Sistema de información para mejorar las colaboraciones dinámicas en el Grid

[ES] La principal ventaja de los Grid computacionales sobre otros paradigmas de computación distribuida es su capacidad para coordinar el acceso a datos y recursos, a través de diferentes dominios administrativos, en un entorno virtual interinstitucional. Para ello, el sistema de información juega un papel decisivo en la selección de los recursos que mejor cumplen con los requerimientos de las aplicaciones Grid. Esta tesis de máster presenta un sistema de información para el Grid que proporciona servicios de comunicación a grupos para aplicaciones Grid, de forma transparente y escalable, con el objetivo de soportar colaboraciones dinámicas que puedan ayudar a solucionar problemas que incluyan, solamente, a un subconjunto de los participantes de una organización virtual. En particular, el sistema presentado incluye un mecanismo de entrega de mensajes que permite a las aplicaciones seleccionar los servicios, antes de enviar sus datos a través de sistema Grid de información. Este enfoque mejora substancialmente la protección de los datos contra el acceso no autorizado, y evita la transmisión de mensajes innecesarios a través de la red. El sistema propuesto se basa en la utilización de tecnologías XML y replicación. Introduce varias características avanzadas que, en su conjunto, no están soportadas por ningún middleware Grid, como: múltiples puntos de acceso a la información, persistencia de los datos, soporte para consultas avanzadas con XQuery, y soporte para el estándar industrial WS-Policy. El sistema Grid de información fue probado en condiciones reales de carga de trabajo, en una infraestructura Grid con 50 sitios. La escalabilidad fue evaluada en hasta 1000 mensajes, que pueden contener hasta 10KB de datos, cada uno, y una frecuencia de actualizaciones de 5 minutos. The main advantage of Grid computing over other distributed computing paradigms is its capability to coordinate the access to data and resources in a virtual multi-institutional environment. To this end, the information system plays a decisive role in selecting the services that meet the applications¿ needs. This thesis presents an information system for the Grid that provides transparent and scalable group communication services to standard Grid applications, with the objective of supporting dynamic collaborations that could help address problems that involve only some participants of a virtual organization. In particular, it enables more flexible delivery mechanisms, which allows applications to select the appropriate services before sending their data to the information system. This significantly enhances the protection of data from unauthorized access, and avoids the transmission of unnecessary messages over the network. The proposed information system is based on the use of XML technologies and replication. It introduces several new advanced features that are not currently supported as a whole by any Grid middleware, such as: several entry points to the information, persistent capabilities, support for advanced queries based on XQuery, and support for the industrial standard WS-Policy. The information system has been stress tested under realistic workloads in a Grid infrastructure with 50 sites. Scalability has been evaluated in up to 1000 messages that can be up to 10KB in size each, updated with a frequency of 5 min. PALABRAS CLAVE DESCRIPTORES EN ESPAÑOL Grid ; Sistemas de Información ; ArquitecturasTorres Serrano, E. (2012). Sistema de información para mejorar las colaboraciones dinámicas en el Grid. http://hdl.handle.net/10251/19252Archivo delegad

Técnicas de monitorización y diferenciación de servicios para la asignación de recursos en entornos de computación Grid, en base a indicadores de nivel de servicio

El fortalecimiento de las infraestructuras de computación Grid, como plataforma para el acceso a recursos de cómputo y de almacenamiento en forma de servicios en Internet, ha dado lugar a una nueva necesidad: vincular las solicitudes de los usuarios con los servicios más apropiados, con el objetivo de mejorar la eficiencia de utilización de los recursos que forman parte del Grid, a la vez que mejorar las prestaciones de los trabajos ejecutados en el mismo. Esta necesidad se traduce, en la práctica, en la demanda de nuevos mecanismos de planificación de trabajos y de gestión de recursos, que permitan dotar a las infraestructuras Grid con nuevas estrategias para proporcionar niveles de servicio diferentes a diferentes perfiles de usuarios, proyectos y aplicaciones, y todo ello sobre la base de los requerimientos de calidad de servicio (Quality of Service o QoS) de cada perfil, formalizados en un contrato de nivel de servicio (Service Level Agreements o SLA). Por estas razones, proporcionar QoS en entornos de computación Grid es un área de investigación muy activa, a la vez que muy importante para la evolución del Grid hacia una infraestructura de propósito general que soporte modelos de negocio complejos. Sin embargo, a pesar de los avances en las técnicas de planificación y de gestión de recursos, el soporte para QoS en entornos de computación Grid es todavía muy limitado y, hasta el momento, no existe una solución definitiva para el problema. En este trabajo proponemos un nuevo modelo para la asignación de recursos en el Grid, en base a requerimientos de QoS. Como parte de este modelo, los servicios Grid son evaluados periódicamente a través de casos de prueba representativos, que son ejecutados en los recursos y que sirven para determinar la capacidad de los mismos para funcionar con unas prestaciones y una disponibilidad determinadas. A la vez, los recursos deben ser continuamente monitorizados para conocer su estado.Torres Serrano, E. (2010). Técnicas de monitorización y diferenciación de servicios para la asignación de recursos en entornos de computación Grid, en base a indicadores de nivel de servicio [Tesis doctoral no publicada]. Universitat Politècnica de València. https://doi.org/10.4995/Thesis/10251/7768Palanci

Enhancing Privacy and Authorization Control Scalability in the Grid through Ontologies

© 2009 IEEE. Personal use of this material is permitted. Permission from IEEE must be obtained for all other uses, in any current or future media, including reprinting/republishing this material for advertising or promotional purposes, creating new collective works, for resale or redistribution to servers or lists, or reuse of any copyrighted component of this work in other works.The use of data Grids for sharing relevant data has proven to be successful in many research disciplines. However, the use of these environments when personal data are involved (such as in health) is reduced due to its lack of trust. There are many approaches that provide encrypted storages and key shares to prevent the access from unauthorized users. However, these approaches are additional layers that should be managed along with the authorization policies. We present in this paper a privacy-enhancing technique that uses encryption and relates to the structure of the data and their organizations, providing a natural way to propagate authorization and also a framework that fits with many use cases. The paper describes the architecture and processes, and also shows results obtained in a medical imaging platform.Manuscript received November 19, 2007; revised July 27, 2008. First published August 4,2008; cur-rent version published January 4,2009. This work was supported in part by the Spanish Ministry of Education and Science to develop the project "ngGrid-New Generation Components for the Efficient Exploitation of eScience Infrastructures," under Grant TIN2006-12860 and in part by the Structural Funds of the European Regional Development Fund (ERDF).Blanquer Espert, I.; Hernández García, V.; Segrelles Quilis, JD.; Torres Serrano, E. (2009). Enhancing Privacy and Authorization Control Scalability in the Grid through Ontologies. IEEE Transactions on Information Technology in Biomedicine. 13(1):16-24. https://doi.org/10.1109/TITB.2008.2003369S162413

A Systematic Approach for Using DICOM Structured Reports in Clinical Processes: Focus on Breast Cancer

The final publication is available at Springer via http://dx.doi.org/10.1007/s10278-014-9728-6.This paper describes a methodology for redesigning the clinical processes to manage diagnosis, follow-up, and response to treatment episodes of breast cancer. This methodology includes three fundamental elements: (1) identification of similar and contrasting cases that may be of clinical relevance based upon a target study, (2) codification of reports with standard medical terminologies, and (3) linking and indexing the structured reports obtained with different techniques in a common system. The combination of these elements should lead to improvements in the clinical management of breast cancer patients. The motivation for this work is the adaptation of the clinical processes for breast cancer created by the Valencian Community health authorities to the new techniques available for data processing. To achieve this adaptation, it was necessary to design nine Digital Imaging and Communications in Medicine (DICOM) structured report templates: six diagnosis templates and three summary templates that combine reports from clinical episodes. A prototype system is also described that links the lesion to the reports. Preliminary tests of the prototype have shown that the interoperability among the report templates allows correlating parameters from different reports. Further work is in progress to improve the methodology in order that it can be applied to clinical practice.We thank the subject matter experts for sharing their insights through this study. We are especially appreciative of the efforts of the Radiology Unit and Medical Oncology Unit teams at the University Hospital Dr. Peset. This work was partially supported by the Vicerectorat d'Investigacio de la Universitat Politecnica de Valencia (UPVLC) to develop the project "Mejora del proceso diagnostico del cancer de mama" with reference UPV-FE-2013-8.Medina, R.; Torres Serrano, E.; Segrelles Quilis, JD.; Blanquer Espert, I.; Martí Bonmatí, L.; Almenar-Cubells, D. (2015). A Systematic Approach for Using DICOM Structured Reports in Clinical Processes: Focus on Breast Cancer. Journal of Digital Imaging. 28(2):132-145. doi:10.1007/s10278-014-9728-6S132145282Ratib O: Imaging informatics: From image management to image navigation. Yearb Med Inform 2009; 167–172Oakley J. Digital Imaging: A Primer for Radiographers, Radiologists and Health Care Professionals. Cambridge University Press, 2003.Prokosch HU, Dudeck J: Hospital information systems: Design and development characteristics, impact and future architecture. Elsevier health sciences, 1995Foster I, Kesselman C, Tuecke S. The anatomy of the grid: Enabling scalable virtual organizations. Int J High Perform Comput Appl 2001; 15(3):200–222.Oram A: Peer-to-Peer: Harnessing the power of disruptive technologies. O’Reilly Media, 2001National Institute of Standards and Technology. The NIST Definition of Cloud Computing. 2011. http://csrc.nist.gov/publications/nistpubs/800-145/SP800-145.pdf (accessed 29 Jan 2013)Oster S, Langella S, Hastings S, Ervin D, Madduri R, Phillips J, Kurc T, Siebenlist F, Covitz P, Shanbhag K, Foster I, Saltz J. caGrid 1.0: An enterprise grid infrastructure for biomedical research. J Am Med Inform Assoc 2008; 15:138–149.Natter MD, Quan J, Ortiz DM, et al. An i2b2-based, generalizable, open source, self-scaling chronic disease registry. J Am Med Inform Assoc 2013; 20:172–179.Ohno-Machado L, Bafna V, Boxwala AA, et al. iDASH: Integrating data for analysis, anonymization, and sharing. J Am Med Inform Assoc 2012; 19:196–201.Channin DS, Mongkolwat P, Kleper V, Rubin DL. Computing human image annotation. Conf Proc IEEE Eng Med Biol Soc 2009; 1:7065–8.Sittig DF, Wright A, Osheroff JA, et al. Grand challenges in clinical decision support. J Biomed Inform 2008; 41(2):387–392.Wagholikar KB, Sundararajan V, Deshpande AW. Modeling paradigms for medical diagnostic decision support: a survey and future directions. J Med Syst 2012; 36(5):3029–3049.Rubin DL. Creating and curating a terminology for radiology: Ontology modeling and analysis. J Digit Imaging 2008; 21(4):355–362.Kahn CE, Jr., Langlotz CP, Burnside ES, Carrino JA, Channin DS, Hovsepian DM, et al. Toward best practices in radiology reporting. Radiology 2009; 252(3):852–856.Taira PK, Soderlang SG, JAbovits RM. Automatic structuring of radiology free-text reports. Radiographics 2001; 21(1); 237–245.Fujii H, Yamagishi H, Ando Y, Tsukamoto N, Kawaguchi O, Kasamatsu T, et al. Structuring of free-text diagnostic report. Stud. Health Technol. Inform. 2007; 129: 669–673.Murff HJ, FitzHenry F, Matheny ME, Gentry N, Kotter KL, Crimin K, Dittus RS, Rosen AK, Elkin PL, Brown SH, Speroff T. Automated identification of postoperative complications within an electronic medical record using natural language processing. JAMA 2011; 306(8):848–855.Clunie DA: DICOM structured reporting. PixelMed Publishing, 2000D’Avolio LW, Nguyen TM, Farwell WR, Chen Y, Fitzmeyer F, Harris OM, Fiore LD. Evaluation of a generalizable approach to clinical information retrieval using the automated retrieval console (ARC). J Am Med Inform Assoc 2012; 17:375–382.Napel SA, Beaulieu CF, Redriguez C, Cui J, Xu J, Grupta A, et al. Automated retrieval of CT images of liver lesions on the basis of image similarity: Method and preliminary results. Radiology 2010; 256(1): 243–252.Langlotz CP. RadLex: A new method for indexing online educational materials. Radiographics 2006; 26(6):1595–1597.Crestania F, Vegas J, de la Fuente P. A graphical user interface for the retrieval of hierarchically structured documents. Inf Process Manag 2004; 40(2):269–289.Weiss DL, Langlotz CP. Structured reporting: Patient care enhancement or productivity nightmare? Radiology 2008. 249(3):739–747.Yen PY, Bakken S. Review of health information technology usability study methodologies. J Am Med Inform Assoc 2012; 19(3):413–422.Patrick R, Julien G, Christian L, Antoine G. Automatic medical encoding with SNOMED categories. BMC Med Inform Decis Mak 2008; 8(Suppl 1): S1–S6.Lopez-Garcia P, Boeker M, Illarramendi A, Schulz S. Usability-driven pruning of large ontologies: The case of SNOMED CT, J Am Med Inform Assoc 2012; 19:e102-e109.World Health Organization. International Statistical Classification of Diseases and Related Health Problems 10th Revision. http://apps.who.int/classifications/apps/icd/icd10online/ (accessed 29 Jan 2013)American College of Radiology (ACR) Breast Imaging Reporting and Data System Atlas (BI-RADS® Atlas)World Health Organization. International Classification of Diseases for Oncology, 3rd Edition (ICD-O-3). http://www.who.int/classifications/icd/adaptations/oncology/en/index.html (accessed 29 Jan 2013)Greene FL. TNM: Our language of cancer. CA Cancer J Clin 2004; 54(3):129–130.American Joint Committee of Cancer (AJCC). AJCC Cancer Staging Manual. Seventh Edition. Springer, 2010Hussein R, Engelmann U, Schroeter A, Meinzer HP. DICOM structured reporting: Part 1. Overview and characteristics, Radiographics 2004; 24(3):891–896.Sluis D, Lee KP, Mankovich N. DICOM SR - integrating structured data into clinical information systems. Medicamundi 2002; 46(2):31–36.Percha B, Nassif H, Lipson J, Burnside E, Rubin D. Automatic classification of mammography reports by BI-RADS breast tissue composition class. J Am Med Inform Assoc 2012; 19(5):913–916.Ciatto S, Houssami N, Apruzzese A, Bassetti E, Brancato B, Carozzi F, Catarzi S, Lamberini MP, Marcelli G, Pellizzoni R, Pesce B, Risso G, Russo F, Scorsolini A. Reader variability in reporting breast imaging according to BI-RADS assessment categories (the Florence experience). Breast 2006; 15(1):44–51.National Electrical Manufacturers Association (NEMA). Digital Imaging and Communications in Medicine (DICOM). Part 16: Content Mapping Resource. http://medical.nema.org/dicom/2004/04_16PU.PDF (accessed 29 Jan 2013)Dolin RH, Alschuler L, Boyer S, Beebe C, Behlen FM, Biron PV, Shvo AS. HL7 clinical document architecture, release 2. J Am Med Inform Assoc 2006; 13:30–39.Blanquer I, Hernández V, Meseguer JE, Segrelles D. Content-based organisation of virtual repositories of DICOM objects. Future Gener Comput Syst 2009; 25(6):627–637.Blanquer I, Hernández V, Segrelles D, Torres E. Enhancing privacy and authorization control scalability in the grid through ontologies. IEEE Trans Inf Technol Biomed 2009; 12(1):16–24.Salavert J, Maestre C, Segrelles D, Blanquer I, Hernández V, Medina R, Martí L: Grid prototype to support cancer of breast diagnostics in clinic practice. Proc of the 4th. Iberian Grid Infrastructure Conf. Netbiblo, 2010Segrelles D, Franco JM, Medina R, Blanquer I, Salavert J, Hernandez V, Martí L, Díaz G, Ramos R, Guevara MA, González N, Loureiro J, Ramos I. Exchanging data for breast cancer diagnosis on heterogeneous grid platforms. Computing and Informatics 2012; 31(1):3–15.Ali MS, Consens M, Lalmas M. Extended structural relevance framework: A framework for evaluating structured document retrieval. Inf Retrieval 2012; 15:558–590.Welter P, Riesmeier J, Fischer B, Grouls C, Kuhl C, Deserno, TM. Bridging the integration gap between imaging and information systems: A uniform data concept for content-based image retrieval in computer-aided diagnosis. J Am Med Inform Assoc 2011; 18:506–510.Jenkins CW. Application prototyping: A case study. Perform Eval Rev 1981; 10(1):21–27.Generalitat Valenciana. Conselleria de Sanitat. Oncoguía de Cáncer de Mama Comunidad Valenciana. http://publicaciones.san.gva.es/publicaciones/documentos/V.2478-2006.pdf (accessed 29 Jan 2013)Maestre C, Segrelles-Quilis JD, Torres E, Blanquer I, Medina R, Hernández V, Martí L. Assessing the usability of a science gateway for medical knowledge bases with TRENCADIS. J Grid Computing 2012; 10:665–688.Lewis J. IBM computer usability satisfaction questionnaires: Psychometric evaluation and instructions for use. Int J Hum-Comput Interact 1995; 7(1):57–78.Lewis JR. Psychometric evaluation of the PSSUQ using data from five years of usability studies. Int J Hum-Comput Interact 2002; 14(3–4):463–488.Shapiro SS, Wilk MB. An analysis of variance test for normality (complete samples). Biometrika 1965; 52(3–4):591–611.Chhatwal J, Alagoz O, Lindstrom MJ, Kahn Jr CE, Shaffer KA, Burnside ES. A logistic regression model based on the national mammography database format to aid breast cancer diagnosis. AJR Am J Roentgenol 2009; 192:1117–1127

OMWS: A Web Service Interface for Ecological Niche Modelling

[EN] Ecological niche modelling (ENM) experiments often involve a high number of tasks to be performed. Such tasks may consume a significant amount of computing resources and take a long time to complete, especially when using personal computers. OMWS is a Web service interface that allows more powerful computing back-ends to be remotely exploited by other applications to carry out ENM tasks. Its latest version includes a new operation that can be used to specify complex workflows in a single request, adding the possibility of using workflow management systems on parallel computing back-end. In this paper we describe the OMWS protocol and compare its most recent version with the previous one by running the same ENM experiment using two functionally equivalent clients, each designed for one of the OMWS interface versions. Different back-end configurations were used to investigate how the performance scales for each protocol version when more processing power is made available. Results show that the new version outperforms (in a factor of 2) the previous one when more computing resources are used.The latest version of OMWS contains improvements coming from different sets of requirements originated from two projects that funded their corresponding implementation: EUBrazilOpenBio14, with grants from the European Commission and the National Council for Scientific and Technological Development of Brazil (CNPq) of the Brazilian Ministry of Science and Technology (MCT), and BioVeL, with grants from the European Commission. Server infrastructure was operated through a provisioning system developed in the frame of the Spanish project CLUVIEM (TIN2013-44390-R) funded by the "Ministerio de Economía y Competitividad".Giovanni, RD.; Torres Serrano, E.; Amaral, RB.; Blanquer Espert, I.; Rebello, V.; Canhos, VP. (2015). OMWS: A Web Service Interface for Ecological Niche Modelling. Biodiversity Informatics. 10:35-44. https://doi.org/10.17161/bi.v10i0.4853S35441

Natural resource exploitation in Western Sahara: new research directions

The authors wish to thank the Leverhulme Trust (through their Early Career scheme) and the Spanish Ministry of Economy, Industry and Competitivity, (CSO2017-86986-P, AEI/FEDER, UE) for funding this research. We would also like to thank Patricia Lalonde for her translations and editorial work, as well as all participants of the 'Analysis of the Management and Exploitation of Natural Resources in Situations of Conflict: The Case of Western Sahara' project (funded by the aforementioned ministry), for their constructive comments on earlier iterations of this paper.This review article provides an overview of research to date with an explicit focus on natural resource exploitation in Western Sahara. It integrates findings from various perspectives and disciplines, and synthesises the research done with a view to revealing gaps and, therefore, potential new research directions. As the issue of natural resource exploitation in Western Sahara has been conceptualised in very different ways and from the perspectives of a variety of disciplines, the authors have opted for a semi-systematic review of the work done encompassing academic, non-academic, and activist backgrounds.Leverhulme TrustSpanish Ministry of Economy, Industry and Competitivity (AEI/FEDER, UE) CSO2017-86986-

Cabbage and fermented vegetables : From death rate heterogeneity in countries to candidates for mitigation strategies of severe COVID-19

Large differences in COVID-19 death rates exist between countries and between regions of the same country. Some very low death rate countries such as Eastern Asia, Central Europe, or the Balkans have a common feature of eating large quantities of fermented foods. Although biases exist when examining ecological studies, fermented vegetables or cabbage have been associated with low death rates in European countries. SARS-CoV-2 binds to its receptor, the angiotensin-converting enzyme 2 (ACE2). As a result of SARS-CoV-2 binding, ACE2 downregulation enhances the angiotensin II receptor type 1 (AT(1)R) axis associated with oxidative stress. This leads to insulin resistance as well as lung and endothelial damage, two severe outcomes of COVID-19. The nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is the most potent antioxidant in humans and can block in particular the AT(1)R axis. Cabbage contains precursors of sulforaphane, the most active natural activator of Nrf2. Fermented vegetables contain many lactobacilli, which are also potent Nrf2 activators. Three examples are: kimchi in Korea, westernized foods, and the slum paradox. It is proposed that fermented cabbage is a proof-of-concept of dietary manipulations that may enhance Nrf2-associated antioxidant effects, helpful in mitigating COVID-19 severity.Peer reviewe

Nrf2-interacting nutrients and COVID-19 : time for research to develop adaptation strategies

There are large between- and within-country variations in COVID-19 death rates. Some very low death rate settings such as Eastern Asia, Central Europe, the Balkans and Africa have a common feature of eating large quantities of fermented foods whose intake is associated with the activation of the Nrf2 (Nuclear factor (erythroid-derived 2)-like 2) anti-oxidant transcription factor. There are many Nrf2-interacting nutrients (berberine, curcumin, epigallocatechin gallate, genistein, quercetin, resveratrol, sulforaphane) that all act similarly to reduce insulin resistance, endothelial damage, lung injury and cytokine storm. They also act on the same mechanisms (mTOR: Mammalian target of rapamycin, PPAR gamma:Peroxisome proliferator-activated receptor, NF kappa B: Nuclear factor kappa B, ERK: Extracellular signal-regulated kinases and eIF2 alpha:Elongation initiation factor 2 alpha). They may as a result be important in mitigating the severity of COVID-19, acting through the endoplasmic reticulum stress or ACE-Angiotensin-II-AT(1)R axis (AT(1)R) pathway. Many Nrf2-interacting nutrients are also interacting with TRPA1 and/or TRPV1. Interestingly, geographical areas with very low COVID-19 mortality are those with the lowest prevalence of obesity (Sub-Saharan Africa and Asia). It is tempting to propose that Nrf2-interacting foods and nutrients can re-balance insulin resistance and have a significant effect on COVID-19 severity. It is therefore possible that the intake of these foods may restore an optimal natural balance for the Nrf2 pathway and may be of interest in the mitigation of COVID-19 severity

Mortality and pulmonary complications in patients undergoing surgery with perioperative SARS-CoV-2 infection: an international cohort study

Background: The impact of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) on postoperative recovery needs to be understood to inform clinical decision making during and after the COVID-19 pandemic. This study reports 30-day mortality and pulmonary complication rates in patients with perioperative SARS-CoV-2 infection. Methods: This international, multicentre, cohort study at 235 hospitals in 24 countries included all patients undergoing surgery who had SARS-CoV-2 infection confirmed within 7 days before or 30 days after surgery. The primary outcome measure was 30-day postoperative mortality and was assessed in all enrolled patients. The main secondary outcome measure was pulmonary complications, defined as pneumonia, acute respiratory distress syndrome, or unexpected postoperative ventilation. Findings: This analysis includes 1128 patients who had surgery between Jan 1 and March 31, 2020, of whom 835 (74·0%) had emergency surgery and 280 (24·8%) had elective surgery. SARS-CoV-2 infection was confirmed preoperatively in 294 (26·1%) patients. 30-day mortality was 23·8% (268 of 1128). Pulmonary complications occurred in 577 (51·2%) of 1128 patients; 30-day mortality in these patients was 38·0% (219 of 577), accounting for 81·7% (219 of 268) of all deaths. In adjusted analyses, 30-day mortality was associated with male sex (odds ratio 1·75 [95% CI 1·28–2·40], p\textless0·0001), age 70 years or older versus younger than 70 years (2·30 [1·65–3·22], p\textless0·0001), American Society of Anesthesiologists grades 3–5 versus grades 1–2 (2·35 [1·57–3·53], p\textless0·0001), malignant versus benign or obstetric diagnosis (1·55 [1·01–2·39], p=0·046), emergency versus elective surgery (1·67 [1·06–2·63], p=0·026), and major versus minor surgery (1·52 [1·01–2·31], p=0·047). Interpretation: Postoperative pulmonary complications occur in half of patients with perioperative SARS-CoV-2 infection and are associated with high mortality. Thresholds for surgery during the COVID-19 pandemic should be higher than during normal practice, particularly in men aged 70 years and older. Consideration should be given for postponing non-urgent procedures and promoting non-operative treatment to delay or avoid the need for surgery. Funding: National Institute for Health Research (NIHR), Association of Coloproctology of Great Britain and Ireland, Bowel and Cancer Research, Bowel Disease Research Foundation, Association of Upper Gastrointestinal Surgeons, British Association of Surgical Oncology, British Gynaecological Cancer Society, European Society of Coloproctology, NIHR Academy, Sarcoma UK, Vascular Society for Great Britain and Ireland, and Yorkshire Cancer Research

PATJ Low Frequency Variants Are Associated with Worse Ischemic Stroke Functional Outcome: A Genome-Wide Meta-Analysis

RATIONALE: Ischemic stroke is among the leading causes of adult disability. Part of the variability in functional outcome after stroke has been attributed to genetic factors but no locus has been consistently associated with stroke outcome. OBJECTIVE: Our aim was to identify genetic loci influencing the recovery process using accurate phenotyping to produce the largest GWAS (genome-wide association study) in ischemic stroke recovery to date. METHODS AND RESULTS: A 12-cohort, 2-phase (discovery-replication and joint) meta-analysis of GWAS included anterior-territory and previously independent ischemic stroke cases. Functional outcome was recorded using 3-month modified Rankin Scale. Analyses were adjusted for confounders such as discharge National Institutes of Health Stroke Scale. A gene-based burden test was performed. The discovery phase (n=1225) was followed by open (n=2482) and stringent joint-analyses (n=1791). Those cohorts with modified Rankin Scale recorded at time points other than 3-month or incomplete data on previous functional status were excluded in the stringent analyses. Novel variants in PATJ (Pals1-associated tight junction) gene were associated with worse functional outcome at 3-month after stroke. The top variant was rs76221407 (G allele, β=0.40, P=1.70×10-9). CONCLUSIONS: Our results identify a set of common variants in PATJ gene associated with 3-month functional outcome at genome-wide significance level. Future studies should examine the role of PATJ in stroke recovery and consider stringent phenotyping to enrich the information captured to unveil additional stroke outcome loci