On the Expressivity and Applicability of Model Representation Formalisms

A number of first-order calculi employ an explicit model representation formalism for automated reasoning and for detecting satisfiability. Many of these formalisms can represent infinite Herbrand models. The first-order fragment of monadic, shallow, linear, Horn (MSLH) clauses, is such a formalism used in the approximation refinement calculus. Our first result is a finite model property for MSLH clause sets. Therefore, MSLH clause sets cannot represent models of clause sets with inherently infinite models. Through a translation to tree automata, we further show that this limitation also applies to the linear fragments of implicit generalizations, which is the formalism used in the model-evolution calculus, to atoms with disequality constraints, the formalisms used in the non-redundant clause learning calculus (NRCL), and to atoms with membership constraints, a formalism used for example in decision procedures for algebraic data types. Although these formalisms cannot represent models of clause sets with inherently infinite models, through an additional approximation step they can. This is our second main result. For clause sets including the definition of an equivalence relation with the help of an additional, novel approximation, called reflexive relation splitting, the approximation refinement calculus can automatically show satisfiability through the MSLH clause set formalism.Comment: 15 page

New results on rewrite-based satisfiability procedures

Program analysis and verification require decision procedures to reason on theories of data structures. Many problems can be reduced to the satisfiability of sets of ground literals in theory T. If a sound and complete inference system for first-order logic is guaranteed to terminate on T-satisfiability problems, any theorem-proving strategy with that system and a fair search plan is a T-satisfiability procedure. We prove termination of a rewrite-based first-order engine on the theories of records, integer offsets, integer offsets modulo and lists. We give a modularity theorem stating sufficient conditions for termination on a combinations of theories, given termination on each. The above theories, as well as others, satisfy these conditions. We introduce several sets of benchmarks on these theories and their combinations, including both parametric synthetic benchmarks to test scalability, and real-world problems to test performances on huge sets of literals. We compare the rewrite-based theorem prover E with the validity checkers CVC and CVC Lite. Contrary to the folklore that a general-purpose prover cannot compete with reasoners with built-in theories, the experiments are overall favorable to the theorem prover, showing that not only the rewriting approach is elegant and conceptually simple, but has important practical implications.Comment: To appear in the ACM Transactions on Computational Logic, 49 page

Discriminability of tryptophan containing dipeptides using quantum control

We show that the coherent manipulation of molecular wavepackets in the excited states of trp-containing dipeptides allows efficient discrimination among them. Optimal dynamic discrimination fails, however, for some dipeptide couples. When considering the limited spectral resources at play (3nm bandwidth at 266nm), we discuss the concept of discriminability, which appears uncorrelated to both static spectra and relaxation lifetime

Comparative chondrogenesis of human cells in a 3D integrated experimental/computational mechanobiology model

We present an integrated experimental–computational mechanobiology model of chondrogenesis. The response of human articular chondrocytes to culture medium perfusion, versus perfusion associated with cyclic pressurisation, versus non-perfused culture, was compared in a pellet culture model, and multiphysic computation was used to quantify oxygen transport and flow dynamics in the various culture conditions. At 2 weeks of culture, the measured cell metabolic activity and the matrix content in collagen type II and aggrecan were greatest in the perfused+ pressurised pellets. The main effects of perfusion alone, relative to static controls, were to suppress collagen type I and GAG contents, which were greatest in the non-perfused pellets. All pellets showed a peripheral layer of proliferating cells, which was thickest in the perfused pellets, and most pellets showed internal gradients in cell density and matrix composition. In perfused pellets, the computed lowest oxygen concentration was 0.075mM (7.5% tension), the maximal oxygen flux was 477.5 nmol/m2/s and the maximal fluid shear stress, acting on the pellet surface, was 1.8mPa (0.018 dyn/cm2). In the non-perfused pellets, the lowest oxygen concentration was 0.003mM (0.3% tension) and the maximal oxygen flux was 102.4nmol/m2/s.Alocal correlationwas observed, between the gradients in pellet properties obtained from histology, and the oxygen fields calculated with multiphysic simulation. Our results showup-regulation of hyalinematrix protein production by human chondrocytes in response to perfusion associated with cyclic pressurisation. These results could be favourably exploited in tissue engineering applications

Improving the Efficiency of Reasoning Through Structure-Based Reformulation

Abstract. We investigate the possibility of improving the efficiency of reasoning through structure-based partitioning of logical theories, combined with partitionbased logical reasoning strategies. To this end, we provide algorithms for reasoning with partitions of axioms in first-order and propositional logic. We analyze the computational benefit of our algorithms and detect those parameters of a partitioning that influence the efficiency of computation. These parameters are the number of symbols shared by a pair of partitions, the size of each partition, and the topology of the partitioning. Finally, we provide a greedy algorithm that automatically reformulates a given theory into partitions, exploiting the parameters that influence the efficiency of computation.

HDL in Immune-Inflammatory Responses: Implications beyond Cardiovascular Diseases

High density lipoproteins (HDL) are heterogeneous particles composed by a vast array of proteins and lipids, mostly recognized for their cardiovascular (CV) protective effects. However, evidences from basic to clinical research have contributed to depict a role of HDL in the modulation of immune-inflammatory response thus paving the road to investigate their involvement in other diseases beyond those related to the CV system. HDL-C levels and HDL composition are indeed altered in patients with autoimmune diseases and usually associated to disease severity. At molecular levels, HDL have been shown to modulate the anti-inflammatory potential of endothelial cells and, by controlling the amount of cellular cholesterol, to interfere with the signaling through plasma membrane lipid rafts in immune cells. These findings, coupled to observations acquired from subjects carrying mutations in genes related to HDL system, have helped to elucidate the contribution of HDL beyond cholesterol efflux thus posing HDL-based therapies as a compelling interventional approach to limit the inflammatory burden of immune-inflammatory diseases

Deslorelin subcutaneous implants in Oryx dammah males for reproductive control

The aim of this study was to assess the effects of the deslorelin subcutaneous implant as a temporary contraceptive method in the Oryx dammah male. For this purpose, deslorelin at different doses, i.e. 14.1 mg and 9.4 mg, was subcutaneously implanted in three males (Phase 1) and one male (Phase 2) adult Oryx dammah, respectively. Quantitative behavior evaluation and androgen concentrations in feces and plasma were assessed before and after implant application. Fecal androgen concentrations observed in treated males were compared with those measured in one orchiectomized male and two females. Fecal androgen concentrations increased up to 15 days after the implant application, then progressively decreased, reaching the basal level at day150 in Phase 1. In Phase 2, levels remained high until day 60 and returned to basal level on day 120. Plasma testosterone concentration was higher on the day of implant application than three months later, but with variable ranges among males. A general increase of activity levels and hierarchical changes were observed after treatment, in accordance with hormonal variations. Despite males cohabiting with two fertile females during the observation period, no births were recorded. However, between the end of Phase 1 and the beginning of Phase 2, i.e. about 10–11 months after the first deslorelin implant, a fertile mating occurred leading to the birth of a calf. Therefore, we can hypothesize a contraceptive effect up to 10 months after the implant. Testicular histology performed on one male at the end of the Phase 2 showed no spermatogenetic activity. Our results suggest that deslorelin implant can be used to temporarily control reproduction in the Oryx dammah male. Behavior and fecal androgen measurements were useful and repeatable, non-invasive methods to monitor response

Quantization of Midisuperspace Models

We give a comprehensive review of the quantization of midisuperspace models. Though the main focus of the paper is on quantum aspects, we also provide an introduction to several classical points related to the definition of these models. We cover some important issues, in particular, the use of the principle of symmetric criticality as a very useful tool to obtain the required Hamiltonian formulations. Two main types of reductions are discussed: those involving metrics with two Killing vector fields and spherically symmetric models. We also review the more general models obtained by coupling matter fields to these systems. Throughout the paper we give separate discussions for standard quantizations using geometrodynamical variables and those relying on loop quantum gravity inspired methods.Comment: To appear in Living Review in Relativit