@article{hepworth-warren_erwin_moore_talbot_young_neault_haugland_robertson_blikslager_2023, title={Risk factors associated with an outbreak of equine coronavirus at a large farm in North Carolina}, volume={10}, ISSN={["2297-1769"]}, DOI={10.3389/fvets.2023.1060759}, abstractNote={BackgroundEquine coronavirus (ECoV) leads to outbreaks with variable morbidity and mortality. Few previous reports of risk factors for infection are available in the literature.}, journal={FRONTIERS IN VETERINARY SCIENCE}, author={Hepworth-Warren, Kate L. and Erwin, Sara J. and Moore, Caroline B. and Talbot, James R. and Young, Kimberly A. S. and Neault, Michael J. and Haugland, Jennifer C. and Robertson, James B. and Blikslager, Anthony T.}, year={2023}, month={Mar} }
 @inbook{norem_rice_erwin_bridges_oesch_weber_2022, title={A Mathematical Framework for Evaluation of SOAR Tools with Limited Survey Data}, url={https://doi.org/10.1007/978-3-030-95484-0_32}, DOI={10.1007/978-3-030-95484-0_32}, abstractNote={Security operation centers (SOCs) all over the world are tasked with reacting to cybersecurity alerts ranging in severity. Security Orchestration, Automation, and Response (SOAR) tools streamline cybersecurity alert responses by SOC operators. SOAR tool adoption is expensive both in effort and finances. Hence, it is crucial to limit adoption to those most worthwhile; yet no research evaluating or comparing SOAR tools exists. The goal of this work is to evaluate several SOAR tools using specific criteria pertaining to their usability. SOC operators were asked to first complete a survey about what SOAR tool aspects are most important. Operators were then assigned a set of SOAR tools for which they viewed demonstration and overview videos, and then operators completed a second survey wherein they were tasked with evaluating each of the tools on the aspects from the first survey. In addition, operators provided an overall rating to each of their assigned tools, and provided a ranking of their tools in order of preference. Due to time constraints on SOC operators for thorough testing, we provide a systematic method of downselecting a large pool of SOAR tools to a select few that merit next-step hands-on evaluation by SOC operators. Furthermore, the analyses conducted in this survey help to inform future development of SOAR tools to ensure that the appropriate functions are available for use in a SOC.}, author={Norem, Savannah and Rice, Ashley E. and Erwin, Samantha and Bridges, Robert A. and Oesch, Sean and Weber, Brian}, year={2022} }
 @article{erwin_childs_ciupe_2020, title={Mathematical model of broadly reactive plasma cell production}, volume={10}, url={http://dx.doi.org/10.1038/s41598-020-60316-8}, DOI={10.1038/s41598-020-60316-8}, abstractNote={Abstract}, number={1}, journal={Scientific Reports}, author={Erwin, S. and Childs, L.M. and Ciupe, S.M.}, year={2020}, month={Dec} }
 @article{lanzas_davies_erwin_dawson_2020, title={On modelling environmentally transmitted pathogens}, volume={10}, url={http://dx.doi.org/10.1098/rsfs.2019.0056}, DOI={10.1098/rsfs.2019.0056}, abstractNote={Many pathogens are able to replicate or survive in abiotic environments. Disease transmission models that include environmental reservoirs and environment-to-host transmission have used a variety of functional forms and modelling frameworks without a clear connection to pathogen ecology or space and time scales. We present a conceptual framework to organize microparasites based on the role that abiotic environments play in their lifecycle. Mean-field and individual-based models for environmental transmission are analysed and compared. We show considerable divergence between both modelling approaches when conditions do not facilitate well mixing and for pathogens with fast dynamics in the environment. We conclude with recommendations for modelling environmentally transmitted pathogens based on the pathogen lifecycle and time and spatial scales of the host–pathogen system under consideration.}, number={1}, journal={Interface Focus}, author={Lanzas, Cristina and Davies, Kale and Erwin, Samantha and Dawson, Daniel}, year={2020}, month={Feb} }
 @article{erwin_foster_jacob_papich_lanzas_2020, title={The effect of enrofloxacin on enteric Escherichia coli: Fitting a mathematical model to in vivo data}, volume={15}, url={https://doi.org/10.1371/journal.pone.0228138}, DOI={10.1371/journal.pone.0228138}, abstractNote={Antimicrobial drugs administered systemically may cause the emergence and dissemination of antimicrobial resistance among enteric bacteria. To develop logical, research-based recommendations for food animal veterinarians, we must understand how to maximize antimicrobial drug efficacy while minimizing risk of antimicrobial resistance. Our objective is to evaluate the effect of two approved dosing regimens of enrofloxacin (a single high dose or three low doses) on Escherichia coli in cattle. We look specifically at bacteria above and below the epidemiological cutoff (ECOFF), above which the bacteria are likely to have an acquired or mutational resistance to enrofloxacin. We developed a differential equation model for the antimicrobial drug concentrations in plasma and colon, and bacteria populations in the feces. The model was fit to animal data of drug concentrations in the plasma and colon obtained using ultrafiltration probes. Fecal E. coli counts and minimum inhibitory concentrations were measured for the week after receiving the antimicrobial drug. We predict that the antimicrobial susceptibility of the bacteria above the ECOFF pre-treatment strongly affects the composition of the bacteria following treatment. Faster removal of the antimicrobial drugs from the colon throughout the study leads to improved clearance of bacteria above the ECOFF in the low dose regimen. If we assume a fitness cost is associated with bacteria above the ECOFF, the increased fitness costs leads to reduction of bacteria above the ECOFF in the low dose study. These results suggest the initial E. coli susceptibility is a strong indicator of how steers respond to antimicrobial drug treatment.}, number={1}, journal={PLOS ONE}, publisher={Public Library of Science (PLoS)}, author={Erwin, Samantha and Foster, Derek M. and Jacob, Megan E. and Papich, Mark G. and Lanzas, Cristina}, editor={Loor, Juan JEditor}, year={2020}, month={Jan}, pages={e0228138} }
 @inbook{clifton_davis_erwin_hamerlinck_veprauskas_wang_zhang_gaff_2018, title={Modeling the Argasid Tick (Ornithodoros moubata) Life Cycle}, volume={14}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85071497558&partnerID=MN8TOARS}, DOI={10.1007/978-3-319-98083-6_4}, abstractNote={The first mathematical models for an argasid tick are developed to explore the dynamics and identify knowledge gaps of these poorly studied ticks. These models focus on Ornithodoros moubata, an important tick species throughout Africa and Europe. Ornithodoros moubata is a known vector for African swine fever (ASF), a catastrophically fatal disease for domesticated pigs in Africa and Europe. In the absence of any previous models for soft-bodied ticks, we propose two mathematical models of the life cycle of O. moubata. One is a continuous-time differential equation model that simplifies the tick life cycle to two stages, and the second is a discrete-time difference equation model that uses four stages. Both models use two host types: small hosts and large hosts, and both models find that either host type alone could support the tick population and that the final tick density is a function of host density. While both models predict similar tick equilibrium values, we observe significant differences in the time to equilibrium. The results demonstrate the likely establishment of these ticks if introduced into a new area even if there is only one type of host. These models provide the basis for developing future models that include disease states to explore infection dynamics and possible management of ASF.}, booktitle={Association for Women in Mathematics Series}, author={Clifton, S.M. and Davis, C.L. and Erwin, S. and Hamerlinck, G. and Veprauskas, A. and Wang, Y. and Zhang, W. and Gaff, H.}, year={2018}, pages={63–87} }
 @article{fletcher_erwin_lanzas_theriot_2018, title={Shifts in the Gut Metabolome and Clostridium difficile Transcriptome throughout Colonization and Infection in a Mouse Model}, volume={3}, ISSN={["2379-5042"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85045201454&partnerID=MN8TOARS}, DOI={10.1128/msphere.00089-18}, abstractNote={
            Clostridium difficile
            is a bacterial pathogen of global significance that is a major cause of antibiotic-associated diarrhea. Antibiotics deplete the indigenous gut microbiota and change the metabolic environment in the gut to one favoring
            C. difficile
            growth. Here we used metabolomics and transcriptomics to define the gut environment after antibiotics and during the initial stages of
            C. difficile
            colonization and infection. We show that amino acids, in particular, proline and branched-chain amino acids, and carbohydrates decrease in abundance over time and that
            C. difficile
            gene expression is consistent with their utilization by the bacterium
            in vivo
            . We employed an integrated approach to analyze the metabolome and transcriptome to identify associations between metabolites and transcripts. This highlighted the importance of key nutrients in the early stages of colonization, and the data provide a rationale for the development of therapies based on the use of bacteria that specifically compete for nutrients that are essential for
            C. difficile
            colonization and disease.
          }, number={2}, journal={MSPHERE}, author={Fletcher, Joshua R. and Erwin, Samantha and Lanzas, Cristina and Theriot, Casey M.}, year={2018} }
 @article{erwin_ciupe_2017, title={Germinal center dynamics during acute and chronic infection}, volume={14}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85012916962&partnerID=MN8TOARS}, DOI={10.3934/mbe.2017037}, abstractNote={The ability of the immune system to clear pathogens is limited during chronic virus infections where potent long-lived plasma and memory B-cells are produced only after germinal center B-cells undergo many rounds of somatic hypermutations. In this paper, we investigate the mechanisms of germinal center B-cell formation by developing mathematical models for the dynamics of B-cell somatic hypermutations. We use the models to determine how B-cell selection and competition for T follicular helper cells and antigen influences the size and composition of germinal centers in acute and chronic infections. We predict that the T follicular helper cells are a limiting resource in driving large numbers of somatic hypermutations and present possible mechanisms that can revert this limitation in the presence of non-mutating and mutating antigen.}, number={3}, journal={Mathematical Biosciences and Engineering}, author={Erwin, S. and Ciupe, S.M.}, year={2017}, pages={655–671} }
 @phdthesis{mathematical models of immune responses to infectious diseases_2017, url={http://hdl.handle.net/10919/77026}, year={2017} }
 @article{verma_erwin_abedi_hontecillas_hoops_leber_bassaganya-riera_ciupe_2017, title={Modeling the Mechanisms by Which HIV-Associated Immunosuppression Influences HPV Persistence at the Oral Mucosa}, volume={12}, url={http://dx.doi.org/10.1371/journal.pone.0168133}, DOI={10.1371/journal.pone.0168133}, abstractNote={Human immunodeficiency virus (HIV)-infected patients are at an increased risk of co-infection with human papilloma virus (HPV), and subsequent malignancies such as oral cancer. To determine the role of HIV-associated immune suppression on HPV persistence and pathogenesis, and to investigate the mechanisms underlying the modulation of HPV infection and oral cancer by HIV, we developed a mathematical model of HIV/HPV co-infection. Our model captures known immunological and molecular features such as impaired HPV-specific effector T helper 1 (Th1) cell responses, and enhanced HPV infection due to HIV. We used the model to determine HPV prognosis in the presence of HIV infection, and identified conditions under which HIV infection alters HPV persistence in the oral mucosa system. The model predicts that conditions leading to HPV persistence during HIV/HPV co-infection are the permissive immune environment created by HIV and molecular interactions between the two viruses. The model also determines when HPV infection continues to persist in the short run in a co-infected patient undergoing antiretroviral therapy. Lastly, the model predicts that, under efficacious antiretroviral treatment, HPV infections will decrease in the long run due to the restoration of CD4+ T cell numbers and protective immune responses.}, number={1}, journal={PLOS ONE}, author={Verma, M. and Erwin, S. and Abedi, V. and Hontecillas, R. and Hoops, S. and Leber, A. and Bassaganya-Riera, J. and Ciupe, S.M.}, year={2017}, month={Jan} }
 @article{erwin_huckaba_he_mccarthy_2013, title={Matrix analysis to model the invasion of alligatorweed (Alternanthera philoxeroides) on Kentucky lakes}, volume={6}, url={http://dx.doi.org/10.1093/jpe/rts024}, DOI={10.1093/jpe/rts024}, abstractNote={Aims Alligatorweed (Alternanthera philoxeroides (Mart.) Griseb.) is an invasive species indigenous to South America. With its rapid invasion of southeastern US waterways, understanding the invasiveness of this plant species is critical for providing possible mechanisms of prevention for resource managers. The aim of this project is to use a matrix model to study the invasion dynamics of alligatorweed under both terrestrial and aquatic environments. The use of this model allows for a deeper understanding of the invasiveness and life history–stage structure of alligatorweed. In particular, matrix analysis can further test the hypothesis that certain life stages of alligatorweed might be more sensitive to control and management. Methods A greenhouse experiment was conducted to study the spread of alligatorweed under both aquatic and terrestrial environments. Utilizing the growth data obtained during the summer of 2010, matrix analysis was used to model the growth of alligatorweed for six different treatments. Transition matrices were generated based on plant measurements taken at different life stages defined by the number of leaves or nodes. These matrices are population projection models whose eigenvalues represent the growth rate of alligatorweed. A high growth rate is a key feature of successful invaders. Residuals were calculated and sensitivity analysis was performed to test the accuracy of the model and importance of each life stage over the entire life cycle of alligatorweed. Important findings The results of this study indicate that in the aquatic habitat, plants at their early life cycle stage are most sensitive to potential control measures. Conversely, in the terrestrial habitat, the most sensitive stage of alligatorweed is at its late life cycle stage, characterized with large-sized plants, thus suggesting the best timing for management and eradication of this invasive species.}, number={2}, journal={Journal of Plant Ecology}, author={Erwin, S. and Huckaba, A. and He, K.S. and McCarthy, M.}, year={2013}, month={Apr}, pages={150–157} }
 @phdthesis{modeling of passive chilled beams for use in efficient control of indoor-air environments_2013, year={2013}, month={Jun} }