Standardizing the influenza neuraminidase inhibition assay among United States public health laboratories conducting virological surveillance.

BACKGROUND: Monitoring influenza virus susceptibility to neuraminidase (NA) inhibitors (NAIs) is vital for detecting drug-resistant variants, and is primarily assessed using NA inhibition (NI) assays, supplemented by NA sequence analysis. However, differences in NI testing methodologies between surveillance laboratories results in variability of 50% inhibitory concentration (IC50) values, which impacts data sharing, reporting and interpretation. In 2011, the Centers for Disease Control and Prevention (CDC), in collaboration with the Association for Public Health Laboratories (APHL) spearheaded efforts to standardize fluorescence-based NI assay testing in the United States (U.S.), with the goal of achieving consistency of IC50 data. METHODS: For the standardization process, three participating state public health laboratories (PHLs), designated as National Surveillance Reference Centers for Influenza (NSRC-Is), assessed the NAI susceptibility of the 2011-12 CDC reference virus panel using stepwise procedures, with support from the CDC reference laboratory. Next, the NSRC-Is assessed the NAI susceptibility of season 2011-12 U.S. influenza surveillance isolates (n = 940), with a large subset (n = 742) tested in parallel by CDC. Subsequently, U.S. influenza surveillance isolates (n = 9629) circulating during the next three influenza seasons (2012-15), were independently tested by the three NSRC-Is (n = 7331) and CDC (n = 2298). RESULTS: The NI assay IC50s generated by respective NSRC-Is using viruses and drugs prepared by CDC were similar to those obtained with viruses and drugs prepared in-house, and were uniform between laboratories. IC50s for U.S. surveillance isolates tested during four consecutive influenza seasons (2011-15) were consistent from season to season, within and between laboratories. CONCLUSION: These results show that the NI assay is robust enough to be standardized, marking the first time IC50 data have been normalized across multiple laboratories, and used for U.S. national NAI susceptibility surveillance.

Using co-occurrence network structure to extract synonymous gene and protein names from MEDLINE abstracts.

BACKGROUND: Text-mining can assist biomedical researchers in reducing information overload by extracting useful knowledge from large collections of text. We developed a novel text-mining method based on analyzing the network structure created by symbol co-occurrences as a way to extend the capabilities of knowledge extraction. The method was applied to the task of automatic gene and protein name synonym extraction. RESULTS: Performance was measured on a test set consisting of about 50,000 abstracts from one year of MEDLINE. Synonyms retrieved from curated genomics databases were used as a gold standard. The system obtained a maximum F-score of 22.21% (23.18% precision and 21.36% recall), with high efficiency in the use of seed pairs. CONCLUSION: The method performs comparably with other studied methods, does not rely on sophisticated named-entity recognition, and requires little initial seed knowledge.

A knowledge-based system for transfusion advice.

A knowledge-based system has been designed for evaluating the appropriateness of transfusion of non-red blood cell blood components. The goal of the system is to assist the blood bank physician in quality assurance efforts by automatically identifying cases of inappropriate transfusion before the blood is issued. Evaluation of a working prototype system shows that it is indeed capable of serving this function. The system identifies and summarizes cases, but it leaves consultation, education, and decision making to the blood bank physician. Small "expert systems" such as this may find use in quality assurance activities throughout the laboratory.

Representing thoughts, words, and things in the UMLS.

The authors describe a framework, based on the Ogden-Richards semiotic triangle, for understanding the relationship between the Unified Medical Language System (UMLS) and the source terminologies from which the UMLS derives its content. They pay particular attention to UMLS's Concept Unique Identifier (CUI) and the sense of "meaning" it represents as contrasted with the sense of "meaning" represented by the source terminologies. The CUI takes on emergent meaning through linkage to terms in different terminology systems. In some cases, a CUI's emergent meaning can differ significantly from the original sources' intended meanings of terms linked by that CUI. Identification of these different senses of meaning within the UMLS is consistent with historical themes of semantic interpretation of language. Examination of the UMLS within such a historical framework makes it possible to better understand the strengths and limitations of the UMLS approach for integrating disparate terminologic systems and to provide a model, or theoretic foundation, for evaluating the UMLS as a Possible World--that is, as a mathematical formalism that represents propositions about some perspective or interpretation of the physical world.

Evaluation of a "lexically assign, logically refine" strategy for semi-automated integration of overlapping terminologies.

OBJECTIVE: To evaluate a "lexically assign, logically refine" (LALR) strategy for merging overlapping healthcare terminologies. This strategy combines description logic classification with lexical techniques that propose initial term definitions. The lexically suggested initial definitions are manually refined by domain experts to yield description logic definitions for each term in the overlapping terminologies of interest. Logic-based techniques are then used to merge defined terms. METHODS: A LALR strategy was applied to 7,763 LOINC and 2,050 SNOMED procedure terms using a common set of defining relationships taken from the LOINC data model. Candidate value restrictions were derived by lexically comparing the procedure's name with other terms contained in the reference SNOMED topography, living organism, function, and chemical axes. These candidate restrictions were reviewed by a domain expert, transformed into terminologic definitions for each of the terms, and then algorithmically classified. RESULTS: The authors successfully defined 5,724 (73%) LOINC and 1,151 (56%) SNOMED procedure terms using a LALR strategy. Algorithmic classification of the defined concepts resulted in an organization mirroring that of the reference hierarchies. The classification techniques appropriately placed more detailed LOINC terms underneath the corresponding SNOMED terms, thus forming a complementary relationship between the LOINC and SNOMED terms. DISCUSSION: LALR is a successful strategy for merging overlapping terminologies in a test case where both terminologies can be defined using the same defining relationships, and where value restrictions can be drawn from a single reference hierarchy. Those concepts not having lexically suggested value restrictions frequently indicate gaps in the reference hierarchy.

Image acquisition context: procedure description attributes for clinically relevant indexing and selective retrieval of biomedical images.

OBJECTIVE: To support clinically relevant indexing of biomedical images and image-related information based on the attributes of image acquisition procedures and the judgments (observations) expressed by observers in the process of image interpretation. DESIGN: The authors introduce the notion of "image acquisition context," the set of attributes that describe image acquisition procedures, and present a standards-based strategy for utilizing the attributes of image acquisition context as indexing and retrieval keys for digital image libraries. METHODS: The authors' indexing strategy is based on an interdependent message/terminology architecture that combines the Digital Imaging and Communication in Medicine (DICOM) standard, the SNOMED (Systematized Nomenclature of Human and Veterinary Medicine) vocabulary, and the SNOMED DICOM microglossary. The SNOMED DICOM microglossary provides context-dependent mapping of terminology to DICOM data elements. RESULTS: The capability of embedding standard coded descriptors in DICOM image headers and image-interpretation reports improves the potential for selective retrieval of image-related information. This favorably affects information management in digital libraries.

Information workstations in clinical pathology.

Multitasking operating systems and expanding networks now permit smooth access to remote computers, peripherals, data, and information resources. Graphic user interfaces and productivity-enhancing software packages reduce the need for training and memorization of commands. New models of desktop computers based on "data-centered" software architecture can enhance workstation usefulness even more. Pathologists need to consider how these tools might improve access to and management of information and knowledge.

Applying the trauma triage rule to blunt trauma patients.

OBJECTIVE: To determine the accuracy of the Baxt Trauma Triage Rule (TTR: systolic blood pressure < 85 mm Hg; Glasgow Coma Scale-motor score < 5; or penetrating trauma to head, neck, or trunk) for prediction of major trauma in an independent data set of blunt trauma patients. METHODS: Retrospective evaluation of the TTR in a cohort of patients identified by Oregon Trauma System entry criteria. Accuracy for prediction of "major trauma" victims was measured using resource-based definitions of major trauma. Participants included 626 adult, blunt trauma patients at a level-I trauma center serving a metropolitan center of more than one million people. RESULTS: Of 524 patients with sufficient registry data to apply the TTR, 95 (18%) and 63 (12%) patients met the criteria for major trauma suggested by Baxt et al. and Emerman et al., respectively. Using the Baxt definition of major trauma, the TTR had a sensitivity of 74% (95% CI: 0.65-0.83) and a specificity of 84% (95% CI: 0.81-0.88). There were 25 significant false-negative results, including 12 patients requiring urgent laparotomy and four patients requiring emergency airway procedures. Using the Emerman definition of major trauma, sensitivity improved modestly to 76% (95% CI: 0.65-0.87) and specificity decreased slightly to 80% (95% CI: 0.77-0.84). CONCLUSIONS: In this blunt trauma population, the Baxt TTR failed to identify a significant number of severely injured patients. Slight alterations in the definition of "major trauma" can significantly affect the performance characteristics of triage instruments.

Knowledge-based systems in laboratory medicine and pathology. A review and survey of the field.

Knowledge-based systems are computer systems designed to handle knowledge-intensive tasks, usually involving reasoning and inference. They are increasingly being applied to problems in laboratory medicine and pathology. In this article we provide a brief introduction to the basic concepts of knowledge-based systems, review some of their published applications, and report on an informal survey of specialists in laboratory medicine and pathology. The survey, sent to 102 individuals, indicated that 24% were involved in developing knowledge-based systems, with most systems at an early stage of development. Recent advances in knowledge-based systems research as well as survey responses suggest that this technology will have increasing value in laboratory medicine and pathology.

A clinical laboratory information systems survey. A challenge for the decade.

In 1990, the College of American Pathologists Informatics Committee surveyed 14,785 laboratorians for their experiences with a clinical laboratory information system. A 16.25% response rate was achieved, representing 2402 questionnaires that were analyzed. Despite the perceived satisfaction of the clinical laboratory information system users with more expensive systems, no economy of scale was demonstrated with increasing system cost through either laboratory staff reduction or increased number of specimens per day. The strongest predictors of system satisfaction were (1) vendor success measured by number of installations and (2) a selection process that involved the pathologist/laboratory director and included a formal request for proposal. The need for integration of clinical laboratory information systems with hospital information systems, as well as the universal adoption of standard productivity terminology, including work load units, was evident.