Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

Proyecto, investigación e innovación en urbanismo, arquitectura y diseño industrial

Actas de congresoLas VII Jornadas de Investigación “Encuentro y Reflexión” y I Jornadas de Investigación de becarios y doctorandos. Proyecto, investigación e innovación en Urbanismo, Arquitectura y Diseño Industrial se centraron en cuatro ejes: el proyecto; la dimensión tecnológica y la gestión; la dimensión social y cultural y la enseñanza en Arquitectura, Urbanismo y Diseño Industrial, sustentados en las líneas prioritarias de investigación definidas epistemológicamente en el Consejo Asesor de Ciencia y Tecnología de esta Universidad Nacional de Córdoba. Con el objetivo de afianzar continuidad, formación y transferencia de métodos, metodología y recursos se incorporó becarios y doctorandos de los Institutos de investigación. La Comisión Honoraria la integraron las tres Secretarias de Investigación de la Facultad, arquitectas Marta Polo, quien fundó y María del Carmen Franchello y Nora Gutiérrez Crespo quienes continuaron la tradición de la buena práctica del debate en la cotidianeidad de la propia Facultad. Los textos que conforman las VII Jornadas son los avances y resultados de las investigaciones realizadas en el bienio 2016-2018.Fil: Novello, María Alejandra. Universidad Nacional de Córdoba. Facultad de Arquitectura, Urbanismo y Diseño; ArgentinaFil: Repiso, Luciana. Universidad Nacional de Córdoba. Facultad de Arquitectura, Urbanismo y Diseño; ArgentinaFil: Mir, Guillermo. Universidad Nacional de Córdoba. Facultad de Arquitectura, Urbanismo y Diseño; ArgentinaFil: Brizuela, Natalia. Universidad Nacional de Córdoba. Facultad de Arquitectura, Urbanismo y Diseño; ArgentinaFil: Herrera, Fernanda. Universidad Nacional de Córdoba. Facultad de Arquitectura, Urbanismo y Diseño; ArgentinaFil: Períes, Lucas. Universidad Nacional de Córdoba. Facultad de Arquitectura, Urbanismo y Diseño; ArgentinaFil: Romo, Claudia. Universidad Nacional de Córdoba. Facultad de Arquitectura, Urbanismo y Diseño; ArgentinaFil: Gordillo, Natalia. Universidad Nacional de Córdoba. Facultad de Arquitectura, Urbanismo y Diseño; ArgentinaFil: Andrade, Elena Beatriz. Universidad Nacional de Córdoba. Facultad de Arquitectura, Urbanismo y Diseño; Argentin

patrimonio intelectual

Actas de congresoLas VI Jornadas se realizaron con la exposición de ponencias que se incluyeron en cuatro ejes temáticos, que se desarrollaron de modo sucesivo para facilitar la asistencia, el intercambio y el debate, distribuidos en tres jornadas. Los ejes temáticos abordados fueron: 1. La enseñanza como proyecto de investigación. Recursos de enseñanza-aprendizaje como mejoras de la calidad educativa. 2. La experimentación como proyecto de investigación. Del ensayo a la aplicabilidad territorial, urbana, arquitectónica y de diseño industrial. 3. Tiempo y espacio como proyecto de investigación. Sentido, destino y usos del patrimonio construido y simbólico. 4. Idea constructiva, formulación y ejecución como proyecto de investigación. Búsqueda y elaboración de resultados que conforman los proyectos de la arquitectura y el diseño

An inaugural diabetic ketoacidosis with acute pancreatitis during COVID-19

International audienc

Temporal deep learning framework for retinopathy prediction in patients with type 1 diabetes

International audienceThe adoption of electronic health records in hospitals has ensured the availability of large datasets that can be used to predict medical complications. The trajectories of patients in real-world settings are highly variable, making longitudinal data modeling challenging. In recent years, significant progress has been made in the study of deep learning models applied to time series; however, the application of these models to irregular medical time series (IMTS) remains limited. To address this issue, we developed a generic deep-learning-based framework for modeling IMTS that facilitates the comparative studies of sequential neural networks (transformers and long short-term memory) and irregular time representation techniques. A validation study to predict retinopathy complications was conducted on 1207 patients with type 1 diabetes in a French database using their historical glycosylated hemoglobin measurements, without any data aggregation or imputation. The transformer-based model combined with the soft one-hot representation of time gaps achieved the highest score: an area under the receiver operating characteristic curve of 88.65%, specificity of 85.56%, sensitivity of 83.33% and an improvement of 11.7% over the same architecture without time information. This is the first attempt to predict retinopathy complications in patients with type 1 diabetes using deep learning and longitudinal data collected from patient visits. This study highlighted the significance of modeling time gaps between medical records to improve prediction performance and the utility of a generic framework for conducting extensive comparative studies

Pancytopénie sévère secondaire à un déficit en folates en dépit d’un dosage de folatesérythrocytaires normal

International audienceWe report the case of an alcoholic patient with severe pancytopenia with lowplasma folate level but normal erythrocyte folates and cobalamin levels. The bone marrow smear concluded to a pancytopenia due to folates and/or cobalamin deficiency. Severe pancytopenia due to acute plasma folate deficiency can be observed despite normal erythrocyte folates level which reflects the organism’s folates store.Nous rapportons un cas de pancytopénie sévère avec dosage en folates sériques isolément bas contrastant avec des folates érythrocytaires et vitamine B12 normaux, chez un patient alcoolique. Le myélogramme montrait un aspect de moelle carentielle en ces vitamines. Ce cas met en lumière la possibilité de survenue d’une pancytopénie sévère secondaire à une carence en folates, en dépit d’un dosage normal de folates érythrocytaires, qui est un indicateur des apports en folates des 3 derniers mois (durée de vie du globule rouge) et donc des réserves de l’organisme

R-spondin2, a novel target of NOBOX: identification of variants in a cohort of women with primary ovarian insufficiency

Abstract Background R-spondin2 (Rspo2) is a secreted agonist of the canonical Wnt/β-catenin signaling pathway. Rspo2 plays a key role in development of limbs, lungs and hair follicles, and more recently during ovarian follicle development. Rspo2 heterozygous deficient female mice become infertile around 4 months of age mimicking primary ovarian insufficiency (POI). The study aimed to investigate the regulation of RSPO2 and its potential involvement in pathophysiology of POI. Methods We cloned the RSPO2 promoter and performed transcriptional assays to determine if RSPO2 can be regulated by NOBOX, an ovarian transcription factor. Then, we evaluated 100 infertile women after obtaining a detailed history of the disease and follicle-stimulating hormone measurements, besides karyotype determination and fragile-X premutation syndrome investigation. All exons, intron-exon boundaries and untranslated regions of the RSPO2 gene were identified by sequencing, and the results were statistically analyzed. Results We found that RSPO2 can be regulated by NOBOX via the presence of NOBOX Binding Element in its promoter. Among 9 identified variants in POI women, 4 of them were equally homozygous, 4 have never been described (c.-359C > G, c.-190G > A, c.-170 + 13C > T and c.-169-8 T > A), only one c.557 T > C was predicted to alter a single amino acid in the RSPO2 protein (p.Leu186Pro). Conclusions RSPO2 is a novel target gene of the NOBOX key transcription factor, confirming its important role during the follicular growth in ovary. However, RSPO2 mutations are rare or uncommon in women with POI

Diagnostic Challenge in PLIN1-Associated Familial Partial Lipodystrophy

International audienc

Pegvisomant treatment in acromegaly in clinical practice: Final results of the French ACROSTUDY (312 patients)

International audienc