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  • SDSN - Greece
  • 2013-2022
  • Publications
  • Instruct-ERIC

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Artini M.; Assante M.; Atzori C.; Baglioni M.; +25 Authors

    InfraScience is a research group of the National Research Council of Italy - Institute of Information Science and Technologies (CNR - ISTI) based in Pisa, Italy. This report documents the research activity performed by this group in 2022 to highlight the major results. In particular, the InfraScience group confronted with research challenges characterising Data Infrastructures, e-Science, and Intelligent Systems. The group activity is pursued by closely connecting research and development and by promoting and supporting open science. In fact, the group is leading the development of two large scale infrastructures for Open Science, i.e. D4Science and OpenAIRE. During 2022 InfraScience members contributed to the publishing of several papers, to the research and development activities of 18 research projects (15 funded by EU), to the organization of conferences and training events, to several working groups and task forces.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ CNR ExploRAarrow_drop_down
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    CNR ExploRA
    Report . 2022
    Data sources: CNR ExploRA
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    ISTI Open Portal
    Report . 2022
    Data sources: ISTI Open Portal
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ CNR ExploRAarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      CNR ExploRA
      Report . 2022
      Data sources: CNR ExploRA
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ISTI Open Portal
      Report . 2022
      Data sources: ISTI Open Portal
  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Sharma, Raju Prasad; Kumar, Vikas; Schuhmacher, Marta; Kolodkin, Alexey; +1 Authors

    By their definition, inadvertent exposure to endocrine disrupting compounds (EDCs) intervenes with the endocrine signalling system, even at low dose. On the one hand, some EDCs are used as important pharmaceutical drugs that one would not want to dismiss. On the other hand, these pharmaceutical drugs are having off-target effects and increasingly significant exposure to the general population with unwanted health implications. Flutamide, one of the top pharmaceutical products marketed all over the world for the treatment of prostate cancer, is also a pollutant. Its therapeutic action mainly depends on targeting the androgen receptors and inhibiting the androgen action that is essential for growth and survival of prostate tissue. Currently flutamide is of concern with respect to its categorization as an endocrine disruptor. In this work we have developed a physiologically based pharmacokinetic (PBPK) model of flutamide that could serve as a standard tool for its human risk assessment. First we built the model for rat (where many parameters have been measured). The rat PBPK model was extrapolated to human where the re-parameterization involved human-specific physiology, metabolic kinetics derived from in-vitro studies, and the partition coefficient same as the rat model. We have harmonized the model by integrating different sets of in-vitro, in-vivo and physiological data into a PBPK model. Then the model was used to simulate different exposure scenarios and the results were compared against the observed data. Both uncertainty and sensitivity analysis was done. Since this new whole-body PBPK model can predict flutamide concentrations not only in plasma but also in various organs, the model may have clinical applications in efficacy and safety assessment of flutamide. The model can also be used for reverse dosimetry in the context of interpreting the available biomonitoring data to estimate the degree to which the population is currently being exposed, and a tool for the pharmaceutical companies to validate the estimated Permitted Daily Exposure (PDE) for flutamide.

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    Environmental Research
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    License: CC BY ND SA
    Data sources: UnpayWall
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    image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
    NARCIS
    Article . 2020
    Data sources: NARCIS
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      Environmental Research
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      Data sources: UnpayWall
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      image/svg+xml Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao Closed Access logo, derived from PLoS Open Access logo. This version with transparent background. http://commons.wikimedia.org/wiki/File:Closed_Access_logo_transparent.svg Jakob Voss, based on art designer at PLoS, modified by Wikipedia users Nina and Beao
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      Article . 2020
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Aarestrup, F. M.; Albeyatti, A.; Armitage, W. J.; Auffray, C.; +48 Authors

    The workshop participants received funding from the European Union Seventh Program for Research, Technological Development and Demonstration (FP7) and Horizon Research and Innovation Program (H2020) and other European Union programs under the following grant agreements: AETIONOMY (Developing an Aetiology-based Taxonomy of Human Disease—Approaches to Develop a New Taxonomy for Neurological Disorders, IMI-no115568), ANTI-SUPERBUG PCP (ANTISUPERBUG Precommercial Procurement, H2020-no688878), B-CAST (Breast CAncer Stratification understanding the determinants of risk and prognosis of molecular sub-types, H2020-no633784), BRIDGE Health (Bridging information and data generation for evidence-based health policy and research, H2020-no664691), CASyM (Coordinating Action Systems Medicine—Implementation of Systems Medicine across Europe, FP7-n°305033), CENTER-TBI (Collaborative European NeuroTrauma Effectiveness Research in TBI, FP7-no602150), CECM (Centre for New Methods in Computational Diagnostics and Personalized Therapy, H2020-no763734), COLOSSUS (Advancing a Precision Medicine Paradigm in Metastatic Colorectal Cancer: Systems based patient stratification solutions, H2020-no754923), COMPARE (COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe, H2020-no643476), CONNECARE (Personalized Connected Care for Complex Chronic Patients, H2020-no689802), CREATIVE (Collaborative REsearch on ACute Traumatic brain Injury in intensiVe care medicine in Europe, FP7-no602714), DEFORM (Define the global and financial impact of research misconduct H2020-no710246), ECCTR (European Cornea and Cell Transplant Registry, FP7-n°709723), E-COMPARED (European COMPARative Effectiveness Research on online Depression, FP7-no603098), ECRIN-IA (European Clinical Research Infrastructures Network- Integrating Activity, FP7-no284395), EHR4CR (Electronic Health Records Systems for Clinical Research, IMI-no115189) eInfraCentral (European E-infrastructures Services Gateway, H2020-no731049), ELIXIR (European Life-science Infrastructure for Biological Information, FP7-n°211601), ELIXIR-EXCELERATE (Fast track ELIXIR implementation and drive early user exploitation across the life sciences, H2020-no676559), eMEN (e-mental health innovation and transnational implementation platform North West Europe, H2020), EMIF (European Medical Information Framework, IMI-no115372), ERA PerMed (ERA-net Cofund in Personalized Medicine, H2020-no779282), eTRIKS (Delivering European Translational Information and Knowledge Management Services, IMI-1-no115446), EuroPOND (Data-driven models for progression of neurological diseases, H2020-n°666992), EurValve (Personalized Decision Support for Heart Valve disease, H2020-no689617), HBP SGA1/SGA2 (Human Brain Project specific grant agreements, H2020-n°720270/785907), ICT4DEPRESSION (User-friendly ICT tools to enhance self-management and effective treatment of depression in the EU, FP7-n°248778), ImpleMentAll (Towards evidence-based tailored implementation strategies for eHealth, H2020-no733025), INSTRUCT-ULTRA (Releasing the full potential of instruct to expand and consolidate infrastructure services for integrated structural life sciences research, H2020-no731005), MASTERMIND (Management of Mental Disorders through Advanced Technologies, CIP-no621000), MeDALL (Mechanisms of the Development of ALLergy, FP7-n°261357), MedBioinformatics (Creating medically-driven integrative bioinformatics applications focused on oncology, CNS disorders and their comorbidities, H2020-n°634143), MIDAS (Meaningful Integration of Data, Analytics and Services, H2020-no727721), MultipleMS (Multiple manifestations of genetic and non-genetic factors in Multiple Sclerosis disentangled with a multi-omics approach to accelerate personalized medicine, H2020-no733161), myPEBS (Randomized Comparison Of Risk-Stratified versus Standard Breast Cancer Screening European Women Aged 40–74, H2020-no755394), OpenAIRE-Advance (Advancing Open Scholarship, H2020-no777541), OpenMedicine (OpenMedicine, H2020-n°643796), PanCareSurFup (PanCare Childhood and Adolescent Cancer Survival Care and Follow-up Studies, FP7-n°257505), PIONEER (Prostate Cancer DIagnOsis and TreatmeNt Enhancement through the Power of Big Data in EuRope, H2020-IMI-2-n°777492), PREPARE (Platform for European Preparedness Against (Re-)emerging Epidemics, FP7-n°602525), Regions4PerMed (Interregional coordination for a deep and fast uptake of personalized health, H2020-no825812), RD-CONNECT (An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research, FP7-no305344), Solve-RD (Solving the unsolved Rare Diseases, H2020-no779257), SPIDIA4P (SPIDIA for Personalized Medicine-Standardization of generic Pre-analytical procedures for In-vitro DIAgnostics for Personalized Medicine, H2020-no733112), SYSCID (A Systems medicine approach to chronic inflammatory disease, H2020-no733100), SysCLAD (Systems prediction of Chronic Allograft Dysfunction, FP7-n°305457), SYSCOL (Systems Biology of Colorectal Cancer, FP7-no258236), SysMedPD (Systems Medicine of Mitochondrial Parkinson’s Disease, H2020-n°668738), U-BIOPRED (Unbiased BIOmarkers for the PREDiction of respiratory disease outcomes, IMI-n°115010), VPH-share (Virtual Physiological Human: Sharing for Healthcare—A Research Environment, FP7-n°269978). The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) aims to provide the conditions necessary for building a secure, flexible, and decentralized digital health infrastructure. Creating a European Health Research and Innovation Cloud (HRIC) within this environment should enable data sharing and analysis for health research across the EU, in compliance with data protection legislation while preserving the full trust of the participants. Such a HRIC should learn from and build on existing data infrastructures, integrate best practices, and focus on the concrete needs of the community in terms of technologies, governance, management, regulation, and ethics requirements. Here, we describe the vision and expected benefits of digital data sharing in health research activities and present a roadmap that fosters the opportunities while answering the challenges of implementing a HRIC. For this, we put forward five specific recommendations and action points to ensure that a European HRIC: i) is built on established standards and guidelines, providing cloud technologies through an open and decentralized infrastructure; ii) is developed and certified to the highest standards of interoperability and data security that can be trusted by all stakeholders; iii) is supported by a robust ethical and legal framework that is compliant with the EU General Data Protection Regulation (GDPR); iv) establishes a proper environment for the training of new generations of data and medical scientists; and v) stimulates research and innovation in transnational collaborations through public and private initiatives and partnerships funded by the EU through Horizon 2020 and Horizon Europe.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Recolector de Cienci...arrow_drop_down
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    Genome Medicine
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    UPF Digital Repository
    Article . 2020
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    Serveur académique lausannois
    Article . 2020
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      Genome Medicine
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      UCL Discovery
      Article . 2020
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      UPF Digital Repository
      Article . 2020
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      DOAJ
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      Serveur académique lausannois
      Article . 2020
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    Authors: F. M. Aarestrup; A. Albeyatti; W. J. Armitage; Auffray, C.; +48 Authors

    Additional file 1. National health record systems.

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    Authors: Mercedes Ramírez-Escudero; Mercedes V. del Pozo; Julia Marín-Navarro; Beatriz González; +4 Authors

    Metagenomics has opened up a vast pool of genes for putative, yet uncharacterized, enzymes. It widens our knowledge on the enzyme diversity world and discloses new families for which a clear classification is still needed, as is exemplified by glycoside hydrolase family-3 (GH3) proteins. Herein, we describe a GH3 enzyme (GlyA1) from resident microbial communities in strained ruminal fluid. The enzyme is a β-glucosidase/β-xylosidase that also shows β-galactosidase, β-fucosidase, α-arabinofuranosidase, and α-arabinopyranosidase activities. Short cello- and xylo-oligosaccharides, sophorose and gentibiose, are among the preferred substrates, with the large polysaccharide lichenan also being hydrolyzed by GlyA1. The determination of the crystal structure of the enzyme in combination with deletion and site-directed mutagenesis allowed identification of its unusual domain composition and the active site architecture. Complexes of GlyA1 with glucose, galactose, and xylose allowed picturing the catalytic pocket and illustrated the molecular basis of the substrate specificity. A hydrophobic platform defined by residues Trp-711 and Trp-106, located in a highly mobile loop, appears able to allocate differently β-linked bioses. GlyA1 includes an additional C-terminal domain previously unobserved in GH3 members, but crystallization of the full-length enzyme was unsuccessful. Therefore, small angle x-ray experiments have been performed to investigate the molecular flexibility and overall putative shape. This study provided evidence that GlyA1 defines a new subfamily of GH3 proteins with a novel permuted domain topology. Phylogenetic analysis indicates that this topology is associated with microbes inhabiting the digestive tracts of ruminants and other animals, feeding on chemically diverse plant polymeric materials. This work was supported by Grants BIO2013-48779-C4-2-R, BIO2013-48779-C4-3-R, and BIO2014-54494-R from the Spanish Ministry of Economy and Competitiveness; ERA Net IB2 Project MetaCat through the Spanish Ministry of Economy and Competitiveness Grant PCIN-2014-107; United Kingdom's Biotechnology and Biological Sciences Research Council Grant BB/M029085/1; European Union's Horizon 2020 Research and Innovation Program (Blue Growth, Unlocking the potential of Seas and Oceans) Grant 634486, and the European Regional Development Fund (ERDF). Peer reviewed

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    Journal of Biological Chemistry
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    https://doi.org/10.1074/jbc.M1...
    Other literature type . Article . 2016 . Peer-reviewed
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      Journal of Biological Chemistry
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      https://doi.org/10.1074/jbc.M1...
      Other literature type . Article . 2016 . Peer-reviewed
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Artini M.; Assante M.; Atzori C.; Baglioni M.; +25 Authors

    InfraScience is a research group of the National Research Council of Italy - Institute of Information Science and Technologies (CNR - ISTI) based in Pisa, Italy. This report documents the research activity performed by this group in 2022 to highlight the major results. In particular, the InfraScience group confronted with research challenges characterising Data Infrastructures, e-Science, and Intelligent Systems. The group activity is pursued by closely connecting research and development and by promoting and supporting open science. In fact, the group is leading the development of two large scale infrastructures for Open Science, i.e. D4Science and OpenAIRE. During 2022 InfraScience members contributed to the publishing of several papers, to the research and development activities of 18 research projects (15 funded by EU), to the organization of conferences and training events, to several working groups and task forces.

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    Report . 2022
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    Authors: Sharma, Raju Prasad; Kumar, Vikas; Schuhmacher, Marta; Kolodkin, Alexey; +1 Authors

    By their definition, inadvertent exposure to endocrine disrupting compounds (EDCs) intervenes with the endocrine signalling system, even at low dose. On the one hand, some EDCs are used as important pharmaceutical drugs that one would not want to dismiss. On the other hand, these pharmaceutical drugs are having off-target effects and increasingly significant exposure to the general population with unwanted health implications. Flutamide, one of the top pharmaceutical products marketed all over the world for the treatment of prostate cancer, is also a pollutant. Its therapeutic action mainly depends on targeting the androgen receptors and inhibiting the androgen action that is essential for growth and survival of prostate tissue. Currently flutamide is of concern with respect to its categorization as an endocrine disruptor. In this work we have developed a physiologically based pharmacokinetic (PBPK) model of flutamide that could serve as a standard tool for its human risk assessment. First we built the model for rat (where many parameters have been measured). The rat PBPK model was extrapolated to human where the re-parameterization involved human-specific physiology, metabolic kinetics derived from in-vitro studies, and the partition coefficient same as the rat model. We have harmonized the model by integrating different sets of in-vitro, in-vivo and physiological data into a PBPK model. Then the model was used to simulate different exposure scenarios and the results were compared against the observed data. Both uncertainty and sensitivity analysis was done. Since this new whole-body PBPK model can predict flutamide concentrations not only in plasma but also in various organs, the model may have clinical applications in efficacy and safety assessment of flutamide. The model can also be used for reverse dosimetry in the context of interpreting the available biomonitoring data to estimate the degree to which the population is currently being exposed, and a tool for the pharmaceutical companies to validate the estimated Permitted Daily Exposure (PDE) for flutamide.

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    Environmental Research
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    Authors: Aarestrup, F. M.; Albeyatti, A.; Armitage, W. J.; Auffray, C.; +48 Authors

    The workshop participants received funding from the European Union Seventh Program for Research, Technological Development and Demonstration (FP7) and Horizon Research and Innovation Program (H2020) and other European Union programs under the following grant agreements: AETIONOMY (Developing an Aetiology-based Taxonomy of Human Disease—Approaches to Develop a New Taxonomy for Neurological Disorders, IMI-no115568), ANTI-SUPERBUG PCP (ANTISUPERBUG Precommercial Procurement, H2020-no688878), B-CAST (Breast CAncer Stratification understanding the determinants of risk and prognosis of molecular sub-types, H2020-no633784), BRIDGE Health (Bridging information and data generation for evidence-based health policy and research, H2020-no664691), CASyM (Coordinating Action Systems Medicine—Implementation of Systems Medicine across Europe, FP7-n°305033), CENTER-TBI (Collaborative European NeuroTrauma Effectiveness Research in TBI, FP7-no602150), CECM (Centre for New Methods in Computational Diagnostics and Personalized Therapy, H2020-no763734), COLOSSUS (Advancing a Precision Medicine Paradigm in Metastatic Colorectal Cancer: Systems based patient stratification solutions, H2020-no754923), COMPARE (COllaborative Management Platform for detection and Analyses of (Re-)emerging and foodborne outbreaks in Europe, H2020-no643476), CONNECARE (Personalized Connected Care for Complex Chronic Patients, H2020-no689802), CREATIVE (Collaborative REsearch on ACute Traumatic brain Injury in intensiVe care medicine in Europe, FP7-no602714), DEFORM (Define the global and financial impact of research misconduct H2020-no710246), ECCTR (European Cornea and Cell Transplant Registry, FP7-n°709723), E-COMPARED (European COMPARative Effectiveness Research on online Depression, FP7-no603098), ECRIN-IA (European Clinical Research Infrastructures Network- Integrating Activity, FP7-no284395), EHR4CR (Electronic Health Records Systems for Clinical Research, IMI-no115189) eInfraCentral (European E-infrastructures Services Gateway, H2020-no731049), ELIXIR (European Life-science Infrastructure for Biological Information, FP7-n°211601), ELIXIR-EXCELERATE (Fast track ELIXIR implementation and drive early user exploitation across the life sciences, H2020-no676559), eMEN (e-mental health innovation and transnational implementation platform North West Europe, H2020), EMIF (European Medical Information Framework, IMI-no115372), ERA PerMed (ERA-net Cofund in Personalized Medicine, H2020-no779282), eTRIKS (Delivering European Translational Information and Knowledge Management Services, IMI-1-no115446), EuroPOND (Data-driven models for progression of neurological diseases, H2020-n°666992), EurValve (Personalized Decision Support for Heart Valve disease, H2020-no689617), HBP SGA1/SGA2 (Human Brain Project specific grant agreements, H2020-n°720270/785907), ICT4DEPRESSION (User-friendly ICT tools to enhance self-management and effective treatment of depression in the EU, FP7-n°248778), ImpleMentAll (Towards evidence-based tailored implementation strategies for eHealth, H2020-no733025), INSTRUCT-ULTRA (Releasing the full potential of instruct to expand and consolidate infrastructure services for integrated structural life sciences research, H2020-no731005), MASTERMIND (Management of Mental Disorders through Advanced Technologies, CIP-no621000), MeDALL (Mechanisms of the Development of ALLergy, FP7-n°261357), MedBioinformatics (Creating medically-driven integrative bioinformatics applications focused on oncology, CNS disorders and their comorbidities, H2020-n°634143), MIDAS (Meaningful Integration of Data, Analytics and Services, H2020-no727721), MultipleMS (Multiple manifestations of genetic and non-genetic factors in Multiple Sclerosis disentangled with a multi-omics approach to accelerate personalized medicine, H2020-no733161), myPEBS (Randomized Comparison Of Risk-Stratified versus Standard Breast Cancer Screening European Women Aged 40–74, H2020-no755394), OpenAIRE-Advance (Advancing Open Scholarship, H2020-no777541), OpenMedicine (OpenMedicine, H2020-n°643796), PanCareSurFup (PanCare Childhood and Adolescent Cancer Survival Care and Follow-up Studies, FP7-n°257505), PIONEER (Prostate Cancer DIagnOsis and TreatmeNt Enhancement through the Power of Big Data in EuRope, H2020-IMI-2-n°777492), PREPARE (Platform for European Preparedness Against (Re-)emerging Epidemics, FP7-n°602525), Regions4PerMed (Interregional coordination for a deep and fast uptake of personalized health, H2020-no825812), RD-CONNECT (An integrated platform connecting registries, biobanks and clinical bioinformatics for rare disease research, FP7-no305344), Solve-RD (Solving the unsolved Rare Diseases, H2020-no779257), SPIDIA4P (SPIDIA for Personalized Medicine-Standardization of generic Pre-analytical procedures for In-vitro DIAgnostics for Personalized Medicine, H2020-no733112), SYSCID (A Systems medicine approach to chronic inflammatory disease, H2020-no733100), SysCLAD (Systems prediction of Chronic Allograft Dysfunction, FP7-n°305457), SYSCOL (Systems Biology of Colorectal Cancer, FP7-no258236), SysMedPD (Systems Medicine of Mitochondrial Parkinson’s Disease, H2020-n°668738), U-BIOPRED (Unbiased BIOmarkers for the PREDiction of respiratory disease outcomes, IMI-n°115010), VPH-share (Virtual Physiological Human: Sharing for Healthcare—A Research Environment, FP7-n°269978). The European Union (EU) initiative on the Digital Transformation of Health and Care (Digicare) aims to provide the conditions necessary for building a secure, flexible, and decentralized digital health infrastructure. Creating a European Health Research and Innovation Cloud (HRIC) within this environment should enable data sharing and analysis for health research across the EU, in compliance with data protection legislation while preserving the full trust of the participants. Such a HRIC should learn from and build on existing data infrastructures, integrate best practices, and focus on the concrete needs of the community in terms of technologies, governance, management, regulation, and ethics requirements. Here, we describe the vision and expected benefits of digital data sharing in health research activities and present a roadmap that fosters the opportunities while answering the challenges of implementing a HRIC. For this, we put forward five specific recommendations and action points to ensure that a European HRIC: i) is built on established standards and guidelines, providing cloud technologies through an open and decentralized infrastructure; ii) is developed and certified to the highest standards of interoperability and data security that can be trusted by all stakeholders; iii) is supported by a robust ethical and legal framework that is compliant with the EU General Data Protection Regulation (GDPR); iv) establishes a proper environment for the training of new generations of data and medical scientists; and v) stimulates research and innovation in transnational collaborations through public and private initiatives and partnerships funded by the EU through Horizon 2020 and Horizon Europe.

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      DOAJ
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      Serveur académique lausannois
      Article . 2020
      License: CC BY
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    Authors: F. M. Aarestrup; A. Albeyatti; W. J. Armitage; Auffray, C.; +48 Authors

    Additional file 1. National health record systems.

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    Authors: Mercedes Ramírez-Escudero; Mercedes V. del Pozo; Julia Marín-Navarro; Beatriz González; +4 Authors

    Metagenomics has opened up a vast pool of genes for putative, yet uncharacterized, enzymes. It widens our knowledge on the enzyme diversity world and discloses new families for which a clear classification is still needed, as is exemplified by glycoside hydrolase family-3 (GH3) proteins. Herein, we describe a GH3 enzyme (GlyA1) from resident microbial communities in strained ruminal fluid. The enzyme is a β-glucosidase/β-xylosidase that also shows β-galactosidase, β-fucosidase, α-arabinofuranosidase, and α-arabinopyranosidase activities. Short cello- and xylo-oligosaccharides, sophorose and gentibiose, are among the preferred substrates, with the large polysaccharide lichenan also being hydrolyzed by GlyA1. The determination of the crystal structure of the enzyme in combination with deletion and site-directed mutagenesis allowed identification of its unusual domain composition and the active site architecture. Complexes of GlyA1 with glucose, galactose, and xylose allowed picturing the catalytic pocket and illustrated the molecular basis of the substrate specificity. A hydrophobic platform defined by residues Trp-711 and Trp-106, located in a highly mobile loop, appears able to allocate differently β-linked bioses. GlyA1 includes an additional C-terminal domain previously unobserved in GH3 members, but crystallization of the full-length enzyme was unsuccessful. Therefore, small angle x-ray experiments have been performed to investigate the molecular flexibility and overall putative shape. This study provided evidence that GlyA1 defines a new subfamily of GH3 proteins with a novel permuted domain topology. Phylogenetic analysis indicates that this topology is associated with microbes inhabiting the digestive tracts of ruminants and other animals, feeding on chemically diverse plant polymeric materials. This work was supported by Grants BIO2013-48779-C4-2-R, BIO2013-48779-C4-3-R, and BIO2014-54494-R from the Spanish Ministry of Economy and Competitiveness; ERA Net IB2 Project MetaCat through the Spanish Ministry of Economy and Competitiveness Grant PCIN-2014-107; United Kingdom's Biotechnology and Biological Sciences Research Council Grant BB/M029085/1; European Union's Horizon 2020 Research and Innovation Program (Blue Growth, Unlocking the potential of Seas and Oceans) Grant 634486, and the European Regional Development Fund (ERDF). Peer reviewed

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    Journal of Biological Chemistry
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    https://doi.org/10.1074/jbc.M1...
    Other literature type . Article . 2016 . Peer-reviewed
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      Journal of Biological Chemistry
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      https://doi.org/10.1074/jbc.M1...
      Other literature type . Article . 2016 . Peer-reviewed
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