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2013
Silva, JA, Vale TM, Lourenço JM, Paulino H.  2013.  Replicação Parcial com Memória Transacional Distribuída. Proceedings of INForum Simpósio de Informática. :310–321., Lisbon, Portugal: Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa Abstract2013-inforum-js.pdf

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Araújo, A, Barros R, Mateus T, Gaspar D, Neves N, Vicente A, Filonovich SA, Barquinha P, Fortunato E, Ferraria AM, do Rego ABM, Bicho A, Águas H, Martins R.  2013.  Role of a disperse carbon interlayer on the performances of tandem a-Si solar cells. Science and Technology of Advanced Materials. 14(4)
Morgado, L, Dantas JM, Simões T, Londer YY, Pokkuluri PR, Salgueiro CA.  2013.  Role of Met58 in the regulation of electron/proton transfer in trihaem cytochrome PpcA from Geobacter sulfurreducens. Bioscience Reports. 33(1):11-22. AbstractWebsite

The bacterium Gs (Geobacter sulfurreducens) is capable of oxidizing a large variety of compounds relaying electrons out of the cytoplasm and across the membranes in a process designated as extracellular electron transfer. The trihaem cytochrome PpcA is highly abundant in Gs and is most probably the reservoir of electrons destined for the outer surface. In addition to its role in electron transfer pathways, we have previously shown that this protein could perform e-/H+ energy transduction. This mechanism is achieved by selecting the specific redox states that the protein can access during the redox cycle and might be related to the formation of proton electrochemical potential gradient across the periplasmic membrane. The regulatory role of haem III in the functional mechanism of PpcA was probed by replacing Met58, a residue that controls the solvent accessibility of haem III, with serine, aspartic acid, asparagine or lysine. The data obtained from the mutants showed that the preferred e-/H+ transfer pathway observed for PpcA is strongly dependent on the reduction potential of haem III. It is striking to note that one residue can fine tune the redox states that can be accessed by the trihaem cytochrome enough to alter the functional pathways.

Amado, M, Rodrigues P, Poggi F, Freitas J.  2013.  Solar Urban Planning to EU 20-20-20 Targets. Portugal SB 13 - CONTRIBUTION OF SUSTAINABLE BUILDING TO MEET EU 20-20-20 TARGETS. :697-708., Guimaraes, PT: iiSBE PORTUGAL
Dudognon, E, Correia NT, Danède F, Descamps M.  2013.  Solid-Solid Transformation in Racemic Ibuprofen. Pharmaceutical Research. 30(1):81-89.
Dantas, JM, Morgado L, Pokkuluri PR, Turner DL, Salgueiro CA.  2013.  Solution structure of a mutant of the triheme cytochrome PpcA from Geobacter sulfurreducens sheds light on the role of the conserved aromatic residue F15. Biochimica et Biophysica Acta (BBA) - Bioenergetics. 1827(4):484-492. AbstractWebsite

Extracellular electron transfer is one of the physiological hallmarks of Geobacteraceae. Most of the Geobacter species encode for more than 100 c-type cytochromes which are, in general, poorly conserved between individual species. An exception to this is the PpcA family of periplasmic triheme c-type cytochromes, which are the most abundant proteins in these bacteria. The functional characterization of PpcA showed that it has the necessary properties to couple electron/proton transfer, a fundamental step for ATP synthesis. The detailed thermodynamic characterization of a PpcA mutant, in which the strictly conserved residue phenylalanine 15 was replaced by leucine, showed that the global redox network of cooperativities among heme groups is altered, preventing the mutant from performing a concerted electron/proton transfer. In this work, we determined the solution structure of PpcA F15L mutant in the fully reduced state using NMR spectroscopy by producing 15N-labeled protein. In addition, pH-dependent conformational changes were mapped onto the structure. The mutant structure obtained is well defined, with an average pairwise root-mean-square deviation of 0.36 Å for the backbone atoms and 1.14 Å for all heavy atoms. Comparison between the mutant and wild-type structures elucidated the contribution of phenylalanine 15 in the modulation of the functional properties of PpcA.

Borlido, L, Moura L, Azevedo AM, Roque ACA, Aires‐Barros MR, Farinha JPS.  2013.  Stimuli‐Responsive magnetic nanoparticles for monoclonal antibody purification. Biotechnology Journal. 8(6):709–717. AbstractWebsite

Monoclonal antibodies (mAbs) are important therapeutic proteins. One of the challenges facing large-scale production of monoclonal antibodies is the capacity bottleneck in downstream processing, which can be circumvented by using magnetic stimuli-responsive polymer nanoparticles. In this work, stimuli-responsive magnetic particles composed of a magnetic poly(methyl methacrylate) core with a poly(N-isopropylacrylamide-co-acrylic acid) (P(NIPAM-co-AA)) shell cross-linked with N, N'-methylenebisacrylamide were prepared by miniemulsion polymerization. The particles were shown to have an average hydrodynamic diameter of 317 nm at 18°C, which decreased to 277 nm at 41°C due to the collapse of the thermo-responsive shell. The particles were superparamagnetic in behavior and exhibited a saturation magnetization of 12.6 emu/g. Subsequently, we evaluated the potential of these negatively charged stimuli-responsive magnetic particles in the purification of a monoclonal antibody from a diafiltered CHO cell culture supernatant by cation exchange. The adsorption of antibodies onto P(NIPAM-co-AA)-coated nanoparticles was highly selective and allowed for the recovery of approximately 94% of the mAb. Different elution strategies were employed providing highly pure mAb fractions with host cell protein (HCP) removal greater than 98%. By exploring the stimuli-responsive properties of the particles, shorter magnetic separation times were possible without significant differences in product yield and purity.

Ferreira, I, Baptista AC, Leitão JP, Soares J, Fortunato E, Martins R, Borges JP.  2013.  Strongly Photosensitive and Fluorescent F8T2 Electrospun Fibers. Macromol Mater Eng. 298(2):174-180., Number 2 AbstractWebsite

Electrospun fibers of poly[(9,9-dioctylfluorenyl-2,7-diyl)-co-bithiophene] (F8T2) with exceptional electro-optical performance are obtained. The I/T characteristics measured in fibers with 7–15 µm diameter and 1 mm length show a semiconductor behavior; their thermal activation energy is 0.5 eV and the dark conductivity at RT is 5 × 10−9 (Ω cm)−1. Besides exhibiting a photosensitivity of about 60 under white light illumination with a light power intensity of 25 mW · cm−2, the fibers also attain RT photoluminescence in the cyan, yellow, and red wavelength range under ultraviolet, blue, and green light excitation, respectively. Optical microscope images of F8T2 reveal homogeneous electrospun fibers, which are in good agreement with the uniformly radial fluorescence observed.

Alves, C, Rodrigues, L. C., Andrade, J. R., Pawlicka, A., Pereira, Martins, Fortunato, Silva MM.  2013.  Study and Characterization of a Novel Polymer Electrolyte Based on Agar Doped with Magnesium Triflate. Molecular Crystals and Liquid Crystals. 570(1):1-11.
Cerqueira, N, Fernandes P, González P, Moura JJG, Ramos MJ.  2013.  The sulfur-shift: an activation mechanism for periplasmic nitrate reductase and formate dehydrogenase. Inorg Chem. 52:10766-10772.
Almeida, RA, Turano P, Moura I, Moura JJG, Pauleta SR.  2013.  Superoxide reductase: different interaction modes with its two redox partners. ChemBioChem. 14:1858–1866.
Amado, M, Lucas V, Ribeiro M.  2013.  Sustainable Construction: Value of Certification. Proc. of the Intl. Conf. on Advances in Civil, Structural and Environmental Engineering-- ACSEE 2013. :180-187., Zurich, CH: Institute of Research Engineers and Doctors
Amado, Miguel P., Barroso L.  2013.  SUSTAINABLE CONSTRUCTION: WATER USE IN RESIDENTIAL BUILDINGS IN PORTUGAL. International Journal of Sustainable Construction Engineering & Technology. Vol 4(No 2):14-22.
Geraldes, I, Amado MP.  2013.  SUSTENTABILIDADE DA CONSTRUÇÃO DE HABITAÇÃO SOCIAL COM RECURSO A LSF Sustainability of Construction of Social Habitation with LSF. 2º Congresso Internacional da habitação no Espaço Lusófono. :145-146., Lisboa, PT: LNEC
Thorsing, M, Klitgaard JK, Atilano ML, Skov MN, Kolmos HJ, Filipe SR, Kallipolitis BH.  2013.  Thioridazine induces major changes in global gene expression and cell wall composition in methicillin-resistant Staphylococcus aureus USA300. PLoS One. 8:e64518.
Fortes, P, Simões S, Seixas J, Regemorter DV, Ferreira F.  2013.  Top-down and bottom-up modelling to support low-carbon scenarios: climate policy implications. Climate Policy. 13:285–304., Number 3 AbstractWebsite

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Bahubalindruni, Ganga, Tavares, Vitor Grade, Barquinha, Duarte, Candido, de Oliveira, Pedro Guedes, Martins, Fortunato E.  2013.  Transparent Current Mirrors With a-GIZO TFTs: Neural Modeling, Simulation and Fabrication. Journal of Display Technology. 9(12):1001-1006.
Caires, L, Seco JC.  2013.  The Type Discipline of Behavioral Separation. Proceedings of the 40th Symposium on Principles of Programming Languages (POPL). Abstract

We introduce the concept of behavioral separation as a general prin- ciple for disciplining interference in higher-order imperative con- current programs, and present a type-based approach that system- atically develops the concept in the context of an ML-like language extended with concurrency and synchronization primitives. Behav- ioral separation builds on notions originally introduced for behav- ioral type systems and separation logics, but shifts the focus from the separation of static program state properties towards the sep- aration of dynamic usage behaviors of runtime values. Behavioral separation types specify how values may be safely used by client code, and can enforce fine-grained interference control disciplines while preserving compositionality, information hiding, and flexi- bility. We illustrate how our type system, even if based on a small set of general primitives, is already able to tackle fairly challenging program idioms, involving aliasing at various types, concurrency with first-class threads, manipulation of linked data structures, be- havioral borrowing, and invariant-based separation.

Baltazar, LG, Henriques FMA, Jorne F, Cidade MT.  2013.  The use of rheology in the study of the composition effects on the fresh behaviour of hydraulic lime grouts for injection of masonry walls. Rheologica Acta . 52(2):127-138.
Amado, M, Freitas J, Rodrigues E, Ribeiro R.  2013.  Walkability as a Strategy towards Inclusive Communities: Case of a Portuguese Small Town. International Journal of Civil, Architectural Science and Engineering. Vol. nº 7(Nº 8):1-7.
Baumann, M.  2013.  {A constructive technology assessment of stationary energy storage systems: prospective life cycle orientated analysis}. , Number 01/2013: Universidade Nova de Lisboa, IET/CICS.NOVA-Interdisciplinary Centre on Social Sciences, Faculty of Science and Technology Abstract

Environmental concerns over the use of fossil fuels and their resource constraints have increased the interest in generating electric energy from renewable energy sources (RES) to provide a sustainable electricity supply. A main problem of those technologies (wind or solar power generation) is that they are not constant and reliable sources of power. This results inter alia in an increased demand of energy storage technologies. Related stake holders show a big interest in the technical, economic and ecologic aspects of new emerging energy storage systems. This comes especially true for electrochemical energy storage systems as different Li-Ion batteries, Sodium Sulfur or Redox Flow batteries which can be utilized in all grid voltage levels, a wide range of grid applications as well as end user groups (e.g. private households, industry). A prospective and active Constructive Technology Assessment (CTA) can help to minimize potential mismatches, wrong investments, possible social conflicts, and environmental impacts of new energy storage technologies in an early development stage. It is insufficient to exclusively look at the operation phase to assess a technology. Such an approach can lead to misleading interpretations and can furthermore disregard social or ecological impact factors over the whole life cycle. Different energy storage technologies have to be evaluated in a prospective manner with a full integrated sustainability and life cycle approach to form a base for decision making and to support technology developers in order to allow distinctions between more or less sustainable battery technology variations. Therefore CTA is used as a scientific approach using several “neighbouring” engineering orientated disciplines e.g. Life Cycle Analysis (LCA), Social Life Cycle Assessment (SLCA) or Life Cycle Costs (LCC) and their methodologies which were initially developed for other purposes.The aim of the presented PhD Thesis is to make an economic, technological and

Daniel, CI, Chavez FV, Feio G, Portugal CA, Crespo JG, Sebastiao PJ.  2013.  1H NMR relaxometry, viscometry, and PFG NMR studies of magnetic and nonmagnetic ionic liquids. J Phys Chem B. 117:11877-84., Number 39 AbstractWebsite

A study is presented of the molecular dynamics and of the viscosity in pure [Aliquat][Cl] ionic liquid and in a mixture of [Aliquat][Cl] with 1% (v/v) of [Aliquat][FeCl4]. The (1)H spin-lattice relaxation rate, R1, was measured by NMR relaxometry between 8 and 300 MHz. In addition, the translation self-diffusion, D, was measured by pulse field gradient NMR. The ILs' viscosity was measured as a function of an applied magnetic field, B, and it was found that the IL mixture's viscosity decreased with increasing B, whereas the [Aliquat][Cl] viscosity is independent of B. All experimental results were analyzed taking into account the viscosity's magnetic field dependence, assuming a modified Stokes-Einstein diffusion/viscosity relation. The main difference between the relaxation mechanisms responsible for R1 in the two IL systems is related to the additional paramagnetic relaxation contribution associated with the (1)H spins-[FeCl4] paramagnetic moments' interactions. Cross-relaxation cusps in the R1 dispersion, associated with (35)Cl and (1)H nuclear spins in the IL systems, were detected. The R1 model considered was successfully fitted to the experimental results, and it was possible to estimate the value of D at zero field in the case of the IL mixture which was consistent with the values of D measured at 7 and 14.1 T and with the magnetic field dependence estimated from the viscosity measurements. It was observed that a small concentration of [Aliquat][FeCl4] in the [Aliquat][Cl] was enough to produce a "superparamagnetic"-like effect and to change the IL mixture's molecular dynamics and viscosity and to allow for their control with an external magnetic field.

dos Santos, R, Rocha A, Matias A, Duarte C, de Sá-Nogueira I, Lourenco N, Borges JP, Vidinha P.  2013.  Development of antimicrobial Ion Jelly fibers. RSC Adv.. 3:24400-24405.: The Royal Society of Chemistry Abstract

We report a method to obtain electrospun fibers based on ionic liquids and gelatin, exhibiting antimicrobial properties.

Lipinska, ME, Teixeira DMD, Laia CAT, Silva AMG, Rebelo SLH, Freire C.  2013.  beta-Functionalized zinc(II)aminoporphyrins by direct catalytic hydrogenation. Tetrahedron Letters. 54:110-113., Number 1 AbstractWebsite
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Cruz, C, Santos SD, Cabrita EJ, Queiroz JA.  2013.  Binding analysis between l-histidine immobilized and oligonucleotides by SPR and NMR. International Journal of Biological Macromolecules. 56:175-180. Abstract

Saturation transfer difference (STD) NMR technique and surface plasmon resonance (SPR) are used to study amino acid affinity supports–nucleotides interactions with l-histidine amino acid immobilized on a surface as model support. We have immobilized l-histidine ligand on a carboxymethyldextran- modified gold surface intended for surface plasmon resonance and we analyze the binding profiles of synthetic polynucleotides (1–6 base, sugar and backbone) by determining the equilibrium dissociation constant (KD). The SPR binding profile (square-shaped) is identical for all the complexes and the highest binding affinity can be found for polyA6 followed by polyG6 . As expected, the 5′ -mononucleotides have the lowest affinity. To further study the structural aspects of the interaction we investigate the polynucleotide binding preferences to l-histidine chromatography support by STD-NMR spectroscopy. These results revealed that an increase in the number of bases and backbone to 6 units leads to more contacts with the support, where the main driving force for the interaction with polynucleotides are through the base, except for polyC6 , which is mainly through sugar-phosphate backbone. Therefore, the combination of SPR measurements with STD-NMR technique allowed to establish fine details of the molecular recognition process involved in amino acid affinity supports–nucleotides complexes.