Process algebra for event-driven runtime verification: a case study of wireless network management

Runtime verification is analysis based on information extracted from a running system. Traditionally this involves reasoning about system states, for example using trace predicates. We have been investigating runtime verification for event-driven systems and in that context we propose a higher level of abstraction can be useful, namely reasoning at the level of user-perceived system events. And when considering events, then the natural formalism for verification is a form of process algebra

The impact of inter- and intra-species spore density on germination of the food spoilage fungus Aspergillus niger

Aspergilli can be used to produce food but can spoil it as well. Both food production and spoilage are initiated by germination of the conidia of these fungi that have been introduced by inoculation and contamination, respectively. Germination of these spores includes activation, swelling, establishment of cell polarity, and formation of a germ tube. So far, only quantitative single-species germination studies of fungal spores have been performed. Here, spore germination of the food spoilage fungus Aspergillus niger was studied quantitatively in mono-culture or when mixed with other food-relevant aspergilli (Aspergillus nidulans, Aspergillus terreus, Aspergillus clavatus, and Aspergillus oryzae). In the presence of the germination inducing amino acids proline or alanine, but not in the case of the lowly inducing amino acid arginine, the incidence of swelling and germ tube formation was reduced when 35,000 extra conidia of Aspergillus niger were added to wells containing 5000 of these spores. Adding 35,000 spores of one of the other aspergilli also did not have an effect on germination in the presence of arginine, but the germination inhibition was stronger when compared to the extra A. niger spores in the case of alanine. A similar effect was obtained with proline. Together, results show that the germination of A. niger conidia is impacted by the density of its own spores and that of other aspergilli under favorable nutritional conditions. These results increase our understanding of food spoilage by fungi and can be used to optimize food production with fungi

Cover crop identity determines root fungal community and arbuscular mycorrhiza colonization in following main crops

Cover crops (CC) can promote nutrient retention and recycling for main crops yet may also promote soilborne pathogens or suppress beneficial root symbionts such as arbuscular mycorrhizal fungi (AMF). We investigated how root fungal communities of main crop are affected by preceding CC monocultures and mixtures and by main crop identity. We expected that AMF abundance and diversity in main crops are promoted by AM-host CC, and suppressed by non-AM-host CC, and that mixtures of CC species can promote beneficial and suppress pathogenic root fungi. Our full-factorial field experiment comprised crop rotation in sand soil with different CC treatments (monocultures of radish [AM non-host], ryegrass, clover, vetch [AM hosts], mixtures of radish + vetch, ryegrass + clover and fallow) and two main crops (oat and endive). At peak crop growth, we investigated the root fungal communities in the main crops using microscopy and high throughput sequencing (Illumina MiSeq). Cover crop identity was of prime importance and CC legacy overruled main crop identity in determining root fungal communities in main crops. Compared with fallow, CC with ryegrass increased AMF colonization and richness in both main crops and of non-AMF in oat. Legacies of ryegrass, ryegrass + clover and vetch resulted in distinct root fungal communities in the main crops, while the legacy of CC with radish were similar to the legacy of fallow. Root fungal community in crops after clover had highest abundance of representative fungal pathogens in contrast with the other CC treatments that resulted in fungal communities where pathogens were scarce. Oppositely to expected, CC mixtures did not enhance fungal symbionts or suppressed pathogens. Overall, fungal communities in roots of the main crops in our field experiment were determined by the preceding CC species in monoculture, rather than by the CC AMF preference or functional group. This research highlights that the choice of CC determines the root fungal community in main crop which may influence crop quality

A unifying perspective on protocol mediation: interoperability in the Future Internet

Given the highly dynamic and extremely heterogeneous software systems composing the Future Internet, automatically achieving interoperability between software components —without modifying them— is more than simply desirable, it is quickly becoming a necessity. Although much work has been carried out on interoperability, existing solutions have not fully succeeded in keeping pace with the increasing complexity and heterogeneity of modern software, and meeting the demands of runtime support. On the one hand, solutions at the application layer target higher automation and loose coupling through the synthesis of intermediary entities, mediators, to compensate for the differences between the interfaces of components and coordinate their behaviours, while assuming the use of the same middleware solution. On the other hand, solutions to interoperability across heterogeneous middleware technologies do not reconcile the differences between components at the application layer. In this paper we propose a unified approach for achieving interoperability between heterogeneous software components with compatible functionalities across the application and middleware layers. First, we provide a solution to automatically generate cross-layer parsers and composers that abstract network messages into a uniform representation independent of the middleware used. Second, these generated parsers and composers are integrated within a mediation framework to support the deployment of the mediators synthesised at the application layer. More specifically, the generated parser analyses the network messages received from one component and transforms them into a representation that can be understood by the application-level mediator. Then, the application-level mediator performs the necessary data conversion and behavioural coordination. Finally, the composer transforms the representation produced by the application-level mediator into network messages that can be sent to the other component. The resulting unified mediation framework reconciles the differences between software components from the application down to the middleware layers. We validate our approach through a case study in the area of conference management

WormQTL-public archive and analysis web portal for natural variation data in Caenorhabditis spp

Here, we present WormQTL (http://www.wormqtl.org), an easily accessible database enabling search, comparative analysis and meta-analysis of all data on variation in Caenorhabditis spp. Over the past decade, Caenorhabditis elegans has become instrumental for molecular quantitative genetics and the systems biology of natural variation. These efforts have resulted in a valuable amount of phenotypic, high-throughput molecular and genotypic data across different developmental worm stages and environments in hundreds of C. elegans strains. WormQTL provides a workbench of analysis tools for genotype-phenotype linkage and association mapping based on but not limited to R/qtl (http://www.rqtl.org). All data can be uploaded and downloaded using simple delimited text or Excel formats and are accessible via a public web user interface for biologists and R statistic and web service interfaces for bioinformaticians, based on open source MOLGENIS and xQTL workbench software. WormQTL welcomes data submissions from other worm researcher

Reproductive Isolation in a Threespine Stickleback Hybrid Zone

In many estuarine sites, morphological and genetic differences between anadromous and freshwater threespine sticklebacks are maintained despite breeding in sympatry. Here, we investigate the maintenance of this morphological divergence in a natural hybrid zone in the River Tyne, Scotland. We provide a morphological description of the hybrid zone, and using a Bayesian MCMC approach, identified distinct anadromous and freshwater genetic clusters. Anadromous and freshwater sticklebacks breed in spatial and temporal sympatry in the lower reaches of the River Tyne. The frequency of hybrids within these sites (33%) indicates prezygotic isolation is not complete, and suggests that assortative mating is not strong. However, significant heterozygote deficit and cytonuclear disequilibrium in juveniles collected from sympatric sites confirms that barriers to gene flow exist between the morphs in the wild. In addition, we found no evidence of a directional bias in hybridisation, although hybrids with anadromous mothers were more common because anadromous females outnumbered freshwater females within the hybrid zone. We discuss the potential contribution of temporal, spatial, and sexual prezygotic barriers to the observed reproductive isolation as well as postzygotic selection against hybrid zygotes or fry