Using ontologies for modeling context-aware services platforms

This paper discusses the suitability of using ontologies for modeling context-aware services platforms. It addresses the directions of research we are following in the WASP (Web Architectures for Services Platforms) project. For this purpose a simple scenario is considered

A Combined Component-Based Approach for the Design of Distributed Software Systems

Component-based software development enables the construction of software artefacts by assembling binary units of production, distribution and deployment, the so-called components. Several approaches to component-based development have been proposed recently. Most of these approaches are based on the Unified Modeling Language (UML). UML has been increasingly used in component-based development, despite some shortcomings of this language. This paper presents a methodology for the design of component-based applications that combines a model-based approach with a UML-based approach. This combined approach tackles some of the limitations of UML, allowing a better control of the design proces

In Silico Assigned Resistance Genes Confer Bifidobacterium with Partial Resistance to Aminoglycosides but Not to Β-Lactams

peer-reviewedBifidobacteria have received significant attention due to their contribution to human gut health and the use of specific strains as probiotics. It is thus not surprising that there has also been significant interest with respect to their antibiotic resistance profile. Numerous culture-based studies have demonstrated that bifidobacteria are resistant to the majority of aminoglycosides, but are sensitive to β-lactams. However, limited research exists with respect to the genetic basis for the resistance of bifidobacteria to aminoglycosides. Here we performed an in-depth in silico analysis of putative Bifidobacterium-encoded aminoglycoside resistance proteins and β-lactamases and assess the contribution of these proteins to antibiotic resistance. The in silico-based screen detected putative aminoglycoside and β-lactam resistance proteins across the Bifidobacterium genus. Laboratory-based investigations of a number of representative bifidobacteria strains confirmed that despite containing putative β-lactamases, these strains were sensitive to β-lactams. In contrast, all strains were resistant to the aminoglycosides tested. To assess the contribution of genes encoding putative aminoglycoside resistance proteins in Bifidobacterium sp. two genes, namely Bbr_0651 and Bbr_1586, were targeted for insertional inactivation in B. breve UCC2003. As compared to the wild-type, the UCC2003 insertion mutant strains exhibited decreased resistance to gentamycin, kanamycin and streptomycin. This study highlights the associated risks of relying on the in silico assignment of gene function. Although several putative β-lactam resistance proteins are located in bifidobacteria, their presence does not coincide with resistance to these antibiotics. In contrast however, this approach has resulted in the identification of two loci that contribute to the aminoglycoside resistance of B. breve UCC2003 and, potentially, many other bifidobacteria.Fiona Fouhy is in receipt of an Irish Research Council for Science, Engineering and Technology EMBARK scholarship and is a Teagasc Walsh fellow. Research in the PDC laboratory is supported by the Irish Government under the National Development Plan through the Science Foundation Ireland Investigator award 11/PI/1137. Research in the RPR, CS, PDC and DvS laboratories is also supported by the Science Foundation of Ireland-funded Centre for Science, Engineering and Technology, the Alimentary Pharmabiotic Centre (grant no.s 02/CE/B124 and 07/CE/B1368) and a HRB postdoctoral fellowship (Grant no. PDTM/20011/9) awarded to MOCM

Lactococcal 949 group phages recognize a carbohydrate receptor on the host cell surface

Lactococcal bacteriophages represent one of the leading causes of dairy fermentation failure and product inconsistencies. A new member of the lactococcal 949 phage group, named WRP3, was isolated from cheese whey from a Sicilian factory in 2011. The genome sequence of this phage was determined, and it constitutes the largest lactococcal phage genome currently known, at 130,008 bp. Detailed bioinformatic analysis of the genomic region encoding the presumed initiator complex and baseplate of WRP3 has aided in the functional assignment of several open reading frames (ORFs), particularly that for the receptor binding protein required for host recognition. Furthermore, we demonstrate that the 949 phages target cell wall phospho-polysaccharides as their receptors, accounting for the specificity of the interactions of these phages with their lactococcal hosts. Such information may ultimately aid in the identification of strains/strain blends that do not present the necessary saccharidic target for infection by these problematic phages

Towards a norm-driven design of context-aware e-health applications

In this paper, we explore the usefulness of elaborating process models with norms, especially focusing on the Norm Analysis Method (NAM) as an elaboration tool that can be combined with a process modeling tool, such as Petri Net (PN). The PN-NAM combination has been particularly considered in the paper in relation to a challenge that concerns the design of context-aware applications, namely the challenge of specifying and elaborating complex behaviors that may include alternative (context-driven) processes (we assume that a user context space can be defined and that each context state within this space corresponds to an alternative application service behavior). Hence, the main contribution of our paper comprises an adaptability-driven methodological and modeling support to the design of context-aware applications; modeling guidelines are proposed, considered together with corresponding modeling tools (in particular PN and NAM), and partially illustrated by means of an e-Health-related example. Given the multi-disciplinary nature of the e-Health domain, it is expected that the current research will be useful for it. In particular, e-Health system developers might benefit from the relevant methodological and modeling support, proposed in the paper