Virus Diseases Commons^™

Computational Analysis Of Protein Stability And Allosteric Interaction Networks In Distinct Conformational Forms Of The Sars Cov 2 Spike D614g Mutant: Reconciling Functional Mechanisms Through Allosteric Model Of Spike Regulation, Gennady M. Verkhivker, Steve Agajanian, Deniz Oztas, Grace Gupta

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we used an integrative computational approach to examine molecular mechanisms underlying functional effects of the D614G mutation by exploring atomistic modeling of the SARS-CoV-2 spike proteins as allosteric regulatory machines. We combined coarse-grained simulations, protein stability and dynamic fluctuation communication analysis with network-based community analysis to examine structures of the native and mutant SARS-CoV-2 spike proteins in different functional states. Through distance fluctuations communication analysis, we probed stability and allosteric communication propensities of protein residues in the native and mutant SARS-CoV-2 spike proteins, providing evidence that the D614G mutation can enhance long-range signaling of the allosteric spike …

Exploring Social Determinants Of Covid-19 Related Sickness And Suffering In The Bronx, Hamida Chumpa

Student Theses and Dissertations

Through a positivistic and phenomenological approach, the study examines social determinants of COVID-19 related sickness and suffering in the Bronx, New York City, New York, ZIP codes 10462, 10472, 10467, 10458, 10474, and 10464. I utilize a violence paradigm (structural and everyday violence) to describe the social determinants of risk and sickness-related suffering and deploy an assemblage framework to shed light on how these determinants create negative synergies that undermine wellbeing and render certain communities vulnerable to extreme suffering. The mixed methods include 64 surveys and eight interviews. Analysis methods include a descriptive analysis of survey results and a thematic …

Trend Of Research Visualization Of Covid-19 Complications In Pubmed Database Using Scientometric Analysis From 2020 To March 20, 2021, Dr. Abeel Naseer, Dr. Muhammad Shoaib, Mr. Nusrat Ali, Dr. Muhammad Bilal

Library Philosophy and Practice (e-journal)

This study focused to evaluate the published articles on PubMed whose focus was to study the different relations between COVID 19, and different complications caused due to it. The main complications that were used to formulate this study are Deep Venous Thrombosis (DVT), Stroke, Pulmonary Embolism, Disseminated Intravascular Coagulation (DIC), Myocardial Infarction (MI), anosmia, and pneumonia. The data was extracted from the PubMed database on March 20, 2021at 03:20 PM, PST with the period of 2020 to March 20, 2021. We used Biblioshiny, VOSviewer, and MS Excel software to analyze data and found 2375 published documents. The results revealed that …

Neurocognitive Impairment In People Living With Human Immunodeficiency Virus (Hiv): Risk Factors And Mortality, Zaeema Naveed

Theses & Dissertations

Despite the widespread use of combination antiretroviral therapy (cART), HIV-associated neurocognitive impairment (NCI) persists in people living with HIV (PLWH) with clinical and public health implications. Studies have generated inconsistent results regarding etiological factors for NCI in PLWH and a brief user-friendly predictive tool is desirable in clinical practice to assess the probability of having NCI in PLWH. Furthermore, factors associated with clinically meaningful decline in neurocognitive status and survival disadvantage for patients with NCI are understudied in the post-cART era. The goal of this dissertation was to investigate factors associated with baseline NCI and neurocognitive decline and the association …

Fire Service Covid-19 Infection Prevention And Control Policy Comparison, Saaddedine Dichari

Theses & Dissertations

To date, there have been over 2.7 million deaths and more than 126 million cases attributed to the COVID-19 pandemic (JHU, 2021). This pandemic has affected nearly every aspect of daily life. Among those impacted are U.S. firefighters, as they provide many services beyond simply extinguishing structure fires and are frequently dual certified as emergency medical technicians. Many of the victims of this pandemic have relied on first responders to provide them with emergency medical care and hospital transport. When caring for these infected patients, firefighters have an increased risk of exposure and must be provided with adequate …

Time Series Forecasting Of Covid-19 Deaths In Massachusetts, Andrew Disher

Honors Program Theses and Projects

The aim of this study was to use data provided by the Department of Public Health in the state of Massachusetts on its online dashboard to produce a time series model to accurately forecast the number of new confirmed deaths that have resulted from the spread of CoViD-19. Multiple different time series models were created, which can be classified as either an Auto-Regressive Integrated Moving Average (ARIMA) model or a Regression Model with ARIMA Errors. Two ARIMA models were created to provide a baseline forecasting performance for comparison with the Regression Model with ARIMA Errors, which used the number of …

Mathematical Models Of Covid-19, Kate Faria

Honors Program Theses and Projects

For more than a year, the COVID-19 pandemic has been a major public health issue, affecting the lives of most people around the world. With both people’s health and the economy at great risks, governments rushed to control the spread of the virus. Containment measures were heavily enforced worldwide until a vaccine was developed and distributed. Although researchers today know more about the characteristics of the virus, a lot of work still needs to be done in order to completely remove the disease from the population. However, this is true for most of the infectious diseases in existence, including Influenza, …

Covid-19: Exploring The Probability Of Disease Extinction - A Modeling And Simulation Study, Donald Porchia

Electronic Theses and Dissertations, 2020-2023

There are two distinct topics considered in this dissertation. The first is the formulation of a compartmental model using reactive social distancing in which disease transmission changes as a function of the state variables of the model; in this case, the cumulative incidence. The model assumes a single strain epidemic of Covid-19 in the United States and is used to estimate the cumulative number of deaths due to the epidemic where incidence data is used to calibrate and validate the model. The second topic concerns the use of the stochastic threshold to determine disease persistence or extinction. The Covid-19 pandemic …

On The Front Line: Uri's Response To Covid-19 And The Role Of The Student-Run Emergency Medical Services, Michael C. Brennan

Senior Honors Projects

The COVID-19 pandemic has affected all aspects of society, including universities, and we are just beginning to understand its impacts. This project looks at how universities have responded to the pandemic by focusing on the University of Rhode Island, the largest university in the state of Rhode Island. A key aspect of this project is a timeline that documents the policies implemented by URI leadership and relevant policies adopted by the State of Rhode Island. The timeline also includes data about the number of cases at URI and state-wide, as well as figures for the number of students in isolation …

Efficiency With Covid-19: Home Vs. Dillon’S Rule States, Jason Kolb

Political Science Theses and Capstones

How does a state measure success when dealing with a pandemic like Covid-19? Can Dillon’s Rule keep their citizens happy and protected during a pandemic better then Home Rule? When local governments wait for the state to create policies, is this the best option for the state? Data will show a trend that states with a higher preemption rate have kept the death rate lower when dealing with the Covid-19 pandemic

Changes In Body Mass Index Among Antiretroviral Therapy Naïve People Living With Hiv In Southeastern Nigeria, John O. Olawepo, Jennifer R. Pharr, Chad L. Cross, Babayemi O. Olakunde, Chinedu Aniekwe, Mercy Niyang, Raisa Kabir, Ayodotun Olutola

Environmental & Global Health Faculty Research

The proportion of people living with HIV (PLHIV) who are overweight or obese is rising, leading to a double epidemic of HIV and obesity. The purpose of this retrospective longitudinal study was to examine changes in body mass index (BMI) among PLHIV who were new to antiretroviral therapy (ART) in two states in Southeastern Nigeria. The BMI at baseline and 12 months were compared and the difference in proportions in each BMI category was tested. The association between the BMI at 12 months and the demographic and/or clinical variables was examined using multiway analysis of covariance. The study included 2,146 …

Preprocedure Covid-19 Testing In Early Phase Of Pandemic, Renuka Jain, Bradley Kruger, Robert Citronberg, Stacie Kroboth, Ana Cristina Perez Moreno, Bijoy K. Khandheria

Journal of Patient-Centered Research and Reviews

The COVID-19 pandemic led to a nationwide shutdown of elective medical procedures. Upon resumption of services, preprocedure nasopharyngeal swab testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was introduced for all patients requiring surgical or other aerosol-generating procedures. We investigated preprocedure COVID-19 testing in one of the largest U.S. health systems. Patients included in this retrospective, observational study were asymptomatic and scheduled for a procedure or surgery. All patients underwent a nasopharyngeal swab test for SARS-CoV-2 performed 24–72 hours prior to a planned procedure. Clinical demographics, type of procedure, test results, and subsequent procedure status were evaluated. Of 38,608 …

Ua94/6/1 Covid-19 Diary, Kaleb Workman

Student/Alumni Personal Papers

Reflections of COVID-19 by Gatton Academy of Mathematics & Science student Kaleb Workman.

Defining Septicemia Incidence And Mortality In South Carolina Through Access To Health Care, Behavioral Health, And Low Socio-Economic Status, Raeann Vossberg

Senior Theses

This study aims to provide an in-depth view of septicemia mortality and incidence in the state of South Carolina through the lenses of socio-economic factors, access to healthcare, and behavioral health factors. This study was conducted using data from the South Carolina Revenue and Fiscal Affairs Office, utilizing their Hospitalization, Inpatient, Emergency Department, and Outpatient data both separately and combined depending on the data point, along with additional data sources for support (see works cited). We hypothesize that the higher rates of septicemia mortality and incidence in the southeastern United States, as well as in South Carolina in particular, could …

Mental Health Of Children And Adolescents Amidst Covid-19 And Past Pandemics: A Rapid Systematic Review, Salima Meherali, Neelam Punjani, Samantha Louie-Poon, Komal Abdul Rahim, Jai K. Das, Rehana A. Salam, Zohra S. Lassi

School of Nursing & Midwifery

Background: The COVID‑19 pandemic and associated public health measures have disrupted the lives of people around the world. It is already evident that the direct and indirect psychological and social effects of the COVID‑19 pandemic are insidious and affect the mental health of young children and adolescents now and will in the future. The aim and objectives of this knowledge-synthesis study were to identify the impact of the pandemic on children's and adolescent's mental health and to evaluate the effectiveness of different interventions employed during previous and the current pandemic to promote children's and adolescents' mental health.
Methodology: We conducted …

H1n1 Influenza Virus (Swine Flu): A Comprehensive Insight Into Escalating Catch-22 Scenarios, Muhammad Shahzaib, Ehsan Ul Haq

The University of Louisville Journal of Respiratory Infections

Introduction: Viruses have always been a major cause of various disastrous pandemics in mankind’s history. H1N1 became a threat when its original strain was first discovered back in the swine flu pandemic of 2009. It became highly catastrophic on a large scale because none of the therapeutic interventions and methodologies that were already present at the time were effective against the virus.

Methods: A vast amount of literature and research is available regarding H1N1 influenza from different reputable sources online. The data were gathered with the contrasting and relative situations of 1918 and 2009 pandemics in mind. The overall extracted …

Nih Funding For Vaccine Readiness Before The Covid-19 Pandemic, Anthony E. Kiszewski, Ekaterina Galkina Cleary, Matthew J. Jackson, Fred D. Ledley

Natural & Applied Sciences Faculty Publications

Rapid development of vaccines for COVID-19 has relied on the application of existing vaccine technologies. This work examines the maturity of ten technologies employed in candidate vaccines (as of July 2020) and NIH funding for published research on these technologies from 2000–2019. These technologies vary from established platforms, which have been used successfully in approved products, to emerging technologies with no prior clinical validation. A robust body of published research on vaccine technologies was supported by 16,358 fiscal years of NIH funding totaling $17.2 billion from 2000–2019. During this period, NIH funding for published vaccine research against specific pandemic threats …

Lack Of Association Of The Abo Blood Group With Covid-19 Risk And Severity In Hospitalized Patients In Louisville, Ky, Rafael Fernandez-Botran, Meredith Cahill, Raghava S. Ambadapoodi, Evelyn Exposito Gonzalez, Stephen P. Furmanek, Ruth Carrico, Jose Bordon, Julio A. Ramirez

The University of Louisville Journal of Respiratory Infections

Background: The potential association of the ABO blood group with the risk of COVID-19 and its severity has attracted a lot of interest since the start of the pandemic. While a number of studies have reported an increased risk associated with blood type A and a reduced risk with type O, other studies have did not found a significant effect. This study aimed to define the prevalence of different ABO blood groups in hospitalized COVID-19 patients in the Louisville, KY area and to investigate whether an association exists between the blood group and disease severity.

Methods: This was a retrospective …

Antimicrobial Resistance And Covid-19: Intersections And Implications, Gwenan M. Knight, Rebecca E. Glover, C Finn Mcquaid, Ioana D. Olaru, Karin Gallandat, Quentin J. Leclerc, Naomi M. Fuller, Sam J. Willcocks, Rumina Hasan, Esther Van Kleef, Clare Ir Chandler

Department of Pathology and Laboratory Medicine

Before the coronavirus 2019 (COVID-19) pandemic began, antimicrobial resistance (AMR) was among the top priorities for global public health. Already a complex challenge, AMR now needs to be addressed in a changing healthcare landscape. Here, we analyse how changes due to COVID-19 in terms of antimicrobial usage, infection prevention, and health systems affect the emergence, transmission, and burden of AMR. Increased hand hygiene, decreased international travel, and decreased elective hospital procedures may reduce AMR pathogen selection and spread in the short term. However, the opposite effects may be seen if antibiotics are more widely used as standard healthcare pathways break …

Long-Term Dynamics Of The Kidney Disease Epidemic Among Hiv-Infected Individuals, Heather Gudaz, Henry A. Ogu, Elissa J. Schwartz

Spora: A Journal of Biomathematics

One of many risks facing HIV+ individuals is the development of kidney dysfunction and end stage kidney disease (ESKD). A differential equation-based mathematical model was developed to assess the impact of antiretroviral therapy on the progression to kidney disease and on reducing mortality due to kidney failure. Analytical and numerical predictions of long-term HIV+ ESKD prevalence show that therapy can lead to either extremely low levels of disease prevalence or increased prevalence, depending on drug efficacy levels and mechanisms of action. Maintenance of HIV+ ESKD prevalence below one individual is possible with sufficient efficacy (e.g., 99%) against the progression from …

Epidemiology And Outcomes Of Hospitalized Adults With Sars-Cov-2 Community-Acquired Pneumonia In Louisville, Kentucky, Julio A. Ramirez, T'Shura Ali, Thomas Chandler, Stephen P. Furmanek, Daniya Sheikh, Vidyulata Salunkhe, Steven Gootee, Mohammad Tahboub, William A. Mattingly, Demetra Antimisiaris, Jiapeng Huang, Jose Bordon, Rodrigo Cavallazzi, Paul Schulz, William P. Mckinney, Dawn Balcom, Mark Burns, Ruth Carrico, Forest W. Arnold, Cerid Covid-19 Study Group

The University of Louisville Journal of Respiratory Infections

Background: During the ongoing pandemic of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), SARS-CoV-2 community-acquired pneumonia (CAP) has been the primary cause of hospitalization. The objective of this study was to evaluate the clinical characteristics and outcomes of 1,013 patients hospitalized with SARS-CoV-2 CAP from September 2020 through March 2021 in Louisville, Kentucky.

Methods: This was a retrospective observational study of 1,013 patients hospitalized with SARS-CoV-2 CAP at eight of the adult hospitals in the city of Louisville from September 2020 through March 2021. Patients with 1) a positive reverse transcriptase-polymerase chain reaction (RT-PCR) for SARS-CoV-2, 2) fever, cough, or …

Healthcare Of Indigenous Amazonian Peoples In Response To Covid-19: Marginality, Discrimination And Revaluation Of Ancestral Knowledge In Ucayali, Peru, Doreen Montag, Marco Barboza, Lizardo Cauper, Ivan Brehaut, Isaac Alva, Aoife Bennett, José Sanchez-Choy, Juan Pablo Sarmiento Barletti, Pilar Valenzuela, José Manuyama, Italo García Murayari, Miguel Guimaraes Vásquez, Celso Aguirre Panduro, Angela Giattino, Edwin Julio Palomino Cadenas, Rodrigo Lazo, Carlos A. Delgado, Alfonso Nino, Elaine C. Flores, Maria Amalia Pesantes, Juan Pablo Murillo, Luisa Elvira Belaunde, Sergio Recuenco, Robert Chuquimbalqui, Carol Zavaleta-Cortijo

World Languages and Cultures Faculty Articles and Research

"Systematic and persistent discrimination against Indigenous Peoples translates into differential health outcomes when analysed through ethnicity and/or mother tongue.1 In Peru, morbidity and mortality rates among Indigenous Peoples for COVID-19 appear to confirm this.2 The COVID-19 pandemic has highlighted the historical structural violence against Indigenous Peoples that currently takes a disproportionate toll in the Peruvian Amazon. This equally applies to Indigenous Andean Peoples and Afro Peruvians. Indigenous Peoples in voluntary isolation and those in initial contact are at highest health risk in this pandemic as they have no previous immunity against common infectious diseases, and lack access to public healthcare …

Ua94/6/1 Covid-19: The New Plague, Kaylene Bliss

Student/Alumni Personal Papers

COVID-19 personal narrative written by student Kaylene Bliss for History 241 class.

Association Between Race/Ethnicity And Covid-19 Disease Outcomes In The United States: A Qualitative Systematic Review Of The Literature, Jacob Smith

MEDI 9331 Scholarly Activities Clinical Years

Background/Objective: As studies have shown disparities in coronavirus disease-19 prevalence and severity, we sought to evaluate differences in outcomes of acute SARS-CoV-2 infection by race/ethnicity.

Design: Systematic review

Data Source: Studies from PubMed were included.

Review methods: Articles published in English language from January 1, 2019 through March 22, 2020. Studies included were observational studies that examined racial or ethnic disparities in SARS-CoV-2 infection outcomes in the United States. One reviewer performed data extraction.

Results: Out of a possible 1,944 articles, 99 observational studies (82 individual-level and 17 population-level) were included. Differential rates of hospitalization or otherwise severe illness …

Use Of Lymesim 2.0 To Assess The Potential For Single And Integrated Management Methods To Control Blacklegged Ticks (Ixodes Scapularis; Acari: Ixodidae) And Transmission Of Lyme Disease Spirochetes, Shravani Chitineni, Elizabeth R. Gleim, Holly D. Gaff

Undergraduate Honors Theses

Annual Lyme disease cases continue to rise in the U.S. making it the most reported vector-borne illness in the country. The pathogen (Borrelia burgdorferi) and primary vector (Ixodes scapularis; blacklegged tick) dynamics of Lyme disease are complicated by the multitude of vertebrate hosts and varying environmental factors, making models an ideal tool for exploring disease dynamics in a time- and cost-effective way. In the current study, LYMESIM 2.0, a mechanistic model, was used to explore the effectiveness of three commonly used tick control methods: habitat-targeted acaricide (spraying), rodent-targeted acaricide (bait boxes), and white-tailed deer targeted acaricide (4-poster …

The Intellectual Property Of Covid-19, Ana Santos Rutschman

All Faculty Scholarship

The response to COVID-19 is indissolubly tied to intellectual property. In an increasingly globalized world in which infectious disease pathogens travel faster and wider than before, the development of vaccines, treatments and other forms of medical technology has become an integral part of public health preparedness and response frameworks. The development of these technologies, and to a certain extent the allocation and distribution of resulting outputs, is informed by intellectual property regimes. These regimes influence the commitment of R&D resources, shape scientific collaborations and, in some cases, may condition the widespread availability of emerging technologies. As seen throughout this chapter, …

Epigenetic Mechanisms Underlying Hiv-Infection Induced Susceptibility Of Cd4+ T Cells To Enhanced Activation-Induced Fasl Expression And Cell Death., Smita Ghare, Paula M. Chilton, Aakarsha V. Rao, Swati Joshi-Barve, Paula Peyrani, Andrea Reyes-Vega, Craig J. Mcclain, Kendall Bryant, Robert L. Cook, Mathew Freiberg, Shirish Barve

Faculty and Staff Scholarship

Background:

Chronic immune activation and CD4⁺ T cell depletion are significant pathogenic features of HIV infection. Expression of Fas ligand (FasL), a key mediator of activation-induced cell death in T cells, is elevated in people living with HIV-1 infection (PLWH). However, the epigenetic mechanisms underlying the enhanced induction of FasL expression in CD4⁺ T lymphocytes in PLWH are not completely elucidated. Hence, the current work examined the effect of HIV infection on FasL promoter-associated histone modifications and transcriptional regulation in CD4⁺ T lymphocytes in PLWH.

Method:

Flow cytometric analysis was performed to examine the Fas-FasL expression on …

Decomposing Differences In Coronavirus Disease 2019-Related Case-Fatality Rates Across Seventeen Nations, Ashley Wendell Kranjac, Dinko Kranjac

Sociology Faculty Articles and Research

As of 1 November 2020, estimated case-fatality rates associated with coronavirus disease 2019 are not uniformly patterned across the world and differ substantially in magnitude. Given the global spatial heterogeneity in case-fatality rates, we applied the Blinder-Oaxaca regression decomposition technique to identify how putative sociodemographic, structural, and environmental sources influence variation in case-fatality rates. We show that compositional and associational differences in country-level risk factors explain a substantial proportion of the coronavirus disease 2019-related case-fatality rate gap across nations. Asian countries fair better vis-à-vis case-fatality rate differences mainly due to variation in returns to sociodemographic, structural, and environmental sources among …

Ua94/6/1 Covid-19 Diary, Daniel Myers

Student/Alumni Personal Papers

COVID-19 diary submitted to WKU Archives by student Daniel Myers for fall semester 2020.

Ua94/6/1 Covid-19 Diary, Michaela Snyder

Student/Alumni Personal Papers

COVID-19 diary submitted to WKU Archives by student Michaela Snyder for fall 2020 semester.