Mining protein structure data

The principal topic of this work is the application of data mining techniques, in particular of machine learning, to the discovery of knowledge in a protein database. In the first chapter a general background is presented. Namely, in section 1.1 we overview the methodology of a Data Mining project and its main algorithms. In section 1.2 an introduction to the proteins and its supporting file formats is outlined. This chapter is concluded with section 1.3 which defines that main problem we pretend to address with this work: determine if an amino acid is exposed or buried in a protein, in a discrete way (i.e.: not continuous), for five exposition levels: 2%, 10%, 20%, 25% and 30%. In the second chapter, following closely the CRISP-DM methodology, whole the process of construction the database that supported this work is presented. Namely, it is described the process of loading data from the Protein Data Bank, DSSP and SCOP. Then an initial data exploration is performed and a simple prediction model (baseline) of the relative solvent accessibility of an amino acid is introduced. It is also introduced the Data Mining Table Creator, a program developed to produce the data mining tables required for this problem. In the third chapter the results obtained are analyzed with statistical significance tests. Initially the several used classifiers (Neural Networks, C5.0, CART and Chaid) are compared and it is concluded that C5.0 is the most suitable for the problem at stake. It is also compared the influence of parameters like the amino acid information level, the amino acid window size and the SCOP class type in the accuracy of the predictive models. The fourth chapter starts with a brief revision of the literature about amino acid relative solvent accessibility. Then, we overview the main results achieved and finally discuss about possible future work. The fifth and last chapter consists of appendices. Appendix A has the schema of the database that supported this thesis. Appendix B has a set of tables with additional information. Appendix C describes the software provided in the DVD accompanying this thesis that allows the reconstruction of the present work.

Social network analysis applied to knowledge creation and transfer in the portuguese agricultural R&D field: an exploratory study

Paper presented at the 9th European Conference on Knowledge Management, Southampton Solent University, Southampton, UK, 4-5 Sep. 2008. URL: http://academic-conferences.org/eckm/eckm2008/eckm08-home.htm

Structure to function studies in UDP-glucose dehydrogenases and nitroreductases

The thesis is divided into two parts corresponding to structural studies on two different proteins. The first part concerns the study of two UDP-glucose dehydrogenases (UGDs) from Sphingomonas elodea ATCC 31461 and Burkholderia cepacia IST 408, both involved in exopolysaccharide production. Their relevance arises because some of these bacterial exopolysaccharides are valuable as established biotechnological products, the former case, whilst others are highly problematic, when used by pathogens in biofilm formation over biological surfaces, as the latter case, namely in the human lungs. The goal of these studies is to increase our knowledge regarding UGDs structural properties, which can potentiate either the design of activity enhancers to respond to the increased demand of useful biofilms, or the design of inhibitors of biofilm production, in order to fight invading pathogens present in several infections. The thesis reports the production and crystallisation of both proteins, the determination of initial phases by single-wavelength anomalous dispersion (SAD) in S. elodea crystals using a seleno-methionine isoform, and phasing of B. cepacia crystals by molecular replacement (MR) using the S. elodea model, as well as the refinement, structural analysis and comparison between the several UGDs structures available during this work.(...)

Research and development expenditure in the business sector as indicator of knowledge economy: the Portuguese experience

The objective of the paper is to help to understand recent changes in the structure of R&D activities, by analyzing data on the expenditure of the business sector in research and development (R&D). The results are framed in an international context, through comparison with indicators from the most developed countries, divided by technological intensity and economic activity. The study reveals that the indicators of Portuguese R&D expenditure in the business sector are closely linked both to fiscal policy and to high foreign direct investment in knowledge-intensive industries. It also links these indicators to phenomena such as the abundance of skilled labor in pharmaceutical industries and the government intervention in some sectors of the economy (namely health and rail transportation).

User friendly knowledge acquisition system for medical devices actuation

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

From Consciousness to Knowledge – The Explanatory Power of Revelation

Epistemology in philosophy of mind is a difficult endeavor. Those who believe that our phenomenal life is different from other domains suggest that self-knowledge about phenomenal properties is certain and therefore privileged. Usually, this so called privileged access is explained by the idea that we have direct access to our phenomenal life. This means, in contrast to perceptual knowledge, self-knowledge is non-inferential. It is widely believed that, this kind of directness involves two different senses: an epistemic sense and a metaphysical sense. Proponents of this view often claim that this is due to the fact that we are acquainted with our current experiences. The acquaintance thesis, therefore, is the backbone in justifying privileged access. Unfortunately the whole approach has a profound flaw. For the thesis to work, acquaintance has to be a genuine explanation. Since it is usually assumed that any knowledge relation between judgments and the corresponding objects are merely causal and contingent (e.g. in perception), the proponent of the privileged access view needs to show that acquaintance can do the job. In this thesis, however, I claim that the latter cannot be done. Based on considerations introduced by Levine, I conclude that this approach involves either the introduction of ontologically independent properties or a rather obscure knowledge relation. A proper explanation, however, cannot employ either of the two options. The acquaintance thesis is, therefore, bound to fail. Since the privileged access intuition seems to be vital to epistemology within the philosophy of mind, I will explore alternative justifications. After discussing a number of options, I will focus on the so called revelation thesis. This approach states that by simply having an experience with phenomenal properties, one is in the position to know the essence of those phenomenal properties. I will argue that, after finding a solution for the controversial essence claim, this thesis is a successful replacement explanation which maintains all the virtues of the acquaintance account without necessarily introducing ontologically independent properties or an obscure knowledge relation. The overall solution consists in qualifying the essence claim in the relevant sense, leaving us with an appropriate ontology for phenomenal properties. On the one hand, this avoids employing mysterious independent properties, since this ontological view is physicalist in nature. On the other hand, this approach has the right kind of structure to explain privileged self-knowledge of our phenomenal life. My final conclusion consists in the claim that the privileged access intuition is in fact veridical. It cannot, however, be justified by the popular acquaintance approach, but rather, is explainable by the controversial revelation thesis.

Evolução paleogeográfica e paleobiogeográfica do Caloviano-Kimeridgiano do Algarve

The littoral and the «barrocal» of the Algarve correspond in part to a meso-cenozoic sedimentary basin with a deeping south monocline structure, cut by North-South faults and by two East-West longitudinal flexures. The lithostratigraphic and chronostratigraphic study of the Jurassic formations, undertaken during the last years, allow a better knowledge of the paleogeographic and paleobiogeographic evolution of these formations and particularly of the Callovian-Kimmeridgian. Lower Callovian facies, being similar from Sagres in the West to beyond Tavira, show the uniformity of the sedimentary conditions. Since Middle Callovian, the beginning of the regressive cycle is responsible for a major unconformity between Dogger and Malm. During the Lower Oxfordian a new sedimentary cycle begins with a transgression afecting the region south of the Albufeira-São Brás de Alportel-Tavira line thus originating a gulf centered in the Loulé area which rapidly diminishes since the Lower Kimmeridgian. The faunistic affinities are always tipically tethyan although some classic boreal fauna exist, in contrast with the Northern Tagus basin (where affinities are sub-boreal during the Callovian).

The isolation and characterization of cytochrome c nitrite reductase subunits (NrfA and NrfH) from Desulfovibrio desulfuricans ATCC 27774

Eur. J. Biochem. 270, 3904–3915 (2003)

Effects of team task structure on team climate for innovation and team outcomes

In this cross-sectional study we analyzed, whether team climate for innovation mediates the relationship between team task structure and innovative behavior, job satisfaction, affective organizational commitment, and work stress. 310 employees in 20 work teams of an automotive company participated in this study. 10 teams had been changed from a restrictive to a more self-regulating team model by providing task variety, autonomy, team-specific goals, and feedback in order to increase team effectiveness. Data support the supposed causal chain, although only with respect to team innovative behavior all required effects were statistically significant. Longitudinal designs and larger samples are needed to prove the assumed causal relationships, but results indicate that implementing self-regulating teams might be an effective strategy for improving innovative behavior and thus team and company effectiveness.

Main features of the labour policy in Portugal

In this working paper is presented information on the Portuguese labour market developed with the support of the European project WORKS-“Work organisation and restructuring in the knowledge society”. Is still a on the process article and thus commentaries are welcome. The structure is based on the following topics: a) The employment policy (Time regimes - time use, flexibility, part-time work, work-life balance -, and the work contracts regimes – wages, contract types, diversity); b) Education and training (skilling outcomes, rules on retraining and further training, employability schemes, transferability of skills); c) Equal opportunities (relevance of equal opportunity regulation for restructuring outcomes, the role of gender and age regulation); d) Restructuring effects (policy on transfer of personnel, policy on redundancies, and participation or voice in restructuring).

The Gap Between Knowledge and Action: Obstacles, Restraints and Deficits During the Execution of Refurbishments

This article outlines the initial draft of a PhD project which investigates refurbishment or rehabilitation projects in two German cities. The study focuses on obstacles, restraints and deficits as well as factors of success, which can be identified during the execution of the refurbishments. Moreover the study examines the process of the refurbishment itself, the general conditions under which the refurbishments are being executed as well as the implementation of sustainability criteria. First the article gives a short summary of the theoretical considerations of the study. In this respect it shortly outlines the global conditions of urban development and conducting challenges for cities in the 21st century, guiding principles of a sustainable urban development as well as goals of sustainable refurbishments. Finally the article shortly describes the case studies and presents the initial results of the empirical work.

The sociological perspective on the knowledge-based society: assumptions, facts and visions

The paper will present the central discourse of the knowledge-based society. Already in the 1960s the debate of the industrial society already raised the question whether there can be considered a paradigm shift towards a knowledge-based society. Some prominent authors already foreseen ‘knowledge’ as the main indicator in order to displace ‘labour’ and ‘capital’ as the main driving forces of the capitalistic development. Today on the political level and also in many scientific disciplines the assumption that we are already living in a knowledge-based society seems obvious. Although we still do not have a theory of the knowledge-based society and there still exist a methodological gap about the empirical indicators, the vision of a knowledge-based society determines at least the perception of the Western societies. In a first step the author will pinpoint the assumptions about the knowledge-based society on three levels: on the societal, on the organisational and on the individual level. These assumptions are relied on the following topics: a) The role of the information and communication technologies; b) The dynamic development of globalisation as an ‘evolutionary’ process; c) The increasing importance of knowledge management within organisations; d) The changing role of the state within the economic processes. Not only the differentiation between the levels but also the revision of the assumptions of a knowledge-based society will show that the ‘topics raised in the debates’ cannot be considered as the results of a profound societal paradigm shift. However what seems very impressive is the normative and virtual shift towards a concept of modernity, which strongly focuses on the role of technology as a driving force as well as on the global economic markets, which has to be accepted. Therefore – according to the official debate - the successful adaptation of these processes seems the only way to meet the knowledge-based society. Analysing the societal changes on the three levels, the label ‘knowledge-based society’ can be seen critically. Therefore the main question of Theodor W. Adorno during the 16th Congress of Sociology in 1968 did not loose its actuality. Facing the societal changes he asked whether we are still living in the industrial society or already in a post-industrial state. Thinking about the knowledge-based society according to these two options, this exercise would enrich the whole debate in terms of social inequality, political, economic exclusion processes and at least the power relationship between social groups.

Change Processes and Future Perspectives in the Knowledge Society. The Example of Clothing and Textile Industry

The paper examines change processes und future perspectives in the knowledge society. It presents the clothing and textile industry as an example for a transforming industry in a global economy. The paper reviews existing future studies, which have surveyed change processes and future developments in the clothing and textile industry. Main goals of the review are the identification of changes in work and the description of the restructuring of global value chains within the clothing and textile sector. The paper also highlights major current trends, drivers of change and future prospects in this sector.

The First WORKS Conference on Transformation of Work in a Global Knowledge Economy

The relationship between the changes of the global economy and individual working conditions formed the background of the first WORKS conference “The transformation of work in a global knowledge economy: towards a conceptual framework”, held in Chania, Greece from 21st – 22nd September, 2006 and attended by around 50 European researchers. Experts from academia and trade unions from all over the world were invited to give insights into their field of research, contributing to one of the main topics of the conference: (i) globalisation and organisational restructuring, (ii) workers’ organisation, the quality of working life and the gender dimension and (iii) global experiences and recommendations.

Into a new phase of the research on restructuring of work in the knowledge society: the Third WORKS General Assembly in Sofia (Bulgaria)

The WORKS Project started two years ago (2005), involving the efforts of research institutes of 13 European countries with the main purpose of improving the understanding of the major changes in work in the knowledge-based society, taking account both of global forces and the regional diversity within Europe. This research meeting in Sofia (Bulgaria) aimed to present synthetically the massive amount of data collected in the case studies (occupational and organisational) and with the quantitative research during last year.