Biosurveillance 2.0

Google Disease Trends

noreply@blogger.com (Anonymous) — Thu, 29 Mar 2012 01:57:00 +0000

Novel Influenza A(H1N1) Media Tags

noreply@blogger.com (Anonymous) — Sat, 19 Nov 2011 23:23:00 +0000

Tag

How SMS is Changing the World

noreply@blogger.com (Anonymous) — Sun, 16 Oct 2011 09:09:00 +0000

via

From Tally Sticks, to Clouds, to .... Zombies

noreply@blogger.com (Anonymous) — Sun, 22 May 2011 06:22:00 +0000

From Tally Sticks, to Clouds, to ... Zombies: The Future of Technology on Prezi

Diseases and Disasters (Dis2): Riff’s Performance

noreply@blogger.com (Anonymous) — Fri, 26 Nov 2010 06:04:00 +0000

A couple of years ago, I introduced Riff; a hybrid (event-based and indicator-based) disease surveillance platform, at the International Society for Disease Surveillance (ISDS) [the original concept is fully described here - more up-to-date information can be found on InSTEDD's website here]. Riff was designed to streamline the collaboration between human experts dealing with diverse streams of information and enabling them with machine learning algorithms that can learn quickly and accurately classify the information for detection, prediction and response to health-related events (such as disease outbreaks or pandemics). On Jan 17^th 2010, the Thomson Reuters Foundation used Riff [after prior adoption in their EIS system; an Emergency Information Service for survivors of natural disasters (early work can be found in Nico’s Blog here)] to launch a first-of-its kind, free disaster-information service for the people of Port Au Prince, Haiti. This allowed survivors of Haiti's earthquake to receive critical information by text message directly to their phones, free of charge.

Earlier this year; April 2010, I setup a Riff space; Diseases and Disasters (or Dis²), for providing timely situation awareness from credible and reliable [gold standard of a sort] online reports on diseases and disasters in the world provided primarily by BioCaster and HealthMap. This already tagged and verified information provided Riff’s classifier with a great training opportunity that I had to monitor closely and correct at the beginning for both features (e.g., condition, type of disease transmission, severity, etc.) and geo-location of where the event actually occurred as shown here:

Conditions Tracked in Dis2 Proportional to their Coverage since April 19, 2010

%Conditions Tracked in Dis2 since April 19, 2010

Location of Conditions Tracked in Dis2 Proportional to their Coverage since April 19, 2010

Location (Heatmap) of Conditions Tracked in Dis2 since April 19, 2010

In collaboration with the Humanitarian FOSS Project; supported by a group of computing faculty and open source proponents at Trinity College, Wesleyan University, and Connecticut College (Open Source ALPACA Light Parsing And Classifying Application (ALPACA) and Open Source e-dop for Disease Ontology Prediction for Riff), we developed a Support Vector Machines (or SVM) for automatic feature extraction, data classification and tagging. Riff’s classifier performed incredibly well in the Dis²collaborative space with very little training at the outset; 83% (95% CI: 81-85%) True Positive rate as shown here:

Riff's Performance in the Dis2 Collaborative Space (True Positive and False Negative Ratios)

Riff is an Open Source Project, you can download its source code here and help further enhance its performance.

Acknowledgment

Nicolás di Tada and Eduardo (Ed) Jezierski: InSTEDD, Palo Alto, CA, USA
Nigel Collier: BioCaster - National Institute of Informatics and PRESTO Japan Science and Technology (JST) Corporation, Tokyo, Japan
John Brownstein and Clark Freifeld: HealthMap - Children’s Hospital Informatics Program at Harvard-Massachusetts Institute of Technology, Division of Health Sciences and Technology, Division of Emergency Medicine, Children’s Hospital Boston, Boston, Massachusetts, USA
Humanitarian FOSS Project

Cholera-Related Media Reports Worldwide

noreply@blogger.com (Anonymous) — Sat, 23 Oct 2010 07:32:00 +0000

Cholera-Related Media Reports Worldwide

Salmonella Media Coverage in the US - Summer 2010

noreply@blogger.com (Anonymous) — Sat, 28 Aug 2010 10:38:00 +0000

Salmonella Outbreak Media Coverage in US - Summer 2010

My Book on Biosurveillance: Methods and Case Studies

noreply@blogger.com (Anonymous) — Mon, 02 Aug 2010 22:54:00 +0000

Biosurveillance: Methods and Case Studies

My new book on Biosurveillance is scheduled for release on September 17th, 2010. The book

Provides a synopsis of current state-of-the-art practices as well as a starting point for the development and evaluation of new methods
Covers applied research and complete case studies in biosurveillance that focus on local, regional and national implementation
Presents techniques from other fields, such as intelligence and engineering
Explores future innovations in biosurveillance, including advances in analytical methods, modeling, and simulation
Addresses policy and organizational issues related to the construction of biosurveillance systems

“While having its roots in 21st Century infectious disease threats to health on a grand scale, biosurveillance has come to encompass a broader scope of the science and practice of managing population health-related data and information so that effective action can be taken to mitigate adverse health effects from urgent threats. This expansive scope is reflected in the diverse collection of reports and perspectives brought together in this text, Biosurveillance." — From the Foreword by Daniel M. Sosin, MD, MPH, Centers for Disease Control and Prevention (CDC).

Table of Content

Timeliness of Data Sources, Lynne Dailey, PhD, MPH, BSc.
Simulating and Evaluating Biosurveillance Datasets, Thomas H. Lotze, Galit Shmueli, Lotze, Shmueli, Yahav Inbal Yahav, and Robert H. Smith
Remote Sensing-Based Modeling of Infectious Disease Transmission, Richard K. Kiang, Farida Adimi, Radina P. Soebiyanto
Integrating Human Capabilities into Biosurveillance Systems: A Study of Biosurveillance and Situation Awareness, Cheryl A. Bolstad, Haydee M. Cuevas, Jingjing Wang-Costello, Mica R. Endsley, Walton John Page, and Taha Kass-Hout
The Role of Zoos in Biosurveillance, Julia Chosy, PhD, Janice Mladonick, and Tracey McNamara, DVM
HealthMap, Amy L. Sonricker, MPH, Clark C. Freifeld, Mikaela Keller, PhD, John S. Brownstein, PhD
The Role of SMS Text Messaging to Improve Public Health Response, Elizabeth Avery Gomez, Ph.D.
Using Prediction Markets to Forecast Infectious Diseases, Philip M. Polgreen, MD, MPH, and Forrest D. Nelson, PhD
The Role of Data Aggregation in Public Health and Food Safety Surveillance, Artur Dubrawski
Introduction to China’s Infectious Disease Surveillance System, Jin Shuigao and Ma Jiaqi
Biosurveillance and Public Health Practice: A Case Study of North Carolina’s NC DETECT System, S. Cornelia Kaydos-Daniels, PhD, MSPH; Lucia Rojas Smith, DrPH,, MPH; Amy I. Ising, MSIS; Clifton Barnett, MSIS; Tonya Farris, MPH;, Anna E. Waller, ScD; and Scott Wetterhall, MD, MPH
Aberration Detection in R Illustrated by Danish mortality monitoring, Michael Höhl and, Anne Mazick
User Requirements toward a Real-Time Biosurveillance Program, Nuwan Waidyanatha and Suma Prashant
Using Common Alerting Protocol to Support a Real-Time Biosurveillance Program in Sri Lanka and India, Gordon A. Gow and Nuwan Waidyanatha
Navigating the Information Storm: Web-Based Global Health Surveillance in BioCaster, Nigel Collier, Son Doan, Reiko Matsuda Goodwin, John McCrae, Mike Conway, Mika Shigematsu, and Ai Kawazoe
A Snapshot of Situation Awareness: Using the NC DETECT System to Monitor the 2007 Heat Wave, David B. Rein
Linking Detection to Effective Response, Scott F. Wetterhall, MD, MPH, Taha A. Kass-Hout, MD, MS , and David L. Buckeridge, MD, PhD

By reading this book, I hope you reap from it lessons and insights to apply in your work for a lifetime.

Riff: A Social Network and Collaborative Platform for Public Health Disease Surveillance

noreply@blogger.com (Anonymous) — Sat, 10 Jul 2010 00:37:00 +0000

From back of the napkin concept, to initial prototype and production, and finally to implementation, here is the story of Riff...

View more presentations from Taha Kass-Hout, MD, MS.

Dengue Fever in Florida (in the US?)

noreply@blogger.com (Anonymous) — Mon, 21 Jun 2010 04:28:00 +0000

An outbreak in Key West, Fla., has re-emerged in April 2010. Historically, dengue was in Florida in the early 1900, but locally-acquired cases had not been confirmed since then until August 2009. The recent Florida outbreak might have gone unnoticed if it hadn't been for an astute physician in upstate New York who identified the first case in Rochester, N.Y., involving a patient who had just returned from a week-long visit to Key West.

In the US, dengue fever has rarely been an issue outside of the Texas-Mexico border region, but currently it is estimated that more than half of the US population live in places which contain one or both of mosquito species capable of transmitting the dengue fever virus creating conditions more favorable for an outbreak. Dengue is now [starting last year] a reportable disease in the US due to its increasing threat.

Dengue fever is characterized by agonizing aching in the bones, joints and muscles, a pounding headache, pain behind the eyes, a high fever and a classic rash. There is no cure or vaccine, only preventative and supportive care.

You can collaborate around Dengue on Riff here

Upper Big Branch South Mine Explosion: Could Data Mining Have Prevented a Coal Mine Disaster?

noreply@blogger.com (Anonymous) — Fri, 09 Apr 2010 21:28:00 +0000

The April 5^th explosion at the Upper Big Branch South Mine (Performance Coal Co.) in Whitesville, W.VA. got me wondering, what type of data was available that somehow would have suggested this mine was at a dangerous point. I was able to find the citation information published on the United States Department of Labor, Mine Safety & Health Administration (MSHA) [under Data Transparency at MSHA]. My colleague Paul McMurray and I found that out of the 124 total citations in 2010, ~43% (53 citations) were issued in the month of March 2010 with a potential penalty of $1,077,339 [where we expressed it as the maximum penalty assigned a given standard historic citation since 2007-01-01)]. It’s also worth noting that this mine had over 500 citations in 2009 (~46% of all violations since 2007). Without exploring the data for other mines, these numbers seem to be high enough by themselves to suggest that this mine could have been a candidate for a greater level of scrutiny by federal, state and local authorities that are responsible to overlook mines safety.

The following table shows the Upper Big Branch Mine-South Citations, Orders and Safecards Detail Issued for March 2010 [Google Fusion Table (collaborative online spreadsheet)]. Further analysis [e.g., data mining] should look into the type of standards to see if we can categorize the various violations of these standards [e.g., ventilation problems, escape routes, etc.].

Riff: Heatmap of Latest Information Tagged with "Influenza"

noreply@blogger.com (Anonymous) — Sat, 03 Apr 2010 20:26:00 +0000

Link to Riff here

BreathEasy - A Mobile PHR App for Adults with Asthma and Depression or Anxiety

noreply@blogger.com (Anonymous) — Sun, 07 Mar 2010 03:30:00 +0000

My Colleague; Dr. Barbara Massoudi with RTI, recently received funding from the Robert Wood Johnson (RWJ) Foundation for Project HealthDesign (a Personal Health Record (PHR) platform) Round II. In this round, Barbara and her team will be developing a mobile PHR application to assist people with asthma and depression or anxiety. The mobile app (Android-based for the initial prototype) will help these patients track observations of daily living (ODLs) related to their conditions at any time of the day. You can read more on the project here.

Official google.org Blog: Google Flu Trends in 121 U.S. cities

noreply@blogger.com (Anonymous) — Wed, 13 Jan 2010 02:22:00 +0000

Official google.org Blog: Google Flu Trends in 121 U.S. cities

2009, AMIA Spring Congress

noreply@blogger.com (Anonymous) — Mon, 01 Jun 2009 16:39:00 +0000

Last week, I presented Evolve; InSTEDD's Global Early Warning and Response System, at the 2009, American Medical Informatics Association (AMIA) Spring Congress. The conference took place at the Walt Disney World Swan , May 28th–30th, in Orlando, Florida, USA. Here is the presentation:

View more OpenOffice presentations from Taha Kass-hout.

Influenza A(H1N1) Media Hype: Mid-March 2009 thru May 19, 2009

noreply@blogger.com (Anonymous) — Fri, 22 May 2009 04:56:00 +0000

Data source: A(H1N1) Evolve Collaborative Workspace

Note: Tag cloud was created on Many Eyes © IBM

Note: Tag cloud was created on Many Eyes © IBM

Note: Map was created on Many Eyes © IBM

Related Links:

Tracking A(H1N1) using Evolve
Low volume Evolve announcements on Twitter
Extremely Affordable Health Innovations
MBDS ICT and Technology Forum
Best Poster Award for Improving Public Health Investigation and Response at the Seventh Annual International Society for Disease Surveillance Conference
Collaborative Analytics and Environment for Linking Early Event Detection to an Effective Response

Oswego in the Cloud: Demo with US CDC to Synchronize Epi Info™ Data Using Mesh4x

noreply@blogger.com (Anonymous) — Sat, 16 May 2009 21:31:00 +0000

Enrique Nieves Jr (Acting Director, Division of Integrated Surveillance Systems and Services (DISSS), CDC, NCPHI) and Jay Jones describe a Mesh4x demonstration we did with US CDC to "...synchronize data using Epi Info™". You can see their recent publication in the PanAfrican Medical Journal titled: Epi Info™: Now an Open-source application that continues a long and productive “life” through CDC support and funding.

Related Links:

Epi Info™ and Mesh4x Prototype Demonstration with US CDC
Empowering Epidemiologists to Share Information, Anytime, Anywhere: Epi Info™ and Mesh4x
Epi Info™ current website on CDC.gov (available for download Epi Info™ 3.5.1 (last accessed May 16th, 2009))
Epi Info™ Friends Group on Google
InSTEDD Mesh4X

Tracking A(H1N1) using Riff

noreply@blogger.com (Anonymous) — Fri, 15 May 2009 04:44:00 +0000

Last week, InSTEDD's CEO; Dr. Eric Rasmussen, blogged about the Riff workspace we stood up earlier to further aid experts and responders collaborating around emerging reports related to the 2009 A(H1N1) pandemic influenza. To-date, there's been massive news coverage around the event, but in order to make sense of it all, a group of experts (with a backgrounds in public health, international relations, diplomacy, social work, and emergency response) volunteered their time to collaborate around the various streams of information (listed below).

One by-product of this ongoing effort is that the information is appropriately tagged and geo-located. The A(H1N1) workspace allows you to subscribe to all the information or to a filter of your own. The tags include information beyond just a disease category, symptom, or syndrome, but we also tried to capture other important information; such as policy issues (e.g., vaccination, school closure, travel advisory, etc.). However, our primary goal is not to become another information source, rather to be able to provide a good situational awareness of the event in order to respond effectively. We are trying to address the following problems that are inherent in the current early detection systems:

Classic problem: too much data, not enough information. Why aren’t the key indicators noticed earlier?
Noisy data—low reliability—
Need to keep the human in the loop (a lot of this is still an art).
Sources not always obvious - we saw emerging sources of information, like the citizen reporting over a Google map (in the past much attention was paid to sources like Internet search queries (e.g., Eysenbach, Ginsberg, Polgreen, Hulth, and Cooper), over the counter medications sales (e.g., Wagner/RODS Lab), absenteeism (e.g., Wagner/RODS Lab), as opposed to ER chief complaints or routine disease surveillance hierarchical systems).
Threat profile keeps changing- is not known for something like a SARS/SARI (e.g., Swine Flu or other things like it).
Political and Organizational Boundaries (Note that we weren't able to perfectly communicate the first indications of SARS, or the outbreaks of H5N1 in China, and we saw that happen again with the H1N1 Swine outbreak).
Need to set up the need for shared collaboration spaces and geographic distribution. Not only do we need human experts in the loop, but they need to share the hunches and concerns. Discussion needs to identify communities of interest. Different specialists are involved based on the nature of the threat.

I particularly applaud the effort by HealthMappers (Dr. Brownstein, et al) for quickly putting together an A(H1N1) mashup (or the New England Journal of Medicine HealthMap) which tracks the cases (confirmed, suspect, dead, or ruled out) alongside with the informal sources that HealthMap continuously monitors and moderates. HealthMap and BioCaster also setup moderated tweets on Twitter that are timely, reliable and of high quality.

Information Sources:

The Challenge Ahead:

While all this is important, I'd like to emphasize the fact that the best data is still coming from old-fashioned shoe leather epidemiology. We have to be true to ourselves and remember that, with all the information, new tools, open networks of collaborators, etc., we still missed the early indication(s) of the A(H1N1) outbreak. I remember when I was in the trenches of SARS back in 2003, we didn't have the breadth and depth of the information nor the tools we currently have. This calls for an action to rethink our strategies around early detection especially for emerging infectious diseases...

Related Links:

Low volume Riff announcements on Twitter
Extremely Affordable Health Innovations
MBDS ICT and Technology Forum
Best Poster Award for Improving Public Health Investigation and Response at the Seventh Annual International Society for Disease Surveillance Conference
Collaborative Analytics and Environment for Linking Early Event Detection to an Effective Response

Extremely Affordable Health Innovations

noreply@blogger.com (Anonymous) — Fri, 15 May 2009 03:27:00 +0000

Nico and I presented Evolve at the “Extremely Affordable Health Innovations”; A Grameen Health initiative in collaboration with World Health Care Congress (WHCC), which took place on April 14th-16th, 2009 in Washington D.C. The winners, by category and overall, are listed here. We won the best poster in the Community Monitoring category. The poster will be on display again on May 131h-141h, 2009 at WHCC Europe in Brussels, Belgium.
Evolve: InSTEDD's Global Early Warning and Response SystemView more presentations from Taha Kass-hout.

Related Links:

Low volume Evolve announcements on Twitter
Extremely Affordable Health Innovations
MBDS ICT and Technology Forum
Best Poster Award for Improving Public Health Investigation and Response at the Seventh Annual International Society for Disease Surveillance Conference
Collaborative Analytics and Environment for Linking Early Event Detection to an Effective Response

MBDS ICT and Technology Forum

noreply@blogger.com (Anonymous) — Thu, 14 May 2009 19:16:00 +0000

I presented the following at the Mekong Basin Disease Surveillance (MBDS), Information Communication and Technology Forum which took place April 2nd–3rd, 2009 in Mukdahan Province, Thailand.

I. ICT Developments in Mobile Technology for Global Public Health: InSTEDD Collaboration Tools

View more presentations from Taha Kass-hout.

Photo Credit: Dr. Moe Ko Oo MBDS Coordinator

II. Using GeoChat for a Cross-Border Field Simulation Exercise

III. MBDS SE Asia Collaborative Early Warning & Response workspace (using Evolve)

View more presentations from Taha Kass-hout.

At the end of the forum, Ed and I answered questions related to the utility and feasibility of GeoChat and Evolve in the various MBDS member countries.

Photo Credit: Dr. Moe Ko Oo MBDS Coordinator

Official google.org Blog: New resources for non-profit and humanitarian mapping

noreply@blogger.com (Anonymous) — Wed, 13 May 2009 16:29:00 +0000

Official google.org Blog: New resources for non-profit and humanitarian mapping

InSTEDD Collaboration Technology for Public Health and Humanitarian Action and Global Development

noreply@blogger.com (Anonymous) — Mon, 02 Mar 2009 21:16:00 +0000

I gave a talk today on InSTEDD collaboration technologies and platform at the CDC Focus On Users: Underserved Populations Conference, March 2-3, 2009. This conference is co-sponsored by CDC's National Center for Health Marketing, the U.S. Department of Health and Human Services, Georgia State University Department of Communication, the Pew Internet & American Life Project, and the National Public Health Information Coalition.

Collaboration Technology for Public Health and Humanitarian Action and Global Development.

View more presentations from Taha Kass-hout. (tags: kass-hout tools)

Open Collaboration Experiment around Emergency Alerts, Disasters, Market Recalls, and More...

noreply@blogger.com (Anonymous) — Sun, 01 Mar 2009 23:43:00 +0000

We set up two open collaboration spaces around up-to-date notifications and alerts on the following:

- Emergency Preparedness & Response alerts, Recent Outbreaks and Incidents, Clinician Outreach and Communication Activity (COCA), and Public Service Announcements for Hurricanes from US CDC

- Recalls, market withdrawals and safety alerts from the the U.S. Food and Drug Administration (FDA)

These spaces offer a suite of collaborative features, including: commenting, tagging (adding your own keywords), mapping (user generated and automated), relating multiple alerts, searching and filtering, specifying a time window, adding attachments, subscribing (currently in the form of a web-friendly format also known as RSS, but in the very near future we will support email subscription), and more. The two spaces are also equipped with an intelligent process (referred to as machine-learning algorithm) that "learns" from inputs provided by the users (e.g., adding a keyword (tag), or correcting the mapping of an item). This intelligent process quickly and accurately learns from users inputs (with 95% confidence based on previous tests) and starts suggesting tags as well as correcting itself and offering even better results over time (by simply accepting or rejecting a suggested tag or an automatically mapped location).

Have you an alert or item you like to share with the community? You can easily contribute that alert by clicking the "Add Item" feature.

We invite you to try it and help us spread the good word by inviting others as well. We look forward to your feedback and comments in order to make this tool as useful as it can possibly be. If you have thoughts or questions you can contact us at info@instedd.org or email me directly at: kasshout@instedd.org.

Atmospheric CO2 Levels: Green, Orange, Red...

noreply@blogger.com (Anonymous) — Tue, 17 Feb 2009 09:25:00 +0000

Since 412,000 BCE, atmospheric CO2 levels ranged; in a cyclical motion, from 182-299 ppmv. CO2 levels started an upward trend after 1604 and rose above the maximum historic threshold of 300 ppmv in 1912. A most recent recording of CO2 level from the Mauna Loa Observatory was at 381.9 ppmv in 2006.

I assembled the data in a Google Doc from the following sources:

Recent CO2 records:
- Mauna Loa Observatory atmospheric CO2 Data [1958 - present]

Historical paleoclimatic CO2 records:
- Law Dome, Antarctica DE08, DE08-2, and DSS ice cores [1006 - 1978]
- Vostok ice core Data in thousands of years BCE [-412,080 - -337]

Internet Search Queries on CO2 Levels (Source Google Insights for Search):

Internet Search Queries on Global Warming (Source Google Insights for Search):

Acknowledgments:
- Rafal Raciborski, Ph.D. candidate, Department of Political Science, Emory University - for scaling the x-axis

Thanks for reading my blog last year!

noreply@blogger.com (Anonymous) — Fri, 23 Jan 2009 03:08:00 +0000