A generic framework for the analysis and specialization of logic programs

The relationship between abstract interpretation and partial deduction has received considerable attention and (partial) integrations have been proposed starting from both the partial deduction and abstract interpretation perspectives. In this work we present what we argüe is the first fully described generic algorithm for efñcient and precise integration of abstract interpretation and partial deduction. Taking as starting point state-of-the-art algorithms for context-sensitive, polyvariant abstract interpretation and (abstract) partial deduction, we present an algorithm which combines the best of both worlds. Key ingredients include the accurate success propagation inherent to abstract interpretation and the powerful program transformations achievable by partial deduction. In our algorithm, the calis which appear in the analysis graph are not analyzed w.r.t. the original definition of the procedure but w.r.t. specialized definitions of these procedures. Such specialized definitions are obtained by applying both unfolding and abstract executability. Our framework is parametric w.r.t. different control strategies and abstract domains. Different combinations of such parameters correspond to existing algorithms for program analysis and specialization. Simultaneously, our approach opens the door to the efñcient computation of strictly more precise results than those achievable by each of the individual techniques. The algorithm is now one of the key components of the CiaoPP analysis and specialization system.

Some issues in analysis and specialization of modular ciao-prolog programs

Separating programs into modules is a well-known technique which has proven very useful in program development and maintenance. Starting by introducing a number of possible scenarios, in this paper we study different issues which appear when developing analysis and specialization techniques for modular logic programming. We discuss a number of design alternatives and their consequences for the different scenarios considered and describe where applicable the decisions made in the Ciao system analyzer and specializer. In our discussion we use the module system of Ciao Prolog. This is both for concreteness and because Ciao Prolog is a second-generation Prolog system which has been designed with global analysis and specialization in mind, and which has a strict module system. The aim of this work is not to provide a theoretical basis on modular analysis and specialization, but rather to discuss some interesting practical issues.

Towards Integrating Partial Evaluation in a Specialization Framework based on Generic Abstract Interpretation

Abstract is not available

Specialization and optimization of constraint programs with dynamic scheduling

In this report we discuss some of the issues involved in the specialization and optimization of constraint logic programs with dynamic scheduling. Dynamic scheduling, as any other form of concurrency, increases the expressive power of constraint logic programs, but also introduces run-time overhead. The objective of the specialization and optimization is to reduce as much as possible such overhead automatically, while preserving the semantics of the original programs. This is done by program transformation based on global analysis. We present implementation techniques for this purpose and report on experimental results obtained from an implementation of the techniques in the context of the CIAO compiler.

Mathematical and Numerical Modeling in Maritime Geomechanics

A theoretical and numerical framework to model the foundation of marine offshore structures is presented. The theoretical model is composed by a system of partial differential equations describing coupling between seabed solid skeleton and pore fluids (water, air, oil,…) combined with a system of ordinary differential equations describing the specific constitutive relation of the seabed soil skeleton. Once the theoretical model is described, the finite element numerical procedure to achieve an approximate solution of the governing equations is outlined. In order to validate the proposed theoretical and numerical framework the seaward tilt mechanism induced by the action of breaking waves over a vertical breakwater is numerically reproduced. The results numerically attained are in agreement with the main conclusions drawn from the literature associated with this failure mechanism

Test Analysis Tool (TATo). A new tool for standardization of time series in maritime and port environment

During the last decades, Puertos del Estado and research groups have developed a huge effort on numerical an physical monitoring. This effort has led to the necessity to implement a tool to standardize, store and process all gathered data. The Test Analysis Tool (TATo) is described in the paper.

National Museum of Maritime Archeology

In collaboration with Antón García Abril.

Retablissement des manufactures et du commerce d'Espagne [Texto impreso] : ouvrage dividé en deux parties : la premiere, qui considere principalement les manufactures d'Espagne. La seconde, qui traite de son commerce maritime

Segunda parte con portadilla propia : Retablissement des manufactures et du commerce d'espagne. Seconde partie ...

Differential elimination by differential specialization of Sylvester style matrices

Differential resultant formulas are defined, for a system $\cP$ of $n$ ordinary Laurent differential polynomials in $n-1$ differential variables. These are determinants of coefficient matrices of an extended system of polynomials obtained from $\cP$ through derivations and multiplications by Laurent monomials. To start, through derivations, a system $\ps(\cP)$ of $L$ polynomials in $L-1$ algebraic variables is obtained, which is non sparse in the order of derivation. This enables the use of existing formulas for the computation of algebraic resultants, of the multivariate sparse algebraic polynomials in $\ps(\cP)$, to obtain polynomials in the differential elimination ideal generated by $\cP$. The formulas obtained are multiples of the sparse differential resultant defined by Li, Yuan and Gao, and provide order and degree bounds in terms of mixed volumes in the generic case.

Molecular adaptation of Ammonia Monooxygenase during independent pH specialization in Thaumarchaeota

Acknowledgements. This work was funded by Natural Environment Research Council Fellowship NE/J019151/1 and by institutional funding from within the University of Aberdeen.

Espin Contains an Additional Actin-binding Site in Its N Terminus and Is a Major Actin-bundling Protein of the Sertoli Cell–Spermatid Ectoplasmic Specialization Junctional Plaque

The espins are actin-binding and -bundling proteins localized to parallel actin bundles. The 837-amino-acid “espin” of Sertoli cell–spermatid junctions (ectoplasmic specializations) and the 253-amino-acid “small espin” of brush border microvilli are splice isoforms that share a C-terminal 116-amino-acid actin-bundling module but contain different N termini. To investigate the roles of espin and its extended N terminus, we examined the actin-binding and -bundling properties of espin constructs and the stoichiometry and developmental accumulation of espin within the ectoplasmic specialization. An espin construct bound to F-actin with an approximately threefold higher affinity (Kd = ∼70 nM) than small espin and was ∼2.5 times more efficient at forming bundles. The increased affinity appeared to be due to an additional actin-binding site in the N terminus of espin. This additional actin-binding site bound to F-actin with a Kd of ∼1 μM, decorated actin stress fiber-like structures in transfected cells, and was mapped to a peptide between the two proline-rich peptides in the N terminus of espin. Espin was detected at ∼4–5 × 106 copies per ectoplasmic specialization, or ∼1 espin per 20 actin monomers and accumulated there coincident with the formation of parallel actin bundles during spermiogenesis. These results suggest that espin is a major actin-bundling protein of the Sertoli cell–spermatid ectoplasmic specialization.

Evolutionary specialization of the nuclear targeting apparatus

The α- and β-karyopherins (Kaps), also called importins, mediate the nuclear transport of proteins. All α-Kaps contain a central domain composed of eight approximately 40 amino acid, tandemly arranged, armadillo-like (Arm) repeats. The number and order of these repeats have not changed since the common origin of fungi, plants, and mammals. Phylogenetic analysis suggests that the various α-Kaps fall into two groups, α1 and α2. Whereas animals encode both types, the yeast genome encodes only an α1-Kap. The β-Kaps are characterized by 14–15 tandemly arranged HEAT motifs. We show that the Arm repeats of α-Kaps and the HEAT motifs of β-Kaps are similar, suggesting that the α-Kaps and β-Kaps (and for that matter, all Arm and HEAT repeat-containing proteins) are members of the same protein superfamily. Phylogenetic analysis indicates that there are at least three major groups of β-Kaps, consistent with their proposed cargo specificities. We present a model in which an α-independent β-Kap progenitor gave rise to the α-dependent β-Kaps and the α-Kaps.

Feeding specialization and host-derived chemical defense in Chrysomeline leaf beetles did not lead to an evolutionary dead end

Combination of molecular phylogenetic analyses of Chrysomelina beetles and chemical data of their defensive secretions indicate that two lineages independently developed, from an ancestral autogenous metabolism, an energetically efficient strategy that made the insect tightly dependent on the chemistry of the host plant. However, a lineage (the interrupta group) escaped this subordination through the development of a yet more derived mixed metabolism potentially compatible with a large number of new host-plant associations. Hence, these analyses on leaf beetles document a mechanism that can explain why high levels of specialization do not necessarily lead to “evolutionary dead ends.”

Molecular organization of the postsynaptic specialization

A specific set of molecules including glutamate receptors is targeted to the postsynaptic specialization of excitatory synapses in the brain, gathering in a structure known as the postsynaptic density (PSD). Synaptic targeting of glutamate receptors depends on interactions between the C-terminal tails of receptor subunits and specific PDZ domain-containing scaffold proteins in the PSD. These scaffold proteins assemble a specialized protein complex around each class of glutamate receptor that functions in signal transduction, cytoskeletal anchoring, and trafficking of the receptors. Among the glutamate receptor subtypes, the N-methyl-d-aspartate receptor is relatively stably integrated in the PSD, whereas the α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor moves in and out of the postsynaptic membrane in highly dynamic fashion. The distinctive cell biological behaviors of N-methyl-d-aspartate and α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptors can be explained by their differential interactions with cytoplasmic proteins.