Supporting NAT traversal and secure communications in a protocol implementation framework

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para obtenção do Grau de Mestre em Engenharia Electrotécnica e de Computadores

Planning and verification of multipath routing protocols

Conventionally the problem of the best path in a network refers to the shortest path problem. However, for the vast majority of networks present nowadays this solution has some limitations which directly affect their proper functioning, as well as an inefficient use of their potentialities. Problems at the level of large networks where graphs of high complexity are commonly present as well as the appearing of new services and their respective requirements, are intrinsically related to the inability of this solution. In order to overcome the needs present in these networks, a new approach to the problem of the best path must be explored. One solution that has aroused more interest in the scientific community considers the use of multiple paths between two network nodes, where they can all now be considered as the best path between those nodes. Therefore, the routing will be discontinued only by minimizing one metric, where only one path between nodes is chosen, and shall be made by the selection of one of many paths, thereby allowing the use of a greater diversity of the present paths (obviously, if the network consents). The establishment of multi-path routing in a given network has several advantages for its operation. Its use may well improve the distribution of network traffic, improve recovery time to failure, or it can still offer a greater control of the network by its administrator. These factors still have greater relevance when networks have large dimensions, as well as when their constitution is of high complexity, such as the Internet, where multiple networks managed by different entities are interconnected. A large part of the growing need to use multipath protocols is associated to the routing made based on policies. Therefore, paths with different characteristics can be considered with equal level of preference, and thus be part of the solution for the best way problem. To perform multi-path routing using protocols based only on the destination address has some limitations but it is possible. Concepts of graph theory of algebraic structures can be used to describe how the routes are calculated and classified, enabling to model the routing problem. This thesis studies and analyzes multi-path routing protocols from the known literature and derives a new algebraic condition which allows the correct operation of these protocols without any network restriction. It also develops a range of software tools that allows the planning and the respective verification/validation of new protocols models according to the study made.

A Logic and tool for local reasoning about security protocols

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia Informática

The role of the efflux mechanisms in multidrug resistance in Mycobacterium tuberculosis

Abstract The emergence of multi and extensively drug resistant tuberculosis (MDRTB and XDRTB) has increased the concern of public health authorities around the world. The World Health Organization has defined MDRTB as tuberculosis (TB) caused by organisms resistant to at least isoniazid and rifampicin, the main first-line drugs used in TB therapy, whereas XDRTB refers to TB resistant not only to isoniazid and rifampicin, but also to a fluoroquinolone and to at least one of the three injectable second-line drugs, kanamycin, amikacin and capreomycin. Resistance in Mycobacterium tuberculosis is mainly due to the occurrence of spontaneous mutations and followed by selection of mutants by subsequent treatment. However, some resistant clinical isolates do not present mutations in any genes associated with resistance to a given antibiotic, which suggests that other mechanism(s) are involved in the development of drug resistance, namely the presence of efflux pump systems that extrude the drug to the exterior of the cell, preventing access to its target. Increased efflux activity can occur in response to prolonged exposure to subinhibitory concentrations of anti-TB drugs, a situation that may result from inadequate TB therapy. The inhibition of efflux activity with a non-antibiotic inhibitor may restore activity of an antibiotic subject to efflux and thus provide a way to enhance the activity of current anti-TB drugs. The work described in this thesis foccus on the study of efflux mechanisms in the development of multidrug resistance in M. tuberculosis and how phenotypic resistance, mediated by efflux pumps, correlates with genetic resistance. In order to accomplish this goal, several experimental protocols were developed using biological models such as Escherichia coli, the fast growing mycobacteria Mycobacterium smegmatis, and Mycobacterium avium, before their application to M. tuberculosis. This approach allowed the study of the mechanisms that result in the physiological adaptation of E. coli to subinhibitory concentrations of tetracycline (Chapter II), the development of a fluorometric method that allows the detection and quantification of efflux of ethidium bromide (Chapter III), the characterization of the ethidium bromide transport in M. smegmatis (Chapter IV) and the contribution of efflux activity to macrolide resistance in Mycobacterium avium complex (Chapter V). Finally, the methods developed allowed the study of the role of efflux pumps in M. tuberculosis strains induced to isoniazid resistance (Chapter VI). By this manner, in Chapter II it was possible to observe that the physiological adaptation of E. coli to tetracycline results from an interplay between events at the genetic level and protein folding that decrease permeability of the cell envelope and increase efflux pump activity. Furthermore, Chapter III describes the development of a semi-automated fluorometric method that allowed the correlation of this efflux activity with the transport kinetics of ethidium bromide (a known efflux pump substrate) in E. coli and the identification of efflux inhibitors. Concerning M. smegmatis, we have compared the wild-type M. smegmatis mc2155 with knockout mutants for LfrA and MspA for their ability to transport ethidium bromide. The results presented in Chapter IV showed that MspA, the major porin in M. smegmatis, plays an important role in the entrance of ethidium bromide and antibiotics into the cell and that efflux via the LfrA pump is involved in low-level resistance to these compounds in M. smegmatis. Chapter V describes the study of the contribution of efflux pumps to macrolide resistance in clinical M. avium complex isolates. It was demonstrated that resistance to clarithromycin was significantly reduced in the presence of efflux inhibitors such as thioridazine, chlorpromazine and verapamil. These same inhibitors decreased efflux of ethidium bromide and increased the retention of [14C]-erythromycin in these isolates. Finaly, the methods developed with the experimental models mentioned above allowed the study of the role of efflux pumps on M. tuberculosis strains induced to isoniazid resistance. This is described in Chapter VI of this Thesis, where it is demonstrated that induced resistance to isoniazid does not involve mutations in any of the genes known to be associated with isoniazid resistance, but an efflux system that is sensitive to efflux inhibitors. These inhibitors decreased the efflux of ethidium bromide and also reduced the minimum inhibitory concentration of isoniazid in these strains. Moreover, expression analysis showed overexpression of genes that code for efflux pumps in the induced strains relatively to the non-induced parental strains. In conclusion, the work described in this thesis demonstrates that efflux pumps play an important role in the development of drug resistance, namely in mycobacteria. A strategy to overcome efflux-mediated resistance may consist on the use of compounds that inhibit efflux activity, restoring the activity of antimicrobials that are efflux pump substrates, a useful approach particularly in TB where the most effective treatment regimens are becoming uneffective due to the increase of MDRTB/XDRTB.

A proteomic approach toward the selection of proteins with enhanced intrinsic conformational stability

Journal of Proteome Research (2006)5: 2720-2726

Enterococcus and biocides: mechanisms of tolerance and selection for vancomycin resistance

Dissertation presented to obtain a Doctoral degree in Biology, Instituto de Tecnologia Química e Biológica, Universidade Nova de Lisboa.

Mental health promotion during pregnancy and early childhood : an action- research project in primary health care

ABSTRACT – Background: Primary Health Care (PHC) is usually the first contact with the health system, and health professionals are key mediators for enabling citizens to take care of their health. In Portugal, great improvements have been achieved in the biometric indicators of maternal and child health during the last decades. Nevertheless, scant attention has been paid to the mental health dimension, in spite of the recognition of its importance, being pregnancy and early childhood crucial opportunities in the lifecycle for mental health promotion, especially in the early years of life, with a strong impact in the health of the child. The impact of early attachment between mother and baby on maternal and child health has long been recognized. This attachment can be influenced by some factors, as the mother’s emotional adjustment. Attention to these factors may facilitate implementation of both positive conditions and preventative measures. Family support during the transition to parenthood has been highlighted as an effective measure and PHC professionals are in a privileged position as information sources as well as mediators. Aims: The project we present describes an action-research process developed together among academic researchers and health professionals to embrace these issues. We intend to enable health professionals to support families in the transition to parenthood thereby promoting children’s mental health. Approach: The project is driven by a participatory approach intended to lead to reorganization of health care during pregnancy and early childhood. Effective change happens when those involved are interested and motivated, what makes their participation so important. Reflection about current practices and needs, and knowledge about evidence-based interventions have been guiding the selection of changes to introduce in clinical practice for family support and development of parenthood skills and self-confidence. Development: We summarize the main steps in development: the initial assessment and the picture taken from the community under study; the decision making process; the training programme of PHC professionals in action; the review of the protocols of maternal consultation, home visits and antenatal education; the implementation planning; the plan for evaluation the effectiveness of the changes introduced in the delivery of maternal and child health care units. The already developed work has shown that motivation, leadership and organizational issues are decisive for process development.-------------------------- RESUMO - Os Cuidados de Saúde Primários são habitualmente o primeiro contacto com o sistema de saúde e os profissionais de saúde são mediadores chave na capacitação dos cidadãos para cuidarem da sua saúde. Em Portugal, nas últimas décadas, têm-se alcançado grandes melhorias nos indicadores biométricos de saúde materno-infantil. Contudo, tem-se dedicado pouca atenção à dimensão de saúde mental, apesar do reconhecimento da sua importância. A gravidez e primeira infância têm sido apontadas como uma oportunidade crucial no ciclo de vida para a promoção da saúde mental. É dado especial enfoque aos primeiros tempos de vida, dado o forte impacto na saúde da criança. O impacte da vinculação precoce entre a mãe e o bebé na saúde da mãe e da criança há muito que é reconhecido. Esta vinculação pode ser influenciada por vários factores, nomeadamente pelo ajustamento emocional da mãe. A focalização nestes aspectos pode facilitar a criação de condições favoráveis e a implementação de medidas preventivas. O suporte familiar durante o período de transição para a parentalidade tem sido enfatizado como uma medida eficaz e os Cuidados de Saúde Primários estão numa posição privilegiada como fontes de informação e como mediadores. O projecto que apresentamos descreve um processo de investigação- acção desenvolvido em parceria entre investigadores académicos e profissionais de saúde para abordar os aspectos referidos. Pretende-se capacitar os profissionais de saúde para apoiarem as famílias na transição para a parentalidade, promovendo assim a saúde mental das crianças. O projecto baseia-se numa abordagem participativa, direccionada para a reorganização dos cuidados durante a gravidez e primeiros tempos de vida. A mudança efectiva acontece quando os envolvidos estão interessados e motivados, o que torna a sua participação tão importante. A reflexão acerca das práticas e necessidades actuais e o conhecimento acerca de intervenções baseadas na evidência têm guiado a selecção das alterações a introduzir na prática clínica, no sentido de promover o suporte familiar e o desenvolvimento de competências parentais e auto-confiança. Neste artigo, apresentamos as etapas principais do desenvolvimento do projecto: avaliação inicial da comunidade em estudo; processo de tomada de decisão; programa de formação dos profissionais dos Cuidados de Saúde Primários; revisão dos protocolos da consulta de saúde materna, visita domiciliária e educação pré-natal; planeamento da implementação; plano de avaliação da efectividade das alterações introduzidas na prestação de cuidados. O trabalho já desenvolvido tem mostrado que a motivação, liderança e aspectos

Biogenic amines in wine: gene transcription as a tool for selection of Oenococcus oeni starter strains

Dissertation presented to obtain the Ph.D degree in Biology

Segregated modeling and selection of populations for polyhydroxyalkanoate production by mixed microbial cultures

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

Selection of a co-operation agreement between EMOVE – Innovative Technologies and WavEC – Wave Energy Center

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

Market selection and market entry recommendations for a non-profit organization's first international venture

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

Calibration, selection and mosaicing of SMART-1 AMIE images

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

Intrusion tolerant routing with data consensus in wireless sensor networks

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Production of polyhydroxyalkanoates from cheese whey - pH effect on the acidogenic fermentation stage and nutrient needs of the culture selection stage

Dissertação para obtenção do Grau de Mestre em Biotecnologia

Establishing a cell biology platform: isolation and preservation of human blood products

Dissertação para obtenção do Grau de Mestre em Genética Molecular e Biomedicina