Mucosa-Associated Microbiota in Barrett’s Esophagus, Dysplasia, and Esophageal Adenocarcinoma Differ Similarly Compared With Healthy Controls

INTRODUCTION: Alterations in the composition of the human gut microbiome and its metabolites have been linked to gut epithelial neoplasia. We hypothesized that differences in mucosa-adherent Barrett’s microbiota could link to risk factors, providing risk of progression to neoplasia. METHODS: Paired biopsies from both diseased and nonaffected esophagus (as well as gastric cardia and gastric juice for comparison) from patients with intestinal metaplasia (n 5 10), low grade dysplasia (n 5 10), high grade dysplasia (n 5 10), esophageal adenocarcinoma (n 5 12), and controls (n 5 10) were processed for mucosa-associated bacteria and analyzed by 16S ribosomal ribonucleic acid V4 gene DNA sequencing. Taxa composition was tested using a generalized linear model based on the negative binomial distribution and the log link functions of the R Bioconductor package edgeR. RESULTS: The microbe composition of paired samples (disease vs nondisease) comparing normal esophagus with intestinal metaplasia, low grade dysplasia, high grade dysplasia, and adenocarcinoma showed significant decreases in the phylum Planctomycetes and the archaean phylum Crenarchaeota (P \u3c 0.05, false discovery rate corrected) in diseased tissue compared with healthy controls and intrasample controls (gastric juice and unaffected mucosa). Genera Siphonobacter, Balneola, Nitrosopumilus, and Planctomyces were significantly decreased (P \u3c 0.05, false discovery rate corrected), representing \u3c10% of the entire genus community. These changes were unaffected by age, tobacco use, or sex for Crenarcha. DISCUSSSION: There are similar significant changes in bacterial genera in Barrett’s esophagealmucosa, dysplasia, and adenocarcinoma compared with controls and intrapatient unaffected esophagus. Further work will establish the biologic plausibility of these specific microbes’ contributions to protection from or induction of esophageal epithelial dysplasia. Includes supplemental file

A conceptual architecture for semantic web services development and deployment

Several extensions of the Web Services Framework (WSF) have been proposed. The combination with Semantic Web technologies introduces a notion of semantics, which can enhance scalability through automation. Service composition to processes is an equally important issue. Ontology technology – the core of the Semantic Web – can be the central building block of an extension endeavour. We present a conceptual architecture for ontology-based Web service development and deployment. The development of service-based software systems within the WSF is gaining increasing importance. We show how ontologies can integrate models, languages, infrastructure, and activities within this architecture to support reuse and composition of semantic Web services

Extending OWL-S for the Composition of Web Services Generated With a Legacy Application Wrapper

Despite numerous efforts by various developers, web service composition is still a difficult problem to tackle. Lot of progressive research has been made on the development of suitable standards. These researches help to alleviate and overcome some of the web services composition issues. However, the legacy application wrappers generate nonstandard WSDL which hinder the progress. Indeed, in addition to their lack of semantics, WSDLs have sometimes different shapes because they are adapted to circumvent some technical implementation aspect. In this paper, we propose a method for the semi automatic composition of web services in the context of the NeuroLOG project. In this project the reuse of processing tools relies on a legacy application wrapper called jGASW. The paper describes the extensions to OWL-S in order to introduce and enable the composition of web services generated using the jGASW wrapper and also to implement consistency checks regarding these services.Comment: ICIW 2012, The Seventh International Conference on Internet and Web Applications and Services, Stuttgart : Germany (2012

Towards a service-oriented e-infrastructure for multidisciplinary environmental research

Research e-infrastructures are considered to have generic and thematic parts. The generic part provids high-speed networks, grid (large-scale distributed computing) and database systems (digital repositories and data transfer systems) applicable to all research commnities irrespective of discipline. Thematic parts are specific deployments of e-infrastructures to support diverse virtual research communities. The needs of a virtual community of multidisciplinary envronmental researchers are yet to be investigated. We envisage and argue for an e-infrastructure that will enable environmental researchers to develop environmental models and software entirely out of existing components through loose coupling of diverse digital resources based on the service-oriented achitecture. We discuss four specific aspects for consideration for a future e-infrastructure: 1) provision of digital resources (data, models & tools) as web services, 2) dealing with stateless and non-transactional nature of web services using workflow management systems, 3) enabling web servce discovery, composition and orchestration through semantic registries, and 4) creating synergy with existing grid infrastructures

Approaches to Semantic Web Services: An Overview and Comparison

Abstract. The next Web generation promises to deliver Semantic Web Services (SWS); services that are self-described and amenable to automated discovery, composition and invocation. A prerequisite to this, however, is the emergence and evolution of the Semantic Web, which provides the infrastructure for the semantic interoperability of Web Services. Web Services will be augmented with rich formal descriptions of their capabilities, such that they can be utilized by applications or other services without human assistance or highly constrained agreements on interfaces or protocols. Thus, Semantic Web Services have the potential to change the way knowledge and business services are consumed and provided on the Web. In this paper, we survey the state of the art of current enabling technologies for Semantic Web Services. In addition, we characterize the infrastructure of Semantic Web Services along three orthogonal dimensions: activities, architecture and service ontology. Further, we examine and contrast three current approaches to SWS according to the proposed dimensions

Issues about the Adoption of Formal Methods for Dependable Composition of Web Services

Web Services provide interoperable mechanisms for describing, locating and invoking services over the Internet; composition further enables to build complex services out of simpler ones for complex B2B applications. While current studies on these topics are mostly focused - from the technical viewpoint - on standards and protocols, this paper investigates the adoption of formal methods, especially for composition. We logically classify and analyze three different (but interconnected) kinds of important issues towards this goal, namely foundations, verification and extensions. The aim of this work is to individuate the proper questions on the adoption of formal methods for dependable composition of Web Services, not necessarily to find the optimal answers. Nevertheless, we still try to propose some tentative answers based on our proposal for a composition calculus, which we hope can animate a proper discussion

ASIME 2018 White Paper. In-Space Utilisation of Asteroids: Asteroid Composition -- Answers to Questions from the Asteroid Miners

In keeping with the Luxembourg government's initiative to support the future use of space resources, ASIME 2018 was held in Belval, Luxembourg on April 16-17, 2018. The goal of ASIME 2018: Asteroid Intersections with Mine Engineering, was to focus on asteroid composition for advancing the asteroid in-space resource utilisation domain. What do we know about asteroid composition from remote-sensing observations? What are the potential caveats in the interpretation of Earth-based spectral observations? What are the next steps to improve our knowledge on asteroid composition by means of ground-based and space-based observations and asteroid rendez-vous and sample return missions? How can asteroid mining companies use this knowledge? ASIME 2018 was a two-day workshop of almost 70 scientists and engineers in the context of the engineering needs of space missions with in-space asteroid utilisation. The 21 Questions from the asteroid mining companies were sorted into the four asteroid science themes: 1) Potential Targets, 2) Asteroid-Meteorite Links, 3) In-Situ Measurements and 4) Laboratory Measurements. The Answers to those Questions were provided by the scientists with their conference presentations and collected by A. Graps or edited directly into an open-access collaborative Google document or inserted by A. Graps using additional reference materials. During the ASIME 2018, first day and second day Wrap-Ups, the answers to the questions were discussed further. New readers to the asteroid mining topic may find the Conversation boxes and the Mission Design discussions especially interesting.Comment: Outcome from the ASIME 2018: Asteroid Intersections with Mine Engineering, Luxembourg. April 16-17, 2018. 65 Pages. arXiv admin note: substantial text overlap with arXiv:1612.0070

Evaluation of Common Methods for Sampling Invertebrate Pollinator Assemblages: Net Sampling Out-Perform Pan Traps

Methods for sampling ecological assemblages strive to be efficient, repeatable, and representative. Unknowingly, common methods may be limited in terms of revealing species function and so of less value for comparative studies. The global decline in pollination services has stimulated surveys of flower-visiting invertebrates, using pan traps and net sampling. We explore the relative merits of these two methods in terms of species discovery, quantifying abundance, function, and composition, and responses of species to changing floral resources. Using a spatially-nested design we sampled across a 5000 km2 area of arid grasslands, including 432 hours of net sampling and 1296 pan trap-days, between June 2010 and July 2011. Net sampling yielded 22% more species and 30% higher abundance than pan traps, and better reflected the spatio-temporal variation of floral resources. Species composition differed significantly between methods; from 436 total species, 25% were sampled by both methods, 50% only by nets, and the remaining 25% only by pans. Apart from being less comprehensive, if pan traps do not sample flower-visitors, the link to pollination is questionable. By contrast, net sampling functionally linked species to pollination through behavioural observations of flower-visitation interaction frequency. Netted specimens are also necessary for evidence of pollen transport. Benefits of net-based sampling outweighed minor differences in overall sampling effort. As pan traps and net sampling methods are not equivalent for sampling invertebrate-flower interactions, we recommend net sampling of invertebrate pollinator assemblages, especially if datasets are intended to document declines in pollination and guide measures to retain this important ecosystem service. © 2013 Popic et al