Produção Lean com visualização do fluxo de trabalho em 3D

Magazine Digital eUAU - Março 2011

Desenvolvimento de dispositivos microfluídicos 3D em papel para utilização em biossensores

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Data-centric concurrency control on the java programming language

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Produção de espumas 3D porosas por auto-organização de nanofibras de policaprolactona

Dissertação para obtenção do Grau de Mestre em Engenharia Biomédica

Evaluation of chemotherapeutic potential of natural extracts using 3D models of colon cancer

Dissertation to obtain master degree in Biotechnology

Modelação 3D de teores de depósitos minerais condicionados por tipos de mineralização. O caso de estudo do depósito mineral do Zambujal, Minas de Neves-Corvo

Dissertação para obtenção do Grau de Mestre em Engenharia Geológica (Georrecursos)

Estruturas 3D porosas com gradiente de funcionalidade produzidas por Freeze-casting

Dissertação para obtenção do Grau de Mestre em Engenharia de Materiais

Child programming: an adequate domain specific language for programming specific robots

Dissertação para obtenção do Grau de Mestre em Engenharia Informática

Optimization of breast tomosynthesis image reconstruction using parallel computing

Breast cancer is the most common cancer among women, being a major public health problem. Worldwide, X-ray mammography is the current gold-standard for medical imaging of breast cancer. However, it has associated some well-known limitations. The false-negative rates, up to 66% in symptomatic women, and the false-positive rates, up to 60%, are a continued source of concern and debate. These drawbacks prompt the development of other imaging techniques for breast cancer detection, in which Digital Breast Tomosynthesis (DBT) is included. DBT is a 3D radiographic technique that reduces the obscuring effect of tissue overlap and appears to address both issues of false-negative and false-positive rates. The 3D images in DBT are only achieved through image reconstruction methods. These methods play an important role in a clinical setting since there is a need to implement a reconstruction process that is both accurate and fast. This dissertation deals with the optimization of iterative algorithms, with parallel computing through an implementation on Graphics Processing Units (GPUs) to make the 3D reconstruction faster using Compute Unified Device Architecture (CUDA). Iterative algorithms have shown to produce the highest quality DBT images, but since they are computationally intensive, their clinical use is currently rejected. These algorithms have the potential to reduce patient dose in DBT scans. A method of integrating CUDA in Interactive Data Language (IDL) is proposed in order to accelerate the DBT image reconstructions. This method has never been attempted before for DBT. In this work the system matrix calculation, the most computationally expensive part of iterative algorithms, is accelerated. A speedup of 1.6 is achieved proving the fact that GPUs can accelerate the IDL implementation.

Amorphous silicon e 3D sensors applied to object detection

Nowadays, existing 3D scanning cameras and microscopes in the market use digital or discrete sensors, such as CCDs or CMOS for object detection applications. However, these combined systems are not fast enough for some application scenarios since they require large data processing resources and can be cumbersome. Thereby, there is a clear interest in exploring the possibilities and performances of analogue sensors such as arrays of position sensitive detectors with the final goal of integrating them in 3D scanning cameras or microscopes for object detection purposes. The work performed in this thesis deals with the implementation of prototype systems in order to explore the application of object detection using amorphous silicon position sensors of 32 and 128 lines which were produced in the clean room at CENIMAT-CEMOP. During the first phase of this work, the fabrication and the study of the static and dynamic specifications of the sensors as well as their conditioning in relation to the existing scientific and technological knowledge became a starting point. Subsequently, relevant data acquisition and suitable signal processing electronics were assembled. Various prototypes were developed for the 32 and 128 array PSD sensors. Appropriate optical solutions were integrated to work together with the constructed prototypes, allowing the required experiments to be carried out and allowing the achievement of the results presented in this thesis. All control, data acquisition and 3D rendering platform software was implemented for the existing systems. All these components were combined together to form several integrated systems for the 32 and 128 line PSD 3D sensors. The performance of the 32 PSD array sensor and system was evaluated for machine vision applications such as for example 3D object rendering as well as for microscopy applications such as for example micro object movement detection. Trials were also performed involving the 128 array PSD sensor systems. Sensor channel non-linearities of approximately 4 to 7% were obtained. Overall results obtained show the possibility of using a linear array of 32/128 1D line sensors based on the amorphous silicon technology to render 3D profiles of objects. The system and setup presented allows 3D rendering at high speeds and at high frame rates. The minimum detail or gap that can be detected by the sensor system is approximately 350 μm when using this current setup. It is also possible to render an object in 3D within a scanning angle range of 15º to 85º and identify its real height as a function of the scanning angle and the image displacement distance on the sensor. Simple and not so simple objects, such as a rubber and a plastic fork, can be rendered in 3D properly and accurately also at high resolution, using this sensor and system platform. The nip structure sensor system can detect primary and even derived colors of objects by a proper adjustment of the integration time of the system and by combining white, red, green and blue (RGB) light sources. A mean colorimetric error of 25.7 was obtained. It is also possible to detect the movement of micrometer objects using the 32 PSD sensor system. This kind of setup offers the possibility to detect if a micro object is moving, what are its dimensions and what is its position in two dimensions, even at high speeds. Results show a non-linearity of about 3% and a spatial resolution of < 2µm.

Writing/erasing 3D micro and nano wrinkles in flexible elastomers for volatile organic compounds sensor

Micro/nano wrinkled patterns on cross-linked urethane/urea polymeric flexible free standing films with two soft segments, polypropylene oxide and polybutadiene, can be induced by UV-irradiation. The ability to write/erase these 3D structures, in a controlled manner, is the main focus of this work. The imprinting of the wrinkled structures was accomplished by swelling in an appropriate solvent followed by drying the membranes after the cross-linking process and UV irradiation. The surface tailoring of the elastomeric membranes was imaged by optical microscopy, scanning electronic microscopy and by atomic force microscopy. To erase the wrinkled structures the elastomers were swollen. The swelling as well as the sol/gel fraction and the UV radiation were tuned in order to control the wrinkles characteristics. It was found that the wrinkles wavelength, in the order of microns (1±0,25μm), was stamped by the UV radiation intensity and exposure time while the wrinkles' amplitude, in the order of nanometers (150-450 nm), was highly dependent on the swelling and sol/gel fraction. A prototype for volatile organic compounds detection was developed taking advantage of the unique 3D micro/nano wrinkles features.

Towards an algorithmic skeleton framework for programming the Intel R Xeon PhiTM processor

The Intel R Xeon PhiTM is the first processor based on Intel’s MIC (Many Integrated Cores) architecture. It is a co-processor specially tailored for data-parallel computations, whose basic architectural design is similar to the ones of GPUs (Graphics Processing Units), leveraging the use of many integrated low computational cores to perform parallel computations. The main novelty of the MIC architecture, relatively to GPUs, is its compatibility with the Intel x86 architecture. This enables the use of many of the tools commonly available for the parallel programming of x86-based architectures, which may lead to a smaller learning curve. However, programming the Xeon Phi still entails aspects intrinsic to accelerator-based computing, in general, and to the MIC architecture, in particular. In this thesis we advocate the use of algorithmic skeletons for programming the Xeon Phi. Algorithmic skeletons abstract the complexity inherent to parallel programming, hiding details such as resource management, parallel decomposition, inter-execution flow communication, thus removing these concerns from the programmer’s mind. In this context, the goal of the thesis is to lay the foundations for the development of a simple but powerful and efficient skeleton framework for the programming of the Xeon Phi processor. For this purpose we build upon Marrow, an existing framework for the orchestration of OpenCLTM computations in multi-GPU and CPU environments. We extend Marrow to execute both OpenCL and C++ parallel computations on the Xeon Phi. We evaluate the newly developed framework, several well-known benchmarks, like Saxpy and N-Body, will be used to compare, not only its performance to the existing framework when executing on the co-processor, but also to assess the performance on the Xeon Phi versus a multi-GPU environment.

Produção de matrizes porosas 3D baseadas em réplicas invertidas de cristais coloidais

A Engenharia de Tecidos surge da necessidade recorrente de regenerar ou recriar órgãos e tecidos danificados devido a vários tipos de trauma. A carência de funcionalidades resultante pode ser resolvida através da implantação de substitutos bio-sintéticos. O presente trabalho consiste na produção de matrizes porosas 3D baseadas em réplicas invertidas de cristais coloidais com futura aplicação em substituintes ósseos sintéticos para fraturas de não-união. O substituinte ósseo consiste numa estrutura denominada Inverse colloidal crystal (ICC), em que a sua organização singular resulta numa homogénea proliferação celular e num aumento das propriedades mecânicas, quando comparada com outros substituintes. O primeiro passo para a obtenção desta estrutura é a produção de microesferas de poliestireno, por uma técnica baseada em microfluídica. Posteriormente as microesferas são empacotadas resultando numa estrutura coesa com ligações entre microesferas vizinhas. O preenchimento dos espaços vazios entre microesferas pelo biomaterial pretendido e posterior remoção das microesferas dá origem à estrutura porosa do ICC. ICCs poliméricos (ϕCs = 1,00) e compósitos (ϕCs = 0,86 e ϕHA = 0,14; ϕCs = 0,67 e ϕHA = 0,33; ϕCs = ϕHA = 0,50) são produzidos e as suas propriedades mecânicas são testadas através de ensaios de compressão e comparadas com outros substituintes sintéticos. Para avaliação do comportamento dos materiais em contacto com meio biológico, foram realizados testes de citotoxicidade que revelaram uma viabilidade celular acima dos 80% em todos os ICCs.

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.

Machine ethics via logic programming

Machine ethics is an interdisciplinary field of inquiry that emerges from the need of imbuing autonomous agents with the capacity of moral decision-making. While some approaches provide implementations in Logic Programming (LP) systems, they have not exploited LP-based reasoning features that appear essential for moral reasoning. This PhD thesis aims at investigating further the appropriateness of LP, notably a combination of LP-based reasoning features, including techniques available in LP systems, to machine ethics. Moral facets, as studied in moral philosophy and psychology, that are amenable to computational modeling are identified, and mapped to appropriate LP concepts for representing and reasoning about them. The main contributions of the thesis are twofold. First, novel approaches are proposed for employing tabling in contextual abduction and updating – individually and combined – plus a LP approach of counterfactual reasoning; the latter being implemented on top of the aforementioned combined abduction and updating technique with tabling. They are all important to model various issues of the aforementioned moral facets. Second, a variety of LP-based reasoning features are applied to model the identified moral facets, through moral examples taken off-the-shelf from the morality literature. These applications include: (1) Modeling moral permissibility according to the Doctrines of Double Effect (DDE) and Triple Effect (DTE), demonstrating deontological and utilitarian judgments via integrity constraints (in abduction) and preferences over abductive scenarios; (2) Modeling moral reasoning under uncertainty of actions, via abduction and probabilistic LP; (3) Modeling moral updating (that allows other – possibly overriding – moral rules to be adopted by an agent, on top of those it currently follows) via the integration of tabling in contextual abduction and updating; and (4) Modeling moral permissibility and its justification via counterfactuals, where counterfactuals are used for formulating DDE.