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End date: 2023 × End date: 2022 × Type: Article × Subject: Anatomy ×

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    Anatomy and the type concept in biology show that ontologies must be adapted to the diagnostic needs of research
    (London : BioMed Central, 2022) Vogt, Lars; Mikó, István; Bartolomaeus, Thomas
    Background: In times of exponential data growth in the life sciences, machine-supported approaches are becoming increasingly important and with them the need for FAIR (Findable, Accessible, Interoperable, Reusable) and eScience-compliant data and metadata standards. Ontologies, with their queryable knowledge resources, play an essential role in providing these standards. Unfortunately, biomedical ontologies only provide ontological definitions that answer What is it? questions, but no method-dependent empirical recognition criteria that answer How does it look? questions. Consequently, biomedical ontologies contain knowledge of the underlying ontological nature of structural kinds, but often lack sufficient diagnostic knowledge to unambiguously determine the reference of a term. Results: We argue that this is because ontology terms are usually textually defined and conceived as essentialistic classes, while recognition criteria often require perception-based definitions because perception-based contents more efficiently document and communicate spatial and temporal information—a picture is worth a thousand words. Therefore, diagnostic knowledge often must be conceived as cluster classes or fuzzy sets. Using several examples from anatomy, we point out the importance of diagnostic knowledge in anatomical research and discuss the role of cluster classes and fuzzy sets as concepts of grouping needed in anatomy ontologies in addition to essentialistic classes. In this context, we evaluate the role of the biological type concept and discuss its function as a general container concept for groupings not covered by the essentialistic class concept. Conclusions: We conclude that many recognition criteria can be conceptualized as text-based cluster classes that use terms that are in turn based on perception-based fuzzy set concepts. Finally, we point out that only if biomedical ontologies model also relevant diagnostic knowledge in addition to ontological knowledge, they will fully realize their potential and contribute even more substantially to the establishment of FAIR and eScience-compliant data and metadata standards in the life sciences.
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    A block copolymer templated approach for the preparation of nanoporous polymer structures and cellulose fiber hybrids by ozone treatment
    (Cambridge : RSC Publ., 2022) Gemmer, Lea; Hu, Qiwei; Niebuur, Bart-Jan; Kraus, Tobias; Balzer, Bizan N.; Gallei, Markus
    Functional amphiphilic block copolymers (BCPs) are versatile, smart, and promising materials that are often used as soft templates in nanoscience. BCPs generally feature the capability of microphase-separation leading to various interesting morphologies at the nanometer length scale. Materials derived from BCPs can be converted into porous structures while retaining the underlying morphology of the matrix material. Here, a convenient and scalable approach for the fabrication of porous functional polyvinylpyridines (P2VP) is introduced. The BCP polyisoprene-block-P2VP (PI-b-P2VP) is obtained via sequential anionic polymerization of the respective monomers and used to form either BCP films in the bulk state or a soft template in a composite with cellulose fibers. Cross-linking of the BCPs with 1,4-diiodobutane is conducted and subsequently PI domains are selectively degraded inside the materials using ozone, while preserving the porous and tailor-made P2VP nanostructure. Insights into the feasibility of the herein presented strategy is supported by various polymer characterization methods comprising nuclear magnetic resonance (NMR), size exclusion chromatography (SEC), and differential scanning calorimetry (DSC). The resulting bulk- and composite materials are investigated regarding their morphology and pore formation by scanning electron microscopy (SEM), atomic force microscopy (AFM) and small-angle X-ray scattering (SAXS). Furthermore, chemical conversions were examined by energy dispersive X-ray spectroscopy (EDS), attenuated total reflection Fourier-transformation infrared spectroscopy (ATR-FTIR) and water contact angle (WCA) measurements. By this convenient strategy the fabrication of functional porous P2VP in the bulk state and also within sustainable cellulose composite materials is shown, paving the synthetic strategy for the generation of a new family of stimuli-responsive sustainable materials.