| 1. |
- Petzold, Andreas, et al.
(författare)
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Opinion : New directions in atmospheric research offered by research infrastructures combined with open and data-intensive science
- 2024
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Ingår i: Atmospheric Chemistry and Physics. - 1680-7316. ; 24:9, s. 5369-5388
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Forskningsöversikt (refereegranskat)abstract
- The acquisition and dissemination of essential information for understanding global biogeochemical interactions between the atmosphere and ecosystems and how climate-ecosystem feedback loops may change atmospheric composition in the future comprise a fundamental prerequisite for societal resilience in the face of climate change. In particular, the detection of trends and seasonality in the abundance of greenhouse gases and short-lived climate-Active atmospheric constituents is an important aspect of climate science. Therefore, easy and fast access to reliable, long-Term, and high-quality observational environmental data is recognised as fundamental to research and the development of environmental forecasting and assessment services. In our opinion article, we discuss the potential role that environmental research infrastructures in Europe (ENVRI RIs) can play in the context of an integrated global observation system. In particular, we focus on the role of the atmosphere-centred research infrastructures ACTRIS (Aerosol, Clouds and Trace Gases Research Infrastructure), IAGOS (In-service Aircraft for a Global Observing System), and ICOS (Integrated Carbon Observation System), also referred to as ATMO-RIs, with their capabilities for standardised collection and provision of long-Term and high-quality observational data, complemented by rich metadata. The ATMO-RIs provide data through open access and offer data interoperability across different research fields including all fields of environmental sciences and beyond. As a result of these capabilities in data collection and provision, we elaborate on the novel research opportunities in atmospheric sciences which arise from the combination of open-Access and interoperable observational data, tools, and technologies offered by data-intensive science and the emerging collaboration platform ENVRI-Hub, hosted by the European Open Science Cloud (EOSC).
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| 2. |
- Ahlström, Anders, et al.
(författare)
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The dominant role of semi-arid ecosystems in the trend and variability of the land CO2 sink
- 2015
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Ingår i: Science. - : American Association for the Advancement of Science (AAAS). - 1095-9203 .- 0036-8075. ; 348:6237, s. 895-899
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Tidskriftsartikel (refereegranskat)abstract
- The growth rate of atmospheric carbon dioxide (CO2) concentrations since industrialization is characterized by large interannual variability, mostly resulting from variability in CO2 uptake by terrestrial ecosystems (typically termed carbon sink). However, the contributions of regional ecosystems to that variability are not well known. Using an ensemble of ecosystem and land-surface models and an empirical observation-based product of global gross primary production, we show that the mean sink, trend, and interannual variability in CO2 uptake by terrestrial ecosystems are dominated by distinct biogeographic regions. Whereas the mean sink is dominated by highly productive lands (mainly tropical forests), the trend and interannual variability of the sink are dominated by semi-arid ecosystems whose carbon balance is strongly associated with circulation-driven variations in both precipitation and temperature.
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| 3. |
- Gorski, Mathias, et al.
(författare)
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Genetic loci and prioritization of genes for kidney function decline derived from a meta-analysis of 62 longitudinal genome-wide association studies
- 2022
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Ingår i: Kidney International. - : Elsevier. - 0085-2538 .- 1523-1755. ; 102:3, s. 624-639
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Tidskriftsartikel (refereegranskat)abstract
- Estimated glomerular filtration rate (eGFR) reflects kidney function. Progressive eGFR-decline can lead to kidney failure, necessitating dialysis or transplantation. Hundreds of loci from genome-wide association studies (GWAS) for eGFR help explain population cross section variability. Since the contribution of these or other loci to eGFR-decline remains largely unknown, we derived GWAS for annual eGFR-decline and meta-analyzed 62 longitudinal studies with eGFR assessed twice over time in all 343,339 individuals and in high-risk groups. We also explored different covariate adjustment. Twelve genomewide significant independent variants for eGFR-decline unadjusted or adjusted for eGFR- baseline (11 novel, one known for this phenotype), including nine variants robustly associated across models were identified. All loci for eGFR-decline were known for cross-sectional eGFR and thus distinguished a subgroup of eGFR loci. Seven of the nine variants showed variant- by-age interaction on eGFR cross section (further about 350,000 individuals), which linked genetic associations for eGFR-decline with agedependency of genetic cross- section associations. Clinically important were two to four-fold greater genetic effects on eGFR-decline in high-risk subgroups. Five variants associated also with chronic kidney disease progression mapped to genes with functional in- silico evidence (UMOD, SPATA7, GALNTL5, TPPP). An unfavorable versus favorable nine-variant genetic profile showed increased risk odds ratios of 1.35 for kidney failure (95% confidence intervals 1.03- 1.77) and 1.27 for acute kidney injury (95% confidence intervals 1.08-1.50) in over 2000 cases each, with matched controls). Thus, we provide a large data resource, genetic loci, and prioritized genes for kidney function decline, which help inform drug development pipelines revealing important insights into the age-dependency of kidney function genetics.
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| 4. |
- Huber, Robert, et al.
(författare)
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Integrating data and analysis technologies within leading environmental research infrastructures : Challenges and approaches
- 2021
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Ingår i: Ecological Informatics. - : Elsevier BV. - 1574-9541. ; 61
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Tidskriftsartikel (refereegranskat)abstract
- When researchers analyze data, it typically requires significant effort in data preparation to make the data analysis ready. This often involves cleaning, pre-processing, harmonizing, or integrating data from one or multiple sources and placing them into a computational environment in a form suitable for analysis. Research infrastructures and their data repositories host data and make them available to researchers, but rarely offer a computational environment for data analysis. Published data are often persistently identified, but such identifiers resolve onto landing pages that must be (manually) navigated to identify how data are accessed. This navigation is typically challenging or impossible for machines. This paper surveys existing approaches for improving environmental data access to facilitate more rapid data analyses in computational environments, and thus contribute to a more seamless integration of data and analysis. By analysing current state-of-the-art approaches and solutions being implemented by world‑leading environmental research infrastructures, we highlight the existing practices to interface data repositories with computational environments and the challenges moving forward. We found that while the level of standardization has improved during recent years, it still is challenging for machines to discover and access data based on persistent identifiers. This is problematic in regard to the emerging requirements for FAIR (Findable, Accessible, Interoperable, and Reusable) data, in general, and problematic for seamless integration of data and analysis, in particular. There are a number of promising approaches that would improve the state-of-the-art. A key approach presented here involves software libraries that streamline reading data and metadata into computational environments. We describe this approach in detail for two research infrastructures. We argue that the development and maintenance of specialized libraries for each RI and a range of programming languages used in data analysis does not scale well. Based on this observation, we propose a set of established standards and web practices that, if implemented by environmental research infrastructures, will enable the development of RI and programming language independent software libraries with much reduced effort required for library implementation and maintenance as well as considerably lower learning requirements on users. To catalyse such advancement, we propose a roadmap and key action points for technology harmonization among RIs that we argue will build the foundation for efficient and effective integration of data and analysis.
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| 5. |
- Moor, Kathrin, et al.
(författare)
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High-avidity IgA protects the intestine by enchaining growing bacteria
- 2017
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Ingår i: Nature. - : NATURE PUBLISHING GROUP. - 0028-0836 .- 1476-4687. ; 544:7651, s. 498-
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Tidskriftsartikel (refereegranskat)abstract
- Vaccine-induced high-avidity IgA can protect against bacterial enteropathogens by directly neutralizing virulence factors or by poorly defined mechanisms that physically impede bacterial interactions with the gut tissues ('immune exclusion')(1-3). IgA-mediated cross-linking clumps bacteria in the gut lumen and is critical for protection against infection by non-typhoidal Salmonella enterica subspecies enterica serovar Typhimurium (S. Typhimurium). However, classical agglutination, which was thought to drive this process, is efficient only at high pathogen densities (>= 10(8) non-motile bacteria per gram). In typical infections, much lower densities(4,5) (10(0)-10(7) colony-forming units per gram) of rapidly dividing bacteria are present in the gut lumen. Here we show that a different physical process drives formation of clumps in vivo: IgA-mediated cross-linking enchains daughter cells, preventing their separation after division, and clumping is therefore dependent on growth. Enchained growth is effective at all realistic pathogen densities, and accelerates pathogen clearance from the gut lumen. Furthermore, IgA enchains plasmid-donor and -recipient clones into separate clumps, impeding conjugative plasmid transfer in vivo. Enchained growth is therefore a mechanism by which IgA can disarm and clear potentially invasive species from the intestinal lumen without requiring high pathogen densities, inflammation or bacterial killing. Furthermore, our results reveal an untapped potential for oral vaccines in combating the spread of antimicrobial resistance.
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| 6. |
- Petzold, Andreas, et al.
(författare)
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Creating ENVRI-hub, the Open-Access Platform of the Environmental Sciences Community in Europe
- 2021
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Ingår i: ; , s. 04-53
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Environmental research infrastructures designed for monitoring all domains of the Earth system (oceans, atmosphere, ecosystems, and solid earth) contribute to global observing systems and serve as crucial information sources for environmental scientists in their quest for understanding and interpreting the complex Earth System. The EU funded ENVRI-FAIR project builds on the Environmental Research Infrastructure (ENVRI) community that includes principal European producers and providers of environmental research data and services. The backbone of the project is the existing IT infrastructure of participating research infrastructures. ENVRI-FAIR targets the development and implementation of both technical frameworks and policy solutions that make scientific boundaries seamlessly traversable for environmental scientists and prepare a holistic approach to Earth system science for the new Open Science paradigm. Cross-discipline harmonization and standardization activities, together with the implementation of joint data management and access structures at the research infrastructure level, facilitate the strategic coordination of observation systems, required for interdisciplinary science. ENVRI-FAIR will create the open access ENVRI-hub delivering environmental and earth science services provided by the contributing environmental research infrastructures. The architecture and functionalities of the ENVRI-hub are driven by the applications, use cases and user needs, and will be based on three main pillars: (1) the ENVRI Knowledge Base and Training Platform as resources for knowledge, services, training, and other digital assets; (2) the ENVRI Catalogue as machine-actionable interface to the ENVRI ecosystem; and (3) interdisciplinary use cases as demonstrators for the capabilities of service provision among environmental research infrastructures and across science clusters. The architecture, design features, technology developments and associated policies are designed in anticipation of interoperation with the European Open Science Cloud (EOSC). The ENVRI-hub is intended to act as a key platform for researchers, other users and developers planning to include ENVRI data-services in their workflows through EOSC resources.
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| 7. |
- Petzold, Andreas, et al.
(författare)
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ENVRI-Hub Design and Architecture White Paper
- 2023
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- ENVRI-FAIR is the connection of the ESFRI Cluster of Environmental Research Infrastructures (ENVRI) to the European Open Science Cloud (EOSC). The high-impact ambition of ENVRI-FAIR is to establish the technical preconditions for the successful implementation of a virtual, federated machine-to-machine interface to access environmental data and services provided by the contributing ENVRIs. This interface is called the ENVRI-Hub. Full integration of services across RIs and even subdomains is continuously progressing at ENVRIs with focus on environmental data and scientific research objectives. Each RI is specialized in a specific number of parameters related to its specific competences. For users that require a broader or the full spectrum of environmental parameters, the ENVRI-Hub will offer a platform that reflects the complexity and diversity of the ENVRI landscape, while preserving their specific structures and addressing the requirements they were designed for.The ENVRI-Hub will be a federated system of harmonized subdomain/RI-specific systems of data policies and management, access platforms and virtual research environments. The system will be completely open source, modular and scalable and build on the experience available in the consortium and already operational systems. Figure 1 shows the key features of the ENVRI-Hub.The ENVRI-Hub community metadata and data store is foreseen to be based on semantic web technology, ontologies, and open linked data, allowing integration of the vocabularies and metadata standards developed in the implementation work packages of ENVRI-FAIR. The cross-subdomain development will create large benefits in efficiency and robustness of the ENVRI-hub system. It will enable true interoperability of access to metadata and data objects across the RIs and subdomains and thus facilitate the development of (joint) higher-level services. By following a strict modular design, the developments can be (re-)used in the different RIs. All components should contain couplers to the EOSC services, like AAI, data storage solutions and catalogue of services, to enable the seamless integration of ENVRIs data and services into EOSC.
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| 8. |
- Stocker, Markus, et al.
(författare)
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Persistent identification of instrument
- 2020
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Ingår i: Data Science Journal. - : Ubiquity Press, Ltd.. - 1683-1470. ; 19:1
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Tidskriftsartikel (refereegranskat)abstract
- Instruments play an essential role in creating research data. Given the importance of instruments and associated metadata to the assessment of data quality and data reuse, globally unique, persistent and resolvable identification of instruments is crucial. The Research Data Alliance Working Group Persistent Identification of Instruments (PIDINST) developed a community-driven solution for persistent identification of instruments which we present and discuss in this paper. Based on an analysis of 10 use cases, PIDINST developed a metadata schema and prototyped schema implementation with DataCite and ePIC as representative persistent identifier infrastructures and with HZB (Helmholtz-Zentrum Berlin für Materialien und Energie) and BODC (British Oceanographic Data Centre) as representative institutional instrument providers. These implementations demonstrate the viability of the proposed solution in practice. Moving forward, PIDINST will further catalyse adoption and consolidate the schema by addressing new stakeholder requirements.
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