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Epidemics

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https://www.readbyqxmd.com/read/28641948/optimally-capturing-latency-dynamics-in-models-of-tuberculosis-transmission
#1
Romain Ragonnet, James M Trauer, Nick Scott, Michael T Meehan, Justin T Denholm, Emma S McBryde
Although different structures are used in modern tuberculosis (TB) models to simulate TB latency, it remains unclear whether they are all capable of reproducing the particular activation dynamics empirically observed. We aimed to determine which of these structures replicate the dynamics of progression accurately. We reviewed 88 TB-modelling articles and classified them according to the latency structure employed. We then fitted these different models to the activation dynamics observed from 1352 infected contacts diagnosed in Victoria (Australia) and Amsterdam (Netherlands) to obtain parameter estimates...
June 16, 2017: Epidemics
https://www.readbyqxmd.com/read/28552262/inferring-epidemiological-dynamics-of-infectious-diseases-using-tajima-s-d-statistic-on-nucleotide-sequences-of-pathogens
#2
Kiyeon Kim, Ryosuke Omori, Kimihito Ito
The estimation of the basic reproduction number is essential to understand epidemic dynamics, and time series data of infected individuals are usually used for the estimation. However, such data are not always available. Methods to estimate the basic reproduction number using genealogy constructed from nucleotide sequences of pathogens have been proposed so far. Here, we propose a new method to estimate epidemiological parameters of outbreaks using the time series change of Tajima's D statistic on the nucleotide sequences of pathogens...
May 1, 2017: Epidemics
https://www.readbyqxmd.com/read/28487207/effectiveness-of-personal-protective-measures-in-reducing-pandemic-influenza-transmission-a-systematic-review-and-meta-analysis
#3
REVIEW
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; I(2)=0%), and facemask use provided a non-significant protective effect (OR=0...
April 30, 2017: Epidemics
https://www.readbyqxmd.com/read/28576351/publicly-available-software-tools-for-decision-makers-during-an-emergent-epidemic-systematic-evaluation-of-utility-and-usability
#4
REVIEW
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...
April 26, 2017: Epidemics
https://www.readbyqxmd.com/read/28461081/mathematical-modeling-of-ovine-footrot-in-the-uk-the-effect-of-dichelobacter-nodosus-and-fusobacterium-necrophorum-on-the-disease-dynamics
#5
Jolene Atia, Emma Monaghan, Jasmeet Kaler, Kevin Purdy, Laura Green, Matt Keeling
Dichelobacter nodosus is a virulent, invasive, anaerobic bacterium that is believed to be the causative agent of ovine footrot, an infectious bacterial disease of sheep that causes lameness. Another anaerobe, Fusobacterium necrophorum, has been intimately linked with the disease occurrence and severity. Here we examine data from a longitudinal study of footrot on one UK farm, including quantitative PCR (qPCR) estimates of bacterial load of D. nodosus and F. necrophorum. The data is at foot level; all feet were monitored for five weeks assessing disease severity (healthy, interdigital dermatitis (ID), or severe footrot (SFR)) and bacterial load (number of bacteria/swab)...
April 12, 2017: Epidemics
https://www.readbyqxmd.com/read/28416219/displacement-of-sexual-partnerships-in-trials-of-sexual-behavior-interventions-a-model-based-assessment-of-consequences
#6
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...
April 2, 2017: Epidemics
https://www.readbyqxmd.com/read/28479050/corrigendum-to-impact-of-waning-acquired-immunity-and-asymptomatic-infections-on-case-control-studies-for-enteric-pathogens-epidemics-17-2016-56-63
#7
https://www.readbyqxmd.com/read/28262588/population-effect-of-influenza-vaccination-under-co-circulation-of-non-vaccine-variants-and-the-case-for-a-bivalent-a-h3n2-vaccine-component
#8
Colin J Worby, Jacco Wallinga, Marc Lipsitch, Edward Goldstein
Some past epidemics of different influenza subtypes (particularly A/H3N2) in the US saw co-circulation of vaccine-type and variant strains. There is evidence that natural infection with one influenza subtype offers short-term protection against infection with another influenza subtype (henceforth, cross-immunity). This suggests that such cross-immunity for strains within a subtype is expected to be strong. Therefore, while vaccination effective against one strain may reduce transmission of that strain, this may also lead to a reduction of the vaccine-type strain's ability to suppress spread of a variant strain...
June 2017: Epidemics
https://www.readbyqxmd.com/read/28189386/characterising-pandemic-severity-and-transmissibility-from-data-collected-during-first-few-hundred-studies
#9
Andrew J Black, Nicholas Geard, James M McCaw, Jodie McVernon, Joshua V Ross
Early estimation of the probable impact of a pandemic influenza outbreak can assist public health authorities to ensure that response measures are proportionate to the scale of the threat. Recently, frameworks based on transmissibility and severity have been proposed for initial characterization of pandemic impact. Data requirements to inform this assessment may be provided by "First Few Hundred" (FF100) studies, which involve surveillance-possibly in person, or via telephone-of household members of confirmed cases...
June 2017: Epidemics
https://www.readbyqxmd.com/read/28169133/gender-asymmetry-in-concurrent-partnerships-and-hiv-prevalence
#10
Ka Yin Leung, Kimberly A Powers, Mirjam Kretzschmar
The structure of the sexual network of a population plays an essential role in the transmission of HIV. Concurrent partnerships, i.e. partnerships that overlap in time, are important in determining this network structure. Men and women may differ in their concurrent behavior, e.g. in the case of polygyny where women are monogamous while men may have concurrent partnerships. Polygyny has been shown empirically to be negatively associated with HIV prevalence, but the epidemiological impacts of other forms of gender-asymmetric concurrency have not been formally explored...
June 2017: Epidemics
https://www.readbyqxmd.com/read/28139388/a-comparative-analysis-of-chikungunya-and-zika-transmission
#11
Julien Riou, Chiara Poletto, Pierre-Yves Boëlle
The recent global dissemination of Chikungunya and Zika has fostered public health concern worldwide. To better understand the drivers of transmission of these two arboviral diseases, we propose a joint analysis of Chikungunya and Zika epidemics in the same territories, taking into account the common epidemiological features of the epidemics: transmitted by the same vector, in the same environments, and observed by the same surveillance systems. We analyse eighteen outbreaks in French Polynesia and the French West Indies using a hierarchical time-dependent SIR model accounting for the effect of virus, location and weather on transmission, and based on a disease specific serial interval...
June 2017: Epidemics
https://www.readbyqxmd.com/read/28089780/co-feeding-transmission-facilitates-strain-coexistence-in-borrelia-burgdorferi-the-lyme-disease-agent
#12
S L States, C I Huang, S Davis, D M Tufts, M A Diuk-Wasser
Coexistence of multiple tick-borne pathogens or strains is common in natural hosts and can be facilitated by resource partitioning of the host species, within-host localization, or by different transmission pathways. Most vector-borne pathogens are transmitted horizontally via systemic host infection, but transmission may occur in the absence of systemic infection between two vectors feeding in close proximity, enabling pathogens to minimize competition and escape the host immune response. In a laboratory study, we demonstrated that co-feeding transmission can occur for a rapidly-cleared strain of Borrelia burgdorferi, the Lyme disease agent, between two stages of the tick vector Ixodes scapularis while feeding on their dominant host, Peromyscus leucopus...
June 2017: Epidemics
https://www.readbyqxmd.com/read/28038869/modelling-and-bayesian-analysis-of-the-abakaliki-smallpox-data
#13
Jessica E Stockdale, Theodore Kypraios, Philip D O'Neill
The celebrated Abakaliki smallpox data have appeared numerous times in the epidemic modelling literature, but in almost all cases only a specific subset of the data is considered. The only previous analysis of the full data set relied on approximation methods to derive a likelihood and did not assess model adequacy. The data themselves continue to be of interest due to concerns about the possible re-emergence of smallpox as a bioterrorism weapon. We present the first full Bayesian statistical analysis using data-augmentation Markov chain Monte Carlo methods which avoid the need for likelihood approximations and which yield a wider range of results than previous analyses...
June 2017: Epidemics
https://www.readbyqxmd.com/read/28027840/defining-epidemics-in-computer-simulation-models-how-do-definitions-influence-conclusions
#14
Carolyn Orbann, Lisa Sattenspiel, Erin Miller, Jessica Dimka
Computer models have proven to be useful tools in studying epidemic disease in human populations. Such models are being used by a broader base of researchers, and it has become more important to ensure that descriptions of model construction and data analyses are clear and communicate important features of model structure. Papers describing computer models of infectious disease often lack a clear description of how the data are aggregated and whether or not non-epidemic runs are excluded from analyses. Given that there is no concrete quantitative definition of what constitutes an epidemic within the public health literature, each modeler must decide on a strategy for identifying epidemics during simulation runs...
June 2017: Epidemics
https://www.readbyqxmd.com/read/28007549/estimation-of-age-specific-rates-of-reactivation-and-immune-boosting-of-the-varicella-zoster-virus
#15
Isabella Marinelli, Alies van Lier, Hester de Melker, Andrea Pugliese, Michiel van Boven
Studies into the impact of vaccination against the varicella zoster virus (VZV) have increasingly focused on herpes zoster (HZ), which is believed to be increasing in vaccinated populations with decreasing infection pressure. This idea can be traced back to Hope-Simpson's hypothesis, in which a person's immune status determines the likelihood that he/she will develop HZ. Immunity decreases over time, and can be boosted by contact with a person experiencing varicella (exogenous boosting) or by a reactivation attempt of the virus (endogenous boosting)...
June 2017: Epidemics
https://www.readbyqxmd.com/read/28359662/assessing-the-transmission-dynamics-of-measles-in-japan-2016
#16
Hiroshi Nishiura, Kenji Mizumoto, Yusuke Asai
OBJECTIVES: Despite the verification of measles elimination, Japan experienced multiple generations of measles transmission following importation events in 2016. The purpose of the present study was to analyze the transmission dynamics of measles in Japan, 2016, estimating the transmission potential in the partially vaccinated population. METHODS: All diagnosed measles cases were notified to the government, and the present study analyzed two pieces of datasets independently, i...
March 22, 2017: Epidemics
https://www.readbyqxmd.com/read/28351673/elucidating-transmission-dynamics-and-host-parasite-vector-relationships-for-rodent-borne-bartonella-spp-in-madagascar
#17
Cara E Brook, Ying Bai, Emily O Yu, Hafaliana C Ranaivoson, Haewon Shin, Andrew P Dobson, C Jessica E Metcalf, Michael Y Kosoy, Katharina Dittmar
Bartonella spp. are erythrocytic bacteria transmitted via arthropod vectors, which infect a broad range of vertebrate hosts, including humans. We investigated transmission dynamics and host-parasite-vector relationships for potentially zoonotic Bartonella spp. in invasive Rattus rattus hosts and associated arthropod ectoparasites in Madagascar. We identified five distinct species of Bartonella (B. elizabethae 1, B. elizabethae 2, B. phoceensis 1, B. rattimassiliensis 1, and B. tribocorum 1) infecting R. rattus rodents and their ectoparasites...
March 16, 2017: Epidemics
https://www.readbyqxmd.com/read/28395850/the-impact-of-stratified-immunity-on-the-transmission-dynamics-of-influenza
#18
Hsiang-Yu Yuan, Marc Baguelin, Kin O Kwok, Nimalan Arinaminpathy, Edwin van Leeuwen, Steven Riley
Although empirical studies show that protection against influenza infection in humans is closely related to antibody titres, influenza epidemics are often described under the assumption that individuals are either susceptible or not. Here we develop a model in which antibody titre classes are enumerated explicitly and mapped onto a variable scale of susceptibility in different age groups. Fitting only with pre- and post-wave serological data during 2009 pandemic in Hong Kong, we demonstrate that with stratified immunity, the timing and the magnitude of the epidemic dynamics can be reconstructed more accurately than is possible with binary seropositivity data...
March 12, 2017: Epidemics
https://www.readbyqxmd.com/read/28365331/on-the-duration-of-the-period-between-exposure-to-hiv-and-detectable-infection
#19
Bernhard P Konrad, Darlene Taylor, Jessica M Conway, Gina S Ogilvie, Daniel Coombs
HIV infection cannot be detected immediately after exposure because plasma viral loads are too small initially. The duration of this phase of infection (the "eclipse period") is difficult to estimate because precise dates of exposure are rarely known. Therefore, the reliability of clinical HIV testing during the first few weeks of infection is unknown, creating anxiety among HIV-exposed individuals and their physicians. We address this by fitting stochastic models of early HIV infection to detailed viral load records for 78 plasma donors, taken during the period of exposure and infection...
March 11, 2017: Epidemics
https://www.readbyqxmd.com/read/28431862/application-of-the-cdc-ebolaresponse-modeling-tool-to-disease-predictions
#20
Robert H Gaffey, Cécile Viboud
Model-based predictions were critical in eliciting a vigorous international public health response to the 2014 Ebola Virus Disease outbreak in West Africa. Here, we describe the performances of an extension of the CDC-initiated EbolaResponse Modeling tool to the Ebola Forecasting Challenge, which offered a controlled environment for epidemiological predictions. In the EbolaResponse tool, transmission risks and proportions of population affected by interventions were fitted to data via least square fitting. Prediction performances were evaluated for 5 prediction time points of 4 synthetic outbreaks...
March 10, 2017: Epidemics
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