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2016
Cavero, AM, Melo MJ, Miranda MA, Castro R, Casanova C.  2016.  Beatus manuscripts under the microscope: the Alcobaca Beatus and the Iberian Cistercian tradition revisited, 2016. Journal of Medieval Iberian Studies. 8(2):217-251. AbstractWebsite
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Cordeiro, M, Giestas L, Lima JC, Baptista PMV.  2016.  BioCode gold-nanobeacon for the detection of fusion transcripts causing chronic myeloid leukemia, 2016. Journal of Nanobiotechnology. 14 AbstractWebsite
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Tron, A, Gago S, McClenaghan ND, Parola AJ, Pina F.  2016.  A blue 4 ',7-diaminoflavylium cation showing an extended pH range stability, 2016. Physical Chemistry Chemical Physics. 18(13):8920-8925. AbstractWebsite
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Gomis-Berenguer, A, Iniesta J, Moro A, Maurino V, Lima JC, Ania CO.  2016.  Boosting visible light conversion in the confined pore space of nanoporous carbons, 2016. Carbon. 96:98-104. AbstractWebsite
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Gomis-Berenguer, A, Iniesta J, Moro A, Maurino V, Lima JC, Ania CO.  2016.  Boosting visible light conversion in the confined pore space of nanoporous carbons (vol 96, pg 98, 2015), 2016. Carbon. 98:187-187. AbstractWebsite
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Moretto, S, Robinson D, Schippl J, Moniz AB.  2016.  Beyond Visions: Survey to the High-speed Train Industry. 6th Transport Research Arena. :1839-1846. Abstract

In Europe, the technology development of high-speed trains is increasingly exposed to societal needs, driven by ICT advancements, external to traditional design. Together with the liberalisation of the rail markets and increase pressures from other transport modes leads to an unprecedented situation where planers, operators and suppliers of high-speed have to take decision in this complex and competitive environment.
In such broadening of elements influencing design and, thus, product development process, from the survey here to be presented, it was not observed technology options assessment or strategic agenda setting from visions shifting in the same way.
For the high-speed train industry this new trend requires going beyond the visions of the past 15 to 20 years’ practices of “sector endogenous” and structurally closed strategic methods approaches to a broader interaction with the widening of societal actors now capable of being active contributors to innovation from digitalization.
This way to understand the European industry readiness for undertaking such supra systemic challenge, this paper presents the results from a survey conducted by the authors to 74 representatives of the high-speed train innovation chain regarding to which extent societal embedding is considered in the drafting of their visions and technology development projects.
This work becomes even more pertinent if considered that the debate is now open in the railway industry (not exclusive to high-speed trains) as they are launching the joint initiative SHIFT2RAIL, revise ERRAC (the European Rail Research Advisory Council) mandate and enter in a new research cycle with the European research framework Horizon 2020.

Moretto, S, Robinson D, Schippl J, Moniz AB.  2016.  Beyond Visions: Survey to the High-speed Train Industry. Transportation Research Procedia. 14:1839-1846. AbstractWebsite

In Europe, the technology development of high-speed trains is increasingly exposed to societal needs, driven by ICT advancements, external to traditional design. Together with the liberalisation of the rail markets and increase pressures from other transport modes leads to an unprecedented situation where planers, operators and suppliers of high-speed have to take decision in this complex and competitive environment.
In such broadening of elements influencing design and, thus, product development process, from the survey here to be presented, it was not observed technology options assessment or strategic agenda setting from visions shifting in the same way.
For the high-speed train industry this new trend requires going beyond the visions of the past 15 to 20 years’ practices of “sector endogenous” and structurally closed strategic methods approaches to a broader interaction with the widening of societal actors now capable of being active contributors to innovation from digitalization.
This way to understand the European industry readiness for undertaking such supra systemic challenge, this paper presents the results from a survey conducted by the authors to 74 representatives of the high-speed train innovation chain regarding to which extent societal embedding is considered in the drafting of their visions and technology development projects.
This work becomes even more pertinent if considered that the debate is now open in the railway industry (not exclusive to high-speed trains) as they are launching the joint initiative SHIFT2RAIL, revise ERRAC (the European Rail Research Advisory Council) mandate and enter in a new research cycle with the European research framework Horizon 2020.

Batista, MKS, Mestre AS, Matos I, Fonseca IM, Carvalho AP.  2016.  Biodiesel production waste as promising biomass precursor of reusable activated carbons for caffeine removal. RSC Adv.. 6:45419-45427.: The Royal Society of Chemistry AbstractWebsite

Biodiesel production generates low particle size rapeseed waste (recovered from warehouse air filtration systems) that was herein explored as promising biomass precursor of chemically activated carbons. The influence of several experimental parameters on the porosity development was investigated. No benefit was observed when solution impregnation was made nor a significant dependence of the biomass : K2CO3 ratio was observed and{,} as expected{,} high porosity development was obtained only for treatments at 700 [degree]C. Microporous materials with apparent surface area around 1000 m2 g-1 were obtained comparing favorably with literature data regarding activated carbons from rapeseed processing by-products. A selected lab-made sample and two commercial carbons were tested as adsorbents of caffeine from aqueous solution. Although commercial materials present a quicker adsorption rate{,} regarding adsorption capacity the lab-made sample reaches the same value attained by a benchmark material. The regeneration tests made over the rapeseed derived carbon through heat treatments at 600 [degree]C for 1 hour under N2 flow proved that at least two exhaustion-regeneration cycles can be made since the material retains a caffeine adsorption capacity similar to that of the fresh carbon. Therefore{,} a waste management problem of biodiesel industry - rapeseed residue - can be transformed in a valuable material with promising properties for environmental remediation processes.

do Fraga, AC, Quitete CPB, Ximenes VL, Sousa-Aguiar EF, Fonseca IM, Rego AMB.  2016.  Biomass derived solid acids as effective hydrolysis catalysts. Journal of Molecular Catalysis A: Chemical. 422:248-257. AbstractWebsite

The conversion of cellulose into products with higher added value often includes a depolymerization step to obtain glucose, its fundamental unity. The depolymerization reaction is carried out via hydrolysis of the β-1,4-glycosidic bond. The search for a solid acid catalyst capable of breaking these bonds is gaining increasing prominence in the literature. In this regard, sulfonated carbons have shown promising results. This work evaluated the use of a residue from the extraction of palm oil as raw material for the production of sulfonated carbons. The raw material was carbonized and sulfonated. The obtained solid acids were tested in the hydrolysis of cellobiose, a dimer of glucose often used as a model compound for cellulose. The hydrolysis reaction is the first step in converting renewable carbon sources into chemical products and biofuels. Some aspects were investigated, as the effect of carbonization temperature on the concentration of sulfonic groups, the results showing that the content thereof reached a maximum value at 300°C. Regarding the hydrolysis of cellobiose, it has been identified that there is a relationship between the concentration of sulfonic acid groups and the activity of these catalysts. However, there is a drop in the turnover number as the amount of sulfonic acid sites increases. This was related to a preferred position sulfonation mechanism. Furthermore, sulfonated carbons showed higher activity than the commercial acid resins, indicating that this material may be a good option for the generation of solid acid catalysts.

2015
Ventura, MG, Paninho AI, Nunes AVM, Fonseca IM, Branco LC.  2015.  Biocompatible locust bean gum mesoporous matrices prepared by ionic liquids and a scCO(2) sustainable system, 2015. Rsc Advances. 5(130):107700-107706. AbstractWebsite
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Coutinho, ML, Miller AZ, Macedo MF.  2015.  Biological colonization and biodeterioration of architectural ceramic materials: An overview, 2015. Journal of Cultural Heritage. 16(5):759-777. AbstractWebsite
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Dantas, JM, Silva e Sousa M, Salgueiro CA, Bruix M.  2015.  Backbone, side chain and heme resonance assignments of cytochrome OmcF from Geobacter sulfurreducens. Biomolecular NMR Assignments. 9(2):365-368. AbstractWebsite

Gene knockout studies on Geobacter sulfurreducens (Gs) cells showed that the outer membrane cytochrome OmcF is involved in respiratory pathways leading to the extracellular reduction of Fe(III) citrate and U(VI) oxide. In addition, microarray analysis of OmcF-deficient mutant versus the wild-type strain revealed that many of the genes with decreased transcript level were those whose expression is upregulated in cells grown with a graphite electrode as electron acceptor. This suggests that OmcF also regulates the electron transfer to electrode surfaces and the concomitant electrical current production by Gs in microbial fuel cells. Extracellular electron transfer processes (EET) constitute nowadays the foundations to develop biotechnological applications in biofuel production, bioremediation and bioenergy. Therefore, the structural characterization of OmcF is a fundamental step to understand the mechanisms underlying EET. Here, we report the complete assignment of the heme proton signals together with (1)H, (13)C and (15)N backbone and side chain assignments of the OmcF, excluding the hydrophobic residues of the N-terminal predicted lipid anchor.

Dantas, JM, Salgueiro CA, Bruix M.  2015.  Backbone, side chain and heme resonance assignments of the triheme cytochrome PpcD from Geobacter sulfurreducens. Biomol NMR Assign. 9(1):211-214. AbstractWebsite

Gene knock-out studies on Geobacter sulfurreducens (Gs) cells showed that the periplasmic triheme cytochrome PpcD is involved in respiratory pathways leading to the extracellular reduction of Fe(III) and U(VI) oxides. More recently, it was also shown that the gene encoding for PpcD has higher transcript abundance when Gs cells utilize graphite electrodes as sole electron donors to reduce fumarate. This sets PpcD as the first multiheme cytochrome to be involved in Gs respiratory pathways that bridge the electron transfer between the cytoplasm and cell exterior in both directions. Nowadays, extracellular electron transfer (EET) processes are explored for several biotechnological applications, which include bioremediation, bioenergy and biofuel production. Therefore, the structural characterization of PpcD is a fundamental step to understand the mechanisms underlying EET. However, compared to non-heme proteins, the presence of numerous proton-containing groups in the redox centers presents additional challenges for protein signal assignment and structure calculation. Here, we report the complete assignment of the heme proton signals together with 1H, 13C and 15N backbone and side chain assignments of the reduced form of PpcD.

Fernandes, CSM, Gonçalves B, Sousa M, Martins DL, Barroso T, Pina AS, Peixoto C, Aguiar-Ricardo A, Roque ACA.  2015.  Biobased Monoliths for Adenovirus Purification. ACS Applied Materials & Interfaces. 7(12):6605-6612., Number 12 AbstractWebsite

Adenoviruses are important platforms for vaccine development and vectors for gene therapy, increasing the demand for high titers of purified viral preparations. Monoliths are macroporous supports regarded as ideal for the purification of macromolecular complexes, including viral particles. Although common monoliths are based on synthetic polymers as methacrylates, we explored the potential of biopolymers processed by clean technologies to produce monoliths for adenovirus purification. Such an approach enables the development of disposable and biodegradable matrices for bioprocessing. A total of 20 monoliths were produced from different biopolymers (chitosan, agarose, and dextran), employing two distinct temperatures during the freezing process (−20 °C and −80 °C). The morphological and physical properties of the structures were thoroughly characterized. The monoliths presenting higher robustness and permeability rates were further analyzed for the nonspecific binding of Adenovirus serotype 5 (Ad5) preparations. The matrices presenting lower nonspecific Ad5 binding were further functionalized with quaternary amine anion-exchange ligand glycidyltrimethylammonium chloride hydrochloride by two distinct methods, and their performance toward Ad5 purification was assessed. The monolith composed of chitosan and poly(vinyl) alcohol (50:50) prepared at −80 °C allowed 100% recovery of Ad5 particles bound to the support. This is the first report of the successful purification of adenovirus using monoliths obtained from biopolymers processed by clean technologies.

Coutinho, MAGLD.  2015.  Biological colonization on majolica glazed tiles: biodeterioration, bioreceptivity and mitigation strategies. Departamento de Conservação e Restauro, FCT-NOVA. , Caparica
Mendes, MJ, Morawiec S, Mateus T, Lyubchyk A, Águas H, Ferreira I, Fortunato E, Martins R, Priolo F, Crupi I.  2015.  Broadband light trapping in thin film solar cells with self-organized plasmonic nano-colloids. Nanotechnology. 26(13):135202. AbstractWebsite

The intense light scattered from metal nanoparticles sustaining surface plasmons makes them attractive for light trapping in photovoltaic applications. However, a strong resonant response from nanoparticle ensembles can only be obtained if the particles have monodisperse physical properties. Presently, the chemical synthesis of colloidal nanoparticles is the method that produces the highest monodispersion in geometry and material quality, with the added benefits of being low-temperature, low-cost, easily scalable and of allowing control of the surface coverage of the deposited particles. In this paper, novel plasmonic back-reflector structures were developed using spherical gold colloids with appropriate dimensions for pronounced far-field scattering. The plasmonic back reflectors are incorporated in the rear contact of thin film n-i-p nanocrystalline silicon solar cells to boost their photocurrent generation via optical path length enhancement inside the silicon layer. The quantum efficiency spectra of the devices revealed a remarkable broadband enhancement, resulting from both light scattering from the metal nanoparticles and improved light incoupling caused by the hemispherical corrugations at the cells' front surface formed from the deposition of material over the spherically shaped colloids.

2014
Silva, JA, Lourenço JM, Paulino H.  2014.  Boosting Locality in Multi-version Partial Data Replication, 2014. : Universidade Nova de Lisboa2014-silva.pdf
Atilano, ML, Pereira PM, Vaz F, Catalão MJ, Reed P, Grilo IR, Sobral RG, Ligoxygakis P, Pinho MG, Filipe SR.  2014.  Bacterial autolysins trim cell surface peptidoglycan to prevent detection by the Drosophila innate immune system. eLife. 3:e02277.
Otelo-Cardoso, AR, Schwuchow V, Rodrigues D, Cabrita EJ, Leimkühler S, Romão MJ, Santos-Silva T.  2014.  Biochemical, Stabilization and Crystallization Studies on a Molecular Chaperone (PaoD) Involved in the Maturation of Molybdoenzymes.. PLoS One. 9(1) Abstract

Molybdenum and tungsten enzymes require specific chaperones for folding and cofactor insertion. PaoD is the chaperone of the periplasmic aldehyde oxidoreductase PaoABC. It is the last gene in the paoABCD operon in Escherichia coli and its presence is crucial for obtaining mature enzyme. PaoD is an unstable, 35 kDa, protein. Our biochemical studies showed that it is a dimer in solution with a tendency to form large aggregates, especially after freezing/thawing cycles. In order to improve stability, PaoD was thawed in the presence of two ionic liquids [C4mim]Cl and [C2OHmim]PF6 and no protein precipitation was observed. This allowed protein concentration and crystallization using polyethylene glycol or ammonium sulfate as precipitating agents. Saturation transfer difference – nuclear magnetic resonance (STD-NMR) experiments have also been performed in order to investigate the effect of the ionic liquids in the stabilization process, showing a clear interaction between the acidic ring protons of the cation and, most likely, negatively charged residues at the protein surface. DLS assays also show a reduction of the overall size of the protein aggregates in presence of ionic liquids. Furthermore, cofactor binding studies on PaoD showed that the protein is able to discriminate between molybdenum and tungsten bound to the molybdenum cofactor, since only a Mo-MPT form of the cofactor remained bound to PaoD.

Dhadge, VL, Hussain A, Azevedo AM, Aires-Barros MR, Roque ACA.  2014.  Boronic acid-modified magnetic materials for antibody purification. J. R. Soc. Interface. 11(91):20130875. AbstractWebsite

Aminophenyl boronic acids can form reversible covalent ester interactions with cis-diol-containing molecules, serving as a selective tool for binding glycoproteins as antibody molecules that possess oligosaccharides in both the Fv and Fc regions. In this study, amino phenyl boronic acid (APBA) magnetic particles (MPs) were applied for the magnetic separation of antibody molecules. Iron oxide MPs were firstly coated with dextran to avoid non-specific binding and then with 3-glycidyloxypropyl trimethoxysilane to allow further covalent coupling of APBA (APBA_MP). When contacted with pure protein solutions of human IgG (hIgG) and bovine serum albumin (BSA), APBA_MP bound 170 ± 10 mg hIgG g−1 MP and eluted 160 ± 5 mg hIgG g−1 MP, while binding only 15 ± 5 mg BSA g−1 MP. The affinity constant for the interaction between hIgG and APBA_MP was estimated as 4.9 × 105 M−1 (Ka) with a theoretical maximum capacity of 492 mg hIgG adsorbed g−1 MP (Qmax), whereas control particles bound a negligible amount of hIgG and presented an estimated theoretical maximum capacity of 3.1 mg hIgG adsorbed g−1 MP (Qmax). APBA_MPs were also tested for antibody purification directly from CHO cell supernatants. The particles were able to bind 98% of IgG loaded and to recover 95% of pure IgG (purity greater than 98%) at extremely mild conditions.

Morawiec, S, Mendes MJ, Filonovich SA, Mateus T, Mirabella S, Águas H, Ferreira I, Simone F, Fortunato E, Martins R, Priolo F, Crupi I.  2014.  Broadband photocurrent enhancement in a-Si:H solar cells with plasmonic back reflectors. Opt. Express. 22(104):A1059-A1070. AbstractWebsite

Plasmonic light trapping in thin film silicon solar cells is a promising route to achieve high efficiency with reduced volumes of semiconductor material. In this paper, we study the enhancement in the opto-electronic performance of thin a-Si:H solar cells due to the light scattering effects of plasmonic back reflectors (PBRs), composed of self-assembled silver nanoparticles (NPs), incorporated on the cells’ rear contact. The optical properties of the PBRs are investigated according to the morphology of the NPs, which can be tuned by the fabrication parameters. By analyzing sets of solar cells built on distinct PBRs we show that the photocurrent enhancement achieved in the a-Si:H light trapping window (600 – 800 nm) stays in linear relation with the PBRs diffuse reflection. The best-performing PBRs allow a pronounced broadband photocurrent enhancement in the cells which is attributed not only to the plasmon-assisted light scattering from the NPs but also to the front surface texture originated from the conformal growth of the cell material over the particles. As a result, remarkably high values of Jsc and Voc are achieved in comparison to those previously reported in the literature for the same type of devices.

Otrelo-Cardoso, AR, Schwuchow V, Rodrigues D, Cabrita EJ, Leimkuehler S, Romao MJ, Santos-Silva T.  2014.  Biochemical, Stabilization and Crystallization Studies on a Molecular Chaperone (PaoD) Involved in the Maturation of Molybdoenzymes. Plos One. 9, Number 1 AbstractWebsite
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2013
Bernacka-Wójcik, I, Lopes {PA }, Vaz {AC}, Veigas {BMR}, Wojcik {PJ}, Simões P, Barata D, Fortunato {EMC}, Baptista {PMRV}, Águas {HMB}, de Martins {RFP}.  2013.  Bio-microfluidic platform for gold nanoprobe based DNA detection-application to Mycobacterium tuberculosis, oct. Biosensors & Bioelectronics. 48:87–93.: Elsevier Abstract

We have projected and fabricated a microfluidic platform for DNA sensing that makes use of an optical colorimetric detection method based on gold nanoparticles. The platform was fabricated using replica moulding technology in PDMS patterned by high-aspect-ratio SU-8 moulds. Biochips of various geometries were tested and evaluated in order to find out the most efficient architecture, and the rational for design, microfabrication and detection performance is presented. The best biochip configuration has been successfully applied to the DNA detection of Mycobacterium tuberculosis using only 3 mu l on DNA solution (i.e. 90 ng of target DNA), therefore a 20-fold reduction of reagents volume is obtained when compared with the actual state of the art.

Rondao, R, de Melo JSS, Pina J, Melo MJ, Vitorino T, Parola AJ.  2013.  Brazilwood Reds: The (Photo)Chemistry of Brazilin and Brazilein, 2013. Journal of Physical Chemistry A. 117:10650-10660. AbstractWebsite

The ground and excited state (in the singlet state, S-1) acid-base equilibria, together with the photophysical properties of the two main constituents of brazilwood, brazilin and brazilein, have been investigated in aqueous solutions in the pH range: -1 < pH < 10. Brazilin is the colorless reduced form of brazilein where three ground and three excited state species (BredHn, with n = 2-4 representing the protonated hydroxyl groups) are observed with two corresponding acidity constants: pK(a1) = 6.6 and pK(a2) = 9.4 (pK(a1)(*) = 4.7 and pK(a2)(*) = 9.9, obtained from the Forster cycle). In the case of brazilein, three ground species (pK(a1) = 6.5 and pK(a2) = 9.5) and four excited state species were identified (again from the Forster cycle: pK(a1)(*) = 3.9 and pK(a2)(*) = 9.8). The colorless species (brazilin) presents a high fluorescence quantum yield (phi(F) = 0.33) and competitive radiative channel (k(F) = 1.3 x 10(9) s(-1)) over radiationless processes (k(NR) = 2.6 x 10(9) s(-1)). In contrast to this behavior, brazilein displays a phi(F) value 2 orders of magnitude lower and a dominance of the radiationless decay pathways, which is suggested to be linked to an excited state proton transfer leading to a quinoidal-like structure. This is further supported by time-resolved data (obtained in a ps time domain). The overall data indicates that brazilin is more prone to degradation than brazilein, mainly due to the high efficiency of the racliationless decay channel (likely through internal conversion), which confers a stabilizing inherent characteristic to the latter. In the case of brazilein, the efficiency of the radiationless channel is linked to an excited state intramolecular proton transfer resulting from an excited state equilibrium involving neutral and zwitterionic tautomeric species of this compound. Furthermore, a theoretical study has been performed with the determination of the optimized ground-state and excited molecular geometries for the two compounds together with the prediction of the lowest vertical one-electron excitation energy and the relevant molecular orbital contours and charge densities changes using density functional theory calculations. These were found to corroborate differences in acidity in the ground and excited states.

Qu, X, Latino DA, Aires-de-Sousa J.  2013.  A big data approach to the ultra-fast prediction of DFT-calculated bond energies. J. Cheminform.. 5(1):34.Website