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2009
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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Ribeiro, Celso, Paulo J. Gomes, Paulo A. Ribeiro, Maria Raposo, Hugo Águas, Pedro Mendonça dos Santos, Beatriz Borges, and Pedro Brogueira. "Polymeric Film Sensors based on PAH-PAZO Ionic Self-assembled Multi-nanolayers." BIODEVICES. 2009. 458-461. 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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Santos, JM, and AJL Phillips. "Resolving the complex of Diaporthe (Phomopsis) species occurring on Foeniculum vulgare in Portugal." Fungal Diversity. 34 (2009): 111-125. Abstract
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Amaro, P., J. P. Santos, F. Parente, A. Surzhykov, and P. Indelicato. "Resonance effects on the two-photon emission from hydrogenic ions." Physical Review A (Atomic, Molecular, and Optical Physics). 79 (2009): 062504. AbstractWebsite
A theoretical study of the all two-photon transitions from initial bound states with ni=2,3 in hydrogenic ions is presented. High-precision values of relativistic decay rates for ions with nuclear charge in the range 1<=Z<=92 are obtained through the use of finite basis sets for the Dirac equation constructed from B splines. We also report the spectral (energy) distributions of several resonant transitions, which exhibit interesting structures, such as zeros in the emission spectrum, indicating that two-photon emission is strongly suppressed at certain frequencies. We compare two different approaches (the line profile approach and the QED approach based on the analysis of the relativistic two-loop self-energy) to regularize the resonant contribution to the decay rate. Predictions for the pure two-photon contributions obtained in these approaches are found to be in good numerical agreement.
Amaro, P., J. P. Santos, F. Parente, A. Surzhykov, and P. Indelicato. "Resonance effects on the two-photon emission from hydrogenic ions." Physical Review A. 79 (2009): 062504. AbstractWebsite

A theoretical study of the all two-photon transitions from initial bound states with ni=2,3 in hydrogenic ions is presented. High-precision values of relativistic decay rates for ions with nuclear charge in the range 1<=Z<=92 are obtained through the use of finite basis sets for the Dirac equation constructed from B splines. We also report the spectral (energy) distributions of several resonant transitions, which exhibit interesting structures, such as zeros in the emission spectrum, indicating that two-photon emission is strongly suppressed at certain frequencies. We compare two different approaches (the line profile approach and the QED approach based on the analysis of the relativistic two-loop self-energy) to regularize the resonant contribution to the decay rate. Predictions for the pure two-photon contributions obtained in these approaches are found to be in good numerical agreement.

Honzí?ek, J., A. Mukhopadhyay, T. Santos-Silva, MJ Romão, and C. C. Romão. "Ring-functionalized molybdenocene complexes." Organometallics. 28 (2009): 2871-2879. 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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Silva, V., L. B. Oliveira, J. R. Fernandes, M. P. Vestias, and H. C. Neto. "Run-Time Reconfigurable Array Using Magnetic RAM." Digital System Design, Architectures, Methods and Tools, 2009. DSD'09. 12th Euromicro Conference on. IEEE, 2009. 74-81. 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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Figueiredo, Ondina M., Teresa Pereira Silva, João Pedro Veiga, and Isabel M. Dias. "Speciation state of cobalt in blue glazes: a XAFS study on XVI cent. chinese blue-&-white porcelains." EMRS 2009 Spring Meeting, Symposium R-X-Ray Techniques for Advanced Materials, Nanostructures and Thin Films from Laboratory Sources to Synchronotron Radiation, June 8-12, 2009. 2009. Abstract
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Sergeant, K., C. Pinheiro, JF Hausman, and al.et. "Taking Advantage of Nonspecific Trypsin Cleavages for the Identification of Seed Storage Proteins in Cereals." JOURNAL OF PROTEOME RESEARCH. 8 (2009): 3182-3190. Abstract
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Sergeant, K., C. Pinheiro, JF Hausman, and al.et. "Taking Advantage of Nonspecific Trypsin Cleavages for the Identification of Seed Storage Proteins in Cereals." JOURNAL OF PROTEOME RESEARCH. 8 (2009): 3182-3190. Abstract
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Silva, V., J. R. Fernandes, L. B. Oliveira, H. C. Neto, R. ferreira, S. Freitas, and P. P. Freitas. "Thermal Assisted Switching Magnetic Tunnel Junctions as FPGA Memory Elements." Mixed Design of Integrated Circuits & Systems, 2009. MIXDES'09. MIXDES-16th International Conference. IEEE, 2009. 332-336. Abstract
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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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Neshataeva, Ekaterina, Tilmar Kuemmell, André Ebbers, Gerd Bacher, David J. Rogers, VE Sandana, Hosseini F. Teherani, M. Razeghi, HJ Drouhin, and R. Martins. "Zinc Oxide Materials and Devices IV (Proceedings Volume)." (2009). Abstract
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Conrath, Katja, Alice S. Pereira, Carlos E. Martins, Cristina G. Timoteo, Pedro Tavares, Silvia Spinelli, Joerg Kinne, Christophe Flaudrops, Christian Cambillau, Serge Muyldermans, Isabel Moura, Jose J. G. Moura, Mariella Tegoni, and Aline Desmyter. "{Camelid nanobodies raised against an integral membrane enzyme, nitric oxide reductase}." Protein science : a publication of the Protein Society. 18 (2009): 619-628. Abstract
Nitric Oxide Reductase (NOR) is an integral membrane protein performing the reduction of NO to N2O. NOR is composed of two subunits: the large one (NorB) is a bundle of 12 transmembrane helices (TMH). It contains a b type heme and a binuclear iron site, which is believed to be the catalytic site, comprising a heme b and a non-hemic iron. The small subunit (NorC) harbors a cytochrome c and is attached to the membrane through a unique TMH. With the aim to perform structural and functional studies of NOR, we have immunized dromedaries with NOR and produced several antibody fragments of the heavy chain (VHHs, also known as nanobodies (TM)). These fragments have been used to develop a faster NOR purification procedure, to proceed to crystallization assays and to analyze the electron transfer of electron donors. BIAcore experiments have revealed that up to three VHHs can bind concomitantly to NOR with affinities in the nanomolar range. This is the first example of the use of VHHs with an integral membrane protein. Our results indicate that VHHs are able to recognize with high affinity distinct epitopes on this class of proteins, and can be used as versatile and valuable tool for purification, functional study and crystallization of integral membrane proteins.
Said, R., N. Ali, C. A. A. Ghumman, O. M. N. D. Teodoro, and W. Ahmed. "{Characterisation of DLC Films Deposited Using Titanium Isopropoxide (TIPOT) at Different Flow Rates}." Journal of nanoscience and nanotechnology. 9 (2009): 4298-4304. Abstract

In recent years, there has been growing interest in the search for advanced biomaterials for biomedical applications, such as human implants and surgical cutting tools. It is known that both carbon and titanium exhibit good biocompatibility and have been used as implants in the human body. It is highly desirable to deposit biocompatible thin films onto a range of components in order to impart biocompatibility and to minimise wear in implants. Diamond like carbon (DLC) is a good candidate material for achieving biocompatibility and low wear rates. In this study, thin films of diamond-like-carbon DLC were deposited onto stainless steel (316) substrates using C2H2, argon and titanium isopropoxide (TIPOT) precursors. Argon was used to generate the plasma in the plasma enhanced vapour deposition (PECVD) system. A critical coating feature governing the performance of the component during service is film thickness. The as-grown films were in the thickness range 90-100 nm and were found to be dependent on TIPOT flow rate. Atomic force microscopy (AFM) was used to characterise the surface roughness of the samples. As the flow rate of TIPOT increased the average roughness was found to increase in conjunction with the film thickness. Raman spectroscopy was used to investigate the chemical structure of amorphous carbon matrix. Surface tension values were calculated using contact angle measurements. In general, the trend of the surface tension results exhibited an opposite trend to that of the contact angle. The elemental composition of the samples was characterised using a VG ToF SIMS (IX23LS) instrument and X-ray photoelectron spectroscopy (XPS). Surprisingly, SIMS and XPS results showed that the DLC samples did not show evidence of titanium since no peaks representing to titanium appeared on the SIMS/XPS spectra.

Martí, A., E. Antolín, P. G. Linares, E. Cánovas, D. {Fuertes Marrón}, C. Tablero, M. Mendes, A. Mellor, I. Tobías, M. Y. Levy, E. Hernández, A. Luque, C. D. Farmer, C. R. Stanley, R. P. Campion, J. L. Hall, S. V. Novikov, C. T. Foxon, R. Scheer, B. Marsen, H. W. Schock, M. Picault, and C. Chaix. "{IBPOWER: Intermediate band materials and solar cells for photovoltaics with high efficiency and reduced cost}." Conference Record of the IEEE Photovoltaic Specialists Conference. 2009. Abstract
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