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.

Framework for the semantic alignment of enterprise’s domain knowledge

Nowadays, the consumption of goods and services on the Internet are increasing in a constant motion. Small and Medium Enterprises (SMEs) mostly from the traditional industry sectors are usually make business in weak and fragile market sectors, where customized products and services prevail. To survive and compete in the actual markets they have to readjust their business strategies by creating new manufacturing processes and establishing new business networks through new technological approaches. In order to compete with big enterprises, these partnerships aim the sharing of resources, knowledge and strategies to boost the sector’s business consolidation through the creation of dynamic manufacturing networks. To facilitate such demand, it is proposed the development of a centralized information system, which allows enterprises to select and create dynamic manufacturing networks that would have the capability to monitor all the manufacturing process, including the assembly, packaging and distribution phases. Even the networking partners that come from the same area have multi and heterogeneous representations of the same knowledge, denoting their own view of the domain. Thus, different conceptual, semantic, and consequently, diverse lexically knowledge representations may occur in the network, causing non-transparent sharing of information and interoperability inconsistencies. The creation of a framework supported by a tool that in a flexible way would enable the identification, classification and resolution of such semantic heterogeneities is required. This tool will support the network in the semantic mapping establishments, to facilitate the various enterprises information systems integration.

Methodological framework for detection of harmonisation breaking in service environments

As the complexity of markets and the dynamicity of systems evolve, the need for interoperable systems capable of strengthening enterprise communication effectiveness increases. This is particularly significant when it comes to collaborative enterprise networks, like manufacturing supply chains, where several companies work, communicate, and depend on each other, in order to achieve a specific goal. Once interoperability is achieved, that is once all network parties are able to communicate with and understand each other, organisations are able to exchange information along a stable environment that follows agreed laws. However, as markets adapt to new requirements and demands, an evolutionary behaviour is triggered giving space to interoperability problems, thus disrupting the sustainability of interoperability and raising the need to develop monitoring activities capable of detecting and preventing unexpected behaviour. This work seeks to contribute to the development of monitoring techniques for interoperable SOA-based enterprise networks. It focuses on the automatic detection of harmonisation breaking events during real-time communications, and strives to develop and propose a methodological approach to handle these disruptions with minimal or no human intervention, hence providing existing service-based networks with the ability to detect and promptly react to interoperability issues.

Development and validation of gold nanoprobes for human SNP detection towards commercial application

Conventional molecular techniques for detection and characterization of relevant nucleic acid (i.e. DNA) sequences are, nowadays, cumbersome, expensive and with reduced portability. The main objective of this dissertation consisted in the optimization and validation of a fast and low-cost colorimetric nanodiagnostic methodology for the detection of single nucleotide polymorphisms (SNPs). This was done considering SNPs associated to obesity of commercial interest for STAB VIDA, and subsequent evaluation of other clinically relevant targets. Also, integration of this methodology into a microfluidic platform envisaging portability and application on points-of-care (POC) was achieved. To warrant success in pursuing these objectives, the experimental work was divided in four sections: i) genetic association of SNPs to obesity in the Portuguese population; ii) optimization and validation of the non-cross-linking approach for complete genotype characterization of these SNPs; iii) incorporation into a microfluidic platform; and iv) translation to other relevant commercial targets. FTO dbSNP rs#:9939609 carriers had higher body mass index (BMI), total body fat mass, waist perimeter and 2.5 times higher risk to obesity. AuNPs functionalized with thiolated oligonucleotides (Au-nanoprobes) were used via the non-cross-linking to validate a diagnostics approach against the gold standard technique - Sanger Sequencing - with high levels of sensitivity (87.50%) and specificity (91.67%). A proof-of-concept POC microfluidic device was assembled towards incorporation of the molecular detection strategy. In conclusion a successful framework was developed and validated for the detection of SNPs with commercial interest for STAB VIDA, towards future translation into a POC device.

Contribution to drug discovery and development for tauopathies using yeast as a model

This work aimed to contribute to drug discovery and development (DDD) for tauopathies, while expanding our knowledge on this group of neurodegenerative disorders, including Alzheimer’s disease (AD). Using yeast, a recognized model for neurodegeneration studies, useful models were produced for the study of tau interaction with beta-amyloid (Aβ), both AD hallmark proteins. The characterization of these models suggests that these proteins co-localize and that Aβ1-42, which is toxic to yeast, is involved in tau40 phosphorylation (Ser396/404) via the GSK-3β yeast orthologue, whereas tau seems to facilitate Aβ1-42 oligomerization. The mapping of tau’s interactome in yeast, achieved with a tau toxicity enhancer screen using the yeast deletion collection, provided a novel framework, composed of 31 genes, to identify new mechanisms associated with tau pathology, as well as to identify new drug targets or biomarkers. This genomic screen also allowed to select the yeast strain mir1Δ-tau40 for development of a new GPSD2TM drug discovery screening system. A library of unique 138 marine bacteria extracts, obtained from the Mid-Atlantic Ridge hydrothermal vents, was screened with mir1Δ-tau40. Three extracts were identified as suppressors of tau toxicity and constitute good starting points for DDD programs. mir1Δ strain was sensitive to tau toxicity, relating tau pathology with mitochondrial function. SLC25A3, the human homologue of MIR1, codes for the mitochondrial phosphate carrier protein (PiC). Resorting to iRNA, SLC25A3 expression was silenced in human neuroglioma cells, as a first step towards the engineering of a neural model for replicating the results obtained in yeast. This model is essential to understand the mechanisms of tau toxicity at the mitochondrial level and to validate PiC as a relevant drug target. The set of DDD tools here presented will foster the development of innovative and efficacious therapies, urgently needed to cope with tau-related disorders of high human and social-economic impact.

Development of biomimetic microengineered hydrogel fibers for tendon regeneration

Musculoskeletal diseases are one of the leading causes of disability worldwide. Tendon injuries are responsible for substantial morbidity, pain and disability. Tissue engineering strategies aim at translating tendon structure into biomimetic materials. The main goal of the present study is to develop microengineered hydrogel fibers through the combination of microfabrication and chemical interactions between oppositely charged polyelectrolytes. For this, methacrylated hyaluronic acid (MeHA) and chondroitin sulfate (MeCS) were combined with chitosan (CHT). Hydrogel fibers were obtained by injecting polymer solutions (either MeHA or MeHA/MeCS and CHT) in separate microchannels that join at a y-junction, with the materials interacting upon contact at the interface. To evaluate cell behavior, human tendon derived cells (hTDCs) were isolated from tendon surplus samples during orthopedic surgeries and seeded on top of the fibers. hTDCs adhered to the surface of the fibers, remaining viable, and were found to be expressing CD44, the receptor for hyaluronic acid. The synthesis of hydrogel fibers crosslinkable through both physical and chemical mechanisms combined with microfabrication technology allows the development of biomimetic structures with parallel fibers being formed towards the replication of tendon tissue architecture.

Thermo-compression molding of chitosan with a deep eutectic mixture for biofilms development

Supplementary information available at: http://www.rsc.org/suppdata/c5/gc/c5gc02231b/c5gc02231b1.pdf

An automated framework for the management of P2P traffic in ISP infrastructures

Peer-to-Peer (P2P) is nowadays a widely used paradigm underpinning the deployment of several Internet services and applications. However, the management of P2P traffic aggregates is not an easy task for Internet Service Providers (ISPs). In this perspective, and considering an expectable proliferation in the use of such ap- plications, future networks require the development of smart mechanisms fostering an easier coexistence between P2P applications and ISP infrastructures. This paper aims to contribute for such research efforts presenting a framework incorporating useful mechanisms to be activated by network administrators, being also able to operate as an automated management tool dealing with P2P traffic aggregates.

Step towards multiplatform framework for supporting pediatric and neonatology care unit decision process

Children are an especially vulnerable population, particularly in respect to drug administration. It is estimated that neonatal and pediatric patients are at least three times more vulnerable to damage due to adverse events and medication errors than adults are. With the development of this framework, it is intended the provision of a Clinical Decision Support System based on a prototype already tested in a real environment. The framework will include features such as preparation of Total Parenteral Nutrition prescriptions, table pediatric and neonatal emergency drugs, medical scales of morbidity and mortality, anthropometry percentiles (weight, length/height, head circumference and BMI), utilities for supporting medical decision on the treatment of neonatal jaundice and anemia and support for technical procedures and other calculators and widespread use tools. The solution in development means an extension of INTCare project. The main goal is to provide an approach to get the functionality at all times of clinical practice and outside the hospital environment for dissemination, education and simulation of hypothetical situations. The aim is also to develop an area for the study and analysis of information and extraction of knowledge from the data collected by the use of the system. This paper presents the architecture, their requirements and functionalities and a SWOT analysis of the solution proposed.

Development of an integral viscoelastic flow solver in OpenFOAM®

The usual high cost of commercial codes, and some technical limitations, clearly limits the employment of numerical modelling tools in both industry and academia. Consequently, the number of companies that use numerical code is limited and there a lot of effort put on the development and maintenance of in-house academic based codes. Having in mind the potential of using numerical modelling tools as a design aid, of both products and processes, different research teams have been contributing to the development of open source codes/libraries. In this framework, any individual can take advantage of the available code capabilities and/or implement additional features based on his specific needs. These type of codes are usually developed by large communities, which provide improvements and new features in their specific fields of research, thus increasing significantly the code development process. Among others, OpenFOAM® multi-physics computational library, developed by a very large and dynamic community, nowadays comprises several features usually only available in their commercial counterparts; e.g. dynamic meshes, large diversity of complex physical models, parallelization, multiphase models, to name just a few. This computational library is developed in C++ and makes use of most of all language capabilities to facilitate the implementation of new functionalities. Concerning the field of computational rheology, OpenFOAM® solvers were recently developed to deal with the most relevant differential viscoelastic rheological models, and stabilization techniques are currently being verified. This work describes the implementation of a new solver in OpenFOAM® library, able to cope with integral viscoelastic models based on the deformation field method. The implemented solver is verified through the comparison of the predicted results with analytical solutions, results published in the literature and by using the Method of Manufactured Solutions.

Development of magnetoelectric CoFe2O4/poly(vinylidene fluoride) microspheres

Magnetoelectric microspheres based on piezoelectric poly(vinylidene fluoride) (PVDF) and magnetrostrictive CoFe2O4 (CFO), a novel morphology for polymer-based ME material, have been developed by an electrospray process. The CFO nanoparticles content in the (3-7 μm diameter) microspheres reaches values up to 27 wt.%, despite their concentration in the starting solution reaching values up to 70 wt.%. Additionally, the inclusion of magnetostrictive nanoparticles into the polymer spheres has no relevant effect on the piezoelectric β-phase content (≈60%), crystallinity (40%) and the onset degradation temperature (460º-465ºC) of the polymer matrix. The multiferroic microspeheres show a maximum piezoelectric reponse |d33|≈30 pC.N-1, leading to a magnetoelectric response of Δ|d33|≈5 pC.N-1 obtained when a 220 mT DC magnetic field was applied. It is also shown that the interface between CFO nanoparticles and PVDF (from 0 to 55%) has a strong influence on the ME response of the microspheres. The simplicity and the scalability of the processing method suggest a large application potential of this novel magnetoelectric geometry in areas such as tissue engineering, sensors and actuators.

Brazil's global aspirations and their implications for the relationship with Argentina in the framework of MERCOSUR

Dissertação de mestrado em Relações Internacionais

Caso de demonstração de uma framework para automatização do teste de APIs de aplicações SaaS

Dissertação de mestrado integrado em Engenharia e Gestão de Sistemas de Informação

Development of advanced cell/tissue culture systems, based on enhanced polymeric scaffolds and sophisticated bioreactors, for tissue engineering applications

Programa Doutoral em Engenharia Biomédica

Pervasive business intelligence: a marketing intelligence framework proposal

Doctoral Thesis in Information Systems and Technologies Area of Information Systems and Technology