7 research outputs found

    Modular Logic Programming: Full Compositionality and Conflict Handling for Practical Reasoning

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    With the recent development of a new ubiquitous nature of data and the profusity of available knowledge, there is nowadays the need to reason from multiple sources of often incomplete and uncertain knowledge. Our goal was to provide a way to combine declarative knowledge bases – represented as logic programming modules under the answer set semantics – as well as the individual results one already inferred from them, without having to recalculate the results for their composition and without having to explicitly know the original logic programming encodings that produced such results. This posed us many challenges such as how to deal with fundamental problems of modular frameworks for logic programming, namely how to define a general compositional semantics that allows us to compose unrestricted modules. Building upon existing logic programming approaches, we devised a framework capable of composing generic logic programming modules while preserving the crucial property of compositionality, which informally means that the combination of models of individual modules are the models of the union of modules. We are also still able to reason in the presence of knowledge containing incoherencies, which is informally characterised by a logic program that does not have an answer set due to cyclic dependencies of an atom from its default negation. In this thesis we also discuss how the same approach can be extended to deal with probabilistic knowledge in a modular and compositional way. We depart from the Modular Logic Programming approach in Oikarinen & Janhunen (2008); Janhunen et al. (2009) which achieved a restricted form of compositionality of answer set programming modules. We aim at generalising this framework of modular logic programming and start by lifting restrictive conditions that were originally imposed, and use alternative ways of combining these (so called by us) Generalised Modular Logic Programs. We then deal with conflicts arising in generalised modular logic programming and provide modular justifications and debugging for the generalised modular logic programming setting, where justification models answer the question: Why is a given interpretation indeed an Answer Set? and Debugging models answer the question: Why is a given interpretation not an Answer Set? In summary, our research deals with the problematic of formally devising a generic modular logic programming framework, providing: operators for combining arbitrary modular logic programs together with a compositional semantics; We characterise conflicts that occur when composing access control policies, which are generalisable to our context of generalised modular logic programming, and ways of dealing with them syntactically: provided a unification for justification and debugging of logic programs; and semantically: provide a new semantics capable of dealing with incoherences. We also provide an extension of modular logic programming to a probabilistic setting. These goals are already covered with published work. A prototypical tool implementing the unification of justifications and debugging is available for download from http://cptkirk.sourceforge.net

    Characterization of the coiled-coil domain-containing protein 124 (Ccdc124) as a novel centrosome and midbody component involved in cytokinesis

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    Ankara : The Department of Molecular Biology and Genetics and the Graduate School of Engineering and Science of Bilkent Univ., 2013.Thesis (Ph. D.) -- Bilkent University, 2013.Includes bibliographical references leaves 114-124.Cytokinetic abscission is the cellular process leading to physical separation of two postmitotic sister cells by severing the intercellular bridge. During cell division several functional complexes accumulate at the bridge connecting the two sister cells. The most noticeable structural component of the intercellular bridge is a transient organelle termed as midbody. This novel organelle is localized at a central region, which marks the site of cytokinetic abscission. Despite its major role in completion of cell divison, our understanding of spatiotemporal regulation of midbody assembly is incomplete. In this thesis work, we first characterizated the coiled-coil domain-containing protein-124 (Ccdc124), a eukaryotic protein conserved from fungi-to-man, at the molecular level. We identified that at the sub-cellular level Ccdc124 is localized at centrosomes and the midbody depending on stages of the cell cycle. In interphase cells, as well as in mitosis, the protein is localized to centrosomes. However at later stages of cytokinesis (lateanaphase/ telophase) Ccdc124 translocates to the midbody. Knockdown of Ccdc124 in human HeLa cells leads to accumulation of enlarged and multinucleated cells; however, centrosome maturation was not affected. Similarly, in preliminary in vivo assays involving down-regulation of Ccdc124-homologue in zebra fish early embryos, we observed multinuclear embryonic cells. Furthermore, we have validated a previously observed in vitro interaction in our laboratory between Ccdc124 and the Ras guanine nucleotide exchange factor 1B (RasGEF1B) by co-immunoprecipitation assays. As RasGEF1B is strictly a Rap2 GTP-binding protein specific nucleotide exchange factor, this result has suggested a possible involvement of Rap2 in cytokinesis related events. Thus, subsequently, we assessed the sub-cellular localization of Rap2 in synchronized cells during cytokinesis. We found that even though it does not play a role in cell division, Rap2 is localized to the midbody. This result establishes a functional link between cytokinesis and activation of localized Rap2 signaling at the midbody. Data presented in this thesis work indicate that Ccdc124 is a novel factor operating both for proper progression of late cytokinetic stages in eukaryotes, and for establishment of Rap2 signaling dependent cellular functions proximal to the abscission site.Akıllılar, Pelin TelkoparanPh.D
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