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BackgroundAlthough electronic health records (EHRs) have been widely used in secondary assessments, clinical documents are relatively less utilized owing to the lack of standardized clinical text frameworks across different institutions. ObjectiveThis study aimed to develop a framework for processing unstructured clinical documents of EHRs and integration with standardized structured data. MethodsWe developed a framework known as Staged Optimization of Curation, Regularization, and Annotation of clinical text (SOCRATex). SOCRATex has the following four aspects: (1) extracting clinical notes for the target population and preprocessing the data, (2) defining the annotation schema with a hierarchical structure, (3) performing document-level hierarchical annotation using the annotation schema, and (4) indexing annotations for a search engine system. To test the usability of the proposed framework, proof-of-concept studies were performed on EHRs. We defined three distinctive patient groups and extracted their clinical documents (ie, pathology reports, radiology reports, and admission notes). The documents were annotated and integrated into the Observational Medical Outcomes Partnership (OMOP)-common data model (CDM) database. The annotations were used for creating Cox proportional hazard models with different settings of clinical analyses to measure (1) all-cause mortality, (2) thyroid cancer recurrence, and (3) 30-day hospital readmission. ResultsOverall, 1055 clinical documents of 953 patients were extracted and annotated using the defined annotation schemas. The generated annotations were indexed into an unstructured textual data repository. Using the annotations of pathology reports, we identified that node metastasis and lymphovascular tumor invasion were associated with all-cause mortality among colon and rectum cancer patients (both P=.02). The other analyses involving measuring thyroid cancer recurrence using radiology reports and 30-day hospital readmission using admission notes in depressive disorder patients also showed results consistent with previous findings. ConclusionsWe propose a framework for hierarchical annotation of textual data and integration into a standardized OMOP-CDM medical database. The proof-of-concept studies demonstrated that our framework can effectively process and integrate diverse clinical documents with standardized structured data for clinical research.

PurposeTo determine whether germline BRCA (gBRCA) pathogenic variants are associated with decreased ovarian reserve.Materials and methodsAn individual patient-level data meta-analysis was performed using five data sets on 828 evaluable women who were tested for gBRCA. Of those, 250 carried gBRCA, whereas 578 had tested negative and served as controls. Of the women with gBRCA, four centers studied those affected with breast cancer (n = 161) and one studied unaffected individuals (n = 89). The data were adjusted for the center, age, body mass index, smoking, and oral contraceptive pill use before the final analysis. Anti-Müllerian hormone (AMH) levels in affected women were drawn before presystemic therapy.ResultsThe mean age of women with versus without gBRCA1/2 (34.1 ± 4.9 v 34.3 ± 4.8 years; P = .48) and with gBRCA1 versus gBRCA2 (33.7 ± 4.9 v 34.6 ± 4.8 years; P = .16) was similar. After the adjustments, women with gBRCA1/2 had significantly lower AMH levels compared with controls (23% lower; 95% CI, 4 to 38; P = .02). When the adjusted analysis was limited to affected women (157 with gBRCA v 524 without, after exclusions), the difference persisted (25% lower; 95% CI, 9 to 38; P = .003). The serum AMH levels were lower in women with gBRCA1 (33% lower; 95% CI, 12 to 49; P = .004) but not gBRCA2 compared with controls (7% lower; 95% CI, 31% lower to 26% higher; P = .64).ConclusionYoung women with gBRCA pathogenic variants, particularly those affected and with gBRCA1, have lower serum AMH levels compared with controls. They may need to be preferentially counseled about the possibility of shortened reproductive lifespan because of diminished ovarian reserve.

Sex determination of birds is essential for ecological studies, but visually distinguishing the sex of monomorphic birds in the field is challenging. We investigated intersexual morphological differences in the Eurasian Tree Sparrow (Passer montanus saluratus), which is known as a sexually monomorphic species. We caught 198 adult Eurasian Tree Sparrows (104 males and 94 females), collected data on their morphological characteristics, and determined their sex using polymerase chain reaction to amplify sex-chromosome-linked CHD gene introns. Wing length was longer in males than in females, and badge sizes were significantly larger in males. Discriminant function analysis using badge size and wing length classified sex with an accuracy of 86.9%. In accordance with a previous paper, our study considers that the sex of Eurasian Tree Sparrows can be distinguished with reasonable accuracy by the badge size and wing length in wild populations. Received 6 January 2022. Accepted 16 July 2022. Key words: badge size, CHD gene intron, discriminant function analysis, monomorphism, sex determination, wing length. La determination del sexo do las aves cs esencial en estudios ecologicos. pero la determinacion visual del sexo en aves monomoriicas en campo es un reto. lnvcstigamos diferencias morfologicas intersexuales en el gorrion molinero eurasiatico (Passer montanus saluratus), que es conocido como una especie sexualmente monomorfica. Capturamos 198 gorriones molineros curasiaticos adultos (104 machos y 94 hembras), tomamos datos dc sus caracteristicas morfologicas y detenninamos su sexo usando rcaccion en cadena de polimerasa para ampliticar los introncs del gen CHD ligados al cromosoma sexual. La longitud del ala era mayor en machos que en hembras y los tamanos de las manchas eran significativamente mayorcs en machos que en hembras. Un analisis de funcidn discriminante usando tamano dc las manchas y longitud de! ala ctasifico el sexo con una precision de 86.9%. Tal y como se dijo en un articulo anterior, nuestro cstudio considers que el sexo de los gorriones molineros curasiaticos puede ser distinguido con una precision razonablc utilizando el tamano de la mancha y la longitud del ala en poblaciones silvestres. Palabras clave: analisis de funcidn discriminante. determinacion de sexo. intron del gen CHD. longitud dc ala, monomorfismo. tamano de mancha., Sex identification is essential for studying the biology of avian breeding, but it is difficult to visually distinguish the sex of monomorphic species. Sexual monomorphism appears in 30% of all [...]