QSAR modeling of antitubercular activity of diverse organic compounds

Tuberculosis (TB) is a worldwide infectious disease that has shown over time extremely high mortality levels. The urgent need to develop new antitubercular drugs is due to the increasing rate of appearance of multi-drug resistant strains to the commonly used drugs, and the longer durations of therapy and recovery, particularly in immuno-compromised patients. The major goal of the present study is the exploration of data from different families of compounds through the use of a variety of machine learning techniques so that robust QSAR-based models can be developed to further guide in the quest for new potent anti-TB compounds. Eight QSAR models were built using various types of descriptors (from ADRIANA.Code and Dragon software) with two publicly available structurally diverse data sets, including recent data deposited in PubChem. QSAR methodologies used Random Forests and Associative Neural Networks. Predictions for the external evaluation sets obtained accuracies in the range of 0.76-0.88 (for active/inactive classifications) and Q(2)=0.66-0.89 for regressions. Models developed in this study can be used to estimate the anti-TB activity of drug candidates at early stages of drug development (C) 2011 Elsevier B.V. All rights reserved.

Increase of the delivered energy probability in DES using a fuzzy probabilistic modeling

The paper proposes a methodology to increase the probability of delivering power to any load point by identifying new investments in distribution energy systems. The proposed methodology is based on statistical failure and repair data of distribution components and it uses a fuzzy-probabilistic modeling for the components outage parameters. The fuzzy membership functions of the outage parameters of each component are based on statistical records. A mixed integer nonlinear programming optimization model is developed in order to identify the adequate investments in distribution energy system components which allow increasing the probability of delivering power to any customer in the distribution system at the minimum possible cost for the system operator. To illustrate the application of the proposed methodology, the paper includes a case study that considers a 180 bus distribution network.

Lightweight user modeling – a case study

In the context of previous publications, we propose a new lightweight UM process, intended to work as a tourism recommender system in a commercial environment. The new process tackles issues like cold start, gray sheep and over specialization through a rich user model and the application of a gradual forgetting function to the collected user action history. Also, significant performance improvements were achieved regarding the previously proposed UM process.

Modeling group decision meeting participants with an Agent-based approach

This paper aims to present a multi-agent model for a simulation, whose goal is to help one specific participant of multi-criteria group decision making process.This model has five main intervenient types: the human participant, who is using the simulation and argumentation support system; the participant agents, one associated to the human participant and the others simulating the others human members of the decision meeting group; the directory agent; the proposal agents, representing the different alternatives for a decision (the alternatives are evaluated based on criteria); and the voting agent responsiblefor all voting machanisms.At this stage it is proposed a two phse algorithm. In the first phase each participantagent makes his own evaluation of the proposals under discussion, and the voting agent proposes a simulation of a voting process.In the second phase, after the dissemination of the voting results,each one ofthe partcipan agents will argue to convince the others to choose one of the possible alternatives. The arguments used to convince a specific participant are dependent on agent knowledge about that participant. This two-phase algorithm is applied iteratively.

Modeling Allee Effect from Beta(p, 2) Densities

In this work we develop and investigate generalized populational growth models, adjusted from Beta(p, 2) densities, with Allee effect. The use of a positive parameter leads the presented generalization, which yields some more flexible models with variable extinction rates. An Allee limit is incorporated so that the models under study have strong Allee effect.

Study of the one dimensional and transient bioheat transfer equation: Multi-layer solution development and applications

: In this work we derive an analytical solution given by Bessel series to the transient and one-dimensional (1D) bioheat transfer equation in a multi-layer region with spatially dependent heat sources. Each region represents an independent biological tissue characterized by temperature-invariant physiological parameters and a linearly temperature dependent metabolic heat generation. Moreover, 1D Cartesian, cylindrical or spherical coordinates are used to define the geometry and temperature boundary conditions of first, second and third kinds are assumed at the inner and outer surfaces. We present two examples of clinical applications for the developed solution. In the first one, we investigate two different heat source terms to simulate the heating in a tumor and its surrounding tissue, induced during a magnetic fluid hyperthermia technique used for cancer treatment. To obtain an accurate analytical solution, we determine the error associated with the truncated Bessel series that defines the transient solution. In the second application, we explore the potential of this model to study the effect of different environmental conditions in a multi-layered human head model (brain, bone and scalp). The convective heat transfer effect of a large blood vessel located inside the brain is also investigated. The results are further compared with a numerical solution obtained by the Finite Element Method and computed with COMSOL Multi-physics v4.1 (c). (c) 2013 Elsevier Ltd. All rights reserved.

User modeling and recommendation strategies for tourism

Mestrado em Engenharia Informática

An application of structural equation modeling of test dispositional optimism as mediator or moderator in quality of life in patients with chronic disease

The aim of the present study was to test a hypothetical model to examine if dispositional optimism exerts a moderating or a mediating effect between personality traits and quality of life, in Portuguese patients with chronic diseases. A sample of 540 patients was recruited from central hospitals in various districts of Portugal. All patients completed self-reported questionnaires assessing socio-demographic and clinical variables, personality, dispositional optimism, and quality of life. Structural equation modeling (SEM) was used to analyze the moderating and mediating effects. Results suggest that dispositional optimism exerts a mediator rather than a moderator role between personality traits and quality of life, suggesting that “the expectation that good things will happen” contributes to a better general well-being and better mental functioning.

Monte Carlo modeling and simulations of the High Definition (HD120) micro MLC and validation against measurements for a 6 MV beam

Purpose: The most recent Varian® micro multileaf collimator(MLC), the High Definition (HD120) MLC, was modeled using the BEAMNRCMonte Carlo code. This model was incorporated into a Varian medical linear accelerator, for a 6 MV beam, in static and dynamic mode. The model was validated by comparing simulated profiles with measurements. Methods: The Varian® Trilogy® (2300C/D) accelerator model was accurately implemented using the state-of-the-art Monte Carlo simulation program BEAMNRC and validated against off-axis and depth dose profiles measured using ionization chambers, by adjusting the energy and the full width at half maximum (FWHM) of the initial electron beam. The HD120 MLC was modeled by developing a new BEAMNRC component module (CM), designated HDMLC, adapting the available DYNVMLC CM and incorporating the specific characteristics of this new micro MLC. The leaf dimensions were provided by the manufacturer. The geometry was visualized by tracing particles through the CM and recording their position when a leaf boundary is crossed. The leaf material density and abutting air gap between leaves were adjusted in order to obtain a good agreement between the simulated leakage profiles and EBT2 film measurements performed in a solid water phantom. To validate the HDMLC implementation, additional MLC static patterns were also simulated and compared to additional measurements. Furthermore, the ability to simulate dynamic MLC fields was implemented in the HDMLC CM. The simulation results of these fields were compared with EBT2 film measurements performed in a solid water phantom. Results: Overall, the discrepancies, with and without MLC, between the opened field simulations and the measurements using ionization chambers in a water phantom, for the off-axis profiles are below 2% and in depth-dose profiles are below 2% after the maximum dose depth and below 4% in the build-up region. On the conditions of these simulations, this tungsten-based MLC has a density of 18.7 g cm− 3 and an overall leakage of about 1.1 ± 0.03%. The discrepancies between the film measured and simulated closed and blocked fields are below 2% and 8%, respectively. Other measurements were performed for alternated leaf patterns and the agreement is satisfactory (to within 4%). The dynamic mode for this MLC was implemented and the discrepancies between film measurements and simulations are within 4%. Conclusions: The Varian® Trilogy® (2300 C/D) linear accelerator including the HD120 MLC was successfully modeled and simulated using the Monte CarloBEAMNRC code by developing an independent CM, the HDMLC CM, either in static and dynamic modes.

User modeling In adaptive hypermedia educational systems

This document is a survey in the research area of User Modeling (UM) for the specific field of Adaptive Learning. The aims of this document are: To define what it is a User Model; To present existing and well known User Models; To analyze the existent standards related with UM; To compare existing systems. In the scientific area of User Modeling (UM), numerous research and developed systems already seem to promise good results, but some experimentation and implementation are still necessary to conclude about the utility of the UM. That is, the experimentation and implementation of these systems are still very scarce to determine the utility of some of the referred applications. At present, the Student Modeling research goes in the direction to make possible reuse a student model in different systems. The standards are more and more relevant for this effect, allowing systems communicate and to share data, components and structures, at syntax and semantic level, even if most of them still only allow syntax integration.

Convergência para NZEB de um edifício classificado

Dissertação para obtenção do grau de Mestre em Engenharia Civil na Área de Edificações

Simulação e programação offline de robôs industriais afectos a tarefas de lixagem

Este trabalho teve o intuito de testar a viabilidade da programação offline para tarefas de lixamento na empresa Grohe Portugal. Para tal era necessário perceber o que é a programação offline e para isso foi efectuada uma pesquisa referente a essa temática, onde ficou evidente que a programação offline é em tudo semelhante à programação online, tendo apenas como principal diferença o facto de não usar o robô propriamente dito durante o desenvolvimento do programa. Devido à ausência do robô, a programação offline exige que se conheça detalhadamente a célula de trabalho, bem como todas as entradas e saídas associadas à célula, sendo que o conhecimento das entradas e saídas pode ser contornada carregando um backup do robô ou carregando os módulos de sistema. No entanto os fabricantes habitualmente não fornecem informação detalhada sobre as células de trabalho, o que dificulta o processo de implementação da unidade no modelo 3D para a programação offline. Após este estudo inicial, foi efectuado um estudo das características inerentes a cada uma das células existentes, com o objectivo de se obter uma melhor percepção de toda a envolvente relacionada com as tarefas de lixamento. Ao longo desse estudo efectuaram-se vários testes para validar os diversos programas desenvolvidos, bem como para testar a modelação 3D efectuada. O projecto propriamente dito consistiu no desenvolvimento de programas offline de forma a minimizar o impacto (em especial o tempo de paragem) da programação de novos produtos. Todo o trabalho de programação era até então feito utilizando o robô, o que implicava tempos de paragem que podiam ser superiores a três dias. Com o desenvolvimento dos programas em modo offline conseguiu-se reduzir esse tempo de paragem dos robôs para pouco mais de um turno (8h), existindo apenas a necessidade de efectuar algumas afinações e correcções nos movimentos de entrada, saída e movimentações entre rotinas e unidades, uma vez que estes movimentos são essenciais ao bom acabamento da peça e convém que seja suaves. Para a realização e conclusão deste projecto foram superadas diversas etapas, sendo que as mais relevantes foram: - A correcta modelação 3D da célula, tendo em conta todo o cenário envolvente, para evitar colisões do robô com a célula; - A adaptação da programação offline para uma linguagem mais usual aos afinadores, ou seja, efectuar a programação com targets inline e criar diferentes rotinas para cada uma das partes da peça, facilitando assim a afinação; - A habituação à programação recorrendo apenas ao uso de módulos para transferir os programas para a célula, bem como a utilização de entradas, saídas e algumas rotinas e funcionalidades já existentes.

Neural-network approach to modeling liquid crystals in complex confinement

Finding the structure of a confined liquid crystal is a difficult task since both the density and order parameter profiles are nonuniform. Starting from a microscopic model and density-functional theory, one has to either (i) solve a nonlinear, integral Euler-Lagrange equation, or (ii) perform a direct multidimensional free energy minimization. The traditional implementations of both approaches are computationally expensive and plagued with convergence problems. Here, as an alternative, we introduce an unsupervised variant of the multilayer perceptron (MLP) artificial neural network for minimizing the free energy of a fluid of hard nonspherical particles confined between planar substrates of variable penetrability. We then test our algorithm by comparing its results for the structure (density-orientation profiles) and equilibrium free energy with those obtained by standard iterative solution of the Euler-Lagrange equations and with Monte Carlo simulation results. Very good agreement is found and the MLP method proves competitively fast, flexible, and refinable. Furthermore, it can be readily generalized to the richer experimental patterned-substrate geometries that are now experimentally realizable but very problematic to conventional theoretical treatments.

Biomechanical modeling and simulation of the spider crab (maja brachydactyla)

Uma linha de pesquisa e desenvolvimento na área da robótica, que tem recebido atenção crescente nos últimos anos, é o desenvolvimento de robôs biologicamente inspirados. A ideia é adquirir conhecimento de seres biológicos, cuja evolução ocorreu ao longo de milhões de anos, e aproveitar o conhecimento assim adquirido para implementar a locomoção pelos mesmos métodos (ou pelo menos usar a inspiração biológica) nas máquinas que se constroem. Acredita-se que desta forma é possível desenvolver máquinas com capacidades semelhantes às dos seres biológicos em termos de capacidade e eficiência energética de locomoção. Uma forma de compreender melhor o funcionamento destes sistemas, sem a necessidade de desenvolver protótipos dispendiosos e com longos tempos de desenvolvimento é usar modelos de simulação. Com base nestas ideias, o objectivo deste trabalho passa por efectuar um estudo da biomecânica da santola (Maja brachydactyla), uma espécie de caranguejo comestível pertencente à família Majidae de artrópodes decápodes, usando a biblioteca de ferramentas SimMechanics da aplicação Matlab / Simulink. Esta tese descreve a anatomia e locomoção da santola, a sua modelação biomecânica e a simulação do seu movimento no ambiente Matlab / SimMechanics e SolidWorks.

Three-dimensional modeling of tongue during speech using MRI data

The tongue is the most important and dynamic articulator for speech formation, because of its anatomic aspects (particularly, the large volume of this muscular organ comparatively to the surrounding organs of the vocal tract) and also due to the wide range of movements and flexibility that are involved. In speech communication research, a variety of techniques have been used for measuring the three-dimensional vocal tract shapes. More recently, magnetic resonance imaging (MRI) becomes common; mainly, because this technique allows the collection of a set of static and dynamic images that can represent the entire vocal tract along any orientation. Over the years, different anatomical organs of the vocal tract have been modelled; namely, 2D and 3D tongue models, using parametric or statistical modelling procedures. Our aims are to present and describe some 3D reconstructed models from MRI data, for one subject uttering sustained articulations of some typical Portuguese sounds. Thus, we present a 3D database of the tongue obtained by stack combinations with the subject articulating Portuguese vowels. This 3D knowledge of the speech organs could be very important; especially, for clinical purposes (for example, for the assessment of articulatory impairments followed by tongue surgery in speech rehabilitation), and also for a better understanding of acoustic theory in speech formation.