Topology of the world trade web

Economy, and consequently trade, is a fundamental part of human social organization which, until now, has not been studied within the network modeling framework. Here we present the first, to the best of our knowledge, empirical characterization of the world trade web, that is, the network built upon the trade relationships between different countries in the world. This network displays the typical properties of complex networks, namely, scale-free degree distribution, the small-world property, a high clustering coefficient, and, in addition, degree-degree correlation between different vertices. All these properties make the world trade web a complex network, which is far from being well described through a classical random network description.

The EU-ADR Web Platform: delivering advanced pharmacovigilance tools

PURPOSE: Pharmacovigilance methods have advanced greatly during the last decades, making post-market drug assessment an essential drug evaluation component. These methods mainly rely on the use of spontaneous reporting systems and health information databases to collect expertise from huge amounts of real-world reports. The EU-ADR Web Platform was built to further facilitate accessing, monitoring and exploring these data, enabling an in-depth analysis of adverse drug reactions risks.METHODS: The EU-ADR Web Platform exploits the wealth of data collected within a large-scale European initiative, the EU-ADR project. Millions of electronic health records, provided by national health agencies, are mined for specific drug events, which are correlated with literature, protein and pathway data, resulting in a rich drug-event dataset. Next, advanced distributed computing methods are tailored to coordinate the execution of data-mining and statistical analysis tasks. This permits obtaining a ranked drug-event list, removing spurious entries and highlighting relationships with high risk potential.RESULTS: The EU-ADR Web Platform is an open workspace for the integrated analysis of pharmacovigilance datasets. Using this software, researchers can access a variety of tools provided by distinct partners in a single centralized environment. Besides performing standalone drug-event assessments, they can also control the pipeline for an improved batch analysis of custom datasets. Drug-event pairs can be substantiated and statistically analysed within the platform's innovative working environment.CONCLUSIONS: A pioneering workspace that helps in explaining the biological path of adverse drug reactions was developed within the EU-ADR project consortium. This tool, targeted at the pharmacovigilance community, is available online at https://bioinformatics.ua.pt/euadr/. Copyright © 2012 John Wiley & Sons, Ltd.

Desarrollo de una web semántica

Amb aquest projecte es vol solucionar aquesta manca d'accés a la informació i sobretot disposar d'un sistema que relacioni "tot amb tot", és a dir, muntar un sistema únic per documentar xarxa (física) independentment de l'element que es vulgui documentar. La idea és basar el projecte de documentació en una web semàntica basada en wiki semàntica amb un motor de cerca MediaWiki.

O2, the Oberta in Open Access : institutional repository

Tríptic informatiu sobre la publicació de documents amb accés obert en el repositori institucional de la UOC, O2 (La Oberta en obert). Aquest informa sobre quins documents hi poden publicar els membres de la comunitat UOC, com fer-ho i els serveis de valor afegit per a tots els usuaris (web 2.0, subscripció per RSS o correu electrònic, exportació al gestor bibliogràfic Refworks, etc.) i per a la recerca (lligam amb l'aplicació d'avaluació de la recerca GIR i informació del factor d'impacte de la revista a SCOPUS, IN-RECS/IN-RECJ i MIAR).

Ciencia 2.0 : aplicación de la web social a la investigación

REBIUN study on Science 2.0 and social web applications for research. There are three categories: share research, share resources and share results. Describes the applications and selected resources of interest: scientific social networks, scientific databases, research platforms, surveys, concept maps, file sharing, bibliographic management, social bookmarking, citation indexes, blogs and wikis, science news, open access. The services are evaluated and the report describes his interest to libraries.

Going with the consumer towards the social Web environment : a review of extant knowledge

The social Web environment cannot be explained without taking into account the use made by consumers of the web technologies in the field of e-commerce. Starting with a systematic background of the growing body of research on marketing and consumer behaviour on the Web; this article presents a critical review of the main contributions on this theme, integrating also the research field of consumer behaviour in the social Web environment. It concludes with some managerial guidelines for successful use of the social Web in the commercial activities and in the establishment of fruitful relationships between the consumers and the brand.

eggNOG v4.0: nested orthology inference across 3686 organisms

With the increasing availability of various 'omics data, high-quality orthology assignment is crucial for evolutionary and functional genomics studies. We here present the fourth version of the eggNOG database (available at http://eggnog.embl.de) that derives nonsupervised orthologous groups (NOGs) from complete genomes, and then applies a comprehensive characterization and analysis pipeline to the resulting gene families. Compared with the previous version, we have more than tripled the underlying species set to cover 3686 organisms, keeping track with genome project completions while prioritizing the inclusion of high-quality genomes to minimize error propagation from incomplete proteome sets. Major technological advances include (i) a robust and scalable procedure for the identification and inclusion of high-quality genomes, (ii) provision of orthologous groups for 107 different taxonomic levels compared with 41 in eggNOGv3, (iii) identification and annotation of particularly closely related orthologous groups, facilitating analysis of related gene families, (iv) improvements of the clustering and functional annotation approach, (v) adoption of a revised tree building procedure based on the multiple alignments generated during the process and (vi) implementation of quality control procedures throughout the entire pipeline. As in previous versions, eggNOGv4 provides multiple sequence alignments and maximum-likelihood trees, as well as broad functional annotation. Users can access the complete database of orthologous groups via a web interface, as well as through bulk download.

Building a usable and accessible semantic web interaction platform

Semantic Web applications take off is being slower than expected, at least with respect to “real-world” applications and users. One of the main reasons for this lack of adoption is that most Semantic Web user interfaces are still immature from the usability and accessibility points of view. This is due to the novelty of these technologies, but this also motivates the exploration of alternative interaction paradigms, different from the “traditional” Web or Desktop applications ones. Our proposal is realized in the Rhizomer platform, which explores the possibilities of the object–action interaction paradigm at the Web scale. This paradigm is well suited for heterogeneous resource spaces such as those common in the Semantic Web. Resources, described by metadata, correspond to the objects in the paradigm. Semantic web services, which are dynamically associated to these objects, correspond to the actions. The platform is being put into practice in the context of a research project in order to build an open application for media distribution based on Semantic Web technologies. Moreover, its usability and accessibility have been evaluated in this real setting and compared to similar systems.

Micromorphological characterization and lithification of microbial mats from the Ebro Delta (Spain)

The structural organization of microbial mats from the Ebro Delta (Spain) and their accretion and partial lithification processes were explored using scanning electron microscopy in back-scattered electron mode and low-temperature scanning electron microscopy. Two differentiated zones were distinguished in a transverse section of a fragment taken from the mat at a depth of 2.5 mm. The first consisted of an upper layer in which the dominant microorganisms, Microcoleus spp., actively grew in an embedded slack matrix of exopolysaccharides. Microcoleus filaments were oriented parallel to the surface and to each other, with filaments below arranged perpendicularly to one another but without crossing. Most of the minerals present were allochthonous grains of calcium phosphate biocorroded by cyanobacteria. The second zone was below a depth of 1 mm and made up of accretion layers with large deposits of calcium carbonate and smaller amounts of calcium phosphate of biological origin. The predominance of a particular type of mineral precipitation with a characteristic external shape and/or texture within a zone, e.g., sponge-like deposits of calcium phosphate, appears to depend on the taxa of the prevailing microorganisms

Semantic Web applications: a framework for industry and business exploitation – What is needed for the adoption of the Semantic Web from the market and industry

In recent years, Semantic Web (SW) research has resulted in significant outcomes. Various industries have adopted SW technologies, while the ‘deep web’ is still pursuing the critical transformation point, in which the majority of data found on the deep web will be exploited through SW value layers. In this article we analyse the SW applications from a ‘market’ perspective. We are setting the key requirements for real-world information systems that are SW-enabled and we discuss the major difficulties for the SW uptake that has been delayed. This article contributes to the literature of SW and knowledge management providing a context for discourse towards best practices on SW-based information systems.

A web ontologies framework for digital rights management

In order to improve the management of copyright in the Internet, known as Digital Rights Management, there is the need for a shared language for copyright representation. Current approaches are based on purely syntactic solutions, i.e. a grammar that defines a rights expression language. These languages are difficult to put into practise due to the lack of explicit semantics that facilitate its implementation. Moreover, they are simple from the legal point of view because they are intended just to model the usage licenses granted by content providers to end-users. Thus, they ignore the copyright framework that lies behind and the whole value chain from creators to end-users. Our proposal is to use a semantic approach based on semantic web ontologies. We detail the development of a copyright ontology in order to put this approach into practice. It models the copyright core concepts for creation, rights and the basic kinds of actions that operate on content. Altogether, it allows building a copyright framework for the complete value chain. The set of actions operating on content are our smaller building blocks in order to cope with the complexity of copyright value chains and statements and, at the same time, guarantee a high level of interoperability and evolvability. The resulting copyright modelling framework is flexible and complete enough to model many copyright scenarios, not just those related to the economic exploitation of content. The ontology also includes moral rights, so it is possible to model this kind of situations as it is shown in the included example model for a withdrawal scenario. Finally, the ontology design and the selection of tools result in a straightforward implementation. Description Logic reasoners are used for license checking and retrieval. Rights are modelled as classes of actions, action patterns are modelled also as classes and the same is done for concrete actions. Then, to check if some right or license grants an action is reduced to check for class subsumption, which is a direct functionality of these reasoners.

Ultrasonic and LIDAR sensors for electronic canopy characterization in vineyards: advances to improve pesticide application methods

Canopy characterization is a key factor to improve pesticide application methods in tree crops and vineyards. Development of quick, easy and efficient methods to determine the fundamental parameters used to characterize canopy structure is thus an important need. In this research the use of ultrasonic and LIDAR sensors have been compared with the traditional manual and destructive canopy measurement procedure. For both methods the values of key parameters such as crop height, crop width, crop volume or leaf area have been compared. Obtained results indicate that an ultrasonic sensor is an appropriate tool to determine the average canopy characteristics, while a LIDAR sensor provides more accuracy and detailed information about the canopy. Good correlations have been obtained between crop volume (CVU) values measured with ultrasonic sensors and leaf area index, LAI (R2 = 0.51). A good correlation has also been obtained between the canopy volume measured with ultrasonic and LIDAR sensors (R2 = 0.52). Laser measurements of crop height (CHL) allow one to accurately predict the canopy volume. The proposed new technologies seems very appropriate as complementary tools to improve the efficiency of pesticide applications, although further improvements are still needed.

A user-friendly web portal for T-Coffee on supercomputers

Background: Parallel T-Coffee (PTC) was the first parallel implementation of the T-Coffee multiple sequence alignment tool. It is based on MPI and RMA mechanisms. Its purpose is to reduce the execution time of the large-scale sequence alignments. It can be run on distributed memory clusters allowing users to align data sets consisting of hundreds of proteins within a reasonable time. However, most of the potential users of this tool are not familiar with the use of grids or supercomputers. Results: In this paper we show how PTC can be easily deployed and controlled on a super computer architecture using a web portal developed using Rapid. Rapid is a tool for efficiently generating standardized portlets for a wide range of applications and the approach described here is generic enough to be applied to other applications, or to deploy PTC on different HPC environments. Conclusions: The PTC portal allows users to upload a large number of sequences to be aligned by the parallel version of TC that cannot be aligned by a single machine due to memory and execution time constraints. The web portal provides a user-friendly solution.

Review. Characterization and selection of hexaploid wheats containing resistance to Heterodera avenae or Mayetiola destructor introgressed from Aegilops

Cereal cyst nematode (CCN, Heterodera avenae) and Hessian fly (HF, Mayetiola destructor) are two major pests affecting wheat crops worldwide including important cereal areas of Spain. Aegilops ventricosa and Ae. triuncialis were used as donors in a strategy to introduce resistance genes (RG) for these pests in hexaploid wheat (Triticum aestivum L.). Two 42 chromosomes introgression lines have been derived from Ae. ventricosa: H-93-8 and H-93-33 carrying genes Cre2 and H27 conferring resistance to CCN and HF, respectively. Line TR-3531 with 42 chromosomes has been derived from Ae. triuncialis and carries RGs conferring resistance for CCN (Cre7) and for HF (H30). Alien material has been incorporated in lines H-93 by chromosomal substitution and recombination, while in line TR-3531 homoeologous recombination affecting small DNA fragments has played a major role. It has been demonstrated that Cre2, Cre7, H27 and H30 are major single dominant genes and not allelic of other previously described RGs. Biochemical and molecular-biology studies of the defense mechanism triggered by Cre2 and Cre7 have revealed specific induction of peroxidase and other antioxidant enzymes. In parallel to these basic studies advanced lines carrying resistance genes for CNN and/or HF have been developed. Selection was done using molecular markers for eventually «pyramiding» resistance genes. Several isozyme and RAPD markers have been described and, currently, new markers based on transposable elements and NBS-LRR sequences are being developed. At present, two advanced lines have already been included at the Spanish Catalogue of Commercial Plant Varieties.

Indicadores de calidad de la producción en la Web of Science de diez profesores del Área de Personalidad, Evaluación y Tratamiento Psicológico: aportaciones adicionales al estudio de Olivas-Ávila y Musi-Lechuga

Los rankings de productividad científica resultan cada vez más relevantes, tanto a nivel individual como institucional. Garantizar que se basan en información confiable y exhaustiva es, por tanto, importante. Este estudio indica que la posición de los individuos en esa clase de ranking puede cambiar sustancialmente cuando se consideran diversos indicadores bibliométricos internacionalmente reconocidos. Se usa, como ilustración, el caso de los diez profesores del área de ‘Personalidad, Evaluación y Tratamiento Psicológico’ consignados en el reciente análisis de Olivas-Ávila y Musi-Lechuga (Psicothema 2010. Vol. 22, nº 4, pp. 909-916).