Development of 3D in vitro models for prediction of hepatic metabolism and toxicity

The development of human cell models that recapitulate hepatic functionality allows the study of metabolic pathways involved in toxicity and disease. The increased biological relevance, cost-effectiveness and high-throughput of cell models can contribute to increase the efficiency of drug development in the pharmaceutical industry. Recapitulation of liver functionality in vitro requires the development of advanced culture strategies to mimic in vivo complexity, such as 3D culture, co-cultures or biomaterials. However, complex 3D models are typically associated with poor robustness, limited scalability and compatibility with screening methods. In this work, several strategies were used to develop highly functional and reproducible spheroid-based in vitro models of human hepatocytes and HepaRG cells using stirred culture systems. In chapter 2, the isolation of human hepatocytes from resected liver tissue was implemented and a liver tissue perfusion method was optimized towards the improvement of hepatocyte isolation and aggregation efficiency, resulting in an isolation protocol compatible with 3D culture. In chapter 3, human hepatocytes were co-cultivated with mesenchymal stem cells (MSC) and the phenotype of both cell types was characterized, showing that MSC acquire a supportive stromal function and hepatocytes retain differentiated hepatic functions, stability of drug metabolism enzymes and higher viability in co-cultures. In chapter 4, a 3D alginate microencapsulation strategy for the differentiation of HepaRG cells was evaluated and compared with the standard 2D DMSO-dependent differentiation, yielding higher differentiation efficiency, comparable levels of drug metabolism activity and significantly improved biosynthetic activity. The work developed in this thesis provides novel strategies for 3D culture of human hepatic cell models, which are reproducible, scalable and compatible with screening platforms. The phenotypic and functional characterization of the in vitro systems performed contributes to the state of the art of human hepatic cell models and can be applied to the improvement of pre-clinical drug development efficiency of the process, model disease and ultimately, development of cell-based therapeutic strategies for liver failure.

The accuracy of the escrowed dividend model on the value of European options on a stock paying discrete dividend

This project characterizes the accuracy of the escrowed dividend model on the value of European options on a stock paying discrete dividend. A description of the escrowed dividend model is provided, and a comparison between this model and the benchmark model is realized. It is concluded that options on stocks with either low volatility, low dividend yield, low ex-dividend to maturity ratio or that are deep in or out of the money are reasonably priced with the escrowed dividend model.

Produção e caracterização de espumas 3D obtidas por electrofiação para aplicação em engenharia de tecidos

A produção de estruturas tridimensionais poliméricas tem sido foco de estudo por parte da Engenharia de Células e Tecidos, pelo que mimetizam melhor as condições in vivo dos tecidos. A conjugação das propriedades eléctricas com arquitectura 3D permite uma regeneração tecidual mais eficaz. Desta forma este estudo incidiu na construção de scaffolds, que conjugasse as propriedades mecânicas, eléctricas e biológicas num só suporte. O processo utilizado para produção de scaffolds baseou-se na electrofiação de soluções poliméricas de PCL (8% m/m) com incorporação de óxido de grafeno em diferentes concentrações: 0.01%, 0.1% e 0.25% (m/V). Foram avaliados os parâmetros de electrofiação que permitiram a organização tridimensional. A composição química e a morfologia das membranas foram avaliadas por FTIR-ATR e por microscopia electrónica de varrimento (MEV), respectivamente. Através de ensaios de tracção e de permeabilidade estudou-se a influência de óido de grafeno na matriz polimérica. Foram feitas experiências de redução de óxido de grafeno nas fibras electrofiadas, tanto nas membranas como das espumas, através do uso de vapores de hidrazina. Este mecanismo mostrou-se ineficaz, uma vez que afectou a sua morfologia. As espumas foram avaliadas quanto à sua bioactividade e propriedades mecânicas (ensaios de compressão). Também foram realizados testes de viabilidade celular nas membranas e de adesão celular nas espumas, de forma a avaliar o seu potencial para aplicação biomédica. Os resultados destes ensaios revelaram que óxido de grafeno não apresenta efeitos citotóxicos para o organismo e a sua presença promove a adesão celular ao scaffold.

Jogo 3D online para reabilitação de pacientes afásicos

Esta plataforma foi projetada como auxílio complementar ao processo de reabilitação de doentes afásicos lusófonos. Uma gama de exercícios são disponibilizados de forma a induzir diferentes estímulos (compreensão escrita e auditiva e expressão escrita) sendo a grande maioria destes realizados dentro de um ambiente virtual em três dimensões onde o utilizador (dependendo da tarefa) pode interagir com objetos presentes dentro de uma casa. A principal particularidade desta plataforma reside no facto desta estar alojada online, dispensando instalações e permitindo um acompanhamento mais próximo por parte do terapeuta da fala do progresso feito pelo paciente. A ferramenta desenvolvida está disponível para visualização e teste no endereço www.weblisling.net.

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.

Compaction quality control on site of earthworks - A comparative study

The capacity to use geologic materials (soil and rock) that are available in the surrounding environment is inherent to the human civilization and has contributed to the evolution of societies throughout the course of history. The use of these materials in the construction of structures such as houses, roads, railways or dams, stirred the improvement of socioeconomic and environmental conditions. Several reports of structural problems on embankments can be found throughout history. A considerable number of those registers can be linked to inadequate compaction, demonstrating the importance of guaranteeing a suitable quality of soil compaction. Various methodologies and specifications of compaction quality control on site of earthworks, based on the fill moisture content and dry unit weight, were developed during the 20th century. Two widely known methodologies are the conventional and nuclear techniques. The conventional methods are based on the use of the field sand cone test (or similar) and sampling of material for laboratory-based testing to evaluate the fill dry unit weight and water content. The nuclear techniques measure both parameters in the field using a nuclear density gauge. A topic under discussion in the geotechnical community, namely in Portugal, is the comparison between the accuracy of the nuclear gauge and sand cone test results for assessing the compaction and density ratio of earth fills, particularly for dams. The main purpose of this dissertation is to compare both of them. The data used were acquired during the compaction quality control operations at the Coutada/Tamujais dam trial embankment and core construction. This is a 25 m high earth dam located in Vila Velha de Rodão, Portugal. To analyse the spatial distribution of the compaction parameters (water content and compaction ratio), a 3D model was also developed. The main results achieved are discussed and finally some considerations are put forward on the suitability of both techniques to ensure fill compaction quality and on additional research to complement the conclusions obtained.

Building 3D City Models: Testing and Comparing Laser Scanning and Low-Cost UAV Data Using FOSS Technologies

Contém resumo

Improving accuracy of inflation forecasts using macroeconomic information

This thesis examines the effects of macroeconomic factors on inflation level and volatility in the Euro Area to improve the accuracy of inflation forecasts with econometric modelling. Inflation aggregates for the EU as well as inflation levels of selected countries are analysed, and the difference between these inflation estimates and forecasts are documented. The research proposes alternative models depending on the focus and the scope of inflation forecasts. I find that models with a Generalized AutoRegressive Conditional Heteroskedasticity (GARCH) in mean process have better explanatory power for inflation variance compared to the regular GARCH models. The significant coefficients are different in EU countries in comparison to the aggregate EU-wide forecast of inflation. The presence of more pronounced GARCH components in certain countries with more stressed economies indicates that inflation volatility in these countries are likely to occur as a result of the stressed economy. In addition, other economies in the Euro Area are found to exhibit a relatively stable variance of inflation over time. Therefore, when analysing EU inflation one have to take into consideration the large differences on country level and focus on those one by one.

Development of human central nervous system 3D in vitro models for preclinical research

Neurological disorders are a major concern in modern societies, with increasing prevalence mainly related with the higher life expectancy. Most of the current available therapeutic options can only control and ameliorate the patients’ symptoms, often be-coming refractory over time. Therapeutic breakthroughs and advances have been hampered by the lack of accurate central nervous system (CNS) models. The develop-ment of these models allows the study of the disease onset/progression mechanisms and the preclinical evaluation of novel therapeutics. This has traditionally relied on genetically engineered animal models that often diverge considerably from the human phenotype (developmentally, anatomically and physiologically) and 2D in vitro cell models, which fail to recapitulate the characteristics of the target tissue (cell-cell and cell-matrix interactions, cell polarity). The in vitro recapitulation of CNS phenotypic and functional features requires the implementation of advanced culture strategies that enable to mimic the in vivo struc-tural and molecular complexity. Models based on differentiation of human neural stem cells (hNSC) in 3D cultures have great potential as complementary tools in preclinical research, bridging the gap between human clinical studies and animal models. This thesis aimed at the development of novel human 3D in vitro CNS models by integrat-ing agitation-based culture systems and a wide array of characterization tools. Neural differentiation of hNSC as 3D neurospheres was explored in Chapter 2. Here, it was demonstrated that human midbrain-derived neural progenitor cells from fetal origin (hmNPC) can generate complex tissue-like structures containing functional dopaminergic neurons, as well as astrocytes and oligodendrocytes. Chapter 3 focused on the development of cellular characterization assays for cell aggregates based on light-sheet fluorescence imaging systems, which resulted in increased spatial resolu-tion both for fixed samples or live imaging. The applicability of the developed human 3D cell model for preclinical research was explored in Chapter 4, evaluating the poten-tial of a viral vector candidate for gene therapy. The efficacy and safety of helper-dependent CAV-2 (hd-CAV-2) for gene delivery in human neurons was evaluated, demonstrating increased neuronal tropism, efficient transgene expression and minimal toxicity. The potential of human 3D in vitro CNS models to mimic brain functions was further addressed in Chapter 5. Exploring the use of 13C-labeled substrates and Nucle-ar Magnetic Resonance (NMR) spectroscopy tools, neural metabolic signatures were evaluated showing lineage-specific metabolic specialization and establishment of neu-ron-astrocytic shuttles upon differentiation. Chapter 6 focused on transferring the knowledge and strategies described in the previous chapters for the implementation of a scalable and robust process for the 3D differentiation of hNSC derived from human induced pluripotent stem cells (hiPSC). Here, software-controlled perfusion stirred-tank bioreactors were used as technological system to sustain cell aggregation and dif-ferentiation. The work developed in this thesis provides practical and versatile new in vitro ap-proaches to model the human brain. Furthermore, the culture strategies described herein can be further extended to other sources of neural phenotypes, including pa-tient-derived hiPSC. The combination of this 3D culture strategy with the implemented characterization methods represents a powerful complementary tool applicable in the drug discovery, toxicology and disease modeling.

GEOCHEMISTRY AND GEOCHRONOLOGY OF SURFICIAL ACRE BASIN SEDIMENTS (WESTERN AMAZONIA): KEY INFORMATION FOR CLIMATE RECONSTRUCTION.

Geochemical and geochronological analyses of samples of surficial Acre Basin sediments and fossils indicate an extensive fluvial-lacustrine system, occupying this region, desiccated slowly during the last glacial cycle (LGC). This research documents direct evidence for aridity in western Amazonia during the LGC and is important in establishing boundary conditions for LGC climate models as well as in correlating marine and continental (LGC) climate conditions.

Genetic algorithm for shipping route estimation with long-range tracking data : automatic reconstruction of shipping routes based on the historical ship positions for maritime safety applications

Ship tracking systems allow Maritime Organizations that are concerned with the Safety at Sea to obtain information on the current location and route of merchant vessels. Thanks to Space technology in recent years the geographical coverage of the ship tracking platforms has increased significantly, from radar based near-shore traffic monitoring towards a worldwide picture of the maritime traffic situation. The long-range tracking systems currently in operations allow the storage of ship position data over many years: a valuable source of knowledge about the shipping routes between different ocean regions. The outcome of this Master project is a software prototype for the estimation of the most operated shipping route between any two geographical locations. The analysis is based on the historical ship positions acquired with long-range tracking systems. The proposed approach makes use of a Genetic Algorithm applied on a training set of relevant ship positions extracted from the long-term storage tracking database of the European Maritime Safety Agency (EMSA). The analysis of some representative shipping routes is presented and the quality of the results and their operational applications are assessed by a Maritime Safety expert.

PHB-HV 3D Scaffold supports osteoblast growth

Bone tissue engineering requires a biocompatible scaffold that supports cell growth and enhances the native repair process. Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHB-HV) is a biodegradable 3D scaffold with 88.1 â 0.3% porosity and pore size of 163.5 â 0.1 mm. Previous studies demonstrated the potential of PHB-HV as a scaffold in spinal cord repair. The aim of this study was to evaluate PHB-HV as a scaffold for bone regeneration by assessing the cytocompatability of this scaffold.

Cell encapsulated hydrogel microspheres as "building blocks" for producing 3D constructs

Cell encapsulation within hydrogel microspheres shows great promise in the field of tissue engineering and regenerative medicine (TERM). However, the assembling of microspheres as building blocks to produce complex tissues is a hard task because of their inability to place along length scales in space. We propose a proof-of-concept strategy to produce 3D constructs using cell encapsulated as building blocks by perfusion based LbL technique. This technique exploits the â bindingâ potential of multilayers apart from coating

Análisis mecánico de albañilería arqueológica de adobe bajo cargas de compresión uniaxial: El caso de Huaca de la Luna

This article presents an experimental and numerical study for the mechanical characterization under uniaxial compressive loading of the adobe masonry of one of the most emblematic archaeological complex in Peru, 'Huaca de la Luna' (100-650AD). Compression tests of prisms were carried out with original material brought to the laboratory. For measuring local deformations in the tests, displacement transducers were used which were complemented by a digital image correlation system which allowed a better understanding of the failure mechanism. The tests were then numerically simulated by modelling the masonry as a continuum media. Several approaches were considered concerning the geometrical modelling, namely 2D and 3D simplified models, and 3D refined models based on a photogrammetric reconstruction. The results showed a good approximation between the numerical prediction and the experimental response in all cases. However, the 3D models with irregular geometries seem to reproduce better the cracking pattern observed in the tests.

The role of temporary accommodation buildings for post-disaster housing reconstruction

The number of houses damaged or destroyed after disasters is frequently large, and re-housing of homeless people is one of the most important tasks of reconstruction programmes. Reconstruction works often last long and during that time, it is essential to provide victims with the minimum conditions to live with dignity, privacy, and protection. This research intends to demonstrate the crucial role of temporary accommodation buildings to provide spaces where people can live and gradually resume their life until they have a permanent house. The study also aims to identify the main problems of temporary accommodation strategies and to discuss some principles and guidelines in order to reach better design solutions. It is found that temporary accommodation is an issue that goes beyond the simple provision of buildings, since the whole space for temporary settlement is important. Likewise, temporary accommodation is a process that should start before a disaster occurs, as a preventive pre-planning. In spite of being temporary constructions, these housing buildings are one of the most important elements to provide in emergency scenarios, contributing for better recovery and reconstruction actions.