Ética e estética em LUDWIG WITTGENSTEIN

Dissertação de Doutoramento em Antropologia Filosófica (Ética e Estética)

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.

Synechocystis ferredoxin/ferredoxin-NADP+-reductase/NADP+ complex: Structural model obtained by NMR-restrained docking

FEBS Letters 579 (2005) 4585–4590

A further investigation of the cytochrome b5–cytochrome c complex

J Biol Inorg Chem (2003) 8: 777–786

Integrating protein structural information

Dissertação apresentada para obtenção de Grau de Doutor em Bioquímica,Bioquímica Estrutural, pela Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia

Multiple sequence alignment correction using constraints

Trabalho apresentado no âmbito do European Master in Computational Logics, como requisito parcial para obtenção do grau de Mestre em Computational Logics

A further investigation of the cytochrome b5–cytochrome c complex

J Biol Inorg Chem (2003) 8: 777–786 DOI 10.1007/s00775-003-0479-y

Recent droughts and the impact of North Atlantic Oscillation in Iberia; a spatiotemporal analysis based on vegetation temperature condition Index (VTCI)

Dissertation submitted in partial fulfillment of the requirements for the Degree of Master of Science in Geospatial Technologies.

Emissão e omissão no Wittgenstein de Rorty

O trabalho de Ludwig Wittgenstein é uma das mais constantes referências no percurso de Richard Rorty, cujos escritos, por sua vez, assumem um papel de relevo no âmbito do comentário wittgensteiniano. Apesar de abundarem os textos que contestam a leitura que Rorty faz de Wittgenstein, não há nenhum que, de forma global, vise analisar o modo como se desenrola tal leitura. Na parte I, faremos, pois, o retrato da leitura que Rorty faz de Wittgenstein, recorrendo aos três artigos que o norte-americano escreveu sobre o pensador austríaco: “Keeping Philosophy Pure: an Essay on Wittgenstein”, publicado em 1982, no livro Consequences of Pragmatism – Essays 1972-1980; “Wittgenstein, Heidegger, and the reification of language”, publicado, em 1991, no segundo volume dos Philosophical Papers de Rorty; e “Wittgenstein and the Linguistic Turn”, publicado em 2007, no quarto e último volume dos Philosophical Papers. Na parte II, procuraremos pôr em relevo três implicações democráticas do pensamento de Ludwig Wittgenstein, as quais, apesar de não mencionadas por Rorty, não só são compatíveis com o seu pragmatismo como, sobretudo, estabelecem uma conexão que Rorty não fez: aquela que liga o Rorty leitor de Wittgenstein ao Rorty que reflecte sobre os fundamentos da democracia. A defesa da democracia e a leitura de Wittgenstein surgem separadas no pensamento de Rorty; a sugestão que permeia a parte II é que teria sido mais frutífero, para Rorty e de acordo com os seus próprios parâmetros, estabelecer uma conexão entre o trabalho de Wittgenstein e a reflexão acerca da democracia. Argumenta-se que a pertinência de tal conexão permite concluir que Rorty rejeitou precipitadamente os termos terapia, metafísica e humanidade, na medida em que os mesmos, desde que entendidos num determinado sentido, são úteis para pensar a democracia como exigindo uma certa terapia, como o sistema que privilegia uma pluralidade de metafísicas ou como o modo de convívio no qual a humanidade consiste num espaço relacional de intercâmbio linguístico.

A cor como abrigo: a arquitectura como cuidado

A presente tese intitulada “A cor como abrigo: a arquitectura como cuidado” tem por objectivo fortalecer a ligação entre a “Teoria das Cores” de Goethe e a arquitectura. Para isso a nossa estratégia foi recuperar os conceitos de espaço e corpo. Ambos começam por ser tomados como realidades físicas mas pouco a pouco vai-se mostrando que tal coisa como uma abordagem ‘puramente física’ do espaço e do corpo não é possível - talvez porque não exista. Mesmo a medicina (ao contrario do que possamos pensar primeiro) é uma ciência que não só reconhece o carácter diáfano do corpo como diariamente luta para ir além de uma concepção do corpo enquanto coisa física por perceber que o corpo é determinado por formas e funções mas sobretudo como tomado por forças. Um exemplo extremo desta interacção entre espaço e corpo (ligados através da arquitectura), onde o carácter diáfano de ambos ganha evidência, é na arquitectura de hospitais, que abordamos por último: “o que é um espaço vivido que tem por principal função restaurar o corpo do seu estado de doença?” As referencias principais são J.W. Goethe, Ludwig Wittgenstein, Edmund Husserl, Gilles Deleuze, Christian Norberg- Schulz, Frank Lloyd Wright and Tadao Ando. *********************************************************************This PhD research thesis titled: "Colour as shelter: architecture as care" has as its main goal to strengthen an existing relation between Goethe's Theory of Colours and Architecture. In order to do that our strategy was to use space and body as guiding concepts. Both start as being considered from a pure physical point of view but as our theme develops we see that a “pure physical point of view” concerning space and body it is not possible – perhaps because it does not exist. Medicine (unlike we may think at first) it is a science that not only acknowledges the diaphanous character of the body as daily, tries to go beyond the conception of body as physical thing understanding that the body is determined by forms and functions but mostly taken by forces. An extreme example of the interaction between space and body (linked through architecture), where the diaphanous character of both is evident, is Healthcare architecture: "what is a lived space that has as main function to restore the body of its illness"? Main references are: J.W. Goethe, Ludwig Wittgenstein, Edmund Husserl, Gilles Deleuze, Christian Norberg-Schulz, Frank Lloyd Wright and Tadao Ando.

Botnet cluster identification

Botnets are a group of computers infected with a specific sub-set of a malware family and controlled by one individual, called botmaster. This kind of networks are used not only, but also for virtual extorsion, spam campaigns and identity theft. They implement different types of evasion techniques that make it harder for one to group and detect botnet traffic. This thesis introduces one methodology, called CONDENSER, that outputs clusters through a self-organizing map and that identify domain names generated by an unknown pseudo-random seed that is known by the botnet herder(s). Aditionally DNS Crawler is proposed, this system saves historic DNS data for fast-flux and double fastflux detection, and is used to identify live C&Cs IPs used by real botnets. A program, called CHEWER, was developed to automate the calculation of the SVM parameters and features that better perform against the available domain names associated with DGAs. CONDENSER and DNS Crawler were developed with scalability in mind so the detection of fast-flux and double fast-flux networks become faster. We used a SVM for the DGA classififer, selecting a total of 11 attributes and achieving a Precision of 77,9% and a F-Measure of 83,2%. The feature selection method identified the 3 most significant attributes of the total set of attributes. For clustering, a Self-Organizing Map was used on a total of 81 attributes. The conclusions of this thesis were accepted in Botconf through a submited article. Botconf is known conferênce for research, mitigation and discovery of botnets tailled for the industry, where is presented current work and research. This conference is known for having security and anti-virus companies, law enforcement agencies and researchers.

Adidas AG

UNL - NSBE