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Epidemics

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https://www.readbyqxmd.com/read/29773482/a-model-for-leptospire-dynamics-and-control-in-the-norway-rat-rattus-norvegicus-the-reservoir-host-in-urban-slum-environments
#1
Amanda Minter, Peter J Diggle, Federico Costa, James Childs, Albert I Ko, Mike Begon
Leptospirosis is a zoonosis that humans can contract via contact with animal reservoirs directly or with water contaminated with their urine. The primary reservoir of pathogenic leptospires within urban slum environments is the Norway rat (Rattus norvegicus). Motivated by the annual outbreaks of human leptospirosis in slum urban settings, the within population infection dynamics of the Norway rat were investigated in Pau da Lima, an community in Salvador, Brazil. A mechanistic model of the dynamics of leptospire infection was informed by extensive field and laboratory data was developed and explored analytically...
May 5, 2018: Epidemics
https://www.readbyqxmd.com/read/29673815/role-of-animal-movement-and-indirect-contact-among-farms-in-transmission-of-porcine-epidemic-diarrhea-virus
#2
Kimberly VanderWaal, Andres Perez, Montse Torremorrell, Robert M Morrison, Meggan Craft
Epidemiological models of the spread of pathogens in livestock populations primarily focus on direct contact between farms based on animal movement data, and in some cases, local spatial spread based on proximity between premises. The roles of other types of indirect contact among farms is rarely accounted for. In addition, data on animal movements is seldom available in the United States. However, the spread of porcine epidemic diarrhea virus (PEDv) in U.S. swine represents one of the best documented emergences of a highly infectious pathogen in the U...
April 12, 2018: Epidemics
https://www.readbyqxmd.com/read/29685498/using-state-space-models-to-predict-the-abundance-of-juvenile-and-adult-sea-lice-on-atlantic-salmon
#3
Adel Elghafghuf, Raphael Vanderstichel, Sophie St-Hilaire, Henrik Stryhn
Sea lice are marine parasites affecting salmon farms, and are considered one of the most costly pests of the salmon aquaculture industry. Infestations of sea lice on farms significantly increase opportunities for the parasite to spread in the surrounding ecosystem, making control of this pest a challenging issue for salmon producers. The complexity of controlling sea lice on salmon farms requires frequent monitoring of the abundance of different sea lice stages over time. Industry-based data sets of counts of lice are amenable to multivariate time-series data analyses...
April 11, 2018: Epidemics
https://www.readbyqxmd.com/read/29655934/age-difference-between-heterosexual-partners-in-britain-implications-for-the-spread-of-chlamydia-trachomatis
#4
Joost H Smid, Victor Garcia, Nicola Low, Catherine H Mercer, Christian L Althaus
Heterosexual partners often differ in age. Integrating realistic patterns of sexual mixing by age into dynamic transmission models has been challenging. The effects of these patterns on the transmission of sexually transmitted infections (STI) including Chlamydia trachomatis (chlamydia), the most common bacterial STI are not well understood. We describe age mixing between new heterosexual partners using age- and sex-specific data about sexual behavior reported by people aged 16-63 years in the 2000 and 2010 British National Surveys of Sexual Attitudes and Lifestyles...
March 31, 2018: Epidemics
https://www.readbyqxmd.com/read/29576516/contagion-the-bbc-four-pandemic-the-model-behind-the-documentary
#5
Petra Klepac, Stephen Kissler, Julia Gog
To mark the centenary of the 1918 influenza pandemic, the broadcasting network BBC have put together a 75-min documentary called 'Contagion! The BBC Four Pandemic'. Central to the documentary is a nationwide citizen science experiment, during which volunteers in the United Kingdom could download and use a custom mobile phone app called BBC Pandemic, and contribute their movement and contact data for a day. As the 'maths team', we were asked to use the data from the app to build and run a model of how a pandemic would spread in the UK...
March 21, 2018: Epidemics
https://www.readbyqxmd.com/read/29576517/transmission-dynamics-of-influenza-in-two-major-cities-of-uganda
#6
Wan Yang, Matthew J Cummings, Barnabas Bakamutumaho, John Kayiwa, Nicholas Owor, Barbara Namagambo, Timothy Byaruhanga, Julius J Lutwama, Max R O'Donnell, Jeffrey Shaman
In this paper, we report the epidemic characteristics of the three co-circulating influenza viruses (i.e., A/H1N1, A/H3N2, and B) in two tropical African cities-Kampala and Entebbe, Uganda-over an eight-year period (2008-2015). Using wavelet methods, we show that influenza epidemics recurred annually during the study period. In most months, two or more influenza viruses co-circulated at the same time. However, the epidemic timing differed by influenza (sub)type. Influenza A/H3N2 caused epidemics approximately every 2 years in both cities and tended to alternate with A/H1N1 or B...
March 19, 2018: Epidemics
https://www.readbyqxmd.com/read/29567063/robust-qualitative-estimation-of-time-varying-contact-rates-in-uncertain-epidemics
#7
Marco Tulio Angulo, Jorge X Velasco-Hernandez
We will inevitably face new epidemics where the lack of long time-series data and the uncertainty about the outbreak dynamics make difficult to obtain quantitative predictions. Here we present an algorithm to qualitatively infer time-varying contact rates from short time-series data, letting us predict the start, relative magnitude and decline of epidemic outbreaks. Using real time-series data of measles, dengue, and the current zika outbreak, we demonstrate our algorithm can outperform existing algorithms based on estimating reproductive numbers...
March 15, 2018: Epidemics
https://www.readbyqxmd.com/read/29548927/identifying-genotype-specific-elevated-risk-areas-and-associated-herd-risk-factors-for-bovine-tuberculosis-spread-in-british-cattle
#8
R J Orton, M Deason, P R Bessell, D M Green, R R Kao, L C M Salvador
Bovine tuberculosis (bTB) is a chronic zoonosis with major health and economic impact on the cattle industry. Despite extensive control measures in cattle and culling trials in wildlife, the reasons behind the expansion of areas with high incidence of bTB breakdowns in Great Britain remain unexplained. By balancing the importance of cattle movements and local transmission on the observed pattern of cattle outbreaks, we identify areas at elevated risk of infection from specific Mycobacterium bovis genotypes...
March 1, 2018: Epidemics
https://www.readbyqxmd.com/read/29506911/results-from-the-second-year-of-a-collaborative-effort-to-forecast-influenza-seasons-in-the-united-states
#9
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
https://www.readbyqxmd.com/read/28351674/a-simple-approach-to-measure-transmissibility-and-forecast-incidence
#10
Pierre Nouvellet, Anne Cori, Tini Garske, Isobel M Blake, Ilaria Dorigatti, Wes Hinsley, Thibaut Jombart, Harriet L Mills, Gemma Nedjati-Gilani, Maria D Van Kerkhove, Christophe Fraser, Christl A Donnelly, Neil M Ferguson, Steven Riley
Outbreaks of novel pathogens such as SARS, pandemic influenza and Ebola require substantial investments in reactive interventions, with consequent implementation plans sometimes revised on a weekly basis. Therefore, short-term forecasts of incidence are often of high priority. In light of the recent Ebola epidemic in West Africa, a forecasting exercise was convened by a network of infectious disease modellers. The challenge was to forecast unseen "future" simulated data for four different scenarios at five different time points...
March 2018: Epidemics
https://www.readbyqxmd.com/read/29567064/the-distribution-of-district-level-leprosy-incidence-in-india-is-geometric-stable-consistent-with-subcriticality
#11
Thomas M Lietman, Lee Worden, Fengchen Liu, Travis C Porco
Mathematical models predict that the community-level incidence of a controlled infectious disease across a region approaches a geometric distribution. This could hold over larger regions, if new cases remain proportional to existing cases. Leprosy has been disappearing for centuries, making an excellent candidate for testing this hypothesis. Here, we show the annual new case detection rate of leprosy in Indian districts to be consistent with a geometric distribution. For 2008-2013, goodness-of-fit testing was unable to exclude the geometric, and the shape parameter of the best fit negative binomial distribution was close to unity (0...
February 14, 2018: Epidemics
https://www.readbyqxmd.com/read/29456072/acute-illness-from-campylobacter-jejuni-may-require-high-doses-while-infection-occurs-at-low-doses
#12
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
https://www.readbyqxmd.com/read/29666018/a-bayesian-evidence-synthesis-approach-to-estimate-disease-prevalence-in-hard-to-reach-populations-hepatitis-c-in-new-york-city
#13
Sarah Tan, Susanna Makela, Daliah Heller, Kevin Konty, Sharon Balter, Tian Zheng, James H Stark
Existing methods to estimate the prevalence of chronic hepatitis C (HCV) in New York City (NYC) are limited in scope and fail to assess hard-to-reach subpopulations with highest risk such as injecting drug users (IDUs). To address these limitations, we employ a Bayesian multi-parameter evidence synthesis model to systematically combine multiple sources of data, account for bias in certain data sources, and provide unbiased HCV prevalence estimates with associated uncertainty. Our approach improves on previous estimates by explicitly accounting for injecting drug use and including data from high-risk subpopulations such as the incarcerated, and is more inclusive, utilizing ten NYC data sources...
February 3, 2018: Epidemics
https://www.readbyqxmd.com/read/29415865/assessing-the-variability-in-transmission-of-bovine-tuberculosis-within-spanish-cattle-herds
#14
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
https://www.readbyqxmd.com/read/29366873/modeling-marek-s-disease-virus-transmission-a-framework-for-evaluating-the-impact-of-farming-practices-and-evolution
#15
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
https://www.readbyqxmd.com/read/29279186/digital-dermatitis-in-dairy-cattle-the-contribution-of-different-disease-classes-to-transmission
#16
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
https://www.readbyqxmd.com/read/29279187/the-importance-of-being-urgent-the-impact-of-surveillance-target-and-scale-on-mosquito-borne-disease-control
#17
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
https://www.readbyqxmd.com/read/29329958/contact-tracing-for-the-control-of-infectious-disease-epidemics-chronic-wasting-disease-in-deer-farms
#18
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
https://www.readbyqxmd.com/read/29306640/species-interactions-may-help-explain-the-erratic-periodicity-of-whooping-cough-dynamics
#19
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
https://www.readbyqxmd.com/read/29273280/epidemix-an-interactive-multi-model-application-for-teaching-and-visualizing-infectious-disease-transmission
#20
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
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