Complex Dynamics of defective interfering baculoviruses during serial passage in insect cells

Defective interfering (DI) viruses are thought to cause oscillations in virus levels, known as the ‘Von Magnus effect’. Interference by DI viruses has been proposed to underlie these dynamics, although experimental tests of this idea have not been forthcoming. For the baculoviruses, insect viruses commonly used for the expression of heterologous proteins in insect cells, the molecular mechanisms underlying DI generation have been investigated. However, the dynamics of baculovirus populations harboring DIs have not been studied in detail. In order to address this issue, we used quantitative real-time PCR to determine the levels of helper and DI viruses during 50 serial passages of Autographa californica multiple nucleopolyhedrovirus (AcMNPV) in Sf21 cells. Unexpectedly, the helper and DI viruses changed levels largely in phase, and oscillations were highly irregular, suggesting the presence of chaos. We therefore developed a simple mathematical model of baculovirus-DI dynamics. This theoretical model reproduced patterns qualitatively similar to the experimental data. Although we cannot exclude that experimental variation (noise) plays an important role in generating the observed patterns, the presence of chaos in the model dynamics was confirmed with the computation of the maximal Lyapunov exponent, and a Ruelle-Takens-Newhouse route to chaos was identified at decreasing production of DI viruses, using mutation as a control parameter. Our results contribute to a better understanding of the dynamics of DI baculoviruses, and suggest that changes in virus levels over passages may exhibit chaos.

Complex dynamics in the trajectory control of redundant manipulators

Redundant manipulators allow the trajectory optimization, the obstacle avoidance, and the resolution of singularities. For this type of manipulators, the kinematic control algorithms adopt generalized inverse matrices that may lead to unpredictable responses. Motivated by these problems this paper studies the complexity revealed by the trajectory planning scheme when controlling redundant manipulators. The results reveal fundamental properties of the chaotic phenomena and give a deeper insight towards the development of superior trajectory control algorithms.

Discretization of complex-order algorithms for control applications

In this article we describe several methods for the discretization of the differintegral operator sa, where α = u + jv is a complex value. The concept of the conjugated-order differintegral is also introduced, which enables the use of complex-order differintegrals while still producing real-valued time responses and transfer functions. The performance of the resulting approximations is analysed in both the time and frequency domains. Several results are presented that demonstrate its utility in control system design.

Complex-order dynamics in hexapod locomotion

This paper studies the dynamics of foot–ground interaction in hexapod locomotion systems. For that objective the robot motion is characterized in terms of several locomotion variables and the ground is modelled through a non-linear spring-dashpot system, with parameters based on the studies of soil mechanics. Moreover, it is adopted an algorithm with foot-force feedback to control the robot locomotion. A set of model-based experiments reveals the influence of the locomotion velocity on the foot–ground transfer function, which presents complex-order dynamics.

Vision based obstacle detection for all-terrain robots

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

Sistemas de prevenção de cuidados de saúde

A tomada de decisão na saúde pode-se tornar um processo complexo e moroso. A complexidade associada ao processo de decisão na saúde advém da diversidade de opções clinicamente razoáveis, ou seja, nenhuma opção se sobrepõem _a outra, visto que cada uma possui os seus riscos e benefícios, que são normalmente interpretados de modo diferente entre os indivíduos. Desta forma, cabe ao paciente e _a sua equipa médica optarem pela opção que melhor se enquadra na situação clínica do paciente Para tornar este processo menos complexo, cada vez mais se utiliza as chamadas "ferramentas de decisão", que se caraterizam por fornecer informação sobre as diferentes opções clínicas, traduzindo-se numa diminuição da dificuldade da tomada de decisão. De uma forma geral, as ferramentas de decisão são desenvolvidas com o intuito de facilitar a tomada de decisão, através do aumento do conhecimento científico sobre um determinado problema (tomada de decisão informada) e uma mudança de atitude do paciente face aos seus cuidados de saúde. Na realização da presente dissertação foi desenvolvido um sistema de informação na web, que engloba informação relativa ao rastreio do cancro da próstata. Este sistema também surge acoplado a um conjunto de componentes de decisão, que têm como objetivo auxiliar os indivíduos no processo de decisão para a realização do rastreio do cancro da próstata, assim como a prevenção de doenças relacionadas com a próstata. A implementação desta aplicação web teve como base as necessidades do indivíduo, ou seja informações clínicas sobre possíveis riscos e benefícios associados ao rastreio, assim como fornecer uma maior interatividade com o utilizador. A primeira versão da aplicação já foi testada e avaliada através da participação de um conjunto de indivíduos que compõem o público-alvo para este tipo de aplicações. Os resultados obtidos permitiram concluir que os requisitos definidos para esta aplicação, permitem o aumento do conhecimento do indivíduo e o auxílio na tomada de decisão para a realização do rastreio do cancro da próstata.

Afetação de recursos em sistemas de produção

O problema do escalonamento, por ser um dos factores fundamentais na tomada de decisão para uma boa gestão das operações, tem sido alvo de um amplo estudo, tanto na sua componente teórica como na sua componente prática. A importância de um escalonamento correto das operações é preponderante, quando as pequenas diferenças, em termos de tempos de produção, podem ter um grande impacto na competitividade da organização. Em muitas unidades produtivas, existem máquinas capazes de realizar as mesmas operações com diferentes desempenhos. Isto pode dever-se à necessidade de flexibilizar os recursos ou mesmo a uma atualização da capacidade produtiva. Embora os problemas de máquinas diferentes em paralelo tenham sido alvo de um vasto estudo, muitos deles não são passíveis de ser resolvidos através de métodos exatos. O problema de minimização do makespan (Rm||Cmax), é NP-hard, sendo habitualmente abordado através de heurísticas. Entre as heurísticas utilizadas em problemas de minimização do makespan em máquinas diferentes em paralelo, é possível identificar duas filosofias de afectação: a que utiliza os tempos de processamento para alocar as tarefas e a que utiliza as datas de conclusão. Nesta dissertação, pretende-se dar uma contribuição para a resolução do problema de afectação de recursos em sistemas de produção. Para tal, foram propostas as heurísticas OMTC 3 e Suffrage One. A contribuição consiste na proposta de versões híbridas e modificadas das heurística MCT e Suffrage, uma vez identificadas várias características que podem limitar o seu desempenho, como o facto da heurística MCT alocar as tarefas numa ordem aleatória ou a heurística Suffrage alocar mais que uma tarefa por iteração. Finalmente, procedeu-se à realização de testes computacionais, para avaliar o desempenho das heurísticas propostas. Os testes realizados permitiram concluir que a heurística OMTC 3 apresentou um melhor desempenho que a heurística MCT.

Recomendação de conteúdos multimédia

A quantidade e variedade de conteúdos multimédia actualmente disponíveis cons- tituem um desafio para os utilizadores dado que o espaço de procura e escolha de fontes e conteúdos excede o tempo e a capacidade de processamento dos utilizado- res. Este problema da selecção, em função do perfil do utilizador, de informação em grandes conjuntos heterogéneos de dados é complexo e requer ferramentas específicas. Os Sistemas de Recomendação surgem neste contexto e são capazes de sugerir ao utilizador itens que se coadunam com os seus gostos, interesses ou necessidades, i.e., o seu perfil, recorrendo a metodologias de inteligência artificial. O principal objectivo desta tese é demonstrar que é possível recomendar em tempo útil conteúdos multimédia a partir do perfil pessoal e social do utilizador, recorrendo exclusivamente a fontes públicas e heterogéneas de dados. Neste sen- tido, concebeu-se e desenvolveu-se um Sistema de Recomendação de conteúdos multimédia baseado no conteúdo, i.e., nas características dos itens, no historial e preferências pessoais e nas interacções sociais do utilizador. Os conteúdos mul- timédia recomendados, i.e., os itens sugeridos ao utilizador, são provenientes da estação televisiva britânica, British Broadcasting Corporation (BBC), e estão classificados de acordo com as categorias dos programas da BBC. O perfil do utilizador é construído levando em conta o historial, o contexto, as preferências pessoais e as actividades sociais. O YouTube é a fonte do histo- rial pessoal utilizada, permitindo simular a principal fonte deste tipo de dados - a Set-Top Box (STB). O historial do utilizador é constituído pelo conjunto de vídeos YouTube e programas da BBC vistos pelo utilizador. O conteúdo dos vídeos do YouTube está classificado segundo as categorias de vídeo do próprio YouTube, sendo efectuado o mapeamento para as categorias dos programas da BBC. A informação social, que é proveniente das redes sociais Facebook e Twit- ter, é recolhida através da plataforma Beancounter. As actividades sociais do utilizador obtidas são filtradas para extrair os filmes e séries que são, por sua vez, enriquecidos semanticamente através do recurso a repositórios abertos de dados interligados. Neste caso, os filmes e séries são classificados através dos géneros da IMDb e, posteriormente, mapeados para as categorias de programas da BBC. Por último, a informação do contexto e das preferências explícitas, através da classificação dos itens recomendados, do utilizador são também contempladas. O sistema desenvolvido efectua recomendações em tempo real baseado nas actividades das redes sociais Facebook e Twitter, no historial de vídeos Youtube e de programas da BBC vistos e preferências explícitas. Foram realizados testes com cinco utilizadores e o tempo médio de resposta do sistema para criar o conjunto inicial de recomendações foi 30 s. As recomendações personalizadas são geradas e actualizadas mediante pedido expresso do utilizador.

Development of procedures for the simulation of atmospheric flows over complex terrain, using OpenFOAM

The main purpose of this work was the development of procedures for the simulation of atmospheric ows over complex terrain, using OpenFOAM. For this aim, tools and procedures were developed apart from this code for the preprocessing and data extraction, which were thereafter applied in the simulation of a real case. For the generation of the computational domain, a systematic method able to translate the terrain elevation model to a native OpenFOAM format (blockMeshDict) was developed. The outcome was a structured mesh, in which the user has the ability to de ne the number of control volumes and its dimensions. With this procedure, the di culties of case set up and the high computation computational e ort reported in literature associated to the use of snappyHexMesh, the OpenFOAM resource explored until then for the accomplishment of this task, were considered to be overwhelmed. Developed procedures for the generation of boundary conditions allowed for the automatic creation of idealized inlet vertical pro les, de nition of wall functions boundary conditions and the calculation of internal eld rst guesses for the iterative solution process, having as input experimental data supplied by the user. The applicability of the generated boundary conditions was limited to the simulation of turbulent, steady-state, incompressible and neutrally strati ed atmospheric ows, always recurring to RaNS (Reynolds-averaged Navier-Stokes) models. For the modelling of terrain roughness, the developed procedure allowed to the user the de nition of idealized conditions, like an uniform aerodynamic roughness length or making its value variable as a function of topography characteristic values, or the using of real site data, and it was complemented by the development of techniques for the visual inspection of generated roughness maps. The absence and the non inclusion of a forest canopy model limited the applicability of this procedure to low aerodynamic roughness lengths. The developed tools and procedures were then applied in the simulation of a neutrally strati ed atmospheric ow over the Askervein hill. In the performed simulations was evaluated the solution sensibility to di erent convection schemes, mesh dimensions, ground roughness and formulations of the k - ε and k - ω models. When compared to experimental data, calculated values showed a good agreement of speed-up in hill top and lee side, with a relative error of less than 10% at a height of 10 m above ground level. Turbulent kinetic energy was considered to be well simulated in the hill windward and hill top, and grossly predicted in the lee side, where a zone of ow separation was also identi ed. Despite the need of more work to evaluate the importance of the downstream recirculation zone in the quality of gathered results, the agreement between the calculated and experimental values and the OpenFOAM sensibility to the tested parameters were considered to be generally in line with the simulations presented in the reviewed bibliographic sources.

Type inference for conversation types

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia Informática

Functional domains of Bacillus subtilis transcription factor AraR and identification of aminoacids important for nucleoprotein complex assembly and effector-binding.

Journal of Bacteriology (Apr 2006) 3024-3036

Impact of the Meteorology Conditions on the Particulate Matter Dispersion from an Industrial Complex into Urban and Suburban Areas

The aim of this work was to assess the influence of meteorological conditions on the dispersion of particulate matter from an industrial zone into urban and suburban areas. The particulate matter concentration was related to the most important meteorological variables such as wind direction, velocity and frequency. A coal-fired power plant was considered to be the main emission source with two stacks of 225 m height. A middle point between the two stacks was taken as the centre of two concentric circles with 6 and 20 km radius delimiting the sampling area. About 40 sampling collectors were placed within this area. Meteorological data was obtained from a portable meteorological station placed at approximately 1.7 km to SE from the stacks. Additional data was obtained from the electrical company that runs the coal power plant. These data covers the years from 2006 to the present. A detailed statistical analysis was performed to identify the most frequent meteorological conditions concerning mainly wind speed and direction. This analysis revealed that the most frequent wind blows from Northwest and North and the strongest winds blow from Northwest. Particulate matter deposition was obtained in two sampling campaigns carried out in summer and in spring. For the first campaign the monthly average flux deposition was 1.90 g/m2 and for the second campaign this value was 0.79 g/m2. Wind dispersion occurred predominantly from North to South, away from the nearest residential area, located at about 6 km to Northwest from the stacks. Nevertheless, the higher deposition fluxes occurred in the NW/N and NE/E quadrants. This study was conducted considering only the contribution of particulate matter from coal combustion, however, others sources may be present as well, such as road traffic. Additional chemical analyses and microanalysis are needed to identify the source linkage to flux deposition levels.

Consistency and Context Management in a Multi Agent Belief Revision Testbed

Multi-agent architectures are well suited for complex inherently distributed problem solving domains. From the many challenging aspects that arise within this framework, a crucial one emerges: how to incorporate dynamic and conflicting agent beliefs? While the belief revision activity in a single agent scenario is concentrated on incorporating new information while preserving consistency, in a multi-agent system it also has to deal with possible conflicts between the agents perspectives. To provide an adequate framework, each agent, built as a combination of an assumption based belief revision system and a cooperation layer, was enriched with additional features: a distributed search control mechanism allowing dynamic context management, and a set of different distributed consistency methodologies. As a result, a Distributed Belief Revision Testbed (DiBeRT) was developed. This paper is a preliminary report presenting some of DiBeRT contributions: a concise representation of external beliefs; a simple and innovative methodology to achieve distributed context management; and a reduced inter-agent data exchange format.

An Intelligent Distributed System for Environmental Management

Environmental management is a complex task. The amount and heterogeneity of the data needed for an environmental decision making tool is overwhelming without adequate database systems and innovative methodologies. As far as data management, data interaction and data processing is concerned we here propose the use of a Geographical Information System (GIS) whilst for the decision making we suggest a Multi-Agent System (MAS) architecture. With the adoption of a GIS we hope to provide a complementary coexistence between heterogeneous data sets, a correct data structure, a good storage capacity and a friendly user’s interface. By choosing a distributed architecture such as a Multi-Agent System, where each agent is a semi-autonomous Expert System with the necessary skills to cooperate with the others in order to solve a given task, we hope to ensure a dynamic problem decomposition and to achieve a better performance compared with standard monolithical architectures. Finally, and in view of the partial, imprecise, and ever changing character of information available for decision making, Belief Revision capabilities are added to the system. Our aim is to present and discuss an intelligent environmental management system capable of suggesting the more appropriate land-use actions based on the existing spatial and non-spatial constraints.

A Hybrid Simulated Annealing approach to handle Energy Resource Management considering an intensive use of Electric Vehicles

The massification of electric vehicles (EVs) can have a significant impact on the power system, requiring a new approach for the energy resource management. The energy resource management has the objective to obtain the optimal scheduling of the available resources considering distributed generators, storage units, demand response and EVs. The large number of resources causes more complexity in the energy resource management, taking several hours to reach the optimal solution which requires a quick solution for the next day. Therefore, it is necessary to use adequate optimization techniques to determine the best solution in a reasonable amount of time. This paper presents a hybrid artificial intelligence technique to solve a complex energy resource management problem with a large number of resources, including EVs, connected to the electric network. The hybrid approach combines simulated annealing (SA) and ant colony optimization (ACO) techniques. The case study concerns different EVs penetration levels. Comparisons with a previous SA approach and a deterministic technique are also presented. For 2000 EVs scenario, the proposed hybrid approach found a solution better than the previous SA version, resulting in a cost reduction of 1.94%. For this scenario, the proposed approach is approximately 94 times faster than the deterministic approach.