Petri net based development of globally-asynchronous locally-synchronous distributed embedded systems

Dissertação para obtenção do Grau de Doutor em Engenharia Electrotécnica e de Computadores

Development of composite particles for pulmonary delivery

In this work, biocompatible and biodegradable poly(D-L-lactide-co-glycolide) (PLGA) microparticles with the potential for use as a controlled release system of vaccines and other drugs to the lung were manufactured using supercritical CO2, through the Supercritical Assisted Atomization (SAA) technique. After performing a controlled variance in production parameters (temperature, pressure, CO2/solution flow ratio) PLGA microparticles were characterized and later used to encapsulate active pharmaceutical ingredients (API). Bovine serum albumin (BSA) was chosen as model protein and vaccine, while sildenafil was the chosen drug to treat pulmonary artery hypertension and their effect on the particles characteristics was evaluated. All the produced formulations were characterized in relation to their morphology (Morphologi G3 and scanning electronic microscopy (SEM)), to their physical-chemical properties (X-ray diffraction (XRD, differential scanning calorimetry (DSC), Fourier transform infrared (FTIR)) and aerodynamic performance using an in vitro aerosolization study – Andersen cascade impactor (ACI) - to obtain data such as the fine particle fraction (FPF) and the mass median aerodynamic diameter (MMAD). Furthermore, pharmacokinetic, biodegradability and biocompatibility tests were performed in order to verify the particle suitability for inhalation. The resulting particles showed aerodynamic diameters between the 3 and 5 μm, yields up to 58% and FPF percentages rounding the 30%. Taken as a whole, the produced microparticles do present the necessary requests to make them appropriate for pulmonary delivery.

Precast concrete wall-foundation connection. Development of a seismic dissipative connection

Seismic events are a major factor to consider in structural design of buildings in many countries. With the purpose of saving lives, most of the design codes lead to structural solutions that withstand large seismic actions without collapsing, but without taking into account a possible usage of the structures after the earthquake. As a result, it is necessary to consider the time needed to repair/retrofit the damaged structures (i.e. the downtime) since this period of inactivity may result in huge financial implications for the occupants of the buildings. In order to minimise the damages and simplify repair operations, structural solutions with rocking systems and negligible residual displacements have been developed during the last two decades. Systems with precast concrete rocking walls were studied with the aim of investigat- ing suitable and convenient structural alternatives to minimise the damage in case of an earthquake. Experimental, numerical and analytical analyses on post-tensioned solutions, with and without energy dissipation devices, were carried out in this research. The energy dissipation devices were made from steel angles that were further developed during the research. Different solutions for these devices were experimentally tested under cyclic loading and the results are presented. Numerical and analytical work on steel angles was also carried out. Regarding the concrete rocking wall systems, two concrete rocking wall systems were studied: post-tensioned walls and post-tensioned walls with energy dissipation devices. In the latter, the solution was to fix them externally to the wall, allowing their easy replacement after an earthquake. It is shown that the dissipaters are a viable solution for use in precast concrete rocking wall systems. A building case study is presented. The comparison between a traditional monolithic system and a hybrid solution was carried out, allowing the evaluation of the efficiency of the solution that was developed.

Phage display as a tool for development of novel therapeutics for breast cancer

Phage display technology is a powerful platform for the generation of highly specific human monoclonal antibodies (Abs) with potential use in clinical applications. Moreover, this technique has also proven to be a reliable approach in identifying and validating new cancer-related targets. For scientific or medical applications, different types of Ab libraries can be constructed. The use of Fab Immune libraries allows the production of high quality and affinity antigen-specific Abs. In this work, two immune human phage display IgG Fab libraries were generated from the Ab repertoire of 16 breast cancer patients, in order to obtain a tool for the development of new therapeutic Abs for breast cancer, a condition that has great impact worldwide. The generated libraries are estimated to contain more than 108 independent clones and a diversity over 90%. Libraries validation was pursued by selection against BSA, a foreign and highly immunogenic protein, and HER2, a well established cancer target. Preliminary results suggested that phage pools with affinity for these antigens were selected and enriched. Individual clones were isolated, however, it was not possible to obtain enough data to further characterize them. Selection against the DLL1 protein was also performed, once it is a known ligand of the Notch pathway, whose deregulation is associated to breast cancer, making it an interesting target for the generation of function-blocking Abs. Selection resulted in the isolation of a clone with low affinity and Fab expression levels. The validation process was not completed and further effort will have to be put in this task in the future. Although immune libraries concept implies limited applicability, the library reported here has a wide range of use possibilities, since it was not restrained to a single antigen but instead thought to be used against any breast cancer associated target, thus being a valuable tool.

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.

Development of novel ionic liquids based on biological molecules

Ionic Liquids (ILs) belong to a class of compounds with unusual properties: very low vapour pressure; high chemical and thermal stability and the ability to dissolve a wide range of substances. A new field in research is evaluating the possibility to use natural chiral biomolecules for the preparation of chiral ionic liquids (CILs). This important challenge in synthetic chemistry can open new avenues of research in order to avoid some problems related with the intrinsic biodegradability and toxicity associated to conventional ILs. The research work developed aimed for the synthesis of CILs, their characterization and possible applications, based on biological moieties used either as chiral cations or anions, depending on the synthetic manipulation of the derivatives. Overall, a total of 28 organic salts, including CILs were synthesized: 9 based on L-cysteine derivatives, 12 based on L-proline, 3 based on nucleosides and 4 based on nucleotides. All these new CILs were completely characterized and their chemical and physical properties were evaluated. Some CILs based on L-cysteine have been applied for discrimination processes, including resolution of racemates and as a chiral catalyst for asymmetric Aldol condensation. L-proline derived CILs were also studied as chiral catalysts for Michael reaction. In parallel, the interactions of macrocyclic oligosugars called cyclodextrins (CDs) with several ILs were studied. It was possible to improve the solubility of CDs in water and serum. Additionally, fatty acids and steroids showed an increase in water solubility when ILs-CDs systems were used. The development of efficient and selective ILs-CDs systems is indispensable to expand the range of their applications in host-guest interactions, drug delivery systems or catalytic reactions. Novel salts derived from nucleobases were used in order to enhance the fluorescence in aqueous solution. Additionally, preliminary studies regarding ethyl lactate as an alternative solvent for asymmetric organocatalysis were performed.

Development of novel active pharmaceutical ionic liquids and salts based on antibiotics and anti-fungal drugs

Ionic Liquids (ILs) are class of compounds, which have become popular since the mid-1990s. Despite the fact that ILs are defined by one physical property (melting point), many of the potential applications are now related to their biological properties. The use of a drug as a liquid can avoid some problems related to polymorphism which can influence a drug´s solubility and thus its dosages. Also, the arrangement of the anion or cation with a specific drug might be relevant in order to: a) change the correspondent biopharmaceutical drug classification system; b) for the drug formulation process and c) the change the Active Pharmaceutical Ingredients’ (APIs). The main goal of this Thesis is the synthesis and study of physicochemical and biological properties of ILs as APIs from beta-lactam antibiotics (ampicillin, penicillin G and amoxicillin) and from the anti-fungal Amphotericin B. All the APIs used here were neutralized in a buffer appropriate hydroxide cations. The cation hydroxide was obtained on Amberlite resin (in the OH form) in order to exchange halides. The biological studies of these new compounds were made using techniques like the micro dilution and colorimetric methods. Overall a total of 19 new ILs were synthesised (6 ILs based on ampicillin, 4 ILs, based on amoxicillin, 6 ILs based on penicillin G and 4 ILs based on amphotericin B) and characterized by spectroscopic and analytical methods in order to confirm their structure and purity. The study of the biological properties of the synthesised ILs showed that some have antimicrobial activity against bacteria and yeast cells, even in resistant bacteria. Also this work allowed to show that ILs based on ampicillin could be used as anti-tumour agents. This proves that with a careful selection of the organic cation, it is possible to provoke important physico-chemical and biological alteration in the properties of ILs-APIs with great impact, having in mind their applications.

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.

Analysis, testing and development of safe cleaning methods of rusted stone material

Three different treatments were applied on several specimens of dolomitic and calcitic marble, properly stained with rust to mimic real situations (the stone specimens were exposed to the natural environment for about six months in contact with rusted iron). Thirty six marble specimens, eighteen calcitic and eighteen dolomitic, were characterized before and after treatment and monitored throughout the cleaning tests. The specimens were characterized by SEM-EDS (Scanning Electron Microscopy coupled with Energy Dispersion System), XRD (XRay Diffraction), XRF (X-Ray Fluorescence), FTIR (Fourier Transform Infrared Spectroscopy) and color measurements. It was also made a microscopic and macroscopic analysis of the stone surface along with the tests of short and long term capillary absorption. A series of test trials were conducted in order to understand which concentrations and contact times best suits to this purpose, to confirm what had been written to date in the literature. We sought to develop new methods of treatment application, skipping the usual methods of applying chemical treatments on stone substrates, with the use of cellulose poultice, resorting to the agar, a gel already used in many other areas, being something new in this area, which possesses great applicability in the field of conservation of stone materials. After the application of the best methodology for cleaning, specimens were characterized again in order to understand which treatment was more effective and less harmful, both for the operator and the stone material. Very briefly conclusions were that for a very intense and deep penetration into the stone, a solution of 3.5% of SDT buffered with ammonium carbonate to pH around 7 applied with agar support would be indicated. For rust stains in its initial state, the use of Ammonium citrate at a concentration of 5% buffered with ammonium to pH 7 could be applied more than once until satisfactory results appear.

Analysis of panoramio photo tags in order to extract land use information

In the recent past, hardly anyone could predict this course of GIS development. GIS is moving from desktop to cloud. Web 2.0 enabled people to input data into web. These data are becoming increasingly geolocated. Big amounts of data formed something that is called "Big Data". Scientists still don't know how to deal with it completely. Different Data Mining tools are used for trying to extract some useful information from this Big Data. In our study, we also deal with one part of these data - User Generated Geographic Content (UGGC). The Panoramio initiative allows people to upload photos and describe them with tags. These photos are geolocated, which means that they have exact location on the Earth's surface according to a certain spatial reference system. By using Data Mining tools, we are trying to answer if it is possible to extract land use information from Panoramio photo tags. Also, we tried to answer to what extent this information could be accurate. At the end, we compared different Data Mining methods in order to distinguish which one has the most suited performances for this kind of data, which is text. Our answers are quite encouraging. With more than 70% of accuracy, we proved that extracting land use information is possible to some extent. Also, we found Memory Based Reasoning (MBR) method the most suitable method for this kind of data in all cases.

Use of Poisson spatiotemporal regression models for the Brazilian Amazon Forest: malaria count data

INTRODUCTION: Malaria is a serious problem in the Brazilian Amazon region, and the detection of possible risk factors could be of great interest for public health authorities. The objective of this article was to investigate the association between environmental variables and the yearly registers of malaria in the Amazon region using Bayesian spatiotemporal methods. METHODS: We used Poisson spatiotemporal regression models to analyze the Brazilian Amazon forest malaria count for the period from 1999 to 2008. In this study, we included some covariates that could be important in the yearly prediction of malaria, such as deforestation rate. We obtained the inferences using a Bayesian approach and Markov Chain Monte Carlo (MCMC) methods to simulate samples for the joint posterior distribution of interest. The discrimination of different models was also discussed. RESULTS: The model proposed here suggests that deforestation rate, the number of inhabitants per km², and the human development index (HDI) are important in the prediction of malaria cases. CONCLUSIONS: It is possible to conclude that human development, population growth, deforestation, and their associated ecological alterations are conducive to increasing malaria risk. We conclude that the use of Poisson regression models that capture the spatial and temporal effects under the Bayesian paradigm is a good strategy for modeling malaria counts.

Development of cognitive abilities of children infected with helminths through health education

INTRODUCTION: The aim of this study was to evaluate the effect of health education in learning and cognitive development of children infected, previously treated in an endemic area for helminthiasis. METHODS: It is a longitudinal, experimental, with random allocation of participants. The study included 87 children of both sexes enrolled in the school hall of Maranhão, State of Minas Gerais, Brazil, and divided into two groups: intervention and control. Initially the children were submitted to the parasitological fecal examination for infection diagnosis and, when positive, they were treated. For the data collection, a structured questionnaire and the psychological tests Raven, Wisc-III and DAP III were applied, before and after the educational intervention. For the group comparison, the Mann Whitney test was used, and established significance level of 5%. RESULTS: It was found that previously infected children who received the educational intervention, children showed higher performance than the control group in strutured questionnaire (p<0.05). CONCLUSIONS: It is acceptable to suppose the positive influence and the importance in the use of educational interventions in the cognitive recovery and learning of children previously treated with anthelmintics.

Barriers preventing the successful integration of mental health services into Primary Health Care in Nigeria : a mixed methods approach

RESUMO: A Nigéria tem uma população estimada em cerca de 170 milhões de pessoas. O número de profissionais de saúde mental é muito diminuto, contando apenas com 150 psiquiatras o que perfaz aproximadamente um rácio de psiquiatra: população de mais de 1:1 milhão de pessoas. O Plano Nacional de Saúde Mental de 1991 reconheceu esta insuficiência e recomendou a integração dos serviços de saúde mental nos cuidados de saúde primários (CSP). Depois de mais de duas décadas, essa política não foi ainda implementada. Este estudo teve como objetivos mapear a estrutura organizacional dos serviços de saúde mental da Nigéria, e explorar os desafios e barreiras que impedem a integração bem-sucedida dos serviços de saúde mental nos cuidados de saúde primários, isto segundo a perspectiva dos profissionais dos cuidados de saúde primários. Com este objetivo, desenvolveu-se um estudo exploratório sequencial e utilizou-se um modelo misto para a recolha de dados. A aplicação em simultâneo de abordagens qualitativas e quantitativas permitiram compreender os problemas relacionados com a integração dos serviços de saúde mental nos CSP na Nigéria. No estudo qualitativo inicial, foram realizadas entrevistas com listagens abertas a 30 profissionais dos CSP, seguidas de dois grupos focais com profissionais dos CSP de duas zonas governamentais do estado de Oyo de forma a obter uma visão global das perspectivas destes profissionais locais sobre os desafios e barreiras que impedem uma integração bem-sucedida dos serviços de saúde mental nos CSP. Subsequentemente, foram realizadas entrevistas com quatro pessoas-chave, especificamente coordenadores e especialistas em saúde mental. Os resultados do estudo qualitativo foram utilizados para desenvolver um questionário para análise quantitativa das opiniões de uma amostra maior e mais representativa dos profissionais dos CSP do Estado de Oyo, bem como de duas zonas governamentais locais do Estado de Osun. As barreiras mais comummente identificadas a partir deste estudo incluem o estigma e os preconceitos sobre a doença mental, a formação inadequada dos profissionais dos CPS sobre saúde mental, a perceção pela equipa dos CSP de baixa prioridade de ação do Governo, o medo da agressão e violência pela equipa dos CSP, bem como a falta de disponibilidade de fármacos. As recomendações para superar estes desafios incluem a melhoria sustentada dos esforços da advocacia à saúde mental que vise uma maior valorização e apoio governamental, a formação e treino organizados dos profissionais dos cuidados primários, a criação de redes de referência e de apoio com instituições terciárias adjacentes, e o engajamento da comunidade para melhorar o acesso aos serviços e à reabilitação, pelas pessoas com doença mental. Estes resultados fornecem indicações úteis sobre a perceção das barreiras para a integração bem sucedida dos serviços de saúde mental nos CSP, enquanto se recomenda uma abordagem holística e abrangente. Esta informação pode orientar as futuras tentativas de implementação da integração dos serviços de saúde mental nos cuidados primários na Nigéria.------------ABSTRACT: Nigeria has an estimated population of about 170 million people but the number of mental health professionals is very small, with about 150 psychiatrists. This roughly translates to a psychiatrist:population ratio of more than 1:1 million people. The National Mental Health Policy of 1991 recognized this deficiency and recommended the integration of mental health into primary health care (PHC) delivery system. After more than two decades, this policy has yet to be implemented. This study aimed to map out the organizational structure of the mental health systems in Nigeria, and to explore the challenges and barriers preventing the successful integration of mental health into primary health care, from the perspective of the primary health care workers. A mixed methods exploratory sequential study design was employed, which entails the use of sequential timing in the combined methods of data collection. A combination of qualitative and uantitative approaches in sequence, were utilized to understand the problems of mental health services integration into PHC in Nigeria. The initial qualitative phase utilized free listing interviews with 30 PHC workers, followed by two focus group discussions with primary care workers from two Local Government Areas (LGA) of Oyo State to gain useful insight into the local perspectives of PHC workers about the challenges and barriers preventing successful integration of mental health care services into PHC. Subsequently, 4 key informant interviews with PHC co-ordinators and mental health experts were carried out. The findings from the qualitative study were utilized to develop a quantitative study questionnaire to understand the opinions of a larger and more representative sample of PHC staff in two more LGAs of Oyo State, as well as 2 LGAs from Osun State. The common barriers identified from this study include stigma and misconceptions about mental illness, inadequate training of PHC staff about mental health, low government priority, fear of aggression and violence by the PHC staff, as well as non-availability of medications. Recommendations for overcoming these challenges include improved and sustained efforts at mental health advocacy to gain governmental attention and support, organized training and retraining for primary care staff, establishment of referral and supportive networks with neighbouring tertiary facilities and community engagement to improve service utilization and rehabilitation of mentally ill persons. These findings provide useful insight into the barriers to the successful integration of mental health into PHC, while recommending a holistic and comprehensive approach. This information can guide future attempts to implement the integration of mental health into primary care in Nigeria.

HAART: a risk factor for development of porphyria cutanea tarda?

Porphyria cutanea tarda (PCT) is caused by inherited or acquired partial deficiency of the uroporphyrinogen-decarboxylase (Uro-D) enzyme activity. It is the most common form of porphyria. The main triggering factors to the development of porphyria cutanea tarda are alcohol, hepatitis C virus and human immunodeficiency virus. There are several reports of PCT associated with drugs, among them, antiretroviral therapy. We describe three HIV-positive patients, which showed photosensitivity as well as the emergence of tense blisters on sun-exposed areas during the use of highly active antiretroviral therapy (HAART) and discuss the possibility of PCT after the use of these drugs by those patients.

Development of a fundus camera for analysis of photoreceptor directionality in the healthy retina

The Stiles-Crawford effect (SCE) is the well-known phenomenon in which the brightness of light perceived by the human eye depends upon its entrance point in the pupil. This physiological characteristic is due to the directional sensitivity of the cone photoreceptors in the retina and it displays an approximately Gaussian dependency which is altered in a number of pathologies. Retinal imaging, a widely spread clinical practice, may be used to evaluate the SCE and thus serve as diagnostic tool. Nonetheless, its use for such a purpose is still underdeveloped and far from the clinical reality. In this project a fundus camera was built and used to assess the cone photoreceptor directionality by reflective imaging of the retina in healthy individuals. The physical and physiological implications of its development are addressed in detail in the text: the optical properties of the human eye, illumination issues, acquiring a retinal image formed by the eye, among others. A full description of the developmental process that led to the final measuring method and results is also given. The developed setup was successfully used to obtain high quality images of the eye fundus and in particular the parafoveal cone photoreceptors. The SCE was successfully observed and characterized. Even though considerable improvements could be done to the measurement method, the project showed the feasibility of using retinal imaging to evaluate the SCE thus motivating its usage in a clinical environment.