Selecting Essential Information for Biosurveillance—A Multi-Criteria Decision Analysis

The National Strategy for Biosurveillancedefines biosurveillance as “the process of gathering, integrating, interpreting, and communicating essential information related to all-hazards threats or disease activity affecting human, animal, or plant health to achieve early detection and warning, contribute to overall situational awareness of the health aspects of an incident, and to enable better decision-making at all levels.” However, the strategy does not specify how “essential information” is to be identified and integrated into the current biosurveillance enterprise, or what the metrics qualify information as being “essential”. Thequestion of data stream identification and selection requires a structured methodology that can systematically evaluate the tradeoffs between the many criteria that need to be taken in account. Multi-Attribute Utility Theory, a type of multi-criteria decision analysis, can provide a well-defined, structured approach that can offer solutions to this problem. While the use of Multi-Attribute Utility Theoryas a practical method to apply formal scientific decision theoretical approaches to complex, multi-criteria problems has been demonstrated in a variety of fields, this method has never been applied to decision support in biosurveillance.We have developed a formalized decision support analytic framework that can facilitate identification of “essential information” for use in biosurveillance systems or processes and we offer this framework to the global BSV community as a tool for optimizing the BSV enterprise. To demonstrate utility, we applied the framework to the problem of evaluating data streams for use in an integrated global infectious disease surveillance system.     

Global mapping of infectious disease

The primary aim of this review was to evaluate the state of knowledge of the geographical distribution of all infectious diseases of clinical significance to humans. A systematic review was conducted to enumerate cartographic progress, with respect to the data available for mapping and the methods currently applied. The results helped define the minimum information requirements for mapping infectious disease occurrence, and a quantitative framework for assessing the mapping opportunities for all infectious diseases. This revealed that of 355 infectious diseases identified, 174 (49%) have a strong rationale for mapping and of these only 7 (4%) had been comprehensively mapped. A variety of ambitions, such as the quantification of the global burden of infectious disease, international biosurveillance, assessing the likelihood of infectious disease outbreaks and exploring the propensity for infectious disease evolution and emergence, are limited by these omissions. An overview of the factors hindering progress in disease cartography is provided. It is argued that rapid improvement in the landscape of infectious diseases mapping can be made by embracing non-conventional data sources, automation of geo-positioning and mapping procedures enabled by machine learning and information technology, respectively, in addition to harnessing labour of the volunteer ‘cognitive surplus’ through crowdsourcing.     

A Review of Evaluations of Electronic Event-Based Biosurveillance Systems

Electronic event-based biosurveillance systems (EEBS’s) that use near real-time information from the internet are an increasingly important source of epidemiologic intelligence. However, there has not been a systematic assessment of EEBS evaluations, which could identify key uncertainties about current systems and guide EEBS development to most effectively exploit web-based information for biosurveillance. To conduct this assessment, we searched PubMed and Google Scholar to identify peer-reviewed evaluations of EEBS’s. We included EEBS’s that use publicly available internet information sources, cover events that are relevant to human health, and have global scope. To assess the publications using a common framework, we constructed a list of 17 EEBS attributes from published guidelines for evaluating health surveillance systems. We identified 11 EEBS’s and 20 evaluations of these EEBS’s. The number of published evaluations per EEBS ranged from 1 (Gen-Db, GODsN, MiTAP) to 8 (GPHIN, HealthMap). The median number of evaluation variables assessed per EEBS was 8 (range, 3–15). Ten published evaluations contained quantitative assessments of at least one key variable. No evaluations examined usefulness by identifying specific public health decisions, actions, or outcomes resulting from EEBS outputs. Future EEBS assessments should identify and discuss critical indicators of public health utility, especially the impact of EEBS’s on public health response.     

Monitoring and surveillance for rare health-related events: a review from the veterinary perspective

Disease monitoring and surveillance systems (MOSSs) have become one of the major components of veterinary activity. Such systems are used to assess the existing levels of prevalence, the effectiveness of control programmes and, after disease eradication, to document the continued absence of disease from a given region or zone. With decreasing disease or infection prevalence, traditional approaches become less reliable and increasingly costly. The objective of this work was to summarize and discuss methodological issues related to veterinary (animal health) MOSSs. There are considerable inconsistencies in the use of the terms 'monitoring' and 'surveillance'. Passive as well as active MOSS have their disadvantages when used for rare health-related events such as emerging and re-emerging diseases. There is a need for evaluation and improvement of these approaches. Integrated systems that call for the use of several parallel surveillance activities seem to be the favoured approach, and analytical methods to combine MOSS data from various sources into a population prevalence, or probability of disease freedom, are under development. The health and safety of the animal and human generations depends on our continuous ability to detect, monitor and control newly emerging or re-emerging livestock diseases and zoonoses rapidly. Uniform surveillance definitions, sound scientifically based approaches that use the resources and data available, and a pool of researchers and veterinary public health officials with sufficient training in epidemiology, are critically important to handle this challenging task.     

Nephele streaming: stream processing under QoS constraints at scale

The ability to process large numbers of continuous data streams in a near-real-time fashion has become a crucial prerequisite for many scientific and industrial use cases in recent years. While the individual data streams are usually trivial to process, their aggregated data volumes easily exceed the scalability of traditional stream processing systems. At the same time, massively-parallel data processing systems like MapReduce or Dryad currently enjoy a tremendous popularity for data-intensive applications and have proven to scale to large numbers of nodes. Many of these systems also provide streaming capabilities. However, unlike traditional stream processors, these systems have disregarded QoS requirements of prospective stream processing applications so far. In this paper we address this gap. First, we analyze common design principles of today’s parallel data processing frameworks and identify those principles that provide degrees of freedom in trading off the QoS goals latency and throughput. Second, we propose a highly distributed scheme which allows these frameworks to detect violations of user-defined QoS constraints and optimize the job execution without manual interaction. As a proof of concept, we implemented our approach for our massively-parallel data processing framework Nephele and evaluated its effectiveness through a comparison with Hadoop Online. For an example streaming application from the multimedia domain running on a cluster of 200 nodes, our approach improves the processing latency by a factor of at least 13 while preserving high data throughput when needed.     

Molecular detection of vertebrates in stream water: a demonstration using Rocky Mountain tailed frogs and Idaho giant salamanders

Stream ecosystems harbor many secretive and imperiled species, and studies of vertebrates in these systems face the challenges of relatively low detection rates and high costs. Environmental DNA (eDNA) has recently been confirmed as a sensitive and efficient tool for documenting aquatic vertebrates in wetlands and in a large river and canal system. However, it was unclear whether this tool could be used to detect low-density vertebrates in fast-moving streams where shed cells may travel rapidly away from their source. To evaluate the potential utility of eDNA techniques in stream systems, we designed targeted primers to amplify a short, species-specific DNA fragment for two secretive stream amphibian species in the northwestern region of the United States (Rocky Mountain tailed frogs, Ascaphus montanus, and Idaho giant salamanders, Dicamptodon aterrimus). We tested three DNA extraction and five PCR protocols to determine whether we could detect eDNA of these species in filtered water samples from five streams with varying densities of these species in central Idaho, USA. We successfully amplified and sequenced the targeted DNA regions for both species from stream water filter samples. We detected Idaho giant salamanders in all samples and Rocky Mountain tailed frogs in four of five streams and found some indication that these species are more difficult to detect using eDNA in early spring than in early fall. While the sensitivity of this method across taxa remains to be determined, the use of eDNA could revolutionize surveys for rare and invasive stream species. With this study, the utility of eDNA techniques for detecting aquatic vertebrates has been demonstrated across the majority of freshwater systems, setting the stage for an innovative transformation in approaches for aquatic research.     

Biosurveillance where it happens: state and local capabilities and needs

In recent years, improved biosurveillance has become a bipartisan national security priority. As has been pointed out by the National Biosurveillance Advisory Subcommittee and others, building a national biosurveillance enterprise requires having strong biosurveillance systems at the state and local levels, and additional policies are needed to strengthen their biosurveillance capabilities. Because of the foundational role that state and local health departments play in biosurveillance, we sought to determine to what extent state and local health departments have the right capabilities in place to provide the information needed to detect and manage an epidemic or public health emergency-both for state and local outbreak management and for reporting to federal agencies during national public health crises. We also sought to identify those policies or actions that would improve state and local biosurveillance and make recommendations to federal policymakers who are interested in improving national biosurveillance capabilities.     

Climate change and alpine stream biology: progress,challenges, and opportunities for the future

In alpine regions worldwide, climate change is dramatically altering ecosystems and affecting biodiversity in many ways. For streams, receding alpine glaciers and snowfields, paired with altered precipitation regimes, are driving shifts in hydrology, species distributions, basal resources, and threatening the very existence of some habitats and biota. Alpine streams harbour substantial species and genetic diversity due to significant habitat insularity and environmental heterogeneity. Climate change is expected to affect alpine stream biodiversity across many levels of biological resolution from micro‐ to macroscopic organisms and genes to communities. Herein, we describe the current state of alpine stream biology from an organism‐focused perspective. We begin by reviewing seven standard and emerging approaches that combine to form the current state of the discipline. We follow with a call for increased synthesis across existing approaches to improve understanding of how these imperiled ecosystems are responding to rapid environmental change. We then take a forward‐looking viewpoint on how alpine stream biologists can make better use of existing data sets through temporal comparisons, integrate remote sensing and geographic information system (GIS) technologies, and apply genomic tools to refine knowledge of underlying evolutionary processes. We conclude with comments about the future of biodiversity conservation in alpine streams to confront the daunting challenge of mitigating the effects of rapid environmental change in these sentinel ecosystems.     

Xenosurveillance: A Novel Mosquito-Based Approach for Examining the Human-Pathogen Landscape

BackgroundGlobally, regions at the highest risk for emerging infectious diseases are often the ones with the fewest resources. As a result, implementing sustainable infectious disease surveillance systems in these regions is challenging. The cost of these programs and difficulties associated with collecting, storing and transporting relevant samples have hindered them in the regions where they are most needed. Therefore, we tested the sensitivity and feasibility of a novel surveillance technique called xenosurveillance. This approach utilizes the host feeding preferences and behaviors of Anopheles gambiae, which are highly anthropophilic and rest indoors after feeding, to sample viruses in human beings. We hypothesized that mosquito bloodmeals could be used to detect vertebrate viral pathogens within realistic field collection timeframes and clinically relevant concentrations.Conclusions/SignificanceTogether, these data demonstrate the feasibility of xenosurveillance and in doing so validated a simple and non-invasive surveillance tool that could be used to complement current biosurveillance efforts.     

SAGES: a suite of freely-available software tools for electronic disease surveillance in resource-limited settings

Public health surveillance is undergoing a revolution driven by advances in the field of information technology. Many countries have experienced vast improvements in the collection, ingestion, analysis, visualization, and dissemination of public health data. Resource-limited countries have lagged behind due to challenges in information technology infrastructure, public health resources, and the costs of proprietary software. The Suite for Automated Global Electronic bioSurveillance (SAGES) is a collection of modular, flexible, freely-available software tools for electronic disease surveillance in resource-limited settings. One or more SAGES tools may be used in concert with existing surveillance applications or the SAGES tools may be used en masse for an end-to-end biosurveillance capability. This flexibility allows for the development of an inexpensive, customized, and sustainable disease surveillance system. The ability to rapidly assess anomalous disease activity may lead to more efficient use of limited resources and better compliance with World Health Organization International Health Regulations.     

The key to enabling biosurveillance is cooperative technology development

The world population will continue to face biological threats, whether they are naturally occurring or intentional events. The speed with which diseases can emerge and spread presents serious challenges, because the impact on public health, the economy, and development can be huge. The U.S. government recognizes that global public health can also have an impact on national security. This global perspective manifests itself in U.S. policy documents that clearly articulate the importance of biosurveillance in providing early warning, detection, and situational awareness of infectious disease threats in order to mount a rapid response and save lives. In this commentary, we suggest that early recognition of infectious disease threats, whether naturally occurring or man-made, requires a globally distributed array of interoperable hardware and software fielded in sufficient numbers to create a network of linked collection nodes. We argue that achievement of this end state will require a degree of cooperation that does not exist at this time-either across the U.S. federal government or among our global partners. Successful fielding of a family of interoperable technologies will require interagency research, development, and purchase ("acquisition") of biosurveillance systems through cooperative ventures that likely will involve our strategic allies and public-private partnerships. To this end, we propose leveraging an existing federal interagency group to integrate the acquisition of technologies to enable global biosurveillance.     

Assessing channel-forming characteristics of an impacted headwater stream in Ohio, USA

Since the start of European settlement in Ohio the landscape has been greatly modified to accommodate anthropogenic land uses. This, in turn, has altered the hydrologic characteristics of many streams from those that are stable channel systems in dynamic equilibrium to those of modified incised channels that are more characteristic of anthropogenic influences. As stream restoration practices gain importance and prevalence there is a need to prioritize project funds based on the restoration potential of a stream. Regional curves that relate channel-forming geometry to drainage area, and applications of channel-forming discharge concepts, are tools that are used in making restoration and management decisions. Regional curves are usually developed for unmodified natural streams and/or gaged river systems and not for small, ungaged modified channels that are common throughout agricultural areas or mixed use watersheds. This study focuses on the development and potential usefulness of regional curves and channel-forming discharge concepts for Mac-o-chee Creek, a small, ungaged headwater stream system in Ohio. Results show that these approaches and a weight of evidence analysis could be useful in providing information for management and restoration decisions on these small stream systems as well as aiding in the assessment and modeling of trends within these streams with dynamic hydrologic conditions due to changes in land use/land cover.     

Food web complexity and allometric scaling relationships in stream mesocosms: implications for experimentation

1. Mesocosms are used extensively by ecologists to gain a mechanistic understanding of ecosystems based on the often untested assumption that these systems can replicate the key attributes of natural assemblages. 2. Previous investigations of stream mesocosm utility have explored community composition, but here for the first time, we extend the approach to consider the replicability and realism of food webs in four outdoor channels (4 m(2)). 3. The four food webs were similarly complex, consisting of diverse assemblages (61-71 taxa) with dense feeding interactions (directed connectance 0.09-0.11). Mesocosm food web structural attributes were within the range reported for 82 well-characterized food webs from natural streams and rivers. When compared with 112 additional food webs from standing freshwater, marine, estuarine and terrestrial environments, stream food webs (including mesocosms) had similar characteristic path lengths, but typically lower mean food chain length and exponents for the species-link relationship. 4. Body size (M) abundance (N) allometric scaling coefficients for trivariate taxonomic mesocosm food webs (-0.53 to -0.49) and individual size distributions (-0.60 to -0.58) were consistent and similar to those from natural systems, suggesting that patterns of energy flux between mesocosm consumers and resources were realistic approximations. 5. These results suggest that stream mesocosms of this scale can support replicate food webs with a degree of biocomplexity that is comparable to 'natural' streams. The findings highlight the potential value of mesocosms as model systems for performing experimental manipulations to test ecological theories, at spatiotemporal scales of relevance to natural ecosystems.     

Status assessment in acid-sensitive and non-acid-sensitive Maryland coastal planin streams using an integrated biological,chemical, physical,and land-use approach

This study was designed to: (1) evaluate the ecological status of acid-sensitive and non acid-sensitive Maryland coastal plain streams using biological (Index of biotic Integrity [IBI] for fish), chemical and physical habitat conditions; (2) determine if a low IBI for coastal plain stream fish can be related to stream sensitivity from acidic inputs and (3) correlate land use activities and watershed size in the coastal plain streams with biological, chemical and physical conditions. IBI values obtained using 12 community metrics for Maryland coastal plain stream fish demonstrated that there were no significant differences in these values when acid-sensitive and non-acid-sensitive streams were compared. However, other complementary data in acid-sensitive streams such as absence of the acid-sensitive species, blacknose dace and higher numbers and biomass of tolerant species suggested that these streams may be impacted. IBI values were also found to be negatively correlated with various trace metals in acid-sensitive streams but not in non-acid-sensitive areas. Chemical conditions such as trace metals and nutrients were associated with land use activities. Highest concentrations of trace metals (chromium, nickel, and cadmium) were found in streams with the highest percentage of low residential housing. Nitrate concentrations were significantly higher in streams found in agricultural areas than in forested areas. Agriculturally dominated streams with highest nitrate concentrations (> 10 mg l^-1) also contained the highest percentage of livestock feeding operations. The mean IBI score for streams draining agricultural land was higher than the mean value for forested streams when all streams were compared. However, when several streams that were only marginally forested (< 50%) were removed from the analysis, the IBI scores did not differ significantly by land use. Two physical habitat indices exhibited a strong associated with each other. Each habitat index also correlated with IBI values.     

Overview and application of the AQEM assessment system

The main objective of the European Union (EU) funded project AQEM¹was to develop a framework of an assessment system for streams in Europe based on benthic macroinvertebrates that fulfils the requirements of the EU Water Framework Directive. Initial assessment methods for 28 European stream types and more generally applicable tools for stream biomonitoring in Europe were generated. The development of the system was based on a newly collected data set covering stream types in Austria, the Czech Republic, Germany, Greece, Italy, The Netherlands, Portugal and Sweden. Altogether, 901 benthic invertebrate samples were taken using a standardised multi-habitat sampling procedure and a large number of parameters describing the streams and their catchments was recorded for all sampling sites. From the stream and catchment characteristics measures of stress were derived. A large number of metrics was tested independently for each of the stream types, to identify the response of each metric to degradation of a site. This process resulted in up to 18 core metrics for the individual stream types, which were combined into a different multimetric index in each country. The multimetric AQEM assessment system is used to classify a stream stretch into an Ecological Quality Class ranging from 5 (high quality) to 1 (bad quality) and often provides information on the possible causes of degradation. AQEM provides a taxa list of 9557 European macroinvertebrate taxa with associated autecological information, a software package for performing all the calculations necessary for applying the multimetric AQEM assessment system and a manual describing all aspects of the application of the system from site selection to data interpretation.     

Mouse-human comparative map resources on the Web

Comparative maps have been a valuable resource for extrapolating biological information among organisms. The relationship between mouse and human maps provides a framework for integrating information from each species and thereby increasing the utility of all available data such as gene location, structure and function. This review describes the various public resources, both databases and web sites, containing genome-wide mouse-human comparative map information available through the World-Wide Web. We will focus on the use and applicability of these resources in their current form and consider future potential directions.     

A complete categorization of multiscale models of infectious disease systems

Modelling of infectious disease systems has entered a new era in which disease modellers are increasingly turning to multiscale modelling to extend traditional modelling frameworks into new application areas and to achieve higher levels of detail and accuracy in characterizing infectious disease systems. In this paper we present a categorization framework for categorizing multiscale models of infectious disease systems. The categorization framework consists of five integration frameworks and five criteria. We use the categorization framework to give a complete categorization of host-level immuno-epidemiological models (HL-IEMs). This categorization framework is also shown to be applicable in categorizing other types of multiscale models of infectious diseases beyond HL-IEMs through modifying the initial categorization framework presented in this study. Categorization of multiscale models of infectious disease systems in this way is useful in bringing some order to the discussion on the structure of these multiscale models.     

Fluvial landscape ecology: addressing uniqueness within the river discontinuum

1. As rivers and streams are patchy and strongly hierarchical systems, a hierarchical patch dynamics perspective can be used as a framework for visualising interactions between structure and function in fluvial landscapes. The perspective is useful for addressing fundamental attributes of lotic ecosystems, such as heterogeneity, hierarchy, directionality and process feedback occurring across spatial scales and for illustrating spatio‐temporal linkages between disparate concepts in lotic system ecology such as the River Continuum Concept, the Serial Discontinuity Concept, the Flood Pulse Concept and the Hyporheic Corridor Concept. 2. At coarse spatial scales, the hierarchical patch dynamics perspective describes each river network as a unique, patchy discontinuum from headwaters to mouth. The discontinuum is comprised of a longitudinal series of alternating stream segments with different geomorphological structures. Each confluence in the steam network further punctuates the discontinuum because the sudden change in stream characteristics can create a `gap' in the expected pattern of downstream transitions. The discontinuum view recognises general trends in habitat characteristics along the longitudinal profile, but creates a framework for studying and understanding the ecological importance of each stream's individual pattern of habitat transitions along longitudinal, lateral or vertical vectors at any scale. 3. Object‐oriented modelling and programming techniques provide a means for developing robust, quantitative simulation models that describe the dynamic structure of patch hierarchies. Such models can simulate how the structure and function of lotic ecosystems are influenced by the landscape context of the system (the ecological conditions within which the system is set) and the metastructure (structural characteristics and juxtaposition) of finer‐scale patches comprising the system. 4. A simple object‐oriented, multiscale, discontinuum model of solute transformation and biological response along a stream channel illustrates how changing the branching pattern of a stream and the arrangement of its component patches along the downstream profile will result in substantial changes in predicted patterns of solute concentration and biotic community structure. 5. The importance of context, structure, and metastructure in determining lotic ecosystem function serves to underscore 27 ) concept that `every stream is likely to be individual.' Advancing the discipline of fluvial landscape ecology provides an excellent opportunity to develop general concepts and tools that address the individual character of each stream network and integrate the concept of `uniqueness within the river discontinuum' into our ecological understanding of rivers and streams.     

A probabilistic framework for nutrient uptake length

The nutrient uptake length, the average displacement of a nutrient in a stream before being taken up by the biota, is an important quantity to characterize and compare streams and rivers, or to quantify certain aspects of their related ecosystems. This concept has been widely used for almost 30 years now, and uptake lengths have been estimated for several nutrients in many systems, but it also suffers from a number of limitations, one of them being the requirement of a spatially homogeneous stream or river. We combine recently advocated, transport-based models of stream processes with current concepts of dispersal theory into a novel framework for nutrient uptake length. The framework is based on the theory for dispersal kernels in terrestrial systems, where the entire distribution of dispersal distances is calculated and not only the average. Within this framework, we can re-derive all previous results and formulae for uptake length, and we can include spatially heterogeneous stream environments. In addition, we propose a number of new characteristic quantities that can complement nutrient uptake length when evaluating the health of a stream system or the impact of a source of nutrients. We illustrate our method with two examples of spatially non-homogeneous streams: point-source input of nutrients (e.g., wastewater treatment plant) and diffuse lateral input (e.g., agricultural run-off), and we show how to measure the relative contribution of the two sources to the uptake length and other characteristics.