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Biomedical subjects

Alexander C Yu

Publications and source records attributed to Alexander C Yu.

3 recordsLinked to original sources

Representation of ophthalmology concepts by electronic systems: intercoder agreement among physicians using controlled terminologies.

OBJECTIVE: To assess intercoder agreement for ophthalmology concepts by 3 physician coders using 5 controlled terminologies (International Classification of Diseases 9, Clinical Modification [ICD9CM]; Current Procedural Terminology, fourth edition; Logical Observation Identifiers, Names, and Codes [LOINC]; Systematized Nomenclature of Medicine, Clinical Terms [SNOMED-CT]; and Medical Entities Dictionary). DESIGN: Noncomparative case series. PARTICIPANTS: Five complete ophthalmology case presentations selected from a publicly available journal. METHODS: Each case was parsed into discrete concepts. Electronic or paper browsers were used independently by 3 physician coders to assign a code for every concept in each terminology. A match score representing adequacy of assignment for each concept was assigned on a 3-point scale (0, no match; 1, partial match; 2, complete match). For every concept, the level of intercoder agreement was determined by 2 methods: (1) based on exact code matching with assignment of complete agreement when all coders assigned the same code, partial agreement when 2 coders assigned the same code, and no agreement when all coders assigned different codes, and (2) based on manual review for semantic equivalence of all assigned codes by an independent ophthalmologist to classify intercoder agreement for each concept as complete agreement, partial agreement, or no agreement. Subsequently, intercoder agreement was calculated in the same manner for the subset of concepts judged to have adequate coverage by each terminology, based on receiving a match score of 2 by at least 2 of the 3 coders. MAIN OUTCOME MEASURES: Intercoder agreement in each controlled terminology: complete, partial, or none. RESULTS: Cases were parsed into 242 unique concepts. When all concepts were analyzed by manual review, the proportion of complete intercoder agreement ranged from 12% (LOINC) to 44% (SNOMED-CT), and the difference in intercoder agreement between LOINC and all other terminologies was statistically significant (P<0.004). When only concepts with adequate terminology were analyzed by manual review, the proportion of complete intercoder agreement ranged from 33% (LOINC) to 64% (ICD9CM), and there were no statistically significant differences in intercoder agreement among any pairs of terminologies. CONCLUSIONS: The level of intercoder agreement for ophthalmic concepts in existing controlled medical terminologies is imperfect. Intercoder reproducibility is essential for accurate and consistent electronic representation of medical data.

Decision Support Systems, Clinical↗

Methods in biomedical ontology.

Research on ontologies is becoming widespread in the biomedical informatics community. At the same time, it has become apparent that the challenges of properly constructing and maintaining ontologies have proven more difficult than many workers in the field initially expected. Discovering general, feasible methods has thus become a central activity for many of those hoping to reap the benefits of ontologies. This paper reviews current methods in the construction, maintenance, alignment, and evaluation of ontologies.

Animals↗

Development of multiorgan pathology in the wpk rat model of polycystic kidney disease.

Rodent models of polycystic kidney disease (PKD) have provided valuable insight into the cellular changes associated with cystogenesis in humans. The present study characterizes the morphology of renal and extrarenal pathology of autosomal recessive PKD induced by the wpk gene in Wistar rats. In wpk(-/-) rats, proximal tubule and collecting duct cysts develop in utero and eventually consume the kidney. Increased apoptosis, mitosis, and extracellular tenascin deposition parallel cyst development. Extrarenal pathology occurs in the immune system (thymic and splenic hypoplasia) and central nervous system (CNS; hypoplasia to agenesis of the corpus callosum with severe hydrocephalus). Severity of hydrocephalus varied inversely with size of the corpus callosum. In wpk(-/-) rats, the corpus callosum exhibits relatively few axons that cross the midline. This CNS pathology is similar to that described in three human renal cystic syndromes: orofaciodigital, genitopatellar, and cerebrorenal-digital syndromes. Collecting duct and ventricular ependymal cilia appear morphologically normal. To determine if rodent background strain and the presence of modifier genes affect severity of the disease, we crossed the Wistar-wpk rat with Brown Norway (BN) and Long Evan (LE) rats and found the degree of renal and cerebral pathology was diminished as evidenced by lower kidney weight as a percent of body weight and serum urea nitrogen concentration in cystic rats on LE or BN strains as well as less prominent cranial enlargement. Crosses with BN rats allowed us to localize the wpk gene on chromosome 5 very close to the D5Rat73 marker. The wpk gene lies within a chromosomal region known to harbor a PKD modifier locus. In summary, the types of renal and cerebral pathology seen in the Wistar wpk rat are a unique combination seen only in this rodent model.

Agenesis of Corpus Callosum↗