Clinical decision support system for point of care use: ontology driven design and software implementation

OBJECTIVES: The objective of this research was to design a clinical decision support system (CDSS) that supports heterogeneous clinical decision problems and runs on multiple computing platforms. Meeting this objective required a novel design to create an extendable and easy to maintain clinical CDSS for point of care support. The proposed solution was evaluated in a proof of concept implementation. METHODS: Based on our earlier research with the design of a mobile CDSS for emergency triage we used ontology-driven design to represent essential components of a CDSS. Models of clinical decision problems were derived from the ontology and they were processed into executable applications during runtime. This allowed scaling applications' functionality to the capabilities of computing platforms. A prototype of the system was implemented using the extended client-server architecture and Web services to distribute the functions of the system and to make it operational in limited connectivity conditions. RESULTS: The proposed design provided a common framework that facilitated development of diversified clinical applications running seamlessly on a variety of computing platforms. It was prototyped for two clinical decision problems and settings (triage of acute pain in the emergency department and postoperative management of radical prostatectomy on the hospital ward) and implemented on two computing platforms-desktop and handheld computers. CONCLUSIONS: The requirement of the CDSS heterogeneity was satisfied with ontology-driven design. Processing of application models described with the help of ontological models allowed having a complex system running on multiple computing platforms with different capabilities. Finally, separation of models and runtime components contributed to improved extensibility and maintainability of the system.

On the Vertex Separation of Cactus Graphs

This paper is part of a work in progress whose goal is to construct a fast, practical algorithm for the vertex separation (VS) of cactus graphs. We prove a \main theorem for cacti", a necessary and sufficient condition for the VS of a cactus graph being k. Further, we investigate the ensuing ramifications that prevent the construction of an algorithm based on that theorem only.

Semantic Description of Web Services and Possibilities of BPEL4WS

The using of the upsurge of semantics web technologies gives a possibility for an increasing of the flexibility, extensibility and consistency of the existent industrial standards for modeling of web services. In the paper the types of semantic description of web services and the degree of their realization in BPEL4WS (Business Process Execution Language for Web Services) respectively on the abstract and executable level are treated. The methods for using of BPEL4WS for the purposes of semantic web services in the direction of their semi-automatic integration are suggested.

Architecture of Extensible Computations Driven Systems

Никола Вълчанов, Тодорка Терзиева, Владимир Шкуртов, Антон Илиев - Една от основните области на приложения на компютърната информатика е автоматизирането на математическите изчисления. Информационните системи покриват различни области като счетоводство, електронно обучение/тестване, симулационни среди и т. н. Те работят с изчислителни библиотеки, които са специфични за обхвата на системата. Въпреки, че такива системи са перфектни и работят безпогрешно, ако не се поддържат остаряват. В тази работа описваме механизъм, който използва динамично библиотеките за изчисления и взема решение по време на изпълнение (интелигентно или интерактивно) за това как и кога те да се използват. Целта на тази статия е представяне на архитектура за системи, управлявани от изчисления. Тя се фокусира върху ползите от използването на правилните шаблони за дизайн с цел да се осигури разширяемост и намаляване на сложността.

Manageable Workflows for Processing Parallel Sequencing Data

ACM Computing Classification System (1998): D.2.11, D.1.3, D.3.1, J.3, C.2.4.

An aspect-oriented approach to designing role-based access control services

Access control (AC) limits access to the resources of a system only to authorized entities. Given that information systems today are increasingly interconnected, AC is extremely important. The implementation of an AC service is a complicated task. Yet the requirements to an AC service vary a lot. Accordingly, the design of an AC service should be flexible and extensible in order to save development effort and time. Unfortunately, with conventional object-oriented techniques, when an extension has not been anticipated at the design time, the modification incurred by the extension is often invasive. Invasive changes destroy design modularity, further deteriorate design extensibility, and even worse, they reduce product reliability. ^ A concern is crosscutting if it spans multiple object-oriented classes. It was identified that invasive changes were due to the crosscutting nature of most unplanned extensions. To overcome this problem, an aspect-oriented design approach for AC services was proposed, as aspect-oriented techniques could effectively encapsulate crosscutting concerns. The proposed approach was applied to develop an AC framework that supported role-based access control model. In the framework, the core role-based access control mechanism is given in an object-oriented design, while each extension is captured as an aspect. The resulting framework is well-modularized, flexible, and most importantly, supports noninvasive adaptation. ^ In addition, a process to formalize the aspect-oriented design was described. The purpose is to provide high assurance for AC services. Object-Z was used to specify the static structure and Predicate/Transition net was used to model the dynamic behavior. Object-Z was extended to facilitate specification in an aspect-oriented style. The process of formal modeling helps designers to enhance their understanding of the design, hence to detect problems. Furthermore, the specification can be mathematically verified. This provides confidence that the design is correct. It was illustrated through an example that the model was ready for formal analysis. ^

Sets and Supersets

Peer reviewed

Sets and Supersets

Peer reviewed

A New Method for Modeling Free Surface Flows and Fluid-structure Interaction with Ocean Applications

The computational modeling of ocean waves and ocean-faring devices poses numerous challenges. Among these are the need to stably and accurately represent both the fluid-fluid interface between water and air as well as the fluid-structure interfaces arising between solid devices and one or more fluids. As techniques are developed to stably and accurately balance the interactions between fluid and structural solvers at these boundaries, a similarly pressing challenge is the development of algorithms that are massively scalable and capable of performing large-scale three-dimensional simulations on reasonable time scales. This dissertation introduces two separate methods for approaching this problem, with the first focusing on the development of sophisticated fluid-fluid interface representations and the second focusing primarily on scalability and extensibility to higher-order methods.

We begin by introducing the narrow-band gradient-augmented level set method (GALSM) for incompressible multiphase Navier-Stokes flow. This is the first use of the high-order GALSM for a fluid flow application, and its reliability and accuracy in modeling ocean environments is tested extensively. The method demonstrates numerous advantages over the traditional level set method, among these a heightened conservation of fluid volume and the representation of subgrid structures.

Next, we present a finite-volume algorithm for solving the incompressible Euler equations in two and three dimensions in the presence of a flow-driven free surface and a dynamic rigid body. In this development, the chief concerns are efficiency, scalability, and extensibility (to higher-order and truly conservative methods). These priorities informed a number of important choices: The air phase is substituted by a pressure boundary condition in order to greatly reduce the size of the computational domain, a cut-cell finite-volume approach is chosen in order to minimize fluid volume loss and open the door to higher-order methods, and adaptive mesh refinement (AMR) is employed to focus computational effort and make large-scale 3D simulations possible. This algorithm is shown to produce robust and accurate results that are well-suited for the study of ocean waves and the development of wave energy conversion (WEC) devices.

Combining Taxonomies using Word2vec

Taxonomies have gained a broad usage in a variety of fields due to their extensibility, as well as their use for classification and knowledge organization. Of particular interest is the digital document management domain in which their hierarchical structure can be effectively employed in order to organize documents into content-specific categories. Common or standard taxonomies (e.g., the ACM Computing Classification System) contain concepts that are too general for conceptualizing specific knowledge domains. In this paper we introduce a novel automated approach that combines sub-trees from general taxonomies with specialized seed taxonomies by using specific Natural Language Processing techniques. We provide an extensible and generalizable model for combining taxonomies in the practical context of two very large European research projects. Because the manual combination of taxonomies by domain experts is a highly time consuming task, our model measures the semantic relatedness between concept labels in CBOW or skip-gram Word2vec vector spaces. A preliminary quantitative evaluation of the resulting taxonomies is performed after applying a greedy algorithm with incremental thresholds used for matching and combining topic labels.

Développement de matériaux à base de protéines extraites du byssus de la moule bleue Mytilus edulis

Le byssus est un amas de fibres que les moules produisent afin de s’ancrer aux surfaces immergées sous l’eau. Ces fibres sont pourvues de propriétés mécaniques impressionnantes combinant rigidité, élasticité et ténacité élevées. De plus, elles possèdent un comportement d’auto-guérison de leurs propriétés mécaniques en fonction du temps lorsque la contrainte initialement appliquée est retirée. Les propriétés mécaniques de ces fibres sont le résultat de l’agencement hiérarchique de protéines de type copolymère blocs riches en collagène et de la présence de métaux formant des liens sacrificiels réversibles avec certains acides aminés comme les DOPA et les histidines. Bien que cette fibre soit très intéressante pour la production de matériaux grâce à son contenu élevé en collagène potentiellement biocompatible, cette ressource naturelle est traitée comme un déchet par les mytiliculteurs. L’objectif de cette thèse était de valoriser cette fibre en extrayant les protéines pour générer une nouvelle classe de matériaux biomimétiques. Un hydrolysat de protéines de byssus (BPH) riche en acides aminés chargés, i.e. ~30 % mol, et permettant de former des films a pu être généré. Lorsque solubilisé à pH 10.5, le BPH forme un hydrogel contenant des structures en triple hélice de collagène et des feuillets β anti-parallèles intra- et inter-moléculaires. Suite à l’évaporation de l’eau, le film de BPH résultant est insoluble en milieu aqueux à cause des structures secondaires très stables agissant comme points de réticulation effectifs. Les propriétés mécaniques des films de BPH sont modulables en fonction du pH. Au point isoélectrique (pI = 4.5), les interactions électrostatiques entre les charges opposées agissent comme points de réticulation et augmentent la rigidité des films et leur contrainte à la rupture sans affecter la déformation à la rupture. À pH plus élevé ou plus bas que le pI, les performances mécaniques des films sont plus faibles à cause de la répulsion entre les groupements fonctionnels de même charge qui interagissent plutôt avec les molécules d’eau et causent le gonflement de la matrice protéique des films. Le BPH contenant un nombre élevé d’acides aminés chargés et réactifs, nous avons pu réticuler les films de manière covalente à l’aide d’EDC ou de glutaraldéhyde. Les propriétés mécaniques des films sont modulables en fonction de la concentration d’EDC utilisée lors de la réticulation ou en employant du glutaraldéhyde comme agent réticulant. Les films sont à la fois plus rigides et plus forts avec un degré de réticulation élevé, mais perdent leur extensibilité à mesure que les segments libres de s’étirer lors d’une traction deviennent entravés par les points de réticulation. La réticulation augmente également la résistance à la dégradation enzymatique par la collagénase, les films les plus fortement réticulés lui étant pratiquement insensibles. La spectroscopie infrarouge montre enfin que la réticulation entraîne une transition de feuillets β anti-parallèles inter-moléculaires vers des structures de type hélices de collagène/PPII hydratées. Des liens sacrificiels ont été formés dans les films de BPH par traitement au pI et/ou avec différents métaux, i.e. Na+, Ca2+, Fe3+, afin de moduler les propriétés mécaniques statiques et d’évaluer le rôle de ces traitements sur le comportement d’auto-guérison lors de tests mécaniques cycliques avec différents temps de repos. Plus la valence des ions métalliques ajoutés augmente, plus les propriétés mécaniques statiques affichent un module, une contrainte à la rupture et une ténacité élevés sans toutefois affecter la déformation à la rupture, confirmant la formation de liens sacrificiels. Les tests mécaniques cycliques montrent que les traitements au pI ou avec Ca2+ créent des liens sacrificiels ioniques réversibles qui mènent à un processus d’auto-guérison des performances mécaniques dépendant du pH. L’ajout de Fe3+ à différentes concentrations module les performances mécaniques sur un plus large intervalle et la nature plus covalente de son interaction avec les acides aminés permet d’atteindre des valeurs nettement plus élevées que les autres traitements étudiés. Le Fe3+ permet aussi la formation de liens sacrificiels réversibles menant à l’auto-guérison des propriétés mécaniques. Les spectroscopies Raman et infrarouge confirment que le fer crée des liaisons avec plusieurs acides aminés, dont les histidines et les DOPA. Les résultats dans leur ensemble démontrent que les films de BPH sont des hydrogels biomimétiques du byssus qui peuvent être traités ou réticulés de différentes façons afin de moduler leurs performances mécaniques. Ils pourraient ainsi servir de matrices pour des applications potentielles dans le domaine pharmaceutique ou en ingénierie tissulaire.

Proteomic and phosphoproteomic analysis of polyethylene glycol-induced osmotic stress in root tips of common bean (Phaseolus vulgaris L.)

Previous studies have shown that polyethylene glycol (PEG)-induced osmotic stress (OS) reduces cell-wall (CW) porosity and limits aluminium (Al) uptake by root tips of common bean (Phaseolus vulgaris L.). A subsequent transcriptomic study suggested that genes related to CW processes are involved in adjustment to OS. In this study, a proteomic and phosphoproteomic approach was applied to identify OS-induced protein regulation to further improve our understanding of how OS affects Al accumulation. Analysis of total soluble proteins in root tips indicated that, in total, 22 proteins were differentially regulated by OS; these proteins were functionally categorized. Seventy-seven per- cent of the total expressed proteins were involved in metabolic pathways, particularly of carbohydrate and amino acid metabolism. An analysis of the apoplastic proteome revealed that OS reduced the level of five proteins and increased that of seven proteins. Investigation of the total soluble phosphoproteome suggested that dehydrin responded to OS with an enhanced phosphorylation state without a change in abundance. A cellular immunolocalization analysis indicated that dehydrin was localized mainly in the CW. This suggests that dehydrin may play a major protective role in the OS-induced physical breakdown of the CW structure and thus maintenance of the reversibility of CW extensibility during recovery from OS. The proteomic and phosphoproteomic analyses provided novel insights into the complex mechanisms of OS-induced reduction of Al accumulation in the root tips of common bean and highlight a key role for modification of CW structure.

Développement de matériaux à base de protéines extraites du byssus de la moule bleue Mytilus edulis

Le byssus est un amas de fibres que les moules produisent afin de s’ancrer aux surfaces immergées sous l’eau. Ces fibres sont pourvues de propriétés mécaniques impressionnantes combinant rigidité, élasticité et ténacité élevées. De plus, elles possèdent un comportement d’auto-guérison de leurs propriétés mécaniques en fonction du temps lorsque la contrainte initialement appliquée est retirée. Les propriétés mécaniques de ces fibres sont le résultat de l’agencement hiérarchique de protéines de type copolymère blocs riches en collagène et de la présence de métaux formant des liens sacrificiels réversibles avec certains acides aminés comme les DOPA et les histidines. Bien que cette fibre soit très intéressante pour la production de matériaux grâce à son contenu élevé en collagène potentiellement biocompatible, cette ressource naturelle est traitée comme un déchet par les mytiliculteurs. L’objectif de cette thèse était de valoriser cette fibre en extrayant les protéines pour générer une nouvelle classe de matériaux biomimétiques. Un hydrolysat de protéines de byssus (BPH) riche en acides aminés chargés, i.e. ~30 % mol, et permettant de former des films a pu être généré. Lorsque solubilisé à pH 10.5, le BPH forme un hydrogel contenant des structures en triple hélice de collagène et des feuillets β anti-parallèles intra- et inter-moléculaires. Suite à l’évaporation de l’eau, le film de BPH résultant est insoluble en milieu aqueux à cause des structures secondaires très stables agissant comme points de réticulation effectifs. Les propriétés mécaniques des films de BPH sont modulables en fonction du pH. Au point isoélectrique (pI = 4.5), les interactions électrostatiques entre les charges opposées agissent comme points de réticulation et augmentent la rigidité des films et leur contrainte à la rupture sans affecter la déformation à la rupture. À pH plus élevé ou plus bas que le pI, les performances mécaniques des films sont plus faibles à cause de la répulsion entre les groupements fonctionnels de même charge qui interagissent plutôt avec les molécules d’eau et causent le gonflement de la matrice protéique des films. Le BPH contenant un nombre élevé d’acides aminés chargés et réactifs, nous avons pu réticuler les films de manière covalente à l’aide d’EDC ou de glutaraldéhyde. Les propriétés mécaniques des films sont modulables en fonction de la concentration d’EDC utilisée lors de la réticulation ou en employant du glutaraldéhyde comme agent réticulant. Les films sont à la fois plus rigides et plus forts avec un degré de réticulation élevé, mais perdent leur extensibilité à mesure que les segments libres de s’étirer lors d’une traction deviennent entravés par les points de réticulation. La réticulation augmente également la résistance à la dégradation enzymatique par la collagénase, les films les plus fortement réticulés lui étant pratiquement insensibles. La spectroscopie infrarouge montre enfin que la réticulation entraîne une transition de feuillets β anti-parallèles inter-moléculaires vers des structures de type hélices de collagène/PPII hydratées. Des liens sacrificiels ont été formés dans les films de BPH par traitement au pI et/ou avec différents métaux, i.e. Na+, Ca2+, Fe3+, afin de moduler les propriétés mécaniques statiques et d’évaluer le rôle de ces traitements sur le comportement d’auto-guérison lors de tests mécaniques cycliques avec différents temps de repos. Plus la valence des ions métalliques ajoutés augmente, plus les propriétés mécaniques statiques affichent un module, une contrainte à la rupture et une ténacité élevés sans toutefois affecter la déformation à la rupture, confirmant la formation de liens sacrificiels. Les tests mécaniques cycliques montrent que les traitements au pI ou avec Ca2+ créent des liens sacrificiels ioniques réversibles qui mènent à un processus d’auto-guérison des performances mécaniques dépendant du pH. L’ajout de Fe3+ à différentes concentrations module les performances mécaniques sur un plus large intervalle et la nature plus covalente de son interaction avec les acides aminés permet d’atteindre des valeurs nettement plus élevées que les autres traitements étudiés. Le Fe3+ permet aussi la formation de liens sacrificiels réversibles menant à l’auto-guérison des propriétés mécaniques. Les spectroscopies Raman et infrarouge confirment que le fer crée des liaisons avec plusieurs acides aminés, dont les histidines et les DOPA. Les résultats dans leur ensemble démontrent que les films de BPH sont des hydrogels biomimétiques du byssus qui peuvent être traités ou réticulés de différentes façons afin de moduler leurs performances mécaniques. Ils pourraient ainsi servir de matrices pour des applications potentielles dans le domaine pharmaceutique ou en ingénierie tissulaire.

TcT: Tyrolean Complexity Tool

International audience

A relação diagnóstica em contexto de creche e jardim-de-infância

O presente estudo enquadra-se no domínio das Ciências da Educação e na área específica da Análise da Acão Educativa. Não se afastando das preocupações inscritas nos objetivos de um mestrado de autor "A Criança em Diferentes Contextos Educativos”, também se compagina com as nossas determinações pessoais e profissionais, empreendidas na convicção da investigação como um projeto de vida. Para o efeito, arquitetámos o nosso universo de estudo a partir da observação naturalista em sete salas de creche e de jardim-de-infância do distrito de Évora. Da população estudada fizeram parte diferentes acores educativos, entre eles, as crianças dos 3 meses aos 6 anos de idade, as educadoras e as auxiliares de Acão educativa. Pretendemos, a partir dos sinais emitidos pelas crianças, retirar indicadores de necessidades educativas, para compreender as atitudes e comportamentos dos agentes educativos (educadores e auxiliares) na sua prática pedagógica, inferindo das suas próprias necessidades formativas. Procurámos saber como eram feitos os diagnósticos de necessidades (educativas das crianças e formativas dos educadores) e como organizavam a sua relação com outros acores educativos, no sentido de um desenvolvimento holístico da criança. Dada a natureza e o objeto de estudo, optámos por uma metodologia qualitativa de carácter interpretativo, configurada num estudo de caso. Utilizámos a linha de Investigação-Acão/Formação, preconizada por Luís Barbosa, integrada na sua "Escola Sensível e Transformacionista", que radica os seus fundamentos na ideia de que o jardim-de-infância, tal como outra qualquer organização educativa, deve ser um "Observatório de Caracterização de necessidades educativas das crianças e formativas dos sues agentes educativos”, gerido na perspetiva da mudança. Neste enquadramento de ideias, ao qual aderimos por convicção, utilizámos, para caracterizar o real, a Observação como técnica privilegiada, pese embora as limitações que lhe são subjacentes. Minimizámos este facto, triangulando os dados com entrevistas semiestruturadas e notas de campo. Suportámo-nos da Técnica do Espelhamento, da Pedagogia de Ajuda, da Renomeação de Experiências e da Extensibilidade de Si, às quais, pela sua importância demos ênfase no enquadramento teórico. O nosso estudo permitiu-nos inferir que, a relação diagnostica nos processos de ensino/aprendizagem, naqueles contextos, parece estar correlacionada com o facto de que os agentes educativos ainda necessitam de adquirir um leque variado de competências, relacionadas com o Saber-Ser e o Saber-Estar, que lhes permitam atitudes relacionais pró-activas e maior sensibilidade para captar as emoções e as sensações das crianças. Este facto vem corroborar o facto de termos verificado que os agentes educativos não usam o diagnóstico de necessidades como âncora de organização das suas práticas educativas o que não contribui de forma sustentável para a promoção do bem-estar e do desenvolvimento integral da criança. ABSTRACT: The present study lies within the field of Educational Sciences in the specific area of analysis of education. Not moving away from the concerns listed in the goals of an author master degree "The Child in Different Educational Contexts”, it also fits our personal and professional decisions, undertaken in the belief of research as a project of life. We chose the universe of our study from naturalistic observation in seven rooms of Nurseries and Infant Schools in the district of Évora. The study population consisted of children from three months to six years old, educators and assistants of education. From signals emitted by children, we intended to take indicators of educational needs to understand the attitudes and behavior of the educators and their assistants in their pedagogical practice, inferring their own educational needs. We tried to know how the diagnoses of needs were made (educational needs of the children and training needs of the educators) and how they organized their relationship with other educational agents towards a holistic development of children. Considering the nature and purpose of the study we opted for a qualitative methodology of interpretative nature, in a case study. We used the action research training line, advocated by Luís Barbosa in his work "Escola Sensível e Transformacionista" (Sensitive and Transformational School), whose reason lies in the idea that Infant Schools, like other educational organizations, should be centers for the characterization of children’s educational needs and educational agents' formative needs, managed in terms of change. ln this framework of ideas, that we adopted by conviction, we used the observation as the main technique, despite its limitations. To minimize them we triangulated the data with semi structured interviews and field notes. We used the techniques of Mirroring, Pedagogy of Help, renaming of Experiences and Extensibility of Yourself, and, because of their importance, we focused on them in the theoretical framework. This study allowed us to infer that the diagnostic relationship in the teaching­learning processes, in those contexts, seem to be correlated with the fact that the educational agents still need to acquire a wide range of skills related to the Know How To Be, to provide them with proactive relational attitudes and a bigger sensibility to get the children's emotions and sensations. We also found that the educational agents don't use a diagnostic of needs as anchor of the organization of their educational practices, what does not contribute in a sustainable way for the promotion of the well being and integral development of the child.