939 research outputs found
Enhancing spatial detection accuracy for syndromic surveillance with street level incidence data
<p>Abstract</p> <p>Background</p> <p>The Department of Defense Military Health System operates a syndromic surveillance system that monitors medical records at more than 450 non-combat Military Treatment Facilities (MTF) worldwide. The Electronic Surveillance System for Early Notification of Community-based Epidemics (ESSENCE) uses both temporal and spatial algorithms to detect disease outbreaks. This study focuses on spatial detection and attempts to improve the effectiveness of the ESSENCE implementation of the spatial scan statistic by increasing the spatial resolution of incidence data from zip codes to street address level.</p> <p>Methods</p> <p>Influenza-Like Illness (ILI) was used as a test syndrome to develop methods to improve the spatial accuracy of detected alerts. Simulated incident clusters of various sizes were superimposed on real ILI incidents from the 2008/2009 influenza season. Clusters were detected using the spatial scan statistic and their displacement from simulated loci was measured. Detected cluster size distributions were also evaluated for compliance with simulated cluster sizes.</p> <p>Results</p> <p>Relative to the ESSENCE zip code based method, clusters detected using street level incidents were displaced on average 65% less for 2 and 5 mile radius clusters and 31% less for 10 mile radius clusters. Detected cluster size distributions for the street address method were quasi normal and sizes tended to slightly exceed simulated radii. ESSENCE methods yielded fragmented distributions and had high rates of zero radius and oversized clusters.</p> <p>Conclusions</p> <p>Spatial detection accuracy improved notably with regard to both location and size when incidents were geocoded to street addresses rather than zip code centroids. Since street address geocoding success rates were only 73.5%, zip codes were still used for more than one quarter of ILI cases. Thus, further advances in spatial detection accuracy are dependant on systematic improvements in the collection of individual address information.</p
Data-driven Disease Surveillance
The recent and still ongoing pandemic of SARS-CoV-2 has shown that an infectious disease outbreak can have serious consequences on public health and economy. In this situation, public health officials constantly aim to control and reduce the number of infections in order to avoid overburdening health care system. Besides minimizing personal contact through political measures, a fundamental approach to contain the spread of diseases is to isolate infected individuals. The effectiveness of the latter approach strongly depends on a timely detection of the outbreak as the tracking of individuals can quickly become infeasible when the number of cases increases. Hence, a key factor in the containment of an infectious disease is the early detection of a potential larger outbreak, commonly known as outbreak detection.
For this purpose, epidemiologists rely on a variety of statistical surveillance methods in order to maintain an overview of the current situation of infections by either monitoring confirmed cases or cases with early symptoms. Mainly based on statistical hypothesis testing, these methods automatically raise an alarm if an unexpected increase in the number of infections is observed. The practical usefulness of such methods highly depends on the trade-off between the ability to detect outbreaks and the chances of raising a false alarm. However, this hypothesis-based approach to disease surveillance has several limitations. On the one hand, it is a hand-crafted approach which requires domain knowledge to set up the statistical methods, especially if early symptoms are monitored. On the other hand, outbreaks of emerging infectious diseases with different symptom patterns are likely to be missed by such a surveillance system.
In this thesis, we focus on data-driven disease surveillance and address these challenges in the following ways. To support epidemiologists in the process of defining reliable disease patterns for monitoring cases with early symptoms, we present a novel approach to discover such patterns in historic data. With respect to supervised learning, we propose a fusion classifier which can combine the output of multiple statistical methods using the univariate time series of infection counts as the only source of information. In addition, we develop algorithms based on unsupervised learning which frame the task of outbreak detection as a general anomaly detection task. This even includes the surveillance of emerging infectious diseases. Therefore, we contribute a novel framework and propose a new approach based on sum-product networks to monitor multiple disease patterns simultaneously. Our results show that data-driven approaches are ideal to assist epidemiologists by processing large amounts of data that cannot fully be understood and analyzed by humans. Most significantly, the incorporation of additional information into the surveillance through machine learning techniques shows reliable and promising results
Prediction of infectious disease epidemics via weighted density ensembles
Accurate and reliable predictions of infectious disease dynamics can be
valuable to public health organizations that plan interventions to decrease or
prevent disease transmission. A great variety of models have been developed for
this task, using different model structures, covariates, and targets for
prediction. Experience has shown that the performance of these models varies;
some tend to do better or worse in different seasons or at different points
within a season. Ensemble methods combine multiple models to obtain a single
prediction that leverages the strengths of each model. We considered a range of
ensemble methods that each form a predictive density for a target of interest
as a weighted sum of the predictive densities from component models. In the
simplest case, equal weight is assigned to each component model; in the most
complex case, the weights vary with the region, prediction target, week of the
season when the predictions are made, a measure of component model uncertainty,
and recent observations of disease incidence. We applied these methods to
predict measures of influenza season timing and severity in the United States,
both at the national and regional levels, using three component models. We
trained the models on retrospective predictions from 14 seasons (1997/1998 -
2010/2011) and evaluated each model's prospective, out-of-sample performance in
the five subsequent influenza seasons. In this test phase, the ensemble methods
showed overall performance that was similar to the best of the component
models, but offered more consistent performance across seasons than the
component models. Ensemble methods offer the potential to deliver more reliable
predictions to public health decision makers.Comment: 20 pages, 6 figure
Pandemetrics: systematically assessing, monitoring, and controlling the evolution of a pandemic
The still ongoing pandemic of SARS-CoV-2 virus and COVID-19 disease, affecting the population worldwide, has demonstrated the need of more accurate methodologies for assessing, monitoring, and controlling an outbreak of such devastating proportions. Authoritative attempts have been made in traditional fields of medicine (epidemiology, virology, infectiology) to address these shortcomings, mainly by relying on mathematical and statistical modeling. However, here, we propose approaching the methodological work from a different, and to some extent alternative, standpoint. Applied systematically, the concepts and tools of statistical engineering and quality management, developed not only in healthcare settings, but also in other scientific contexts, can be very useful in assessing, monitoring, and controlling pandemic events. We propose a methodology based on a set of tools and techniques, formulas, graphs, and tables to support the decision-making concerning the management of a pandemic like COVID-19. This methodological body is hereby named Pandemetrics. This name intends to emphasize the peculiarity of our approach to measuring, and graphically presenting the unique context of the COVID-19 pandemic
Data-Centric Epidemic Forecasting: A Survey
The COVID-19 pandemic has brought forth the importance of epidemic
forecasting for decision makers in multiple domains, ranging from public health
to the economy as a whole. While forecasting epidemic progression is frequently
conceptualized as being analogous to weather forecasting, however it has some
key differences and remains a non-trivial task. The spread of diseases is
subject to multiple confounding factors spanning human behavior, pathogen
dynamics, weather and environmental conditions. Research interest has been
fueled by the increased availability of rich data sources capturing previously
unobservable facets and also due to initiatives from government public health
and funding agencies. This has resulted, in particular, in a spate of work on
'data-centered' solutions which have shown potential in enhancing our
forecasting capabilities by leveraging non-traditional data sources as well as
recent innovations in AI and machine learning. This survey delves into various
data-driven methodological and practical advancements and introduces a
conceptual framework to navigate through them. First, we enumerate the large
number of epidemiological datasets and novel data streams that are relevant to
epidemic forecasting, capturing various factors like symptomatic online
surveys, retail and commerce, mobility, genomics data and more. Next, we
discuss methods and modeling paradigms focusing on the recent data-driven
statistical and deep-learning based methods as well as on the novel class of
hybrid models that combine domain knowledge of mechanistic models with the
effectiveness and flexibility of statistical approaches. We also discuss
experiences and challenges that arise in real-world deployment of these
forecasting systems including decision-making informed by forecasts. Finally,
we highlight some challenges and open problems found across the forecasting
pipeline.Comment: 67 pages, 12 figure
Improving \u3ci\u3eAedes\u3c/i\u3e Mosquito Surveillance and La Crosse Virus Screening in Eastern Tennessee
La Crosse virus (LACV), transmitted by infected Aedes triseriatus, Ae. albopictus, and Ae. japonicus mosquitoes is the leading cause of pediatric arboviral encephalitis. Severe cases of LAC encephalitis occur in individuals 16-years-old or younger and may cause permanent neurological damage or fatality. No vaccines exist making mosquito control and disease prevention crucial to public health. Effective screening and surveillance practices are key components to these goals. While a number of standard mosquito surveillance methods exist, continuous testing and improved understanding of vector biology to determine the best ways to implement these methods is important. Additionally, the current standard for screening LACV, RT-PCR, is time consuming, expensive, and inaccessible by many laboratories. I hypothesized that different LACV vectors would be active at different times (objective 1) and that a more efficient molecular method for virus detection can be developed (objective 2). For objective 1, I collected mosquitoes from 19 sites around Knox County from June-September in 2015 using traps previously found to be effective for monitoring LACV vectors. Nets were changed twice a day during “work” or “off-work” hours (9:00-17:00 or 17:00-9:00). Mosquitoes were identified and trap and time of day recorded. A total of 1,223 Aedes albopictus, 49 Ae. japonicus, and 90 Ae. triseriatus were collected. Significantly more LACV vectors were collected from 17:00-9:00. For objective 2, using a positive control, a reverse transcriptase loop mediated isothermal amplification (RT-LAMP) method of virus detection was developed and a dilution series was conducted to compare the developed assay to the standard. Both assays were found equally effective at detecting LACV, but the RT-LAMP is preferable for cost effectiveness and reduced detection time. This thesis provides research laboratories, health departments, and citizens with important vector surveillance information and an accurate and inexpensive method of screening for the virus. Surveillance information will make it easier for mosquito control districts to effectively monitor vectors. The diagnostic assay can be used in field-lab settings and will provide accurate results in a shorter time than with traditional methods. Together, the increased efficiency in vector surveillance and virus detection provide rapid and accurate results for low cost
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