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- ItemAdvancing Research Data Management in Universities of Science and Technology(Meyrin : CERN, 2020-02-13) Björnemalm, Matthias; Cappellutti, Federica; Dunning, Alastair; Gheorghe, Dana; Goraczek, Malgorzata Zofia; Hausen, Daniela; Hermann, Sibylle; Kraft, Angelina; Martinez Lavanchy, Paula; Prisecaru, Tudor; Sànchez, Barbara; Strötgen, RobertThe white paper ‘Advancing Research Data Management in Universities of Science and Technology’ shares insights on the state-of-the-art in research data management, and recommendations for advancement. A core part of the paper are the results of a survey, which was distributed to our member institutions in 2019 and addressed the following aspects of research data management (RDM): (i) the establishment of a RDM policy at the university; (ii) the provision of suitable RDM infrastructure and tools; and (iii) the establishment of RDM support services and trainings tailored to the requirements of science and technology disciplines. The paper reveals that while substantial progress has been made, there is still a long way to go when it comes to establishing “advanced-degree programmes at our major universities for the emerging field of data scientist”, as recommended in the seminal 2010 report ‘Riding the Wave’, and our white paper offers concrete recommendations and best practices for university leaders, researchers, operational staff, and policy makers. The topic of RDM has become a focal point in many scientific disciplines, in Europe and globally. The management and full utilisation of research data are now also at the top of the European agenda, as exemplified by Ursula von der Leyen addressat this year’s World Economic Forum.However, the implementation of RDM remains divergent across Europe. The white paper was written by a diverse team of RDM specialists, including data scientists and data stewards, with the work led by the RDM subgroup of our Task Force Open Science. The writing team included Angelina Kraft (Head of Lab Research Data Services at TIB, Leibniz University Hannover) who said: “The launch of RDM courses and teaching materials at universities of science and technology is a first important step to motivate people to manage their data. Furthermore, professors and PIs of all disciplines should actively support data management and motivate PhD students to publish their data in recognised digital repositories.” Another part of the writing team was Barbara Sanchez (Head of Centre for Research Data Management, TU Wien) and Malgorzata Goraczek (International Research Support / Data Management Support, TU Wien) who added:“A reliable research data infrastructure is a central component of any RDM service. In addition to the infrastructure, proper RDM is all about communication and cooperation. This includes bringing tools, infrastructures, staff and units together.” Alastair Dunning (Head of 4TU.ResearchData, Delft University of Technology), also one of the writers, added: “There is a popular misconception that better research data management only means faster and more efficient computers. In this white paper, we emphasise the role that training and a culture of good research data management must play.”
- ItemAmoeboid Cell Migration through Regular Arrays of Micropillars under Confinement(New York : Cold Spring Harbor Laboratory, 2022) Sadjadi, Zeinab; Vesperini, Doriane; Laurent, Annalena M.; Barnefske, Lena; Terriac, Emmanuel; Lautenschläger, Franziska; Rieger, HeikoMigrating cells often encounter a wide variety of topographic features—including the presence of obstacles—when navigating through crowded biological environments. Unravelling the impact of topography and crowding on the dynamics of cells is key to better understand many essential physiological processes such as the immune response. We study how migration and search efficiency of HL-60 cells differentiated into neutrophils in quasi two-dimensional environments are influenced by the lateral and vertical confinement and spatial arrangement of obstacles. A microfluidic device is designed to track the cells in confining geometries between two parallel plates with distance h, in which identical micropillars are arranged in regular pillar forests. We find that at each cell-pillar contact event, the cell spends a finite time near the pillar surface, which is independent of the height h and the interpillar spacing e. At low pillar density regime, the directional persistence of cells reduces with decreasing h or e, influencing their diffusivity and first-passage properties. The dynamics is strikingly different at high pillar density regime, where the cells are in simultaneous contact with more than one pillar; the cell velocity and persistence are distinctly higher compared to dilute pillar configurations with the same h. Our simulations reveal that the interplay between cell persistence and cell-pillar interactions can dramatically affect cell diffusivity and, thus, its first-passage properties.
- ItemA tale of two 'opens': intersections between Free and Open Source Software and Open Scholarship(Charlottesville, VA : Center for Open Science, 2020) Tennant, Jonathan P.; Agrawal, Ritwik; Baždarić, Ksenija; Brassard, David; Crick, Tom; Dunleavy, Daniel J.; Evans, Thomas Rhys; Gardner, Nicholas; Gonzalez-Marquez, Monica; Graziotin, Daniel; Greshake Tzovaras, Bastian; Gunnarson, Daniel; Havemann, Johanna; Hosseini, Mohammad; Katz, Daniel S.; Knöchelmann, Marcel; Lahti, Leo; Madan, Christopher R.; Manghi, Paolo; Marocchino, Alberto; Masuzzo, Paola; Murray-Rust, Peter; Narayanaswamy, Sanjay; Nilsonne, Gustav; Pacheco-Mendoza, Josmel; Penders, Bart; Pourret, Olivier; Rera, Michael; Samuel, John; Steiner, Tobias; Stojanovski, Jadranka; Uribe Tirado, Alejandro; Vos, Rutger; Worthington, Simon; Yarkoni, TalThere is no clear-cut boundary between Free and Open Source Software and Open Scholarship, and the histories, practices, and fundamental principles between the two remain complex. In this study, we critically appraise the intersections and differences between the two movements. Based on our thematic comparison here, we conclude several key things. First, there is substantial scope for new communities of practice to form within scholarly communities that place sharing and collaboration/open participation at their focus. Second, Both the principles and practices of FOSS can be more deeply ingrained within scholarship, asserting a balance between pragmatism and social ideology. Third, at the present, Open Scholarship risks being subverted and compromised by commercial players. Fourth, the shift and acceleration towards a system of Open Scholarship will be greatly enhanced by a concurrent shift in recognising a broader range of practices and outputs beyond traditional peer review and research articles. In order to achieve this, we propose the formulation of a new type of institutional mandate. We believe that there is substantial need for research funders to invest in sustainable open scholarly infrastructure, and the communities that support them, to avoid the capture and enclosure of key research services that would prevent optimal researcher behaviours. Such a shift could ultimately lead to a healthier scientific culture, and a system where competition is replaced by collaboration, resources (including time and people) are shared and acknowledged more efficiently, and the research becomes inherently more rigorous, verified, and reproducible.
- ItemRegulating bacterial behavior within hydrogels of tunable viscoelasticity(New York : Cold Spring Harbor Laboratory, 2022) Bhusari, Shardul; Sankaran, Shrikrishnan; del Campo, AránzazuEngineered living materials (ELMs) are a new class of materials in which living organism incorporated into diffusive matrices uptake a fundamental role in material’s composition and function. Understanding how the spatial confinement in 3D affects the behavior of the embedded cells is crucial to design and predict ELM’s function, regulate and minimize their environmental impact and facilitate their translation into applied materials. This study investigates the growth and metabolic activity of bacteria within an associative hydrogel network (Pluronic-based) with mechanical properties that can be tuned by introducing a variable degree of acrylate crosslinks. Individual bacteria distributed in the hydrogel matrix at low density form functional colonies whose size is controlled by the extent of permanent crosslinks. With increasing stiffness and decreasing plasticity of the matrix, a decrease in colony volumes and an increase in their sphericity is observed. Protein production surprisingly follows a different pattern with higher production yields occurring in networks with intermediate permanent crosslinking degrees. These results demonstrate that, bacterial mechanosensitivity can be used to control and regulate the composition and function of ELMs by thoughtful design of the encapsulating matrix, and by following design criteria with interesting similarities to those developed for 3D culture of mammalian cells.
- ItemDiscussion on Existing Standards and Quality Criteria in Nanosafety Research : Summary of the NanoS-QM Expert Workshop(Zenodo, 2021) Binder, Kunigunde; Bonatto Minella, Christian; Elberskirchen, Linda; Kraegeloh, Annette; Liebing, Julia; Petzold, Christiane; Razum, Matthias; Riefler, Norbert; Schins, Roel; Sofranko, Adriana; van Thriel, Christoph; Unfried, KlausThe partners of the research project NanoS-QM (Quality- and Description Standards for Nanosafety Research Data) identified and invited relevant experts from research institutions, federal agencies, and industry to evaluate the traceability of the results generated with the existing standards and quality criteria. During the discussion it emerged that numerous studies seem to be of insufficient quality for regulatory purposes or exhibit weaknesses with regard to data completeness. Deficiencies in study design could be avoided by more comprehensive use of appropriate standards, many of which already exist. The use of Electronic Laboratory Notebooks (ELNs) that allow for early collection of metadata and enrichment of datasets could be one solution to enable data re-use and simplify quality control. Generally, earlier provision and curation of data and metadata indicating their quality and completeness (e.g. guidelines, standards, standard operating procedures (SOPs) that were used) would improve their findability, accessibility, interoperability, and reusability (FAIR) in the nanosafety research field.
- ItemAnalysis of Knowledge Tracing performance on synthesised student data(Hannover : Technische Informationsbibliothek, 2024) Pagonis, Panagiotis; Hartung, Kai; Wu, Di; Georges, Munir; Gröttrup, SörenKnowledge Tracing (KT) aims to predict the future performance of students by tracking the development of their knowledge states. Despite all the recent progress made in this field, the application of KT models in education systems is still restricted from the data perspectives: 1) limited access to real life data due to data protection concerns, 2) lack of diversity in public datasets, 3) noises in benchmark datasets such as duplicate records. To resolve these problems, we simulated student data with three statistical strategies based on public datasets and tested their performance on two KT baselines. While we observe only minor performance improvement with additional synthetic data, our work shows that using only synthetic data for training can lead to similar performance as real data.
- ItemKnowledge Graphs - Working Group Charter (NFDI section-metadata) (1.2)(Genève : CERN, 2023) Stocker, Markus; Rossenova, Lozana; Shigapov, Renat; Betancort, Noemi; Dietze, Stefan; Murphy, Bridget; Bölling, Christian; Schubotz, Moritz; Koepler, OliverKnowledge Graphs are a key technology for implementing the FAIR principles in data infrastructures by ensuring interoperability for both humans and machines. The Working Group "Knowledge Graphs" in Section "(Meta)data, Terminologies, Provenance" of the German National Research Data Infrastructure (Nationale Forschungsdateninfrastruktur (NFDI) e.V.) aims to promote the use of knowledge graphs in all NFDI consortia, to facilitate cross-domain data interlinking and federation following the FAIR principles, and to contribute to the joint development of tools and technologies that enable transformation of structured and unstructured data into semantically reusable knowledge across different domains.
- ItemPID Network Deutschland: Netzwerk für die Förderung von persistenten Identifikatoren in Wissenschaft und Kultur(Potsdam : Helmholtz Open Science Office, 2023) Bertelmann, Roland; Buys, Matthew; Kett, Jürgen; Pampel, Heinz; Pieper, Dirk; Scholze, Frank; Sens, Irina; Burger, Felix; Dreyer, Britta; Glagla-Dietz, Stephanie; Hagemann- Wilholt, Stephanie; Hartmann, Sarah; Schrader, Antonia C.; Schirrwagen, Jochen; Summann, Friedrich; Vierkant, Paul[No abstract available]
- ItemWorkshop on PIDs within NFDI: Report of the Working Group “Persistent Identifiers (PID)” of the Section Common Infrastructures of the NFDI(Zenodo, 2023) Arend, Daniel; Bach, Janete; Elger, Kirsten; Göller, Sandra; Hagemann-Wilholt, Stephanie; Krahl, Rolf; Lange, Matthias; Linke, David; Mayer, Desiree; Mutschke, Peter; Reimer, Lorenz; Scheidgen, Markus; Schrader, Antonia C.; Selzer, Michael; Wieder, PhilippIn order to gain an overview of the current state of the discussion on PIDs and for the identification of use cases for the initiation phase of a PID service within the NFDI basic services, the working group Persistent Identifier of the Section Common Infrastructures of the NFDI hosted an online workshop in January 2023. In the course of the workshop, members of nine different NFDI consortia presented the current application of PIDs in their consortia.
- ItemConcept for Setting up the Persistent Identifier Services Working Group in the NFDI Section "Common Infrastructures"(Zenodo, 2022) Bingert, Sven; Brase, Jan; Burger, Felix; Dreyer, Britta; Hagemann-Wilholt, Stephanie; Vierkant, Paul; Wieder, PhilippThe aim of this NFDI working group is to develop a common strategy for the implementation and extension of PID services that is closely aligned with the needs of NFDI consortia. Resulting solutions should enable FAIR research workflows balancing out generic metadata requirements for PIDs that maximise resource discoverability on the one hand and subject-specific needs on the other. At the technical level, the partners want to realise interoperability between PID types and established systems and build on a high level of maturity here; jointly developed services should be able to be rolled out for the entire NFDI.