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2014
Santos, TG, Lopes N, MacHado M, Vilaça P, Miranda RM.  2014.  Surface reinforcement of AA5083-H111 by friction stir processing assisted by electrical current, 2014. Journal of Materials Processing Technology. 216:375-380.: Elsevier Ltd AbstractWebsite
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Gaspar, D, Pimentel AC, Mendes MJ, Mateus T, Falcão BP, Leitão JP, Soares J, Araújo A, Vicente A, Filonovich SA, Águas H, Martins R, Ferreira I.  2014.  Ag and Sn Nanoparticles to Enhance the Near-Infrared Absorbance of a-Si:H Thin Films. Plasmonics. 9(5):1015–1023. AbstractWebsite

Silver (Ag) and tin (Sn) nanoparticles (NPs) were deposited by thermal evaporation onto heated glass substrates with a good control of size, shape and surface coverage. This process has the advantage of allowing the fabrication of thin-film solar cells with incorporated NPs without vacuum break, since it does not require chemical processes or post-deposition annealing. The X-ray diffraction, TEM and SEM properties are correlated with optical measurements and amorphous silicon hydrogenated (a-Si:H) films deposited on top of both types of NPs show enhanced absorbance in the near-infrared. The results are interpreted with electromagnetic modelling performed with Mie theory. A broad emission in the near-infrared region is considerably increased after covering the Ag nanoparticles with an a-Si:H layer. Such effect may be of interest for possible down-conversion mechanisms in novel photovoltaic devices.

Veigas, B, Fernandes AR, Baptista PV.  2014.  AuNPs for identification of molecular signatures of resistance. Front Microbiol. 5:455.14veigasfm.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.
Silva, J, Rodrigues AS, Videira PA, Lasri J, Charmier AJ, Pombeiro AJL, Fernandes AR.  2014.  Characterization of the antiproliferative potential and biological targets of a trans ketoimine platinum complex. Inorg Chim Acta. 423:156-167.
Viciosa, MT, Alves NM, Oliveira T, Dionísio M, Mano JF.  2014.  Confinement Effects on the Dynamic Behavior of Poly(D,L-lactic acid) upon Incorporation in alpha-Cyclodextrin. the Journal of Physical Chemistry B. 118(24):6972–6981.Website
Dias, RJ, Vale TM, Lourenço JM.  2014.  Framework Support for the Efficient Implementation of Multi-Version Algorithms. Transactional Memory: Foundations, Algorithms, Tools, and Applications. (Rachid Guerraoui, Paolo Romano, Eds.).: Springer Abstractdias_vale_lourenco.pdf

Software Transactional Memory algorithms associate metadata with the memory locations accessed during a transaction’s lifetime. This metadata may be stored in an external table and accessed by way of a function that maps the address of each memory location with the table entry that keeps its metadata (this is the out-place or external scheme); or alternatively may be stored adjacent to the associated memory cell by wrapping them together (the in-place scheme). In transactional memory multi-version algorithms, several versions of the same memory location may exist. The efficient implementation of these algorithms requires a one-to-one correspondence between each memory location and its list of past versions, which is stored as metadata. In this chapter we address the matter of the efficient implementation of multi-version algorithms in Java by proposing and evaluating a novel in-place metadata scheme for the Deuce framework. This new scheme is based in Java Bytecode transformation techniques and its use requires no changes to the application code. Experimentation indicates that multi-versioning STM algorithms implemented using our new in-place scheme are in average 6× faster than when implemented with the out-place scheme.

de Almeida, MP, Pereira E, Baptista P, Gomes I, Figueiredo S, Soares L, Franco R.  2014.  Gold Nanoparticles as (bio)chemical Sensors. Comprehensive Analytical Chemistry; Gold Nanoparticles in Analytical Chemistry . (Valcárcel, M., López-Lorente, A.I., Eds.).:529–567., Amsterdam: Elsevier
Gouveia, JP, Bilo N, Gargiulo M, Giannakidis G, Gregório V, Duncan I, Nunes V, Robinson D, Seixas J, Valentim A.  2014.  InSMART - Integrative Smart City Planning - The case of Households in Évora. Urban Futures Squaring Circles: Proceedings, International Conference on Urban Futures Squaring Circles 2050,. , Calouste Gulbenkian Foundation: Institute of Social Sciences of the University of Lisbon and Calouste Gulbenkian Foundation Abstract

European policy has acknowledged the significance of local and regional communities for the
deployment of new low carbon technologies and their potential for sustainable energy production and use.
Several initiatives and programmes (e.g. Covenant of Mayors) have been set up to engage European cities in the
effort towards a low carbon future. At the same time, there is a critical need to improve comprehensive city
planning driven by an integrated approach and focused on cost benefit assessment towards sustainable energy
use. Hence, innovative tools and models to assess and perform in-depth analysis of the alternative measures
towards efficient energy use, will help pave the way to fully capture the potential of each city in the most
efficient (economically, socially and technically) way.
The InSMART concept brings together four European cities: Évora (Portugal), Cesena (Italy), Nottingham (UK)
and Trikala (Greece), and scientific organizations of these countries, to establish a methodology for enhancing
sustainable planning for city needs through an integrative and multidisciplinary planning approach, aiming to
developing detailed sustainable energy action plans. Such an approach will identify the optimum mix of short,
medium and long term projects and investments, addressing the efficiency of energy flows across various city
sectors with regards to economic, environmental and social criteria and will highlight priority actions.
Tools and models, like Geographic Information System, buildings models (CitySim and EnergyPlus) and
transport-based energy and carbon model, as well as a technological partial equilibrium energy model (TIMES),
are used to analyse, all the relevant sectors (buildings, industries, transports, waste and water management).
Furthermore, the cities buildings stocks are being characterized through an extensive 110-question survey
(around 410 door-to-door interviews) and will be modelled through a typology approach. Four hundred 20-
question surveys are also being carried out to evaluate transport and mobility patterns, supported on travel diaries and fulfilling different quotas for several variables (geographic location, days of the week, age and working
status) in order to assure representativeness of the data collected.
The main differences between rural and urban areas results from the building surveys and high-resolution
electricity consumption from smart meters for the Portuguese city of Évora are highlighted.

Gouveia, JP, Seixas J, Bilo N, Valentim A, Nunes V, Giannakidis G, Robinson D, Irons D, Gargiulo M.  2014.  Integrative Smart City Planning - Buildings and Mobility in Évora. 4th IAEE European Energy Conference - Sustainable Energy Policy and Strategies for Europe. , LUISS University, Rome, Italy.
Carvalho, T, Augusto V, Rocha A, Lourenco NMT, Correia NT, Barreiros S, Vidinha P, Cabrita EJ, Dionisio M.  2014.  Ion Jelly Conductive Properties Using Dicyanamide-Based Ionic Liquids. Journal of Physical Chemistry B. 118(31):9445-9459. Abstract

The thermal behavior and transport properties of several ion jellys (IJs), a composite that results from the combination of gelatin with an ionic liquid (IL), were investigated by dielectric relaxation spectroscopy (DRS), differential scanning calorimetry (DSC), and pulsed field gradient nuclear magnetic resonance spectroscopy (PFG NMR). Four different ILs containing the dicyanamide anion were used: 1-butyl-3-methylimidazolium dicyanamide (BMIMDCA), 1-ethyl-3-methylimidazolium dicyanamide (EMIMDCA), 1-butyl-1-methylpyrrolidinium dicyanamide (BMPyrDCA), and 1-butylpyridinium dicyanamide (BPyDCA); the bulk ILs were also investigated for comparison. A glass transition was detected by DSC for all materials, ILs and IJs, allowing them to be classified as glass formers. Additionally, an increase in the glass transition temperature upon dehydration was observed with a greater extent for IJs, attributed to a greater hindrance imposed by the gelatin matrix after water removal, rendering the IL less mobile. While crystallization is observed for some ILs with negligible water content, it was never detected for any IJ upon thermal cycling, which persist always as fully amorphous materials. From DRS measurements, conductivity and diffusion coefficients for both cations (D+) and anions (D–) were extracted. D+ values obtained by DRS reveal excellent agreement with those obtained from PFG NMR direct measurements, obeying the same VFTH equation over a large temperature range (ΔT ≈ 150 K) within which D+ varies around 10 decades. At temperatures close to room temperature, the IJs exhibit D values comparable to the most hydrated (9%) ILs. The IJ derived from EMIMDCA possesses the highest conductivity and diffusion coefficient, respectively, 10–2 S·cm–1 and 10–10 m2·s–1. For BMPyrDCA the relaxational behavior was analyzed through the complex permittivity and modulus formalism allowing the assignment of the detected secondary relaxation to a Johari–Goldstein process. Besides the relevant information on the more fundamental nature providing physicochemical details on ILs behavior, new doorways are opened for practical applications by using IJ as a strategy to produce novel and stable electrolytes for different electrochemical devices.

Carvalho, T, Augusto V, Rocha A, Lourenço NMT, Correia NT, Barreiros S, Vidinha P, Cabrita EJ, Dionísio M.  2014.  Ion jelly conductive properties using dicyanamide-based ionic liquids. The Journal of Physical Chemistry B. 118(31):9445-9459.Website
Veigas, Bruno, Branquinho, R., Pinto, Joana, Wojcik, Pawel Jerzy, Martins, Fortunato, Baptista PV.  2014.  Ion sensing (EIS) real-time quantitative monitorization of isothermal DNA amplification. Biosensors and Bioelectronics. 52:50-55.
Costa, Veigas, Bruno, Jacob, Jorge M., Santos, GMC, Santos, GMC, Baptista, Ana Catarina, Martins, Inacio, Joao, Fortunato E.  2014.  A low cost, safe, disposable, rapid and self-sustainable paper-based platform for diagnostic testing: lab-on-paper. Nanotechnology. 25(9):12pp..
Rodrigues, AC, Viciosa MT, F. Danède, Affouard F, N. T. Correia.  2014.  Molecular Mobility of Amorphous S-Flurbiprofen: A Dielectric Relaxation Spectroscopy Approach. Molecular Pharmaceutics. 11(1):112-130.Website
Nunes, TG, Viciosa MT, N. T. Correia, F. Danède, Nunes RG, Diogo HP.  2014.  A Stable Amorphous Statin: Solid-State NMR and Dielectric Studies on Dynamic Heterogeneity of Simvastatin. Molecular Pharmaceutics. 11(3):727-737.Website
Silva, MA, Valente RC, Pokkuluri PR, Turner DL, Salgueiro CA, Catarino T.  2014.  Thermodynamic and kinetic characterization of two methyl-accepting chemotaxis heme sensors from Geobacter sulfurreducens reveals the structural origin of their functional difference. Biochim Biophys Acta. 1837(6):920-928. AbstractWebsite

The periplasmic sensor domains GSU582 and GSU935 are part of methyl-accepting chemotaxis proteins of the bacterium Geobacter sulfurreducens containing one c-type heme and a PAS-like fold. Their spectroscopic properties were shown previously to share similar spectral features. In both sensors, the heme group is in the high-spin form in the oxidized state and low-spin after reduction and binding of a methionine residue. Therefore, it was proposed that this redox-linked ligand switch might be related to the signal transduction mechanism. We now report the thermodynamic and kinetic characterization of the sensors GSU582 and GSU935 by visible spectroscopy and stopped-flow techniques, at several pH and ionic strength values. Despite their similar spectroscopic features, the midpoint reduction potentials and the rate constants for reduction by dithionite are considerably different in the two sensors. The reduction potentials of both sensors are negative and well framed within the typical anoxic subsurface environments in which Geobacter species predominate. The midpoint reduction potentials of sensor GSU935 are lower than those of GSU582 at all pH and ionic strength values and the same was observed for the reduction rate constants. The origin of the different functional properties of these closely related sensors is rationalized in the terms of the structures. The results suggest that the sensors are designed to function in different working potential ranges, allowing the bacteria to trigger an adequate cellular response in different anoxic subsurface environments. These findings provide an explanation for the co-existence of two similar methyl-accepting chemotaxis proteins in G. sulfurreducens.

Velasco, LF, Lima JC, Ania C.  2014.  Visible-Light Photochemical Activity of Nanoporous Carbons under Monochromatic Light. Angewandte Chemie International Edition. 53:1-4. Abstract

By using monochromatic light the ability of semiconductor-free nanoporous carbons to convert the low-energy photons from the visible spectrum into chemical reactions (i.e. phenol photooxidation) is demonstrated. Data shows that the onset wavelength of the photochemical activity can be tuned by surface functionalization, with enhanced visible-light conversion upon introducing N-containing groups.

Viegas, MC, Moniz A, Santos PT.  2014.  Artisanal fishermen contribution for the integrated and sustainable coastal management - application of strategic SWOT analysis. Procedia - Social and Behavioral Sciences. 2014:257-267. AbstractWebsite
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Barreira, G, Ferreira ASD, Vidinha P, Cabral JMS, Martinho JMG, Lima JC, Cabrita EJ, Barreiros S.  2014.  Assessing diffusion in enzyme loaded sol-gel matrices. Rsc Advances. 4:25099-25105., Number 48 AbstractWebsite
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Barreira, G, Ferreira ASD, Vidinha P, Cabral JMS, Martinho JMG, Lima JC, Cabrita EJ, Barreiros S.  2014.  Assessing diffusion in enzyme loaded sol–gel matrices. RSC Advances. 4:25099-25105. Abstract

Pulsed field gradient spin echo high resolution magic angle spinning nuclear magnetic resonance spectroscopy is a powerful technique to characterize confined biosystems. We used this approach to assess the diffusion of solvent and reaction species within sol–gel matrices differing in enzyme loading.

Otero, V, Sanches D, Montagner C, Vilarigues M, Carlyle L, Lopes JA, Melo MJ.  2014.  Characterisation of metal carboxylates by Raman and infrared spectroscopy in works of art. Journal of Raman Spectroscopy. 45:1197-1206., Number 11-12 AbstractWebsite
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Ferreira, JP, Viveiros R, Lourenco A, da Silva MS, Rosatella A, Casimiro T, Afonso CAM.  2014.  Integrated desulfurization of diesel by combination of metal-free oxidation and product removal by molecularly imprinted polymers. RSC Adv.. 4:54948-54952.: The Royal Society of Chemistry AbstractWebsite

The production of ultra-low-sulfur diesel is an important worldwide demand. In this work a novel integrated method for desulfurization of diesel is proposed based on the combination of Bronsted acid catalyzed oxidation and the selective removal of the oxidized products using a molecularly imprinted polymer (MIP) produced in supercritical carbon dioxide (scCO2). The biphasic oxidation reaction of dibenzothiophene sulfone (DBT){,} as model substrate{,} and H2O2 as oxidant{,} was optimized by testing different acid catalysts{,} and also different phase transfer catalysts (PTC){,} including two different ionic liquids (ILs) trihexyl(tetradecyl)phosphoniumchloride [P6{,}6{,}6{,}14]Cl and Aliquat[registered sign]. The products of the efficient oxidation of DBT{,} dibenzothiophene sulfoxide (DBTSO) and dibenzothiophene sulfone (DBTSO2){,} were then selectively removed from real diesel using the MIP.

Martins, ANC, Simeonov SP, Frija LMT, Viveiros R, Lourenço A, da Silva MS, Casimiro T, Afonso CAM.  2014.  Isolation, analytical quantification and seasonal variation of labdanolic acid from the Portuguese-grown Cistus ladaniferus. Industrial Crops and Products. 60:226-232. AbstractWebsite
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Sa, S, Gawande MB, Velhinho A, Veiga JP, Bundaleski N, Trigueiro J, Tolstogouzov A, Teodoro OMND, Zboril R, Varma RS, Branco PS.  2014.  Magnetically recyclable magnetite-palladium (Nanocat-Fe-Pd) nanocatalyst for the Buchwald-Hartwig reaction. GREEN CHEMISTRY. 16:3494-3500., Number 7 Abstract
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