Global Functional Atlas of \u3cem\u3eEscherichia coli\u3c/em\u3e Encompassing Previously Uncharacterized Proteins

One-third of the 4,225 protein-coding genes of Escherichia coli K-12 remain functionally unannotated (orphans). Many map to distant clades such as Archaea, suggesting involvement in basic prokaryotic traits, whereas others appear restricted to E. coli, including pathogenic strains. To elucidate the orphans’ biological roles, we performed an extensive proteomic survey using affinity-tagged E. coli strains and generated comprehensive genomic context inferences to derive a high-confidence compendium for virtually the entire proteome consisting of 5,993 putative physical interactions and 74,776 putative functional associations, most of which are novel. Clustering of the respective probabilistic networks revealed putative orphan membership in discrete multiprotein complexes and functional modules together with annotated gene products, whereas a machine-learning strategy based on network integration implicated the orphans in specific biological processes. We provide additional experimental evidence supporting orphan participation in protein synthesis, amino acid metabolism, biofilm formation, motility, and assembly of the bacterial cell envelope. This resource provides a “systems-wide” functional blueprint of a model microbe, with insights into the biological and evolutionary significance of previously uncharacterized proteins

Accessing RDF(S) data resources in service-based Grid infrastructures

We describe the results of the RDF(S) activity within the Open Grid Forum (http://www.ogf.org) (OGF) Database Access and Integration Services (DAIS) Working Group (http://forge.gridforum.org/projects/dais-wg) whose objective is to develop standard service-based grid access mechanisms for data expressed in RDF and RDF Schema. We produce two specifications, focused on the provision of SPARQL querying capabilities for accessing RDF data and a set of RDF Schema ontology handling primitives for creating, retrieving, updating, and deleting RDF data. In this paper we present a set of use cases that justify this work and an overview of these specifications, which will enter in editorial process at OGF25. We conclude by outlining the future work that will be made in the context of this standardization process

Peer-to-Peer Grids

We describe Peer-to-Peer Grids built around Integration of technologies from the peer-to-peer and Grid fields. We focus on the role of Web services linked by a powerful event service using uniform XML interfaces and application level routing. We describe how a rich synchronous and asynchronous collaboration environment can support virtual communities built on top of such infrastructure. Universal access mechanisms are discussed

Semantic technologies: from niche to the mainstream of Web 3? A comprehensive framework for web Information modelling and semantic annotation

Context: Web information technologies developed and applied in the last decade have considerably changed the way web applications operate and have revolutionised information management and knowledge discovery. Social technologies, user-generated classification schemes and formal semantics have a far-reaching sphere of influence. They promote collective intelligence, support interoperability, enhance sustainability and instigate innovation. Contribution: The research carried out and consequent publications follow the various paradigms of semantic technologies, assess each approach, evaluate its efficiency, identify the challenges involved and propose a comprehensive framework for web information modelling and semantic annotation, which is the thesis’ original contribution to knowledge. The proposed framework assists web information modelling, facilitates semantic annotation and information retrieval, enables system interoperability and enhances information quality. Implications: Semantic technologies coupled with social media and end-user involvement can instigate innovative influence with wide organisational implications that can benefit a considerable range of industries. The scalable and sustainable business models of social computing and the collective intelligence of organisational social media can be resourcefully paired with internal research and knowledge from interoperable information repositories, back-end databases and legacy systems. Semantified information assets can free human resources so that they can be used to better serve business development, support innovation and increase productivity

HTTP Mailbox - Asynchronous RESTful Communication

We describe HTTP Mailbox, a mechanism to enable RESTful HTTP communication in an asynchronous mode with a full range of HTTP methods otherwise unavailable to standard clients and servers. HTTP Mailbox allows for broadcast and multicast semantics via HTTP. We evaluate a reference implementation using ApacheBench (a server stress testing tool) demonstrating high throughput (on 1,000 concurrent requests) and a systemic error rate of 0.01%. Finally, we demonstrate our HTTP Mailbox implementation in a human assisted web preservation application called "Preserve Me".Comment: 13 pages, 6 figures, 8 code blocks, 3 equations, and 3 table

UBIDEV: a homogeneous service framework for pervasive computing environments

This dissertation studies the heterogeneity problem of pervasive computing system from the viewpoint of an infrastructure aiming to provide a service-oriented application model. From Distributed System passing through mobile computing, pervasive computing is presented as a step forward in ubiquitous availability of services and proliferation of interacting autonomous entities. To better understand the problems related to the heterogeneous and dynamic nature of pervasive computing environments, we need to analyze the structure of a pervasive computing system from its physical and service dimension. The physical dimension describes the physical environment together wit the technology infrastructure that characterizes the interactions and the relations within the environment; the service dimension represents the services (being them software or not) the environment is able to provide [Nor99]. To better separate the constrains and the functionalities of a pervasive computing system, this dissertation classifies it in terms of resources, context, classification, services, coordination and application. UBIDEV, as the key result of this dissertation, introduces a unified model helping the design and the implementation of applications for heterogeneous and dynamic environments. This model is composed of the following concepts: • Resource: all elements of the environment that are manipulated by the application, they are the atomic abstraction unit of the model. • Context: all information coming from the environment that is used by the application to adapts its behavior. Context contains resources and services and defines their role in the application. • Classification: the environment is classified according to the application ontology in order to ground the generic conceptual model of the application to the specific environment. It defines the basic semantic level of interoperability. • Service: the functionalities supported by the system; each service manipulates one or more resources. Applications are defined as a coordination and adaptation of services. • Coordination: all aspects related to service composition and execution as well as the use of the contextual information are captured by the coordination concept. • Application Ontology: represents the viewpoint of the application on the specific context; it defines the high level semantic of resources, services and context. Applying the design paradigm proposed by UBIDEV, allows to describe applications according to a Service Oriented Architecture[Bie02], and to focus on application functionalities rather than their relations with the physical devices. Keywords: pervasive computing, homogenous environment, service-oriented, heterogeneity problem, coordination model, context model, resource management, service management, application interfaces, ontology, semantic services, interaction logic, description logic.Questa dissertazione studia il problema della eterogeneit`a nei sistemi pervasivi proponendo una infrastruttura basata su un modello orientato ai servizi. I sistemi pervasivi sono presentati come un’evoluzione naturale dei sistemi distribuiti, passando attraverso mobile computing, grazie ad una disponibilit`a ubiqua di servizi (sempre, ovunque ed in qualunque modo) e ad loro e con l’ambiente stesso. Al fine di meglio comprendere i problemi legati allintrinseca eterogeneit`a dei sistemi pervasivi, dobbiamo prima descrivere la struttura fondamentale di questi sistemi classificandoli attraverso la loro dimensione fisica e quella dei loro servizi. La dimensione fisica descrive l’ambiente fisico e tutti i dispositivi che fanno parte del contesto della applicazione. La dimensione dei servizi descrive le funzionalit`a (siano esse software o no) che l’ambiente `e in grado di fornire [Nor99]. I sistemi pervasivi vengono cos`ı classificati attraverso una metrica pi `u formale del tipo risorse, contesto, servizi, coordinazione ed applicazione. UBIDEV, come risultato di questa dissertazione, introduce un modello uniforme per la descrizione e lo sviluppo di applicazioni in ambienti dinamici ed eterogenei. Il modello `e composto dai seguenti concetti di base: • Risorse: gli elementi dell’ambiente fisico che fanno parte del modello dellapplicazione. Questi rappresentano l’unit`a di astrazione atomica di tutto il modello UBIDEV. • Contesto: le informazioni sullo stato dell’ambiente che il sistema utilizza per adattare il comportamento dell’applicazione. Il contesto include informazioni legate alle risorse, ai servizi ed alle relazioni che li legano. • Classificazione: l’ambiente viene classificato sulla base di una ontologia che rappresenta il punto di accordo a cui tutti i moduli di sistema fanno riferimento. Questa classificazione rappresenta il modello concettuale dell’applicazione che si riflette sull’intero ambiente. Si definisce cos`ı la semantica di base per tutto il sistema. • Servizi: le funzionalit`a che il sistema `e in grado di fornire; ogni servizio `e descritto in termini di trasformazione di una o pi `u risorse. Le applicazioni sono cos`ı definite in termini di cooperazione tra servizi autonomi. • Coordinazione: tutti gli aspetti legati alla composizione ed alla esecuzione di servizi cos`ı come l’elaborazione dell’informazione contestuale. • Ontologia dell’Applicazione: rappresenta il punto di vista dell’applicazione; definisce la semantica delle risorse, dei servizi e dell’informazione contestuale. Applicando il paradigma proposto da UBIDEV, si possono descrivere applicazioni in accordo con un modello Service-oriented [Bie02] ed, al tempo stesso, ridurre l’applicazione stessa alle sue funzionalit`a di alto livello senza intervenire troppo su come queste funzionalit` a devono essere realizzate dalle singole componenti fisiche

A Survey on Wireless Sensor Network Security

Wireless sensor networks (WSNs) have recently attracted a lot of interest in the research community due their wide range of applications. Due to distributed nature of these networks and their deployment in remote areas, these networks are vulnerable to numerous security threats that can adversely affect their proper functioning. This problem is more critical if the network is deployed for some mission-critical applications such as in a tactical battlefield. Random failure of nodes is also very likely in real-life deployment scenarios. Due to resource constraints in the sensor nodes, traditional security mechanisms with large overhead of computation and communication are infeasible in WSNs. Security in sensor networks is, therefore, a particularly challenging task. This paper discusses the current state of the art in security mechanisms for WSNs. Various types of attacks are discussed and their countermeasures presented. A brief discussion on the future direction of research in WSN security is also included.Comment: 24 pages, 4 figures, 2 table

Cross-Platform Text Mining and Natural Language Processing Interoperability - Proceedings of the LREC2016 conference

No abstract available

Cross-Platform Text Mining and Natural Language Processing Interoperability - Proceedings of the LREC2016 conference

No abstract available