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2011
M. Goulão, A. Moreira, J. Araújo, and J. Santos. "Streamlining scenario modeling with Model-Driven Development: A case study." Proceedings of the Model-Driven Requirements Engineering Workshop (MoDRE 2011), at the 19th International Requirements Engineering Conference (RE 2011). IEEE Computer Society, 2011. 55-63. Abstract

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P. Patricio, V. Amaral, J. Araújo, and R. Monteiro. "Towards a Unified Goal-Oriented Language." IEEE COMPSAC 2011 proceedings. IEEE Computer Society, 2011. Abstract

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Dias, Ricardo, João Louren{\c c}o, and Nuno Pregui{\c c}a. "Efficient and Correct Transactional Memory Programs Combining Snapshot Isolation and Static Analysis." Proceedings of the 3nd USENIX conference on Hot topics in parallelism (HotPar’11). HotPar’11. Usenix Association, 2011. Abstract
Concurrent programs may suffer from concurrency anomalies that may lead to erroneous and unpredictable program behaviors. To ensure program correctness, these anomalies must be diagnosed and corrected. This paper addresses the detection of both low- and high-level anomalies in the Transactional Memory setting. We propose a static analysis procedure and a framework to address Transactional Memory anomalies. We start by dealing with the classic case of low-level dataraces, identifying concurrent accesses to shared memory cells that are not protected within the scope of a memory transaction. Then, we address the case of high-level dataraces, bringing the programmer’s attention to pairs of memory transactions that were misspecified and should have been combined into a single transaction. Our framework was applied to a set of programs, collected form different sources, containing well known low- and high-level anomalies. The framework demonstrated to be accurate, confirming the effectiveness of using static analysis techniques to precisely identify concurrency anomalies in Transactional Memory programs.
Caires, L., Jorge A. Perez, J. C. Seco, Hugo T. Vieira, and Lúcio Ferrão. "Type-based Access Control in Data-Centric Systems." Programming Languages and Systems, 20th European Symposium on Programming, ESOP 2011. Ed. Gilles Barthe. Lecture Notes in Computer Science. Springer-Verlag, 2011.
P. Varela, J. Araújo, I. Brito, and A. Moreira. "Aspect-Oriented Analysis for Software Product Lines Requirements Engineering." 26th Symposium On Applied Computing, ACM SAC 2011. ACM Press, 2011. 654-671. Abstract

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Martins, R., Rybarczyk Y., and Fonseca J. "3D game for the rehabilitation of aphasic patients." 4th Annual Conference in Science and Art of Video Games. Porto, Portugal 2011. copy.pdf
Catarino, I., and C. Paine. "3He gas gap heat switch." Cryogenics. 51 (2011): 45-48. Abstract

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Oliveira, Luís Picciochi, and João M. Lourenço. "Aceleração de Computações Científicas com Processadores Heterogéneos." InForum 2011: Proceedings of InForum Simpósio de Informática. Coimbra: Universidade do Coimbra, 2011. Abstractinforum-pitxyoki.pdf

Actualmente o mercado residencial de computadores inclui não só multiprocessadores com diversos núcleos (CPUs) como também placas gráficas (GPUs) cuja capacidade de processamento tem evoluído a um ritmo exponencial. Este poder computacional pode ser utilizado para outros fins para além do processamento gráfico, tal como o processamento de algoritmos comuns em computação científica. Neste artigo é apresentada, discutida e avaliada a framework Cheetah, uma framework que distribui programas computacionalmente exigentes sobre uma rede de CPUs e GPUs. Um programador que utilize a Cheetah apenas necessita de especificar o seu programa como um conjunto de kernels OpenCL, relegando para a framework a distribuição destes pelas unidades de processamento disponíveis. O programa pode assim escalar à medida que são adicionados novos recursos computacionais, sem quaisquer esforços adicionais de adaptação ou recompilação. Os testes realizados demonstraram a capacidade de a framework providenciar aceleracçõs até duas ordens de grandeza com um esforço de desenvolvimento reduzido, mesmo quando na presença de recursos computacionais limitados.

Freitas, F., V. D. Alves, and M. A. M. Reis. "Advances in bacterial exopolysaccharides: from production to biotechnological applications." Trends in Biotechnology . 29.8 (2011): 388-398.freitas_2011_trends_biotechnol_298_388-398.pdf
Azevedo, S. G., H. Carvalho, and V. Cruz-Machado. "Agile Index: Automotive Supply Chain." World Academy of Science, Engineering and Technology. 79 (2011): 784-790. AbstractWebsite

The supply chains (SCs) have to appeal to new management paradigms to improve their ability to respond rapidly and cost effectively to unpredictable changes in markets and increasing levels of environmental turbulence, both in terms of volume and variety. In this highly demanded context, the Agile paradigm provides the capabilities to SC quickly adapt to changes in the market requirements. The purpose of this paper is to suggest an Agile Index to assess the agility of the automotive companies and corresponding SCs.The proposed integrated assessment model incorporates Agile practices weighted according to their importance to the automotive SC competitiveness and obtained from the Delphi technique.

Estêvão M. S., Carvalho L. C. R., Ferreira Fernandes Marques L. E. M. M. "Analysis of the antioxidant activity of an indole library: cyclic voltammetry versus ROS scavenging activity." Tetrahedron Lett.. 52 (2011): 101-106.
Rybarczyk, Y., Rybarczyk P., Oliveira N., and Vernay D. "Application Internet pour l’évaluation stratégique et personnalisée des situations de handicap." Symposium sur l’Ingénierie de l’Information Médicale’11. Toulouse, France 2011.
Costa, J. C., M. D. Ortigueira, and AG Batista. "ARMA Modelling of Sleep Spindles." Second IFIP WG 5.5/SOCOLNET Doctoral Conference on Computing, Electrical and Industrial Systems. Doceis, 2011.
Moreira, Felismina T. C., Rosa A. F. Dutra, João P. C. Noronha, and Goreti M. F. Sales. "Artificial antibodies for Troponin T by its imprinting on the surface of Multiwalled Carbon Nanotubes: its use as sensory surfaces." Biosensors and Bioelectronics. 28.1 (2011): 243-250.
Micaelo, Rui, Jaime Ribeiro, Maria Azevedo, and Nuno Azevedo. "Asphalt compaction study: micromechanical modelling of a simplified lab compaction procedure." Road Materials and Pavement Design. 12.3 (2011): 461-491.Website
Barros, M. T., and A. M. Faísca-Phillips. "Asymmetric Organocatalytic Reactions for the Synthesis of Heterocycles." Heterocyclic Targets in Advanced Organic Synthesis. Eds. M. C. Carreiras, and J. Marco-Contelles. Kerala, India: Research Signpost, 2011. 1-50.
Araújo, João, Vítor H. Fernandes, Manuel M. Jesus, Victor Maltcev, and James D. Mitchell. "Automorphisms of partial endomorphism semigroups." Publicationes Mathematicae Debrecen. 79.1-2 (2011): 23-39.
Araújo, João, Vítor H. Fernandes, Manuel M. Jesus, Victor Maltcev, and James D. Mitchell. "Automorphisms of partial endomorphism semigroups." Publ. Math.. 79 (2011): 23-39. Abstract

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Lucas, V., and M. P. Amado Avaliação da Construção Sustentável. iiSBE. Lisboa, Portugal: iiSBE - UM, 2011.
Amado, M. P., T. Lopes, E. R. Moura, J. C. Freitas, and M. R. Ribeiro Avaliação da Sustentabilidade do PDM. 6º CLEM 2011. Maputo, Moçambique: INEGI, 2011.
Viegas, Aldino, Joao Manso, Marta C. Corvo, Manuel M. B. Marques, and Eurico J. Cabrita. "Binding of ibuprofen, ketorolac and diclofenac to COX-1 and COX-2 studied by saturation transfer difference NMR." Journal of Medicinal Chemistry. 54.24 (2011): 8555-8562. AbstractWebsite

Saturation Transfer Difference-NMR (STD-NMR) spectroscopy has emerged as a powerful screening tool and a straightforward way to study the binding epitopes of active compounds in early stage lead discovery in pharmaceutical research. Here we report the application of STD NMR to characterize the binding of the anti-inflammatory drugs ibuprofen, diclofenac and ketorolac to COX-1 and COX-2. Using well-studied COX inhibitors and by comparing STD signals with crystallographic structures we show that there is a relation between the orientations of ibuprofen and diclofenac in the COX-2 active site and the relative STD responses detected in the NMR experiments. Based on this analysis we propose that ketorolac should bind to the COX-2 active site in similar orientation as that of diclofenac. We also show that the combination of STD NMR with competition experiments constitutes a valuable tool to address the recently proposed behavior of COX-2 as functional heterodimers and complement enzyme activity studies in the effort to rationalize COX inhibition mechanisms.

Viegas A., Manso J., Marques Manuel Cabrita M. B. E. J. *. "Binding of Ibuprofen, Ketorolac, and Diclofenac to COX-1 and COX-2 Studied by Saturation Transfer Difference NMR." J. Med. Chem.. 54 (2011): 8555-8562.
Cortez, João, Ekaterina Vorobieva, Daniel Gralheira, Inês Osório, Leonor Soares, Nuno Vale, Eulália Pereira, Paula Gomes, and Ricardo Franco. "Bionanoconjugates of tyrosinase and peptide-derivatised gold nanoparticles for biosensing of phenolic compounds." Journal of Nanoparticle Research. 13.3 (2011): 1101-1113.cortez_et_al_j_nanopart_res_13_2011_1101-1113.pdf
Dias, A. M., A. S. Marcos, A. Hussain, and A. C. A. Roque. "A biotechnological perspective on the application of iron oxide magnetic colloids modified with polysaccharides." Biotechnology Advances. 29 (2011): 142-155.