Open Access. Powered by Scholars. Published by Universities.®

Diseases Commons

Open Access. Powered by Scholars. Published by Universities.®

Virus Diseases

Institution
Keyword
Publication Year
Publication
Publication Type
File Type

Articles 61 - 90 of 2715

Full-Text Articles in Diseases

A Novel Mathematical Model Of Hiv Transmission Incorporating The Effects Of Treatment And Pre-Exposure Prophylaxis: Sensitivity Analysis And Numerical Simulations, Erick Manuel Delgado Moya Dec 2025

A Novel Mathematical Model Of Hiv Transmission Incorporating The Effects Of Treatment And Pre-Exposure Prophylaxis: Sensitivity Analysis And Numerical Simulations, Erick Manuel Delgado Moya

Mathematical Modelling and Numerical Simulation with Applications

Human immunodeficiency virus (HIV) continues to be a public health problem in many countries of the world, and Pre-exposure prophylaxis (PrEP) is a preventive method for HIV, which has shown great efficacy and is in use worldwide. This work presents a new mathematical model for HIV transmission incorporating PrEP use and evaluates the impact of PrEP along with its increasing use in a population. The construction of the model takes into account three forms of diagnosis: diagnosis of individuals in risky sexual contact, diagnosis after risky contact (diagnosis in the undiagnosed infected compartment), and diagnosis associated with attempting to enter …


Mathematical Analysis And Numerical Simulation Of A Fractional-Order Sir-Si Model For Malaria Transmission Dynamics, Gassan A. M. O. Farah, Abdulaziz Y. A. Mukhtar, Kailash C. Patidar Dec 2025

Mathematical Analysis And Numerical Simulation Of A Fractional-Order Sir-Si Model For Malaria Transmission Dynamics, Gassan A. M. O. Farah, Abdulaziz Y. A. Mukhtar, Kailash C. Patidar

Mathematical Modelling and Numerical Simulation with Applications

This study investigates the complex transmission dynamics of malaria, a critical global health challenge, with a focus on the African continent. We introduce a novel approach that employs Fractional Differential Equations (FDEs) to advance the understanding of malaria spread and control. Specifically, we develop a new SIR-SI model using the Caputo fractional operator, which captures the memory effects and time-delay characteristics inherent in real-world epidemiological systems. A detailed analysis of the model's solvability and uniqueness is conducted using fixed-point theory. To obtain an analytical solution, the system is solved via the Laplace transform method, with solutions expressed in closed form …


Long Covid Incidence Across Sars-Cov-2 Lineages And Identification Of Conserved Spike Targets For Multivalent Vaccines, Grace J. Kim, Md Ashad Alam, Judy S. Crabtree, Rebecca Rose, Susanna L. Lamers, San Chu, Ronald Horswell, Daniel Fort, Lucio Miele Dec 2025

Long Covid Incidence Across Sars-Cov-2 Lineages And Identification Of Conserved Spike Targets For Multivalent Vaccines, Grace J. Kim, Md Ashad Alam, Judy S. Crabtree, Rebecca Rose, Susanna L. Lamers, San Chu, Ronald Horswell, Daniel Fort, Lucio Miele

School of Graduate Studies Faculty Publications

Background: Long COVID remains poorly characterized at the genomic level. The primary aim of this study was to examine the relationship between viral sequences and the incidence of Long COVID at a tertiary care center in Louisiana between April 2020 and December 2022. A secondary aim was analysis of the Spike protein to identify conserved regions for multivalent vaccine targets. Method: To estimate Long COVID incidence across variants, we linked 4,789 SARS-CoV-2 sequences to 3,090 de-identified patient electronic health record information. The base population was defined as any patient with an International Classification of Diseases-10-Clinical Modification COVID-19 diagnosis code (U07.1) …


Presenteeism Among Health Care Personnel With Covid-19, James C. Crosby, Eliezer Santos Leon, Brian Chinnock, Karisa K. Harland, Anusha Krishnadasan, Nicholas M. Mohr, Ian D. Plumb, Melissa Briggs Hagen, Kelli Wallace, David A. Talan, Project Prevent Network, Anne Zepeski, Tracy Young, Howard A. Smithline, Lilly C. Lee, Stephen C. Lim, Et Al Dec 2025

Presenteeism Among Health Care Personnel With Covid-19, James C. Crosby, Eliezer Santos Leon, Brian Chinnock, Karisa K. Harland, Anusha Krishnadasan, Nicholas M. Mohr, Ian D. Plumb, Melissa Briggs Hagen, Kelli Wallace, David A. Talan, Project Prevent Network, Anne Zepeski, Tracy Young, Howard A. Smithline, Lilly C. Lee, Stephen C. Lim, Et Al

School of Medicine Faculty Publications

IMPORTANCE: Presenteeism-defined as continuing to work during an illness-poses a public health risk in the workplace and is especially hazardous within health care institutions where vulnerable patients may be exposed to nosocomial infections. Understanding the frequency and characteristics of health care personnel (HCP) who report presenteeism while ill with COVID-19 may help mitigate SARS-CoV-2 spread in hospitals and other health care institutions. OBJECTIVES: To determine the frequency of presenteeism among HCP with symptomatic COVID-19, and to evaluate the demographic, occupational, and clinical factors associated with it. DESIGN, SETTING, AND PARTICIPANTS: This is an observational cohort study that uses data from …


Identifying Barriers For Community Pharmacies As Vaccines For Children (Vfc) Providers In Rural Alabama: Opportunities For Solutions, Myra Bajwa Dec 2025

Identifying Barriers For Community Pharmacies As Vaccines For Children (Vfc) Providers In Rural Alabama: Opportunities For Solutions, Myra Bajwa

Honors Theses

Significant Human papillomavirus (HPV) vaccination disparities exist between rural and urban areas in the US. A primary contributor is low access to preventive care in rural areas. Among the most promising strategies to overcome this is increasing access through offering HPV vaccination in non-traditional, convenient health settings such as pharmacies. In rural areas, community pharmacies are trusted, convenient pillars of the community. In Alabama, community pharmacies are eligible for enrollment in the Vaccines for Children (VFC) Program, a federally-funded program that provides free vaccines to children and adolescents under 18 years old who are uninsured, underinsured, American Indian, or Alaska …


Adaptive Compulsion, Amanda A. Santos Dec 2025

Adaptive Compulsion, Amanda A. Santos

Electronic Theses, Projects, and Dissertations

Adaptive

Adjective

Adap.tive ( ə-ˈdap-tiv)

of, relating to, or being a heritable trait that serves a specific function and improves an organism's fitness or survival

Compulsion

Noun

Com.pul.sion (kəm-ˈpəl-shən)

a repetitive behavior or mental act that a person feels driven to perform to alleviate the anxiety and distress caused by an unwanted thought or urge, known as an obsession.

For years we have lived in unprecedented times. From the worldwide quarantine in 2020 resulting from the pandemic, to our current US political crisis. The constant barrage of events is overwhelming and demoralizing.

The work in this gallery is a display …


High Prevalence And Atypical Genotype Distribution Of Oral Human Papillomavirus In An East African Hiv Cohort: A Cross-Sectional Study, Ian G. Munabi, Adriane Kamulegeya, Dunstan Kalanzi, David P. Kateete, Fred Collins Semitala, Catherine-Lutalo Mwesigwa, Samuel Kalungi, Jennifer E. Cameron, Kimon Divaris, William Buwembo Nov 2025

High Prevalence And Atypical Genotype Distribution Of Oral Human Papillomavirus In An East African Hiv Cohort: A Cross-Sectional Study, Ian G. Munabi, Adriane Kamulegeya, Dunstan Kalanzi, David P. Kateete, Fred Collins Semitala, Catherine-Lutalo Mwesigwa, Samuel Kalungi, Jennifer E. Cameron, Kimon Divaris, William Buwembo

School of Medicine Faculty Publications

BACKGROUND: Globally, Human Papillomavirus type 16 (HPV-16) is the predominant genotype associated with oropharyngeal cancers. However, little is known about the prevalence and type distribution of Oral Human Papillomavirus (OHPV) in people living with HIV (PLWHIV) in the East African region. The objective of this study was to document the prevalence and circulating genotypes of OHPV infection in a large cohort of PLWHIV attending an urban HIV clinic in Eastern Africa METHODS: This was a cross-sectional study among 1,715 participants of the Makerere University Joint AIDS Program clinic, located in Kampala, Uganda, in East Africa. A salivary sample was collected …


Hpv Prevention In Men: A Narrative Review Of Strategies, Risks, And Public Health Implications, Martin S. Lipsky, Bayler Gunnell, Justin Nguyen, Samantha Lee, Geo Wolfe, Man Hung Nov 2025

Hpv Prevention In Men: A Narrative Review Of Strategies, Risks, And Public Health Implications, Martin S. Lipsky, Bayler Gunnell, Justin Nguyen, Samantha Lee, Geo Wolfe, Man Hung

Institute on Aging Publications

Human papillomavirus (HPV) is the most common sexually transmitted infection worldwide, impacting both males and females. In men, HPV causes genital warts, more than 90% of anal cancers, and 60% of oropharyngeal cancers. Given that one in three men are infected with HPV worldwide, there is a pressing need for enhanced public health strategies focusing on prevention. This comprehensive narrative review presents an overview of HPV in men, key risk factors, and primary prevention in men. The most effective preventive measure for HPV in males is vaccination. Males at high risk for HPV include those who smoke, have human immunodeficiency …


Nirsevimab Effectiveness Against Intensive Care Unit Admission For Respiratory Syncytial Virus In Infants - 24 States, December 2024-April 2025, Laura D. Zambrano, Regina M. Simeone, Margaret M. Newhams, Amanda B. Payne, Natasha B. Halasa, Amber O. Orzel-Lockwood, Jemima M. Calixte, Satoshi Kamidani, Hillary Crandall, Melissa A. Cameron, Jennifer E. Schuster, Aline B. Maddux, Kathleen Chiotos, Katherine Irby, Steven L. Shein, Mary Allen Staat, Lora M. Martin, Samina S. Bhumbra, Ryan A. Nofziger, Jigar C. Chauhan, Danielle M. Zerr, Shira J. Gertz, Judith A. Guzman-Cottrill, Michele Kong, Janet R. Hume, Bria M. Coates, Kelly N. Michelson, Tamara T. Bradford, Et Al Nov 2025

Nirsevimab Effectiveness Against Intensive Care Unit Admission For Respiratory Syncytial Virus In Infants - 24 States, December 2024-April 2025, Laura D. Zambrano, Regina M. Simeone, Margaret M. Newhams, Amanda B. Payne, Natasha B. Halasa, Amber O. Orzel-Lockwood, Jemima M. Calixte, Satoshi Kamidani, Hillary Crandall, Melissa A. Cameron, Jennifer E. Schuster, Aline B. Maddux, Kathleen Chiotos, Katherine Irby, Steven L. Shein, Mary Allen Staat, Lora M. Martin, Samina S. Bhumbra, Ryan A. Nofziger, Jigar C. Chauhan, Danielle M. Zerr, Shira J. Gertz, Judith A. Guzman-Cottrill, Michele Kong, Janet R. Hume, Bria M. Coates, Kelly N. Michelson, Tamara T. Bradford, Et Al

School of Medicine Faculty Publications

Respiratory syncytial virus (RSV) is a leading cause of intensive care unit (ICU) admission and respiratory failure among infants (children aged < year) in the United States. In August 2023, CDC’s Advisory Committee on Immunization Practices recommended nirsevimab, a long-acting monoclonal antibody, to protect against RSV-associated lower respiratory tract infection among all infants aged < 8 months born during or entering their first RSV season. Following licensure, nirsevimab effectiveness has been demonstrated against RSV-associated infant hospitalization, but evidence regarding effectiveness against RSV-associated critical illness is limited. In a 27-hospital case-control investigation, nirsevimab effectiveness against both RSV-associated infant ICU admission and acute respiratory failure (illness requiring continuous positive airway pressure, bilevel positive airway pressure, or invasive mechanical ventilation) after hospital admission was evaluated during December 1, 2024-April 15, 2025. Among 457 case-patients who received a positive RSV test result and 302 control patients who received a negative RSV test result admitted to an ICU with respiratory symptoms, 14% and 45%, respectively, had received nirsevimab ≥ 7 days before symptom onset. Nirsevimab was 80% effective (95% CI = 70%-86%) against RSV-associated ICU admission and 83% effective (95% CI = 74%-90%) against acute respiratory failure when received a median of 52 days (IQR = 32-89 days) and 50 days (IQR = 32-86 days) before onset for each respective endpoint. These estimates support the recommendation for use of nirsevimab as a prevention strategy to protect infants against severe outcomes from RSV infection.


Rabies Virus-Vectored Lyme Disease Vaccine Provides Long-Term Protection Against Tick-Transmitted Borrelia Burgdorferi, Shantel Rios, Bibek Bhattachan, Christoph Wirblich, Anisha Chandwani, Kruthi Vavilikolanu, Jacob F. Myers, Chrysoula Kitsou, Utpal Pal, Matthias J. Schnell Nov 2025

Rabies Virus-Vectored Lyme Disease Vaccine Provides Long-Term Protection Against Tick-Transmitted Borrelia Burgdorferi, Shantel Rios, Bibek Bhattachan, Christoph Wirblich, Anisha Chandwani, Kruthi Vavilikolanu, Jacob F. Myers, Chrysoula Kitsou, Utpal Pal, Matthias J. Schnell

Department of Microbiology and Immunology Faculty Papers

Lyme disease (LD) cases have doubled globally. LD is a tick-borne illness caused by the Borrelia burgdorferi sensu lato (Bb). If untreated, Bb can disseminate to distal organs, causing carditis, arthritis, and meningitis. Currently, no FDA-approved human LD vaccine exists on the market. This study used two approaches to incorporate OspA into the rabies virus (RABV) vaccine vector. We used the RABV-glycoprotein tail (RVG tail) and the Hendra virus (HeV) glycoprotein tail (HVG tail) to incorporate OspA, creating BNSP333-OspA-RVG and BNSP333-OspA-HVG, respectively. Both vaccines produced type-1 biased anti-OspA antibodies, but only BNSP333-OspA-HVG induced neutralizing antibodies and protected against Bb infection. …


Evolutionary Pathways Of Drug Resistance To Long-Acting Prep In Initial Hiv Infection, Yeona Kang, Katharine Gurski, Yanping Ma Nov 2025

Evolutionary Pathways Of Drug Resistance To Long-Acting Prep In Initial Hiv Infection, Yeona Kang, Katharine Gurski, Yanping Ma

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.


Increasing Pediatric Hpv Vaccination Rates, Brooke A. Nicholas Nov 2025

Increasing Pediatric Hpv Vaccination Rates, Brooke A. Nicholas

Dissertations

Increasing Pediatric HPV Vaccination Rates

Abstract

Problem: The human papillomavirus (HPV) is a sexually transmitted infection that affects more than 80% of the population within the United States (Eisenhauer et al., 2020). HPV can develop into cervical, anogenital, and oropharyngeal cancers (Eisenhauer et al., 2020). About 4,000 individuals die from cervical cancer alone each year (O’Leary, 2022). The HPV vaccine, though recommended by the ACIP and AAP, is below national vaccination rates in comparison to other vaccines (O’Leary, 2022).

Methods: This quality improvement project is a non-randomized controlled trial that observed HPV vaccine dose completion rates for patients aged 9-14 …


Impact On Oral Health Of The Post-Covid-19 Infections: A Systematic Review, Aouatif Aouidate, Hanane Ouddoud, Loubna Bahije Oct 2025

Impact On Oral Health Of The Post-Covid-19 Infections: A Systematic Review, Aouatif Aouidate, Hanane Ouddoud, Loubna Bahije

International Arab Journal of Dentistry

Introduction: The COVID-19 pandemic has been associated with a diverse range of oral health implications, including mucosal lesions, periodontitis, and disruptions of the oral microbiota. Since airborne particles primarily transmit COVID-19, understanding its potential impact on oral health is crucial for dental care and infection control.

Objectives: This systematic review aimed to evaluate the effects of post-COVID-19 infections on oral health, highlighting clinical manifestations, periodontal disease associations, and microbiota disturbances.

Methods: Electronic literature searches were conducted between January 2020 and July 2024 by one author across several databases, including PubMed/MEDLINE, Scopus, Cochrane Library, EMBASE, ScienceDirect, Google Scholar, …


Human Papillomavirus Vaccine Uptake Among U.S. Medical Residents In High-Exposure-Risk Specialties – A National Study, Madison Oxford, Christina Stetter, Arpit Dave Sep 2025

Human Papillomavirus Vaccine Uptake Among U.S. Medical Residents In High-Exposure-Risk Specialties – A National Study, Madison Oxford, Christina Stetter, Arpit Dave

Graduate Medical Education Research Journal

Background. HPV vaccination is not required for the United States (U.S.) medical residents, despite their potentially high risk of iatrogenic exposure to the virus. We aim to evaluate vaccination status, patterns of HPV vaccine uptake, and perceived risk of iatrogenic infection among residents in high-exposure-risk specialties.

Methods. In spring 2023, an anonymous online survey was distributed via program directors and coordinators of all Accreditation Council for Graduate Medical Education (ACGME)-accredited Obstetrics & Gynecology, Family Medicine, Otolaryngology, and Dermatology training programs to assess residents’ vaccination status, HPV exposure, and HPV vaccine knowledge.

Results. Responses from 537 residents at programs located in …


Allosteric Control Overcomes Steric Limitations For Neutralizing Antibodies Targeting Conserved Binding Epitopes Of The Sars-Cov-2 Spike Protein: Exploring The Intersection Of Binding, Allostery, And Immune Escape With A Multimodal Computational Approach, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker Sep 2025

Allosteric Control Overcomes Steric Limitations For Neutralizing Antibodies Targeting Conserved Binding Epitopes Of The Sars-Cov-2 Spike Protein: Exploring The Intersection Of Binding, Allostery, And Immune Escape With A Multimodal Computational Approach, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Understanding the atomistic basis of multi-layer mechanisms employed by broadly reactive neutralizing antibodies of the SARS-CoV-2 spike protein without directly blocking receptor engagement remains an important challenge in coronavirus immunology. Class 4 antibodies represent an intriguing case: they target a deeply conserved, cryptic epitope on the receptor-binding domain yet exhibit variable neutralization potency across subgroups F1 (CR3022, EY6A, COVA1-16), F2 (DH1047), and F3 (S2X259). The molecular basis for this variability is not fully understood. Here, we employed a multi-modal computational approach integrating atomistic and coarse-grained molecular dynamics simulations, binding free energy calculations, mutational scanning, and dynamic network analysis to elucidate …


Zika Virus Impairs Autophagic Flux In Trabecular Meshwork, And Inhibition Of Autophagy Restricts Ocular Viral Transmission And Associated Pathology, Faraz Ahmad, Prince Kumar, Pallav Singh, Trupti Joshi, Pawan Kumar Singh Sep 2025

Zika Virus Impairs Autophagic Flux In Trabecular Meshwork, And Inhibition Of Autophagy Restricts Ocular Viral Transmission And Associated Pathology, Faraz Ahmad, Prince Kumar, Pallav Singh, Trupti Joshi, Pawan Kumar Singh

Biomedical Sciences

Zika virus (ZIKV) is the lone member of Flavivirus family known to cause congenital glaucoma following in utero exposure. The molecular mechanisms of ZIKV-induced glaucoma remain elusive, with no known therapeutic modalities. Autophagy plays a dual role in viral infections and glaucoma pathogenesis. However, how ZIKV  interferes with autophagic pathways in the trabecular meshwork (TM) and whether autophagy contributes to ZIKV-induced ocular complications remains elusive. Here, we investigated the role of autophagy in ZIKV ocular pathogenesis utilizing a primary human trabecular meshwork cells (HTMC) and IFNAR1-/- mouse model of ocular infection. Our results show that ZIKV permissively infects HTMC, elicits …


Enhancing Preparedness: A Genetic Study Of Sar-Cov-2 And Other Microbial Public Health Threats In Wastewater From A College Town, Christian N. Hutchinson Sep 2025

Enhancing Preparedness: A Genetic Study Of Sar-Cov-2 And Other Microbial Public Health Threats In Wastewater From A College Town, Christian N. Hutchinson

Master's Theses

Problem

The SARS-CoV-2 (COVID-19) pandemic revealed both the systemic vulnerabilities of our healthcare system as well as the importance of timely, localized data for informing public health responses. Traditional testing approaches were essential but often failed to capture the full extent of viral spread, especially in those with mild or asymptomatic conditions that relied on at home testing. This underreporting hindered effective allocation of resources and made developing effective intervention strategies difficult. We also realized the potential for wastewater surveillance to be applied to tracking antimicrobial resistance gene markers. Taken together, this approach should have important implications for improving public …


Hiv-1 Controllers Possess A Unique Cd8+ T Cell Activation Phenotype And Loss Of Control Is Associated With Increased Expression Of Exhaustion Markers, Amber D. Jones, Zachary Capriotti, Erin Santos, Angel Lin, Rachel Van Duyne, Stephen Smith, Zachary Klase Aug 2025

Hiv-1 Controllers Possess A Unique Cd8+ T Cell Activation Phenotype And Loss Of Control Is Associated With Increased Expression Of Exhaustion Markers, Amber D. Jones, Zachary Capriotti, Erin Santos, Angel Lin, Rachel Van Duyne, Stephen Smith, Zachary Klase

Kimmel Cancer Center Papers, Presentations, and Grand Rounds

BACKGROUND: HIV-1 controllers are a rare population of individuals that exhibit spontaneous control of HIV-1 infection without antiretroviral therapy. Understanding the mechanisms by which HIV-1 controllers maintain and eventually lose this ability would be highly valuable in HIV-1 cure or vaccine research. Previous work revealed the ability of CD8+ T cells isolated from HIV-1 controllers to suppress HIV-1 replication in matched CD4+ T cells and PBMCs ex vivo and suggested the loss of control may be tied to CD8+ T cell exhaustion.

RESULTS: We explored whether CD8+ T cell exhaustion plays a role in the maintenance and loss of control …


Variability In Long Covid Definitions And Validation Of Published Prevalence Rates, Lauren E. Wisk, Michelle L'Hommedieu, Kate Diaz Roldan, Imtiaz Ebna Mannan, Erica S. Spatz, Robert A. Weinstein, Arjun K. Venkatesh, Michael Gottlieb, Ryan Huebinger, Kristin L. Rising, Juan Carlos C. Montoy, Kari A. Stephens, Robert M. Rodriguez, Mandy J. Hill, Kelli N. O'Laughlin, Nicole L. Gentile, Ahamed H. Idris, Shu-Xia Li, Michelle Santangelo, Efrat R. Kean, Samuel A. Mcdonald, Kristyn Gatling, Joann G Elmore Aug 2025

Variability In Long Covid Definitions And Validation Of Published Prevalence Rates, Lauren E. Wisk, Michelle L'Hommedieu, Kate Diaz Roldan, Imtiaz Ebna Mannan, Erica S. Spatz, Robert A. Weinstein, Arjun K. Venkatesh, Michael Gottlieb, Ryan Huebinger, Kristin L. Rising, Juan Carlos C. Montoy, Kari A. Stephens, Robert M. Rodriguez, Mandy J. Hill, Kelli N. O'Laughlin, Nicole L. Gentile, Ahamed H. Idris, Shu-Xia Li, Michelle Santangelo, Efrat R. Kean, Samuel A. Mcdonald, Kristyn Gatling, Joann G Elmore

Jefferson Center for Connected Care Faculty Papers

IMPORTANCE: Long COVID definitions vary widely, and no consensus exists on how to accurately measure its prevalence, complicating both clinical care and research.

OBJECTIVE: To assess long COVID prevalence using various definitions from published literature.

DESIGN, SETTING, AND PARTICIPANTS: This prospective, multicenter cohort study used data from the longitudinal Innovative Support for Patients With SARS-CoV-2 Infections Registry (INSPIRE). Participants aged 18 years or older with symptoms suggestive of COVID-19 illness at the time of their index SARS-CoV-2 test enrolled at 8 sites across the US from December 11, 2020, through August 29, 2022, with follow-up surveys collected through February 28, …


Dynamic Mutational Profiling Of Binding Interactions And Allosteric Networks In Conformational Ensembles Of The Sars-Cov-2 Spike Protein Complexes With Classes Of Antibodies Targeting Cryptic Binding Sites: Confluence Of Binding And Allostery Determines Molecular Mechanisms And Hotspots Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker Aug 2025

Dynamic Mutational Profiling Of Binding Interactions And Allosteric Networks In Conformational Ensembles Of The Sars-Cov-2 Spike Protein Complexes With Classes Of Antibodies Targeting Cryptic Binding Sites: Confluence Of Binding And Allostery Determines Molecular Mechanisms And Hotspots Of Immune Escape, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The ongoing evolution of SARS-CoV-2 variants has underscored the need to understand not only the structural basis of antibody recognition but also the dynamic and allosteric mechanisms that could underlie complexity of broad and escape-resistant neutralization. In this study, we employed a multi-scale approach integrating structural analysis, hierarchical molecular simulations, mutational scanning and network-based allosteric modeling to dissect how Class 4 antibodies (represented by S2X35, 25F9, and SA55) and Class 5 antibodies (represented by S2H97, WRAIR-2063 and WRAIR-2134) can modulate conformational behavior, binding energetics, allosteric interactions and immune escape patterns of the SARS-CoV-2 spike protein. Using hierarchical simulations of the …


The Effect Of Hcv On Methadone Dose During Pregnancy, Sarah Boudova, Neel S. Iyer, Danielle M. Tholey, Jonathan M. Fenkel, Rupsa C. Boelig Aug 2025

The Effect Of Hcv On Methadone Dose During Pregnancy, Sarah Boudova, Neel S. Iyer, Danielle M. Tholey, Jonathan M. Fenkel, Rupsa C. Boelig

Department of Obstetrics and Gynecology Faculty Papers

Pregnancy is a time of high patient motivation to initiate treatment for opioid use disorder (OUD). Hepatic drug metabolism can be altered by pregnancy and hepatitis C virus (HCV) infection. We aimed to examine the impact of HCV during pregnancy on methadone dosing. Retrospective chart review of all pregnant patients with OUD admitted for initiation of methadone from 1/2020-6/2022. Associations were examined using Student's T-tests, chi-squared tests, Fisher's exact tests and univariate and multivariate linear regression. We identified 191 pregnancies initiated on methadone, of which 188 were screened for HCV. 111 (59.0%) were HCV Antibody (Ab)+, of whom 108 were …


Genotype Distribution Of Human Papillomavirus Among Women With Cervical Cancer Stratified By Hiv Status In Tanzania, Alita Mrema, Mamsau Ngoma, Emmanuel L. Lugina, Atukuzwe Kahakwa, Chacha Josiah Mwita, Salama Iddy, Eulade Rugengamizi, Kandali Samwel, John Ngowi, Salum J. Lidenge, Charles Wood, Julius Mwaiselage Aug 2025

Genotype Distribution Of Human Papillomavirus Among Women With Cervical Cancer Stratified By Hiv Status In Tanzania, Alita Mrema, Mamsau Ngoma, Emmanuel L. Lugina, Atukuzwe Kahakwa, Chacha Josiah Mwita, Salama Iddy, Eulade Rugengamizi, Kandali Samwel, John Ngowi, Salum J. Lidenge, Charles Wood, Julius Mwaiselage

School of Medicine Faculty Publications

Background Cervical cancer (CC) is the leading cancer among women in Tanzania, especially among those between the ages of 15 and 44. The prevalence of high-risk Human papillomavirus (HR-HPV)-16/18 women in the general population at any given time is 3.3%. HR-HPVs 16 or 18 are the primary cause of CC. The distribution of HPV genotypes among women with CC according to HIV status is unknown in Tanzania. This study aimed to determine the HPV genotype distribution according to HIV status among women with CC in Tanzania. Methods This cross-sectional study was done at Ocean Road Cancer Institute (ORCI) in Tanzania …


Host-Virus Interaction Dynamics Using Sulfolobus Spindle-Shaped Virus And Host Sulfolobales System, Yeasin Ahmed Aug 2025

Host-Virus Interaction Dynamics Using Sulfolobus Spindle-Shaped Virus And Host Sulfolobales System, Yeasin Ahmed

Graduate Theses and Dissertations

The Sulfolobus Spindle-shaped virus (SSV) is among the most studied archaeal viruses, particularly in extreme environments. This virus predominantly infects multiple Crenarchaea from the Sulfolobaceae family. These hosts thrive in extreme environmental conditions, such as sulfuric hot springs, with a pH of 2 to 4 and a temperature of 76-80˚C. Sulfolobales exhibit a wide geographical distribution across volcanic hot springs. The Sulfolobus Spindle-shaped Virus (SSV), encompassing strains such as SSV1 and SSV8, employs a non-lytic replication strategy in hosts belonging to the order Sulfolobales. The SSV-Sulfolobales system can be cultured in liquid and gellan gum solid media. A comprehensive study …


Multiscale Modeling And Dynamic Mutational Profiling Of Binding Energetics And Immune Escape For Class I Antibodies With Sars-Cov-2 Spike Protein: Dissecting Mechanisms Of High Resistance To Viral Escape Against Emerging Variants, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker Jul 2025

Multiscale Modeling And Dynamic Mutational Profiling Of Binding Energetics And Immune Escape For Class I Antibodies With Sars-Cov-2 Spike Protein: Dissecting Mechanisms Of High Resistance To Viral Escape Against Emerging Variants, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The rapid evolution of SARS-CoV-2 has underscored the need for a detailed understanding of antibody binding mechanisms to combat immune evasion by emerging variants. In this study, we investigated the interactions between Class I neutralizing antibodies—BD55-1205, BD-604, OMI-42, P5S-1H1, and P5S-2B10—and the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein using multiscale modeling, which combined molecular simulations with the ensemble-based mutational scanning of the binding interfaces and binding free energy computations. A central theme emerging from this work is that the unique binding strength and resilience to immune escape of the BD55-1205 antibody are determined by leveraging a broad epitope …


Implementation Of A Human Papillomavirus Vaccination Toolkit Postpartum, Eriola Arapi Jul 2025

Implementation Of A Human Papillomavirus Vaccination Toolkit Postpartum, Eriola Arapi

Dissertations

Problem: Despite strong recommendations from the Centers for Disease Control and

Prevention (CDC, 2021) for HPV vaccination in individuals aged 9 to 26, postpartum women

are often overlooked as a target population. Every year in the U.S., oncogenic human

papillomavirus (HPV) infection causes approximately 330,000 cases of precancerous cervical

dysplasia and 12,000 cases of cervical cancer, the most common female cancer attributable to

HPV (Wang et al., 2024). Many providers miss the opportunity to offer the vaccine during the

postpartum hospital stay and the six-week visit—when patients are insured, motivated, and

more accessible.

Methods: This quality improvement (QI) project used …


Current Trends In Clinical Trials For Merkel Cell Carcinoma (Mcc), Tilak Patel, Rachel Butz, Brian Boulmay, Vilija Vaitaitis Jul 2025

Current Trends In Clinical Trials For Merkel Cell Carcinoma (Mcc), Tilak Patel, Rachel Butz, Brian Boulmay, Vilija Vaitaitis

School of Medicine Faculty Publications

Merkel cell carcinoma (MCC) is a rare, aggressive neuroendocrine cutaneous malignancy with high rates of recurrence and metastasis. The treatment of MCC has historically involved surgery, radiation, and chemotherapy; however, current clinical trials are investigating immunotherapies, intratumoral injections, and combination therapies to improve outcomes. This review explores the current trends in clinical trials for MCC, highlighting recent advances in management.


The Effects Of A Mindfulness-Based Intervention On Depression And Anxiety In The Long-Covid Population, Rachel Welbel, Elizabeth Rutha, Jeffrey Ording, Douglas Wang, Jana Hirschtick Jul 2025

The Effects Of A Mindfulness-Based Intervention On Depression And Anxiety In The Long-Covid Population, Rachel Welbel, Elizabeth Rutha, Jeffrey Ording, Douglas Wang, Jana Hirschtick

Journal of Patient-Centered Research and Reviews

Long-COVID is a complicated, post-viral syndrome involving multiple body systems and can present with neuropsychiatric symptoms. Little has been reported about the neuropsychiatric symptoms of long-COVID, and validated treatments do not yet exist. There is prior evidence that mindfulnessbased strategies have been helpful for those with chronic illnesses; shown significant decreases in anxiety, stress, and depression; and enhanced quality of life. In this study, we report on the utility of a mindfulness-based intervention on levels of anxiety and depression in a long-COVID population. Our hospital system founded both a “Covid Recovery Clinic” (CRC) and a “Post-COVID Resilience Program” (PCRP). The …


Improving Hiv Nonoccupational Postexposure Prophylaxis Completion In Survivors Of Sexual Assault, Rebecca Aden Jul 2025

Improving Hiv Nonoccupational Postexposure Prophylaxis Completion In Survivors Of Sexual Assault, Rebecca Aden

Doctor of Nursing Practice Final Project Abstract

PURPOSE

This project aimed to increase adherence to HIV nonoccupational postexposure prophylaxis (nPEP) among adult survivors of sexual assault using a 24-hour nurse-led callback intervention to reinforce patient education and support treatment completion.

BACKGROUND

This project was implemented within a public healthcare system’s forensic nursing program. Sexual assault survivors face an elevated risk of HIV transmission, yet completion of the 28-day nPEP regimen often remains below 40%. Barriers to completion include limited understanding, gaps in follow-up, as well as psychosocial and socioeconomic challenges.

METHODOLOGY

The FADE QI framework was utilized for this project. The population included adult, non-incarcerated patients who …


Kshv Vil6 Inhibits Functional B Cell Maturation During De Novo Infection, Wajd Zakir, Jessica M. Osborn, Jennifer Totonchy Jul 2025

Kshv Vil6 Inhibits Functional B Cell Maturation During De Novo Infection, Wajd Zakir, Jessica M. Osborn, Jennifer Totonchy

Pharmacy Faculty Articles and Research

Despite causative links to lymphoproliferative disorders, little is known about early events governing KSHV infection in B lymphocytes. IL-6 signaling plays a critical role in KSHV-mediated disease, with human IL-6 (hIL6) levels correlating with viral load and disease progression. This dynamic is even more complex due to the coexistence of hIL6 and KSHV-encoded viral IL-6 (vIL6) in these diseases. We hypothesize that hIL6 and vIL6 play critical, separable and collective roles in the early stages of KSHV infection in B cells. In this study, we use our ex vivo model of KSHV infection in human tonsil lymphocytes to investigate the …


Orofacial Manifestations Of Highly Active Antiretroviral Therapy (Haart) And Pre-Exposure Prophylaxis (Prep): Implications For Dental Care And Guidelines For Management, Alec Donelian, Yuedi Yu, Ezzard Rolle Dds, Alison Newgard Dds Jul 2025

Orofacial Manifestations Of Highly Active Antiretroviral Therapy (Haart) And Pre-Exposure Prophylaxis (Prep): Implications For Dental Care And Guidelines For Management, Alec Donelian, Yuedi Yu, Ezzard Rolle Dds, Alison Newgard Dds

The New York State Dental Journal

HAART and PrEP have demonstrated reduction of HIV-related mortality and HIV infection, respectively. A range of orofacial side effects has been associated with both HAART and PrEP. As PrEP usage has increased, there has also been an increase in sexually transmitted infections that have orofacial symptoms. As oral health-care providers, it is important that we recognize these orofacial side effects and symptoms. Further, we offer clinical recommendations for dental professionals treating patients who are on either HAART or PrEP and their associated risk factors.