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2014
João, C, Vasconcelos J, Silva JC, Borges JP.  2014.  An Overview of Inverted Colloidal Crystal Systems for Tissue Engineering, 2014. Tissue Engineering Part B-Reviews. 20:437-454. AbstractWebsite

Scaffolding is at the heart of tissue engineering but the number of techniques available for turning biomaterials into scaffolds displaying the features required for a tissue engineering application is somewhat limited. Inverted colloidal crystals (ICCs) are inverse replicas of an ordered array of monodisperse colloidal particles, which organize themselves in packed long-range crystals. The literature on ICC systems has grown enormously in the past 20 years, driven by the need to find organized macroporous structures. Although replicating the structure of packed colloidal crystals (CCs) into solid structures has produced a wide range of advanced materials (e.g., photonic crystals, catalysts, and membranes) only in recent years have ICCs been evaluated as devices for medical/pharmaceutical and tissue engineering applications. The geometry, size, pore density, and interconnectivity are features of the scaffold that strongly affect the cell environment with consequences on cell adhesion, proliferation, and differentiation. ICC scaffolds are highly geometrically ordered structures with increased porosity and connectivity, which enhances oxygen and nutrient diffusion, providing optimum cellular development. In comparison to other types of scaffolds, ICCs have three major unique features: the isotropic three-dimensional environment, comprising highly uniform and size-controllable pores, and the presence of windows connecting adjacent pores. Thus far, this is the only technique that guarantees these features with a long-range order, between a few nanometers and thousands of micrometers. In this review, we present the current development status of ICC scaffolds for tissue engineering applications.

Santos, TG, Martins J, Mendes L, Miranda RM.  2014.  Process developments in FSW, 2014. 8th International Conference on Management Science and Engineering Management, ICMSEM 2014. 281:1015-1021.: Springer Verlag AbstractWebsite
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Miranda, RM, Gandra JP, Vilaca P, Quintino L, Santos TG.  2014.  Surface modification by solid state processing, 2014. Surface Modification by Solid State Processing. :1-183.: Elsevier Ltd. AbstractWebsite
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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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Correia, IL, Franco IS, de Sá-Nogueira I.  2014.  Towards Novel Amino Acid-Base Contacts in Gene Regulatory Proteins: AraR – A Case Study, 11. PLoS ONE. 9:e111802., Number 11: Public Library of Science AbstractWebsite

AraR is a transcription factor involved in the regulation of carbon catabolism in Bacillus subtilis. This regulator belongs to the vast GntR family of helix-turn-helix (HTH) bacterial metabolite-responsive transcription factors. In this study, AraR-DNA specific interactions were analysed by an in vitro missing-contact probing and validated using an in vivo model. We show that amino acid E30 of AraR, a highly conserved residue in GntR regulators, is indirectly responsible for the specificity of amino acid-base contacts, and that by mutating this residue it will be possible to achieve new specificities towards DNA contacts. The results highlight the importance in DNA recognition and binding of highly conserved residues across certain families of transcription factors that are located in the DNA-binding domain but not predicted to specifically contact bases on the DNA. These new findings not only contribute to a more detailed comprehension of AraR-operator interactions, but may also be useful for the establishment of a framework of rules governing protein-DNA recognition.

Mendes, LM.  2014.  100% Renewable Cities: Transition Strategies.. 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
Simão, J.  2014.  An Adaptive Java Runtime Environment for Cloud Computing. Instituto Superior Técnico.
Pina, AS, Batalha IL, Roque ACA.  2014.  Affinity Tags in Protein Purification and Peptide Enrichment: An Overview. Protein Downstream Processing: Design, Development and Application of High and Low-Resolution Methods. (Labrou, Nikolaos, Ed.).:147-168.: Springer Abstract

The reversible interaction between an affinity ligand and a complementary receptor has been widely explored in purification systems for several biomolecules. The development of tailored affinity ligands highly specific towards particular target biomolecules is one of the options in affinity purification systems. However, both genetic and chemical modifications on proteins and peptides widen the application of affinity ligand-tag receptor pairs towards universal capture and purification strategies. In particular, this chapter will focus on two case studies highly relevant for biotechnology and biomedical areas, namely, the affinity tags and receptors employed on the production of recombinant fusion proteins and the chemical modification of phosphate groups on proteins and peptides and the subsequent specific capture and enrichment, a mandatory step before further proteomic analysis.

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.

Neves, N, Lagoa A, Calado J, do Rego BAM, Fortunato E, Martins R, Ferreira I.  2014.  Al-doped ZnO nanostructured powders by emulsion detonation synthesis – Improving materials for high quality sputtering targets manufacturing. J. Eur. Ceram. Soc.. 34(10):2325-2338. AbstractWebsite

Emulsion detonation synthesis method was used to produce undoped and Al-doped ZnO nanostructured powders (0.5–2.0 wt.% Al2O3). The synthesized powders present a controlled composition and a morphology which is independent on the doping level. The XRD results indicate wurtzite as the single phase for undoped ZnO and the presence of gahnite as secondary phase for Al-doped ZnO powders. The sintering behavior of each powder was studied based on their linear shrinkage and shrinkage rate curves, showing the high sinterability of the powders. Activation energies for densification in the earlier stage were calculated for all compositions and possible sintering mechanisms are suggested depending on the doping level. The high chemical homogeneity and sinterability and the lower electrical resistivity of the bulk Al-doped sintered samples demonstrates the feasibility of emulsion detonation synthesis for the production of high quality Al-doped ZnO powders to be used in ceramic sputtering targets manufacture.

Soares, PIP, Ferreira I, Borges JP.  2014.  Application of Hyperthermia for Cancer Treatment: Recent Patents Review. Topics in Anti-Cancer Research, Vol. 3. (Atta-ur-Rahman, Khurshid Zaman, Eds.).:342-383.: Bentham Science Publishers Abstract

Cancer is one of the main causes of death in the world and its incidence increases every day. Current treatments are insufficient and present many breaches. Hyperthermia is an old concept and was early established as a cancer treatment option, mainly in superficial cancers. More recently, the concept of intracellular hyperthermia emerged wherein magnetic particles are concentrated at the tumor site and remotely heated using an applied magnetic field to achieve hyperthermic temperatures (42-45ºC). Many patents have been registered in this area since the year 2000. This chapter presents the most relevant information organized in two main categories according to the use or not of nanotechnology. The patents without nanotechnology were divided into the following subcategories: 1) external Radio-Frequency devices; 2) hyperthermic perfusion; 3) frequency enhancers; 4) applying heat to the target site using a catheter; and 5) injection of magnetic and ferroelectric particles. The patents with nanotechnology were divided into three subcategories: 1) hyperthermia devices; 2) nanoparticles; and 3) nanostructures. The use of magnetic nanoparticles is a very promising treatment approach since it may be used for diagnostic and treatment. Magnetic nanoparticle could be applied to detect and diagnose the tumor and to carry a pharmacological active drug to be delivered in the tumor site or apply hyperthermia through an external magnetic field.

Soares, PIP, Ferreira IMM, Borges JPMR.  2014.  Application of hyperthermia for cancer treatment: recent patents review. Topics in anti-cancer research. :342-383., USA: Bentham Science Publishers Abstract

Cancer is one of the main causes of death in the world and its incidence increases every
day. Current treatments are insufficient and present many breaches. Hyperthermia is an old
concept and was early established as a cancer treatment option, mainly in superficial
cancers. More recently, the concept of intracellular hyperthermia emerged wherein magnetic
particles are concentrated at the tumor site and remotely heated using an applied magnetic
field to achieve hyperthermic temperatures (42-45ºC). Many patents have been registered in
this area since the year 2000. This chapter presents the most relevant information organized
in two main categories according to the use or not of nanotechnology.

Silva, J, Fernandes AR, Baptista PV.  2014.  Application of Nanotechnology in Drug Delivery. Application of Nanotechnology in Drug Delivery. (Ali Demir Sezer, Ed.)., Rijeka: InTech, Chapters published application_of_nanotechnology_in_drug_delivery.pdf
Nunes, CI, Brás JL, Najmudin S, Moura JJG, Moura I, Carepo M.  2014.  ArsC3 from Desulfovibrio alaskensis G20, a cation and sulfate-independent highly efficient arsenate reductase. J Biol Inorg Chem. 19:1277-1285.
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.
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.

Borges, JP, Canejo JP, Fernandes S, Brogueira P, Godinho MH.  2014.  Cellulose-Based Liquid Crystalline Composite Systems. Nanocellulose Polymer Nanocomposites: Fundamentals and Applications. (Thakur, Vijay Kumar, Ed.).:215-235., Hoboken, NJ, USA: John Wiley & Sons, Inc.
Pina, AS, Lowe CR, Roque ACA.  2014.  Challenges and opportunities in the purification of recombinant tagged proteins. Biotechnology Advances. 32(2):366-381. AbstractWebsite

The purification of recombinant proteins by affinity chromatography is one of the most efficient strategies due to the high recovery yields and purity achieved. However, this is dependent on the availability of specific affinity adsorbents for each particular target protein. The diversity of proteins to be purified augments the complexity and number of specific affinity adsorbents needed, and therefore generic platforms for the purification of recombinant proteins are appealing strategies. This justifies why genetically encoded affinity tags became so popular for recombinant protein purification, as these systems only require specific ligands for the capture of the fusion protein through a pre-defined affinity tag tail. There is a wide range of available affinity pairs “tag-ligand” combining biological or structural affinity ligands with the respective binding tags. This review gives a general overview of the well-established “tag-ligand” systems available for fusion protein purification and also explores current unconventional strategies under development.

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.
Silva, TF, Martins LM, Guedes da Silva MF, Kuznetsov ML, Fernandes AR, Silva A, Pan CJ, Lee JF, Hwang BJ, Pombeiro AJ.  2014.  Cobalt complexes with pyrazole ligands as catalyst precursors for the peroxidative oxidation of cyclohexane: X-ray absorption spectroscopy studies and biological applications. Chem Asian J. 9(4):1132-43.14silvacaj.pdf
Contreras, J, Martins R, Wojcik P, Filonovich S, Águas H, Gomes L, Fortunato E, Ferreira I.  2014.  Color sensing ability of an amorphous silicon position sensitive detector array system. Sensor Actuat. A-Phys.. 205:26-37. AbstractWebsite

The color sensing ability of a data acquisition prototype system integrating a 32 linear array of 1D amorphous silicon position sensitive detectors (PSD) was analyzed. Besides being used to reproduce a 3D profile of highly reflective surfaces, here we show that it can also differentiate primary red, green, blue (RGB) and derived colors. This was realized by using an incident beam with a RGB color combination and adequate integration times taking into account that a color surface mostly reflects its corresponding color. A mean colorimetric error of 25.7 was obtained. Overall, we show that color detection is possible via the use of this sensor array system, composed by a simpler amorphous silicon pin junction.

Baltazar, LG, Henriques FMA, Jorne F, Cidade MT.  2014.  Combined effect of superplasticizer, silica fume and temperature in the performance of natural hydraulic lime grouts. Construction & Building Materials . 50:584-597.