TY - THES A1 - Gebser, Martin T1 - Proof theory and algorithms for answer set programming T1 - Beweistheorie und Algorithmen für die Antwortmengenprogrammierung N2 - Answer Set Programming (ASP) is an emerging paradigm for declarative programming, in which a computational problem is specified by a logic program such that particular models, called answer sets, match solutions. ASP faces a growing range of applications, demanding for high-performance tools able to solve complex problems. ASP integrates ideas from a variety of neighboring fields. In particular, automated techniques to search for answer sets are inspired by Boolean Satisfiability (SAT) solving approaches. While the latter have firm proof-theoretic foundations, ASP lacks formal frameworks for characterizing and comparing solving methods. Furthermore, sophisticated search patterns of modern SAT solvers, successfully applied in areas like, e.g., model checking and verification, are not yet established in ASP solving. We address these deficiencies by, for one, providing proof-theoretic frameworks that allow for characterizing, comparing, and analyzing approaches to answer set computation. For another, we devise modern ASP solving algorithms that integrate and extend state-of-the-art techniques for Boolean constraint solving. We thus contribute to the understanding of existing ASP solving approaches and their interconnections as well as to their enhancement by incorporating sophisticated search patterns. The central idea of our approach is to identify atomic as well as composite constituents of a propositional logic program with Boolean variables. This enables us to describe fundamental inference steps, and to selectively combine them in proof-theoretic characterizations of various ASP solving methods. In particular, we show that different concepts of case analyses applied by existing ASP solvers implicate mutual exponential separations regarding their best-case complexities. We also develop a generic proof-theoretic framework amenable to language extensions, and we point out that exponential separations can likewise be obtained due to case analyses on them. We further exploit fundamental inference steps to derive Boolean constraints characterizing answer sets. They enable the conception of ASP solving algorithms including search patterns of modern SAT solvers, while also allowing for direct technology transfers between the areas of ASP and SAT solving. Beyond the search for one answer set of a logic program, we address the enumeration of answer sets and their projections to a subvocabulary, respectively. The algorithms we develop enable repetition-free enumeration in polynomial space without being intrusive, i.e., they do not necessitate any modifications of computations before an answer set is found. Our approach to ASP solving is implemented in clasp, a state-of-the-art Boolean constraint solver that has successfully participated in recent solver competitions. Although we do here not address the implementation techniques of clasp or all of its features, we present the principles of its success in the context of ASP solving. N2 - Antwortmengenprogrammierung (engl. Answer Set Programming; ASP) ist ein Paradigma zum deklarativen Problemlösen, wobei Problemstellungen durch logische Programme beschrieben werden, sodass bestimmte Modelle, Antwortmengen genannt, zu Lösungen korrespondieren. Die zunehmenden praktischen Anwendungen von ASP verlangen nach performanten Werkzeugen zum Lösen komplexer Problemstellungen. ASP integriert diverse Konzepte aus verwandten Bereichen. Insbesondere sind automatisierte Techniken für die Suche nach Antwortmengen durch Verfahren zum Lösen des aussagenlogischen Erfüllbarkeitsproblems (engl. Boolean Satisfiability; SAT) inspiriert. Letztere beruhen auf soliden beweistheoretischen Grundlagen, wohingegen es für ASP kaum formale Systeme gibt, um Lösungsmethoden einheitlich zu beschreiben und miteinander zu vergleichen. Weiterhin basiert der Erfolg moderner Verfahren zum Lösen von SAT entscheidend auf fortgeschrittenen Suchtechniken, die in gängigen Methoden zur Antwortmengenberechnung nicht etabliert sind. Diese Arbeit entwickelt beweistheoretische Grundlagen und fortgeschrittene Suchtechniken im Kontext der Antwortmengenberechnung. Unsere formalen Beweissysteme ermöglichen die Charakterisierung, den Vergleich und die Analyse vorhandener Lösungsmethoden für ASP. Außerdem entwerfen wir moderne Verfahren zum Lösen von ASP, die fortgeschrittene Suchtechniken aus dem SAT-Bereich integrieren und erweitern. Damit trägt diese Arbeit sowohl zum tieferen Verständnis von Lösungsmethoden für ASP und ihrer Beziehungen untereinander als auch zu ihrer Verbesserung durch die Erschließung fortgeschrittener Suchtechniken bei. Die zentrale Idee unseres Ansatzes besteht darin, Atome und komposite Konstrukte innerhalb von logischen Programmen gleichermaßen mit aussagenlogischen Variablen zu assoziieren. Dies ermöglicht die Isolierung fundamentaler Inferenzschritte, die wir in formalen Charakterisierungen von Lösungsmethoden für ASP selektiv miteinander kombinieren können. Darauf aufbauend zeigen wir, dass unterschiedliche Einschränkungen von Fallunterscheidungen zwangsläufig zu exponentiellen Effizienzunterschieden zwischen den charakterisierten Methoden führen. Wir generalisieren unseren beweistheoretischen Ansatz auf logische Programme mit erweiterten Sprachkonstrukten und weisen analytisch nach, dass das Treffen bzw. Unterlassen von Fallunterscheidungen auf solchen Konstrukten ebenfalls exponentielle Effizienzunterschiede bedingen kann. Die zuvor beschriebenen fundamentalen Inferenzschritte nutzen wir zur Extraktion inhärenter Bedingungen, denen Antwortmengen genügen müssen. Damit schaffen wir eine Grundlage für den Entwurf moderner Lösungsmethoden für ASP, die fortgeschrittene, ursprünglich für SAT konzipierte, Suchtechniken mit einschließen und darüber hinaus einen transparenten Technologietransfer zwischen Verfahren zum Lösen von ASP und SAT erlauben. Neben der Suche nach einer Antwortmenge behandeln wir ihre Aufzählung, sowohl für gesamte Antwortmengen als auch für Projektionen auf ein Subvokabular. Hierfür entwickeln wir neuartige Methoden, die wiederholungsfreies Aufzählen in polynomiellem Platz ermöglichen, ohne die Suche zu beeinflussen und ggf. zu behindern, bevor Antwortmengen berechnet wurden. KW - Wissensrepräsentation und -verarbeitung KW - Antwortmengenprogrammierung KW - Beweistheorie KW - Algorithmen KW - Knowledge Representation and Reasoning KW - Answer Set Programming KW - Proof Theory KW - Algorithms Y1 - 2011 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus-55425 ER - TY - JOUR A1 - Durzinsky, Markus A1 - Marwan, Wolfgang A1 - Ostrowski, Max A1 - Schaub, Torsten A1 - Wagler, Annegret T1 - Automatic network reconstruction using ASP JF - Theory and practice of logic programming N2 - Building biological models by inferring functional dependencies from experimental data is an important issue in Molecular Biology. To relieve the biologist from this traditionally manual process, various approaches have been proposed to increase the degree of automation. However, available approaches often yield a single model only, rely on specific assumptions, and/or use dedicated, heuristic algorithms that are intolerant to changing circumstances or requirements in the view of the rapid progress made in Biotechnology. Our aim is to provide a declarative solution to the problem by appeal to Answer Set Programming (ASP) overcoming these difficulties. We build upon an existing approach to Automatic Network Reconstruction proposed by part of the authors. This approach has firm mathematical foundations and is well suited for ASP due to its combinatorial flavor providing a characterization of all models explaining a set of experiments. The usage of ASP has several benefits over the existing heuristic algorithms. First, it is declarative and thus transparent for biological experts. Second, it is elaboration tolerant and thus allows for an easy exploration and incorporation of biological constraints. Third, it allows for exploring the entire space of possible models. Finally, our approach offers an excellent performance, matching existing, special-purpose systems. Y1 - 2011 U6 - https://doi.org/10.1017/S1471068411000287 SN - 1471-0684 VL - 11 SP - 749 EP - 766 PB - Cambridge Univ. Press CY - New York ER - TY - GEN A1 - Gebser, Martin A1 - Schaub, Torsten A1 - Thiele, Sven A1 - Veber, Philippe T1 - Detecting inconsistencies in large biological networks with answer set programming T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We introduce an approach to detecting inconsistencies in large biological networks by using answer set programming. To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and high-throughput profiles of cell activity. We then present an approach based on answer set programming to check the consistency of large-scale data sets. Moreover, we extend this methodology to provide explanations for inconsistencies by determining minimal representations of conflicts. In practice, this can be used to identify unreliable data or to indicate missing reactions. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 561 KW - answer set programming KW - bioinformatics KW - consistency KW - diagnosis Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412467 SN - 1866-8372 IS - 561 ER - TY - JOUR A1 - Mileo, Alessandra A1 - Schaub, Torsten A1 - Merico, Davide A1 - Bisiani, Roberto T1 - Knowledge-based multi-criteria optimization to support indoor positioning JF - Annals of mathematics and artificial intelligence N2 - Indoor position estimation constitutes a central task in home-based assisted living environments. Such environments often rely on a heterogeneous collection of low-cost sensors whose diversity and lack of precision has to be compensated by advanced techniques for localization and tracking. Although there are well established quantitative methods in robotics and neighboring fields for addressing these problems, they lack advanced knowledge representation and reasoning capacities. Such capabilities are not only useful in dealing with heterogeneous and incomplete information but moreover they allow for a better inclusion of semantic information and more general homecare and patient-related knowledge. We address this problem and investigate how state-of-the-art localization and tracking methods can be combined with Answer Set Programming, as a popular knowledge representation and reasoning formalism. We report upon a case-study and provide a first experimental evaluation of knowledge-based position estimation both in a simulated as well as in a real setting. KW - Knowledge representation KW - Answer Set Programming KW - Wireless Sensor Networks KW - Localization KW - Tracking Y1 - 2011 U6 - https://doi.org/10.1007/s10472-011-9241-2 SN - 1012-2443 SN - 1573-7470 VL - 62 IS - 3-4 SP - 345 EP - 370 PB - Springer CY - Dordrecht ER - TY - GEN A1 - Gebser, Martin A1 - Kaminski, Roland A1 - Schaub, Torsten T1 - Complex optimization in answer set programming T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Preference handling and optimization are indispensable means for addressing nontrivial applications in Answer Set Programming (ASP). However, their implementation becomes difficult whenever they bring about a significant increase in computational complexity. As a consequence, existing ASP systems do not offer complex optimization capacities, supporting, for instance, inclusion-based minimization or Pareto efficiency. Rather, such complex criteria are typically addressed by resorting to dedicated modeling techniques, like saturation. Unlike the ease of common ASP modeling, however, these techniques are rather involved and hardly usable by ASP laymen. We address this problem by developing a general implementation technique by means of meta-prpogramming, thus reusing existing ASP systems to capture various forms of qualitative preferences among answer sets. In this way, complex preferences and optimization capacities become readily available for ASP applications. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 554 KW - answer set programming KW - preference handling KW - complex optimization KW - meta-programming Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412436 SN - 1866-8372 IS - 554 ER - TY - GEN A1 - Durzinsky, Markus A1 - Marwan, Wolfgang A1 - Ostrowski, Max A1 - Schaub, Torsten A1 - Wagler, Annegret T1 - Automatic network reconstruction using ASP T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - Building biological models by inferring functional dependencies from experimental data is an important issue in Molecular Biology. To relieve the biologist from this traditionally manual process, various approaches have been proposed to increase the degree of automation. However, available approaches often yield a single model only, rely on specific assumptions, and/or use dedicated, heuristic algorithms that are intolerant to changing circumstances or requirements in the view of the rapid progress made in Biotechnology. Our aim is to provide a declarative solution to the problem by appeal to Answer Set Programming (ASP) overcoming these difficulties. We build upon an existing approach to Automatic Network Reconstruction proposed by part of the authors. This approach has firm mathematical foundations and is well suited for ASP due to its combinatorial flavor providing a characterization of all models explaining a set of experiments. The usage of ASP has several benefits over the existing heuristic algorithms. First, it is declarative and thus transparent for biological experts. Second, it is elaboration tolerant and thus allows for an easy exploration and incorporation of biological constraints. Third, it allows for exploring the entire space of possible models. Finally, our approach offers an excellent performance, matching existing, special-purpose systems. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 560 KW - regulatory networks KW - biological networks KW - answer Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412419 SN - 1866-8372 IS - 560 ER - TY - JOUR A1 - Gebser, Martin A1 - Schaub, Torsten A1 - Thiele, Sven A1 - Veber, Philippe T1 - Detecting inconsistencies in large biological networks with answer set programming JF - Theory and practice of logic programming N2 - We introduce an approach to detecting inconsistencies in large biological networks by using answer set programming. To this end, we build upon a recently proposed notion of consistency between biochemical/genetic reactions and high-throughput profiles of cell activity. We then present an approach based on answer set programming to check the consistency of large-scale data sets. Moreover, we extend this methodology to provide explanations for inconsistencies by determining minimal representations of conflicts. In practice, this can be used to identify unreliable data or to indicate missing reactions. KW - answer set programming KW - bioinformatics KW - consistency KW - diagnosis Y1 - 2011 U6 - https://doi.org/10.1017/S1471068410000554 SN - 1471-0684 VL - 11 IS - 5-6 SP - 323 EP - 360 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Gebser, Martin A1 - Kaminski, Roland A1 - Schaub, Torsten T1 - Complex optimization in answer set programming JF - Theory and practice of logic programming N2 - Preference handling and optimization are indispensable means for addressing nontrivial applications in Answer Set Programming (ASP). However, their implementation becomes difficult whenever they bring about a significant increase in computational complexity. As a consequence, existing ASP systems do not offer complex optimization capacities, supporting, for instance, inclusion-based minimization or Pareto efficiency. Rather, such complex criteria are typically addressed by resorting to dedicated modeling techniques, like saturation. Unlike the ease of common ASP modeling, however, these techniques are rather involved and hardly usable by ASP laymen. We address this problem by developing a general implementation technique by means of meta-prpogramming, thus reusing existing ASP systems to capture various forms of qualitative preferences among answer sets. In this way, complex preferences and optimization capacities become readily available for ASP applications. KW - Answer Set Programming KW - Preference Handling KW - Complex optimization KW - Meta-Programming Y1 - 2011 U6 - https://doi.org/10.1017/S1471068411000329 SN - 1471-0684 VL - 11 IS - 3 SP - 821 EP - 839 PB - Cambridge Univ. Press CY - New York ER - TY - JOUR A1 - Gebser, Martin A1 - Kaufmann, Benjamin A1 - Kaminski, Roland A1 - Ostrowski, Max A1 - Schaub, Torsten A1 - Schneider, Marius T1 - Potassco the Potsdam answer set solving collection JF - AI communications : AICOM ; the European journal on artificial intelligence N2 - This paper gives an overview of the open source project Potassco, the Potsdam Answer Set Solving Collection, bundling tools for Answer Set Programming developed at the University of Potsdam. KW - Answer set programming KW - declarative problem solving Y1 - 2011 U6 - https://doi.org/10.3233/AIC-2011-0491 SN - 0921-7126 VL - 24 IS - 2 SP - 107 EP - 124 PB - IOS Press CY - Amsterdam ER - TY - JOUR A1 - Naze, Y. A1 - Broos, Patrick S. A1 - Oskinova, Lidia M. A1 - Townsley, L. K. A1 - Cohen, David H. A1 - Corcoran, M. F. A1 - Evans, N. R. A1 - Gagne, M. A1 - Moffat, Anthony F. J. A1 - Pittard, J. M. A1 - Rauw, G. A1 - Ud-Doula, A. A1 - Walborn, N. R. T1 - GLOBAL X-RAY PROPERTIES OF THE O AND B STARS IN CARINA JF - ASTROPHYSICAL JOURNAL SUPPLEMENT SERIES N2 - The key empirical property of the X-ray emission from O stars is a strong correlation between the bolometric and X-ray luminosities. In the framework of the Chandra Carina Complex Project, 129 O and B stars have been detected as X-ray sources; 78 of those, all with spectral type earlier than B3, have enough counts for at least a rough X-ray spectral characterization. This leads to an estimate of the L-X-L-BOL ratio for an exceptional number of 60 O stars belonging to the same region and triples the number of Carina massive stars studied spectroscopically in X-rays. The derived log(L-X/L-BOL) is -7.26 for single objects, with a dispersion of only 0.21 dex. Using the properties of hot massive stars listed in the literature, we compare the X-ray luminosities of different types of objects. In the case of O stars, the L-X-L-BOL ratios are similar for bright and faint objects, as well as for stars of different luminosity classes or spectral types. Binaries appear only slightly harder and slightly more luminous in X-rays than single objects; the differences are not formally significant (at the 1% level), except for the L-X-L-BOL ratio in the medium (1.0-2.5 keV) energy band. Weak-wind objects have similar X-ray luminosities but they display slightly softer spectra compared with "normal" O stars with the same bolometric luminosity. Discarding three overluminous objects, we find a very shallow trend of harder emission in brighter objects. The properties of the few B stars bright enough to yield some spectral information appear to be different overall (constant X-ray luminosities, harder spectra), hinting that another mechanism for producing X-rays, besides wind shocks, might be at work. However, it must be stressed that the earliest and X-ray brightest among these few detected objects are similar to the latest O stars, suggesting a possibly smooth transition between the two processes. KW - ISM: individual objects (Carina nebula) KW - stars: massive KW - X-rays: stars Y1 - 2011 U6 - https://doi.org/10.1088/0067-0049/194/1/7 SN - 0067-0049 VL - 194 IS - 1 PB - IOP PUBLISHING LTD CY - BRISTOL ER - TY - JOUR A1 - Townsley, Leisa K. A1 - Broos, Patrick S. A1 - Corcoran, Michael F. A1 - Feigelson, Eric D. A1 - Gagne, Marc A1 - Montmerle, Thierry A1 - Oey, M. S. A1 - Smith, Nathan A1 - Garmire, Gordon P. A1 - Getman, Konstantin V. A1 - Povich, Matthew S. A1 - Evans, Nancy Remage A1 - Naze, Yael A1 - Parkin, E. R. A1 - Preibisch, Thomas A1 - Wang, Junfeng A1 - Wou, Scott J. A1 - Chu, You-Hua A1 - Cohen, David H. A1 - Gruendl, Robert A. A1 - Hamaguchi, Kenji A1 - King, Robert R. A1 - Mac Low, Mordecai-Mark A1 - McCaughrean, Mark J. A1 - Moffat, Anthony F. J. A1 - Oskinova, Lidia M. A1 - Pittard, Julian M. A1 - Stassun, Keivan G. A1 - Ud-Doula, Asif A1 - Walborn, Nolan R. A1 - Waldron, Wayne L. A1 - Churchwell, Ed A1 - Nictiols, J. S. A1 - Owocki, Stanley P. A1 - Schulz, Norbert S. T1 - An introduction to the chandra carina complex project JF - The astrophysical journal : an international review of spectroscopy and astronomical physics ; Supplement series N2 - The Great Nebula in Carina provides an exceptional view into the violent massive star formation and feedback that typifies giant H II regions and starburst galaxies. We have mapped the Carina star-forming complex in X-rays, using archival Chandra data and a mosaic of 20 new 60 ks pointings using the Chandra X-ray Observatory's Advanced CCD Imaging Spectrometer, as a testbed for understanding recent and ongoing star formation and to probe Carina's regions of bright diffuse X-ray emission. This study has yielded a catalog of properties of > 14,000 X-ray point sources;> 9800 of them have multiwavelength counterparts. Using Chandra's unsurpassed X-ray spatial resolution, we have separated these point sources from the extensive, spatially-complex diffuse emission that pervades the region; X-ray properties of this diffuse emission suggest that it traces feedback from Carina's massive stars. In this introductory paper, we motivate the survey design, describe the Chandra observations, and present some simple results, providing a foundation for the 15 papers that follow in this special issue and that present detailed catalogs, methods, and science results. KW - H II regions KW - stars: massive KW - stars: pre-main sequence KW - X-rays: individual (Carina) KW - X-rays: ISM KW - X-rays: stars Y1 - 2011 U6 - https://doi.org/10.1088/0067-0049/194/1/1 SN - 0067-0049 VL - 194 IS - 1 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Gebser, Martin A1 - Sabuncu, Orkunt A1 - Schaub, Torsten T1 - An incremental answer set programming based system for finite model computation JF - AI communications : AICOM ; the European journal on artificial intelligence N2 - We address the problem of Finite Model Computation (FMC) of first-order theories and show that FMC can efficiently and transparently be solved by taking advantage of a recent extension of Answer Set Programming (ASP), called incremental Answer Set Programming (iASP). The idea is to use the incremental parameter in iASP programs to account for the domain size of a model. The FMC problem is then successively addressed for increasing domain sizes until an answer set, representing a finite model of the original first-order theory, is found. We implemented a system based on the iASP solver iClingo and demonstrate its competitiveness by showing that it slightly outperforms the winner of the FNT division of CADE's 2009 Automated Theorem Proving (ATP) competition on the respective benchmark collection. KW - Incremental answer set programming KW - finite model computation Y1 - 2011 U6 - https://doi.org/10.3233/AIC-2011-0496 SN - 0921-7126 VL - 24 IS - 2 SP - 195 EP - 212 PB - IOS Press CY - Amsterdam ER - TY - GEN A1 - Guerrero, Martín A. A1 - Chu, You-Hua A1 - Hamann, Wolf-Rainer A1 - Oskinova, Lidia M. A1 - Schönberner, Detlef A1 - Todt, Helge Tobias A1 - Steffen, Matthias A1 - Ruiz, Nieves A1 - Gruendl, Robert A. A1 - Blair, William P. T1 - Ablation and wind mass-loading in the born-again planetary nebula A 30 T2 - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe N2 - We present XMM-Newton and Chandra observations of the born-again planetary nebula A 30. These X-ray observations reveal a bright unresolved source at the position of the central star whose X-ray luminosity exceeds by far the model expectations for photospheric emission and for shocks within the stellar wind. We suggest that a “born-again hot bubble” may be responsible for this X-ray emission. Diffuse X-ray emission associated with the petal-like features and one of the H-poor knots seen in the optical is also found. The weakened emission of carbon lines in the spectrum of the diffuse emission can be interpreted as the dilution of stellar wind by mass-loading or as the detection of material ejected during a very late thermal pulse. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 563 KW - planetary nebulae: individual (A 30) KW - X-rays: ISM Y1 - 2019 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-412341 SN - 1866-8372 IS - 563 ER - TY - GEN A1 - Todt, Helge Tobias A1 - Peña, Miriam A1 - Zühlke, Julia A1 - Oskinova, Lidia M. A1 - Hamann, Wolf-Rainer A1 - Gräfener, Götz T1 - Weak emission line central stars of planetary nebulae T2 - Planetary Nebulae: an Eye to the Future N2 - To understand the evolution and morphology of planetary nebulae, a detailed knowledge of their central stars is required. Central stars that exhibit emission lines in their spectra, indicating stellar mass-loss allow to study the evolution of planetary nebulae in action. Emission line central stars constitute about 10 % of all central stars. Half of them are practically hydrogen-free Wolf-Rayet type central stars of the carbon sequence, [WC], that show strong emission lines of carbon and oxygen in their spectra. In this contribution we address the weak emission-lines central stars (wels). These stars are poorly analyzed and their hydrogen content is mostly unknown. We obtained optical spectra, that include the important Balmer lines of hydrogen, for four weak emission line central stars. We present the results of our analysis, provide spectral classification and discuss possible explanations for their formation and evolution. T3 - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 462 KW - stars: AGB and post-AGB KW - stars: Wolf-Rayet KW - stars: abundances Y1 - 2018 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-413775 ER - TY - JOUR A1 - Fettke, Jörg A1 - Nunes-Nesi, Adriano A1 - Fernie, Alisdair A1 - Steup, Martin T1 - Identification of a novel heteroglycan-interacting protein, HIP 1.3, from Arabidopsis thaliana JF - Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants N2 - Plastidial degradation of transitory starch yields mainly maltose and glucose. Following the export into the cytosol, maltose acts as donor for a glucosyl transfer to cytosolic heteroglycans as mediated by a cytosolic transglucosidase (DPE2; EC 2.4.1.25) and the second glucosyl residue is liberated as glucose. The cytosolic phosphorylase (Pho2/PHS2; EC 2.4.1.1) also interacts with heteroglycans using the same intramolecular sites as DPE2. Thus, the two glucosyl transferases interconnect the cytosolic pools of glucose and glucose 1-phosphate. Due to the complex monosaccharide pattern, other heteroglycan-interacting proteins (Hips) are expected to exist. Identification of those proteins was approached by using two types of affinity chromatography. Heteroglycans from leaves of Arabidopsis thaliana (Col-0) covalently bound to Sepharose served as ligands that were reacted with a complex mixture of buffer-soluble proteins from Arabidopsis leaves. Binding proteins were eluted by sodium chloride. For identification, SDS-PAGE, tryptic digestion and MALDI-TOF analyses were applied. A strongly interacting polypeptide (approximately 40 kDa; designated as HIP1.3) was observed as product of locus At1g09340. Arabidopsis mutants deficient in HIP1.3 were reduced in growth and contained heteroglycans displaying an altered monosaccharide pattern. Wild type plants express HIP1.3 most strongly in leaves. As revealed by immuno fluorescence, HIP1.3 is located in the cytosol of mesophyll cells but mostly associated with the cytosolic surface of the chloroplast envelope membranes. In an HIP1.3-deficient mutant the immunosignal was undetectable. Metabolic profiles from leaves of this mutant and wild type plants as well were determined by GC-MS. As compared to the wild type control, more than ten metabolites, such as ascorbic acid, fructose, fructose bisphosphate, glucose, glycine, were elevated in darkness but decreased in the light. Although the biochemical function of HIP1.3 has not yet been elucidated, it is likely to possess an important function in the central carbon metabolism of higher plants. KW - Arabidopsis thaliana KW - Carbohydrate binding proteins KW - Cytosolic heteroglycans KW - Maltose metabolism KW - Starch metabolism Y1 - 2011 U6 - https://doi.org/10.1016/j.jplph.2010.09.008 SN - 0176-1617 VL - 168 IS - 12 SP - 1415 EP - 1425 PB - Elsevier CY - Jena ER - TY - JOUR A1 - Rohrmann, Johannes A1 - Tohge, Takayuki A1 - Alba, Rob A1 - Osorio, Sonia A1 - Caldana, Camila A1 - McQuinn, Ryan A1 - Arvidsson, Samuel Janne A1 - van der Merwe, Margaretha J. A1 - Riano-Pachon, Diego Mauricio A1 - Müller-Röber, Bernd A1 - Fei, Zhangjun A1 - Nesi, Adriano Nunes A1 - Giovannoni, James J. A1 - Fernie, Alisdair T1 - Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development JF - The plant journal N2 - Maturation of fleshy fruits such as tomato (Solanum lycopersicum) is subject to tight genetic control. Here we describe the development of a quantitative real-time PCR platform that allows accurate quantification of the expression level of approximately 1000 tomato transcription factors. In addition to utilizing this novel approach, we performed cDNA microarray analysis and metabolite profiling of primary and secondary metabolites using GC-MS and LC-MS, respectively. We applied these platforms to pericarp material harvested throughout fruit development, studying both wild-type Solanum lycopersicum cv. Ailsa Craig and the hp1 mutant. This mutant is functionally deficient in the tomato homologue of the negative regulator of the light signal transduction gene DDB1 from Arabidopsis, and is furthermore characterized by dramatically increased pigment and phenolic contents. We choose this particular mutant as it had previously been shown to have dramatic alterations in the content of several important fruit metabolites but relatively little impact on other ripening phenotypes. The combined dataset was mined in order to identify metabolites that were under the control of these transcription factors, and, where possible, the respective transcriptional regulation underlying this control. The results are discussed in terms of both programmed fruit ripening and development and the transcriptional and metabolic shifts that occur in parallel during these processes. KW - transcription factor KW - Solanum lycopersicum KW - quantitative RT-PCR KW - microarray KW - metabolomics KW - fleshy fruit ripening Y1 - 2011 U6 - https://doi.org/10.1111/j.1365-313X.2011.04750.x SN - 0960-7412 VL - 68 IS - 6 SP - 999 EP - 1013 PB - Wiley-Blackwell CY - Malden ER - TY - JOUR A1 - Huber, Christian A1 - Klamroth, Tillmann T1 - Explicitly time-dependent coupled cluster singles doubles calculations of laser-driven many-electron dynamics JF - The journal of chemical physics : bridges a gap between journals of physics and journals of chemistry N2 - We report explicitly time-dependent coupled cluster singles doubles (TD-CCSD) calculations, which simulate the laser-driven correlated many-electron dynamics in molecular systems. Small molecules, i.e., HF, H(2)O, NH(3), and CH(4), are treated mostly with polarized valence double zeta basis sets. We determine the coupled cluster ground states by imaginary time propagation for these molecules. Excited state energies are obtained from the Fourier transform of the time-dependent dipole moment after an ultrashort, broadband laser excitation. The time-dependent expectation values are calculated from the complex cluster amplitudes using the corresponding configuration interaction singles doubles wave functions. Also resonant laser excitations of these excited states are simulated, in order to explore the limits for the numerical stability of our current TD-CCSD implementation, which uses time-independent molecular orbitals to form excited configurations. Y1 - 2011 U6 - https://doi.org/10.1063/1.3530807 SN - 0021-9606 VL - 134 IS - 5 PB - American Institute of Physics CY - Melville ER -