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.

Spectroscopic characterization of natural dyes by their non-invasive identification on pre-Columbian codices: the Maya yellow

Mesoamerican cultures had a strong tradition of written and pictorial manuscripts, called the codices. In studies already performed it was found the use of Maya Blue, made from a mixture of indigo and a clay called palygorskite, forming an incredibly stable material where the dye is trapped inside the nanotubes of the clay, after heating. However, a bigger challenge lies in the study of the yellows used, for these civilizations might have used this clay-dye mixture to produce their yellow colorants. As a first step, it was possible to provide identification, by non-invasive methods, of two colorants (a flavonoid and a carotenoid). While the flavonoid absorbed between 368-379 nm, the carotenoid would absorb around 455 nm. A temperature study also conducted allowed to set 140ºC as the desirable temperature to heat the samples without degrading them. FT-IR, conventional Raman and SERS allowed us to understand the existence of a reaction between the dyes and the clays (palygorskite and kaolinite), however it is difficult to understand it in a molecular point of view. As a second step, five species of Mexican dyes were selected on the basis of historical sources. The Maya yellow samples were produced adapting the recipe proposed by Reyes-Valerio, supporting the yellow dyes extracted from the dried plants on the clays, with addition of water, and then heated at 140ºC. It was found that the addition of water in palygorskite would increase the pH, hence deprotonating the molecules having a clear negative effect in the color. A second recipe was developed, without the addition of water; however, it was found that the use of water based binders would still alter the color of the samples with palygorskite. In this case, kaolinite without heating yield better results as a Maya yellow hybrid. It was found that the Maya chemistry might not have been the same for all the colors. The Mesoamericans might have found that different dyes could work better to their desires if matched with different clays. It was noticeable that for a clear distinction between flavonoids and carotenoids the reflectance and emission studies suffice, but when clay is added, Raman techniques will perform better. For this reason, conventional Raman and SERS were employed in order to create a database for the Mesoamerican dyestuffs for a future identification.

Novel Cryopreservation Strategies for Cell‐Therapies and Pre‐Clinical Research

The expanding need for complex biologics for therapeutic applications, in‐vitro pharmacology and toxicology studies and fundamental research demands the production of banks of well‐characterized and safety‐tested stocks of a large number of cell/tissue samples. This implies the development of effective cryopreservation methodologies that can cope with process scalability and automation and must reflect the biological and physical properties of the cells as these can be significantly altered by the process.

Dissecting gastrointestinal dysfunction and inflammation in a “pre-motor” rodent model of Parkinson’s disease

Research on Parkinson’s disease (PD) has mainly focused on the degeneration of the dopaminergic neurons of nigro-striatal (NS) pathway; also, post-mortem studies have demonstrated that the noradrenergic and the serotonergic transmitter systems are also affected (Jellinger, 1999). Degeneration of these neuronal cell bodies is generally thought to start prior to the loss of dopaminergic neurons in the NS pathway and precedes the appearance of the motor symptoms that are the “hallmark” of PD. Gastrointestinal (GI) motility is often disturbed in PD, manifesting chiefly as impaired gastric emptying and constipation. These GI dysfunction symptoms may be the result of a loss in noradrenergic and serotonergic innervation. GI deficits were evaluated using an organ bath technique. Groups treated with different combinations of neurotoxins (6-OHDA alone, 6-OHDA + pCA or 6-OHDA + DSP-4) presented significant differences in gut contractility compared to control groups. Since a substantial body of literature suggests the presence of an inflammatory process in parkinsonian state (Whitton, 2007), changes in pro-inflammatory cytokines in the gut were assessed using a cytokine microarray. It has been found in this work that groups with a combined dopaminergic and noradrenergic lesion have a significant increase in both expressions of IL-13 and VEGF. IL-6 also shows a decrease in treatment groups; however this decrease did not reach statistical significance. The therapeutic value of Exendin-4 (EX-4) was evaluated. It has been previously demonstrated that EX-4, a glucagon-like peptide-1 receptor (GLP-1R) agonist, is neuroprotective in rodent models of PD (Harkavyi et al., 2008). In this thesis it has been found that EX-4 was able to reverse a decrease in gut contractility obtained through intracerebral bilateral 6-OHDA injection. Although more studies are required, EX-4 could be used as a possible therapy for the GI symptoms prominent in the early stages of PD.

Image processing for displacement measurements

Since the invention of photography humans have been using images to capture, store and analyse the act that they are interested in. With the developments in this field, assisted by better computers, it is possible to use image processing technology as an accurate method of analysis and measurement. Image processing's principal qualities are flexibility, adaptability and the ability to easily and quickly process a large amount of information. Successful examples of applications can be seen in several areas of human life, such as biomedical, industry, surveillance, military and mapping. This is so true that there are several Nobel prizes related to imaging. The accurate measurement of deformations, displacements, strain fields and surface defects are challenging in many material tests in Civil Engineering because traditionally these measurements require complex and expensive equipment, plus time consuming calibration. Image processing can be an inexpensive and effective tool for load displacement measurements. Using an adequate image acquisition system and taking advantage of the computation power of modern computers it is possible to accurately measure very small displacements with high precision. On the market there are already several commercial software packages. However they are commercialized at high cost. In this work block-matching algorithms will be used in order to compare the results from image processing with the data obtained with physical transducers during laboratory load tests. In order to test the proposed solutions several load tests were carried out in partnership with researchers from the Civil Engineering Department at Universidade Nova de Lisboa (UNL).

Mobile image processing to support educational geometry games

The mobile IT era is here, it is still growing and expanding at a steady rate and, most of all, it is entertaining. Mobile devices are used for entertainment, whether social through the so-called social networks, or private through web browsing, video watching or gaming. Youngsters make heavy use of these devices, and even small children show impressive adaptability and skill. However not much attention is directed towards education, especially in the case of young children. Too much time is usually spent in games which only purpose is to keep children entertained, time that could be put to better use such as developing elementary geometric notions. Taking advantage of this pocket computer scenario, it is proposed an application geared towards small children in the 6 – 9 age group that allows them to consolidate knowledge regarding geometric shapes, forming a stepping stone that leads to some fundamental mathematical knowledge to be exercised later on. To achieve this goal, the application will detect simple geometric shapes like squares, circles and triangles using the device’s camera. The novelty of this application will be a core real-time detection system designed and developed from the ground up for mobile devices, taking into account their characteristic limitations such as reduced processing power, memory and battery. User feedback was be gathered, aggregated and studied to assess the educational factor of the application.

La Cène ou la figure du banquet comme image de crise morale chez Zeng Fanzhi

Les yeux et les masques sont prévalents dans les oeuvres du peintre chinois contemporain Zeng Fanzhi (né en 1964), comme métaphore du jeu de pouvoir qui oppose les individus à l’appareil social et politique. Son oeuvre La Cène, d’après Leonard de Vinci, est un exemple frappant de cette préoccupation. Cet essai examine l’utilisation par l’artiste de cette représentation occidentale d’une crise morale (une trahison qui mène à la mort du Christ) pour exprimer la dystopie qui marque la Chine contemporaine. L’interprétation par Zeng de l’oeuvre de Vinci témoigne d’une compréhension profonde de sa signification à la Renaissance comme conflit entre le pouvoir terrestre et spirituel, auquel il surimpose la fonction du banquet dans la culture chinoise comme lieu de lutte politique. Un nihilisme détaché imprègne ce travail, à l’instar de l’interprétation métaphorique du banquet de Platon par Søren Kierkegaard, In Vino Veritas.

Crowdfunding campaigns: Perceived quality and success

Research in Crowdfunding is an emerging priority within the field of Entrepreneurship. Hundreds of platforms provide nowadays multiple Crowdfunding schemes which are intended to make it easier for entrepreneurs and others to collect money from the crowd. However, only a few campaigns become successful as others don’t reach the pre-established funding goal. It is thus necessary to keep on understanding the dynamics of these platforms and the factors which justify success. The asymmetry of information has been shown to be a delicate issue as people perceive quality in different manners. As so, this research aims to understand which components of perceived quality mostly influence investments decisions. Mainly Entrepreneurship and Marketing theories were explored along the way. This is research follows a causal approach where nineteen hypotheses are tested. An experimental survey was conducted and data was collected from 127 people who were asked to evaluate one of the most important pieces of any Crowdfunding campaign – the pitch video – and consequently invest on the presented products.

Portuguese footwear

This case study deals with the reasons why the Portuguese Footwear Cluster evolved from a small industry focused on the Portuguese internal market into a high-tech industry capable of designing and producing some of the best and most expensive shoes in the world. It went from using the low labor costs of an under-developed economy to produce long series of shoes for pre-designated brands in Northern Europe to having the ability to produce some of the highest quality shoes in the world, in small orders, designed and delivered in record timing, while offering a service of excellence. In 1960, when Portugal became a founding member of EFTA, the footwear industry in Portugal was globally irrelevant, producing low quality shoes directed to the puny internal market and its African colonies. The new free trade zone with economies much more developed that itself, led to the transfer of the labor-intensive, low skilled manufacture from the UK and Scandinavian countries to Portugal. Mostly through joint ventures, the industry was able to mechanize itself so it could produce shoes in long series at low prices. It grew based on that model up until the 1990s, when the emergence of the Asian countries meant either a different strategy or extinction. Taking advantage of a clarified leadership of its trade association, it used the European funds made available to it during the 1990s, to modernize its factory floors, so it could become more nimble and flexible, expand its design capabilities and dramatically change its image abroad. The role of the trade association, APICCAPS, was instrumental throughout the process going well beyond what came to be expected of trade associations. It used its privileged position to provide understanding regarding the current situation and competitive landscape, alerting for changes ahead and at the same time providing a strategic vision on how to deal with the challenges. Moreover, it helped companies get the resources they needed by creating a research center in collaboration with a University, by creating a process that allowed companies to learn from each other via the show casing of projects sponsored by the association or by helping industrials traveling to locations where new customers could be found. The case study provides insight on how the trade association leadership, which has no formal authority over its members, was able to guide and motivate an industry through a consistent positive approach. That approach focused on the solutions, on the opportunities and on the success stories of companies in the cluster rather than on what was wrong or needed to be addressed. Based on this case, one could use the leadership role of the trade association to discuss and change leaders’ roles and styles in other sectors or even companies.