TY - GEN A1 - Willner, Arne P. A1 - Massonne, Hans-Joachim A1 - Ring, Uwe A1 - Sudo, Masafumi A1 - Thomson, Stuart N. T1 - P–T evolution and timing of a late Palaeozoic fore-arc system and its heterogeneous Mesozoic overprint in north-central Chile (latitudes 31–32° S) T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - In the late Palaeozoic fore-arc system of north-central Chile at latitudes 31-32 degrees S (from the west to the east) three lithotectonic units are telescoped within a short distance by a Mesozoic strikeslip event (derived peak P-T conditions in brackets): (1) the basally accreted Choapa Metamorphic Complex (CMC; 350-430 degrees C, 6-9 kbar), (2) the frontally accreted Arrayan Formation (AF; 280-320 degrees C, 4-6 kbar) and (3) the retrowedge basin of the Huentelauquen Formation (HF; 280-320 degrees C, 3-4 kbar). In the CMC, Ar-Ar spot ages locally date white-mica formation at peak P-T conditions and during early exhumation at 279-242 Ma. In a local garnet mica-schist intercalation (570-585 degrees C, 11-13 kbar) Ar-Ar spot ages refer to the ascent from the subduction channel at 307-274 Ma. Portions of the CMC were isobarically heated to 510-580 degrees C at 6.6-8.5 kbar. The age of peak P-T conditions in the AF can only vaguely be approximated at >= 310 Ma by relict fission-track ages consistent with the observation that frontal accretion occurred prior to basal accretion. Zircon fission-track dating indicates cooling below similar to 280 degrees C at similar to 248 Ma in the CMC and the AF, when a regional unconformity also formed. Ar-Ar white-mica spot ages in parts of the CMC and within the entire AF and HF point to heterogeneous resetting during Mesozoic extensional and shortening events at similar to 245-240 Ma, similar to 210-200 Ma, similar to 174-159 Ma and similar to 142-127 Ma. The zircon fission-track ages are locally reset at 109-96 Ma. All resetting of Ar-Ar white-mica ages is proposed to have occurred by in situ dissolution/precipitation at low temperature in the presence of locally penetrating hydrous fluids. Hence syn-and postaccretionary events in the fore-arc system can still be distinguished and dated in spite of its complex heterogeneous postaccretional overprint. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 597 KW - Ar-Ar white-mica dating KW - zircon fission-track dating KW - accretionary prism KW - frontal accretion KW - basal accretion KW - thermal overprint KW - age resetting Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-414909 SN - 1866-8372 IS - 597 ER - TY - GEN A1 - Vink, Jorick Sandor A1 - Heger, Alexander A1 - Krumholz, Mark R. A1 - Puls, Joachim A1 - Banerjee, Shiladitya A1 - Castro, Norberto A1 - Chen, K.-J. A1 - Chenè, A.-N. A1 - Crowther, P. A. A1 - Daminelli, A. A1 - Gräfener, G. A1 - Groh, J. H. A1 - Hamann, Wolf-Rainer A1 - Heap, S. A1 - Herrero, A. A1 - Kaper, L. A1 - Najarro, F. A1 - Oskinova, Lida A1 - Roman-Lopes, A. A1 - Rosen, A. A1 - Sander, A. A1 - Shirazi, M. A1 - Sugawara, Y. A1 - Tramper, F. A1 - Vanbeveren, D. A1 - Voss, R. A1 - Wofford, A. A1 - Zhang, Y. T1 - Very massive stars in the local universe T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Recent studies have claimed the existence of very massive stars (VMS) up to 300 M⊙ in the local Universe. As this finding may represent a paradigm shift for the canonical stellar upper-mass limit of 150 M⊙, it is timely to discuss the status of the data, as well as the far-reaching implications of such objects. We held a Joint Discussion at the General Assembly in Beijing to discuss (i) the determination of the current masses of the most massive stars, (ii) the formation of VMS, (iii) their mass loss, and (iv) their evolution and final fate. The prime aim was to reach broad consensus between observers and theorists on how to identify and quantify the dominant physical processes. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 601 KW - stars: massive stars KW - stars: mass-loss KW - stars: stellar evolution Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-415220 SN - 1866-8372 IS - 601 ER - TY - GEN A1 - Su, Yingna A1 - Kliem, Bernhard A1 - van Ballegooijen, Adriaan A1 - Deluca, Edward T1 - Numerical simulations of the CME on 2010 April 8 T2 - Solar and Astrophysical Dynamos and Magnetic Activity N2 - We present 3D zero-beta ideal MHD simulations of the solar flare/CME event that occurred in Active Region 11060 on 2010 April 8. The initial magnetic configurations of the two simulations are stable nonlinear force-free field and unstable magnetic field models constructed by Su et al. (2011) using the flux rope insertion method. The MHD simulations confirm that the stable model relaxes to a stable equilibrium, while the unstable model erupts as a CME. Comparisons between observations and MHD simulations of the CME are also presented. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 674 KW - Sun: coronal mass ejections (CMEs) KW - Sun: flares KW - Sun: magnetic fields Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-414887 SN - 1866-8372 IS - 674 SP - 575 EP - 576 ER - TY - GEN A1 - Saki, Adel A1 - Moazzen, Mohssen A1 - Oberhänsli, Roland T1 - Mineral chemistry and thermobarometry of the staurolite-chloritoid schists from Poshtuk, NW Iran T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - The Poshtuk metapelitic rocks in northwestern Iran underwent two main phases of regional and contact metamorphism. Microstructures, textural features and field relations indicate that these rocks underwent a polymetamorphic history. The dominant metamorphic assemblage of the metapelites is garnet, staurolite, chloritoid, chlorite, muscovite and quartz, which grew mainly syntectonically during the later contact metamorphic event. Peak metamorphic conditions of this event took place at 580 ◦ C and ∼ 3–4 kbar, indicating that this event occurred under high-temperature and low-pressure conditions (HT/LP metamorphism), which reflects the high heat flow in this part of the crust. This event is mainly controlled by advective heat input through magmatic intrusions into all levels of the crust. These extensive Eocene metamorphic and magmatic activities can be associated with the early Alpine Orogeny, which resulted in this area from the convergence between the Arabian and Eurasian plates, and the Cenozoic closure of the Tethys oceanic tract(s). T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 578 KW - thermobarometry KW - HT/LP metamorphism KW - Poshtuk metapelites KW - northwestern Iran Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-413942 SN - 1866-8372 IS - 578 SP - 1077 EP - 1088 ER - TY - GEN A1 - Powell, Anahid E. A1 - Lenhard, Michael T1 - Control of organ size in plants T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - The size of plant organs, such as leaves and flowers, is determined by an interaction of genotype and environmental influences. Organ growth occurs through the two successive processes of cell proliferation followed by cell expansion. A number of genes influencing either or both of these processes and thus contributing to the control of final organ size have been identified in the last decade. Although the overall picture of the genetic regulation of organ size remains fragmentary, two transcription factor/microRNA-based genetic pathways are emerging in the control of cell proliferation. However, despite this progress, fundamental questions remain unanswered, such as the problem of how the size of a growing organ could be monitored to determine the appropriate time for terminating growth. While genetic analysis will undoubtedly continue to advance our knowledge about size control in plants, a deeper understanding of this and other basic questions will require including advanced live-imaging and mathematical modeling, as impressively demonstrated by some recent examples. This should ultimately allow the comparison of the mechanisms underlying size control in plants and in animals to extract common principles and lineage-specific solutions. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 898 KW - BHLH transcription factor KW - genome-wide association KW - arabidopsis-thaliana KW - cell-proliferation KW - leaf development KW - developing leaves KW - petal growth KW - gene family KW - tor kinase KW - auxin Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-438029 SN - 1866-8372 IS - 898 ER - TY - GEN A1 - Ostrowski, Max A1 - Schaub, Torsten H. T1 - ASP modulo CSP BT - the clingcon system T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We present the hybrid ASP solver clingcon, combining the simple modeling language and the high performance Boolean solving capacities of Answer Set Programming (ASP) with techniques for using non-Boolean constraints from the area of Constraint Programming (CP). The new clingcon system features an extended syntax supporting global constraints and optimize statements for constraint variables. The major technical innovation improves the interaction between ASP and CP solver through elaborated learning techniques based on irreducible inconsistent sets. A broad empirical evaluation shows that these techniques yield a performance improvement of an order of magnitude. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 579 KW - answer set KW - constraints KW - logic KW - SMT Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-413908 SN - 1866-8372 IS - 579 ER - TY - GEN A1 - Oskinova, Lida A1 - Guerrero, Martín A. A1 - Hénault-Brunet, Vincent A1 - Sun, W. A1 - Chu, You-Hua A1 - Evans, Chris A1 - Gallagher, John S. A1 - Gruendl, Robert A. A1 - Reyes-Iturbide, Jorge T1 - The slow X-ray pulsar SXP 1062 and associated supernova remnant in the Wing of the Small Magellanic Cloud T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - SXP 1062 is an exceptional case of a young neutron star in a wind-fed high-mass X-ray binary associated with a supernova remnant. A unique combination of measured spin period, its derivative, luminosity and young age makes this source a key probe for the physics of accretion and neutron star evolution. Theoretical models proposed to explain the properties of SXP 1062 shall be tested with new data. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 591 KW - stars: emission-line KW - Be KW - X-rays: binaries KW - pulsars: individual (SXP 1062) Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-415135 SN - 1866-8372 IS - 591 ER - TY - GEN A1 - Oskinova, Lida A1 - Feldmeier, Achim A1 - Kretschmar, Peter T1 - Clumped stellar winds in supergiant high-mass X-ray binaries T2 - Postprint der universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - The clumping of massive star winds is an established paradigm, which is confirmed by multiple lines of evidence and is supported by stellar wind theory. We use the results from time-dependent hydrodynamical models of the instability in the line-driven wind of a massive supergiant star to derive the time-dependent accretion rate on to a compact object in the Bondi-Hoyle-Lyttleton approximation. The strong density and velocity fluctuations in the wind result in strong variability of the synthetic X-ray light curves. Photoionization of inhomogeneous winds is different from the photoinization of smooth winds. The degree of ionization is affected by the wind clumping. The wind clumping must also be taken into account when comparing the observed and model spectra of the photoionized stellar wind. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 573 KW - accretion KW - instabilities KW - stars: mass loss KW - X-rays: binaries Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-413916 SN - 1866-8372 IS - 573 SP - 287 EP - 288 ER - TY - GEN A1 - Nishikawa, K.-I. A1 - Zhang, B. A1 - Choi, E. J. A1 - Min, K. W. A1 - Niemiec, J. A1 - Medvedev, M. A1 - Hardee, P. A1 - Mizuno, Y. A1 - Nordlund, A. A1 - Frederiksen, J. A1 - Sol, H. A1 - Pohl, Martin A1 - Hartmann, D. H. A1 - Fishman, G.J. T1 - Radiation from accelerated particles in shocks T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Recent PIC simulations of relativistic electron-positron (electron-ion) jets injected into a stationary medium show that particle acceleration occurs in the shocked regions. Simulations show that the Weibel instability is responsible for generating and amplifying highly nonuniform, small-scale magnetic fields and for particle acceleration. These magnetic fields contribute to the electron’s transverse eflection behind the shock. The “jitter” radiation from deflected electrons in turbulent magnetic fields has properties different from synchrotron radiation calculated in a uniform magnetic field. This jitter radiation may be important for understanding the complex time evolution and/or spectral structure of gamma-ray bursts, relativistic jets in general, and supernova remnants. In order to calculate radiation from first principles and go beyond the standard synchrotron model, we have used PIC simulations. We present synthetic spectra to compare with the spectra obtained from Fermi observations. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 600 KW - relativistic jets KW - Weibel instability KW - magnetic field generation KW - particle acceleration KW - radiation Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-413128 SN - 1866-8372 IS - 600 SP - 371 EP - 372 ER - TY - GEN A1 - Morris, Penelope J. A1 - Salt, Carina A1 - Raila, Jens A1 - Brenten, Thomas A1 - Kohn, Barbara A1 - Schweigert, Florian J. A1 - Zentek, Jürgen T1 - Safety evaluation of vitamin A in growing dogs T2 - Potsprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The safe upper limit for inclusion of vitamin A in complete diets for growing dogs is uncertain, with the result that current recommendations range from 5.24 to 104.80 mu mol retinol (5000 to 100 000 IU vitamin A)/4184 kJ (1000 kcal) metabolisable energy (ME). The aim of the present study was to determine the effect of feeding four concentrations of vitamin A to puppies from weaning until 1 year of age. A total of forty-nine puppies, of two breeds, Labrador Retriever and Miniature Schnauzer, were randomly assigned to one of four treatment groups. Following weaning at 8 weeks of age, puppies were fed a complete food supplemented with retinyl acetate diluted in vegetable oil and fed at 1ml oil/100 g diet to achieve an intake of 5.24, 13.10, 78.60 and 104.80 mu mol retinol (5000, 12 500, 75 000 and 100 000 IU vitamin A)/4184 kJ (1000 kcal) ME. Fasted blood and urine samples were collected at 8, 10, 12, 14, 16, 20, 26, 36 and 52 weeks of age and analysed for markers of vitamin A metabolism and markers of safety including haematological and biochemical variables, bone-specific alkaline phosphatase, cross-linked carboxyterminal telopeptides of type I collagen and dual-energy X-ray absorptiometry. Clinical examinations were conducted every 4 weeks. Data were analysed by means of a mixed model analysis with Bonferroni corrections for multiple endpoints. There was no effect of vitamin A concentration on any of the parameters, with the exception of total serum retinyl esters, and no effect of dose on the number, type and duration of adverse events. We therefore propose that 104.80 mu mol retinol (100 000 IU vitamin A)/4184 kJ (1000 kcal) is a suitable safe upper limit for use in the formulation of diets designed for puppy growth. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 686 KW - puppies KW - dogs KW - Retinol KW - Retinyl esters KW - vitamin A Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-414929 IS - 686 ER - TY - GEN A1 - Martins, Fabrice A1 - Bergemann, Maria A1 - Bestenlehner, Joachim M. A1 - Crowther, Paul A. A1 - Hamann, Wolf-Rainer A1 - Najarro, Francisco A1 - Nieva, Maria Fernanda A1 - Przybilla, Norbert A1 - Freimanis, Juris A1 - Hou, Weizhen A1 - Kaper, Lex T1 - SpS5 - II. Stellar and wind parameters T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The development of infrared observational facilities has revealed a number of massive stars in obscured environments throughout the Milky Way and beyond. The determination of their stellar and wind properties from infrared diagnostics is thus required to take full advantage of the wealth of observations available in the near and mid infrared. However, the task is challenging. This session addressed some of the problems encountered and showed the limitations and successes of infrared studies of massive stars. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 688 KW - infrared: stars KW - stars: early-type KW - stars: late-type KW - stars: fundamental parameters KW - stars: mass loss KW - stars: abundances Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-414956 SN - 1866-8372 IS - 688 ER - TY - GEN A1 - Lenhard, Michael T1 - All's well that ends well BT - arresting cell proliferation in leaves T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - The transition from cell proliferation to cell expansion is critical for determining leaf size. Andriankaja et al. (2012) demonstrate that in leaves of dicotyledonous plants, a basal proliferation zone is maintained for several days before abruptly disappearing, and that chloroplast differentiation is required to trigger the onset of cell expansion. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 906 KW - arabidopsis-thaliana KW - genetic-control KW - growth KW - size KW - curvature Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-438035 SN - 1866-8372 IS - 906 SP - 9 EP - 11 ER - 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 - Krügel, André A1 - Vitu, Françoise A1 - Engbert, Ralf T1 - Fixation positions after skipping saccades BT - a single space makes a large difference T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - During reading, saccadic eye movements are generated to shift words into the center of the visual field for lexical processing. Recently, Krugel and Engbert (Vision Research 50:1532-1539, 2010) demonstrated that within-word fixation positions are largely shifted to the left after skipped words. However, explanations of the origin of this effect cannot be drawn from normal reading data alone. Here we show that the large effect of skipped words on the distribution of within-word fixation positions is primarily based on rather subtle differences in the low-level visual information acquired before saccades. Using arrangements of "x" letter strings, we reproduced the effect of skipped character strings in a highly controlled single-saccade task. Our results demonstrate that the effect of skipped words in reading is the signature of a general visuomotor phenomenon. Moreover, our findings extend beyond the scope of the widely accepted range-error model, which posits that within-word fixation positions in reading depend solely on the distances of target words. We expect that our results will provide critical boundary conditions for the development of visuomotor models of saccade planning during reading. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 856 KW - eye movements KW - reading KW - motor control KW - skipping Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-432887 SN - 1866-8372 IS - 856 SP - 1556 EP - 1561 ER - TY - GEN A1 - Krippendorff, Ben-Fillippo A1 - Oyarzún, Diego A. A1 - Huisinga, Wilhelm T1 - Predicting the F(ab)-mediated effect of monoclonal antibodies in vivo by combining cell-level kinetic and pharmacokinetic modelling T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Cell-level kinetic models for therapeutically relevant processes increasingly benefit the early stages of drug development. Later stages of the drug development processes, however, rely on pharmacokinetic compartment models while cell-level dynamics are typically neglected. We here present a systematic approach to integrate cell-level kinetic models and pharmacokinetic compartment models. Incorporating target dynamics into pharmacokinetic models is especially useful for the development of therapeutic antibodies because their effect and pharmacokinetics are inherently interdependent. The approach is illustrated by analysing the F(ab)-mediated inhibitory effect of therapeutic antibodies targeting the epidermal growth factor receptor. We build a multi-level model for anti-EGFR antibodies by combining a systems biology model with in vitro determined parameters and a pharmacokinetic model based on in vivo pharmacokinetic data. Using this model, we investigated in silico the impact of biochemical properties of anti-EGFR antibodies on their F(ab)-mediated inhibitory effect. The multi-level model suggests that the F(ab)-mediated inhibitory effect saturates with increasing drug-receptor affinity, thereby limiting the impact of increasing antibody affinity on improving the effect. This indicates that observed differences in the therapeutic effects of high affinity antibodies in the market and in clinical development may result mainly from Fc-mediated indirect mechanisms such as antibody-dependent cell cytotoxicity. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 958 KW - cell-level kinetics KW - pharmacokinetic models KW - therapeutic proteins KW - EGFR Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431051 SN - 1866-8372 IS - 958 SP - 125 EP - 139 ER - TY - GEN A1 - Kleessen, Sabrina A1 - Nikoloski, Zoran T1 - Dynamic regulatory on/off minimization for biological systems under internal temporal perturbations T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Background: Flux balance analysis (FBA) together with its extension, dynamic FBA, have proven instrumental for analyzing the robustness and dynamics of metabolic networks by employing only the stoichiometry of the included reactions coupled with adequately chosen objective function. In addition, under the assumption of minimization of metabolic adjustment, dynamic FBA has recently been employed to analyze the transition between metabolic states. Results: Here, we propose a suite of novel methods for analyzing the dynamics of (internally perturbed) metabolic networks and for quantifying their robustness with limited knowledge of kinetic parameters. Following the biochemically meaningful premise that metabolite concentrations exhibit smooth temporal changes, the proposed methods rely on minimizing the significant fluctuations of metabolic profiles to predict the time-resolved metabolic state, characterized by both fluxes and concentrations. By conducting a comparative analysis with a kinetic model of the Calvin-Benson cycle and a model of plant carbohydrate metabolism, we demonstrate that the principle of regulatory on/off minimization coupled with dynamic FBA can accurately predict the changes in metabolic states. Conclusions: Our methods outperform the existing dynamic FBA-based modeling alternatives, and could help in revealing the mechanisms for maintaining robustness of dynamic processes in metabolic networks over time. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 852 KW - metabolic network KW - metabolite concentration KW - flux rate KW - flux balance analysis KW - qualitative comparative analysis Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431128 SN - 1866-8372 IS - 852 ER - TY - GEN A1 - Jing, Runchun A1 - Ambrose, Michael A. A1 - Knox, Maggie R. A1 - Smykal, Petr A1 - Hybl, Miroslav A1 - Ramos, Á. A1 - Caminero, Constantino A1 - Burstin, Judith A1 - Duc, Gerard A1 - van Soest, L. J. M. A1 - Święcicki, W. K. A1 - Pereira, M. Graca A1 - Vishnyakova, Margarita A1 - Davenport, Guy F. A1 - Flavell, Andrew J. A1 - Ellis, T. H. Noel T1 - Genetic diversity in European Pisum germplasm collections T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - The distinctness of, and overlap between, pea genotypes held in several Pisum germplasm collections has been used to determine their relatedness and to test previous ideas about the genetic diversity of Pisum. Our characterisation of genetic diversity among 4,538 Pisum accessions held in 7 European Genebanks has identified sources of novel genetic variation, and both reinforces and refines previous interpretations of the overall structure of genetic diversity in Pisum. Molecular marker analysis was based upon the presence/absence of polymorphism of retrotransposon insertions scored by a high-throughput microarray and SSAP approaches. We conclude that the diversity of Pisum constitutes a broad continuum, with graded differentiation into sub-populations which display various degrees of distinctness. The most distinct genetic groups correspond to the named taxa while the cultivars and landraces of Pisum sativum can be divided into two broad types, one of which is strongly enriched for modern cultivars. The addition of germplasm sets from six European Genebanks, chosen to represent high diversity, to a single collection previously studied with these markers resulted in modest additions to the overall diversity observed, suggesting that the great majority of the total genetic diversity collected for the Pisum genus has now been described. Two interesting sources of novel genetic variation have been identified. Finally, we have proposed reference sets of core accessions with a range of sample sizes to represent Pisum diversity for the future study and exploitation by researchers and breeders. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 871 KW - germplasm collection KW - insertion polymorphism KW - retrotransposon insertion KW - broad continuum KW - SSAP marker Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-434743 SN - 1866-8372 IS - 871 SP - 367 EP - 380 ER - TY - GEN A1 - Hoppe, Sebastian A1 - Bier, Frank Fabian A1 - von Nickisch-Rosenegk, Markus T1 - Microarray-based method for screening of immunogenic proteins from bacteria T2 - Postprints der Universität Potsdam Mathematisch-Naturwissenschaftliche Reihe N2 - Background: Detection of immunogenic proteins remains an important task for life sciences as it nourishes the understanding of pathogenicity, illuminates new potential vaccine candidates and broadens the spectrum of biomarkers applicable in diagnostic tools. Traditionally, immunoscreenings of expression libraries via polyclonal sera on nitrocellulose membranes or screenings of whole proteome lysates in 2-D gel electrophoresis are performed. However, these methods feature some rather inconvenient disadvantages. Screening of expression libraries to expose novel antigens from bacteria often lead to an abundance of false positive signals owing to the high cross reactivity of polyclonal antibodies towards the proteins of the expression host. A method is presented that overcomes many disadvantages of the old procedures. Results: Four proteins that have previously been described as immunogenic have successfully been assessed immunogenic abilities with our method. One protein with no known immunogenic behaviour before suggested potential immunogenicity. We incorporated a fusion tag prior to our genes of interest and attached the expressed fusion proteins covalently on microarrays. This enhances the specific binding of the proteins compared to nitrocellulose. Thus, it helps to reduce the number of false positives significantly. It enables us to screen for immunogenic proteins in a shorter time, with more samples and statistical reliability. We validated our method by employing several known genes from Campylobacter jejuni NCTC 11168. Conclusions: The method presented offers a new approach for screening of bacterial expression libraries to illuminate novel proteins with immunogenic features. It could provide a powerful and attractive alternative to existing methods and help to detect and identify vaccine candidates, biomarkers and potential virulence-associated factors with immunogenic behaviour furthering the knowledge of virulence and pathogenicity of studied bacteria. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 726 KW - expression library KW - immunogenic protein KW - false positive signal KW - polyclonal seron KW - standard western blot Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-429815 SN - 1866-8372 IS - 726 ER - TY - GEN A1 - Hische, Manuela A1 - Larhlimi, Abdelhalim A1 - Schwarz, Franziska A1 - Fischer-Rosinský, Antje A1 - Bobbert, Thomas A1 - Assmann, Anke A1 - Catchpole, Gareth S. A1 - Pfeiffer, Andreas F. H. A1 - Willmitzer, Lothar A1 - Selbig, Joachim A1 - Spranger, Joachim T1 - A distinct metabolic signature predictsdevelopment of fasting plasma glucose T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Background High blood glucose and diabetes are amongst the conditions causing the greatest losses in years of healthy life worldwide. Therefore, numerous studies aim to identify reliable risk markers for development of impaired glucose metabolism and type 2 diabetes. However, the molecular basis of impaired glucose metabolism is so far insufficiently understood. The development of so called 'omics' approaches in the recent years promises to identify molecular markers and to further understand the molecular basis of impaired glucose metabolism and type 2 diabetes. Although univariate statistical approaches are often applied, we demonstrate here that the application of multivariate statistical approaches is highly recommended to fully capture the complexity of data gained using high-throughput methods. Methods We took blood plasma samples from 172 subjects who participated in the prospective Metabolic Syndrome Berlin Potsdam follow-up study (MESY-BEPO Follow-up). We analysed these samples using Gas Chromatography coupled with Mass Spectrometry (GC-MS), and measured 286 metabolites. Furthermore, fasting glucose levels were measured using standard methods at baseline, and after an average of six years. We did correlation analysis and built linear regression models as well as Random Forest regression models to identify metabolites that predict the development of fasting glucose in our cohort. Results We found a metabolic pattern consisting of nine metabolites that predicted fasting glucose development with an accuracy of 0.47 in tenfold cross-validation using Random Forest regression. We also showed that adding established risk markers did not improve the model accuracy. However, external validation is eventually desirable. Although not all metabolites belonging to the final pattern are identified yet, the pattern directs attention to amino acid metabolism, energy metabolism and redox homeostasis. Conclusions We demonstrate that metabolites identified using a high-throughput method (GC-MS) perform well in predicting the development of fasting plasma glucose over several years. Notably, not single, but a complex pattern of metabolites propels the prediction and therefore reflects the complexity of the underlying molecular mechanisms. This result could only be captured by application of multivariate statistical approaches. Therefore, we highly recommend the usage of statistical methods that seize the complexity of the information given by high-throughput methods. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 850 KW - prediction KW - fasting glucose KW - type 2 diabetes KW - metabolomics KW - plasma KW - random forest KW - metabolite KW - regression KW - biomarker Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-427400 SN - 1866-8372 IS - 850 ER - TY - GEN A1 - Gröbel, Thomas A1 - Stange, Irina T1 - Die Geschichte des Standortes Potsdam-Golm 1935-1991 N2 - Die Ausstellung "Die Geschichte des Standortes Potsdam-Golm 1935 bis 1991" zeigt die wechselvolle Historie des jetzigen Universitäts- und Wissenschaftsstandortes. Die Ursprünge finden sich in der 1935 errichteten General-Wever-Kaserne. Nach der Beendigung des Zweiten Weltkrieges und bis zur Wende nutzten sowohl die sowjetische Armee als auch das Ministerium für Staatssicherheit das Gelände. Thematisiert werden unter anderem die militärische Zentralregion Brandenburg, die Herausbildung der Geheimdiensthochschule von 1951 bis 1990, die Lehre an dieser Einrichtung, das Studienleben und die Forschungstätigkeit sowie die Nutzung des Standortes nach 1990. Die Ausstellung besteht aus 13 mit zahlreichen Fotos versehenen Tafeln. Y1 - 2012 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-72648 ER - TY - GEN A1 - Gebser, Martin A1 - Kaufmann, Benjamin A1 - Schaub, Torsten H. T1 - Multi-threaded ASP solving with clasp T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We present the new multi-threaded version of the state-of-the-art answer set solver clasp. We detail its component and communication architecture and illustrate how they support the principal functionalities of clasp. Also, we provide some insights into the data representation used for different constraint types handled by clasp. All this is accompanied by an extensive experimental analysis of the major features related to multi-threading in clasp. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 586 KW - propositional satisfiability KW - clause elimination KW - parallel execution KW - SAT KW - algorithm KW - platypus KW - systems KW - search KW - solver Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-413977 SN - 1866-8372 IS - 586 ER - TY - GEN A1 - Diercke, Andrea A1 - Arlt, Rainer A1 - Denker, Carsten T1 - Digitization of Spörer’s sunspot drawings T2 - Postprints der Universität Potsdam : Mathematisch Naturwissenschaftliche Reihe N2 - Much of our knowledge about the solar dynamo is based on sunspot observations. It is thus desirable to extend the set of positional and morphological data of sunspots into the past. Gustav Spörer observed in Germany from Anklam (1861–1873) and Potsdam (1874–1894). He left detailed prints of sunspot groups, which we digitized and processed to mitigate artifacts left in the print by the passage of time. After careful geometrical correction, the sunspot data are now available as synoptic charts for almost 450 solar rotation periods. Individual sunspot positions can thus be precisely determined and spot areas can be accurately measured using morphological image processing techniques. These methods also allow us to determine tilt angles of active regions (Joy’s law) and to assess the complexity of an active region. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 577 KW - sun: sunspots KW - sun: photosphere KW - sun: activity KW - techniques: image processing KW - astronomical databases: miscellaneous KW - history and philosophy of astronomy Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-413922 SN - 1866-8372 IS - 577 SP - 63 EP - 64 ER - TY - GEN A1 - Dallmeyer, Anne A1 - Claussen, Martin A1 - Wang, Yongbo A1 - Herzschuh, Ulrike T1 - Spatial variability of Holocene changes in the annual precipitation pattern BT - a model-data synthesis for the Asian monsoon region T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - This study provides a detailed analysis of the mid-Holocene to present-day precipitation change in the Asian monsoon region. We compare for the first time results of high resolution climate model simulations with a standardised set of mid-Holocene moisture reconstructions. Changes in the simulated summer monsoon characteristics (onset, withdrawal, length and associated rainfall) and the mechanisms causing the Holocene precipitation changes are investigated. According to the model, most parts of the Indian subcontinent received more precipitation (up to 5 mm/day) at mid-Holocene than at present-day. This is related to a stronger Indian summer monsoon accompanied by an intensified vertically integrated moisture flux convergence. The East Asian monsoon region exhibits local inhomogeneities in the simulated annual precipitation signal. The sign of this signal depends on the balance of decreased pre-monsoon and increased monsoon precipitation at mid-Holocene compared to present-day. Hence, rainfall changes in the East Asian monsoon domain are not solely associated with modifications in the summer monsoon circulation but also depend on changes in the mid-latitudinal westerly wind system that dominates the circulation during the pre-monsoon season. The proxy-based climate reconstructions confirm the regional dissimilarities in the annual precipitation signal and agree well with the model results. Our results highlight the importance of including the pre-monsoon season in climate studies of the Asian monsoon system and point out the complex response of this system to the Holocene insolation forcing. The comparison with a coarse climate model simulation reveals that this complex response can only be resolved in high resolution simulations. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 905 KW - Asian monsoon KW - holocene KW - precipitation KW - climate modelling KW - moisture reconstructions Y1 - 2020 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-432771 SN - 1866-8372 IS - 905 ER -