Structural investigation of the Bacillus subtilis morphogenic factor RodZ

A thesis to obtain a Master degree in Structural and Functional Biochemistry

Maintaining the correctness of transactional memory programs

Dissertação para obtenção do Grau de Doutor em Engenharia Informática

Things we see: Portuguese anthropology on material culture

Part of the objects that anthropologists can now find in Lisbon result from the existence of networks with rather diverse historical, social and cultural origins, linking Angola, Mozambique, Cape Verde, Guinea-Bissau, Brazil and Portugal, as well as the countries which have attracted all these countries’ diasporas. The publishing of papers by Portuguese and Brazilian anthropologists in this dossier dedicated to consumption might come to generate a productive collaboration between researchers from both countries, which for over five centuries have seen arriving from the other side of the Atlantic strange objects that, in turn, have taken the routes of the diasporas mentioned above, from luxurious and whimsical items as the indigenous leaders’ feathers and the carriages of the Portuguese royalty, to common and irreplaceable goods as the havaianas.

Learnings from real cases route-to-market redesign within the Portuguese lubricants sector

A Work Project, presented as part of the requirements for the Award of a Masters Degree in Management from the NOVA – School of Business and Economics

Regulation and function of the cell wall polymer lipoteichoic acid in staphylococcus aureus

A thesis submitted for the Degree of Master in Medical microbiology

From a project to an organisation: a Strategic Communication’s approach

Relatório de Estágio apresentado para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Ciências da Comunicação, área de especialização em Comunicação Estratégica

A distributed platform for the volunteer execution of workflows on a local area network

Thesis submitted in fulfilment of the requirements for the Degree of Master of Science in Computer Science

Design of a tool to study the fate of Chlamydia trachomatis infected cells

Chlamydia trachomatis has a unique obligate intracellular developmental cycle that ends by the lysis of the cell and/or the extrusion of the bacteria in order to allow for re-infections. While Chlamydia trachomatis infections are often asymptomatic the diagnosis of Chlamydia trachomatis is usually late, occurring after manifestation of persistency. Investigations on the consequences of long-term infections and the molecular mechanisms behind it will reveal light to what extent bacteria can modulate host cell function and what the ultimate fate of host cells after clearance of an infection is. Such studies on the host cell fate could be greatly facilitated if the infected cells become permanently marked during and after the infection. Therefore, this project intends to develop a new genetic tool that would allow permanently labeling of Chlamydia trachomatis host cells. The plan was to generate a Chlamydia trachomatis strain that encodes a recombinant CRE recombinase, fused to a secretory effector function of the Chlamydia type 3 secretion system (T3SS). Upon translocation into the host cell, this recombinant CRE enzyme could then, owing to its site-specific recombination function, switch a reporter gene contained in the host cell genome. To this end, the reporter line carried a membrane-tagged tdTomato (mT) gene flanked by two LoxP sequences followed by a GFP gene. The translocation of the recombinant CRE recombinase into this cell line was designed to trigger the recombination of the LoxP sites whereby the cells would turn from red fluorescence to green as an irreversible label of the infected cells. Successful execution of this mechanism would allow to draw a direct link between Chlamydia trachomatis infection and the subsequent fate of the infected cell.

O Arquivo Gama Lobo Salema (sécs. XV – XX): temas e problemas entre a História e a Arquivística

Longe das premissas de «objectividade» e «cientificidade» positivistas, que promoviam a Arquivística como «ciência auxiliar» da História, os arquivistas como “guardiães passivos” 2 da documentação ao ser- viço dos historiadores e os arquivos como “resíduos naturais e orgânicos da actividade humana” 3 virginal- mente conservados ao longo dos séculos, as últimas décadas trouxeram novos pressupostos lançados por uma, também ela, «Nova Arquivística», progressivamente sintonizada com os desafios pós-modernistas com as exigências da Era da Informação. Autónoma, metamorfoseada e ao abrigo de um novo paradigma, esta «ciência» arquivística renovada depressa contaminou a sua antiga disciplina-mãe ao chamar particular atenção para a necessidade de rever algumas das tendências - ou “resíduos tóxicos” 5 para usar uma expressão de Patrick Geary – de herança positivista. Dessa contaminação resultaram dois movimentos essenciais que marcam o compasso de diversas das principais discussões hoje tecidas acerca da metodologia e da teoria da História: o archival turn (“viragem arquivística”), sobretudo animado pela produção científica ligada aos EUA, Inglaterra e Canáda; e o tournant documentaire (“viragem documental”), propagado por autores oriundos de França, Bélgica, Espanha, Itália e, em menor medida, Portugal. Apesar de cada uma destas viragens apresentar características específicas ambas partilham, no entanto, uma mesma essência que aponta precisamente para a concepção dos arquivos (tanto os conjuntos documentais como as instituições) não só como “place of study”, isto é, como espaços e repositórios de informação passível de ser recolhida para a análise de dado objecto de estudo mas também como objectos de estudo em si mesmos, per se merecedores de um esforço problematizante. Esta centralidade ocupada pelos conjuntos documentais, pelos arquivos-instituição e, consequentemente, pelo trabalho desenvolvido pelos arquivistas provocou, por seu turno, um intenso questionamento de algumas das mais enraizadas «evidências» cultivadas no seio da Historiografia.

Humor and the framing of the public sphere and public opinion in Portugal (1797-1834)

In his Answer to the Question: What is Enlightenment (1784), Kant puts forward his belief that the vocation to think freely, which humankind is endowed with, is bound to make sure that “the public use of reason” will at last act “even on the fundamental principles of government and the state [will] find it agreeable to treat man – who is now more than a machine – in accord with his dignity”. The critical reference to La Mettrie (1747), by opposing the machine to human dignity, will echo, in the dawn of the 20th century, in Bergson’s attempt to explain humor. Besides being exclusive to humans, humor is also a social phenomenon. Freud (1905) assures that pleasure originated by humor is collective, it results from a “social process”: jokes need an audience, a “third party”, in order to work and have fun. Assuming humor as a social and cultural phenomenon, this paper intends to sustain that it played a role in the framing of the public sphere and of public opinion in Portugal during the transition from Absolute Monarchy to Liberalism. The search for the conditions which made possible the critical exercise of sociability is at the root of the creation of the public sphere in the sense developed by Habermas (1962), whose perspective, however, has been questioned by those who point 2 out the alleged idealism of the concept – as opposed, for example, to Bakhtin (1970), whose work stresses diversity and pluralism. This notwithstanding, the concept of public sphere is crucial to the building of public opinion, which is, in turn, indissoluble from the principle of publicity, as demonstrated by Bobbio (1985). This paper discusses the historical evolution of the concept of public opinion from Ancient Greece doxa, through Machiavelli’s “humors” (1532), the origin of the expression in Montaigne (1580) and the contributions of Hobbes (1651), Locke (1690), Swift (1729), Rousseau (1762) or Hume (1777), up to the reflection of Lippman (1922) and Bourdieu’s critique (1984). It maintains that humor, as it appears in Portuguese printed periodicals from 1797 (when Almocreve de Petas was published for the first time) to the end of the civil war (1834) – especially in those edited by José Daniel Rodrigues da Costa but also in O Piolho Viajante, by António Manuel Policarpo da Silva, or in the ones written by José Agostinho de Macedo, as well as in a political “elite minded” periodical such as Correio Braziliense –, contributed to the framing of the public sphere and of public opinion in Portugal.

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.

Brotherly love and filial obedience: the commemorative programme of the Avis princes at Santa Maria da Vitória, Batalha

This dissertation focuses on a rare 15th century commemorative programme that has thus far received little scholarly attention: the collective monument erected in the Founder’s Chapel, at the Monastery of Santa Maria da Vitória, Batalha, to house the remains of four Avis princes, members of what would become known as ‘the Illustrious Generation’. A patron is proposed for the commission of this erudite monument - the princes’ eldest brother, king Duarte I - arguing its integration into a broader propaganda programme to glorify the memory of the Avis dynasty founder, king João I. The dissertation then proceeds to discuss various highly innovative features of the monument, such as its pseudo-architectural character, its use of sophisticated heraldry and personal badges, the apparent absence of religious iconography on the tombs and, importantly, the collective nature of the programme, key to its interpretation. Using a semiotic approach, a discussion is also offered on the way the various formal, iconographic and conceptual novelties of the princes’ monument impacted on the 15th century monumental landscape in Portugal. Finally, the monument and the chapel housing it are looked at through the prism of the various readings that successive generations of viewers have projected onto it, from the time of its creation to the turn of the 20th century, in order to offer a more comprehensive understanding of the object as it stands today.

New visualization model for large scale biosignals analysis

Benefits of long-term monitoring have drawn considerable attention in healthcare. Since the acquired data provides an important source of information to clinicians and researchers, the choice for long-term monitoring studies has become frequent. However, long-term monitoring can result in massive datasets, which makes the analysis of the acquired biosignals a challenge. In this case, visualization, which is a key point in signal analysis, presents several limitations and the annotations handling in which some machine learning algorithms depend on, turn out to be a complex task. In order to overcome these problems a novel web-based application for biosignals visualization and annotation in a fast and user friendly way was developed. This was possible through the study and implementation of a visualization model. The main process of this model, the visualization process, comprised the constitution of the domain problem, the abstraction design, the development of a multilevel visualization and the study and choice of the visualization techniques that better communicate the information carried by the data. In a second process, the visual encoding variables were the study target. Finally, the improved interaction exploration techniques were implemented where the annotation handling stands out. Three case studies are presented and discussed and a usability study supports the reliability of the implemented work.

Bits, Atoms, and Information Sharing: new opportunities for participation

The particular characteristics and affordances of technologies play a significant role in human experience by defining the realm of possibilities available to individuals and societies. Some technological configurations, such as the Internet, facilitate peer-to-peer communication and participatory behaviors. Others, like television broadcasting, tend to encourage centralization of creative processes and unidirectional communication. In other instances still, the affordances of technologies can be further constrained by social practices. That is the case, for example, of radio which, although technically allowing peer-to-peer communication, has effectively been converted into a broadcast medium through the legislation of the airwaves. How technologies acquire particular properties, meanings and uses, and who is involved in those decisions are the broader questions explored here. Although a long line of thought maintains that technologies evolve according to the logic of scientific rationality, recent studies demonstrated that technologies are, in fact, primarily shaped by social forces in specific historical contexts. In this view, adopted here, there is no one best way to design a technological artifact or system; the selection between alternative designs—which determine the affordances of each technology—is made by social actors according to their particular values, assumptions and goals. Thus, the arrangement of technical elements in any technological artifact is configured to conform to the views and interests of those involved in its development. Understanding how technologies assume particular shapes, who is involved in these decisions and how, in turn, they propitiate particular behaviors and modes of organization but not others, requires understanding the contexts in which they are developed. It is argued here that, throughout the last century, two distinct approaches to the development and dissemination of technologies have coexisted. In each of these models, based on fundamentally different ethoi, technologies are developed through different processes and by different participants—and therefore tend to assume different shapes and offer different possibilities. In the first of these approaches, the dominant model in Western societies, technologies are typically developed by firms, manufactured in large factories, and subsequently disseminated to the rest of the population for consumption. In this centralized model, the role of users is limited to selecting from the alternatives presented by professional producers. Thus, according to this approach, the technologies that are now so deeply woven into human experience, are primarily shaped by a relatively small number of producers. In recent years, however, a group of three interconnected interest groups—the makers, hackerspaces, and open source hardware communities—have increasingly challenged this dominant model by enacting an alternative approach in which technologies are both individually transformed and collectively shaped. Through a in-depth analysis of these phenomena, their practices and ethos, it is argued here that the distributed approach practiced by these communities offers a practical path towards a democratization of the technosphere by: 1) demystifying technologies, 2) providing the public with the tools and knowledge necessary to understand and shape technologies, and 3) encouraging citizen participation in the development of technologies.

Land cover mapping analysis and urban growth modeling using remote sensing techniques

The rapid growth of big cities has been noticed since 1950s when the majority of world population turned to live in urban areas rather than villages, seeking better job opportunities and higher quality of services and lifestyle circumstances. This demographic transition from rural to urban is expected to have a continuous increase. Governments, especially in less developed countries, are going to face more challenges in different sectors, raising the essence of understanding the spatial pattern of the growth for an effective urban planning. The study aimed to detect, analyse and model the urban growth in Greater Cairo Region (GCR) as one of the fast growing mega cities in the world using remote sensing data. Knowing the current and estimated urbanization situation in GCR will help decision makers in Egypt to adjust their plans and develop new ones. These plans should focus on resources reallocation to overcome the problems arising in the future and to achieve a sustainable development of urban areas, especially after the high percentage of illegal settlements which took place in the last decades. The study focused on a period of 30 years; from 1984 to 2014, and the major transitions to urban were modelled to predict the future scenarios in 2025. Three satellite images of different time stamps (1984, 2003 and 2014) were classified using Support Vector Machines (SVM) classifier, then the land cover changes were detected by applying a high level mapping technique. Later the results were analyzed for higher accurate estimations of the urban growth in the future in 2025 using Land Change Modeler (LCM) embedded in IDRISI software. Moreover, the spatial and temporal urban growth patterns were analyzed using statistical metrics developed in FRAGSTATS software. The study resulted in an overall classification accuracy of 96%, 97.3% and 96.3% for 1984, 2003 and 2014’s map, respectively. Between 1984 and 2003, 19 179 hectares of vegetation and 21 417 hectares of desert changed to urban, while from 2003 to 2014, the transitions to urban from both land cover classes were found to be 16 486 and 31 045 hectares, respectively. The model results indicated that 14% of the vegetation and 4% of the desert in 2014 will turn into urban in 2025, representing 16 512 and 24 687 hectares, respectively.