2022, Włodarczyk-Biegun, Małgorzata K., Villiou, Maria, Koch, Marcus, Muth, Christina, Wang, Peixi, Ott, Jenna, del Campo, Aranzazu

The 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.

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, Philipp

In 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.

2022, Bingert, Sven, Brase, Jan, Burger, Felix, Dreyer, Britta, Hagemann-Wilholt, Stephanie, Vierkant, Paul, Wieder, Philipp

The 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.

2023, Stocker, Markus, Rossenova, Lozana, Shigapov, Renat, Betancort, Noemi, Dietze, Stefan, Murphy, Bridget, Bölling, Christian, Schubotz, Moritz, Koepler, Oliver

Knowledge 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.

2022, de Miguel-Jiménez, Adrián, Ebeling, Bastian, Paez, Julieta I., Fink-Straube, Claudia, Pearson, Samuel, del Campo, Aranzazu

Crosslinking 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.

2024-02, Sigle, Stefan, Werner, Patrick, Schweizer, Simon, Caldeira, Liliana, Hosch, René, Dyrba, Martin, Fegeler, Christian, Sigle, Stefan, Werner, Patrick, Schweizer, Simon, Caldeira, Liliana, Hosch, René, Dyrba, Martin, Fegeler, Christian, Grönke, Ana, Seletkov, Dmitrii, Kotter, Elmar, Nensa, Felix, Wehrle, Julius, Kaufmes, Kevin, Scherer, Lucas, Nolden, Marco, Boeker, Martin, Schmidt, Marvin, Pelka, Obioma, Braren, Rickmer, Stump, Shura-Roman, Graetz, Teresa, Pogarell, Tobias, Susetzky, Tobias, Wieland, Tobias, Parmar, Vicky, Wang, Yuanbin

Artificial Intelligence (AI) in research and clinical contexts is transforming the areas of medical and life sciences permanently. Aspects like findability, accessibility, interoperability, and reusability are often neglected for AI-based inference services. The Open Medical Inference (OMI) protocol aims to support remote inference by addressing the aforementioned aspects. Key component of the proposed protocol is an interoperable registry for remote inference services, which addresses the issue of findability for algorithms. It is complemented by information on how to invoke services remotely. Together, these components lay the basis for the implementation of distributed inference services beyond organizational borders. The OMI protocol considers prior work for aspects like data representation and transmission standards wherever possible. Based on Business Process Modeling of prototypical use cases for the service registry and common inference processes, a generic information model for remote services was inferred. Based on this model, FHIR resources were identified to represent AI-based services. The OMI protocol is first introduced using AI-services in radiology but is designed to be generalizable to other application domains as well. It provides an accessible, open specification as blueprint for the introduction and implementation of remote inference services.

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, Klaus

The 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.

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.

2024, Beutter, C. N. L., Block, N., Berger, S., Edo-Ferrando, P., Heinz, B., Läufer, K., Lang, B., Mächtlen, K., Münkel, S., Rannert, D., Zwerenz-Kopp, F., Fegeler, C.

Im Rahmen einer Projektgruppe haben sich sowohl Versorger (ÄrztInnen, KrebsberatungsstellenmitarbeiterInnen oder PsychoonkologInnen) sowie Betroffene mit einer regulären Integration von Lebensqualitätsdaten in der Versorgung befasst. Dabei wurde ein digitales System konzipiert, dass eine alltagsnahe und longitudinale Erhebung ermöglicht. Im working paper wurde über alle Teilnehmenden hinweg eine Problemidentifikation der derzeitigen IST-Situation integriert, um anhand dieser Probleme und Hemmschwellen ein übergreifendes Lösungskonzept zu erarbeiten. Im Lösungsraum wurden sowohl spezifische Anforderungen seitens der Versorger als auch PatientInnen zusammengefasst und gegenübergestellt. Dabei wurde ebenfalls die Vernetzung der einzelnen Akteure untereinander beleuchtet sowie die Thematik der Datenspende angerissen.

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]