Dynamic Multicore Processing for Pandemic Influenza Simulation.

Pandemic simulation is a useful tool for analyzing outbreaks and exploring the impact of variations in disease, population, and intervention models. Unfortunately, this type of simulation can be quite time-consuming especially for large models and significant outbreaks, which makes it difficult to run the simulations interactively and to use simulation for decision support during ongoing outbreaks. Improved run-time performance enables new applications of pandemic simulations, and can potentially allow decision makers to explore different scenarios and intervention effects. Parallelization of infection-probability calculations and multicore architectures can take advantage of modern processors to achieve significant run-time performance improvements. However, because of the varying computational load during each simulation run, which originates from the changing number of infectious persons during the outbreak, it is not useful to us the same multicore setup during the simulation run. The best performance can be achieved by dynamically changing the use of the available processor cores to balance the overhead of multithreading with the performance gains of parallelization.

A Flexible Simulation Architecture for Pandemic Influenza Simulation.

Simulation is an important resource for studying the dynamics of pandemic influenza and predicting the potential impact of interventions. However, there are several challenges for the design of such simulator architectures. Specifically, it is difficult to develop simulators that combine flexibility with run-time performance. This tradeoff is problematic in the pandemic-response setting because it makes it challenging to extend and adapt simulators for ongoing situations where rapid results are indispensable. Simulation architectures based on aspect-oriented programming can model specific concerns of the simulator and can allow developers to rapidly extend the simulator in new ways without sacrificing run-time performance. It is possible to use such aspects in conjunction with separate simulation models, which define community, disease, and intervention properties. The implication of this research for pandemic response is that aspects can add a novel layer of flexibility to simulation environments, which enables modelers to extend the simulator run-time component to new requirements that go beyond the original modeling framework.

Performance of eHealth data sources in local influenza surveillance: a 5-year open cohort study.

BACKGROUND: There is abundant global interest in using syndromic data from population-wide health information systems--referred to as eHealth resources--to improve infectious disease surveillance. Recently, the necessity for these systems to achieve two potentially conflicting requirements has been emphasized. First, they must be evidence-based; second, they must be adjusted for the diversity of populations, lifestyles, and environments. OBJECTIVE: The primary objective was to examine correlations between data from Google Flu Trends (GFT), computer-supported telenursing centers, health service websites, and influenza case rates during seasonal and pandemic influenza outbreaks. The secondary objective was to investigate associations between eHealth data, media coverage, and the interaction between circulating influenza strain(s) and the age-related population immunity. METHODS: An open cohort design was used for a five-year study in a Swedish county (population 427,000). Syndromic eHealth data were collected from GFT, telenursing call centers, and local health service website visits at page level. Data on mass media coverage of influenza was collected from the major regional newspaper. The performance of eHealth data in surveillance was measured by correlation effect size and time lag to clinically diagnosed influenza cases. RESULTS: Local media coverage data and influenza case rates showed correlations with large effect sizes only for the influenza A (A) pH1N1 outbreak in 2009 (r=.74, 95% CI .42-.90; P<.001) and the severe seasonal A H3N2 outbreak in 2011-2012 (r=.79, 95% CI .42-.93; P=.001), with media coverage preceding case rates with one week. Correlations between GFT and influenza case data showed large effect sizes for all outbreaks, the largest being the seasonal A H3N2 outbreak in 2008-2009 (r=.96, 95% CI .88-.99; P<.001). The preceding time lag decreased from two weeks during the first outbreaks to one week from the 2009 A pH1N1 pandemic. Telenursing data and influenza case data showed correlations with large effect sizes for all outbreaks after the seasonal B and A H1 outbreak in 2007-2008, with a time lag decreasing from two weeks for the seasonal A H3N2 outbreak in 2008-2009 (r=.95, 95% CI .82-.98; P<.001) to none for the A p H1N1 outbreak in 2009 (r=.84, 95% CI .62-.94; P<.001). Large effect sizes were also observed between website visits and influenza case data. CONCLUSIONS: Correlations between the eHealth data and influenza case rates in a Swedish county showed large effect sizes throughout a five-year period, while the time lag between signals in eHealth data and influenza rates changed. Further research is needed on analytic methods for adjusting eHealth surveillance systems to shifts in media coverage and to variations in age-group related immunity between virus strains. The results can be used to inform the development of alert-generating eHealth surveillance systems that can be subject for prospective evaluations in routine public health practice.

Intentions to perform non-pharmaceutical protective behaviors during influenza outbreaks in Sweden: a cross-sectional study following a mass vaccination campaign.

Failure to incorporate the beliefs and attitudes of the public into theoretical models of preparedness has been identified as a weakness in strategies to mitigate infectious disease outbreaks. We administered a cross-sectional telephone survey to a representative sample (n = 443) of the Swedish adult population to examine whether self-reported intentions to improve personal hygiene and increase social distancing during influenza outbreaks could be explained by trust in official information, self-reported health (SF-8), sociodemographic factors, and determinants postulated in protection motivation theory, namely threat appraisal and coping appraisal. The interviewees were asked to make their appraisals for two scenarios: a) an influenza with low case fatality and mild lifestyle impact; b) severe influenza with high case fatality and serious disturbances of societal functions. Every second respondent (50.0%) reported high trust in official information about influenza. The proportion that reported intentions to take deliberate actions to improve personal hygiene during outbreaks ranged between 45-85%, while less than 25% said that they intended to increase social distancing. Multiple logistic regression models with coping appraisal as the explanatory factor most frequently contributing to the explanation of the variance in intentions showed strong discriminatory performance for staying home while not ill (mild outbreaks: Area under the curve [AUC] 0.85 (95% confidence interval 0.82;0.89), severe outbreaks AUC 0.82 (95% CI 0.77;0.85)) and acceptable performance with regard to avoiding public transportation (AUC 0.78 (0.74;0.82), AUC 0.77 (0.72;0.82)), using handwash products (AUC 0.70 (0.65;0.75), AUC 0.76 (0.71;0.80)), and frequently washing hands (AUC 0.71 (0.66;0.76), AUC 0.75 (0.71;0.80)). We conclude that coping appraisal was the explanatory factor most frequently included in statistical models explaining self-reported intentions to carry out non-pharmaceutical health actions in the Swedish outlined context, and that variations in threat appraisal played a smaller role in these models despite scientific uncertainties surrounding a recent mass vaccination campaign.

Age as a determinant for dissemination of seasonal and pandemic influenza: an open cohort study of influenza outbreaks in Östergötland County, Sweden.

An understanding of the occurrence and comparative timing of influenza infections in different age groups is important for developing community response and disease control measures. This study uses data from a Scandinavian county (population 427.000) to investigate whether age was a determinant for being diagnosed with influenza 2005-2010 and to examine if age was associated with case timing during outbreaks. Aggregated demographic data were collected from Statistics Sweden, while influenza case data were collected from a county-wide electronic health record system. A logistic regression analysis was used to explore whether case risk was associated with age and outbreak. An analysis of variance was used to explore whether day for diagnosis was also associated to age and outbreak. The clinical case data were validated against case data from microbiological laboratories during one control year. The proportion of cases from the age groups 10-19 (p<0.001) and 20-29 years old (p<0.01) were found to be larger during the A pH1N1 outbreak in 2009 than during the seasonal outbreaks. An interaction between age and outbreak was observed (p<0.001) indicating a difference in age effects between circulating virus types; this interaction persisted for seasonal outbreaks only (p<0.001). The outbreaks also differed regarding when the age groups received their diagnosis (p<0.001). A post-hoc analysis showed a tendency for the young age groups, in particular the group 10-19 year olds, led outbreaks with influenza type A H1 circulating, while A H3N2 outbreaks displayed little variations in timing. The validation analysis showed a strong correlation (r = 0.625;p<0.001) between the recorded numbers of clinically and microbiologically defined influenza cases. Our findings demonstrate the complexity of age effects underlying the emergence of local influenza outbreaks. Disentangling these effects on the causal pathways will require an integrated information infrastructure for data collection and repeated studies of well-defined communities.

Requirements and design of the PROSPER protocol for implementation of information infrastructures supporting pandemic response: a Nominal Group study.

BACKGROUND: Advanced technical systems and analytic methods promise to provide policy makers with information to help them recognize the consequences of alternative courses of action during pandemics. Evaluations still show that response programs are insufficiently supported by information systems. This paper sets out to derive a protocol for implementation of integrated information infrastructures supporting regional and local pandemic response programs at the stage(s) when the outbreak no longer can be contained at its source. METHODS: Nominal group methods for reaching consensus on complex problems were used to transform requirements data obtained from international experts into an implementation protocol. The analysis was performed in a cyclical process in which the experts first individually provided input to working documents and then discussed them in conferences calls. Argument-based representation in design patterns was used to define the protocol at technical, system, and pandemic evidence levels. RESULTS: The Protocol for a Standardized information infrastructure for Pandemic and Emerging infectious disease Response (PROSPER) outlines the implementation of information infrastructure aligned with pandemic response programs. The protocol covers analyses of the community at risk, the response processes, and response impacts. For each of these, the protocol outlines the implementation of a supporting information infrastructure in hierarchical patterns ranging from technical components and system functions to pandemic evidence production. CONCLUSIONS: The PROSPER protocol provides guidelines for implementation of an information infrastructure for pandemic response programs both in settings where sophisticated health information systems already are used and in developing communities where there is limited access to financial and technical resources. The protocol is based on a generic health service model and its functions are adjusted for community-level analyses of outbreak detection and progress, and response program effectiveness. Scientifically grounded reporting principles need to be established for interpretation of information derived from outbreak detection algorithms and predictive modeling.

A neighborhood susceptibility index for planning of local physical interventions in response to pandemic influenza outbreaks.

The global spread of a novel A (H1N1) influenza virus in 2009 has highlighted the possibility of a devastating pandemic similar to the 'Spanish flu' of 1917-1918. Responding to such pandemics requires careful planning for the early phases where there is no availability of pandemic vaccine. We set out to compute a Neighborhood Influenza Susceptibility Index (NISI) describing the vulnerability of local communities of different geo-socio-physical structure to a pandemic influenza outbreak. We used a spatially explicit geo-physical model of Linköping municipality (pop. 136,240) in Sweden, and employed an ontology-modeling tool to define simulation models and transmission settings. We found considerable differences in NISI between neighborhoods corresponding to primary care areas with regard to early progress of the outbreak, as well as in terms of the total accumulated share of infected residents counted after the outbreak. The NISI can be used in local preparations of physical response measures during pandemics.

Population-based simulations of influenza pandemics: validity and significance for public health policy.

OBJECTIVE: To examine the validity and usefulness of pandemic simulations aimed at informing practical decision-making in public health. METHODS: We recruited a multidisciplinary group of nine experts to assess a case-study simulation of influenza transmission in a Swedish county. We used a non-statistical nominal group technique to generate evaluations of the plausibility, formal validity (verification) and predictive validity of the simulation. A health-effect assessment structure was used as a framework for data collection. FINDINGS: The unpredictability of social order during disasters was not adequately addressed by simulation methods; even minor disruptions of the social order may invalidate key infrastructural assumptions underpinning current pandemic simulation models. Further, a direct relationship between model flexibility and computation time was noted. Consequently, simulation methods cannot, in practice, support integrated modifications of microbiological, epidemiological and spatial submodels or handle multiple parallel scenarios. CONCLUSION: The combination of incomplete surveillance data and simulation methods that neglect social dynamics limits the ability of national public health agencies to provide policy-makers and the general public with the critical and timely information needed during a pandemic.

Impact of precautionary behaviors during outbreaks of pandemic influenza: modeling of regional differences.

Using time geographic theory for representation of population mixing, we set out to analyze the relative impact from precautionary behaviors on outbreaks of pandemic influenza in Europe and Asia. We extended an existing simulator environment with behavioral parameters from a population survey to model different behaviors. We found that precautionary behaviors even among a minority of the population can have a decisive effect on the probability of the outbreak to propagate. The results also display that assumptions strongly influences the outcome. Depending on the interpretation of how many "children" are kept from "school", R(0) changes from a range where outbreak progression is possible to a range where it is improbable in both European (R(0)=1.77/1.23) and Asian (R(0)=1.70/1.05) conditions. We conclude that unprompted distancing can have a decisive effect on pandemic propagation. An important response strategy can be to promote voluntary precautionary behavior shown to reduce disease transmission.

A discrete time-space geography for epidemiology: from mixing groups to pockets of local order in pandemic simulations.

The World Health Organization urges all nations to develop and maintain national influenza preparedness plans. Important components of such plans are forecasts of morbidity and mortality based on local social and geographic conditions. Most methodologies for simulations of epidemic outbreaks are implicitly based on the assumption that the frequency and duration of social contacts that lead to disease transmission is affected by geography, i.e. the spatial distribution of physical meeting places. In order to increase the effectiveness of the present methods for simulation of infectious disease outbreaks, the aim of this study is to examine two social geographic issues related to such models. We display how the social geographic characteristics of mixing networks, in particular when these significantly deviate from the random-mixing norm, can be represented in order to enhance the understanding and prediction of epidemic patterns in light of a possible future destructive influenza pandemic. We conclude that social geography, social networks and simulation models of directly transmitted infectious diseases are fundamentally linked.

Ontology based modeling of pandemic simulation scenarios.

Computer-based simulation of influenza outbreaks in local communities can help researchers, epidemiologists, and decision makers better understand the impact of the community structure on the reproduction rate of disease, and the relative benefits of different types of prevention and interventions. The goal of scenario modeling is to develop a description of scenario components, such as the disease, the community, and interventions. An ontology-based representation of the scenario model together with a modeling tool, which is based on an extension to Protégé, assist scenario developers in formulating simulation specifications. This approach allows the exploration of new ideas by rapidly formulating and reconstructing scenarios from novel components.

Mobile phone computing for in-situ cognitive behavioral therapy.

Cognitive behavioral therapy (CBT) for psychological disorders is becoming increasingly popular on the Internet. However, when using this workstation approach, components such as training and learning relaxation skills, problem solving, exposure exercises, and sleep management guidance must be done in the domestic environment. This paper describes design concepts for providing spatially explicit CBT with mobile phones. We reviewed and analyzed a set of treatment manuals to distinguish elements of CBT that can be improved and supported using mobile phone applications. The key advantage of mobile computing support in CBT is that multimedia can be applied to record, scale, and label anxiety-provoking situations where the need arises, which helps the CBT clients formulate and convey their thoughts and feelings to relatives and friends, as well as to therapists at subsequent treatment sessions.