Leveraging electronic healthcare record standards and semantic web technologies for the identification of patient cohorts

Introduction The secondary use of Electronic Healthcare Records (EHRs) often requires the identification of patient cohorts. In this context, an important problem is the heterogeneity of clinical data sources, which can be overcome with the combined use of standardized information models, Virtual Health Records, and semantic technologies, since each of them contributes to solving aspects related to the semantic interoperability of EHR data. Our main objective is to develop methods allowing for a direct use of EHR data for the identification of patient cohorts leveraging current EHR standards and semantic web technologies. Materials and Methods We propose to take advantage of the best features of working with EHR standards and ontologies. Our proposal is based on our previous results and experience working with both technological infrastructures. Our main principle is to perform each activity at the abstraction level with the most appropriate technology available. This means that part of the processing will be performed using archetypes (i.e., data level) and the rest using ontologies (i.e., knowledge level). Our approach will start working with EHR data in proprietary format, which will be first normalized and elaborated using EHR standards and then transformed into a semantic representation, which will be exploited by automated reasoning. Results We have applied our approach to protocols for colorectal cancer screening. The results comprise the archetypes, ontologies and datasets developed for the standardization and semantic analysis of EHR data. Anonymized real data has been used and the patients have been successfully classified by the risk of developing colorectal cancer. Conclusion This work provides new insights in how archetypes and ontologies can be effectively combined for EHR-driven phenotyping. The methodological approach can be applied to other problems provided that suitable archetypes, ontologies and classification rules can be designed.This work was supported by the Ministerio de Economia y Competitividad and the FEDER program through grants TIN2010-21388-C01 and TIN2010-21388-C02. MCLG was supported by the Fundacion Seneca through grant 15555/FPI/2010.Fernández-Breis, JT.; Maldonado Segura, JA.; Marcos, M.; Legaz-García, MDC.; Moner Cano, D.; Torres-Sospedra, J.; Esteban-Gil, A.... (2013). Leveraging electronic healthcare record standards and semantic web technologies for the identification of patient cohorts. Journal of the American Medical Informatics Association. 20(E2):288-296. https://doi.org/10.1136/amiajnl-2013-001923S28829620E2Cuggia, M., Besana, P., & Glasspool, D. (2011). Comparing semi-automatic systems for recruitment of patients to clinical trials. International Journal of Medical Informatics, 80(6), 371-388. doi:10.1016/j.ijmedinf.2011.02.003Sujansky, W. 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(2011). Integrating reasoning and clinical archetypes using OWL ontologies and SWRL rules. Journal of Biomedical Informatics, 44(2), 343-353. doi:10.1016/j.jbi.2010.11.005Tao C Wongsuphasawat K Clark K . Towards event sequence representation, reasoning and visualization for EHR data. Proceedings of the 2nd ACM SIGHIT International Health Informatics Symposium (IHI'12). New York, NY, USA: ACM:801–6.Bodenreider O . Biomedical ontologies in action: role in knowledge management, data integration and decision support. IMIA Yearbook of Medical Informatics 2008;67–79.Beale T . Archetypes. 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International Journal of Medical Informatics, 78(8), 559-570. doi:10.1016/j.ijmedinf.2009.03.006SAXON XSLT and XQuery processor. http://saxon.sourceforge.net/ (accessed Jun 2013).NCBO Bioportal. http://bioportal.bioontology.org/ (accessed Jun 2013).The Protégé Ontology Editor and Knowledge Acquisition System. http://protege.stanford.edu/ (accessed Jun 2013).Semantic Web Integration Tool. http://sele.inf.um.es/swit (accessed Jun 2013).Hermit Reasoner. http://www.hermit-reasoner.com/ (accessed Jun 2013).The OWLAPI. http://owlapi.sourceforge.net/ (accessed Jun 2013).Institute for Health Metrics and Evaluation. Global Burden of Disease. http://www.healthmetricsandevaluation.org/gbd (accessed Jun 2013).Segnan N Patnick J von Karsa L . European guidelines for quality assurance in colorectal cancer screening and diagnosis 2010. First Edition. European Union. ISBN 978-92-79-16435-4.W3C. 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Lysyl oxidase-like 2 (LOXL2), a new regulator of cell polarity required for metastatic dissemination of basal-like breast carcinomas

Basal-like breast carcinoma is characterized by the expression of basal/ myoepithelial markers, undifferentiated phenotype, highly aggressive behaviour and frequent triple negative status (ESR , PR , Her2neu ). We have previously shown that epithelial–mesenchymal transition (EMT) occurs in basal-like breast tumours and identified Lysyl-oxidase-like 2 (LOXL2) as an EMT player and poor prognosis marker in squamous cell carcinomas. We now show that LOXL2 mRNA is overexpressed in basal-like human breast carcinomas. Breast carcinoma cell lines with basal-like phenotype show a specific cytoplasmic/perinuclear LOXL2 expression, and this subcellular distribution is significantly associated with distant metastatic incidence in basal-like breast carcinomas. LOXL2 silencing in basal-like carcinoma cells induces a mesenchymal-epithelial transition (MET) associated with a decrease of tumourigenicity and suppression of metastatic potential. Mechanistic studies indicate that LOXL2 maintains the mesenchymal phenotype of basal-like carcinoma cells by a novel mechanism involving transcriptional downregulation of Lgl2 and claudin1 and disorganization of cell polarity and tight junction complexes. Therefore, intracellular LOXL2 is a new candidate marker of basal-like carcinomas and a target to block metastatic dissemination of this aggressive breast tumour subtypeThis work was supported by grants from the Spanish Ministry of Science and Innovation, MICINN, (SAF2007-53061; SAF2010-21143; Consolider Ingenio CSD2007/00017, to AC; SAF2007-63075; SAF2010-20175 to GM-B); Fundacion Mutua Madrileña (2007, 2009 to AC and GM-B); Instituto de Salud Carlos III (ISCIII) (PI 080971 to JP), and Junta de Andalucıa (PI-0384/2007; PI 080971, P07-CVI- 03100 to JP). FS and A Martı´n are recipients of JAE-pre and JAE-postdoc contracts from the Spanish Research Council (CSIC), respectively; MAC is founded by the RETICS (ISCIII)

Primer consenso en leucemia linfocítica crónica de la agrupación mexicana para el estudio de la hematología: epidemiología, diagnóstico y tratamiento

La leucemia linfocítica crónica (LLC) es la leucemia crónica menos frecuente en México. En consideración a los avances recientes, a una mejor clasificación pronóstica y a la introducción de nuevas modalidades terapéuticas, la Agrupación Mexicana para el Estudio de la Hematología organizó el primer consenso mexicano en leucemia linfocítica crónica. Este consenso se llevó a cabo en Cancún, Quintana Roo, México, en Septiembre del 2007. Los objetivos de esta reunión fueron actualizar y compartir los conocimientos de la enfermedad entre los especialistas mexicanos, con el fin de mejorar el diagnóstico y el pronóstico de la LLC en México. En el artículo se discute los aspectos clínicos, diagnósticos y terapéuticos de la LLC

Mapa de series, geoseries y geopermaseries de vegetación de España (Memoria del mapa de vegetación potencial de España). Parte II

Peer Reviewe

HCV-coinfection is related to an increased HIV-1 reservoir size in cART-treated HIV patients: a cross-sectional study

In HIV-1/HCV-coinfected patients, chronic HCV infection leads to an increased T-lymphocyte immune activation compared to HIV-monoinfected patients, thereby likely contributing to increase HIV-1 reservoir that is the major barrier for its eradication. Our objective was to evaluate the influence of HCV coinfection in HIV-1 viral reservoir size in resting (r) CD4+ T-cells (CD25-CD69-HLADR-). Multicenter cross-sectional study of 97 cART-treated HIV-1 patients, including 36 patients with HIV and HCV-chronic co-infection without anti-HCV treatment, 32 HIV patients with HCV spontaneous clearance and 29 HIV-monoinfected patients. rCD4+ T-cells were isolated and total DNA was extracted. HIV viral reservoir was measured by Alu-LTR qPCR. Differences between groups were calculated with a generalized linear model. Overall, 63.9% were men, median age of 41 years and Caucasian. Median CD4+ and CD8+ T-lymphocytes were 725 and 858 cells/mm 3 , respectively. CD4+ T nadir cells was 305 cells/mm 3 . Proviral HIV-1 DNA size was significantly increased in chronic HIV/HCV-coinfected compared to HIV-monoinfected patients (206.21 ± 47.38 vs. 87.34 ± 22.46, respectively; P = 0.009), as well as in spontaneously clarified HCV co-infected patients when compared to HIV-monoinfected individuals (136.20 ± 33.20; P = 0.009). HIV-1/HCV co-infected patients showed a larger HIV-1 reservoir size in comparison to HIV-monoinfected individuals. This increase could lead to a greater complexity in the elimination of HIV-1 reservoir in HIV-1/HCV-coinfected individuals, which should be considered in the current strategies for the elimination of HIV-1 reservoir.Financial support was provided by the Instituto de Salud Carlos III to VB (PI15CIII/00031), by the Spanish Ministry of Economy and Competitiveness to MC (SAF2016–78480-R) and The SPANISH AIDS Research Network RD16CIII/0002/0001, RD16CIII/0002/0002 and RD16/0025/0013 - ISCIII – FEDER. MRLP is supported by ISCIII - Subdirección General de Evaluacion and European Funding for Regional Development (FEDER) (PIE 13/00040 and RD12/0017/0017 RETIC de SIDA). C.P. is supported by the Portuguese Fundação para a Ciência e Tecnologia (FCT) (grant number SFRH/ BPD/77448/2011 is part of the EDCTP2 programme supported by the European Union). V.B., A.F.R. and N.R. are supported by the Miguel Servet programme from Fondo de Investigación Sanitaria (ISCIII) (grant number CP13/00098, CP14/CIII/00010 and CP14/00198, respectively)

Psychometric characteristics of the Spanish version of instruments to measure neck pain disability

[EN] Background. The NDI, COM and NPQ are evaluation instruments for disability due to NP. There was no Spanish version of NDI or COM for which psychometric characteristics were known. The objectives of this study were to translate and culturally adapt the Spanish version of the Neck Disability Index Questionnaire (NDI), and the Core Outcome Measure (COM), to validate its use in Spanish speaking patients with non-specific neck pain (NP), and to compare their psychometric characteristics with those of the Spanish version of the Northwick Pain Questionnaire (NPQ). Methods. Translation/re-translation of the English versions of the NDI and the COM was done blindly and independently by a multidisciplinary team. The study was done in 9 primary care Centers and 12 specialty services from 9 regions in Spain, with 221 acute, subacute and chronic patients who visited their physician for NP: 54 in the pilot phase and 167 in the validation phase. Neck pain (VAS), referred pain (VAS), disability (NDI, COM and NPQ), catastrophizing (CSQ) and quality of life (SF-12) were measured on their first visit and 14 days later. Patients' self-assessment was used as the external criterion for pain and disability. In the pilot phase, patients' understanding of each item in the NDI and COM was assessed, and on day 1 test-retest reliability was estimated by giving a second NDI and COM in which the name of the questionnaires and the order of the items had been changed. Results. Comprehensibility of NDI and COM were good. Minutes needed to fill out the questionnaires [median, (P25, P75)]: NDI. 4 (2.2, 10.0), COM: 2.1 (1.0, 4.9). Reliability: [ICC, (95%CI)]: NDI: 0.88 (0.80, 0.93). COM: 0.85 (0.75,0.91). Sensitivity to change: Effect size for patients having worsened, not changed and improved between days 1 and 15, according to the external criterion for disability: NDI: -0.24, 0.15, 0.66; NPQ: -0.14, 0.06, 0.67; COM: 0.05, 0.19, 0.92. Validity: Results of NDI, NPQ and COM were consistent with the external criterion for disability, whereas only those from NDI were consistent with the one for pain. Correlations with VAS, CSQ and SF-12 were similar for NDI and NPQ (absolute values between 0.36 and 0.50 on day 1, between 0.38 and 0.70 on day 15), and slightly lower for COM (between 0.36 and 0.48 on day 1, and between 0.33 and 0.61 on day 15). Correlation between NDI and NPQ: r = 0.84 on day 1, r = 0.91 on day 15. Correlation between COM and NPQ: r = 0.63 on day 1, r = 0.71 on day 15. Conclusion. Although most psychometric characteristics of NDI, NPQ and COM are similar, those from the latter one are worse and its use may lead to patients' evolution seeming more positive than it actually is. NDI seems to be the best instrument for measuring NP-related disability, since its results are the most consistent with patient's assessment of their own clinical status and evolution. It takes two more minutes to answer the NDI than to answer the COM, but it can be reliably filled out by the patient without assistanceS

Recicland, demostration on the management of organic and inorganic waste from agriculture

La agricultura protegida que se desarrolla principalmente en el litoral oriental andaluz es una actividad de gran importancia económica y social para Andalucía. Sin embargo, el crecimiento exponencial de la superficie de invernadero ha dado lugar a un incremento del volumen de residuos agrarios. Además, este sistema agrícola está evolucionando hacia nuevas técnicas de cultivo que implican, no sólo la generación de residuos, sino también una mayor diversificación que hace más complicada su gestión. El principal problema para la gestión de estos residuos agrarios no está sólo en su dispersión geográfica, sino también en su estacionalidad, ya que se genera gran cantidad en determinados periodos anuales, coincidiendo con la finalización de las campañas agrícolas. Por este motivo, la capacidad máxima de recogida y almacenamiento y el proceso de gestión están condicionados por el volumen generado al finalizar los ciclos de cultivo. En este contexto, surge el proyecto RECICLAND que pretende palear dichos problemas y contribuir a la gestión sostenible de los residuos generados en los procesos productivos. Concretamente, el objetivo general de este proyecto es desarrollar actividades demostrativas piloto, informando de modo práctico sobre diferentes técnicas para la gestión específica de residuos inorgánicos y restos vegetales. Para ello, se ha establecido un área de reciclaje, junto con actividades de transferencia (jornadas prácticas, visitas, vídeos demostrativos y publicaciones) en el Centro IFAPA La Mojonera (Almería).Protected agriculture, which takes place mainly on the eastern coast of Andalusia, constitutes the major economic and social activity for this region. However, greenhouse area exponential growth has led to an increase in the volume of agricultural waste. In addition, this agricultural system is evolving towards new cultivation techniques that not only involve the generation of waste, but also a greater diversification that makes its management hard to tackle. The main issue regarding management of this agricultural waste is not only its geographical dispersion, but also its seasonality, as a large quantity is generated during certain periods of the year, coinciding with the end of agricultural campaigns. Indeed, the maximum collection and storage capacity and the management process itself are conditioned by the volume generated at the end of cropping cycles. In this context, the RECICLAND project arises, which aims to alleviate these problems and contribute to the sustainable management of the waste generated in the production processes. Specifically, the general objective of project is to develop pilot demonstration activities, providing practical information on different techniques for the specific management of inorganic waste and plant debris. For this purpose, a recycling area has been set up, where transference activities such as practical workshops, guide visits, demonstration, videos, and publications are being carried out in IFAPA La Mojonera (Almería)

Características de los ambientes de aprendizaje online para una práctica docente de calidad. Indicadores de evaluación

Contribuir a la mejora de la calidad de la enseñanza y de los resultados de aprendizaje constituye uno de los retos en el sistema universitario actual que exige un gran esfuerzo de coordinación en las acciones de investigación e innovación a desarrollar. Para alcanzar este propósito, desde el grupo de investigación EDUTIC-ADEI (VIGROB-039) de la Universidad de Alicante se ha promovido la constitución de una red docente interdepartamental e interuniversitaria que pretende investigar sobre cómo debe ser la enseñanza online que se desarrolla en el ámbito universitario. Para ello, se ha abordado el concepto de ambiente de aprendizaje en este contexto virtual con el fin de delimitar los parámetros que deben definir una enseñanza de calidad cuando hablamos de e-learning, Masive Open Online Courses [MOOCs], Personal Learning Environment [PLE], etc. La investigación, pues, ahonda en los aspectos curriculares que conforman dichos ambientes de aprendizaje online con el fin de delimitar los parámetros de una enseñanza virtual de calidad

Effect of viral storm in patients admitted to intensive care units with severe COVID-19 in Spain: a multicentre, prospective, cohort study

Background: The contribution of the virus to the pathogenesis of severe COVID-19 is still unclear. We aimed to evaluate associations between viral RNA load in plasma and host response, complications, and deaths in critically ill patients with COVID-19. Methods: We did a prospective cohort study across 23 hospitals in Spain. We included patients aged 18 years or older with laboratory-confirmed SARS-CoV-2 infection who were admitted to an intensive care unit between March 16, 2020, and Feb 27, 2021. RNA of the SARS-CoV-2 nucleocapsid region 1 (N1) was quantified in plasma samples collected from patients in the first 48 h following admission, using digital PCR. Patients were grouped on the basis of N1 quantity: VIR-N1-Zero ([removed]2747 N1 copies per mL). The primary outcome was all-cause death within 90 days after admission. We evaluated odds ratios (ORs) for the primary outcome between groups using a logistic regression analysis. Findings: 1068 patients met the inclusion criteria, of whom 117 had insufficient plasma samples and 115 had key information missing. 836 patients were included in the analysis, of whom 403 (48%) were in the VIR-N1-Low group, 283 (34%) were in the VIR-N1-Storm group, and 150 (18%) were in the VIR-N1-Zero group. Overall, patients in the VIR-N1-Storm group had the most severe disease: 266 (94%) of 283 patients received invasive mechanical ventilation (IMV), 116 (41%) developed acute kidney injury, 180 (65%) had secondary infections, and 148 (52%) died within 90 days. Patients in the VIR-N1-Zero group had the least severe disease: 81 (54%) of 150 received IMV, 34 (23%) developed acute kidney injury, 47 (32%) had secondary infections, and 26 (17%) died within 90 days (OR for death 0·30, 95% CI 0·16–0·55; p<0·0001, compared with the VIR-N1-Storm group). 106 (26%) of 403 patients in the VIR-N1-Low group died within 90 days (OR for death 0·39, 95% CI 0·26–0·57; p[removed]11 página

Now, the part of intuition. Research, Art and Creation, 2018

Catálogo de Exposición del Máster en Investigación en Arte y Creación de la UCM. Muestra celebrada del 25 de septiembre al 10 de octubre de 2018 en la Sala de Exposiciones de la Facultad de Bellas Artes. C / Pintor el Greco 2, Ciudad Universitaria. 28040 Madrid. Comisariado de Javier Mañero Rodicio.Exhibition catalog of the Master in Art and Creation Research of the UCM. September 25 to October 10, 2018 in the Exhibition Hall of the Faculty of Fine Arts. C / Pintor El Greco 2, University City. 28040 Madrid. Curated by Javier Mañero Rodicio.Fac. de Bellas ArtesFALSEFacultad de Bellas Artes. Universidad Complutense de Madrid.pu