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2009
Martins, R., Leandro Raniero, Luis Pereira, Daniel Costa, Hugo Aguas, Sonia Pereira, Leonardo Silva, A. Gonçalves, I. Ferreira, and E. Fortunato. "Nanostructured silicon and its application to solar cells, position sensors and thin film transistors." Philosophical Magazine. 89 (2009): 2699-2721. Abstract
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Mateus, O., SCR Maidment, and NA Christiansen. "A new long-necked {'}sauropod-mimic{'} stegosaur and the evolution of the plated dinosaurs." Proceedings of the Royal Society B: Biological Sciences. 276 (2009): 1815-1821. Abstract
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Capelo, J. L., R. Carreira, M. Diniz, L. Fernandes, M. Galesio, C. Lodeiro, H. M. Santos, and G. Vale. "Overview on modern approaches to speed up protein identification workflows relying on enzymatic cleavage and mass spectrometry-based techniques." Analytica Chimica Acta. 650 (2009): 151-159. AbstractWebsite
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Fortunato, E., Nuno Correia, Pedro Barquinha, Claudia Costa, Luis Pereira, Goncalo Goncalves, and Rodrigo Martins. "Paper Field Effect Transistor." Zinc Oxide Materials and Devices Iv. Eds. F. H. Teherani, C. W. Litton, and D. J. Rogers. Vol. 7217. Proceedings of SPIE, 7217. 2009. Abstract
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Chaves, M. M., J. Flexas, and C. Pinheiro. "Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell." Annals of Botany. 103 (2009): 551-560. AbstractWebsite

Plants are often subjected to periods of soil and atmospheric water deficits during their life cycle as well as, in many areas of the globe, to high soil salinity. Understanding how plants respond to drought, salt and co-occurring stresses can play a major role in stabilizing crop performance under drought and saline conditions and in the protection of natural vegetation. Photosynthesis, together with cell growth, is among the primary processes to be affected by water or salt stress. The effects of drought and salt stresses on photosynthesis are either direct (as the diffusion limitations through the stomata and the mesophyll and the alterations in photosynthetic metabolism) or secondary, such as the oxidative stress arising from the superimposition of multiple stresses. The carbon balance of a plant during a period of salt/water stress and recovery may depend as much on the velocity and degree of photosynthetic recovery, as it depends on the degree and velocity of photosynthesis decline during water depletion. Current knowledge about physiological limitations to photosynthetic recovery after different intensities of water and salt stress is still scarce. From the large amount of data available on transcript-profiling studies in plants subjected to drought and salt it is becoming apparent that plants perceive and respond to these stresses by quickly altering gene expression in parallel with physiological and biochemical alterations; this occurs even under mild to moderate stress conditions. From a recent comprehensive study that compared salt and drought stress it is apparent that both stresses led to down-regulation of some photosynthetic genes, with most of the changes being small (ratio threshold lower than 1) possibly reflecting the mild stress imposed. When compared with drought, salt stress affected more genes and more intensely, possibly reflecting the combined effects of dehydration and osmotic stress in salt-stressed plants.

Chaves, M. M., J. Flexas, and C. Pinheiro. "Photosynthesis under drought and salt stress: regulation mechanisms from whole plant to cell." Annals of Botany. 103 (2009): 551-560. AbstractWebsite
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Freire, Filipe, Maria Joao Romao, Anjos L. Macedo, Susana S. Aveiro, Brian J. Goodfellow, and Ana Luisa Carvalho. "Preliminary structural characterization of human SOUL, a haem-binding protein." Acta Crystallographica Section F-Structural Biology and Crystallization Communications. 65 (2009): 723-726. Abstract
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Martins, M. C., J. P. Marques, A. M. Costa, J. P. Santos, F. Parente, S. Schlesser, Le E. - O. Bigot, and P. Indelicato. "Production and decay of sulfur excited species in an electron-cyclotron-resonance ion-source plasma." Physical Review A (Atomic, Molecular, and Optical Physics). 80 (2009): 032501. AbstractWebsite
The most important processes for the creation of S12+ to S14+ ions excited states from the ground configurations of S9+ to S14+ ions in an electron cyclotron resonance ion source, leading to the emission of K x-ray lines, are studied. Theoretical values for inner-shell excitation and ionization cross sections, including double-KL and triple-KLL ionizations, transition probabilities and energies for the de-excitation processes, are calculated in the framework of the multiconfiguration Dirac-Fock method. With reasonable assumptions about the electron energy distribution, a theoretical Kalpha x-ray spectrum is obtained, which is compared to recent experimental data.
Martins, M. C., J. P. Marques, A. M. Costa, J. P. Santos, F. Parente, S. Schlesser, E. O. Le Bigot, and P. Indelicato. "Production and decay of sulfur excited species in an electron-cyclotron-resonance ion-source plasma." Physical Review A. 80 (2009): 032501. AbstractWebsite

The most important processes for the creation of S12+ to S14+ ions excited states from the ground configurations of S9+ to S14+ ions in an electron cyclotron resonance ion source, leading to the emission of K x-ray lines, are studied. Theoretical values for inner-shell excitation and ionization cross sections, including double-KL and triple-KLL ionizations, transition probabilities and energies for the de-excitation processes, are calculated in the framework of the multiconfiguration Dirac-Fock method. With reasonable assumptions about the electron energy distribution, a theoretical Kalpha x-ray spectrum is obtained, which is compared to recent experimental data.

Torosantucci, Antonella, Paola Chiani, Carla Bromuro, Flavia De Bernardis, Angelina S. Palma, Yan Liu, Giuseppina Mignogna, Bruno Maras, Marisa Colone, Annarita Stringaro, Silvia Zamboni, Ten Feizi, and Antonio Cassone. "Protection by Anti-beta-Glucan Antibodies Is Associated with Restricted beta-1,3 Glucan Binding Specificity and Inhibition of Fungal Growth and Adherence." Plos One. 4 (2009). Abstract
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Chaves, I., C. Pinheiro, JAP Paiva, S. Planchon, K. Sergeant, J. Renaut, JA Graca, G. Costa, AV Coelho, and CPP Ricardo. "Proteomic evaluation of wound-healing processes in potato (Solanum tuberosum L.) tuber tissue." PROTEOMICS. 9 (2009): 4154-4175. Abstract
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Chaves, I., C. Pinheiro, JAP Paiva, S. Planchon, K. Sergeant, J. Renaut, JA Graca, G. Costa, AV Coelho, and CPP Ricardo. "Proteomic evaluation of wound-healing processes in potato (Solanum tuberosum L.) tuber tissue." PROTEOMICS. 9 (2009): 4154-4175. Abstract
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Viciosa, M. T., N. T. Correia, M. Salmeron Sanchez, AL Carvalho, MJ Romao, J. L. Gomez Ribelles, and M. Dionisio. "Real-Time Monitoring of Molecular Dynamics of Ethylene Glycol Dimethacrylate Glass Former." Journal of Physical Chemistry B. 113 (2009): 14209-14217. Abstract
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Childs, Robert A., Angelina S. Palma, Steve Wharton, Tatyana Matrosovich, Yan Liu, Wengang Chai, Maria A. Campanero-Rhodes, Yibing Zhang, Markus Eickmann, Makoto Kiso, Alan Hay, Mikhail Matrosovich, and Ten Feizi. "Receptor-binding specificity of pandemic influenza A (H1N1) 2009 virus determined by carbohydrate microarray." Nature Biotechnology. 27 (2009): 797-799. Abstract
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Santos, S., Alberto Cardoso, A. Santos, and P. Gil Robust Monitoring and Fault Tolerance in Wireless Sensor Networks. n/a, 2009. Abstract
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Martins, Rodrigo, P. Barquinha, L. Pereira, N. Correia, G. GONCALVES, I. Ferreira, and E. Fortunato. "Selective floating gate non‐volatile paper memory transistor." physica status solidi (RRL)-Rapid Research Letters. 3.9 (2009): 308-310. Abstract
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Martins, Rodrigo, LuÍs Pereira, Pedro Barquinha, Nuno Correia, Gonçalo Gonçalves, Isabel Ferreira, Carlos Dias, N. Correia, M. Dionísio, and M. Silva. "Self‐sustained n‐type memory transistor devices based on natural cellulose paper fibers." Journal of Information Display. 10.4 (2009): 149-157. Abstract
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Cardoso, Alberto, S. Santos, A. Santos, and P. Gil. "Simulation Platform for Wireless Sensor Networks based on the TrueTime Toolbox." IECON 2009 - 35th Annual Conference of the IEEE Industrial Electronics Society. n/a 2009. Abstract
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Gomes, J., Alberto Cardoso, and P. Gil. "Slope instability and landslides in Tua river basin and its relations with recent train disasters." Geomorphology 2009 - 7th International Conference on Geomorphology (ANZIAG). n/a 2009. Abstract
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Agra, A., D. M. Cardoso, J. O. Cerdeira, M. Miranda, and E. Rocha. "Solving huge size instances of the optimal diversity management problem." Journal of Mathematical Sciences. 161 (2009): 956-960. Abstract
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Cipriano, F., Ouerdiane Vilela Mendes H. R. "Stochastic Solution of a KPP-Type Nonlinear Fractional Differential Equation." Fractional Calculus and Applied Analysis. 12 (2009): 47-56. AbstractWebsite

Mathematics Subject Classification: 26A33, 76M35, 82B31A stochastic solution is constructed for a fractional generalization of the KPP (Kolmogorov, Petrovskii, Piskunov) equation. The solution uses a fractional generalization of the branching exponential process and propagation processes which are spectral integrals of Levy processes.

Pinto, R. M., A. A. Dias, and M. L. Costa. "Theoretical study of the molecular properties of methyl 2-azidopropionate and methyl 3-azidopropionate." Journal of Molecular Structure: THEOCHEM. 894 (2009): 80-87. AbstractWebsite

An extensive conformational analysis was carried at ab initio and DFT levels of theory on two molecules - methyl 2-azidopropionate (N3CH3CHCOOCH3) and methyl 3-azidopropionate (N3CH2CH2COOCH3). In each case, the lowest energy conformers were characterized and the energy barriers between them were estimated. Ionization energies and vibrational frequencies were also computed, in order to support future spectroscopic studies with ultraviolet photoelectron spectroscopy (UVPES) and matrix isolation infrared spectroscopy (Matrix Isolation FTIR).

Costa, P. M., H. M. Santos, I. Peres, M. H. Costa, S. Alves, J. L. Capelo-Martinez, and M. S. Diniz. "Toxicokinetics of waterborne trivalent arsenic in the freshwater bivalve corbicula fluminea." Archives of Environmental Contamination and Toxicology. 57 (2009): 338-347. AbstractWebsite
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Pereira, P., M. H. Fino, and F. V. Coito. "Using discrete-variable optimization for CMOS spiral inductor design." Proc. Int Microelectronics (ICM) Conf. 2009. 324-327. Abstract

In this paper a discrete-variable optimization methodology for the automatic design of CMOS integrated spiral inductors is introduced. The use of discrete variable optimization procedure offers the designer the possibility for exploring the design space exclusively in those points available for the technology under use. Further user-defined constraints between layout parameters may also be incorporated as a way of taking into account design heuristics. A comparison between using discrete-variable optimization and a continuous optimization procedure followed by a discretization of the results is presented, where the benefits of the proposed methodology are presented. An application using the proposed methodology was developed in Matlab and the optimization toolbox is used. For the sake of simplicity the pi-model has been used for characterizing the inductor. The validity of the design results is checked against circuit simulation with ASITIC.