Satisfiability of constraint specifications on XML documents

Jose Meseguer is one of the earliest contributors in the area of Algebraic Specification. In this paper, which we are happy to dedicate to him on the occasion of his 65th birthday, we use ideas and methods coming from that area with the aim of presenting an approach for the specification of the structure of classes of XML documents and for reasoning about them. More precisely, we specify the structure of documents using sets of constraints that are based on XPath and we present inference rules that are shown to define a sound and complete refutation procedure for checking satisfiability of a given specification using tableaux.Peer ReviewedPostprint (author's final draft

Borrowed contexts for attributed graphs

Borrowed context graph transformation is a simple and powerful technique developed by Ehrig and König that allow us to derive labeled transitions and bisimulation congruences for graph transformation systems or, in general, for pocess calculi that can be defined in terms of graph transformation systems. Moreover, the same authors have also shown how to use this technique for the verification of bisimilarity. In principle, the main results about borrowed context transformation do not apply only to plain graphs, but they are generic in the sense that they apply to all categories tha satisfy certain properties related to the notion of adhesivity. In particular, this is the case of attributed graphs. However, as we show in the paper, the techniques used for checking bisimilarity are not equally generic and, in particular they fail, if we want to apply them to attributed graphs. To solve this problem, in this paper, we define a special notion of symbolic graph bisimulation and show how it can be used to check bisimilarity of attributed graphs.Postprint (published version

Candida albicans pathogenicity mechanisms

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Controlling Reuse in Pattern-Based Model-to-Model Transformations

Model-to-model transformation is a central activity in Model-Driven Engineering that consists of transforming models from a source to a target language. Pattern-based model-to-model transformation is our approach for specifying transformations in a declarative, relational and formal style. The approach relies on patterns describing allowed or forbidden relations between two models. These patterns are compiled into operational mechanisms to perform forward and backward transformations. Inspired by QVT-Relations, in this paper we incorporate into our framework the so-called check-before-enforce semantics, which checks the existence of suitable elements before creating them (i.e. it promotes reuse). Moreover, we enable the use of keys in order to describe when two elements are considered equal. The presented techniques are illustrated with a bidirectional transformation between Web Services Description Language and Enterprise Java Beans models.Work partially supported by the Spanish Ministry of Science and Innovation, with projects METEORIC (TIN2008-02081) and FORMALISM (TIN2007-66523), and the R&D program of the Community of Madrid (S2009/TIC-1650, project “e-Madrid”). Moreover, part of this work was done during a post-doctoral stay of the first author at the University of York, and sabbatical leaves of the second and third authors to the University of York and TU Berlin respectively, all with financial support from the Spanish Ministry of Science and Innovation (grant refs. JC2009-00015, PR2009-0019 and PR2008-0185).Publicad

Abstract Constraint Data Types

Martin Wirsing is one of the earliest contributors to the area of Algebraic Specification (e.g., [2]), which he explored in a variety of domains over many years. Throughout his career, he has also inspired countless researchers in related areas. This paper is inspired by one of the domains that he explored thirty years or so after his first contributions when leading the FET Integrated Project SENSORIA [14]: the use of constraint systems to deal with non-functional requirements and preferences [13,8]. Following in his footsteps, we provide an extension of the traditional notion of algebraic data type specification to encompass soft-constraints as formalised in [1]. Finally, we relate this extension with institutions [6] and recent work on graded consequence in institutions [3].Peer ReviewedPostprint (author’s final draft

Hsp90 orchestrates transcriptional regulation by Hsf1 and cell wall remodelling by MAPK signalling during thermal adaptation in a pathogenic yeast

Acknowledgments We thank Rebecca Shapiro for creating CaLC1819, CaLC1855 and CaLC1875, Gillian Milne for help with EM, Aaron Mitchell for generously providing the transposon insertion mutant library, Jesus Pla for generously providing the hog1 hst7 mutant, and Cathy Collins for technical assistance.Peer reviewedPublisher PD

Cold-water corals research in the lab and in the field: (1) growth rates of four CWC species maintained in aquaria, (2) new research areas: the Galicia Bank and the Avilés canyon (Atlantic and Cantabrian Sea), a scientific and methodological approach

Growth rates of 4 Cold-water Coral (CWC) species (Madrepora occulata, Lophe/ia pertusa, Desmophyllum cristagalli and Dendrophyllia cornigera) from the Mediterranean Sea have been measured under the same and controlled laboratory conditions over a nine months period. Results showed that M. occulata grew faster than the other three species, which presented similar growth rates. These results are discussed and also compared with the growth of tropical coral species maintained in aquaria, but in different light and temperature conditions, which corresponded to the usual culture conditions of these corals. It appeared that the zooxanthellate tropical coral Galaxea fascicularis exhibited similar growth rates than the CWC M. oculata. Further we present new research areas on the Atlantic and Cantabrian continental margin, the Galicia Bank and the Aviles canyon, which are part of the zones studied in the Spanish LIFE project INDEMARES, as well as possible targets as Marine Protected Areas (MPAs) for the NATURA 2000 network. Both areas are studied considering an ecosystem approach, aboarding an integrated study of the physical scenario (hydrography, geomorphology), all ecosystem compartments (fish, endo-, epi-, and suprabenthic and benthopelagic fauna) and the trophic relationships between them. All this information, together with the study of the impact of the fisheries working in the areas, will be integrated in a trophodynamic mass-balance model and will be used to identify vulnerable ecosystems (VE) (as the CWC habitats are) and essential fish habitats (EFH). This methodological approach offers a holistic view of these deep-sea ecosystems and can be used to design more effective and successful management strategies for MPA