@article{MileoSchaubMericoetal.2011, author = {Mileo, Alessandra and Schaub, Torsten and Merico, Davide and Bisiani, Roberto}, title = {Knowledge-based multi-criteria optimization to support indoor positioning}, series = {Annals of mathematics and artificial intelligence}, volume = {62}, journal = {Annals of mathematics and artificial intelligence}, number = {3-4}, publisher = {Springer}, address = {Dordrecht}, issn = {1012-2443}, doi = {10.1007/s10472-011-9241-2}, pages = {345 -- 370}, year = {2011}, abstract = {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.}, language = {en} } @misc{GebserKaminskiSchaub2011, author = {Gebser, Martin and Kaminski, Roland and Schaub, Torsten}, title = {Complex optimization in answer set programming}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {554}, issn = {1866-8372}, doi = {10.25932/publishup-41243}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-412436}, pages = {19}, year = {2011}, abstract = {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.}, language = {en} } @misc{DurzinskyMarwanOstrowskietal.2011, author = {Durzinsky, Markus and Marwan, Wolfgang and Ostrowski, Max and Schaub, Torsten and Wagler, Annegret}, title = {Automatic network reconstruction using ASP}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {560}, issn = {1866-8372}, doi = {10.25932/publishup-41241}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-412419}, pages = {18}, year = {2011}, abstract = {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.}, language = {en} } @article{GebserSchaubThieleetal.2011, author = {Gebser, Martin and Schaub, Torsten and Thiele, Sven and Veber, Philippe}, title = {Detecting inconsistencies in large biological networks with answer set programming}, series = {Theory and practice of logic programming}, volume = {11}, journal = {Theory and practice of logic programming}, number = {5-6}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {1471-0684}, doi = {10.1017/S1471068410000554}, pages = {323 -- 360}, year = {2011}, abstract = {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.}, language = {en} } @article{GebserKaminskiSchaub2011, author = {Gebser, Martin and Kaminski, Roland and Schaub, Torsten}, title = {Complex optimization in answer set programming}, series = {Theory and practice of logic programming}, volume = {11}, journal = {Theory and practice of logic programming}, number = {3}, publisher = {Cambridge Univ. Press}, address = {New York}, issn = {1471-0684}, doi = {10.1017/S1471068411000329}, pages = {821 -- 839}, year = {2011}, abstract = {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.}, language = {en} } @article{GebserKaufmannKaminskietal.2011, author = {Gebser, Martin and Kaufmann, Benjamin and Kaminski, Roland and Ostrowski, Max and Schaub, Torsten and Schneider, Marius}, title = {Potassco the Potsdam answer set solving collection}, series = {AI communications : AICOM ; the European journal on artificial intelligence}, volume = {24}, journal = {AI communications : AICOM ; the European journal on artificial intelligence}, number = {2}, publisher = {IOS Press}, address = {Amsterdam}, issn = {0921-7126}, doi = {10.3233/AIC-2011-0491}, pages = {107 -- 124}, year = {2011}, abstract = {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.}, language = {en} } @article{NazeBroosOskinovaetal.2011, author = {Naze, Y. and Broos, Patrick S. and Oskinova, Lidia M. and Townsley, L. K. and Cohen, David H. and Corcoran, M. F. and Evans, N. R. and Gagne, M. and Moffat, Anthony F. J. and Pittard, J. M. and Rauw, G. and Ud-Doula, A. and Walborn, N. R.}, title = {GLOBAL X-RAY PROPERTIES OF THE O AND B STARS IN CARINA}, series = {ASTROPHYSICAL JOURNAL SUPPLEMENT SERIES}, volume = {194}, journal = {ASTROPHYSICAL JOURNAL SUPPLEMENT SERIES}, number = {1}, publisher = {IOP PUBLISHING LTD}, address = {BRISTOL}, issn = {0067-0049}, doi = {10.1088/0067-0049/194/1/7}, pages = {20}, year = {2011}, abstract = {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.}, language = {en} } @article{TownsleyBroosCorcoranetal.2011, author = {Townsley, Leisa K. and Broos, Patrick S. and Corcoran, Michael F. and Feigelson, Eric D. and Gagne, Marc and Montmerle, Thierry and Oey, M. S. and Smith, Nathan and Garmire, Gordon P. and Getman, Konstantin V. and Povich, Matthew S. and Evans, Nancy Remage and Naze, Yael and Parkin, E. R. and Preibisch, Thomas and Wang, Junfeng and Wou, Scott J. and Chu, You-Hua and Cohen, David H. and Gruendl, Robert A. and Hamaguchi, Kenji and King, Robert R. and Mac Low, Mordecai-Mark and McCaughrean, Mark J. and Moffat, Anthony F. J. and Oskinova, Lidia M. and Pittard, Julian M. and Stassun, Keivan G. and Ud-Doula, Asif and Walborn, Nolan R. and Waldron, Wayne L. and Churchwell, Ed and Nictiols, J. S. and Owocki, Stanley P. and Schulz, Norbert S.}, title = {An introduction to the chandra carina complex project}, series = {The astrophysical journal : an international review of spectroscopy and astronomical physics ; Supplement series}, volume = {194}, journal = {The astrophysical journal : an international review of spectroscopy and astronomical physics ; Supplement series}, number = {1}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {0067-0049}, doi = {10.1088/0067-0049/194/1/1}, pages = {28}, year = {2011}, abstract = {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.}, language = {en} } @article{GebserSabuncuSchaub2011, author = {Gebser, Martin and Sabuncu, Orkunt and Schaub, Torsten}, title = {An incremental answer set programming based system for finite model computation}, series = {AI communications : AICOM ; the European journal on artificial intelligence}, volume = {24}, journal = {AI communications : AICOM ; the European journal on artificial intelligence}, number = {2}, publisher = {IOS Press}, address = {Amsterdam}, issn = {0921-7126}, doi = {10.3233/AIC-2011-0496}, pages = {195 -- 212}, year = {2011}, abstract = {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.}, language = {en} } @misc{GuerreroChuHamannetal.2011, author = {Guerrero, Mart{\´i}n A. and Chu, You-Hua and Hamann, Wolf-Rainer and Oskinova, Lidia M. and Sch{\"o}nberner, Detlef and Todt, Helge Tobias and Steffen, Matthias and Ruiz, Nieves and Gruendl, Robert A. and Blair, William P.}, title = {Ablation and wind mass-loading in the born-again planetary nebula A 30}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {563}, issn = {1866-8372}, doi = {10.25932/publishup-41234}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-412341}, pages = {2}, year = {2011}, abstract = {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.}, language = {en} } @misc{TodtPenaZuehlkeetal.2011, author = {Todt, Helge Tobias and Pe{\~n}a, Miriam and Z{\"u}hlke, Julia and Oskinova, Lidia M. and Hamann, Wolf-Rainer and Gr{\"a}fener, G{\"o}tz}, title = {Weak emission line central stars of planetary nebulae}, series = {Planetary Nebulae: an Eye to the Future}, journal = {Planetary Nebulae: an Eye to the Future}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-413775}, pages = {2}, year = {2011}, abstract = {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.}, language = {en} } @article{FettkeNunesNesiFernieetal.2011, author = {Fettke, J{\"o}rg and Nunes-Nesi, Adriano and Fernie, Alisdair and Steup, Martin}, title = {Identification of a novel heteroglycan-interacting protein, HIP 1.3, from Arabidopsis thaliana}, series = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants}, volume = {168}, journal = {Journal of plant physiology : biochemistry, physiology, molecular biology and biotechnology of plants}, number = {12}, publisher = {Elsevier}, address = {Jena}, issn = {0176-1617}, doi = {10.1016/j.jplph.2010.09.008}, pages = {1415 -- 1425}, year = {2011}, abstract = {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.}, language = {en} } @article{RohrmannTohgeAlbaetal.2011, author = {Rohrmann, Johannes and Tohge, Takayuki and Alba, Rob and Osorio, Sonia and Caldana, Camila and McQuinn, Ryan and Arvidsson, Samuel Janne and van der Merwe, Margaretha J. and Riano-Pachon, Diego Mauricio and M{\"u}ller-R{\"o}ber, Bernd and Fei, Zhangjun and Nesi, Adriano Nunes and Giovannoni, James J. and Fernie, Alisdair}, title = {Combined transcription factor profiling, microarray analysis and metabolite profiling reveals the transcriptional control of metabolic shifts occurring during tomato fruit development}, series = {The plant journal}, volume = {68}, journal = {The plant journal}, number = {6}, publisher = {Wiley-Blackwell}, address = {Malden}, issn = {0960-7412}, doi = {10.1111/j.1365-313X.2011.04750.x}, pages = {999 -- 1013}, year = {2011}, abstract = {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.}, language = {en} }