A clustering approach for vehicle routing problems with hard time windows

Dissertação para obtenção do Grau de Mestre em Logica Computicional

Development of principle culture medium formulations for Saccharomyces cerevisiae

Saccharomyces cerevisiae as well as other microorganisms are frequently used in industry with the purpose of obtain different kind of products that can be applied in several areas (research investigation, pharmaceutical compounds, etc.). In order to obtain high yields for the desired product, it is necessary to make an adequate medium supplementation during the growth of the microorganisms. The higher yields are typically reached by using complex media, however the exact formulation of these media is not known. Moreover, it is difficult to control the exact composition of complex media, leading to batch-to-batch variations. So, to overcome this problem, some industries choose to use defined media, with a defined and known chemical composition. However these kind of media, many times, do not reach the same high yields that are obtained by using complex media. In order to obtain similar yield with defined media the addition of many different compounds has to be tested experimentally. Therefore, the industries use a set of empirical methods with which it is tried to formulate defined media that can reach the same high yields as complex media. In this thesis, a defined medium for Saccharomyces cerevisiae was developed using a rational design approach. In this approach a given metabolic network of Saccharomyces cerevisiae is divided into a several unique and not further decomposable sub networks of metabolic reactions that work coherently in steady state, so called elementary flux modes. The EFMtool algorithm was used in order to calculate the EFM’s for two Saccharomyces cerevisiae metabolic networks (amino acids supplemented metabolic network; amino acids non-supplemented metabolic network). For the supplemented metabolic network 1352172 EFM’s were calculated and then divided into: 1306854 EFM’s producing biomass, and 18582 EFM’s exclusively producing CO2 (cellular respiration). For the non-supplemented network 635 EFM’s were calculated and then divided into: 215 EFM’s producing biomass; 420 EFM’s producing exclusively CO2. The EFM’s of each group were normalized by the respective glucose consumption value. After that, the EFMs’ of the supplemented network were grouped again into: 30 clusters for the 1306854 EFMs producing biomass and, 20 clusters for the 18582 EFM’s producing CO2. For the non-supplemented metabolic network the respective EFM’s of each metabolic function were grouped into 10 clusters. After the clustering step, the concentrations of the other medium compounds were calculated by considering a reasonable glucose amount and by accounting for the proportionality between the compounds concentrations and the glucose ratios. The approach adopted/developed in this thesis may allow a faster and more economical way for media development.

LAY USE OF AMAZONIAN PLANTS FOR THE TREATMENT OF TUBERCULOSIS

The Brazilian State of Amazonas has a high incidence of Tuberculosis, 91.4 in 10,000 habitants (SESAU, 1994) and resistant strains of Mycobacterium tuberculosis are frequently being found in the region (SALEM et.al, 1990). These problems have been associated with side effects caused by the antibiotics used to treat Tuberculosis, which have in rum been associated with treatment non-compliance (PATTISAPU, 1984). To resolve this problem a cost effective alternative treatment for Tuberculosis with few or no side effects, needs to be found. Amazonas has an abundance of plants, many of which are used by the lay population for medicinal purposes. A survey was carried out in five towns of the region, interviewing patients receiving treatment for Tuberculosis, to find out whether and which plants have been used to treat Tuberculosis. Results showed that the majority of patients in the sample had used medicinal plants before or after diagnosis of Tuberculoses. Thirteen different plants were recorded for this purpose. Chenopodium ambrosioides L, popularly known as Mastruz, was the most commonly used, followed by Caesalpinia ferrea Mart. Jucá and Spilanthes acmella DC. Jambu. This study concentrates on Mastruz as it was used more frequently than the other medicinal plants. No significant effects on baciloscopy test results were found when Mastruz was used before diagnosis. ln-vitro laboratory tests have also not shown any tuberculocidal effects for Mastruz. Further tests are being carried out on the other medicinal plants.

Reverse engineering of web applications

The MAP-i Doctoral Program of the Universities of Minho, Aveiro and Porto

Design de superfície biomimética para aplicação em atividades desportivas

Tese de Doutoramento Engenharia Têxtil.

Sustentabilidade no Design: uma abordagem aos resíduos limpos das indústrias do calçado

Dissertação de mestrado em Design e Marketing

A dimensão interna da responsabilidade social nas organizações: equilíbrio entre o trabalho e a vida familiar

Dissertação de mestrado em Sociologia (área de especialização em Organizações e Trabalho)

A Grid Supercomputing Enviroment for High Demand Computational Applications

Despite the huge increase in processor and interprocessor network performace, many computational problems remain unsolved due to lack of some critical resources such as floating point sustained performance, memory bandwidth, etc... Examples of these problems are found in areas of climate research, biology, astrophysics, high energy physics (montecarlo simulations) and artificial intelligence, among others. For some of these problems, computing resources of a single supercomputing facility can be 1 or 2 orders of magnitude apart from the resources needed to solve some them. Supercomputer centers have to face an increasing demand on processing performance, with the direct consequence of an increasing number of processors and systems, resulting in a more difficult administration of HPC resources and the need for more physical space, higher electrical power consumption and improved air conditioning, among other problems. Some of the previous problems can´t be easily solved, so grid computing, intended as a technology enabling the addition and consolidation of computing power, can help in solving large scale supercomputing problems. In this document, we describe how 2 supercomputing facilities in Spain joined their resources to solve a problem of this kind. The objectives of this experience were, among others, to demonstrate that such a cooperation can enable the solution of bigger dimension problems and to measure the efficiency that could be achieved. In this document we show some preliminary results of this experience and to what extend these objectives were achieved.

Dynamical modeling and analysis of large cellular regulatory networks.

The dynamical analysis of large biological regulatory networks requires the development of scalable methods for mathematical modeling. Following the approach initially introduced by Thomas, we formalize the interactions between the components of a network in terms of discrete variables, functions, and parameters. Model simulations result in directed graphs, called state transition graphs. We are particularly interested in reachability properties and asymptotic behaviors, which correspond to terminal strongly connected components (or "attractors") in the state transition graph. A well-known problem is the exponential increase of the size of state transition graphs with the number of network components, in particular when using the biologically realistic asynchronous updating assumption. To address this problem, we have developed several complementary methods enabling the analysis of the behavior of large and complex logical models: (i) the definition of transition priority classes to simplify the dynamics; (ii) a model reduction method preserving essential dynamical properties, (iii) a novel algorithm to compact state transition graphs and directly generate compressed representations, emphasizing relevant transient and asymptotic dynamical properties. The power of an approach combining these different methods is demonstrated by applying them to a recent multilevel logical model for the network controlling CD4+ T helper cell response to antigen presentation and to a dozen cytokines. This model accounts for the differentiation of canonical Th1 and Th2 lymphocytes, as well as of inflammatory Th17 and regulatory T cells, along with many hybrid subtypes. All these methods have been implemented into the software GINsim, which enables the definition, the analysis, and the simulation of logical regulatory graphs.

Institutional fragmentation and coordination initiatives in western European welfare states

As a result of recent welfare state transformations, and most notably the reorientation of welfare states towards activation, the internal fragmentation of social security systems has emerged as a key policy problem in many western European countries. The types of response that have been adopted, however, vary substantially across countries, ranging from the encouragement of inter-agency collaboration to the outright merger of agencies. The purpose of this exploratory article is twofold. First, by proposing the concept of coordination initiatives, it tries to develop a better conceptualization of the cross-national diversity in responses to the fragmentation problem. Second, starting from existing theories of welfare state development and policy change, it presents first hypotheses accounting for the variation observed in coordination initiatives.

Expression of mosquito active toxin genes by a Colombian native strain of the gram-negative bacterium Asticcacaulis excentricus

Mosquito control with biological insecticides, such as Bacillus sp. toxins, has been used widely in many countries. However, rapid sedimentation away from the mosquito larvae feeding zone causes a low residual effect. In order to overcome this problem, it has been proposed to clone the Bacillus toxin genes in aquatic bacteria which are able to live in the upper part of the water column. Two strains of Asticcacaulis excentricus were chosen to introduce the B. sphaericus binary toxin gene and B. thuringiensis subsp. medellin cry11Bb gene cloned in suitable vectors. In feeding experiments with these aquatic bacteria, it was shown that Culex quinquefasciatus, Aedes aegypti, and Anopheles albimanus larvae were able to survive on a diet based on this wild bacterium. A. excentricus recombinant strains were able to express both genes, but the recombinant strain expressing the B. sphaericus binary toxin was toxic to mosquito larvae. Crude protease A. excentricus extracts did not degrade the Cry11Bb toxin. The flotability studies indicated that the recombinant A. excentricus strains remained in the upper part of the water column longer than the wild type Bacillus strains.

Profitability, uncertainty and multi-product firm product proliferation: The Spanish car industry

This article studies how product introduction decisions relate to profitability and uncertainty in the context of multi-product firms and product differentiation. These two features, common to many modern industries, have not received much attention in the literature as compared to the classical problem of firm entry, even if the determinants of firm and product entry are quite different. The theoretical predictions about the sign of the impact of uncertainty on product entry are not conclusive. Therefore, an econometric model relating firms’ product introduction decisions with profitability and profit uncertainty is proposed. Firm’s estimated profits are obtained from a structural model of product demand and supply, and uncertainty is proxied by profits’ variance. The empirical analysis is carried out using data on the Spanish car industry for the period 1990-2000. The results show a positive relationship between product introduction and profitability, and a negative one with respect to profit variability. Interestingly, the degree of uncertainty appears to be a driving force of entry stronger than profitability, suggesting that the product proliferation process in the Spanish car market may have been mainly a consequence of lower uncertainty rather than the result of having a more profitable market. Keywords: Product introduction, entry, uncertainty, multiproduct firms, automobile JEL codes: L11, L13

Cuestiones de pintura y miniatura en Cerdeña: modelos, intercambios y relaciones internacionales en la segunda mitad del siglo XV

Durante el siglo XV Cerdeña desempeña, gracias a su posicionamiento geográfico en el centro del Mediterráneo, un papel muy importante en la red de comercio internacional. Este movimiento económico-cultural fomenta una extensa producción artística que está caracterizada por depender fuertemente de la presencia en la isla de talleres y artistas catalanes. Al día de hoy se conoce muy poco la presencia y las características de la pintura del gótico tardío en la Cerdeña. Las dificultades encontradas por los investigadores en la reconstrucción de la historia del arte sarda de esta época son numerosas y difíciles de solucionar. El problema depende de la falta de fuentes documentales (directas e indirectas), de la gran dispersión de muchísimas obras, de la inaccesibilidad de unas de las obras más interesantes; del desplazamiento casi total de las obras de su sitio original, y del total anonimato de la mayoría de los artistas. En estas condiciones la única solución para alcanzar nuevos elementos científicos es: integrar los conocimientos procedente de las fuentes documentales; ampliar la practica metodológica (multidisciplinariedad), conectar el tejido sardo (pintura, miniatura, grabados) con el ámbito internacional. El objetivo final es introducir la pintura sarda en un contexto más amplio, para poder descubrir el sistema de modelos y de relaciones artísticas, que la conectan con el mundo artístico mediterráneo. El trabajo de este primer año ha sido particularmente intenso y complicado por las dificultades encontradas en ponerse en un tema tan vasto como lo de la pintura y los modelos figurativos de la segunda mitad del siglo XV. Principales objetivos: averiguar toda la bibliografía conocida sobre el tema e intentar ampliar los estudios cada vez que se encontraban indicios sobre posibles autores y obras sardas; empezar el trabajo de catalogación de las obras pictóricas (conocidas o recien descubiertas.)

Ecologia del tram final del riu Ebre: la comunitat de macròfits i macroinvertebrats associats

Durant els últims anys al tram final del riu Ebre s’han produit canvis molt importants a l’ecosistema fluvial: l’augment de la transparència de l’aigua ha comportat una proliferació massiva de macròfits que ha provocat canvis en l’estructura tròfica i en la composició de les comunitats biològiques, representant un greu perill per espècies amenaçades com Margaritifera auricularia. A més del problema ecològic, els macròfits estan provocant molts problemes socio-econòmics perjudicant les captacions d’aigua (centrals nuclears, hidroelèctriques i regadius), creant problemes per a la navegació fluvial, i afavorint la proliferació d’espècies molestes com la mosca negra (Simulium erythrocephalum). Entre les diferents causes que podrien explicar aquests canvis en l’ecosistema hi ha: la disminució del fòsfor dissolt, la regularització i la disminució de cabals, i l’aparició d’espècies introduides com el musclo zebra. Segurament es tractarà d’un efecte combinat de les diferents causes però és necessari analitzar-les per tal de conèixer quines tenen més incidència i així, poder proposar mesures de gestió per als problemes ecològics que pateix el tram final de l’Ebre. Al present projecte de tesi (inclós en el projecte d’I+D: efectes de la millora de la qualitat de l'aigua i de l'alteració del règim de cabals sobre les comunitats biològiques del tram final del riu Ebre) s’estudiarà la comunitat de macròfits i macroinvertebrats associats per tal de determinar el paper que tenen en el canvis que s’han produit al riu durant els últims anys.

Profitability, uncertainty and multi-product firm product proliferation: The Spanish car industry

This article studies how product introduction decisions relate to profitability and uncertainty in the context of multi-product firms and product differentiation. These two features, common to many modern industries, have not received much attention in the literature as compared to the classical problem of firm entry, even if the determinants of firm and product entry are quite different. The theoretical predictions about the sign of the impact of uncertainty on product entry are not conclusive. Therefore, an econometric model relating firms’ product introduction decisions with profitability and profit uncertainty is proposed. Firm’s estimated profits are obtained from a structural model of product demand and supply, and uncertainty is proxied by profits’ variance. The empirical analysis is carried out using data on the Spanish car industry for the period 1990-2000. The results show a positive relationship between product introduction and profitability, and a negative one with respect to profit variability. Interestingly, the degree of uncertainty appears to be a driving force of entry stronger than profitability, suggesting that the product proliferation process in the Spanish car market may have been mainly a consequence of lower uncertainty rather than the result of having a more profitable market