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2012
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.

Jorne, F, Henriques FMA, Baltazar LG.  2012.  Avaliação da técnica de injecção de grout recorrendo ao ensaio de ultra-sons e tomografia ultra-sónica (in portuguese), 18th-20th Decemb. Proceedings of the 4th National Congress on Construction. , Coimbra, Portugal
Baltazar, LG, Henriques FMA, Jorne F.  2012.  Grout optimisation for old masonry consolidation, 18th-20th Decemb. Proceedings of the 4th National Congress on Construction. , Coimbra, Portugal
Kanudia, A, Boavida D, van den Broek M, Cabal H, Gargiulo M, Gouveia JP, Labriet M, Seixas J, Tosato GC.  2012.  CCS infrastructure development scenarios for the integrated Iberian Peninsula and Morocco energy system, 18-22 November. GHGT_11, Conference session #9 on “CCS technology assessment and system integration”. , Kyoto International Conference Center, Japan
van den Broek, M, Mesquita P, Carneiro J, Silva J, Berghout N, Ramirez A, Gouveia JP, Seixas J, Cabal H, Martinez R, Rimi A, Boavida D, Tosato GC.  2012.  Region specific challenges of a CO2 pipeline infrastructure in the West Mediterranean area - Model results versus stakeholder views., 18-22 November. GHGT_11, on “CCS technology assessment and system integration”. , Kyoto International Conference Center, Japan.
Baltazar, LG, Henriques FMA, Jorne F.  2012.  Hydraulic lime grouts for masonry injection – effects of admixtures on the fresh grout properties, 15th - 17th Octo. Proceedings of the 8th International Conference on Structural Analysis of Historical Constructions. , Wroclaw, Poland
Brás, A, Henriques FMA, Cidade MT.  2012.  - Rheological behaviour of hydraulic lime-based grouts. Shear-time and temperature dependence. Mechanics of Time-Dependent Materials. DOI 10.1007/s11043-012-9202-0
Tana, M, Bianchi A, Sclocco R, Franchin T, Cerutti S, Leal A.  2012.  . Parcel-Based Connectivity Analysis of fMRI Data for the Study of Epileptic Seizure Propagation.. Brain Topography . (DOI:10.1007/s10548-012-0225-2)
Brecher, C, Breitbach T, Müller S, Mayer MP, Odenthal B, Schlick C, Herfs W.  2012.  3D Assembly Group Analysis for Cognitive Automation. Journal of Robotics. 2012(1):1-18. AbstractWebsite

A concept that allows the cognitive automation of robotic assembly processes is introduced. An assembly cell comprised of two robots was designed to verify the concept. For the purpose of validation a customer-defined part group consisting of Hubelino bricks is assembled. One of the key aspects for this process is the verification of the assembly group. Hence a software component was designed that utilizes the Microsoft Kinect to perceive both depth and color data in the assembly area. This information is used to determine the current state of the assembly group and is compared to a CAD model for validation purposes. In order to efficiently resolve erroneous situations, the results are interactively accessible to a human expert. The implications for an industrial application are demonstrated by transferring the developed concepts to an assembly scenario for switch-cabinet systems.

Neves, Nuno, Barros, R., Antunes, Elsa, Calado, João, Fortunato, Martins, Ferreira I.  2012.  Aluminum doped zinc oxide sputtering targets obtained from nanostructured powders: Processing and application. Journal of the European Ceramic Society. 32(16):4381-4391.
Bahubalindruni, Ganga, Tavares, Vitor Grade, Barquinha, Duarte, Candido, Martins, Fortunato, de Oliveira PG.  2012.  Basic analog circuits with a-GIZO thin-film transistors: Modeling and simulation. 2012 International Conference on Synthesis, Modeling, Analysis and Simulation Methods and Applications to Circuit Design (SMACD).
Barroso, T, Roque ACA, Aguiar-Ricardo A.  2012.  Bioinspired and Sustainable Chitosan Based Monoliths for Antibody Capture and Release. RSC ADV. 2(30):11285-11294. AbstractWebsite

Chitosan-based monoliths activated by plasma technology induced the coupling of a robust biomimetic ligand, previously reported as an artificial Protein A, with high yields while minimizing the environmental impact of the procedure. Due to the high porosity, good mechanical and tunable physicochemical properties of the affinity chitosan-based monoliths, it is possible to achieve high binding capacities (150 ± 10 mg antibody per gram support), and to recover 90 ± 5% of the bound protein with 98% purity directly from cell-culture extracts. Therefore, the chitosan-based monoliths prepared by clean processes exhibit a remarkable performance for the one-step capture and recovery of pure antibodies or other biological molecules with biopharmaceutical relevance.

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
Sandu, ICA, Schäfer S, Magrini D, Bracci S, Roque ACA.  2012.  Cross-Section and Staining-Based Techniques for Investigating Organic Materials in Painted and Polychrome Works of Art: A Review.. Microscopy and Microanalysis. 18(4):860-875. AbstractWebsite

The article presents a review of the use of cross-section and staining techniques for investigating natural organic materials (mainly proteinaceous and oil-based binders/varnishes) in painted and polychrome artworks, considering the requirements of conservation practice and routine diagnostics. The reviewed literature calls attention to the importance of using cross sections to prepare samples for optical microscopy and to different properties of embedding resins; the most appropriate instrumental conditions for optical microscopy; and the advantages and disadvantages of the most common staining techniques. A few case studies were selected to illustrate the use of autofluorescence (intrinsic fluorescence) and induced fluorescence (using specific staining tests and fluorophore-labeled antibodies) for mapping and identifying organic paint materials in cross sections. New directions of research in cross-section analyses and fluorescence-based techniques for the identification and mapping of artistic materials are presented. The complementary use of different stains on the same cross section, further exploration of intrinsic and induced fluorescence of aged versus fresh materials, and applicability of cross-section observation and staining as complementary methods for assessing the effectiveness of restoration treatments, such as cleaning and consolidation, are discussed in the last section of the article.

Soares, PIP, Dias S, Novo C, Ferreira I, Borges JP.  2012.  Doxorubicin vs. ladirubicin: methods for improving osteosarcoma treatment. Mini reviews in medicinal chemistry. 12(12):1239–1249., Number 12: Bentham Science Publishers AbstractWebsite

Osteosarcoma is the most common primary bone tumor in children and adolescents, with a 5-year disease free survival rate of 70%. Current chemotherapy regimens comprise a group of chemotherapeutic agents in which doxorubicin is included. However, tumor resistance to anthracyclines and cardiotoxicity are limiting factors for its usage. Liposomal formulations of doxorubicin improve its anti-cancer effects but are still insufficient. The research in this area has lead to the production of anthracyclines analogues, such as ladirubicin, the leading compound of alkylcyclines. This new anticancer agent has shown promising results in vivo and in vitro, being effective against osteosarcoma cell lines, including those with a multidrug resistant phenotype. In phase I clinical trials, this molecule caused mild side effects and did not induce significant cardiotoxicity at doses ranging from 1 to 16 mg/m2, resulting in a peak plasma concentration (Cmax) ranging from 0.5 to 1.5 μM. The recommended doses for phase II studies were 12 and 14 mg/m2 in heavily and minimally pretreated/non-pretreated patients, respectively. Phase II clinical trials in ovary, breast, colorectal cancer, NSCLC and malignant melanoma are underway. Given the improved molecular targeting efficacy of these new compounds, ongoing approaches have sought to improve drug delivery systems, to improve treatment efficacy while reducing systemic toxicity. The combination of these two approaches may be a good start for the discovery of new treatment for osteosarcoma.

Grosso, AR, {De Almeida} SF, Braga J, Carmo-fonseca M, de Almeida SF, Braga J, Almeida FD, Carmo-fonseca M, Res G, Almeida FD, Grosso AR, Carmo-fonseca M.  2012.  Dynamic transitions in RNA polymerase II density profiles during transcription termination. Genome research. 22:1447–1456., Number 8 AbstractWebsite

Eukaryotic protein-coding genes are transcribed by RNA polymerase II (RNAPII) through a cycle composed of three main phases: initiation, elongation, and termination. Recent studies using chromatin immunoprecipitation coupled to high-throughput sequencing suggest that the density of RNAPII molecules is higher at the 3'-end relative to the gene body. Here we show that this view is biased due to averaging density profiles for "metagene" analysis. Indeed, the majority of genes exhibit little, if any, detectable accumulation of polymerases during transcription termination. Compared with genes with no enrichment, genes that accumulate RNAPII at the 3'-end are shorter, more frequently contain the canonical polyadenylation [poly(A)] signal AATAAA and G-rich motifs in the downstream sequence element, and have higher levels of expression. In 1% to 4% of actively transcribing genes, the RNAPII enriched at the 3'-end is phosphorylated on Ser5, and we provide evidence suggesting that these genes have their promoter and terminator regions juxtaposed. We also found a striking correlation between RNAPII accumulation and nucleosome organization, suggesting that the presence of nucleosomes after the poly(A) site induces pausing of polymerases, leading to their accumulation. Yet we further observe that nucleosome occupancy at the 3'-end of genes is dynamic and correlates with RNAPII density. Taken together, our results provide novel insight to transcription termination, a fundamental process that remains one of the least understood stages of the transcription cycle.

Golshahi, S., Rozati, S.M., Botelho do Rego, A.M., Wang, J., Elangovan, E., Martins, Fortunato E.  2012.  Effect of substrate temperature on the properties of pyrolytically deposited nitrogen-doped zinc oxide thin films . Materials Science and Engineering: B. 178(1):103-108.
Pimenta, AFR, Baptista AC, Carvalho T, Brogueira P, Lourenço N, Afonso C, Barreiros S, Vidinha P, Borges JP.  2012.  Electrospinning of Ion Jelly fibers. Materials Letters. 83:161-164. AbstractWebsite

Ion Jelly materials combine the chemical versatility and conductivity of an ionic liquid (IL) with the morphological versatility of a biopolymer (gelatin). They exhibit very interesting properties, such as conductivities up to 10− 4 S cm− 1, and high thermostability up to 180 °C, and have been used successfully to design electrochromic windows. In this work we report on the preparation of Ion Jelly fibers through electrospinning in order to obtain high surface area conductive materials. We have used the IL 1-(2-hydroxyethyl)-3-methyl-imidazolium tetrafluoroborate ([C2OHmim]BF4), which exhibits conveniently high ionic conductivity (over 10− 3 S cm− 1) and electrochemical stability (electrochemical window over 6.0 V). The morphology of the obtained fibers was quantified using Scanning Electron Microscopy (SEM) and Atomic Force Microscopy (AFM). We found that on average the effect of the IL on fiber diameter differs for lower and higher IL concentrations and that this effect was correlated with the initial conductivity and viscosity of Ion Jelly electrospinning solution. Moreover we also found that conductivities of Ion Jelly fibers are of the same order of magnitude as the conductivities of Ion Jelly dense films (~ 10− 4 S cm− 1). To the best of our knowledge, this is the first report on the incorporation of an IL into gelatin fibers using electrospinning. This opens up new opportunities for the application of gelatin fibers in electrochemical and biomedical devices.

Franco, PQ, João C, Silva JC, Borges JP.  2012.  Electrospun hydroxyapatite fibers from a simple sol–gel system. Materials Letters. 67(1):233–236., Number 1: Elsevier AbstractWebsite

This work reports the production of hydroxyapatite (HA) sub-micron fibers by combining electrospinning and a non-alkoxide sol–gel system, using cheap precursors. Phosphorus pentoxide (P2O5) and calcium nitrate tetrahydrate (Ca(NO3)2.4H2O) were used as precursors of phosphorus and calcium, respectively. The fibers were electrospun from a mixture of the gel formed from the system Ca(NO3)2.4H2O/P2O5 with polymeric solutions of polyvinylpyrrolidone (PVP) in water and ethanol/water mixtures. The fibers were analyzed for their morphology (Scanning Electron Microscopy, SEM), chemical composition (Fourier Transform Infrared Spectroscopy, FTIR) and structure (X-ray diffraction, XRD). The fibers obtained were composed mainly of type B carbonated HA with traces of β-tricalcium phosphate (β-TCP). SEM analysis revealed that increasing the concentration of water in the solvent system, used in the preparation of electrospinning solutions, led to fibers with smaller diameters and narrower diameter distribution.

Miller, A. Z., Hernández-Mariné, M., Jurado, V., Dionísio, A., Barquinha, Fortunato, Afonso, M. J., Chaminé, H. I., Saiz-Jimenez C.  2012.  Enigmatic reticulated filaments in subsurface granite. Environmental Microbiology Reports. 4(6):596–603.
Morgado, L, Dantas JM, Bruix M, Londer YY, Salgueiro CA.  2012.  Fine Tuning of Redox Networks on Multiheme Cytochromes from Geobacter sulfurreducens Drives Physiological Electron/Proton Energy Transduction. Bioinorganic Chemistry and Applications. 2012(Article ID 298739):1-9. AbstractWebsite

The bacterium Geobacter sulfurreducens (Gs) can grow in the presence of extracellular terminal acceptors, a property that is currently explored to harvest electricity from aquatic sediments and waste organic matter into microbial fuel cells. A family composed of five triheme cytochromes (PpcA-E) was identified in Gs. These cytochromes play a crucial role by bridging the electron transfer from oxidation of cytoplasmic donors to the cell exterior and assisting the reduction of extracellular terminal acceptors. The detailed thermodynamic characterization of such proteins showed that PpcA and PpcD have an important redox-Bohr effect that might implicate these proteins in the e−/H+ coupling mechanisms to sustain cellular growth. The physiological relevance of the redox-Bohr effect in these proteins was studied by determining the fractional contribution of each individual redox-microstate at different pH values. For both proteins, oxidation progresses from a particular protonated microstate to a particular deprotonated one, over specific pH ranges. The preferred e−/H+ transfer pathway established by the selected microstates indicates that both proteins are functionally designed to couple e−/H+ transfer at the physiological pH range for cellular growth.

Borlido, L, Azevedo AM, Sousa AG, Oliveira PH, Roque ACA, Aires-Barros MR.  2012.  Fishing human monoclonal antibodies from a CHO cell supernatant with boronic acid magnetic particles. Journal of Chromatography B. 903:163-170. AbstractWebsite

In this work we have evaluated the potential of boronic acid functionalized magnetic particles for the one-step capture of a human monoclonal antibody (mAb) from a Chinese hamster ovary (CHO) cell culture supernatant. For comparison, Protein A coated magnetic particles were also used. The most important factor influencing the overall process yield and product purity in boronic acid particles was found to be the binding pH. Basic pH values promoted higher purities while resulting in decreased yields due to the competing effects of molecules such as glucose and lactate present in the cell culture supernatant. After optimization, the particles were successfully used in a multi-cycle purification process of the mAb from the CHO feedstock. Boronic acid particles were able to achieve an average overall yield of 86% with 88% removal of CHO host cell proteins (HCP) when the binding was performed at pH 7.4, while at pH 8.5 these values were 58% and 97%, respectively. In both cases, genomic DNA removal was in excess of 97%. Comparatively, Protein A particles recorded an average overall yield of 80% and an HCP removal greater than 99%. The adsorption of the mAb to the boronic acid particles was shown to be mediated by strong affinity interactions. Overall, boronic acid based purification processes can offer a cost-effective alternative to Protein A as the direct capturing step from the mammalian cell culture.

Guirgis, BSS, e Cunha CSá, Gomes I, Cavadas M, Silva I, Doria G, Blatch GL, Baptista PV, Pereira E, Azzazy HME, Mota MM, Prudêncio M, Franco R.  2012.  GOLD NANOPARTICLES-BASED FLUORESCENCE IMMUNOASSAY FOR MALARIA ANTIGEN DETECTION. Anal. Bioanal. Chem.. 402:1019-1027.
Veigas, Bruno, Jacob, Jorge M., Costa, Santos, GMC, Viveiros, Miguel, Inacio, Joao, Martins, Barquinha, Fortunato, Baptista PV.  2012.  Gold on paper-paper platform for Au-nanoprobe TB detection. Lab on a Chip. 12:4802-4808.
Santos, S, Marques V, Pires M, Silveira L, Oliveira H, Lanca V, Brito D, Madeira H, Esteves JF, Freitas A, Carreira IM, Gaspar IM, Monteiro C, Fernandes AR.  2012.  High resolution melting: improvements in the genetic diagnosis of hypertrophic cardiomyopathy in a Portuguese cohort. BMC Med Genet. 13:17.12santosbmcmg.pdf
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