LRA Collection:
http://hdl.handle.net/2381/1116
2014-04-18T23:19:54ZAn empirical evaluation of extendible arrays
http://hdl.handle.net/2381/28738
Title: An empirical evaluation of extendible arrays
Authors: Joannou, Stelios; Raman, Rajeev
Editors: Pardalos, PM; Rebennack, S
Abstract: We study the performance of several alternatives for implementing extendible arrays, which allow random access to elements stored
in them, whilst allowing the arrays to be grown and shrunk. The study
not only looks at the basic operations of grow/shrink and accessing data, but also the effects of memory fragmentation on performance.
Description: The final publication is
available at link.springer.com2014-04-09T10:40:44ZCell-cycle regulation of NOTCH signaling during C. elegans vulval development
http://hdl.handle.net/2381/28643
Title: Cell-cycle regulation of NOTCH signaling during C. elegans vulval development
Authors: Nusser-Stein, Stefanie; Beyer, Antje; Rimann, Ivo; Adamczyk, Magdalene; Piterman, Nir; Hajnal, Alex; Fisher, Jasmin
Abstract: C. elegans vulval development is one of the best‐characterized systems to study cell fate specification during organogenesis. The detailed knowledge of the signaling pathways determining vulval precursor cell (VPC) fates permitted us to create a computational model based on the antagonistic interactions between the epidermal growth factor receptor (EGFR)/RAS/MAPK and the NOTCH pathways that specify the primary and secondary fates, respectively. A key notion of our model is called bounded asynchrony, which predicts that a limited degree of asynchrony in the progression of the VPCs is necessary to break their equivalence. While searching for a molecular mechanism underlying bounded asynchrony, we discovered that the termination of NOTCH signaling is tightly linked to cell‐cycle progression. When single VPCs were arrested in the G1 phase, intracellular NOTCH failed to be degraded, resulting in a mixed primary/secondary cell fate. Moreover, the G1 cyclins CYD‐1 and CYE‐1 stabilize NOTCH, while the G2 cyclin CYB‐3 promotes NOTCH degradation. Our findings reveal a synchronization mechanism that coordinates NOTCH signaling with cell‐cycle progression and thus permits the formation of a stable cell fate pattern.2014-03-07T13:50:41ZStrongly complete logics for coalgebras
http://hdl.handle.net/2381/28587
Title: Strongly complete logics for coalgebras
Authors: Kurz, Alexander; Rosicky, Jiri
Abstract: Coalgebras for a functor model different types of transition systems in a uniform way. This paper focuses on a uniform account of finitary logics for set-based coalgebras. In particular, a general construction of a logic from an arbitrary set-functor is given and proven to be strongly complete under additional assumptions. We proceed in three parts. Part I argues that sifted colimit preserving functors are those functors that preserve universal algebraic structure. Our main theorem here states that a functor preserves sifted colimits if and only if it has a finitary presentation by operations and equations. Moreover, the presentation of the category of algebras for the functor is obtained compositionally from the presentations of the underlying category and of the functor. Part II investigates algebras for a functor over ind-completions and extends the theorem of J{'o}nsson and Tarski on canonical extensions of Boolean algebras with operators to this setting. Part III shows, based on Part I, how to associate a finitary logic to any finite-sets preserving functor T. Based on Part II we prove the logic to be strongly complete under a reasonable condition on T.2014-02-14T10:52:40ZCompleteness for the coalgebraic cover modality
http://hdl.handle.net/2381/28586
Title: Completeness for the coalgebraic cover modality
Authors: Kupke, Clemens; Kurz, Alexander; Venema, Yde
Abstract: We study the finitary version of the coalgebraic logic introduced by L.Moss. The syntax of this logic, which is introduced uniformly with respect to a coalgebraic type functor, required to preserve weak pullbacks, extends that of classical propositional logic with a so-called coalgebraic cover modality depending on the type functor. Its semantics is defined in terms of a categorically defined relation lifting operation. As the main contributions of our paper we introduce a derivation system, and prove that it provides a sound and complete axiomatization for the collection of coalgebraically valid inequalities. Our soundness and completeness proof is algebraic, and we employ Pattinson's stratification method, showing that our derivation system can be stratified in countably many layers, corresponding to the modal depth of the formulas involved. In the proof of our main result we identify some new concepts and obtain some auxiliary results of independent interest. We survey properties of the notion of relation lifting, induced by an arbitrary but fixed set functor. We introduce a category of Boolean algebra presentations, and establish an adjunction between it and the category of Boolean algebras. Given the fact that our derivation system involves only formulas of depth one, it can be encoded as a endo-functor on Boolean algebras. We show that this functor is finitary and preserves embeddings, and we prove that the Lindenbaum-Tarski algebra of our logic can be identified with the initial algebra for this functor.2014-02-14T10:40:06ZSuccinct representations of permutations and functions
http://hdl.handle.net/2381/28330
Title: Succinct representations of permutations and functions
Authors: Munro, J. Ian; Raman, Rajeev; Raman, Venkatesh; Rao, Satti Srinivasa
Abstract: We investigate the problem of succinctly representing an arbitrary permutation, π, on {0, . . . , n−1} so that π[superscript k](i) can be computed quickly for any i and any (positive or negative) integer power k. A representation taking (1 + ϵ)n lg n + O(1) bits suffices to compute arbitrary powers in constant time, for any positive constant ϵ ≤ 1. A representation taking the optimal ⌈lg n!⌉ + o(n) bits can be used to compute arbitrary powers in O(lg n/ lg lg n) time.
We then consider the more general problem of succinctly representing an arbitrary function, f : [n] → [n] so that f[superscript k](i) can be computed quickly for any i and any integer power k. We give a representation that takes (1 + ϵ)n lg n + O(1) bits, for any positive constant ϵ ≤ 1, and computes arbitrary positive powers in constant time. It can also be used to compute f[superscript k](i), for any negative integer k, in optimal O(1+ | f[superscript k](i) |) time. We place emphasis on the redundancy, or the space beyond the information-theoretic lower bound that the data structure uses in order to support operations efficiently. A number of lower bounds have recently been shown on the redundancy of data structures. These lower bounds confirm the space–time optimality of some of our solutions.
Furthermore, the redundancy of one of our structures "surpasses" a recent lower bound by Golynski [Golynski, SODA 2009], thus demonstrating the limitations of this lower bound.
Description: NOTICE: this is the author’s version of a work that was accepted for publication in Theoretical Computer Science. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. A definitive version was subsequently published in Theoretical Computer Science, 2012, 438, pp. 47-88, DOI: 10.1016/j.tcs.2012.03.005.2013-10-28T12:29:09ZAttitudes towards User Experience (UX) Measurement
http://hdl.handle.net/2381/28125
Title: Attitudes towards User Experience (UX) Measurement
Authors: Law, Lai-Chong; van Schaik, Paul
Editors: Wiedenbeck, S
Abstract: User experience (UX), as an immature research area, is still haunted by the challenges of defining the scope of UX in general and operationalising experiential qualities in particular. To explore the basic question whether UX constructs are measurable, we conducted semi-structured interviews with eleven UX professionals where a set of questions in relation to UX measurement were explored. The interviewees expressed scepticism as well as ambivalence towards UX measures and shared anecdotes related to such measures in different contexts. Besides, the data suggested that design-oriented UX professionals tended to be sceptical about UX measurement. To examine whether such an attitude prevailed in the HCI community, we conducted a survey with essentially the same set of questions used in the interviews. Altogether 367 responses were received; 170 of them were valid and analysed. The survey provided empirical evidence on this issue as a baseline for progress in UX measurement. Overall, results indicated that attitude was favourable and there were nuanced views on details of UX measurement, implying good prospects for its acceptance, given further progress in research and education in UX measurement where UX modelling grounded in theories can play a crucial role. Mutual recognition of the value of objective measures and subjective accounts of user experience can enhance the maturity of this area.2013-09-03T14:47:00ZPCTL model checking of Markov chains: Truth and falsity as winning strategies in games
http://hdl.handle.net/2381/26567
Title: PCTL model checking of Markov chains: Truth and falsity as winning strategies in games
Authors: Fecher, H; Huth, M; Piterman, N; Wagner, D2012-10-24T09:21:52ZA hierarchy of reverse bisimulations on stable configuration structures
http://hdl.handle.net/2381/26332
Title: A hierarchy of reverse bisimulations on stable configuration structures
Authors: Phillips, I; Ulidowski, I2012-10-24T09:21:34ZEnriched Logical Connections
http://hdl.handle.net/2381/21632
Title: Enriched Logical Connections
Authors: Kurz, A; Velebil, J2012-10-24T09:10:17ZSoft constraints of difference and equality
http://hdl.handle.net/2381/21619
Title: Soft constraints of difference and equality
Authors: Hebrard, E; Marx, D; O'Sullivan, B; Razgon, I2012-10-24T09:10:16ZFinitary functors: From set to Preord and Poset
http://hdl.handle.net/2381/21606
Title: Finitary functors: From set to Preord and Poset
Authors: Balan, A; Kurz, A2012-10-24T09:10:16ZRelation liftings on preorders and posets
http://hdl.handle.net/2381/21605
Title: Relation liftings on preorders and posets
Authors: Bílková, M; Kurz, A; Petrişan, D; Velebil, J2012-10-24T09:10:16ZRigorous protocol design in practice: An optical packet-switch MAC in HOL
http://hdl.handle.net/2381/20790
Title: Rigorous protocol design in practice: An optical packet-switch MAC in HOL
Authors: Biltcliffe, A; Ridge, T; Sewell, P; Dales, M; Jansen, S2012-10-24T09:08:59ZVerifying Distributed Systems: the Operational Approach
http://hdl.handle.net/2381/20789
Title: Verifying Distributed Systems: the Operational Approach
Authors: Ridge, T2012-10-24T09:08:59ZEfficient algorithms for finding a longest common increasing subsequence
http://hdl.handle.net/2381/20787
Title: Efficient algorithms for finding a longest common increasing subsequence
Authors: Chan, W-T; Zhang, Y; Ye, D; Fung, SPY; Zhu, H2012-10-24T09:08:59ZThe semantics of x86-CC multiprocessor machine code
http://hdl.handle.net/2381/20788
Title: The semantics of x86-CC multiprocessor machine code
Authors: Sarkar, S; Sewell, P; Nardelli, FZ; Owens, S; Ridge, T; Braibant, T; Myreen, MO; Alglave, J2012-10-24T09:08:59ZAlgebraic semantics for coalgebraic logics
http://hdl.handle.net/2381/20607
Title: Algebraic semantics for coalgebraic logics
Authors: Kupke, C; Kurz, A; Pattinson, D2012-10-24T09:08:51ZModal logics are coalgebraic
http://hdl.handle.net/2381/20598
Title: Modal logics are coalgebraic
Authors: Cîrstea, C; Kurz, A; Pattinson, D; Schröder, L; Venema, Y2012-10-24T09:08:51ZWeak factorizations, fractions and homotopies
http://hdl.handle.net/2381/20602
Title: Weak factorizations, fractions and homotopies
Authors: Kurz, A; Rosický, J2012-10-24T09:08:51ZFamilies of symmetries as efficient models of resource binding
http://hdl.handle.net/2381/20603
Title: Families of symmetries as efficient models of resource binding
Authors: Ciancia, V; Kurz, A; Montanari, U2012-10-24T09:08:51ZOn universal algebra over nominal sets
http://hdl.handle.net/2381/20601
Title: On universal algebra over nominal sets
Authors: Kurz, A; Petrian, D2012-10-24T09:08:51ZCoalgebras and modal expansions of logics
http://hdl.handle.net/2381/20606
Title: Coalgebras and modal expansions of logics
Authors: Kurz, A; Palmigiano, A2012-10-24T09:08:51ZMeasuring teachers' readiness for E-learning in higher education institutions associated with the subject of electricity in Turkey
http://hdl.handle.net/2381/20593
Title: Measuring teachers' readiness for E-learning in higher education institutions associated with the subject of electricity in Turkey
Authors: Akaslan, D; Law, EL-C2012-10-24T09:08:51ZPresenting functors on many-sorted varieties and applications
http://hdl.handle.net/2381/20599
Title: Presenting functors on many-sorted varieties and applications
Authors: Kurz, A; Petrian, D2012-10-24T09:08:51ZCoalgebraic representations of distributive lattices with operators
http://hdl.handle.net/2381/20605
Title: Coalgebraic representations of distributive lattices with operators
Authors: Bonsangue, MM; Kurz, A; Rewitzky, IM2012-10-24T09:08:51ZModelling user experience - An agenda for research and practice
http://hdl.handle.net/2381/20594
Title: Modelling user experience - An agenda for research and practice
Authors: Law, EL-C; Van Schaik P2012-10-24T09:08:51ZOn coalgebras over algebras
http://hdl.handle.net/2381/20595
Title: On coalgebras over algebras
Authors: Balan, A; Kurz, A2012-10-24T09:08:51ZStone coalgebras
http://hdl.handle.net/2381/20608
Title: Stone coalgebras
Authors: Kupke, C; Venema, Y; Kupke, C; Kurz, A2012-10-24T09:08:51ZEquational presentations of functors and monads
http://hdl.handle.net/2381/20597
Title: Equational presentations of functors and monads
Authors: Velebil, J; Kurz, A2012-10-24T09:08:51ZForeword: Special issue on coalgebraic logic
http://hdl.handle.net/2381/20596
Title: Foreword: Special issue on coalgebraic logic
Authors: Doberkat, E-E; Kurz, A2012-10-24T09:08:51ZMuMHR: Multi-path, multi-hop hierarchical routing
http://hdl.handle.net/2381/20604
Title: MuMHR: Multi-path, multi-hop hierarchical routing
Authors: Hammoudeh, M; Gaura, E; Kurz, A2012-10-24T09:08:51ZCoalgebra and logic: A brief overview
http://hdl.handle.net/2381/20600
Title: Coalgebra and logic: A brief overview
Authors: Kurz, A; Palmigiano, A; Venema, Y2012-10-24T09:08:51ZFixed-parameter tractability of multicut parameterized by the size of the cutset
http://hdl.handle.net/2381/20526
Title: Fixed-parameter tractability of multicut parameterized by the size of the cutset
Authors: Marx, D; Razgon, I2012-10-24T09:08:48ZSingular Artin monoids of finite coxeter type are automatic
http://hdl.handle.net/2381/20517
Title: Singular Artin monoids of finite coxeter type are automatic
Authors: Corran, R; Hoffmann, M; Thomas, RM; Kuske, D2012-10-24T09:08:47ZPreface
http://hdl.handle.net/2381/20366
Title: Preface
Authors: Ulidowski, I2012-10-24T09:08:39ZPreface. Hybrid automata and oscillatory behaviour in biological systems
http://hdl.handle.net/2381/20367
Title: Preface. Hybrid automata and oscillatory behaviour in biological systems
Authors: Cannata, N; Merelli, E; Ulidowski, I2012-10-24T09:08:39ZEditorial for special section on dependencies and interactions with aspects
http://hdl.handle.net/2381/20341
Title: Editorial for special section on dependencies and interactions with aspects
Authors: Chitchyan, R; Fabry, J; Katz, S; Rensink, A2012-10-24T09:08:37ZPreface
http://hdl.handle.net/2381/20320
Title: Preface
Authors: Bonchi, F; Grohmann, D; Spoletini, P; Troina, A; Tuosto, E2012-10-24T09:08:36ZPreface
http://hdl.handle.net/2381/20294
Title: Preface
Authors: Cannata, N; Merelli, E; Ulidowski, I2012-10-24T09:08:34ZOn a class of semigroups with symmetric presentations
http://hdl.handle.net/2381/20276
Title: On a class of semigroups with symmetric presentations
Authors: Campbell, CM; Robertson, EF; Thomas, RM2012-10-24T09:08:33ZReidemeister-Schreier type rewriting for semigroups
http://hdl.handle.net/2381/20273
Title: Reidemeister-Schreier type rewriting for semigroups
Authors: Campbell, CM; Robertson, EF; Ruškuc, N; Thomas, RM2012-10-24T09:08:33ZReversibility and Models for Concurrency
http://hdl.handle.net/2381/20214
Title: Reversibility and Models for Concurrency
Authors: Phillips, I; Ulidowski, I2012-10-24T09:08:29ZPredictive modeling of signaling crosstalk during C. elegans vulval development.
http://hdl.handle.net/2381/20178
Title: Predictive modeling of signaling crosstalk during C. elegans vulval development.
Authors: Fisher, J; Piterman, N; Hajnal, A; Henzinger, TA
Abstract: Caenorhabditis elegans vulval development provides an important paradigm for studying the process of cell fate determination and pattern formation during animal development. Although many genes controlling vulval cell fate specification have been identified, how they orchestrate themselves to generate a robust and invariant pattern of cell fates is not yet completely understood. Here, we have developed a dynamic computational model incorporating the current mechanistic understanding of gene interactions during this patterning process. A key feature of our model is the inclusion of multiple modes of crosstalk between the epidermal growth factor receptor (EGFR) and LIN-12/Notch signaling pathways, which together determine the fates of the six vulval precursor cells (VPCs). Computational analysis, using the model-checking technique, provides new biological insights into the regulatory network governing VPC fate specification and predicts novel negative feedback loops. In addition, our analysis shows that most mutations affecting vulval development lead to stable fate patterns in spite of variations in synchronicity between VPCs. Computational searches for the basis of this robustness show that a sequential activation of the EGFR-mediated inductive signaling and LIN-12 / Notch-mediated lateral signaling pathways is key to achieve a stable cell fate pattern. We demonstrate experimentally a time-delay between the activation of the inductive and lateral signaling pathways in wild-type animals and the loss of sequential signaling in mutants showing unstable fate patterns; thus, validating two key predictions provided by our modeling work. The insights gained by our modeling study further substantiate the usefulness of executing and analyzing mechanistic models to investigate complex biological behaviors.2012-10-24T09:08:25ZEditorial
http://hdl.handle.net/2381/20162
Title: Editorial
Authors: Mosses, PD; Ulidowski, I2012-10-24T09:08:22ZModel-driven development of reactive information systems: From graph transformation rules to JML contracts
http://hdl.handle.net/2381/20157
Title: Model-driven development of reactive information systems: From graph transformation rules to JML contracts
Authors: Heckel, R; Lohmann, M2012-10-24T09:08:21ZOperational Semantics of Reversibility in Process Algebra
http://hdl.handle.net/2381/20124
Title: Operational Semantics of Reversibility in Process Algebra
Authors: Phillips, I; Ulidowski, I2012-10-24T09:07:58ZGuest editorial to the special issue on language engineering for model-driven software development
http://hdl.handle.net/2381/20121
Title: Guest editorial to the special issue on language engineering for model-driven software development
Authors: Bézivin, J; Heckel, R2012-10-24T09:07:58ZStyle-based modeling and refinement of service-oriented architectures: A graph transformation-base approach
http://hdl.handle.net/2381/20107
Title: Style-based modeling and refinement of service-oriented architectures: A graph transformation-base approach
Authors: Baresi, L; Heckel, R; Thöne, S; Varró, D2012-10-24T09:07:57ZA Logic for Application Level QoS
http://hdl.handle.net/2381/20099
Title: A Logic for Application Level QoS
Authors: Hirsch, D; Lluch-Lafuente, A; Tuosto, E2012-10-24T09:07:57ZAn observational model for spatial logics
http://hdl.handle.net/2381/20054
Title: An observational model for spatial logics
Authors: Tuosto, E; Vieira, HT2012-10-24T09:07:54Z