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1.  Analytic Biosurveillance Methods for Resource-Limited Settings 
PMCID: PMC4050823
alerting; control chart; exponential smoothing; SAGES; resourcelimited
2.  SAGES Update: Electronic Disease Surveillance in Resource-Limited Settings 
The Suite for Automated Global Electronic bioSurveillance (SAGES) is a collection of modular, flexible, open-source software tools for electronic disease surveillance in resource-limited settings. This demonstration will illustrate several new innovations and update attendees on new users in Africa and Asia.
The new 2005 International Health Regulations (IHR), a legally binding instrument for all 194 WHO member countries, significantly expanded the scope of reportable conditions and are intended to help prevent and respond to global public health threats. SAGES aims to improve local public health surveillance and IHR compliance with particular emphasis on resource-limited settings. More than a decade ago, in collaboration with the US Department of Defense (DoD), the Johns Hopkins University Applied Physics Laboratory (JHU/APL) developed the Electronic Surveillance System for the Early Notification of Community-based Epidemics (ESSENCE). ESSENCE collects, processes, and analyzes non-traditional data sources (i.e. chief complaints from hospital emergency departments, school absentee data, poison control center calls, over-the-counter pharmaceutical sales, etc.) to identify anomalous disease activity in a community. The data can be queried, analyzed, and visualized both temporally and spatially by the end user. The current SAGES initiative leverages the experience gained in the development of ESSENCE, and the analysis and visualization components of SAGES are built with the same features in mind.
SAGES tools are organized into four categories: 1) data collection, 2) analysis & visualization, 3) communications, and 4) modeling/simulation/evaluation. Within each category, SAGES offers a variety of tools compatible with surveillance needs and different types or levels of information technology infrastructure. SAGES tools are built in a modular nature, which allows for the user to select one or more tools to enhance an existing surveillance system or use the tools en masse for an end-to-end electronic disease surveillance capability. Thus, each locality can select tools from SAGES based upon their needs, capabilities, and existing systems to create a customized electronic disease surveillance system. New OpenESSENCE developments include improved data query ability, improved mapping functionality, and enhanced training materials. New cellular phone developments include the ability to concatenate single SMS messages sent by simple or Smart Android cell phones. This ‘multiple-SMS’ message ability allows use of SMS technology to send and receive health information exceeding normal SMS message length in a manner transparent to the users.
The SAGES project is intended to enhance electronic disease surveillance capacity in resource-limited settings around the world. We have combined electronic disease surveillance tools developed at JHU/APL with other freely-available, interoperable software tools to create SAGES. We believe this suite of tools will facilitate local and regional electronic disease surveillance, regional public health collaborations, and international disease reporting. SAGES development, funded by the US Armed Forces Health Surveillance Center, continues as we add new international collaborators. SAGES tools are currently deployed in locations in Africa, Asia and South America, and are offered to other interested countries around the world.
PMCID: PMC3692858
software; surveillance; electronic; open-source
3.  Tweeting Fever: Are Tweet Extracts a Valid Surrogate Data Source for Dengue Fever? 
To determine whether Twitter data contains information on dengue-like illness and whether the temporal trend of such data correlates with the incidence dengue or dengue-like illness as identified by city and national health authorities.
Dengue fever is a major cause of morbidity and mortality in the Republic of the Philippines (RP) and across the world. Early identification of geographic outbreaks can help target intervention campaigns and mitigate the severity of outbreaks. Electronic disease surveillance can improve early identification but, in most dengue endemic areas data pre-existing digital data are not available for such systems. Data must be collected and digitized specifically for electronic disease surveillance. Twitter, however, is heavily used in these areas; for example, the RP is among the top 20 producers of tweets in the world. If social media could be used as a surrogate data source for electronic disease surveillance, it would provide an inexpensive pre-digitized data source for resource-limited countries. This study investigates whether Twitter extracts can be used effectively as a surrogate data source to monitor changes in the temporal trend of dengue fever in Cebu City and the National Capitol Region surrounding Manila (NCR) in the RP.
We obtained two sources of ground truth incidence for dengue. The first was daily dengue fever incidence for Cebu City and the NCR taken from the Philippines Integrated Disease Surveillance and Response System (PIDSR). The second ground truth source was fever incidence from Cebu City for 2011. The Cebu City Health Office (CCHO) has monitored fever incidence as a surrogate for dengue fever since the 1980s. Tweets from Cebu City, and the NCR were collected prospectively thru Twitter’s public application program interface. The Cebu City fever ground truth data set was smoothed with a seven day moving average to facilitate comparison to the PIDSR and Twitter data. A vocabulary of words and phrases describing fever and dengue fever in the tweets collected were identified and used to mark relevant tweets. A subset of these ‘fever’ tweets that mentioned fever related to a medical situation were identified. The incidence and the temporal pattern of these medically-relevant tweets were compared with the incidence and pattern of fever and dengue fever in the two ground truth data sets. Pearson correlation coefficient was used to compare the correlation among the different data sets. Noted lag periods were adjusted by moving the data in time and re-computing the correlation coefficient.
26,023,103 tweets were collected from the two geographic regions: 10,303,366 from Cebu City and 15,719,767 tweets from the NCR. 8,814 (0.02%) Tweets contained the word fever and 4099 (0.01% of total) mentioned fever in a medically-relevant context, for example. “…I have a fever…” vs. “…football fever….” The medically-relevant tweets were compared with both ground truth data sets. The correlation between the Tweets and each of the incidence data sets is shown below.
Tweets containing medically-relevant fever references were correlated (p<0.0001) with both fever and dengue fever incidence in the ground truth data sets. The signal indicating fever in the medically-related tweets led the incidence data significantly: by 6 days for the Cebu City fever incidence; and by 12 days for the PIDSR dengue fever incidence. Temporal adjustment to account for observed lag periods increased the correlation coefficient by about one-third in both cases. This was a limited pilot study, but it suggests that Twitter extracts may provide a valid and timely surrogate data source to monitor dengue fever in this population. Further study of the correlation of Twitter and dengue in other areas, and of Twitter with other illnesses is warranted.
PMCID: PMC3692911
Dengue; Social Media; Twitter
4.  Developing open source, self-contained disease surveillance software applications for use in resource-limited settings 
Emerging public health threats often originate in resource-limited countries. In recognition of this fact, the World Health Organization issued revised International Health Regulations in 2005, which call for significantly increased reporting and response capabilities for all signatory nations. Electronic biosurveillance systems can improve the timeliness of public health data collection, aid in the early detection of and response to disease outbreaks, and enhance situational awareness.
As components of its Suite for Automated Global bioSurveillance (SAGES) program, The Johns Hopkins University Applied Physics Laboratory developed two open-source, electronic biosurveillance systems for use in resource-limited settings. OpenESSENCE provides web-based data entry, analysis, and reporting. ESSENCE Desktop Edition provides similar capabilities for settings without internet access. Both systems may be configured to collect data using locally available cell phone technologies.
ESSENCE Desktop Edition has been deployed for two years in the Republic of the Philippines. Local health clinics have rapidly adopted the new technology to provide daily reporting, thus eliminating the two-to-three week data lag of the previous paper-based system.
OpenESSENCE and ESSENCE Desktop Edition are two open-source software products with the capability of significantly improving disease surveillance in a wide range of resource-limited settings. These products, and other emerging surveillance technologies, can assist resource-limited countries compliance with the revised International Health Regulations.
PMCID: PMC3458896  PMID: 22950686
Electronic biosurveillance; Software development; Public health; Disease outbreak; Resource-limited settings
5.  SAGES: A Suite of Freely-Available Software Tools for Electronic Disease Surveillance in Resource-Limited Settings 
PLoS ONE  2011;6(5):e19750.
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.
PMCID: PMC3091876  PMID: 21572957
6.  Bayesian Information Fusion Networks for Biosurveillance Applications 
This study introduces new information fusion algorithms to enhance disease surveillance systems with Bayesian decision support capabilities. A detection system was built and tested using chief complaints from emergency department visits, International Classification of Diseases Revision 9 (ICD-9) codes from records of outpatient visits to civilian and military facilities, and influenza surveillance data from health departments in the National Capital Region (NCR). Data anomalies were identified and distribution of time offsets between events in the multiple data streams were established. The Bayesian Network was built to fuse data from multiple sources and identify influenza-like epidemiologically relevant events. Results showed increased specificity compared with the alerts generated by temporal anomaly detection algorithms currently deployed by NCR health departments. Further research should be done to investigate correlations between data sources for efficient fusion of the collected data.
PMCID: PMC3002118  PMID: 19717809
7.  Syndromic Surveillance: Adapting Innovations to Developing Settings 
PLoS Medicine  2008;5(3):e72.
The tools and strategies of syndromic surveillance, say the authors, hold promise for improving public health security in developing countries.
PMCID: PMC2270304  PMID: 18366250
8.  Weekly Rifapentine/Isoniazid or Daily Rifampin/Pyrazinamide for Latent Tuberculosis in Household Contacts 
Rationale: Treatment of latent tuberculosis (TB) infection with weekly rifapentine and isoniazid is a potentially effective alternative to current therapies.
Objectives: To compare the efficacy of weekly rifapentine/isoniazid to daily rifampin/pyrazinamide in preventing TB in household contacts of patients with pulmonary TB in Brazil.
Methods: Contacts of patients with TB were randomized to rifapentine 900 mg/isoniazid 900 mg once weekly for 12 wk or rifampin 450–600 mg/pyrazinamide 750–1,500 mg daily for 8 wk and followed for at least 2 yr.
Measurements: TB rates, adverse events, and adherence to therapy.
Main Results: A total of 399 household contacts were enrolled, 206 in the rifapentine/isoniazid arm and 193 in the rifampin/pyrazinamide arm. The median age was 34 yr, median weight was 63 kg, 60% of participants were female, and only one patient was HIV infected. Rifapentine/isoniazid was well tolerated, but the trial was halted by the investigators before completion because of unanticipated hepatotoxicity in the rifampin/pyrazinamide arm. Twenty of 193 participants (10%) receiving rifampin/pyrazinamide experienced grade 3 or 4 hepatotoxicity, compared with 2 of 206 participants (1%) on rifapentine/isoniazid (p < 0.001). There were no hospitalizations or deaths due to hepatotoxicity, and all participants' liver enzyme levels returned to normal during follow-up. During follow-up, four cases of active TB developed, three in the rifapentine/isoniazid group and one in the rifampin/pyrazinamide group (1.46 vs. 0.52%; difference, 0.94%; 95% confidence interval, −1.6 to 3.7%).
Conclusions: Rifapentine/isoniazid was better tolerated than rifampin/pyrazinamide and was associated with good protection against TB. Rifapentine/isoniazid weekly for 12 wk is likely a promising therapy for latent TB infection.
PMCID: PMC2662911  PMID: 16474028
controlled clinical trial; latent tuberculosis; pyrazinamide; rifampin; rifapentine
9.  Event Communication in a Regional Disease Surveillance System 
When real-time disease surveillance is practiced in neighboring states within a region, public health users may benefit from easily sharing their concerns and findings regarding potential health threats. To better understand the need for this capability, an event communications component (ECC) was added to the National Capital Region Disease Surveillance System, an operational biosurveillance system employed in the District of Columbia and in surrounding Maryland and Virginia counties. Through usage analysis and user survey methods, we assessed the value of the enhanced system in daily operational use and during two simulated exercises. Results suggest that the system has utility for regular users of the system as well as suggesting several refinements for future implementations.
PMCID: PMC2655862  PMID: 18693883

Results 1-9 (9)