@article{farthing_jolley_nickel_hill_stwalley_reske_kwon_olsen_burnham_dubberke_et al._2023, title={Early coronavirus disease 2019 (COVID-19) pandemic effects on individual-level risk for healthcare-associated infections in hospitalized patients}, volume={6}, ISSN={["1559-6834"]}, DOI={10.1017/ice.2023.83}, abstractNote={Abstract}, journal={INFECTION CONTROL AND HOSPITAL EPIDEMIOLOGY}, author={Farthing, Trevor S. and Jolley, Ashlan and Nickel, Katelin B. and Hill, Cherie and Stwalley, Dustin and Reske, Kimberly A. and Kwon, Jennie H. and Olsen, Margaret A. and Burnham, Jason P. and Dubberke, Erik R. and et al.}, year={2023}, month={Jun} }
 @article{lacy_igoe_das_farthing_lloyd_lanzas_odoi_lenhart_2023, title={Modeling impact of vaccination on COVID-19 dynamics in St. Louis}, volume={17}, ISSN={["1751-3766"]}, DOI={10.1080/17513758.2023.2287084}, abstractNote={The region of St. Louis, Missouri, has displayed a high level of heterogeneity in COVID-19 cases, hospitalization, and vaccination coverage. We investigate how human mobility, vaccination, and time-varying transmission rates influenced SARS-CoV-2 transmission in five counties in the St. Louis area. A COVID-19 model with a system of ordinary differential equations was developed to illustrate the dynamics with a fully vaccinated class. Using the weekly number of vaccinations, cases, and hospitalization data from five counties in the greater St. Louis area in 2021, parameter estimation for the model was completed. The transmission coefficients for each county changed four times in that year to fit the model and the changing behaviour. We predicted the changes in disease spread under scenarios with increased vaccination coverage. SafeGraph local movement data were used to connect the forces of infection across various counties.}, number={1}, journal={JOURNAL OF BIOLOGICAL DYNAMICS}, author={Lacy, Alexanderia and Igoe, Morganne and Das, Praachi and Farthing, Trevor and Lloyd, Alun L. and Lanzas, Cristina and Odoi, Agricola and Lenhart, Suzanne}, year={2023}, month={Dec} }
 @article{farthing_lanzas_2021, title={Assessing the efficacy of interventions to control indoor SARS-Cov-2 transmission: An agent-based modeling approach}, volume={37}, ISSN={["1878-0067"]}, DOI={10.1016/j.epidem.2021.100524}, abstractNote={Nonpharmaceutical interventions for minimizing indoor SARS-CoV-2 transmission continue to be critical tools for protecting susceptible individuals from infection, even as effective vaccines are produced and distributed globally. We developed a spatially-explicit agent-based model for simulating indoor respiratory pathogen transmission during discrete events taking place in a single room within a sub-day time frame, and used it to compare effects of four interventions on reducing secondary SARS-CoV-2 attack rates during a superspreading event by simulating a well-known case study. We found that preventing people from moving within the simulated room and efficacious mask usage appear to have the greatest effects on reducing infection risk, but multiple concurrent interventions are required to minimize the proportion of susceptible individuals infected. Social distancing had little effect on reducing transmission if individuals were randomly relocated within the room to simulate activity-related movements during the gathering. Furthermore, our results suggest that there is potential for ventilation airflow to expose susceptible people to aerosolized pathogens even if they are relatively far from infectious individuals. Maximizing the vertical aerosol removal rate is paramount to successful transmission-risk reduction when using ventilation systems as intervention tools.}, journal={EPIDEMICS}, author={Farthing, Trevor S. and Lanzas, Cristina}, year={2021}, month={Dec} }
 @article{farthing_lanzas_2021, title={Assessing the efficacy of interventions to control indoor SARS-Cov-2 transmission: an agent-based modeling approach}, volume={1}, url={https://doi.org/10.1101/2021.01.21.21250240}, DOI={10.1101/2021.01.21.21250240}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Farthing, Trevor S. and Lanzas, Cristina}, year={2021}, month={Jan} }
 @article{farthing_dawson_sanderson_seger_lanzas_2021, title={Combining epidemiological and ecological methods to quantify social effects on Escherichia coli transmission}, volume={8}, ISSN={["2054-5703"]}, url={https://doi.org/10.1098/rsos.210328}, DOI={10.1098/rsos.210328}, abstractNote={
            Enteric microparasites like
            Escherichia coli
            use multiple transmission pathways to propagate within and between host populations. Characterizing the relative transmission risk attributable to host social relationships and direct physical contact between individuals is paramount for understanding how microparasites like
            E. coli
            spread within affected communities and estimating colonization rates. To measure these effects, we carried out commensal
            E. coli
            transmission experiments in two cattle (
            Bos taurus
            ) herds, wherein all individuals were equipped with real-time location tracking devices. Following transmission experiments in this model system, we derived temporally dynamic social and contact networks from location data. Estimated social affiliations and dyadic contact frequencies during transmission experiments informed pairwise accelerated failure time models that we used to quantify effects of these sociobehavioural variables on weekly
            E. coli
            colonization risk in these populations. We found that sociobehavioural variables alone were ultimately poor predictors of
            E. coli
            colonization in feedlot cattle, but can have significant effects on colonization hazard rates (
            p
            ≤ 0.05). We show, however, that observed effects were not consistent between similar populations. This work demonstrates that transmission experiments can be combined with real-time location data collection and processing procedures to create an effective framework for quantifying sociobehavioural effects on microparasite transmission.
          }, number={10}, journal={ROYAL SOCIETY OPEN SCIENCE}, author={Farthing, Trevor S. and Dawson, Daniel E. and Sanderson, Mike W. and Seger, Hannah and Lanzas, Cristina}, year={2021}, month={Oct} }
 @article{machado_farthing_andraud_nunes lopes_lanzas_2021, title={Modelling the role of mortality-based response triggers on the effectiveness of African swine fever control strategies}, volume={10}, ISSN={["1865-1682"]}, url={https://doi.org/10.1111/tbed.14334}, DOI={10.1111/tbed.14334}, abstractNote={African swine fever (ASF) is considered the most impactful transboundary swine disease. In the absence of effective vaccines, control strategies are heavily dependent on mass depopulation and shipment restrictions. Here, we developed a nested multiscale model for the transmission of ASF, combining a spatially explicit network model of animal shipments with a deterministic compartmental model for the dynamics of two ASF strains within 3 km × 3 km pixels in one Brazilian state. The model outcomes are epidemic duration, number of secondary infected farms and pigs, and distance of ASF spread. The model also shows the spatial distribution of ASF epidemics. We analyzed quarantine-based control interventions in the context of mortality trigger thresholds for the deployment of control strategies. The mean epidemic duration of a moderately virulent strain was 11.2 days, assuming the first infection is detected (best-case scenario), and 15.9 days when detection is triggered at 10% mortality. For a highly virulent strain, the epidemic duration was 6.5 days and 13.1 days, respectively. The distance from the source to infected locations and the spatial distribution was not dependent on strain virulence. Under the best-case scenario, we projected an average number of infected farms of 23.77 farms and 18.8 farms for the moderate and highly virulent strains, respectively. At 10% mortality-trigger, the predicted number of infected farms was on average 46.27 farms and 42.96 farms, respectively. We also demonstrated that the establishment of ring quarantine zones regardless of size (i.e. 5 km, 15 km) was outperformed by backward animal movement tracking. The proposed modelling framework provides an evaluation of ASF epidemic potential, providing a ranking of quarantine-based control strategies that could assist animal health authorities in planning the national preparedness and response plan.}, journal={TRANSBOUNDARY AND EMERGING DISEASES}, publisher={Wiley}, author={Machado, Gustavo and Farthing, Trevor S. and Andraud, Mathieu and Nunes Lopes, Francisco Paulo and Lanzas, Cristina}, year={2021}, month={Oct} }
 @article{farthing_lanzas_2021, title={When can we stop wearing masks? Agent-based modeling to identify when vaccine coverage makes nonpharmaceutical interventions for reducing SARS-CoV-2 infections redundant in indoor gatherings}, volume={4}, url={https://doi.org/10.1101/2021.04.19.21255737}, DOI={10.1101/2021.04.19.21255737}, abstractNote={Abstract}, publisher={Cold Spring Harbor Laboratory}, author={Farthing, Trevor S. and Lanzas, Cristina}, year={2021}, month={Apr} }
 @article{farthing_dawson_sanderson_lanzas_2020, title={Accounting for space and uncertainty in real‐time location system‐derived contact networks}, url={https://doi.org/10.1002/ece3.6225}, DOI={10.1002/ece3.6225}, abstractNote={Abstract}, journal={Ecology and Evolution}, author={Farthing, Trevor S. and Dawson, Daniel E. and Sanderson, Michael W. and Lanzas, Cristina}, year={2020}, month={Jun} }
 @article{farthing_muir_brady_2020, title={Three Bermudagrass-suppression techniques have little effect on soil-nutrient availability and microbial communities 200 days after application}, volume={145}, DOI={10.1016/j.apsoil.2019.09.002}, abstractNote={Cynodon dactylon (Bermudagrass) is a highly competitive invasive plant dominating many southern grasslands. Glyphosate (N-(phosphonomethyl)glycine) is often used in conjunction with other herbicides and land-management practices to remove Bermudagrass in preparation for native-grassland restoration projects. Studies evaluating glyphosate-induced effects on soil ecology, however, often disregard potential for herbicide × or herbicide × mechanical treatment interactions. Therefore, our objective was to evaluate three chemical Bermudagrass-removal methods (i.e., repeated glyphosate application, repeated glyphosate application + imidazolinone herbicide use, repeated glyphosate application + mechanical above-ground biomass removal), previously described by Farthing et al. (2018), at research sites in Stephenville and McGregor, TX USA. We sought to determine if inter-treatment differences in soil pH, multiple element concentrations, and microbial diversity existed. We applied treatments to 355-m2 plots throughout summer 2015 and collected soil samples in April–July 2016 (216–249 and 218–259 days following final herbicide applications in Stephenville, and McGregor, respectively). We observed differences (P ≤ 0.05) in soil pH and NO3-N relative to untreated controls at the McGregor site, however, we were unable to observe differences directly related to treatments. Microbial communities differed (P ≤ 0.05) between locations, but treatments had no effect on soil-bacteria or archaea species richness and Shannon diversity. We did find that ≈1% of Operational Taxonomic Units appeared to be differentially abundant following treatments, but it is unclear whether differences are connected to glyphosate application. Our findings were generally consistent with previous research indicating herbicide use induces few-to-no long-term shifts in soil microbial communities, but our results highlight the necessity for microbiological field-study designs to include multiple locations.}, journal={Applied Soil Ecology}, publisher={Elsevier BV}, author={Farthing, Trevor S. and Muir, James P. and Brady, Jeff A.}, year={2020}, month={Jan} }
 @article{dawson_farthing_sanderson_lanzas_2019, title={Transmission on empirical dynamic contact networks is influenced by data processing decisions}, volume={26}, ISSN={["1755-4365"]}, url={https://doi.org/10.1016/j.epidem.2018.08.003}, DOI={10.1016/j.epidem.2018.08.003}, abstractNote={Dynamic contact data can be used to inform disease transmission models, providing insight into the dynamics of infectious diseases. Such data often requires extensive processing for use in models or analysis. Therefore, processing decisions can potentially influence the topology of the contact network and the simulated disease transmission dynamics on the network. In this study, we examine how four processing decisions, including temporal sampling window (TSW), spatial threshold of contact (SpTh), minimum contact duration (MCD), and temporal aggregation (daily or hourly) influence the information content of contact data (indicated by changes in entropy) as well as disease transmission model dynamics. We found that changes made to information content by processing decisions translated to significant impacts to the transmission dynamics of disease models using the contact data. In particular, we found that SpTh had the largest independent influence on information content, and that some output metrics (R0, time to peak infection) were more sensitive to changes in information than others (epidemic extent). These findings suggest that insights gained from transmission modeling using dynamic contact data can be influenced by processing decisions alone, emphasizing the need to carefully consideration them prior to using contact-based models to conduct analyses, compare different datasets, or inform policy decisions.}, journal={EPIDEMICS}, publisher={Elsevier BV}, author={Dawson, Daniel E. and Farthing, Trevor S. and Sanderson, Michael W. and Lanzas, Cristina}, year={2019}, month={Mar}, pages={32–42} }
 @article{farthing_muir_falk_murray_2018, title={Efficacy of Seven Invasive-Bermudagrass Removal Strategies in Three Texas Ecoregions}, volume={36}, ISSN={["1543-4079"]}, DOI={10.3368/er.36.4.306}, abstractNote={Cynodon dactylon (Bermudagrass) is an invasive grass found in some southwestern U.S. grasslands and is linked to decreased wildlife abundance. Cynodon dactylon removal is a necessary first step in many native grassland restoration projects. We evaluated seven C. dactylon removal methods in three Texas ecoregions, seeking to determine which most effectively suppressed C. dactylon growth in varying environmental conditions. We applied treatments to 355-m2 plots throughout summer 2015 and measured aboveground, living plant biomass, height, canopy cover, and species richness within plots in April–July 2016. Six treatments reduced (p ≤ 0.05) C. dactylon canopy cover compared to untreated controls at all study sites: single and repeated glyphosate herbicide applications—with or without shredding C. dactylon to 3-cm height two weeks prior, a single imazapyr herbicide application, and a glyphosate, imazapic, and imazapyr herbicide combination all resulted in ≥ 98.60% C. dactylon canopy cover and biomass reduction. A single glyphosate application reduced C. dactylon canopy cover 72.13 ± 27.74% compared to controls. Shredding grass and overseeding Vicia villosa (hairy vetch) reduced (p ≤ 0.05) C. dactylon biomass 49.45 ± 6.92% and height 13.58 ± 0.04% but did not decrease canopy cover relative to controls in any ecoregion. Overseeding V. villosa and shredding C. dactylon prior to herbicide application resulted in greater volunteer plant species richness and greater above-soil biomass. Treatment ability to suppress C. dactylon growth was similar across ecoregions. This implies land managers may use C. dactylon-suppression methodologies standardized for the entire state of Texas and likely beyond. By utilizing our results to effectively suppress C. dactylon, pastures can be prepared for conversion to native rangeland and prairie ecosystems.}, number={4}, journal={ECOLOGICAL RESTORATION}, publisher={University of Wisconsin Press}, author={Farthing, Trevor S. and Muir, James P. and Falk, Anthony D. and Murray, Darrel}, year={2018}, month={Dec}, pages={306–314} }