Modelling and verifying smell-free architectures with the Archery language

Architectural (bad) smells are design decisions found in software architectures that degrade the ability of systems to evolve. This paper presents an approach to verify that a software architecture is smellfree using the Archery architectural description language. The language provides a core for modelling software architectures and an extension for specifying constraints. The approach consists in precisely specifying architectural smells as constraints, and then verifying that software architectures do not satisfy any of them. The constraint language is based on a propositional modal logic with recursion that includes: a converse operator for relations among architectural concepts, graded modalities for describing the cardinality in such relations, and nominals referencing architectural elements. Four architectural smells illustrate the approach.

Basic constraints between two vectors

This chapter deals with the characterization of the basic constraints between two vectors. This issue plays a crucial role in the formulation of constraint equations for mechanical joints. In particular, relations between two parallel and two perpendicular vectors are derived. Moreover, formulation for a vector that connects two generic points is presented. The material described here is developed under the framework of multibody systems formulation for spatial systems.

Kinematic joints constraints

"Series title: Springerbriefs in applied sciences and technology, ISSN 2191-530X"

Equations of motion for constrained systems

"Series title: Springerbriefs in applied sciences and technology, ISSN 2191-530X"

A critical evaluation of methods for the reconstruction of tissue-specific models

Under the framework of constraint based modeling, genome-scale metabolic models (GSMMs) have been used for several tasks, such as metabolic engineering and phenotype prediction. More recently, their application in health related research has spanned drug discovery, biomarker identification and host-pathogen interactions, targeting diseases such as cancer, Alzheimer, obesity or diabetes. In the last years, the development of novel techniques for genome sequencing and other high-throughput methods, together with advances in Bioinformatics, allowed the reconstruction of GSMMs for human cells. Considering the diversity of cell types and tissues present in the human body, it is imperative to develop tissue-specific metabolic models. Methods to automatically generate these models, based on generic human metabolic models and a plethora of omics data, have been proposed. However, their results have not yet been adequately and critically evaluated and compared. This work presents a survey of the most important tissue or cell type specific metabolic model reconstruction methods, which use literature, transcriptomics, proteomics and metabolomics data, together with a global template model. As a case study, we analyzed the consistency between several omics data sources and reconstructed distinct metabolic models of hepatocytes using different methods and data sources as inputs. The results show that omics data sources have a poor overlapping and, in some cases, are even contradictory. Additionally, the hepatocyte metabolic models generated are in many cases not able to perform metabolic functions known to be present in the liver tissue. We conclude that reliable methods for a priori omics data integration are required to support the reconstruction of complex models of human cells.

Da previsibilidade da notícia às vantagens da agenda jornalística: uma reflexão a partir do Rádio Clube Português

Dissertação de mestrado em Ciências da Comunicação (área de especialização em Informação e Jornalismo)

Multibody systems formulation

"Series: Solid mechanics and its applications, vol. 226"

Atividades de campo no ensino da Geologia: opiniões de professores portugueses sobre formas ideais de as usar

Devido à elevada dimensão espacial e temporal da maior parte dos fenómenos geológicos, não é possível reproduzir no laboratório os fenómenos a estudar, pelo que, se o professor de Geologia pretender colocar os alunos em contato com esses fenómenos, terá que organizar uma saída de campo para que as necessárias e adequadas atividades sejam realizadas no lugar onde esses fenómenos ocorrem. Contudo, e apesar de professores e alunos reconhecerem diversas potencialidades didáticas das saídas de campo, os professores raramente as organizam e justificam isso com base em diversos impedimentos. Neste artigo relatam-se os resultados de um estudo em que 233 professores portugueses de Biologia e Geologia foram inquiridos acerca de formas ideais de integrar as atividades de campo na componente de Geologia, no 3º ciclo do Ensino Básico (n=102) e no Ensino Secundário (n=131). Os resultados sugerem que as práticas que os professores gostariam de implementar, caso não houvesse constrangimentos à realização de atividades de campo, não seriam, na maior parte dos casos, muito diferentes das práticas implementadas que são relatadas na literatura. Esta falta de exigência e de ousadia por parte dos professores, no que concerne ao modo como as atividades de campo deveriam ser utilizadas, sugere a necessidade de a formação inicial e contínua de professores contemplar uma abordagem adequada das saídas de campo e de as escolas se reorganizarem para facilitarem a organização, fundamentada, das mesmas.

Influência do clima afectivo induzido pelo treinador no comportamento táctico e estado afectivo dos jogadores

O presente estudo tem como objectivo perceber como o clima afectivo (positivo ou negativo) induzido pelo treinador influencia o comportamento táctico e o estado afectivo percepcionado pelos jogadores de futebol Sub-15 do Campeonato Distrital da Associação de Futebol de Lisboa. Seleccionaram-se três equipas que constituíram os três grupos do estudo: grupo de afectividade positiva (GAP), grupo de afectividade negativa (GAN) e o grupo controlo (GC). Após um pré-teste, à excepção do GC, com manifestação de afectividade neutra pelo treinador, os grupos experimentais foram submetidos a situações de afectividade positiva e negativa, durante três sessões de treino. Após este período de intervenção, realizou-se um pós-teste. Avaliou-se afectos percepcionados pelos jogadores, através da escala PANAS e o comportamento táctico, através da largura de jogo da equipa, com base na recolha de dados posicionais, verificando-se a regularidade da largura de jogo através da entropia amostral (SampEn). Foram encontradas diferenças significativas na regularidade do comportamento no GAN ̅ e ̅ mas não se encontraram diferenças nos afectos percepcionados pelos jogadores em nenhum dos grupos. Encontrou-se igualmente uma tendência positiva na largura da equipa no GAP. Os resultados sugerem que o clima afectivo do treinador apresenta-se como um constrangimento ambiental que influência o comportamento táctico dos jogadores. O clima afectivo positivo estabeleceu um aumento da largura da equipa, mostrando-se viável à procura de comportamentos adaptativos para a consecução de objectivos estabelecidos.

Endogenous capacity utilization and the asymmetric effects of monetary policy

This paper investigates the role of variable capacity utilization as a source of asymmetries in the relationship between monetary policy and economic activity within a dynamic stochastic general equilibrium framework. The source of the asymmetry is directly linked to the bottlenecks and stock-outs that emerge from the existence of capacity constraints in the real side of the economy. Money has real effects due to the presence of rigidities in households' portfolio decisions in the form of a Luces-Fuerst 'limited participation' constraint. The model features variable capacity utilization rates across firms due to demand uncertainty. A monopolistic competitive structure provides additional effects through optimal mark-up changes. The overall message of this paper for monetary policy is that the same actions may have different effects depending on the capacity utilization rate of the economy.

Preliminary study of cooperation in hybrid ad-hoc networks

In this paper, we present a first approach to evolve a cooperative behavior in ad hoc networks. Since wireless nodes are energy constrained, it may not be in the best interest of a node to always accept relay requests. On the other hand, if all nodes decide not to expend energy in relaying, then network throughput will drop dramatically. Both these extreme scenarios are unfavorable to the interests of a user. In this paper we deal with the issue of user cooperation in ad hoc networks by developing the algorithm called Generous Tit-For-Tat. We assume that nodes are rational, i.e., their actions are strictly determined by self-interest, and that each node is associated with a minimum lifetime constraint. Given these lifetime constraints and the assumption of rational behavior, we study the added behavior of the network.

The fourth extracellular loop of the alpha subunit of Na,K-ATPase. Functional evidence for close proximity with the second extracellular loop.

Na,K-ATPase is the main active transport system that maintains the large gradients of Na(+) and K(+) across the plasma membrane of animal cells. The crystal structure of a K(+)-occluding conformation of this protein has been recently published, but the movements of its different domains allowing for the cation pumping mechanism are not yet known. The structure of many more conformations is known for the related calcium ATPase SERCA, but the reliability of homology modeling is poor for several domains with low sequence identity, in particular the extracellular loops. To better define the structure of the large fourth extracellular loop between the seventh and eighth transmembrane segments of the alpha subunit, we have studied the formation of a disulfide bond between pairs of cysteine residues introduced by site-directed mutagenesis in the second and the fourth extracellular loop. We found a specific pair of cysteine positions (Y308C and D884C) for which extracellular treatment with an oxidizing agent inhibited the Na,K pump function, which could be rapidly restored by a reducing agent. The formation of the disulfide bond occurred preferentially under the E2-P conformation of Na,K-ATPase, in the absence of extracellular cations. Using recently published crystal structure and a distance constraint reproducing the existence of disulfide bond, we performed an extensive conformational space search using simulated annealing and showed that the Tyr(308) and Asp(884) residues can be in close proximity, and simultaneously, the SYGQ motif of the fourth extracellular loop, known to interact with the extracellular domain of the beta subunit, can be exposed to the exterior of the protein and can easily interact with the beta subunit.

Metodología de diseño de filtros CRF/SCF basada en modelos de resonadores BAW acoplados acústicamente

La creixent utilització de sistemes de comunicacions mòbils ha impulsat la demanda de filtres passabanda miniaturitzats d'elevades prestacions operant en el rang de freqüències de microones. Els Film Bulk Acoustic Resonators (FBAR) estan esdevenint la principal alternativa als filtres basats en ressonadors Surface Acoustic Wave (SAW) o als basats en ressonadors ceràmics. Els Stacked Crystal Filters (SCF) i els Coupled Resonator Filters (CRF) són configuracions FBAR que permeten assolir una excel·lent atenuació en la banda de refús. Aquest treball presenta un innovador circuit equivalent elèctric que modela el CRF. Llavors, es desenvolupa una metodologia de síntesi de filtres per al SCF i per al CRF utilitzant els seus circuits equivalents elèctrics. La metodologia de disseny presentada permet obtenir les dimensions de l'estructura del filtre acústic partint de les especificacions del filtre i de les restriccions pròpies de la tecnologia. S'han implementat diferents respostes de Chebyshev per a sistemes de comunicacions reals per tal de validar el procediment de disseny dels filtres obtenint els resultats esperats.

Structure-function relationships of the alpha1b-adrenergic receptor.

The alpha1b-adrenergic receptor (AR) is a member of the large superfamily of seven transmembrane domain (TMD) G protein-coupled receptors (GPCR). Combining site-directed mutagenesis of the alpha1b-AR with computational simulations of receptor dynamics, we have explored the conformational changes underlying the process of receptor activation, i.e. the transition between the inactive and active states. Our findings suggest that the structural constraint stabilizing the alpha1b-AR in the inactive form is a network of H-bonding interactions amongst conserved residues forming a polar pocket and R143 of the DRY sequence at the end of TMDIII. We have recently reported that point mutations of D142, of the DRY sequence and of A293 in the distal portion of the third intracellular loop resulted in ligand-independent (constitutive) activation of the alpha1b-AR. These constitutively activating mutations could induce perturbations resulting in the shift of R143 out of the polar pocket. The main role of R143 may be to mediate receptor activation by triggering the exposure of several basic amino acids of the intracellular loops towards the G protein. Our investigation has been extended also to the biochemical events involved in the desensitization process of alpha1b-AR. Our results indicate that immediately following agonist-induced activation, the alpha1b-AR can undergo rapid agonist-induced phosphorylation and desensitization. Different members of the G protein coupled receptor kinase family can play a role in agonist-induced regulation of the alpha1b-AR. In addition, constitutively active alpha1b-AR mutants display different phosphorylation and internalization features. The future goal is to further elucidate the molecular mechanism underlying the complex equilibrium between activation and inactivation of the alpha1b-AR and its regulation by pharmacological substances. These findings can help to elucidate the mechanism of action of various agents displaying properties of agonists or inverse agonists at the adrenergic system.

Constrained school choice: an experimental study

The literature on school choice assumes that families can submit a preference list over all the schools they want to be assigned to. However, in many real-life instances families are only allowed to submit a list containing a limited number of schools. Subjects' incentives are drastically affected, as more individuals manipulate their preferences. Including a safety school in the constrained list explains most manipulations. Competitiveness across schools play an important role. Constraining choices increases segregation and affects the stability and efficiency of the final allocation. Remarkably, the constraint reduces significantly the proportion of subjects playing a dominated strategy.