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2007
Cardoso A. S., Marques M. M. B., Srinivasan Prabhakar Lobo N. S. A. M. "A synthetic strategy using Witkop's pyrroloindole for (-)-debromoflustramine B, (+)-ent-debromoflustramine B and (+)-ent-debromoflustramide B ." Tetrahedron. 63 (2007): 10211-10225.
J. Araújo, and E. Baniassad TAOSD - Special Issue on Early Aspects. Transactions on Aspect Oriented Software Development (TAOSD) }note = { Edition of this journal number., 2007. Abstract

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Lourenço, João M., and Gonçalo Cunha. "Testing patterns for software transactional memory engines." Proceedings of the 5th Workshop on Parallel and Distributed Systems: Testing, Analysis, and Debugging (PADTAD'07). {PADTAD}'07. New York, NY, USA: ACM, 2007. 36-42. Abstractpadtad21s.pdf

The emergence of multi-core processors is promoting the use of concurrency and multithreading. To raise the abstraction level of synchronization constructs is fundamental to ease the development of concurrent software, and Software Transactional Memory (STM) is a good approach towards such goal. However, execution environment issues such as the processor instruction set, caching policy, and memory model, may have strong influence upon the reliability of STM engines. This paper addresses the testing of STM engines aiming at improving their reliability and independence from execution environment. From our experience with porting and extending a specific STM engine, we report on some of the bugs found and synthesize some testing patterns that proved to be useful at testing STM engines.

M. Alferez, U. Kulesza, A. Garcia, A. Moreira, J. Araújo, and Vasco Amaral. "Towards Volatility Analysis in Software Product Line Engineering." Second International Workshop on Aspect-Oriented Product Line Engineering held in conjunction with GPCE'07 (Generative Programming and Component Engineering). Salzburg, Austria 2007. Abstract

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M. S. Tabares, A. Moreira, R. Anaya, F. Arango, and J. Araújo. "A Traceability Method for Crosscutting Concerns with transformation rules." Workshop on Early Aspects at ICSE: Aspect-oriented requirements engineering and architectural design, 28th International Conference on Software Engineering (ICSE 2007). ACM Press, 2007. Abstract

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Barbosa, Luís, Jácome Cunha, and Joost Visser. "A Type-Level Approach to Component Prototyping." International Workshop on Synthesis and Analysis of Component Connectors: in Conjunction with the 6th ESEC/FSE Joint Meeting. SYANCO '07. New York, NY, USA: ACM, 2007. 23-36. Abstractsyanco07.pdf

Algebraic theories for modeling components and their interactions offer abstraction over the specifics of component states and interfaces. For example, such theories deal with forms of sequential composition of two components in a manner independent of the type of data stored in the states of the components, and independent of the number and types of methods offered by the interfaces of the combinators. General purpose programming languages do not offer this level of abstraction, which implies that a gap must be bridged when turning component models into implementations. In this paper, we present an approach to prototyping of component-based systems that employs so-called type-level programming (or compile-time computation) to bridge the gap between abstract component models and their type-safe implementation in a functional programming language. We demonstrate our approach using Barbosa's model of components as generalized Mealy machines. For this model, we develop a combinator library in Haskell, which uses type-level programming with two effects. Firstly, wiring between components is computed during compilation. Secondly, the well-formedness of the component compositions is guarded by Haskell's strong type system.

Cipriano, Fernanda, and Ana Bela Cruzeiro. "Variational principle for diffusions on the diffeomorphism group with the \(H^2\) metric." Mathematical analysis of random phenomena. Proceedings of the international conference, Hammamet, Tunisia, September 12–17, 2005. Hackensack, NJ: World Scientific, 2007. 85-91. Abstract

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Cipriano, Fernanda, and Ana Bela Cruzeiro. "Variational principle for diffusions on the diffeomorphism group with the \(H^2\) metric." Mathematical analysis of random phenomena. Proceedings of the international conference, Hammamet, Tunisia, September 12–17, 2005. Hackensack, NJ: World Scientific, 2007. 85-91. Abstract

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Bentes, L., R. Ayouchi, C. Santos, R. Schwarz, P. Sanguino, O. Conde, M. Peres, T. Monteirod, and O. Teodoro. "{ZnO films grown by laser ablation with and without oxygen CVD}." Superlattices and Microstructures. 42 (2007): 152-157. Abstract2007_emrs_superlatticeszno.pdf

In the presentwork we have studied the properties of zinc oxide (ZnO) thin films grown by laser ablation of ZnO targets under different substrate temperature and background oxygen conditions. The ZnO layers were deposited with a Pulsed Laser Deposition (PLD) system on pre-nitrided (0001) sapphire (Al2O3), using the base line of a Nd:YAG laser at 1064 nm. The films were characterized by different structural and optical methods, including X-ray diffraction (XRD), scanning electron microscopy (SEM), optical transmission spectroscopy, and steady-state photoluminescence (PL). XRD analysis with rocking curves and $þeta$–2$þeta$ scans indicates preferential growth along the c-axis direction with a full width at half maximum (FWHM) smaller than 1.5◦. Low-temperature photoluminescence (PL) showed strong excitonic emission near 3.36 eV between 9 and 65 K

Águas, H., Pereira Costa Barquinha Pereira Fortunato Martins S. D. P. "3 dimensional polymorphous silicon based metal-insulator-semiconductor position sensitive detectors." Thin Solid Films. 515 (2007): 7530-7533. AbstractWebsite

In this work we investigate the properties of a polymorphous silicon (pm-Si:H) metal-insulator-semiconductor (MIS) structure used in 3D position sensitive detectors (PSD). For the first time a 3D sensor made-up by pm-Si:H/SiO2/Au layers is presented. MIS structures present several advantages over p-i-n structures, such as easier fabrication, fast response time and higher resolution. The 1D MIS PSD that constitute the array were extensively studied aiming its application in 3D pattern recognition. The results obtained show that MIS PSD can achieve non-linearities below 2% and sensitivities of 3.2 μA/cm over 6 mm length sensors. The miniaturization of the sensors length to arrays of 6 and 16 mm, respectively showed average non-linearities of about 1.9% for the 16 mm sensor which proved to be the best solution for this MIS structure. © 2006 Elsevier B.V. All rights reserved.

Aguas, H., S. Pereira, D. Costa, P. Barquinha, L. Pereira, E. Fortunato, and R. Martins. "3 dimensional polymorphous silicon based metal-insulator-semiconductor position sensitive detectors." Thin Solid Films. 515 (2007): 7530-7533. Abstract
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Fortunato, Elvira, Pedro Barquinha, Luis Pereira, Gongalo Goncalves, and Rodrigo Martins Advanced materials for the next generation of thin film transistors. Eds. C. H. Chen, and Y. S. Tsai. Idmc'07: Proceedings of the International Display Manufacturing Conference 2007., 2007. AbstractWebsite
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Fortunato, E., Barquinha Pereira Gonçalves Martins P. L. G. "Advanced materials for the next generation of thin film transistors." IDMC 2007 - International Display Manufacturing Conference and FPD Expo - Proceedings. 2007. 371-373. Abstract

Staggered bottom gate transparent thin film transistors (TTFTs) have been produced by rf magnetron sputtering at room temperature, using amorphous indium-zinc-oxide (IZO) semiconductor, for the channel as well as for the drain and source regions. The obtained TTFTs operate in the enhancement mode with threshold voltages of 2.4 V, saturation mobility of 22.7 cm2/Vs, gate voltage swing of 0.44 V/dec and an ON/OFF current ratio of 7×10 7. The high performances presented by these TTFTs produced at room temperature, make these TFTs a promising candidate for flexible, wearable, disposable portable electronics as well as battery-powered applications.

Fortunato, E., Barquinha Pimentel Pereira Gonçalves Martins P. A. L. "Amorphous IZO TTFTs with saturation mobilities exceeding 100 cm2/Vs." Physica Status Solidi - Rapid Research Letters. 1 (2007): R34-R36. AbstractWebsite

In this paper we demonstrate the use of amorphous binary In2O3-ZnO oxides simultaneously as active channel layer and as source/drain regions in transparent thin film transistor (TTFT), processed at room temperature by rf sputtering. The TTFTs operate in the enhancement mode and their performances are thickness dependent. The best TTFTs exhibit saturation mobilities higher than 102 cm2/Vs, threshold voltages lower than 6 V, gate voltage swing of 0.8 V/dec and an on/off current ratio of 107. This mobility is at least two orders of magnitude higher than that of conventional amorphous silicon TFTs and comparable to or even better than other polycrystal-line semiconductors. © 2007 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

c Martins, R.a, Baptista Raniero Doria Silva Franco Fortunato P. b L. a. "Amorphous/nanocrystalline silicon biosensor for the specific identification of unamplified nucleic acid sequences using gold nanoparticle probes." Applied Physics Letters. 90 (2007). AbstractWebsite

Amorphous/nanocrystalline silicon p i′ i i′ n devices fabricated on micromachined glass substrates are integrated with oligonucleotide-derivatized gold nanoparticles for a colorimetric detection method. The method enables the specific detection and quantification of unamplified nucleic acid sequences (DNA and RNA) without the need to functionalize the glass surface, allowing for resolution of single nucleotide differences between DNA and RNA sequences-single nucleotide polymorphism and mutation detection. The detector's substrate is glass and the sample is directly applied on the back side of the biosensor, ensuring a direct optical coupling of the assays with a concomitant maximum photon capture and the possibility to reuse the sensor. © 2007 American Institute of Physics.

Araújo, João, and Janusz Konieczny. "Automorphisms of endomorphism monoids of relatively free bands." Proc. Edinb. Math. Soc. (2). 50 (2007): 1-21. AbstractWebsite
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Caires, L., J. C. Seco, and Hugo T. Vieira Automotive and Finance Case Studies in the Conversation Calculus. Departamento de Informática FCT/UNL, 2007.
Timoteo, C. G., C. Pantana, A. G. Duarte, F. Folgosa, AS Pereira, and P. Tavares. "The Catalytic center of a Desaturase from Arabidopsis thaliana." J Biol Inorg Chem. 12 (2007): S93. Abstract
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Pereira, L.a, Aguas Beckers Martins Fortunato Martins H. a M. b. "Characterization of nickel induced crystallized silicon by spectroscopic ellipsometry." Materials Research Society Symposium Proceedings. Vol. 910. 2007. 529-534. Abstract

In this work Spectroscopic Ellipsometry (SE) was used to study metal induced crystallization (MIC) on amorphous silicon films in order to analyze the influence of different annealing conditions on their structural properties. The variation of the metal thickness has shown to be determinant on the time needed to full crystallize silicon films. Films of 100 nm thickness crystallize after 2h at 500°C using 1 nm of Ni deposited on it. When reducing the average metal thickness down to 0.05 nm the same silicon film will need almost 10 hours to be totally crystallized. Using a new approach on the modelling procedure of the SE data we show to be possible to determine the Ni remaining inside the crystallized films. The method consists in using Ni as reference on the Bruggeman Effective Medium Approximation (BEMA) layer that will simulated the optical response of the crystallized silicon. Silicon samples and metal layers with different thicknesses were analyzed and this new method has shown to be sensible to changes on the initial metal/silicon ratio. The nickel distribution inside the silicon layers was independently measured by Rutherford Backscattering Spectroscopy (RBS) to check the data obtained from the proposed approach. © 2006 Materials Research Society.

Fisher, K., D. J. Lowe, P. Tavares, AS Pereira, BH HUYNH, D. Edmondson, and W. E. Newton. "Conformations generated during turnover of the Azotobacter vinelandii nitrogenase MoFe protein and their relationship to physiological function." Journal of Inorganic Biochemistry. 101 (2007): 1649-1656. AbstractWebsite

Various S = 3/2 EPR signals elicited from wild-type and variant Azotobacter vinelandii nitrogenase MoFe proteins appear to reflect different conformations assumed by the FeMo-cofactor with different protonation states. To determine whether these presumed changes in protonation and conformation reflect catalytic capacity, the responses (particularly to changes in electron flux) of the alpha H195Q, alpha H195N, and alpha Q191 K variant MoFe proteins (where His at position 195 in the alpha subunit is replaced by Gln/Asn or Gln at position alpha-191 by Lys), which have strikingly different substrate-reduction properties, were studied by stopped-flow or rapid-freeze techniques. Rapid-freeze EPR at low electron flux (at 3-fold molar excess of wild-type Fe protein) elicited two transient FeMo-cofactor-based EPR signals within 1 s of initiating turnover under N-2 with the alpha H195Q and alpha H195N variants, but not with the alpha Q191K variant. No EPR signals attributable to P cluster oxidation were observed for any of the variants under these conditions. Furthermore, during turnover at low electron flux with the wild-type, alpha H195Q or alpha H195N MoFe protein, the longer-time 430-nm absorbance increase, which likely reflects P cluster oxidation, was also not observed (by stopped-flow spectrophotometry); it did, however, occur for all three MoFe proteins under higher electron flux. No 430-nm absorbance increase occurred with the alpha Q191K variant, not even at higher electron flux. This putative lack of involvement of the P cluster in electron transfer at low electron flux was confirmed by rapid-freeze Fe-57 Mossbauer spectroscopy, which clearly showed FeMo-factor reduction without P cluster oxidation. Because the wild-type, alpha H195Q and alpha H195N MoFe proteins can bind N-2, but alpha Q195K cannot, these results suggest that P cluster oxidation occurs only under high electron flux as required for N-2 reduction. (C) 2007 Elsevier Inc. All rights reserved.

Campagnolo, M. L., and J. O. Cerdeira. "Contextual classification of remotely sensed images with integer linear programming." Proceedings of the International Symposium CompIMAGE 2006 - Computational Modelling of Objects Represented in Images: Fundamentals, Methods and Applications (2007): 123-128. Abstract
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Gaspar, A., T. Avelar, and O. Mateus. "Criacionismo e Sociedade no Séc. XX."  Evolução e Criacionismo: Uma Relação Impossível. Lisboa 2007. 133-160. Abstract
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Santos-Silva, T., JM Dias, A. Dolla, M. - C. Durand, L. L. Gon?alves, J. Lampreia, I. Moura, and MJ Romão. "Crystal Structure of the 16 Heme Cytochrome from Desulfovibrio gigas: A Glycosylated Protein in a Sulphate-reducing Bacterium." Journal of Molecular Biology. 370 (2007): 659-673. Abstract
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Alagador, D., and J. O. Cerdeira. "Designing spatially-explicit reserve networks in the presence of mandatory sites." Biological Conservation. 137 (2007): 254-262. Abstract
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