Implementation of membrane processes for improvement of the detection of food contaminants

The EM3E Master is an Education Programme supported by the European Commission, the European Membrane Society (EMS), the European Membrane House (EMH), and a large international network of industrial companies, research centres and universities (http://www.em3e.eu)

Usefulness of zebrafish model to assess glomerular and tubular alterations induced by tenofovir

Tenofovir (TFV) is one of the most used antiretroviral drugs. However, it is associated with tubular damage with mitochondria as a possible target. Tubulopathy precedes glomerular dysfunction, thus classic markers of renal function like the glomerular filtration rate (GFR) do not detect early TFV damage. Prediction and management of drug induced renal injury (DIRI) rely on the mechanisms of the drug insult and in optimal animal models to explore it. Zebrafish (Danio rerio) offers unique advantages for assessing DIRI, since the pronephros is structurally very similar to its human counterpart and is fully developed at 3.5 days postfertilization. The main aim of the present work was to evaluate the effects of TFV, as well as its pro-drug, tenofovir disoproxil fumarate (TDF), on the GFR and in mitochondria morphology in tubular cells of zebrafish larvae. Lethality curves were performed to understand the relationship between drug concentration and lethality. LC10 was selected to explore the renal function using the FITC-inulin assay and to analyze the mitochondrial toxicity by electron microscopy on larvae exposed to TDF, TFV, paracetamol and gentamicin (positive controls) or water (negative control). Lethality curves showed that gentamicin was the most lethal drug, followed by TDF, TFV and paracetamol. Gentamicin and paracetamol decreased the GFR, but no differences were found for either TDF or TFV, when compared to controls (%FITC Control = 33±8; %FITC TDF = 35±10; %FITC TFV = 30±10; %FITC Gentamicin = 46±17; %FITC Paracetamol = 83±14). Tubular mitochondria from treated larvae were notably different from non-treated larvae, showing swelling, irregular shapes, decreased mitochondria network, cristae disruption and loss of matrix granules. These results are in agreement with the effects of these drugs in humans and thus, demonstrate that zebrafish larvae can be a good model to assess the functional and structural damage associated with DIRI.

Harvest control rule vs optimal harvesting of an age-structured population: The case of the Ibero-Atlantic Sardine Fishery

Research Masters

Establishing guidelines for obtaining optimal cell sources to use in tendon tissue engineering strategies

Cell-based approaches in tissue engineering (TE) have been barely explored for the treatment of tendon and ligament (T/L) tissues, requiring the establishment of a widely available cell source with tenogenic potential. As T/L cells are scarce, stem cells may provide a good alternative. Understanding how resident cells behave in vitro, might be useful for recapitulating the tenogenic potential of stem cells for tendon TE applications. Therefore, we propose to isolate and characterize human T/L-derived cells (hTDCs and hLDCs) and compare their regenerative potential with stem cells from adipose tissue (hASCs) and amniotic fluid (hAFSCs)(1). T/L cells were isolated using different procedures and stem cells isolated as described elsewhere(1). Moreover, T/L cells were stimu- lated into the three mesenchymal lineages, using standard differentia- tion media. Cells were characterized for the typical stem cell markers as well as T/L related markers, namely tenascin-C, collagen I and III, decorin and scleraxis, using different complementary techniques such as real time RT-PCR, immunocytochemistry and flow cytometry. No differences were observed between T/L in gene expression and protein deposition. T/L cells were mostly positive for stem ness markers (CD73/CD90/CD105), and have the potential to differentiate towards osteogenesis, chondrogenesis and adipogenesis, demonstrated by the positive staining for AlizarinRed, SafraninO, ToluidineBlue and OilRed. hASCs and hAFSCs exhibit positive expression of all tenogenic mark- ers, although at lower levels than hTDCs and hLDCs. Nevertheless, stem cells availability is key factor in TE strategies, despite that it’s still required optimization to direct their tenogenic phenotype.

An immunity based configuration for multilayer single featured biometric authentication algorithms

Immune systems have been used in the last years to inspire approaches for several computational problems. This paper focus on behavioural biometric authentication algorithms’ accuracy enhancement by using them more than once and with different thresholds in order to first simulate the protection provided by the skin and then look for known outside entities, like lymphocytes do. The paper describes the principles that support the application of this approach to Keystroke Dynamics, an authentication biometric technology that decides on the legitimacy of a user based on his typing pattern captured on he enters the username and/or the password and, as a proof of concept, the accuracy levels of one keystroke dynamics algorithm when applied to five legitimate users of a system both in the traditional and in the immune inspired approaches are calculated and the obtained results are compared.

Towards automated test and validation of SIP solutions

IP networks are currently the major communication infrastructure used by an increasing number of applications and heterogeneous services, including voice services. In this context, the Session Initiation Protocol (SIP) is a signaling protocol widely used for controlling multimedia communication sessions such as voice or video calls over IP networks, thus performing vital functions in an extensive set of public and enter- prise solutions. However, the SIP protocol dissemination also entails some challenges, such as the complexity associated with the testing/validation processes of IMS/SIP networks. As a consequence, manual IMS/SIP testing solutions are inherently costly and time consuming tasks, being crucial to develop automated approaches in this specific area. In this perspective, this article presents an experimental approach for automated testing/validation of SIP scenarios in IMS networks. For that purpose, an automation framework is proposed allowing to replicate the configuration of SIP equipment from the pro- duction network and submit such equipment to a battery of tests in the testing network. The proposed solution allows to drastically reduce the test and validation times when compared with traditional manual approaches, also allowing to enhance testing reliability and coverage. The automation framework comprises of some freely available tools which are conveniently integrated with other specific modules implemented within the context of this work. In order to illustrate the advantages of the proposed automated framework, a real case study taken from a PT Inovação customer is presented comparing the time required to perform a manual SIP testing approach with the one time required when using the proposed auto- mated framework. The presented results clearly corroborate the advantages of using the presented framework.

Towards effective control of P2P traffic aggregates in network infrastructures

Nowadays, many P2P applications proliferate in the Internet. The attractiveness of many of these systems relies on the collaborative approach used to exchange large resources without the dependence and associated constraints of centralized approaches where a single server is responsible to handle all the requests from the clients. As consequence, some P2P systems are also interesting and cost-effective approaches to be adopted by content-providers and other Internet players. However, there are several coexistence problems between P2P applications and In- ternet Service Providers (ISPs) due to the unforeseeable behavior of P2P traffic aggregates in ISP infrastructures. In this context, this work proposes a collaborative P2P/ISP system able to underpin the development of novel Traffic Engi- neering (TE) mechanisms contributing for a better coexistence between P2P applications and ISPs. Using the devised system, two TE methods are described being able to estimate and control the impact of P2P traffic aggregates on the ISP network links. One of the TE methods allows that ISP administrators are able to foresee the expected impact that a given P2P swarm will have in the underlying network infrastructure. The other TE method enables the definition of ISP friendly P2P topologies, where specific network links are protected from P2P traffic. As result, the proposed system and associated mechanisms will contribute for improved ISP resource management tasks and to foster the deployment of innovative ISP-friendly systems.

Automated network resilience optimization using computational intelligence methods

This paper presents an automated optimization framework able to provide network administrators with resilient routing configurations for link-state protocols, such as OSPF or IS-IS. In order to deal with the formulated NP-hard optimization problems, the devised framework is underpinned by the use of computational in- telligence optimization engines, such as Multi-objective Evolutionary Algorithms (MOEAs). With the objective of demonstrating the framework capabilities, two il- lustrative Traffic Engineering methods are described, allowing to attain routing con- figurations robust to changes in the traffic demands and maintaining the network stable even in the presence of link failure events. The presented illustrative results clearly corroborate the usefulness of the proposed automated framework along with the devised optimization methods.

Modeling microbes: New methods for integrated metabolic and regulatory network reconstruction

PhD Thesis in Bioengineering

In silico constraint-based strain optimization methods: the quest for optimal cell factories

Shifting from chemical to biotechnological processes is one of the cornerstones of 21st century industry. The production of a great range of chemicals via biotechnological means is a key challenge on the way toward a bio-based economy. However, this shift is occurring at a pace slower than initially expected. The development of efficient cell factories that allow for competitive production yields is of paramount importance for this leap to happen. Constraint-based models of metabolism, together with in silico strain design algorithms, promise to reveal insights into the best genetic design strategies, a step further toward achieving that goal. In this work, a thorough analysis of the main in silico constraint-based strain design strategies and algorithms is presented, their application in real-world case studies is analyzed, and a path for the future is discussed.

Cost optimal strategies for the renovation of residential neighbourhoods towards energy and emissions neutrality – Rainha Dona Leonor case study

Buildings are one of the major consumers of energy in Europe. This makes them an important target when aiming to reduce the energy consumptions and carbon emissions. The majority of the European building stock has already some decades and so it needs renovation in order to keep its functionality. Taking advantage of these interventions, the energy performance of the buildings may also be improved. In Portugal the renovation techniques, both regarding energy efficiency measures as well as measures for the use of renewable energy sources, are normally planned at the building scale. It is important to explore the possibility of having large scale interventions, has it has been done in other countries, namely at neighbourhood scale with district energy system in order to optimize the results in terms of costs and environmental impact.

Abstract computation in schizophrenia detection through artificial neural network based systems

Schizophrenia stands for a long-lasting state of mental uncertainty that may bring to an end the relation among behavior, thought, and emotion; that is, it may lead to unreliable perception, not suitable actions and feelings, and a sense of mental fragmentation. Indeed, its diagnosis is done over a large period of time; continuos signs of the disturbance persist for at least 6 (six) months. Once detected, the psychiatrist diagnosis is made through the clinical interview and a series of psychic tests, addressed mainly to avoid the diagnosis of other mental states or diseases. Undeniably, the main problem with identifying schizophrenia is the difficulty to distinguish its symptoms from those associated to different untidiness or roles. Therefore, this work will focus on the development of a diagnostic support system, in terms of its knowledge representation and reasoning procedures, based on a blended of Logic Programming and Artificial Neural Networks approaches to computing, taking advantage of a novel approach to knowledge representation and reasoning, which aims to solve the problems associated in the handling (i.e., to stand for and reason) of defective information.

Thrombophilia screening: An artificial neural network approach

Thrombotic disorders have severe consequences for the patients and for the society in general, being one of the main causes of death. These facts reveal that it is extremely important to be preventive; being aware of how probable is to have that kind of syndrome. Indeed, this work will focus on the development of a decision support system that will cater for an individual risk evaluation with respect to the surge of thrombotic complaints. The Knowledge Representation and Reasoning procedures used will be based on an extension to the Logic Programming language, allowing the handling of incomplete and/or default data. The computational framework in place will be centered on Artificial Neural Networks.

Biochemical and physical surface functionalization of polycaprolactone as a key mediator of osteogenic differentiation and vascularized tissue morphogenesis

Tese de Doutoramento em Engenharia de Tecidos, Medicina Regenerativa e Células Estaminais.

Modelos de apoio às decisão na conceção e planeamento de um armazém

Programa Doutoral em Engenharia Industrial e de Sistemas.