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2009
Najmudin, S., C. Bonifacio, A. G. Duarte, S. R. Pauleta, I. Moura, J. J. Moura, and MJ Romao. "Crystallization and crystallographic analysis of the apo form of the orange protein (ORP) from Desulfovibrio gigas." Acta Crystallogr Sect F Struct Biol Cryst Commun. 65 (2009): 730-2. AbstractWebsite

The orange-coloured protein (ORP) from Desulfovibrio gigas is a 12 kDa protein that contains a novel mixed-metal sulfide cluster of the type [S(2)MoS(2)CuS(2)MoS(2)]. Diffracting crystals of the apo form of ORP have been obtained. Data have been collected for the apo form of ORP to 2.25 A resolution in-house and to beyond 2.0 A resolution at ESRF, Grenoble. The crystals belonged to a trigonal space group, with unit-cell parameters a = 43, b = 43, c = 106 A.

Moura, J., L. Krippahl, S. Pauleta, R. Almeida, and S. Del Acqua. "Molecular interactions/electron transfer protein complexes using Docking algorithms, spectroscopy (NMR) and site direct mutagenesis." Febs Journal. 276 (2009): 11. AbstractWebsite
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MP, Ribeiro, Espiga A, Silva D, Baptista P, Henriques J, Ferreira C, Silva JC, Borges JP, Pires E, Chaves P, and Correia IJ. "Development of a new chitosan hydrogel for wound dressing." WOUND REPAIR AND REGENERATION. 17 (2009): 817-824. Abstract
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Neagu, E. R., C. J. Dias, MC Lança, and J. N. Marat-Mendes. "The study of molecular movements in dielectrics using isothermal and non- isotehermal current measurements." 183 (2009): –-. Abstract
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C, Henriques, Vidinha R, Botequim D, Borges JP, and Silva JAMC. "A Systematic Study of Solution and Processing Parameters on Nanofiber Morphology Using a New Electrospinning Apparatus." JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY. 9 (2009): 3535-3545. Abstract
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Najmudin, S., C. Bonifacio, A. G. Duarte, S. R. Pauleta, I. Moura, JJG Moura, and MJ Romao. "Crystallization and crystallographic analysis of the apo form of the orange protein (ORP) from Desulfovibrio gigas. (vol F65, pg 730, 2009)." Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 65 (2009): 856. AbstractWebsite
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Bakalova, Snezhana M., Filipe J. S. Duarte, Miglena K. Georgieva, Eurico J. Cabrita, and Gil A. Santos. "An Alternative Mechanism for Diels-Alder Reactions of Evans Auxiliary Derivatives." Chemistry-a European Journal. 15 (2009): 7665-7677. Abstract
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Duarte, Filipe J. S., Eurico J. Cabrita, Gernot Frenking, and Gil A. Santos. "Density Functional Study of Proline-Catalyzed Intramolecular Baylis-Hillman Reactions." Chemistry-a European Journal. 15 (2009): 1734-1746. Abstract
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Martins, Rodrigo, Luis Pereira, Pedro Barquinha, Goncalo Goncalves, Isabel Ferreira, Carlos Dias, N. Correia, M. Dionisio, M. Silva, Nuno Correia, and Elvira Fortunato. "Self-sustained n-Type Memory Transistor Devices Based on Natural Cellulose Paper Fibers." Journal of Information Display. 10 (2009): 149-157. AbstractWebsite
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Paulino, Hervé, Paulo Cancela, and Tiago Franco. "Orchestration of Middleware Services." On the Move to Meaningful Internet Systems: OTM 2009 Workshops, Confederated International Workshops and Posters. Eds. Pilar Herrero Robert Meersman, and Tharam S. Dillon. Lecture Notes in Computer Science. Springer-Verlag, 2009. 1-3. Abstract
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Valtchev, {Stanimir Stoyanov}, and DEE Group Author. "Control strategy for efficient operation of super-resonant SLSR (contactless) converters." -. 2009. 527-530. Abstract

A new faster control method is presented, inattempt to achieve stable operation and higher efficiency of anySeries Loaded Series Resonant (SLSR) power converter, andespecially when the application requires contactless energytransfer. This instantaneously reacting control method is basedon calculated individual energy portions delivered to theresonant circuit. Its viability is demonstrated by simulation of ananalogue circuit implementation.

Leite, {João Alexandre Carvalho Pinheiro}, and {José Júlio Alves} Alferes. "Resource allocation with answer-set programming." IFAAMAS. Eds. C. Sierra, C. Castelfranchi, KS Decker, and JS Sichman. Vol. 1. IFAAMAS, 2009. 649-656. Abstract
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Bonfait, G., I. Catarino, J. Afonso, D. Martins, M. Linder, and L. Duband. "20 K Energy Storage Unit." Cryogenics. 49 (2009): 326-333. Abstract

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Schoch, CL, PW Crous, JZ Groenewald, EWA Boehm, TI Burgess, J. de Gruyter, GS de Hoog, LJ Dixon, M. Grube, C. Gueidan, Y. Harada, S. Hatakeyama, K. Hirayama, T. Hosoya, SM Huhndorf, KD Hyde, EBG Jones, J. Kohlmeyer, A. Kruys, YM Li, R. Lucking, HT Lumbsch, L. Marvanova, JS Mbatchou, AH Mcvay, AN Miller, GK Mugambi, L. Muggia, MP Nelsen, P. Nelson, CA Owensby, AJL Phillips, S. Phongpaichit, SB Pointing, V. Pujade-Renaud, HA Raja, ER Plata, B. Robbertse, C. Ruibal, J. Sakayaroj, T. Sano, L. Selbmann, CA Shearer, T. Shirouzu, B. Slippers, S. Suetrong, K. Tanaka, B. Volkmann-Kohlmeyer, MJ WINGFIELD, AR Wood, JHC Woudenberg, H. Yonezawa, Y. Zhang, and JW Spatafora. "A class-wide phylogenetic assessment of Dothideomycetes." Studies in Mycology. 64 (2009): 1-15. Abstract

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Dimitrovová, Z., and J. N. Varandas. "Critical velocity of a load moving on a beam with a sudden change of foundation stiffness: Applications to high-speed trains." Computers & Structures. 87 (2009): 1224-1232. Abstract

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Martins, D., I. Catarino, U. Schroder, J. Ricardo, R. Patricio, L. Duband, and G. Bonfait. "CUSTOMIZABLE GAS-GAP HEAT SWITCH." CEC 20. Tucson, AZ, USA: Advances in Cryogenic Engineering, 55, pp. 1652-7 (2010), 2009. Abstract

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Afonso, J., I. Catarino, D. Martins, J. Ricardo, R. Patricio, L. Duband, and G. Bonfait. "Energy Storage Unit: solid state demonstrators at 20 K and 6 K." Space Cryogenics Workshop. Arcadia, CA, USA: Cryogenic Society of America, 2009. Abstract

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Catarino, I., J. Afonso, D. Martins, L. Duband, and G. Bonfait. "Gas gap thermal switches using neon or hydrogen and sorption pump." Vacuum. 83 (2009): 1270-1273. Abstract

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Catarino, I., L. Duband, and G. Bonfait. "Hydrogen and Neon Gas-Gap Heat Switch." Cryocoolers. 15 (2009): 553-559. Abstract

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Lourenço, João M., Nuno Preguiça, Ricardo J. Dias, João Nuno Silva, João Garcia, and Luís Veiga NGenVM: New Generation Execution Environments. EuroSys. Nuremberg, Germany, 2009. Abstractngenvm-poster.pdf

This document describes a work-in-progress development of NGen-VM, a distributed infrastructure that manages execution environments with run-time and programming language support targeting applications developed in the Java programming language, deployed over clusters of many-core computers. For each running application or suite of related applications, a dedicated single-system image will be provided, regardless of the concurrent threads running on a single machine (on several cores) or scattered on different computers. Such system images rely on a single model for concurrency management (Transactional Shared Memory Model), in order fill the gap between the hardware infrastructure of clusters of many-core nodes and the application runtime that is independent from that hardware infrastructure. Interactions between threads in the same tasks will be supported by a Transactional Memory framework that provides the programming language with Atomic and Isolated code regions. Interactions between thread on different machines will also use the Transactional Memory model, but now resorting to a Distributed Shared Memory abstraction.

Lourenço, João M., Ricardo J. Dias, João Luís, Miguel Rebelo, and Vasco Pessanha. "Understanding the Behavior of Transactional Memory Applications." Proceedings of the 7th Workshop on Parallel and Distributed Systems: Testing, Analysis, and Debugging (PADTAD'09). {PADTAD}'09. New York, NY, USA: ACM, 2009. 31-39. Abstractpadtad2009.pdf

Transactional memory is a new trend in concurrency control that was boosted by the advent of multi-core processors and the near to come many-core processors. It promises the performance of finer grain with the simplicity of coarse grain threading. However, there is a clear absence of software development tools oriented to the transactional memory programming model, which is confirmed by the very small number of related scientific works published until now. This paper describes ongoing work. We propose a very low overhead monitoring framework, developed specifically for monitoring TM computations, that collects the transactional events into a single log file, sorted in a global order. This framework is then used by a visualization tool to display different types of charts from two categories: statistical charts and thread-time space diagrams. These last diagrams are interactive, allowing to identify conflicting transactions. We use the visualization tool to analyse the behavior of two different, but similar, testing applications, illustrating how it can be used to better understand the behavior of these transactional memory applications.

Dias, Ricardo J., and João M. Lourenço. "Unifying Memory and Database Transactions." Proceedings of the 15th International Euro-Par Conference on Parallel Processing. {Euro-Par}'09. Berlin, Heidelberg: Springer-Verlag, 2009. 349-360. Abstracteuropar2009-umadt.pdf

Software Transactional Memory is a concurrency control technique gaining increasing popularity, as it provides high-level concurrency control constructs and eases the development of highly multi-threaded applications. But this easiness comes at the expense of restricting the operations that can be executed within a memory transaction, and operations such as terminal and file I/O are either not allowed or incur in serious performance penalties. Database I/O is another example of operations that usually are not allowed within a memory transaction. This paper proposes to combine memory and database transactions in a single unified model, benefiting from the ACID properties of the database transactions and from the speed of main memory data processing. The new unified model covers, without differentiating, both memory and database operations. Thus, the users are allowed to freely intertwine memory and database accesses within the same transaction, knowing that the memory and database contents will always remain consistent and that the transaction will atomically abort or commit the operations in both memory and database. This approach allows to increase the granularity of the in-memory atomic actions and hence, simplifies the reasoning about them.

Roque, A. A., Tiago A. N. Silva, J. M. F. Calado, and J. C. Q. Dias An Approach to Fault Diagnosis of Rolling Bearings. Vol. 4. WSEAS TRANSACTIONS on SYSTEMS and CONTROL, 4.4. World Scientific and Engineering Academy and Society (WSEAS), 2009. Abstract
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Costa, P. M., S. Caeiro, M. S. Diniz, J. Lobo, M. Martins, A. M. Ferreira, M. Caetano, C. Vale, T. Á. DelValls, and M. H. Costa. "Biochemical endpoints on juvenile Solea senegalensis exposed to estuarine sediments: The effect of contaminant mixtures on metallothionein and CYP1A induction." Ecotoxicology. 18 (2009): 988-1000. AbstractWebsite
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Freitas, A. C., F. Ferreira, A. M. Costa, R. Pereira, S. C. Antunes, F. Gonçalves, T. A. P. Rocha-Santos, M. S. Diniz, L. Castro, I. Peres, and A. C. Duarte. "Biological treatment of the effluent from a bleached kraft pulp mill using basidiomycete and zygomycete fungi." Science of the Total Environment. 407 (2009): 3282-3289. AbstractWebsite
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