Modelos Deformáveis em Imagem Médica

Modelos deformáveis são actualmente bastante utilizados em imagem médica pois, através da utilização de princípios físicos, simulam de forma bastante satisfatória o comportamento dos objectos reais.Basicamente os modelos deformáveis são inicializados junto dos objectos a considerar, por processos automáticos ou semi-automáticos, e a aproximação para a posição final desejada é conseguida através de um processo de minimização de energia. Esta minimização de energia é verificada quando o modelo atinge o equilíbrio, entre as suas forças internas e as forças externas originadas pelos dados e por eventuais forças impostas pelo utilizador.Neste relatório são apresentados os fundamentos dos modelos deformáveis e indicados alguns exemplos de aplicação em imagem médica, nomeadamente na segmentação, no emparelhamento, no alinhamento e na reconstrução de dados 2D e 3D.Palavras-chave: Contornos activos, imagem médica, modelos deformáveis.Deformable models are currently very used in medical image since, through the use of physical principles, they simulate quite satisfactory the real objects behavior.Basically the deformable models are placed in the image near to the objects to be considered, by automatic or semi-automatic processes, and the approach to the desired final position is obtained through an energy minimization process. This energy minimization is verified when the model reaches the equilibrium, between its internal forces and the external forces originated by the data and eventual forces imposed by the user.In this report are presented the deformable models fundaments and indicated some application examples in medical imaging field, namely in segmentation, matching, alignment and in the reconstruction of 2D and 3D data.Keywords: Active contours, deformable models, medical image

Análise de Movimento Não Rígido em Visão por Computador

Neste artigo são apresentadas várias metodologias actualmente existentes, no domínio da Visão por Computador, para a análise de movimento não rígido e são indicados diversos exemplos de aplicações. Assim o movimento não rígido é classificado e, para cada classe resultante, são indicadas as restrições e as condições inerentes e verificados alguns trabalhos realizados no seu âmbito. Como as questões de análise de movimento e modelização da forma se tornam inseparáveis quando se considera o movimento do tipo não rígido, a modelização sugere uma classificação possível da forma não rígida e do movimento. Assim são também apresentados modelos de forma para objectos deformáveis e indicados vários exemplos de aplicações. Com este estudo, de certo modo aprofundado, das várias metodologias, e suas aplicações, existentes no domínio da análise de movimento não rígido, espera-se contribuir para o seu desenvolvimento, dada a actual carência de boas revisões do estado da arte neste domínio.In this article several methodologies actually existent, in the Computer Vision domain, for non-rigid movement analysis are presented and several examples of applications are indicated. Thus the non-rigid movement is classified and, for each resulting class, the restrictions and the inherent conditions are presented and some works accomplished in its ambit are verified. As the questions of movement and shape analysis becomes non-separable when its considered the movement of the non-rigid type, the shape models also suggests a possible classification of the non-rigid shape and of the movement. Thus shape models for deformable objects will be presented and some examples of applications indicated. With this study, in certain way deep, of several methodologies, and its applications, existent in the domain of the non-rigid movement analysis, the authors hope to contribute for its development, given the actual lack of good state of the art revisions in this domain

Análise de Movimento Não Rígido em Visão por Computador

Neste artigo são apresentadas várias metodologias actualmente existentes, no domínio da Visão por Computador, para a análise de movimento não rígido e são indicados diversos exemplos de aplicações. Assim o movimento não rígido é classificado e, para cada classe resultante, são indicadas as restrições e as condições inerentes e verificados alguns trabalhos realizados no seu âmbito. Como as questões de análise de movimento e modelização da forma se tornam inseparáveis quando se considera o movimento do tipo não rígido, a modelização sugere uma classificação possível da forma não rígida e do movimento. Assim são também apresentados modelos de forma para objectos deformáveis e indicados vários exemplos de aplicações. Com este estudo, de certo modo aprofundado, das várias metodologias, e suas aplicações, existentes no domínio da análise de movimento não rígido, espera-se contribuir para o seu desenvolvimento, dada a actual carência de boas revisões do estado da arte neste domínio

Microalgae from aeroterrestrial environments: scenedesmus vacuolatus as a potential resource for mass cultivation

Microalgae are promising microorganisms deserving attention within the vast array of new biotechnologies. They are employed in many commercial applications: human and animal nutrition, pharmaceutical and cosmetical components, wastewater treatments. One of the critical factor for the industrial uses of microalgae is the production of biomass. So two types of cultivation system have been developed to increase the biomass production: liquid cultivations and immobilized cultivations. Moreover the biomass production depends on the type of organisms. Scenedesmus vacuolatus is known to have high biomass productivity among green algae, and has been frequently tested for biotechnological applications. Understanding the real potentiality of cultivation of this alga still needs new experimental evidences. In my dissertation, I focus the attention to the possible use of Scenedesmus vacuolatus as a model organism for massive cultivation and, consequently, to develop an industrial production, either in liquid- or immobilized-culture systems. To assess potential applications of Scenedesmus vacuolatus in the fields of biomass production, it is necessary to characterize its growth and photosynthetic activity. Different sets of experiments have been carried out in both type of cultivations liquid and immobilized. Firstly, I analyze several Scenedesmus vacuolatus strains and I prove the best candidate for my experiments is 053. Secondly, in liquid culture, thanks to the support of kinetic model I highlight the bottleneck of the photosynthesis process in photobioreactor in different operating conditions is photoinhibition. Moreover, in liquid culture, Scenedesmus vacuolatus shows a very good growth performances in enclosed photobioreactors achieving high biomass in presence of 2% CO2. Thirdly, in the study of immobilized cultivation, thanks to the combination of photograph imaging analysis and pulse amplitude modulation fluorimetry, I study the first steps of the adhesion process of this microalga in submerged condition and analyze its physiological state. Also in this case, Scenedesmus vacuolatus shows positive outcomes: it has a good ability of attachment and the adhesion process is scarcely influenced by the kind of carrier used. Eventually, by studying growth of Scenedesmus vacuolatus on a on a porous substrate bioreactor (the Twin Layer system), the performances of Scenedesmus vacuolatus in liquid systems are shown lower than that ones in attached cultivation and also in this case the addition of CO2 is necessary to increase the productivity. Comparison with data obtained from other organisms in other experiments on porous substrate bioreactor shows that immobilized cultivation of Scenedesmus vacuolatus based on Twin-layer system allows to achieve very good values of biomass productivity and light yield and confirms that also in immobilized cultivation Scenedesmus vacuolatus is a good candidate for industrial uses

A four-dimensional probabilistic atlas of the human brain

The authors describe the development of a four-dimensional atlas and reference system that includes both macroscopic and microscopic information on structure and function of the human brain in persons between the ages of 18 and 90 years. Given the presumed large but previously unquantified degree of structural and functional variance among normal persons in the human population, the basis for this atlas and reference system is probabilistic. Through the efforts of the International Consortium for Brain Mapping (ICBM), 7,000 subjects will be included in the initial phase of database and atlas development. For each subject, detailed demographic, clinical, behavioral, and imaging information is being collected. In addition, 5,800 subjects will contribute DNA for the purpose of determining genotype-phenotype-behavioral correlations. The process of developing the strategies, algorithms, data collection methods, validation approaches, database structures, and distribution of results is described in this report. Examples of applications of the approach are described for the normal brain in both adults and children as well as in patients with schizophrenia. This project should provide new insights into the relationship between microscopic and macroscopic structure and function in the human brain and should have important implications in basic neuroscience, clinical diagnostics, and cerebral disorders

Biosynthesis and regulation of cyclic lipopeptides in Pseudomonas fluorescens

Cyclic lipopeptides (CLPs) are surfactant and antibiotic metabolites produced by a variety of bacterial genera. For the genus Pseudomonas, many structurally different CLPs have been identified. CLPs play an important role in surface motility of Pseudomonas strains, but also in virulence and attachment/detachment to and from surfaces. In this Ph.D. thesis project, two new CLP biosynthesis clusters were identified in Pseudomonas fluorescens and fully sequenced. In P. fluorescens strain SBW25, the viscosin biosynthesis cluster was identified by bioinformatic analyses of the genome followed by genetic and chemical analyses. For P. fluorescens strain SS101, the genes for massetolide biosynthesis were identified via random mutagenesis followed by cloning, sequencing and chemical analyses. Biosynthesis of viscosin and massetolide is governed by three nonribosomal peptide synthetase (NRPS) genes, designated viscABC and massABC, respectively. The viscosin and massetolide biosynthesis gene clusters are very similar, but different from CLP gene clusters described for other Pseudomonas as the viscA and massA genes are physically disconnected from viscBC and massBC, respectively. Viscosin differs from massetolide A only at position number four in the peptide moiety, which is a valine in viscosin and an isoleucine in massetolide A. Because of the modular structure of the NRPSs and the co-linearity of the assembly process, transfer of the mass genes of strain SS101 into strain SBW25 resulted in the production of both massetolide A and viscosin, demonstrating that the assembly line for CLP biosynthesis in Pseudomonas can be altered leading to the production of non-native products. Compared to the understanding of CLP biosynthesis, not so much is known about the regulation. This thesis shows that the GacA/GacS two-component system regulates massetolide and viscosin biosynthesis in strains SS101 and SBW25, respectively. No indications were found that massetolide or viscosin biosynthesis is regulated by quorum sensing via N-acylhomoserine lactones. Site-directed mutagenesis of the LuxR-type regulator genes luxR-vA and luxR-vBC flanking the viscosin biosynthesis cluster resulted in a loss of viscosin production, indicating that both LuxR-type transcriptional regulators are important for viscosin biosynthesis in strain SBW25. Phylogenetic analyses further suggested that these LuxR-type transcriptional regulators do not contain the autoinducerbinding domain found for the quorum sensing-associated LuxR regulator in Vibrio fischeri. Instead, the LuxR-type regulator genes flanking the massetolide and viscosin biosynthesis genes are closely related to the LuxR-type regulators identified for syringomycin/ syringopeptin biosynthesis and appear to belong to a separate LuxR-type regulator subfamily, different from the autonomous effector domain protein GerE. Via random mutagenesis and subsequent screening for massetolide-deficient mutants, also other regulator genes were identified including clpP. ClpP is a serine protease that plays a crucial role in intracellular refolding and degradation of proteins, which is an essential process for the viability of cells. ClpP was shown to affect transcription of luxR-mA, thereby regulating transcription of the massetolide biosynthesis genes. Results further suggested that, at the transcriptional level, ClpPmediated regulation of massetolide biosynthesis operates independently from regulation by the GacA/GacS two-component system. In conclusion, the results of this thesis led to the identification of several genes and previously unknown pathways involved in regulation of CLP biosynthesis and highlighted the complexity of the signaling cascades underlying CLP biosynthesis in Pseudomonas. CLPs have diverse functions for the producing bacterial strains, including a role in motility, biofilm formation, antimicrobial activity and virulence. Also in establishment and persistence in plant environments, CLPs were shown to confer a competitive advantage. A new function of CLPs, identified in a collaboration with Mark Mazzola (USDA) and presented in this thesis, is their protective effects against predation by protozoa. In vitro assays showed that both massetolide and viscosin can lyse the trophozoites of Naeglaria americana and that wild type strains SS101 and SBW25 were substantially less sensitive to protozoan grazing than their CLP-deficient mutants. Also in soil containing N. americana, population densities of wild type strains SS101 and SBW25 were significantly higher compared to the massetolide and viscosin-deficient mutants, showing that CLP production confers a competitive advantage in survival in complex environments. Moreover, transcription of the CLP-biosynthesis genes increased significantly upon protozoan grazing, indicating that the Pseudomonas strains sense the protozoa and react by producing CLPs as defense compounds. Which signal triggers the induction of the CLP biosynthesis genes is not known yet and currently under investigation. Based on these results, we postulate that CLPs are an important component of the preingestional defense mechanisms of bacteria against protozoan predation, not only due to their lytic effects on protozoa, but also because CLPs contribute to evasion of protozoan grazing via altered cell surface properties, swimming and swarming, and microcolony and biofilm formation. <br/

BOLD Noise Assumptions in fMRI

This paper discusses the assumption of Gaussian noise in the blood-oxygenation-dependent (BOLD) contrast for functional MRI (fMRI). In principle, magnitudes in MRI images follow a Rice distribution. We start by reviewing differences between Rician and Gaussian noise. An analytic expression is derived for the null (resting-state) distribution of the difference between two Rician distributed images. This distribution is shown to be symmetric, and an exact expression for its standard deviation is derived. This distribution can be well approximated by a Gaussian, with very high precision for high SNR, and high precision for lower SNR. Tests on simulated and real MR images show that subtracting the time-series mean in fMRI yields asymmetrically distributed temporal noise. Subtracting a resting-state time series from the first results in symmetric and nearly Gaussian noise. This has important consequences for fMRI analyses using standard statistical tests

A four-dimensional probabilistic atlas of the human brain

The authors describe the development of a four-dimensional atlas and reference system that includes both macroscopic and microscopic information on structure and function of the human brain in persons between the ages of 18 and 90 years. Given the presumed large but previously unquantified degree of structural and functional variance among normal persons in the human population, the basis for this atlas and reference system is probabilistic. Through the efforts of the International Consortium for Brain Mapping (ICBM), 7,000 subjects will be included in the initial phase of database and atlas development. For each subject, detailed demographic, clinical, behavioral, and imaging information is being collected. In addition, 5,800 subjects will contribute DNA for the purpose of determining genotype– phenotype–behavioral correlations. The process of developing the strategies, algorithms, data collection methods, validation approaches, database structures, and distribution of results is described in this report. Examples of applications of the approach are described for the normal brain in both adults and children as well as in patients with schizophrenia. This project should provide new insights into the relationship between microscopic and macroscopic structure and function in the human brain and should have important implications in basic neuroscience, clinical diagnostics, and cerebral disorders

Austrian High-Performance-Computing meeting (AHPC2020)

This booklet is a collection of abstracts presented at the AHPC conference

Padrão: um sistema de descoberta de conhecimento em bases de dados geo-referenciadas

A Descoberta de Conhecimento em Bases de Dados está associada à identi…cação de relacionamentos implícitos existentes nos dados analisados. O processo global de descoberta de conhecimento, que se desenrola em várias fases, inclui a gestão dos algoritmos de Data Mining, utilizados para extrair padrões dos dados, e a interpretação dos padrões encontrados pelos mesmos. Um caso particular da Descoberta de Conhecimento em Bases de Dados diz respeito à exploração de dados geo-referenciados, isto é, dados que incluem referências a objectos geográ… cos, localizações ou partes de uma divisão territorial. A análise destes dados impõe a veri…cação da componente espacial associada aos mesmos (distâncias, direcções, adjacências, ...), e a sua in‡uência nos restantes dados explorados, já que um objecto geográ…co pode ser afectado por acontecimentos veri…cados em objectos vizinhos. Os algoritmos de Data Mining disponíveis em ferramentas de descoberta de conhecimento tradicionais, que permitem a exploração de dados armazenados em bases de dados relacionais, não estão preparados para a análise desta componente, motivando: i) o desenvolvimento de novos algoritmos; ii) a adaptação de algoritmos já existentes; iii) a utilização de sistemas gestores de bases de dados espaciais ou sistemas de informação geográ…ca, que permitam a incorporação da componente espacial dos dados no processo de descoberta de conhecimento. A existência nas bases de dados organizacionais de identi…cadores geográ…cos qualitativos, como moradas, os quais possibilitam a geo-referenciação da informação através de sistemas de posicionamento indirecto, conduziu à identi…cação de uma abordagem alternativa à análise de dados espaciais, utilizada neste trabalho, que permite a integração da componente espacial dos dados, no processo de descoberta de conhecimento, através da utilização de estratégias de raciocínio espacial qualitativo. Os princípios estabelecidos para o Padrão, o sistema proposto nesta tese, representam uma nova abordagem na análise de dados espaciais, que apresenta como vantagens: o facto de permitir utilizar uma diversidade de técnicas de Data Mining, já disponíveis para dados não espaciais; o suprimir a necessidade de caracterização geométrica das entidades geográ…cas referenciadas; e o permitir aos algoritmos de Data Mining analisar simultaneamente dados geoespaciais e dados não espaciais, não condicionando ou limitando os resultados que podem ser obtidos. A apresentação de um estudo de caso, com a análise de uma base de dados de grande dimensão, permitiu constatar a utilidade do sistema Padrão na exploração de bases de dados geo-referenciadas, nomeadamente, na identi…cação de relacionamentos implícitos existentes entre os dados geo-espaciais e os dados não espaciais analisados.Knowledge Discovery in Databases is a process that aims the discovery of associations within data sets. Data Mining is the central step of this process. It corresponds to the application of algorithms for identifying patterns within data. Other steps are related to incorporating prior domain knowledge and interpretation of results. Geo-referenced data sets constitute a special case that demands a particular approach within the knowledge discovery process. Geo-referenced data sets include allusion to geographic objects, locations or administrative sub-divisions of a region. The geographic location and extension of those objects have implicit relationships of spatial neighbourhood. The Data Mining algorithms have to take this spatial neighbourhood into account when looking for associations among data. Data Mining algorithms available in traditional knowledge discovery tools, developed for the analysis of relational databases, are not prepared for the analysis of this spatial component. This situation led to: i) the development of new algorithms capable of dealing with spatial relationships; ii) the adaptation of existing algorithms in order to enable them no deal with those spatial relationships; iii) the integration of the capabilities for spatial analysis of spatial database management systems or geographic information systems with the tools normally used in the knowledge discovery process. Most of the geographic attributes normally found out in organisational databases (e.g., addresses) correspond to a type of spatial information that can be described using indirect positioning systems. This work proposes a new approach - the Padrão system - to the analysis of spatial data based on qualitative spatial reasoning strategies that allow the integration of the spatial component in the knowledge discovery process. The main advantages of this approach include: the use of already existing Data Mining algorithms applied to the analysis of non-spatial data; avoid the geometric characterisation of spatial objects; and enable that Data Mining algorithms deal with geo-spatial and non-spatial data simultaneously thus imposing no limits and constraints to the results achieved. The e¢cacy and usefulness of Padrão has been tested with a case study where a large database has been subject to a knowledge discovery process. The results con…rm that Padrão enables the identification of implicit relationships among geo-spatial and non-spatial data.PRODEP II - acção 5.2, concurso n.º3/98, Doutoramentos