BigraphER: rewriting and analysis engine for bigraphs

BigraphER is a suite of open-source tools providing an effi- cient implementation of rewriting, simulation, and visualisation for bigraphs, a universal formalism for modelling interacting systems that evolve in time and space and first introduced by Milner. BigraphER consists of an OCaml library that provides programming interfaces for the manipulation of bigraphs, their constituents and reaction rules, and a command-line tool capable of simulating Bigraphical Reactive Systems (BRSs) and computing their transition systems. Other features are native support for both bigraphs and bigraphs with sharing, stochastic reaction rules, rule priorities, instantiation maps, parameterised controls, predicate checking, graphical output and integration with the probabilistic model checker PRISM

A Consideration of Biomarkers to be Used for Evaluation of Inflammation in Human Nutritional Studies

To monitor inflammation in a meaningful way, the markers used must be valid: they must reflect the inflammatory process under study and they must be predictive of future health status. In 2009, the Nutrition and Immunity Task Force of the International Life Sciences Institute, European Branch, organized an expert group to attempt to identify robust and predictive markers, or patterns or clusters of markers, which can be used to assess inflammation in human nutrition studies in the general population. Inflammation is a normal process and there are a number of cells and mediators involved. These markers are involved in, or are produced as a result of, the inflammatory process irrespective of its trigger and its location and are common to all inflammatory situations. Currently, there is no consensus as to which markers of inflammation best represent low-grade inflammation or differentiate between acute and chronic inflammation or between the various phases of inflammatory responses. There are a number of modifying factors that affect the concentration of an inflammatory marker at a given time, including age, diet and body fatness, among others. Measuring the concentration of inflammatory markers in the bloodstream under basal conditions is probably less informative compared with data related to the concentration change in response to a challenge. A number of inflammatory challenges have been described. However, many of these challenges are poorly standardised. Patterns and clusters may be important as robust biomarkers of inflammation. Therefore, it is likely that a combination of multiple inflammatory markers and integrated readouts based upon kinetic analysis following defined challenges will be the most informative biomarker of inflammation. Copyright © ILSI Europe 2013.Peer Reviewe

Bibliography on the Scyphozoa with selected references on Hydrozoa and Anthozoa

Our goal in assembling this bibliography has been to bring together literature references on all aspects of scyphozoan research. Compilation was begun in 1967 as a card file of references to publications on the Scyphozoa; selected references to hydrozoan and anthozoan studies that were considered relevant to the study of scyphozoans were included. In 1968, a major research program on the jellyfish of Chesapeake Bay was initiated at the Virginia Institute of Marine Science (VIMS) under Dr. E. B. Joseph, and work on the bibliography became an integral part of the program. In 1969 we began converting the bibliography into a form suitable for wider distribution, and in February 1970 a preliminary draft was completed. The present bibliography is an expanded and revised version of the preliminary draft

Trend-based analysis of a population model of the AKAP scaffold protein

We formalise a continuous-time Markov chain with multi-dimensional discrete state space model of the AKAP scaffold protein as a crosstalk mediator between two biochemical signalling pathways. The analysis by temporal properties of the AKAP model requires reasoning about whether the counts of individuals of the same type (species) are increasing or decreasing. For this purpose we propose the concept of stochastic trends based on formulating the probabilities of transitions that increase (resp. decrease) the counts of individuals of the same type, and express these probabilities as formulae such that the state space of the model is not altered. We define a number of stochastic trend formulae (e.g. weakly increasing, strictly increasing, weakly decreasing, etc.) and use them to extend the set of state formulae of Continuous Stochastic Logic. We show how stochastic trends can be implemented in a guarded-command style specification language for transition systems. We illustrate the application of stochastic trends with numerous small examples and then we analyse the AKAP model in order to characterise and show causality and pulsating behaviours in this biochemical system

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

Spin and orbital dynamics through the metal-to-insulator transition in Cd2_2Os2_2O7_7 probed with high-resolution RIXS

High-resolution resonant inelastic x-ray scattering (RIXS) measurements ($\Delta$E = 46 meV) have been performed on Cd$_2$Os$_2$O$_7$ through the metal-to-insulator transition (MIT). A magnetic excitation at 125 meV evolves continuously through the MIT, in agreement with recent Raman scattering results, and provides further confirmation for an all-in, all-out magnetic ground state. Asymmetry of this feature is likely a result of coupling between the electronic and magnetic degrees of freedom. We also observe a broad continuum of interband excitations centered at 0.3 eV energy loss. This is indicative of significant hybridization between Os 5$d$ and O 2$p$ states, and concurrent itinerant nature of the system. In turn, this suggests a possible break down of the free-ion model for Cd$_2$Os$_2$O$_7$.Comment: Accepted in Physical Review B (10 pages

Flame Evolution During Type Ia Supernovae and the Deflagration Phase in the Gravitationally Confined Detonation Scenario

We develop an improved method for tracking the nuclear flame during the deflagration phase of a Type Ia supernova, and apply it to study the variation in outcomes expected from the gravitationally confined detonation (GCD) paradigm. A simplified 3-stage burning model and a non-static ash state are integrated with an artificially thickened advection-diffusion-reaction (ADR) flame front in order to provide an accurate but highly efficient representation of the energy release and electron capture in and after the unresolvable flame. We demonstrate that both our ADR and energy release methods do not generate significant acoustic noise, as has been a problem with previous ADR-based schemes. We proceed to model aspects of the deflagration, particularly the role of buoyancy of the hot ash, and find that our methods are reasonably well-behaved with respect to numerical resolution. We show that if a detonation occurs in material swept up by the material ejected by the first rising bubble but gravitationally confined to the white dwarf (WD) surface (the GCD paradigm), the density structure of the WD at detonation is systematically correlated with the distance of the deflagration ignition point from the center of the star. Coupled to a suitably stochastic ignition process, this correlation may provide a plausible explanation for the variety of nickel masses seen in Type Ia Supernovae.Comment: 14 pages, 10 figures, accepted to the Astrophysical Journa

A dedicated vascular access clinic for children on haemodialysis: Two years' experience

BACKGROUND: Arteriovenous fistula (AVF) formation for long-term haemodialysis in children is a niche discipline with little data for guidance. We developed a dedicated Vascular Access Clinic that is run jointly by a transplant surgeon, paediatric nephrologist, dialysis nurse and a clinical vascular scientist specialised in vascular sonography for the assessment and surveillance of AVFs. We report the experience and 2-year outcomes of this clinic. METHODS: Twelve new AVFs were formed and 11 existing AVFs were followed up for 2 years. All children were assessed by clinical and ultrasound examination. RESULTS: During the study period 12 brachiocephalic, nine basilic vein transpositions and two radiocephalic AVFs were followed up. The median age (interquartile range) and weight of those children undergoing new AVF creation were 9.4 (interquartile 3-17) years and 26.9 (14-67) kg, respectively. Pre-operative ultrasound vascular mapping showed maximum median vein and artery diameters of 3.0 (2-5) and 2.7 (2.0-5.3) mm, respectively. Maturation scans 6 weeks after AVF formation showed a median flow of 1277 (432-2880) ml/min. Primary maturation rate was 83 % (10/12). Assisted maturation was 100 %, with two patients requiring a single angioplasty. For the 11 children with an existing AVF the maximum median vein diameter was 14.0 (8.0-26.0) mm, and the median flow rate was 1781 (800-2971) ml/min at a median of 153 weeks after AVF formation. Twenty-two AVFs were used successfully for dialysis, a median kt/V of 1.97 (1.8-2.9), and urea reduction ratio of 80.7 % (79.3-86 %) was observed. One child was transplanted before the AVF was used. CONCLUSIONS: A multidisciplinary vascular clinic incorporating ultrasound assessment is key to maintaining young children on chronic haemodialysis via an AVF

Organization of Ecosystems in the Vicinity of a Novel Phase Transition

It is shown that an ecosystem in equilibrium is generally organized in a state which is poised in the vicinity of a novel phase transition.Comment: 4 pages, 2 figure