Towards a European Collaborative Data Infrastructure

The EUDAT project is a pan-European data initiative that started in October 2011. The project brings together a unique consortium of 25 partners - including research communities, national data and high performance computing (HPC) centres, technology providers, and funding agencies - from 13 countries. EUDAT aims to build a sustainable cross-disciplinary and cross-national data infrastructure that provides a set of shared services for accessing and preserving research data. The design and deployment of these services is being coordinated by multi-disciplinary task forces comprising representatives from research communities and data centres. This short paper presents the achievements of the project during its first year and describes the services that have been chosen to meet the requirements of the initial research communities involved in the project.CSC — IT Center for Science Ltd., FI-02101 Espoo, Finland, SARA, Science Park 140, 1098 XG Amsterdam, The Netherlands, Max Planck Institute for Psycholinguistics, PO Box 310, 6500 AH Nijmegen, The Netherlands

EOSC Authentication and Authorization Infrastructure (AAI) : Report from the EOSC Executive Board Working Group (WG) Architecture AAI Task Force (TF)

The EOSC Architecture Working Group has assigned the AAI Task Force (AAI TF) the task to establish a common global ecosystem for identity and access control infrastructures for the European Open Science Cloud (EOSC). Since the EOSC is part of an international environment of research and education, the principles established by the EOSC AAI subtask must be globally viable. The EOSC AAI TF has produced a set of deliverables: - EOSC AAI First Principles & Requirements - EOSC AAI Baseline Architecture - EOSC AAI Federation participation guidelines (participation policy and technical framework) - EOSC AAI Best Practise

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer.

Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM -/- patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors

The FANCM:p.Arg658* truncating variant is associated with risk of triple-negative breast cancer

Abstract: Breast cancer is a common disease partially caused by genetic risk factors. Germline pathogenic variants in DNA repair genes BRCA1, BRCA2, PALB2, ATM, and CHEK2 are associated with breast cancer risk. FANCM, which encodes for a DNA translocase, has been proposed as a breast cancer predisposition gene, with greater effects for the ER-negative and triple-negative breast cancer (TNBC) subtypes. We tested the three recurrent protein-truncating variants FANCM:p.Arg658*, p.Gln1701*, and p.Arg1931* for association with breast cancer risk in 67,112 cases, 53,766 controls, and 26,662 carriers of pathogenic variants of BRCA1 or BRCA2. These three variants were also studied functionally by measuring survival and chromosome fragility in FANCM−/− patient-derived immortalized fibroblasts treated with diepoxybutane or olaparib. We observed that FANCM:p.Arg658* was associated with increased risk of ER-negative disease and TNBC (OR = 2.44, P = 0.034 and OR = 3.79; P = 0.009, respectively). In a country-restricted analysis, we confirmed the associations detected for FANCM:p.Arg658* and found that also FANCM:p.Arg1931* was associated with ER-negative breast cancer risk (OR = 1.96; P = 0.006). The functional results indicated that all three variants were deleterious affecting cell survival and chromosome stability with FANCM:p.Arg658* causing more severe phenotypes. In conclusion, we confirmed that the two rare FANCM deleterious variants p.Arg658* and p.Arg1931* are risk factors for ER-negative and TNBC subtypes. Overall our data suggest that the effect of truncating variants on breast cancer risk may depend on their position in the gene. Cell sensitivity to olaparib exposure, identifies a possible therapeutic option to treat FANCM-associated tumors

EOSC interoperability framework

This document has been developed by the Interoperability Task Force of the EOSC Executive Board FAIR Working Group, with participation from the Architecture WG. Achieving interoperability within EOSC is essential in order for the federation of services that will compose EOSC to provide added value for service users. In the context of the FAIR principles, interoperability is discussed in relation to the fact that “research data usually need to be integrated with other datain addition, the data need to interoperate with applications or workflows for analysis, storage, and processing”. Our view on interoperability does not only consider data but also the many other research artefacts that may be used in the context of research activity, such as software code, scientific workflows, laboratory protocols, open hardware designs, etc. It also considers the need to make services and e-infrastructures as interoperable as possible. This document identifies the general principles that should drive the creation of the EOSC Interoperability Framework (EOSC IF), and organises them into the four layers that are commonly considered in other interoperability frameworks (e.g., the European Interoperability Framework - EIF): technical, semantic, organisational and legal interoperability. For each of these layers, a catalogue of problems and needs, as well as challenges and high-level recommendations have been proposed, which should be considered in the further development and implementation of the EOSC IF components. Such requirements and recommendations have been developed after an extensive review of related literature as well as by running interviews with stakeholders from ERICs (European Research Infrastructure Consortia), ESFRI (European Strategy Forum on Research Infrastructures) projects, service providers and research communities. Some examples of such requirements are: “every semantic artefact that is being maintained in EOSC must have sufficient associated documentation, with clear examples of usage and conceptual diagrams”, or “Coarse-grained and fine-grained dataset (and other research object) search tools need to be made available”, etc. The document finally contains a proposal for the management of FAIR Digital Objects in the context of EOSC and a reference architecture for the EOSC Interoperability Framework that is inspired by and extends the European Interoperability Reference Architecture (EIRA), identifying the main building blocks required

EOSC Interoperability Framework Reference Architecture (Version 2.0)

The EOSC Interoperability Framework Reference Architecture contains framework definitions and uses abstract Building Blocks as a tool to group functionality that will be needed to meet the requirements for the EOSC Interoperability Framework (EOSC-IF). The base of the EOSC-IF Reference Architecture has been derived from the European Interoperability Reference Architecture (EIRA) developed by ISA2. This is made available as an Archimate file

Hydrogen atom cleaning of archeological artefacts

For the development of H+ and H0 beams a new method was developed based on the expansion of a cascade arc plasma. A partial aim was to develop an intense beam of at. hydrogen. The result was a 100 A equiv. hydrogen atom beam with an energy conversion efficiency of typically 30-40%. The resulting hydrogen plasma was also used to do preliminary expts. on restoration treatment of archeol. artifacts according to the method of S. Veprek, et al. The present high d. atom rich plasma beam wit

Vibrational kinetics of CO2 in non-thermal plasma

During the presentation I will discuss the development of two diagnostics to increase our current level of understanding of the vibrational kinetics within CO2 discharges, with the intention to ultimately contribute to a controlled and efficient dissociation process. The diagnostic techniques are (1) time resolved in situ Fourier transform infrared (FTIR) spectroscopy and (2) spatiotemporally resolved in situ rotational Raman spectroscopy. Both techniques are used to obtain information about the rovibrational density distributions in the electronic ground state of CO2 in a pulsed glow discharge. During the active part of the plasma pulse a clear non-equilibrium is observed between the rotational and the ν3, and the (ν1, ν2) and ν3 vibrational density distributions. The results provide ample experimental foundation to expand our knowledge on CO2 vibrations and dissociation, especially through comparison with numerical models. This work has received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 81339