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All sources NASA NTRS DOE OSTI

DOE OSTI2017

NBIC Biofeeds: A Digital Tool for Open Source Biosurveillance across Federal Agencies

The National Biosurveillance Integration Center (NBIC) is developing a scalable, flexible open source data collection, analysis, and dissemination tool to support biosurveillance operations by the U.S. Department of Homeland Security (DHS) and its federal interagency partners. The NBIC integrates, analyzes, and distributes key information about health and disease events to help ensure the nation’s responses are well-informed, save lives, and minimize economic impact. NBIC serves as a bridge between Federal, State, Local, Territorial, and Tribal entities to conduct biosurveillance across human, animal, plant, and environmental domains. The integration of information enables early warning and shared situational awareness of biological events to inform critical decisions directing response and recovery efforts. To meet its mission objectives, NBIC utilizes a variety of datasets, including open source information, to provide comprehensive coverage of biological events occurring across the globe. NBIC Biofeeds is a digital tool designed to improve the efficiency of reviewing and analyzing large volumes of open source reporting by biosurveillance analysts on a daily basis; moreover, the system provides a mechanism to disseminate tailored feeds allowing NBIC to better meet the specific information needs of individual, interagency partners. The tool is currently under development by the Department of Energy (DOE), Pacific Northwest National Laboratory (PNNL)and it is in a testing and evaluation phase supported by NBIC biosurveillance subject matter experts. Integration with the Defense Threat Reduction Agency (DTRA), Biosurveillance Ecosystem(BSVE) is also underway. NBIC Biofeeds Version 1 is expected to be fully operational in Fiscal Year 2017. The PNNL is applying agile methodology to streamline the build of NBIC Biofeeds to specifications required for operational use by NBIC and its federal interagency partners. Biosurveillance, analytics, and system engineering subject matter experts provide guidance on the implementation of features in the tool to ensure functionality aligns with operational workflows and production support. PNNL is leveraging software from a previous government effort to repurpose the technology to meet NBIC needs. NBIC Biofeeds incorporates the open source, document-orientated MongoDB database to capture user- and system-generated metadata on hundreds of thousands of records, in part, to establish baselines to aid prospective and retrospective analysis on emerging biological events. NBIC Biofeeds integrates a biosurveillance taxonomy (uniquely developed by NBIC),which includes input from interagency partners to recognize critical characteristics of a biological event. In NBIC Biofeeds Version1, metadata capture of reported events is done manually by NBIC analysts; however, moving forward in Version 2, the tool will be further automated to flag significant reporting on biological events with a human remaining in the loop to confirm the validity of the system-generated tags. To serve as a one-stop tool for open source biosurveillance, NBIC Biofeeds automatically harvests information from thousands of websites, utilizing third party aggregators, paid subscriptions to data feeds, and scraping of high priority sources. Users can develop desired queries for automatic updating, leverage a unique review and curation mechanism, and further analyze data from topical, geographic, and temporal visualization features in the tool. To meet NBIC’s information sharing needs, the tool allows for design of tailored RSS feeds and electronic message-based delivery of analysis on biological events, intended for recipients in the government with unique missions around human, animal, plant, and environmental health. Through current testing and evaluation – underway by biosurveillance subject matter experts – NBIC Biofeeds is demonstrating value in supporting open source biosurveillance by the Center for more rapid recognition and sharing of key event characteristics. Centralizing access and analysis of this data set into a single system is increasing the efficiency of daily, global biosurveillance, while enhancing the value of information identified through use of the querying, curation, and production support features in the tool.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

NBIC Biofeeds: Deploying a New, Digital Tool for Open Source Biosurveillance across Federal Agencies

The National Biosurveillance Integration Center (NBIC) is deploying a scalable, flexible open source data collection, analysis, and dissemination tool to support biosurveillance operations by the U.S. Department of Homeland Security (DHS) and its federal interagency partners.IntroductionNBIC integrates, analyzes, and distributes key information about health and disease events to help ensure the nation’s responses are well-informed, save lives, and minimize economic impact. To meet its mission objectives, NBIC utilizes a variety of data sets, including open source information, to provide comprehensive coverage of biological events occurring across the globe. NBIC Biofeeds is a digital tool designed to improve the efficiency of analyzing large volumes of open source reporting and increase the number of relevant insights gleaned from this dataset. Moreover, the tool provides a mechanism to disseminate tailored, electronic message notifications in near-real time so that NBIC can share specific information of interest to its interagency partners in a timely manner. NBIC intends to implement operational use of the capability in FY 2018. The core components of the system are data collection, curation, and dissemination of information deemed important by NBIC subject matter experts. NBIC Biofeeds has captured information from more than 70,000 unique sources published from around the globe and presents, on average, 9,000 new biosurveillance-relevant articles to users each day. NBIC leverages a variety of data feeds, including third party aggregators like Google and subscription-based feeds such as HealthMap, as well as Really Simple Syndication (RSS) feeds and web-scraping of highly relevant sources. The NBIC biosurveillance taxonomy imbedded in the tool consists of more than 600 metadata targets that cover key information for understanding the significance of an active biological event, including etiologic agents, impact to humans and animals (e.g., infection severity, healthcare workers involved, type of host), social disruption, infrastructure strain, countermeasures engaged, and ‘red flag’ characteristics (e.g., pathogen appearance in a new geographic area, unusual clinical signs). This taxonomy serves as a foundation for data curation and can be tailored by NBIC partners to more directly meet their own mission objectives. At this time, metadata is predominately captured by NBIC analysts, who manually tag information, which triggers the population of three automatically-disseminated products from the tool: 1) the NBIC Daily Biosurveillance Review, 2) immediate and daily summary email notifications, and 3) custom-designed RSS feeds. These products are meant for individual recipients in the federal interagency and for consumption by other biosurveillance information technology systems, such as the Department of Defense, Defense Threat Reduction Agency (DTRA) Biosurveillance Ecosystem (BSVE). NBIC is working in partnership with DTRA to integrate NBIC Biofeeds as an application directly into the BSVE and further develop the BSVE as an all-in-one platform for biosurveillance data analytics. To improve the efficiency and effectiveness of gaining insights using NBIC Biofeeds, developers of the tool at the Pacific Northwest National Laboratory (PNNL) are researching and testing a variety of advanced analytics techniques focused on: 1) article relevancy ratings to improve the review of queried data, 2) significance ratings to elucidate the perceived severity of an event based on reported characteristics, 3) full-text article retrieval and storage for improved machine-tagging, and 4) anomaly detection for emerging threats. Testing and implementation of new analytic capabilities in NBIC Biofeeds is planned for this fiscal year. NBIC Biofeeds was developed to serve as a sophisticated and powerful open source biosurveillance technology of value to the federal government by providing information to stakeholders conducting open source biosurveillance as well as those consuming biosurveillance information. In FY 2018, NBIC Biofeeds will begin operational use by NBIC and an initial set of users in various federal agencies. User accounts for testing purposes will be available to other federal partners, and a broad scope of federal stakeholders can receive products directly from NBIC Biofeeds based on their interests. NBIC Biofeeds is expected to enable more rapid recognition and enhanced analysis of emerging biological events by NBIC analysts. NBIC anticipates other federal agencies with biosurveillance missions will find this technology of value and intends to offer use of the platform to those federal partners that can benefit from access to the tool and information generated from NBIC Biofeeds.

NBIC↗

DOE OSTI2014

Advancing a Framework to Enable Characterization and Evaluation of Data Streams Useful for Biosurveillance

In recent years, biosurveillance has become the buzzword under which a diverse set of ideas and activities regarding detecting and mitigating biological threats are incorporated depending on context and perspective. Increasingly, biosurveillance practice has become global and interdisciplinary, requiring information and resources across public health, One Health, and biothreat domains. Even within the scope of infectious disease surveillance, multiple systems, data sources, and tools are used with varying and often unknown effectiveness. Evaluating the impact and utility of state-of-the-art biosurveillance is, in part, confounded by the complexity of the systems and the information derived from them. We present a novel approach conceptualizing biosurveillance from the perspective of the fundamental data streams that have been or could be used for biosurveillance and to systematically structure a framework that can be universally applicable for use in evaluating and understanding a wide range of biosurveillance activities. Moreover, the Biosurveillance Data Stream Framework and associated definitions are proposed as a starting point to facilitate the development of a standardized lexicon for biosurveillance and characterization of currently used and newly emerging data streams. Criteria for building the data stream framework were developed from an examination of the literature, analysis of information on operational infectious disease biosurveillance systems, and consultation with experts in the area of biosurveillance. To demonstrate utility, the framework and definitions were used as the basis for a schema of a relational database for biosurveillance resources and in the development and use of a decision support tool for data stream evaluation.

47 OTHER INSTRUMENTATION↗

DOE OSTI2016

A Conceptual Architecture for National Biosurveillance: Moving Beyond Situational Awareness to Enable Digital Detection of Emerging Threats

Despite numerous calls for improvement, the U.S. biosurveillance enterprise remains a patchwork of uncoordinated systems that fail to take advantage of the rapid progress in information processing, communication, and analytics made in the past decade. By synthesizing components from the extensive biosurveillance literature, we propose a conceptual framework for a national biosurveillance architecture and provide suggestions for implementation. The framework differs from the current federal biosurveillance development pathway in that it is not focused on systems useful for “situational awareness,” but is instead focused on the long-term goal of having true warning capabilities. Therefore, a guiding design objective is the ability to digitally detect emerging threats that span jurisdictional boundaries, because attempting to solve the most challenging biosurveillance problem first provides the strongest foundation to meet simpler surveillance objectives. Core components of the vision are: (1) a whole-of-government approach to support currently disparate federal surveillance efforts that have a common data need, including those for food safety, vaccine and medical product safety, and infectious disease surveillance; (2) an information architecture that enables secure, national access to electronic health records, yet does not require that data be sent to a centralized location for surveillance analysis; (3) an inference architecture that leverages advances in ‘big data’ analytics and learning inference engines—a significant departure from the statistical process control paradigm that underpins nearly all current syndromic surveillance systems; and, (4) an organizational architecture with a governance model aimed at establishing national biosurveillance as a critical part of the U.S. national infrastructure. Although it will take many years to implement, and a national campaign of education and debate to acquire public buy-in for such a comprehensive system, the potential benefits warrant increased consideration within the U.S. government.

45 MILITARY TECHNOLOGY, WEAPONRY, AND NATIONAL DEF↗

DOE OSTI2021

How Cooperative Engagement Programs Strengthen Sequencing Capabilities for Biosurveillance and Outbreak Response

The threat of emerging and re-emerging infectious diseases continues to be a challenge to public and global health security. Cooperative biological engagement programs act to build partnerships and collaborations between scientists and health professionals to strengthen capabilities in biosurveillance. Biosurveillance is the systematic process of detecting, reporting, and responding to especially dangerous pathogens and pathogens of pandemic potential before they become outbreaks, epidemics, and pandemics. One important tool in biosurveillance is next generation sequencing. Expensive sequencing machines, reagents, and supplies make it difficult for countries to adopt this technology. Cooperative engagement programs help by providing funding for technical assistance to strengthen sequencing capabilities. Through workshops and training, countries are able to learn sequencing and bioinformatics, and implement these tools in their biosurveillance programs. Cooperative programs have an important role in building and sustaining collaborations among institutions and countries. One of the most important pieces in fostering these collaborations is trust. Trust provides the confidence that a successful collaboration will benefit all parties involved. With sequencing, this enables the sharing of pathogen samples and sequences. Obtaining global sequencing data helps to identify unknown etiological agents, track pathogen evolution and infer transmission networks throughout the duration of a pandemic. Having sequencing technology in place for biosurveillance generates the capacity to provide real-time data to understand and respond to pandemics. We highlight the need for these programs to continue to strengthen sequencing in biosurveillance. By working together to strengthen sequencing capabilities, trust can be formed, benefitting global health in the face of biological threats.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Biosurveillance Data Stream Framework: A Novel Approach to Characterization and Evaluation

Multiple data sources are used in a variety of biosurveillance systems. With the advent of new technologies, globalization, high performance computing, and "big data" opportunities, there are seemingly unlimited potential data streams that could be useful in biosurveillance. Data streams have not been universally defined in either the literature or by specific biosurveillance systems. Furthermore, the definitions and framework that we have developed enable a characterization methodology that facilitates understanding of data streams and can be universally applicable for use in evaluating and understanding a wide range of biosurveillance activities- filling a gap recognized in both the public health and biosurveillance communities.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens

Viral pathogens can rapidly evolve, adapt to novel hosts, and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a novel computational approach called FEVER (Fast Evaluation of Viral Emerging Risks) to design assays that simultaneously accomplish: 1) broad-coverage biosurveillance of an entire group of viruses, 2) accurate diagnosis of an outbreak strain, and 3) mutation typing to detect variants of public health importance. We demonstrate the application of FEVER to generate assays to simultaneously 1) detect sarbecoviruses for biosurveillance; 2) diagnose infections specifically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and 3) perform rapid mutation typing of the D614G SARS-CoV-2 spike variant associated with increased pathogen transmissibility. These FEVER assays had a high in silico recall (predicted positive) up to 99.7% of 525,708 SARS-CoV-2 sequences analyzed and displayed sensitivities and specificities as high as 92.4% and 100% respectively when validated in 100 clinical samples. The D614G SARS-CoV-2 spike mutation PCR test was able to identify the single nucleotide identity at position 23,403 in the viral genome of 96.6% SARS-CoV-2 positive samples without the need for sequencing. This study demonstrates the utility of FEVER to design assays for biosurveillance, diagnostics, and mutation typing to rapidly detect, track, and mitigate future outbreaks and pandemics caused by emerging viruses.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2018

Text-based Analytics for Biosurveillance

The ability to prevent, mitigate, or control a biological threat depends on how quickly the threat is identified and characterized. Ensuring the timely delivery of data and analytics is an essential aspect of providing adequate situational awareness in the face of a disease outbreak. This chapter outlines an analytic pipeline for supporting an advanced early warning system that can integrate multiple data sources and provide situational awareness of potential and occurring disease situations. The pipeline, includes real-time automated data analysis founded on natural language processing (NLP), semantic concept matching, and machine learning techniques, to enrich content with metadata related to biosurveillance. Online news articles are presented as an example use case for the pipeline, but the processes can be generalized to any textual data. In this chapter, the mechanics of a streaming pipeline are briefly discussed as well as the major steps required to provide targeted situational awareness. The text-based analytic pipeline includes various processing steps as well as identifying article relevance to biosurveillance (e.g., relevance algorithm) and article feature extraction (who, what, where, why, how, and when). The ability to prevent, mitigate, or control a biological threat depends on how quickly the threat is identified and characterized. Ensuring the timely delivery of data and analytics is an essential aspect of providing adequate situational awareness in the face of a disease outbreak. This chapter outlines an analytic pipeline for supporting an advanced early warning system that can integrate multiple data sources and provide situational awareness of potential and occurring disease situations. The pipeline, includes real-time automated data analysis founded on natural language processing (NLP), semantic concept matching, and machine learning techniques, to enrich content with metadata related to biosurveillance. Online news articles are presented as an example use case for the pipeline, but the processes can be generalized to any textual data. In this chapter, the mechanics of a streaming pipeline are briefly discussed as well as the major steps required to provide targeted situational awareness. The text-based analytic pipeline includes various processing steps as well as identifying article relevance to biosurveillance (e.g., relevance algorithm) and article feature extraction (who, what, where, why, how, and when).

Biomedical NLP↗

DOE OSTI2018

Machine Learning for Identifying Relevance to Biosurveillance in Multilingual Text

Objective: The objective is to develop an ensemble of machine learning algorithms to identify multilingual, online articles that are relevant to biosurveillance. Language morphology varies widely across languages and must be accounted for when designing algorithms. Here, we compare the performance of a word embedding-based approach and a topic modeling approach with machine learning algorithms to determine the best method for Chinese, Arabic, and French languages. Introduction: Global biosurveillance is an extremely important, yet challenging task. One form of global biosurveillance comes from harvesting open source online data (e.g. news, blogs, reports, RSS feeds). The information derived from this data can be used for timely detection and identification of biological threats all over the world. However, the more inclusive the data harvesting procedure is to ensure that all potentially relevant articles are collected, the more data that is irrelevant also gets harvested. This issue can become even more complex when the online data is in a non-native language. Foreign language articles not only create language-specific issues for Natural Language Processing (NLP), but also add a significant amount of translation costs. Previous work shows success in the use of combinatory monolingual classifiers in specific applications, e.g., legal domain [1]. A critical component for a comprehensive, online harvesting biosurveillance system is the capability to identify relevant foreign language articles from irrelevant ones based on the initial article information collected, without the additional cost of full text retrieval and translation.

Machine learning↗

DOE OSTI2013

An Overview of Internet biosurveillance

Internet biosurveillance utilizes unstructured data from diverse Web-based sources to provide early warning and situational awareness of public health threats. The scope of source coverage ranges from local based media in the vernacular to international media in widely read languages. Internet biosurveillance is a timely modality available to government and public health officials, health care workers, and the public and private sector, serving as a real-time complementary approach to traditional indicator-based public health disease surveillance methods. Internet biosurveillance also supports the broader activity of epidemic intelligence. This review covers the current state of the field of Internet biosurveillance and provides a perspective on the future of the field.

digital disease detection↗

DOE OSTI2017

Landscape of international event-based biosurveillance

Event-based biosurveillance is a scientific discipline in which diverse sources of data, many of which are available from the Internet, are characterized prospectively to provide information on infectious disease events. Biosurveillance complements traditional public health surveillance to provide both early warning of infectious disease events and situational awareness. The Global Health Security Action Group of the Global Health Security Initiative is developing a biosurveillance capability that integrates and leverages component systems from member nations. This work discusses these biosurveillance systems and identifies needed future studies.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2015

ORBiT: Oak Ridge biosurveillance toolkit for public health dynamics

Background: The digitization of health-related information through electronic health records (EHR) and electronic healthcare reimbursement claims and the continued growth of self-reported health information through social media provides both tremendous opportunities and challenges in developing effective biosurveillance tools. With novel emerging infectious diseases being reported across different parts of the world, there is a need to build systems that can track, monitor and report such events in a timely manner. Further, it is also important to identify susceptible geographic regions and populations where emerging diseases may have a significant impact. Methods: In this paper, we present an overview of Oak Ridge Biosurveillance Toolkit (ORBiT), which we have developed specifically to address data analytic challenges in the realm of public health surveillance. In particular, ORBiT provides an extensible environment to pull together diverse, large-scale datasets and analyze them to identify spatial and temporal patterns for various biosurveillance-related tasks. Results: We demonstrate the utility of ORBiT in automatically extracting a small number of spatial and temporal patterns during the 2009-2010 pandemic H1N1 flu season using claims data. These patterns provide quantitative insights into the dynamics of how the pandemic flu spread across different parts of the country. We discovered that the claims data exhibits multi-scale patterns from which we could identify a small number of states in the United States (US) that act as “bridge regions” contributing to one or more specific influenza spread patterns. Similar to previous studies, the patterns show that the south-eastern regions of the US were widely affected by the H1N1 flu pandemic. Several of these south-eastern states act as bridge regions, which connect the north-east and central US in terms of flu occurrences. Conclusions: These quantitative insights show how the claims data combined with novel analytical techniques can provide important information to decision makers when an epidemic spreads throughout the country. Taken together ORBiT provides a scalable and extensible platform for public health surveillance.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2014

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.

47 OTHER INSTRUMENTATION↗

DOE OSTI2013

A Systematic Evaluation of Traditional and Non-Traditional Data Streams for Integrated Global Biosurveillance (Final Report)

Living in a closely connected and highly mobile world presents many new mechanisms for rapid disease spread and in recent years, global disease surveillance has become a high priority. In addition, much like the contribution of non-traditional medicine to curing diseases, non-traditional data streams are being considered of value in disease surveillance. Los Alamos National Laboratory (LANL) was tasked by the Defense Threat Reduction Agency (DTRA)-Joint Science and Technology Office (JSTO) to determine the relevance of data streams for an integrated global biosurveillance system through the use of defined metrics and methodologies. The long-term, broad objective of this project was to provide information and analysis that can be leveraged from existing and developing national and international disease surveillance systems and methodologies, to create a global disease monitoring system, ultimately providing decision makers with timely information to prepare for and mitigate the spread of disease. Specifically, this project evaluated data streams that are currently being used in surveillance systems and data streams that had the potential for being used in surveillance to enable early disease detection. LANL’s focus was on infectious disease surveillance and the term “biosurveillance” will be used to refer to this scope hereafter. Data stream evaluation was conducted using two different methods: Multi criteria decision analysis (MCDA) using a tool called Logical Decisions ® that assigns utility scores to data streams based on weighted metrics and assigned values specific to data stream categories; and a Surveillance Window concept developed at LANL that assigns a window or windows of time specific to a disease within which information coming from various data streams can be determined to have utility. A cross method analysis was performed between the surveillance window based evaluation and the MCDA-based evaluation to identify data stream categories that showed high utility for both methods. In addition, algorithms that can integrate useful data streams to facilitate early disease detection were also examined. This project provided an understanding of data streams relevant to early warning, early detection and monitoring of disease outbreaks. The report describes the results of LANL’s evaluation of 16 data stream categories using the two methods, and recommendations for next steps. The project evolved significantly over its course, and significant improvements in our approaches were made compared to the initial proposed processes. A key outcome of this effort was that LANL was able to bring together several diverse entities involved in disease surveillance and lay the foundation for new collaborations that straddled military and civilian health surveillance. The robust evaluation framework developed by LANL has generated significant interest and there is interest in adopting this framework for various applications both within disease surveillance as well as other public health initiatives. Finally, LANL developed the Biosurveillance Resource Directory (BRD), a relational database that underwent pilot testing by members of the human, plant and animal disease surveillance community. The BRD is intended to be a global resource to facilitate rapid information access.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2021

Digital Biosurveillance for Zoonotic Disease Detection in Kenya

Infectious disease surveillance is crucial for early detection and situational awareness of disease outbreaks. Digital biosurveillance monitors large volumes of open-source data to flag potential health threats. This study investigates the potential of digital surveillance in the detection of the top five priority zoonotic diseases in Kenya: Rift Valley fever (RVF), anthrax, rabies, brucellosis, and trypanosomiasis. Open-source disease events reported between August 2016 and October 2020 were collected and key event-specific information was extracted using a newly developed disease event taxonomy. A total of 424 disease reports encompassing 55 unique events belonging to anthrax (43.6%), RVF (34.6%), and rabies (21.8%) were identified. Most events were first reported by news media (78.2%) followed by international health organizations (16.4%). News media reported the events 4.1 (±4.7) days faster than the official reports. There was a positive association between official reporting and RVF events (odds ratio (OR) 195.5, 95% confidence interval (CI); 24.01–4756.43, p < 0.001) and a negative association between official reporting and local media coverage of events (OR 0.03, 95% CI; 0.00–0.17, p = 0.030). This study highlights the usefulness of local news in the detection of potentially neglected zoonotic disease events and the importance of digital biosurveillance in resource-limited settings.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

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

This paper proposes the use of Multi-Attribute Utility Theory to address the issue of identifying and selecting essential information for inclusion into a biosurveillance system or process. Additionally, we developed a decision support framework that can facilitate identifying data streams for use in biosurveillance systems or processes and demonstrated utility by applying the framework to the problem of evaluating data streams for use in an global infectious disease surveillance system.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

What’s in Your Pocket? Trends in Mobile Apps for Biosurveillance and Decision-Making

Mobile applications offer tremendous potential for collecting data for biosurveillance through participatory surveillance and the integration of new and traditional data streams. This panel features epidemiologists, data scientists, and technology partners who will address the full application lifecycle -- from the assessment of the specific demand, resource, and technology specifications, to implementation and evaluation-- of several innovative apps. Audience engagement using a new web app will gather input on other uses of mobile apps for data collection, visualization, and analyses. The panel and audience discussion will be compiled into guidance for future development of mobile apps for biosurveillance purposes to advance population health.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2014

Sigma: Strain-level inference of genomes from metagenomic analysis for biosurveillance

Motivation: Metagenomic sequencing of clinical samples provides a promising technique for direct pathogen detection and characterization in biosurveillance. Taxonomic analysis at the strain level can be used to resolve serotypes of a pathogen in biosurveillance. Sigma was developed for strain-level identification and quantification of pathogens using their reference genomes based on metagenomic analysis. Results: Sigma provides not only accurate strain-level inferences, but also three unique capabilities: (i) Sigma quantifies the statistical uncertainty of its inferences, which includes hypothesis testing of identified genomes and confidence interval estimation of their relative abundances; (ii) Sigma enables strain variant calling by assigning metagenomic reads to their most likely reference genomes; and (iii) Sigma supports parallel computing for fast analysis of large datasets. In conclusion, the algorithm performance was evaluated using simulated mock communities and fecal samples with spike-in pathogen strains. Availability and Implementation: Sigma was implemented in C++ with source codes and binaries freely available at http://sigma.omicsbio.org.

59 BASIC BIOLOGICAL SCIENCES↗