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.

Trials, tricks and transparency: how disclosure rules affect clinical knowledge

Scandals of selective reporting of clinical trial results by pharmaceutical firms have underlined the need for more transparency in clinical trials. We provide a theoretical framework which reproduces incentives for selective reporting and yields three key implications concerning regulation. First, a compulsory clinical trial registry complemented through a voluntary clinical trial results database can implement full transparency (the existence of all trials as well as their results is known). Second, full transparency comes at a price. It has a deterrence effect on the incentives to conduct clinical trials, as it reduces the firms'gains from trials. Third, in principle, a voluntary clinical trial results database without a compulsory registry is a superior regulatory tool; but we provide some qualified support for additional compulsory registries when medical decision-makers cannot anticipate correctly the drug companies' decisions whether to conduct trials. Keywords: pharmaceutical firms, strategic information transmission, clinical trials, registries, results databases, scientific knowledge JEL classification: D72, I18, L15

Teacher strategies to elicit knowledge from students in the CLIL classroom: the purpose of questions in controlled patterns of teacher-student interaction

This Master Dissertation comprises two parts: a personal reflection and an empirical study. The personal reflection reviews the process of professionalization undergone by its author throughout the Master. The empirical study tackles teacher strategies to elicit knowledge from students in the CLIL classroom and more specifically the purpose of questions in controlled patterns of teacher-student interaction. The theories of relevant authors such as Vigotsky, Mercer and Tsui are used as a framework to analyze the data presented. The analysis shows the different strategies to elicit knowledge used by the teacher and the appropriateness of her questions in the analyzed interaction

Implementació d'una funcionalitat en un framework per una aplicació J2EE

En el present projecte utilitzarem els coneixements sobre els frameworks adquirits al llarg del treball per complir la raó última d'aquest projecte: la modificació d'un framework per tal d'ampliar o millorar el seu rendiment en l'aplicació J2EE. En concret consistirà en la implementació d¿un validador en el framework JSF.

Integration in strategic alliances : a conceptual framework of IT use in marketing as NPD key factor

En una economia basada en el coneixement, la innovació del producte es considera un factor clau a l'hora de determinar la competitivitat, la productivitat i el creixement d'una companyia. No obstant això, l'experiència de les companyies demostra la necessitat d'un nou model de gestió de la innovació del producte: una gestió basada en el màrqueting, en què la cooperació i l'ús intensiu de les tecnologies de la informació i de la comunicació (TIC) són especialment importants. En els darrers anys, la bibliografia sobre màrqueting ha analitzat el paper de la cooperació en l'èxit del procés d'innovació. No obstant això, fins ara pocs treballs han estudiat el paper que té l'ús de les TIC en el màrqueting en l'èxit del desenvolupament de nous productes (NPD, New Product Development en anglès). És una omissió curiosa, tenint en compte que el nou entorn competitiu és definit per una economia i una societat basades principalment en l'ús intensiu de les TIC i del coneixement. L'objectiu d'aquest treball és investigar el paper que l'ús de les TIC en el màrqueting té en el procés de desenvolupament de nous productes, com a element que reforça la integració d'agents al projecte, afavorint l'establiment de relacions dirigides a la cooperació i l'adquisició d'intel·ligència de mercat útil en el procés de desenvolupament de nous productes. L'estudi d'una mostra de 2.038 companyies de tots els sectors de l'activitat econòmica a Catalunya ens permet contrastar hipòtesis inicials i establir un perfil de companyia innovadora basat en les importants relacions que hi ha entre la innovació, l'ús de TIC en el màrqueting i la integració. Sobresurten dues idees en la nostra anàlisi. En primer lloc, l'ús intensiu de les TIC en el màrqueting fa que la companyia sigui més innovadora, ja que percep que el seu ús ajuda a superar barreres a la innovació i accelera els processos, que es tornen més eficients. En segon lloc, incrementant l'ús de les TIC en el màrqueting es fa augmentar la predisposició de la companyia a integrar agents particulars en l'entorn de negoci en el desenvolupament del procés d'innovació i a col·laborar-hi, de manera que es millora el grau d'adaptació del nou producte a les demandes del mercat.

On heuristic and linear models of judgment: Mapping the demand for knowledge

Research on judgment and decision making presents a confusing picture of human abilities. For example, much research has emphasized the dysfunctional aspects of judgmental heuristics, and yet, other findings suggest that these can be highly effective. A further line of research has modeled judgment as resulting from as if linear models. This paper illuminates the distinctions in these approaches by providing a common analytical framework based on the central theoretical premise that understanding human performance requires specifying how characteristics of the decision rules people use interact with the demands of the tasks they face. Our work synthesizes the analytical tools of lens model research with novel methodology developed to specify the effectiveness of heuristics in different environments and allows direct comparisons between the different approaches. We illustrate with both theoretical analyses and simulations. We further link our results to the empirical literature by a meta-analysis of lens model studies and estimate both human andheuristic performance in the same tasks. Our results highlight the trade-off betweenlinear models and heuristics. Whereas the former are cognitively demanding, the latterare simple to use. However, they require knowledge and thus maps of when andwhich heuristic to employ.

A knowledge based signal processing approach to tonic identification in indian classical music

In this paper, we describe several techniques for detecting tonic pitch value in Indian classical music. In Indian music, the raga is the basic melodic framework and it is built on the tonic. Tonic detection is therefore fundamental for any melodic analysis in Indian classical music. This workexplores detection of tonic by processing the pitch histograms of Indian classic music. Processing of pitch histograms using group delay functions and its ability to amplify certain traits of Indian music in the pitch histogram, is discussed. Three different strategies to detect tonic, namely, the concert method, the template matching and segmented histogram method are proposed. The concert method exploits the fact that the tonic is constant over a piece/concert.templatematchingmethod and segmented histogrammethodsuse the properties: (i) the tonic is always present in the background, (ii) some notes are less inflected and dominant, to detect the tonic of individual pieces. All the three methods yield good results for Carnatic music (90−100% accuracy), while for Hindustanimusic, the templatemethod works best, provided the v¯adi samv¯adi notes for a given piece are known (85%).

Integration in strategic alliances : a conceptual framework of IT use in marketing as NPD key factor

En una economia basada en el coneixement, la innovació del producte es considera un factor clau a l'hora de determinar la competitivitat, la productivitat i el creixement d'una companyia. No obstant això, l'experiència de les companyies demostra la necessitat d'un nou model de gestió de la innovació del producte: una gestió basada en el màrqueting, en què la cooperació i l'ús intensiu de les tecnologies de la informació i de la comunicació (TIC) són especialment importants. En els darrers anys, la bibliografia sobre màrqueting ha analitzat el paper de la cooperació en l'èxit del procés d'innovació. No obstant això, fins ara pocs treballs han estudiat el paper que té l'ús de les TIC en el màrqueting en l'èxit del desenvolupament de nous productes (NPD, New Product Development en anglès). És una omissió curiosa, tenint en compte que el nou entorn competitiu és definit per una economia i una societat basades principalment en l'ús intensiu de les TIC i del coneixement. L'objectiu d'aquest treball és investigar el paper que l'ús de les TIC en el màrqueting té en el procés de desenvolupament de nous productes, com a element que reforça la integració d'agents al projecte, afavorint l'establiment de relacions dirigides a la cooperació i l'adquisició d'intel·ligència de mercat útil en el procés de desenvolupament de nous productes. L'estudi d'una mostra de 2.038 companyies de tots els sectors de l'activitat econòmica a Catalunya ens permet contrastar hipòtesis inicials i establir un perfil de companyia innovadora basat en les importants relacions que hi ha entre la innovació, l'ús de TIC en el màrqueting i la integració. Sobresurten dues idees en la nostra anàlisi. En primer lloc, l'ús intensiu de les TIC en el màrqueting fa que la companyia sigui més innovadora, ja que percep que el seu ús ajuda a superar barreres a la innovació i accelera els processos, que es tornen més eficients. En segon lloc, incrementant l'ús de les TIC en el màrqueting es fa augmentar la predisposició de la companyia a integrar agents particulars en l'entorn de negoci en el desenvolupament del procés d'innovació i a col·laborar-hi, de manera que es millora el grau d'adaptació del nou producte a les demandes del mercat.

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.

Collaborative explicit plasticity framework: a conceptual scheme for the generation of plastic and group-aware user interfaces

The advent of new advances in mobile computing has changed the manner we do our daily work, even enabling us to perform collaborative activities. However, current groupware approaches do not offer an integrating and efficient solution that jointly tackles the flexibility and heterogeneity inherent to mobility as well as the awareness aspects intrinsic to collaborative environments. Issues related to the diversity of contexts of use are collected under the term plasticity. A great amount of tools have emerged offering a solution to some of these issues, although always focused on individual scenarios. We are working on reusing and specializing some already existing plasticity tools to the groupware design. The aim is to offer the benefits from plasticity and awareness jointly, trying to reach a real collaboration and a deeper understanding of multi-environment groupware scenarios. In particular, this paper presents a conceptual framework aimed at being a reference for the generation of plastic User Interfaces for collaborative environments in a systematic and comprehensive way. Starting from a previous conceptual framework for individual environments, inspired on the model-based approach, we introduce specific components and considerations related to groupware.

A logic programming framework for possibilistic argumentation: formalization and logical properties

In the last decade defeasible argumentation frameworks have evolved to become a sound setting to formalize commonsense, qualitative reasoning. The logic programming paradigm has shown to be particularly useful for developing different argument-based frameworks on the basis of different variants of logic programming which incorporate defeasible rules. Most of such frameworks, however, are unable to deal with explicit uncertainty, nor with vague knowledge, as defeasibility is directly encoded in the object language. This paper presents Possibilistic Logic Programming (P-DeLP), a new logic programming language which combines features from argumentation theory and logic programming, incorporating as well the treatment of possibilistic uncertainty. Such features are formalized on the basis of PGL, a possibilistic logic based on G¨odel fuzzy logic. One of the applications of P-DeLP is providing an intelligent agent with non-monotonic, argumentative inference capabilities. In this paper we also provide a better understanding of such capabilities by defining two non-monotonic operators which model the expansion of a given program P by adding new weighed facts associated with argument conclusions and warranted literals, respectively. Different logical properties for the proposed operators are studied

A framework for the analysis of CLIL lecturers’ discourse from a genre perspective

Internationalization strategies and the European Space of Higher Education are causing a growing interest in English medium instruction (EMI). University linguistic and internationalization policies are attempting to provide lectures with the required training and education. Linguists can supply not only the knowledge of the language but the knowledge about language which may enable lecturers to increase their academic language competence autonomously. This paper presents a framework for the analysis of lecturers’ discourse to trigger reflection about the linguistic needs in CLIL/EMI contexts.