Gene expression regulation and lineage evolution: the North and South tale of the hybrid polyploid Squalius alburnoides complex

The evolution of hybrid polyploid vertebrates, their viability and their perpetuation over evolutionary time have always been questions of great interest. However, little is known about the impact of hybridization and polyploidization on the regulatory networks that guarantee the appropriate quantitative and qualitative gene expression programme. The Squalius alburnoides complex of hybrid fish is an attractive system to address these questions, as it includes a wide variety of diploid and polyploid forms, and intricate systems of genetic exchange. Through the study of genome-specific allele expression of seven housekeeping and tissue-specific genes, we found that a gene copy silencing mechanism of dosage compensation exists throughout the distribution range of the complex. Here we show that the allele-specific patterns of silencing vary within the complex, according to the geographical origin and the type of genome involved in the hybridization process. In southern populations, triploids of S. alburnoides show an overall tendency for silencing the allele from the minority genome, while northern population polyploids exhibit preferential biallelic gene expression patterns, irrespective of genomic composition. The present findings further suggest that gene copy silencing and variable expression of specific allele combinations may be important processes in vertebrate polyploid evolution.

Quality assurance and quality control in mammography: a review of available guidance worldwide

Objectives - Review available guidance for quality assurance (QA) in mammography and discuss its contribution to harmonise practices worldwide. Methods - Literature search was performed on different sources to identify guidance documents for QA in mammography available worldwide in international bodies, healthcare providers, professional/scientific associations. The guidance documents identified were reviewed and a selection was compared for type of guidance (clinical/technical), technology and proposed QA methodologies focusing on dose and image quality (IQ) performance assessment. Results - Fourteen protocols (targeted at conventional and digital mammography) were reviewed. All included recommendations for testing acquisition, processing and display systems associated with mammographic equipment. All guidance reviewed highlighted the importance of dose assessment and testing the Automatic Exposure Control (AEC) system. Recommended tests for assessment of IQ showed variations in the proposed methodologies. Recommended testing focused on assessment of low-contrast detection, spatial resolution and noise. QC of image display is recommended following the American Association of Physicists in Medicine guidelines. Conclusions - The existing QA guidance for mammography is derived from key documents (American College of Radiology and European Union guidelines) and proposes similar tests despite the variations in detail and methodologies. Studies reported on QA data should provide detail on experimental technique to allow robust data comparison. Countries aiming to implement a mammography/QA program may select/prioritise the tests depending on available technology and resources.

Cooperative framework for open real-time systems

Actualmente, os sistemas embebidos estão presentes em toda a parte. Embora grande parte da população que os utiliza não tenha a noção da sua presença, na realidade, se repentinamente estes sistemas deixassem de existir, a sociedade iria sentir a sua falta. A sua utilização massiva deve-se ao facto de estarem practicamente incorporados em quase os todos dispositivos electrónicos de consumo, telecomunicações, automação industrial e automóvel. Influenciada por este crescimento, a comunidade científica foi confrontada com novos problemas distribuídos por vários domínios científicos, dos quais são destacados a gestão da qualidade de serviço e gestão de recursos - domínio encarregue de resolver problemas relacionados com a alocação óptima de recursos físicos, tais como rede, memória e CPU. Existe na literatura um vasto conjunto de modelos que propõem soluções para vários problemas apresentados no contexto destes domínios científicos. No entanto, não é possível encontrar modelos que lidem com a gestão de recursos em ambientes de execução cooperativos e abertos com restrições temporais utilizando coligações entre diferentes nós, de forma a satisfazer os requisitos não funcionais das aplicações. Devido ao facto de estes sistemas serem dinâmicos por natureza, apresentam a característica de não ser possível conhecer, a priori, a quantidade de recursos necessários que uma aplicação irá requerer do sistema no qual irá ser executada. Este conhecimento só é adquirido aquando da execução da aplicação. De modo a garantir uma gestão eficiente dos recursos disponíveis, em sistemas que apresentam um grande dinamismo na execução de tarefas com e sem restrições temporais, é necessário garantir dois aspectos fundamentais. O primeiro está relacionado com a obtenção de garantias na execução de tarefas de tempo-real. Estas devem sempre ser executadas dentro da janela temporal requirida. O segundo aspecto refere a necessidade de garantir que todos os recursos necessários à execução das tarefas são fornecidos, com o objectivo de manter os níveis de performance quer das aplicações, quer do próprio sistema. Tendo em conta os dois aspectos acima mencionados, o projecto CooperatES foi especificado com o objectivo de permitir a dispositivos com poucos recursos uma execução colectiva de serviços com os seus vizinhos, de modo a cumprir com as complexas restrições de qualidade de serviço impostas pelos utilizadores ou pelas aplicações. Decorrendo no contexto do projecto CooperatES, o trabalho resultante desta tese tem como principal objectivo avaliar a practicabilidade dos conceitos principais propostos no âmbito do projecto. O trabalho em causa implicou a escolha e análise de uma plataforma, a análise de requisitos, a implementação e avaliação de uma framework que permite a execução cooperativa de aplicações e serviços que apresentem requisitos de qualidade de serviço. Do trabalho desenvolvido resultaram as seguintes contribuições: Análise das plataformas de código aberto que possam ser utilizadas na implementação dos conceitos relacionados com o projecto CooperatES; Critérios que influenciaram a escolha da plataforma Android e um estudo focado na análise da plataforma sob uma perspectiva de sistemas de tempo-real; Experiências na implementação dos conceitos do projecto na plataforma Android; Avaliação da practicabilidade dos conceitos propostos no projecto CooperatES; Proposta de extensões que permitam incorporar características de sistemas de tempo real abertos na plataforma Android.

Tuneable micro- and nano-periodic structures in urethane/urea networks

Micro- and nano-patterned materials are of great importance for the design of new nanoscale electronic, optical and mechanical devices, ranging from sensors to displays. A prospective system that can support a designed functionality is elastomeric polyurethane thin films with nano- or micromodulated surface structures ("wrinkles"). These wrinkles can be induced on different lengthscales by mechanically stretching the films, without the need for any sophisticated lithographic techniques. In the present article we focus on the experimental control of the wrinkling process. A simple model for wrinkle formation is also discussed, and some preliminary results reported. Hierarchical assembly of these tunable structures paves the way for the development of a new class of materials with a wide range of applications, from electronics to biomedicine.

Amperometric and spectrophotometric determination of carbaryl in natural waters and commercial formulations

The work presented describes the development and evaluation of two flow-injection analysis (FIA) systems for the automated determination of carbaryl in spiked natural waters and commercial formulations. Samples are injected directly into the system where they are subjected to alkaline hydrolysis thus forming 1-naphthol. This product is readily oxidised at a glassy carbon electrode. The electrochemical behaviour of 1-naphthol allows the development of an FIA system with an amperometric detector in which 1-naphthol determination, and thus measurement of carbaryl concentration, can be performed. Linear response over the range 1.0×10–7 to 1.0×10–5 mol L–1, with a sampling rate of 80 samples h–1, was recorded. The detection limit was 1.0×10–8 mol L–1. Another FIA manifold was constructed but this used a colorimetric detector. The methodology was based on the coupling of 1-naphthol with phenylhydrazine hydrochloride to produce a red complex which has maximum absorbance at 495 nm. The response was linear from 1.0×10–5 to 1.5×10–3 mol L–1 with a detection limit of 1.0×10–6 mol L–1. Sample-throughput was about 60 samples h–1. Validation of the results provided by the two FIA methodologies was performed by comparing them with results from a standard HPLC–UV technique. The relative deviation was <5%. Recovery trials were also carried out and the values obtained ranged from 97.0 to 102.0% for both methods. The repeatability (RSD, %) of 12 consecutive injections of one sample was 0.8% and 1.6% for the amperometric and colorimetric systems, respectively.

INDEPTH: timeliness assessment of ethernet/IP-based systems

The continuous improvement of Ethernet technologies is boosting the eagerness of extending their use to cover factory-floor distributed real time applications. Indeed, it is remarkable the considerable amount of research work that has been devoted to the timing analysis of Ethernet-based technologies in the past few years. It happens, however, that the majority of those works are restricted to the analysis of sub-sets of the overall computing and communication system, thus without addressing timeliness in a holistic fashion. To this end, we address an approach, based on simulation, aiming at extracting temporal properties of commercial-off-the-shelf (COTS) Ethernet-based factory-floor distributed systems. This framework is applied to a specific COTS technology, Ethernet/IP. We reason about the modeling and simulation of Ethernet/IP-based systems, and on the use of statistical analysis techniques to provide useful results on timeliness. The approach is part of a wider framework related to the research project INDEPTH NDustrial-Ethernet ProTocols under Holistic analysis.

Water quality in lakes and reservoirs in China

Dissertation elaborated for the partial fulfilment of the requirements of the Master Degree in Civil Engineering in the Speciality Area of Hydarulics

An architecture for reliable distributed computer-controlled systems

In Distributed Computer-Controlled Systems (DCCS), both real-time and reliability requirements are of major concern. Architectures for DCCS must be designed considering the integration of processing nodes and the underlying communication infrastructure. Such integration must be provided by appropriate software support services. In this paper, an architecture for DCCS is presented, its structure is outlined, and the services provided by the support software are presented. These are considered in order to guarantee the real-time and reliability requirements placed by current and future systems.

Simulation model for driving dynamics, energy use and power supply

Dissertação para obtenção do grau de Mestre em Engenharia Electrotécnica Ramo de Energia

Power Producers Trading Electricity in Both Pool and Forward Markets

The electricity industry throughout the world, which has long been dominated by vertically integrated utilities, has experienced major changes. Deregulation, unbundling, wholesale and retail wheeling, and real-time pricing were abstract concepts a few years ago. Today market forces drive the price of electricity and reduce the net cost through increased competition. As power markets continue to evolve, there is a growing need for advanced modeling approaches. This article addresses the challenge of maximizing the profit (or return) of power producers through the optimization of their share of customers. Power producers have fixed production marginal costs and decide the quantity of energy to sell in both day-ahead markets and a set of target clients, by negotiating bilateral contracts involving a three-rate tariff. Producers sell energy by considering the prices of a reference week and five different types of clients with specific load profiles. They analyze several tariffs and determine the best share of customers, i.e., the share that maximizes profit. © 2014 IEEE.

Analysis of the respiratory dynamics during normal breathing by means of pseudo phase plots and pressure-volume loops

This paper reports on the analysis of tidal breathing patterns measured during noninvasive forced oscillation lung function tests in six individual groups. The three adult groups were healthy, with prediagnosed chronic obstructive pulmonary disease, and with prediagnosed kyphoscoliosis, respectively. The three children groups were healthy, with prediagnosed asthma, and with prediagnosed cystic fibrosis, respectively. The analysis is applied to the pressure–volume curves and the pseudophaseplane loop by means of the box-counting method, which gives a measure of the area within each loop. The objective was to verify if there exists a link between the area of the loops, power-law patterns, and alterations in the respiratory structure with disease. We obtained statistically significant variations between the data sets corresponding to the six groups of patients, showing also the existence of power-law patterns. Our findings support the idea that the respiratory system changes with disease in terms of airway geometry and tissue parameters, leading, in turn, to variations in the fractal dimension of the respiratory tree and its dynamics.

Automatic learning for the classification of chemical reactions and in statistical thermodynamics

This Thesis describes the application of automatic learning methods for a) the classification of organic and metabolic reactions, and b) the mapping of Potential Energy Surfaces(PES). The classification of reactions was approached with two distinct methodologies: a representation of chemical reactions based on NMR data, and a representation of chemical reactions from the reaction equation based on the physico-chemical and topological features of chemical bonds. NMR-based classification of photochemical and enzymatic reactions. Photochemical and metabolic reactions were classified by Kohonen Self-Organizing Maps (Kohonen SOMs) and Random Forests (RFs) taking as input the difference between the 1H NMR spectra of the products and the reactants. The development of such a representation can be applied in automatic analysis of changes in the 1H NMR spectrum of a mixture and their interpretation in terms of the chemical reactions taking place. Examples of possible applications are the monitoring of reaction processes, evaluation of the stability of chemicals, or even the interpretation of metabonomic data. A Kohonen SOM trained with a data set of metabolic reactions catalysed by transferases was able to correctly classify 75% of an independent test set in terms of the EC number subclass. Random Forests improved the correct predictions to 79%. With photochemical reactions classified into 7 groups, an independent test set was classified with 86-93% accuracy. The data set of photochemical reactions was also used to simulate mixtures with two reactions occurring simultaneously. Kohonen SOMs and Feed-Forward Neural Networks (FFNNs) were trained to classify the reactions occurring in a mixture based on the 1H NMR spectra of the products and reactants. Kohonen SOMs allowed the correct assignment of 53-63% of the mixtures (in a test set). Counter-Propagation Neural Networks (CPNNs) gave origin to similar results. The use of supervised learning techniques allowed an improvement in the results. They were improved to 77% of correct assignments when an ensemble of ten FFNNs were used and to 80% when Random Forests were used. This study was performed with NMR data simulated from the molecular structure by the SPINUS program. In the design of one test set, simulated data was combined with experimental data. The results support the proposal of linking databases of chemical reactions to experimental or simulated NMR data for automatic classification of reactions and mixtures of reactions. Genome-scale classification of enzymatic reactions from their reaction equation. The MOLMAP descriptor relies on a Kohonen SOM that defines types of bonds on the basis of their physico-chemical and topological properties. The MOLMAP descriptor of a molecule represents the types of bonds available in that molecule. The MOLMAP descriptor of a reaction is defined as the difference between the MOLMAPs of the products and the reactants, and numerically encodes the pattern of bonds that are broken, changed, and made during a chemical reaction. The automatic perception of chemical similarities between metabolic reactions is required for a variety of applications ranging from the computer validation of classification systems, genome-scale reconstruction (or comparison) of metabolic pathways, to the classification of enzymatic mechanisms. Catalytic functions of proteins are generally described by the EC numbers that are simultaneously employed as identifiers of reactions, enzymes, and enzyme genes, thus linking metabolic and genomic information. Different methods should be available to automatically compare metabolic reactions and for the automatic assignment of EC numbers to reactions still not officially classified. In this study, the genome-scale data set of enzymatic reactions available in the KEGG database was encoded by the MOLMAP descriptors, and was submitted to Kohonen SOMs to compare the resulting map with the official EC number classification, to explore the possibility of predicting EC numbers from the reaction equation, and to assess the internal consistency of the EC classification at the class level. A general agreement with the EC classification was observed, i.e. a relationship between the similarity of MOLMAPs and the similarity of EC numbers. At the same time, MOLMAPs were able to discriminate between EC sub-subclasses. EC numbers could be assigned at the class, subclass, and sub-subclass levels with accuracies up to 92%, 80%, and 70% for independent test sets. The correspondence between chemical similarity of metabolic reactions and their MOLMAP descriptors was applied to the identification of a number of reactions mapped into the same neuron but belonging to different EC classes, which demonstrated the ability of the MOLMAP/SOM approach to verify the internal consistency of classifications in databases of metabolic reactions. RFs were also used to assign the four levels of the EC hierarchy from the reaction equation. EC numbers were correctly assigned in 95%, 90%, 85% and 86% of the cases (for independent test sets) at the class, subclass, sub-subclass and full EC number level,respectively. Experiments for the classification of reactions from the main reactants and products were performed with RFs - EC numbers were assigned at the class, subclass and sub-subclass level with accuracies of 78%, 74% and 63%, respectively. In the course of the experiments with metabolic reactions we suggested that the MOLMAP / SOM concept could be extended to the representation of other levels of metabolic information such as metabolic pathways. Following the MOLMAP idea, the pattern of neurons activated by the reactions of a metabolic pathway is a representation of the reactions involved in that pathway - a descriptor of the metabolic pathway. This reasoning enabled the comparison of different pathways, the automatic classification of pathways, and a classification of organisms based on their biochemical machinery. The three levels of classification (from bonds to metabolic pathways) allowed to map and perceive chemical similarities between metabolic pathways even for pathways of different types of metabolism and pathways that do not share similarities in terms of EC numbers. Mapping of PES by neural networks (NNs). In a first series of experiments, ensembles of Feed-Forward NNs (EnsFFNNs) and Associative Neural Networks (ASNNs) were trained to reproduce PES represented by the Lennard-Jones (LJ) analytical potential function. The accuracy of the method was assessed by comparing the results of molecular dynamics simulations (thermal, structural, and dynamic properties) obtained from the NNs-PES and from the LJ function. The results indicated that for LJ-type potentials, NNs can be trained to generate accurate PES to be used in molecular simulations. EnsFFNNs and ASNNs gave better results than single FFNNs. A remarkable ability of the NNs models to interpolate between distant curves and accurately reproduce potentials to be used in molecular simulations is shown. The purpose of the first study was to systematically analyse the accuracy of different NNs. Our main motivation, however, is reflected in the next study: the mapping of multidimensional PES by NNs to simulate, by Molecular Dynamics or Monte Carlo, the adsorption and self-assembly of solvated organic molecules on noble-metal electrodes. Indeed, for such complex and heterogeneous systems the development of suitable analytical functions that fit quantum mechanical interaction energies is a non-trivial or even impossible task. The data consisted of energy values, from Density Functional Theory (DFT) calculations, at different distances, for several molecular orientations and three electrode adsorption sites. The results indicate that NNs require a data set large enough to cover well the diversity of possible interaction sites, distances, and orientations. NNs trained with such data sets can perform equally well or even better than analytical functions. Therefore, they can be used in molecular simulations, particularly for the ethanol/Au (111) interface which is the case studied in the present Thesis. Once properly trained, the networks are able to produce, as output, any required number of energy points for accurate interpolations.

Power producers trading electricity in both pool and forward markets

The electricity industry throughout the world, which has long been dominated by vertically integrated utilities, has experienced major changes. Deregulation, unbundling, wholesale and retail wheeling, and real-time pricing were abstract concepts a few years ago. Today market forces drive the price of electricity and reduce the net cost through increased competition. As power markets continue to evolve, there is a growing need for advanced modeling approaches. This article addresses the challenge of maximizing the profit (or return) of power producers through the optimization of their share of customers. Power producers have fixed production marginal costs and decide the quantity of energy to sell in both day-ahead markets and a set of target clients, by negotiating bilateral contracts involving a three-rate tariff. Producers sell energy by considering the prices of a reference week and five different types of clients with specific load profiles. They analyze several tariffs and determine the best share of customers, i.e., the share that maximizes profit. © 2014 IEEE.

A Logic and tool for local reasoning about security protocols

Trabalho apresentado no âmbito do Mestrado em Engenharia Informática, como requisito parcial para obtenção do grau de Mestre em Engenharia Informática

Densities and refractive indices for the ternary mixture methanol/propan-1-Ol/acetonitrile

Refractive indices, n(D), and densities, rho, at 298.15 K were measured for the ternary mixture methanol (MeOH)/propan-1-ol (1-PrOH)/acetonitrile (MeCN) for a total of 22 mole fractions, along with 18 mole fractions of each of the corresponding binary mixtures, methanol/propan-1-ol, propan-1-ol/acetonitrile and methanol/acetonitrile. The variation of excess refractive indices and excess molar volumes with composition was modeled by the Redlich-Kister polynomial function in the case of binary mixtures and by the Cibulka equation for the ternary mixture. A thermodynamic approach to excess refractive indices, recently proposed by other authors, was applied for the first time to ternary liquid mixtures. Structural effects were identified and interpreted both in the binary and ternary systems. A complex relationship between excess refractive indices and excess molar volumes was identified, revealing all four possible sign combinations between these two properties. Structuring of the mixtures was also discussed on the basis of partial molar volumes of the binary and ternary mixtures.