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

Embryo and larval biology of the deepsea octocoral Dentomuricea aff. meteor under different temperature regimes

Deep-sea octocorals are common habitat-formers in deep-sea ecosystems, however, our knowledge on their early life history stages is extremely limited. The present study focuses on the early life history of the species Dentomuricea aff. meteor, a common deep-sea octocoral in the Azores. The objective was to describe the embryo and larval biology of the target species under two temperature regimes, corresponding to the minimum and maximum temperatures in its natural environment during the spawning season. At temperature of 13 ±0.5 °C, embryos of the species reached the planula stage after 96h and displayed a median survival of 11 days. Planulae displayed swimming only after stimulation, swimming speed was 0.24 ±0.16 mm s−1 and increased slightly but significantly with time. Under a higher temperature (15 °C ±0.5 °C) embryos reached the planula stage 24 h earlier (after 72 h), displayed a median survival of 16 days and had significantly higher swimming speed (0.3 ±0.27 mm s−1). Although the differences in survival were not statistically significant, our results highlight how small changes in temperature can affect embryo and larval characteristics with potential cascading effects in larval dispersal and success. In both temperatures, settlement rates were low and metamorphosis occurred even without settlement. Such information is rarely available for deep-sea corals, although essential to achieve a better understanding of dispersal, connectivity and biogeographical patterns of benthic species.Versión del edito

Constraints for behavioural specifications

Behavioural specifications with constraints for the incremental development of algebraic specifications are presented. The behavioural constraints correspond to the completely defined subparts of a given incomplete behavioural specification. Moreover, the local observability criteria used within a behavioural constraint could not coincide with the global criteria used in the behavioural specification. This is absolutely needed because, otherwise, some constraints could involve only non observable sorts and therefore have trivial semantics. Finally, the extension operations and completion operations for refining specifications are defined. The extension operations correspond to horizontal refinements and build larger specifications on top of existing ones in a conservative way. The completion operations correspond to vertical refinements, they add detail to an incomplete behavioural specification and they do restrict the class of models.Postprint (published version

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

Les comunitats de coralls al canó de cap de Creus

En la darrera dècada, les comunitats de coralls blancs han despertat l’interès dels científics a nivell mundial a causa, en part a la seva rellevància ecològica i en part a la seva desconeixença. Els escrits antics, des d’inicis del segle XX se sap que aquestes comunitats eren molt abundants en el límit de la plataforma continental a la Mediterrània entre 150 i 400 m de fondària. Actualment estan confinats a indrets on les activitats pesqueres de ròssec no les hagin malmès i és urgent trobar i avaluar el seu estat per promoure la seva conservació.Un dels indretsmés on es pot confirmar la presència i bon estat de conservació en la Mediterrània és el canó submarí de cap de Creus. Sobretot a la paret del sud del canó s’han pogut estudiar poblacions molt importants del corall Madrepora oculata i algunes petites poblacions de Lophelia pertusa. Les colònies d’aquests coralls configuren un hàbitat singular i de gran diversitat resultat, en part, de l’elevada producció biològica de l’àrea del cap de Creus i també perquè la seva localització a la paret del canó ha dificultat la destrucció encara que avui en dia les línies de palangre són l’amenaça més directa per a la seva supervivència.In the last decade, colonies of white coral have become of interest to scientists worldwide, partly because of their ecological relevance and partly because they are still little known. From older writings from the beginning of the twentieth century we know that these colonies were very frequent on themargins of the continental shelf in the Mediterranean between 150 and 400m deep. Nowadays, they are confined to areas where trawling activities have not destroyed them and it is urgent to find and evaluate its current state in order to promote its conservation. Another Mediterranean area where it can be found, and well-conserved, is the submarine channel of the Cap de Creus. Especially on the south side of the channel, important colonies of the Madrepora oculata coral have been studied and some smaller ones of Lophelia pertusa. These coral colonies make up a unique habitat of great diversity as a result of, in part, the elevated biological production of the Cap de Creus area. And also because their situation on the channel’s wall has protected them from destruction, although longline fishing represents a direct threat against its survival still today

Contrasting metabolic strategies of two co‑occurring deep‑sea octocorals

The feeding biology of deep-sea octocorals remains poorly understood, as attention is more often directed to reef building corals. The present study focused on two common deep-water octocoral species in the Azores Archipelago, Dentomuricea aff. meteor and Viminella flagellum, aiming at determining their ability to exploit different food sources. We adopted an experimental approach, with three different food sources, including live phytoplankton, live zooplankton and dissolved organic matter (DOM), that were artificially enriched with 13C and 15N (C and N tracers). The presence of tracers was subsequently followed in the coral tissue, C respiration and particulate organic C and N (POC and PON) release. In both species, feeding with zooplankton resulted in significantly higher incorporation of tracers in all measured variables, compared to the other food sources, highlighting the importance of zooplankton for major physiological processes. Our results revealed contrasting metabolic strategies between the two species, with D. aff. meteor acquiring higher amounts of prey and allocating higher percentage to respiration and release of POC and PON than V. flagellum. Such metabolic differences can shape species fitness and distributions and have further ecological implications on the ecosystem function of communities formed by different octocoral species.Versión del edito

A road map for defining Good Environmental Status in the deep-sea

The development of tools to assess the Good Environmental Status (GES) in the Deep Sea (DS) is one of the aspects that ATLAS WP3 is addressing. GES assessment in the DS is challenging due to 1) the lack of baseline data, 2) the remoteness of the DS ecosystems, and 3) the limitations of the sampling methods currently available. Throughout the duration of the project, ATLAS will develop a suitable approach to address GES in the DS. During the 2nd General Assembly, we will present a draft for a “road map” to address GES in the DS as well some of the aspects discussed during the 2017 ICES WG on Deep Sea Ecosystems. The temporal and spatial scale at which GES should be assessed in the deep-sea is an important aspect to be considered. Due to the data limited situation and challenges posed to monitoring, it may well be the case that GES will have to be assessed at large spatial and temporal scales when comparing the shallower waters of the European Seas. For similar reasons, the type of indicators to be used may have to be simplified and likely be based on high-level analyses related to traits, pressures/risks, and habitat /ecosystem resilience. Ultimately, the results of the combined analyses of GES descriptors might bring to a potential refining or redefinition of the GES concept for the deep-sea

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

Benthic suspension feeders, key players in Antartic marine ecosystems?

Ja fa un cert temps que hom accepta, de manera general i a partir d'estudis de la columna d'aigua en mar obert, que en les comunitats marines de l'oceà Antàrtic hi ha un període prolongat d'activitat hivernal mínima que s'estén al llarg de sis mesos com a mínim, que és el temps que dura l'hivern austral. Tanmateix, investigacions recents en algunes espècies d'invertebrats suspensívors (filtradors) bentònics litorals han suggerit que el període d'inactivitat potser dura només unes poques setmanes. Això planteja una interessant qüestió: què és el que permet que aquests organismes antàrtics mengin, i per tant romanguin actius, durant períodes molt més llargs del que fins ara s'havia cregut? Hom ha suggerit adaptacions especials a menjar en concentracions molt baixes d'aliment, o bé a usar eficientment l'abundància ocasional d'aliment enmig de llargs períodes d'escassedat. Molts animals suspensívors podrien usar fonts alternatives al seu aliment usual, el fito- i el zooplàncton; per exemple, la ?fracció fina' de matèria orgànica, o microplàncton (bacteris, ciliats i flagel·lats, junt amb carboni inorgànic particulat d'orígens diversos), que hom ha demostrat recentment que té un paper molt més significatiu del que hom creia a l'hora de complementar la dieta i de subvenir a les demandes energètiques de moltes espècies de suspensívors. També s'ha esmentat el possible paper de la resuspensió de sediments i, atès l'elevat valor alimentari del component orgànic dels sediments antàrtics, àdhuc de fons pregons, serà interessant investigar més en aquesta línia. Observacions recents relacionades amb la dieta natural (captura de preses) d'algunes espècies d'aigües somes porten a suposar que alguns suspensívors antàrtics, si més no, tenen taxes de creixement i reproducció que són similars a les assenyalades per a espècies d'aigües temperades.For quite some time it was generally accepted, from water column and open sea studies, that in Antarctic marine communities there is a prolonged period of minimal winter activity which lasts for at least six months during the Southern winter. However, recent studies on certain littoral benthic suspension feeders have suggested that the period of inactivity may last only a few weeks. This raises the question of what allows these organisms to feed, and hence remain active, for considerably longer periods than previously thought. Special adaptations to feeding at low levels of food concentration, or to using occasional food abundance followed by long periods of starvation have been suggested. Many suspension feeders might use alternative food sources to phytoand zooplankton, e.g., the «fine fraction» of organic matter, or microplankton (bacteria, ciliates, and flagellates including POC of several origins), which has recently been shown to play a much more significant role than expected in complementing the diet and meeting energy demands in many species of suspension feeders. The possible role of sediment resuspension has also been reported, and given the high food value of the organic component of sediments even on deep bottoms further research would be of interest. Recent observations related to the natural diet (prey capture) of several shallow species lead to the assumption that part of Antarctic suspension feeders have similar growth and reproduction rates to those reported for temperate waters. Efficient food assimilation may contribute to our understanding of the continuous reproduction state observed in octocorals and, also, of the development of tridimensionally structured communities which are suspension-feeder dominated, highly diversified, and have a high biomass

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