Camelid nanobodies raised against an integral membrane enzyme, nitric oxide reductase

Protein Sci. 2009 Mar;18(3):619-28. doi: 10.1002/pro.69.

A framework for semantic checking of information systems

Dissertação para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores

Molecular determinants of ligand specificity in carbohydrate-binding modules: an NMR and X-ray crystallography integrated study

Dissertação para obtenção do Grau de Doutor em Bioquímica – Ramo Bioquímica Estrutural

Linked Data based Health Information Representation, Visualization and Retrieval System on the Semantic Web

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

Insights into Campylobacter jejuni Desulforubrerythrin catalytic mechanism

Dissertation presented to obtain the Master Degree in Molecular Genetics and Biomedicine

Lime mortars with rice husk ash for ancient masonry

HMC08 - 1st Historical Mortars Conference: Characterization, Diagnosis, Conservation, Repair and Compatibility, LNEC, Lisbon, 24-26 September 2008

The Edges of Areal Units: a case study in the heterogeneous effects of assessment district edges

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

Durability to marine environment of innovative products for consolidation and chromatic reintegration of historical renders

9th International Masonry Conference 2014, 7-9 July, Universidade do Minho, Guimarães

A knowledge-based framework to facilitate E-training implementation

Dissertação para obtenção do Grau de Mestre em Engenharia Eletrotécnica e de Computadores

Assessment of Notch1 ligands production - key protein targets in breast cancer

Cell-to-cell communication is required for many biological processes in development and adult life. One of the most common systems utilized by a wide range of eukaryotes is the Notch signalling pathway. Four Notch receptors and five ligands have been identified in mammals that interact via their extracellular domains leading to transcription activation. Studies have shown that the Notch ligands expression is undetectable in normal breast tissues, but moderate to high expression has been detected in breast cancer. Thus, any of the Notch1 ligands can be studied as possible therapeutic targets for breast cancer. To study Notch pathway proteins there is the need to obtain stable protein solutions. E. coli is the host of excellence for recombinant proteins for the ease of use, fast growth and high cell densities. However, the expression of mammalian proteins in such systems may overwhelm the bacterial cellular machinery, which does not possess the ability for post-translational modifications, or dedicated compartments for protein synthesis. Mammalian cells are therefore preferred, despite their technical and financial increased demands. We aim to determine the best expression and purification conditions for the different ligand protein constructs, to develop specific function-blocking antibodies using the Phage Display technology. Moreover, we propose to crystallize the Notch1 ligands alone and in complex with the phage display selected antibodies, unveiling molecular details. hJag2DE3 and hDll1DE6 proteins were purified from refolded inclusion bodies or mammalian cell culture supernatants, respectively, and purity was confirmed by SDS-PAGE (>95%). Protein produced in mammalian cells showed to be more stable, apparently with the physiological disulfide pattern, contrary to what was observed in the refolded protein. Several nano-scale crystallization experiments were set up in 96-well plates, but no positive result was obtained. We will continue to pursue for the best expression for the Notch ligand constructs in both expression systems.

Evaporation from porous building materials and its cooling potential

Evaporative cooling is a traditional strategy to improve summer comfort, which has gained renewed relevance in the context of the transition to a greener economy. Here, the potential for evaporative cooling of two common porous building materials, natural stone and ceramic brick, was evaluated. The work has relevance also to the protection of built heritage becauseevaporation underlies the problems of dampness and salt crystallization, which are so harmful and frequent in this heritage. It was observed that the drying rate of the materials is, in some cases, higher than the evaporation rate of a free water surface. Surface area measurements by a three-dimensional optical technique suggested, as probable cause of this behavior, that surface irregularity gives rise to a large effective surface of evaporation in the material. Surface temperature measurements by infrared were performed afterward during evaporation experiments outside during a hot summer day in Lisbon. Their results indicate that ordinary building materials can be very efficient evaporative media and, thus, may help in achieving higher energy efficiency while maintaining a simultaneous constructive or architectural function.

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.

Semantic enrichment of knowledge sources supported by domain ontologies

This thesis introduces a novel conceptual framework to support the creation of knowledge representations based on enriched Semantic Vectors, using the classical vector space model approach extended with ontological support. One of the primary research challenges addressed here relates to the process of formalization and representation of document contents, where most existing approaches are limited and only take into account the explicit, word-based information in the document. This research explores how traditional knowledge representations can be enriched through incorporation of implicit information derived from the complex relationships (semantic associations) modelled by domain ontologies with the addition of information presented in documents. The relevant achievements pursued by this thesis are the following: (i) conceptualization of a model that enables the semantic enrichment of knowledge sources supported by domain experts; (ii) development of a method for extending the traditional vector space, using domain ontologies; (iii) development of a method to support ontology learning, based on the discovery of new ontological relations expressed in non-structured information sources; (iv) development of a process to evaluate the semantic enrichment; (v) implementation of a proof-of-concept, named SENSE (Semantic Enrichment kNowledge SourcEs), which enables to validate the ideas established under the scope of this thesis; (vi) publication of several scientific articles and the support to 4 master dissertations carried out by the department of Electrical and Computer Engineering from FCT/UNL. It is worth mentioning that the work developed under the semantic referential covered by this thesis has reused relevant achievements within the scope of research European projects, in order to address approaches which are considered scientifically sound and coherent and avoid “reinventing the wheel”.

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.

Crystallographic studies of proteins involved in the mRNA localization mechanisms in Drosophila melanogaster and amidation of the peptidoglycan residues in Staphylococcus aureus

Part of the work described in this chapter, was the subject of the following publication: D. Vieira, T. a. Figueiredo, A. Verma, R. G. Sobral, A. M. Ludovice, H. de Lencastre, and J. Trincao, “Purification, crystallization and preliminary X-ray diffraction analysis of GatD, a glutamine amidotransferase-like protein from Staphylococcus aureus peptidoglycan,” Acta Crystallogr. Sect. F Struct. Biol. Commun., vol. 70, no. 5, pp. 1–4, Apr. 2014.