Purification of complex biopharmaceuticals with new processes, advanced analytics and computer-aided process design tools

Dissertação para obtenção do Grau de Mestre em Biotecnologia

Target-specific multiphysics modeling for thermal medicine applications

Dissertation to obtain the degree of Doctor of Philosophy in Biomedical Engineering

Integration of Membrane Filtration and Photolysis Processes for Drinking Water Treatment

Dissertation presented to obtain the Ph.D degree in Engineering and Technology Sciences, Chemical Engineering.

Understanding the microbial ecology and ecophysiology of enhanced biological phosphorus removal processes through metabolic modelling and experimental studies

Dissertation to obtain the degree of Master in Chemical and Biochemical Engineering

Controlling gene expression in enterobacteriaceae: studies on sRNAs and strategies for synthetic biology

Dissertation presented to obtain the Master Degree in Molecular, Genetics and Biomedicine

Héraldique des sceaux du clergé séculier portugais au Moyen Âge

Ce n’est que dans les dernières années que l’héraldique au Portugal a entamé le processus de rénovation qui, en France, a commencé il y a déjà quelques décennies. Dans ce processus, l’étude de l’héraldique médiévale a été peu contemplé, restant pratiquement à faire, en bonne partir dû à l’absence d’armoriaux antérieurs au XVe siècle qui permettent de connaître les armes utilisées par les familles et les diverses entités portugaises. Pour cette raison, les sceaux portant des représentations héraldiques ont une importance extrême, car ils constituent très fréquemment la seule source pour l’étude des armoiries, ayant en plus l’avantage d’être datés avec précision et liées à des personnages ou entités qui sont connues. Cependant, la sigillographie portugaise se trouve aussi dans une phase de son évolution qui, n’étant plus embryonnaire, est encore une phase de formation. Il nous manque des catalogues, des dépouillages systématiques, des études approfondies qui permettent aux héraldistes de faire leurs recherches. C’est dans ce contexte qui est née ce partenariat entre deux médiévalistes très intéressés à la sigillographie et un spécialiste d’héraldique, qui ensemble ont décidé d’entamer l’étude des origines des représentations héraldiques dans les sceaux portugais, en commençant par les sceaux du clergé séculier, qui constitue le sujet par excellence de la recherche des deux historiens. Dans ce vaste univers sigillaire, qui concerne des personnes d’une grande variété d’origines sociales, y compris la noblesse et la riche bourgeoisie urbaine, les éléments héraldiques semblent avoir émergé seulement à partir de la fin du XIIIe siècle, et d’une façon timide. Le XIVe siècle assiste à sa diffusion dans les sceaux d’évêques, dignités et chanoines, mais ce n’est qu’au XVe siècle que l’héraldique s’impose, gagnant même une place primordiale dans quelques représentations sigillographiques. Le but de cette communication sera donc l’analyse du processus d’héraldisation des sceaux du clergé séculier portugais, entre les dernières décennies du XIIIe et le XVe siècle, pour évaluer comme s’est procédé, dans le cas portugais, le phénomène d’«acculturation héraldique» de l’emblématique épiscopale et cléricale.

Staging the Scientist: The Representation of Science and its Processes in American and British Drama

Dissertação apresentada para cumprimento dos requisitos necessários à obtenção do grau de Mestre em Estudos Ingleses e Norte Americanos

Standardization of project management processes

Software development is a discipline that is almost as old as the history of computers. With the advent of the Internet and all of its related technologies, software development has been on high demand. But, and especially in SME (small and medium enterprise), this was not accompanied with a comparable effort to develop a set of sustainable and standardized activities of project management, which lead to increasing inefficiencies and costs. Given the actual economic situation, it makes sense to engage in an effort to reduce said inefficiencies and rising costs. For that end, this work will analyze the current state of software development’s project management processes on a Portuguese SME, along with its problems and inefficiencies in an effort to create a standardized model to manage software development, with special attention given to critical success factors in an agile software development environment, while using the best practices in process modeling. This work also aims to create guidelines to correctly integrate these changes in the existing IS structure of a company.

Application of NMR RDC’s, relaxation and self-diffusion for the study of dynamic processes of small molecules in solution

Spin-lattice Relaxation, self-Diffusion coefficients and Residual Dipolar Couplings (RDC’s) are the basis of well established Nuclear Magnetic Resonance techniques for the physicochemical study of small molecules (typically organic compounds and natural products with MW < 1000 Da), as they proved to be a powerful and complementary source of information about structural dynamic processes in solution. The work developed in this thesis consists in the application of the earlier-mentioned NMR techniques to explore, analyze and systematize patterns of the molecular dynamic behavior of selected small molecules in particular experimental conditions. Two systems were chosen to investigate molecular dynamic behavior by these techniques: the dynamics of ion-pair formation and ion interaction in ionic liquids (IL) and the dynamics of molecular reorientation when molecules are placed in oriented phases (alignment media). The application of NMR spin-lattice relaxation and self-diffusion measurements was applied to study the rotational and translational molecular dynamics of the IL: 1-butyl-3-methylimidazolium tetrafluoroborate [BMIM][BF4]. The study of the cation-anion dynamics in neat and IL-water mixtures was systematically investigated by a combination of multinuclear NMR relaxation techniques with diffusion data (using by H1, C13 and F19 NMR spectroscopy). Spin-lattice relaxation time (T1), self-diffusion coefficients and nuclear Overhauser effect experiments were combined to determine the conditions that favor the formation of long lived [BMIM][BF4] ion-pairs in water. For this purpose and using the self-diffusion coefficients of cation and anion as a probe, different IL-water compositions were screened (from neat IL to infinite dilution) to find the conditions where both cation and anion present equal diffusion coefficients (8% water fraction at 25 ºC). This condition as well as the neat IL and the infinite dilution were then further studied by 13C NMR relaxation in order to determine correlation times (c) for the molecular reorientational motion using a mathematical iterative procedure and experimental data obtained in a temperature range between 273 and 353 K. The behavior of self-diffusion and relaxation data obtained in our experiments point at the combining parameters of molar fraction 8 % and temperature 298 K as the most favorable condition for the formation of long lived ion-pairs. When molecules are subjected to soft anisotropic motion by being placed in some special media, Residual Dipolar Couplings (RDCs), can be measured, because of the partial alignment induced by this media. RDCs are emerging as a powerful routine tool employed in conformational analysis, as it complements and even outperforms the approaches based on the classical NMR NOE or J3 couplings. In this work, three different alignment media have been characterized and evaluated in terms of integrity using 2H and 1H 1D-NMR spectroscopy, namely the stretched and compressed gel PMMA, and the lyotropic liquid crystals CpCl/n-hexanol/brine and cromolyn/water. The influence that different media and degrees of alignment have on the dynamic properties of several molecules was explored. Different sized sugars were used and their self-diffusion was determined as well as conformation features using RDCs. The results obtained indicate that no influence is felt by the small molecules diffusion and conformational features studied within the alignment degree range studied, which was the 3, 5 and 6 % CpCl/n-hexanol/brine for diffusion, and 5 and 7.5 % CpCl/n-hexanol/brine for conformation. It was also possible to determine that the small molecules diffusion verified in the alignment media presented close values to the ones observed in water, reinforcing the idea of no conditioning of molecular properties in such media.

A solution for estimates in software development projects

The Corporate world is becoming more and more competitive. This leads organisations to adapt to this reality, by adopting more efficient processes, which result in a decrease in cost as well as an increase of product quality. One of these processes consists in making proposals to clients, which necessarily include a cost estimation of the project. This estimation is the main focus of this project. In particular, one of the goals is to evaluate which estimation models fit the Altran Portugal software factory the most, the organization where the fieldwork of this thesis will be carried out. There is no broad agreement about which is the type of estimation model more suitable to be used in software projects. Concerning contexts where there is plenty of objective information available to be used as input to an estimation model, model-based methods usually yield better results than the expert judgment. However, what happens more frequently is not having this volume and quality of information, which has a negative impact in the model-based methods performance, favouring the usage of expert judgement. In practice, most organisations use expert judgment, making themselves dependent on the expert. A common problem found is that the performance of the expert’s estimation depends on his previous experience with identical projects. This means that when new types of projects arrive, the estimation will have an unpredictable accuracy. Moreover, different experts will make different estimates, based on their individual experience. As a result, the company will not directly attain a continuous growing knowledge about how the estimate should be carried. Estimation models depend on the input information collected from previous projects, the size of the project database and the resources available. Altran currently does not store the input information from previous projects in a systematic way. It has a small project database and a team of experts. Our work is targeted to companies that operate in similar contexts. We start by gathering information from the organisation in order to identify which estimation approaches can be applied considering the organization’s context. A gap analysis is used to understand what type of information the company would have to collect so that other approaches would become available. Based on our assessment, in our opinion, expert judgment is the most adequate approach for Altran Portugal, in the current context. We analysed past development and evolution projects from Altran Portugal and assessed their estimates. This resulted in the identification of common estimation deviations, errors, and patterns, which lead to the proposal of metrics to help estimators produce estimates leveraging past projects quantitative and qualitative information in a convenient way. This dissertation aims to contribute to more realistic estimates, by identifying shortcomings in the current estimation process and supporting the self-improvement of the process, by gathering as much relevant information as possible from each finished project.

Trans-Synaptic Signaling by Activity-Dependent Cleavage of Neuroligin-1

Throughout the brain, patterns of activity in postsynaptic neurons influence the properties of synaptic inputs. Such feedback regulation is central to neural network stability that underlies proper information processing and feature representation in the central nervous system. At the cellular level, tight coupling of presynaptic and postsynaptic function is fundamental to neural computation and synaptic plasticity. The cohort of protein complexes at the pre and postsynaptic membrane allows for tight synapse-specific segregation and integration of diverse molecular and electrical signals.(...)

Petites villes européenes au bas Moyen Âge: perspectives de recherche

Fundação para a Ciência e Tecnologia,

Storage of water molecules into biomimetic heterostructures: the role of roughness

The development of devices based on heterostructured thin films of biomolecules conveys a huge contribution on biomedical field. However, to achieve high efficiency of these devices, the storage of water molecules into these heterostructures, in order to maintain the biological molecules hydrated, is mandatory. Such hydrated environment may be achieved with lipids molecules which have the ability to rearrange spontaneously into vesicles creating a stable barrier between two aqueous compartments. Yet it is necessary to find conditions that lead to the immobilization of whole vesicles on the heterostructures. In this work, the conditions that govern the deposition of open and closed liposomes of 1.2-dipalmitoyl-sn-Glycero-3-[Phospho-rac-(1-glycerol)] (sodium Salt) (DPPG) onto polyelectrolytes cushions prepared by the layer-by-layer (LbL) method were analyzed. Electronic transitions of DPPG molecules as well as absorption coefficients were obtained by vacuum ultraviolet spectroscopy, while the elemental composition of the heterostructures was characterized by x-ray photoelectron spectroscopy (XPS). The presence of water molecules in the films was inferred by XPS and infrared spectroscopy. Quartz crystal microbalance (QCM) data analysis allowed to conclude that, in certain cases, the DPPG adsorbed amount is dependent of the bilayers number already adsorbed. Moreover, the adsorption kinetics curves of both adsorbed amount and surface roughness allowed to determine the kinetics parameters that are related with adsorption processes namely, electrostatic forces, liposomes diffusion and lipids re-organization on surface. Scaling exponents attained from atomic force microscopy images statistical analysis demonstrate that DPPG vesicles adsorption mechanism is ruled by the diffusion Villain model confirming that adsorption is governed by electrostatic forces. The power spectral density treatment enabled a thorough description of the accessible surface of the samples as well as of its inner structural properties. These outcomes proved that surface roughness influences the adsorption of DPPG liposomes onto surfaces covered by a polyelectrolyte layer. Thus, low roughness was shown to induce liposome rupture creating a lipid bilayer while high roughness allows the adsorption of whole liposomes. In addition, the fraction of open liposomes calculated from the normalized maximum adsorbed amounts decreases with the cushion roughness increase, allowing us to conclude that the surface roughness is a crucial variable that governs the adsorption of open or whole liposomes. This conclusion is fundamental for the development of well-designed sensors based on functional biomolecules incorporated in liposomes. Indeed, LbL films composed of polyelectrolytes and liposomes with and without melanin encapsulated were successfully applied to sensors of olive oil.

Relating the spatial component and users interests to improve applications based on questions, petitions and participatory processes

Nowadays, participatory processes attending the need for real democracy and transparency in governments and collectives are more needed than ever. Immediate participation through channels like social networks enable people to give their opinion and become pro-active citizens, seeking applications to interact with each other. The application described in this dissertation is a hybrid channel of communication of questions, petitions and participatory processes based on Public Participation Geographic Information System (PPGIS), Participation Geographic Information System (PGIS) and ‘soft’ (subjective data) Geographic Information System (SoftGIS) methodologies. To achieve a new approach to an application, its entire design is focused on the spatial component related with user interests. The spatial component is treated as main feature of the system to develop all others depending on it, enabling new features never seen before in social actions (questions, petitions and participatory processes). Results prove that it is possible to develop a working application mainly using open source software, with the possibility of spatial and subject filtering, visualizing and free download of actions within application. The resulting application empowers society by releasing soft data and defines a new breaking approach, unseen so far.

Enhancement of an implemented rating model and impact on existing risk management processes: A hands-on approach from financial supplier risk management within the automotive industry

The purpose of this paper is to conduct a methodical drawback analysis of a financial supplier risk management approach which is currently implemented in the automotive industry. Based on identified methodical flaws, the risk assessment model is further developed by introducing a malus system which incorporates hidden risks into the model and by revising the derivation of the most central risk measure in the current model. Both methodical changes lead to significant enhancements in terms of risk assessment accuracy, supplier identification and workload efficiency.