Diffusional kurtosis imaging using a fast heuristic constrained linear least squares algorithm: a plugin for OsiriX

Diffusion Kurtosis Imaging (DKI) is a fairly new magnetic resonance imag-ing (MRI) technique that tackles the non-gaussian motion of water in biological tissues by taking into account the restrictions imposed by tissue microstructure, which are not considered in Diffusion Tensor Imaging (DTI), where the water diffusion is considered purely gaussian. As a result DKI provides more accurate information on biological structures and is able to detect important abnormalities which are not visible in standard DTI analysis. This work regards the development of a tool for DKI computation to be implemented as an OsiriX plugin. Thus, as OsiriX runs under Mac OS X, the pro-gram is written in Objective-C and also makes use of Apple’s Cocoa framework. The whole program is developed in the Xcode integrated development environ-ment (IDE). The plugin implements a fast heuristic constrained linear least squares al-gorithm (CLLS-H) for estimating the diffusion and kurtosis tensors, and offers the user the possibility to choose which maps are to be generated for not only standard DTI quantities such as Mean Diffusion (MD), Radial Diffusion (RD), Axial Diffusion (AD) and Fractional Anisotropy (FA), but also DKI metrics, Mean Kurtosis (MK), Radial Kurtosis (RK) and Axial Kurtosis (AK).The plugin was subjected to both a qualitative and a semi-quantitative analysis which yielded convincing results. A more accurate validation pro-cess is still being developed, after which, and with some few minor adjust-ments the plugin shall become a valid option for DKI computation

Experimental design methodologies for the identification of Michaelis-Menten type kinetics

The main objective of this work was to investigate the application of experimental design techniques for the identification of Michaelis-Menten kinetic parameters. More specifically, this study attempts to elucidate the relative advantages/disadvantages of employing complex experimental design techniques in relation to equidistant sampling when applied to different reactor operation modes. All studies were supported by simulation data of a generic enzymatic process that obeys to the Michaelis-Menten kinetic equation. Different aspects were investigated, such as the influence of the reactor operation mode (batch, fed-batch with pulse wise feeding and fed-batch with continuous feeding) and the experimental design optimality criteria on the effectiveness of kinetic parameters identification. The following experimental design optimality criteria were investigated: 1) minimization of the sum of the diagonal of the Fisher information matrix (FIM) inverse (A-criterion), 2) maximization of the determinant of the FIM (D-criterion), 3) maximization of the smallest eigenvalue of the FIM (E-criterion) and 4) minimization of the quotient between the largest and the smallest eigenvalue (modified E-criterion). The comparison and assessment of the different methodologies was made on the basis of the Cramér-Rao lower bounds (CRLB) error in respect to the parameters vmax and Km of the Michaelis-Menten kinetic equation. In what concerns the reactor operation mode, it was concluded that fed-batch (pulses) is better than batch operation for parameter identification. When the former operation mode is adopted, the vmax CRLB error is lowered by 18.6 % while the Km CRLB error is lowered by 26.4 % when compared to the batch operation mode. Regarding the optimality criteria, the best method was the A-criterion, with an average vmax CRLB of 6.34 % and 5.27 %, for batch and fed-batch (pulses), respectively, while presenting a Km’s CRLB of 25.1 % and 18.1 %, for batch and fed-batch (pulses), respectively. As a general conclusion of the present study, it can be stated that experimental design is justified if the starting parameters CRLB errors are inferior to 19.5 % (vmax) and 45% (Km), for batch processes, and inferior to 42 % and to 50% for fed-batch (pulses) process. Otherwise equidistant sampling is a more rational decision. This conclusion clearly supports that, for fed-batch operation, the use of experimental design is likely to largely improve the identification of Michaelis-Menten kinetic parameters.

Auxiliary mechanisms for telerobotics

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

Segmentation of striatal brain structures from high resolution pet images

Dissertation presented at the Faculty of Science and Technology of the New University of Lisbon in fulfillment of the requirements for the Masters degree in Electrical Engineering and Computers

Design of New Materials for Passive Vibration Control

The objective of this contribution is to extend the models of cellular/composite material design to nonlinear material behaviour and apply them for design of materials for passive vibration control. As a first step a computational tool allowing determination of optimised one-dimensional isolator behaviour was developed. This model can serve as a representation for idealised macroscopic behaviour. Optimal isolator behaviour to a given set of loads is obtained by generic probabilistic metaalgorithm, simulated annealing. Cost functional involves minimization of maximum response amplitude in a set of predefined time intervals and maximization of total energy absorbed in the first loop. Dependence of the global optimum on several combinations of leading parameters of the simulated annealing procedure, like neighbourhood definition and annealing schedule, is also studied and analyzed. Obtained results facilitate the design of elastomeric cellular materials with improved behaviour in terms of dynamic stiffness for passive vibration control.

Creation and extension of ontologies for describing communications in the context of organizations

Thesis submitted to Faculdade de Ciências e Tecnologia of the Universidade Nova de Lisboa, in partial fulfillment of the requirements for the degree of Master in Computer Science

Iberian peninsula ecosystem carbon fluxes: a model-data integration study

Dissertação apresentada para obtenção do Grau de Doutor em Engenharia do Ambiente pela Universidade Nova de Lisboa,Faculdade de Ciências e Tecnologia

Tectónica da cadeia da Arrábida

Geociências, Museu Nac. Hist. Nat. Univ. Lisboa, nº 2, 35-84

Every normal logic program has a 2-valued semantics: theory, extensions, applications, implementations

Trabalho apresentado no âmbito do Doutoramento em Informática, como requisito parcial para obtenção do grau de Doutor em Informática

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.

Design of New Materials for Passive Vibration Control

The aim of this contribution is to extend the techniques of composite materials design to non-linear material behaviour and apply it for design of new materials for passive vibration control. As a first step a computational tool allowing determination of macroscopic optimized one-dimensional isolator behaviour was developed. Voigt, Maxwell, standard and more complex material models can be implemented. Objective function considers minimization of the initial reaction and/or displacement peak as well as minimization of the steady-state amplitude of reaction and/or displacement. The complex stiffness approach is used to formulate the governing equations in an efficient way. Material stiffness parameters are assumed as non-linear functions of the displacement. The numerical solution is performed in the complex space. The steady-state solution in the complex space is obtained by an iterative process based on the shooting method which imposes the conditions of periodicity with respect to the known value of the period. Extension of the shooting method to the complex space is presented and verified. Non-linear behaviour of material parameters is then optimized by generic probabilistic meta-algorithm, simulated annealing. Dependence of the global optimum on several combinations of leading parameters of the simulated annealing procedure, like neighbourhood definition and annealing schedule, is also studied and analyzed. Procedure is programmed in MATLAB environment.

Risk-based decision support system for life cycle management of industrials plants

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

Linear amplification with multiple nonlinear devices

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

Design and implementation of 3D buildings integration for a Webgl-Based Virtual Globe: a case study of Valencian Cadastre and Fide Building Mode

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

Structure-function relationships in a glycosyltransferase, a phosphatase and an oxidoreductase

Dissertation presented to obtain the Ph.D degree in Biochemistry