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An Open-Data-Driven Agent-Based Model To Simulate Infectious Disease Outbreaks, Elizabeth Hunter, Brian Mac Namee, John D. Kelleher

Articles

Agent-based models are a tool that can be used to better understand the dynamics of an infectious disease outbreak. An infectious disease outbreak is influenced by many factors including vaccination or immunity levels, population density, and the age structure of the population. We hypothesize that these factors along with interactions of factors and the actions of individuals would lead to outbreaks of different size and severity even in two towns that appear similar on paper. Thus, it is necessary to implement a model that is able to capture these interactions and the actions of individuals. Using openly available data we …

Interference And Control Of The Nosocomial Transmission Of Methicillin-Resistant Staphylococcus Aureus, Sen Pei, Flaviano Morone, Fredrik Liljeros, Hernan Makse, Jeffrey L. Shaman

Publications and Research

Methicillin-resistant Staphylococcus aureus (MRSA) is a continued threat to human health in both community and healthcare settings. In hospitals, control efforts would benefit from accurate estimation of asymptomatic colonization and infection importation rates from the community. However, developing such estimates remains challenging due to limited observation of colonization and complicated transmission dynamics within hospitals and the community. Here, we develop an inference framework that can estimate these key quantities by combining statistical filtering techniques, an agent-based model, and real-world patient-to-patient contact networks, and use this framework to infer nosocomial transmission and infection importation over an outbreak spanning 6 years in …

Retrospective Review Of Alternative Antibiotic Use In Patients With A Reported Penicillin Allergy At A Community Hospital, Rita Chamoun, Monica Tadros, Amy Montes, Heidi Clarke, Radhan Gopalani

All Publications

No abstract provided.

Improving Satisfaction For Patients With Diabetic Foot Ulcer Using A Diagnosis Specific Written Education Packet, Douglas W. Kozeluh

Doctor of Nursing Practice Scholarly Projects

Diabetes mellitus is a significant health care concern affecting 30.2 million Americans in 2015. One of the most common, costly, and serious sequela of diabetes is diabetic foot ulceration (DFU), which may lead to lower extremity amputation. Up to 50% of DFUs and lower extremity amputations can be prevented through effective patient education (PE). PE provided through written information is one intervention designed to improve patient understanding and self-management practices in order to reduce the risks and complications of DFU. The purpose of this Doctorate in Nursing Practice (DNP) project was to determine if implementation of a DFU specific written …

Vertical Transmission Of Zika Virus In Aedes Aegypti And Aedes Albopictus, Stephanie Cantu

Honors Theses

Arboviruses such as Zika (ZIKV), dengue, chikungunya are responsible causing over 4 million people to live with debilitating conditions and may produce long-term health consequences. Zika virus, a newly emerging arbovirus, has potentially severe neurological complications and a potential to cause severe birth defects. There are no current vaccines for Zika virus, and the primary method for control the spread of this disease is through early detection and vector control. Assessing and quantifying viral transmission patterns is critical for successful control efforts. Zika virus shows some unique (among arboviruses) transmission patterns, notably the ability to be sexually transmitted. One aspect …

Microbiota Metabolic Product Deoxycholic Acid Prevents Campylobacter Jejuni Chicken Colonization Through Modulating Ceca Anaerobes, Bilal Ali Alrubaye

Graduate Theses and Dissertations

Campylobacter jejuni is a prevalent infectious enteritis mainly foodborne from chickens. Despite of reducing C. jejuni food contamination dramatically decreases campylobacteriosis, few effective approaches are available for the bacterial reduction in chickens. The aim of this study was to use microbial metabolic product deoxycholic acid (DCA) to reduce C. jejuni chicken colonization. Broiler chicks were fed 0 or 1.5 g/kg DCA, lithocholic acid (LCA), or urodeoxycholic acid (UDCA) in diets or orally gavaged with cholic acid (CA, 1.5g/kg body weight). Birds were also transplanted with DCA modulated anaerobes (DCA-Anearo) or aerobes (DCA-Aero). Birds were infected with 109 CFU/bird human clinical …

Risky Business: Millennials’ Protection Motivation Factors For Norovirus Outbreaks On College Campuses, Dylan Conrad Martinez

Graduate Theses and Dissertations

The risk and severity of hNoV transmission is obscurely recognized to foodservice millennial customers. Most commonly associated with cruise ships, consumers are not aware of its full potential to strike at other locations, especially college campuses. For the foodservice industry and the university community, it is imperative that a proactive method for increasing millennials’ motivation to practice mitigation methods emerges to reduce future hNoV outbreaks on college campuses. Research has shown that students can play a major role in the spread of hNoV on college campuses. Therefore, the purpose of these studies is to examine motivations for health protective behaviors …

The Role Of Non-Neuronal Acetylcholine In Urogenital Chlamydial Infection, Jessica R. Lockhart

Electronic Theses and Dissertations

Chlamydia trachomatiscauses a bacterial sexually transmitted infection, Chlamydia, that is often chronic and casues reproductive complications in women. We hypothesized that Chlamydia infection increases local acetylcholine (ACh) production, which regulates the host’s inflammatory response to the infection. Female mice infected with C. muridarumwere sacrificed at days 3, 9, 15, and 21 post-infection, genital tract tissues harvested, and immunohistochemistry performed to enumerate ACh-producing cells. Infection increased the number of ACh-producing cells in cervical tissue at days 3,15, and 21 post-infection (pi), uterine tissue at day 3 and 9 pi, and ovarian tissue day 3, 15, and 21 pi. These …

Examining The Impact Of Hiv Medical And Social Case Management Program On Viral Load For Clients Living With Hiv/Aids In Nebraska, Abdulla Munir

Capstone Experience: Master of Public Health

Abstract

Case management (CM) is one of the standard practices that has been implemented since 1990 to help people living with HIV/AIDS (PLWHA) in the United States. The program is designed for low-income populations and it aims to address the barriers related to access to health care and improve the HIV outcomes. Previous studies identified a positive association with the provision of CM and improvement in viral outcomes. Increasing the viral suppression rates among HIV diagnosed individuals proved to reduce the risk of transmitting the infection, and disease incidence. Although CM program is provided to Nebraskans diagnosed with HIV, but …

A Comparison Of Agent-Based Models And Equation Based Models For Infectious Disease Epidemiology, Elizabeth Hunter, Brian Mac Namee, John D. Kelleher

Articles

There are two main methods that are used to model the spread of an infectious disease: agent-based modelling and equation based modelling. In this paper, we compare the results from an example implementation of each method, and show that although the agent-based model takes longer to setup and run, it provides additional information that is not available when using an equation based model. Specifically, the ability of the agent-based model to capture heterogeneous mixing and agent interactions enables it to give a better overall view of an outbreak. We compare the performance of both models by simulating a measles outbreak …

Quantitative Microbial Risk Assessment For Parts, Ground, And Msc Poultry Product Including Intervention Analysis And Exploration Of Enterobacteriaceae As An Indicator Organism In Poultry Processing, Leigh Ann Parette

Graduate Theses and Dissertations

Samples collected at five different large bird poultry processing facilities over a period of 7 months from prescald to post debone locations were enumerated for Enterobacteriaceae, Salmonella spp., and Campylobacter spp. and the results were used to create Quantitative Microbial Risk Analyses (QMRA) models for parts, ground, and mechanically separated chicken (MSC) products. Sensitivity analyses indicated the points in the process at which reductions would be most advantageous to the endpoint and simulation models were run to test reductions required to meet the current USDA performance standards.

These data were analyzed to determine the reductions from one node (location) to …

Risk Stratification Of Febrile Infants ≤60 Days Old Without Routine Lumbar Puncture., Paul L. Aronson, Marie E. Wang, Eugene D. Shapiro, Samir S. Shah, Adrienne G. Deporre, Russell J Mcculloh, Christopher M. Pruitt, Sanyukta Desai, Lise E. Nigrovic, Richard D. Marble, Rianna C. Leazer, Sahar N. Rooholamini, Laura F. Sartori, Fran Balamuth, Christopher Woll, Mark I. Neuman, Febrile Young Infant Research Collaborative

Manuscripts, Articles, Book Chapters and Other Papers

Video Abstract: media-1vid110.1542/5840460609001PEDS-VA_2018-1879

OBJECTIVES: To evaluate the Rochester and modified Philadelphia criteria for the risk stratification of febrile infants with invasive bacterial infection (IBI) who do not appear ill without routine cerebrospinal fluid (CSF) testing.

METHODS: We performed a case-control study of febrile infants ≤60 days old presenting to 1 of 9 emergency departments from 2011 to 2016. For each infant with IBI (defined as a blood [bacteremia] and/or CSF [bacterial meningitis] culture with growth of a pathogen), controls without IBI were matched by site and date of visit. Infants were excluded if they appeared ill or had a …

Triatomines: Trypanosomatids, Bacteria, And Viruses Potential Vectors?, Caroline Barreto Viera, Yanna Reis Praça, Kaio Luis Da Silva Bentes, Paula Beatriz Santiago, Sofia Marcelino Martins Silva, Gabriel Dos Santos Silva, Flávia Nader Motta, Izabela Marques Dourado Bastos, Jaime Martins De Santana, Carla Nunes De Araújo

Harold W. Manter Laboratory of Parasitology: Library Materials

Triatominae bugs are the vectors of Chagas disease, a major concern to public health especially in Latin America, where vector-borne Chagas disease has undergone resurgence due mainly to diminished triatomine control in many endemic municipalities. Although the majority of Triatominae species occurs in the Americas, species belonging to the genus Linshcosteus occur in India, and species belonging to the Triatoma rubrofasciata complex have been also identified in Africa, the Middle East, South-East Asia, and in the Western Pacific. Not all of Triatominae species have been found to be infected with Trypanosoma cruzi, but the possibility of establishing vector transmission …

Azithromycin For Early Pseudomonas Infection In Cystic Fibrosis. The Optimize Randomized Trial., Nicole Mayer-Hamblett, George Retsch-Bogart, Margaret Kloster, Frank Accurso, Margaret Rosenfeld, Gary Albers, Philip Black, Perry Brown, Annemarie Cairns, Stephanie D. Davis, Gavin R. Graff, Gwendolyn S. Kerby, David Orenstein, Rachael Buckingham, Bonnie W. Ramsey, Optimize Study Group

Manuscripts, Articles, Book Chapters and Other Papers

RATIONALE: New isolation of Pseudomonas aeruginosa (Pa) is generally treated with inhaled antipseudomonal antibiotics such as tobramycin inhalation solution (TIS). A therapeutic approach that complements traditional antimicrobial therapy by reducing the risk of pulmonary exacerbation and inflammation may ultimately prolong the time to Pa recurrence.

OBJECTIVES: To test the hypothesis that the addition of azithromycin to TIS in children with cystic fibrosis and early Pa decreases the risk of pulmonary exacerbation and prolongs the time to Pa recurrence.

METHODS: The OPTIMIZE (Optimizing Treatment for Early Pseudomonas aeruginosa Infection in Cystic Fibrosis) trial was a multicenter, double-blind, randomized, placebo-controlled, 18-month trial …

Triatomines: Trypanosomatids, Bacteria, And Viruses Potential Vectors? [Review], Caroline Barreto Vieira, Yanna Reis Praça, Kaio Luís Da Silva Bentes, Paula Beatriz Santiago, Sofia Marcelino Martins Silva, Gabriel Dos Santos Silva, Flávia Nader Motta, Izabela Marques Dorado Bastos, Jaime Martins De Santana, Carla Nunes De Araújo

Harold W. Manter Laboratory of Parasitology: Library Materials

Triatominae bugs are the vectors of Chagas disease, a major concern to public health especially in Latin America, where vector-borne Chagas disease has undergone resurgence due mainly to diminished triatomine control in many endemic municipalities. Although the majority of Triatominae species occurs in the Americas, species belonging to the genus Linshcosteus occur in India, and species belonging to the Triatoma rubrofasciata complex have been also identified in Africa, the Middle East, South-East Asia, and in the Western Pacific. Not all of Triatominae species have been found to be infected with Trypanosoma cruzi, but the possibility of establishing vector transmission …

Hidden Cost Of Disease In A Free-Ranging Ungulate: Brucellosis Reduces Mid-Winter Pregnancy In Elk, Gavin C. Cotterill, Paul C. Cross, Arthur D. Middleton, Jared D. Rogerson, Brandon M. Scurlock, Johan T. Du Toit

Wildland Resources Faculty Publications

Demonstrating disease impacts on the vital rates of free‐ranging mammalian hosts typically requires intensive, long‐term study. Evidence for chronic pathogens affecting reproduction but not survival is rare, but has the potential for wide‐ranging effects. Accurately quantifying disease‐associated reductions in fecundity is important for advancing theory, generating accurate predictive models, and achieving effective management. We investigated the impacts of brucellosis (Brucella abortus) on elk (Cervus canadensis) productivity using serological data from over 6,000 captures since 1990 in the Greater Yellowstone Ecosystem, USA. Over 1,000 of these records included known age and pregnancy status. Using Bayesian multilevel models, …

Design, Synthesis, And Evaluation Of Amphiphilic Cyclic And Linear Peptides Composed Of Hydrophobic And Positively-Charged Amino Acids As Antibacterial Agents, Neda Riahifard, Saghar Mozaffari, Taibah Aldakhil, Francisco Nunez, Qamar Alshammari, Saud Alshammari, Jason Yamaki, Keykavous Parang, Rakesh Kumar Tiwari

Pharmacy Faculty Articles and Research

Antimicrobial peptides (AMPs) contain amphipathic structures and are derived from natural resources. AMPs have been found to be effective in treating the infections caused by antibiotic-resistant bacteria (ARB), and thus, are potential lead compounds against ARB. AMPs’ physicochemical properties, such as cationic nature, amphiphilicity, and their size, will provide the opportunity to interact with membrane bilayers leading to damage and death of microorganisms. Herein, AMP analogs of [R₄W₄] were designed and synthesized by changing the hydrophobicity and cationic nature of the lead compound with other amino acids to provide insights into a structure-activity relationship against selected …

Vancomycin Delays Clindamycin-Induced Fatality In The Hamster Model Of Clostridioides [Clostridium] Difficile Infection, Amelia E. Fox-King, Chrisabelle Mefferd, Jacqueline R. Phan, Nancy O. Nou, Ernesto Abel-Santos, Brian P. Hedlund

LSAMP Poster Presentations

Antibiotics can leave the host gut microbiome susceptible to Clostridioides [Clostridium] difficile colonization and lethal toxin production. For instance, clindamycin-induced susceptibility to C. difficile infection (CDI) results in rapid fatality in hamster models, yet vancomycin has been shown to offer increased survival in hamsters challenged with C. difficile. We aim to develop an antibiotic treatment that will facilitate CDI susceptibility without prompt fatality in hamster models. An antibiotic regimen starting with a continuous vancomycin treatment along with a single clindamycin dosage is thought to reduce the major disruption in the indigenous gut microbiome and prevent clindamycin-induced death. …

A Mathematical Model Of The Inflammatory Response To Pathogen Challenge, Lester Caudill, Fiona Lynch

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Simulating Antibiotic Resistance In The Computer Lab And Biology Lab: Ideas For Undergraduate Projects, Anne E. Yust

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

Nocardia Brasiliensis Infection After Hurricane Irma: Two Case Reports, Sarah Al-Obaydi Md, James Demaio, Nemer Dabage Md

Infectious Disease

Background: Although an increase in skin and soft tissue infections has been well documented after natural disasters, cases of Nocardia brasiliensis infection have not been included in prior reports. We present two cases of N. brasiliensis lymphadenitis that occurred in Manatee County, Florida after Hurricane Irma.

Methods: Case 1-A 75 year old immune competent male may have injured his arm while retrieving a golf ball approximately four weeks after Hurricane Irma. Ten days later he presented to the hospital with an abscess on his left forearm and a lymphadenitis extending nearly to the axilla. Despite treatment with vancomycin, the lymph …

8th Annual Postdoctoral Science Symposium, University Of Texas Md Anderson Cancer Center Postdoctoral Association

Annual Postdoctoral Science Symposium Abstracts

The mission of the Annual Postdoctoral Science Symposium (APSS) is to provide a platform for talented postdoctoral fellows throughout the Texas Medical Center to present their work to a wider audience. The MD Anderson Postdoctoral Association convened its inaugural Annual Postdoctoral Science Symposium (APSS) on August 4, 2011.

The APSS provides a professional venue for postdoctoral scientists to develop, clarify, and refine their research as a result of formal reviews and critiques of faculty and other postdoctoral scientists. Additionally, attendees discuss current research on a broad range of subjects while promoting academic interactions and enrichment and developing new collaborations.

Mrsa In The United States, Sweden, And Syria, Derek J. Lillestolen

Montview Journal of Research & Scholarship

Methicillin-resistant Staphylococcus aureus (MRSA) is an opportunistic pathogen that is resistant to many broad and narrow-spectrum antibiotics commonly used in the treatment of S. aureus. There has been much fanfare about MRSA, receiving nicknames like “superbug” because of its varying degrees of resistance to the most common broad and narrow-spectrum antibiotics such as penicillin, oxacillin, methicillin and amoxicillin (2). The reality, however, is that MRSA is still susceptible to certain antibiotics and can be treated effectively. This study displays the factors which help and hurt MRSA treatments. There is shown a strong link between the prescription of broad-spectrum antibiotics …

Epidemiology Of Diabetic Foot Infection In The Metro-Detroit Area With A Focus On Independent Predictors For Pathogens Resistant To Recommended Empiric Antimicrobial Therapy, Oryan Henig, Jason M. Pogue, Raymond Cha, Paul E. Kilgore, Umar Hayat, Mahmoud Ja'ara, Raza Muhamad Ali, Salman Mahboob, Rahul Pansare, Kathryn Deeds, Bushra Joarder, Hyndavi Kandala, Sorabh Dhar, Keith S. Kaye

Department of Pharmacy Practice

Background. The polymicrobial nature of diabetic foot infection (DFI) and the emergence of antimicrobial resistance have complicated DFI treatment. Current treatment guidelines for deep DFI recommend coverage of methicillin-resistant Staphylococcus aureus (MRSA) and susceptible Enterobacteriaceae. This study aimed to describe the epidemiology of DFI and to identify predictors for DFI associated with multidrug-resistant organisms (MDROs) and pathogens resistant to recommended treatment (PRRT).

Methods. Adult patients admitted to Detroit Medical Center from January 2012 to December 2015 with DFI and positive cultures were included. Demographics, comorbidities, microbiological history, sepsis severity, and antimicrobial use within 3 months before DFI were obtained …

Interfering With Dna Decondensation As A Strategy Against Mycobacteria, Enzo M. Scutigliani, Edwin R. Scholl, Anita E. Grootemaat, Sadhana Khanal, Jakub A. Kochan, Przemek M. Krawczyk, Eric A. Reits, Atefeh Garzan, Huy X. Ngo, Keith D. Green, Sylvie Garneau-Tsodikova, Jan M. Ruijter, Henk A. Van Veen, Nicole N. Van Der Wel

Pharmaceutical Sciences Faculty Publications

Tuberculosis is once again a major global threat, leading to more than 1 million deaths each year. Treatment options for tuberculosis patients are limited, expensive and characterized by severe side effects, especially in the case of multidrug-resistant forms. Uncovering novel vulnerabilities of the pathogen is crucial to generate new therapeutic strategies. Using high resolution microscopy techniques, we discovered one such vulnerability of Mycobacterium tuberculosis. We demonstrate that the DNA of M. tuberculosis can condense under stressful conditions such as starvation and antibiotic treatment. The DNA condensation is reversible and specific for viable bacteria. Based on these observations, we hypothesized …

Rapid Development Of Hepatocellular Carcinoma After Eradication Of Hepatitis C Virus With Directly Acting Antiviral Treatment, Fakhar Ali Qazi Arisar, Saeed Hamid

Section of Gastroenterology

Hepatitis C is a major risk factor for the development of hepatocellular carcinoma (HCC), arising typically on a background of liver cirrhosis. Treatment of hepatitis C has been revolutionized by the addition of oral direct-acting antivirals (DAAs) with sustained virological response (SVR) rates above 90%. There is a recent concern under debate about the increased risk of early HCC recurrence in patients with chronic hepatitis C who were treated with direct-acting antivirals. Nonetheless, these reports mostly focused on patients who were cirrhotic and were already treated for HCC. We report 4 cases of treatment naive, chronic hepatitis C patients who …

Hla-C Downregulation By Hiv-1 Adapts To Host Hla Genotype, Nathaniel D. Batchel, Gisele Umviligihozo, Suzanne Pickering, Talia Mota, Hua Liang, Gregory Q. Del Prete, Pramita Chatterjee, Guinevere Q. Lee, Rasmi Thomas, Mark A. Brockman, Stuart Neil, Mary Carrington, Bosco M. Bwana, David Bangsberg, Multiple Additional Authors

OHSU-PSU School of Public Health Faculty Publications and Presentations

HIV-1 can downregulate HLA-C on infected cells, using the viral protein Vpu, and the magnitude of this downregulation varies widely between primary HIV-1 variants. The selection pressures that result in viral downregulation of HLA-C in some individuals, but preservation of surface HLA-C in others are not clear. To better understand viral immune evasion targeting HLA-C, we have characterized HLA-C downregulation by a range of primary HIV-1 viruses. 128 replication competent viral isolates from 19 individuals with effective anti-retroviral therapy, show that a substantial minority of individuals harbor latent reservoir virus which strongly downregulates HLA-C. Untreated infections display no change in …

Mechanisms Adopted By Dengue-2 Viruses To Induce Autophagy In Mammalian Cells, Sounak Ghosh Roy

Dissertations, Theses, and Capstone Projects

Dengue, the most rapidly spreading flavivirus, threatens to affect almost half of the human global population. We previously showed that dengue-2 protects canine kidney cells (MDCK) from cytotoxic chemicals. We showed, independently, that cell protection, as well as viral replication and maturation, are positively regulated by PI3K-dependent autophagy. However, we had not identified the specific pathway that induces autophagy in infected cells. The current study explores the role of a specific branch of the endoplasmic reticulum (ER) stress-mediated Unfolded Protein Response (UPR), the PERK/eIF2α/ATF4 pathway in the induction of autophagy by …

Strategies Involving The Food-Derived Agent Curcumin To Eliminate Brain Cancer, Sumit Mukherjee

Dissertations, Theses, and Capstone Projects

Glioblastoma (GBM) is one of the most deadly forms of cancer with a mean 5-year survival rate of ≤5%. We have used the non-invasive strategy of long-term intranasal (IN) delivery of a glioblastoma-directed adduct of curcumin (CC), CC-CD68Ab, into the brain of murine GBM cell line GL261-implanted mice to study the therapeutic effect of CC on GBM remission. The treatment caused GBM tumor remission in 50% of GL261-implanted GBM mice. A similar rescue rate (60%) was also achieved through long-term intraperitoneal (i.p) infusion of a highly bioavailable phosphotidylcholine (PC)-encapsulated formulation of CC, Curcumin Phytosome Meriva (CCP), into the GL261-implanted GBM …

The Association Of Qsofa, Sofa, And Sirs With Mortality In Emergency Department Pneumonia, Ian D. Mecham, Nathan C. Dean, Emily L. Wilson, Al R. Jephson, Michael J. Lanpsa

The University of Louisville Journal of Respiratory Infections

Objective: To determine the association between 30-day mortality with Systemic Inflammatory Response Syndrome (SIRS), Sequential Organ Failure Assessment (SOFA), and quick SOFA (qSOFA) in emergency department patients with pneumonia. Secondary outcomes included the association of sepsis scores with hospital admission and direct ICU admission.

Methods: This is a secondary analysis of a pneumonia population conducted in the emergency department of 3 tertiary care medical centers and 4 community hospitals. Adult immunocompetent patients diagnosed with pneumonia were included from 3 twelve-month periods spanning December 2009 to October 2015. We generated area under the receiver operating characteristic curve (AUC) values for …