Therapeutics bioconjugates: evaluation of iminoboronates as payload delivery system for cancer

The advent of bioconjugation impacted deeply the world of sciences and technology. New biomolecules were found, biological processes were understood, and novel methodologies were formed due to the fast expansion of this area. The possibility of creating new effective therapies for diseases like cancer is one of big applications of this now big area of study. Off target toxicity was always the problem of potent small molecules with high activity towards specific tumour targets. However, chemotherapy is now selective due to powerful linkers that connect targeting molecules with affinity to interesting biological receptors and cytotoxic drugs. This linkers must have very specific properties, such as high stability in plasma, no toxicity, no interference with ligand affinity nor drug potency, and at the same time, be able to lyse once inside the target molecule to release the therapeutic warhead. Bipolar environments between tumour intracellular and extracellular medias are usually exploited by this linkers in order to complete this goal. The work done in this thesis explores a new model for that same task, specific cancer drug delivery. Iminoboronates were studied due to its remarkable selective stability towards a wide pH range and endogenous molecules. A fluorescence probe was design to validate this model by creating an Off/On system and determine the payload release location in situ. A process was optimized to synthetize the probe 8-(1-aminoethyl)-7-hydroxy-coumarin (1) through a reductive amination reaction in a microwave reactor with 61 % yield. A method to conjugate this probe to ABBA was also optimized, obtaining the iminoboronate in good yields in mild conditions. The iminoboronate model was studied regarding its stability in several simulated biological environments and each half-life time was determined, showing the conjugate is stable most of the cases except in tumour intracellular systems. The construction of folate-ABBA-coumarin bioconjugate have been made to complete this evaluation. The ability to be uptaken by a cancer cell through endocytosis process and the conjugation delivery of coumarin fluorescence payload are two features to hope for in this construct.

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.

Sonae MC: The road model of Kaizen

Sonae MC is considered the first success case of Kaizen in the retail industry. Before becoming a true role model for so many companies, there was a long road to walk. However, it may still be hard to understand the steps taken on the way. How could a training program develop into an integral continuous improvement system, and how did it affect the company – its people, culture, operations and strategy? How was it possible to get everyone on board? How could it be sustained until today, when Kaizen usually fails in the West? What were the critical factors for success?

PALEOENVIRONMENTAL MODEL FOR THE LATE CENOZOIC OF SOUTHWESTERN AMAZONIA: PALEONTOLOGY AND GEOLOGY

Our study provides paleontological and geological data substantiating a paleoenvironmental model for the upper Miocene-Pliocene of Southwestern Amazonia. The extensive Late Tertiary sediments of The Solimões Formation, outcropping in Southwestern Amazonia, were deposited by a complex megafan system, originating in the high Peruvian Andes. The megafan system was the sedimentological response to the Andean Quechua tectonic phase of Tertiary age, producing sediments that fdled the foreland basin of Southwestern Amazonia. Occurrences of varied vertebrate fossil assemblages of the Huayquerian-Montehermosan Mammal age collected in these sediments support this interpretation. The fauna includes several genera and species of fishes, reptiles, birds, mammals and appears to be one that could have lived in or near a riverine habitat. In the Late Pliocene, the megafan system became inactive as a result of the influence of the Diaguita Tectonical Phase.

A decision support system for a waste collection vehicle routing problem

The selective collection of municipal solid waste for recycling is a very complex and expensive process, where a major issue is to perform cost-efficient waste collection routes. Despite the abundance of commercially available software for fleet management, they often lack the capability to deal properly with sequencing problems and dynamic revision of plans and schedules during process execution. Our approach to achieve better solutions for the waste collection process is to model it as a vehicle routing problem, more specifically as a team orienteering problem where capacity constraints on the vehicles are considered, as well as time windows for the waste collection points and for the vehicles. The final model is called capacitated team orienteering problem with double time windows (CTOPdTW).We developed a genetic algorithm to solve routing problems in waste collection modelled as a CTOPdTW. The results achieved suggest possible reductions of logistic costs in selective waste collection.

A spatial multicriteria model for urban accessibility mapping

Accessibility is nowadays an important issue for the development of cities. It is seen as a priority in order toguarantee equal access to fundamental rights, to improve the quality of life of citizens and to ensure that everyone, regardless of age, mobility or ability, have equal access to all the resources and benefits cities have to offer. Consequently, factors closely related to the accessibility have gained a higher relevance for identifying and assessing the location of urban facilities. The main goal of the paper is to present an accessibility evaluation model applied in Santarém, in Brazil, a city located midway between the larger cities of Belem and Manaus. The research instruments, sampling method and data analysis proposed for mapping urban accessibility are described. Daily activities were used to identify and group key destinations. The model was implemented within a geographic information system and integrates the individualâ s perspective through the definition of each key destination weight, reflecting their significance for daily activities in the urban area. Accessibility to key destinations was mapped over 24 districts of the city of Santarém. The results of this model application can support city administration decision-making for new investments in order to improve urban quality of life.

A GIS extension model to calculate urban heat island intensity based on urban geometry

This paper presents a simulation model, which was incorporated into a Geographic Information System (GIS), in order to calculate the maximum intensity of urban heat islands based on urban geometry data. The method-ology of this study stands on a theoretical-numerical basis (Okeâ s model), followed by the study and selection of existing GIS tools, the design of the calculation model, the incorporation of the resulting algorithm into the GIS platform and the application of the tool, developed as exemplification. The developed tool will help researchers to simulate UHI in different urban scenarios.

Generic system for human-computer gesture interaction: applications on sign language recognition and robotic soccer refereeing

Hand gestures are a powerful way for human communication, with lots of potential applications in the area of human computer interaction. Vision-based hand gesture recognition techniques have many proven advantages compared with traditional devices, giving users a simpler and more natural way to communicate with electronic devices. This work proposes a generic system architecture based in computer vision and machine learning, able to be used with any interface for human-computer interaction. The proposed solution is mainly composed of three modules: a pre-processing and hand segmentation module, a static gesture interface module and a dynamic gesture interface module. The experiments showed that the core of visionbased interaction systems could be the same for all applications and thus facilitate the implementation. For hand posture recognition, a SVM (Support Vector Machine) model was trained and used, able to achieve a final accuracy of 99.4%. For dynamic gestures, an HMM (Hidden Markov Model) model was trained for each gesture that the system could recognize with a final average accuracy of 93.7%. The proposed solution as the advantage of being generic enough with the trained models able to work in real-time, allowing its application in a wide range of human-machine applications. To validate the proposed framework two applications were implemented. The first one is a real-time system able to interpret the Portuguese Sign Language. The second one is an online system able to help a robotic soccer game referee judge a game in real time.

Generic system for human-computer gesture interaction

Hand gestures are a powerful way for human communication, with lots of potential applications in the area of human computer interaction. Vision-based hand gesture recognition techniques have many proven advantages compared with traditional devices, giving users a simpler and more natural way to communicate with electronic devices. This work proposes a generic system architecture based in computer vision and machine learning, able to be used with any interface for humancomputer interaction. The proposed solution is mainly composed of three modules: a pre-processing and hand segmentation module, a static gesture interface module and a dynamic gesture interface module. The experiments showed that the core of vision-based interaction systems can be the same for all applications and thus facilitate the implementation. In order to test the proposed solutions, three prototypes were implemented. For hand posture recognition, a SVM model was trained and used, able to achieve a final accuracy of 99.4%. For dynamic gestures, an HMM model was trained for each gesture that the system could recognize with a final average accuracy of 93.7%. The proposed solution as the advantage of being generic enough with the trained models able to work in real-time, allowing its application in a wide range of human-machine applications.

Analysis of output properties of the Peroxiredoxin/Thioredoxin/Thioredoxin reductase system

Dissertação de mestrado em Bioinformática

Improving selective collection of urban waste using a business intelligence system

Today recovering urban waste requires effective management services, which usually imply sophisticated monitoring and analysis mechanisms. This is essential for the smooth running of the entire recycling process as well as for planning and control urban waste recovering. In this paper we present a business intelligence system especially designed and im- plemented to support regular decision-making tasks on urban waste management processes. The system provides a set of domain-oriented analytical tools for studying and characterizing poten- tial scenarios of collection processes of urban waste, as well as for supporting waste manage- ment in urban areas, allowing for the organization and optimization of collection services. In or- der to clarify the way the system was developed and the how it operates, particularly in process visualization and data analysis, we also present the organization model of the system, the ser- vices it disposes, and the interface platforms for exploring data.

Integrated management systems: A model for maturity assessment

Maturity models are adopted to minimise our complexity perception over a truly complex phenomenon. In this sense, maturity models are tools that enable the assessment of the most relevant variables that impact on the outputs of a specific system. Ideally a maturity model should provide information concerning the qualitative and quantitative relationships between variables and how they affect the latent variable, that is, the maturity level. Management systems (MSs) are implemented worldwide and by an increasing number of companies. Integrated management systems (IMSs) consider the implementation of one or several MSs usually coexisting with the quality management subsystem (QMS). It is intended in this chapter to report a model based on two components that enables the assessment of the IMS maturity, considering the key process agents (KPAs) identified through a systematic literature review and the results collected from two surveys.

Refinement and variability techniques in model transformation of software requirements

Tese de Doutoramento em Tecnologias e Sistemas de Informação

Different module placements in a modular façade system for natural ventilation

Nowadays natural ventilation has gained prominence because its correct use can reduce energy consumption for cooling systems and improve thermal comfort among users. In this paper, we report on the modelling initiative, based on the wind tunnel tests that were carried out for the determination of the influence of natural ventilation in buildings. Indeed, the renewal of air in a closed environment without using an air conditioning system with mechanical elements can lead to energy savings and, in addition, provide air quality.The wind tunnel tests were carried out by varying the positioning of six ventilation modules in the façade system configuration. The modules were positioned below the window-sill (ventilated window-sill) as well as separately above and below the façade. The wind speed measurements were taken inside and outside the model for the different façades configurations to evaluate the best performance in relation to natural ventilation. The results supported the positioning of the six ventilation modules below the window-sill, forming a â ventilated window-sillâ as the most effective natural ventilation solution.

Study of natural ventilation for a modular façade system in wind tunnel tests

Wind tunnel tests are a reliable tool to determine the effect of natural ventilation on buildings. This paper presents results of wind tunnel tests conducted to evaluate the influence of ventilation modules positioning on a façade system. Modules positioning was modified, resulting in different façade configurations. The tests were carried out with the use of a model, varying the position of the ventilation modules in the façade configuration. The cases tested were six ventilation modules positioned below the window-sill (ventilated window-sill), and three ventilation modules positioned above and below the façade. The façade system proposed was movable and interchangeable so that the same basic model could be used to test the possibilities for ventilation. Wind speed measurements were taken inside and outside the model for the different façades configurations to evaluate the best performance in relation to natural ventilation. Singleâ sided and Cross ventilation were considered for wind speed measurements. Results show the use of six ventilation modules positioned below the window-sill, forming "a ventilated window-sill" is the best solution in terms of natural ventilation.