Tuberculosis: new era for diagnosis and surveillance using whole-genome sequencing-based approaches

Tuberculosis (TB) has been declared as a global public health emergency by the WHO since 1993. It still accounts for almost 2 million deaths each year, making it the ninth leading cause of death worldwide. The major obstacle for an effective TB control is antimicrobial resistance, thus, to be successful, new strategies must be addressed, for instance, the implementation of new rapid TB diagnostic technologies that could translate into early treatment initiation and blocking of transmission chains. Considering the major constraints regarding the isolation and time of growth of M. tuberculosis strains, the main goal of this PhD dissertation was to acknowledge the potential of the use of WGS-based methodologies for routine diagnostic and epidemiological surveillance. We evaluated several software for in silico prediction of antibiotic resistance and developed bioinformatics pipelines for surveillance purposes, in particular for the identification of transmission chains. As they revealed high sensitivity, these approaches are already implemented in the routine of the Portuguese National Reference Laboratory (NRL). We also recognised the possibility to use these same approaches directly to samples collected from TB patients, lowering the time-to-results, for a complete drug resistance pattern and phylogeny analysis, for five to eight days. The validation of this methodology is ongoing and will be implemented in a near future. Additionally, and according to the new recommendations for TB treatment, we have initiated studies to identify new mutations associated with resistance to the recently adopted drugs, in order to enrich the available databases and improve the performance of the genotypic diagnostics pipelines. This PhD dissertation highlights WGS-based methodologies as powerful tools to surpass the difficulties of phenotypic TB diagnosis and surveillance and to provide a much more rapid information regarding resistance prediction and eventual transmission chains. It also supported the technological transition performed at the NRL for TB surveillance

Tattoo and fear of commitment : temporary tattoos, their influence on consumer behavior and acceptance in the Portuguese market

Although temporary tattoos have been in the market for some time, some brands decided to create online stores dedicated exclusively to the promotion and sale of this type of tattoos, specifically the so-called "stickers" or "transfers". Through this concept, they give the hypothesis to a client, of testing a future permanent tattoo or usufruct only of a new accessory in the body. For this reason, this highly customizable service could be a threat to the permanent tattoo industry. However this will not be the focus, but rather how it might be an alternative for those who have some fear related to the permanent tattoo industry, whether financial, psychological or physiological. The primary objective of this study is to identify, in the Portuguese market, the attractiveness of this new service of temporary tattoos, the drivers and the factors that could be compromising in the purchase, the tattooed people and the not tattooed. Even though there were several limitations in this study, in general, the service of temporary tattoos showed to have potential in the Portuguese market. The reasons that were chosen for the participants to order a temporary tattoo were related to a choice associated with the permanent tattoo industry. However, in addition to the points mentioned above, other variables were considered in this conclusion, namely the participants' possible concerns about the service of temporary tattoos and the variables in which the participants showed themselves willing to give more money.Apesar das tatuagens temporárias já existirem há algum tempo no mercado, algumas marcas decidiram criar lojas online que se dedicam exclusivamente à promoção e venda deste tipo de tatuagens, mais especificamente as chamadas “stickers” ou “transfers”. Através deste conceito, dão a hipótese a um cliente, de testar uma futura tatuagem permanente ou usufruir apenas de um novo acessório no corpo. Por essa razão, este serviço altamente personalizável, poderá ser uma ameaça à indústria das tatuagens permanentes. Contudo, esse não será o foco, mas sim, de que forma é que esta poderá ser uma alternativa para aqueles que tenham algum tipo de receio relacionado com a indústria das tatuagens permanentes, seja relativamente à dimensão financeira, psicológica ou fisiológica. O principal objetivo deste estudo é identificar, no mercado português, a atratibilidade deste novo serviço das tatuagens temporárias, os drivers e os fatores que poderão ser comprometedores na compra, nas pessoas tatuadas e nos não tatuadas. Independentemente de terem existido várias limitações neste estudo, no geral, o serviço das tatuagens temporárias mostrou ter potencial no mercado Português. As razões que mais foram escolhidas para os participantes encomendarem uma tatuagem temporária, estiveram relacionadas com uma escolha relacionada com indústria das tatuagens permanentes. Contudo, existiram outras variáveis que foram consideradas nesta conclusão, nomeadamente, as preocupações hipotéticas dos participantes sobre o serviço das tatuagens temporárias e as variáveis em que os participantes se mostraram a dispostos a dar mais dinheiro

Etnobotânica do Nordeste Português: saberes, plantas e usos

Publicação complementar em papel do Relatório final das actividades do projecto entregue à FCT on-lineEsta publicação descreve todas as actividades realizadas no âmbito do projecto Etnobotânica do Nordeste Português e em particular os resultados obtidos através da realização de estudos de caso e da aplicação de diversas metodologias etnográficas.FC

When the young think that every plant is parsley. Social variability of ethnobotanical knowledge and plant categorization in two rural areas from Portugal

Resumo de comunicação oral apresentada no V ICEBThe ethnobotanical research in two Portuguese natural protected areas allows us to discuss the process of perceiving plants and building plant knowledge and the cultural transformations in the conceptions of plant, nature and environment in rural contexts that face social and economical changes.FCT e Instituto Gulbenkian de Ciênci

Importance of local knowledge in plant resources management and conservation in two protected areas from Trás-os-Montes, Portugal

Many European protected areas were legally created to preserve and maintain biological diversity, unique natural features and associated cultural heritage. Built over centuries as a result of geographical and historical factors interacting with human activity, these territories are reservoirs of resources, practices and knowledge that have been the essential basis of their creation. Under social and economical transformations several components of such areas tend to be affected and their protection status endangered

Why is wild-life more important than people? Conservation strategies, perceptions and contradictions in two protected areas from Trás-os-Montes

Portuguese authorities for nature conservation have been engaged in comprehensive resource networks and effective legislation and regulations for protected areas putting together different efforts to sustain biodiversity and to enlist the full range of partners. It appears that the involvement and participation of local communities was the essential basis on which protected areas would build a system of management which has integrity, security and success, particularly those including human settlements. Nevertheless, conservation measures were mostly designed by outsiders who were culturally detached and parks boundaries were mainly based on environmental criteria. Two important natural protected areas, located in the most north-eastern part of Portugal (Trás-os- Montes), have a great diversity of natural and semi-natural habitats and humanized landscapes which are repositories of nature and cultural heritage. The territories of the Natural Park of Montesinho and the Natural Park of Douro International are the result of many geographical and historical factors and represent harmonious integration of human activity with nature, allowing ecological diversity to be maintained and valued. Based on key-informants' opinions we explore their personal experience with the parks authorities and their ideas about the management of these protected areas. Key-informants main argument is that national conservation networks and strategies did not take into account regional identity, people background and local believes and habits. Moreover, it is perceived that most of the initiatives have never recognized the vital role of human activity in such areas maintenance and the contribution of local knowledge (LK) to the current environment. Many occurrences decreased the intrinsic value of regional landscapes which were considered part of the cultural heritage and had embedded intangible values such as dwelling, spiritual and aesthetical values, local tradition, neighborly and inter-generational relations. Local ideas of nature have determined distinguishable values of plants and animals and outlined different orientations towards predatory actions.Cultibos yerbas i saberes Fundo EDP Biodiversidad

When the young think that every plant is parsley! Social variability of ethno-botanical knowledge and plant categorization in two rural areas in Portugal

Ethnobotanical research in two Portuguese natural protected areas (Montesinho Natural Park and Douro International Natural Park) is the basis to discuss the process of perceiving plants and nature in rural contexts facing social and economic changes. The main argument is that people select and invoke different ethnobotanical knowledge and classificatory principles which are required considering different social attempts and activities in plant categorization. Pile sort tests carried out with 79 informants show that people develop concepts and integrate a diversified knowledge during plant categorization processes. The social variability of plant categorization seems to be related to age and gender differences. Younger people who are nowadays driven away from agricultural activities have quite different perceptions of plants. Criteria of categorization are different when applied by men or women. Cognitive mechanisms addressed during categorisation tasks are influenced by each person’s social background and daily practices. Data also reflect the cultural dynamics in rural contexts: non-transmitted practices, transitional knowledge and changes in nature conceptions

Gendered plants and plant categorization by gender: Classificatory and “storied” knowledge in trás-os-montes, portugal

Background: An anthropomorphizing process arises out of classification systems, whereby analogy is drawn between the social differences of gender and the morphological and biological characteristics used to designate or classify plants. On the other side, it is observed that men and women categorize plants differently on the basis of their practices and knowledge. This paper addresses two assumptions: the consistent cognitive mechanisms of attributing gender to plants in classifications and the local differentiation of knowledge and social variability of categorization of plants based on gender. Methods: The data presented results from research carried out in Portugal in two rural villages, using participant observation, structured ethnobotanical interviews and free pile sorting task (79 interlocutors; among them 11 local experts). A literature review provided some examples from studies conducted in other contexts, which have been used to analyze and discuss our findings. Results: Gender differentiations are present in plants naming and identification. Plants morphologically similar can take different designations or have the same name with gender variations depending on people’s perceptions of female or male features. The survey conducted in these Portuguese case studies shows also a gender variability of knowledge, although knowledge about plants is usually quite shared. Conclusions: The mechanism of plant differentiation using gender attributes seems to be transcultural. However, the plant classification by gender must be explained from a local standpoint and knowledge about plants should be understood as a “storied knowledge”.The data presented were collected in the project “Ethnobotany of the Northeastern Region of Portugal: local knowledge, plants and uses”, founded by FCT - Fundação Ciência e Tecnologia, Portugal (References: - POCTI/ANT/48629/2002; POCI/ANT/59395/2004). The Frazão-Moreira personal data from Wadane (Mauritania) were gathered in the micro-project “Arabic gum. From caravans to the local appropriation in Mauritanian oasis modernity”, included in “Portuguese castles abroad. Heritage and cultural cooperation between Portugal and Arab-Islamic countries”, founded by FCT (Reference: POCTI/ANT/48629/2002; Silva 2013).info:eu-repo/semantics/publishedVersio

Normalização em ética e responsabilidade social: desenvolvimentos em Portugal

A Organização Internacional de Normalização (ISO) está a desenvolver a Norma Internacional de Responsabilidade Social (Norma ISO 26000), com publicação prevista para 2008, que constituirá um guia sobre esta matéria, tendo encorajado por outro lado todos os países participantes a desenvolver as suas próprias normas nacionais sobre a mesma temática. Portugal vem participando nestes esforços através da APEE (Associação Portuguesa de Ética Empresarial), na sua qualidade de Organismo de Normalização Sectorial para os domínios da Ética Empresarial e Responsabilidade Social, que lançou as Comissões Técnicas CT 164 Responsabilidade Social e CT 165 Ética Empresarial, no âmbito do Sistema Português de Normalização. A CT 164 tem o mandato de acompanhar e contribuir para os desenvolvimentos da Norma ISO e, ainda mais importante, de elaborar uma Norma Portuguesa de Responsabilidade Social (RS), como resposta ao interesse crescente por parte das empresas e de outras organizações em actuar reconhecidamente em prol da sustentabilidade, e ao repto da própria ISO, que encorajou os diversos países a elaborarem as suas normas nacionais de RS. É de referir que o trabalho em Portugal se tem desenvolvido em articulação com o da também recém-criada CT 165 Ética Empresarial, cujo principal objectivo é o desenvolvimento de uma norma sobre a elaboração e implementação de códigos de ética em organizações. Por outro lado, o Fórum de Ética e Responsabilidade Social é composto por entidades representativas de seis categorias de partes interessadas (stakeholders), definidas pela ISO, ou seja, Empresas, Organizações Laborais, Organizações Não Governamentais, Organizações de Consumidores, Organizações Governamentais e Serviços, Suporte, Investigação e Outros. O Fórum tem a função de Mirror Committee do ISO/TMB/WG SR e, sobretudo, de contribuir activamente para o desenvolvimento dos projectos de Normas Portuguesas de Responsabilidade Social e de Elaboração e Implementação de Códigos de Ética em organizações, em estreita colaboração com a CT 164 e a CT 165

Low-Cost Indoor Localisation Based on Inertial Sensors, Wi-Fi and Sound

The average life expectancy has been increasing in the last decades, creating the need for new technologies to improve the quality of life of the elderly. In the Ambient Assisted Living scope, indoor location systems emerged as a promising technology capable of sup porting the elderly, providing them a safer environment to live in, and promoting their autonomy. Current indoor location technologies are divided into two categories, depend ing on their need for additional infrastructure. Infrastructure-based solutions require expensive deployment and maintenance. On the other hand, most infrastructure-free systems rely on a single source of information, being highly dependent on its availability. Such systems will hardly be deployed in real-life scenarios, as they cannot handle the absence of their source of information. An efficient solution must, thus, guarantee the continuous indoor positioning of the elderly. This work proposes a new room-level low-cost indoor location algorithm. It relies on three information sources: inertial sensors, to reconstruct users’ trajectories; environ mental sound, to exploit the unique characteristics of each home division; and Wi-Fi, to estimate the distance to the Access Point in the neighbourhood. Two data collection protocols were designed to resemble a real living scenario, and a data processing stage was applied to the collected data. Then, each source was used to train individual Ma chine Learning (including Deep Learning) algorithms to identify room-level positions. As each source provides different information to the classification, the data were merged to produce a more robust localization. Three data fusion approaches (input-level, early, and late fusion) were implemented for this goal, providing a final output containing complementary contributions from all data sources. Experimental results show that the performance improved when more than one source was used, attaining a weighted F1-score of 81.8% in the localization between seven home divisions. In conclusion, the evaluation of the developed algorithm shows that it can achieve accurate room-level indoor localization, being, thus, suitable to be applied in Ambient Assisted Living scenarios.O aumento da esperança média de vida nas últimas décadas, criou a necessidade de desenvolvimento de tecnologias que permitam melhorar a qualidade de vida dos idosos. No âmbito da Assistência à Autonomia no Domicílio, sistemas de localização indoor têm emergido como uma tecnologia promissora capaz de acompanhar os idosos e as suas atividades, proporcionando-lhes um ambiente seguro e promovendo a sua autonomia. As tecnologias de localização indoor atuais podem ser divididas em duas categorias, aquelas que necessitam de infrastruturas adicionais e aquelas que não. Sistemas dependentes de infrastrutura necessitam de implementação e manutenção que são muitas vezes dispendiosas. Por outro lado, a maioria das soluções que não requerem infrastrutura, dependem de apenas uma fonte de informação, sendo crucial a sua disponibilidade. Um sistema que não consegue lidar com a falta de informação de um sensor dificilmente será implementado em cenários reais. Uma solução eficiente deverá assim garantir o acompanhamento contínuo dos idosos. A solução proposta consiste no desenvolvimento de um algoritmo de localização indoor de baixo custo, baseando-se nas seguintes fontes de informação: sensores inerciais, capazes de reconstruir a trajetória do utilizador; som, explorando as características dis tintas de cada divisão da casa; e Wi-Fi, responsável pela estimativa da distância entre o ponto de acesso e o smartphone. Cada fonte sensorial, extraída dos sensores incorpora dos no dispositivo, foi, numa primeira abordagem, individualmente otimizada através de algoritmos de Machine Learning (incluindo Deep Learning). Como os dados das diversas fontes contêm informação diferente acerca das mesmas características do sistema, a sua fusão torna a classificação mais informada e robusta. Com este objetivo, foram implementadas três abordagens de fusão de dados (input data, early and late fusion), fornecendo um resultado final derivado de contribuições complementares de todas as fontes de dados. Os resultados experimentais mostram que o desempenho do algoritmo desenvolvido melhorou com a inclusão de informação multi-sensor, alcançando um valor para F1- score de 81.8% na distinção entre sete divisões domésticas. Concluindo, o algoritmo de localização indoor, combinando informações de três fontes diferentes através de métodos de fusão de dados, alcançou uma localização room-level e está apto para ser aplicado num cenário de Assistência à Autonomia no Domicílio