Discovering multi-scale co-occurrence patterns of asthma and influenza with the Oak Ridge bio-surveillance toolkit
Abstract
Here, we describe a data-driven unsupervised machine learning approach to extract geo-temporal co-occurrence patterns of asthma and the flu from large-scale electronic healthcare reimbursement claims (eHRC) datasets. Specifically, we examine the eHRC data from 2009 to 2010 pandemic H1N1 influenza season and analyze whether different geographic regions within the United States (US) showed an increase in co-occurrence patterns of the flu and asthma. Our analyses reveal that the temporal patterns extracted from the eHRC data show a distinct lag time between the peak incidence of the asthma and the flu. While the increased occurrence of asthma contributed to increased flu incidence during the pandemic, this co-occurrence is predominant for female patients. The geo-temporal patterns reveal that the co-occurrence of the flu and asthma are typically concentrated within the south-east US. Further, in agreement with previous studies, large urban areas (such as New York, Miami, and Los Angeles) exhibit co-occurrence patterns that suggest a peak incidence of asthma and flu significantly early in the spring and winter seasons. Together, our data-analytic approach, integrated within the Oak Ridge Bio-surveillance Toolkit platform, demonstrates how eHRC data can provide novel insights into co-occurring disease patterns.
- Authors:
-
- Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
- IMS Government Solutions (IMSGS), Inc., Fairfax, VA (United States)
- Univ. of Pittsburgh, Pittsburgh, PA (United States)
- Publication Date:
- Research Org.:
- Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1286929
- Grant/Contract Number:
- AC05-00OR22725
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Frontiers in Public Health
- Additional Journal Information:
- Journal Volume: 3; Journal Issue: 1; Journal ID: ISSN 2296-2565
- Publisher:
- Frontiers Research Foundation
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 60 APPLIED LIFE SCIENCES; 97 MATHEMATICS AND COMPUTING; disease co-occurrence; non-negative matrix factorization; public health surveillance; asthma; flu; electronic healthcare reimbursement claims
Citation Formats
Ramanathan, Arvind, Pullum, Laura L., Hobson, Tanner C., Stahl, Christopher G., Steed, Chad A., Valkova, Silvia, Quinn, Shannon, and Chennubhotla, Chakra. Discovering multi-scale co-occurrence patterns of asthma and influenza with the Oak Ridge bio-surveillance toolkit. United States: N. p., 2015.
Web. doi:10.3389/fpubh.2015.00182.
Ramanathan, Arvind, Pullum, Laura L., Hobson, Tanner C., Stahl, Christopher G., Steed, Chad A., Valkova, Silvia, Quinn, Shannon, & Chennubhotla, Chakra. Discovering multi-scale co-occurrence patterns of asthma and influenza with the Oak Ridge bio-surveillance toolkit. United States. https://doi.org/10.3389/fpubh.2015.00182
Ramanathan, Arvind, Pullum, Laura L., Hobson, Tanner C., Stahl, Christopher G., Steed, Chad A., Valkova, Silvia, Quinn, Shannon, and Chennubhotla, Chakra. Mon .
"Discovering multi-scale co-occurrence patterns of asthma and influenza with the Oak Ridge bio-surveillance toolkit". United States. https://doi.org/10.3389/fpubh.2015.00182. https://www.osti.gov/servlets/purl/1286929.
@article{osti_1286929,
title = {Discovering multi-scale co-occurrence patterns of asthma and influenza with the Oak Ridge bio-surveillance toolkit},
author = {Ramanathan, Arvind and Pullum, Laura L. and Hobson, Tanner C. and Stahl, Christopher G. and Steed, Chad A. and Valkova, Silvia and Quinn, Shannon and Chennubhotla, Chakra},
abstractNote = {Here, we describe a data-driven unsupervised machine learning approach to extract geo-temporal co-occurrence patterns of asthma and the flu from large-scale electronic healthcare reimbursement claims (eHRC) datasets. Specifically, we examine the eHRC data from 2009 to 2010 pandemic H1N1 influenza season and analyze whether different geographic regions within the United States (US) showed an increase in co-occurrence patterns of the flu and asthma. Our analyses reveal that the temporal patterns extracted from the eHRC data show a distinct lag time between the peak incidence of the asthma and the flu. While the increased occurrence of asthma contributed to increased flu incidence during the pandemic, this co-occurrence is predominant for female patients. The geo-temporal patterns reveal that the co-occurrence of the flu and asthma are typically concentrated within the south-east US. Further, in agreement with previous studies, large urban areas (such as New York, Miami, and Los Angeles) exhibit co-occurrence patterns that suggest a peak incidence of asthma and flu significantly early in the spring and winter seasons. Together, our data-analytic approach, integrated within the Oak Ridge Bio-surveillance Toolkit platform, demonstrates how eHRC data can provide novel insights into co-occurring disease patterns.},
doi = {10.3389/fpubh.2015.00182},
journal = {Frontiers in Public Health},
number = 1,
volume = 3,
place = {United States},
year = {Mon Aug 03 00:00:00 EDT 2015},
month = {Mon Aug 03 00:00:00 EDT 2015}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
Influenza Vaccination in Children with Asthma
journal, February 2004
- Bueving, Herman J.; Bernsen, Roos M. D.; de Jongste, Johan C.
- American Journal of Respiratory and Critical Care Medicine, Vol. 169, Issue 4
The Parable of Google Flu: Traps in Big Data Analysis
journal, March 2014
- Lazer, D.; Kennedy, R.; King, G.
- Science, Vol. 343, Issue 6176
Developing a Social Media System for Biosurveillance
journal, March 2014
- Waters, Julie; Howard, Kristina; Baker, Heather
- Online Journal of Public Health Informatics, Vol. 6, Issue 1
An exploratory study of a text classification framework for Internet-based surveillance of emerging epidemics
journal, January 2011
- Torii, Manabu; Yin, Lanlan; Nguyen, Thang
- International Journal of Medical Informatics, Vol. 80, Issue 1
Asthma, influenza, and vaccination
journal, December 2006
- Glezen, W.
- Journal of Allergy and Clinical Immunology, Vol. 118, Issue 6
A Brief Targeted Review of Susceptibility Factors, Environmental Exposures, Asthma Incidence, and Recommendations for Future Asthma Incidence Research
journal, April 2006
- Yeatts, Karin; Sly, Peter; Shore, Stephanie
- Environmental Health Perspectives, Vol. 114, Issue 4
Comparison: Flu Prescription Sales Data from a Retail Pharmacy in the US with Google Flu Trends and US ILINet (CDC) Data as Flu Activity Indicator
journal, August 2012
- Patwardhan, Avinash; Bilkovski, Robert
- PLoS ONE, Vol. 7, Issue 8
Syndemics and Public Health: Reconceptualizing Disease in Bio-Social Context
journal, December 2003
- Singer, Merill; Clair, Scott
- Medical Anthropology Quarterly, Vol. 17, Issue 4
Social and News Media Enable Estimation of Epidemiological Patterns Early in the 2010 Haitian Cholera Outbreak
journal, January 2012
- Chunara, Rumi; Andrews, Jason R.; Brownstein, John S.
- The American Journal of Tropical Medicine and Hygiene, Vol. 86, Issue 1
Viruses as precipitants of asthma symptoms. I. Epidemiology
journal, March 1992
- Pattemore, P. K.; Johnston, S. L.; Bardin, P. G.
-
Clinical
Experimental Allergy, Vol. 22, Issue 3
Electronic Health Records in Hospitals [Correspondence]
journal, July 2009
- ,
- New England Journal of Medicine, Vol. 361, Issue 4, p. 421-422
Assessing Google Flu Trends Performance in the United States during the 2009 Influenza Virus A (H1N1) Pandemic
journal, August 2011
- Cook, Samantha; Conrad, Corrie; Fowlkes, Ashley L.
- PLoS ONE, Vol. 6, Issue 8
Categorical Dimensions of Human Odor Descriptor Space Revealed by Non-Negative Matrix Factorization
journal, September 2013
- Castro, Jason B.; Ramanathan, Arvind; Chennubhotla, Chakra S.
- PLoS ONE, Vol. 8, Issue 9
National Trends in Treatment of Type 2 Diabetes Mellitus, 1994-2007
journal, October 2008
- Alexander, G. Caleb; Sehgal, Niraj L.; Moloney, Rachael M.
- Archives of Internal Medicine, Vol. 168, Issue 19
Viral Respiratory Infection and the Link to Asthma
journal, October 2008
- Gern, James E.
- Pediatric Infectious Disease Journal, Vol. 27, Issue 10
ORBiT: Oak Ridge biosurveillance toolkit for public health dynamics
journal, December 2015
- Ramanathan, Arvind; Pullum, Laura L.; Hobson, Tanner C.
- BMC Bioinformatics, Vol. 16, Issue S17
Influenza — Interpandemic as Well as Pandemic Disease
journal, December 2005
- Dolin, Raphael
- New England Journal of Medicine, Vol. 353, Issue 24
Detecting influenza epidemics using search engine query data
journal, February 2009
- Ginsberg, Jeremy; Mohebbi, Matthew H.; Patel, Rajan S.
- Nature, Vol. 457, Issue 7232
Electronic Health Records in Ambulatory Care [Correspondence]
journal, October 2008
- ,
- New England Journal of Medicine, Vol. 359, Issue 17, p. 1848-1849
Off-label Prescribing Among Office-Based Physicians
journal, May 2006
- Radley, David C.; Finkelstein, Stan N.; Stafford, Randall S.
- Archives of Internal Medicine, Vol. 166, Issue 9
Oral Oseltamivir Improves Pulmonary Function and Reduces Exacerbation Frequency for Influenza-Infected Children With Asthma
journal, March 2005
- Johnston, Sebastian L.; Ferrero, Fernando; Garcia, Maria Luz
- Pediatric Infectious Disease Journal, Vol. 24, Issue 3
Ethics in Public Health Research
journal, May 2008
- Myers, Julie; Frieden, Thomas R.; Bherwani, Kamal M.
- American Journal of Public Health, Vol. 98, Issue 5
Review: Use of Electronic Medical Records for Health Outcomes Research
journal, March 2009
- Dean, Bonnie B.; Lam, Jessica; Natoli, Jaime L.
- Medical Care Research and Review, Vol. 66, Issue 6
Influenza Vaccination Among Adults with Asthma
journal, August 2009
- Lu, Peng-jun; Euler, Gary L.; Callahan, David B.
- American Journal of Preventive Medicine, Vol. 37, Issue 2
Synchrony, Waves, and Spatial Hierarchies in the Spread of Influenza
journal, March 2006
- Viboud, C.; Bjornstad, O. N.; Smith, D. L.
- Science, Vol. 312, Issue 5772
Estimating Effect of Antiviral Drug Use during Pandemic (H1N1) 2009 Outbreak, United States
journal, September 2011
- Atkins, Charisma
- Emerging Infectious Diseases, Vol. 17, Issue 9
Positive matrix factorization: A non-negative factor model with optimal utilization of error estimates of data values
journal, June 1994
- Paatero, Pentti; Tapper, Unto
- Environmetrics, Vol. 5, Issue 2
Electronic Health Records
journal, July 2005
- Ambinder, Edward P.
- Journal of Oncology Practice, Vol. 1, Issue 2
Influenza vaccine in patients with asthma
journal, February 2006
- Hanania, Nicola A.; Atmar, Robert L.; Castro, Mario
- Expert Review of Vaccines, Vol. 5, Issue 1
The Use of Twitter to Track Levels of Disease Activity and Public Concern in the U.S. during the Influenza A H1N1 Pandemic
journal, May 2011
- Signorini, Alessio; Segre, Alberto Maria; Polgreen, Philip M.
- PLoS ONE, Vol. 6, Issue 5
Assessing seasonal dynamics of Guillain-Barré syndrome with search engine query data
journal, February 2019
- Giordano, Antonino; Vabanesi, Marco; Dalla Costa, Gloria
- Neurological Sciences, Vol. 40, Issue 5
Public health surveillance with electronic medical records: at risk of surveillance bias and overdiagnosis
journal, April 2013
- Chiolero, A.; Santschi, V.; Paccaud, F.
- The European Journal of Public Health, Vol. 23, Issue 3
Least squares formulation of robust non-negative factor analysis
journal, May 1997
- Paatero, Pentti
- Chemometrics and Intelligent Laboratory Systems, Vol. 37, Issue 1
An overview of Internet biosurveillance
journal, November 2013
- Hartley, D. M.; Nelson, N. P.; Arthur, R. R.
- Clinical Microbiology and Infection, Vol. 19, Issue 11
Discovering Conformational Sub-States Relevant to Protein Function
journal, January 2011
- Ramanathan, Arvind; Savol, Andrej J.; Langmead, Christopher J.
- PLoS ONE, Vol. 6, Issue 1
Influenza Vaccine Compliance Among Pediatric Asthma Patients: What Is the Better Method of Notification?
journal, December 2006
- Moore, Maj Meredith L.; Parker, Maj Amy L.
- Pediatric Asthma, Allergy & Immunology, Vol. 19, Issue 4
National Use of Postmenopausal Hormone Therapy
journal, January 2004
- Hersh, Adam L.; Stefanick, Marcia L.; Stafford, Randall S.
- JAMA, Vol. 291, Issue 1
Clinical pearls for preventing, diagnosing, and treating seasonal and 2009 H1N1 influenza infection in patients with asthma
journal, November 2009
- Rank, Matthew A.; Li, James T.
- Journal of Allergy and Clinical Immunology, Vol. 124, Issue 5
The role of Respiratory Viruses in Acute and Chronic Asthma
journal, June 2000
- Tuffaha, Amjad; Gern, James E.; Lemanske, Robert F.
- Clinics in Chest Medicine, Vol. 21, Issue 2
How Common Are Electronic Health Records In The United States? A Summary Of The Evidence
journal, January 2006
- Jha, Ashish K.; Ferris, Timothy G.; Donelan, Karen
- Health Affairs, Vol. 25, Issue Suppl1
Use of Electronic Health Records in U.S. Hospitals
journal, April 2009
- Jha, Ashish K.; DesRoches, Catherine M.; Campbell, Eric G.
- New England Journal of Medicine, Vol. 360, Issue 16
Electronic Health Records
journal, July 2005
- Ambinder, Edward P.
- Journal of Oncology Practice, Vol. 1, Issue 2, 57-63
Electronic Health Records in Ambulatory Care — A National Survey of Physicians
journal, July 2008
- DesRoches, Catherine M.; Campbell, Eric G.; Rao, Sowmya R.
- New England Journal of Medicine, Vol. 359, Issue 1
Definition, structure, content, use and impacts of electronic health records: A review of the research literature
journal, May 2008
- Hayrinen, K.; Saranto, K.; Nykanen, P.
- International Journal of Medical Informatics, Vol. 77, Issue 5
Review: Use of Electronic Medical Records for Health Outcomes Research
journal, March 2009
- Dean, Bonnie B.; Lam, Jessica; Natoli, Jaime L.
- Medical Care Research and Review, Vol. 66, Issue 6
Digital Disease Detection — Harnessing the Web for Public Health Surveillance
journal, May 2009
- Brownstein, John S.; Freifeld, Clark C.; Madoff, Lawrence C.
- New England Journal of Medicine, Vol. 360, Issue 21
Influenza vaccination in children with asthma in Health Maintenance Organizations
journal, April 2000
- Kramarz, Piotr; DeStefano, Frank; Gargiullo, Paul M.
- Vaccine, Vol. 18, Issue 21
Routine and Influenza Vaccination Rates in Children with Asthma
journal, April 1998
- Chung, Esther K.; Casey, Rosemary; Pinto-Martin, Jennifer A.
- Annals of Allergy, Asthma & Immunology, Vol. 80, Issue 4
Influenza-Associated Deaths among Children in the United States, 2003–2004
journal, December 2005
- Bhat, Niranjan; Wright, Jennifer G.; Broder, Karen R.
- New England Journal of Medicine, Vol. 353, Issue 24
Influenza Vaccination Among Adults with Asthma
journal, August 2009
- Lu, Peng-jun; Euler, Gary L.; Callahan, David B.
- American Journal of Preventive Medicine, Vol. 37, Issue 2
Influenza Vaccine Compliance Among Pediatric Asthma Patients: What Is the Better Method of Notification?
journal, December 2006
- Moore, Maj Meredith L.; Parker, Maj Amy L.
- Pediatric Asthma, Allergy & Immunology, Vol. 19, Issue 4
Discovering Conformational Sub-States Relevant to Protein Function
journal, January 2011
- Ramanathan, Arvind; Savol, Andrej J.; Langmead, Christopher J.
- PLoS ONE, Vol. 6, Issue 1
Categorical Dimensions of Human Odor Descriptor Space Revealed by Non-Negative Matrix Factorization
journal, September 2013
- Castro, Jason B.; Ramanathan, Arvind; Chennubhotla, Chakra S.
- PLoS ONE, Vol. 8, Issue 9
Positive matrix factorization: A non-negative factor model with optimal utilization of error estimates of data values
journal, June 1994
- Paatero, Pentti; Tapper, Unto
- Environmetrics, Vol. 5, Issue 2
Synchrony, Waves, and Spatial Hierarchies in the Spread of Influenza
journal, March 2006
- Viboud, C.; Bjornstad, O. N.; Smith, D. L.
- Science, Vol. 312, Issue 5772
A Brief Targeted Review of Susceptibility Factors, Environmental Exposures, Asthma Incidence, and Recommendations for Future Asthma Incidence Research
journal, April 2006
- Yeatts, Karin; Sly, Peter; Shore, Stephanie
- Environmental Health Perspectives, Vol. 114, Issue 4
Public health surveillance with electronic medical records: at risk of surveillance bias and overdiagnosis
journal, April 2013
- Chiolero, A.; Santschi, V.; Paccaud, F.
- The European Journal of Public Health, Vol. 23, Issue 3
Off-label Prescribing Among Office-Based Physicians
journal, May 2006
- Radley, David C.; Finkelstein, Stan N.; Stafford, Randall S.
- Archives of Internal Medicine, Vol. 166, Issue 9
National Use of Postmenopausal Hormone Therapy
journal, January 2004
- Hersh, Adam L.; Stefanick, Marcia L.; Stafford, Randall S.
- JAMA, Vol. 291, Issue 1
Estimating Effect of Antiviral Drug Use during Pandemic (H1N1) 2009 Outbreak, United States
journal, September 2011
- Atkins, Charisma
- Emerging Infectious Diseases, Vol. 17, Issue 9
Prescription Drug Spending Trends In The United States: Looking Beyond The Turning Point
journal, January 2008
- Aitken, Murray; Berndt, Ernst R.; Cutler, David M.
- Health Affairs, Vol. 27, Issue Suppl1
National Trends in Treatment of Type 2 Diabetes Mellitus, 1994-2007
journal, October 2008
- Alexander, G. Caleb; Sehgal, Niraj L.; Moloney, Rachael M.
- Archives of Internal Medicine, Vol. 168, Issue 19
Detecting influenza epidemics using search engine query data
journal, February 2009
- Ginsberg, Jeremy; Mohebbi, Matthew H.; Patel, Rajan S.
- Nature, Vol. 457, Issue 7232
Comparison: Flu Prescription Sales Data from a Retail Pharmacy in the US with Google Flu Trends and US ILINet (CDC) Data as Flu Activity Indicator
journal, August 2012
- Patwardhan, Avinash; Bilkovski, Robert
- PLoS ONE, Vol. 7, Issue 8
Reassessing Google Flu Trends Data for Detection of Seasonal and Pandemic Influenza: A Comparative Epidemiological Study at Three Geographic Scales
journal, October 2013
- Olson, Donald R.; Konty, Kevin J.; Paladini, Marc
- PLoS Computational Biology, Vol. 9, Issue 10
Developing a Social Media System for Biosurveillance
journal, March 2014
- Waters, Julie; Howard, Kristina; Baker, Heather
- Online Journal of Public Health Informatics, Vol. 6, Issue 1
An overview of Internet biosurveillance
journal, November 2013
- Hartley, D. M.; Nelson, N. P.; Arthur, R. R.
- Clinical Microbiology and Infection, Vol. 19, Issue 11
An exploratory study of a text classification framework for Internet-based surveillance of emerging epidemics
journal, January 2011
- Torii, Manabu; Yin, Lanlan; Nguyen, Thang
- International Journal of Medical Informatics, Vol. 80, Issue 1
Crowdsourcing, citizen sensing and sensor web technologies for public and environmental health surveillance and crisis management: trends, OGC standards and application examples
journal, January 2011
- Kamel Boulos, Maged N.; Resch, Bernd; Crowley, David N.
- International Journal of Health Geographics, Vol. 10, Issue 1
The Use of Twitter to Track Levels of Disease Activity and Public Concern in the U.S. during the Influenza A H1N1 Pandemic
journal, May 2011
- Signorini, Alessio; Segre, Alberto Maria; Polgreen, Philip M.
- PLoS ONE, Vol. 6, Issue 5
Twitter as a Sentinel in Emergency Situations: Lessons from the Boston Marathon Explosions
journal, January 2013
- Cassa, Christopher; Chunara, Rumi; Mandl, Kenneth
- PLoS Currents
Social and News Media Enable Estimation of Epidemiological Patterns Early in the 2010 Haitian Cholera Outbreak
journal, January 2012
- Chunara, Rumi; Andrews, Jason R.; Brownstein, John S.
- The American Journal of Tropical Medicine and Hygiene, Vol. 86, Issue 1
Assessing Google Flu Trends Performance in the United States during the 2009 Influenza Virus A (H1N1) Pandemic
journal, August 2011
- Cook, Samantha; Conrad, Corrie; Fowlkes, Ashley L.
- PLoS ONE, Vol. 6, Issue 8
The Parable of Google Flu: Traps in Big Data Analysis
journal, March 2014
- Lazer, D.; Kennedy, R.; King, G.
- Science, Vol. 343, Issue 6176
Syndemics and Public Health: Reconceptualizing Disease in Bio-Social Context
journal, December 2003
- Singer, Merill; Clair, Scott
- Medical Anthropology Quarterly, Vol. 17, Issue 4
Viruses as precipitants of asthma symptoms. I. Epidemiology
journal, March 1992
- Pattemore, P. K.; Johnston, S. L.; Bardin, P. G.
-
Clinical
Experimental Allergy, Vol. 22, Issue 3
Viral respiratory infection and the link to asthma
journal, January 2004
- Gern, James E.
- Pediatric Infectious Disease Journal, Vol. 23, Issue 1
Asthma, influenza, and vaccination
journal, December 2006
- Glezen, W.
- Journal of Allergy and Clinical Immunology, Vol. 118, Issue 6
Influenza vaccine in patients with asthma
journal, February 2006
- Hanania, Nicola A.; Atmar, Robert L.; Castro, Mario
- Expert Review of Vaccines, Vol. 5, Issue 1
Clinical pearls for preventing, diagnosing, and treating seasonal and 2009 H1N1 influenza infection in patients with asthma
journal, November 2009
- Rank, Matthew A.; Li, James T.
- Journal of Allergy and Clinical Immunology, Vol. 124, Issue 5
The Safety of Inactivated Influenza Vaccine in Adults and Children with Asthma
journal, November 2001
- ,
- New England Journal of Medicine, Vol. 345, Issue 21, p. 1529-1536
Oral Oseltamivir Improves Pulmonary Function and Reduces Exacerbation Frequency for Influenza-Infected Children With Asthma
journal, March 2005
- Johnston, Sebastian L.; Ferrero, Fernando; Garcia, Maria Luz
- Pediatric Infectious Disease Journal, Vol. 24, Issue 3