From SNPs to pathways: integration of functional effect of sequence variations on models of cell signalling pathways

Background: Single nucleotide polymorphisms (SNPs) are the most frequent type of sequence variation between individuals, and represent a promising tool for finding genetic determinants of complex diseases and understanding the differences in drug response. In this regard, it is of particular interest to study the effect of non-synonymous SNPs in the context of biological networks such as cell signalling pathways. UniProt provides curated information about the functional and phenotypic effects of sequence variation, including SNPs, as well as on mutations of protein sequences. However, no strategy has been developed to integrate this information with biological networks, with the ultimate goal of studying the impact of the functional effect of SNPs in the structure and dynamics of biological networks. Results: First, we identified the different challenges posed by the integration of the phenotypic effect of sequence variants and mutations with biological networks. Second, we developed a strategy for the combination of data extracted from public resources, such as UniProt, NCBI dbSNP, Reactome and BioModels. We generated attribute files containing phenotypic and genotypic annotations to the nodes of biological networks, which can be imported into network visualization tools such as Cytoscape. These resources allow the mapping and visualization of mutations and natural variations of human proteins and their phenotypic effect on biological networks (e.g. signalling pathways, protein-protein interaction networks, dynamic models). Finally, an example on the use of the sequence variation data in the dynamics of a network model is presented. Conclusion: In this paper we present a general strategy for the integration of pathway and sequence variation data for visualization, analysis and modelling purposes, including the study of the functional impact of protein sequence variations on the dynamics of signalling pathways. This is of particular interest when the SNP or mutation is known to be associated to disease. We expect that this approach will help in the study of the functional impact of disease-associated SNPs on the behaviour of cell signalling pathways, which ultimately will lead to a better understanding of the mechanisms underlying complex diseases.

Genetic characterization of the ABO blood group in Neandertals

Background: The high polymorphism rate in the human ABO blood group gene seems to be related to susceptibility to different pathogens. It has been estimated that all genetic variation underlying the human ABO alleles appeared along the human lineage, after the divergence from the chimpanzee lineage. A paleogenetic analysis of the ABO blood group gene in Neandertals allows us to directly test for the presence of the ABO alleles in these extinct humans. Results: We have analysed two male Neandertals that were retrieved under controlled conditions at the El Sidron site in Asturias (Spain) and that appeared to be almost free of modern human DNA contamination. We find a human specific diagnostic deletion for blood group O (O01 haplotype) in both Neandertal individuals. Conclusion: These results suggest that the genetic change responsible for the O blood group in humans predates the human and Neandertal divergence. A potential selective event associated with the emergence of the O allele may have therefore occurred after humans separated from their common ancestor with chimpanzees and before the human-Neandertal population divergence.

@neurIST infrastructure for advanced disease management through integration of heterogeneous data, computing, and complex processing services

The increasing volume of data describing humandisease processes and the growing complexity of understanding, managing, and sharing such data presents a huge challenge for clinicians and medical researchers. This paper presents the@neurIST system, which provides an infrastructure for biomedical research while aiding clinical care, by bringing together heterogeneous data and complex processing and computing services. Although @neurIST targets the investigation and treatment of cerebral aneurysms, the system’s architecture is generic enough that it could be adapted to the treatment of other diseases.Innovations in @neurIST include confining the patient data pertaining to aneurysms inside a single environment that offers cliniciansthe tools to analyze and interpret patient data and make use of knowledge-based guidance in planning their treatment. Medicalresearchers gain access to a critical mass of aneurysm related data due to the system’s ability to federate distributed informationsources. A semantically mediated grid infrastructure ensures that both clinicians and researchers are able to seamlessly access andwork on data that is distributed across multiple sites in a secure way in addition to providing computing resources on demand forperforming computationally intensive simulations for treatment planning and research.

CLFP intrinsic constraints-based group management of blended learning situations

When applying a Collaborative Learning Flow Pattern (CLFP) to structure sequences of activities in real contexts, one of the tasks is to organize groups of students according to the constraints imposed by the pattern. Sometimes,unexpected events occurring at runtime force this pre-defined distribution to be changed. In such situations, an adjustment of the group structures to be adapted to the new context is needed. If the collaborative pattern is complex, this group redefinitionmight be difficult and time consuming to be carried out in real time. In this context, technology can help on notifying the teacher which incompatibilitiesbetween the actual context and the constraints imposed by the pattern. This chapter presents a flexible solution for supporting teachers in the group organization profiting from the intrinsic constraints defined by a CLFPs codified in IMS Learning Design. A prototype of a web-based tool for the TAPPS and Jigsaw CLFPs and the preliminary results of a controlled user study are alsopresented as a first step towards flexible technological systems to support grouping tasks in this context.

Effects of prison work programmes on the employability of ex-prisioners

This paper presents the main results of a study that relates information from the prison system with information for the Spanish Social Security in order to study the employability of the former inmates of prisons in Catalonia, Spain who obtained final release from 1/1/2004 to 31/12/2007. The results show that 43.6% of the ex-prisoners find a job after serving their sentences, but their integration in the labour market tends to be fragile, confirming that it is a very vulnerable group. It was also found that prison work has a favourable effect on employability and that vocational training could be useful for those who have not previously worked and have no education or job skills.

Why do workers leave unions? - group differences in a Spanish Union Federation

This study analyses the characteristics of members leaving a Spanishunion federation – Catalonia branch of Workers’ Commissions(CCOO-Catalonia), together with their reasons for leaving using avariety of data sources. Our findings indicate that higher union attritionamong members in instable employment (i.e. casual employment andlow seniority). In general, union leavers confirm that their job situationis an important reason for leaving the union. We therefore concludethat efforts made by the union to retain members in vulnerable labormarket positions are important in reducing high rates of union attritionin Spain.

Societat de la vigilància 25 anys desprès de 1984 a Catalunya i UK

Desprès de un any de treball, el grup ha detectat que la relació entre protecció de dades i vídeo vigilància constitueix el nus central de la preocupació internacional en torn a la anomenada “Societat de la Vigilància”. Paral•lelament, ha constatat que a l’Estat Espanyol hi ha pocs grups que treballin aquesta cruïlla temàtica, raó per la qual la representació ibèrica en els grups de recerca europeus era minsa. Per aquestes raons, el grup ha dedicat els esforços a: 1) desenvolupar un marc teòric que faci possible entendre l’entramat legislatiu, sociològic i fenomènic de la video vigilància a Catalunya, a l’estat Espanyol, i a Europa. 2) dur a terme accions de recerca empírica qualitativa i quantitativa i relacionar-les amb aquest marc teòric. 3) crear vincles de col•laboració amb investigadors catalans, espanyols, anglesos i fins i tot europeus, començant una etapa d’integració a les xarxes de recerca en funcionament o en estat latent. En funció de les característiques de la convocatòria i del tema original que ens ocupava (la relació entre la mes coneguda obra de George Orwell -1984- i la situació actual del control social a Catalunya i al Regne Unit), s’ha posat especial èmfasi en l’establiment de vincles amb investigadors del Regne Unit; com a conseqüència, s’ha treballat amb dos de les persones “associades” al projecte (Phillip Carney i David Porteous) intercanviant dades, informació i dissenyant accions, en una col•laboració que té projecció en el futur immediat -amb la publicació d’un llibre conjunt- i mediat -mitjançant la integració de investigadors participants en aquest projecte en altres accions de recerca d’abast europeu-. Les accions realitzades en funció d’això explicat es descriuen en aquesta memòria, acompanyades d’un breu resum de les troballes mes significatives.

PhD Students’ Research Group Social Capital in Two Countries: A Clustering Approach with Duocentred Network Measures

The article examines the structure of the collaboration networks of research groups where Slovenian and Spanish PhD students are pursuing their doctorate. The units of analysis are student-supervisor dyads. We use duocentred networks, a novel network structure appropriate for networks which are centred around a dyad. A cluster analysis reveals three typical clusters of research groups. Those which are large and belong to several institutions are labelled under a bridging social capital label. Those which are small, centred in a single institution but have high cohesion are labelled as bonding social capital. Those which are small and with low cohesion are called weak social capital groups. Academic performance of both PhD students and supervisors are highest in bridging groups and lowest in weak groups. Other variables are also found to differ according to the type of research group. At the end, some recommendations regarding academic and research policy are drawn

Interbank market integration under asymmetric information

We argue that the main barrier to an integrated international interbankmarket is the existence of asymmetric information between differentcountries, which may prevail in spite of monetary integration or successfulcurrency pegging. In order to address this issue, we study the scope forinternational interbank market integration with unsecured lending whencross-country information is noisy. We find not only that an equilibriumwith integrated markets need not always exist, but also that when it does,the integrated equilibrium may coexist with one of interbank marketsegmentation. Therefore, market deregulation, per se, does not guaranteethe emergence of an integrated interbank market. The effect of a repo marketwhich, a priori, was supposed to improve efficiency happens to be morecomplex: it reduces interest rate spreads and improves upon the segmentationequilibrium, but\ it may destroy the unsecured integrated equilibrium, sincethe repo market will attract the best borrowers. The introduction of othertransnational institutional arrangements, such as multinational banking,correspondent banking and the existence of "too-big-to-fail" banks mayreduce cross country interest spreads and provide more insurance againstcountry wide liquidity shocks. Still, multinational banking, as theintroduction of repos, may threaten the integrated interbank marketequilibrium.