PORGY: a Visual Analytics Platform for System Modelling and Analysis Based on Graph Rewriting

PORGY is a visual environment for rule-based modelling based on port graphs and port graph rewrite rules whose application is steered by rewriting strategies. The focus of this demonstration is the visual and interactive features offered by PORGY, which facilitate an exploratory approach to model, simu- late and analyse different ways of applying the rules while recording the model evolution, as well as tracking and plotting system parameters

Labelled Graph Strategic Rewriting for Social Networks

We develop an algebraic approach, based on labelled-graph strategic rewriting , for the study of social networks, specifically network generation and propagation mechanisms. This approach sheds a new light on these problems, and leads to new or improved generation and propagation algorithms. We argue that relevant concepts are provided by three ingredients: labelled graphs to represent networks of data or users, rewrite rules to describe concurrent local transformations, and strategies to express control. We show how these techniques can be used to generate random networks that are suitable for social network analysis, simulate different propagation mechanisms, and analyse and compare propagation models by extracting common rules and differences, thus leading to improved algorithms. We illustrate with examples the flexibility of the approach

Labelled Graph Strategic Rewriting for Social Networks

International audienceWe propose an algebraic and logical approach to the study of social networks, where network components and processes are directly defined by labelled port graph strategic rewriting. Data structures attached to graph elements (nodes, ports and edges) model local and global knowledge in the network, rewrite rules express elementary and local transformations , and strategies control the global evolution of the network. We show how this approach can be used to generate random networks, simulate existing propagation and dissemination mechanisms, and design new, improved algorithms

Endotoxin-induced myocardial dysfunction in senescent rats

INTRODUCTION: Aging is associated with a decline in cardiac contractility and altered immune function. The aim of this study was to determine whether aging alters endotoxin-induced myocardial dysfunction. METHODS: Senescent (24 month) and young adult (3 month) male Wistar rats were treated with intravenous lipopolysaccharide (LPS) (0.5 mg/kg (senescent and young rats) or 5 mg/kg (young rats only)), or saline (senescent and young control groups). Twelve hours after injection, cardiac contractility (isolated perfused hearts), myofilament Ca(2+ )sensitivity (skinned fibers), left ventricular nitric oxide end-oxidation products (NOx and NO(2)) and markers of oxidative stress (thiobarbituric acid reactive species (TBARS) and antioxidant enzymes) were investigated. RESULTS: LPS (0.5 mg/kg) administration resulted in decreased contractility in senescent rats (left ventricular developed pressure (LVDP), 25 ± 4 vs 53 ± 4 mmHg/g heart weight in control; P < 0.05) of amplitude similar to that in young rats with LPS 5 mg/kg (LVDP, 48 ± 7 vs 100 ± 7 mmHg/g heart weight in control; P < 0.05). In contrast to young LPS rats (0.5 and 5 mg/kg LPS), myofilament Ca(2+ )sensitivity was unaltered in senescent LPS hearts. Myocardial NOx and NO(2 )were increased in a similar fashion by LPS in young (both LPS doses) and senescent rats. TBARS and antioxidant enzyme activities were unaltered by sepsis whatever the age of animals. CONCLUSION: Low dose of LPS induced a severe myocardial dysfunction in senescent rats. Ca(2+ )myofilament responsiveness, which is typically reduced in myocardium of young adult septic rats, however, was unaltered in senescent rats. If these results are confirmed in in vivo conditions, they may provide a cellular explanation for the divergent reports on ventricular diastolic function in septic shock. In addition, Ca(2+)-sensitizing agents may not be as effective in aged subjects as in younger subjects

Porgy Strategy Language: User Manual

This document provides concrete syntax illustrated with ex-amples for the Porgy’s strategy language and the language for rulealgorithm and conditions. Porgy is a visual, interactive modelling tool based on port graph rewriting. In Porgy, system states are represented by port graphs, and the dynamic evolution of the system is defined via port graph rewrite rules. Strategy expressions are used to control the application of rules, more precisely, strategy expressions indicate both the rule to be applied at each step in a rewriting derivation, and the position in the graph where the rule is applied (the latter is done via focusing constructs). Some of the strategy constructs are strongly inspired from term rewriting languages such as Elan [Borovansk´yBorovansk´y et al., 1998], Stratego [Visser, 2001] and Tom [Balland et al., 2007]. Focusing operators are not present in term rewriting languages (although they rely on implicit traversal strategies). The direct management of positions in strategy expressions, via the distinguished position and banned subgraphs in the target graph and in a located port graph rewrite rule are original features of the language and are managed using positioning constructs. This document describes the concrete syntax of strategy expressions, explains how the different kinds of constructs are used, and provides examples

PORGY : a Visual Analytics Platform for System Modelling and Analysis Based on Graph Rewriting

Atelier Visualisation d'informations, interaction et fouille de données, Conférence EGC2017We propose PORGY 1 a visual modelling framework (Fig. 1) designed for specifying, simulating , and analysing complex systems. PORGY is built on top of the open-source visualisation framework TULIP 2. PORGY is based on the use of port graphs with attributes to represent system states. In a port graph, edges connect to nodes at specific points, called ports. Nodes, ports and edges describe the system components and their relationships, while attributes encapsulate the data values associated with entity. We use graph transformations based on port graph rewrite rules to describe the evolution of the system. FIG. 1 – Overview of PORGY: (1) editing a graph; (2) editing a rule; (3) all available rules; (4) the derivation tree, a complete trace of the computing history; (5) editing a strategy

Share - Publish - Store - Preserve. Methodologies, Tools and Challenges for 3D Use in Social Sciences and Humanities

Through this White Paper, which gathers contributions from experts of 3D data as well as professionals concerned with the interoperability and sustainability of 3D research data, the PARTHENOS project aims at highlighting some of the current issues they have to face, with possible specific points according to the discipline, and potential practices and methodologies to deal with these issues. During the workshop, several tools to deal with these issues have been introduced and confronted with the participants experiences, this White Paper now intends to go further by also integrating participants feedbacks and suggestions of potential improvements. Therefore, even if the focus is put on specific tools, the main goal is to contribute to the development of standardized good practices related to the sharing, publication, storage and long-term preservation of 3D data

Antiretroviral-naive and -treated HIV-1 patients can harbour more resistant viruses in CSF than in plasma

Objectives The neurological disorders in HIV-1-infected patients remain prevalent. The HIV-1 resistance in plasma and CSF was compared in patients with neurological disorders in a multicentre study. Methods Blood and CSF samples were collected at time of neurological disorders for 244 patients. The viral loads were >50 copies/mL in both compartments and bulk genotypic tests were realized. Results On 244 patients, 89 and 155 were antiretroviral (ARV) naive and ARV treated, respectively. In ARV-naive patients, detection of mutations in CSF and not in plasma were reported for the reverse transcriptase (RT) gene in 2/89 patients (2.2%) and for the protease gene in 1/89 patients (1.1%). In ARV-treated patients, 19/152 (12.5%) patients had HIV-1 mutations only in the CSF for the RT gene and 30/151 (19.8%) for the protease gene. Two mutations appeared statistically more prevalent in the CSF than in plasma: M41L (P = 0.0455) and T215Y (P = 0.0455). Conclusions In most cases, resistance mutations were present and similar in both studied compartments. However, in 3.4% of ARV-naive and 8.8% of ARV-treated patients, the virus was more resistant in CSF than in plasma. These results support the need for genotypic resistance testing when lumbar puncture is performe

Wheat receptor-kinase-like protein Stb6 controls gene-for-gene resistance to fungal pathogen Zymoseptoria tritici

Deployment of fast-evolving disease-resistance genes is one of the most successful strategies used by plants to fend off pathogens. In gene-for-gene relationships, most cloned disease-resistance genes encode intracellular nucleotide-binding leucine-rich-repeat proteins (NLRs) recognizing pathogensecreted isolate-specific avirulence (Avr) effectors delivered to the host cytoplasm. This process often triggers a localized hypersensitive response, which halts further disease development. Here we report the map-based cloning of the wheat Stb6 gene and demonstrate that it encodes a conserved wallassociated receptor kinase (WAK)-like protein, which detects the presence of a matching apoplastic effector and confers pathogen resistance without a hypersensitive response. This report demonstrates gene-for-gene disease resistance controlled by this class of proteins in plants. Moreover, Stb6 is, to our knowledge, the first cloned gene specifying resistance to Zymoseptoria tritici, an important foliar fungal pathogen affecting wheat and causing economically damaging septoria tritici blotch (STB) disease