Automated Benchmarking of Incremental SAT and QBF Solvers

Incremental SAT and QBF solving potentially yields improvements when sequences of related formulas are solved. An incremental application is usually tailored towards some specific solver and decomposes a problem into incremental solver calls. This hinders the independent comparison of different solvers, particularly when the application program is not available. As a remedy, we present an approach to automated benchmarking of incremental SAT and QBF solvers. Given a collection of formulas in (Q)DIMACS format generated incrementally by an application program, our approach automatically translates the formulas into instructions to import and solve a formula by an incremental SAT/QBF solver. The result of the translation is a program which replays the incremental solver calls and thus allows to evaluate incremental solvers independently from the application program. We illustrate our approach by different hardware verification problems for SAT and QBF solvers.Comment: camera-ready version (8 pages + 2 pages appendix), to appear in the proceedings of the 20th International Conference on Logic for Programming, Artificial Intelligence and Reasoning (LPAR), LNCS, Springer, 201

Dynamic and combinatorial control of gene expression by nuclear retinoic acid receptors (RARs)

Nuclear retinoic acid receptors (RARs) are transcriptional regulators controlling the expression of specific subsets of genes in a ligand-dependent manner. The basic mechanism for switching on transcription of cognate target genes involves RAR binding at specific response elements and a network of interactions with coregulatory protein complexes, the assembly of which is directed by the C-terminal ligand-binding domain of RARs. In addition to this scenario, new roles for the N-terminal domain and the ubiquitin-proteasome system recently emerged. Moreover, the functions of RARs are not limited to the regulation of cognate target genes, as they can transrepress other gene pathways. Finally, RARs are also involved in nongenomic biological activities such as the activation of translation and of kinase cascades. Here we will review these mechanisms, focusing on how kinase signaling and the proteasome pathway cooperate to influence the dynamics of RAR transcriptional activity

Analysis of Dialogical Argumentation via Finite State Machines

Dialogical argumentation is an important cognitive activity by which agents exchange arguments and counterarguments as part of some process such as discussion, debate, persuasion and negotiation. Whilst numerous formal systems have been proposed, there is a lack of frameworks for implementing and evaluating these proposals. First-order executable logic has been proposed as a general framework for specifying and analysing dialogical argumentation. In this paper, we investigate how we can implement systems for dialogical argumentation using propositional executable logic. Our approach is to present and evaluate an algorithm that generates a finite state machine that reflects a propositional executable logic specification for a dialogical argumentation together with an initial state. We also consider how the finite state machines can be analysed, with the minimax strategy being used as an illustration of the kinds of empirical analysis that can be undertaken.Comment: 10 page

Understanding Gentzen and Frege Systems for QBF

Recently Beyersdorff, Bonacina, and Chew [10] introduced a natural class of Frege systems for quantified Boolean formulas (QBF) and showed strong lower bounds for restricted versions of these systems. Here we provide a comprehensive analysis of the new extended Frege system from [10], denoted EF + ∀red, which is a natural extension of classical extended Frege EF. Our main results are the following: Firstly, we prove that the standard Gentzen-style system G*1 p-simulates EF + ∀red and that G*1 is strictly stronger under standard complexity-theoretic hardness assumptions. Secondly, we show a correspondence of EF + ∀red to bounded arithmetic: EF + ∀red can be seen as the non-uniform propositional version of intuitionistic S12. Specifically, intuitionistic S12 proofs of arbitrary statements in prenex form translate to polynomial-size EF + ∀red proofs, and EF + ∀red is in a sense the weakest system with this property. Finally, we show that unconditional lower bounds for EF + ∀red would imply either a major breakthrough in circuit complexity or in classical proof complexity, and in fact the converse implications hold as well. Therefore, the system EF + ∀red naturally unites the central problems from circuit and proof complexity. Technically, our results rest on a formalised strategy extraction theorem for EF + ∀red akin to witnessing in intuitionistic S12 and a normal form for EF + ∀red proofs

Incrementally Computing Minimal Unsatisfiable Cores of QBFs via a Clause Group Solver API

We consider the incremental computation of minimal unsatisfiable cores (MUCs) of QBFs. To this end, we equipped our incremental QBF solver DepQBF with a novel API to allow for incremental solving based on clause groups. A clause group is a set of clauses which is incrementally added to or removed from a previously solved QBF. Our implementation of the novel API is related to incremental SAT solving based on selector variables and assumptions. However, the API entirely hides selector variables and assumptions from the user, which facilitates the integration of DepQBF in other tools. We present implementation details and, for the first time, report on experiments related to the computation of MUCs of QBFs using DepQBF's novel clause group API.Comment: (fixed typo), camera-ready version, 6-page tool paper, to appear in proceedings of SAT 2015, LNCS, Springe

Affinity purification of human DNA repair/transcription factor TFIIH using epitope-tagged xeroderma pigmentosum B protein

TFIIH is a high molecular weight complex with a remarkable dual function in nucleotide excision repair and initiation of RNA polymerase II transcription. Mutations in the largest subunits, the XPB and XPD helicases, are associated with three inherited disorders: xeroderma pigmentosum, Cockayne's syndrome, and trichothiodystrophy. To facilitate the purification and biochemical characterization of this intricate complex, we generated a cell line stably expressing tagged XPB, allowing the

Antibacterial Effect of Chitosan–Gold Nanoparticles and Computational Modeling of the Interaction between Chitosan and a Lipid Bilayer Model

Pathogenic bacteria have the ability to develop antibiotic resistance mechanisms. Their action consists mainly in the production of bacterial enzymes that inactivate antibiotics or the appearance of modifications that prevent the arrival of the drug at the target point or the alteration of the target point itself, becoming a growing problem for health systems. Chitosan–gold nanoparticles (Cs-AuNPs) have been shown as effective bactericidal materials avoiding damage to human cells. In this work, Cs-AuNPs were synthesized using chitosan as the reducing agent, and a systematic analysis of the influence of the synthesis parameters on the size and zeta potential of the Cs-AuNPs and their UV-vis spectra was carried out. We used a simulation model to characterize the interaction of chitosan with bacterial membranes, using a symmetric charged bilayer and two different chitosan models with different degrees of the chitosan amine protonation as a function of pH, with the aim to elucidate the antibacterial mechanism involving the cell wall disruption. The Cs-AuNP antibacterial activity was evaluated to check the simulation model.Fil: Fuster, M.G.. Universidad de Murcia. Facultad de Química; EspañaFil: Montalbán, M. G.. Universidad de Murcia. Facultad de Química; EspañaFil: Carissimi, G.. Universidad de Murcia. Facultad de Química; EspañaFil: Lima, Beatriz Viviana. Universidad Nacional de San Juan. Facultad de Ingeniería. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan; ArgentinaFil: Feresin, Gabriela Egly. Universidad Nacional de San Juan. Facultad de Ingeniería. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Juan; ArgentinaFil: Cano, M.. Universidad de Cordoba. Instituto Universitario de Investigación En Química Fina y Nanoquímica.; EspañaFil: Giner Casares, J. J.. Universidad de Cordoba. Instituto Universitario de Investigación En Química Fina y Nanoquímica.; EspañaFil: López Cascales, J.J.. Universidad Politécnica de Cartagena; EspañaFil: Enriz, Ricardo Daniel. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - San Luis. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis. Universidad Nacional de San Luis. Facultad de Ciencias Físico Matemáticas y Naturales. Instituto Multidisciplinario de Investigaciones Biológicas de San Luis; ArgentinaFil: Víllora, G.. Universidad de Murcia. Facultad de Química; Españ

The Cockayne syndrome B protein, involved in transcription-coupled DNA repair, resides in an RNA polymerase II-containing complex

Transcription-coupled repair (TCR), a subpathway of nucleotide excision repair (NER) defective in Cockayne syndrome A and B (CSA and CSB), is responsible for the preferential removal of DNA lesions from the transcribed strand of active genes, permitting rapid resumption of blocked transcription. Here we demonstrate by microinjection of antibodies against CSB and CSA gene products into living primary fibroblasts, that both proteins are required for TCR and for recovery of RNA synthesis after UV damage in vivo but not for basal transcription itself. Furthermore, immunodepletion showed that CSB is not required for in vitro NER or transcription. Its central role in TCR suggests that CSB interacts with other repair and transcription proteins. Gel filtration of repair- and transcription-competent whole cell extracts provided evidence that CSB and CSA are part of large complexes of different sizes. Unexpectedly, there was no detectable association of CSB with several candidate NER and transcription proteins. However, a minor but significant portion (10-15%) of RNA polymerase II was found to be tightly associated with CSB. We conclude that within cell-free extracts, CSB is not stably associated with the majority of core NER or transcription components, but is part of a distinct complex involving RNA polymerase II. These findings suggest that CSB is implicated in, but not essential for, transcription, and support the idea that Cockayne syndrome is due to a combined repair and transcription deficiency

Building Strategies into QBF Proofs

Strategy extraction is of great importance for quantified Boolean formulas (QBF), both in solving and proof complexity. So far in the QBF literature, strategy extraction has been algorithmically performed from proofs. Here we devise the first QBF system where (partial) strategies are built into the proof and are piecewise constructed by simple operations along with the derivation. This has several advantages: (1) lines of our calculus have a clear semantic meaning as they are accompanied by semantic objects; (2) partial strategies are represented succinctly (in contrast to some previous approaches); (3) our calculus has strategy extraction by design; and (4) the partial strategies allow new sound inference steps which are disallowed in previous central QBF calculi such as Q-Resolution and long-distance Q-Resolution. The last item (4) allows us to show an exponential separation between our new system and the previously studied reductionless long-distance resolution calculus. Our approach also naturally lifts to dependency QBFs (DQBF), where it yields the first sound and complete CDCL-style calculus for DQBF, thus opening future avenues into CDCL-based DQBF solving

The DLV System for Knowledge Representation and Reasoning

This paper presents the DLV system, which is widely considered the state-of-the-art implementation of disjunctive logic programming, and addresses several aspects. As for problem solving, we provide a formal definition of its kernel language, function-free disjunctive logic programs (also known as disjunctive datalog), extended by weak constraints, which are a powerful tool to express optimization problems. We then illustrate the usage of DLV as a tool for knowledge representation and reasoning, describing a new declarative programming methodology which allows one to encode complex problems (up to $\Delta^P_3$-complete problems) in a declarative fashion. On the foundational side, we provide a detailed analysis of the computational complexity of the language of DLV, and by deriving new complexity results we chart a complete picture of the complexity of this language and important fragments thereof. Furthermore, we illustrate the general architecture of the DLV system which has been influenced by these results. As for applications, we overview application front-ends which have been developed on top of DLV to solve specific knowledge representation tasks, and we briefly describe the main international projects investigating the potential of the system for industrial exploitation. Finally, we report about thorough experimentation and benchmarking, which has been carried out to assess the efficiency of the system. The experimental results confirm the solidity of DLV and highlight its potential for emerging application areas like knowledge management and information integration.Comment: 56 pages, 9 figures, 6 table