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2012
Marques, JP, Indelicato P, Parente F.  2012.  Relativistic multiconfiguration calculations of the 2s22p 2P3/2 level lifetime along the boron isoelectronic sequence, Dec 27. The European Physical Journal D. 66:324. AbstractWebsite
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Santos, JP, Costa AM, Martins MC, Parente F, Indelicato P.  2012.  Modeling praseodymium K X-ray lines in an electron beam ion trap, Aug 16. The European Physical Journal D. 66:202., Number 8 AbstractWebsite

We study the most important processes for the creation of excited states in He-like through C- like praseodymium ions from the ions ground configurations, leading to the emission of K X-ray lines. Theoretical values for inner-shell excitation and ionization cross sections, transition probabilities and energies for the deexcitation processes, are calculated in the framework of the multi-configuration Dirac- Fock method, including QED corrections. Using these calculated values, a theoretical Kα X-ray spectrum is obtained, which is compared to recent experimental data obtained in the Livermore Super-EBIT electron beam ion trap facility.

Pereira, MMA.  2012.  Chiral Ionic Liquids from Carbohydrates: Synthesis and Properties, AUG. MINI-REVIEWS IN ORGANIC CHEMISTRY. 9:243-260., Number 3 Abstract
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Guerra, M, Parente F, Indelicato P, Santos JP.  2012.  Modified binary encounter Bethe model for electron-impact ionization, Apr 01. International Journal of Mass Spectrometry. 313:1.: Elsevier B.V. AbstractWebsite

Theoretical expressions for ionization cross sections by electron impact based on the binary encounter Bethe (BEB) model, valid from ionization threshold up to relativistic energies, are proposed.The new modified BEB (MBEB) and its relativistic counterpart (MRBEB) expressions are simpler than the BEB (nonrelativistic and relativistic) expressions because they require only one atomic parameter, namely the binding energy of the electrons to be ionized, and use only one scaling term for the ionization of all sub-shells.The new models are used to calculate the K-, L- and M-shell ionization cross sections by electron impact for several atoms with Z from 6 to 83. Comparisons with all, to the best of our knowledge, available experimental data show that this model is as good or better than other models, with less complexity.

Machado, D, dos Couto {IMSL}, Perdigão J, Rodrigues L, Portugal I, Baptista P, Veigas B, Amaral L, Bettencourt {MV}.  2012.  Contribution of Efflux to the Emergence of Isoniazid and Multidrug Resistance in Mycobacterium tuberculosis., apr. PLoS ONE. 7, Number 4: PLOS - Public Library of Science Abstract
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Martins, SMA, Branco PCS, Pereira AMDRL.  2012.  An Efficient Methodology for the Synthesis of 3-Styryl Coumarins, APR. JOURNAL OF THE BRAZILIAN CHEMICAL SOCIETY. 23:688-693., Number 4 Abstract
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Amado, M, Poggi F.  2012.  Sustentabilidade em edíficios de habitação: um novo sistema de habitação, 26 April. CCRSEEL. , Lisbon: Gabinete de Planeamento Físico e Gestão Ambiental da Faculdade de Ciências e Tecnologia da UNL
Rosado, LS, Santos TG, Ramos PM, Vilaça P, Piedade M.  2012.  A differential planar eddy currents probe: Fundamentals, modeling and experimental evaluation, 2012. NDT and E International. 51:85-93. AbstractWebsite
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Leydet, Y, Gavara R, Petrov V, Diniz AM, Parola AJ, Lima JC, Pina F.  2012.  The effect of self-aggregation on the determination of the kinetic and thermodynamic constants of the network of chemical reactions in 3-glucoside anthocyanins, 2012. Phytochemistry. 83:125-135. AbstractWebsite

The six most common 3-glucoside anthocyanins, pelargonidin-3-glucoside, peonidin-3-glucoside, delphinidin-3-glucoside, malvidin-3-glucoside, cyanidin-3-glucoside and petunidin-3-glucoside were studied in great detail by NMR, UV-vis absorption and stopped flow. For each anthocyanin, the thermodynamic and kinetic constants of the network of chemical reactions were calculated at different anthocyanin concentration, from 6 x 10(-6) M up to 8 x 10(-4) M; an increasing of the flavylium cation acidity constant to give quinoidal base and a decreasing of the flavylium cation hydration constant to give hemiketal were observed by increasing the anthocyanin concentration. These effects are attributed to the self-aggregation of the flavylium cation and quinoidal base, which is stronger in the last case. The UV-vis and H-1 NMR spectral variations resulting from the increasing of the anthocyanin concentration were discussed in terms of two aggregation models; monomer-dimer and isodesmic, the last one considering the formation of higher order aggregates possessing the same aggregation constant of the dimer. The self-aggregation constant of flavylium cation at pH = 1.0, calculated by both models increases by increasing the number of methoxy (-OCH3) or hydroxy (-OH) substituents following the order: myrtillin (2 -OH), oenin (2 -OCH3), 3-OGI-petunidin (1 -OH, 1 -OCH3), kuromanin (1 -OH), 3-OGI-peonidin (1 -OCH3) and callistephin (none). Evidence for flavylium aggregates possessing a shape between J and H was achieved, as well as for the formation of higher order aggregates. (C) 2012 Elsevier Ltd. All rights reserved.

Rondao, R, de Melo JS, Melo MJ, Parola AJ.  2012.  Excited-State Isomerization of Leuco Indigo, 2012. Journal of Physical Chemistry A. 116:2826-2832. AbstractWebsite

The photoreaction of indigo and two other derivatives in its reduced (leuco) form was investigated by absorption and fluorescence (steady-state and time-resolved) techniques. The fluorescence quantum yield (phi(F)) dependence with the UV irradiation time was found to increase up to a value of phi(F) approximate to 0.2-0.3 (after 16 min) for indigo and phi(F) = 0.2 (at similar to 150 min) for its derivative 4,4'-dibutoxy-7,7'-dimethoxy-5,5'-dinitroindigo (DBMNI). With a model compound, where rotation around the central C-C bond is blocked, the phi(F) value was found constant with the UV irradiation time. Time-resolved fluorescence revealed that initially the decays are fitted with a biexponential law (with 0.12 and 2.17 ns), ending with an almost monoexponential decay (similar to 2.17 ns). Quantum yields for the isomerization photoreaction (phi(R)) were also obtained for indigo and DBMNI with values of 0.9 and 0.007, respectively. The results are rationalized in terms of a photoisomerization (conversion) reaction occurring in the first excited singlet state of trans to cis forms of leuco indigo.

Trindade, AC, Canejo JP, Patrício P, Brogueira P, Teixeira PI, Godinho MH.  2012.  Hierarchical wrinkling on elastomeric Janus spheres, 2012. Journal of Materials Chemistry. 22(41):22044-22049.: The Royal Society of Chemistry AbstractWebsite

Hierarchical wrinkling on elastomeric Janus spheres is permanently imprinted by swelling, for different lengths of time, followed by drying the particles in an appropriate solvent. First-order buckling with a spatial periodicity (λ11) of the order of a few microns and hierarchical structures comprising of 2nd order buckling with a spatial periodicity (λ12) of the order of hundreds of nanometers have been obtained. The 2nd order buckling features result from a Grinfeld surface instability due to the diffusion of the solvent and the presence of sol molecules.

Petrov, V, Parola AJ, Pina F.  2012.  Isomerization between 2-(2,4-Dihydroxystyryl)-1-benzopyrylium and 7-Hydroxy-2-(4-hydroxystyryl)-1-benzopyrylium, 2012. Journal of Physical Chemistry A. 116:8107-8118. AbstractWebsite

2-Phenyl-1-benzopyrylium (flavylium) and 2-styryl-1-benzopyrylium (styrylflavylium) cations establish in aqueous solution a series of equilibria defining chemical reaction networks responsive to several stimuli (pH, light, redox potential). Control over the mole fraction distribution of species by applying the appropiate stimuli defines a horizontal approach to supramolecular chemistry, in agreement with the customary bottom-up approach toward complex systems. In this work, we designed an asymmetric styrylchalcone able to cyclize in two different ways, producing two isomeric styrylflavylium cations whose chemical reaction networks are thus interconnected. The chemical reaction networks of 2-(2,4-dihydroxystyryl)-1-benzopyrylium (AH(+)) and 7-hydroxy-2-(4-hydroxystyryl)-1-benzopyrylium (AH(iso)(+)) comprise the usual species observed in flavylium-derived networks, in this case, the styryl derivatives of quinoidal bases, hemiketals, and chalcones. The thermodynamics and kinetics of the crossed networks were characterized by the use of UV-vis absorption and NMR spectroscopy as well as time-resolved pH jumps followed by stopped-flow. The two styrylflavylium cations are connected (isomerize) through two alternative intermediates, the asymmetric trans-styrylchalcone (Ct) and a spiropyran-type intermediate (SP). At pH = 1, AH(+) slowly evolves (k(obs) approximate to 10(-5) s(-1)) to a mixture containing 62% AH(iso)(+),s0 through the Ct intermediate, while at pH = 5, the SP intermediate is involved. The observed rate constants for the conversion of the styrylflavylim cations into equilibrium mixtures containing essentially Ct follow a pH-dependent bell-shaped curve in both networks. While at pH = 1 in the dark, AH(+) evolves to an equilibrium mixture containing predominantly AH(iso)(+) irradiation at lambda > 435 nm induces the opposite conversion.

Matos Filipe, L, Santos TG, Valtchev S, Pamies Teixeira J, Miranda RM.  2012.  New method employing the electrical impedance for monitoring mechanical damage evolution in glass-reinforced: Applications to riveted joints, 2012. Materials and Design. 42:25-31. AbstractWebsite
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Gago, S, Petrov V, Parola AJ, Pina F.  2012.  Synthesis, characterization and photochromism of 3 '-butoxyflavylium derivatives, 2012. Journal of Photochemistry and Photobiology a-Chemistry. 244:54-64. AbstractWebsite

The compounds 3'-butoxy-7-methoxyflavylium and 3'-butoxy-7-hydroxyflavylium were synthesized and the respective equilibrium and rate constants determined by two complementary techniques, pH jumps and flash photolysis. An experimental strategy based on these two techniques allowed calculation of all the equilibrium and rate constants of the system carried out for the first time in flavylium compounds lacking of the high cis-trans isomerization barrier. Irradiation of the trans-chalcone gives rise to the formation of the cis-chalcone still during the lifetime of the flash, which disappears through two parallel reactions: (i) one leading to the recovery of the trans-chalcone and the other, (ii) forming flavylium cation via hemiketal. This last reaction is globally dependent on pH and at less acidic pH the system reverts back to the trans-chalcone. The highest yield of colour production upon the flash takes place in the pH range 2-3.5. (c) 2012 Elsevier B.V. All rights reserved.

Gago, S, Petrov V, Diniz AM, Parola AJ, Cunha-Silva L, Pina F.  2012.  Unidirectional Switching between Two Flavylium Reaction Networks by the Action of Alternate Stimuli of Acid and Base, 2012. Journal of Physical Chemistry A. 116:372-380. AbstractWebsite

The introduction of an ester group in the flavylium core allowed the reversible conversion between two different flavylium compounds each one exhibiting its own reaction network. An unidirectional switching cycle between 7-diethylamino-2-(4-(methoxy-carbonyl)phenyl)-1-benzopyrylium and 2-(4-carboxyphenyl)-7-diethylamino-1-benzopyrylium was achieved by means of alternate acid and base stimuli. Addition of base to a methanolic solution of the ester derivative gives rise to the trans-chalcone of the parent carboxylic acid, which upon acidification of the solution forms the respective flavylium cation. This species esterifies under very acidic conditions to restore the original methyl ester derivative. The chemical reaction networks of both compounds were fully characterized from their thermodynamic and kinetic aspects, by a series of pH jumps followed by UV-vis absorption and emission spectroscopy, stopped flow and H-down arrow NMR. The crystal structure of the trans-chalcone of the ester derivative was unveiled showing a supramolecular structure involving hydrogen bonding.

Santana, SDF, Pina AS, Roque ACA.  2012.   Immobilization of enterokinase on magnetic supports for the cleavage of fusion proteins. Journal of Biotechnology. 161:378–382. AbstractWebsite

Magnetic nanobiocatalysts for tag cleavage on fusion proteins have been prepared by immobilizing
enterokinase (EK) onto iron oxide magnetic nanoparticles coated with biopolymers. Two different
chemistries have been explored for the covalent coupling of EK, namely carbodiimide (EDC coupling)
and maleimide activation (Sulfo coupling). Upon immobilization, EK initial activity lowered but EDC coupling lead to higher activity retention. Regarding the stability ofthe nanobiocatalysts,thesewere recycled
up to ten times with the greater activity losses observed in the first two cycles. The immobilized EK also
proved to cleave a control fusion protein and to greatly simplify the separation of the enzyme from the
reaction mixture.

Fontes, CMGA, Correia ISá, Romão MJ, Sá-Nogueira I, Prates JAM, Ferreira LMA.  2012.  Editorial of the 9th Carbohydrate Bioengineering Meeting (CBM9).. Biocatalysis and Biotransformation. 30:273-273., Number 3
Contreras, Javier, Idzikowski, Marek, Pereira, Filonovich, Sergej Alexandrovich, Fortunato, Martins, Ferreira I.  2012.  Amorphous Silicon Position Sensitive Detector Array for Fast 3-D Object Profiling. IEEE SENSORS JOURNAL. 12(4):812-820.
Cardoso, MM, Peça IN, Roque ACA.  2012.  Antibody-Conjugated Nanoparticles for Therapeutic Applications. Current Medicinal Chemistry. 19(19):3103-3127. AbstractWebsite

A great challenge to clinical development is the delivery of chemotherapeutic agents, known to cause severe toxic effects, directly to diseased sites which increase the therapeutic index whilst minimizing off-target side effects. Antibody-conjugated nanoparticles offer great opportunities to overcome these limitations in therapeutics. They combine the advantages given by the nanoparticles with the ability to bind to their target with high affinity and improve cell penetration given by the antibodies. This specialized vehicle, that can encapsulate several chemotherapeutic agents, can be engineered to possess the desirable properties, allowing overcoming the successive physiological conditions and to cross biological barriers and reach a specific tissue or cell. Moreover, antibody-conjugated nanoparticles have shown the ability to be internalized through receptor-mediated endocytosis and accumulate in cells without being recognized by the P-glycoprotein, one of the main mediators of multi-drug resistance, resulting in an increase in the intracellular concentration of drugs. Also, progress in antibody engineering has allowed the manipulation of the basic antibody structure for raising and tailoring specificity and functionality. This review explores recent developments on active drug targeting by nanoparticles functionalized with monoclonal antibodies (polymeric micelles, liposomes and polymeric nanoparticles) and summarizes the opportunities of these targeting strategies in the therapy of serious diseases (cancer, inflammatory diseases, infectious diseases, and thrombosis).

Dell'Acqua, S, Pauleta SR, Moura JJ, Moura I.  2012.  Biochemical characterization of the purple form of Marinobacter hydrocarbonoclasticus nitrous oxide reductase. Philos Trans R Soc Lond B Biol Sci. 367(1593):1204-1212.
Silva, TF, Martins LM, da Silva MFG, Fernandes AR, Silva A, Borralho PM, Santos S, Rodrigues CM, Pombeiro AJ.  2012.  Cobalt complexes bearing scorpionate ligands: synthesis, characterization, cytotoxicity and DNA cleavage. Dalton Trans. 41(41):12888-97.12silvadt.pdf
Gomes, I, Feio MJ, Santos NC, Eaton P, Serro AP, Saramago B, Pereira E, Franco R.  2012.  CONTROLLED ADSORPTION OF CYTOCHROME C TO NANOSTRUCTURED GOLD SURFACES. J. Nanopart. Res. . 14:1321.
Dias, RJ, Vale TM, Lourenço JM.  2012.  Efficient Support for In-Place Metadata in Transactional Memory. Euro-Par 2012 Parallel Processing. 7484(Kaklamanis, Christos, Papatheodorou, Theodore, Spirakis, PaulG., Eds.).:589–600., Rhodes, Greece: Springer Berlin Heidelberg Abstract2012-europar.pdf

Implementations of Software Transactional Memory (STM) algorithms associate metadata with the memory locations accessed during a transaction’s lifetime. This metadata may be stored either in-place, by wrapping every memory cell in a container that includes the memory cell itself and the corresponding metadata; or out-place (also called external), by resorting to a mapping function that associates the memory cell address with an external table entry containing the corresponding metadata. The implementation techniques for these two approaches are very different and each STM framework is usually biased towards one of them, only allowing the efficient implementation of STM algorithms following that approach, hence inhibiting the fair comparison with STM algorithms falling into the other. In this paper we introduce a technique to implement in-place metadata that does not wrap memory cells, thus overcoming the bias by allowing STM algorithms to directly access the transactional metadata. The proposed technique is available as an extension to the DeuceSTM framework, and enables the efficient implementation of a wide range of STM algorithms and their fair (unbiased) comparison in a common STM infrastructure. We illustrate the benefits of our approach by analyzing its impact in two popular TM algorithms with two different transactional workloads, TL2 and multi-versioning, with bias to out-place and in-place respectively.