SpatialOne: End-to-End analysis of visium data at scale.

MOTIVATION: Spatial transcriptomics allow to quantify mRNA expression within the spatial context. Nonetheless, in-depth analysis of spatial transcriptomics data remains challenging and difficult to scale due to the number of methods and libraries required for that purpose. RESULTS: Here we present SpatialOne, an end-to-end pipeline designed to simplify the analysis of 10x Visium data by combining multiple state-of-the-art computational methods to segment, deconvolve and quantify spatial information; this approach streamlines the analysis of reproducible spatial-data at scale. AVAILABILITY AND IMPLEMENTATION: SpatialOne source code and execution examples are available at https://github.com/Sanofi-Public/spatialone-pipeline. SpatialOne is distributed as a docker container image. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Eficacia de un protocolo para el diagnóstico y tratamiento del síncope en una población no seleccionada / Efficacy of a protocol for the diagnosis and management of syncope in an unselected population

Fundamento y objetivo: Valorar la eficacia de un protocolo basado en las Guías Europeas para el manejo y diagnóstico del síncope y aplicado por un equipo multidisciplinario en una población no seleccionada.Pacientes y método: Fueron estudiados prospectivamente 402 pacientes no seleccionados en un hospital comarcal entre noviembre de 2003 y noviembre de 2008 mediante un protocolo basado en las Guías Europeas. Resultados:Se consiguió el diagnóstico en un 83,3% de los pacientes y un 26,6% precisaron ingreso hospitalario. Por cada 100 casos, se calculó el número de tests diagnósticos efectuados y su rendimiento (porcentaje de positivos/efectuados): tabla basculante 31-rendimiento 62,4%, ecocardiografía 17-8,3%, Holter 16-13,2%, tomografía computarizada (TC) craneal 5,2-0%, ergometría 1,9-0%, TC tórax 1,4-16%, estudio electrofisiológico 1,2-33%, Holter insertable 0,7-33%.Conclusiones: Este estudio muestra un alto porcentaje de diagnósticos con un bajo número de pruebas diagnósticas, destacando el rendimiento de la tabla basculante. El estudio de pacientes no seleccionados de síncope mediante un protocolo basado en las Guías Europeas y aplicado por un equipo multidisciplinario fue muy efectivo (AU)

Background and objective: To evaluate the efficacy of a protocol based on European guidelines for the management and diagnosis of syncope applied by a multidisciplinary team in unselected patients. Patients and methods: 402 unselected patients were followed prospectively in a second-level country hospital, between November 2003 and November 2008 with a protocol based on European Guidelines.Result: : Syncope was diagnosed in 83.3% of patients and 26.6% required hospitalization. For every 100 cases, the number of tests carried out and their performance (percentage of positive diagnostic tests/number of tests carried out) was calculated. Tilt test: 31 and performance: 62.4%, Doppler-echocardiography. 17-8.3%, Holter 16-13.2%, cranial CT 5.2-0%, ergometry 1.9-0%, chest CT 1.4-16%, EPS 1.2-33%, ILR 0.7-33%.Conclusions: This study shows a high percentage of diagnoses with low number of tests carried out, emphasizing the performance of tilt test. The study of unselected patients with a protocol based on European Guidelines for the management and diagnosis of syncope applied by a multidisciplinary team was very effective (AU)