A constraint specification approach to building flexible workflows

Process support systems, such as workflows, are being used in a variety of domains. However, most areas of application have focused on traditional production-style processes, which are characterised by predictability and repetitiveness. Application in non-traditional domains with highly flexible process is still largely unexplored. Such flexible processes are characterised by lack of ability to completely predefine and/or an explosive number of alternatives. Accordingly we define flexibility as the ability of the process to execute on the basis of a partially defined model where the full specification is made at runtime and may be unique to each instance. In this paper, we will present an approach to building workflow models for such processes. We will present our approach in the context of a non-traditional domain for workflow, deployment, which is, degree programs in tertiary institutes. The primary motivation behind our approach is to provide the ability to model flexible processes without introducing non-standard modelling constructs. This ensures that the correctness and verification of the language is preserved. We propose to build workflow schemas from a standard set of modelling constructs and given process constraints. We identify the fundamental requirements for constraint specification and classify them into selection, termination and build constraints. We will detail the specification of these constraints in a relational model. Finally, we will demonstrate the dynamic building of instance specific workflow models on the basis of these constraints

Patterns of Interactions in Complex Social Networks Based on Coloured Motifs Analysis

Coloured network motifs are small subgraphs that enable to discover and interpret the patterns of interaction within the complex networks. The analysis of three-nodes motifs where the colour of the node reflects its high – white node or low – black node centrality in the social network is presented in the paper. The importance of the vertices is assessed by utilizing two measures: degree prestige and degree centrality. The distribution of motifs in these two cases is compared to mine the interconnection patterns between nodes. The analysis is performed on the social network derived from email communication

Towards insect inspired visual sensors for robots

Flying insects display a repertoire of complex behaviours that are facilitated by their non-standard visual system that if understood would offer solutions for weight- and power- constrained robotic platforms such as micro unmanned aerial vehicles (MUAVs). Crucial to this goal is revealing the specific features of insect eyes that engineered solutions would benefit from possessing, however progress in exploration of the design space has been limited by challenges in accurately replicating insect vision. Here we propose that emerging ray-tracing technologies are ideally placed to realise the high-fidelity replication of the insect visual perspective in a rapid, modular and adaptive framework allowing development of technical specifications for a new class of bio-inspired sensor. A proof-of-principle insect eye renderer is shown and insights into research directions it affords discussed

CONTEST : a Controllable Test Matrix Toolbox for MATLAB

Large, sparse networks that describe complex interactions are a common feature across a number of disciplines, giving rise to many challenging matrix computational tasks. Several random graph models have been proposed that capture key properties of real-life networks. These models provide realistic, parametrized matrices for testing linear system and eigenvalue solvers. CONTEST (CONtrollable TEST matrices) is a random network toolbox for MATLAB that implements nine models. The models produce unweighted directed or undirected graphs; that is, symmetric or unsymmetric matrices with elements equal to zero or one. They have one or more parameters that affect features such as sparsity and characteristic pathlength and all can be of arbitrary dimension. Utility functions are supplied for rewiring, adding extra shortcuts and subsampling in order to create further classes of networks. Other utilities convert the adjacency matrices into real-valued coefficient matrices for naturally arising computational tasks that reduce to sparse linear system and eigenvalue problems

Patterns of subnet usage reveal distinct scales of regulation in the transcriptional regulatory network of Escherichia coli

The set of regulatory interactions between genes, mediated by transcription factors, forms a species' transcriptional regulatory network (TRN). By comparing this network with measured gene expression data one can identify functional properties of the TRN and gain general insight into transcriptional control. We define the subnet of a node as the subgraph consisting of all nodes topologically downstream of the node, including itself. Using a large set of microarray expression data of the bacterium Escherichia coli, we find that the gene expression in different subnets exhibits a structured pattern in response to environmental changes and genotypic mutation. Subnets with less changes in their expression pattern have a higher fraction of feed-forward loop motifs and a lower fraction of small RNA targets within them. Our study implies that the TRN consists of several scales of regulatory organization: 1) subnets with more varying gene expression controlled by both transcription factors and post-transcriptional RNA regulation, and 2) subnets with less varying gene expression having more feed-forward loops and less post-transcriptional RNA regulation.Comment: 14 pages, 8 figures, to be published in PLoS Computational Biolog

Recent insights into the molecular mechanisms of the NLRP3 inflammasome activation

Inflammasomes are high-molecular-weight protein complexes that are formed in the cytosolic compartment in response to danger- or pathogen-associated molecular patterns. These complexes enable activation of an inflammatory protease caspase-1, leading to a cell death process called pyroptosis and to proteolytic cleavage and release of pro-inflammatory cytokines interleukin (IL)-1beta and IL-18. Along with caspase-1, inflammasome components include an adaptor protein, ASC, and a sensor protein, which triggers the inflammasome assembly in response to a danger signal. The inflammasome sensor proteins are pattern recognition receptors belonging either to the NOD-like receptor (NLR) or to the AIM2-like receptor family. While the molecular agonists that induce inflammasome formation by AIM2 and by several other NLRs have been identified, it is not well understood how the NLR family member NLRP3 is activated. Given that NLRP3 activation is relevant to a range of human pathological conditions, significant attempts are being made to elucidate the molecular mechanism of this process. In this review, we summarize the current knowledge on the molecular events that lead to activation of the NLRP3 inflammasome in response to a range of K (+) efflux-inducing danger signals. We also comment on the reported involvement of cytosolic Ca (2+) fluxes on NLRP3 activation. We outline the recent advances in research on the physiological and pharmacological mechanisms of regulation of NLRP3 responses, and we point to several open questions regarding the current model of NLRP3 activation

Acid–base physiology over tidal periods in the mussel Mytilus edulis: size and temperature are more influential than seawater pH

This is the final version. Available on open access from the Royal Society via the DOI in this recordData accessibility: Additional data available in the Dryad Digital Respoitory: https://doi.org/10.5061/dryad.k11r5b9 [44].Ocean acidification (OA) studies to date have typically used stable open-ocean pH and CO2 values to predict the physiological responses of intertidal species to future climate scenarios, with few studies accounting for natural fluctuations of abiotic conditions or the alternating periods of emersion and immersion routinely experienced during tidal cycles. Here, we determine seawater carbonate chemistry and the corresponding in situ haemolymph acid–base responses over real time for two populations of mussel (Mytilus edulis) during tidal cycles, demonstrating that intertidal mussels experience daily acidosis during emersion. Using these field data to parameterize experimental work we demonstrate that air temperature and mussel size strongly influence this acidosis, with larger mussels at higher temperatures experiencing greater acidosis. There was a small interactive effect of prior immersion in OA conditions (pHNBS 7.7/pCO2 930 µatm) such that the haemolymph pH measured at the start of emersion was lower in large mussels exposed to OA. Critically, the acidosis induced in mussels during emersion in situ was greater (ΔpH approximately 0.8 units) than that induced by experimental OA (ΔpH approximately 0.1 units). Understanding how environmental fluctuations influence physiology under current scenarios is critical to our ability to predict the responses of key marine biota to future environmental changes.University of Exeter—Plymouth Marine Laboratory scholarship fundNatural Environment Research Council (NERC

Transcriptional adaptation of Mycobacterium tuberculosis within macrophages: Insights into the phagosomal environment

Little is known about the biochemical environment in phagosomes harboring an infectious agent. To assess the state of this organelle we captured the transcriptional responses of Mycobacterium tuberculosis (MTB) in macrophages from wild-type and nitric oxide (NO) synthase 2–deficient mice before and after immunologic activation. The intraphagosomal transcriptome was compared with the transcriptome of MTB in standard broth culture and during growth in diverse conditions designed to simulate features of the phagosomal environment. Genes expressed differentially as a consequence of intraphagosomal residence included an interferon � – and NO-induced response that intensifies an iron-scavenging program, converts the microbe from aerobic to anaerobic respiration, and induces a dormancy regulon. Induction of genes involved in the activation and �-oxidation of fatty acids indicated that fatty acids furnish carbon and energy. Induction of �E-dependent, sodium dodecyl sulfate–regulated genes and genes involved in mycolic acid modification pointed to damage and repair of the cell envelope. Sentinel genes within the intraphagosomal transcriptome were induced similarly by MTB in the lungs of mice. The microbial transcriptome thus served as a bioprobe of the MTB phagosomal environment

On the convergence of quadrature formulas connected with multipoint Padé-type approximants

29 pages, no figures.-- MSC2000 codes: 41A55, 41A21.MR#: MR1408352 (97e:41066)Zbl#: Zbl 0856.41027^aLet $I(F)= \int^1_{- 1} F(x)\omega(x) dx$, where $\omega$ is a complex valued integrable function. We consider quadrature formulas for $I(F)$ which are exact with respect to rational functions with prescribed poles contained in \overline{\bbfC}\backslash [- 1, 1]. Their rate of convergence is studied.The research by the first three authors (P.G.-V., M.J.P., R.O.) was partially supported by the HCM project ROLLS, under Contract CHRX-CT93-0416. Research by the fourth author (G.L.L.) was carried out while on a visit at Universidad de La Laguna. This visit was made possible by a travel grant from CDE-IMU.Publicad