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2011
Dell'acqua, S., S. R. Pauleta, I. Moura, and JJG Moura. "The tetranuclear copper active site of nitrous oxide reductase: the CuZ center." Journal of Biological Inorganic Chemistry. 16 (2011): 183-194. AbstractWebsite

This review focuses on the novel CuZ center of nitrous oxide reductase, an important enzyme owing to the environmental significance of the reaction it catalyzes, reduction of nitrous oxide, and the unusual nature of its catalytic center, named CuZ. The structure of the CuZ center, the unique tetranuclear copper center found in this enzyme, opened a novel area of research in metallobiochemistry. In the last decade, there has been progress in defining the structure of the CuZ center, characterizing the mechanism of nitrous oxide reduction, and identifying intermediates of this reaction. In addition, the determination of the structure of the CuZ center allowed a structural interpretation of the spectroscopic data, which was supported by theoretical calculations. The current knowledge of the structure, function, and spectroscopic characterization of the CuZ center is described here. We would like to stress that although many questions have been answered, the CuZ center remains a scientific challenge, with many hypotheses still being formed.

Dell'acqua, S., I. Moura, J. J. Moura, and S. R. Pauleta. "The electron transfer complex between nitrous oxide reductase and its electron donors." J Biol Inorg Chem. 16 (2011): 1241-54. AbstractWebsite

Identifying redox partners and the interaction surfaces is crucial for fully understanding electron flow in a respiratory chain. In this study, we focused on the interaction of nitrous oxide reductase (N(2)OR), which catalyzes the final step in bacterial denitrification, with its physiological electron donor, either a c-type cytochrome or a type 1 copper protein. The comparison between the interaction of N(2)OR from three different microorganisms, Pseudomonas nautica, Paracoccus denitrificans, and Achromobacter cycloclastes, with their physiological electron donors was performed through the analysis of the primary sequence alignment, electrostatic surface, and molecular docking simulations, using the bimolecular complex generation with global evaluation and ranking algorithm. The docking results were analyzed taking into account the experimental data, since the interaction is suggested to have either a hydrophobic nature, in the case of P. nautica N(2)OR, or an electrostatic nature, in the case of P. denitrificans N(2)OR and A. cycloclastes N(2)OR. A set of well-conserved residues on the N(2)OR surface were identified as being part of the electron transfer pathway from the redox partner to N(2)OR (Ala495, Asp519, Val524, His566 and Leu568 numbered according to the P. nautica N(2)OR sequence). Moreover, we built a model for Wolinella succinogenes N(2)OR, an enzyme that has an additional c-type-heme-containing domain. The structures of the N(2)OR domain and the c-type-heme-containing domain were modeled and the full-length structure was obtained by molecular docking simulation of these two domains. The orientation of the c-type-heme-containing domain relative to the N(2)OR domain is similar to that found in the other electron transfer complexes.

Da Silva, M. S., R. Viveiros, P. I. Morgado, A. Aguiar-Ricardo, I. J. Correia, and T. Casimiro. "Development of 2-(dimethylamino)ethyl methacrylate-based molecular recognition devices for controlled drug delivery using supercritical fluid technology." International Journal of Pharmaceutics. 416.1 (2011): 61-68. AbstractWebsite
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Da Silva, M. S., F. L. Nobrega, A. Aguiar-Ricardo, E. J. Cabrita, and T. Casimiro. "Development of molecularly imprinted co-polymeric devices for controlled delivery of flufenamic acid using supercritical fluid technology." Journal of Supercritical Fluids. 58.1 (2011): 150-157. AbstractWebsite
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Costa, E., J. De-Carvalho, T. Casimiro, C. L. da Silva, M. T. Cidade, and A. Aguiar-Ricardo. "Tailoring thermoresponsive microbeads in supercritical carbon dioxide for biomedical applications." Journal of Supercritical Fluids. 56.3 (2011): 292-298. AbstractWebsite
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Craciunescu, Corneliu M., Karimbi. K. Mahesh, Rui JC Silva, Francisco M. BRAZ FERNANDES, Y. Brechet, E. Clouet, A. Deschamps, A. Finel, and F. Soisson. "Structural Transitions in a Co2NiGa Ferromagnetic Shape Memory Alloy." Solid-Solid Phase Transformations in Inorganic Materials, Pts 1-2. 172-174 (2011): 202-207. Abstract
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De Frémont, P., H. Clavier, V. Rosa, T. Avilés, and P. Braunstein. "Synthesis, characterization, and reactivity of cationic gold(I) α-diimine complexes." Organometallics. 30.8 (2011): 2241-2251. AbstractWebsite
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Valtchev, {Stanimir Stoyanov}, and DEE Group Author. "Actions for Broadening the Engineering Culture of the European Student with an Insight to the Future Needs of the Global (European) Labour Market." Proceedings of the First International Conference of the European Polytechnical University. 2011. 78-82. Abstract
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Valtchev, {Stanimir Stoyanov}, and DEE Group Author. "Energy Harvesting and the Human Health." Proceedings of the First International Conference of the European Polytechnical University. 2011. 451-460. Abstract
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Valtchev, {Stanimir Stoyanov}, {Jorge Joaquim} Pamies-Teixeira, and DEE Group Author High Level Education Through Research Training Networks: A Potential StrategyTo Build Knowledge In EV/HEV. Vol. NA., 2011. Abstract
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Valtchev, {Stanimir Stoyanov}, and DEE Group Author. "An UHF Wireless Power Harvesting System - Analysis and Design." PES 2011: Proceedings of extended abstracts. 2011. 141-142. Abstract

This paper presents a system to harvest electromagnetic energy from the environment. The proposed solution differs from others already existent in the literature because it makes possible to harvest energy from a large frequency spectrum. Typically the existing energy harvesting systems only gather energy from one specific source, thus not taking advantage of the several RF sources existing in one place. The full system and its componentsare simulated and implemented, and the results obtained are shown. The system harvest energy from UHF sources, and converts the harvested energy to a DC voltage, in order to feed electronic devices. This conversion is made through the utilization of a voltage multiplier, followed by a voltage regulator.

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.
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.
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.
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.
Rybarczyk, Y., and Mestre D. "Body schema deformation in teleoperation: effect of sensori-motor contingences." Psychology Research. 1.1 (2011): 26-41.
Duarte, Susana, Helena Carvalho, and V. Cruz Machado. "The Commitments Between Lean, Agile, Resilient and Green Supply Chain Paradigms." GLASGOW, SCOTLAND: UNIVERSITY OF STRATHCLYDE, 2011. 68-82. Abstract

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Dinis, R., and M. P. Amado Contributos para a Reabilitação Sustentável de Edifícios. 6º CLEM 2011. Maputo, Moçambique: INEGI, 2011.
Bragança, H., D. Rigling, E. Diogo, J. Capelo, A. Phillips, and R. Tenreiro. "Cryphonectria naterciae : A new species in the Cryphonectria-Endothia complex and diagnostic molecular markers based on microsatellite primed PCR." Fungal Biology. 115 (2011): 852-861.
Lourenço, João, Diogo Sousa, Bruno C. Teixeira, and Ricardo J. Dias. "Detecting concurrency anomalies in transactional memory programs." Comput. Sci. Inf. Syst.. 8.2 (2011): 533-548. Abstractcomsis-2011.pdf

Software transactional memory is a promising programming model that adapts many concepts borrowed from the databases world to control concurrent accesses to main memory (RAM). This paper discusses how to support revertible operations, such as memory allocation and release, within software libraries that will be used in software memory transactional contexts. The proposal is based in the extension of the transaction life cycle state diagram with new states associated to the execution of user-defined handlers. The proposed approach is evaluated in terms of functionality and performance by way of a use case study and performance tests. Results demonstrate that the proposal and its current implementation are flexible, generic and efficient

Dias, Ricardo J., João M. Lourenço, and João Costa Seco Detection of Snapshot Isolation Anomalies in Software Transactional Memory: A Statical Analysis Approach. Departamento de Informática FCT/UNL, 2011. Abstract

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Rybarczyk, Y., Rybarczyk P., Oliveira N., and Vernay D. "e-ESPOIR: a user-friendly web-based tool for disability evaluation." 11th conference of the Association for the Advancement of Assistive Technology in Europe. Maastricht, Netherlands 2011.
Duarte, Filipe J. S., Snezhana M. Bakalova, Eurico J. Cabrita, and Gil A. Santos. "Lewis Acid Catalyzed Reactions of Chiral Imidazolidinones and Oxazolidinones: Insights on the Role of the Catalyst." Journal of Organic Chemistry. 76.17 (2011): 6997-7004. Abstract

The mechanism proposed by Evans to justify the selectivity obtained in Lewis acid catalyzed Diels-Alder reactions of cyclopentadiene with acyloxazolidinones has been generalized and used in the rationalization of selectivities obtained in many other systems. However, we recently proposed an alternative mechanism, on the basis of open-chain mono- and bicomplexes, that avoids the need for chelates and explains the selectivity obtained by Evans. In this manuscript we apply our proposal to the catalyzed conjugated addition of amines to acylimidazolidinones, reported by Cardillo, and we clearly show that aluminum chelates are not involved in the reaction, as they induce no selectivity, while Cardillo observed high experimental selectivities. Our data equally show that bicomplexes with carbonyl parallel orientation, proposed by Cardillo to justify the experimental selectivity with nonchelating Lewis acids, indeed induce the opposite selectivity and have also to be dismissed. On the other hand, our mechanistic proposal allows for the full rationalization of the data obtained by Cardillo with aluminum, boron, or zinc Lewis acids and supports our previous proposal on DA cycloadditions of dienes to Evans chiral auxiliary derivatives.