Burrows-wheeler transform in secondary memory

Master’s Thesis in Computer Engineering

Sequencing cutting patterns with colored interval graphs

The problem addressed here originates in the industry of flat glass cutting and wood panel sawing, where smaller items are cut from larger items accordingly to predefined cutting patterns. In this type of industry the smaller pieces that are cut from the patterns are piled around the machine in stacks according to the size of the pieces, which are moved to the warehouse only when all items of the same size have been cut. If the cutting machine can process only one pattern at a time, and the workspace is limited, it is desirable to set the sequence in which the cutting patterns are processed in a way to minimize the maximum number of open stacks around the machine. This problem is known in literature as the minimization of open stacks (MOSP). To find the best sequence of the cutting patterns, we propose an integer programming model, based on interval graphs, that searches for an appropriate edge completion of the given graph of the problem, while defining a suitable coloring of its vertices.

Models and tools for value systems analysis in collaborative environments

Dissertation to obtain the degree of Doctor in Electrical and Computer Engineering, specialization of Collaborative Networks

Estimation of infection rate in epidemic models with multiple populations

Dissertação para obtenção do Grau de Mestre em Matemática e Aplicações Especialização em Actuariado, Estatística e Investigação Operacional

An agent-based evolutionary approach for manufacturing system layout design

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

Molecular analysis of the dengue virus type 1 and 2 in Brazil based on sequences of the genomic envelope-nonstructural protein 1 junction region

The genomic sequences of the Envelope-Non-Structural protein 1 junction region (E/NS1) of 84 DEN-1 and 22 DEN-2 isolates from Brazil were determined. Most of these strains were isolated in the period from 1995 to 2001 in endemic and regions of recent dengue transmission in São Paulo State. Sequence data for DEN-1 and DEN-2 utilized in phylogenetic and split decomposition analyses also include sequences deposited in GenBank from different regions of Brazil and of the world. Phylogenetic analyses were done using both maximum likelihood and Bayesian approaches. Results for both DEN-1 and DEN-2 data are ambiguous, and support for most tree bipartitions are generally poor, suggesting that E/NS1 region does not contain enough information for recovering phylogenetic relationships among DEN-1 and DEN-2 sequences used in this study. The network graph generated in the split decomposition analysis of DEN-1 does not show evidence of grouping sequences according to country, region and clades. While the network for DEN-2 also shows ambiguities among DEN-2 sequences, it suggests that Brazilian sequences may belong to distinct subtypes of genotype III.

Towards a Mobile Three-dimensional Modelling System for Underground Structures

Robotica 2012: 12th International Conference on Autonomous Robot Systems and Competitions April 11, 2012, Guimarães, Portugal

Application of Visual-Inertial SLAM for 3D Mapping of Underground Environments

The underground scenarios are one of the most challenging environments for accurate and precise 3d mapping where hostile conditions like absence of Global Positioning Systems, extreme lighting variations and geometrically smooth surfaces may be expected. So far, the state-of-the-art methods in underground modelling remain restricted to environments in which pronounced geometric features are abundant. This limitation is a consequence of the scan matching algorithms used to solve the localization and registration problems. This paper contributes to the expansion of the modelling capabilities to structures characterized by uniform geometry and smooth surfaces, as is the case of road and train tunnels. To achieve that, we combine some state of the art techniques from mobile robotics, and propose a method for 6DOF platform positioning in such scenarios, that is latter used for the environment modelling. A visual monocular Simultaneous Localization and Mapping (MonoSLAM) approach based on the Extended Kalman Filter (EKF), complemented by the introduction of inertial measurements in the prediction step, allows our system to localize himself over long distances, using exclusively sensors carried on board a mobile platform. By feeding the Extended Kalman Filter with inertial data we were able to overcome the major problem related with MonoSLAM implementations, known as scale factor ambiguity. Despite extreme lighting variations, reliable visual features were extracted through the SIFT algorithm, and inserted directly in the EKF mechanism according to the Inverse Depth Parametrization. Through the 1-Point RANSAC (Random Sample Consensus) wrong frame-to-frame feature matches were rejected. The developed method was tested based on a dataset acquired inside a road tunnel and the navigation results compared with a ground truth obtained by post-processing a high grade Inertial Navigation System and L1/L2 RTK-GPS measurements acquired outside the tunnel. Results from the localization strategy are presented and analyzed.

Groundtruth system for underwater benchmarking

Oceans - San Diego, 2013

Multi-robot cooperative stereo for outdoor scenarios

13th International Conference on Autonomous Robot Systems (Robotica), 2013

Método de correspondência para sistemas de visão multi-câmara

Os sistemas de perceção visual são das principais fontes de informação sensorial utilizadas pelos robôs autónomos, para localização e navegação em diferentes meios de operação. O objetivo passa por obter uma grande quantidade de informação sobre o ambiente que a câmara está a visualizar, processar e extrair informação que permita realizar as tarefas de uma forma e ciente. Uma informação em particular que os sistemas de visão podem fornecer, e a informação tridimensional acerca do meio envolvente. Esta informação pode ser adquirida recorrendo a sistemas de visão monoculares ou com múltiplas câmaras. Nestes sistemas a informação tridimensional pode ser obtida recorrendo a técnica de triangulação, tirando partido do conhecimento da posição relativa entre as câmaras. No entanto, para calcular as coordenadas de um ponto tridimensional no referencial da câmara e necessário existir correspondência entre pontos comuns às imagens adquiridas pelo sistema. No caso de más correspondências a informação 3D e obtida de forma incorreta. O problema associado à correspondência de pontos pode ser agravado no caso das câmaras do sistema terem características intrínsecas diferentes nomeadamente: resolução, abertura da lente, distorção. Outros fatores como as orientações e posições das câmaras também podem condicionar a correspondência de pontos. Este trabalho incide sobre problemática de correspondência de pontos existente no processo de cálculo da informação tridimensional. A presente dissertação visa o desenvolvimento de uma abordagem de correspondência de pontos para sistemas de visão no qual é conhecida a posição relativa entre câmaras.

Energy Harvesting for Autonomous Underwater Vehicles

In this study, energy production for autonomous underwater vehicles is investigated. This project is part of a bigger project called TURTLE. The autonomous vehicles perform oceanic researches at seabed for which they are intended to be kept operational underwater for several months. In order to ful l a long-term underwater condition, powerful batteries are combined with \micro- scale" energy production on the spot. This work tends to develop a system that generates power up to a maximum of 30 W. Latter energy harvesting structure consists basically of a turbine combined with a generator and low-power electronics to adjust the achieved voltage to a required battery charger voltage. Every component is examined separately hence an optimum can be de ned for all, and subsequently also an overall optimum. Di erent design parameters as e.g. number of blades, solidity ratio and cross-section area are compared for di erent turbines, in order to see what is the most feasible type. Further, a generator is chosen by studying how ux distributions might be adjusted to low velocities, and how cogging torque can be excluded by adapted designs. Low-power electronics are con gured in order to convert and stabilize heavily varying three-phase voltages to a constant, recti ed voltage which is usable for battery storage. Clearly, di erent component parameters as maximum power and torque are matched here to increase the overall power generation. Furthermore an overall maximum power is set up for achieving a maximum power ow at load side. Due to among others typical low velocities of about 0.1 to 0.5 m/s, and constructing limits of the prototype, the vast range of components is restricted to only a few that could be used. Hence, a helical turbine is combined in a direct drive mode to a coreless-stator axial- ux permanent-magnet generator, from which the output voltage is adjusted subsequently by a recti er, impedance matching unit, upconverter circuit and an overall control unit to regulate di erent component parameters. All these electronics are combined in a closed-loop design to involve positive feedback signals. Furthermore a theoretical con guration for the TURTLE vehicle is described in this work and a solution is proposed that might be implemented, for which several design tests are performable in a future study.

Geomecânica aplicada à estabilidade de explorações mineiras bench and fill: o caso do jazigo de Feitais, Minas de Aljustrel

Este trabalho pretende abordar a importância de um estudo geomecânico no apoio à otimização e estabilidade de explorações subterrâneas por subníveis, com criação de bancadas e posterior enchimento. O presente envolveu um estudo geológico-geotécnico em quinze galerias situadas a muro, teto e corpo da mineralização com o levantamento das características mais relevantes do maciço rochoso para aplicação das classificações geomecânicas, englobando uma amostragem de mais de 1780 descontinuidades, obtendo um modelo cartográfico subterrâneo com um panorama geral da qualidade do maciço rochoso intercetado pelas escavações nas diferentes zonas. Os dados dos levantamentos de campo levaram à criação de uma base de dados com a aplicação das classificações geomecânicas Q-System, RMR e GSI, por galeria e, em seguida, por zona, com proposta de classe de sustimento a aplicar em cada local, pelo ábaco de Barton, em conjunto com a determinação de parâmetros geomecânicos fundamentais ao refinamento do conhecimento geológico-geotécnico das unidades litológicas em estudo. Na parte final, focando a localização da massa mineralizada de Feitais é efetuada uma abordagem relativa à estabilidade das cavidades geradas pelo desmonte em bancada entre subníveis, com respetivo dimensionamento das larguras admissíveis, em condições de segurança, através da relação entre o número de estabilidade e raio hidráulico, pelo método do gráfico de estabilidade. Com esta metodologia de caracterização geológico geotécnica, é pretendido efetuar um ponto de partida à criação de um modelo geomecânico comportamental do jazigo de Feitais, Mina de Aljustrel, contando com um processo inicial de apoio ao planeamento mineiro aplicado ao método de desmonte em bancada e posterior enchimento por subníveis, atuando nos parâmetros de estabilidade e apoio à extração, favorecendo assim a segurança das operações de trabalho em conjunto com um apoio de otimização da extração.

Diffusion characteristics of ethylene glycol in skeletal muscle

Part of the optical clearing study in biological tissues concerns the determination of the diffusion characteristics of water and optical clearing agents in the subject tissue. Such information is sufficient to characterize the time dependence of the optical clearing mechanisms—tissue dehydration and refractive index (RI) matching. We have used a simple method based on collimated optical transmittance measurements made from muscle samples under treatment with aqueous solutions containing different concentrations of ethylene glycol (EG), to determine the diffusion time values of water and EG in skeletal muscle. By representing the estimated mean diffusion time values from each treatment as a function of agent concentration in solution, we could identify the real diffusion times for water and agent. These values allowed for the calculation of the correspondent diffusion coefficients for those fluids. With these results, we have demonstrated that the dehydration mechanism is the one that dominates optical clearing in the first minute of treatment, while the RI matching takes over the optical clearing operations after that and remains for a longer time of treatment up to about 10 min, as we could see for EG and thin tissue samples of 0.5 mm.

The characteristic time of glucose diffusion measured for muscle tissue at optical clearing

The study of agent diffusion in biological tissues is very important to understand and characterize the optical clearing effects and mechanisms involved: tissue dehydration and refractive index matching. From measurements made to study the optical clearing, it is obvious that light scattering is reduced and that the optical properties of the tissue are controlled in the process. On the other hand, optical measurements do not allow direct determination of the diffusion properties of the agent in the tissue and some calculations are necessary to estimate those properties. This fact is imposed by the occurrence of two fluxes at optical clearing: water typically directed out of and agent directed into the tissue. When the water content in the immersion solution is approximately the same as the free water content of the tissue, a balance is established for water and the agent flux dominates. To prove this concept experimentally, we have measured the collimated transmittance of skeletal muscle samples under treatment with aqueous solutions containing different concentrations of glucose. After estimating the mean diffusion time values for each of the treatments we have represented those values as a function of glucose concentration in solution. Such a representation presents a maximum diffusion time for a water content in solution equal to the tissue free water content. Such a maximum represents the real diffusion time of glucose in the muscle and with this value we could calculate the corresponding diffusion coefficient.