ELIXIR Ethics Policy

The purpose of many ELIXIR Services is to facilitate the open sharing of research data. While data and knowledge provided by ELIXIR Services will be accessible to researchers, this does not mean that the use of data is unencumbered: restrictions on the use of data may arise due to legal (e.g. data protection requirements, copyright protection, or license restrictions) or ethical considerations. Especially for ELIXIR Services managing data from human research participants that are used in the context of clinical and health research, gaining and deserving the trust of patients, study participants and donors concerning the proper handling of their data is of utmost importance for research to proceed and generate benefits for society. The ELIXIR Ethics Policy provides evidence that an adequate level of protection of personal data including sensitive data is in place throughout ELIXIR - including across national borders - which increases the acceptance of clauses in consent forms concerning data deposition with ELIXIR Services. ELIXIR Services are formally defined and must meet specific criteria based on the ELIXIR founding documents. Every ELIXIR Service involving personal data must have a regulatory framework ensuring that these data are made available for research in a way that is compliant with all relevant (e.g. EU-level, national and local or internal) legal and ethical requirements. At the same time, ELIXIR is a distributed infrastructure and its Nodes are independent organisations. The Node providing an ELIXIR Service is responsible for the implementation of the requirements of the ELIXIR Ethics Policy. Consequently, the Policy does not prescribe how the specific requirements are met; this is up to the Node. The Ethics Policy, which is a specific requirement of the ELIXIR founding documents, consolidates requirements that are shared across all ELIXIR Members and Services. It imposes no additional constraints on the use of data contributed to ELIXIR Services than those provided by the Data Controller/Provider or existing legal and ethical requirements. ELIXIR Services do not assume the ownership of the data they hold, but provide a platform where data controllers/data providers can share their data with the community. One of the major achievements made during the development of the ELIXIR Ethics Policy is the clear definition of responsibilities with respect to the provision of data underlying regulatory requirements into those to be met by the individual researcher or investigator or body of researchers or investigators that submits data for access and use in the context of an ELIXIR Service (the “data provider”), the ELIXIR Service, and the individual researcher or investigator or group of researchers or investigators that accesses and/or uses data made available as part of an ELIXIR Service (the “data user”). The ELIXIR Ethics Policy is accompanied by a document providing background and context for the requirements of the policy (Annex 2). The background document will be updated continually and expanded to include more in-depth explanations of the requirements included in the policy, where they originate, how they can be implemented, and a clarification of how the policy relates to guidance provided by other relevant initiatives (such as the GA4GH, among others)

Man vs. Machine

Historically, technological innovations have substituted human labor for decades and if the revolutionary technological developments continue, substitution may happen at an increasing pace. This increasing pace might place high demands on society to quickly adapt if high levels of technological unemployment are to be avoided. This paper examines how the computerization of society may affect the labor market in Sweden. Our research question is: - How susceptible is the Swedish labor market for computerization? The method used to answer this question is based on a method from an American report that conducted a similar survey on the U.S. labor market. The method is based on the job description for each profession and the bottlenecks to computerization. Given its tasks and requirements each profession is given a certain probability of computerization. Our results suggests that 36 percent of Swedish jobs has a high probability to be computerized within one to two decades. Most are in professions such as manufacturing, transport, forestry and hotel- and foodservices. Those professions that are least likely to be computerized are within industries such as nursing and education

Structure of the PPARα and -γ Ligand Binding Domain in Complex with AZ 242; Ligand Selectivity and Agonist Activation in the PPAR Family

AbstractBackground: The peroxisome proliferator-activated receptors (PPAR) are ligand-activated transcription factors belonging to the nuclear receptor family. The roles of PPARα in fatty acid oxidation and PPARγ in adipocyte differentiation and lipid storage have been characterized extensively. PPARs are activated by fatty acids and eicosanoids and are also targets for antidyslipidemic drugs, but the molecular interactions governing ligand selectivity for specific subtypes are unclear due to the lack of a PPARα ligand binding domain structure.Results: We have solved the crystal structure of the PPARα ligand binding domain (LBD) in complex with the combined PPARα and -γ agonist AZ 242, a novel dihydro cinnamate derivative that is structurally different from thiazolidinediones. In addition, we present the crystal structure of the PPARγ_LBD/AZ 242 complex and provide a rationale for ligand selectivity toward the PPARα and -γ subtypes. Heteronuclear NMR data on PPARα in both the apo form and in complex with AZ 242 shows an overall stabilization of the LBD upon agonist binding. A comparison of the novel PPARα/AZ 242 complex with the PPARγ/AZ 242 complex and previously solved PPARγ structures reveals a conserved hydrogen bonding network between agonists and the AF2 helix.Conclusions: The complex of PPARα and PPARγ with the dual specificity agonist AZ 242 highlights the conserved interactions required for receptor activation. Together with the NMR data, this suggests a general model for ligand activation in the PPAR family. A comparison of the ligand binding sites reveals a molecular explanation for subtype selectivity and provides a basis for rational drug design

Principles of data management and sharing at European Research Infrastructures

Under the umbrella of the BioMedBridges project, fourteen research infrastructures in the biological, biomedical and environmental sciences developed commonly agreed principles of data management and sharing. The document makes key recommendations on how data management and sharing via the research infrastructures can be supported and encouraged: The RIs encourage data sharing and reuse and support the notion that public funders should encourage Open Access to data from publicly funded research where possible. Some data may only be shared under certain conditions and with appropriate safekeeping mechanisms in place, such as personally identifiable data, data subject to ethical or legal restrictions, or restrictions for intellectual property protection. To encourage data sharing, systematic reward and recognition mechanisms are necessary. Proposals for publicly funded research at RIs should include a data management plan concerning the deposition of data in long-term archives that addresses specific resources and activities (including standardisation of data production and curation/annotation). Funding for tools and activities connected to data deposition must be available. Systems, services and resources must be in place to facilitate straightforward data deposition by researchers, including support concerning the necessary data use agreements and consent forms for data with data protection or intellectual property requirements. Systems are also needed to capture and track data provenance and use. To ensure necessary trust by data providers or depositors, RIs must guarantee high standards of security and traceability

Demonstrating public value to funders and other stakeholders—the journey of ELIXIR, a virtual and distributed research infrastructure for life science data

Open Science is a founding principle of ELIXIR, a pan-European research infrastructure for life science data, with 21 Member countries plus the European Molecular Biology Laboratory. The mission of ELIXIR is to coordinate bioinformatics resources so that they form a single, integrated and pan-European infrastructure, which can be used freely by academic and private-sector researchers across the globe. As a recipient of public and charitable funding, ELIXIR must demonstrate its value, and the need to produce evidence in support of this is intensifying. Our practice-led journey towards demonstrating public value is articulated around five main challenges and, for each, we present our pragmatic approach for tackling it. We begin by showing how we are working towards demystifying what research infrastructures do. We then shed light on the sort of evidence our funders and other stakeholders are asking us for, how this evidence varies in nature and scope, and our tactics to satisfy them. We follow-on by providing our thoughts on possible barriers and solutions to embedding impact evaluation in our activities. Finally, we provide lessons learned, which we believe are sufficiently transferable and will be inspirational to other research infrastructures as they embark on their own journeys to demonstrate public value.publishedVersio

Seasonal variations in carbon, nitrogen and phosphorus concentrations and C:N:P stoichiometry in different organs of a Larix principis-rupprechtii Mayr. plantation in the Qinling Mountains, China

Understanding how concentrations of elements and their stoichiometry change with plant growth and age is critical for predicting plant community responses to environmental change. Weusedlong-term field experiments to explore how the leaf, stem and root carbon (C), nitrogen (N) and phosphorous (P) concentrations and their stoichiometry changed with growth and stand age in a L.principis-rupprechtii Mayr. plantation from 2012–2015 in the Qinling Mountains, China. Our results showed that the C, N and P concentrations and stoichiometric ratios in different tissues of larch stands were affected by stand age, organ type andsampling month and displayed multiple correlations with increased stand age in different growing seasons. Generally, leaf C and N concentrations were greatest in the fast-growing season, but leaf P concentrations were greatest in the early growing season. However, no clear seasonal tendencies in the stem and root C, N and P concentrations were observed with growth. In contrast to N and P, few differences were found in organ-specific C concentrations. Leaf N:P was greatest in the fast-growing season, while C:N and C:P were greatest in the late-growing season. No clear variations were observed in stem and root C:N, C:P andN:Pthroughout the entire growing season, but leaf N:P was less than 14, suggesting that the growth of larch stands was limited by N in our study region. Compared to global plant element concentrations and stoichiometry, the leaves of larch stands had higher C, P, C:NandC:PbutlowerNandN:P,andtherootshadgreater PandC:NbutlowerN,C:Pand N:P. Our study provides baseline information for describing the changes in nutritional elements with plant growth, which will facilitates plantation forest management and restoration, and makes avaluable contribution to the global data pool on leaf nutrition and stoichiometry

FAIR+E pathogen data for surveillance and research: lessons from COVID-19

The COVID-19 pandemic has exemplified the importance of interoperable and equitable data sharing for global surveillance and to support research. While many challenges could be overcome, at least in some countries, many hurdles within the organizational, scientific, technical and cultural realms still remain to be tackled to be prepared for future threats. We propose to (i) continue supporting global efforts that have proven to be efficient and trustworthy toward addressing challenges in pathogen molecular data sharing; (ii) establish a distributed network of Pathogen Data Platforms to (a) ensure high quality data, metadata standardization and data analysis, (b) perform data brokering on behalf of data providers both for research and surveillance, (c) foster capacity building and continuous improvements, also for pandemic preparedness; (iii) establish an International One Health Pathogens Portal, connecting pathogen data isolated from various sources (human, animal, food, environment), in a truly One Health approach and following FAIR principles. To address these challenging endeavors, we have started an ELIXIR Focus Group where we invite all interested experts to join in a concerted, expert-driven effort toward sustaining and ensuring high-quality data for global surveillance and research

COMPASSO mission and its iodine clock: outline of the clock design

One of the limiting factors for GNSS geolocation capabilities is the clock technology deployed on the satellites and the knowledge of the satellite position. Consequently, there are numerous ongoing efforts to improve the stability of space-deployable clocks for next-generation GNSS. The COMPASSO mission is a German Aerospace Center (DLR) project to demonstrate high-performance quantum optical technologies in space with two laser-based absolute frequency references, a frequency comb and a laser communication and ranging terminal establishing a link with the ground station located in Oberpfaffenhofen, Germany. A successful mission will strongly improve the timing stability of space-deployable clocks, demonstrate time transfer between different clocks and allow for ranging in the mm-range. Thus, the technology is a strong candidate for future GNSS satellite clocks and offers possibilities for novel satellite system architectures and can improve the performance of scientific instruments as well. The COMPASSO payload will be delivered to the international space station in 2025 for a mission time of 2 years. In this article, we will highlight the key systems and functionalities of COMPASSO, with the focus set to the absolute frequency references

The COVID-19 Data Portal: accelerating SARS-CoV-2 and COVID-19 research through rapid open access data sharing.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic will be remembered as one of the defining events of the 21st century. The rapid global outbreak has had significant impacts on human society and is already responsible for millions of deaths. Understanding and tackling the impact of the virus has required a worldwide mobilisation and coordination of scientific research. The COVID-19 Data Portal (https://www.covid19dataportal.org/) was first released as part of the European COVID-19 Data Platform, on April 20th 2020 to facilitate rapid and open data sharing and analysis, to accelerate global SARS-CoV-2 and COVID-19 research. The COVID-19 Data Portal has fortnightly feature releases to continue to add new data types, search options, visualisations and improvements based on user feedback and research. The open datasets and intuitive suite of search, identification and download services, represent a truly FAIR (Findable, Accessible, Interoperable and Reusable) resource that enables researchers to easily identify and quickly obtain the key datasets needed for their COVID-19 research