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2011
Giestas, L, Lima JC, Baptista PV.  2011.  Coupling single base extension to a spectral codification tool for increased throughput screening. Journal of Biotechnology. 154:199-204., Number 4 Abstract
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Coelho, C, Gonzalez PJ, Moura JJG, Moura I, Trincao J, Romao MJ.  2011.  The Crystal Structure of Cupriavidus necator Nitrate Reductase in Oxidized and Partially Reduced States. Journal of Molecular Biology. 408:932-948., Number 5 AbstractWebsite
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Mukhopadhyay, A, Kladova AV, Bursakov SA, Gavel YO, Calvete JJ, Shnyrov VL, Moura I, Moura JJG, Romao MJ, Trincao J.  2011.  Crystal structure of the zinc-, cobalt-, and iron-containing adenylate kinase from Desulfovibrio gigas: a novel metal-containing adenylate kinase from Gram-negative bacteria. Journal of Biological Inorganic Chemistry. 16:51-61., Number 1 AbstractWebsite
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Brito Palma, LFF, Coito FJ, Gil P, Neves-Silva R.  2011.  Design of Adaptive PCA Controllers for SISO Systems. World Congress. 18:5483–5488., Number 1 Abstract

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da Silva, MS, Viveiros R, Morgado PI, Aguiar-Ricardo A, Correia IJ, Casimiro T.  2011.  Development of 2-(dimethylamino)ethyl methacrylate-based molecular recognition devices for controlled drug delivery using supercritical fluid technology. International Journal of Pharmaceutics. 416:61-68., Number 1 AbstractWebsite

This work reports the development of a novel potential body-friendly oral drug delivery system, which consists of a biocompatible molecularly imprinted polymer (MIP), with pH sensitive character and low cross-linking degree (20.2 wt%), synthesized and processed in supercritical carbon dioxide. The \{MIP\} is synthesized using 2-(dimethylamino)ethyl methacrylate (DMAEMA) as functional monomer and ethylene glycol dimethacrylate (EGDMA) as cross-linker, and ibuprofen as molecular recognition template. The imprinted matrix was able to show a higher affinity towards ibuprofen than its corresponding non-imprinted polymer (NIP) meaning that the molecular imprinting in scCO2 was efficient even using a low crosslinking degree. \{MIP\} showed a significant molecular recognition towards the template, presenting higher drug uptake ability in the supercritical impregnation step, loading 33.1 wt% of ibuprofen compared to only 10.2 wt% for the \{NIP\} polymer. In vitro drug release experiments, simulating an oral administration, showed different release profiles at pH 2.2 and pH 7.4. Zeta potential measurements were performed to both \{MIP\} and \{NIP\} showing that the imprinting process has a significant influence on the charge of the polymeric particles. Cytotoxicity assays performed with human colorectal carcinoma-derived Caco-2 cells demonstrated that the polymers are biocompatible and could be potentially used in drug delivery applications.

da Silva, MS, Nobrega FL, Aguiar-Ricardo A, Cabrita EJ, Casimiro T.  2011.  Development of molecularly imprinted co-polymeric devices for controlled delivery of flufenamic acid using supercritical fluid technology. The Journal of Supercritical Fluids. 58:150-157., Number 1 AbstractWebsite

This work reports the development of a novel class of affinity co-polymeric materials using supercritical fluid technology. Polymeric materials with molecular recognition to flufenamic acid, were first synthesized in supercritical carbon dioxide (scCO2) using the drug as template. Molecularly imprinted co-polymers of methacrylic acid (MAA) or N-isopropyl acrylamide (NIPAAm) crosslinked with ethylene glycol dimethacrylate (EGDMA) were synthesized using different crosslinking degrees and template:monomer ratios, at 65 °C and 21 MPa. High-pressure \{NMR\} experiments confirmed that the nature of the interactions between the drug and the functional monomers during the polymerization step are mainly hydrogen bonds. scCO2-assisted impregnation revealed that the imprinted matrices were able to uptake higher amounts of flufenamic acid. This effect was particularly evidenced in the more crosslinked matrices, with P(MAA–EGDMA) imprinted copolymers binding up to 101.5 mg drug/g polymer against only 50.5 mg/g in the non-imprinted copolymer. In vitro drug delivery experiments showed that imprinted co-polymers release the drug in a more sustained way than the corresponding non-imprinted matrices. Overall it was shown that supercritical fluid technology is a viable approach for the development of self-assembly molecular recognition polymers with potential application in controlled drug delivery systems.

Carneiro, M, Batista AG, Ortigueira MD.  2011.  EEG artifact removal with ICA analysis. Doctoral Conference on Computing, Electrical and Industrial Systems, DoCEIS 2011. Abstract
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Cardoso, NV, Batista AG, Ortigueira MD.  2011.  EEG Features Extraction for Sleep Classification and Spindle Detection. Doctoral Conference on Computing on Computing, Electrical and Industrial Systems. Abstract
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Branco, A, Branco LC, Pina F.  2011.  Electrochromic and magnetic ionic liquids. Chemical Communications. 47:2300-2302., Number 8 AbstractWebsite
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Gomes, AC, Bruno SM, Gago S, Lopes RP, Machado DA, Carminatti AP, Valente AA, Pillinger M, Goncalves IS.  2011.  Epoxidation of cyclooctene using soluble or MCM-41-supported molybdenum tetracarbonyl-pyridylimine complexes as catalyst precursors. Journal of Organometallic Chemistry. 696:3543-3550., Number 22 AbstractWebsite
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Rosa, JP, Lima JC, Baptista PV.  2011.  Experimental photophysical characterization of fluorophores in the vicinity of gold nanoparticles. Nanotechnology. 22, Number 41 Abstract
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Rosa, {JP }, Lima {JC }, Baptista {PV }.  2011.  Experimental photophysical characterization of fluorophores in the vicinity of gold nanoparticles. Nanotechnology. 22, Number 41: IOP Publishing Abstract

We propose an experimental-based tool for dealing with fluorescence modulation close to nanoparticles for application in studies of fluorophores in the vicinity of gold nanoparticles (AuNPs), typically addressed via theoretical models. We performed a photophysical characterization of fluorophores in the vicinity of AuNPs, showing that correct Phi(F) determination suffers from a local pH effect, and address the observed radiative enhancement. Our approach is based on the experimental assurance that the reference fluorophores are in the same optical conditions as those of the AuNP-fluorophore conjugates. We demonstrate the relevance for introducing corrections for the inner filter effect and the reabsorption of the emitted light caused by AuNPs. The proposed approach could circumvent the need for theoretical based corrections and allow for more accurate determination of fluorescence emission in the vicinity of gold nanoparticles.

Ortigueira, MD.  2011.  Fractional Calculus for Scientists and Engineers. Fractional Calculus for Scientists and Engineers. 84: Springer-Verlag AbstractWebsite
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Ortigueira, MD.  2011.  The Fractional Quantum Derivative and the Fractional Linear Scale Invariant Systems. Fractional Calculus for Scientists and Engineers. 84:123–144.: Springer-Verlag Abstract

The normal way of introducing the notion of derivative is by means of the limit of an incremental ratio that can assume three forms, depending the used translations as we saw in Chaps. 1 and 4. On the other hand, in those derivatives the limit operation is done over a set of points uniformly spaced: a linear scale was used. Here we present an alternative derivative, that is valid only for t {\ensuremath{>}} 0 or t {\ensuremath{<}} 0 and uses an exponential scale

Freitas, F, Alves VD, Torres CAV, Cruz M, Sousa I, Melo MJ, Ramos AM, Reis MAM.  2011.  Fucose-containing exopolysaccharide produced by the newly isolated Enterobacter strain A47 DSM 23139. Carbohydrate Polymers. 83:159-165., Number 1 AbstractWebsite
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Ortigueira, MD, Trujillo JJ.  2011.  Generalized Gru?nwald?Letnikov Fractional Derivative and Its Laplace and Fourier Transforms Journal of Computational and Nonlinear Dynamics. 6:034501., Number 3 AbstractWebsite

The generalized Grünwald?Letnikov fractional derivative is analyzed in this paper. Its Laplace and Fourier transforms are computed, and some current results are criticized. It is shown that only the forward derivative of a sinusoid exists. This result is used to define the frequency response of a fractional linear system.

Neves, P, Amarante TR, Gomes AC, Coelho AC, Gago S, Pillinger M, Goncalves IS, Silva CM, Valente AA.  2011.  Heterogeneous oxidation catalysts formed in situ from molybdenum tetracarbonyl complexes and tert-butyl hydroperoxide. Applied Catalysis a-General. 395:71-77., Number 1-2 AbstractWebsite
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Ferraz, R, Branco LC, Prudencio C, Noronha JP, Petrovski Z.  2011.  Ionic Liquids as Active Pharmaceutical Ingredients. Chemmedchem. 6:975-985., Number 6 AbstractWebsite
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Machado, A, Redol P, Branco L, Vilarigues M.  2011.  Ionic liquids for medieval stained glass cleaning: a new frontier. ICOM-CC Lisbon. :1-9. Abstract
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Duarte, FJS, Bakalova SM, Cabrita EJ, Santos GA.  2011.  Lewis Acid Catalyzed Reactions of Chiral Imidazolidinones and Oxazolidinones: Insights on the Role of the Catalyst. Journal of Organic Chemistry. 76:6997-7004. Abstract

The mechanism proposed by Evans to justify the selectivity obtained in Lewis acid catalyzed Diels-Alder reactions of cyclopentadiene with acyloxazolidinones has been generalized and used in the rationalization of selectivities obtained in many other systems. However, we recently proposed an alternative mechanism, on the basis of open-chain mono- and bicomplexes, that avoids the need for chelates and explains the selectivity obtained by Evans. In this manuscript we apply our proposal to the catalyzed conjugated addition of amines to acylimidazolidinones, reported by Cardillo, and we clearly show that aluminum chelates are not involved in the reaction, as they induce no selectivity, while Cardillo observed high experimental selectivities. Our data equally show that bicomplexes with carbonyl parallel orientation, proposed by Cardillo to justify the experimental selectivity with nonchelating Lewis acids, indeed induce the opposite selectivity and have also to be dismissed. On the other hand, our mechanistic proposal allows for the full rationalization of the data obtained by Cardillo with aluminum, boron, or zinc Lewis acids and supports our previous proposal on DA cycloadditions of dienes to Evans chiral auxiliary derivatives.

Antunes, R, Coito F, Duarte-Ramos H.  2011.  A Linear Approach towards Modeling Human Behavior. Technological Innovation for Sustainability. :305–314.: Springer Abstract

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Lourenço, LM, Seco JC, Martins F.  2011.  Linguagem Intermédia Tipificada para Máquina de Pilha Concorrente com Objectos. Simpósio de Informática (INForum). Abstract
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Timoteo, CG, Pereira AS, Martins CE, Naik SG, Duarte AG, Moura JJG, Tavares P, Huynh BH, Moura I.  2011.  Low-Spin Heme b(3) in the Catalytic Center of Nitric Oxide Reductase from Pseudomonas nautica. Biochemistry. {50}:{4251-4262}., Number {20} Abstract

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.

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