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2011
Santos, JM, K. Vrandečić, J. Ćosić, T. Duvnjak, and AJL Phillips. "Resolving the complex of Diaporthe/Phomopsis species on soybean in Croatia." Persoonia. 27 (2011): 9-19.
Dias, Ricardo J., Dino Distefano, João M. Lourenço, and João Costa Seco StarTM: Automatic Verification of Snapshot Isolation in Transactional Memory Java Programs. Departamento de Informática FCT/UNL, 2011. Abstractddls11.pdf

This paper presents StarTM , an automatic verification tool for transactional memory Java programs executing under relaxed isolation levels. We certify which transactions in a program are safe to execute under Snapshot Isolation without triggering the write-skew anomaly, opening the way to run-time optimizations that may lead to considerable performance enhancements.
Our tool builds on a novel shape analysis technique based on Separation Logic to statically approximate the read- and write-sets of a transactional memory Java program. This technique is particularly challenging due to the presence of dynamically allocated memory.
We implement our technique and apply our tool to a set of intricate examples. We corroborate known results, certifying some of the examples for safe execution under Snapshot Isolation by proving the absence of write-skew anomalies. In other cases we identify transactions that potentially trigger the write-skew anomaly.

Dias, MI, Ondina M. Figueiredo, Antónia M. Matos, A. Pais, Maria Isabel Prudêncio, Teresa Pereira Silva, Christopher Ian Burbidge, A. L. Rodrigues, and João Pedro Veiga. "Datação, autenticidade, materiais e pigmentos. Estudos laboratoriais sobre faiança portuguesa e porcelana chinesa produzida para o mercado português, séculos XVI a XVIII." IX Congresso Ibérico de Arqueometria (CIA). 2011. Abstract
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Louren{\c c}o, João, Diogo Sousa, Bruno C. Teixeira, and Ricardo Dias. "Detecting concurrency anomalies in transactional memory programs." Comput. Sci. Inf. Syst.. 8 (2011). Abstract
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
Neagu, E. R., C. J. Dias, M. C. Lanca, R. Igreja, P. Inacio, J. N. Marat-Mendes, and Ieee Discrimination between Space Charge and Dipolar Contributions in Ferroelectric Polymers., 2011. Abstract

The final thermally stimulated discharge current method allows a better selection of the experimental conditions for sample polarization. By decreasing the ratio between the charging time and the discharging time, the apparent peak is of the same order of magnitude as the genuine peaks and there is only a partial overlap between then. Two peaks have been identified for polyamide 11, one associated with the glass transition around 60 degrees C and the second associated with the Curie transition around 96 degrees C.

R., Neagu E., C. Dias, Lança M. Carmo, Igreja R., Inacio P., and Marat-Mendes J. N. "Discrimination between Space Charge and Dipolar Contributions in Ferroelectric Polymers." 14th International Symposium on Electrets. International Symposium on Electrets. 2011. Abstract

The final thermally stimulated discharge current method allows a better selection of the experimental conditions for sample polarization. By decreasing the ratio between the charging time and the discharging time, the apparent peak is of the same order of magnitude as the genuine peaks and there is only a partial overlap between then. Two peaks have been identified for polyamide 11, one associated with the glass transition around 60 °C and the second associated with the Curie transition around 96 °C.

Neagu, E. R., C. J. Dias, M. C. Lanca, R. Igreja, P. Inacio, J. N. Marat-Mendes, and Ieee Discrimination between Space Charge and Dipolar Contributions in Ferroelectric Polymers., 2011. AbstractWebsite

The final thermally stimulated discharge current method allows a better selection of the experimental conditions for sample polarization. By decreasing the ratio between the charging time and the discharging time, the apparent peak is of the same order of magnitude as the genuine peaks and there is only a partial overlap between then. Two peaks have been identified for polyamide 11, one associated with the glass transition around 60 degrees C and the second associated with the Curie transition around 96 degrees C.

Neagu, E. R., C. J. Dias, M. C. Lanca, R. Igreja, P. Inacio, J. N. Marat-Mendes, and Ieee. "Discrimination between Space Charge and Dipolar Contributions in Ferroelectric Polymers." 2011 14th International Symposium on Electrets (Ise) (2011): 145-146. Abstract
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Mendonça, E., M. Diniz, L. Silva, I. Peres, L. Castro, J. B. Correia, and A. Picado. "Effects of diamond nanoparticle exposure on the internal structure and reproduction of Daphnia magna." Journal of Hazardous Materials. 186 (2011): 265-271. AbstractWebsite
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M.C., LANÇA, NEAGU E.R., DIAS C.J., GIL L., and MARAT-MENDES J.N. "Electrical properties of cork and derivatives." 23.3/4 (2011). Abstract
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Diniz, M. S., R. Pereira, A. C. Freitas, T. A. P. Rocha-Santos, L. Castro, I. Peres, and A. C. Duarte. "Evaluation of the sub-lethal toxicity of bleached kraft pulp mill effluent to carassius auratus and dicentrarchus labrax." Water, Air, and Soil Pollution. 217 (2011): 35-45. AbstractWebsite
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Igreja, Rui, and C. J. Dias. "Extension to the analytical model of the interdigital electrodes capacitance for a multi-layered structure." Sensors and Actuators a-Physical. 172 (2011): 392-399. Abstract

Interdigital electrodes (IE) are one of the most used transducers in different technical and analytical applications with the particular importance in the field of chemical and biological sensors. With the recent demand for lab-on-a-chip devices and the need for sensors miniaturization it becomes common the use of such transducers in structures with several dielectric layers (either substrates or superstrates). In a previous a work we proposed a model for the computation of the capacitance of these multi-layered structures using the techniques of conformal mapping and partial capacitance. Until now, that model has been used in applications where the permittivity of consecutive layers monotonically decreases from layer to layer (as we move away from the electrodes plane) giving excellent results. New applications, such as the use of Si/SiO2 substrates (to promote very smooth surfaces for electrodes deposition) or the use of passivation layers for the protection of electrodes (e.g. from liquids), among others, represent a new challenge for the computation of the overall capacitance since in these devices the permittivity can decrease from layer to layer. Under these conditions the original partial capacitance technique needs to be modified to include these new configurations. In this work we will discuss a new approach, splitting the concept of partial capacitance in parallel partial capacitance and serial partial capacitance where new conformal mapping transformations are proposed for the latter case. Hence this novel approach will extend our previous analytical model in order to account for the cases where there is a decrease in the permittivity from layer to layer. The results are compared with finite element simulation and experimental results. (C) 2011 Elsevier B.V. All rights reserved.

Igreja, R., and C. J. Dias. "Extension to the analytical model of the interdigital electrodes capacitance for a multi-layered structure." Sensors and Actuators a-Physical. 172 (2011): 392-399. AbstractWebsite
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Carvalho, H., S. G. Azevedo, S. Duarte, and V. Cruz-Machado. "Green and Lean Paradigms Influence on Sustainable Business Development of Manufacturing Supply Chains." International Journal of Green Computing. 2 (2011): 45-62. 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 (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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Pinheiro, Carla, Carla Antonio, Maria Fernanda Ortuno, Petre I. Dobrev, Wolfram Hartung, Jane Thomas-Oates, Candido Pinto Ricardo, Radomira Vankova, Manuela M. Chaves, and Julie C. Wilson. "Initial water deficit effects on Lupinus albus photosynthetic performance, carbon metabolism, and hormonal balance: metabolic reorganization prior to early stress responses." Journal of Experimental Botany. 62 (2011): 4965-4974. AbstractWebsite

The early (2-4 d) effects of slowly imposed soil water deficit on Lupinus albus photosynthetic performance, carbon metabolism, and hormonal balance in different organs (leaf blade, stem stele, stem cortex, and root) were evaluated on 23-d-old plants (growth chamber assay). Our work shows that several metabolic adjustments occurred prior to alteration of the plant water status, implying that water deficit is perceived before the change in plant water status. The slow, progressive decline in soil water content started to be visible 3 d after withholding water (3 DAW). The earliest plant changes were associated with organ-specific metabolic responses (particularly in the leaves) and with leaf conductance and only later with plant water status and photosynthetic rate (4 DAW) or photosynthetic capacity (according to the Farquhar model; 6 DAW). Principal component analysis (PCA) of the physiological parameters, the carbohydrate and the hormone levels and their relative values, as well as leaf water-soluble metabolites full scan data (LC-MS/MS), showed separation of the different sampling dates. At 6 DAW classically described stress responses are observed, with plant water status, ABA level, and root hormonal balance contributing to the separation of these samples. Discrimination of earlier stress stages (3 and 4 DAW) is only achieved when the relative levels of indole-3-acetic acid (IAA), cytokinins (Cks), and carbon metabolism (glucose, sucrose, raffinose, and starch levels) are taken into account. Our working hypothesis is that, in addition to single responses (e.g. ABA increase), the combined alterations in hormone and carbohydrate levels play an important role in the stress response mechanism. Response to more advanced stress appears to be associated with a combination of cumulative changes, occurring in several plant organs. The carbohydrate and hormonal balance in the leaf (IAA to bioactive-Cks; soluble sugars to IAA and starch to IAA; relative abundances of the different soluble sugars) flag the initial responses to the slight decrease in soil water availability (10-15% decrease). Further alterations in sucrose to ABA and in raffinose to ABA relative values (in all organs) indicate that soil water availability continues to decrease. Such alterations when associated with changes in the root hormone balance indicate that the stress response is initiated. It is concluded that metabolic balance (e.g. IAA/bioactive Cks, carbohydrates/IAA, sucrose/ABA, raffinose/ABA, ABA/IAA) is relevant in triggering adjustment mechanisms.

Pinheiro, Carla, Carla Antonio, Maria Fernanda Ortuno, Petre I. Dobrev, Wolfram Hartung, Jane Thomas-Oates, Candido Pinto Ricardo, Radomira Vankova, Manuela M. Chaves, and Julie C. Wilson. "Initial water deficit effects on Lupinus albus photosynthetic performance, carbon metabolism, and hormonal balance: metabolic reorganization prior to early stress responses." Journal of Experimental Botany. 62 (2011): 4965-4974. AbstractWebsite
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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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Antunes, R., F. Coito, and H. Duarte-Ramos. "A Linear Approach towards Modeling Human Behavior." Technological Innovation for Sustainability (2011): 305-314. Abstract
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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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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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