TY - GEN A1 - Larhlimi, Abdelhalim A1 - David, Laszlo A1 - Selbig, Joachim A1 - Bockmayr, Alexander T1 - F2C2 BT - a fast tool for the computation of flux coupling in genome-scale metabolic networks T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background: Flux coupling analysis (FCA) has become a useful tool in the constraint-based analysis of genome-scale metabolic networks. FCA allows detecting dependencies between reaction fluxes of metabolic networks at steady-state. On the one hand, this can help in the curation of reconstructed metabolic networks by verifying whether the coupling between reactions is in agreement with the experimental findings. On the other hand, FCA can aid in defining intervention strategies to knock out target reactions. Results: We present a new method F2C2 for FCA, which is orders of magnitude faster than previous approaches. As a consequence, FCA of genome-scale metabolic networks can now be performed in a routine manner. Conclusions: We propose F2C2 as a fast tool for the computation of flux coupling in genome-scale metabolic networks. F2C2 is freely available for non-commercial use at https://sourceforge.net/projects/f2c2/files/. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 921 KW - balance analysis KW - reconstruction KW - pathways KW - models KW - metabolic network KW - couple reaction KW - reversible reaction KW - linear programming problem KW - coupling relationship Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-432431 SN - 1866-8372 IS - 921 ER - TY - GEN A1 - Laudan, Jonas A1 - Rözer, Viktor A1 - Sieg, Tobias A1 - Vogel, Kristin A1 - Thieken, Annegret T1 - Damage assessment in Braunsbach 2016 BT - data collection and analysis for an improved understanding of damaging processes during flash floods T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Flash floods are caused by intense rainfall events and represent an insufficiently understood phenomenon in Germany. As a result of higher precipitation intensities, flash floods might occur more frequently in future. In combination with changing land use patterns and urbanisation, damage mitigation, insurance and risk management in flash-flood-prone regions are becoming increasingly important. However, a better understanding of damage caused by flash floods requires ex post collection of relevant but yet sparsely available information for research. At the end of May 2016, very high and concentrated rainfall intensities led to severe flash floods in several southern German municipalities. The small town of Braunsbach stood as a prime example of the devastating potential of such events. Eight to ten days after the flash flood event, damage assessment and data collection were conducted in Braunsbach by investigating all affected buildings and their surroundings. To record and store the data on site, the open-source software bundle KoBoCollect was used as an efficient and easy way to gather information. Since the damage driving factors of flash floods are expected to differ from those of riverine flooding, a post-hoc data analysis was performed, aiming to identify the influence of flood processes and building attributes on damage grades, which reflect the extent of structural damage. Data analyses include the application of random forest, a random general linear model and multinomial logistic regression as well as the construction of a local impact map to reveal influences on the damage grades. Further, a Spearman's Rho correlation matrix was calculated. The results reveal that the damage driving factors of flash floods differ from those of riverine floods to a certain extent. The exposition of a building in flow direction shows an especially strong correlation with the damage grade and has a high predictive power within the constructed damage models. Additionally, the results suggest that building materials as well as various building aspects, such as the existence of a shop window and the surroundings, might have an effect on the resulting damage. To verify and confirm the outcomes as well as to support future mitigation strategies, risk management and planning, more comprehensive and systematic data collection is necessary. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 653 KW - building damage KW - mai 29th KW - flow KW - vulnerability KW - 2016-origin KW - pathways KW - Germany KW - impacts KW - model Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-418392 SN - 1866-8372 IS - 653 ER - TY - GEN A1 - Moradian, Hanieh A1 - Roch, Toralf A1 - Lendlein, Andreas A1 - Gossen, Manfred T1 - mRNA transfection-induced activation of primary human monocytes and macrophages BT - Dependence on carrier system and nucleotide modifcation T2 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Monocytes and macrophages are key players in maintaining immune homeostasis. Identifying strategies to manipulate their functions via gene delivery is thus of great interest for immunological research and biomedical applications. We set out to establish conditions for mRNA transfection in hard-to-transfect primary human monocytes and monocyte-derived macrophages due to the great potential of gene expression from in vitro transcribed mRNA for modulating cell phenotypes. mRNA doses, nucleotide modifications, and different carriers were systematically explored in order to optimize high mRNA transfer rates while minimizing cell stress and immune activation. We selected three commercially available mRNA transfection reagents including liposome and polymer-based formulations, covering different application spectra. Our results demonstrate that liposomal reagents can particularly combine high gene transfer rates with only moderate immune cell activation. For the latter, use of specific nucleotide modifications proved essential. In addition to improving efficacy of gene transfer, our findings address discrete aspects of innate immune activation using cytokine and surface marker expression, as well as cell viability as key readouts to judge overall transfection efficiency. The impact of this study goes beyond optimizing transfection conditions for immune cells, by providing a framework for assessing new gene carrier systems for monocyte and macrophage, tailored to specific applications. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1403 KW - sirna transfection KW - mediated delivery KW - gene delivery KW - efficient KW - immunogenicity KW - lipoplexes KW - cells KW - therapeutics KW - polarization KW - pathways Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-515694 SN - 1866-8372 IS - 1 ER -