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<?xml version="1.0" encoding="UTF-8"?>
<html xmlns="http://www.w3.org/1999/xhtml">
<head charset="UTF-8">
<title>classificationP</title>
<link rel="stylesheet" type="text/css" href="http://ajax.aspnetcdn.com/ajax/jquery.dataTables/1.9.4/css/jquery.dataTables.css"/>
<script src="http://ajax.aspnetcdn.com/ajax/jQuery/jquery-1.8.2.min.js" charset="UTF-8" type="text/javascript"> </script>
<script src="http://ajax.aspnetcdn.com/ajax/jquery.dataTables/1.9.4/jquery.dataTables.min.js" charset="UTF-8" type="text/javascript"> </script>
<script charset="UTF-8" type="text/javascript">$(function() { $("#results").dataTable(); }) </script>
</head>
<body>
<div class="bs-example table-responsive">
<table class="table table-striped table-bordered table-hover" id="results">
<thead>
<tr>
<th>articles</th>
<th>bibliography</th>
<th>dic:funder</th>
<th>word:frequencies</th>
</tr>
</thead>
<tbody>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4018281" target="separate" title="remote PDF on server">PMC4018281</a>
<a href="PMC4018281/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="Seroepidemiology and molecular epidemiology of enterovirus 71 in Russia.">
<i>titl: </i>Seroepidemiology and molecular ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
</span>
<span class="jour" title="">
<i>jour: </i>
</span>
<br/>
<span class="abst" title="Enterovirus 71 (EV71) is an emerging human pathogen causing massive epidemics of hand, foot and mouth disease with severe neurological complications in Asia. EV71 also circulates in Europe, however it does not cause large outbreaks. The reason for distinct epidemiological patterns of EV71 infection in Europe and Asia and the risk of EV71 epidemic in Europe and Russia remain unknown. Seroepidemiology of EV71 and molecular epidemiology of occasional EV71 isolates were studied to explore circulation of EV71 in Russia. In six regions of Russian Federation, seroprevalence of EV71 in sera collected in 2008 ranged from 5% to 20% in children aged 1-2 years and from 19% to 83% in children aged 3-5 years. The seroprevalence among elder children was significantly higher (41-83% vs. 19-27%) in Asian regions of Russia. EV71 strains identified in Russia in 2001-2011 belonged to subtypes C1 and C2, while genotype C4 that was causing epidemics in Asia since 1998 emerged in 2009 and became dominant in 2013.">
<i>abst: </i>Enterovirus 71 (EV71) is an em ...
</span>
</div>
</td>
<td>
<div title="2">
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/borders" target="separate">borders</a>
</span>
<br/>
</div>
</td>
<td>
<div title="14">
<span>
<a href="http://en.wikipedia.org/wiki/from" target="separate">from x 32</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/{background" target="separate">{background x 29</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/The" target="separate">The x 26</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/seroprevalence" target="separate">seroprevalence x 27</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/children" target="separate">children x 26</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4063664" target="separate" title="remote PDF on server">PMC4063664</a>
<a href="PMC4063664/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="An HIV epidemic model based on viral load dynamics: value in assessing empirical trends in HIV virulence and community viral load.">
<i>titl: </i>An HIV epidemic model based on ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
</span>
<span class="jour" title="">
<i>jour: </i>
</span>
<br/>
<span class="abst" title="Trends in HIV virulence have been monitored since the start of the AIDS pandemic, as studying HIV virulence informs our understanding of HIV epidemiology and pathogenesis. Here, we model changes in HIV virulence as a strictly evolutionary process, using set point viral load (SPVL) as a proxy, to make inferences about empirical SPVL trends from longitudinal HIV cohorts. We develop an agent-based epidemic model based on HIV viral load dynamics. The model contains functions for viral load and transmission, SPVL and disease progression, viral load trajectories in multiple stages of infection, and the heritability of SPVL across transmissions. We find that HIV virulence evolves to an intermediate level that balances infectiousness with longer infected lifespans, resulting in an optimal SPVL∼4.75 log10 viral RNA copies/mL. Adaptive viral evolution may explain observed HIV virulence trends: our model produces SPVL trends with magnitudes that are broadly similar to empirical trends. With regard to variation among studies in empirical SPVL trends, results from our model suggest that variation may be explained by the specific epidemic context, e.g. the mean SPVL of the founding lineage or the age of the epidemic; or improvements in HIV screening and diagnosis that results in sampling biases. We also use our model to examine trends in community viral load, a population-level measure of HIV viral load that is thought to reflect a population's overall transmission potential. We find that community viral load evolves in association with SPVL, in the absence of prevention programs such as antiretroviral therapy, and that the mean community viral load is not necessarily a strong predictor of HIV incidence.">
<i>abst: </i>Trends in HIV virulence have b ...
</span>
</div>
</td>
<td>
<div title="7">
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a> x 5
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/strong" target="separate">strong</a> x 2
</span>
<br/>
</div>
</td>
<td>
<div title="56">
<span>
<a href="http://en.wikipedia.org/wiki/set" target="separate">set x 29</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/and" target="separate">and x 237</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/log" target="separate">log x 46</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/HIV" target="separate">HIV x 120</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/virulence" target="separate">virulence x 41</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4318579" target="separate" title="remote PDF on server">PMC4318579</a>
<a href="PMC4318579/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="HIV competition dynamics over sexual networks: first comer advantage conserves founder effects.">
<i>titl: </i>HIV competition dynamics over ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
</span>
<span class="jour" title="">
<i>jour: </i>
</span>
<br/>
<span class="abst" title="Outside Africa, the global phylogeography of HIV is characterized by compartmentalized local epidemics that are typically dominated by a single subtype, which indicates strong founder effects. We hypothesized that the competition of viral strains at the epidemic level may involve an advantage of the resident strain that was the first to colonize a population. Such an effect would slow down the invasion of new strains, and thus also the diversification of the epidemic. We developed a stochastic modelling framework to simulate HIV epidemics over dynamic contact networks. We simulated epidemics in which the second strain was introduced into a population where the first strain had established a steady-state epidemic, and assessed whether, and on what time scale, the second strain was able to spread in the population. Simulations were parameterized based on empirical data; we tested scenarios with varying levels of overall prevalence. The spread of the second strain occurred on a much slower time scale compared with the initial expansion of the first strain. With strains of equal transmission efficiency, the second strain was unable to invade on a time scale relevant for the history of the HIV pandemic. To become dominant over a time scale of decades, the second strain needed considerable (>25%) advantage in transmission efficiency over the resident strain. The inhibition effect was weaker if the second strain was introduced while the first strain was still in its growth phase. We also tested how possible mechanisms of interference (inhibition of superinfection, depletion of highly connected hubs in the network, one-time acute peak of infectiousness) contribute to the inhibition effect. Our simulations confirmed a strong first comer advantage in the competition dynamics of HIV at the population level, which may explain the global phylogeography of the virus and may influence the future evolution of the pandemic.">
<i>abst: </i>Outside Africa, the global phy ...
</span>
</div>
</td>
<td>
<div title="18">
<span>
<a href="http://en.wikipedia.org/wiki/strong" target="separate">strong</a> x 12
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/orange" target="separate">orange</a> x 3
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/borders" target="separate">borders</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/project" target="separate">project</a>
</span>
</div>
</td>
<td>
<div title="66">
<span>
<a href="http://en.wikipedia.org/wiki/epidemics" target="separate">epidemics x 23</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/was" target="separate">was x 97</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/also" target="separate">also x 31</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/were" target="separate">were x 54</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/its" target="separate">its x 25</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4355742" target="separate" title="remote PDF on server">PMC4355742</a>
<a href="PMC4355742/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="Multi-scale modeling for the transmission of influenza and the evaluation of interventions toward it.">
<i>titl: </i>Multi-scale modeling for the t ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
</span>
<span class="jour" title="">
<i>jour: </i>
</span>
<br/>
<span class="abst" title="Mathematical modeling of influenza epidemic is important for analyzing the main cause of the epidemic and finding effective interventions towards it. The epidemic is a dynamic process. In this process, daily infections are caused by people's contacts, and the frequency of contacts can be mainly influenced by their cognition to the disease. The cognition is in turn influenced by daily illness attack rate, climate, and other environment factors. Few existing methods considered the dynamic process in their models. Therefore, their prediction results can hardly be explained by the mechanisms of epidemic spreading. In this paper, we developed a heterogeneous graph modeling approach (HGM) to describe the dynamic process of influenza virus transmission by taking advantage of our unique clinical data. We built social network of studied region and embedded an Agent-Based Model (ABM) in the HGM to describe the dynamic change of an epidemic. Our simulations have a good agreement with clinical data. Parameter sensitivity analysis showed that temperature influences the dynamic of epidemic significantly and system behavior analysis showed social network degree is a critical factor determining the size of an epidemic. Finally, multiple scenarios for vaccination and school closure strategies were simulated and their performance was analyzed.">
<i>abst: </i>Mathematical modeling of influ ...
</span>
</div>
</td>
<td>
<div title="11">
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a> x 9
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/strong" target="separate">strong</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/project" target="separate">project</a>
</span>
<br/>
</div>
</td>
<td/>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4372574" target="separate" title="remote PDF on server">PMC4372574</a>
<a href="PMC4372574/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="Superinfection between influenza and RSV alternating patterns in San Luis Potosí State, México.">
<i>titl: </i>Superinfection between influen ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
</span>
<span class="jour" title="">
<i>jour: </i>
</span>
<br/>
<span class="abst" title="The objective of this paper is to explain through the ecological hypothesis superinfection and competitive interaction between two viral populations and niche (host) availability, the alternating patterns of Respiratory Syncytial Virus (RSV) and influenza observed in a regional hospital in San Luis Potosí State, México using a mathematical model as a methodological tool. The data analyzed consists of community-based and hospital-based Acute Respiratory Infections (ARI) consultations provided by health-care institutions reported to the State Health Service Epidemiology Department from 2003 through 2009.">
<i>abst: </i>The objective of this paper is ...
</span>
</div>
</td>
<td>
<div title="12">
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a> x 8
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/strong" target="separate">strong</a> x 2
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/orange" target="separate">orange</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/k" target="separate">k</a>
</span>
<br/>
</div>
</td>
<td>
<div title="24">
<span>
<a href="http://en.wikipedia.org/wiki/cases" target="separate">cases x 25</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/epidemic" target="separate">epidemic x 21</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/for" target="separate">for x 120</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/time" target="separate">time x 22</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/{background" target="separate">{background x 29</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4395159" target="separate" title="remote PDF on server">PMC4395159</a>
<a href="PMC4395159/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="SNPer: an R library for quantitative variant analysis on single nucleotide polymorphisms among influenza virus populations.">
<i>titl: </i>SNPer: an R library for quanti ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
</span>
<span class="jour" title="">
<i>jour: </i>
</span>
<br/>
<span class="abst" title="Influenza virus (IFV) can evolve rapidly leading to genetic drifts and shifts resulting in human and animal influenza epidemics and pandemics. The genetic shift that gave rise to the 2009 influenza A/H1N1 pandemic originated from a triple gene reassortment of avian, swine and human IFVs. More minor genetic alterations in genetic drift can lead to influenza drug resistance such as the H274Y mutation associated with oseltamivir resistance. Hence, a rapid tool to detect IFV mutations and the potential emergence of new virulent strains can better prepare us for seasonal influenza outbreaks as well as potential pandemics. Furthermore, identification of specific mutations by closely examining single nucleotide polymorphisms (SNPs) in IFV sequences is essential to classify potential genetic markers associated with potentially dangerous IFV phenotypes. In this study, we developed a novel R library called "SNPer" to analyze quantitative variants in SNPs among IFV subpopulations. The computational SNPer program was applied to three different subpopulations of published IFV genomic information. SNPer queried SNPs data and grouped the SNPs into (1) universal SNPs, (2) likely common SNPs, and (3) unique SNPs. SNPer outperformed manual visualization in terms of time and labor. SNPer took only three seconds with no errors in SNP comparison events compared with 40 hours with errors using manual visualization. The SNPer tool can accelerate the capacity to capture new and potentially dangerous IFV strains to mitigate future influenza outbreaks.">
<i>abst: </i>Influenza virus (IFV) can evol ...
</span>
</div>
</td>
<td>
<div title="2">
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/interface" target="separate">interface</a>
</span>
<br/>
</div>
</td>
<td>
<div title="13">
<span>
<a href="http://en.wikipedia.org/wiki/the" target="separate">the x 140</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/and" target="separate">and x 102</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/data" target="separate">data x 28</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/The" target="separate">The x 37</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/{background" target="separate">{background x 29</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4405370" target="separate" title="remote PDF on server">PMC4405370</a>
<a href="PMC4405370/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="Spatial structure, transmission modes and the evolution of viral exploitation strategies.">
<i>titl: </i>Spatial structure, transmissio ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
</span>
<span class="jour" title="">
<i>jour: </i>
</span>
<br/>
<span class="abst" title="Spatial structure and local migration are predicted to promote the evolution of less aggressive host exploitation strategies in horizontally transmitted pathogens. Here we explore the effect of spatial structure on the evolution of pathogens that can use both horizontal and vertical routes of transmission. First, we analyse theoretically how vertical transmission can alter evolutionary trajectories and confirm that space can impede the spread of virulent pathogens. Second, we test this prediction using the latent phage λ which transmits horizontally and vertically in Escherichia coli populations. We show that the latent phage λ wins competition against the virulent mutant λcI857 in spatially structured epidemics, but loses when spatial structure is eroded. The vertical transmission of phage λ immunizes its local host pool against superinfection and prevents the spread of the virulent λcI857. This effect breaks down when mixing facilitates horizontal transmission to uninfected hosts. We thus confirm the importance of spatial structure for the evolutionary maintenance of prudent infection strategies in latent viruses.">
<i>abst: </i>Spatial structure and local mi ...
</span>
</div>
</td>
<td>
<div title="2">
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/strong" target="separate">strong</a>
</span>
<br/>
</div>
</td>
<td>
<div title="28">
<span>
<a href="http://en.wikipedia.org/wiki/transmission" target="separate">transmission x 57</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/infected" target="separate">infected x 27</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/host" target="separate">host x 33</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/can" target="separate">can x 21</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/virulent" target="separate">virulent x 22</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4510129" target="separate" title="remote PDF on server">PMC4510129</a>
<a href="PMC4510129/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="Genetic Characterization of a Novel HIV-1 Circulating Recombinant Form (CRF74_01B) Identified among Intravenous Drug Users in Malaysia: Recombination History and Phylogenetic Linkage with Previously Defined Recombinant Lineages.">
<i>titl: </i>Genetic Characterization of a ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
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<span class="jour" title="">
<i>jour: </i>
</span>
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<span class="abst" title="In many parts of Southeast Asia, the HIV-1 epidemic has been driven by the sharing of needles and equipment among intravenous drug users (IDUs). Over the last few decades, many studies have proven time and again that the diversity of HIV-1 epidemics can often be linked to the route of infection transmission. That said, the diversity and complexity of HIV-1 molecular epidemics in the region have been increasing at an alarming rate, due in part to the high tendency of the viral RNA to recombine. This scenario was exemplified by the discovery of numerous circulating recombinant forms (CRFs), especially in Thailand and Malaysia. In this study, we characterized a novel CRF designated CRF74_01B, which was identified in six epidemiologically unlinked IDUs in Kuala Lumpur, Malaysia. The near-full length genomes were composed of CRF01_AE and subtype B', with eight breakpoints dispersed in the gag-pol and nef regions. Remarkably, this CRF shared four and two recombination hotspots with the previously described CRF33_01B and the less prevalent CRF53_01B, respectively. Genealogy-based Bayesian phylogenetic analysis of CRF74_01B genomic regions showed that it is closely related to both CRF33_01B and CRF53_01B. This observation suggests that CRF74_01B was probably a direct descendent from specific lineages of CRF33_01B, CRF53_01B and subtype B' that could have emerged in the mid-1990s. Additionally, it illustrated the active recombination processes between prevalent HIV-1 subtypes and recombinants in Malaysia. In summary, we report a novel HIV-1 genotype designated CRF74_01B among IDUs in Kuala Lumpur, Malaysia. The characterization of the novel CRF74_01B is of considerable significance towards the understanding of the genetic diversity and population dynamics of HIV-1 circulating in the region.">
<i>abst: </i>In many parts of Southeast Asi ...
</span>
</div>
</td>
<td>
<div title="2">
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a> x 2
</span>
<br/>
</div>
</td>
<td>
<div title="12">
<span>
<a href="http://en.wikipedia.org/wiki/HIV-" target="separate">HIV- x 37</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/and" target="separate">and x 106</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/{background" target="separate">{background x 29</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/from" target="separate">from x 24</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/with" target="separate">with x 26</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4520691" target="separate" title="remote PDF on server">PMC4520691</a>
<a href="PMC4520691/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="Forecasting Influenza Epidemics in Hong Kong.">
<i>titl: </i>Forecasting Influenza Epidemic ...
</span>
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<span class="date" title="">
<i>date: </i>
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<span class="jour" title="">
<i>jour: </i>
</span>
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<span class="abst" title="Recent advances in mathematical modeling and inference methodologies have enabled development of systems capable of forecasting seasonal influenza epidemics in temperate regions in real-time. However, in subtropical and tropical regions, influenza epidemics can occur throughout the year, making routine forecast of influenza more challenging. Here we develop and report forecast systems that are able to predict irregular non-seasonal influenza epidemics, using either the ensemble adjustment Kalman filter or a modified particle filter in conjunction with a susceptible-infected-recovered (SIR) model. We applied these model-filter systems to retrospectively forecast influenza epidemics in Hong Kong from January 1998 to December 2013, including the 2009 pandemic. The forecast systems were able to forecast both the peak timing and peak magnitude for 44 epidemics in 16 years caused by individual influenza strains (i.e., seasonal influenza A(H1N1), pandemic A(H1N1), A(H3N2), and B), as well as 19 aggregate epidemics caused by one or more of these influenza strains. Average forecast accuracies were 37% (for both peak timing and magnitude) at 1-3 week leads, and 51% (peak timing) and 50% (peak magnitude) at 0 lead. Forecast accuracy increased as the spread of a given forecast ensemble decreased; the forecast accuracy for peak timing (peak magnitude) increased up to 43% (45%) for H1N1, 93% (89%) for H3N2, and 53% (68%) for influenza B at 1-3 week leads. These findings suggest that accurate forecasts can be made at least 3 weeks in advance for subtropical and tropical regions.">
<i>abst: </i>Recent advances in mathematica ...
</span>
</div>
</td>
<td>
<div title="1">
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a>
</span>
<br/>
</div>
</td>
<td>
<div title="39">
<span>
<a href="http://en.wikipedia.org/wiki/for" target="separate">for x 166</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/The" target="separate">The x 39</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/more" target="separate">more x 29</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/and" target="separate">and x 214</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/model" target="separate">model x 29</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4608293" target="separate" title="remote PDF on server">PMC4608293</a>
<a href="PMC4608293/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="Strategic information is everyone's business: perspectives from an international stakeholder meeting to enhance strategic information data along the HIV Cascade for people who inject drugs.">
<i>titl: </i>Strategic information is every ...
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<span class="date" title="">
<i>date: </i>
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<span class="jour" title="">
<i>jour: </i>
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<span class="abst" title="People who inject drugs (PWID) are at increased HIV transmission risk because of unsafe injecting practices and a host of other individual, network, and structural factors. Thus, PWID have a great need for services within the Cascade of HIV prevention, diagnosis, care, and treatment (HIV Cascade). Yet the systems that monitor their progress through the Cascade are often lacking. Subsequently, fewer reliable data are available to guide programs targeting this key population (KP). Programmatic data, which are helpful in tracking PWID through the Cascade, also are limited because not all countries have harm reduction programming from which to estimate Cascade indicators. Also, due to stigma and the illegal nature of drug use, PWID may not disclose their drug use behavior or HIV status when accessing services. Consequently, PWID appear to have low HIV testing rates and, for those living with HIV, lower access to health services and lower viral suppression rates than do other KP groups. This commentary, based on outcomes from an international stakeholder meeting, identifies data gaps and proposes solutions to strengthen strategic information (SI), the systematic collection, analysis, and dissemination of information, to optimize HIV prevention, care, and treatment programming for PWID.">
<i>abst: </i>People who inject drugs (PWID) ...
</span>
</div>
</td>
<td>
<div title="3">
<span>
<a href="http://en.wikipedia.org/wiki/project" target="separate">project</a> x 2
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/strong" target="separate">strong</a>
</span>
<br/>
</div>
</td>
<td>
<div title="10">
<span>
<a href="http://en.wikipedia.org/wiki/HIV" target="separate">HIV x 65</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/{background" target="separate">{background x 29</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/for" target="separate">for x 70</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/and" target="separate">and x 194</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/are" target="separate">are x 42</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4634195" target="separate" title="remote PDF on server">PMC4634195</a>
<a href="PMC4634195/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="HIV Transmission Networks in the San Diego-Tijuana Border Region.">
<i>titl: </i>HIV Transmission Networks in t ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
</span>
<span class="jour" title="">
<i>jour: </i>
</span>
<br/>
<span class="abst" title="HIV sequence data can be used to reconstruct local transmission networks. Along international borders, like the San Diego-Tijuana region, understanding the dynamics of HIV transmission across reported risks, racial/ethnic groups, and geography can help direct effective prevention efforts on both sides of the border.We gathered sociodemographic, geographic, clinical, and viral sequence data from HIV infected individuals participating in ten studies in the San Diego-Tijuana border region. Phylogenetic and network analysis was performed to infer putative relationships between HIV sequences. Correlates of identified clusters were evaluated and spatiotemporal relationships were explored using Bayesian phylogeographic analysis.After quality filtering, 843 HIV sequences with associated demographic data and 263 background sequences from the region were analyzed, and 138 clusters were inferred (2-23 individuals). Overall, the rate of clustering did not differ by ethnicity, residence, or sex, but bisexuals were less likely to cluster than heterosexuals or men who have sex with men (p = 0.043), and individuals identifying as white (p ≤ 0.01) were more likely to cluster than other races. Clustering individuals were also 3.5 years younger than non-clustering individuals (p < 0.001). Although the sampled San Diego and Tijuana epidemics were phylogenetically compartmentalized, five clusters contained individuals residing on both sides of the border.This study sampled ~ 7% of HIV infected individuals in the border region, and although the sampled networks on each side of the border were largely separate, there was evidence of persistent bidirectional cross-border transmissions that linked risk groups, thus highlighting the importance of the border region as a "melting pot" of risk groups.NIH, VA, and Pendleton Foundation.">
<i>abst: </i>HIV sequence data can be used ...
</span>
</div>
</td>
<td>
<div title="4">
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a> x 2
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/borders" target="separate">borders</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/project" target="separate">project</a>
</span>
<br/>
</div>
</td>
<td>
<div title="27">
<span>
<a href="http://en.wikipedia.org/wiki/and" target="separate">and x 178</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/(.%)" target="separate">(.%) x 43</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/from" target="separate">from x 64</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/San" target="separate">San x 71</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/risk" target="separate">risk x 27</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4642928" target="separate" title="remote PDF on server">PMC4642928</a>
<a href="PMC4642928/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="Strain Interactions as a Mechanism for Dominant Strain Alternation and Incidence Oscillation in Infectious Diseases: Seasonal Influenza as a Case Study.">
<i>titl: </i>Strain Interactions as a Mecha ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
</span>
<span class="jour" title="">
<i>jour: </i>
</span>
<br/>
<span class="abst" title="BACKGROUND:Many human infectious diseases are caused by pathogens that have multiple strains and show oscillation in infection incidence and alternation of dominant strains which together are referred to as epidemic cycling. Understanding the underlying mechanisms of epidemic cycling is essential for forecasting outbreaks of epidemics and therefore important for public health planning. Current theoretical effort is mainly focused on the factors that are extrinsic to the pathogens themselves ("extrinsic factors") such as environmental variation and seasonal change in human behaviours and susceptibility. Nevertheless, co-circulation of different strains of a pathogen was usually observed and thus strains interact with one another within concurrent infection and during sequential infection. The existence of these intrinsic factors is common and may be involved in the generation of epidemic cycling of multi-strain pathogens. METHODS AND FINDINGS:To explore the mechanisms that are intrinsic to the pathogens themselves ("intrinsic factors") for epidemic cycling, we consider a multi-strain SIRS model including cross-immunity and infectivity enhancement and use seasonal influenza as an example to parameterize the model. The Kullback-Leibler information distance was calculated to measure the match between the model outputs and the typical features of seasonal flu (an outbreak duration of 11 weeks and an annual attack rate of 15%). Results show that interactions among strains can generate seasonal influenza with these characteristic features, provided that: the infectivity of a single strain within concurrent infection is enhanced 2-7 times that within a single infection; cross-immunity as a result of past infection is 0.5-0.8 and lasts 2-9 years; while other parameters are within their widely accepted ranges (such as a 2-3 day infectious period and the basic reproductive number of 1.8-3.0). Moreover, the observed alternation of the dominant strain among epidemics emerges naturally from the best fit model. Alternative modelling that also includes seasonal forcing in transmissibility shows that both external mechanisms (i.e. seasonal forcing) and the intrinsic mechanisms (i.e., strain interactions) are equally able to generate the observed time-series in seasonal flu. CONCLUSIONS:The intrinsic mechanism of strain interactions alone can generate the observed patterns of seasonal flu epidemics, but according to Kullback-Leibler information distance the importance of extrinsic mechanisms cannot be excluded. The intrinsic mechanism illustrated here to explain seasonal flu may also apply to other infectious diseases caused by polymorphic pathogens.">
<i>abst: </i>BACKGROUND:Many human infectio ...
</span>
</div>
</td>
<td>
<div title="14">
<span>
<a href="http://en.wikipedia.org/wiki/strong" target="separate">strong</a> x 9
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a> x 5
</span>
<br/>
</div>
</td>
<td>
<div title="56">
<span>
<a href="http://en.wikipedia.org/wiki/The" target="separate">The x 57</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/transmission" target="separate">transmission x 33</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/during" target="separate">during x 27</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/this" target="separate">this x 23</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/mean" target="separate">mean x 28</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4666598" target="separate" title="remote PDF on server">PMC4666598</a>
<a href="PMC4666598/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="Socio-economic and Climate Factors Associated with Dengue Fever Spatial Heterogeneity: A Worked Example in New Caledonia.">
<i>titl: </i>Socio-economic and Climate Fac ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
</span>
<span class="jour" title="">
<i>jour: </i>
</span>
<br/>
<span class="abst" title="BACKGROUND/OBJECTIVES:Understanding the factors underlying the spatio-temporal distribution of infectious diseases provides useful information regarding their prevention and control. Dengue fever spatio-temporal patterns result from complex interactions between the virus, the host, and the vector. These interactions can be influenced by environmental conditions. Our objectives were to analyse dengue fever spatial distribution over New Caledonia during epidemic years, to identify some of the main underlying factors, and to predict the spatial evolution of dengue fever under changing climatic conditions, at the 2100 horizon. METHODS:We used principal component analysis and support vector machines to analyse and model the influence of climate and socio-economic variables on the mean spatial distribution of 24,272 dengue cases reported from 1995 to 2012 in thirty-three communes of New Caledonia. We then modelled and estimated the future evolution of dengue incidence rates using a regional downscaling of future climate projections. RESULTS:The spatial distribution of dengue fever cases is highly heterogeneous. The variables most associated with this observed heterogeneity are the mean temperature, the mean number of people per premise, and the mean percentage of unemployed people, a variable highly correlated with people's way of life. Rainfall does not seem to play an important role in the spatial distribution of dengue cases during epidemics. By the end of the 21st century, if temperature increases by approximately 3 °C, mean incidence rates during epidemics could double. CONCLUSION:In New Caledonia, a subtropical insular environment, both temperature and socio-economic conditions are influencing the spatial spread of dengue fever. Extension of this study to other countries worldwide should improve the knowledge about climate influence on dengue burden and about the complex interplay between different factors. This study presents a methodology that can be used as a step by step guide to model dengue spatial heterogeneity in other countries.">
<i>abst: </i>BACKGROUND/OBJECTIVES:Understa ...
</span>
</div>
</td>
<td>
<div title="10">
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a> x 4
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/strong" target="separate">strong</a> x 3
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/orange" target="separate">orange</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/borders" target="separate">borders</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/project" target="separate">project</a>
</span>
</div>
</td>
<td>
<div title="74">
<span>
<a href="http://en.wikipedia.org/wiki/number" target="separate">number x 36</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/one" target="separate">one x 22</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/unemployed" target="separate">unemployed x 24</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/year" target="separate">year x 22</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/temperature" target="separate">temperature x 99</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4684369" target="separate" title="remote PDF on server">PMC4684369</a>
<a href="PMC4684369/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="Human Social Behavior and Demography Drive Patterns of Fine-Scale Dengue Transmission in Endemic Areas of Colombia.">
<i>titl: </i>Human Social Behavior and Demo ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
</span>
<span class="jour" title="">
<i>jour: </i>
</span>
<br/>
<span class="abst" title="Dengue is known to transmit between humans and A. aegypti mosquitoes living in neighboring houses. Although transmission is thought to be highly heterogeneous in both space and time, little is known about the patterns and drivers of transmission in groups of houses in endemic settings. We carried out surveys of PCR positivity in children residing in 2-block patches of highly endemic cities of Colombia. We found high levels of heterogeneity in PCR positivity, varying from less than 30% in 8 of the 10 patches to 56 and 96%, with the latter patch containing 22 children simultaneously PCR positive (PCR22) for DEN2. We then used an agent-based model to assess the likely eco-epidemiological context of this observation. Our model, simulating daily dengue dynamics over a 20 year period in a single two block patch, suggests that the observed heterogeneity most likely derived from variation in the density of susceptible people. Two aspects of human adaptive behavior were critical to determining this density: external social relationships favoring viral introduction (by susceptible residents or infectious visitors) and immigration of households from non-endemic areas. External social relationships generating frequent viral introduction constituted a particularly strong constraint on susceptible densities, thereby limiting the potential for explosive outbreaks and dampening the impact of heightened vectorial capacity. Dengue transmission can be highly explosive locally, even in neighborhoods with significant immunity in the human population. Variation among neighborhoods in the density of local social networks and rural-to-urban migration is likely to produce significant fine-scale heterogeneity in dengue dynamics, constraining or amplifying the impacts of changes in mosquito populations and cross immunity between serotypes.">
<i>abst: </i>Dengue is known to transmit be ...
</span>
</div>
</td>
<td>
<div title="12">
<span>
<a href="http://en.wikipedia.org/wiki/strong" target="separate">strong</a> x 5
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a> x 4
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/sparks" target="separate">sparks</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/project" target="separate">project</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/bp" target="separate">bp</a>
</span>
</div>
</td>
<td>
<div title="39">
<span>
<a href="http://en.wikipedia.org/wiki/was" target="separate">was x 31</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/model" target="separate">model x 25</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/The" target="separate">The x 34</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/each" target="separate">each x 37</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/this" target="separate">this x 22</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4704709" target="separate" title="remote PDF on server">PMC4704709</a>
<a href="PMC4704709/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="The Genomic Signature of Population Reconnection Following Isolation: From Theory to HIV.">
<i>titl: </i>The Genomic Signature of Popul ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
</span>
<span class="jour" title="">
<i>jour: </i>
</span>
<br/>
<span class="abst" title="Ease of worldwide travel provides increased opportunities for organisms not only to colonize new environments but also to encounter related but diverged populations. Such events of reconnection and secondary contact of previously isolated populations are widely observed at different time scales. For example, during the quaternary glaciation, sea water level fluctuations caused temporal isolation of populations, often to be followed by secondary contact. At shorter time scales, population isolation and reconnection of viruses are commonly observed, and such events are often associated with epidemics and pandemics. Here, using coalescent theory and simulations, we describe the temporal impact of population reconnection after isolation on nucleotide differences and the site frequency spectrum, as well as common summary statistics of DNA variation. We identify robust genomic signatures of population reconnection after isolation. We utilize our development to infer the recent evolutionary history of human immunodeficiency virus 1 (HIV-1) in Asia and South America, successfully retrieving the successive HIV subtype colonization events in these regions. Our analysis reveals that divergent HIV-1 subtype populations are currently admixing in these regions, suggesting that HIV-1 may be undergoing a process of homogenization, contrary to popular belief.">
<i>abst: </i>Ease of worldwide travel provi ...
</span>
</div>
</td>
<td>
<div title="92">
<span>
<a href="http://en.wikipedia.org/wiki/k" target="separate">k</a> x 64
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/total" target="separate">total</a> x 19
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/strong" target="separate">strong</a> x 7
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/project" target="separate">project</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/bp" target="separate">bp</a>
</span>
</div>
</td>
<td>
<div title="47">
<span>
<a href="http://en.wikipedia.org/wiki/model" target="separate">model x 23</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/and" target="separate">and x 376</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/from" target="separate">from x 62</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/can" target="separate">can x 25</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/pairwise" target="separate">pairwise x 42</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4707738" target="separate" title="remote PDF on server">PMC4707738</a>
<a href="PMC4707738/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="Virus evolution and transmission in an ever more connected world.">
<i>titl: </i>Virus evolution and transmissi ...
</span>
<br/>
<span class="date" title="">
<i>date: </i>
</span>
<span class="jour" title="">
<i>jour: </i>
</span>
<br/>
<span class="abst" title="The frequency and global impact of infectious disease outbreaks, particularly those caused by emerging viruses, demonstrate the need for a better understanding of how spatial ecology and pathogen evolution jointly shape epidemic dynamics. Advances in computational techniques and the increasing availability of genetic and geospatial data are helping to address this problem, particularly when both information sources are combined. Here, we review research at the intersection of evolutionary biology, human geography and epidemiology that is working towards an integrated view of spatial incidence, host mobility and viral genetic diversity. We first discuss how empirical studies have combined viral spatial and genetic data, focusing particularly on the contribution of evolutionary analyses to epidemiology and disease control. Second, we explore the interplay between virus evolution and global dispersal in more depth for two pathogens: human influenza A virus and chikungunya virus. We discuss the opportunities for future research arising from new analyses of human transportation and trade networks, as well as the associated challenges in accessing and sharing relevant spatial and genetic data.">
<i>abst: </i>The frequency and global impac ...
</span>
</div>
</td>
<td>
<div title="2">
<span>
<a href="http://en.wikipedia.org/wiki/strong" target="separate">strong</a> x 2
</span>
<br/>
</div>
</td>
<td>
<div title="28">
<span>
<a href="http://en.wikipedia.org/wiki/has" target="separate">has x 21</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/transmission" target="separate">transmission x 30</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/influenza" target="separate">influenza x 48</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/can" target="separate">can x 25</a>
</span>
<br/>
<span>
<a href="http://en.wikipedia.org/wiki/from" target="separate">from x 44</a>
</span>
</div>
</td>
</tr>
<tr>
<td title="fixme">
<a href="http://europepmc.org/articles/PMC4735166" target="separate" title="remote PDF on server">PMC4735166</a>
<a href="PMC4735166/scholarly.html" target="separate" title="HTML on local server">local</a>
</td>
<td>
<div>
<span class="titl" title="Assessing herd immunity against rubella in Japan: a retrospective seroepidemiological analysis of age-dependent transmission dynamics.">
<i>titl: </i>Assessing herd immunity agains ...