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/

Concurrent constraint programming with process mobility

We propose an extension of concurrent constraint programming with primitives for process migration within a hierarchical network, and we study its semantics. To this purpose, we first investigate a "pure " paradigm for process migration, namely a paradigm where the only actions are those dealing with transmissions of processes. Our goal is to give a structural definition of the semantics of migration; namely, we want to describe the behaviour of the system, during the transmission of a process, in terms of the behaviour of the components. We achieve this goal by using a labeled transition system where the effects of sending a process, and requesting a process, are modeled by symmetric rules (similar to handshaking-rules for synchronous communication) between the two partner nodes in the network. Next, we extend our paradigm with the primitives of concurrent constraint programming, and we show how to enrich the semantics to cope with the notions of environment and constraint store. Finally, we show how the operational semantics can be used to define an interpreter for the basic calculus.

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

Graphical Encoding of a Spatial Logic for the pi-Calculus

This paper extends our graph-based approach to the verification of spatial properties of π-calculus specifications. The mechanism is based on an encoding for mobile calculi where each process is mapped into a graph (with interfaces) such that the denotation is fully abstract with respect to the usual structural congruence, i.e., two processes are equivalent exactly when the corresponding encodings yield isomorphic graphs. Behavioral and structural properties of π-calculus processes expressed in a spatial logic can then be verified on the graphical encoding of a process rather than on its textual representation. In this paper we introduce a modal logic for graphs and define a translation of spatial formulae such that a process verifies a spatial formula exactly when its graphical representation verifies the translated modal graph formula

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

The relationship between [OIII]5007A equivalent width and obscuration in AGN

In this paper we study the relationship between the equivalent width (EW) of the [OIII]5007A narrow emission line in AGN and the level of obscuration. To this end, we combine the results of a systematic spectral analysis, both in the optical and in the X-rays, on a statistically complete sample of ~170 X-ray selected AGN from the XMM-Newton Bright Serendipitous Source sample (XBS). We find that the observed large range of [OIII]5007A equivalent widths observed in the sample (from a few A up to 500A) is well explained as a combination of an intrinsic spread, probably due to the large range of covering factors of the Narrow Line Region, and the effect of absorption. The intrinsic spread is dominant for EW below 40-50A while absorption brings the values of EW up to ~100-150A, for moderate levels of absorption (AV~0.5-2 mag) or up to ~500A for AV>2 mag. In this picture, the absorption has a significant impact on the observed EW also in type~1 AGN. Using numerical simulations we find that this model is able to reproduce the [OIII]5007A EW distribution observed in the XBS sample and correctly predicts the shape of the EW distribution observed in the optically selected sample of QSO taken from the SDSS survey.Comment: 7 pages, 5 figures. Accepted for publication in MNRA

Phagosomal Proteins of \u3ci\u3eDictyostelium discoideum\u3c/i\u3e

In recognizing food particles, Dictyostelium cell-surface molecules initiate cytoskeletal rearrangements that result in phagosome formation. After feeding D. discoideum cells latex beads, early phagosomes were isolated on sucrose step gradients. Protein analyses of these vesicles showed that they contained glycoproteins and surface-labeled species corresponding to integral plasma membrane proteins. Cytoskeletal proteins also were associated with phagosomes, including myosin II, actin and a 30 kDa-actin bundling protein. As seen by the acridine orange fluorescence of vesicles containing bacteria, phagosomes were acidified rapidly by a vacuolar H+-ATPase that was detected by immunoblotting. Except for the loss of cytoskeletal proteins, few other changes over time were noted in the protein profiles of phagosomes, suggesting that phagosome maturation was incomplete. The indigestibility of the beads possibly inhibited further endocytic processing, which has been observed by others. Since nascent phagosomes contained molecules of both the cytoskeleton and plasma membrane, they will be useful in studies aimed at identifying specific protein associations occurring between membrane proteins and the cytoskeleton during phagocytosis