Combining Free Text and Structured Electronic Medical Record Entries to Detect Acute Respiratory Infections

The electronic medical record (EMR) contains a rich source of information that could be harnessed for epidemic surveillance. We asked if structured EMR data could be coupled with computerized processing of free-text clinical entries to enhance detection of acute respiratory infections (ARI).A manual review of EMR records related to 15,377 outpatient visits uncovered 280 reference cases of ARI. We used logistic regression with backward elimination to determine which among candidate structured EMR parameters (diagnostic codes, vital signs and orders for tests, imaging and medications) contributed to the detection of those reference cases. We also developed a computerized free-text search to identify clinical notes documenting at least two non-negated ARI symptoms. We then used heuristics to build case-detection algorithms that best combined the retained structured EMR parameters with the results of the text analysis.An adjusted grouping of diagnostic codes identified reference ARI patients with a sensitivity of 79%, a specificity of 96% and a positive predictive value (PPV) of 32%. Of the 21 additional structured clinical parameters considered, two contributed significantly to ARI detection: new prescriptions for cough remedies and elevations in body temperature to at least 38°C. Together with the diagnostic codes, these parameters increased detection sensitivity to 87%, but specificity and PPV declined to 95% and 25%, respectively. Adding text analysis increased sensitivity to 99%, but PPV dropped further to 14%. Algorithms that required satisfying both a query of structured EMR parameters as well as text analysis disclosed PPVs of 52-68% and retained sensitivities of 69-73%.Structured EMR parameters and free-text analyses can be combined into algorithms that can detect ARI cases with new levels of sensitivity or precision. These results highlight potential paths by which repurposed EMR information could facilitate the discovery of epidemics before they cause mass casualties

Doctor of Philosophy

dissertationElectronic Health Records (EHRs) provide a wealth of information for secondary uses. Methods are developed to improve usefulness of free text query and text processing and demonstrate advantages to using these methods for clinical research, specifically cohort identification and enhancement. Cohort identification is a critical early step in clinical research. Problems may arise when too few patients are identified, or the cohort consists of a nonrepresentative sample. Methods of improving query formation through query expansion are described. Inclusion of free text search in addition to structured data search is investigated to determine the incremental improvement of adding unstructured text search over structured data search alone. Query expansion using topic- and synonym-based expansion improved information retrieval performance. An ensemble method was not successful. The addition of free text search compared to structured data search alone demonstrated increased cohort size in all cases, with dramatic increases in some. Representation of patients in subpopulations that may have been underrepresented otherwise is also shown. We demonstrate clinical impact by showing that a serious clinical condition, scleroderma renal crisis, can be predicted by adding free text search. A novel information extraction algorithm is developed and evaluated (Regular Expression Discovery for Extraction, or REDEx) for cohort enrichment. The REDEx algorithm is demonstrated to accurately extract information from free text clinical iv narratives. Temporal expressions as well as bodyweight-related measures are extracted. Additional patients and additional measurement occurrences are identified using these extracted values that were not identifiable through structured data alone. The REDEx algorithm transfers the burden of machine learning training from annotators to domain experts. We developed automated query expansion methods that greatly improve performance of keyword-based information retrieval. We also developed NLP methods for unstructured data and demonstrate that cohort size can be greatly increased, a more complete population can be identified, and important clinical conditions can be detected that are often missed otherwise. We found a much more complete representation of patients can be obtained. We also developed a novel machine learning algorithm for information extraction, REDEx, that efficiently extracts clinical values from unstructured clinical text, adding additional information and observations over what is available in structured text alone

Utilização de técnicas de text mining sobre registos clínicos de epilepsia em crianças, para auxílio ao diagnóstico e classificação

Dissertação apresentado à Escola Superior de Tecnologia e Gestão do IPL para obtenção do grau de Mestre em Engenharia Informática - Computação Móvel, orientada pelo Doutor Rui Rijo e pela Doutora Catarina Silva.A informação médica tem aumentado continuamente ao longo do tempo, produzindo-se quantidades elevadíssimas de dados. A análise e a extração desses dados oferecem possibilidades de reduzir o esforço e o tempo na sugestão e classificação de um diagnóstico. O processamento dos dados médicos representa um grande desafio, considerando que estes dados são geralmente apresentados em texto livre e com vocabulário técnico específico. Entre os dados mais ricos e relevantes encontram-se os registos clínicos. A análise de registos clínicos é complexa pois para a realização de um diagnóstico correto é necessário ter em conta várias características como sintomas, exames, historial do paciente, tratamentos, medicamentos, entre outros. Além disso, esta análise requer um domínio de diferentes áreas de conhecimento para a realização de um diagnóstico fiável, entre outras data mining, text mining, registos clínicos eletrónicos, e a área clínica. Estes diagnósticos devem ainda ser classificados segundo normalizações, para que o médico possa tomar procedimentos e prescrever tratamentos mais corretos segundo determinadas classificações. O presente trabalho sugere uma abordagem que incide na área de epilepsia infantil, analisando e extraindo informação relevante de registos clínicos eletrónicos, para ajudar os médicos a tomar decisões, tais como identificar e classificar diagnósticos, ajudar na prescrição de tratamentos, medicamentos e na sugestão de procedimentos. A epilepsia infantil é complexa e não linear, uma vez que os médicos têm de analisar diferentes causas, entre outras, genéticas, estruturais, metabólicas, e um diagnóstico errado pode modificar a vida de uma criança. Os registos clínicos reais e anónimos foram fornecidos e transcritos com a ajuda do serviço de pediatria do Hospital Santo André. Os resultados alcançados são promissores, estando no entanto ainda longe dos desejados para permitir uma sugestão e classificação de diagnósticos de forma precisa e segura. Esta abordagem permite ainda uma classificação dos diagnósticos baseadas em normalizações, de forma a sugerir os melhores procedimentos, prognósticos e tratamentos dependendo da classificação encontrada. Desta forma, será possível ajudar a reduzir o erro médico na classificação de diagnósticos, o erro na prescrição, e aumentar a eficácia no processamento dos dados médicos, poupando tempo e dinheiro

Summary of notifiable infectious diseases and conditions -- United States, 2014

Published October 14, 2016, for 2014The Summary of Notifiable Infectious Diseases and Conditions\u2014United States, 2014 (hereafter referred to as the summary) contains the official statistics, in tabular and graphic form, for the reported occurrence of nationally notifiable infectious diseases and conditions in the United States for 2014. Unless otherwise noted, data are final totals for 2014 reported as of June 30, 2015. These statistics are collected and compiled from reports sent by U.S. state and territory, New York City, and District of Columbia health departments to the National Notifiable Diseases Surveillance System (NNDSS), which is operated by CDC in collaboration with the Council of State and Territorial Epidemiologists (CSTE). This summary is available at http://www.cdc.gov/mmwr/mmwr_nd/index.html. This site also includes summary publications from previous years.The Highlights section presents noteworthy epidemiologic and prevention information for 2014 for selected infectious diseases and conditions and additional information to aid in the interpretation of surveillance and infectious diseases- and conditions-trend data. Part 1 contains tables showing incident (new) cases and incidence rates for the nationally notifiable infectious diseases and conditions reported during 2014; these tables do not include rows for conditions with zero cases reported in 2014 (Tables 1,2,3,4,5, and 6).* The tables provide the number of cases reported to CDC for 2014 and the distribution of cases by MMWR month, geographic location, and demographic characteristics (e.g., age, sex, race, and ethnicity). Part 1 also includes a table with the reported incidence of notifiable diseases during 2004\u20132014 and a table enumerating deaths associated with specified notifiable infectious diseases and conditions reported to CDC\u2019s National Center for Health Statistics (NCHS) during 2008\u20132014 (Tables 7 and 8). Part 2 contains graphs and maps that depict summary data for selected notifiable infectious diseases and conditions described in tabular form in Part 1. Historical notifiable disease data, annotated as Part 3 in previous releases of this summary, will no longer be included in this report. Historical notifiable disease data during 1944\u20132013 are available online in previous years\u2019 summaries (http://www.cdc.gov/mmwr/mmwr_nd). The Selected Reading section presents general and disease-specific references for notifiable infectious diseases and conditions. These references provide additional information on surveillance and epidemiologic concerns, diagnostic concerns, and infectious disease-control activities. To increase the usefulness of future editions, comments regarding the current report and descriptions of how information is or could be used are invited. Comments should be e-mailed to [email protected] with the following subject line: \u201cAnnual Summary\u201d.Suggested citation for this article: Adams DA, Thomas KR, Jajosky R, et al. Summary of Notifiable Infectious Diseases and Conditions \u2014 United States, 2014. MMWR Morb Mortal Wkly Rep 2016;63:1-152 DOI: http://dx.doi.org/10.15585/mmwr.mm6354a1.201627736829664

THE PERCEIVED AND REAL VALUE OF HEALTH INFORMATION EXCHANGE IN PUBLIC HEALTH SURVEILLANCE

Indiana University-Purdue University Indianapolis (IUPUI)Public health agencies protect the health and safety of populations. A key function of public health agencies is surveillance or the ongoing, systematic collection, analysis, interpretation, and dissemination of data about health-related events. Recent public health events, such as the H1N1 outbreak, have triggered increased funding for and attention towards the improvement and sustainability of public health agencies’ capacity for surveillance activities. For example, provisions in the final U.S. Centers for Medicare and Medicaid Services (CMS) “meaningful use” criteria ask that physicians and hospitals report surveillance data to public health agencies using electronic laboratory reporting (ELR) and syndromic surveillance functionalities within electronic health record (EHR) systems. Health information exchange (HIE), organized exchange of clinical and financial health data among a network of trusted entities, may be a path towards achieving meaningful use and enhancing the nation’s public health surveillance infrastructure. Yet the evidence on the value of HIE, especially in the context of public health surveillance, is sparse. In this research, the value of HIE to the process of public health surveillance is explored. Specifically, the study describes the real and perceived completeness and usefulness of HIE in public health surveillance activities. To explore the real value of HIE, the study examined ELR data from two states, comparing raw, unedited data sent from hospitals and laboratories to data enhanced by an HIE. To explore the perceived value of HIE, the study examined public health, infection control, and HIE professionals’ perceptions of public health surveillance data and information flows, comparing traditional flows to HIE-enabled ones. Together these methods, along with the existing literature, triangulate the value that HIE does and can provide public health surveillance processes. The study further describes remaining gaps that future research and development projects should explore. The data collected in the study show that public health surveillance activities vary dramatically, encompassing a wide range of paper and electronic methods for receiving and analyzing population health trends. Few public health agencies currently utilize HIE-enabled processes for performing surveillance activities, relying instead on direct reporting of information from hospitals, physicians, and laboratories. Generally HIE is perceived well among public health and infection control professionals, and many of these professionals feel that HIE can improve surveillance methods and population health. Human and financial resource constraints prevent additional public health agencies from participating in burgeoning HIE initiatives. For those agencies that do participate, real value is being added by HIEs. Specifically, HIEs are improving the completeness and semantic interoperability of ELR messages sent from clinical information systems. New investments, policies, and approaches will be necessary to increase public health utilization of HIEs while improving HIEs’ capacity to deliver greater value to public health surveillance processes

Biochemical and epidemiological investigations of non-steroidal anti-inflammatory drug usage and related side effects in equids

Non-steroidal anti-inflammatory drugs (NSAIDs) are widely used in equine veterinary practice. These drugs exert their effect by inhibiting cyclooxygenase (COX) enzymes, which control prostaglandin production, a major regulator of tissue perfusion. Two isoforms of COX enzymes exist: COX-1 is physiologically present in tissues, while COX-2 is up-regulated during inflammation and has been indicated as responsible for the negative effects of an inflammatory response. Evidence suggests that NSAIDs that inhibit only COX-2, preserving the physiological function of COX-1 might have a safer profile. Studies that evaluate the effect of NSAIDs on COX enzymes are all performed under experimental conditions and none uses actual clinical patients. The biochemical investigations in this work focus on describing the effect on COX enzymes activity of flunixin meglumine and phenylbutazone, two non-selective COX inhibitors and firocoxib, a COX-2 selective inhibitor, in clinical patients undergoing elective surgery. A separate epidemiological investigation was aimed at describing the impact that the findings of biochemical data have on a large population of equids. Electronic medical records (EMRs) from 454,153 equids were obtained from practices in the United Kingdom, United States of America and Canada. Information on prevalence and indications for NSAIDs use was extracted from the EMRs via a text mining technique, improved from the literature and described and validated within this Thesis. Further the prevalence of a clinical sign compatible with NSAID toxicity, such as diarrhoea, is reported along with analysis evaluating NSAID administration in light of concurrent administration of other drugs and comorbidities. This work confirms findings from experimental settings that NSAIDs firocoxib is COX-2 selective and that flunixin meglumine and phenylbutazone are non-selective COX inhibitors and therefore their administration carries a greater risk of toxicity. However the impact of this finding needs to be interpreted with caution as epidemiological data suggest that the prevalence of toxicity is in fact small and the use of these drugs at the labelled dose is quite safe