfunction, and metabolic exhaustion; and prolonged immunoparalysis culminating in persistent inflammation, immunosuppression, and catabolism syndrome (PICS). Key mechanisms linking these phases, including the co-existence of hyper- and hypo-inflammatory states, are synthesized alongside relevant clinical biomarkers such as IL-6, HLA-DR, and single-cell immune profiles. This review highlights …

Beyond Health Reform: The Aca And The Social Drivers Of Health, Wendy E. Parmet, Jasmine M. Howard

Seton Hall Journal of Legislation and Public Policy

No abstract provided.

A Tractable Nematode Model For The Emerging Fungal Pathogen, Candida Auris, Melissa Martinez

Dissertations and Theses (Open Access)

Candida auris is an emerging multidrug-resistant opportunistic fungal pathogen. It

poses a significant threat to immunocompromised patients and those with prolonged stays in

healthcare facilities. C. auris spreads rapidly in health care facilities through enhanced

colonization of skin and abiotic surfaces. The genetic factors contributing to this ability and to

the virulence, drug resistance, and stress-tolerant nature of C. auris are largely unknown.

Current animal models of C. auris infections are not well standardized and report conflicting

results. Additional animal models of virulence are needed, especially those amenable to high-

throughput analysis. The nematode Caenorhabditis elegans has been validated as …

Characterization Of Staphylococcus Aureus Clinical Isolates From Deep Musculoskeletal Infections For An In Vitro Biofilm Model For Phage Therapy, Raquel C. Luna

Dissertations and Theses (Open Access)

The rise of multidrug-resistant (MDR) infections is a growing concern in the treatment of deep musculoskeletal infections (MSKIs) and orthopaedic device-related infections (ODRIs). Staphylococcus aureus is responsible for about one third of these infections due to its strong biofilm forming capacity, presence on human skin, and the large number of antibiotic-resistant variants. Bacteriophage (phage) therapy is now being considered as a treatment for MDR MSKIs/ODRIs. We are investigating the use of phage encapsulated into or adsorbed onto biodegradable microspheres for local delivery to the site of these MDR infections. We determined that the anti-staphylococcal phage K effectively lyses the S. …

From Antigen Presentation To Tumor Control: Mechanisms Of Type I Conventional Dendritic Cell-Based Cancer Vaccines, Josue E. Pineda

Dissertations and Theses (Open Access)

Type 1 conventional dendritic cells (cDC1s) are important for generating and sustaining antitumor immunity. Accordingly, the abundance of cDC1s in human tumors correlates with improved outcomes in cancer. Capitalizing on this role, we previously demonstrated that vaccination with in vitro-derived murine cDC1s elicits durable tumor control in multiple preclinical models; however, the immunological mechanisms underlying the efficacy of cDC1 vaccination remain unclear. Here, we examined whether in vitro-derived cDC1s resemble tumor-infiltrating DC populations and whether MHC-I and MHC-II antigen presentation contribute to cDC1-mediated tumor control following vaccination in melanoma.

As expected, MHC-I- or MHC-II-deficiency had minimal impact on …

Understanding Epigenomic Landscapes In Cancer Progression And Immunotherapy Response, Jonathan Schulz

Dissertations and Theses (Open Access)

Nonmutational epigenomic reprogramming has emerged as a key hallmark of cancer that plays crucial roles in tumor evolution during its progression and response to therapy. However, the extent and nature of epigenomic reprogramming remains poorly understood. This dissertation examines how epigenetic regulation shapes cancer progression and response to immunotherapy. Working at the intersection of cancer biology and computational genomics, it develops analytical frameworks for characterizing chromatin structure and DNA methylation across diverse tumor contexts and uses these frameworks to address two complementary biological questions: how promoter-associated chromatin organization varies across cancer types, and how epigenetic perturbation modulates tumor immunogenicity in …

An Integrated Framework For Early Detection And Transmissibility Assessment Of Emerging Variants In Wastewater, Xingwen Chen, Tin Phan, Wei Lin Lee, Katie Clark, Steven F Rhode, Samantha Brozak, Bruce Pell, Tsultrim Palden, Mats Leifels, Anna Gitter, Yang Kuang, Stefan Wuertz, Janelle Thompson, Kristina D Mena, Eric J Alm, Fuqing Wu

Faculty, Staff and Student Publications

Tracking the emergence of new viral variants is critical for epidemic preparedness, but remains challenging because variants typically circulate at low prevalence during the early phase of outbreaks. Here, we present an integrated framework that combines sensitive variant detection in wastewater with quantitative assessment of transmissibility through dynamic epidemic modeling. Using the SARS-CoV-2 Omicron variant as a proof of concept, we developed a novel nested allele-specific RT-qPCR assay (NAS-PCR) that achieved a thousand-fold increase in sensitivity compared with allele-specific RT-qPCR (limit of detection: 0.5 copies/μl). NAS-PCR detected Omicron in wastewater samples from the Greater Boston area starting in September 2021, …

Identifying And Exploring The Presence Of Antibiotic Resistant Escherichia Coli In Private Groundwater Sources In Southeastern Ontario Via Machine Learning, Madeleine Kelly, Paul Hynds, R. Stephen Brown, Kevin Mcdermott, Ioan Petculescu, Rhiannon Punch, Anna Majury

Research Outputs: 2025-Present

According to the World Health Organization, antibiotic resistance represents one of the top global public health and development threats. The environment serves as a significant reservoir and transmission pathway for antibiotic-resistant bacteria (ARB), with anthropogenic activities introducing resistant bacteria, resistance genes, and antibiotic residues to soils and aquatic systems, thereby promoting development and dissemination of resistance. Groundwater has recently been highlighted as an important reservoir for antibiotic-resistant bacteria, with over four million Canadian residents currently relying on private groundwater wells (Statistics Canada, 2024). While groundwater is increasingly acknowledged as a reservoir of ARB, the influence of external drivers affecting their …

Abnormal Trafficking And Processing Of Multiple Matrix Metalloproteinases Drive Cartilage Defects In Congenital Disorders Of Glycosylation, Chia-Lun Wu

All Dissertations

Congenital Disorders of Glycosylation (CDG) are rare metabolic diseases caused by defects in glycosylation. Despite identification of over 200 CDG types, the mechanisms linking glycosylation defects to diverse clinical phenotypes remain unclear. This dissertation uses zebrafish models of PMM2-CDG and STT3-CDG to redefine CDG pathogenesis, shifting from a simple glycan deficiency model to one involving disrupted cellular spatial organization.

We identify a protease-dependent pathway underlying craniofacial cartilage defects. Specifically, defective proteolytic processing of N-cadherin, a key adhesion molecule in chondrogenesis, is a central driver of pathology. We further uncover an unconventional trafficking mechanism in which ER stress and altered secretory …

Enhancing Food Security In Stann Creek, Belize Using Meat Rabbits: Engineering Perspective, Lindsey Garretson

Biological and Agricultural Engineering Undergraduate Honors Theses

The purpose of this paper is to discuss the engineering perspective within the overall project of using meat rabbits to enhance food security and nutrition within Stann Creek, Belize. From the engineering perspective, the overarching goals were like the overarching project goals including the construction and materials required guide within the manual, designing potential upgrades to the design including a solar and battery system and an automatic watering system, and to design the system to be “practically sustainable” where possible. The constraints for this project included cost, the size of land dedicated for the rabbitry, and the operational and environmental …

A Mass Disabling Event: Why California Courts Must Protect Workers’ Families From Take-Home Covid, Ellery Armstrong

Seattle Journal for Social Justice

No abstract provided.

Understanding The Role Of Toxs As A Bile Sensing Component Of The Toxrs Virulence Regulatory System In Vibrio Spp., Minje Kim

Dartmouth College Ph.D Dissertations

Pathogenic Vibrio bacteria, such as V. cholerae and V. parahaemolyticus, colonize in the human small intestine to cause severe gastrointestinal disease. During the infection, these bacteria encounter bile salts, antimicrobial cholesterol metabolites secreted into the intestine. Pathogenic Vibrio species have evolved to utilize bile salts as signals to regulate virulence. The signaling depends in part on ToxRS, a conserved co-component transmembrane transcription regulator. ToxRS consists of the transcription factor ToxR and its membrane-tethered binding partner ToxS. ToxS is required for ToxR stability and full transcriptional activity. Although bile salts are known to influence ToxRS-dependent virulence gene expression, the molecular …

Drug Repurposing Against Giardia Targeting Lipid Rafts, Extracellular Vesicles, And Sphingolipid Synthesis, Breanna Chantal Pence

Open Access Theses & Dissertations

Giardia lamblia is a protozoan parasite responsible for the intestinal disease giardiasis worldwide. Giardia is one of the major intestinal parasites in the world, with over 500,000 new cases annually. Symptoms of giardiasis include diarrhea, abdominal pain, and nausea. Children are particularly vulnerable to giardiasis, with cases of malnutrition, stunted growth, and cognitive impairment in countries where the disease is endemic. Giardia consists of two morphologic forms: an infective cyst which transmits the disease and a motile trophozoite which attaches to the epithelium of the small intestine during infection. Metronidazole is a common treatment for giardiasis, but cases of toxicity …

Determining Zap-70 Signaling Pathways Mediated By Ccr7 In Tcr T Cell Activation, Vivian Torres

Open Access Theses & Dissertations

Activation of T lymphocytes is the main event that occurs in the adaptive immune response after engagement of the T cell receptor (TCR) with the peptide of the major histocompatibility complex (pMHC) molecules that are demonstrated by antigen presenting cells [1]. A key step in this process is the recruitment and activation of the zeta chain associated protein of 70 kDa (ZAP-70). ZAP-70 couples TCR engagement to downstream intracellular signaling pathways through phosphorylation of tyrosine residues within intracellular tyrosine activation motifs (ITAMs) [2]. Although there have been extensive studies on the signaling response through TCR activation, the regulatory influence of …

From Covid-19 To Influenza: Transforming Public Health Surveillance Through Freeze-Drying Innovations, Rui Dong

Open Access Theses & Dissertations

Public health surveillance increasingly relies on wastewater-based epidemiology (WBE) as a non-invasive, community-level early warning system for infectious diseases like COVID-19 and influenza. However, detecting minute viral concentrations in complex wastewater matrices remains a significant analytical challenge. Traditional concentrating methods, such as ultrafiltration, are limited by high performance variability and significant viral signal loss due to necessary pretreatment steps, such as pre-clarification, which inadvertently discard solid-associated viral fractions. To address these limitations, this dissertation introduces and evaluates freeze-drying as a novel, pretreatment-free concentrating method for wastewater viral surveillance. By sublimating water, freeze-drying uniquely retains both liquid and solid-phase viruses within …

Exploring The Correlation Between Malnutrition And Food And Nutrition Insecurity In Inflammatory Bowel Disease, Heather Burr

All Graduate Theses and Dissertations, Fall 2023 to Present

Inflammatory Bowel Disease (IBD) may increase the risk of malnutrition because of nausea, vomiting, diarrhea and restrictive eating. In addition, patients with IBD may experience food and nutrition insecurity. Therefore, we conducted an online survey to assess risk of malnutrition and food and nutrition insecurity among adult patients with IBD in outpatient and community settings. Patients were recruited between July and December 2025, aiming to reach adults in the Rocky Mountain Region diagnosed with IBD. Data collected included demographics, health-related factors, risk of nutrition insecurity, risk of food insecurity, and barriers and facilitators to dietary management of IBD.

Fifty-seven patients …

Human Papillomavirus (Hpv) Vaccine Acceptance: A Mixed-Methods Study And Randomized Controlled Trial Examining Messengers Of Hpv Vaccine Information Among Hispanic Parents, Alyssa Andrea Martinez

Open Access Theses & Dissertations

Hispanics make up 19.5% of the U.S. population, making them the nation's largest ethnic minority. Hispanics are disproportionately impacted by health outcomes, including many different types of cancers that are caused by the Human Papillomavirus (HPV). An HPV vaccine is available that can prevent 90% of HPV associated cancers. The purpose of this mixed-methods study and randomized experiment is to develop and test data-driven digital health messages to promote the HPV vaccine in Hispanic parents. Four specific aims were conducted among three major studies. Aim 1 (Study 1): A cross-sectional survey was conducted to obtain preliminary evidence on trusted messengers …

Characterization Of The Antiviral Activity Of Mouse Schlafen Proteins, Wendy Paola Alvarez Leal

Open Access Theses & Dissertations

The goal of this work was to characterize the anti-viral role of mouse Schlafen8 and Schlafen9. Expression of these proteins is induced by type I interferon in response to viral infections. Importantly, their human functional orthologs exhibit anti-viral functions, and the structural element required for these activities are conserved in Schlafen8 and Schlafen9. Therefore, it is expected that these proteins will also impair viral replication. An important limitation in this field is that the anti-viral function of human SLFNs has been evidenced only in in vitro cellular models. No informative mutations have been described in human populations so far. Thus, …

Exploring A 'Fishy' Solution: Uncovering Human Norovirus Using A Zebrafish Model, Sahaana Chandran

Graduate Theses and Dissertations

Human norovirus (HuNoV) is the leading cause of acute gastroenteritis worldwide; however, the lack of robust laboratory culture systems and reliable animal models has limited progress in understanding viral replication and developing effective intervention strategies. While alternative models such as the zebrafish system have been explored, gaps remain in evaluating their ability to support replication across diverse HuNoV strains and in identifying factors that influence infectivity. This dissertation provides a comprehensive investigation into the use of the zebrafish model for studying viral replication, host interactions, and potential inhibition strategies. Initial studies focused on optimizing viral delivery methods using Tulane virus …

Bats And Bacteria: Infection Dynamics At The Human-Wildlife Interface, Isabella Katherine Deanglis

Graduate Theses and Dissertations

As the second most diverse mammalian order, bats host an array of pathogens, some of which are known to infect humans. Synanthropic bats share spaces with humans, resulting in bat-borne pathogen exposure. While most bat-borne disease research has focused on viral pathogens, bats host numerous bacterial pathogens with zoonotic potential. By integrating a global meta-analysis with field studies in Sub-Saharan Africa, I characterize the structural attributes that facilitate shared interfaces, the bacterial pathogens present in synanthropic bats of rural Kenya, and the physiological and environmental dynamics influencing odds of infection in these synanthropic bats. Finally, I evaluate the clinical relevance …

Low-Abundance And Fragmentary Helicobacter Pylori Dna Detected In Phenotypically Negative Gastric Biopsies Using Targeted Sequencing, Fabien Mbaya-Tshibangu, Alain Cimuanga-Mukanya, Evariste Tshibangu-Kabamba, Nadine Kayiba-Kalenda, Tressy Kalenga-Ngomba, Patrick Ngoma-Kisoko, Gunturu Revathi, Junko Akada, Benoît Mbiya-Mukinayi, Augustin Tshibaka Kabongo

Pathology, East Africa

Accurate detection and monitoring of antimicrobial resistance (AMR) in Helicobacter pylori mainly rely on phenotypic methods and culture, which can sometimes fail when bacterial load is low or after recent treatment. We investigated whether gastric biopsies classified as H. pylori-negative by standard diagnostic techniques still contain detectable bacterial DNA, including regions linked to AMR, and assessed whether selected DNA fragments can mediate allelic exchange in vitro. Gastric biopsies from 46 dyspeptic patients in the Democratic Republic of the Congo (including 23 phenotypically positive and 23 phenotypically negative individuals) were analyzed using long-read amplicon sequencing of seven resistance-associated loci, selective whole-genome …

Optimized Ultrasound Imaging Of Phase-Change Nanodroplets, Charles R Dyall, Dmitry Nevozhay, Andy Liu, Trevor M Mitcham, George J Lu, Konstantin V Sokolov, Richard R Bouchard

Faculty, Staff and Student Publications

Phase-change nanodroplets (PCNDs) continue to generate significant research interest due to their potential to extravasate into tissue, to be targeted for molecular imaging and drug delivery, and to undergo an induced phase-change to "activated" microbubbles (MBs) for ultrasound (US) imaging. To accurately quantify molecular markers, however, one assumes a consistent proportion of PCNDs in a region of interest (ROI) are stably activated and imaged. Herein we present a framework for developing a diagnostic sequence that is optimized for PCND activation uniformity, contrast, and acquisition time. To develop this framework, activation was examined at three scales of increasing complexity: single, adjacent, …

Potential Impact Of Parasites In The Transmission Of Chronic Wasting Disease, Paulina Soto, Rodrigo Morales

Faculty, Staff and Student Publications

No abstract provided.

Long Covid Persistence And Surveillance Gaps Across 58 Us Hospitals, Jiazi Tian, Alaleh Azhir, Matthew Decaro, Ngan Chau, Jonas Hügel, Michele Morris, Jingya Cheng, Pedram Fard, Ingrid V Bassett, Douglas S Bell, Elmer V Bernstam, Shyam Visweswaran, Jeffrey G Klann, Shawn N Murphy, Hossein Estiri

Faculty, Staff and Student Publications

Importance: Surveillance of postacute sequelae of SARS-CoV-2 infection (PASC) depends on diagnostic coding systems that capture fewer than one-half of affected individuals, rendering millions invisible to health systems and policymakers.

Objective: To quantify the gap between true PASC burden and diagnostic code-based estimates, determine the proportion representing chronic disease, and characterize organ system heterogeneity and temporal trends across diverse populations.

Design, setting, and participants: This retrospective cohort study used electronic health record data from 58 hospitals and affiliated clinics in 4 US regions, from 2017 to 2025. Adults (aged ≥18 years) with laboratory-confirmed SARS-CoV-2 infection or a COVID-19 diagnosis code …