Towards a Notion of Distributed Time for Petri Nets

We set the ground for research on a timed extension of Petri nets where time parameters are associated with tokens and arcs carry constraints that qualify the age of tokens required for enabling. The novelty is that, rather than a single global clock, we use a set of unrelated clocks --- possibly one per place --- allowing a local timing as well as distributed time synchronisation. We give a formal definition of the model and investigate properties of local versus global timing, including decidability issues and notions of processes of the respective models

Preserving Topology and Elasticity for Embedded Deformable Models

International audienceIn this paper we introduce a new approach for the embedding of linear elastic deformable models. Our technique results in significant improvements in the efficient physically based simulation of highly detailed objects. First, our embedding takes into account topological details, that is, disconnected parts that fall into the same coarse element are simulated independently. Second, we account for the varying material properties by computing stiffness and interpolation functions for coarse elements which accurately approximate the behaviour of the embedded material. Finally, we also take into account empty space in the coarse embeddings, which provides a better simulation of the boundary. The result is a straightforward approach to simulating complex deformable models with the ease and speed associated with a coarse regular embedding, and with a quality of detail that would only be possible at much finer resolution

On computing fixpoints in well-structured regular model checking, with applications to lossy channel systems

We prove a general finite convergence theorem for "upward-guarded" fixpoint expressions over a well-quasi-ordered set. This has immediate applications in regular model checking of well-structured systems, where a main issue is the eventual convergence of fixpoint computations. In particular, we are able to directly obtain several new decidability results on lossy channel systems.Comment: 16 page

Wochenende — modular and flexible alignment-based shotgun metagenome analysis

Background: Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of read mapping location, normalization options, growth dynamics and functional gene repertoires. Current read classification tools use non-standard output formats, or do not fully show information on mapping location. As reference datasets are not perfect, portrayal of mapping information is critical for judging results effectively. Results: Our alignment-based pipeline, Wochenende, incorporates flexible quality control, trimming, mapping, various filters and normalization. Results are completely transparent and filters can be adjusted by the user. We observe stringent filtering of mismatches and use of mapping quality sharply reduces the number of false positives. Further modules allow genomic visualization and the calculation of growth rates, as well as integration and subsequent plotting of pipeline results as heatmaps or heat trees. Our novel normalization approach additionally allows calculation of absolute abundance profiles by comparison with reads assigned to the human host genome. Conclusion: Wochenende has the ability to find and filter alignments to all kingdoms of life using both short and long reads, and requires only good quality reference genomes. Wochenende automatically combines multiple available modules ranging from quality control and normalization to taxonomic visualization. Wochenende is available at https://github.com/MHH-RCUG/nf_wochenende

Compositionality for Quantitative Specifications

We provide a framework for compositional and iterative design and verification of systems with quantitative information, such as rewards, time or energy. It is based on disjunctive modal transition systems where we allow actions to bear various types of quantitative information. Throughout the design process the actions can be further refined and the information made more precise. We show how to compute the results of standard operations on the systems, including the quotient (residual), which has not been previously considered for quantitative non-deterministic systems. Our quantitative framework has close connections to the modal nu-calculus and is compositional with respect to general notions of distances between systems and the standard operations

GATA4 controls regionalization of tissue immunity and commensal-driven immunopathology

There is growing recognition that regionalization of bacterial colonization and immunity along the intestinal tract has an important role in health and disease. Yet, the mechanisms underlying intestinal regionalization and its dysregulation in disease are not well understood. This study found that regional epithelial expression of the transcription factor GATA4 controls bacterial colonization and inflammatory tissue immunity in the proximal small intestine by regulating retinol metabolism and luminal IgA. Furthermore, in mice without jejunal GATA4 expression, the commensal segmented filamentous bacteria promoted pathogenic inflammatory immune responses that disrupted barrier function and increased mortality upon Citrobacter rodentium infection. In celiac disease patients, low GATA4 expression was associated with metabolic alterations, mucosal Actinobacillus, and increased IL-17 immunity. Taken together, these results reveal broad impacts of GATA4-regulated intestinal regionalization on bacterial colonization and tissue immunity, highlighting an elaborate interdependence of intestinal metabolism, immunity, and microbiota in homeostasis and disease.</p

HIV Prevalence, Risks for HIV Infection, and Human Rights among Men Who Have Sex with Men (MSM) in Malawi, Namibia, and Botswana

BACKGROUND: In the generalized epidemics of HIV in southern Sub-Saharan Africa, men who have sex with men have been largely excluded from HIV surveillance and research. Epidemiologic data for MSM in southern Africa are among the sparsest globally, and HIV risk among these men has yet to be characterized in the majority of countries. METHODOLOGY: A cross-sectional anonymous probe of 537 men recruited with non-probability sampling among men who reported ever having had sex with another man in Malawi, Namibia, and Botswana using a structured survey instrument and HIV screening with the OraQuick(c) rapid test kit. PRINCIPAL FINDINGS: The HIV prevalence among those between the ages of 18 and 23 was 8.3% (20/241); 20.0% (42/210) among those 24-29; and 35.7% (30/84) among those older than 30 for an overall prevalence of 17.4% (95% CI 14.4-20.8). In multivariate logistic regressions, being older than 25 (aOR 4.0, 95% CI 2.0-8.0), and not always wearing condoms during sex (aOR 2.6, 95% CI 1.3-4.9) were significantly associated with being HIV-positive. Sexual concurrency was common with 16.6% having ongoing concurrent stable relationships with a man and a woman and 53.7% had both male and female sexual partners in proceeding 6 months. Unprotected anal intercourse was common and the use of petroleum-based lubricants was also common when using condoms. Human rights abuses, including blackmail and denial of housing and health care was prevalent with 42.1% (222/527) reporting at least one abuse. CONCLUSIONS: MSM are a high-risk group for HIV infection and human rights abuses in Malawi, Namibia, and Botswana. Concurrency of sexual partnerships with partners of both genders may play important roles in HIV spread in these populations. Further epidemiologic and evaluative research is needed to assess the contribution of MSM to southern Africa's HIV epidemics and how best to mitigate this. These countries should initiate and adequately fund evidence-based and targeted HIV prevention programs for MSM

Developing general cultural awareness in a monocultural English as a foreign language context in a Mexican university: a wiki-based critical incident approach

© 2013 Association for Language Learning. This article explores what the ‘intercultural turn’ might mean in the case of teaching English to speakers of other languages (TESOL). The discussion is contextualised in what has been termed the ‘expanding circle’ of English and focuses on an English as a foreign language (EFL) class in a Mexican university, a context where the full implications of a shift from EFL to English as a lingua franca (ELF) have yet to be addressed. We consider how the intercultural turn might be understood in this Mexican context and then present the rationale for, and design of, a technology-based (wiki) extra-curricular pilot project which adopted less of an EFL/cultural and more of an ELF/intercultural approach. We evaluate the evidence from this small-scale project in terms of students\u27 developing general cultural awareness and suggest that this type of project, an example of the intercultural turn, might be more widely applicable in similar ‘expanding circle’ EFL contexts

The methodology of surveillance for antimicrobial resistance and healthcare-associated infections in Europe (SUSPIRE): a systematic review of publicly available information.

OBJECTIVES: Surveillance is a key component of any control strategy for healthcare-associated infections (HAIs) and antimicrobial resistance (AMR), and public availability of methodologic aspects is crucial for the interpretation of the data. We sought to systematically review publicly available information for HAIs and/or AMR surveillance systems organized by public institutions or scientific societies in European countries. METHODS: A systematic review of scientific and grey literature following the Preferred Reporting Items for Systematic Reviews and Meta-analyses (PRISMA) guidelines was performed. Information on HAIs and/or AMR surveillance systems published until 31 October 2016 were included. RESULTS: A total of 112 surveillance systems were detected; 56 from 20 countries were finally included. Most exclusions were due to lack of publicly available information. Regarding AMR, the most frequent indicator was the proportion of resistant isolates (27 of 34 providing information, 79.42%); only 18 (52.9%) included incidence rates; the data were only laboratory based in 33 (78.5%) of the 42 providing this information. Regarding HAIs in intensive care units, all 22 of the systems providing data included central line-associated bloodstream infections, and 19 (86.3%) included ventilator-associated pneumonia and catheter-associated urinary tract infections; incidence density was the most frequent indicator. Regarding surgical site infections, the most frequent procedures included were hip prosthesis, colon surgery and caesarean section (21/22, 95.5%). CONCLUSIONS: Publicly available information about the methods and indicators of the surveillance system is frequently lacking. Despite the efforts of European Centre for Disease Control and Prevention (ECDC) and other organizations, wide heterogeneity in procedures and indicators still exists

A General Framework for Architecture Composability

Architectures depict design principles: paradigms that can be understood by all, allow thinking on a higher plane and avoiding low-level mistakes. They provide means for ensuring correctness by construction by enforcing global properties characterizing the coordination between components. An architecture can be considered as an operator A that, applied to a set of components B, builds a composite component A(B) meeting a characteristic property Φ. Architecture composability is a basic and common problem faced by system designers. In this paper, we propose a formal and general framework for architecture composability based on an associative, commutative and idempotent architecture composition operator ⊕. The main result is that if two architectures A1 and A2 enforce respectively safety properties Φ1 and Φ2 , the architecture A1 ⊕ A2 enforces the property Φ1 ∧ Φ2 , that is both properties are preserved by architecture composition. We also establish preservation of liveness properties by architecture composition. The presented results are illustrated by a running example and a case study