@misc{KaminskiSchaubSiegeletal.2013, author = {Kaminski, Roland and Schaub, Torsten and Siegel, Anne and Videla, Santiago}, title = {Minimal intervention strategies in logical signaling networks with ASP}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {4-5}, issn = {1866-8372}, doi = {10.25932/publishup-41570}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415704}, pages = {675 -- 690}, year = {2013}, abstract = {Proposing relevant perturbations to biological signaling networks is central to many problems in biology and medicine because it allows for enabling or disabling certain biological outcomes. In contrast to quantitative methods that permit fine-grained (kinetic) analysis, qualitative approaches allow for addressing large-scale networks. This is accomplished by more abstract representations such as logical networks. We elaborate upon such a qualitative approach aiming at the computation of minimal interventions in logical signaling networks relying on Kleene's three-valued logic and fixpoint semantics. We address this problem within answer set programming and show that it greatly outperforms previous work using dedicated algorithms.}, language = {en} } @misc{DammhahnGoodman2014, author = {Dammhahn, Melanie and Goodman, Steven M.}, title = {Trophic niche differentiation and microhabitat utilization revealed by stable isotope analyses in a dry-forest bat assemblage at Ankarana, northern Madagascar}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, issn = {1866-8372}, doi = {10.25932/publishup-41515}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415157}, pages = {97 -- 109}, year = {2014}, abstract = {Bats are important components in tropical mammal assemblages. Unravelling the mechanisms allowing multiple syntopic bat species to coexist can provide insights into community ecology. However, dietary information on component species of these assemblages is often difficult to obtain. Here we measuredstable carbon and nitrogen isotopes in hair samples clipped from the backs of 94 specimens to indirectly examine whether trophic niche differentiation and microhabitat segregation explain the coexistence of 16 bat species at Ankarana, northern Madagascar. The assemblage ranged over 4.4\% in delta N-15 and was structured into two trophic levels with phytophagous Pteropodidae as primary consumers (c. 3\% enriched over plants) and different insectivorous bats as secondary consumers (c. 4\% enriched over primary consumers). Bat species utilizing different microhabitats formed distinct isotopic clusters (metric analyses of delta C-13-delta N-15 bi-plots), but taxa foraging in the same microhabitat did not show more pronounced trophic differentiation than those occupying different microhabitats. As revealed by multivariate analyses, no discernible feeding competition was found in the local assemblage amongst congeneric species as compared with non-congeners. In contrast to ecological niche theory, but in accordance with studies on New and Old World bat assemblages, competitive interactions appear to be relaxed at Ankarana and not a prevailing structuring force.}, language = {en} } @misc{BanbaraSohTamuraetal.2013, author = {Banbara, Mutsunori and Soh, Takehide and Tamura, Naoyuki and Inoue, Katsumi and Schaub, Torsten}, title = {Answer set programming as a modeling language for course timetabling}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {594}, issn = {1866-8372}, doi = {10.25932/publishup-41546}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415469}, pages = {783 -- 798}, year = {2013}, abstract = {The course timetabling problem can be generally defined as the task of assigning a number of lectures to a limited set of timeslots and rooms, subject to a given set of hard and soft constraints. The modeling language for course timetabling is required to be expressive enough to specify a wide variety of soft constraints and objective functions. Furthermore, the resulting encoding is required to be extensible for capturing new constraints and for switching them between hard and soft, and to be flexible enough to deal with different formulations. In this paper, we propose to make effective use of ASP as a modeling language for course timetabling. We show that our ASP-based approach can naturally satisfy the above requirements, through an ASP encoding of the curriculum-based course timetabling problem proposed in the third track of the second international timetabling competition (ITC-2007). Our encoding is compact and human-readable, since each constraint is individually expressed by either one or two rules. Each hard constraint is expressed by using integrity constraints and aggregates of ASP. Each soft constraint S is expressed by rules in which the head is the form of penalty (S, V, C), and a violation V and its penalty cost C are detected and calculated respectively in the body. We carried out experiments on four different benchmark sets with five different formulations. We succeeded either in improving the bounds or producing the same bounds for many combinations of problem instances and formulations, compared with the previous best known bounds.}, language = {en} } @misc{ChechkinZaidLomholtetal.2013, author = {Chechkin, Aleksei V. and Zaid, Irwin M. and Lomholt, Michael A. and Sokolov, Igor M. and Metzler, Ralf}, title = {Bulk-mediated surface diffusion on a cylinder in the fast exchange limit}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch Naturwissenschaftliche Reihe}, number = {593}, issn = {1866-8372}, doi = {10.25932/publishup-41548}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415480}, pages = {114 -- 126}, year = {2013}, abstract = {In various biological systems and small scale technological applications particles transiently bind to a cylindrical surface. Upon unbinding the particles diffuse in the vicinal bulk before rebinding to the surface. Such bulk-mediated excursions give rise to an effective surface translation, for which we here derive and discuss the dynamic equations, including additional surface diffusion. We discuss the time evolution of the number of surface-bound particles, the effective surface mean squared displacement, and the surface propagator. In particular, we observe sub- and superdiffusive regimes. A plateau of the surface mean-squared displacement reflects a stalling of the surface diffusion at longer times. Finally, the corresponding first passage problem for the cylindrical geometry is analysed.}, language = {en} } @misc{OskinovaGuerreroHenaultBrunetetal.2012, author = {Oskinova, Lidia M. and Guerrero, Mart{\´i}n A. and H{\´e}nault-Brunet, Vincent and Sun, W. and Chu, You-Hua and Evans, Chris and Gallagher, John S. and Gruendl, Robert A. and Reyes-Iturbide, Jorge}, title = {The slow X-ray pulsar SXP 1062 and associated supernova remnant in the Wing of the Small Magellanic Cloud}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {591}, issn = {1866-8372}, doi = {10.25932/publishup-41513}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-415135}, pages = {3}, year = {2012}, abstract = {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.}, language = {en} } @misc{GebserHarrisonKaminskietal.2015, author = {Gebser, Martin and Harrison, Amelia and Kaminski, Roland and Lifschitz, Vladimir and Schaub, Torsten}, title = {Abstract gringo}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {592}, issn = {1866-8372}, doi = {10.25932/publishup-41475}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414751}, pages = {15}, year = {2015}, abstract = {This paper defines the syntax and semantics of the input language of the ASP grounder gringo. The definition covers several constructs that were not discussed in earlier work on the semantics of that language, including intervals, pools, division of integers, aggregates with non-numeric values, and lparse-style aggregate expressions. The definition is abstract in the sense that it disregards some details related to representing programs by strings of ASCII characters. It serves as a specification for gringo from Version 4.5 on.}, language = {en} } @misc{WestburyHartmannBarlowetal.2018, author = {Westbury, Michael V. and Hartmann, Stefanie and Barlow, Axel and Wiesel, Ingrid and Leo, Viyanna and Welch, Rebecca and Parker, Daniel M. and Sicks, Florian and Ludwig, Arne and Dalen, Love and Hofreiter, Michael}, title = {Extended and continuous decline in effective population size results in low genomic diversity in the world's rarest hyena species, the brown hyena}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {589}, issn = {1866-8372}, doi = {10.25932/publishup-41413}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414132}, pages = {13}, year = {2018}, abstract = {Hyenas (family Hyaenidae), as the sister group to cats (family Felidae), represent a deeply diverging branch within the cat-like carnivores (Feliformia). With an estimated population size of <10,000 individuals worldwide, the brown hyena (Parahyaena brunnea) represents the rarest of the four extant hyena species and has been listed as Near Threatened by the IUCN. Here, we report a high-coverage genome from a captive bred brown hyena and both mitochondrial and low-coverage nuclear genomes of 14 wild-caught brown hyena individuals from across southern Africa. We find that brown hyena harbor extremely low genetic diversity on both the mitochondrial and nuclear level, most likely resulting from a continuous and ongoing decline in effective population size that started similar to 1 Ma and dramatically accelerated towards the end of the Pleistocene. Despite the strikingly low genetic diversity, we find no evidence of inbreeding within the captive bred individual and reveal phylogeographic structure, suggesting the existence of several potential subpopulations within the species.}, language = {en} } @misc{DammhahnRakotondramananaGoodman2015, author = {Dammhahn, Melanie and Rakotondramanana, Claude Fabienne and Goodman, Steven M.}, title = {Coexistence of morphologically similar bats (Vespertilionidae) on Madagascar}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {590}, issn = {1866-8372}, doi = {10.25932/publishup-41472}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414729}, pages = {12}, year = {2015}, abstract = {Based on niche theory, closely related and morphologically similar species are not predicted to coexist due to overlap in resource and habitat use. Local assemblages of bats often contain cryptic taxa, which co-occur despite notable similarities in morphology and ecology. We measured in two different habitat types on Madagascar levels of stable carbon and nitrogen isotopes in hair (n = 103) and faeces (n = 57) of cryptic Vespertilionidae taxa to indirectly examine whether fine-grained trophic niche differentiation explains their coexistence. In the dry deciduous forest (Kirindy), six sympatric species ranged over 6.0\% in delta N-15, i.e. two trophic levels, and 4.2\% in delta C-13 with a community mean of 11.3\% in delta N-15 and - 21.0\% in delta C-13. In the mesic forest (Antsahabe), three sympatric species ranged over one trophic level (delta N-15: 2.4\%, delta C-13: 1.0\%) with a community mean of 8.0\% delta N-15 and - 21.7\% in delta C-13. Multivariate analyses and residual permutation of Euclidian distances in delta C-13- delta N-15 bi-plots revealed in both communities distinct stable isotope signatures and species separation for the hair samples among coexisting Vespertilionidae. Intraspecific variation in faecal and hair stable isotopes did not indicate that seasonal migration might relax competition and thereby facilitate the local co-occurrence of sympatric taxa.}, language = {en} } @misc{HoosKaminskiLindaueretal.2015, author = {Hoos, Holger and Kaminski, Roland and Lindauer, Marius and Schaub, Torsten}, title = {aspeed}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {588}, issn = {1866-8372}, doi = {10.25932/publishup-41474}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-414743}, pages = {26}, year = {2015}, abstract = {Although Boolean Constraint Technology has made tremendous progress over the last decade, the efficacy of state-of-the-art solvers is known to vary considerably across different types of problem instances, and is known to depend strongly on algorithm parameters. This problem was addressed by means of a simple, yet effective approach using handmade, uniform, and unordered schedules of multiple solvers in ppfolio, which showed very impressive performance in the 2011 Satisfiability Testing (SAT) Competition. Inspired by this, we take advantage of the modeling and solving capacities of Answer Set Programming (ASP) to automatically determine more refined, that is, nonuniform and ordered solver schedules from the existing benchmarking data. We begin by formulating the determination of such schedules as multi-criteria optimization problems and provide corresponding ASP encodings. The resulting encodings are easily customizable for different settings, and the computation of optimum schedules can mostly be done in the blink of an eye, even when dealing with large runtime data sets stemming from many solvers on hundreds to thousands of instances. Also, the fact that our approach can be customized easily enabled us to swiftly adapt it to generate parallel schedules for multi-processor machines.}, language = {en} } @misc{DallmeyerClaussenFischeretal.2015, author = {Dallmeyer, Anne and Claussen, M. and Fischer, N. and Haberkorn, K. and Wagner, S. and Pfeiffer, M. and Jin, L. and Khon, Vyacheslav and Wang, Y. and Herzschuh, Ulrike}, title = {The evolution of sub-monsoon systems in the Afro-Asian monsoon region during the Holocene}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {587}, issn = {1866-8372}, doi = {10.25932/publishup-40972}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-409727}, pages = {22}, year = {2015}, abstract = {The recently proposed global monsoon hypothesis interprets monsoon systems as part of one global-scale atmospheric overturning circulation, implying a connection between the regional monsoon systems and an in-phase behaviour of all northern hemispheric monsoons on annual timescales (Trenberth et al., 2000). Whether this concept can be applied to past climates and variability on longer timescales is still under debate, because the monsoon systems exhibit different regional characteristics such as different seasonality (i. e. onset, peak and withdrawal). To investigate the interconnection of different monsoon systems during the pre-industrial Holocene, five transient global climate model simulations have been analysed with respect to the rainfall trend and variability in different sub-domains of the Afro-Asian monsoon region. Our analysis suggests that on millennial timescales with varying orbital forcing, the monsoons do not behave as a tightly connected global system. According to the models, the Indian and North African monsoons are coupled, showing similar rainfall trend and moderate correlation in centennial rainfall variability in all models. The East Asian monsoon changes independently during the Holocene. The dissimilarities in the seasonality of the monsoon sub-systems lead to a stronger response of the North African and Indian monsoon systems to the Holocene insolation forcing than of the East Asian monsoon and affect the seasonal distribution of Holocene rainfall variations. Within the Indian and North African monsoon domain, precipitation solely changes during the summer months, showing a decreasing Holocene precipitation trend. In the East Asian monsoon region, the precipitation signal is determined by an increasing precipitation trend during spring and a decreasing precipitation change during summer, partly balancing each other. A synthesis of reconstructions and the model results do not reveal an impact of the different seasonality on the timing of the Holocene rainfall optimum in the different sub-monsoon systems. Rather they indicate locally inhomogeneous rainfall changes and show that single palaeo-records should not be used to characterise the rainfall change and monsoon evolution for entire monsoon sub-systems.}, language = {en} }