Digital Commons Network^™

Leveraging Large Language Models For Knowledge-Free Weak Supervision In Clinical Natural Language Processing

Faculty, Staff and Student Publications

The performance of deep learning-based natural language processing systems is based on large amounts of labeled training data which, in the clinical domain, are not easily available or affordable. Weak supervision and in-context learning offer partial solutions to this issue, particularly using large language models (LLMs), but their performance still trails traditional supervised methods with moderate amounts of gold-standard data. In particular, inferencing with LLMs is computationally heavy. We propose an approach leveraging fine-tuning LLMs and weak supervision with virtually no domain knowledge that still achieves consistently dominant performance. Using a prompt-based approach, the LLM is used to generate weakly-labeled …

Development Of A Multi-Epitope Peptide Vaccine Against Monkeypox Virus: Immunoinformatics Analysis For South East Asian Hla Alleles, Nelson Chandra, Mochammad Aqilah Herdiansyah, Viol Dhea Kharisma, Arif Nur Muhammad Ansori, Arli Aditya Parikesit

Makara Journal of Science

The monkeypox virus (MPXV), a DNA virus causing zoonotic disease, poses major global public health challenges, with mortality rates between 3%–6%. Although smallpox vaccines provide partial cross-protection, there is a critical need for a dedicated, effective monkeypox (mpox) vaccine. This study aimed to design a multi-epitope peptide-based vaccine specifically adapted to the HLA allele profiles common in Southeast Asian populations, where MPXV cases are rising. Using immunoinformatics, we screened for and detected B and T cell epitopes from the MPXV cell surface antigen and IFN-alpha/beta receptor proteins. The vaccine design was validated through a rigorous evaluation of its antigenicity, immunogenicity, …

Ubiquitous News Coverage And Its Varied Effects In Communicating Protective Behaviors To American Adults In Infectious Disease Outbreaks: Time-Series And Longitudinal Panel Study, Anqi Shao, Kaiping Chen, Branden Johnson, Shaila Miranda, Qidi Xing

Information Systems Faculty Publications and Presentations

Background: Effective communication is essential for promoting preventive behaviors during infectious disease outbreaks like COVID-19. While consistent news can better inform the public about these health behaviors, the public may not adopt them.

Objective: This study aims to explore the role of different media platforms in shaping public discourse on preventive measures to infectious diseases such as quarantine and vaccination, and how media exposure influences individuals’ intentions to adopt these behaviors in the United States.

Methods: This study uses data from 3 selected top national newspapers in the United States, Twitter discussions, and a US nationwide longitudinal panel survey from …

Novel Signaling Pathways Involved In Ybx1 Role In Hepatocellular Carcinoma, Yamile Abuchard Anaya, Ana Ayala Pazzi, Dennis Kwabiah, Veerababu Nagati, Ricardo Pequeno Bracho, Kyle Doxtater, Subhash C. Chauhan, Manish K. Tripathi

Research Symposium

Background: The most prevalent type of liver cancer is hepatocellular carcinoma (HCC), and socioeconomic and health disparities have a major impact on both its incidence and fatality rates. HCC rates are typically greater in areas with poor access to healthcare, high obesity rates, and a high frequency of infectious diseases. Because of risk factors include diabetes, non-alcoholic fatty liver disease (NAFLD), and Hepatitis B and C, HCC is particularly common in the Rio Grande Valley (RGV). The burden of HCC in this underprivileged area is made worse by McAllen, Texas, which regrettably holds the distinction of being the most obese …

Renal Transplant Recipients And Complicated Utis: A Path Toward Next-Generation Care, Rob E. Carpenter

Human Resource Development Faculty Publications and Presentations

Next-generation sequencing (NGS) offers diagnostic potential in managing complicated urinary tract infections (UTIs) in renal transplant recipients by enabling precise pathogen identification and resistance profiling. Integrating NGS into care protocols can improve graft preservation, reduce hospitalizations, and support antimicrobial stewardship. Policies should prioritize its adoption, while research explores cost-effectiveness and clinical outcomes. Medical education must emphasize NGS to prepare clinicians for advanced diagnostic approaches, fostering improved patient outcomes and innovative care solutions. Please cite this paper as: Carpenter RE. Renal transplant recipients and complicated UTIs: a path toward next-generation care. Renal transplant recipients face a heightened risk of complicated urinary …

Impact Of Chromatin On Hiv-1 Latency: A Multi-Dimensional Perspective, Joanna E. Jones, Chelsea E. Gunderson, Brian Wigdahl, Michael R. Nonnemacher

Kimmel Cancer Center Papers, Presentations, and Grand Rounds

Human immunodeficiency virus type 1 (HIV-1) is a retrovirus that infects multiple immune cell types and integrates into host cell DNA termed provirus. Under antiretroviral control, provirus in cells is able to evade targeting by both host immune surveillance and antiretroviral drug regimens. Additionally, the provirus remains integrated for the life of the cell, and clonal expansion establishes a persistent reservoir. As host cells become quiescent following the acute stage of infection, the provirus also enters a latent state characterized by low levels of transcription and virion production. Proviral latency may last years or even decades, but stimuli such as …

Investigating The Ability Of Foxo1 To Maintain Stem Cells, Stella A. Rios, Megan E. Keniry

Research Symposium

Background: Our group discovered that FOXO transcription factors drive stem gene expression in cancer to promote aggressiveness. Work by our group and others demonstrated that FOXO factors universally maintain stem cells including in cancer, embryonic, hematogenic and neuronal contents. Our current efforts are delineating the molecular underpinnings by which FOXO factors halt differentiation to maintain stem cells.

In this project, we are employing myoblasts as a valuable model to examine how Foxo1 maintains stem cells. Foxo1-regulated genes in myoblasts closely parallel its targets in glioblastoma and basal breast cancer stem cells, including targets such as Leukemia Inhibitory Factor, …

Provider Perspectives On The Challenges And Opportunities In Managing Chronic Pain Among Patients With Hiv And A History Of Substance Use Disorder: A Qualitative Study, Sonya A. Bhatia, Isabella Iregui, Amy Knowlton, Tuo-Yen Tseng

Research Symposium

Background: Chronic pain is common in people living with HIV or opioid use disorder and is complex to clinically manage. Opioid dependence treatment, such as Suboxone (combined buprenorphine and naloxone), is associated with improved adherence to antiretroviral therapy, reduced opioid use, and lower overdose risk. While evidence suggests Suboxone can treat opioid use disorder and chronic pain concomitantly, its use as an analgesic remains off-label. Patients with these co-morbidities, especially prevalent among People of Color, are often underdiagnosed and undertreated . This study explored clinicians’ experiences and opinions on managing chronic pain in (mostly Black) persons living with HIV who …

The Relationship Of Physician Associate Student Satisfaction And Academic Performance, Jed Grant, Nancy Hamler

Pacific Journal of Health

Introduction: Patient and student satisfaction are increasingly important factors in healthcare and higher education, respectively. While satisfaction is important, it may not always correlate directly with outcomes, academic performance, or long-term professional accomplishments. Researchers aim to investigate the relationship between student satisfaction and measures of student success. Methods: This retrospective study analyzed data from 215 students over five PA student cohorts for correlations between student satisfaction and academic performance in core clinical medicine courses, program GPA, and PANCE scores. Statistical analysis was performed by data scientists to test for independence and significance. Results: The systems-based clinical medicine course had a …

Let’S Worm In To The Guinea Worm Disease, Rachel Decker

Osmosis Magazine

Imagine living with another organism in your body, cohabiting for months before you are even aware of its presence. Slowly, a lesion starts to form on your leg. The lesion grows bigger everyday, starting at a couple millimeters but growing up to a couple centimeters. The burning sensation starts with the lesion and can only be dimmed by submerging your leg in water. Suddenly, a worm emerges from the lesion along with pus and blood. The patient is infected with Guinea Worm Disease.

The Science Of Tattoos, Isabel Dilandro

Osmosis Magazine

From face paint to temporary stick-on tattoos, children are taught that art on bodies is something beautiful and playful, associated with memories of fun and joy. Why is it then that tattoos get such an infamous reputation? The answer is pretty simple: tattoos are not temporary. But why? How does the ink get there? How does it stay put? In order to understand this process a bit more, it is important to have a basic understanding of the skin’s structure and function.

Osmosis Magazine - Fall 2021

Osmosis Magazine

Osmosis is a student read, led, and written publication from the University of Richmond, focusing on all aspects of healthcare and science.

The Unusual Suspect - Herpes Zoster As The Culprit For Severe Abdominal Pain. A Case Report., Edward Lovering, Ahmad Asif, Sean Sheih, Samuel B Holzman, Yani Zhang

Journal of Community Hospital Internal Medicine Perspectives

Reactivation of herpes zoster leading to disseminated and visceral organ involvement is an uncommon phenomenon and almost always associated with immunocompromised patients. Visceral herpes zoster is a challenging diagnosis to make as patients typically present with severe abdominal pain which precedes the typical rash of herpes zoster. We describe the case of a 68-year-old female who presented to the emergency department with abdominal pain and was subsequently diagnosed with disseminated herpes zoster and found to have underlying monoclonal gammopathy.

Risk Factors, Pathogenesis, Prevention And Clinical Features Of Cardiovascular Implantable Electronic Device (Cied) Infections, Mustafa Shehzad, Humna Younis, Rohail Azhar, Dawood Shehzad, Noor Zara Usman

Journal of Community Hospital Internal Medicine Perspectives

Cardiac implantable electronic devices (CIEDs) are essential therapeutic tools for managing various cardiac conditions but are also associated with the risk of infections, leading to significant morbidity, mortality, and healthcare costs. Risk factors include patient comorbidities, procedural aspects, and device characteristics. Prompt intervention and early recognition of CIED infections, including pocket and systemic infections, are essential for preventing complications. Advanced imaging modalities aid in accurate diagnosis, while a multidisciplinary approach involving infectious disease specialists and cardiologists guides treatment strategies. Tailored antibiotic therapy, along with device removal and lead extraction, is crucial in managing CIED infections. This article emphasizes risk factors, …

Association Of Inflammatory Biomarkers With New Functional Morbidity At Hospital Discharge In Children Who Survive Severe Sepsis, Mallory Perry-Eaddy, Walter Faig, Martha Curley, Scott Weiss

Department of Pediatrics Faculty Papers

OBJECTIVE: New functional morbidity is common in critically ill children who survive sepsis; yet, the underlying biological mechanisms, particularly the impact of inflammation, remain unknown. We sought to test the hypothesis that increased levels of inflammatory biomarkers during the acute phase of pediatric sepsis are associated with new functional morbidity at hospital discharge.

METHODS: We conducted a post hoc secondary analysis of the MitoPSe clinical study, including N = 119 critically ill children who survived sepsis. Data collected included demographic and clinical variables and 31 inflammatory biomarkers collected at three distinct timepoints (within days 1-2 of PICU admission, days 3-5, …

Immunotherapy-Related Neurotoxicity In The Central Nervous System Of Children With Cancer, Jiasen He, Jeremy Connors, Andrew Meador, Shuo Xu, Heather Meador, Juan Fueyo, Gregory K Friedman, Wafik Zaky, Zsila Sadighi, John M Slopis, Ali H Ahmad

Faculty, Staff and Student Publications

Significant gaps remain in our understanding of immunotherapy-related neurotoxicity in pediatric patients, largely because much of our knowledge comes from studies in adults. Accurately identifying the adverse effects of immunotherapy in children is also challenging, owing to variations in terminology and grading systems. Moreover, the manifestation of immunotherapy-related neurotoxicity differs greatly across different diseases, various modalities, dosages, and delivery methods. Combining immunotherapy with other treatments might improve outcomes but introduces new complexities and potential for increased toxicities. Additionally, pediatric patients with intracranial malignancy have unique responses to immunotherapies and distinct neurotoxicity compared to those with extracranial malignancy. Consequently, we must …

The Hidden Faces Behind The Covid-19 Vaccine, Julia Brittain

Osmosis Magazine

When you think about the COVID-19 vaccine, the names Pfizer or Moderna probably come to mind. It’s no surprise that these companies are often mentioned in discussions of the COVID- 19 vaccine. After all, in December 2020, Pfizer-BioNTech became the first biopharmaceutical company to receive emergency use authorization for their COVID-19 vaccine from the FDA, and Moderna followed shortly after.

Osmosis Magazine - Spring 2021

Osmosis Magazine

Osmosis is a student read, led, and written publication from the University of Richmond, focusing on all aspects of healthcare and science.

Mechanisms Of Macrophage Metabolic Activation And Paracrine Wnt Signaling In The Pathogenesis Of Systemic Sclerosis, Emily Ann Morris

Dartmouth College Ph.D Dissertations

Systemic sclerosis (SSc) is a chronic autoimmune disease of unknown etiology. We have previously shown that macrophages (MØs) play a critical role in its pathogenesis; however, the mechanisms driving MØ activation in SSc remain poorly understood. This dissertation investigates the molecular signaling pathways and biochemical mechanisms underlying profibrotic MØ activity in SSc.

First, I identify a novel MØ-specific effect of mycophenolate mofetil (MMF), the standard-of-care treatment for SSc. While MMF is a well characterized lymphostatic, my findings demonstrate that its active metabolite, mycophenolic acid (MPA), is also capable of directly inhibiting myeloid viability and profibrotic MØ activation by suppressing de …

Cardiometabolic Benefits Of A Non-Industrialized-Type Diet Are Linked To Gut Microbiome Modulation, Fuyong Li, Anissa M. Armet, Katri Korpela, Junhong Liu, Rodrigo Margain Quevedo, Francesco Asnicar, Benjamin Seethaler, Tianna B. S. Rusnak, Janis L. Cole, Zhihong Zhang, Shuang Zhao, Adele Gagnon, Edward C. Deehan, Joao F. Mota, Jeffrey A. Bakal, Russell Greiner, Dan Knights, Nicola Segata, Stephan C. Bischoff, Laurie Mereu, Andrea M. Haqq, Catherine J. Field, Liang Li, Carla M. Prado, Jens Walter

Department of Food Science and Technology: Faculty Publications

Industrialization adversely affects the gut microbiome and predisposes individuals to chronic non-communicable diseases. We tested a microbiome restoration strategy comprising a diet that recapitulated key characteristics of non-industrialized dietary patterns (restore diet) and a bacterium rarely found in industrialized microbiomes (Limosilactobacillus reuteri) in a randomized controlled feeding trial in healthy Canadian adults. The restore diet, despite reducing gut microbiome diversity, enhanced the persistence of L. reuteri strain from rural Papua New Guinea (PB-W1) and redressed several microbiome features altered by industrialization. The diet also beneficially altered microbiota-derived plasma metabolites implicated in the etiology of chronic non-communicable diseases. Considerable …

Overcoming Vaccine Hesitancy: Evidence From Italy During The Covid-19 Pandemic, Alessandro Del Ponte, Audrey De Dominicis, Paolo Canofari

Political Science Faculty Articles and Research

Objectives

Study design

Assessing The Biological Impacts And Health Risks Of Uv Radiation In The Context Of Sustainable Development Goals: Review, Ruaa H. Abbas, Lina M. Shaker

AUIQ Complementary Biological System

Ultraviolet (UV) radiation, while essential for certain biological processes, presents significant risks to human health and ecosystems. Increased UV exposure, driven by ozone depletion and climate change, heightens threats such as DNA damage, skin cancer, immune suppression, and eye disorders, directly aligning with Sustainable Development Goal (SDG) 3: Good Health and Well-being. Additionally, UV radiation disrupts marine and terrestrial ecosystems, impacting biodiversity and productivity, relevant to SDGs 14 and 15. This review evaluates the health and environmental impacts of UV radiation and highlights recent advancements in UV monitoring technology. Key findings reveal substantial evidence linking UV exposure to accelerated skin …

Osmosis Magazine, Spring 2017

Osmosis Magazine

Osmosis is a student read, led, and written publication from the University of Richmond, focusing on all aspects of healthcare and science.

Osmosis Magazine, Fall 2016, Alex Long, Kristen Rubenstein, Tony Da Lomba, Mary Burns, Liana Saleh, Nicole D'Ambrosio, Maron Tarekegn, Adrianna Guillard, Maggie Michel, Cassie Gilboy, Annie Scalet, Carew Bartley, Colette Buser, Amanda Focht, Ian Gallagher, Adriana Grimes, Helene Keirns, Miriam Mcbride, Joe Ortolani, Annie Ryan, Danielle Storozynsky, Niamh Sutherburg

Osmosis Magazine

Osmosis is a student read, led, and written publication from the University of Richmond, focusing on all aspects of healthcare and science.

Educating Staff To Use World Health Organization Hand Hygiene Guidelines To Decrease Health Care-Associated Infection, Edith Kplivi

Walden Dissertations and Doctoral Studies

Summary The Doctor of Nursing Practice project was a practice-focused initiative to address increased hospital-associated infections (HAIs) in an outpatient mental health facility. Improper hand hygiene significantly contributes to the spread of HAIs, negatively affecting patient outcomes, increasing healthcare costs, and decreasing patient satisfaction. The practice-focused question was: For nursing staff in an outpatient clinic, will education focused on the World Health Organization (WHO) guidelines on hand hygiene increase knowledge toward the goal of decreasing HAIs? In collaboration with project site leadership, I identified the following gap in practice: Though fundamental hand hygiene practices may be known to healthcare workers, …

Diagnostic Stewardship And The Mitigation Of Treatment Of Asymptomatic Bacteriuria, Raimonda Kathryn Clarke

Walden Dissertations and Doctoral Studies

Urinalyses and urine cultures are being ordered at the facility of concern without regard to patient history/symptomatology, leading to inappropriate treatment of asymptomatic bacteriuria (ASB) and unnecessary antibiotic prescriptions. The following practice-focused question was developed to address this practice concern: Can an educational program focused on diagnostic stewardship and the mitigation of treatment of asymptomatic bacteriuria improve clinician awareness, knowledge, and confidence in identifying and diagnosing asymptomatic bacteriuria in patients over age 65 in the outpatient setting? Thus, the purpose of this doctor of nursing practice (DNP) project was to close the identified knowledge and attitude gap in a moderate-size …

Factors Driving Adolescent Tuberculosis Incidence By Age And Sex In 30 High-Tuberculosis Burden Countries: A Mathematical Modelling Study, Peter J Dodd

Faculty, Staff and Students Publications

INTRODUCTION: During adolescence, tuberculosis incidence rises, with a greater increase in males compared with females. Tuberculosis notifications and estimates infrequently disaggregate adolescent age groups. Moreover, the factors that drive the increases in overall incidence and the male-to-female (MF) ratio remain unclear.

METHODS: We constructed a mechanistic model to estimate cumulative Mycobacterium tuberculosis infection and tuberculosis disease incidence in the WHO’s 30 high-tuberculosis burden countries (HBCs), which represent 86%–90% of global tuberculosis incidence. We derived infection risk from tuberculosis prevalence and assortative social mixing based on sex and age (10–14 years vs 15–19 years old). We adjusted age subgroup-specific risks of …

Systematic Method For Developing Tailored Strategies For Implementing Point-Of-Care Procalcitonin Testing To Guide Antibiotic Prescribing In Swiss Primary Care: A Protocol For A Mixed-Methods Participatory Approach, Aline Wolfensberger, Sophie Cl Gendolla, Jelena Dunaiceva, Catherine Plüss-Suard, Anne Niquille, Anna Nicolet, Joachim Marti, Byron J Powell, Rahel Naef, Noémie Boillat-Blanco, Yolanda Mueller, Lauren Clack

2020-Current year OA Pubs

INTRODUCTION: Antimicrobial resistance is a major global health threat, driven largely by the misuse and overuse of antibiotics. Point-of-care (POC) tests for inflammatory biomarkers like procalcitonin (PCT) have shown promise in reducing unnecessary antibiotic prescriptions. The hybrid type II ImpPro trial aims to evaluate the implementation and effectiveness of POC-PCT on antibiotic prescriptions by primary care physicians (PCP) in French-speaking Switzerland. Implementation is planned to include a multifaceted strategy delivered mainly, but not exclusively, via PCP quality circles. Currently, little guidance exists on how to best tailor the implementation strategies to a specific context. This study protocol describes the comprehensive …

Atypical Dengue Fever With Severe Hematological Manifestations: A Case From The Rio Grande Valley, Elias Arellano Villanueva, Alhasan Asaad, Jose Campo Maldonado

Research Symposium

Background: Dengue fever, a mosquito-borne viral illness, is endemic in tropical regions, including border regions like the Rio Grande Valley while often self-limited, severe presentations such as dengue hemorrhagic fever and dengue shock syndrome highlight its challenges and complexities. This report describes an atypical dengue case with severe hematological manifestations, underscoring the diagnostic challenges and the importance of early recognition, multidisciplinary evaluation, and evidence-based management.

Case Presentation: A 22-year-old Hispanic female with no significant past medical history presented to the ED with hematemesis and fever following her travel to Monterrey, Mexico. Initial symptoms included high fever (107.6°F), chills, diarrhea, vomiting, …

The Influence Of The Covid-19 Pandemic On Spinal Cord Injury Prevalence And Cause Of Injury In Texas: A Four-Year Retrospective Analysis, Blake C. Martin, Daniel Salinas, Kelsey Baker

Research Symposium

Background: COVID-19 was the most significant medical issue since the Spanish Flu and was declared a pandemic on March 11, 2020. Current literature states that during the COVID-19 pandemic, in which about 10% of the global population was affected, there was a decrease in the frequency of trauma injuries observed in the clinic. Of note, spinal cord injury (SCI) has been suggested to show changing epidemiology from the COVID-19 pandemic. For example, a study in Scotland has suggested that the cause of SCI was significantly influenced during the pandemic, with an increase in self-harm. Such epidemiological changes may influence economic …