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- ItemOn Tetrahedralisations Containing Knotted and Linked Line Segments(Amsterdam [u.a.] : Elsevier, 2017) Si, Hang; Ren, Yuxue; Lei, Na; Gu, XianfengThis paper considers a set of twisted line segments in 3d such that they form a knot (a closed curve) or a link of two closed curves. Such line segments appear on the boundary of a family of 3d indecomposable polyhedra (like the Schönhardt polyhedron) whose interior cannot be tetrahedralised without additional vertices added. On the other hand, a 3d (non-convex) polyhedron whose boundary contains such line segments may still be decomposable as long as the twist is not too large. It is therefore interesting to consider the question: when there exists a tetrahedralisation contains a given set of knotted or linked line segments? In this paper, we studied a simplified question with the assumption that all vertices of the line segments are in convex position. It is straightforward to show that no tetrahedralisation of 6 vertices (the three-line-segments case) can contain a trefoil knot. Things become interesting when the number of line segments increases. Since it is necessary to create new interior edges to form a tetrahedralisation. We provided a detailed analysis for the case of a set of 4 line segments. This leads to a crucial condition on the orientation of pairs of new interior edges which determines whether this set is decomposable or not. We then prove a new theorem about the decomposability for a set of n (n ≥ 3) knotted or linked line segments. This theorem implies that the family of polyhedra generalised from the Schonhardt polyhedron by Rambau [1] are all indecomposable.
- ItemCold physical plasma-induced oxidation of cysteine yields reactive sulfur species (RSS)(Amsterdam [u.a.] : Elsevier, 2019) Bruno, Giuliana; Heusler, Thea; Lackmann, Jan-Wilm; Woedtke, Thomas von; Weltmann, Klaus-Dieter; Wende, KristianPurpose: Studying plasma liquid chemistry can reveal insights into their biomedical effects, i.e. to understand the direct and indirect processes triggered by the treatment in a model or clinical application. Due to the reactivity of the sulfur atom, thiols are potential targets for plasma- derived reactive species. Being crucial for protein function and redox signaling pathways, their controllable modification would allow expanding the application range. Additionally, models to control and standardize CAP sources are desired tools for plasma source design. Methods: Cysteine, a ubiquitous amino acid, was used as a tracer compound to scavenge the reactive species produced by an argon plasma jet (kINPen). The resulting product pattern was identified via high-resolution mass spectrometry. The Ellman´s assay was used to screen CAP derived thiol consumption, and long-lived species deposition (hydrogen peroxide, nitrite, nitrate) was monitored in relation to the presence of cysteine. Results: The intensity of cysteine oxidation increased with treatment time and availability of oxygen in the feed gas. A range of products from cysteine was identified, in part indicative for certain treatment conditions. Several non-stable products occur transiently during the plasma treatment. Bioactive reactive sulfur species (RSS) have been found for mild treatment conditions, such as cysteine sulfoxides and cysteine-S-sulfonate. Considering the number of cysteine molecules in the boundary layer and the achieved oxidation state, short-lived species dominate in cysteine conversion. In addition, a boundary layer depletion of the tracer was observed. Conclusion: Translating these data into the in-vivo application, strong direct oxidation of protein thiol groups with subsequent changes in protein biochemistry must be considered. Plasma-derived RSS may in part contribute to the observed biomedical effects of CAP. Care must be taken to control the discharge parameter tightly as chemical dynamics at or in the liquid are subject to change easily. © 2019
- ItemScattering matrices and Dirichlet-to-Neumann maps(Amsterdam [u.a.] : Elsevier, 2017) Behrndt, Jussi; Malamud, Mark M.; Neidhardt, HagenA general representation formula for the scattering matrix of a scattering system consisting of two self-adjoint operators in terms of an abstract operator valued Titchmarsh–Weyl m-function is proved. This result is applied to scattering problems for different self-adjoint realizations of Schrödinger operators on unbounded domains, Schrödinger operators with singular potentials supported on hypersurfaces, and orthogonal couplings of Schrödinger operators. In these applications the scattering matrix is expressed in an explicit form with the help of Dirichlet-to-Neumann maps.
- ItemHow modelers construct energy costs: Discursive elements in Energy System and Integrated Assessment Models(Amsterdam [u.a.] : Elsevier, 2019) Ellenbeck, Saskia; Lilliestam, JohanEnergy system and integrated assessment models (IAMs) are widely used techniques for knowledge production to assess costs of future energy pathways and economic effects of energy/climate policies. With their increased use for policy assessment and increasing dominance in energy policy science, such models attract increasing criticism. In the last years, such models – especially the highly complex IAMs, have been accused of being arbitrary. We challenge this view and argue that the models and their assumptions are not arbitrary, but they are normative and reflect the modelers’ understanding of the functioning of the society, the environment-societal relations and respective appropriate scientific tools and theories – in short: models are shaped by discursive structures, reproducing and reinforcing particular societal discourses. We identify 9 distinct paths, all relating to crucial model decisions, via which discourses enter models: for each of these decisions, there are multiple “correct” answers, in the sense that they can be justified within a particular discourse. We conclude that decisions of modelers about the structure and about assumptions in energy modeling are not arbitrary but contingent to the discursive context the modeler is related to. This has two implications. First, modelers and consumers of model output must reflect on what a model and its assumptions represent, and not only whether are they correct. Second, models hardly need to add more (mathematical) complexity, but rather be reduced and simplified so that they can continue to fulfill their main function as formalized and powerful instruments for thought experiments about future energy pathways.
- ItemComplement activation by carbon nanotubes and its influence on the phagocytosis and cytokine response by macrophages(Amsterdam [u.a.] : Elsevier, 2014) Pondman, K.M.; Sobik, M.; Nayak, A.; Tsolaki, A.G.; Jäkel, A.; Flahaut, E.; Hampel, S.; ten Haken, B.; Sim, R.B.; Kishore, U.Carbon nanotubes (CNTs) have promised a range of applications in biomedicine. Although influenced by the dispersants used, CNTs are recognized by the innate immune system, predominantly by the classical pathway of the complement system. Here, we confirm that complement activation by the CNT used continues up to C3 and C5, indicating that the entire complement system is activated including the formation of membrane-attack complexes. Using recombinant forms of the globular regions of human C1q (gC1q) as inhibitors of CNT-mediated classical pathway activation, we show that C1q, the first recognition subcomponent of the classical pathway, binds CNTs via the gC1q domain. Complement opsonisation of CNTs significantly enhances their uptake by U937 cells, with concomitant downregulation of pro-inflammatory cytokines and up-regulation of anti-inflammatory cytokines in both U937 cells and human monocytes. We propose that CNT-mediated complement activation may cause recruitment of cellular infiltration, followed by phagocytosis without inducing a pro-inflammatory immune response. From the Clinical Editor: This study highlights the importance of the complement system in response to carbon nanontube administration, suggesting that the ensuing complement activation may cause recruitment of cellular infiltration, followed by phagocytosis without inducing a pro-inflammatory immune response.
- ItemCorrecting a fundamental error in greenhouse gas accounting related to bioenergy(Amsterdam [u.a.] : Elsevier, 2012) Haberl, H.; Sprinz, D.; Bonazountas, M.; Cocco, P.; Desaubies, Y.; Henze, M.; Hertel, O.; Johnson, R.K.; Kastrup, U.; Laconte, P.; Lange, E.; Novak, P.; Paavola, J.; Reenberg, A.; van den Hove, S.; Vermeire, T.; Wadhams, P.; Searchinger, T.Many international policies encourage a switch from fossil fuels to bioenergy based on the premise that its use would not result in carbon accumulation in the atmosphere. Frequently cited bioenergy goals would at least double the present global human use of plant material, the production of which already requires the dedication of roughly 75% of vegetated lands and more than 70% of water withdrawals. However, burning biomass for energy provision increases the amount of carbon in the air just like burning coal, oil or gas if harvesting the biomass decreases the amount of carbon stored in plants and soils, or reduces carbon sequestration. Neglecting this fact results in an accounting error that could be corrected by considering that only the use of 'additional biomass' - biomass from additional plant growth or biomass that would decompose rapidly if not used for bioenergy - can reduce carbon emissions. Failure to correct this accounting flaw will likely have substantial adverse consequences. The article presents recommendations for correcting greenhouse gas accounts related to bioenergy.
- ItemAmyloids: From molecular structure to mechanical properties(Amsterdam [u.a.] : Elsevier, 2013) Schleeger, M.; Vandenakker, C.C.; Deckert-Gaudig, T.; Deckert, V.; Velikov, K.P.; Koenderink, G.; Bonn, M.Many proteins of diverse sequence, structure and function self-assemble into morphologically similar fibrillar aggregates known as amyloids. Amyloids are remarkable polymers in several respects. First of all, amyloids can be formed from proteins with very different amino acid sequences; the common denominator is that the individual proteins constituting the amyloid fold predominantly into a β-sheet structure. Secondly, the formation of the fibril occurs through non-covalent interactions between primarily the β-sheets, causing the monomers to stack into fibrils. The fibrils are remarkably robust, considering that the monomers are bound non-covalently. Finally, a common characteristic of fibrils is their unbranched, straight, fiber-like structure arising from the intertwining of the multiple β-sheet filaments. These remarkably ordered and stable nanofibrils can be useful as building blocks for protein-based functional materials, but they are also implicated in severe neurodegenerative diseases. The overall aim of this article is to highlight recent efforts aimed at obtaining insights into amyloid proteins on different length scales. Starting from molecular information on amyloids, single fibril properties and mechanical properties of networks of fibrils are described. Specifically, we focus on the self-assembly of amyloid protein fibrils composed of peptides and denatured model proteins, as well as the influence of inhibitors of fibril formation. Additionally, we will demonstrate how the application of recently developed vibrational spectroscopic techniques has emerged as a powerful approach to gain spatially resolved information on the structure-function relation of amyloids. While spectroscopy provides information on local molecular conformations and protein secondary structure, information on the single fibril level has been developed by diverse microscopic techniques. The approaches to reveal basic mechanical properties of single fibrils like bending rigidity, shear modulus, ultimate tensile strength and fracture behavior are illustrated. Lastly, mechanics of networks of amyloid fibrils, typically forming viscoelastic gels are outlined, with a focus on (micro-) rheological properties. The resulting fundamental insights are essential for the rational design of novel edible and biodegradable protein-based polymers, but also to devise therapeutic strategies to combat amyloid assembly and accumulation during pathogenic disorders.
- ItemLaser Embossing of Micro-and Submicrometer Surface Structures in Copper(Amsterdam [u.a.] : Elsevier, 2012) Ehrhardt, M.; Lorenz, P.; Frost, F.; Zimmer, K.Micro- and submicrometer structures have been transferred from nickel foils into solid copper surfaces by laser microembossing. The developed arrangement for laser microembossing allows a large-area replication using multi- pulse laser scanning scheme, guaranties a low contamination of the embossed surface and enables the utilization of thick workpieces. In the micrometer range the replicated patterns feature a high accuracy regarding the shape. A significant difference between the master and the replication pattern could be observed for the laser embossing of submicrometer patterns. In conclusion, the results show that the proposed laser embossing process is a promising method with a number of applications in microengineering.
- ItemOpening up knowledge systems for better responses to global environmental change(Amsterdam [u.a.] : Elsevier, 2013) Cornell, S.; Berkhout, F.; Tuinstra, W.; Tàbara, J.D.; Jäger, J.; Chabay, I.; de Wit, B.; Langlais, R.; Mills, D.; Moll, P.; Otto, I.M.; Petersen, A.; Pohl, C.; van Kerkhoff, L.Linking knowledge with action for effective societal responses to persistent problems of unsustainability requires transformed, more open knowledge systems. Drawing on a broad range of academic and practitioner experience, we outline a vision for the coordination and organization of knowledge systems that are better suited to the complex challenges of sustainability than the ones currently in place. This transformation includes inter alia: societal agenda setting, collective problem framing, a plurality of perspectives, integrative research processes, new norms for handling dissent and controversy, better treatment of uncertainty and of diversity of values, extended peer review, broader and more transparent metrics for evaluation, effective dialog processes, and stakeholder participation. We set out institutional and individual roadmaps for achieving this vision, calling for well-designed, properly resourced, longitudinal, international learning programs.
- ItemPotentiating anti-tumor immunity with physical plasma(Amsterdam [u.a.] : Elsevier, 2018) Bekeschus, Sander; Clemen, Ramona; Metelmann, Hans-RobertThe age of checkpoint blockage emphasizes the importance of adaptive antitumor immune responses. This arm of immune defense is key in recognizing molecules via specific receptors to distinguish between self and foreign or mutated structures. Antigen-specific T-cells identify non-self epitopes, tumor-associated antigens, or neoepitopes on tumors to carry out attacks on malignant cells. Although tumor cells are immunogenic by nature, they have developed strategies to evade an immune response that would otherwise facilitate their clearance. Several steps in antitumor immunity utilize the toxic and signaling properties of reactive oxygen and nitrogen species (ROS/RNS). Cold physical plasmas are potent generators of such ROS/RNS and are demonstrated to have profound antitumor activity in vitro and in vivo. Here we discuss recent evidence and concepts on how plasmas may boost immunity against pathological cells. Specifically, plasma treatment may enhance the immunogenicity of tumor cells by induction of the immunogenic cancer cell death (ICD) and redox regulation of the antigen-presenting machinery. These aspects provide a rationale for localized plasma-based onco-therapies enhancing systemic antitumor immunity, which eventually may target distant tumor metastasis in cancer patients in a T-cell dependent fashion.