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2010
Neu, Ursula, Melissa S. Maginnis, Angelina S. Palma, Luisa J. Stroeh, Christian D. S. Nelson, Ten Feizi, Walter J. Atwood, and Thilo Stehle. "Structure-Function Analysis of the Human JC Polyomavirus Establishes the LSTc Pentasaccharide as a Functional Receptor Motif." Cell Host & Microbe. 8 (2010): 309-319. Abstract
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Pinto, R. M., R. I. Olariu, J. Lameiras, F. T. Martins, A. A. Dias, G. J. Langley, P. Rodrigues, C. D. Maycock, J. P. Santos, M. F. Duarte, M. T. Fernandez, and M. L. Costa. "Study of selected benzyl azides by UV photoelectron spectroscopy and mass spectrometry." Journal of Molecular Structure. 980 (2010): 163-171. AbstractWebsite
Benzyl azide and the three methylbenzyl azides were synthesized and characterized by mass spectrometry (MS) and ultraviolet photoelectron spectroscopy (UVPES). The electron ionization fragmentation mechanisms for benzyl azide and their methyl derivatives were studied by accurate mass measurements and linked scans at constant B/E. For benzyl azide, in order to clarify the fragmentation mechanism, labelling experiments were performed. From the mass analysis of methylbenzyl azides isomers it was possible to differentiate the isomers ortho, meta and para. The abundance and nature of the ions resulting from the molecular ion fragmentation, for the three distinct isomers of substituted benzyl azides, were rationalized in terms of the electronic properties of the substituent. Concerning the para-isomer, IRC calculations were performed at UHF/6-31G(d) level. The photoionization study of benzyl azide, with He(I) radiation, revealed five bands in the 8-21 eV ionization energies region. From every photoelectron spectrum of methylbenzyl azides isomers it has been identified seven bands, on the same range as the benzyl azide. Interpretation of the photoelectron spectra was accomplished applying Koopmans' theorem to the SCF orbital energies obtained at HF/6-311++G(d, p) level.
Pinto, R. M., R. I. Olariu, J. Lameiras, F. T. Martins, A. A. Dias, G. J. Langley, P. Rodrigues, C. D. Maycock, J. P. Santos, M. F. Duarte, M. T. Fernandez, and M. L. Costa. "Study of selected benzyl azides by UV photoelectron spectroscopy and mass spectrometry." Journal of Molecular Structure. 980 (2010): 163-171. AbstractWebsite

Benzyl azide and the three methylbenzyl azides were synthesized and characterized by mass spectrometry (MS) and ultraviolet photoelectron spectroscopy (UVPES). The electron ionization fragmentation mechanisms for benzyl azide and their methyl derivatives were studied by accurate mass measurements and linked scans at constant B/E. For benzyl azide, in order to clarify the fragmentation mechanism, labelling experiments were performed. From the mass analysis of methylbenzyl azides isomers it was possible to differentiate the isomers ortho, meta and para. The abundance and nature of the ions resulting from the molecular ion fragmentation, for the three distinct isomers of substituted benzyl azides, were rationalized in terms of the electronic properties of the substituent. Concerning the para-isomer, IRC calculations were performed at UHF/6-31G(d) level. The photoionization study of benzyl azide, with He(I) radiation, revealed five bands in the 8-21 eV ionization energies region. From every photoelectron spectrum of methylbenzyl azides isomers it has been identified seven bands, on the same range as the benzyl azide. Interpretation of the photoelectron spectra was accomplished applying Koopmans' theorem to the SCF orbital energies obtained at HF/6-311++G(d, p) level.

Santos, H. M., R. Carreira, M. S. Diniz, M. G. Rivas, C. Lodeiro, JJG Moura, and J. L. Capelo. "Ultrasonic multiprobe as a new tool to overcome the bottleneck of throughput in workflows for protein identification relaying on ultrasonic energy." Talanta. 81 (2010): 55-62. AbstractWebsite
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Figueiredo, Ondina M., Teresa Pereira Silva, and João Pedro Veiga. "An X-ray spectrometry and absorption spectroscopy study of blue-and-white glazes from ancient Chinese porcelains." European Conference on X-ray Spectrometry-EXRS2010. 2010. Abstract
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Figueiredo, Ondina M., Teresa Pereira Silva, and João Pedro Veiga. "An X-ray spectrometry and absorption spectroscopy study of blue-and-white glazes from ancient Chinese porcelains [Abstract]." European Conference on X-ray Spectrometry-EXRS2010. 2010. Abstract
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Santos, J. P., A. M. Costa, J. P. Marques, M. C. Martins, P. Indelicato, and F. Parente. "X-ray-spectroscopy analysis of electron-cyclotron-resonance ion-source plasmas." Physical Review A. 82 (2010): 062516. AbstractWebsite
Analysis of x-ray spectra emitted by highly charged ions in an electron-cyclotron-resonance ion source (ECRIS) may be used as a tool to estimate the charge-state distribution (CSD) in the source plasma. For that purpose, knowledge of the electron energy distribution in the plasma, as well as the most important processes leading to the creation and de-excitation of ionic excited states are needed. In this work we present a method to estimate the ion CSD in an ECRIS through the analysis of the x-ray spectra emitted by the plasma. The method is applied to the analysis of a sulfur ECRIS plasma.
Santos, J. P., A. M. Costa, J. P. Marques, M. C. Martins, P. Indelicato, and F. Parente. "X-ray-spectroscopy analysis of electron-cyclotron-resonance ion-source plasmas." Physical Review A. 82 (2010): 062516. AbstractWebsite

Analysis of x-ray spectra emitted by highly charged ions in an electron-cyclotron-resonance ion source (ECRIS) may be used as a tool to estimate the charge-state distribution (CSD) in the source plasma. For that purpose, knowledge of the electron energy distribution in the plasma, as well as the most important processes leading to the creation and de-excitation of ionic excited states are needed. In this work we present a method to estimate the ion CSD in an ECRIS through the analysis of the x-ray spectra emitted by the plasma. The method is applied to the analysis of a sulfur ECRIS plasma.

Bundaleski, Nenad, Ana G. Silva, Augusto M. C. Moutinho, and Orlando M. N. D. Teodoro. "{Adsorption dynamics of water on the surface of TiO2 (110)}." Journal of Physics: Conference Series. Vol. 012008. 2010. 12008. Abstract

Rutile titanium dioxide TiO2 is used in a number of technological areas. Therefore, in surface science, it has become the most studied oxide surface. Water adsorption on rutile TiO2 (110) has been investigated using the X-ray photoelectron spectroscopy (XPS) and the work function study (WF): water adsorption induces formation of a dipole layer, which locally changes the work function. This can be experimentally observed as the onset shift of the secondary electron energy spectrum. While XPS seems to be insufficiently sensitive to monitor water adsorption on TiO2, there is a clear work function change undoubtedly attributed to the water adsorption. The measurements were done for different water vapour pressures, exposure times, sample temperatures and general surface conditions. Time evolutions of the work function change and the H2O partial pressure, enable us to successfully model the adsorption dynamics and help us understand the observed results. The analysis clearly shows existence of at least three different adsorption sites. Their interplay governs the work function time evolution, while the relative contributions depend on the surface temperature and, presumably, its topography. These results will be discussed in the light of several recent experimental and theoretical studies of this system done by other authors.

Costa, Viviana P., Mara E. M. Braga, Joana P. Guerra, Ana R. C. Duarte, Catarina M. M. Duarte, Eugénio O. B. Leite, Maria H. Gil, and Hermínio C. de Sousa. "{Development of therapeutic contact lenses using a supercritical solvent impregnation method}." Journal of Supercritical Fluids. 52 (2010): 306-316. Abstract

We present some selected results indicating the feasibility of preparing therapeutic finished ophthalmic articles, namely commercially available soft contact lenses, using a supercritical solvent impregnation (SSI) technique. Several commercial soft contact lenses were tested and, among these, four lenses were selected for more complete studies: Nelfilcon A (FocusDailies®, CIBA Vision), Omafilcon A (Proclear® Compatibles, CooperVision), Methafilcon A (Frequency® 55, CooperVision) and Hilafilcon B (SofLens® 59 Comfort, Bausch {&} Lomb). Supercritical carbon dioxide (scCO2) was the chosen supercritical fluid and two ophthalmic drugs were tested: flurbiprofen (a NSAID, hydrophobic) and timolol maleate (an anti-glaucoma drug, hydrophilic). The effects of operational pressure, of impregnation duration and of the addition of a cosolvent (ethanol) were studied on the overall drug loading yields. Depending on the experiment, we employed pressures from 9 up to 16 MPa and impregnation times from 30 up to 180 min. Temperature was kept constant and equal to 313 K. The employed depressurization rates were kept low and between 0.1 and 0.2 MPa/min. Results are discussed in terms of the employed operational conditions and taking in consideration all the possible interactions between supercritical fluids, drugs, cosolvents and the polymers which compose the employed hydrogel contact lenses. In vitro drug release experiments were carried out in order to evaluate the resulting drug release profiles. Obtained results were also compared with drug-loaded contact lenses obtained by conventional drug "soaking" in aqueous solutions. Results also proved that SSI can be considered as a viable, efficient and safe alternative for the impregnation of drugs, including those of hydrophobic character or presenting low aqueous solubility, into commercial soft contact lenses. SSI proved to be a "tunable" process since the variation of the employed operational conditions indicated that it is possible to control the amount of impregnated drug. In the end, the ophthalmic articles were recovered undamaged and without the presence of harmful solvent residues. This method also permits to process already prepared commercial contact lenses, without interfering with their manufacture methods and, after processing, store them for future use. © 2010 Elsevier B.V. All rights reserved.

Said, R., N. Ali, C. A. A. Ghumman, O. M. N. D. Teodoro, W. Ahmed, A. Abuazza, and J. Gracio. "{Effects of Bias Voltage on Diamond Like Carbon Coatings Deposited Using Titanium Isopropoxide ( TIPOT ) and Acetylene / Argon Mixtures onto Various Substrate Materials}." Journal of nanoscience and nanotechnology. 10 (2010): 2552-7. Abstract

RF-PECVD was used to prepare amorphous of carbon (DLC) onto stainless steel 316 and glass substrates. The substrates were negatively biased at between 100 V to 400 V. Thin films of DLC have been deposited using C2H2 and titanium isopropoxide (TIPOT). Argon was used to generate the plasma in the PECVD system chamber. DEKTAK 8 surface stylus profilometer was used to measure the film thickness and the deposition rate was calculated. Micro Raman spectroscopy was employed to determine the chemical structure and bonding present in the films. Composition analysis of the samples was carried out using VGTOF SIMS (IX23LS) instrument. In addition, X-ray photoelectron spectroscopy (XPS) was used to analyze the composition and chemical state of the films. The wettability of the films was examined using the optical contact angle meter (CAM200) system. Two types of liquids with different polarities were used to study changes in the surface energy. The as-grown films were in the thickness range of 200-400 nm. Raman spectroscopy results showed that the I(D)/I(G) ratio decreased when the bias voltage on the stainless steel substrates was increased. This indicates an increase in the graphitic nature of the film deposited. In contrast, on the glass substrates the I(D)/I(G) ratio increased when the bias voltage was increased indicates a greater degree of diamond like character. Chemical composition determined using XPS showed the presence of carbon and oxygen in both samples on glass and stainless steel substrates. Both coatings the contact angle of the films decreased except for 400 V which showed a slight increase. The oxygen is thought to play an important role on the polar component of a-C.

Vasconcelos, J. F., C. Silvestre, P. Oliveira, and B. Guerreiro. "{Embedded UAV model and LASER aiding techniques for inertial navigation systems}." Control Engineering Practice. 18 (2010): 262-278. AbstractWebsite
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Vasconcelos, J. F., C. Silvestre, P. Oliveira, and B. Guerreiro. "{Embedded UAV model and LASER aiding techniques for inertial navigation systems}." Control Engineering Practice. 18 (2010): 262-278. AbstractWebsite
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Santo, V. E., A. R. C. Duarte, M. E. Gomes, J. F. Mano, and R. L. Reis. "{Hybrid 3D structure of poly(d,l-lactic acid) loaded with chitosan/chondroitin sulfate nanoparticles to be used as carriers for biomacromolecules in tissue engineering}." Journal of Supercritical Fluids. 54 (2010). Abstract

In the tissue engineering (TE) field, the concept of producing multifunctional scaffolds, capable not only of acting as templates for cell transplantation but also of delivering bioactive agents in a controlled manner, is an emerging strategy aimed to enhance tissue regeneration. In this work, a complex hybrid release system consisting in a three-dimensional (3D) structure based on poly(d,l-lactic acid) (PDLLA) impregnated with chitosan/chondroitin sulfate nanoparticles (NPs) was developed. The scaffolds were prepared by supercritical fluid foaming at 200 bar and 35 °C, and were then characterized by scanning electron microscopy (SEM) and micro-CT. SEM also allowed to assess the distribution of the NPs within the structure, showing that the particles could be found in different areas of the scaffold, indicating a homogeneous distribution within the 3D structure. Water uptake and weight loss measurements were also carried out and the results obtained demonstrated that weight loss was not significantly enhanced although the entrapment of the NPs in the 3D structure clearly enhances the swelling of the structure. Moreover, the hybrid porous biomaterial displayed adequate mechanical properties for cell adhesion and support. The possibility of using this scaffold as a multifunctional material was further evaluated by the incorporation of a model protein, bovine serum albumin (BSA), either directly into the PDLLA foam or in the NPs that were eventually included in the scaffold. The obtained results show that it is possible to achieve different release kinetics, suggesting that this system is a promising candidate for dual protein delivery system for TE applications. © 2010 Elsevier B.V.

Sabil, Khalik M., Ana Rita C. Duarte, John Zevenbergen, Murni M. Ahmad, Suzana Yusup, Abdul A. Omar, and Cor J. Peters. "{Kinetic of formation for single carbon dioxide and mixed carbon dioxide and tetrahydrofuran hydrates in water and sodium chloride aqueous solution}." International Journal of Greenhouse Gas Control. 4 (2010): 798-805. AbstractWebsite

A laboratory-scale reactor system is built and operated to measure the kinetic of formation for single and mixed carbon dioxide-tetrahydrofuran hydrates. The T-cycle method, which is used to collect the kinetic data, is briefly discussed. For single carbon dioxide hydrate, the induction time decreases with the increase of the initial carbon dioxide pressure up to 2.96. MPa. Beyond this pressure, the induction time is becoming relatively constant with the increase of initial carbon dioxide pressure indicating that the liquid phase is completely supersaturated with carbon dioxide. Experimental results show that the inclusion of tetrahydrofuran reduces the induction time required for hydrate formation. These observations indicate hydrate nucleation process and onset growth are more readily to occur in the presence of tetrahydrofuran. In contrast, the presence of sodium chloride prolongs the induction time due to clustering of water molecules with the ions and the salting-out effects. It is also shown that the degree of subcooling required for hydrate formation is affected by the presence of tetrahydrofuran and sodium chloride in the hydrate forming system. The presence of tetrahydrofuran in the hydrate system significantly reduces the amount of carbon dioxide uptake. The apparent rate constant, k, for those systems are reported. © 2010.

2009
Karlovich, Alexei Yu., and Ilya M. Spitkovsky. "Connectedness of spectra of Toeplitz operators on Hardy spaces with Muckenhoupt weights over Carleson curves." Integral Equations and Operator Theory. 65.1 (2009): 83-114. AbstractWebsite

Harold Widom proved in 1966 that the spectrum of a Toeplitz operator \(T(a)\) acting on the Hardy space \(H^p(\mathbb{T})\) over the unit circle \(\mathbb{T}\) is a connected subset of the complex plane for every bounded measurable symbol \(a\) and \(1 < p < \infty\). In 1972, Ronald Douglas established the connectedness of the essential spectrum of \(T(a)\) on \(H^2(\mathbb{T})\). We show that, as was suspected, these results remain valid in the setting of Hardy spaces \(H^p(\Gamma,w)\), \( 1 < p < \infty \), with general Muckenhoupt weights \(w\) over arbitrary Carleson curves \(\Gamma\).

Xie, X., R. G. Hadt, S. R. Pauleta, P. J. Gonzalez, S. Un, I. Moura, and E. I. Solomon. "A variable temperature spectroscopic study on Paracoccuspantotrophus pseudoazurin: protein constraints on the blue Cu site." J Inorg Biochem. 103 (2009): 1307-13. AbstractWebsite

The blue or Type 1 (T1) copper site of Paracoccuspantotrophus pseudoazurin exhibits significant absorption intensity in both the 450 and 600 nm regions. These are sigma and pi S(Cys) to Cu(2+) charge transfer (CT) transitions. The temperature dependent absorption, EPR, and resonance Raman (rR) vibrations enhanced by these bands indicate that a single species is present at all temperatures. This contrasts the temperature dependent behavior of the T1 center in nitrite reductase [S. Ghosh, X. Xie, A. Dey, Y. Sun, C. Scholes, E. Solomon, Proc. Natl. Acad. Sci. 106 (2009) 4969-4974] which has a thioether ligand that is unconstrained by the protein. The lack of temperature dependence in the T1 site in pseudoazurin indicates the presence of a protein constraint similar to the blue Cu site in plastocyanin where the thioether ligand is constrained at 2.8 A. However, plastocyanin exhibits only pi CT. This spectral difference between pseudoazurin and plastocyanin reflects a coupled distortion of the site where the axial thioether in pseudoazurin is also constrained, but at a shorter Cu-S(Met) bond length. This leads to an increase in the Cu(2+)-S(Cys) bond length, and the site undergoes a partial tetragonal distortion in pseudoazurin. Thus, its ground state wavefunction has both sigma and pi character in the Cu(2+)-S(Cys) bond.

Martins, R., L. Raniero, L. Pereira, D. Costa†, H. Águas, S. Pereira, L. 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. AbstractWebsite
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Tavares, Alexandra Impacto do mercado ibérico de electricidade (MIBEL) no comportamento competitivo dos agentes produtores de energia eléctrica. Eds. Mário Neves, Jorge Sousa, and João Pina. FCT-UNL, 2009. Abstract

A presente Dissertação consiste num estudo do comportamento competitivo de entidades, produtoras e comercializadoras de energia eléctrica, num período de tempo antes e após a entrada em vigor do Mercado Ibérico de Electricidade (MIBEL). Esse período de tempo engloba os meses entre Abril de 2007 e Abril de 2008, sendo que o MIBEL teve início a 1 de Julho de 2007. O estudo incide principalmente no grau de competitividade ou ausência da mesma, que as referidas entidades adoptaram após o começo do MIBEL. Para poder efectuar essa avaliação, recorre-se a uma abordagem baseada em variações conjecturais, que constituem um indicador desse grau de competitividade. Ou seja, as variações conjecturais representam a convicção que determinada empresa X tem face ao comportamento que outra empresa Y adoptará após uma acção efectuada pela empresa X. Por acção depreende-se, por exemplo, uma redução ou um aumento da quantidade de produção de uma empresa. Se o valor da variável conjectural for 0, as empresas encontram-se a concorrer à Cournot. Caso seja -1, as empresas encontram-se em concorrência perfeita. Por outro lado, se o valor da variação conjectural for superior a 0 pode existir uma situação de conluio entre as empresas. De modo a obter estes valores das variações conjecturais, utiliza-se e readapta-se um simulador de mercado diário, denominado SiMEC - Simulador do Mercado Eléctrico e do Carbono. Este simulador, que anteriormente simulava apenas períodos temporais precedentes ao MIBEL, foi reajustado de modo a incluir dados pós MIBEL. Finalmente, são então realizados gráficos comparativos e retiradas conclusões acerca do comportamento das entidades face a alterações na estrutura do mercado de electricidade.

Conrath, K., AS Pereira, C. E. Martins, C. G. Timoteo, P. Tavares, S. Spinelli, J. Kinne, C. Flaudrops, C. Cambillau, S. Muyldermans, I. Moura, J. J. Moura, M. Tegoni, and A. Desmyter. "Camelid nanobodies raised against an integral membrane enzyme, nitric oxide reductase." Protein Sci. 18 (2009): 619-28. AbstractWebsite

Nitric Oxide Reductase (NOR) is an integral membrane protein performing the reduction of NO to N(2)O. 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). 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.

Guerreiro, B. J., C. Silvestre, R. Cunha, C. Cao, and N. Hovakimyan. "{L1 adaptive control for autonomous rotorcraft}." American Control Conference, 2009. 2009. 3250-3255. Abstract
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Guerreiro, B. J., C. Silvestre, R. Cunha, C. Cao, and N. Hovakimyan. "{L1 adaptive control for autonomous rotorcraft}." American Control Conference, 2009. 2009. 3250-3255. Abstract
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Ivanova, G., L. S. Serafim, P. C. Lemos, A. M. Ramos, M. A. M. Reis, and E. J. Cabrita. "Influence of feeding strategies of mixed microbial cultures on the chemical composition and microstructure of copolyesters P(3HB-co-3HV) analyzed by NMR and statistical analysis." Magnetic Resonance in Chemistry. 47 (2009): 497-504. Abstract
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Martins, Rui M. S., NORBERT SCHELL, Paulo R. Gordo, Manuel JP Maneira, Rui JC Silva, and Francisco M. BRAZ FERNANDES. "Development of sputtered Shape Memory Alloy (SMA) Ni-Ti films for actuation in ice cooled environments." Vacuum. 83.10 (2009): 1299-1302. Abstract
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Pedras, B., E. Oliveira, H. Santos, L. Rodriguez, R. Crehuet, T. Aviles, J. L. Capelo, and C. Lodeiro. "A new tripodal poly-imine indole-containing ligand: Synthesis, complexation, spectroscopic and theoretical studies." Inorg Chim Acta. 362 (2009): 2627-2635. AbstractWebsite

A novel flexible tripodal ligand derived from 3-methylindole, ("InTREN" L), and its mononuclear Zn(II), Cu(II), Ni(II), Hg(II) and Pd(II) complexes are described. All compounds gave analytically pure solid samples. Characterisation of the compounds was accomplished by (1)H NMR, IR and absorption spectroscopies, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and elemental analysis and their geometry optimized using density functional theory (DFT).Time-dependent-density functional theory (TD-DFT) calculations have been used to assign the lowest energy absorption bands of the free ligand and the Zn(II) complex. The system is a very good candidate for in situ recognition/coordination effects by MALDI-TOF-MS spectrometry and absorption spectroscopy. The presence of three indole groups in InTREN opens up the possibility to synthesize new three-dimensional self-assembly supramolecular structures. (C) 2008 Elsevier B.V. All rights reserved.