TY - GEN A1 - Hildebrandt, Dieter T1 - A software reference architecture for service-oriented 3D geovisualization systems T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Modern 3D geovisualization systems (3DGeoVSs) are complex and evolving systems that are required to be adaptable and leverage distributed resources, including massive geodata. This article focuses on 3DGeoVSs built based on the principles of service-oriented architectures, standards and image-based representations (SSI) to address practically relevant challenges and potentials. Such systems facilitate resource sharing and agile and efficient system construction and change in an interoperable manner, while exploiting images as efficient, decoupled and interoperable representations. The software architecture of a 3DGeoVS and its underlying visualization model have strong effects on the system's quality attributes and support various system life cycle activities. This article contributes a software reference architecture (SRA) for 3DGeoVSs based on SSI that can be used to design, describe and analyze concrete software architectures with the intended primary benefit of an increase in effectiveness and efficiency in such activities. The SRA integrates existing, proven technology and novel contributions in a unique manner. As the foundation for the SRA, we propose the generalized visualization pipeline model that generalizes and overcomes expressiveness limitations of the prevalent visualization pipeline model. To facilitate exploiting image-based representations (IReps), the SRA integrates approaches for the representation, provisioning and styling of and interaction with IReps. Five applications of the SRA provide proofs of concept for the general applicability and utility of the SRA. A qualitative evaluation indicates the overall suitability of the SRA, its applications and the general approach of building 3DGeoVSs based on SSI. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1131 KW - 3D geovisualization KW - software reference architecture KW - spatial data infrastructure KW - service-oriented architecture KW - standardization KW - image-based representation Y1 - 2021 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-475831 SN - 1866-8372 IS - 1131 ER - TY - GEN A1 - Kersting, Sebastian A1 - Rausch, Valentina A1 - Bier, Frank Fabian A1 - von Nickisch-Rosenegk, Markus T1 - Rapid detection of Plasmodium falciparum with isothermal recombinase polymerase amplification and lateral flow analysis T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Background Nucleic acid amplification is the most sensitive and specific method to detect Plasmodium falciparum. However the polymerase chain reaction remains laboratory-based and has to be conducted by trained personnel. Furthermore, the power dependency for the thermocycling process and the costly equipment necessary for the read-out are difficult to cover in resource-limited settings. This study aims to develop and evaluate a combination of isothermal nucleic acid amplification and simple lateral flow dipstick detection of the malaria parasite for point-of-care testing. Methods A specific fragment of the 18S rRNA gene of P. falciparum was amplified in 10 min at a constant 38°C using the isothermal recombinase polymerase amplification (RPA) method. With a unique probe system added to the reaction solution, the amplification product can be visualized on a simple lateral flow strip without further labelling. The combination of these methods was tested for sensitivity and specificity with various Plasmodium and other protozoa/bacterial strains, as well as with human DNA. Additional investigations were conducted to analyse the temperature optimum, reaction speed and robustness of this assay. Results The lateral flow RPA (LF-RPA) assay exhibited a high sensitivity and specificity. Experiments confirmed a detection limit as low as 100 fg of genomic P. falciparum DNA, corresponding to a sensitivity of approximately four parasites per reaction. All investigated P. falciparum strains (n = 77) were positively tested while all of the total 11 non-Plasmodium samples, showed a negative test result. The enzymatic reaction can be conducted under a broad range of conditions from 30-45°C with high inhibitory concentration of known PCR inhibitors. A time to result of 15 min from start of the reaction to read-out was determined. Conclusions Combining the isothermal RPA and the lateral flow detection is an approach to improve molecular diagnostic for P. falciparum in resource-limited settings. The system requires none or only little instrumentation for the nucleic acid amplification reaction and the read-out is possible with the naked eye. Showing the same sensitivity and specificity as comparable diagnostic methods but simultaneously increasing reaction speed and dramatically reducing assay requirements, the method has potential to become a true point-of-care test for the malaria parasite. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 948 KW - Plasmodium falciparum KW - Recombinase polymerase amplification KW - RPA KW - PCR KW - lateral flow KW - point-of-care testing KW - rapid test KW - isothermal nucleic acid amplification Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431562 SN - 1866-8372 IS - 948 ER - TY - GEN A1 - Thieken, Annegret A1 - Cammerer, Holger A1 - Dobler, Christian A1 - Lammel, Johannes A1 - Schöberl, Fritz T1 - Estimating changes in flood risks and benefits of non-structural adaptation strategies BT - a case study from Tyrol, Austria T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Flood damage has increased significantly and is expected to rise further in many parts of the world. For assessing potential changes in flood risk, this paper presents an integrated model chain quantifying flood hazards and losses while considering climate and land use changes. In the case study region, risk estimates for the present and the near future illustrate that changes in flood risk by 2030 are relatively low compared to historic periods. While the impact of climate change on the flood hazard and risk by 2030 is slight or negligible, strong urbanisation associated with economic growth contributes to a remarkable increase in flood risk. Therefore, it is recommended to frequently consider land use scenarios and economic developments when assessing future flood risks. Further, an adapted and sustainable risk management is necessary to encounter rising flood losses, in which non-structural measures are becoming more and more important. The case study demonstrates that adaptation by non-structural measures such as stricter land use regulations or enhancement of private precaution is capable of reducing flood risk by around 30 %. Ignoring flood risks, in contrast, always leads to further increasing losses-with our assumptions by 17 %. These findings underline that private precaution and land use regulation could be taken into account as low cost adaptation strategies to global climate change in many flood prone areas. Since such measures reduce flood risk regardless of climate or land use changes, they can also be recommended as no-regret measures. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 910 KW - flood risk KW - scenarios KW - adaptation to climate change KW - hazard KW - vulnerability KW - lech catchment Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-432282 SN - 1866-8372 IS - 910 ER - TY - GEN A1 - Böckmann, Christine A1 - Osterloh, Lukas T1 - Runge-Kutta type regularization method for inversion of spheroidal particle distribution from limited optical data T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The Runge-Kutta type regularization method was recently proposed as a potent tool for the iterative solution of nonlinear ill-posed problems. In this paper we analyze the applicability of this regularization method for solving inverse problems arising in atmospheric remote sensing, particularly for the retrieval of spheroidal particle distribution. Our numerical simulations reveal that the Runge-Kutta type regularization method is able to retrieve two-dimensional particle distributions using optical backscatter and extinction coefficient profiles, as well as depolarization information. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 907 KW - inverse ill-posed problem KW - integral equation KW - laser remote sensing KW - inverse scattering KW - aerosol size distribution KW - 65R32 KW - 47A52 KW - 65R20 KW - 78A46 KW - iterative regularization Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-441200 SN - 1866-8372 IS - 907 SP - 150 EP - 165 ER - TY - GEN A1 - Wang, Lifeng A1 - Zöller, Gert A1 - Hainzl, Sebastian T1 - Joint determination of slip and stress drop in a Bayesian inversion approach: BT - a case study for the 2010 M8.8 Maule earthquake T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Stress drop is a key factor in earthquake mechanics and engineering seismology. However, stress drop calculations based on fault slip can be significantly biased, particularly due to subjectively determined smoothing conditions in the traditional least-square slip inversion. In this study, we introduce a mechanically constrained Bayesian approach to simultaneously invert for fault slip and stress drop based on geodetic measurements. A Gaussian distribution for stress drop is implemented in the inversion as a prior. We have done several synthetic tests to evaluate the stability and reliability of the inversion approach, considering different fault discretization, fault geometries, utilized datasets, and variability of the slip direction, respectively. We finally apply the approach to the 2010 M8.8 Maule earthquake and invert for the coseismic slip and stress drop simultaneously. Two fault geometries from the literature are tested. Our results indicate that the derived slip models based on both fault geometries are similar, showing major slip north of the hypocenter and relatively weak slip in the south, as indicated in the slip models of other studies. The derived mean stress drop is 5-6 MPa, which is close to the stress drop of similar to 7 MPa that was independently determined according to force balance in this region Luttrell et al. (J Geophys Res, 2011). These findings indicate that stress drop values can be consistently extracted from geodetic data. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 888 KW - stress drop KW - fault slip KW - Bayesian KW - geodetic measurements Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-435511 SN - 1866-8372 IS - 888 SP - 375 EP - 388 ER - TY - GEN A1 - Wallenta, Daniel T1 - A Lefschetz fixed point formula for elliptic quasicomplexes T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - In a recent paper, the Lefschetz number for endomorphisms (modulo trace class operators) of sequences of trace class curvature was introduced. We show that this is a well defined, canonical extension of the classical Lefschetz number and establish the homotopy invariance of this number. Moreover, we apply the results to show that the Lefschetz fixed point formula holds for geometric quasiendomorphisms of elliptic quasicomplexes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 885 KW - elliptic complexes KW - Fredholm complexes KW - Lefschetz number Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-435471 SN - 1866-8372 IS - 885 SP - 577 EP - 587 ER - TY - GEN A1 - Zulawski, Monika A1 - Schulze, Gunnar A1 - Braginets, Rostyslav A1 - Hartmann, Stefanie A1 - Schulze, Waltraud X T1 - The Arabidopsis Kinome BT - phylogeny and evolutionary insights into functional diversification T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Background Protein kinases constitute a particularly large protein family in Arabidopsis with important functions in cellular signal transduction networks. At the same time Arabidopsis is a model plant with high frequencies of gene duplications. Here, we have conducted a systematic analysis of the Arabidopsis kinase complement, the kinome, with particular focus on gene duplication events. We matched Arabidopsis proteins to a Hidden-Markov Model of eukaryotic kinases and computed a phylogeny of 942 Arabidopsis protein kinase domains and mapped their origin by gene duplication. Results The phylogeny showed two major clades of receptor kinases and soluble kinases, each of which was divided into functional subclades. Based on this phylogeny, association of yet uncharacterized kinases to families was possible which extended functional annotation of unknowns. Classification of gene duplications within these protein kinases revealed that representatives of cytosolic subfamilies showed a tendency to maintain segmentally duplicated genes, while some subfamilies of the receptor kinases were enriched for tandem duplicates. Although functional diversification is observed throughout most subfamilies, some instances of functional conservation among genes transposed from the same ancestor were observed. In general, a significant enrichment of essential genes was found among genes encoding for protein kinases. Conclusions The inferred phylogeny allowed classification and annotation of yet uncharacterized kinases. The prediction and analysis of syntenic blocks and duplication events within gene families of interest can be used to link functional biology to insights from an evolutionary viewpoint. The approach undertaken here can be applied to any gene family in any organism with an annotated genome. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 861 KW - Hide Markov Model KW - Duplication Event KW - Kinase Family KW - Tandem Duplication KW - Segmental Duplication Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-432907 SN - 1866-8372 IS - 861 ER - TY - GEN A1 - Morel, T. A1 - Castro, Norberto A1 - Fossati, Luca A1 - Hubrig, Swetlana A1 - Langer, N. A1 - Przybilla, Norbert A1 - Schöller, Markus A1 - Carroll, Thorsten Anthony A1 - Ilyin, Ilya A1 - Irrgang, Andreas A1 - Oskinova, Lida A1 - Schneider, Fabian R. N. A1 - Simon Díaz, Sergio A1 - Briquet, Maryline A1 - González, Jean-Francois A1 - Kharchenko, Nina A1 - Nieva, M.-F. A1 - Scholz, Ralf-Dieter A1 - de Koter, Alexander A1 - Hamann, Wolf-Rainer A1 - Herrero, Artemio A1 - Maíz Apellániz, Jesus A1 - Sana, Hugues A1 - Arlt, Rainer A1 - Barbá, Rodolfo H. A1 - Dufton, Polly A1 - Kholtygin, Alexander A1 - Mathys, Gautier A1 - Piskunov, Anatoly E. A1 - Reisenegger, Andreas A1 - Spruit, H. A1 - Yoon, S.-C. T1 - The B fields in OB stars (BOB) survey T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The B fields in OB stars (BOB) survey is an ESO large programme collecting spectropolarimetric observations for a large number of early-type stars in order to study the occurrence rate, properties, and ultimately the origin of magnetic fields in massive stars. As of July 2014, a total of 98 objects were observed over 20 nights with FORS2 and HARPSpol. Our preliminary results indicate that the fraction of magnetic OB stars with an organised, detectable field is low. This conclusion, now independently reached by two different surveys, has profound implications for any theoretical model attempting to explain the field formation in these objects. We discuss in this contribution some important issues addressed by our observations (e.g., the lower bound of the field strength) and the discovery of some remarkable objects. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 821 KW - magnetic fields KW - stars: early-type KW - stars: magnetic fields KW - stars: individual (HD 164492C, CPD –57 ◦ 3509, HD 54879, β CMa, ε CMa) Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-415238 SN - 1866-8372 IS - 821 ER - TY - GEN A1 - Kersting, Sebastian A1 - Rausch, Valentina A1 - Bier, Frank Fabian A1 - von Nickisch-Rosenegk, Markus T1 - Multiplex isothermal solid-phase recombinase polymerase amplification for the specific and fast DNA-based detection of three bacterial pathogens T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - We report on the development of an on-chip RPA (recombinase polymerase amplification) with simultaneous multiplex isothermal amplification and detection on a solid surface. The isothermal RPA was applied to amplify specific target sequences from the pathogens Neisseria gonorrhoeae, Salmonella enterica and methicillin-resistant Staphylococcus aureus (MRSA) using genomic DNA. Additionally, a positive plasmid control was established as an internal control. The four targets were amplified simultaneously in a quadruplex reaction. The amplicon is labeled during on-chip RPA by reverse oligonucleotide primers coupled to a fluorophore. Both amplification and spatially resolved signal generation take place on immobilized forward primers bount to expoxy-silanized glass surfaces in a pump-driven hybridization chamber. The combination of microarray technology and sensitive isothermal nucleic acid amplification at 38 °C allows for a multiparameter analysis on a rather small area. The on-chip RPA was characterized in terms of reaction time, sensitivity and inhibitory conditions. A successful enzymatic reaction is completed in <20 min and results in detection limits of 10 colony-forming units for methicillin-resistant Staphylococcus aureus and Salmonella enterica and 100 colony-forming units for Neisseria gonorrhoeae. The results show this method to be useful with respect to point-of-care testing and to enable simplified and miniaturized nucleic acid-based diagnostics. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 730 KW - isothermal amplification KW - RPA KW - microchip KW - DNA sensor KW - point-of-care Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-430479 SN - 1866-8372 IS - 730 SP - 1715 EP - 1723 ER - TY - GEN A1 - Kaiser, Eurika A1 - Noack, Bernd R. A1 - Cordier, Laurent A1 - Spohn, Andreas A1 - Segond, Marc A1 - Abel, Markus A1 - Daviller, Guillaume A1 - Osth, Jan A1 - Krajnovic, Sinisa A1 - Niven, Robert K. T1 - Cluster-based reduced-order modelling of a mixing layer T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - We propose a novel cluster-based reduced-order modelling (CROM) strategy for unsteady flows. CROM combines the cluster analysis pioneered in Gunzburger's group (Burkardt, Gunzburger & Lee, Comput. Meth. Appl. Mech. Engng, vol. 196, 2006a, pp. 337-355) and transition matrix models introduced in fluid dynamics in Eckhardt's group (Schneider, Eckhardt & Vollmer, Phys. Rev. E, vol. 75, 2007, art. 066313). CROM constitutes a potential alternative to POD models and generalises the Ulam-Galerkin method classically used in dynamical systems to determine a finite-rank approximation of the Perron-Frobenius operator. The proposed strategy processes a time-resolved sequence of flow snapshots in two steps. First, the snapshot data are clustered into a small number of representative states, called centroids, in the state space. These centroids partition the state space in complementary non-overlapping regions (centroidal Voronoi cells). Departing from the standard algorithm, the probabilities of the clusters are determined, and the states are sorted by analysis of the transition matrix. Second, the transitions between the states are dynamically modelled using a Markov process. Physical mechanisms are then distilled by a refined analysis of the Markov process, e. g. using finite-time Lyapunov exponent (FTLE) and entropic methods. This CROM framework is applied to the Lorenz attractor (as illustrative example), to velocity fields of the spatially evolving incompressible mixing layer and the three-dimensional turbulent wake of a bluff body. For these examples, CROM is shown to identify non-trivial quasi-attractors and transition processes in an unsupervised manner. CROM has numerous potential applications for the systematic identification of physical mechanisms of complex dynamics, for comparison of flow evolution models, for the identification of precursors to desirable and undesirable events, and for flow control applications exploiting nonlinear actuation dynamics. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 605 KW - low-dimensional models KW - nonlinear dynamical systems KW - shear layers Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-416113 SN - 1866-8372 IS - 605 SP - 365 EP - 414 ER -