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- ItemATMODAT Standard v3.0(Hamburg : DKRZ, 2020) Gasnke, Anette; Kraft, Angelina; Kaiser, Amandine; Heydebreck, Daniel; Lammert, Andrea; Höck, Heinke; Thiemann, Hannes; Voss, Vivien; Grawe, David; Leitl, Bernd; Schlünzen, K. Heinke; Kretzschmar, Jan; Quaas, JohannesWithin the AtMoDat project (Atmospheric Model Data), a standard has been developed which is meant for improving the FAIRness of atmospheric model data published in repositories. The ATMODAT standard includes concrete recommendations related to the maturity, publication and enhanced FAIRness of atmospheric model data. The suggestions include requirements for rich metadata with controlled vocabularies, structured landing pages, file formats (netCDF) and the structure within files. Human- and machine readable landing pages are a core element of this standard, and should hold and present discipline-specific metadata on simulation and variable level. This standard is an updated and translated version of "Bericht über initialen Kernstandard und Kurationskriterien des AtMoDat Projektes (v2.4)
- 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.”
- ItemGelation kinetics of thiol-methylsulfone (MS) hydrogel formulations for 3D cell culture(Washington, D.C. : American Chemical Society, 2022) de Miguel-Jiménez, Adrián; Ebeling, Bastian; Paez, Julieta I.; Fink-Straube, Claudia; Pearson, Samuel; del Campo, AranzazuCrosslinking chemistries that allow hydrogel formation within minutes are essential to achieve homogeneous networks and cell distributions in 3D cell culture. Thiol-methylsulfone (MS) crosslinking chemistry offers minutes-scale gelation under near-physiological conditions showing many desirable attributes for 3D cell encapsulation. Here we investigate the gelation kinetics and mechanical properties of PEG-based hydrogels formed by thiol-tetrazole methylsulfone (TzMS) crosslinking as a function of buffer, crosslinker structure, and degree of TzMS functionalization. Appropriate buffer selection ensured constant pH throughout crosslinking. The formulation containing cell adhesive ligand RGD and enzymatically-degradable peptide VPM gelled in ca. 4 min at pH 7.5, and stiffness could be increased from hundreds of Pascals to > 1 kPa by using excess VPM. The gelation times and stiffnesses for these hydrogels are highly suitable for 3D cell encapsulations, and pave the way for reliable 3D cell culture workflows in pipetting robots.
- 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.
- ItemMetadatenschema für Schulungsmaterialien zum Thema Forschungsdatenmanagement(Meyrin : CERN, 2020-04-27) Biernacka, Katarzyna; Danker, Sarah Ann; Engelhardt, Claudia; Helbig, Kerstin; Hendriks, Sonja; Jacob, Juliane; Jagusch, Gerald; Lanza, Giacomo; Leone, Claudio; Meier, Kristin; Neumann, Janna; Odebrecht, Carolin; Peters, Karsten; Rehwald, Stephanie; Rex, Jessica; Senft, Matthias; Strauch, Annette; Thiemann, Kathrin; Trautwein-Bruns, Ute; Wiljes, Cord; Wuttke, Ulrike; Ziedorn, FraukeDas Dokument enthält ein Metadatenschema für Schulungsmaterialien zum Thema Forschungsdatenmanagement. Dieses Schema wurde von der UAG Schulungen/Fortbildungen der DINI/nestor AG Forschungsdaten erstellt und bei der Materialsammlung von FDM-Schulungsmaterialien unter https://rs.cms.hu-berlin.de/uag_fdm/ umgesetzt.
- 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.
- ItemMelt Electrowriting of Scaffolds with a Porosity Gradient to Mimic the Matrix Structure of the Human Trabecular Meshwork(New York : Cold Spring Harbor Laboratory, 2022) Włodarczyk-Biegun, Małgorzata K.; Villiou, Maria; Koch, Marcus; Muth, Christina; Wang, Peixi; Ott, Jenna; del Campo, AranzazuThe permeability of the Human Trabecular Meshwork (HTM) regulates eye pressure via a porosity gradient across its thickness modulated by stacked layers of matrix fibrils and cells. Changes in HTM porosity are associated with increases in intraocular pressure and the progress of diseases like glaucoma. Engineered HTMs could help to understand the structure-function relation in natural tissues, and lead to new regenerative solutions. Here, melt electrowriting (MEW) is explored as a biofabrication technique to produce fibrillar, porous scaffolds that mimic the multilayer, gradient structure of native HTM. Poly(caprolactone) constructs with a height of 125-500 μm and fiber diameters of 10-12 μm are printed. Scaffolds with a tensile modulus between 5.6 and 13 MPa, and a static compression modulus in the range of 6-360 kPa are obtained by varying the scaffolds design, i.e., density and orientation of the fibers and number of stacked layers. Primary HTM cells attach to the scaffolds, proliferate, and form a confluent layer within 8-14 days, depending on the scaffold design. High cell viability and cell morphology close to that in the native tissue are observed. The present work demonstrates the utility of MEW to reconstruct complex morphological features of natural tissues.
- 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.
- ItemRedox-triggerable Luciferin-Bioinspired Hydrogels as Injectable and Cell-encapsulating Matrices(Washington, D.C. : American Chemical Society, 2022) Jin, Minye; Gläser, Alisa; Paez, Julieta I.Over the past few decades there has been a great interest in developing smart hydrogels that are stimuli-responsive, due to their ability to respond to variations caused by external stimuli. These materials are exploited for biomedical applications such as biosensors, injectable scaffolds, drug delivery and tissue engineering. Recently, our group reported firefly-inspired hydrogel matrices for 3D cell culture. This platform exhibited certain advantages like rapid gelation rate and tunability of mechanical and biological properties. However, this firstly reported system did not allow for fine control of the gelation onset because the crosslinking reaction started as soon as the two precursors were mixed. Moreover, one of its precursors demonstrated poor storage stability in aqueous solution. These limitations restrict its application as injectable matrices. In this article, we endow the luciferin-inspired hydrogels with redox-triggering capability, to overcome the limitations of the previous system and to widen its application range. We achieve this goal by introducing protected macromers as hydrogel polymeric precursors that can be activated in the presence of a mild reductant, to trigger gel formation in situ with high degree of control. We demonstrate that the regulation of intrinsic (e.g., structure of protecting group, reductant type) and extrinsic (e.g., pH, temperature) parameters of the triggering reaction can be used to modulate key materials properties. This novel upgraded redox-triggerable system enables precise control over gelation onset and kinetics, thus facilitating its utilization as injectable hydrogel without negatively impacting its cytocompatibility. Our findings expand the current toolkit of chemically-based stimuli-responsive hydrogels.