Categorization and characterization of transcript-confirmed constitutively and alternatively spliced introns and exons from human

By spliced alignment of human DNA and transcript sequence data we constructed a data set of transcript-confirmed exons and introns from 2793 genes, 796 of which (28%) were seen to have multiple isoforms. We find that over one-third of human exons can translate in more than one frame, and that this is highly correlated with G+C content. Introns containing adenosine at donor site position +3 (A3), rather than guanosine (G3), are more common in low G+C regions, while the converse is true in high G+C regions. These two classes of introns are shown to have distinct lengths, consensus sequences and correlations among splice signals, leading to the hypothesis that A3 donor sites are associated with exon definition, and G3 donor sites with intron definition. Minor classes of introns, including GC-AG, U12-type GT-AG, weak, and putative AG-dependant introns are identified and characterized. Cassette exons are more prevalent in low G+C regions, while exon isoforms are more prevalent in high G+C regions. Cassette exon events outnumber other alternative events, while exon isoform events involve truncation twice as often as extension, and occur at acceptor sites twice as often as at donor sites. Alternative splicing is usually associated with weak splice signals, and in a majority of cases, preserves the coding frame. The reported characteristics of constitutive and alternative splice signals, and the hypotheses offered regarding alternative splicing and genome organization, have important implications for experimental research into RNA processing. The 'AltExtron' data sets are available at http://www.bit.uq.edu.au/altExtron/ and http://www.ebi.ac.uk/similar tothanaraj/altExtron/.

Structural refinement of systems specified in object-z and CSP

This paper is concerned with methods for refinement of specifications written using a combination of Object-Z and CSP. Such a combination has proved to be a suitable vehicle for specifying complex systems which involve state and behaviour, and several proposals exist for integrating these two languages. The basis of the integration in this paper is a semantics of Object-Z classes identical to CSP processes. This allows classes specified in Object-Z to be combined using CSP operators. It has been shown that this semantic model allows state-based refinement relations to be used on the Object-Z components in an integrated Object-Z/CSP specification. However, the current refinement methodology does not allow the structure of a specification to be changed in a refinement, whereas a full methodology would, for example, allow concurrency to be introduced during the development life-cycle. In this paper, we tackle these concerns and discuss refinements of specifications written using Object-Z and CSP where we change the structure of the specification when performing the refinement. In particular, we develop a set of structural simulation rules which allow single components to be refined to more complex specifications involving CSP operators. The soundness of these rules is verified against the common semantic model and they are illustrated via a number of examples.

Mapping Culture and Compromised Art in the Era of Globalization

This work presents an analysis of the cultural and artistic field, positively compromised with social and political questions. The authors start with the categorization of the idea of culture and move to vindication art movements. These movements, which followed the first vanguards and worked from the compromise with “otherness”, are at the origin of the contemporary denomination of political art. In this context, the authors approach the origins of activist art, referring to issues of gender, multiculturalism, globalization, and poverty. The different forms of presenting content are also an object of analysis: from art tradition to the contamination of daily life, from local to global, from street contact to digital.

Towards a Unified Theory of Health-Disease: I. Health as a complex model-object

Theory building is one of the most crucial challenges faced by basic, clinical and population research, which form the scientific foundations of health practices in contemporary societies. The objective of the study is to propose a Unified Theory of Health-Disease as a conceptual tool for modeling health-disease-care in the light of complexity approaches. With this aim, the epistemological basis of theoretical work in the health field and concepts related to complexity theory as concerned to health problems are discussed. Secondly, the concepts of model-object, multi-planes of occurrence, modes of health and disease-illness-sickness complex are introduced and integrated into a unified theoretical framework. Finally, in the light of recent epistemological developments, the concept of Health-Disease-Care Integrals is updated as a complex reference object fit for modeling health-related processes and phenomena.

Coordinated transportation of a large object by a team of three robots

Dynamical systems theory in this work is used as a theoretical language and tool to design a distributed control architecture for a team of three robots that must transport a large object and simultaneously avoid collisions with either static or dynamic obstacles. The robots have no prior knowledge of the environment. The dynamics of behavior is defined over a state space of behavior variables, heading direction and path velocity. Task constraints are modeled as attractors (i.e. asymptotic stable states) of the behavioral dynamics. For each robot, these attractors are combined into a vector field that governs the behavior. By design the parameters are tuned so that the behavioral variables are always very close to the corresponding attractors. Thus the behavior of each robot is controlled by a time series of asymptotical stable states. Computer simulations support the validity of the dynamical model architecture.

Coordinated transportation of a large object by a team of two robots

In this paper dynamical systems theory is used as a theoretical language and tool to design a distributed control architecture for a team of two robots that must transport a large object and simultaneously avoid collisions with obstacles (either static or dynamic). This work extends the previous work with two robots (see [1] and [5]). However here we demonstrate that it’s possible to simplify the architecture presented in [1] and [5] and reach an equally stable global behavior. The robots have no prior knowledge of the environment. The dynamics of behavior is defined over a state space of behavior variables, heading direction and path velocity. Task constrains are modeled as attractors (i.e. asymptotic stable states) of a behavioral dynamics. For each robot, these attractors are combined into a vector field that governs the behavior. By design the parameters are tuned so that the behavioral variables are always very close to the corresponding attractors. Thus the behavior of each robot is controlled by a time series of asymptotic stable states. Computer simulations support the validity of the dynamical model architecture.

Object transportation by multiple mobile robots controlled by attractor dynamics: theory and implementation

Dynamical systems theory is used as a theoretical language and tool to design a distributed control architecture for teams of mobile robots, that must transport a large object and simultaneously avoid collisions with (either static or dynamic) obstacles. Here we demonstrate in simulations and implementations in real robots that it is possible to simplify the architectures presented in previous work and to extend the approach to teams of n robots. The robots have no prior knowledge of the environment. The motion of each robot is controlled by a time series of asymptotical stable states. The attractor dynamics permits the integration of information from various sources in a graded manner. As a result, the robots show a strikingly smooth an stable team behaviour.

Using attractor dynamics to generate decentralized motion control of two mobile robots transporting a long object in coordination

Dynamical systems theory is used here as a theoretical language and tool to design a distributed control architecture for a team of two mobile robots that must transport a long object and simultaneously avoid obstacles. In this approach the level of modeling is at the level of behaviors. A “dynamics” of behavior is defined over a state space of behavioral variables (heading direction and path velocity). The environment is also modeled in these terms by representing task constraints as attractors (i.e. asymptotically stable states) or reppelers (i.e. unstable states) of behavioral dynamics. For each robot attractors and repellers are combined into a vector field that governs the behavior. The resulting dynamical systems that generate the behavior of the robots may be nonlinear. By design the systems are tuned so that the behavioral variables are always very close to one attractor. Thus the behavior of each robot is controled by a time series of asymptotically stable states. Computer simulations support the validity of our dynamic model architectures.

A type system for access control in an object-oriented language

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

Analysis of support for modularity in object teams based on design patterns

Dissertação de Mestrado em Engenharia Informática

Land use / land cover change detection: an object oriented approach, Münster, Germany

Dissertation submitted in partial fulfilment of the requirements for the Degree of Master of Science in Geospatial Technologies

Smart object for 3D interaction

This paper reports on the creation of an interface for 3D virtual environments, computer-aided design applications or computer games. Standard computer interfaces are bound to 2D surfaces, e.g., computer mouses, keyboards, touch pads or touch screens. The Smart Object is intended to provide the user with a 3D interface by using sensors that register movement (inertial measurement unit), touch (touch screen) and voice (microphone). The design and development process as well as the tests and results are presented in this paper. The Smart Object was developed by a team of four third-year engineering students from diverse scientific backgrounds and nationalities during one semester.

Anotação colaborativa de conteúdos utilizando jogos com propósito

Com o crescimento da informação disponível na Web, arquivos pessoais e profissionais, protagonizado tanto pelo aumento da capacidade de armazenamento de dados, como pelo aumento exponencial da capacidade de processamento dos computadores, e do fácil acesso a essa mesma informação, um enorme fluxo de produção e distribuição de conteúdos audiovisuais foi gerado. No entanto, e apesar de existirem mecanismos para a indexação desses conteúdos com o objectivo de permitir a pesquisa e acesso aos mesmos, estes apresentam normalmente uma grande complexidade algorítmica ou exigem a contratação de pessoal altamente qualificado, para a verificação e categorização dos conteúdos. Nesta dissertação pretende-se estudar soluções de anotação colaborativa de conteúdos e desenvolver uma ferramenta que facilite a anotação de um arquivo de conteúdos audiovisuais. A abordagem implementada é baseada no conceito dos “Jogos com Propósito” (GWAP – Game With a Purpose) e permite que os utilizadores criem tags (metadatos na forma de palavras-chave) de forma a atribuir um significado a um objecto a ser categorizado. Assim, e como primeiro objectivo, foi desenvolvido um jogo com o propósito não só de entretenimento, mas também que permita a criação de anotações audiovisuais perante os vídeos que são apresentados ao jogador e, que desta forma, se melhore a indexação e categorização dos mesmos. A aplicação desenvolvida permite ainda a visualização dos conteúdos e metadatos categorizados, e com o objectivo de criação de mais um elemento informativo, permite a inserção de um like num determinado instante de tempo do vídeo. A grande vantagem da aplicação desenvolvida reside no facto de adicionar anotações a pontos específicos do vídeo, mais concretamente aos seus instantes de tempo. Trata-se de uma funcionalidade nova, não disponível em outras aplicações de anotação colaborativa de conteúdos audiovisuais. Com isto, o acesso aos conteúdos será bastante mais eficaz pois será possível aceder, por pesquisa, a pontos específicos no interior de um vídeo.

Extending the learning object definition to represent programming problems

The present generation of eLearning platforms values the interchange of learning objects standards. Nevertheless, for specialized domains these standards are insufficient to fully describe all the assets, especially when they are used as input for other eLearning services. To address this issue we extended an existing learning objects standard to the particular requirements of a specialized domain, namely the automatic evaluation of programming problems. The focus of this paper is the definition of programming problems as learning objects. We introduce a new schema to represent metadata related to automatic evaluation that cannot be conveniently represented using existing standards, such as: the type of automatic evaluation; the requirements of the evaluation engine; or the roles of different assets - tests cases, program solutions, etc. This new schema is being used in an interoperable repository of learning objects, called crimsonHex.