Genome-scale metabolic network reconstruction of Polaromonas sp. strain JS666: analysis of cDCE degradation rates and design of experiments for bioremediation improvement

Release of chloroethene compounds into the environment often results in groundwater contamination, which puts people at risk of exposure by drinking contaminated water. cDCE (cis-1,2-dichloroethene) accumulation on subsurface environments is a common environmental problem due to stagnation and partial degradation of other precursor chloroethene species. Polaromonas sp. strain JS666 apparently requires no exotic growth factors to be used as a bioaugmentation agent for aerobic cDCE degradation. Although being the only suitable microorganism found capable of such, further studies are needed for improving the intrinsic bioremediation rates and fully comprehend the metabolic processes involved. In order to do so, a metabolic model, iJS666, was reconstructed from genome annotation and available bibliographic data. FVA (Flux Variability Analysis) and FBA (Flux Balance Analysis) techniques were used to satisfactory validate the predictive capabilities of the iJS666 model. The iJS666 model was able to predict biomass growth for different previously tested conditions, allowed to design key experiments which should be done for further model improvement and, also, produced viable predictions for the use of biostimulant metabolites in the cDCE biodegradation.

Development of process control strategies exploiting knowledge from systems biology: application to MDCK suspension cells

Madine Darby Canine Kidney (MDCK) cell lines have been extensively evaluated for their potential as host cells for influenza vaccine production. Recent studies allowed the cultivation of these cells in a fully defined medium and in suspension. However, reaching high cell densities in animal cell cultures still remains a challenge. To address this shortcoming, a combined methodology allied with knowledge from systems biology was reported to study the impact of the cell environment on the flux distribution. An optimization of the medium composition was proposed for both a batch and a continuous system in order to reach higher cell densities. To obtain insight into the metabolic activity of these cells, a detailed metabolic model previously developed by Wahl A. et. al was used. The experimental data of four cultivations of MDCK suspension cells, grown under different conditions and used in this work came from the Max Planck Institute, Magdeburg, Germany. Classical metabolic flux analysis (MFA) was used to estimate the intracellular flux distribution of each cultivation and then combined with partial least squares (PLS) method to establish a link between the estimated metabolic state and the cell environment. The validation of the MFA model was made and its consistency checked. The resulted PLS model explained almost 70% of the variance present in the flux distribution. The medium optimization for the continuous system and for the batch system resulted in higher biomass growth rates than the ones obtained experimentally, 0.034 h-1 and 0.030 h-1, respectively, thus reducing in almost 10 hours the duplication time. Additionally, the optimal medium obtained for the continuous system almost did not consider pyruvate. Overall the proposed methodology seems to be effective and both proposed medium optimizations seem to be promising to reach high cell densities.

The World Health Organization Multi-Professional Patient Safety Curriculum : implementation of key modules and its impact on patient safety knowledge, skills, and attitudes of medical students at the University of Algarve

ABSTRACT - Objectives: We attempted to show how the implementation of the key elements of the World Health Organization Patient Safety Curriculum Guide Multi-professional Edition in an undergraduate curriculum affected the knowledge, skills, and attitudes towards patient safety in a graduate entry Portuguese Medical School. Methods: After receiving formal recognition by the WHO as a Complementary Test Site and approval of the organizational ethics committee , the validated pre-course questionnaires measuring the knowledge, skills, and attitudes to patient safety were administered to the 2nd and3rd year students pursuing a four-year course (N = 46). The key modules of the curriculum were implemented over the academic year by employing a variety of learning strategies including expert lecturers, small group problem-based teaching sessions, and Simulation Laboratory sessions. The identical questionnaires were then administered and the impact was measured. The Curriculum Guide was evaluated as a health education tool in this context. Results: A significant number of the respondents, 47 % (n = 22), reported having received some form of prior patient safety training. The effect on Patient Safety Knowledge was assessed by using the percentage of correct pre- and post-course answers to construct 2 × 2 contingency tables and by applying Fishers’ test (two-tailed). No significant differences were detected (p < 0.05). To assess the effect of the intervention on Patient Safety skills and attitudes, the mean and standard deviation were calculated for the pre and post-course responses, and independent samples were subjected to Mann-Whitney’s test. The attitudinal survey indicated a very high baseline incidence of desirable attitudes and skills toward patient safety. Significant changes were detected (p < 0.05) regarding what should happen if an error is made (p = 0.016), the role of healthcare organizations in error reporting (p = 0.006), and the extent of medical error (p = 0.005). Conclusions: The implementation of selected modules of the WHO Patient Safety Curriculum was associated with a number of positive changes regarding patient safety skills and attitudes, with a baseline incidence of highly desirable patient safety attitudes, but no measureable change on the patient safety knowledge, at the University of Algarve Medical School. The significance of these results is discussed along with implications and suggestions for future research.

An agent based architecture to support monitoring in plug and produce manufacturing systems using knowledge extraction

In recent years a set of production paradigms were proposed in order to capacitate manufacturers to meet the new market requirements, such as the shift in demand for highly customized products resulting in a shorter product life cycle, rather than the traditional mass production standardized consumables. These new paradigms advocate solutions capable of facing these requirements, empowering manufacturing systems with a high capacity to adapt along with elevated flexibility and robustness in order to deal with disturbances, like unexpected orders or malfunctions. Evolvable Production Systems propose a solution based on the usage of modularity and self-organization with a fine granularity level, supporting pluggability and in this way allowing companies to add and/or remove components during execution without any extra re-programming effort. However, current monitoring software was not designed to fully support these characteristics, being commonly based on centralized SCADA systems, incapable of re-adapting during execution to the unexpected plugging/unplugging of devices nor changes in the entire system’s topology. Considering these aspects, the work developed for this thesis encompasses a fully distributed agent-based architecture, capable of performing knowledge extraction at different levels of abstraction without sacrificing the capacity to add and/or remove monitoring entities, responsible for data extraction and analysis, during runtime.

Decisions of technology innovation: the role of indicators

This work presents research conducted to understand the role of indicators in decisions of technology innovation. A gap was detected in the literature of innovation and technology assessment about the use and influence of indicators in this type of decision. It was important to address this gap because indicators are often frequent elements of innovation and technology assessment studies. The research was designed to determine the extent of the use and influence of indicators in decisions of technology innovation, to characterize the role of indicators in these decisions, and to understand how indicators are used in these decisions. The latter involved the test of four possible explanatory factors: the type and phase of decision, and the context and process of construction of evidence. Furthermore, it focused on three Portuguese innovation groups: public researchers, business R&D&I leaders and policymakers. The research used a combination of methods to collect quantitative and qualitative information, such as surveys, case studies and social network analysis. This research concluded that the use of indicators is different from their influence in decisions of technology innovation. In fact, there is a high use of indicators in these decisions, but lower and differentiated differences in their influence in each innovation group. This suggests that political-behavioural methods are also involved in the decisions to different degrees. The main social influences in the decisions came mostly from hierarchies, knowledge-based contacts and users. Furthermore, the research established that indicators played mostly symbolic roles in decisions of policymakers and business R&D&I leaders, although their role with researchers was more differentiated. Indicators were also described as helpful instruments to conduct a reasonable interpretation of data and to balance options in innovation and technology assessments studies, in particular when contextualised, described in detail and with discussion upon the options made. Results suggest that there are four main explanatory factors for the role of indicators in these decisions: First, the type of decision appears to be a factor to consider when explaining the role of indicators. In fact, each type of decision had different influences on the way indicators are used, and each type of decision used different types of indicators. Results for policy-making were particularly different from decisions of acquisition and development of products/technology. Second, the phase of the decision can help to understand the role indicators play in these decisions. Results distinguished between two phases detected in all decisions – before and after the decision – as well as two other phases that can be used to complement the decision process and where indicators can be involved. Third, the context of decision is an important factor to consider when explaining the way indicators are taken into consideration in policy decisions. In fact, the role of indicators can be influenced by the particular context of the decision maker, in which all types of evidence can be selected or downplayed. More importantly, the use of persuasive analytical evidence appears to be related with the dispute existent in the policy context. Fourth and last, the process of construction of evidence is a factor to consider when explaining the way indicators are involved in these decisions. In fact, indicators and other evidence were brought to the decision processes according to their availability and capacity to support the different arguments and interests of the actors and stakeholders. In one case, an indicator lost much persuasion strength with the controversies that it went through during the decision process. Therefore, it can be argued that the use of indicators is high but not very influential; their role is mostly symbolic to policymakers and business decisions, but varies among researchers. The role of indicators in these decisions depends on the type and phase of the decision and the context and process of construction of evidence. The latter two are related to the particular context of each decision maker, the existence of elements of dispute and controversies that influence the way indicators are introduced in the decision-making process.

Development and modulation of magnetic responsive supported ionic liquid membranes

The work presented in this thesis aims at developing a new separation process based on the application of supported magnetic ionic liquid membranes, SMILMs, using magnetic ionic liquids, MILs. MILs have attracted growing interest due to their ability to change their physicochemical characteristics when exposed to variable magnetic field conditions. The magnetic responsive behavior of MILs is thus expected to contribute for the development of more efficient separation processes, such as supported liquid membranes, where MILs may be used as a selective carrier. Driven by the MILs behavior, these membranes are expected to switch reversibly their permeability and selectivity by in situ and non-invasive adjustment of the conditions (e.g. intensity, direction vector and uniformity) of an external applied magnetic field. The development of these magnetic responsive membrane processes were anticipated by studies, performed along the first stage of this PhD work, aiming at getting a deep knowledge on the influence of magnetic field on MILs properties. The influence of the magnetic field on the molecular dynamics and structural rearrangement of MILs ionic network was assessed through a 1H-NMR technique. Through the 1H-NMR relaxometry analysis it was possible to estimate the self-diffusion profiles of two different model MILs, [Aliquat][FeCl4] and [P66614][FeCl4]. A comparative analysis was established between the behavior of magnetic and non-magnetic ionic liquids, MILs and ILs, to facilitate the perception of the magnetic field impact on MILs properties. In contrast to ILs, MILs show a specific relaxation mechanism, characterized by the magnetic dependence of their self-diffusion coefficients. MILs self-diffusion coefficients increased in the presence of magnetic field whereas ILs self-diffusion was not affected. In order to understand the reasons underlying the magnetic dependence of MILs self-diffusion, studies were performed to investigate the influence of the magnetic field on MILs’ viscosity. It was observed that the MIL´s viscosity decreases with the increase of the magnetic field, explaining the increase of MILs self-diffusion according to the modified Stokes- Einstein equation. Different gas and liquid transport studies were therefore performed aiming to determine the influence of the magnetic behavior of MILs on solute transport through SMILMs. Gas permeation studies were performed using pure CO2 andN2 gas streams and air, using a series of phosphonium cation based MILs, containing different paramagnetic anions. Transport studies were conducted in the presence and absence of magnetic field at a maximum intensity of 1.5T. The results revealed that gas permeability increased in the presence of the magnetic field, however, without affecting the membrane selectivity. The increase of gas permeability through SMILMs was related to the decrease of the MILs viscosity under magnetic field conditions.(...)

Estrutura Conceptual do Relato Financeiro : Da Definição de um Domínio à Sua Análise para uma Sociedade em Rede

Considerando a língua como um produto da sociedade, mas também como um meio fundamental para o estabelecimento de relações entre os homens, procuramos perceber o seu lugar na sociedade globalizada, com o objectivo de desenvolver uma metodologia de análise terminológica que contribua para uma maior qualidade da comunicação especializada na sociedade em rede. Este trabalho está organizado em duas partes, sendo a primeira dedicada à reflexão sobre o papel da língua na sociedade em rede, focando questões essenciais em torno da tensão existente entre o multilinguismo e a hegemonia do inglês enquanto lingua franca, sobretudo no espaço europeu. Interessa-nos, por um lado, reflectir sobre a definição de políticas linguísticas, concretamente na Europa multilingue dos 28, e, por outro, salientar o papel preponderante que a língua tem na transmissão do conhecimento. A segunda parte deste trabalho concretiza a investigação efectuada na primeira com base na análise do relato financeiro, um domínio do saber que não só é inerentemente multilingue ¾ porque a sua aplicação é transnacional ¾ mas também reflecte a tensão identificada na primeira parte, na medida em que o inglês assume, no mundo dos negócios em geral e nos mercados financeiros em particular, o papel hegemónico de lingua franca. A abordagem terminológica que defendemos é semasiológica para fins onomasiológicos, pelo que partimos da análise do texto de especialidade, organizado em corpora de especialidade. Discutimos subsequentemente os resultados da nossa análise com os especialistas que os irão validar e cuja colaboração em diversos vi momentos do processo de análise terminológica e conceptual é fundamental para garantir a qualidade dos recursos terminológicos produzidos. Nesta óptica, exploramos um corpus de textos legislativos no âmbito do Sistema de Normalização Contabilística (SNC), de modo a delinearmos uma metodologia de trabalho que, no futuro, conduzirá à construção de uma base de dados terminológica do relato financeiro. Concomitantemente, efectuamos também um estudo sobre a Estrutura Conceptual do SNC, para o qual elaboramos uma comparação ao nível da tradução especializada no relato financeiro, com base num corpus paralelo composto pela legislação contabilística internacional endossada pela União Europeia. Utilizamos o corpus paralelo constituído por textos redigidos originalmente em inglês e traduzidos para português, em articulação com o corpus de especialidade criado com a legislação relativa ao normativo contabilístico português, para testar uma metodologia de extracção de equivalentes. Defendemos, por fim, que a harmonização no relato financeiro para além de se reger por políticas contabilísticas comuns, deve ter subjacentes questões terminológicas. É necessário, portanto, harmonizar a terminologia do relato financeiro, possibilitando aos especialistas uma comunicação em português isenta da interferência do inglês herdado das normas internacionais, através dos dois processos que identificamos: a tradução e a adaptação das Normas Internacionais de Contabilidade.

Towards a knowledge society

Economies are moving towards competitive stadiums based on knowledge and innovation. The changing environment and the level of globalization demand important efforts in order to sustain competitive advantages. Portugal has experienced a remarkable evolution since its adhesion to the European Union in several fields: economic development, Research & Development (R&D) consolidation, health parameters and social cohesion. As other developed economies, Portugal started its journey towards a knowledge-based economy and has been consolidating an innovation system during the last 35 years. The following report aims to analyze the evolution of a system since its creation to its last transformation within a globalized context. Challenges such as the lack of maturity of the system, the economic crisis, the European paradox, and closing the gap with other European countries are addressed in the next chapters. Likewise, recommendations on these points are provided by the end of the report as potential solutions.