Genetic regulatory mechanisms by means of extended interactive Petri nets

In our work we have chosen to integrate formalism for knowledge representation with formalism for process representation as a way to specify and regulate the overall activity of a multi-cellular agent. The result of this approach is XP,N, another formalism, wherein a distributed system can be modeled as a collection of interrelated sub-nets sharing a common explicit control structure. Each sub-net represents a system of asynchronous concurrent threads modeled by a set of transitions. XP,N combines local state and control with interaction and hierarchy to achieve a high-level abstraction and to model the complex relationships between all the components of a distributed system. Viewed as a tool XP,N provides a carefully devised conflict resolution strategy that intentionally mimics the genetic regulatory mechanism used in an organic cell to select the next genes to process.

An evolutionary approach to the use of Petri net based models: from parallel controllers to HW/SW co-design

"A workshop within the 19th International Conference on Applications and Theory of Petri Nets - ICATPN’1998"

Feature Nets: behavioural modelling of software product lines

Software product lines (SPL) are diverse systems that are developed using a dual engineering process: (a)family engineering defines the commonality and variability among all members of the SPL, and (b) application engineering derives specific products based on the common foundation combined with a variable selection of features. The number of derivable products in an SPL can thus be exponential in the number of features. This inherent complexity poses two main challenges when it comes to modelling: Firstly, the formalism used for modelling SPLs needs to be modular and scalable. Secondly, it should ensure that all products behave correctly by providing the ability to analyse and verify complex models efficiently. In this paper we propose to integrate an established modelling formalism (Petri nets) with the domain of software product line engineering. To this end we extend Petri nets to Feature Nets. While Petri nets provide a framework for formally modelling and verifying single software systems, Feature Nets offer the same sort of benefits for software product lines. We show how SPLs can be modelled in an incremental, modular fashion using Feature Nets, provide a Feature Nets variant that supports modelling dynamic SPLs, and propose an analysis method for SPL modelled as Feature Nets. By facilitating the construction of a single model that includes the various behaviours exhibited by the products in an SPL, we make a significant step towards efficient and practical quality assurance methods for software product lines.

SOFHIA: a CAD environment to design digital control systems

"Series Title: IFIP - The International Federation for Information Processing, ISSN 1868-4238"

An object-oriented model for rapid prototyping of data path/control systems - a case study

Publicado em "Information control in manufacturing 1998 : (INCOM'98) : advances in industrial engineering : a proceedings volume from the 9th IFAC Symposium, Nancy-Metz, France, 24-26 June 1998. Vol. 2"

Updating of the hierarchical rock mass rating (HRMR) system and a new subsystem developed for weathered granite formations

The RMR system is still very much applied in rock mechanics engineering context. It is based on the evaluation of six weights to obtain a final rating. To obtain the final rating a considerable amount of information is needed concerning the rock mass which can be difficult to obtain in some projects or project stages at least with accuracy. In 2007 an alternative classification scheme based on the RMR, the Hierarchical Rock Mass Rating (HRMR) was presented. The main feature of this system was the adaptation to the level of knowledge existent about the rock mass to obtain the classification of the rock mass since it followed a decision tree approach. However, the HRMR was only valid for hard rock granites with low fracturing degrees. In this work, the database was enlarged with approximately 40% more cases considering other types of granite rock masses including weathered granites and based on this increased database the system was updated. Granite formations existent in the north of Portugal including Porto city are predominantly granites. Some years ago a light rail infrastructure was built in the city of Porto and surrounding municipalities whi h involved considerable challenges due to the high heterogeneity levels of the granite formations and the difficulties involved in their geomechanical characterization. In this work it is intended to provide also a contribution to improve the characterization of these formations with special emphasis to the weathered horizons. A specific subsystem applicable to the weathered formations was developed. The results of the validation of these systems are presented and show acceptable performances in identifying the correct class using less information than with the RMR system.

Multiphasic, multistructured and hierarchical strategies for cartilage regeneration

Cartilage tissue is a complex nonlinear, viscoelastic, anisotropic, and multiphasic material with a very low coefficient of friction, which allows to withstand millions of cycles of joint loading over decades of wear. Upon damage, cartilage tissue has a low self-reparative capacity due to the lack of neural connections, vascularization, and a latent pool of stem/chondroprogenitor cells. Therefore, the healing of articular cartilage defects remains a significant clinical challenge, affecting millions of people worldwide. A plethora of biomaterials have been proposed to fabricate devices for cartilage regeneration, assuming a wide range of forms and structures, such as sponges, hydrogels, capsules, fibers, and microparticles. In common, the fabricated devices were designed taking in consideration that to fully achieve the regeneration of functional cartilage it is mandatory a well-orchestrated interplay of biomechanical properties, unique hierarchical structures, extracellular matrix (ECM), and bioactive factors. In fact, the main challenge in cartilage tissue engineering is to design an engineered device able to mimic the highly organized zonal architecture of articular cartilage, specifically its spatiomechanical properties and ECM composition, while inducing chondrogenesis, either by the proliferation of chondrocytes or by stimulating the chondrogenic differentiation  of stem/chondro-progenitor cells. In this chapter we present the recent advances in the development of innovative and complex biomaterials that fulfill the required structural key elements for cartilage regeneration. In particular, multiphasic, multiscale, multilayered, and hierarchical strategies composed by single or multiple biomaterials combined in a welldefined structure will be addressed. Those strategies include biomimetic scaffolds mimicking the structure of articular cartilage or engineered scaffolds as models of research to fully understand the biological mechanisms that influence the regeneration of cartilage tissue.

Nonlinear behavior of gelatin networks reveals a hierarchical structure

We investigate the strain hardening behavior of various gelatin networks-namely physical gelatin gel, chemically cross-linked gelatin gel, and a hybrid gel made of a combination of the former two-under large shear deformations using the pre-stress, strain ramp, and large amplitude oscillations shear protocols. Further, the internal structures of physical gelatin gels and chemically cross-linked gelatin gels were characterized by small angle neutron scattering (SANS) to enable their internal structures to be correlated with their nonlinear rheology. The Kratky plots of SANS data demonstrate the presence of small cross-linked aggregates within the chemically cross-linked network whereas, in the physical gelatin gels, a relatively homogeneous structure is observed. Through model fitting to the scattering data, we were able to obtain structural parameters, such as the correlation length (ξ), the cross-sectional polymer chain radius (Rc) and the fractal dimension (df) of the gel networks. The fractal dimension df obtained from the SANS data of the physical and chemically cross-linked gels is 1.31 and 1.53, respectively. These values are in excellent agreement with the ones obtained from a generalized nonlinear elastic theory that has been used to fit the stress-strain curves. The chemical cross-linking that generates coils and aggregates hinders the free stretching of the triple helix bundles in the physical gels.

Closed hybrid hierarchical reservoirs based on the deconstruction of the cellular native microenvironment

The stem cell niche organization and dynamics provide valuable cues for the development of mimetic environments that could have potential to stimulate the regenerative process. We propose the use of biodegradable biomaterials to produce closed miniaturised structures able to encapsulate different cell types or bioactive molecules. In particular, capsules are fabricated using the so-called layer-by-layer technology, where the consecutive (nano-sized) layers are well stabilized by electrostatic interactions or other weak forces. Using alginate-based spherical templates containing cells or other elements (e.g. proteins, magnetic nanoparticles, microparticles) it is possible to produce liquefied capsules that may entrap the entire cargo under mild conditions. The inclusion of liquefied micropcapsules may be used to produce hierarchical compartmentalised systems for the delivery of bioactive agents. The presence of solid microparticles inside such capsules offers adequate surface area for adherent cell attachment increasing the biological performance of these hierarchical systems, while maintain both permeability and injectability. We demonstrated that the encapsulation of distinct cell types (including mesenchymal stem cells and endothelial cells) enhances the osteogenic capability of this system, that could be useful in bone tissue engineering applications.

Superhydrophobic surfaces as a tool for the fabrication of hierarchical spherical polymeric carriers

Hierarchical polymeric carriers with high encapsulation efficiencies are fabricated via a biocompatible strategy developed using superhydrophobic (SH) surfaces. The carries are obtained by the incorporation of cell/BSA-loaded dextran-methacrylate (DEXT-MA) microparticles into alginate (ALG) macroscopic beads. Engineered devices like these are expected to boost the development of innovative and customizable systems for biomedical and biotechnological purposes.

Redes de Petri e VHDL na prototipagem rápida de sistemas digitais

O objectivo principal deste artigo é exemplificar a utilização de uma metodologia de especificação de sistemas digitais, baseada em Redes de Petri orientadas por objectos, para obter de uma forma rápida e simplificada um protótipo em VHDL do sistema pretendido. É considerado para exemplificação um sistema digital, para o qual se efectua a especificação no modelo RdP-shobi e a geração automática de código VHDL. Este exemplo permite concluir acerca da utilidade desta metodologia no projecto de sistemas digitais, suportado por princípios de orientação por objectos e por uma ferramenta de EDA desenvolvida propositadamente para o efeito.

Redes de Petri e VHDL na prototipagem rápida de sistemas digitais

O objectivo principal deste artigo é exemplificar a utilização de uma metodologia de especificação de sistemas digitais, baseada em Redes de Petri orientadas por objectos, para obter de uma forma rápida e simplificada um protótipo em VHDL do sistema pretendido. É considerado como exemplo um sistema digital, para o qual se efectua a especificação no modelo RdP-shobi e a partir da qual se pode gerar automaticamente código VHDL. Este exemplo permite demonstrar acerca da capacidade desta metodologia no projecto de sistemas digitais, suportado por princípios de orientação por objectos e por uma ferramenta de EDA concebida para o efeito.

Hierarchical modelling of timber reference properties using probabilistic methods: Maximum Likelihood Method, Bayesian Methods and Probability Networks

In recent decades, an increased interest has been evidenced in the research on multi-scale hierarchical modelling in the field of mechanics, and also in the field of wood products and timber engineering. One of the main motivations for hierar-chical modelling is to understand how properties, composition and structure at lower scale levels may influence and be used to predict the material properties on a macroscopic and structural engineering scale. This chapter presents the applicability of statistic and probabilistic methods, such as the Maximum Likelihood method and Bayesian methods, in the representation of timber’s mechanical properties and its inference accounting to prior information obtained in different importance scales. These methods allow to analyse distinct timber’s reference properties, such as density, bending stiffness and strength, and hierarchically consider information obtained through different non, semi or destructive tests. The basis and fundaments of the methods are described and also recommendations and limitations are discussed. The methods may be used in several contexts, however require an expert’s knowledge to assess the correct statistic fitting and define the correlation arrangement between properties.