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2011
Adams, TL, M. J. Polcyn, O. Mateus, DA Winkler, and LL Jacobs. "First occurrence of the long-snouted crocodyliform Terminonaris (Pholidosauridae) from the Woodbine Formation (Cenomanian) of Texas." Journal of Vertebrate Paleontology. 31 (2011): 712-716. Abstract
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Marques, Filipe J., Carlos A. Coelho, and Barry C. Arnold. "A general near-exact distribution theory for the most common likelihood ratio test statistics used in Multivariate Analysis." Test. 20 (2011): 180-203. Abstract
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Araújo, J., J. D. Mitchell, and Csaba Schneider. "Groups that together with any transformation generate regular semigroups for idempotent generated semigroups." J. Algebra. 343 (2011): 93-106. AbstractWebsite
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de Freitas, J., I. Moldovan, and C. Cismaşiu. "Hybrid-Trefftz displacement element for poroelastic media." Computational Mechanics (2011): 1-15. AbstractWebsite

The elastodynamic response of saturated poroelastic media is modelled approximating independently the solid and seepage displacements in the domain and the force and pressure components on the boundary of the element. The domain and boundary approximation bases are used to enforce on average the dynamic equilibrium and the displacement continuity conditions, respectively. The resulting solving system is Hermitian, except for the damping term, and its coefficients are defined by boundary integral expressions as a Trefftz basis is used to set up the domain approximation. This basis is taken from the solution set of the governing differential equation and models the free-field elastodynamic response of the medium. This option justifies the relatively high levels of performance that are illustrated with the time domain analysis of unbounded domains.

A., Pedrosa, LANÇA M.C., Borges J.P., NEAGU E.R., DIAS C.J., Marat-Mendes, and J.N. "Influence of Polarization on the Bioactivity of Nanopowders of Hydroxyapatite." 14th International Symposium on Electrets. International Symposium on Electrets. 2011. Abstract
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Pedrosa, A., M. C. Lanca, J. P. Borges, E. R. Neagu, C. J. Dias, J. N. Marat-Mendes, and Ieee. "Influence of Polarization on the Bioactivity of Nanopowders of Hydroxyapatite." 2011 14th International Symposium on Electrets (Ise) (2011): 55-56. Abstract
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Pedrosa, A., M. C. Lanca, J. P. Borges, E. R. Neagu, C. J. Dias, J. N. Marat-Mendes, and Ieee Influence of Polarization on the Bioactivity of Nanopowders of Hydroxyapatite., 2011. AbstractWebsite
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Pedrosa, A., M. C. Lanca, J. P. Borges, E. R. Neagu, C. J. Dias, J. N. Marat-Mendes, and Ieee. "Influence of Polarization on the Bioactivity of Nanopowders of Hydroxyapatite." 2011 14th International Symposium on Electrets. International Symposium on Electrets. 2011. 55-56. Abstract
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Valtchev, S., R. Medeiros, S. Valtchev, and B. Klaassens. "An instantaneous regulation for the wired and wireless super-resonant converters." INTELEC, International Telecommunications Energy Conference (Proceedings) (2011). Abstract
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Mollegaard, Karen Mai, Karen Duus, Sofie Dietz Traeholt, Morten Thaysen-Andersen, Yan Liu, Angelina S. Palma, Ten Feizi, Paul R. Hansen, Peter Hojrup, and Gunnar Houen. "The interactions of calreticulin with immunoglobulin G and immunoglobulin Y." Biochimica Et Biophysica Acta-Proteins and Proteomics. 1814 (2011): 889-899. Abstract
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Santos, J. P., A. M. Costa, M. C. Martins, P. Indelicato, and F. Parente. "K X-Ray Energies and Transition Probabilities for He-, Li- and Be-like Praseodymium ions." Journal of Physics: Conference Series. Accepted (2011).
Timoteo, C. G., AS Pereira, C. E. Martins, S. G. Naik, A. G. Duarte, JJG Moura, P. Tavares, BH HUYNH, and I. Moura. "Low-Spin Heme b(3) in the Catalytic Center of Nitric Oxide Reductase from Pseudomonas nautica." Biochemistry. 50 (2011): 4251-4262. AbstractWebsite

Respiratory nitric oxide reductase (NOR) was purified from membrane extract of Pseudomonas (Ps.) nautica cells to homogeneity as judged by polyacrylamide gel electrophoresis. The purified protein is a heterodimer with subunits of molecular masses of 54 and 18 kDa. The gene encoding both subunits was cloned and sequenced. The amino acid sequence shows strong homology with enzymes of the cNOR class. Iron/heme determinations show that one heme c is present in the small subunit (NORC) and that approximately two heme b and one non-heme iron are associated with the large subunit (NORB), in agreement with the available data for enzymes of the cNOR class. Mossbauer characterization of the as-purified, ascorbate-reduced, and dithionite-reduced enzyme confirms the presence of three heme groups (the catalytic heme b(3) and the electron transfer heme b and heme c) and one redox-active non-heme Fe (Fe-B). Consistent with results obtained for other cNORs, heme c and heme b in Ps. nautica cNOR were found to be low-spin while FeB was found to be high-spin. Unexpectedly, as opposed to the presumed high-spin state for heme b(3), the Mossbauer data demonstrate unambiguously that heme b(3) is, in fact, low-spin in both ferric and ferrous states, suggesting that heme b(3) is six-coordinated regardless of its oxidation state. EPR spectroscopic measurements of the as-purified enzyme show resonances at the g similar to 6 and g similar to 2-3 regions very similar to those reported previously for other cNORs. The signals at g = 3.60, 2.99, 2.26, and 1.43 are attributed to the two charge-transfer low-spin ferric heme c and heme b. Previously, resonances at the g similar to 6 region were assigned to a small quantity of uncoupled high-spin Fe-III heme b(3). This assignment is now questionable because heme b(3) is low-spin. On the basis of our spectroscopic data, we argue that the g = 6.34 signal is likely arising from a spin spin coupled binuclear center comprising the low-spin Fe-III heme b(3) and the high-spin Fe-B(III). Activity assays performed under various reducing conditions indicate that heme b(3) has to be reduced for the enzyme to be active. But, from an energetic point of view, the formation of a ferrous heme-NO as an initial reaction intermediate for NO reduction is disfavored because heme [FeNO](7) is a stable product. We suspect that the presence of a sixth ligand in the Fe-II-heme b(3) may weaken its affinity for NO and thus promotes, in the first catalytic step, binding of NO at the Fe-B(II) site. The function of heme b(3) would then be to orient the Fe-B-bound NO molecules for the formation of the N-N bond and to provide reducing equivalents for NO reduction.

Duarte, Susana, and Cruz} {V. Machado. "Manufacturing paradigms in supply chain management." International Journal of Management Science and Engineering Management. 6 (2011): 328-342. Abstract

This paper intends to determine whether the lean, agile, resilient and green paradigms are applied and combined in the actual environment of supply-chain management. A structured literature review on the state of the art was carried out, thus providing a comprehensive understanding on supply-chain management. A classification scheme of supply-chain paradigms was developed where five databases were used to find how these paradigms were being integrated. The research developed provided the confirmation that papers combining more than two paradigms were rare. To date, academicians have not studied the merging of these paradigms in supply-chain management at significant depth.

Xavier, J., J. Morais, N. Dourado, and M. F. S. F. de Moura. "Measurement of mode I and mode II fracture properties of wood-bonded joints." Journal of Adhesion Science and Technology. 25 (2011): 2881-2895. Abstract
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Alves, M., P. Chicau, H. Matias, J. Passarinho, C. Pinheiro, and C. P. Ricardo. "Metabolic analysis revealed altered amino acid profiles in Lupinus albus organs as a result of boron deficiency." Physiologia Plantarum. 142 (2011): 224-232. AbstractWebsite

We analysed the changes in the metabolites of Lupinus albus organs (leaf-blades, petioles, apexes, hypocotyls and roots) as a consequence of B deficiency. The deficiency did not affect malate concentration and induced only minor changes in the sugar content, suggesting that the carbohydrate metabolism is little affected by the deficiency. Contrarily, marked changes in the content of free amino acids were observed, with some specific variations associated with the different organs. These changes indicate that various aspects of metabolism implicated in the amino acid accumulation were affected by B deficiency. Most of the detected changes appear to have implications with some stress responses or signalling processes. Asparagine and proline that increase in many stresses also accumulated in petioles, apexes and hypocotyls. Accumulation of gamma-aminobutyric acid shunt amino acids, indicative of production of reactive oxygen species, occurs in the same three organs and also the roots. The increase in the branched-chain amino acids, observed in all organs, suggests the involvement of B with the cytoskeleton, whereas glycine decrease in leaf-blades and active growing organs (apexes and roots) could be associated with the proposed role of this amino acids in plant signalling in processes that might be associated with the decreased growth rates observed in B deficiency. Despite the admitted importance of free amino acids in plant metabolism, the available information on this matter is scarce. So our results bring new information concerning the effects of B deficiency in the metabolism of the several L. albus organs.

Alves, M., P. Chicau, H. Matias, J. Passarinho, C. Pinheiro, and C. P. Ricardo. "Metabolic analysis revealed altered amino acid profiles in Lupinus albus organs as a result of boron deficiency." Physiologia Plantarum. 142 (2011): 224-232. AbstractWebsite
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Águas, H., I. Bernacka-Wojcik, T. Busani, E. Fortunato, R. Martins, P. Lopes, P. Simões, M. Ferreira, and L. Hilliou. "Microplat project: development status." III Annual Meeting of the I3N–Institute of Nanostructures, Nanomodelling and Nanofabrication, 2011. 2011. 9. Abstract
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Garcia-Alvarez, Begona, Roberto Melero, Fernando M. V. Dias, Jose A. M. Prates, Carlos M. G. A. Fontes, Steven P. Smith, Maria Joao Romao, Ana Luisa Carvalho, and Oscar Llorca. "Molecular Architecture and Structural Transitions of a Clostridium thermocellum Mini-Cellulosome." Journal of Molecular Biology. 407 (2011): 571-580. Abstract
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Marques, Filipe J., and Carlos A. Coelho. "The Multi-sample Block-matrix Sphericity Test." AIP Conference Proceedings. Vol. 1389. AIP, 2011. 1479-1482. Abstract
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Mateus, O., J. Milàn, M. Romano, and M. A. Whyte. "New finds of stegosaur tracks from the Upper Jurassic Lourinhã formation, Portugal." Acta Palaeontologica Polonica. 56 (2011): 651-658. Abstract
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Folgosa, F., C. M. Cordas, J. A. Santos, AS Pereira, JJG Moura, P. Tavares, and I. Moura. "New spectroscopic and electrochemical insights on a class I superoxide reductase: evidence for an intramolecular electron-transfer pathway." Biochemical Journal. 438 (2011): 485-494. AbstractWebsite

SORs (superoxide reductases) are enzymes involved in bacterial resistance to reactive oxygen species, catalysing the reduction of superoxide anions to hydrogen peroxide. So far three structural classes have been identified. Class I enzymes have two ironcentre-containing domains. Most studies have focused on the catalytic iron site (centre II), yet the role of centre I is poorly understood. The possible roles of this iron site were approached by an integrated study using both classical and fast kinetic measurements, as well as direct electrochemistry. A new heterometallic form of the protein with a zinc-substituted centre I, maintaining the iron active-site centre II, was obtained, resulting in a stable derivative useful for comparison with the native all-iron from. Second-order rate constants for the electron transfer between reduced rubredoxin and the different SOR forms were determined to be 2.8 x 10(7) M(-1) . s(-1) and 1.3 x 10(6) M(-1) . s(-1) for SOR(Fe(IIII)-Fe(II)) and for SOR(Fe(IIII)-Fe(III)) forms respectively, and 3.2 x 10(6) M(-1) s(-1) for the SOR(Zn(II)-Fe(III)) form. The results obtained seem to indicate that centre I transfers electrons from the putative physiological donor rubredoxin to the catalytic active iron site (intramolecular process). In addition, electrochemical results show that conformational changes are associated with the redox state of centre I, which may enable a faster catalytic response towards superoxide anion. The apparent rate constants calculated for the SOR-mediated electron transfer also support this observation.

Coelho, Carlos A., and Filipe J. Marques. "On the Exact, Asymptotic and Near-exact Distributions for the Likelihood Ratio Statistics to Test Equality of Several Exponential Distributions." AIP Conference Proceedings. Vol. 1389. AIP, 2011. 1471-1474. Abstract
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Moutinho, Filipe, Lu{\'ı}s Gomes, Paulo E. S. Barbosa, João Paulo Barros, Franklin Ramalho, Jorge Figueiredo, Anikó Costa, and André Monteiro. "Petri Net Based Specification and Verification of Globally-Asynchronous-Locally-Synchronous System." Technological Innovation for Sustainability - Second {IFIP} {WG} 5.5/SOCOLNET Doctoral Conference on Computing, Electrical and Industrial Systems, DoCEIS 2011, Costa de Caparica, Portugal, February 21-23, 2011. Proceedings. 2011. 237-245. Abstract
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