Papers by alexandra silva
Users may download and print one copy of any publication from the public portal for the purpose... more Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim.
Lecture Notes in Computer Science
We present a novel coalgebraic logic for deterministic Mealy machines that is sound, complete and... more We present a novel coalgebraic logic for deterministic Mealy machines that is sound, complete and expressive w.r.t. bisimulation. Every finite Mealy machine corresponds to a finite formula in the language. For the converse, we give a compositional synthesis algorithm which transforms every formula into a finite Mealy machine whose behaviour is exactly the set of causal functions satisfying the formula.
Abundance and distribution of megrims, Lepidorhombus boscii and L. whiffiagonis, in ICES Division Ixa (Portuguese waters
The geographic and bathymetric distribution of megrims off the Portuguese continental coast is de... more The geographic and bathymetric distribution of megrims off the Portuguese continental coast is described, based on a series of groundfish and crustacean surveys carried out by R/V Noruega of IPIMAR during 1990-1993. A log-linear model was used to analyse four-spot megrim data while, in the case of megrim, a visual inspection of raw data was performed. The results suggest an abundance decrease of four-spot megrim from 1990 to 1991. This species occurs mainly at depths greater than 200m and a seasonal abundance pattern is observed but with opposite trends between the north and the south Portuguese coast. A poor 1990 recruitment is also evidenced by the data showing agreement with VPA results. Megrim is also more abundant at the slope and abundance levels show a decline since 1990.
Ecological Indicators, 2015
This study reports the state and causes of eutrophication in the Portuguese continental Exclusive... more This study reports the state and causes of eutrophication in the Portuguese continental Exclusive Economic Zone (EEZ), during a 14-year period (1995-2008), following the European Marine Strategy Framework Directive (MSFD) and using the trophic index TRIX for an integrated evaluation of indicators of eutrophication, and identifies areas where monitoring is needed to improve the eutrophication assessment. A non-continuous dataset for the 8 indicators specified by the MSFD for eutrophication assessment was used, including published and grey data. Eutrophication indicators were validated and thresholds reviewed, considering regional differences. The diatom:flagellate ratio was found a poor indicator of eutrophication as shifts in the diatom:flagellate ratio naturally occur associated with alternating water column turbulence and upwelling, and stratification, and therefore, could not be associated with anthropogenic nutrient enrichment effects. Assessment areas were, as a whole, classified as non-problem areas concerning eutrophication. Although nutrient enrichment was observed in coastal waters, related to river plume influence, nutrient enrichment direct and indirect effects were generally not detectable, possibly due to water column dispersion and mixing processes. Only occasionally, mild eutrophication was found in specific areas under the influence of major river (Douro, Vouga and Guadiana) plumes, associated with high nutrient and phytoplankton biomass levels and seagrass decline, which indicates the need for directed monitoring on eutrophication in those areas.
Lecture Notes in Computer Science, 2013
In automata theory, a machine transitions from one state to the next when it reads an input symbo... more In automata theory, a machine transitions from one state to the next when it reads an input symbol. It is common to also allow an automaton to transition without input. These so-called ε-transitions are convenient, e.g., when one defines the composition of automata. However, they are not necessary, and can be eliminated. Such ε-elimination procedures have been studied separately for different types of automata, including non-deterministic and weighted automata. It has been noted by Hasuo that it is possible to give a coalgebraic account of ε-elimination for some automata using trace semantics (as defined by Hasuo, Jacobs and Sokolova). In this paper, we give a detailed description of the ε-elimination procedure via trace semantics (missing in the literature). We apply this framework to several types of automata, and explore its boundary. In particular, we show that is possible (by careful choice of a monad) to define an ε-removal procedure for all weighted automata over the positive reals (and certain other semirings). Our definition extends the recent proposals by Sakarovitch and Lombardy for these semirings.
Proceedings of the 29th Annual ACM Symposium on Applied Computing, 2014
Quality of Service analysis of composed software systems is an active research area, with the goa... more Quality of Service analysis of composed software systems is an active research area, with the goal of evaluating and improving performance and resource allocation in serviceoriented applications, namely, in the glue code-coordination layer-of such systems. Stochastic Reo offers constructs for service coordination and allows the specification of stochastic values for channels. But its state-of-the-art semantic models fail in several (important) ways. In this paper, we will see how Interactive Markov chains (IMC), proposed as a stochastic compositional model of concurrency, can be effectively used to serve as a compositional semantic model for Stochastic Reo. Treating IMC as a direct semantic model, gives rise to more faithful models and has obvious efficiency advantages. Moreover, tool support that exists for IMC is made available, without significant effort, to verify and reason about the coordination layer modelled as Reo connectors.
Proceedings of the 2006 ACM SIGPLAN workshop on Haskell, 2006
Haskell's type system with multi-parameter constructor classes and functional dependencies allows... more Haskell's type system with multi-parameter constructor classes and functional dependencies allows static (compile-time) computations to be expressed by logic programming on the level of types. This emergent capability has been exploited for instance to model arbitrary-length tuples (heterogeneous lists), extensible records, functions with variable length argument lists, and (homogenous) lists of statically fixed length (vectors). We explain how type-level programming can be exploited to define a strongly-typed model of relational databases and operations on them. In particular, we present a strongly typed embedding of a significant subset of SQL in Haskell. In this model, meta-data is represented by type-level entities that guard the semantic correctness of database operations at compile time. Apart from the standard relational database operations, such as selection and join, we model functional dependencies (among table attributes), normal forms, and operations for database transformation. We show how functional dependency information can be represented at the type level, and can be transported through operations. This means that type inference statically computes functional dependencies on the result from those on the arguments. Our model shows that Haskell can be used to design and prototype typed languages for designing, programming, and transforming relational databases.
Lecture Notes in Computer Science, 2013
Checking language equivalence (or inclusion) of finite automata is a classical problem in Compute... more Checking language equivalence (or inclusion) of finite automata is a classical problem in Computer Science, which has recently received a renewed interest and found novel and more effective solutions, such as approaches based on antichains or bisimulations up-to. Several notions of equivalence (or preorder) have been proposed for the analysis of concurrent systems. Usually, the problem of checking these equivalences is reduced to checking bisimilarity. In this paper, we take a different approach and propose to adapt algorithms for language equivalence to check one prime equivalence in concurrency theory, must testing semantics. To achieve this transfer of technology from language to must semantics, we take a coalgebraic outlook at the problem.
Electronic Proceedings in Theoretical Computer Science, 2011
Process calculi and graph transformation systems provide models of reactive systems with labelled... more Process calculi and graph transformation systems provide models of reactive systems with labelled transition semantics. While the semantics for process calculi is compositional, this is not the case for graph transformation systems, in general. Hence, the goal of this article is to obtain a compositional semantics for graph transformation system in analogy to the structural operational semantics (SOS) for Milner's Calculus of Communicating Systems (CCS). The paper introduces an SOS style axiomatization of the standard labelled transition semantics for graph transformation systems. The first result is its equivalence with the so-called Borrowed Context technique. Unfortunately, the axiomatization is not compositional in the expected manner as no rule captures "internal" communication of subsystems. The main result states that such a rule is derivable if the given graph transformation system enjoys a certain property, which we call "complementarity of actions". Archetypal examples of such systems are interaction nets. We also discuss problems that arise if "complementarity of actions" is violated.
Frontiers in Molecular Biosciences, 2014
Candida albicans is a polymorphic opportunistic fungal pathogen normally residing as commensal on... more Candida albicans is a polymorphic opportunistic fungal pathogen normally residing as commensal on mucosal surfaces, skin and gastrointestinal and genitourinary tracts. However, in immunocompromised patients C. albicans can cause superficial mucosal infections or life-threatening disseminated candidemia. A change in physiological conditions triggers a cascade of molecular events leading to morphogenetic alterations and increased resistance to damage induced by host defenses. The complex biology of this human pathogen is reflected in its morphological plasticity and reinforced by the ability to ambiguously translate the universal leucine CUG codon predominantly as serine, but also as leucine. Mistranslation affects more than half of C. albicans proteome and it is widespread across many biological processes. A previous analysis of CTG-codon containing gene products in C. albicans suggested that codon ambiguity subtly shapes protein function and might have a pivotal role in signaling cascades associated with morphological changes and pathogenesis. In this review we further explore this hypothesis by highlighting the role of ambiguous decoding in macromolecular recognition of key effector proteins associated with the regulation of signal transduction cascades and the cell cycle, which are critical processes for C. albicans morphogenic plasticity under a variety of environmental conditions.
Lecture Notes in Computer Science, 2012
Coalgebra offers a unified theory of state based systems, including infinite streams, labelled tr... more Coalgebra offers a unified theory of state based systems, including infinite streams, labelled transition systems and deterministic automata. In this paper, we use the coalgebraic view on systems to derive, in a uniform way, abstract procedures for checking behavioural equivalence in coalgebras, which perform (a combination of) minimization and determinization. First, we show that for coalgebras in categories equipped with factorization structures, there exists an abstract procedure for equivalence checking. Then, we consider coalgebras in categories without suitable factorization structures: under certain conditions, it is possible to apply the above procedure after transforming coalgebras with reflections. This transformation can be thought of as some kind of determinization. We will apply our theory to the following examples: conditional transition systems and (non-deterministic) automata.
Progress in Oceanography, 2009
Sea surface temperature (SST) and chlorophyll (Chl) maps derived from satellite data, together wi... more Sea surface temperature (SST) and chlorophyll (Chl) maps derived from satellite data, together with wind and phytoplankton cell concentration time-series, are used to characterize the wind forcing and the spatio-temporal SST/Chl variability for periods preceding the summer (June-September) diatom and dinoflagellate blooms. The blooms (concentrations of cells higher than 200 Â 10 3 cells l À1) were identified in the weekly samples collected at the long-term phytoplankton study site in Lisbon Bay, from 2002 to 2005. It is shown that bloom detection at the site occurs either during upwelling events, i.e. when offshore northerly wind speed is greater than 5 m s À1 for more than 5 days, or up to 4 days after wind relaxation. However, no direct relationship was found between the blooms and either the intensity or duration of the wind pulses. The satellite image sequences show that the Chl patterns in Lisbon Bay are strongly linked to the orientation and branching of the upwelling filament rooted at Cape Roca and the westward progression of the warm-core cyclones shed from the slope off Setúbal Bay. High Chl values are typically maintained throughout the upwelling cycle along the inshore boundary of the Roca filament, covering the whole bay during the intense wind phase. During the relaxation phase, there is a Chl increase concurrent with the contraction of the high Chl area to the northern part of the bay, associated with an inshore poleward current. It is proposed that the earlier setup of the offshore stratification conditions and the shedding of a slope eddy favored the bloom of dinoflagellates in July 2004, while the stable position of the main circulation features in July 2002 favored a diatom bloom. The results add further evidence that, in summer, the ocean circulation in the embayments south Cape Roca is dominated by the upwelling dynamics and plays a key role in the development of phytoplankton blooms off central Portugal.
Lecture Notes in Computer Science, 2011
A notion of generalized regular expressions for a large class of systems modeled as coalgebras, a... more A notion of generalized regular expressions for a large class of systems modeled as coalgebras, and an analogue of Kleene's theorem and Kleene algebra, were recently proposed by a subset of the authors of this paper. Examples of the systems covered include infinite streams, deterministic automata and Mealy machines. In this paper, we present a novel algorithm and a tool to decide whether two expressions are bisimilar or not. The procedure is implemented in the automatic theorem prover CIRC, by reducing coinduction to an entailment relation between an algebraic specification and an appropriate set of equations.
Feeding habits of John Dory, Zeus faber, off the Portuguese continental coast
Journal of the Marine Biological Association of the United Kingdom, 1999
The feeding habits of John Dory (Zeus faber) were studied, based on the analysis of stomach conte... more The feeding habits of John Dory (Zeus faber) were studied, based on the analysis of stomach contents from fish sampled in five groundfish surveys. These surveys were carried out off the Portuguese coast during different seasons between 1990 and 1992. The main aspects of feeding biology analysed in this paper are: ontogenetic diet changes, temporal variations in food composition and feeding intensity. Multivariate methods were used to investigate ontogenetic diet shifts. Two main length groups were identified: 8.0–24.9 cm fish, feeding mainly on dragonets and silvery pout, and 25.0–55.9 cm fish whose diet was mainly composed of blue whiting and snipefish. A transitional phase (24.0–30.9 cm fish) with a mixed food composition was observed. This ontogenetic diet shift does not seem to correspond to any important change in body morphology but it does coincide with the onset of sexual maturity in the species.John Dory switched from a diet of small prey species with more pronounced benthi...
Scientia Marina, 2013
Long-term changes in sardine maturation were described using samples collected from landings off ... more Long-term changes in sardine maturation were described using samples collected from landings off the western Portuguese coast since 1947. Estimates of the length at 50% maturity (L 50) were calculated in 44 years of the study period and proved to be good proxies of the maturation length of first-year spawners (Lp 50 of age 0-1 fish). Sardine probability of maturing at a given length declined from the early 1950s to the late 1960s, corresponding to an increase of ca. 2 cm in both L 50 and Lp 50. This trend reversed in the early 1970s and halted in the early to mid-1990s. The tendency for sardine to mature at a lower length was positively correlated with improved body condition in the growing season preceding maturation. Long-term trends in sardine maturation and body condition were parallel to trends in sea surface temperature reported in the literature. The results suggest that maturation at a lower size is directly influenced by increased temperature, and that higher temperatures improve body condition through increased feeding efficiency or a combination of both. We found no evidence that fishing intensity has contributed to long-term changes in sardine maturation.
Scientia Marina, 2013
This study describes changes in abundance and spatial distribution of Atlantic chub mackerel in t... more This study describes changes in abundance and spatial distribution of Atlantic chub mackerel in the Portuguese waters and the Spanish waters of the Gulf of Cadiz using data from acoustic surveys from 1995 to 2010 and data from the fishery since 1958. The distribution and dynamics of chub mackerel and sardine (Sardina pilchardus) are compared and species interactions are discussed. From 2007 to 2009, chub mackerel biomass, as measured acoustically, ranged between 69000 and 238000 t concentrated off the western coast (~50%) and in the Gulf of Cadiz (~30%). Portuguese landings have varied with periods of high landings around 1970 and in recent years. Since 1986 landings have been between 4000 and 23000 t. Both survey catches and commercial landings are taken mainly off the southwestern coast and one-to two-year-old individuals (20-24 cm) predominate in both. Scarcity of larger individuals may be a consequence of their deeper distribution and avoidance of fishing gear, migration of older individuals or a combination of both. In years with high abundance, the fishery expands to the northwestern areas of the Iberian Peninsula. The expansion appears to be caused by improved recruitment although other factors might have contributed (such as targeting to compensate for low sardine catches and the appearance of new markets). The complementary spatial distribution of chub mackerel and sardine and the inverse correlations between their frequency of occurrence, landings and recruitment indices suggest some interaction between the dynamics of the two species, possibly associated with climatic variation.
Proceedings of the National Academy of Sciences, 2010
The free radical theory of aging posits oxidative damage to macromolecules as a primary determina... more The free radical theory of aging posits oxidative damage to macromolecules as a primary determinant of lifespan. Recent studies challenge this theory by demonstrating that in some cases, longevity is enhanced by inactivation of oxidative stress defenses or is correlated with increased, rather than decreased reactive oxygen species and oxidative damage. Here we show that, in Saccharomyces cerevisiae , caloric restriction or inactivation of catalases extends chronological lifespan by inducing elevated levels of the reactive oxygen species hydrogen peroxide, which activate superoxide dismutases that inhibit the accumulation of superoxide anions. Increased hydrogen peroxide in catalase-deficient cells extends chronological lifespan despite parallel increases in oxidative damage. These findings establish a role for hormesis effects of hydrogen peroxide in promoting longevity that have broad implications for understanding aging and age-related diseases.
Information and Computation, 2012
Weighted automata are a generalization of non-deterministic automata where each transition, in ad... more Weighted automata are a generalization of non-deterministic automata where each transition, in addition to an input letter, has also a quantity expressing the weight (e.g. cost or probability) of its execution. As for non-deterministic automata, their behaviours can be expressed in terms of either (weighted) bisimilarity or (weighted) language equivalence. Coalgebras provide a categorical framework for the uniform study of state-based systems and their behaviours. In this work, we show that coalgebras can suitably model weighted automata in two different ways: coalgebras on Set (the category of sets and functions) characterize weighted bisimilarity, while coalgebras on V ect (the category of vector spaces and linear maps) characterize weighted language equivalence. Relying on the second characterization, we show three different procedures for computing weighted language equivalence. The first one consists in a generalizion of the usual partition refinement algorithm for ordinary automata. The second one is the backward version of the first one. The third procedure relies on a syntactic representation of rational weighted languages.
Calcidiscus quadriperforatus and Calcidiscus leptoporus as oceanographic tracers in Lisbon Bay (Portugal)
Estuarine, Coastal and Shelf Science, 2009
A study of the Calcidiscus genus in Lisbon Bay has revealed the presence of Calcidiscus quadriper... more A study of the Calcidiscus genus in Lisbon Bay has revealed the presence of Calcidiscus quadriperforatus and Calcidiscus leptoporus. Samples were collected continuously on a weekly basis for four years (July 2001–May 2005) and on a cruise carried out in summer 2005, covering Lisbon Bay. Calcidiscus quadriperforatus and C. leptoporus developed in the same range of temperature and salinity, 11.5–21.5°C
Autophagy, 2012
of synucleinopathy. 4 Cell proteostasis is maintained by a precisely regulated protein quality co... more of synucleinopathy. 4 Cell proteostasis is maintained by a precisely regulated protein quality control system, consisting of a balance between the folding and refolding of misfolded proteins, by molecular chaperones, and the proteolytic systems, by the UPS and autophagy. 5 Soluble SNCA is degraded by the UPS pathway 6,7 and by chaperone-mediated autophagy (CMA). 8 Nevertheless, studies in yeast and cell line models show that insoluble SNCA and SNCA aggregates interact with the proteasome leading to its inhibition, 7,9-11 an observation also corroborated by assays performed in the substantia nigra of PD brains. 12 Mutant and dopamine-oxidized forms of SNCA also impair the CMA pathway leading to an upregulation of macroautophagy ©2012 Landes Bioscience. Do not distribute.
Uploads
Papers by alexandra silva