Knowledge management for systems biology a general and visually driven framework applied to translational medicine

Background: To enhance our understanding of complex biological systems like diseases we need to put all of the available data into context and use this to detect relations, pattern and rules which allow predictive hypotheses to be defined. Life science has become a data rich science with information about the behaviour of millions of entities like genes, chemical compounds, diseases, cell types and organs, which are organised in many different databases and/or spread throughout the literature. Existing knowledge such as genotype - phenotype relations or signal transduction pathways must be semantically integrated and dynamically organised into structured networks that are connected with clinical and experimental data. Different approaches to this challenge exist but so far none has proven entirely satisfactory. Results: To address this challenge we previously developed a generic knowledge management framework, BioXM™, which allows the dynamic, graphic generation of domain specific knowledge representation models based on specific objects and their relations supporting annotations and ontologies. Here we demonstrate the utility of BioXM for knowledge management in systems biology as part of the EU FP6 BioBridge project on translational approaches to chronic diseases. From clinical and experimental data, text-mining results and public databases we generate a chronic obstructive pulmonary disease (COPD) knowledge base and demonstrate its use by mining specific molecular networks together with integrated clinical and experimental data. Conclusions: We generate the first semantically integrated COPD specific public knowledge base and find that for the integration of clinical and experimental data with pre-existing knowledge the configuration based set-up enabled by BioXM reduced implementation time and effort for the knowledge base compared to similar systems implemented as classical software development projects. The knowledgebase enables the retrieval of sub-networks including protein-protein interaction, pathway, gene - disease and gene - compound data which are used for subsequent data analysis, modelling and simulation. Pre-structured queries and reports enhance usability; establishing their use in everyday clinical settings requires further simplification with a browser based interface which is currently under development.

Discovering the campus together: a mobile and computer-based learning experience

One of the most relevant difficulties faced by first-year undergraduate students is to settle into the educational environment of universities. This paper presents a case study that proposes a computer-assisted collaborative experience designed to help students in their transition from high school to university. This is done by facilitating their first contact with the campus and its services, the university community, methodologies and activities. The experience combines individual and collaborative activities, conducted in and out of the classroom, structured following the Jigsaw Collaborative Learning Flow Pattern. A specific environment including portable technologies with network and computer applications has been developed to support and facilitate the orchestration of a flow of learning activities into a single integrated learning setting. The result is a Computer-Supported Collaborative Blended Learning scenario, which has been evaluated with first-year university students of the degrees of Software and Audiovisual Engineering within the subject Introduction to Information and Communications Technologies. The findings reveal that the scenario improves significantly students’ interest in their studies and their understanding about the campus and services provided. The environment is also an innovative approach to successfully support the heterogeneous activities conducted by both teachers and students during the scenario. This paper introduces the goals and context of the case study, describes how the technology was employed to conduct the learning scenario, the evaluation methods and the main results of the experience.

Rules vs. political discretion: evidence from constitutionally guaranteed transfers to local governments in Brazil

Can rules be used to shield public resources from political interference? The Brazilian constitution and national tax code stipulate that revenue sharing transfers to municipal governments be determined by the size of counties in terms of estimated population. In this paper I document that the population estimates which went into the transfer allocation formula for the year 1991 were manipulated, resulting in significant transfer differentials over the entire 1990's. I test whether conditional on county characteristics that might account for the manipulation, center-local party alignment, party popularity and the extent of interparty fragmentation at the county level are correlated with estimated populations in 1991. Results suggest that revenue sharing transfers were targeted at right-wing national deputies in electorally fragmented counties as well as aligned local executives.

Are rules-based government programs shielded from special-interest politics? Evidence from revenue-sharing transfers in Brazil

Manipulation of government finances for the benefit of narrowly defined groups is usuallythought to be limited to the part of the budget over which politicians exercise discretion inthe short run, such as earmarks. Analyzing a revenue-sharing program between the centraland local governments in Brazil that uses an allocation formula based on local population estimates,I document two main results: first, that the population estimates entering the formulawere manipulated and second, that this manipulation was political in nature. Consistent withswing-voter targeting by the right-wing central government, I find that municipalities withroughly equal right-wing and non-right-wing vote shares benefited relative to opposition orconservative core support municipalities. These findings suggest that the exclusive focus ondiscretionary transfers in the extant empirical literature on special-interest politics may understatethe true scope of tactical redistribution that is going on under programmatic disguise.

Monetary policy rules and macroeconomic stability: Evidence and some theory

We estimate a forward-looking monetary policy reaction function for thepostwar United States economy, before and after Volcker's appointmentas Fed Chairman in 1979. Our results point to substantial differencesin the estimated rule across periods. In particular, interest ratepolicy in the Volcker-Greenspan period appears to have been much moresensitive to changes in expected inflation than in the pre-Volckerperiod. We then compare some of the implications of the estimated rulesfor the equilibrium properties of inflation and output, using a simplemacroeconomic model, and show that the Volcker-Greenspan rule is stabilizing.

Efficient interval scoring rules

Scoring rules that elicit an entire belief distribution through the elicitation of point beliefsare time-consuming and demand considerable cognitive e¤ort. Moreover, the results are validonly when agents are risk-neutral or when one uses probabilistic rules. We investigate a classof rules in which the agent has to choose an interval and is rewarded (deterministically) onthe basis of the chosen interval and the realization of the random variable. We formulatean e¢ ciency criterion for such rules and present a speci.c interval scoring rule. For single-peaked beliefs, our rule gives information about both the location and the dispersion of thebelief distribution. These results hold for all concave utility functions.

Rules or consequences? The role of ethical mindsets in moral dynamics

Recent research on the dynamics of moral behavior has documented two contrastingphenomena - moral consistency and moral balancing. Moral balancing refers to thephenomenon whereby behaving (un)ethically decreases the likelihood of doing so againat a later time. Moral consistency describes the opposite pattern - engaging in(un)ethical behavior increases the likelihood of doing so later on. Three studies supportthe hypothesis that individuals' ethical mindset (i.e., outcome-based versus rule-based)moderates the impact of an initial (un)ethical act on the likelihood of behaving ethicallyin a subsequent occasion. More specifically, an outcome-based mindset facilitates moralbalancing and a rule-based mindset facilitates moral consistency.

Setting the rules of the game: The choice of electoral systems in advanced democracies

The origins of electoral systems have received scant attention in the literature. Looking at the history of electoral rules in the advanced world in the last century, this paper shows that the existing wide variation in electoral rules across nations can be traced to the strategic decisions that the current ruling parties, anticipating the coordinating consequences of different electoral regimes, make to maximize their representation according to the following conditions. On the one hand, as long as the electoral arena does not change substantially and the current electoral regime serves the ruling parties well, the latter have no incentives to modify the electoral regime. On the other hand, as soon as the electoral arena changes (due to the entry of new voters or a change in their preferences), the ruling parties will entertain changing the electoral system, depending on two main conditions: the emergence of new parties and the coordinating capacities of the old ruling parties. Accordingly, if the new parties are strong, the old parties shift from plurality/majority rules to proportional representation (PR) only if the latter are locked into a 'non-Duvergerian' equilibrium; i.e. if no old party enjoys a dominant position (the case of most small European states)--conversely, they do not if a Duvergerian equilibrium exists (the case of Great Britain). Similarly, whenever the new entrants are weak, a non-PR system is maintained, regardless of the structure of the old party system (the case of the USA). The paper discusses as well the role of trade and ethnic and religious heterogeneity in the adoption of PR rules.

Price regulation of plastic money: A critical assessment of Spanish rules

Recent decisions by the Spanish national competition authority (TDC) mandate paymentsystems to include only two costs when setting their domestic multilateral interchange fees(MIF): a fixed processing cost and a variable cost for the risk of fraud. This artificiallowering of MIFs will not lower consumer prices, because of uncompetitive retailing; but itwill however lead to higher cardholders fees and, likely, new prices for point of saleterminals, delaying the development of the immature Spanish card market. Also, to the extent that increased cardholders fees do not offset the fall in MIFs revenue, the task of issuing new cards will be underpaid relatively to the task of acquiring new merchants, causing an imbalance between the two sides of the networks. Moreover, the pricing scheme arising from the decisions will cause unbundling and underprovision of those services whose costs are excluded. Indeed, the payment guarantee and the free funding period will tend to be removed from the package of services currently provided, to be either provided by third parties, by issuers for a separate fee, or not provided at all, especially to smaller and medium-sized merchants. Transaction services will also suffer the consequences that the TDC precludes pricing them in variable terms.

Stochastic evolution of rules for playing normal form games

The evolution of boundedly rational rules for playing normal form games is studied within stationary environments ofstochastically changing games. Rules are viewed as algorithms prescribing strategies for the different normal formgames that arise. It is shown that many of the folk results of evolutionary game theory typically obtained witha fixed game and fixed strategies carry over to the present case. The results are also related to recent experimentson rules and games.

Sweet diversity: Colonial goods and the rise of European living standards after 1492

When did overseas trade start to matter for living standards? Traditional real-wage indices suggest that living standards in Europe stagnated before 1800. In this paper, we argue thatwelfare rose substantially, but surreptitiously, because of an influx of new goods as a result ofoverseas trade. Colonial luxuries such as tea, coffee, and sugar transformed European diets afterthe discovery of America and the rounding of the Cape of Good Hope. These goods became household items in many countries by the end of the 18th century. We use three different methodsto calculate welfare gains based on price data and the rate of adoption of these new colonialgoods. Our results suggest that by 1800, the average Englishman would have been willing to forego 10% or more of his income in order to maintain access to sugar and tea alone. These findings are robust to a wide range of alternative assumptions, data series, and valuation methods.

Veus ignorades: representacions socials, subjectivitat i resiliència en persones grans amb pèrdua d’autonomia funcional

Els processos per a l’aprovació i la implementació de la Llei per a l’Autonomia personal i l’Atenció a les Persones en situació de Dependència (LAPAD) han donat lloc a un intens debat polític i social que, coincidint també amb les millores en la provisió de serveis i els avenços mèdics, ha contribuït a un procés de classificació i d’etiquetatge basats en els dèficits de les persones que es troben en aquestes circumstàncies. Aquesta visió anul·la el subjecte i la seva experiència singular i condiciona l’abordatge dels models d’atenció i de cura. L’estudi pretén fer una aproximació a les persones grans amb pèrdua d’autonomia funcional, fent emergir les seves veus, que expressen com perceben, interpreten, afronten i es reajusten a la nova situació. Partint d’un enfocament constructivista, basat en la subjectivitat, es fa un recorregut sobre els models de la discapacitat que han reeixit en l’activitat científica dels darrers anys, els mecanismes de regulació de les pèrdues que defensen les teories del cicle vital i les aportacions que s’han fet sobre el model de la resiliència aplicat a les persones que envelleixen. El resultats de l’estudi mostren com les representacions i els significats que les persones grans atribueixen a la seva experiència s’inscriuen en les seves trajectòries vitals, donant un sentit únic i singular a la forma de viure i de respondre a la pèrdua d’autonomia funcional i les seves conseqüències. Aquelles que expressen una vivència d’integritat respecte de la vida viscuda, amb predomini d’afectes positius envers un mateix i els altres, que conserven l’esperança i el desig de continuar vivint, s’ajusten a les pèrdues de manera més satisfactòria que aquelles que expressen desconfiança i una certa amargor respecte de la pròpia vida. D’això se’n deriva que els espais d’escolta i d’acompanyament poden ser un recurs vàlid i necessari en el qual, a través de la paraula i el testimoni narrat, el subjecte pugui repensar i resignificar les seves experiències.

Transformation rules form OntoProcED to OntoOKI

This file contains the transformtion rules in SWRL to translate formal specifications of two lower ontology levels (patterns and organization) to the upper level (implementation according to the OKI specification).

Bringing Funds of Family Knowledge to school. The Living Morocco Project (“برغملا شيعلا”)

The purpose of the study, grounded in sociocultural theory, is to describe the funds of knowledge of a Moroccan family living in Catalonia (Spain) in order to document how teachers can use these funds of knowledge to make direct links between students' lives and classroom teaching. The funds of knowledge approach is based on a simple premise: regardless of any socio-economical and sociocultural "deficit" that people may or may not have all families accumulate bodies of beliefs, ideas, skills and abilities based on their experiences (in areas such as their occupation or their religion). The challenge consists in connecting these bodies of educational resources with teaching practice in order to connect the curriculum with students' lives. In doing so, qualitative research can be carried out using several techniques such as self portraits, self-definition tasks, assessment of family artefacts, documenting routines through photographs, or the analysis of a person's significant circle. The results in terms of teaching practices illustrate the variety of ways teachers can make connections between home and school in ways that assist learners in their academic development. In this article, we propose using the term funds of identity to complement the concept of funds of knowledge