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Biomedical subjects

Peter L Elkin

Publications and source records attributed to Peter L Elkin.

18 recordsLinked to original sources
PubMed2005

A controlled trial of automated classification of negation from clinical notes.

BACKGROUND: Identification of negation in electronic health records is essential if we are to understand the computable meaning of the records: Our objective is to compare the accuracy of an automated mechanism for assignment of Negation to clinical concepts within a compositional expression with Human Assigned Negation. Also to perform a failure analysis to identify the causes of poorly identified negation (i.e. Missed Conceptual Representation, Inaccurate Conceptual Representation, Missed Negation, Inaccurate identification of Negation). METHODS: 41 Clinical Documents (Medical Evaluations; sometimes outside of Mayo these are referred to as History and Physical Examinations) were parsed using the Mayo Vocabulary Server Parsing Engine. SNOMED-C was used to provide concept coverage for the clinical concepts in the record. These records resulted in identification of Concepts and textual clues to Negation. These records were reviewed by an independent medical terminologist, and the results were tallied in a spreadsheet. Where questions on the review arose Internal Medicine Faculty were employed to make a final determination. RESULTS: SNOMED-CT was used to provide concept coverage of the 14,792 Concepts in 41 Health Records from John's Hopkins University. Of these, 1,823 Concepts were identified as negative by Human review. The sensitivity (Recall) of the assignment of negation was 97.2% (p < 0.001, Pearson Chi-Square test; when compared to a coin flip). The specificity of assignment of negation was 98.8%. The positive likelihood ratio of the negation was 81. The positive predictive value (Precision) was 91.2% CONCLUSION: Automated assignment of negation to concepts identified in health records based on review of the text is feasible and practical. Lexical assignment of negation is a good test of true Negativity as judged by the high sensitivity, specificity and positive likelihood ratio of the test. SNOMED-CT had overall coverage of 88.7% of the concepts being negated.

Abstracting and Indexing↗
PubMed2005

Use of complementary and alternative medical therapies by patients referred to a fibromyalgia treatment program at a tertiary care center.

OBJECTIVE: To evaluate the frequency and pattern of complementary and alternative medicine (CAM) use in patients referred to a fibromyalgia treatment program at a tertiary care center. PATIENTS AND METHODS: Patients referred to the Mayo Fibromyalgia Treatment Program between February 2003 and July 2003 were invited on their initial visit to participate in a survey regarding CAM use during the previous 6 months. An 85-question survey that addressed different CAM domains was used. RESULTS: Of the 304 patients invited to participate, 289 (95%) completed the survey (263 women and 26 men). Ninety-eight percent of the patients had used some type of CAM therapy during the previous 6 months. The 10 most frequently used CAM treatments were exercise for a specific medical problem (48%), spiritual healing (prayers) (45%), massage therapy (44%), chiropractic treatments (37%), vitamin C (35%), vitamin E (31%), magnesium (29%), vitamin B complex (25%), green tea (24%), and weight-loss programs (20%). CONCLUSION: CAM use is common in patients referred to a fibromyalgia treatment program.

Adolescent↗
PubMed2004

Techniques: Bioprospecting historical herbal texts by hunting for new leads in old tomes.

Ethnobotany has led to the identification of novel pharmacological agents but many challenges to using ethnobotany as a research tool remain. In particular, the loss of traditional knowledge together with the advent of high-throughput screening has made ethnobotanical techniques laborious and potentially unnecessary. However, historical herbal texts provide a preexisting resource that documents the traditional uses of various species as medicines. As generational losses of traditional knowledge accrue, these herbal texts become increasingly valuable. The methodology for extracting useful information contained within these resources had been cumbersome and consuming. However, the application of new bioinformatics data-mining systems to herbal texts holds great promise for identifying novel pharmacotherapeutic leads for bioactive compounds.

Ethnobotany↗
PubMed2004

Sensitivity and specificity of the semiquantitative latex agglutination D-dimer assay for the diagnosis of acute pulmonary embolism as defined by computed tomographic angiography.

OBJECTIVE: To determine the sensitivity and specificity of the semiquantitative latex agglutination plasma fibrin D-dimer assay for the diagnosis of acute pulmonary embolism by using computed tomographic (CT) angiography as the diagnostic reference standard. PATIENTS AND METHODS: From January 1, 1998, to June 26, 2000, patients who had both semiquantitative latex agglutination plasma fibrin D-dimer testing and CT angiography for suspected acute pulmonary embolism were selected for the study. A D-dimer value greater than 250 ng/mL was considered positive for thromboembolic disease. Diagnosis of acute pulmonary embolism was based solely on the interpretation of the CT angiogram. The D-dimer assay results were then compared with the CT angiographic diagnoses. RESULTS: Of 946 CT studies, 172 (18%) were positive for acute pulmonary embolism. The D-dimer assay was positive for 612 (65%) of the 946 patients. For acute pulmonary embolism, the D-dimer assay had a sensitivity of 0.83 (95% confidence interval [CI], 0.76-0.88), a specificity of 039 (95% CI, 036-0.43), a negative likelihood ratio of 0.44 (95 % CI, 032-0.62), and a negative predictive value of 0.91 (95% CI, 0.87-0.94). CONCLUSIONS: The semiquantitative latex agglutination plasma fibrin D-dimer assay had moderate sensitivity and low specificity for the diagnosis of acute pulmonary embolism. When used alone, the results of this test were insufficient to exclude this serious and potentially fatal disorder. Approximately two thirds of our patients had positive D-dimer assays and required further evaluation to exclude acute pulmonary embolism.

Adolescent↗
PubMed2004

VA National Drug File Reference Terminology: a cross-institutional content coverage study.

BACKGROUND: Content coverage studies provide valuable information to potential users of terminologies. We detail the VA National Drug File Reference Terminology's (NDF-RT) ability to represent dictated medication list phrases from the Mayo Clinic. NDF-RT is a description logic-based resource created to support clinical operations at one of the largest healthcare providers in the US. METHODS: Medication list phrases were extracted from dictated patient notes from the Mayo Clinic. Algorithmic mappings to NDF-RT using the SmartAccess Vocabulary Server (SAVS) were presented to two non-VA physicians. The physicians used a terminology browser to determine the accuracy of the algorithmic mapping and the content coverage of NDF-RT. RESULTS: The 509 extracted documents on 300 patients contained 847 medication concepts in medication lists. NDF-RT covered 97.8% of concepts. Of the 18 phrases that NDF-RT did not represent, 10 were for OTC's and food supplements, 5 were for prescription medications, and 3 were missing synonyms. The SAVS engine properly mapped 773 of 810 phrases with an overall sensitivity (precision) was 95.4% and positive predictive value (recall) of 99.9%. CONCLUSIONS: This study demonstrates that NDF-RT has more general utility than its initial design parameters dictated

Abstracting and Indexing↗
PubMed2004

Evaluation of SNOMED coverage of Veterans Health Administration terms.

Veterans Health Administration (VHA) is now evaluating use of SNOMED-CT. This paper reports the first phase of this evaluation, which examines the coverage of SNOMED-CT for problem list entries. Clinician expressions in VA problem lists are quite diverse compared to the content of the current VA terminology Lexicon. We selected a random set of 5054 narratives that were previously "unresolved" against the Lexicon. These narratives were mapped to SNOMED-CT using two automated tools. Experts reviewed a subset of the tools' matched, partly matched, and un-matched narratives. The automated tools produced exact or partial matches for over 90% of the 5054 unresolved narratives. SNOMED-CT has promise as a coding system for clinical problems. In subsequent studies, VA will examine the coverage of SNOMED for other clinical domains, such as drugs, allergies, and physician orders.

Forms and Records Control↗
PubMed2004

Generating complex clinical documents using structured entry and reporting.

Structured entry and reporting in medicine remains an elusive goal. Poor adoption of clinical structured entry for documentation results in part from the inherent complexity of entering patient histories, which are generally unstructured. The authors have developed a structured entry tool that has been adopted by practicing physicians for documentation of clinical encounters. To evaluate the impact of this tool on clinical documentation, the authors have performed two comparative studies investigating note complexity. Authors compared documents generated with a standard dictation/transcription model with documents generated with structured entry. Overall, documents generated with the structured entry and reporting tool contained 64% more concepts (P<0.01) than dictated documents while maintaining the same complexity. Depth and complexity of documentation with the structured entry and reporting tool varied by clinician user and by note sub-section.

Cardiology↗
PubMed2003

A formal representation for messages containing compositional expressions.

Clinically useful controlled vocabularies should represent healthcare concepts completely and with high reliability. Anticipating and pre-coordinating all possible expressions (e.g. 'fracture of the left femur' and 'fracture of the right femur') is not feasible. Variation in practice styles, requirements for the granularity of content, the exponential growth of terminology size, and increased cost of maintaining pre-coordinated terminologies lead us to conclude that no enumerated terminology can ever be truly comprehensive. Compositional terminologies are one potential solution to the problem of content completeness, but carry a risk of generating expressions whose equivalency cannot be easily determined. In order for post-coordinated expressions to be comparable, a sufficiently detailed formal mechanism for information representation is necessary. Comparable data for post-coordinated expressions requires normalization of both the contents and the semantics of the contents of the terminology with the information captured in post-coordinated expressions. In addition, comparable data requires a storage and messaging paradigm robust enough to faithfully represent the information contained within arbitrarily complex compositional expressions. We present a formalism for storing, and sending messages containing compositional expressions using a large-scale reference terminology. It is our intent that this formalism be used to algorithmically determine whether or not messages contain comparable data. In addition, we advocate transmitting the upward transitive closure of subsumption of all concepts, to improve comparability of data and to decrease reliance on locally stored versions of the underlying reference terminology.

Abstracting and Indexing↗
PubMed2003

Primer on medical genomics part V: bioinformatics.

Bioinformatics is the discipline that develops and applies informatics to the field of molecular biology. Although a comprehensive review of the entire field of bioinformatics is beyond the scope of this article, I review the basic tenets of the field and provide a topical sampling of the popular technologies available to clinicians and researchers. These technologies include tools and methods for sequence analysis (nucleotide and protein sequences), rendering of secondary and tertiary structures for these molecules, and protein fold prediction that can lead to rational drug design. I then discuss signaling pathways, new standards for data representation of genes and proteins, and finally the promise of merging these molecular data with the clinical world (the new science of phenomics).

Computational Biology↗
PubMed2003

Data representation in healthcare: a design for a freely-available openly-developed international reference terminology for healthcare.

The importance of data representation in healthcare has been of concern for centuries. In the last fifty years there has been an increasing awareness of the need for formal representations of terminological systems. We propose that terminological system development should be consensus driven and the product of iterative open refinement in order to practically serve the needs of the healthcare community. The system of development and maintenance of such a system must involve recruitment of the best and the brightest in the medical community to take responsibility for insuring the accuracy and completeness of such an effort. We suggest a method for algorithmically building a starting point for such a reference terminology. Further we suggest a distributed authoring environment that would allow domain experts to contribute regardless of their location or language. Open intellectual contribution is the necessary ingredient for a consensus based international health reference terminology.

Algorithms↗
PubMed2003

Coverage of oncology drug indication concepts and compositional semantics by SNOMED-CT.

OBJECTIVE: To evaluate SNOMED-CT 's ability to represent simple and compositional concepts in FDA approved oncology drug indications. METHODS: Oncology drug indications were decomposed into single and compositional concepts. SNOMED-CT's coverage of single concepts and the semantics needed to create compositional concepts were evaluated using automated and manual techniques. RESULTS: SNOMED-CT covered 86.3% of single concepts present in oncology drug indications; 11.3% of indications were covered completely. Coverage was best for concepts describing diseases, anatomy, and patient characteristics. Medications accounted for 50.5% of missing concepts. Excluding drug names, 45.2% of indications were completely represented. SNOMED-CT's semantics completely represented 60.1% of compositional expressions. CONCLUSIONS: SNOMED-CT's overall coverage of the concepts in oncology drug indications was good. Improvements or alternatives are needed for medications and semantics.

Antineoplastic Agents↗
PubMed2003

Adequacy of representation of the National Drug File Reference Terminology Physiologic Effects reference hierarchy for commonly prescribed medications.

The National Drug File Reference Terminology contains a novel reference hierarchy to describe physiologic effects (PE) of drugs. The PE reference hierarchy contains 1697 concepts arranged into two broad categories; organ specific and generalized systemic effects. This investigation evaluated the appropriateness of the PE concepts for classifying a random selection of commonly prescribed medications. Ten physician reviewers classified the physiologic effects of ten drugs and rated the accuracy of the selected term. Inter reviewer agreement, overall confidence, and concept frequencies were assessed and were correlated with the complexity of the drug's known physiologic effects. In general, agreement between reviewers was fair to moderate (kappa 0.08-0.49). The physiologic effects modeled became more disperse with drugs having and inducing multiple physiologic processes. Complete modeling of all physiologic effects was limited by reviewers focusing on different physiologic processes. The reviewers were generally comfortable with the accuracy of the concepts selected. Overall, the PE reference hierarchy was useful for physician reviewers classifying the physiologic effects of drugs. Ongoing evolution of the PE reference hierarchy as it evolves should take into account the experiences of our reviewers.

Drug Therapy↗
PubMed2002

Guideline and quality indicators for development, purchase and use of controlled health vocabularies.

Developers and purchasers of controlled health terminologies require valid mechanisms for comparing terminological systems. By Controlled Health Vocabularies, we refer to terminologies and terminological systems designed to represent clinical data at a granularity consistent with the practice of today's healthcare delivery. Comprehensive criterion for the evaluation of such systems historically have been lacking and the known criteria are inconsistently applied. Although there are many papers which describe specific desirable features of a controlled health vocabulary, to date there is not a consistent guide for evaluators of terminologies to reference, which will help them compare implementations of terminological systems on an equal footing [Methods Inf. Med. 37 (1998) 394, J. Am. Med. Inform. Assoc. 5 (1998) 503]. This guideline serves to fill the gap between academic enumeration of desirable terminological characteristics and the practical implementation or rigorous evaluations which will yield comparable data regarding the quality of one or more controlled health vocabularies.

Guidelines as Topic↗
PubMed2002

Symptomatic hyperthyroidism in a patient taking the dietary supplement tiratricol.

An 87-year-old woman was referred for evaluation of nervousness, tremor, insomnia, and fatigue of 2 months' duration. Initial laboratory evaluation revealed a suppressed thyrotropin level and an elevated triiodothyronine level. A review of her medications revealed that she had started taking several dietary supplements at the recommendation of her chiropractor before the onset of symptoms. One of these was tiratricol (3,5,3'-triiodothyroacetic acid or Triac), a substance sold as a dietary supplement despite classification as a drug by the Food and Drug Administration. Tiratricol has weak thyromimetic effects, can inhibit pituitary thyrotropin secretion, and in higher doses can significantly stimulate metabolism. Such was the case with this patient who presented with signs, symptoms, and biochemical evidence of hyperthyroidism that promptly resolved after discontinuation of tiratricol therapy. To our knowledge, this is the first reported case of documented thyrotoxicosis secondary to tiratricol use. Because tiratricol is still available for sale on several Internet sites, this case emphasizes the importance of inquiring about the use of dietary supplements in all patients. The availability of such products on the Internet increases the already complex task of monitoring patients' use of dietary supplements.

Aged↗
PubMed2002

Internal medicine resident satisfaction with a diagnostic decision support system (DXplain) introduced on a teaching hospital service.

OBJECTIVE: The objective of this study was to determine whether Internal Medicine residents would find the use of an expert system (i.e. Clinical Diagnostic Decision Support System) to be a satisfactory experience when used during a clinical rotation in the hospital setting. Resident willingness to use the instrument was considered to be of particular importance because of growing concerns regarding the educational experience of residents in the hospital. Thus, our first goal was to assess resident satisfaction with the tool, prior to widespread implementation. STUDY POPULATION: Residents on the General Medical Hospital Service at St. Mary's Hospital, Rochester, Minnesota STUDY TYPE: Prospective cohort study METHOD: We provided unrestricted access DXplain, a Web-based Clinical Diagnostic Decision Support System, to five general medical teams in St. Mary's Hospital, Rochester, MN. All residents were particularly encouraged to access the system during the evaluation of new admissions. Usage of the system was recorded electronically each time a user logged on. At the conclusion of the 2 month study period, a survey was sent electronically to each of the participating residents. RESULTS: During the study period, a total of 30 residents (G1 =20, G3= 10) rotated on the five medical services. 29/30 residents responded to the survey. 18/29 indicated that they had used the service, while 11/29 stated that they had not accessed the system. The resident's logged on 117 times to enter a case during the study period, with several entering more than one case per logon. The average number of log-ons per user was 2.4/week. Of the 18 who used the system, 15 found it useful (83.3%), 2 were unsure whether it was useful (11.1%), and 1 (5.6%) did not think it was helpful. However, when asked how often the system led the user to consider novel alternative diagnoses 13/18 (72.2%) responded "almost always to frequently" and 5/18 (27.8%) said "occasionally to sometimes". None of the users felt that the system "rarely" or "never" yielded additional diagnostic considerations. Seventeen out of eighteen users (94.4%) thought the system was "easy to use". When asked if they would like to have such a system regularly available 13/18 (72.2%) responded yes, while 4/18 (22.2%) were unsure. One resident said that they would not like to have DXplain available (5.6%). CONCLUSION: We believe the data reflect a significant level of satisfaction with the system among residents. Their recognition that it frequently led them to consider novel diagnoses suggests it had a positive educational impact.

Attitude of Health Personnel↗
PubMed2002

Initializing the VA medication reference terminology using UMLS metathesaurus co-occurrences.

We developed and evaluated a UMLS Metathesaurus Co-occurrence mining algorithm to connect medications and diseases they may treat. Based on 16 years of co-occurrence data, we created 977 candidate drug-disease pairs for a sample of 100 ingredients (50 commonly prescribed and 50 selected at random). Our evaluation showed that more than 80% of the candidate drug-disease pairs were rated "APPROPRIATE" by physician raters. Additionally, there was a highly significant correlation between the overall frequency of citation and the likelihood that the connection was rated "APPROPRIATE." The drug-disease pairs were used to initialize term definitions in an ongoing effort to build a medication reference terminology for the Veterans Health Administration. Co-occurrence mining is a valuable technique for initializing term definitions in a large-scale reference terminology creation project.

Algorithms↗
PubMedDate not supplied

Optimization of a research web environment for academic internal medicine faculty.

Usability evaluations are a powerful tool that can assist developers in their efforts to optimize the quality of their web environment. This underutilized, experimental method can serve to move applications toward true user-centered design. This article describes the usability methodology and illustrates its importance and application by describing a usability study undertaken at the Mayo Clinic for the purpose of improving an academic research web environment. Academic institutions struggling in an era of declining reimbursements are finding it difficult to maintain academic enterprises on the back of clinical revenues. This may result in declining amounts of time that clinical investigators have to spend in non-patient-related activities. For this reason, we have undertaken to design a web environment, which can minimize the time that a clinician-investigator needs to spend to accomplish academic instrumental activities of daily living. Usability evaluation is a powerful application of human factors engineering, which can improve the utility of web-based Informatics applications.

Computer Simulation↗