Network virtualisation from an operator perspective

Network virtualisation is seen as a promising approach to overcome the so-called “Internet impasse” and bring innovation back into the Internet, by allowing easier migration towards novel networking approaches as well as the coexistence of complementary network architectures on a shared infrastructure in a commercial context. Recently, the interest from the operators and mainstream industry in network virtualisation has grown quite significantly, as the potential benefits of virtualisation became clearer, both from an economical and an operational point of view. In the beginning, the concept has been mainly a research topic and has been materialized in small-scale testbeds and research network environments. This PhD Thesis aims to provide the network operator with a set of mechanisms and algorithms capable of managing and controlling virtual networks. To this end, we propose a framework that aims to allocate, monitor and control virtual resources in a centralized and efficient manner. In order to analyse the performance of the framework, we performed the implementation and evaluation on a small-scale testbed. To enable the operator to make an efficient allocation, in real-time, and on-demand, of virtual networks onto the substrate network, it is proposed a heuristic algorithm to perform the virtual network mapping. For the network operator to obtain the highest profit of the physical network, it is also proposed a mathematical formulation that aims to maximize the number of allocated virtual networks onto the physical network. Since the power consumption of the physical network is very significant in the operating costs, it is important to make the allocation of virtual networks in fewer physical resources and onto physical resources already active. To address this challenge, we propose a mathematical formulation that aims to minimize the energy consumption of the physical network without affecting the efficiency of the allocation of virtual networks. To minimize fragmentation of the physical network while increasing the revenue of the operator, it is extended the initial formulation to contemplate the re-optimization of previously mapped virtual networks, so that the operator has a better use of its physical infrastructure. It is also necessary to address the migration of virtual networks, either for reasons of load balancing or for reasons of imminent failure of physical resources, without affecting the proper functioning of the virtual network. To this end, we propose a method based on cloning techniques to perform the migration of virtual networks across the physical infrastructure, transparently, and without affecting the virtual network. In order to assess the resilience of virtual networks to physical network failures, while obtaining the optimal solution for the migration of virtual networks in case of imminent failure of physical resources, the mathematical formulation is extended to minimize the number of nodes migrated and the relocation of virtual links. In comparison with our optimization proposals, we found out that existing heuristics for mapping virtual networks have a poor performance. We also found that it is possible to minimize the energy consumption without penalizing the efficient allocation. By applying the re-optimization on the virtual networks, it has been shown that it is possible to obtain more free resources as well as having the physical resources better balanced. Finally, it was shown that virtual networks are quite resilient to failures on the physical network.

Analysis of the organic matter associated to sea salt : definition of potential molecular markers based on the volatile composition and presence of glycosidic derivatives and polysaccharides

Sea salt is a natural product obtained from the evaporation of seawater in saltpans due to the combined effect of wind and sunlight. Nowadays, there is a growing interest for protection and re-valorisation of saltpans intrinsically associated to the quality of sea salt that can be evaluated by its physico-chemical properties. These man-made systems can be located in different geographical areas presenting different environmental surroundings. During the crystallization process, organic compounds coming from these surroundings can be incorporated into sea salt crystals, influencing their final composition. The organic matter associated to sea salt arises from three main sources: algae, surrounding bacterial community, and anthropogenic activity. Based on the hypothesis that sea salt contains associated organic compounds that can be used as markers of the product, including saltpans surrounding environment, the aim of this PhD thesis was to identify these compounds. With this purpose, this work comprised: 1) a deep characterisation of the volatile composition of sea salt by headspace solid phase microextraction combined with comprehensive two-dimensional gas chromatography time-of-flight mass spectrometry (HS-SPME/GCGC–ToFMS) methodology, in search of potential sea salt volatile markers; 2) the development of a methodology to isolate the polymeric material potentially present in sea salt, in amounts that allow its characterisation in terms of polysaccharides and protein; and 3) to explore the possible presence of triacylglycerides. The high chromatographic resolution and sensitivity of GC×GC–ToFMS enabled the separation and identification of a higher number of volatile compounds from sea salt, about three folds, compared to unidimentional chromatography (GC–qMS). The chromatographic contour plots obtained revealed the complexity of marine salt volatile composition and confirmed the relevance of GC×GC–ToFMS for this type of analysis. The structured bidimentional chromatographic profile arising from 1D volatility and 2D polarity was demonstrated, allowing more reliable identifications. Results obtained for analysis of salt from two locations in Aveiro and harvested over three years suggest the loss of volatile compounds along the time of storage of the salt. From Atlantic Ocean salts of seven different geographical origins, all produced in 2007, it was possible to identify a sub-set of ten compounds present in all salts, namely 6-methyl-5-hepten-2-one, 2,2,6-trimethylcyclohexanone, isophorone, ketoisophorone, β-ionone-5,6-epoxide, dihydroactinidiolide, 6,10,14-trimethyl-2-pentadecanone, 3-hydroxy-2,4,4-trimethylpentyl 2-methylpropanoate, 2,4,4-trimethylpentane-1,3-diyl bis(2-methylpropanoate), and 2-ethyl-1-hexanol. These ten compounds were considered potential volatile markers of sea salt. Seven of these compounds are carotenoid-derived compounds, and the other three may result from the integration of compounds from anthropogenic activity as metabolites of marine organisms. The present PhD work also allowed the isolation and characterisation, for the first time, of polymeric material from sea salt, using 16 Atlantic Ocean salts. A dialysis-based methodology was developed to isolate the polymeric material from sea salt in amounts that allowed its characterisation. The median content of polymeric material isolated from the 16 salts was 144 mg per kg of salt, e.g. 0.014% (w/w). Mid-infrared spectroscopy and thermogravimetry revealed the main occurrence of sulfated polysaccharides, as well as the presence of protein in the polymeric material from sea salt. Sea salt polysaccharides were found to be rich in uronic acid residues (21 mol%), glucose (18), galactose (16), and fucose (13). Sulfate content represented a median of 45 mol%, being the median content of sulfated polysaccharides 461 mg/g of polymeric material, which accounted for 66 mg/kg of dry salt. Glycosidic linkage composition indicates that the main sugar residues that could carry one or more sulfate groups were identified as fucose and galactose. This fact allowed to infer that the polysaccharides from sea salt arise mainly from algae, due to their abundance and composition. The amino acid profile of the polymeric material from the 16 Atlantic Ocean salts showed as main residues, as medians, alanine (25 mol%), leucine (14), and valine (14), which are hydrophobic, being the median protein content 35 mg/g, i.e. 4,9 mg per kg of dry salt. Beside the occurrence of hydrophobic volatile compounds in sea salt, hydrophobic non-volatile compounds were also detected. Triacylglycerides were obtained from sea salt by soxhlet extraction with n-hexane. Fatty acid composition revealed palmitic acid as the major residue (43 mol%), followed by stearic (13), linolenic (13), oleic (12), and linoleic (9). Sea salt triacylglycerides median content was 1.5 mg per kg of dry salt. Both protein and triacylglycerides seem to arise from macro and microalgae, phytoplankton and cyanobacteria, due to their abundance and composition. Despite the variability resulting from saltpans surrounding environment, this PhD thesis allowed the identification of a sea salt characteristic organic compounds profile based on volatile compounds, polysaccharides, protein, and triacylglycerides.

Perception and software architecture for mobile robotics

When developing software for autonomous mobile robots, one has to inevitably tackle some kind of perception. Moreover, when dealing with agents that possess some level of reasoning for executing their actions, there is the need to model the environment and the robot internal state in a way that it represents the scenario in which the robot operates. Inserted in the ATRI group, part of the IEETA research unit at Aveiro University, this work uses two of the projects of the group as test bed, particularly in the scenario of robotic soccer with real robots. With the main objective of developing algorithms for sensor and information fusion that could be used e ectively on these teams, several state of the art approaches were studied, implemented and adapted to each of the robot types. Within the MSL RoboCup team CAMBADA, the main focus was the perception of ball and obstacles, with the creation of models capable of providing extended information so that the reasoning of the robot can be ever more e ective. To achieve it, several methodologies were analyzed, implemented, compared and improved. Concerning the ball, an analysis of ltering methodologies for stabilization of its position and estimation of its velocity was performed. Also, with the goal keeper in mind, work has been done to provide it with information of aerial balls. As for obstacles, a new de nition of the way they are perceived by the vision and the type of information provided was created, as well as a methodology for identifying which of the obstacles are team mates. Also, a tracking algorithm was developed, which ultimately assigned each of the obstacles a unique identi er. Associated with the improvement of the obstacles perception, a new algorithm of estimating reactive obstacle avoidance was created. In the context of the SPL RoboCup team Portuguese Team, besides the inevitable adaptation of many of the algorithms already developed for sensor and information fusion and considering that it was recently created, the objective was to create a sustainable software architecture that could be the base for future modular development. The software architecture created is based on a series of di erent processes and the means of communication among them. All processes were created or adapted for the new architecture and a base set of roles and behaviors was de ned during this work to achieve a base functional framework. In terms of perception, the main focus was to de ne a projection model and camera pose extraction that could provide information in metric coordinates. The second main objective was to adapt the CAMBADA localization algorithm to work on the NAO robots, considering all the limitations it presents when comparing to the MSL team, especially in terms of computational resources. A set of support tools were developed or improved in order to support the test and development in both teams. In general, the work developed during this thesis improved the performance of the teams during play and also the e ectiveness of the developers team when in development and test phases.

Microbe-mediated recovery of salt marshes contaminated with oil hydrocarbons

Salt marshes are highly productive intertidal habitats that serve as nursery grounds for many commercially and economically important species. Because of their location and physical and biological characteristics, salt marshes are considered to be particularly vulnerable to anthropogenic inputs of oil hydrocarbons. Sediment contamination with oil is especially dangerous for salt marsh vegetation, since low molecular weight aromatic hydrocarbons can affect plants at all stages of development. However, the use of vegetation for bioremediation (phytoremediation), by removal or sequestration of contaminants, has been intensively studied. Phytoremediation is an efficient, inexpensive and environmental friendly approach for the removal of aromatic hydrocarbons, through direct incorporation by the plant and by the intervention of degrading microbial populations in the rhizosphere (microbe-assisted phytoremediation). Rhizosphere microbial communities are enriched in important catabolic genotypes for degradation of oil hydrocarbons (OH) which may have a potential for detoxification of the sediment surrounding the roots. In addition, since rhizosphere bacterial populations may also internalize into plant tissues (endophytes), rhizocompetent AH degrading populations may be important for in planta AH degradation and detoxification. The present study involved field work and microcosms experiments aiming the characterization of relevant plant-microbe interactions in oilimpacted salt marshes and the understanding of the effect of rhizosphere and endosphere bacteria in the role of salt marsh plants as potential phytoremediation agents. In the field approach, molecular tools were used to assess how plant species- and OH pollution affect sediment bacterial composition [bulk sediment and sediment surrounding the roots (rhizosphere) of Halimione portulacoides and Sarcocornia perennis subsp. perennis] in a temperate estuary (Ria de Aveiro, Portugal) chronically exposed to OH pollution. In addition, the 16S rRNA gene sequences retrieved in this study were used to generate in silico metagenomes and to evaluate the distribution of potential bacterial traits in different microhabitats. Moreover, a combination of culture-dependent and -independent approaches was used to investigate the effect of oil hydrocarbons contamination on the structure and function of endophytic bacterial communities of salt marsh plants.Root systems of H. portulacoides and S. perennis subsp. perennis appear to be able to exert a strong influence on bacterial composition and in silico metagenome analysis showed enrichment of genes involved in the process of polycyclic aromatic hydrocarbon (PAH) degradation in the rhizosphere of halophyte plants. The culturable fraction of endophytic degraders was essentially closely related to known OH-degrading Pseudomonas species and endophytic communities revealed sitespecific effects related to the level of OH contamination in the sediment. In order to determine the effects of oil contamination on plant condition and on the responses in terms of structure and function of the bacterial community associated with plant roots (rhizosphere, endosphere), a microcosms approach was set up. The salt marsh plant Halimione portulacoides was inoculated with a previous isolated Pseudomonas sp. endophytic degrader and the 2-methylnaphthalene was used as model PAH contaminant. The results showed that H. portulacoides health and growth were not affected by the contamination with the tested concentration. Moreover, the decrease of 2-methylnaphthalene at the end of experiment, can suggest that H. portulacoides can be considered as a potential plant for future uses in phytoremedition approaches of contaminated salt marsh. The acceleration of hydrocarbon degradation by inoculation of the plants with the hydrocarbon-degrading Pseudomonas sp. could not, however, be demonstrated, although the effects of inoculation on the structure of the endophytic community observed at the end of the experiment indicate that the strain may be an efficient colonizer of H. portulacoides roots. The results obtained in this work suggest that H. portulacoides tolerates moderate concentrations of 2-methylnaphthalene and can be regarded as a promising agent for phytoremedition approaches in salt marshes contaminated with oil hydrocarbons. Plant/microbe interactions may have an important role in the degradation process, as plants support a diverse endophytic bacterial community, enriched in genetic factors (genes and plasmids) for hydrocarbon degradation.

Development of polymeric materials to inhibit bacterial quorum sensing

Bacterial infections are an increasing problem for human health. In fact, an increasing number of infections are caused by bacteria that are resistant to most antibiotics and their combinations. Therefore, the scientific community is currently searching for new solutions to fight bacteria and infectious diseases, without promoting antimicrobial resistance. One of the most promising strategies is the disruption or attenuation of bacterial Quorum Sensing (QS), a refined system that bacteria use to communicate. In a QS event, bacteria produce and release specific small chemicals, signal molecules - autoinducers (AIs) - into the environment. At the same time that bacterial population grows, the concentration of AIs in the bacterial environment increases. When a threshold concentration of AIs is reached, bacterial cells respond to it by altering their gene expression profile. AIs regulate gene expression as a function of cell population density. Phenotypes mediated by QS (QSphenotypes) include virulence factors, toxin production, antibiotic resistance and biofilm formation. In this work, two polymeric materials (linear polymers and molecularly imprinted nanoparticles) were developed and their ability to attenuate QS was evaluated. Both types of polymers should to be able to adsorb bacterial signal molecules, limiting their availability in the extracellular environment, with expected disruption of QS. Linear polymers were composed by one of two monomers (itaconic acid and methacrylic acid), which are known to possess strong interactions with the bacterial signal molecules. Molecularly imprinted polymer nanoparticles (MIP NPs) are particles with recognition capabilities for the analyte of interest. This ability is attained by including the target analyte at the synthesis stage. Vibrio fischeri and Aeromonas hydrophila were used as model species for the study. Both the linear polymers and MIP NPs, tested free in solutions and coated to surfaces, showed ability to disrupt QS by decreasing bioluminescence of V. fischeri and biofilm formation of A. hydrophila. No significant effect on bacterial growth was detected. The cytotoxicity of the two types of polymers to a fibroblast-like cell line (Vero cells) was also tested in order to evaluate their safety. The results showed that both the linear polymers and MIP NPs were not cytotoxic in the testing conditions. In conclusion, the results reported in this thesis, show that the polymers developed are a promising strategy to disrupt QS and reduce bacterial infection and resistance. In addition, due to their low toxicity, solubility and easy integration by surface coating, the polymers have potential for applications in scenarios where bacterial infection is a problem: medicine, pharmaceutical, food industry and in agriculture or aquaculture.

Development of infrared spectroscopy for assessing bacterial quality in foods

Rapid and specific detection of foodborne bacteria that can cause food spoilage or illness associated to its consumption is an increasingly important task in food industry. Bacterial detection, identification, and classification are generally performed using traditional methods based on biochemical or serological tests and the molecular methods based on DNA or RNA fingerprints. However, these methodologies are expensive, time consuming and laborious. Infrared spectroscopy is a reliable, rapid, and economic technique which could be explored as a tool for bacterial analysis in the food industry. In this thesis it was evaluated the potential of IR spectroscopy to study the bacterial quality of foods. In Chapter 2, it was developed a calibration model that successfully allowed to predict the bacterial concentration of naturally contaminated cooked ham samples kept at refrigeration temperature during 8 days. In this part, it was developed the methodology that allowed the best reproducibility of spectra from bacteria colonies with minimal sample preparation, which was used in the subsequent work. Several attempts trying different resolutions and number of scans in the IR were made. A spectral resolution of 4 cm-1, with 32 scans were the settings that allowed the best results. Subsequently, in Chapter 3, it was made an attempt to identify 22 different foodborne bacterial genera/species using IR spectroscopy coupled with multivariate analysis. The principal component analysis, used as an exploratory technique, allowed to form distinct groups, each one corresponding to a different genus, in most of the cases. Then, a hierarchical cluster analysis was performed to further analyse the group formation and the possibility of distinction between species of the same bacterial genus. It was observed that IR spectroscopy not only is suitable to the distinction of the different genera, but also to differentiate species of the same genus, with the simultaneous use of principal component analysis and cluster analysis techniques. The utilization of IR spectroscopy and multivariate statistical analysis were also investigated in Chapter 4, in order to confirm the presence of Listeria monocytogenes and Salmonella spp. isolated from contaminated foods, after growth in selective medium. This would allow to substitute the traditional biochemical and serological methods that are used to confirm these pathogens and that delay the obtainment of the results up to 2 days. The obtained results allowed the distinction of 3 different Listeria species and the distinction of Salmonella spp. from other bacteria that can be mistaken with them. Finally, in chapter 5, high pressure processing, an emerging methodology that permits to produce microbiologically safe foods and extend their shelf-life, was applied to 12 foodborne bacteria to determine their resistance and the effects of pressure in cells. A treatment of 300 MPa, during 15 minutes at room temperature was applied. Gram-negative bacteria were inactivated to undetectable levels and Gram-positive showed different resistances. Bacillus cereus and Staphylococcus aureus decreased only 2 logs and Listeria innocua decreased about 5 logs. IR spectroscopy was performed in bacterial colonies before and after HPP in order to investigate the alterations of the cellular compounds. It was found that high pressure alters bands assigned to some cellular components as proteins, lipids, oligopolysaccharides, phosphate groups from the cell wall and nucleic acids, suggesting disruption of the cell envelopes. In this work, bacterial quantification and classification, as well as assessment of cellular compounds modification with high pressure processing were successfully performed. Taking this into account, it was showed that IR spectroscopy is a very promising technique to analyse bacteria in a simple and inexpensive manner.

Effect of photodynamic therapy on the virulence factors of Staphylococcus aureus

Staphylococcus aureus are Gram-positive bacteria who integrate the human microbiota. Nevertheless, these bacteria can be pathogenic to the humans. Due to the increasing occurrence of antibiotic-resistant S. aureus new approaches to control this pathogen are necessary. The antimicrobial photodynamic inactivation process (PDI) is based in the combined use of a light source, an oxidizing agent like oxygen and an intermediary agent (a photosensitizer). These three components interact to form cytotoxic reactive oxygen species that irreversibly damage vital constituents of the microbial cells and ultimately lead to cell death. In fact, PDI is being shown to be a promising alternative to the antibiotic approach in the inactivation of pathogenic microorganisms. However, information on effects of photosensitization on particular virulence factors is strikingly scarce. The objective of this work was to evaluate the effect of PDI on virulence factors of S. aureus. For this, as photosensitizer the 5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin tetra-iodide (Tetra-Py+-Me) and six strains of S. aureus (one reference strain, one strain with 1 enterotoxin, two strains with 3 enterotoxins and two strains resistant to methicillin, MRSA – one with 5 enterotoxins and the other without enterotoxins) were used. The effect of photosensitization on catalase activity, beta hemolysis, lipases, thermonuclease, enterotoxins, coagulase production and resistance to methicillin was assessed. The results indicate that the expression of some virulence factors in the cells subjected to this therapy is affected. Additionally the susceptibility of the strains to PDI did not decrease upon successive treatments.

Genetic programming and bacterial algorithm for neural networks and fuzzy systems design

In the field of control systems it is common to use techniques based on model adaptation to carry out control for plants for which mathematical analysis may be intricate. Increasing interest in biologically inspired learning algorithms for control techniques such as Artificial Neural Networks and Fuzzy Systems is in progress. In this line, this paper gives a perspective on the quality of results given by two different biologically connected learning algorithms for the design of B-spline neural networks (BNN) and fuzzy systems (FS). One approach used is the Genetic Programming (GP) for BNN design and the other is the Bacterial Evolutionary Algorithm (BEA) applied for fuzzy rule extraction. Also, the facility to incorporate a multi-objective approach to the GP algorithm is outlined, enabling the designer to obtain models more adequate for their intended use.

A hybrid training method for B-spline neural networks

Current and past research has brought up new views related to the optimization of neural networks. For a fixed structure, second order methods are seen as the most promising. From previous works we have shown how second order methods are of easy applicability to a neural network. Namely, we have proved how the Levenberg-Marquard possesses not only better convergence but how it can assure the convergence to a local minima. However, as any gradient-based method, the results obtained depend on the startup point. In this work, a reformulated Evolutionary algorithm - the Bacterial Programming for Levenberg-Marquardt is proposed, as an heuristic which can be used to determine the most suitable starting points, therefore achieving, in most cases, the global optimum.

B-spline and neuro-fuzzy models design with function and derivative equalities

The design of neuro-fuzzy models is still a complex problem, as it involves not only the determination of the model parameters, but also its structure. Of special importance is the incorporation of a priori information in the design process. In this paper two known design algorithms for B-spline models will be updated to account for function and derivatives equality restrictions, which are important when the neural model is used for performing single or multi-objective optimization on-line.

A criança, a publicidade e as práticas alimentares: uma investigação exploratória

Dissertação mest., Ciências da educação, Universidade do Algarve, 2007

A biotecnologia no ensino das ciências do 3º ciclo: desenvolvimento de experiências didácticas utilizando a acção de biocatalisadores imobilizados

Dissertação mest., Biologia e Geologia, Universidade do Algarve, 2007

Paralelização automática de algoritmos matriciais

Tese de dout., Engenharia Electrónica e Computação, Faculdade de Ciências e Tecnologia, Univ. do Algarve, 2003

Variabilidade genómica de Citrus tristeza virus e transformação genética de Citrus aurantium L. com vista à obtenção de resistência

Tese de dout., Biologia, Faculdade de Engenharia de Recursos Naturais, Univ. do Algarve, 2003

Análise das necessidades de formação dos docentes da ESDMI na área das TIC

Dissertação de mest., Ciências da Educação (Educação e Formação de Adultos), Faculdade de Ciências Humanas e Sociais, Univ. do Algarve, 2010