| 1. |
- Bauer, M., et al.
(författare)
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Exploratory study of ultraviolet B (UVB) radiation and age of onset of bipolar disorder
- 2023
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Ingår i: International Journal of Bipolar Disorders. - 2194-7511. ; 11:1
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Tidskriftsartikel (refereegranskat)abstract
- BackgroundSunlight contains ultraviolet B (UVB) radiation that triggers the production of vitamin D by skin. Vitamin D has widespread effects on brain function in both developing and adult brains. However, many people live at latitudes (about > 40 N or S) that do not receive enough UVB in winter to produce vitamin D. This exploratory study investigated the association between the age of onset of bipolar I disorder and the threshold for UVB sufficient for vitamin D production in a large global sample.MethodsData for 6972 patients with bipolar I disorder were obtained at 75 collection sites in 41 countries in both hemispheres. The best model to assess the relation between the threshold for UVB sufficient for vitamin D production and age of onset included 1 or more months below the threshold, family history of mood disorders, and birth cohort. All coefficients estimated at P <= 0.001.ResultsThe 6972 patients had an onset in 582 locations in 70 countries, with a mean age of onset of 25.6 years. Of the onset locations, 34.0% had at least 1 month below the threshold for UVB sufficient for vitamin D production. The age of onset at locations with 1 or more months of less than or equal to the threshold for UVB was 1.66 years younger.ConclusionUVB and vitamin D may have an important influence on the development of bipolar disorder. Study limitations included a lack of data on patient vitamin D levels, lifestyles, or supplement use. More study of the impacts of UVB and vitamin D in bipolar disorder is needed to evaluate this supposition.
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| 2. |
- Escartin, C., et al.
(författare)
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Reactive astrocyte nomenclature, definitions, and future directions
- 2021
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Ingår i: Nature Neuroscience. - : Springer Science and Business Media LLC. - 1097-6256 .- 1546-1726. ; 24, s. 312-325
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Tidskriftsartikel (refereegranskat)abstract
- Reactive astrocytes are astrocytes undergoing morphological, molecular, and functional remodeling in response to injury, disease, or infection of the CNS. Although this remodeling was first described over a century ago, uncertainties and controversies remain regarding the contribution of reactive astrocytes to CNS diseases, repair, and aging. It is also unclear whether fixed categories of reactive astrocytes exist and, if so, how to identify them. We point out the shortcomings of binary divisions of reactive astrocytes into good-vs-bad, neurotoxic-vs-neuroprotective or A1-vs-A2. We advocate, instead, that research on reactive astrocytes include assessment of multiple molecular and functional parameters-preferably in vivo-plus multivariate statistics and determination of impact on pathological hallmarks in relevant models. These guidelines may spur the discovery of astrocyte-based biomarkers as well as astrocyte-targeting therapies that abrogate detrimental actions of reactive astrocytes, potentiate their neuro- and glioprotective actions, and restore or augment their homeostatic, modulatory, and defensive functions. Good-bad binary classifications fail to describe reactive astrocytes in CNS disorders. Here, 81 researchers reach consensus on widespread misconceptions and provide definitions and recommendations for future research on reactive astrocytes.
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| 3. |
- Adamaki, A. K., et al.
(författare)
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Breaking the barriers to interdisciplinarity: Contributions from the Environmental Research Infrastructures
- 2022
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- As science and technology evolve, interdisciplinary targets are anything but static, introducing additional levels of complexity and challenging further the initiatives to break the barriers to interdisciplinary research. For over a decade the community of the Environmental Research Infrastructures, forming the ENVRI cluster, has been building strong foundations to overcome these challenges and benefit the environmental sciences. One of the overarching goals of the ENVRI cluster is to provide more FAIR (Findable, Accessible, Interoperable and Reusable) data and services which will be open to everyone who wishes to get access to environmental observations, from scientists and research communities of scientifically diverse clusters to curious citizens, data scientists and policy makers.Starting with domain-specific use cases we further explore potential cross-domain cases, e.g. in the form of environmental science stories crossing disciplinary boundaries. A set of Jupyter Notebooks developed by the contributing Research Infrastructures (and accessible from a hub of services called the ENVRI-Hub) are promising tools to demonstrate and validate the capabilities of service provision among ENVRIs and across Science Clusters, and act as examples of what a user can achieve through the ENVRI-Hub. In one of the examples we investigate, a user-friendly well-structured Jupyter Notebook that makes use of research infrastructures’ application programming interfaces (APIs) jointly plots in a map the geographical locations of several Marine and Atmospheric stations (where the stations in this example are defined as measurement points actively collecting data). The FAIR principles provide a firm foundation defining the layer that supports the ENVRI-Hub structure and the preliminary results are promising. Considering that the APIs can become discoverable via a common ENVRI catalogue, the ENVRI-Hub aims to make full use of the machine-actionability of such a catalogue in the future to facilitate this kind of use case execution in the Hub itself.Acknowledgement: ENVRI-FAIR has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824068. This work is only possible with the collaboration of the ENVRI-FAIR partners and thanks to the joint efforts of the whole ENVRI team.
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| 4. |
- Petzold, A., et al.
(författare)
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The ENVRI-Hub as a service for accelerating FAIRification of the Environment Domain Research Infrastructures
- 2023
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- European Environmental Research Infrastructures (ENVRIs) on the ESFRI level are core facilities for providing data, research products and services from the four subdomains of Earth system science – Atmosphere, Marine, Solid Earth, and Biodiversity/Terrestrial Ecosystems. The ENVRI Cluster represents the core component of the European environmental research infrastructure landscape, with the ENVRI community as their common forum for collaboration and co-creation. The topics covered by the ENVRIs span the entire range of scientific objectives relevant for Earth system monitoring.The community has developed the ENVRI-Hub as a central platform for accessing interdisciplinary FAIRfied environmental research assets, serving as an essential ENVRI community's interface to the European Open Science Cloud (EOSC). Through the ENVRI-Hub, the ENVRI community shares their FAIRness experience, technologies, and training as well as research products and services. The architecture and functionalities of the ENVRI-Hub are driven by scientific applications, use cases and user needs. Its three main pillars are the ENVRI Knowledge Base as the human interface to the ENVRI ecosystem, the ENVRI Catalogue of Services as the machine-actionable interface to the ENVRI ecosystem, and finally, subdomain and cross-domain scientific use cases as demonstrators for the capabilities of service provision among ENVRIs and across Science Clusters.The Science Demonstrators are being developed by several RIs in parallel. They are the key product to express the ENVRI-Hub’s potential regarding easy access to metadata and services, data discovery, as well as the promotion of interoperability in science across sub-domains. Science Demonstrators are built with Jupyter Notebooks - an open-source web application that allows one to create and share documents that contain live code, equations, visualizations, and narrative text. Uses include cross domain data access, data cleaning and transformation, numerical simulation, statistical modelling, data visualization, machine learning, and much more. The Jupyter Notebook environment forms the nucleus of the future ENVRI Virtual Research Environment.The ENVRI Science Demonstrators and Science Projects in the Horizon 2020 project EOSC Future aim at demonstrating how joint projects can address major challenges for Europe’s societies and how research infrastructures can support Horizon Europe’s missions within the EOSC. Presented Science Demonstrators cover one ENV domain wide service on the collocation of sampling sites, and two science cases from atmospheric and marine research, respectively.Acknowledgement: ENVRI-FAIR has received funding from the EU Horizon 2020 research and innovation programme under grant agreement No 824068. Part of the work is funded by the EU Horizon 2020 project EOSC Future under grant agreement No 101017536. This work is only possible with the collaboration of the ENVRI-FAIR partners and thanks to the joint efforts of the whole ENVRI-Hub team.
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| 5. |
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| 6. |
- Wacker, A, et al.
(författare)
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Secondary structure determination of conserved SARS-CoV-2 RNA elements by NMR spectroscopy
- 2020
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Ingår i: Nucleic acids research. - : Oxford University Press (OUP). - 1362-4962 .- 0305-1048. ; 48:22, s. 12415-12435
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Tidskriftsartikel (refereegranskat)abstract
- The current pandemic situation caused by the Betacoronavirus SARS-CoV-2 (SCoV2) highlights the need for coordinated research to combat COVID-19. A particularly important aspect is the development of medication. In addition to viral proteins, structured RNA elements represent a potent alternative as drug targets. The search for drugs that target RNA requires their high-resolution structural characterization. Using nuclear magnetic resonance (NMR) spectroscopy, a worldwide consortium of NMR researchers aims to characterize potential RNA drug targets of SCoV2. Here, we report the characterization of 15 conserved RNA elements located at the 5′ end, the ribosomal frameshift segment and the 3′-untranslated region (3′-UTR) of the SCoV2 genome, their large-scale production and NMR-based secondary structure determination. The NMR data are corroborated with secondary structure probing by DMS footprinting experiments. The close agreement of NMR secondary structure determination of isolated RNA elements with DMS footprinting and NMR performed on larger RNA regions shows that the secondary structure elements fold independently. The NMR data reported here provide the basis for NMR investigations of RNA function, RNA interactions with viral and host proteins and screening campaigns to identify potential RNA binders for pharmaceutical intervention.
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| 7. |
- Gomes, A. R., et al.
(författare)
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ENVRI-Hub, the open-access platform of the environmental sciences community in Europe: a closer look into the architecture
- 2022
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- The ENVRI-FAIR project brings together the ESFRI environmental research infrastructures (ENVRI) that provide environmental data and services, with the aim of making their resources compliant to the FAIR principles. To achieve this goal , the required work is mostly technical, with the ENVRIs working towards not only improving the FAIRness of their own data and services, but also reflecting their efforts at a higher level by becoming FAIR as a cluster. The approach of this task cannot be linear as it requires harmonization of efforts at different dimensions. To build on a common ground, the most crucial technical gaps have been prioritized and the ENVRIs identify common requirements and design patterns, and collaborate on making good use of existing technical solutions that improve their FAIRness. One of the highest ranked priorities, and obviously among the biggest challenges, is the design of a machine actionable ENVRI Catalogue of Services that also supports the integration into the EOSC. Through this catalogue the service providers will be able to make their assets findable and accessible by mapping their resources into common and rich metadata standards, while by means of a web application the human interaction with the FAIR services can be accomplished. The design of this application, named the ENVRI-Hub, is discussed here. Other aspects related to the ENVRI services, e.g. the use of PIDs, the use of relevant vocabularies, tracking license information and provenance etc. are also investigated. Considering the ENVRI-Hub as a web application, this can act as an integrator by bringing together already existing ENVRI services and interoperable services across research infrastructure boundaries . Exploring the potentials of the ENVRI-Hub already from the design phase, the ingestion of metadata from ENVRI assets such as the ENVRI Knowledge Base, the ENVRI Catalogue of Services and the ENVRI Training Catalogue is investigated, aiming to provide the users with functionalities that are relevant to e.g. the discovery of environmental observations, services, tutorials and other available resources. The chosen architectural pattern for the development of the ENVRI-Hub can be compared to a classical n-tier architecture, comprising 1) a data tier, 2) a logic tier and 3) a presentation tier. To integrate the different ENVRI platforms while preserving the application’s independence, the ENVRI-Hub demonstrator aims to replicate an instance of the Knowledge Base and Catalogue of Services. Following a centralised architectural approach, the ENVRI-Hub serves as a harvester entity, collecting data and metadata from the ENVRI Knowledge Base and the ENVRI Catalogue of Services, therefore bringing together these ENVRI platforms into one single portal.Acknowledgement: ENVRI-FAIR has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824068.This work is only possible with the collaboration of the ENVRI-FAIR partners and thanks to the joint efforts of the whole ENVRI-Hub team.
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| 8. |
- Morcos, M. N. F., et al.
(författare)
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Continuous mitotic activity of primitive hematopoietic stem cells in adult mice
- 2020
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Ingår i: Journal of Experimental Medicine. - : Rockefeller University Press. - 0022-1007 .- 1540-9538. ; 217:6
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Tidskriftsartikel (refereegranskat)abstract
- The proliferative activity of aging hematopoietic stem cells (HSCs) is controversially discussed. Inducible fluorescent histone 2B fusion protein (H2B-FP) transgenic mice are important tools for tracking the mitotic history of murine HSCs in label dilution experiments. A recent study proposed that primitive HSCs symmetrically divide only four times to then enter permanent quiescence. We observed that background fluorescence due to leaky H2B-FP expression, occurring in all H2B-FP transgenes independent of label induction, accumulated with age in HSCs with high repopulation potential. We argue that this background had been misinterpreted as stable retention of induced label. We found cell division-independent half-lives of H2B-FPs to be short, which had led to overestimation of HSC divisional activity. Our data do not support abrupt entry of HSCs into permanent quiescence or sudden loss of regeneration potential after four divisions, but show that primitive HSCs of adult mice continue to cycle rarely.
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| 9. |
- Petzold, A., et al.
(författare)
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Advancing the FAIRness and Openness of Earth system science in Europe
- 2021
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Konferensbidrag (övrigt vetenskapligt/konstnärligt)abstract
- Focused environmental research projects and continuously operating research infrastructures (RIs) designed for monitoring all subdomains of the Earth system 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 and contribute to global observing systems. The EU funded ENVRI-FAIR project [1] builds on the Environmental Research Infrastructure (ENVRI) community that includes principal European producers and providers of environmental research data and services.ENVRI-FAIR targets the development and implementation of both technical frameworks and policy solutions that make subdomain boundaries irrelevant for environmental scientists and prepare 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 RI level, facilitate the strategic coordination of observation systems required for truly interdisciplinary science. ENVRI-FAIR will ultimately create the open access ENVRI-Hub delivering environmental data and services provided by the contributing environmental RIs.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 as the human interface to the ENVRI ecosystem; (2) the ENVRI Catalogue as the machine-actionable interface to the ENVRI ecosystem; and (3) subdomain and cross-domain use cases as demonstrators for the capabilities of service provision among ENVRIs and across Science Clusters. The architecture is designed in anticipation of interoperation with the European Open Science Cloud (EOSC) and is intended to act as a key platform for users and developers planning to include ENVRI services in their workflows.The ENVRI community objectives of sharing FAIRness experience, technologies and training as well as research products and services will be realized by means of the ENVRI-Hub. The architecture, design features, technology developments and associated policies will highlight this example of how ENVRI-FAIR is promoting FAIRness, openness and multidisciplinarity of an entire scientific area by joint developments and implementation efforts.Acknowledgment: ENVRI-FAIR has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 824068.[1] Petzold, A., Asmi, A., Vermeulen, A., Pappalardo, G., Bailo, D., Schaap, D., Glaves, H. M., Bundke, U., and Zhao, Z.: ENVRI-FAIR - Interoperable environmental FAIR data and services for society, innovation and research, 15th IEEE International Conference on eScience 2019, 1-4, doi: http://doi.org/10.1109/eScience.2019.00038, 2019.
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| 10. |
- Schnieders, R, et al.
(författare)
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1H, 13C and 15N chemical shift assignment of the stem-loop 5a from the 5'-UTR of SARS-CoV-2
- 2021
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Ingår i: Biomolecular NMR assignments. - : Springer Science and Business Media LLC. - 1874-270X .- 1874-2718. ; 15:1, s. 203-211
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Tidskriftsartikel (refereegranskat)abstract
- The SARS-CoV-2 (SCoV-2) virus is the causative agent of the ongoing COVID-19 pandemic. It contains a positive sense single-stranded RNA genome and belongs to the genus of Betacoronaviruses. The 5′- and 3′-genomic ends of the 30 kb SCoV-2 genome are potential antiviral drug targets. Major parts of these sequences are highly conserved among Betacoronaviruses and contain cis-acting RNA elements that affect RNA translation and replication. The 31 nucleotide (nt) long highly conserved stem-loop 5a (SL5a) is located within the 5′-untranslated region (5′-UTR) important for viral replication. SL5a features a U-rich asymmetric bulge and is capped with a 5′-UUUCGU-3′ hexaloop, which is also found in stem-loop 5b (SL5b). We herein report the extensive 1H, 13C and 15N resonance assignment of SL5a as basis for in-depth structural studies by solution NMR spectroscopy.
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