Utilidad de los informes estructurados basados en una plataforma web para el diagnóstico por imagen en patología mamaria

El cáncer de mama es una enfermedad con un gran impacto sobre la salud poblacional. A pesar de los avances en esta enfermedad, la mortalidad sigue siendo elevada, por lo que es importante investigar en otros campos y herramientas como por ejemplo en el ámbito de la recogida de datos de forma estandarizada, para recoger información de forma estructurada, decisiones protocolizadas y más objetivas, mejorando esto el pronóstico de la enfermedad. Con respecto a las necesidades actuales referentes fundamentalmente a los sistemas de información, los desarrollos realizados en esta Tesis Doctoral combinan la aplicación de tecnologías y estándares de la información. La hipótesis de trabajo de esta tesis es que los informes estructurados en patología mamaria optimizan los flujos de información en el proceso radiológico con respecto a los informes que emplean el texto plano. Esta optimización se reflejará en una mejor completitud, validez, efectividad y eficacia de los mismos, sin añadir un tiempo excesivo en términos de productividad al introducir la información. Los resultados obtenidos en esta tesis se centran en valorar la importancia del uso de los informes estructurados en el ámbito del cáncer de mama frente al informe convencional comúnmente realizado con texto plano. Con este objetivo se han desarrollado una serie de aportaciones que se detallan a continuación: 1. Incorporación a los flujos de trabajo ya existentes en el cáncer de mama y que afectan a su diagnóstico, tratamiento y seguimiento, de los informes estructurados organizados siguiendo la terminología BI-RADS (estándar de información radiológica) y DICOM-SR (estándar de estructura de informes), para obtener unos flujos de trabajo mejorados. 2. Desarrollo de un prototipo web que permite recoger los datos a través de los informes estandarizados al mismo tiempo que se realiza el informe radiológico estructurado. Estos datos quedan almacenados en una única base de datos para su posterior análisis y uso (como compartir con otros centros, realizar políticas de mejora de salud, facilitar la resolución de casos-problema, evaluar tendencias y extraer casos relacionados). Esta plataforma recoge toda la información necesaria para llevar a cabo un informe mamario completo, ya que incorpora una serie de plantillas consensuadas y específicas para cada técnica de imagen mamaria. 3. Creación de plantillas para los informes de mamografía, ecografía y RM, que reúnen todos los descriptores siguiendo el estándar BI-RADS. Por cada técnica de imagen se ha desarrollado una plantilla y a cada descriptor se le ha asignado su “código universal” según la ontología estándar RADLEX para el caso de la información radiológica y SNOMED-CT para la información no radiológica. Del mismo modo, se recoge en las plantillas si los datos son de obligatorio cumplimiento y la condicionalidad de los campos, para así codificar toda la información correctamente. 4. Mediante unos supuestos clínicos, realizados de manera ciega por varios profesionales de radiodiagnóstico, se ha evaluado el uso del informe estructurado, obteniéndose una mejoría en la completitud, validez, y efectividad de los informes estructurados con respecto al texto plano convencional y, por tanto, una mejora en la eficiencia. Así, empleando el informe estructurado se consiguen informes más rápidos, con una completitud superior al 90% y con una validez y efectividad entorno al 80%. En la evaluación de la mejoría del tiempo empleado y la eficiencia según las técnicas y el personal que las interpreta, se ha constatado que: 4.1. Con el sistema de informes estructurados basado en DICOM-SR se ahorra una media de 26 segundos por cada exploración informada. 4.2. De entre todas las técnicas de imagen, y de forma global, el informe estructurado es más eficiente en la mamografía (al compararla con la RM) y sobretodo en los usuarios más expertos (radiólogos adjuntos y R4+R3 al compararlos con R2). También se ha observado que para los radiólogos adjuntos el informe estructurado es más eficiente en las tres técnicas de imagen, siendo para los residentes expertos R4+R3 más eficiente para la mamografía y para los residentes de menor experiencia R2 más eficiente para la ecografía. 4.3. Si se analiza por técnicas, los informes estructurados son más completos, válidos y efectivos para la ecografía y la RM frente a la mamografía, en todos los subgrupos de usuarios, excepto en el de médicos adjuntos donde los informes para las tres técnicas son igual de completos. Si el análisis es por usuarios, las diferencias se encuentran entre los informes estructurados para los radiólogos más expertos (adjuntos) y los residentes, obteniéndose mejores resultados con una mayor experiencia. 5. No obstante y pese a lograr estandarizar la información con la creación de un prototipo web bien organizado mediante plantillas de cada una de las técnicas de imagen y su codificación siguiendo estándares universales (ontologías como RADLEX y SNOMED-CT), se ha constatado que los datos obtenidos están influenciados por factores asociados a la propia experiencia de los radiólogos. En esta tesis se plasma la creación y análisis de un sistema informático que elimina las variaciones e ineficiencias en la creación de informes radiológicos.Breast cancer is a disease with a major impact on population health. Despite major advances have been done to mitigate this disease, nowadays the mortality rate due to breast cancer still remains high. Therefore, it is crucial to open new lines of research beyond the traditional approaches based on experimental studies. In the last decade, there is an increasing interest in the analysis of large data collections due to the tremendous amount of information that is unused. New tools are needed to dig into the medical reports and to discover new knowledge that could help physicians to design more accurate protocols to manage breast cancer and to improve the prognosis of this disease. This thesis combines new-generation analytics with the use of medical standards to improve the quality of the data. We started our research from the hypothesis that the use of structured data formats to report pathological findings may improve the quality of the information allowing its use in automatic pipelines, compared with traditional free-text reports where many important details are blurred by the lack of precision and ambiguity. Our objective with this thesis is to prove this hypothesis, measuring the improvement by means of 4 quality metrics: completeness, validity, effectiveness and efficiency of the structured reports. To this end, our efforts were focused on evaluating the use of structured reports on breast cancer compared to conventional reports based on free-text. The contributions of this work are listed below: 1. Redesign of the clinical pipelines for the management of breast cancer, introducing structured reports based on standards (BI-RADS terminology and DICOM-SR data format) for diagnosis, treatment and patient outcomes monitoring. 2. Development of a Web-based prototype of a data collection system that allows physicians to introduce their findings in a common database. This prototype uses the most recent advances in security to support analytic operations on the data as well as other common operations, including data sharing among medical centres, information lookup and discovering patterns in the data. Also, the prototype allows users to download medical reports using a standardized data format. 3. Report templates based on the BI-RADS terminology were created for the different imaging techniques available, including mammography, ultrasound and MRI. Other relevant standards are included. In particular, radiological information is annotated with RADLEX ontologies and SNOMED CT terms are used for non-radiological information. All the templates share a common validation scheme where every field is assigned to a specific data type and optional fields are labelled. 4. A usability study was conducted with the participation of real radiologists to evaluate the use of structured reports and to compare the accuracy of the structured reports with the conventional free-text reports. The results of this experiment showed an improvement in the completeness (>90%), validity (>80%) and effectiveness (>80%) of the structured reports over conventional free-text reports. The experiment also measured the efficiency of the participants with the following results: 4.1. Information lookup time was reduced in 26 seconds by using structured reports. 4.2. Mammography was the imaging technique where the shortest times were achieved, especially among expert users. In contrast, introducing ultrasound reports in the system achieved the longest times. 4.3. Experts completed all the reports in the three imaging categories: mammography, ultrasound and MRI, while residents made more mistakes and create incomplete reports when they work with ultrasound and MRI. 5. Despite the improvements achieved with this thesis, the use of standard terminologies, the creation of report templates and the development of tools for the validation of the information are only one part of the solution. There are also human factors, such as the user expertise and the previous experience with computers and technology, affecting the quality of the data collected at the hospitals. 6. Finally, in this thesis we created a computer system that contributes to eliminate inter- and intra-observer variations, helping to improve both the efficiency and the quality of the medical reports

Miape web toolkit: a user-friendly work frame to conncect and share proteomics standards in the lab

Comunicaciones a congreso

Phytoremediation of chrome in tannery effluents using Eichhornia crassipes

El cromo es uno de los mayores contaminantes inorgánicos de las aguas y del suelo en el Paraguay, acarreando serios problemas ambientales. Este metal proviene principalmente de efluentes de curtiembres que son vertidos a cursos de aguas. El objetivo de este trabajo es emplear técnicas de remediación alternativas para el tratamiento de aguas con alto contenido de cromo, utilizando medios naturales (plantas), en un proceso denominado fitorremediación. Ejemplares de Eichhornia crassipes fueron sometidos a una contaminación controlada con Cr3+ durante 20 días y se consideró la máxima concentración tolerada durante todo el periodo del experimento para estudiar la taza y la capacidad de absorción del Cr3+ de la especie. Las constantes cinéticas de este proceso fueron: constante de absorción Kab= 0,10 días -1, y tiempo medio de absorción: t1/2 = 6,8 días. En el efluente final de curtiembre, con 22,4 mg.L-1 de Cr3+, a las 48 horas se produjo una absorción casi completa del cromo suministrado, quedando en el efluente 1,28 mg.L-1 del cromo. Los factores de translocación del cromo para E. crassipes fueron 0,008 y 0,02 en agua de pozo y efluente respectivamente y los factores de bioacumulación 11,6 y 3,2 respectivamente. No se encontraron diferencias significativas entre el contenido de clorofila en los vegetales expuestas en solución de cromo en comparación con el control. Tampoco se encontró oxidación del Cr3+ a Cr6+ medidos espectrofotométricamente.Chromium is one of the largest inorganic pollutants in water and soil in Paraguay, causing serious environmental problems. This metal comes mainly from tannery effluents that are dumped into water courses. The aim of this work was to use alternative remediation techniques for the treatment of waters with high chromium content, using natural media (plants), in a process called phytoremediation. Specimens of Eicchornia crassipes were subjected to controlled contamination with Cr3+ for 20 days and the maximum tolerated concentration during the whole period of the experiment was considered to study the cup and the absorption capacity of Cr3+ from the species. The kinetic constants of this process were: constant absorption: Kab = 0.10 days -1, and absorption half time: t1/2 = 6.8 dys. In the final tannery effluent with 22.4 mg.L-1 of Cr3+, at 48 hours there was almost complete absorption of the chromium supplied, leaving 1.28 mg.L-1 of chromium in the effluent. The chromium translocation factors for E. crassipes were 0.008 and 0.02 in well water and effluent respectively and bioaccumulation factors were 11.6 and 3.2 respectively. No significant differences were found between the chlorophyll content in the plants exposed in chromium solution compared to the control. Neither was oxidation found from Cr3+ to Cr6+ spectrophotometrically measured.Facultad de Ciencias Exacta

Asociación entre Artritis Reumatoidea y otras enfermedades autoinmunes

Objetivos: determinar la frecuencia de enfermedades autoinmunes (EAI) en pacientes con Artritis Reumatoidea (AR) y comparar la frecuencia de EAI entre pacientes con AR y sin AR ni otra EAI reumatológica. Material y Métodos: estudio multicéntrico, observacional, analítico, retrospectivo. Se incluyeron pacientes consecutivos con AR (ACR/EULAR 2010) y como grupo control pacientes con diagnóstico inicial de Osteoartritis primaria (OA).

Occupation and mammographic density: A population-based study (DDM-Occup)

[EN] Introduction: High mammographic density is one of the main risk factors for breast cancer. Although several occupations have been associated with breast cancer, there are no previous occupational studies exploring the association with mammographic density. Our objective was to identify occupations associated with high mammographic density in Spanish female workers. Methods: We conducted a population-based cross-sectional study of occupational determinants of high mammographic density in Spain, based on 1476 women, aged 45-68 years, recruited from seven screening centers within the Spanish Breast Cancer Screening Program network. Reproductive, family, personal, and occupational history data were collected. The latest occupation of each woman was collected and coded according to the 1994 National Classification of Occupations. Mammographic density was assessed from the cranio-caudal mammogram of the left breast using a semi-automated computer-assisted tool. Association between mammographic density and occupation was evaluated by using mixed linear regression models, using log-transformed percentage of mammographic density as dependent variable. Models were adjusted for age, body mass index,menopausal status, parity, smoking, alcohol intake, educational level, type of mammography, first-degree relative with breast cancer, and hormonal replacement therapy use. Screening center and professional reader were included as random effects terms. Results: Mammographic density was higher, although non-statistically significant, among secondary school teachers (e(beta) = 1.41; 95%CI = 0.98-2.03) and nurses (e(beta) = 1.23; 95%CI = 0.96-1.59), whereas workers engaged in the care of people (e(beta) = 0.81; 95%CI = 0.66-1.00) and housewives (e(beta) = 0.87; 95%CI = 0.79-0.95) showed an inverse association with mammographic density. A positive trend for every 5 years working as secondary school teachers was also detected (p-value = 0.035). Conclusions: Nurses and secondary school teachers were the occupations with the highest mammographic density in our study, showing the latter a positive trend with duration of employment. Future studies are necessary to confirm if these results are due to chance or are the result of a true association whose causal hypothesis is, for the moment, unknown.This study was funded by Strategic Action of Intramural Health (Accion Estrategica de Salud Intramural - AESI PI15CIII/00013); the Scientific Foundation of the Spanish Association Against Cancer (Fundacion Cientifica de la Asociacion Espanola Contra el Cancer (AECC) EVP-1178/14); the Research Grant FIS PI060386 & PS09/790 from Spain's Health Research Fund (Fondo de Invesdgacion Sanitaria); the EPY 1306/06 Collaboration Agreement between Astra-Zeneca and the Carlos III Institute of Health; and a grant from the Spanish Federation of Breast Cancer patients (FECMA 485 EPY 1170-10).García-Pérez, J.; Pollán, M.; Pérez-Gómez, B.; González-Sánchez, M.; Cortés Barragán, RA.; Maqueda Blasco, J.; González-Galarzo, MC.... (2017). Occupation and mammographic density: A population-based study (DDM-Occup). Environmental Research. 159:355-361. https://doi.org/10.1016/j.envres.2017.08.02835536115

Resources for research in applied ethics: development of a website

El objetivo de este proyecto es proporcionar recursos para la investigación en bioética y éticas aplicadas, para que los estudiantes puedan disponer de herramientas y materiales útiles para sus trabajos de investigación. Para ello se ha elaborado una página web.The objective of this project is to provide resources for research in bioethics and applied ethics, so that students can have useful tools and materials for their research work. A web page has been developed for this purpose.Universidad Complutense de MadridFac. de Ciencias de la InformaciónFALSEsubmitte

Validation of a Set of Instruments to Assess Patient- and Caregiver-Oriented Measurements in Spinal Muscular Atrophy: Results of the SMA-TOOL Study.

Outcome measures traditionally used in spinal muscular atrophy (SMA) clinical trials are inadequate to assess the full range of disease severity. The aim of this study was to assess the psychometric properties of a set of existing questionnaires and new items, gathering information on the impact of SMA from the patient and caregiver perspectives. This was a multicenter, prospective, noninterventional study including patients with a confirmed diagnosis of 5q-autosomal-recessive SMA aged 8 years and above, or their parents (if aged between 2 and 8 years). The set of outcome measurements included the SMA Independence Scale (SMAIS) patient and caregiver versions, the Neuro-QoL Fatigue Computer Adaptive Test (CAT), the Neuro-QoL Pain Short Form-Pediatric Pain, the PROMIS adult Pain Interference CAT, and new items developed by Fundación Atrofia Muscular España: perceived fatigability, breathing and voice, sleep and rest, and vulnerability. Reliability, construct validity, discriminant validity, and sensitivity to change (4 months from baseline) were measured. A total of 113 patients were included (59.3% 2-17 years old, 59.3% male, and 50.4% with SMA type II). Patients required moderate assistance [mean patient and caregiver SMAIS (SD) scores were 31.1 (12.8) and 7.6 (11.1), respectively]. Perceived fatigability was the most impacted domain, followed by vulnerability. Cronbach's alpha coefficient for perceived fatigability, breathing and voice, and vulnerability total scores were 0.92, 0.88, and 0.85, respectively. The exploratory factor analysis identified the main factors considered in the design, except in the sleep and rest domain. All questionnaires were able to discriminate between the Clinical Global Impression-Severity scores and SMA types. Sensitivity to change was only found for the SMAIS caregiver version and vulnerability items. This set of outcome measures showed adequate reliability, construct validity, and discriminant validity and may constitute a valuable option to measure symptom severity in patients with SMA

Occupation and mammographic density: A population-based study (DDM-Occup)

INTRODUCTION: High mammographic density is one of the main risk factors for breast cancer. Although several occupations have been associated with breast cancer, there are no previous occupational studies exploring the association with mammographic density. Our objective was to identify occupations associated with high mammographic density in Spanish female workers. METHODS: We conducted a population-based cross-sectional study of occupational determinants of high mammographic density in Spain, based on 1476 women, aged 45-68 years, recruited from seven screening centers within the Spanish Breast Cancer Screening Program network. Reproductive, family, personal, and occupational history data were collected. The latest occupation of each woman was collected and coded according to the 1994 National Classification of Occupations. Mammographic density was assessed from the cranio-caudal mammogram of the left breast using a semi-automated computer-assisted tool. Association between mammographic density and occupation was evaluated by using mixed linear regression models, using log-transformed percentage of mammographic density as dependent variable. Models were adjusted for age, body mass index, menopausal status, parity, smoking, alcohol intake, educational level, type of mammography, first-degree relative with breast cancer, and hormonal replacement therapy use. Screening center and professional reader were included as random effects terms. RESULTS: Mammographic density was higher, although non-statistically significant, among secondary school teachers (eβ = 1.41; 95%CI = 0.98-2.03) and nurses (eβ = 1.23; 95%CI = 0.96-1.59), whereas workers engaged in the care of people (eβ = 0.81; 95%CI = 0.66-1.00) and housewives (eβ = 0.87; 95%CI = 0.79-0.95) showed an inverse association with mammographic density. A positive trend for every 5 years working as secondary school teachers was also detected (p-value = 0.035). CONCLUSIONS: Nurses and secondary school teachers were the occupations with the highest mammographic density in our study, showing the latter a positive trend with duration of employment. Future studies are necessary to confirm if these results are due to chance or are the result of a true association whose causal hypothesis is, for the moment, unknown.This study was funded by Strategic Action of Intramural Health (Acción Estratégica de Salud Intramural - AESI PI15CIII/00013); the Scientific Foundation of the Spanish Association Against Cancer (Fundación Científica de la Asociación Española Contra el Cáncer (AECC) – EVP-1178/14); the Research Grant FIS PI060386 & PS09/790 from Spain’s Health Research Fund (Fondo de Investigación Sanitaria); the EPY 1306/06 Collaboration Agreement between Astra-Zeneca and the Carlos III Institute of Health; and a grant from the Spanish Federation of Breast Cancer patients (FECMA 485 EPY 1170-10).S