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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: Sukackaite, Rasa; Cornacchia, Daniela; Jensen, Malene Ringkjøbing; Mas, Philippe J.; +7 Authors

    AbstractRif1 is a conserved protein that plays essential roles in orchestrating DNA replication timing, controlling nuclear architecture, telomere length and DNA repair. However, the relationship between these different roles, as well as the molecular basis of Rif1 function is still unclear. The association of Rif1 with insoluble nuclear lamina has thus far hampered exhaustive characterization of the associated protein complexes. We devised a protocol that overcomes this problem, and were thus able to discover a number of novel Rif1 interactors, involved in chromatin metabolism and phosphorylation. Among them, we focus here on PP1. Data from different systems have suggested that Rif1-PP1 interaction is conserved and has important biological roles. Using mutagenesis, NMR, isothermal calorimetry and surface plasmon resonance we demonstrate that Rif1 is a high-affinity PP1 adaptor, able to out-compete the well-established PP1-inhibitor I2 in vitro. Our conclusions have important implications for understanding Rif1 diverse roles and the relationship between the biological processes controlled by Rif1.

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    Scientific Reports
    Article . 2017
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    Scientific Reports
    Article . 2017 . Peer-reviewed
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    Scientific Reports
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      Scientific Reports
      Article . 2017
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      Scientific Reports
      Article . 2017 . Peer-reviewed
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    Authors: Marquevielle, Julien; Robert, Coralie; Lagrabette, Olivier; Wahid, Mona; +4 Authors

    International audience; KRAS is one of the most mutated oncogenes and still considered an undruggable target. An alternative strategy would consist in targeting its gene rather than the protein, specifically the formation of G-quadruplexes (G4) in its promoter. G4 are secondary structures implicated in biological processes, which can be formed among G-rich DNA (or RNA) sequences. Here we have studied the major conforma-tions of the commonly known KRAS 32R, or simply 32R, a 32 residue sequence within the KRAS Nucle-ase Hypersensitive Element (NHE) region. We have determined the structure of the two major stable con-formers that 32R can adopt and which display slow equilibrium (>ms) with each other. By using different biophysical methods, we found that the nucleotides G9, G25, G28 and G32 are particularly implicated in the exchange between these two conformations. We also showed that a triad at the 3 end further stabilizes one of the G4 conformations, while the second conformer remains more flexible and less stable.

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    HAL-Inserm
    Other literature type . 2020
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    Authors: Hermjakob, Henning; Kleemola, Mari; Moilanen, Katja; Sansone, Susanna-Assunta; +8 Authors

    BY-COVID Work Package 3 is focused on services for the discovery and integration of COVID-19 data by delivering a flexible, tiered metadata discovery system across different domains, metadata standards, and maturity/robustness levels of data sources. This will enable the linking of FAIR data and metadata on SARS-CoV-2 and COVID-19, on other related viruses and diseases, and on socio-economic consequences, across research fields, from omics, clinical, and epidemiological research, to social sciences and humanities. In a series of work package meetings and a workshop, with participation from all other work packages, we have surveyed community metadata standards used by (potential) BY-COVID-19 portal resources (4.1), defined a flexible, three-tiered approach to metadata indexing in the COVID-19 portal (section 4.2), derived common metadata attributes for record level discovery (4.3) and established a workflow with FAIRsharing for resource level metadata capture and exchange (4.4). This work establishes the basis for the further development of the COVID-19 Portal metadata discovery and provides a path for integration of metadata from multi-domain partners in BY-COVID, as well as our ISIDORe sibling project, and relevant external resources. To ensure smooth integration of partner-provided metadata, we will run a technical workshop open to all partners, discussing workflows, metadata attributes and formats, and support tools. Contributor: Morris Swertz (UMCG/BBMRI)

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    Other literature type . Article . 2022
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      Other literature type . Article . 2022
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    Authors: Atherton, Christopher John; Barton, Thomas; Basney, Jim; Broeder, Daan; +36 Authors

    The authors also acknowledge the support and collaboration of many other colleagues in their respective institutes, research communities and IT Infrastructures, together with the funding received by these from many different sources. These include but are not limited to the following: (i) The Worldwide LHC Computing Grid (WLCG) project is a global collaboration of more than 170 computing centres in 43 countries, linking up national and international grid infrastructures. Funding is acknowledged from many national funding bodies and we acknowledge the support of several operational infrastructures including EGI, OSG and NDGF/NeIC. (ii) EGI acknowledges the funding and support received from the European Commission and the many National Grid Initiatives and other members. EOSC-hub receives funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 777536. (iii) The work leading to these results has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. 730941 (AARC2). (iv) Work on the development of ESGF's identity management system has been supported by The UK Natural Environment Research Council and funding from the European Union's Seventh Framework Programme for research, technological development and demonstration through projects IS-ENES (grant agreement no 228203) and IS-ENES2 (grant agreement no 312979). (v) Ludek Matyska and Michal Prochazka acknowledge funding from the RI ELIXIR CZ project funded by MEYS Czech Republic No. LM2015047. (vi) Scott Koranda acknowledges support provided by the United States National Science Foundation under Grant No. PHY-1700765. (vii) GÉANT Association on behalf of the GN4 Phase 2 project (GN4-2).The research leading to these results has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. 731122(GN4-2). (viii) ELIXIR acknowledges support from Research Infrastructure programme of Horizon 2020 grant No 676559 EXCELERATE. (ix) CORBEL life science cluster acknowledges support from Horizon 2020 research and innovation programme under grant agreement No 654248. (x) Mirjam van Daalen acknowledges that the research leading to this result has been supported by the project CALIPSOplus under the Grant Agreement 730872 from the EU Framework Programme for Research and Innovation HORIZON 2020. (xi) EISCAT is an international association supported by research organisations in China (CRIRP), Finland (SA), Japan (NIPR), Norway (NFR), Sweden (VR), and the United Kingdom (NERC). This white-paper expresses common requirements of Research Communities seeking to leverage Identity Federation for Authentication and Authorisation. Recommendations are made to Stakeholders to guide the future evolution of Federated Identity Management in a direction that better satisfies research use cases. The authors represent research communities, Research Services, Infrastructures, Identity Federations and Interfederations, with a joint motivation to ease collaboration for distributed researchers. The content has been edited collaboratively by the Federated Identity Management for Research (FIM4R) Community, with input sought at conferences and meetings in Europe, Asia and North America.

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    https://doi.org/10.5445/ir/100...
    Other literature type . 2018
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    Data sources: Datacite
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    https://zenodo.org/record/1307...
    Article . 2018
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      https://doi.org/10.5445/ir/100...
      Other literature type . 2018
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      https://zenodo.org/record/1307...
      Article . 2018
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    Intrinsically disordered proteins (IDPs) and intrinsically disordered regions (IDRs) are now recognised as major determinants in cellular regulation. This white paper presents a roadmap for future e-infrastructure developments in the field of IDP research within the ELIXIR framework. The goal of these developments is to drive the creation of high-quality tools and resources to support the identification, analysis and functional characterisation of IDPs. The roadmap is the result of a workshop titled "An intrinsically disordered protein user community proposal for ELIXIR" held at the University of Padua. The workshop, and further consultation with the members of the wider IDP community, identified the key priority areas for the roadmap including the development of standards for data annotation, storage and dissemination; integration of IDP data into the ELIXIR Core Data Resources; and the creation of benchmarking criteria for IDP-related software. Here, we discuss these areas of priority, how they can be implemented in cooperation with the ELIXIR platforms, and their connections to existing ELIXIR Communities and international consortia. The article provides a preliminary blueprint for an IDP Community in ELIXIR and is an appeal to identify and involve new stakeholders.

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    Authors: Paradžik, Tina; Ivić, Nives; Filić, Želimira; Manjasetty, Babbu A.; +3 Authors

    The linear chromosome of Streptomyces coelicolor contains two paralogous ssb genes, ssbA and ssbB. Following mutational analysis, we concluded that ssbA is essential, whereas ssbB plays a key role in chromosome segregation during sporulation. In the ssbB mutant, ~30% of spores lacked DNA. The two ssb genes were expressed differently ; in minimal medium, gene expression was prolonged for both genes and significantly upregulated for ssbB. The ssbA gene is transcribed as part of a polycistronic mRNA from two initiation sites, 163 bp and 75 bp upstream of the rpsF translational start codon. The ssbB gene is transcribed as a monocistronic mRNA, from an unusual promoter region, 73 bp upstream of the AUG codon. Distinctive DNA-binding affinities of single-stranded DNA-binding proteins monitored by tryptophan fluorescent quenching and electrophoretic mobility shift were observed. The crystal structure of SsbB at 1.7A° resolution revealed a common OB-fold, lack of the clamp-like structure conserved in SsbA and previously unpublished S-S bridges between the A/B and C/D subunits. This is the first report of the determination of paralogous singlestranded DNA-binding protein structures from the same organism. Phylogenetic analysis revealed frequent duplication of ssb genes in Actinobacteria, whereas their strong retention suggests that they are involved in important cellular functions.

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    Nucleic Acids Research
    Article . 2013 . Peer-reviewed
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    Nucleic Acids Research
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      Nucleic Acids Research
      Article . 2013 . Peer-reviewed
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      Nucleic Acids Research
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    Authors: Tim Schulte; Jonas Lofling; Cecilia Mikaelsson; Alexey Kikhney; +7 Authors

    Streptococcus pneumoniaeis a major human pathogen, and a leading cause of disease and death worldwide. Pneumococcal invasive disease is triggered by initial asymptomatic colonization of the human upper respiratory tract. The pneumococcal serine-rich repeat protein (PsrP) is a lung-specific virulence factor whose functional binding region (BR) binds to keratin-10 (KRT10) and promotes pneumococcal biofilm formation through self-oligomerization. We present the crystal structure of the KRT10-binding domain of PsrP (BR187–385) determined to 2.0 Å resolution. BR187–385adopts a novel variant of the DEv-IgG fold, typical for microbial surface components recognizing adhesive matrix molecules adhesins, despite very low sequence identity. An extended β-sheet on one side of the compressed, two-sided barrel presents a basic groove that possibly binds to the acidic helical rod domain of KRT10. Our study also demonstrates the importance of the other side of the barrel, formed by extensive well-ordered loops and stabilized by short β-strands, for interaction with KRT10.

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    Open Biology
    Other literature type . Article . 2014 . Peer-reviewed
    License: Royal Society Data Sharing and Accessibility
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    Open Biology
    Article . 2014
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    HAL-INSA Toulouse
    Article . 2014
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    Authors: Lucie Kuntová; Ivana Mašlaňová; Radka Obořilová; Hana Šimečková; +10 Authors

    Both temperate and obligately lytic phages have crucial roles in the biology of staphylococci. While superinfection exclusion among closely related temperate phages is a well-characterized phenomenon, the interactions between temperate and lytic phages in staphylococci are not understood. Here, we present a resistance mechanism toward lytic phages of the genus Kayvirus, mediated by the membrane-anchored protein designated PdpSau encoded by Staphylococcus aureus prophages, mostly of the Sa2 integrase type. The prophage accessory gene pdpSau is strongly linked to the lytic genes for holin and ami2-type amidase and typically replaces genes for the toxin Panton-Valentine leukocidin (PVL). The predicted PdpSau protein structure shows the presence of a membrane-binding α-helix in its N-terminal part and a cytoplasmic positively charged C terminus. We demonstrated that the mechanism of action of PdpSau does not prevent the infecting kayvirus from adsorbing onto the host cell and delivering its genome into the cell, but phage DNA replication is halted. Changes in the cell membrane polarity and permeability were observed from 10 min after the infection, which led to prophage-activated cell death. Furthermore, we describe a mechanism of overcoming this resistance in a host-range Kayvirus mutant, which was selected on an S. aureus strain harboring prophage 53 encoding PdpSau, and in which a chimeric gene product emerged via adaptive laboratory evolution. This first case of staphylococcal interfamily phage-phage competition is analogous to some other abortive infection defense systems and to systems based on membrane-destructive proteins. IMPORTANCE. Prophages play an important role in virulence, pathogenesis, and host preference, as well as in horizontal gene transfer in staphylococci. In contrast, broad-host-range lytic staphylococcal kayviruses lyse most S. aureus strains, and scientists worldwide have come to believe that the use of such phages will be successful for treating and preventing bacterial diseases. The effectiveness of phage therapy is complicated by bacterial resistance, whose mechanisms related to therapeutic staphylococcal phages are not understood in detail. In this work, we describe a resistance mechanism targeting kayviruses that is encoded by a prophage. We conclude that the defense mechanism belongs to a broader group of abortive infections, which is characterized by suicidal behavior of infected cells that are unable to produce phage progeny, thus ensuring the survival of the host population. Since the majority of staphylococcal strains are lysogenic, our findings are relevant for the advancement of phage therapy.

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    mBio
    Article . 2023
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    mBio
    Article . 2023 . Peer-reviewed
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      Article . 2023
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    Authors: Bhagwati Khatri; James Keeble; Belinda Dagg; Daryan A. Kaveh; +2 Authors

    AbstractTwo strains of mice (BALB/c and CB6F1) were vaccinated with a range of Bacille Calmette-Guérin (BCG) Danish doses from 3 × 105to 30 CFU/mouse, followed by aerosol infection withMtb(H37Rv or West-Beijing HN878 strain). The results indicated that both strains of mice when infected with HN878 exhibited significant protection in their lungs with BCG doses at 3 × 105—3000 CFU (BALB/c) and 3 × 105—300 CFU (CB6F1). Whereas, a significant protection was seen in both strains of mice with BCG doses at 3 × 105—300 CFU when infected with H37Rv. A significant increase in the frequencies of BCG-specific IFNγ+IL2+TNFα+CD4 T cells in the BCG doses at 3 × 105—3000 CFU (BALB/c) and 3 × 105—300 CFU (CB6F1) was seen. The IFNγ+IL2+TNFα+CD4 T cells correlated with theMtbburden in the lungs of HN878 infected mice (BALB/c and CB6F1) whereas, IFNγ+TNFα+CD4 T cells correlated with the BALB/c mice infected with H37Rv or HN878. The BCG dose at 3000 CFU (an equivalent single human dose in the mice by body weight) is protective in both strains of mice infected with H37Rv or HN878 and may serve an interesting dose to test new TB vaccine in a preclinical animal model.

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    Scientific Reports
    Other literature type . Article . 2021 . Peer-reviewed
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    Scientific Reports
    Article . 2021
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      Other literature type . Article . 2021 . Peer-reviewed
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    Authors: Claudine, Bisson; Nathan B P, Adams; Ben, Stevenson; Amanda A, Brindley; +5 Authors

    Inorganic phosphate is the major bioavailable form of the essential nutrient phosphorus. However, the concentration of phosphate in most natural habitats is low enough to limit microbial growth. Under phosphate-depleted conditions some bacteria utilise phosphite and hypophosphite as alternative sources of phosphorus, but the molecular basis of reduced phosphorus acquisition from the environment is not fully understood. Here, we present crystal structures and ligand binding affinities of periplasmic binding proteins from bacterial phosphite and hypophosphite ATP-binding cassette transporters. We reveal that phosphite and hypophosphite specificity results from a combination of steric selection and the presence of a P-H…π interaction between the ligand and a conserved aromatic residue in the ligand-binding pocket. The characterisation of high affinity and specific transporters has implications for the marine phosphorus redox cycle, and might aid the use of phosphite as an alternative phosphorus source in biotechnological, industrial and agricultural applications. Some bacteria can use inorganic phosphite and hypophosphite as sources of inorganic phosphorus. Here, the authors report crystal structures of the periplasmic proteins that bind these reduced phosphorus species and show that a P-H…π interaction between the ligand and binding site determines their specificity.

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    Authors: Sukackaite, Rasa; Cornacchia, Daniela; Jensen, Malene Ringkjøbing; Mas, Philippe J.; +7 Authors

    AbstractRif1 is a conserved protein that plays essential roles in orchestrating DNA replication timing, controlling nuclear architecture, telomere length and DNA repair. However, the relationship between these different roles, as well as the molecular basis of Rif1 function is still unclear. The association of Rif1 with insoluble nuclear lamina has thus far hampered exhaustive characterization of the associated protein complexes. We devised a protocol that overcomes this problem, and were thus able to discover a number of novel Rif1 interactors, involved in chromatin metabolism and phosphorylation. Among them, we focus here on PP1. Data from different systems have suggested that Rif1-PP1 interaction is conserved and has important biological roles. Using mutagenesis, NMR, isothermal calorimetry and surface plasmon resonance we demonstrate that Rif1 is a high-affinity PP1 adaptor, able to out-compete the well-established PP1-inhibitor I2 in vitro. Our conclusions have important implications for understanding Rif1 diverse roles and the relationship between the biological processes controlled by Rif1.

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    Scientific Reports
    Article . 2017
    Data sources: DOAJ-Articles
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    Scientific Reports
    Article . 2017 . Peer-reviewed
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    Scientific Reports
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      Scientific Reports
      Article . 2017
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      Scientific Reports
      Article . 2017 . Peer-reviewed
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    Authors: Marquevielle, Julien; Robert, Coralie; Lagrabette, Olivier; Wahid, Mona; +4 Authors

    International audience; KRAS is one of the most mutated oncogenes and still considered an undruggable target. An alternative strategy would consist in targeting its gene rather than the protein, specifically the formation of G-quadruplexes (G4) in its promoter. G4 are secondary structures implicated in biological processes, which can be formed among G-rich DNA (or RNA) sequences. Here we have studied the major conforma-tions of the commonly known KRAS 32R, or simply 32R, a 32 residue sequence within the KRAS Nucle-ase Hypersensitive Element (NHE) region. We have determined the structure of the two major stable con-formers that 32R can adopt and which display slow equilibrium (>ms) with each other. By using different biophysical methods, we found that the nucleotides G9, G25, G28 and G32 are particularly implicated in the exchange between these two conformations. We also showed that a triad at the 3 end further stabilizes one of the G4 conformations, while the second conformer remains more flexible and less stable.

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    HAL-Inserm
    Other literature type . 2020
    Data sources: HAL-Inserm
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    Authors: Hermjakob, Henning; Kleemola, Mari; Moilanen, Katja; Sansone, Susanna-Assunta; +8 Authors

    BY-COVID Work Package 3 is focused on services for the discovery and integration of COVID-19 data by delivering a flexible, tiered metadata discovery system across different domains, metadata standards, and maturity/robustness levels of data sources. This will enable the linking of FAIR data and metadata on SARS-CoV-2 and COVID-19, on other related viruses and diseases, and on socio-economic consequences, across research fields, from omics, clinical, and epidemiological research, to social sciences and humanities. In a series of work package meetings and a workshop, with participation from all other work packages, we have surveyed community metadata standards used by (potential) BY-COVID-19 portal resources (4.1), defined a flexible, three-tiered approach to metadata indexing in the COVID-19 portal (section 4.2), derived common metadata attributes for record level discovery (4.3) and established a workflow with FAIRsharing for resource level metadata capture and exchange (4.4). This work establishes the basis for the further development of the COVID-19 Portal metadata discovery and provides a path for integration of metadata from multi-domain partners in BY-COVID, as well as our ISIDORe sibling project, and relevant external resources. To ensure smooth integration of partner-provided metadata, we will run a technical workshop open to all partners, discussing workflows, metadata attributes and formats, and support tools. Contributor: Morris Swertz (UMCG/BBMRI)

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    Authors: Atherton, Christopher John; Barton, Thomas; Basney, Jim; Broeder, Daan; +36 Authors

    The authors also acknowledge the support and collaboration of many other colleagues in their respective institutes, research communities and IT Infrastructures, together with the funding received by these from many different sources. These include but are not limited to the following: (i) The Worldwide LHC Computing Grid (WLCG) project is a global collaboration of more than 170 computing centres in 43 countries, linking up national and international grid infrastructures. Funding is acknowledged from many national funding bodies and we acknowledge the support of several operational infrastructures including EGI, OSG and NDGF/NeIC. (ii) EGI acknowledges the funding and support received from the European Commission and the many National Grid Initiatives and other members. EOSC-hub receives funding from the European Union's Horizon 2020 research and innovation programme under grant agreement No 777536. (iii) The work leading to these results has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. 730941 (AARC2). (iv) Work on the development of ESGF's identity management system has been supported by The UK Natural Environment Research Council and funding from the European Union's Seventh Framework Programme for research, technological development and demonstration through projects IS-ENES (grant agreement no 228203) and IS-ENES2 (grant agreement no 312979). (v) Ludek Matyska and Michal Prochazka acknowledge funding from the RI ELIXIR CZ project funded by MEYS Czech Republic No. LM2015047. (vi) Scott Koranda acknowledges support provided by the United States National Science Foundation under Grant No. PHY-1700765. (vii) GÉANT Association on behalf of the GN4 Phase 2 project (GN4-2).The research leading to these results has received funding from the European Union's Horizon 2020 research and innovation programme under Grant Agreement No. 731122(GN4-2). (viii) ELIXIR acknowledges support from Research Infrastructure programme of Horizon 2020 grant No 676559 EXCELERATE. (ix) CORBEL life science cluster acknowledges support from Horizon 2020 research and innovation programme under grant agreement No 654248. (x) Mirjam van Daalen acknowledges that the research leading to this result has been supported by the project CALIPSOplus under the Grant Agreement 730872 from the EU Framework Programme for Research and Innovation HORIZON 2020. (xi) EISCAT is an international association supported by research organisations in China (CRIRP), Finland (SA), Japan (NIPR), Norway (NFR), Sweden (VR), and the United Kingdom (NERC). This white-paper expresses common requirements of Research Communities seeking to leverage Identity Federation for Authentication and Authorisation. Recommendations are made to Stakeholders to guide the future evolution of Federated Identity Management in a direction that better satisfies research use cases. The authors represent research communities, Research Services, Infrastructures, Identity Federations and Interfederations, with a joint motivation to ease collaboration for distributed researchers. The content has been edited collaboratively by the Federated Identity Management for Research (FIM4R) Community, with input sought at conferences and meetings in Europe, Asia and North America.

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    https://doi.org/10.5445/ir/100...
    Other literature type . 2018
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    Data sources: Datacite
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    https://zenodo.org/record/1307...
    Article . 2018
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      https://doi.org/10.5445/ir/100...
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