Development of new methodologies in sample treatment for proteomics workflow based on enzymatic probe sonication technology and mass spectrometry

Thesis submitted to the Universidade Nova de Lisboa, Faculdade de Ciências e Tecnologia, for the degree of Doctor of Philosophy in Biochemistry

Technology market transfer plan launch of DELIVES to E.U. Market©

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do grau de Mestre em Biotecnologia

How composite indicators of innovation can influence technology policy decision?

Based on the report for Project III of the PhD programme on Technology Assessment and prepared for the Winter School that took place at Universidade Nova de Lisboa, Caparica Campus on the 6th and 7th of December 2010.

The genetic basis of morphological change in convergent evolution of natural populations: identifying candidate genes behind convergent evolution in blind cavefish astyanax mexicanus

Dissertation presented to obtain the Ph.D. degree in Biology at the Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa.

Terminology as a sensemaking social tool

Since the middle of the first decade of this century, several authors have announced the dawn of a new Age, following the Information/ Knowledge Age (1970-2005?). We are certainly living in a Shift Age (Houle, 2007), but no standard designation has been broadly adopted so far, and others, such as Conceptual Age (Pink, 2005) or Social Age (Azua, 2009), are only some of the proposals to name current times. Due to the amount of information available nowadays, meaning making and understanding seem to be common features of this new age of change; change related to (i) how individuals and organizations engage with each other, to (ii) the way we deal with technology, to (iii) how we engage and communicate within communities to create meaning, i.e., also social networking-driven changes. The Web 2.0 and the social networks have strongly altered the way we learn, live, work and, of course, communicate. Within all the possible dimensions we could address this change, we chose to focus on language – a taken-for-granted communication tool, used, translated and recreated in personal and geographical variants, by the many users and authors of the social networks and other online communities and platforms. In this paper, we discuss how the Web 2.0, and specifically social networks, have contributed to changes in the communication process and, in bi- or multilingual environments, to the evolution and freeware use of the so called “international language”: English. Next, we discuss some of the impacts and challenges of this language diversity in international communication in the shift age of understanding and social networking, focusing on specialized networks. Then we point out some skills and strategies to avoid babelization and to build meaningful and effective content in mono or multilingual networks, through the use of common and shared concepts and designations in social network environments. For this purpose, we propose a social and collaborative approach to terminology management, as a shared, strategic and sense making tool for specialized communication in Web 2.0 environments.

Emerging (Bio)Sensing Technology for Assessing and Monitoring Freshwater Contamination – Methods and Applications

Ecological Water Quality - Water Treatment and Reuse

St. Louis encephalitis vírus: first isolation from a human in São Paulo state, Brasil

This paper reports the isolation of St. Louis encephalitis virus (SLEV) from a febrile human case suspected to be dengue, in São Pedro, São Paulo State. A MAC-ELISA done on the patient's acute and convalescent sera was inconclusive and hemagglutination inhibition test detected IgG antibody for flaviviruses. An indirect immunofluorescent assay done on the C6/36 cell culture inoculated with the acute serum was positive for flaviviruses but negative when tested with dengue monoclonal antibodies. RNA extracted from the infected cell culture supernatant was amplified by RT-PCR in the presence of NS5 universal flavivirus primers and directly sequenced. Results of BLAST search indicated that this sequence shares 93% nucleotide similarity with the sequence of SLEV (strain-MSI.7), confirmed by RT-PCR performed with SLEV specific primers. Since SLEV was identified as the cause of human disease, it is necessary to improve surveillance in order to achieve early detection of this agent in the state of São Paulo and in Brazil. This finding is also an alert to health professionals about the need for more complete clinical and epidemiological investigations of febrile illnesses as in the reported case. SLEV infections can be unrecognized or confused with other ones caused by an arbovirus, such as dengue.

Antigenic and genetic characterization of the first rabies virus isolated from the bat Eumops perotis in Brazil

Although the main transmitters of rabies in Brazil are dogs and vampire bats, the role of other species such as insectivorous and frugivorous bats deserves special attention, as the rabies virus has been isolated from 36 bat species. This study describes the first isolation of the rabies virus from the insectivorous bat Eumops perotis. The infected animal was found in the city of Ribeirão Preto, São Paulo. The virus was identified by immunofluorescence antibody test (FAT) in central nervous system (CNS) samples, and the isolation was carried out in N2A cell culture and adult mice. The sample was submitted to antigenic typing using a panel of monoclonal antibodies (CDC/Atlanta/USA). The DNA sequence of the nucleoprotein gene located between nucleotides 102 and 1385 was aligned with homologous sequences from GenBank using the CLUSTAL/W method, and the alignment was used to build a neighbor-joining distance-based phylogenetic tree with the K-2-P model. CNS was negative by FAT, and only one mouse died after inoculation with a suspension from the bat's CNS. Antigenic typing gave a result that was not compatible with the patterns defined by the panel. Phylogenetic analysis showed that the virus isolated segregated into the same cluster related to other viruses isolated from insectivorous bats belonging to genus Nyctinomops ssp. (98.8% nucleotide identity with each other).

Predictors of adherence to the Mediterranean diet from the first to the second trimester of pregnancy

Background: Although changes in eating patterns may occur during gestation, predictors of these changes have not been explored. This study aimed to identify predictors of adherence to the Mediterranean diet (MD) from the first to second trimester of pregnancy. Methods: A prospective study was conducted with 102 pregnant women aged 18-40, from the city of Porto, Portugal. Socio-demographic and lifestyle characteristics were assessed through a questionnaire. Food consumption was assessed with a three-day food diary completed during the first and second trimesters. Participants were categorized according to their change in adherence to the MD into the negative change group (i.e., women who had low adherence in each trimester or had high adherence in the first trimester and then low adherence in the second) and the positive change group (i.e., women who had high adherence in both trimesters or had low adherence in the first trimester and then high adherence in the second). Conditional stepwise logistic regression models were performed to assess the potential predictors of negative MD change. Results: Among the 102 women, 39.2% had negative change from the first to the second trimester. The logistic model´s results show that being married (OR=0.26, 95%CI: 0.10, 0.76) and having a higher intake of vegetables in the first trimester (OR=0.17, 95%CI: 0.10, 0.43) were associated with lower odds of having a negative change in adherence to the MD from the first to second trimester. Conclusion: Marital status and vegetable consumption seem to be associated with a lower occurrence of negative change in adherence to the MD from early to middle pregnancy.

Cardmobili: innovation technology in everyday life

The developments of the internet, the proliferation of the use of Web 2.0 tools, and of the technology in general, are leveraging new ways of people to communicate, collaborate, and interact. This new world and new markets, in a daily change, are enabling the emergence of new innovative enterprises and services, taking advantage of the new technologies and of the global network. Cardmobili is a Portuguese start-up company working in the area of mobile services. This company provides a mobile service to manage rewards and membership cards, enabling users to store them in the cloud, while using mobile applications to present them in store, collecting and using the rewards, sharing cards and information with other users and friends in social networks. Cardmobili is linked to merchants’ loyalty management systems, enabling users to access exclusive offers, delivered to their mobile application and web account. The company provides complete services to make any loyalty or membership program mobile: branding, new customer registration, integration of customer account balance, mobile vouchers, coupons and offers, and mobile communication.

First occurrence of an autochthonous canine case of Leishmania (Leishmania) infantum chagasi in the municipality of Campinas, State of São Paulo, Brazil

An autochthonous case of visceral leishmaniasis is reported in a dog (Canis familiaris) as an apparently natural infection in a non-endemic area. DNA obtained from spleen and liver samples produced the expected fragment in a Leishmania-specific rDNA-based nested-PCR assay. The PCR product, a 490 bp fragment, was sequenced and the nucleotide sequence was identical to that of Leishmania (Leishmania) infantum chagasi. These results are surprising since no autochthonous human or canine cases of visceral leishmaniasis have ever been reported in this municipality. This case suggests that natural transmission of this disease is occurring in this area.

The use of indicators and evidence in governance and policy development of science, technology and innovation

This paper was first presented at the 2012 – EU SPRI Conference “Towards Transformative Governance? - Responses to mission-oriented innovation policy paradigms”, Fraunhofer ISI, June 2012, Karlsruhe

O Futuro dos Centros de Dados

Atualmente, as Tecnologias de Informação (TI) são cada vez mais vitais dentro das organizações. As TI são o motor de suporte do negócio. Para grande parte das organizações, o funcionamento e desenvolvimento das TI têm como base infraestruturas dedicadas (internas ou externas) denominadas por Centro de Dados (CD). Nestas infraestruturas estão concentrados os equipamentos de processamento e armazenamento de dados de uma organização, por isso, são e serão cada vez mais desafiadas relativamente a diversos fatores tais como a escalabilidade, disponibilidade, tolerância à falha, desempenho, recursos disponíveis ou disponibilizados, segurança, eficiência energética e inevitavelmente os custos associados. Com o aparecimento das tecnologias baseadas em computação em nuvem e virtualização, abrese todo um leque de novas formas de endereçar os desafios anteriormente descritos. Perante este novo paradigma, surgem novas oportunidades de consolidação dos CD que podem representar novos desafios para os gestores de CD. Por isso, é no mínimo irrealista para as organizações simplesmente eliminarem os CD ou transforma-los segundo os mais altos padrões de qualidade. As organizações devem otimizar os seus CD, contudo um projeto eficiente desta natureza, com capacidade para suportar as necessidades impostas pelo mercado, necessidades dos negócios e a velocidade da evolução tecnológica, exigem soluções complexas e dispendiosas tanto para a sua implementação como a sua gestão. É neste âmbito que surge o presente trabalho. Com o objetivo de estudar os CD inicia-se um estudo sobre esta temática, onde é detalhado o seu conceito, evolução histórica, a sua topologia, arquitetura e normas existentes que regem os mesmos. Posteriormente o estudo detalha algumas das principais tendências condicionadoras do futuro dos CD. Explorando o conhecimento teórico resultante do estudo anterior, desenvolve-se uma metodologia de avaliação dos CD baseado em critérios de decisão. O estudo culmina com uma análise sobre uma nova solução tecnológica e a avaliação de três possíveis cenários de implementação: a primeira baseada na manutenção do atual CD; a segunda baseada na implementação da nova solução em outro CD em regime de hosting externo; e finalmente a terceira baseada numa implementação em regime de IaaS.

GIS capacity building for risk management to help developing countries:Case of climate change problem in Amhara rural region (Ethiopia)

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

Evolution of the Human Immunodeficiency Virus Type 2 Envelope in the First Years of Infection is Associated with the Dynamics of the Neutralizing Antibody Response

Background: Differently from HIV-1, HIV-2 disease progression usually takes decades without antiretroviral therapy and the majority of HIV-2 infected individuals survive as elite controllers with normal CD4+ T cell counts and low or undetectable plasma viral load. Neutralizing antibodies (Nabs) are thought to play a central role in HIV-2 evolution and pathogenesis. However, the dynamic of the Nab response and resulting HIV-2 escape during acute infection and their impact in HIV-2 evolution and disease progression remain largely unknown. Our objective was to characterize the Nab response and the molecular and phenotypic evolution of HIV-2 in association with Nab escape in the first years of infection in two children infected at birth. Results: CD4+ T cells decreased from about 50% to below 30% in both children in the first five years of infection and the infecting R5 viruses were replaced by X4 viruses within the same period. With antiretroviral therapy, viral load in child 1 decreased to undetectable levels and CD4+ T cells recovered to normal levels, which have been sustained at least until the age of 12. In contrast, viral load increased in child 2 and she progressed to AIDS and death at age 9. Beginning in the first year of life, child 1 raised high titers of antibodies that neutralized primary R5 isolates more effectively than X4 isolates, both autologous and heterologous. Child 2 raised a weak X4-specific Nab response that decreased sharply as disease progressed. Rate of evolution, nucleotide and amino acid diversity, and positive selection, were significantly higher in the envelope of child 1 compared to child 2. Rates of R5-to-X4 tropism switch, of V1 and V3 sequence diversification, and of convergence of V3 to a β-hairpin structure were related with rate of escape from the neutralizing antibodies. Conclusion: Our data suggests that the molecular and phenotypic evolution of the human immunodeficiency virus type 2 envelope are related with the dynamics of the neutralizing antibody response providing further support for a model in which Nabs play an important role in HIV-2 pathogenesis.