Concurrent and Reactive Constraint Programming

The Italian Logic Programming community has given several contributions to the theory of Concurrent Constraint Programming. In particular, in the topics of semantics, verification, and timed extensions. In this paper we review the main lines of research and contributions of the community in this fiel

Modelling concurrent systems specified in a temporal concurrent constraint language -I

In this paper we present an approach to model concurrent systems specified in a temporal concurrent constraint language. Our goal is to construct a framework in which it is possible to apply the Model Checking technique to programs specified in such language. This work is the first step to the framework construction. We present a formalism to transform a specification into a tcc Structure. This structure is a graph representation of the program behavior. Our basic tool is the Timed Concurrent Constraint Programming (tcc) framework defined by Saraswat et al. to describe reactive systems. With this language we take advantage of both the natural properties of the declarative paradigm and of the fact that the notion of time is built into the semantics of the programming language. In fact, on this ground it becomes reasonable to introduce the idea of applying the technique of Model Checking to a finite time interval (introduced by the user). With this restriction we naturally force the space representing the behavior of the program to be finite and hence Model Checking algorithms to be applicable. The graph construction is a completely automatic process that takes as input the tcc specification

Stochastic association of neighboring replicons creates replication factories in budding yeast

Peer reviewedPublisher PD

The new species Neoceroplatus betaryiensis nov. sp. (Diptera: Keroplatidae) from Neotropical Region

The species Neoceroplatus betaryiensis sp. nov. is presented here with the diagnosis of the species with indication of the ZooBank number, making this publication the valid description of the species

Invasive species and amphibian conservation

The recognition that invasive alien species (IAS) are among the greatest threats to biodiversity has stimulated a growing interest in their impacts on native amphibians. Here we describe the multifaceted consequences of biological invasions on native amphibians and identify potential mechanisms and strategies that could better enable the long-Term persistence of native species. IAS can influence amphibian fitness, population size, and community structure via multiple pathways and can exert major, direct impacts through predation, competition, and hybridization. The consequences of indirect impacts, too, such as habitat alteration and the spread of emerging diseases, can be particularly severe in native populations. Native amphibians may respond to IAS by modulating aspects of their behavior, morphology, or life history. Nevertheless, it is still unclear the extent to which phenotypic plasticity and rapid evolution may help native species withstand the impacts of IAS in invaded communities. Practical management strategies focused on prevention, monitoring, and early control are the most effective approaches to allay the impacts of IAS and should be prioritized in proactive conservation plans. Eradications of IAS and mitigation approaches, should IAS become established, are feasible and can greatly improve the status of native populations

A Computational Model of the Secondary Hemostasis Pathway in Reaction Systems

Reaction Systems (RSs) are a computational framework inspired by biochemical mechanisms. An RS defines a finite set of reactions over a finite set of entities (molecules, proteins, etc). Starting from an initial set of entities (the initial state), a computation is performed by applying all reactions to a state in order to produce the following state, giving rise to a sequence of sets of entities. RSs have shown to be a general computational framework whose application ranges from the modeling of biological phenomena to molecular chemistry and computer science. In this paper, we contribute to research on the application of RSs for modeling biological systems. We consider the problem of modeling hemostasis, for which several models have been defined, starting from the 1960s. Previous models are based on sets of ordinary differential equations, while we develop a discrete model in RSs for pathways of the secondary hemostasis. Then, we implement our model in BioReSolve, a computational framework for RSs that we have previously defined which provides tools for the specification and verification of properties. By using the tools in BioReSolve we derive important observations on the model behaviour for hemostasis, and in particular, we study the role of three important inhibitors, verifying that their presence or absence leads to phenomena such as thrombophilia, or thromboembolism, or excessive coagulation, etc. We can also study computationally the causality relations between the molecules involved in the reactions showing which entities play a fundamental role, thus contributing to the design of more effective and specialized drugs. Our work can hence help to show how to model complex biological systems in RSs and derive computationally and biologically relevant properties of the systems

Influence of bulla volume on postbullectomy outcome

Objective: To quantify the contribution of the resected volume and the presence of associated, functionally significant emphysema to the postoperative improvement of pulmonary function after resection of giant lung bullae. Design: Patients undergoing elective surgery for giant bullae who had complete pulmonary function and radiographic studies performed were reviewed retrospectively. Setting: All 25 patients underwent surgery at the thoracic surgery unit of the University of Pisa, Pisa, Italy. Methods: Pulmonary function was assessed before and 12 months after surgery. On the chest radiograph, the location of bullae, and the signs of compression and emphysema were evaluated. The radiographic total lung capacity (TLCX-ray) and the volume of bullae were measured according to the ellipse method. Postoperatively, functional and radiographic changes were analyzed. The percentage change in forced expiratory volume in 1 s(ΔFEV1%) after surgery was the main outcome measure. The influence of factors related to emphysema and bulla volume on the functional improvement postbullectomy was assessed by stepwise multiple regression. Results: Before surgery, the TLCx-ray overestimated the TLC measured by nitrogen washout, with a mean difference between the two measurements of 1.095 L. A close relationship was found between the TLCx-ray and the plethysmographic TLC (n=6; r=0.95). After surgery, dyspnea lessened (P<0.05) and FEV1 increased (P<0.01). Statistically, the radiographic bulla volume was the single most important factor determining the ΔFEV1% (r=0.80, P<0.0001). Conclusions: These findings suggest that the preoperative size of bullae is the most important contributor to the improvement in ventilatory capacity after bullectomy, and that it is possible to predict the expected increase of postoperative FEV1 from preoperative bulla volume