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

Streaming DICOM Real-Time Video and Metadata Flows Outside The Operating Room

International audienceWith the current advancement in the medical world, surgeons are faced with the challenge of handling many sources of medical information in more and more complex and technological Operating Rooms (ORs). Obviously, in the next generation ones, there will be an increasing number of video flows during the surgery (e.g. endoscopes, cameras, ultrasounds, etc.), which can be also displayed all over the OR in order to facilitate the task for the surgeon and to avoid any adverse events or problems related to inadequate communication in the OR. Additionally, other information needs to be shared, pre/post/during an operation, such as the history of the digital images related to the patient in the PACS and the metadata coming from medical sensors. Moreover, these medical videos captured from the OR can be either displayed on a large screen in the OR in order to provide the surgeon with more visibility, in this case via DICOM-RTV, or streamed outside the OR via a P2P solution. The latter one can serve various purposes such as for teaching medical student in real-time or for remote-expertise with a remote senior surgeons. Hence, this paper addresses the challenges of streaming DICOM-RTV video and metadata flows live from the operating room, typically during an ongoing surgery, in real-time to the outside world. A Proof of Concept is also presented in order to demonstrate the feasibility of our solution

Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma

International audienceThe mechanisms of gene amplification in tumour cells are poorly understood and the relationship between extrachromosomal DNA molecules, named double minutes (dmins), and intrachromosomal homogeneously staining regions (hsr) is not documented at nucleotide resolution. Using fluorescent in situ hybridization and whole genome sequencing, we studied a xenografted human oligodendroglioma where the co-amplification of the EGFR and MYC loci was present in the form of dmins at early passages and of an hsr at later passages. The amplified regions underwent multiple rearrangements and deletions during the formation of the dmins and their transformation into hsr. In both forms of amplification, non-homologous end-joining and microhomology-mediated end-joining rather than replication repair mechanisms prevailed in fusions. Small fragments, some of a few tens of base pairs, were associated in contigs. They came from clusters of breakpoints localized hundreds of kilobases apart in the amplified regions. The characteristics of some pairs of junctions suggest that at least some fragments were not fused randomly but could result from the concomi-tant repair of neighbouring breakpoints during the interaction of remote DNA sequences. This characterization at nucleotide resolution of the transition between extra-and intrachromosome amplifications highlights a hitherto uncharacterized organization of the amplified regions suggesting the involvement of new mechanisms in their formation

Federating distributed and heterogeneous information sources in neuroimaging: the NeuroBase Project.

The NeuroBase project aims at studying the requirements for federating, through the Internet, information sources in neuroimaging. These sources are distributed in different experimental sites, hospitals or research centers in cognitive neurosciences, and contain heterogeneous data and image processing programs. More precisely, this project consists in creating of a shared ontology, suitable for supporting various neuroimaging applications, and a computer architecture for accessing and sharing relevant distributed information. We briefly describe the semantic model and report in more details the architecture we chose, based on a media-tor/wrapper approach. To give a flavor of the future deployment of our architecture, we de-scribe a demonstrator that implements the comparison of distributed image processing tools applied to distributed neuroimaging data

OntoVIP: An ontology for the annotation of object models used for medical image simulation.

International audienceThis paper describes the creation of a comprehensive conceptualization of object models used in medical image simulation, suitable for major imaging modalities and simulators. The goal is to create an application ontology that can be used to annotate the models in a repository integrated in the Virtual Imaging Platform (VIP), to facilitate their sharing and reuse. Annotations make the anatomical, physiological and pathophysiological content of the object models explicit. In such an interdisciplinary context we chose to rely on a common integration framework provided by a foundational ontology, that facilitates the consistent integration of the various modules extracted from several existing ontologies, i.e. FMA, PATO, MPATH, RadLex and ChEBI. Emphasis is put on methodology for achieving this extraction and integration. The most salient aspects of the ontology are presented, especially the organization in model layers, as well as its use to browse and query the model repository

A virtual imaging platform for multi-modality medical image simulation.

International audienceThis paper presents the Virtual Imaging Platform (VIP), a platform accessible at http://vip.creatis.insa-lyon.fr to facilitate the sharing of object models and medical image simulators, and to provide access to distributed computing and storage resources. A complete overview is presented, describing the ontologies designed to share models in a common repository, the workflow template used to integrate simulators, and the tools and strategies used to exploit computing and storage resources. Simulation results obtained in four image modalities and with different models show that VIP is versatile and robust enough to support large simulations. The platform currently has 200 registered users who consumed 33 years of CPU time in 2011

The heterochromatic chromosome caps in great apes impact telomere metabolism.

In contrast with the limited sequence divergence accumulated after separation of higher primate lineages, marked cytogenetic variation has been associated with the genome evolution in these species. Studying the impact of such structural variations on defined molecular processes can provide valuable insights on how genome structural organization contributes to organismal evolution. Here, we show that telomeres on chromosome arms carrying subtelomeric heterochromatic caps in the chimpanzee, which are completely absent in humans, replicate later than telomeres on chromosome arms without caps. In gorilla, on the other hand, a proportion of the subtelomeric heterochromatic caps present in most chromosome arms are associated with large blocks of telomere-like sequences that follow a replication program different from that of bona fide telomeres. Strikingly, telomere-containing RNA accumulates extrachromosomally in gorilla mitotic cells, suggesting that at least some aspects of telomere-containing RNA biogenesis have diverged in gorilla, perhaps in concert with the evolution of heterochromatic caps in this species

Evaluation of 16S rRNA gene PCR sensitivity and specificity for diagnosis of prosthetic joint infection: a prospective multicenter cross-sectional study

There is no standard method for the diagnosis of prosthetic joint infection (PJI). The contribution of 16S rRNA gene PCR sequencing on a routine basis remains to be defined. We performed a prospective multicenter study to assess the contributions of 16S rRNA gene assays in PJI diagnosis. Over a 2-year period, all patients suspected to have PJIs and a few uninfected patients undergoing primary arthroplasty (control group) were included. Five perioperative samples per patient were collected for culture and 16S rRNA gene PCR sequencing and one for histological examination. Three multicenter quality control assays were performed with both DNA extracts and crushed samples. The diagnosis of PJI was based on clinical, bacteriological, and histological criteria, according to Infectious Diseases Society of America guidelines. A molecular diagnosis was modeled on the bacteriological criterion (≥ 1 positive sample for strict pathogens and ≥ 2 for commensal skin flora). Molecular data were analyzed according to the diagnosis of PJI. Between December 2010 and March 2012, 264 suspected cases of PJI and 35 control cases were included. PJI was confirmed in 215/264 suspected cases, 192 (89%) with a bacteriological criterion. The PJIs were monomicrobial (163 cases [85%]; staphylococci, n = 108; streptococci, n = 22; Gram-negative bacilli, n = 16; anaerobes, n = 13; others, n = 4) or polymicrobial (29 cases [15%]). The molecular diagnosis was positive in 151/215 confirmed cases of PJI (143 cases with bacteriological PJI documentation and 8 treated cases without bacteriological documentation) and in 2/49 cases without confirmed PJI (sensitivity, 73.3%; specificity, 95.5%). The 16S rRNA gene PCR assay showed a lack of sensitivity in the diagnosis of PJI on a multicenter routine basis

Relationships Linking Amplification Level to Gene Over-Expression in Gliomas

Background: Gene amplification is thought to promote over-expression of genes favouring tumour development. Because amplified regions are usually megabase-long, amplification often concerns numerous syntenic or non-syntenic genes, among which only a subset is over-expressed. The rationale for these differences remains poorly understood. Methodology/Principal Finding: To address this question, we used quantitative RT-PCR to determine the expression level of a series of co-amplified genes in five xenografted and one fresh human gliomas. These gliomas were chosen because we have previously characterised in detail the genetic content of their amplicons. In all the cases, the amplified sequences lie on extra-chromosomal DNA molecules, as commonly observed in gliomas. We show here that genes transcribed in nonamplified gliomas are over-expressed when amplified, roughly in proportion to their copy number, while non-expressed genes remain inactive. When specific antibodies were available, we also compared protein expression in amplified and nonamplified tumours. We found that protein accumulation barely correlates with the level of mRNA expression in some of these tumours. Conclusions/Significance: Here we show that the tissue-specific pattern of gene expression is maintained upon amplification in gliomas. Our study relies on a single type of tumour and a limited number of cases. However, it strongly suggests that, even when amplified, genes that are normally silent in a given cell type play no role in tumour progression