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Matthew Biggerstaff, Michael Johansson, David Alper, Logan C Brooks, Prithwish Chakraborty, David C Farrow, Sangwon Hyun, Sasikiran Kandula, Craig McGowan, Naren Ramakrishnan, Roni Rosenfeld, Jeffrey Shaman, Rob Tibshirani, Ryan J Tibshirani, Alessandro Vespignani, Wan Yang, Qian Zhang, Carrie Reed
Accurate forecasts could enable more informed public health decisions. Since 2013, CDC has worked with external researchers to improve influenza forecasts by coordinating seasonal challenges for the United States and the 10 Health and Human Service Regions. Forecasted targets for the 2014-15 challenge were the onset week, peak week, and peak intensity of the season and the weekly percent of outpatient visits due to influenza-like illness (ILI) 1-4 weeks in advance. We used a logarithmic scoring rule to score the weekly forecasts, averaged the scores over an evaluation period, and then exponentiated the resulting logarithmic score...
February 24, 2018: Epidemics
Peter F M Teunis, Axel Bonačić Marinović, David R Tribble, Chad K Porter, Arno Swart
Data from a set of different studies on the infectivity and pathogenicity of Campylobacter jejuni were analyzed with a multilevel model, allowing for effects of host species (nonhuman primates and humans) and different strains of the pathogen. All challenge studies involved high doses of the pathogen, resulting in all exposed subjects to become infected. In only one study a dose response effect (increasing trend with dose) for infection was observed. High susceptibility to infection with C. jejuni was found in a joint analysis of outbreaks and challenge studies...
February 8, 2018: Epidemics
G Ciaravino, A García-Saenz, S Cabras, A Allepuz, J Casal, I García-Bocanegra, A De Koeijer, S Gubbins, J L Sáez, D Cano-Terriza, S Napp
In Spain, despite years of efforts to eradicate bovine tuberculosis (bTB), the disease is still endemic, with some areas of high prevalence. In this context, the surveillance and control plans may need to be re-evaluated, and understanding the dynamics of bTB spread within Spanish herds may help to develop new strategies for reducing the time for detection of infected herds and for the elimination of bTB from the herds already infected. Here, we developed a compartmental stochastic model to simulate bTB within-herd transmission, fed it with epidemiological data from 22 herds (obtained from a previous work) and carried out parameter inference using Approximate Bayesian Computing methods We also estimated the "Within-herd transmission potential Number" (Rh ), i...
January 31, 2018: Epidemics
David A Kennedy, Patricia A Dunn, Andrew F Read
Marek's disease virus (MDV) is a pathogen of chickens whose control has twice been undermined by pathogen evolution. Disease ecology is believed to be the main driver of this evolution, yet mathematical models of MDV disease ecology have never been confronted with data to test their reliability. Here, we develop a suite of MDV models that differ in the ecological mechanisms they include. We fit these models with maximum likelihood using iterated filtering in 'pomp' to data on MDV concentration in dust collected from two commercial broiler farms...
January 10, 2018: Epidemics
Floor Biemans, Piter Bijma, Natasja M Boots, Mart C M de Jong
Digital Dermatitis (DD) is a claw disease mainly affecting the hind feet of dairy cattle. Digital Dermatitis is an infectious disease, transmitted via the environment, where the infectious "agent" is a combination of bacteria. The standardized classification for DD lesions developed by Döpfer et al. (1997) and extended by Berry et al. (2012) has six distinct classes: healthy (M0), an active granulomatous area of 0-2 cm (M1), an ulcerative lesion of >2 cm (M2), an ulcerative lesion covered by a scab (M3), alteration of the skin (M4), and a combination of M4 and M1 (M4...
December 22, 2017: Epidemics
Samantha R Schwab, Chris M Stone, Dina M Fonseca, Nina H Fefferman
With the emergence or re-emergence of numerous mosquito-borne diseases in recent years, effective methods for emergency vector control responses are necessary to reduce human infections. Current vector control practices often vary significantly between different jurisdictions, and are executed independently and at different spatial scales. Various types of surveillance information (e.g. number of human infections or adult mosquitoes) trigger the implementation of control measures, though the target and scale of surveillance vary locally...
December 16, 2017: Epidemics
Chris Rorres, Maria Romano, Jennifer A Miller, Jana M Mossey, Tony H Grubesic, David E Zellner, Gary Smith
Contact tracing is a crucial component of the control of many infectious diseases, but is an arduous and time consuming process. Procedures that increase the efficiency of contact tracing increase the chance that effective controls can be implemented sooner and thus reduce the magnitude of the epidemic. We illustrate a procedure using Graph Theory in the context of infectious disease epidemics of farmed animals in which the epidemics are driven mainly by the shipment of animals between farms. Specifically, we created a directed graph of the recorded shipments of deer between deer farms in Pennsylvania over a timeframe and asked how the properties of the graph could be exploited to make contact tracing more efficient should Chronic Wasting Disease (a prion disease of deer) be discovered in one of the farms...
December 14, 2017: Epidemics
Samit Bhattacharyya, Matthew J Ferrari, Ottar N Bjørnstad
Incidence of whooping cough exhibits variable dynamics across time and space. The periodicity of this disease varies from annual to five years in different geographic regions in both developing and developed countries. Many hypotheses have been put forward to explain this variability such as nonlinearity and seasonality, stochasticity, variable recruitment of susceptible individuals via birth, immunization, and immune boosting. We propose an alternative hypothesis to describe the variability in periodicity - the intricate dynamical variability of whooping cough may arise from interactions between its dominant etiological agents of Bordetella pertussis and Bordetella parapertussis...
December 14, 2017: Epidemics
Ulrich Muellner, Guillaume Fournié, Petra Muellner, Christina Ahlstrom, Dirk U Pfeiffer
Mathematical models of disease transmission are used to improve our understanding of patterns of infection and to identify factors influencing them. During recent public and animal health crises, such as pandemic influenza, Ebola, Zika, foot-and-mouth disease, models have made important contributions in addressing policy questions, especially through the assessment of the trajectory and scale of outbreaks, and the evaluation of control interventions. However, their mathematical formulation means that they may appear as a "black box" to those without the appropriate mathematical background...
December 11, 2017: Epidemics
Íde Cremin, Oliver Watson, Alastair Heffernan, Natsuko Imai, Norin Ahmed, Sandra Bivegete, Teresia Kimani, Demetris Kyriacou, Preveina Mahadevan, Rima Mustafa, Panagiota Pagoni, Marisa Sophiea, Charlie Whittaker, Leo Beacroft, Steven Riley, Matthew C Fisher
The study of infectious disease outbreaks is required to train today's epidemiologists. A typical way to introduce and explain key epidemiological concepts is through the analysis of a historical outbreak. There are, however, few training options that explicitly utilise real-time simulated stochastic outbreaks where the participants themselves comprise the dataset they subsequently analyse. In this paper, we present a teaching exercise in which an infectious disease outbreak is simulated over a five-day period and subsequently analysed...
December 9, 2017: Epidemics
Jennifer M Ross, Roger Ying, Connie L Celum, Jared M Baeten, Katherine K Thomas, Pamela M Murnane, Heidi van Rooyen, James P Hughes, Ruanne V Barnabas
INTRODUCTION: Mathematical models that incorporate HIV disease progression dynamics can estimate the potential impact of strategies that delay HIV disease progression and reduce infectiousness for persons not on antiretroviral therapy (ART). Suppressive treatment of HIV-positive persons co-infected with herpes simplex virus-2 (HSV-2) with valacyclovir, an HSV-2 antiviral, can lower HIV viral load, but the impact of partially-suppressive valacyclovir relative to fully-suppressive ART on population HIV transmission has not been estimated...
December 5, 2017: Epidemics
Anja Bråthen Kristoffersen, Lars Qviller, Kari Olli Helgesen, Knut Wiik Vollset, Hildegunn Viljugrein, Peder Andreas Jansen
The Norwegian government recently implemented a new management system to regulate salmon farming in Norway, aiming to promote environmentally sustainable growth in the aquaculture industry. The Norwegian coast has been divided into 13 production zones and the volume of salmonid production in the zones will be regulated based on salmon lice effects on wild salmonids. Here we present a model for assessing salmon louse-induced mortality of seaward-migrating post-smolts of Atlantic salmon. The model quantifies expected salmon lice infestations and louse-induced mortality of migrating post-smolt salmon from 401 salmon rivers draining into Norwegian coastal waters...
December 2, 2017: Epidemics
Deborah P Shutt, Carrie A Manore, Stephen Pankavich, Aaron T Porter, Sara Y Del Valle
As South and Central American countries prepare for increased birth defects from Zika virus outbreaks and plan for mitigation strategies to minimize ongoing and future outbreaks, understanding important characteristics of Zika outbreaks and how they vary across regions is a challenging and important problem. We developed a mathematical model for the 2015/2016 Zika virus outbreak dynamics in Colombia, El Salvador, and Suriname. We fit the model to publicly available data provided by the Pan American Health Organization, using Approximate Bayesian Computation to estimate parameter distributions and provide uncertainty quantification...
December 2017: Epidemics
David James Heslop, Abrar Ahmad Chughtai, Chau Minh Bui, C Raina MacIntyre
Epidemics and emerging infectious diseases are becoming an increasing threat to global populations-challenging public health practitioners, decision makers and researchers to plan, prepare, identify and respond to outbreaks in near real-timeframes. The aim of this research is to evaluate the range of public domain and freely available software epidemic modelling tools. Twenty freely utilisable software tools underwent assessment of software usability, utility and key functionalities. Stochastic and agent based tools were found to be highly flexible, adaptable, had high utility and many features, but low usability...
December 2017: Epidemics
Brian G Williams, Christopher Dye
Random mixing in host populations has been a convenient simplifying assumption in the study of epidemics, but neglects important differences in contact rates within and between population groups. For HIV/AIDS, the assumption of random mixing is inappropriate for epidemics that are concentrated in groups of people at high risk, including female sex workers (FSW) and their male clients (MCF), injecting drug users (IDU) and men who have sex with men (MSM). To find out who transmits infection to whom and how that affects the spread and containment of infection remains a major empirical challenge in the epidemiology of HIV/AIDS...
October 26, 2017: Epidemics
Cécile Viboud, Lone Simonsen, Gerardo Chowell, Alessandro Vespignani
No abstract text is available yet for this article.
October 24, 2017: Epidemics
Stéphane Le Vu, Oliver Ratmann, Valerie Delpech, Alison E Brown, O Noel Gill, Anna Tostevin, Christophe Fraser, Erik M Volz
Phylogenetic clustering of HIV sequences from a random sample of patients can reveal epidemiological transmission patterns, but interpretation is hampered by limited theoretical support and statistical properties of clustering analysis remain poorly understood. Alternatively, source attribution methods allow fitting of HIV transmission models and thereby quantify aspects of disease transmission. A simulation study was conducted to assess error rates of clustering methods for detecting transmission risk factors...
October 20, 2017: Epidemics
Marco Ajelli, Qian Zhang, Kaiyuan Sun, Stefano Merler, Laura Fumanelli, Gerardo Chowell, Lone Simonsen, Cecile Viboud, Alessandro Vespignani
The Ebola forecasting challenge organized by the Research and Policy for Infectious Disease Dynamics (RAPIDD) program of the Fogarty International Center relies on synthetic disease datasets generated by numerical simulations of a highly detailed spatially-structured agent-based model. We discuss here the architecture and technical steps of the challenge, leading to datasets that mimic as much as possible the data collection, reporting, and communication process experienced in the 2014-2015 West African Ebola outbreak...
September 20, 2017: Epidemics
Patrick Saunders-Hastings, James A G Crispo, Lindsey Sikora, Daniel Krewski
The goal of this review was to examine the effectiveness of personal protective measures in preventing pandemic influenza transmission in human populations. We collected primary studies from Medline, Embase, PubMed, Cochrane Library, CINAHL and grey literature. Where appropriate, random effects meta-analyses were conducted using inverse variance statistical calculations. Meta-analyses suggest that regular hand hygiene provided a significant protective effect (OR=0.62; 95% CI 0.52-0.73; I2=0%), and facemask use provided a non-significant protective effect (OR=0...
September 2017: Epidemics
Alethea W McCormick, Nadia N Abuelezam, Thomas Fussell, George R Seage, Marc Lipsitch
We investigated the impact of the displacement of sexual activity from adherent recipients of an intervention to others within or outside a trial population on the results from hypothetical trials of different sexual behavior interventions. A short-term model of HIV-prevention interventions that lead to female rejection of male partnership requests showed the impact of displacement expected at the start of a trial. An agent-based model, with sexual mixing and other South African specific demographics, evaluated consequences of displacement for sexual behavior interventions targeting young females in South Africa...
September 2017: Epidemics
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