A type system for components

In modern distributed systems, dynamic reconfiguration, i.e., changing at runtime the communication pattern of a program, is chal- lenging. Generally, it is difficult to guarantee that such modifications will not disrupt ongoing computations. In a previous paper, a solution to this problem was proposed by extending the object-oriented language ABS with a component model allowing the programmer to: i) perform up- dates on objects by means of communication ports and their rebinding; and ii) precisely specify when such updates can safely occur in an object by means of critical sections. However, improper rebind operations could still occur and lead to runtime errors. The present paper introduces a type system for this component model that extends the ABS type system with the notion of ports and a precise analysis that statically enforces that no object will attempt illegal rebinding

Biomarkers in emergency medicine

Researchers navigate the ocean of biomarkers searching for proper targets and optimal utilization of them. Emergency medicine builds up the front line to maximize the utility of clinically validated biomarkers and is the cutting edge field to test the applicability of promising biomarkers emerging from thorough translational researches. The role of biomarkers in clinical decision making would be of greater significance for identification, risk stratification, monitoring, and prognostication of the patients in the critical- and acute-care settings. No doubt basic research to explore novel biomarkers in relation to the pathogenesis is as important as its clinical counterpart. This special issue includes five selected research papers that cover a variety of biomarker- and disease-related topics

Syntactic Markovian Bisimulation for Chemical Reaction Networks

In chemical reaction networks (CRNs) with stochastic semantics based on continuous-time Markov chains (CTMCs), the typically large populations of species cause combinatorially large state spaces. This makes the analysis very difficult in practice and represents the major bottleneck for the applicability of minimization techniques based, for instance, on lumpability. In this paper we present syntactic Markovian bisimulation (SMB), a notion of bisimulation developed in the Larsen-Skou style of probabilistic bisimulation, defined over the structure of a CRN rather than over its underlying CTMC. SMB identifies a lumpable partition of the CTMC state space a priori, in the sense that it is an equivalence relation over species implying that two CTMC states are lumpable when they are invariant with respect to the total population of species within the same equivalence class. We develop an efficient partition-refinement algorithm which computes the largest SMB of a CRN in polynomial time in the number of species and reactions. We also provide an algorithm for obtaining a quotient network from an SMB that induces the lumped CTMC directly, thus avoiding the generation of the state space of the original CRN altogether. In practice, we show that SMB allows significant reductions in a number of models from the literature. Finally, we study SMB with respect to the deterministic semantics of CRNs based on ordinary differential equations (ODEs), where each equation gives the time-course evolution of the concentration of a species. SMB implies forward CRN bisimulation, a recently developed behavioral notion of equivalence for the ODE semantics, in an analogous sense: it yields a smaller ODE system that keeps track of the sums of the solutions for equivalent species.Comment: Extended version (with proofs), of the corresponding paper published at KimFest 2017 (http://kimfest.cs.aau.dk/

Process algebra modelling styles for biomolecular processes

We investigate how biomolecular processes are modelled in process algebras, focussing on chemical reactions. We consider various modelling styles and how design decisions made in the definition of the process algebra have an impact on how a modelling style can be applied. Our goal is to highlight the often implicit choices that modellers make in choosing a formalism, and illustrate, through the use of examples, how this can affect expressability as well as the type and complexity of the analysis that can be performed

Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors

In this paper, we survey five different computational modeling methods. For comparison, we use the activation cycle of G-proteins that regulate cellular signaling events downstream of G-protein-coupled receptors (GPCRs) as a driving example. Starting from an existing Ordinary Differential Equations (ODEs) model, we implement the G-protein cycle in the stochastic Pi-calculus using SPiM, as Petri-nets using Cell Illustrator, in the Kappa Language using Cellucidate, and in Bio-PEPA using the Bio-PEPA eclipse plug in. We also provide a high-level notation to abstract away from communication primitives that may be unfamiliar to the average biologist, and we show how to translate high-level programs into stochastic Pi-calculus processes and chemical reactions.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005

Review of the ELI-NP-GBS low level rf and synchronization systems

The Gamma Beam System (GBS) of ELI-NP is a linac based gamma-source in construction at Magurele (RO) by the European consortium EuroGammaS led by INFN. Photons with tunable energy and with intensity and brilliance well beyond the state of the art will be produced by Compton back-scattering between a high quality electron beam (up to 740 MeV) and a 515 nm intense laser pulse. Production of very intense photon flux with narrow bandwidth requires multi-bunch operation at 100 Hz repetition rate. A total of 13 klystrons, 3 S-band (2856 MHz) and 10 C-band (5712 MHz) will power a total of 14 Travelling Wave accelerating sections (2 S-band and 12 C-band) plus 3 S-band Standing Wave cavities (a 1.6 cell RF gun and 2 RF deflectors). Each klystron is individually driven by a temperature stabilized LLRF module, for a maximum flexibility in terms of accelerating gradient, arbitrary pulse shaping (e.g. to compensate beam loading effects in multi-bunch regime) and compensation of long-term thermal drifts. In this paper, the whole LLRF system architecture and bench test results, the RF reference generation and distribution together with an overview of the synchronization system will be described

Regulating Data Exchange in Service Oriented Applications

We define a type system for COWS, a formalism for specifying and combining services, while modelling their dynamic behaviour. Our types permit to express policies constraining data exchanges in terms of sets of service partner names attachable to each single datum. Service programmers explicitly write only the annotations necessary to specify the wanted policies for communicable data, while a type inference system (statically) derives the minimal additional annotations that ensure consistency of services initial configuration. Then, the language dynamic semantics only performs very simple checks to authorize or block communication. We prove that the type system and the operational semantics are sound. As a consequence, we have the following data protection property: services always comply with the policies regulating the exchange of data among interacting services. We illustrate our approach through a simplified but realistic scenario for a service-based electronic marketplace

Logics for Unranked Trees: An Overview

Labeled unranked trees are used as a model of XML documents, and logical languages for them have been studied actively over the past several years. Such logics have different purposes: some are better suited for extracting data, some for expressing navigational properties, and some make it easy to relate complex properties of trees to the existence of tree automata for those properties. Furthermore, logics differ significantly in their model-checking properties, their automata models, and their behavior on ordered and unordered trees. In this paper we present a survey of logics for unranked trees

A Calculus of Bounded Capacities

Resource control has attracted increasing interest in foundational research on distributed systems. This paper focuses on space control and develops an analysis of space usage in the context of an ambient-like calculus with bounded capacities and weighed processes, where migration and activation require space. A type system complements the dynamics of the calculus by providing static guarantees that the intended capacity bounds are preserved throughout the computation

The Extinction Towards the GRB970228 Field

We determine the local galactic extinction towards the field of gamma-ray burst GRB970228 using a variety of methods. We develop a maximum likelihood method for measuring the extinction by comparing galaxy counts in the field of interest to those in a field of known extinction, and apply this method to the GRB970228 field. We also measure the extinction by comparing the observed stellar spectral energy distributions of stars in the GRB970228 field to the spectral energy distribution of library spectra of the same spectral type. Finally we estimate the extinction using the Balmer emission line ratios of a galaxy in the GRB970228 field, and the neutral hydrogen column density and amount of infrared dust emission toward this field. Combining the results of these methods, we find a best-fit galactic extinction in the optical of $A_V=1.19^{+0.10}_{-0.17}$, which implies a a substantial dimming and change of the spectral slope of the intrinsic GRB970228 afterglow.Comment: 22 pages, including 7 figures. Submitted to Ap