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Epidemiology Commons™

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Full-Text Articles in Epidemiology

From Advisory To Action: The Case For Preserving Paccarb In The Fight Against Antimicrobial Resistance, Leila S. Hojat, Muhammad Dhanani, Amy Y. Kang, Salome O. Chitavi, Robert A. Weinstein, Edward Stenehjem Sep 2026

From Advisory To Action: The Case For Preserving Paccarb In The Fight Against Antimicrobial Resistance, Leila S. Hojat, Muhammad Dhanani, Amy Y. Kang, Salome O. Chitavi, Robert A. Weinstein, Edward Stenehjem

Pharmacy Faculty Articles and Research

The Presidential Advisory Council on Combating Antibiotic-Resistant Bacteria (PACCARB) was established to advise the government on strategies to mitigate antimicrobial resistance (AMR) and its increasing threat to public health and national security. Its members included experts from diverse disciplines such as healthcare, veterinary medicine, industry, public health, and agriculture who were positioned to interface with key stakeholders and the public in an aspirational multidisciplinary approach to combating AMR. The council was successful in elevating AMR as a national priority and played a crucial role in watershed events for antimicrobial stewardship (AS) such as the development of the second National Action …


Mechanisms Of Binding And Immune Escape Resistance For Broadly Neutralizing Antibodies Targeting Distinct Conserved Sars-Cov-2 Spike Epitopes: A Hierarchical Approach Integrating Mutational Profiling And Energy Landscape Analysis, Mohammed Alshahrani, Will Gatlin, Max Ludwick, Lucas Turano, Brandon Foley, Gennady M. Verkhivker Apr 2026

Mechanisms Of Binding And Immune Escape Resistance For Broadly Neutralizing Antibodies Targeting Distinct Conserved Sars-Cov-2 Spike Epitopes: A Hierarchical Approach Integrating Mutational Profiling And Energy Landscape Analysis, Mohammed Alshahrani, Will Gatlin, Max Ludwick, Lucas Turano, Brandon Foley, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The continued evolution of SARS-CoV-2 has enabled an escape from most monoclonal antibodies, yet a subset of broadly neutralizing antibodies targeting three newly identified super-conserved RBD epitopes—SCORE-A, SCORE-B, and SCORE-C—retains remarkable activity against even the most recent JN.1-derived sublineages. Here, we employed an integrated computational framework combining conformational dynamics, mutational scanning, MM-GBSA binding energetics, and frustration profiling to dissect the molecular mechanisms by which XGI antibodies achieve broad neutralization and resistance to immune escape. Structural analysis revealed that all three SCORE epitopes share a common architecture: a highly conserved, minimally frustrated core that provides stable anchoring, flanked by peripheral regions …


Utilizing Machine Learning Techniques For Computer-Aided Covid-19 Screening Based On Clinical Data, Honglun Xu, Andrews T. Anum, Michael Pokojovy, Sreenath Chalil Madathil, Yuxin Wen, Md. Fashiar Rahman, Tzu-Liang Bill Tseng, Scott Moen, Eric Walser Jan 2026

Utilizing Machine Learning Techniques For Computer-Aided Covid-19 Screening Based On Clinical Data, Honglun Xu, Andrews T. Anum, Michael Pokojovy, Sreenath Chalil Madathil, Yuxin Wen, Md. Fashiar Rahman, Tzu-Liang Bill Tseng, Scott Moen, Eric Walser

Engineering Faculty Articles and Research

The COVID-19 pandemic has highlighted the importance of rapid clinical decision-making to facilitate the efficient usage of healthcare resources. Over the past decade, machine learning (ML) has caused a tectonic shift in healthcare, empowering data-driven prediction and decision-making. Recent research demonstrates how ML was used to respond to the COVID-19 pandemic. This paper puts forth new computer-aided COVID-19 disease screening techniques using six classes of ML algorithms (including penalized logistic regression, random forest, artificial neural networks, and support vector machines) and evaluates their performance when applied to a real-world clinical dataset containing patients’ demographic information and vital indices (such as …


A Literature Review Of The United States Of America’S Reliance On Imported Covid Personal Protective Equipment During The Pandemic, Pradip K. Shukla, Izzet Kosar, Hedieh Setayesh Oct 2025

A Literature Review Of The United States Of America’S Reliance On Imported Covid Personal Protective Equipment During The Pandemic, Pradip K. Shukla, Izzet Kosar, Hedieh Setayesh

Business Faculty Articles and Research

This paper provides a literature review of United States of America’s reliance on imported Covid Personal Protective Equipment (PPEs) during the Covid pandemic. The abstracted and cited articles show that the United States was too reliant on imported PPEs, primarily imported from Asia which led to shortages as the cases of Covid surged at various points during the waves of Covid cases. This supply and demand imbalance was not just an inconvenience such as the toilet paper shortage and other supply chain disruptions of basic commodities; this supply and demand imbalance had life and death impacts for many first responders, …


Learning From Covid-19: Clinical Trials, Health Information Technology, And Patient Mortality, Christos Nicolaides, Avinash Collis, Seth Benzell, Indranil Bardhan Oct 2025

Learning From Covid-19: Clinical Trials, Health Information Technology, And Patient Mortality, Christos Nicolaides, Avinash Collis, Seth Benzell, Indranil Bardhan

Economics Faculty Articles and Research

During the COVID-19 pandemic, deaths per case in the United States decreased from 7.46% in April 2020 to 1.76% in April 2021. One mechanism that could explain this decline is a learning effect associated with testing of new treatments by hospitals. Hospitals that participated in clinical trials developed better organizational capabilities to diagnose and treat COVID-19 patients. Simultaneously, hospitals used health information technologies (IT) that integrated health information across healthcare providers to facilitate greater learning and sharing of best practices. Using US county-level data on clinical trial participation, use of health IT, and COVID-19 cases and deaths, we show that …


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 …


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 …


Mutational Scanning And Binding Free Energy Computations Of The Sars-Cov-2 Spike Complexes With Distinct Groups Of Neutralizing Antibodies: Energetic Drivers Of Convergent Evolution Of Binding Affinity And Immune Escape Hotspots, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady M. Verkhivker Feb 2025

Mutational Scanning And Binding Free Energy Computations Of The Sars-Cov-2 Spike Complexes With Distinct Groups Of Neutralizing Antibodies: Energetic Drivers Of Convergent Evolution Of Binding Affinity And Immune Escape Hotspots, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

The rapid evolution of SARS-CoV-2 has led to the emergence of variants with increased immune evasion capabilities, posing significant challenges to antibody-based therapeutics and vaccines. In this study, we conducted a comprehensive structural and energetic analysis of SARS-CoV-2 spike receptor-binding domain (RBD) complexes with neutralizing antibodies from four distinct groups (A–D), including group A LY-CoV016, group B AZD8895 and REGN10933, group C LY-CoV555, and group D antibodies AZD1061, REGN10987, and LY-CoV1404. Using coarse-grained simplified simulation models, rapid energy-based mutational scanning, and rigorous MM-GBSA binding free energy calculations, we elucidated the molecular mechanisms of antibody binding and escape mechanisms, identified key …


Quantitative Characterization And Prediction Of The Binding Determinants And Immune Escape Hotspots For Groups Of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling Of The Sars-Cov-2 Spike Complexes With Antibodies, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady M. Verkhivker Feb 2025

Quantitative Characterization And Prediction Of The Binding Determinants And Immune Escape Hotspots For Groups Of Broadly Neutralizing Antibodies Against Omicron Variants: Atomistic Modeling Of The Sars-Cov-2 Spike Complexes With Antibodies, Mohammed Alshahrani, Vedant Parikh, Brandon Foley, Nishank Raisinghani, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

A growing body of experimental and computational studies suggests that the cross-neutralization antibody activity against Omicron variants may be driven by the balance and tradeoff between multiple energetic factors and interaction contributions of the evolving escape hotspots involved in antigenic drift and convergent evolution. However, the dynamic and energetic details quantifying the balance and contribution of these factors, particularly the balancing nature of specific interactions formed by antibodies with epitope residues, remain largely uncharacterized. In this study, we performed molecular dynamics simulations, an ensemble-based deep mutational scanning of SARS-CoV-2 spike residues, and binding free energy computations for two distinct groups …


Uncovering The Binding Mechanism Of Mutated Omicron Variants Via Computational Strategies, Sajjad Haider, Nadeem Ahmad, Muhammad Shafiq, Ali Raza Siddiqui, Mohammad Nur-E-Alam, Aftab Ahmed, Zaheer Ul-Haq Jan 2025

Uncovering The Binding Mechanism Of Mutated Omicron Variants Via Computational Strategies, Sajjad Haider, Nadeem Ahmad, Muhammad Shafiq, Ali Raza Siddiqui, Mohammad Nur-E-Alam, Aftab Ahmed, Zaheer Ul-Haq

Pharmacy Faculty Articles and Research

The COVID-19 pandemic, triggered by the SARS-CoV-2 virus, has resulted in nearly 630 million cases and 6.60 million fatalities globally, as of November 2022. SARS-CoV-2, a species of the Coronaviridae family, has a single-stranded positive-sense RNA genome as well as four main structural proteins (S, E, M, and N) required for viral entrance into target cells. The spike protein (S) influences this entry through interactions with human angiotensin-converting enzyme 2 (hACE2) receptor. The World Health Organization (WHO) recognized numerous variants of concern (VOCs) that involve Alpha, Beta, Gamma, Delta, and Omicron, having multiple mutations within the spike protein, altering infection …


Impact Of A Pharmacist-Led Hcv Treatment Program At A Federally Qualified Health Center, Jerika T. Lam, Sharon Xavioer Jul 2024

Impact Of A Pharmacist-Led Hcv Treatment Program At A Federally Qualified Health Center, Jerika T. Lam, Sharon Xavioer

Pharmacy Faculty Articles and Research

Pharmacists are key players who can help to eliminate the hepatitis C virus (HCV) epidemic in the United States. This pilot retrospective study evaluated the impact of a pharmacist-led HCV treatment program in a federally qualified health center (FQHC) primary care clinic setting. The primary outcome was to assess sustained virologic response (SVR) rates 12 weeks after patients were initiated and completed their oral direct acting antiviral (DAA) treatment regimens. Methods: This pilot retrospective study included historical analyses of patients who received DAA treatment in the pharmacist-led HCV treatment program in a FQHC clinic between 1 January 2019 and 31 …


Exploring Binding Pockets In The Conformational States Of The Sars-Cov-2 Spike Trimers For The Screening Of Allosteric Inhibitors Using Molecular Simulations And Ensemble-Based Ligand Docking, Grace Gupta, Gennady M. Verkhivker May 2024

Exploring Binding Pockets In The Conformational States Of The Sars-Cov-2 Spike Trimers For The Screening Of Allosteric Inhibitors Using Molecular Simulations And Ensemble-Based Ligand Docking, Grace Gupta, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

Understanding mechanisms of allosteric regulation remains elusive for the SARS-CoV-2 spike protein, despite the increasing interest and effort in discovering allosteric inhibitors of the viral activity and interactions with the host receptor ACE2. The challenges of discovering allosteric modulators of the SARS-CoV-2 spike proteins are associated with the diversity of cryptic allosteric sites and complex molecular mechanisms that can be employed by allosteric ligands, including the alteration of the conformational equilibrium of spike protein and preferential stabilization of specific functional states. In the current study, we combine conformational dynamics analysis of distinct forms of the full-length spike protein trimers and …


Positive Epidemiology, Revisited: The Case For Centering Human Rights And Economic Justice, Farah Qureshi, Christy Denckla, Julia K. Boehm Apr 2024

Positive Epidemiology, Revisited: The Case For Centering Human Rights And Economic Justice, Farah Qureshi, Christy Denckla, Julia K. Boehm

Psychology Faculty Articles and Research

In recent years, a growing body of research in positive epidemiology has sought to expand the traditional focus of epidemiologic research beyond risk factors for disease and towards a more holistic understanding of health that includes the study of positive assets that shape well-being more broadly. While this paradigm shift holds great promise for transforming people’s lives for the better, it is also critiqued for showcasing decontextualized perspectives that could cause great harm to the public’s health if translated uncritically into population-based interventions. In this commentary, we argue for orienting positive epidemiology within a human rights and economic justice framework …


Ensemble-Based Mutational Profiling And Network Analysis Of The Sars-Cov-2 Spike Omicron Xbb Lineages For Interactions With The Ace2 Receptor And Antibodies: Cooperation Of Binding Hotspots In Mediating Epistatic Couplings Underlies Binding Mechanism And Immune Escape, Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker Apr 2024

Ensemble-Based Mutational Profiling And Network Analysis Of The Sars-Cov-2 Spike Omicron Xbb Lineages For Interactions With The Ace2 Receptor And Antibodies: Cooperation Of Binding Hotspots In Mediating Epistatic Couplings Underlies Binding Mechanism And Immune Escape, Nishank Raisinghani, Mohammed Alshahrani, Grace Gupta, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we performed a computational study of binding mechanisms for the SARS-CoV-2 spike Omicron XBB lineages with the host cell receptor ACE2 and a panel of diverse class one antibodies. The central objective of this investigation was to examine the molecular factors underlying epistatic couplings among convergent evolution hotspots that enable optimal balancing of ACE2 binding and antibody evasion for Omicron variants BA.1, BA2, BA.3, BA.4/BA.5, BQ.1.1, XBB.1, XBB.1.5, and XBB.1.5 + L455F/F456L. By combining evolutionary analysis, molecular dynamics simulations, and ensemble-based mutational scanning of spike protein residues in complexes with ACE2, we identified structural stability and binding …


Changes In Real-World Dispensing Of Adhd Stimulants In Youth From 2019 To 2021 In California, Anika Patel, Rishikesh Chavan, Cyril Rakovski, Richard C. Beuttler, Sun Yang Mar 2024

Changes In Real-World Dispensing Of Adhd Stimulants In Youth From 2019 To 2021 In California, Anika Patel, Rishikesh Chavan, Cyril Rakovski, Richard C. Beuttler, Sun Yang

Mathematics, Physics, and Computer Science Faculty Articles and Research

Introduction: Attention-deficit/hyperactivity disorder (ADHD) is one of the most common pediatric neurobehavioral disorders in the U.S. Stimulants, classified as controlled substances, are commonly used for ADHD management. We conducted an analysis of real-world stimulants dispensing data to evaluate the pandemic’s impact on young patients (≤ 26 years) in California.

Methods: Annual prevalence of patients on stimulants per capita across various California counties from 2019 and 2021 were analyzed and further compared across different years, sexes, and age groups. New patients initiating simulants therapy were also examined. A case study was conducted to determine the impact of socioeconomic status on patient …


Real-World Dispensing Of Buprenorphine In California During Prepandemic And Pandemic Periods, Yun Wang, Alexandre Chan, Richard Beuttler, Marc L. Fleming, Todd Schneberk, Michael Nichol, Haibing Lu Jan 2024

Real-World Dispensing Of Buprenorphine In California During Prepandemic And Pandemic Periods, Yun Wang, Alexandre Chan, Richard Beuttler, Marc L. Fleming, Todd Schneberk, Michael Nichol, Haibing Lu

Pharmacy Faculty Articles and Research

Introduction: The opioid overdose crisis in the United States has become a significant national emergency. Buprenorphine, a primary medication for individuals coping with opioid use disorder (OUD), presents promising pharmacokinetic properties for use in primary care settings, and is often delivered as a take-home therapy. The COVID-19 pandemic exacerbated the scarcity of access to buprenorphine, leading to dire consequences for those with OUD. Most existing studies, primarily focused on the immediate aftermath of the COVID-19 outbreak, highlight the challenges in accessing medications for opioid use disorder (MOUDs), particularly buprenorphine. However, these studies only cover a relatively short timeframe. Methods: To …


Dna Barcoding Of Herbal Supplements On The U.S. Commercial Market Associated With The Purported Treatment Of Covid-19, Calin M. Harris, Diane Y. Kim, Chevon R. Jordan, Miranda I. Miranda, Rosalee S. Hellberg Jan 2024

Dna Barcoding Of Herbal Supplements On The U.S. Commercial Market Associated With The Purported Treatment Of Covid-19, Calin M. Harris, Diane Y. Kim, Chevon R. Jordan, Miranda I. Miranda, Rosalee S. Hellberg

Food Science Faculty Articles and Research

Introduction

The COVID-19 pandemic was associated with an increased global use of traditional medicines, including Ayurvedic herbal preparations. Due to their growing demand, their processed nature, and the complexity of the global supply chain, there is an increased risk of adulteration in these products.

Objectives

The objective of this study was to assess the use of DNA barcoding for species identification in herbal supplements on the US market associated with the Ayurvedic treatment of respiratory symptoms.

Methods

A total of 54 commercial products containing Ayurvedic herbs were tested with four DNA barcoding regions (i.e., rbcL, matK, ITS2, and …


Comparative Analysis Of Conformational Dynamics And Systematic Characterization Of Cryptic Pockets In The Sars-Cov-2 Omicron Ba.2, Ba.2.75 And Xbb.1 Spike Complexes With The Ace2 Host Receptor: Confluence Of Binding And Structural Plasticity In Mediating Networks Of Conserved Allosteric Sites, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker Oct 2023

Comparative Analysis Of Conformational Dynamics And Systematic Characterization Of Cryptic Pockets In The Sars-Cov-2 Omicron Ba.2, Ba.2.75 And Xbb.1 Spike Complexes With The Ace2 Host Receptor: Confluence Of Binding And Structural Plasticity In Mediating Networks Of Conserved Allosteric Sites, Mohammed Alshahrani, Grace Gupta, Sian Xiao, Peng Tao, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

In the current study, we explore coarse-grained simulations and atomistic molecular dynamics together with binding energetics scanning and cryptic pocket detection in a comparative examination of conformational landscapes and systematic characterization of allosteric binding sites in the SARS-CoV-2 Omicron BA.2, BA.2.75 and XBB.1 spike full-length trimer complexes with the host receptor ACE2. Microsecond simulations, Markov state models and mutational scanning of binding energies of the SARS-CoV-2 BA.2 and BA.2.75 receptor binding domain complexes revealed the increased thermodynamic stabilization of the BA.2.75 variant and significant dynamic differences between these Omicron variants. Molecular simulations of the SARS-CoV-2 Omicron spike full-length trimer complexes …


Exploring Conformational Landscapes And Cryptic Binding Pockets In Distinct Functional States Of The Sars-Cov-2 Omicron Ba.1 And Ba.2 Trimers: Mutation-Induced Modulation Of Protein Dynamics And Network-Guided Prediction Of Variant-Specific Allosteric Binding Sites, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta Sep 2023

Exploring Conformational Landscapes And Cryptic Binding Pockets In Distinct Functional States Of The Sars-Cov-2 Omicron Ba.1 And Ba.2 Trimers: Mutation-Induced Modulation Of Protein Dynamics And Network-Guided Prediction Of Variant-Specific Allosteric Binding Sites, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta

Mathematics, Physics, and Computer Science Faculty Articles and Research

A significant body of experimental structures of SARS-CoV-2 spike trimers for the BA.1 and BA.2 variants revealed a considerable plasticity of the spike protein and the emergence of druggable binding pockets. Understanding the interplay of conformational dynamics changes induced by the Omicron variants and the identification of cryptic dynamic binding pockets in the S protein is of paramount importance as exploring broad-spectrum antiviral agents to combat the emerging variants is imperative. In the current study, we explore conformational landscapes and characterize the universe of binding pockets in multiple open and closed functional spike states of the BA.1 and BA.2 Omicron …


The Impact Of Vaccinations And Chronic Disease On Covid Death Rates, James L. Doti Aug 2023

The Impact Of Vaccinations And Chronic Disease On Covid Death Rates, James L. Doti

Economics Faculty Articles and Research

This study presents a theoretical and empirical regression model to measure the efficacy of vaccinations in reducing COVID death rates across states over the 3/10/21 to 12/28/22 period. During that period, it was estimated that the availability of vaccinations resulted in a reduction of 427,000 COVID deaths in the nation. To arrive at that estimate, other covariants were held constant. In particular, it was found that chronic disease should be included as an explanatory variable to arrive at unbiased measures of the efficacy of vaccinations in reducing deaths. In addition, the percentage of people over the age of 65 was …


Metapopulation Dynamics Of Sars-Cov-2 Transmission In A Small-Scale Amazonian Society, Thomas Kraft, Edmond Seabright, Sarah Alami, Samuel M. Jenness, Paul L. Hooper, Bret Beheim, Helen Davis, Daniel K. Cummings, Daniel Eid Rodriguez, Maguin Gutierrez Cayuba, Emily J. Miner, Xavier De Lamballerie, Lucia Inchauste, Stéphane Priet, Benjamin Trumble, Jonathan Stieglitz, Hillard Kaplan, Michael Gurven Aug 2023

Metapopulation Dynamics Of Sars-Cov-2 Transmission In A Small-Scale Amazonian Society, Thomas Kraft, Edmond Seabright, Sarah Alami, Samuel M. Jenness, Paul L. Hooper, Bret Beheim, Helen Davis, Daniel K. Cummings, Daniel Eid Rodriguez, Maguin Gutierrez Cayuba, Emily J. Miner, Xavier De Lamballerie, Lucia Inchauste, Stéphane Priet, Benjamin Trumble, Jonathan Stieglitz, Hillard Kaplan, Michael Gurven

ESI Publications

The severity of infectious disease outbreaks is governed by patterns of human contact, which vary by geography, social organization, mobility, access to technology and healthcare, economic development, and culture. Whereas globalized societies and urban centers exhibit characteristics that can heighten vulnerability to pandemics, small-scale subsistence societies occupying remote, rural areas may be buffered. Accordingly, voluntary collective isolation has been proposed as one strategy to mitigate the impacts of COVID-19 and other pandemics on small-scale Indigenous populations with minimal access to healthcare infrastructure. To assess the vulnerability of such populations and the viability of interventions such as voluntary collective isolation, we …


Implementation Of Post-Covid Conditions Management Utilizing Interprofessional Collaboration In A Multi-Facility Healthcare Organization, Jocelin Friedman, Christina Dhesi-Bawa, Kathleen Kennedy, Stephen Lee, Leona Hidalgo Jun 2023

Implementation Of Post-Covid Conditions Management Utilizing Interprofessional Collaboration In A Multi-Facility Healthcare Organization, Jocelin Friedman, Christina Dhesi-Bawa, Kathleen Kennedy, Stephen Lee, Leona Hidalgo

Physical Therapy Faculty Articles and Research

Background: The prevalence of Post-Covid Conditions (PCC) is estimated to affect 10-35% of infected individuals, with upwards of 85% of previously hospitalized individuals reporting prolonged effects. Literature indicates deficiencies in communication between healthcare providers which can negatively affect patients. Due to limited interprofessional communication, there was a scarcity of individuals with PCC receiving comprehensive therapy treatment on an outpatient basis. The multi-system nature of PCC was an indication for interprofessional collaboration and the development of workflows facilitating access to care.

Purpose: This qualitative study investigates the Post-COVID-19 Rehabilitation Program (PCRP) at a California, USA multi-facility healthcare system. The …


Factors Affecting Initiation And Retention Of Medication-Assisted Recovery (Mar) Within A Pilot Pharmacist-Involved Practice Model At A Federally Qualified Healthcare Center (Fqhc) During The Covid-19 Pandemic, Tiffany Nguyen, Thomas Craig Cheetham, Souhiela Fawaz, Richard Beuttler, Sharon Xavioer May 2023

Factors Affecting Initiation And Retention Of Medication-Assisted Recovery (Mar) Within A Pilot Pharmacist-Involved Practice Model At A Federally Qualified Healthcare Center (Fqhc) During The Covid-19 Pandemic, Tiffany Nguyen, Thomas Craig Cheetham, Souhiela Fawaz, Richard Beuttler, Sharon Xavioer

Pharmacy Faculty Articles and Research

Background: During the COVID-19 pandemic, opioid-related overdose deaths increased. Although Medication-Assisted Treatment or Recovery (MAT or MAR) is available, initiation and retention rates vary. The goal of this study was to evaluate clinical, demographic, and Social Determinant of Health factors affecting MAR initiation, on-time initiation of medications, and successful retention in the program. The secondary goal was to evaluate the impact of a novel interprofessional practice model incorporating pharmacists. Methods: A retrospective analysis was conducted using electronic health record data from a pilot MAR Program initiated within a California Federally Qualified Healthcare Center. Results: From September 2019 to August 2020, …


Balancing Functional Tradeoffs Between Protein Stability And Ace2 Binding In The Sars-Cov-2 Omicron Ba.2, Ba.2.75 And Xbb Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic And Energetic Changes, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta May 2023

Balancing Functional Tradeoffs Between Protein Stability And Ace2 Binding In The Sars-Cov-2 Omicron Ba.2, Ba.2.75 And Xbb Lineages: Dynamics-Based Network Models Reveal Epistatic Effects Modulating Compensatory Dynamic And Energetic Changes, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta

Mathematics, Physics, and Computer Science Faculty Articles and Research

Evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity for ACE2, conformational plasticity, protein stability and allosteric modulation. In this study, we systematically characterize conformational dynamics, structural stability and binding affinities of the SARS-CoV-2 Spike Omicron complexes with the host receptor ACE2 for BA.2, BA.2.75, XBB.1 and XBB.1.5 variants. We combined multiscale molecular simulations and dynamic analysis of allosteric interactions together with the ensemble-based mutational scanning of the protein residues and network modeling of epistatic interactions. This multifaceted computational study characterized molecular mechanisms and …


Coarse-Grained Molecular Simulations And Ensemble-Based Mutational Profiling Of Protein Stability In The Different Functional Forms Of The Sars-Cov-2 Spike Trimers: Balancing Stability And Adaptability In Ba.1, Ba.2 And Ba.2.75 Variants, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta Apr 2023

Coarse-Grained Molecular Simulations And Ensemble-Based Mutational Profiling Of Protein Stability In The Different Functional Forms Of The Sars-Cov-2 Spike Trimers: Balancing Stability And Adaptability In Ba.1, Ba.2 And Ba.2.75 Variants, Gennady M. Verkhivker, Mohammed Alshahrani, Grace Gupta

Mathematics, Physics, and Computer Science Faculty Articles and Research

Evolutionary and functional studies have suggested that the emergence of Omicron variants can be determined by multiple fitness tradeoffs including immune escape, binding affinity, conformational plasticity, protein stability, and allosteric modulation. In this study, we embarked on a systematic comparative analysis of the conformational dynamics, electrostatics, protein stability, and allostery in the different functional states of spike trimers for BA.1, BA.2, and BA.2.75 variants. Using efficient and accurate coarse-grained simulations and atomistic reconstruction of the ensembles, we examined the conformational dynamics of the spike trimers that agree with the recent functional studies, suggesting that BA.2.75 trimers are the most stable …


3rd Place Contest Entry: Using The Scientific Method To Combat The Biological And Sociological Effects Of The Covid-19 Pandemic: An Aspiring Healthcare Professional’S Perspective, Isabelle Dhindsa Apr 2023

3rd Place Contest Entry: Using The Scientific Method To Combat The Biological And Sociological Effects Of The Covid-19 Pandemic: An Aspiring Healthcare Professional’S Perspective, Isabelle Dhindsa

Kevin and Tam Ross Undergraduate Research Prize

This is Isabelle Dhindsa's submission for the 2023 Kevin and Tam Ross Undergraduate Research Prize, which won third place. It contains their essay on using library resources, their bibliography, and a sample of their research project on using the scientific method to combat the biological and sociological effects of the COVID-19 pandemic.

Isabelle is a fourth-year student at Chapman University, majoring in Biology. Their faculty mentor is Dr. Carmichael Peters.


Virtual And In Vitro Screening Of Natural Products Identifies Indole And Benzene Derivatives As Inhibitors Of Sars-Cov-2 Main Protease (MPro), Dony Ang, Riley Kendall, Hagop S. Atamian Mar 2023

Virtual And In Vitro Screening Of Natural Products Identifies Indole And Benzene Derivatives As Inhibitors Of Sars-Cov-2 Main Protease (MPro), Dony Ang, Riley Kendall, Hagop S. Atamian

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

The rapid spread of the coronavirus disease 2019 (COVID-19) resulted in serious health, social, and economic consequences. While the development of effective vaccines substantially reduced the severity of symptoms and the associated deaths, we still urgently need effective drugs to further reduce the number of casualties associated with SARS-CoV-2 infections. Machine learning methods both improved and sped up all the different stages of the drug discovery processes by performing complex analyses with enormous datasets. Natural products (NPs) have been used for treating diseases and infections for thousands of years and represent a valuable resource for drug discovery when combined with …


Shot Talk: Development And Pilot Test Of A Theory Of Planned Behavior Campaign To Combat College Student Covid-19 Vaccine Hesitancy, Hannah Ball, Tayah Renea Wozniak, Cailin M. Kuchenbecker Feb 2023

Shot Talk: Development And Pilot Test Of A Theory Of Planned Behavior Campaign To Combat College Student Covid-19 Vaccine Hesitancy, Hannah Ball, Tayah Renea Wozniak, Cailin M. Kuchenbecker

Communication Faculty Articles and Research

Among college students, evidence of relatively lower levels of concern of COVID-19 infection, rapid rates of transmission, and lagging vaccination rates substantiates a need to combat college student COVID-19 vaccine hesitancy. This two-phase study comprised formative research, development, and pilot testing of a campaign to combat COVID-19 vaccine hesitancy among college students. In phase one, focus group discussions with college students (N = 48) uncovered their specific attitudes, subjective norms, and perceived behavioral control toward the COVID-19 vaccine. Thematic analysis revealed concerns about vaccine safety, efficacy, cost, and politicization, as well as perceived barriers to accessing information and the …


Covid-Dynamic: A Large-Scale Longitudinal Study Of Socioemotional And Behavioral Change Across The Pandemic, Tessa Rusch, Yanting Han, Dehua Liang, Amber R. Hopkins, Carolyn V. Lawrence, Uri Maoz, Lynn K. Paul, Damian A. Stanley, The Covid-Dynamic Team Feb 2023

Covid-Dynamic: A Large-Scale Longitudinal Study Of Socioemotional And Behavioral Change Across The Pandemic, Tessa Rusch, Yanting Han, Dehua Liang, Amber R. Hopkins, Carolyn V. Lawrence, Uri Maoz, Lynn K. Paul, Damian A. Stanley, The Covid-Dynamic Team

Pharmacy Faculty Articles and Research

The COVID-19 pandemic has caused enormous societal upheaval globally. In the US, beyond the devastating toll on life and health, it triggered an economic shock unseen since the great depression and laid bare preexisting societal inequities. The full impacts of these personal, social, economic, and public-health challenges will not be known for years. To minimize societal costs and ensure future preparedness, it is critical to record the psychological and social experiences of individuals during such periods of high societal volatility. Here, we introduce, describe, and assess the COVID-Dynamic dataset, a within-participant longitudinal study conducted from April 2020 through January 2021, …


Not A Waste: Wastewater Surveillance To Enhance Public Health, Anna Gitter, Jeremiah Oghuan, Anuja Rajendra Godbole, Carlos A. Chavarria, Carlos Monserrat, Tao Hu, Yun Wang, Anthony W. Maresso, Blake M. Hanson, Kristina D. Mena, Fuqing Wu Jan 2023

Not A Waste: Wastewater Surveillance To Enhance Public Health, Anna Gitter, Jeremiah Oghuan, Anuja Rajendra Godbole, Carlos A. Chavarria, Carlos Monserrat, Tao Hu, Yun Wang, Anthony W. Maresso, Blake M. Hanson, Kristina D. Mena, Fuqing Wu

Pharmacy Faculty Articles and Research

Domestic wastewater, when collected and evaluated appropriately, can provide valuable health-related information for a community. As a relatively unbiased and non-invasive approach, wastewater surveillance may complement current practices towards mitigating risks and protecting population health. Spurred by the COVID-19 pandemic, wastewater programs are now widely implemented to monitor viral infection trends in sewersheds and inform public health decision-making. This review summarizes recent developments in wastewater-based epidemiology for detecting and monitoring communicable infectious diseases, dissemination of antimicrobial resistance, and illicit drug consumption. Wastewater surveillance, a quickly advancing Frontier in environmental science, is becoming a new tool to enhance public health, improve …