7 research outputs found
Modular Logic Programming: Full Compositionality and Conflict Handling for Practical Reasoning
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
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