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2013
Amado, M, Lopes T, Ramalhete I.  2013.  ECO-WALL: MODULAR SOLUTION FOR LOW-COST HOUSES. CISBAT 2013. :121-126., Lausane, CH: EPFL, CH
Martin, KE, Tian Y, Busani T, Medforth CJ, Franco R, van Swol KF, Shelnutt J.  2013.  Effect of pH on the Structure and Composition of Porphyrin Binary Ionic Solids: ZnTPPS/SnTMePyP Nanomaterials. Chemistry of Materials. (25):441-447.
C, N, M.P.F. G, M. E, B.A. S, R.C.C. M, L. R, T. M.  2013.  Effects of ultraviolet excitation on the spectroscopic properties of Sm3+ and Tb3+ doped aluminophosphate glasses. Optical Materials. 35(12):2382-2388. AbstractWebsite

Li2O–BaO–Al2O3–La2O3–P2O5 glasses optically activated with rare earth ions with the 4f5, and 4f8 electronic configuration (Sm3+ and Tb3+, respectively) were analyzed by Raman spectroscopy, absorption, excitation photoluminescence, decay curves and temperature dependent photoluminescence. The spectroscopic characteristics of the as-prepared and heat treated samples at temperatures below and above Tg were studied as well as their room temperature photometric properties under ultraviolet excitation. All the doped glasses exhibit typical signatures of the lanthanides in their trivalent charge state. For the samarium doped glass heat treated at 250 °C (lower than Tg) the Sm2+ luminescence was also observed. The analysis of the luminescence efficiency was performed in the interval range of 14 K to room temperature, where the integrated intensity of the luminescence was found to decrease for the Sm3+ and Tb3+ ions in the studied temperature range. Luminescence decay curves were found to be non-exponential for the 4G5/2 → 6H7/2 and5D3 → 7F4 transitions of the Sm3+ and Tb3+ ions, respectively. The results strongly suggest the occurrence of energy transfer processes through cross relaxation phenomena, mediated by dipole–dipole interaction in all the studied samples. The decay of the 5D4 → 7F5 emission of the Tb3+ ions was found to be single exponential with a time constant of ∼3.1 ms. Based on the spectroscopic characteristics, models for recombination processes are proposed. The room temperature luminance photometric properties with ultraviolet excitation show that the samarium doped glasses have much lower luminance intensity (around 0.3 Cd/m2) when compared with the 6–7 Cd/m2 observed for the terbium doped ones.

Amado, M, Amado A, Poggi F, Correia de Freitas J.  2013.  Efficiency Based Model for Solar Urban Planning. International Journal of Civil, Architectural Science and Engineering. Vol. 7(Nº 12):1-5.
Dias, RJ, Vale TM, Lourenço JM.  2013.  Efficient Support for In-Place Metadata in Java Software Transactional Memory. Concurrency and Computation: Practice & Experience. 25(17):2394–2411.: Wiley Abstract2013-ccpe.pdf

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Baptista, AC, Ferreira I, Borges JP.  2013.  Electrospun fibers in composite materials for medical applications. Journal of Composites and Biodegradable Polymers . 1:56-65. AbstractWebsite

The development of nanoscaled materials has deserved a remarkable interest for biomedical applications. Biological tissues are essentially composite materials with particular mechanical properties that should be carefully considered during the design of innovative biomedical scaffolds. Electrospun membranes are often found in medical applications due to its high specific surface which creates a 3D porous structure that mimics the native extracellular matrix. These electrospun membranes can also be designed to have enhanced mechanical properties, biocompatibility and cellular response making them appealing and inspiring to be used in composites materials.
This paper reviews the new insights in the development of advanced nanostructured composites materials based on electrospun fibers. From tissue engineering to bioelectronics, these composite materials can be found in the most promising research developments for the medical applications.

Poggi, F, Amado MP.  2013.  ENERGIA SOLAR: FATOR NO PROCESSO DE PLANEAMENTO DA CIDADE Solar Energy: Factor in the Process of Planning City. 2º Congresso Internacional da habitação no Espaço Lusófono. :240-241., Lisboa, PT: LNEC
Schmolka, N, Serre K, Grosso AR, Rei M, Pennington DJ, Gomes AQ, Silva-santos B.  2013.  Epigenetic and transcriptional signatures of stable versus plastic differentiation of proinflammatory γδT cell subsets.. Nature immunology. 14:1093–1100., Number 10: Nature Publishing Group AbstractWebsite

Two distinct subsets of γδ T cells that produce interleukin 17 (IL-17) (CD27(-) γδ T cells) or interferon-γ (IFN-γ) (CD27(+) γδ T cells) develop in the mouse thymus, but the molecular determinants of their functional potential in the periphery remain unknown. Here we conducted a genome-wide characterization of the methylation patterns of histone H3, along with analysis of mRNA encoding transcription factors, to identify the regulatory networks of peripheral IFN-γ-producing or IL-17-producing γδ T cell subsets in vivo. We found that CD27(+) γδ T cells were committed to the expression of Ifng but not Il17, whereas CD27(-) γδ T cells displayed permissive chromatin configurations at loci encoding both cytokines and their regulatory transcription factors and differentiated into cells that produced both IL-17 and IFN-γ in a tumor microenvironment.

Rosa, IM.  2013.  Evaluation of the effect of hearing aids using electroencephalographic analysis. Enterprise and Work Innovation Studies. 9(9):29-38. AbstractWebsite

We wonder how it is possible to use the Electroencephalogram (EEG) as a TA instrument, rather than a diagnosis procedure, to evaluate how children hear the sounds. The first concern was related to the definition of concepts, namely the primary and secondary objectives, the importance of the study, the materials and equipment, the procedures, the criteria for inclusion and exclusion and the expected outcomes. We present the main research questions, the proposed methodology and report the first steps of the practical work, some results and a few considerations about the thesis next development.

Maia, MJ.  2013.  Foresight Exercises as a tool for decision-making: the example of two case studies in health. Enterprise and Work Innovation Studies. 9(9):39-66. AbstractWebsite

Healthcare systems are characterized by a rapid technology push and demand. Most decisions taken in this field usually are accompanied by risk and uncertainties. Due to financial constrains (common in every healthcare system), all decision must be made based on evidences of reliable studies. It may be not possible to know the future needs of healthcare systems in general, but it should be possible to foreseen them. This paper aims to shed some light on how prospective analysis can be an adding tool for the decision-making process, by enhancing exploratory and strategic dimension of planning and managing in a sensitive field such as healthcare. In order to provide for a simple overview on foresight exercises applied to health, this paper presents two study-cases that applied different methods. Since different foresight methods were applied, a comparative case-study analysis was applied, taking into consideration the following aspects of the exercise: aim, methodology, stakeholders and outputs. The specific objectives of this report are: to explore the usage of foresight methods applied to healthcare level in two different countries and therefore to understand if there are any similarities in the approach; and based on the analysis results, to develop recommendations for healthcare level decision-making in general. The results of this report can be useful for a better understanding on how foresight methods can be applied in healthcare and their importance. This article can help healthcare professionals, providing them a glimpse of some steps on the use of these foresight methods, so they can be more alert for foresight methodological framework and their practical applications. The knowledge on how to apply foresight methodology can be a differential and potential asset of a well-organized and informed institution, as well as an asset for a shared and participative strategic planning.

Dantas, JM, Tomaz DM, Morgado L, Salgueiro CA.  2013.  Functional characterization of PccH, a key cytochrome for electron transfer from electrodes to the bacterium Geobacter sulfurreducens. FEBS Letters. 587(16):2662-2668. AbstractWebsite

The cytochrome PccH from Geobacter sulfurreducens (Gs) plays a crucial role in current-consuming fumarate-reducing biofilms. Deletion of pccH gene inhibited completely electron transfer from electrodes toward Gs cells. The pccH gene was cloned and the protein heterologously expressed in Escherichia coli. Complementary biophysical techniques including CD, UV-visible and NMR spectroscopy were used to characterize PccH. This cytochrome contains one low-spin c-type heme with His-Met axial coordination and unusual low-reduction potential. This reduction potential is pH-dependent, within the Gs physiological pH range, and is discussed within the context of the electron transfer mechanisms from electrodes to Gs cells.

Barroso, T, Hussain A, Roque ACA, Aguiar‐Ricardo A.  2013.  Functional monolithic platforms: Chromatographic tools for antibody purification. Biotechnology journal. 8(6):671–681. AbstractWebsite

Polymer monoliths are an efficient platform for antibody purification. The use of monoclonal antibodies (mAbs) and engineered antibody structures as therapeutics has increased exponentially over the past few decades. Several approaches use polymer monoliths to purify large quantities of antibody with defined clinical and performance requirements. Functional monolithic supports have attracted a great deal of attention as they offer practical advantages for antibody purification, such as more rapid analysis, smaller sample volume requirements and the opportunity for a greater target molecule enrichment. This review focuses on the development of synthetic and natural polymer-based monoliths for antibody purification. The materials and methods employed in monolith production are discussed, highlighting the properties of each system. We also review the structural characterization techniques available using monolithic systems and their performance under different chromatographic approaches to antibody capture and release. Finally, a summary of monolithic platforms developed for antibody separation is presented, as well as expected trends in research to solve current and future challenges in this field. This review comprises a comprehensive analysis of proposed solutions highlighting the remarkable potential of monolithic platforms.

Alves R.D., L.C. R, J.R. A, Fernandes M., Pinto J.V., L. P, Pawlicka A., R. M, Fortunato E., Bermudez V.D., M.M. S.  2013.  GelatinnZn(CF3SO3)2 Polymer Electrolytes for Electrochromic Devices. Electroanalysis. 25(6):1483-1490.
Rodrigues, R, Grosso AR, Moita L.  2013.  Genome-wide analysis of alternative splicing during dendritic cell response to a bacterial challenge. PloS one. 8:e61975., Number 4 AbstractWebsite

The immune system relies on the plasticity of its components to produce appropriate responses to frequent environmental challenges. Dendritic cells (DCs) are critical initiators of innate immunity and orchestrate the later and more specific adaptive immunity. The generation of diversity in transcriptional programs is central for effective immune responses. Alternative splicing is widely considered a key generator of transcriptional and proteomic complexity, but its role has been rarely addressed systematically in immune cells. Here we used splicing-sensitive arrays to assess genome-wide gene- and exon-level expression profiles in human DCs in response to a bacterial challenge. We find widespread alternative splicing events and splicing factor transcriptional signatures induced by an E. coli challenge to human DCs. Alternative splicing acts in concert with transcriptional modulation, but these two mechanisms of gene regulation affect primarily distinct functional gene groups. Alternative splicing is likely to have an important role in DC immunobiology because it affects genes known to be involved in DC development, endocytosis, antigen presentation and cell cycle arrest.

Franco, R, Pereira E.  2013.  Gold Nanoparticles and Proteins, Interactions. Encyclopedia of Metalloproteins. (Kretsinger, R.H., Uversky, V.N., Permyakov, E.A., Eds.).:908-915., New York: Springer Science+Business Media
Barroso, T, Lourenço A, Araújo M, Bonifácio VDB, Roque ACA, Aguiar-Ricardo A.  2013.  A green approach toward antibody purification: a sustainable biomimetic ligand for direct immobilization on (bio)polymeric supports. Journal of Molecular Recognition. 26(12):662-671.
Carvalho, S, Raposo AC, Martins FB, Grosso AR, Sridhara SC, Rino J, Carmo-fonseca M, de Almeida SF.  2013.  Histone methyltransferase SETD2 coordinates FACT recruitment with nucleosome dynamics during transcription. Nucleic acids research. 41:2881–93., Number 5 AbstractWebsite

Histone H3 of nucleosomes positioned on active genes is trimethylated at Lys36 (H3K36me3) by the SETD2 (also termed KMT3A/SET2 or HYPB) methyltransferase. Previous studies in yeast indicated that H3K36me3 prevents spurious intragenic transcription initiation through recruitment of a histone deacetylase complex, a mechanism that is not conserved in mammals. Here, we report that downregulation of SETD2 in human cells leads to intragenic transcription initiation in at least 11% of active genes. Reduction of SETD2 prevents normal loading of the FACT (FAcilitates Chromatin Transcription) complex subunits SPT16 and SSRP1, and decreases nucleosome occupancy in active genes. Moreover, co-immunoprecipitation experiments suggest that SPT16 is recruited to active chromatin templates, which contain H3K36me3-modified nucleosomes. Our results further show that within minutes after transcriptional activation, there is a SETD2-dependent reduction in gene body occupancy of histone H2B, but not of histone H3, suggesting that SETD2 coordinates FACT-mediated exchange of histone H2B during transcription-coupled nucleosome displacement. After inhibition of transcription, we observe a SETD2-dependent recruitment of FACT and increased histone H2B occupancy. These data suggest that SETD2 activity modulates FACT recruitment and nucleosome dynamics, thereby repressing cryptic transcription initiation.

Cerff, M, Scholz A, Franzreb M, Batalha IL, Roque ACA, Posten C.  2013.  In situ magnetic separation of antibody fragments from Escherichia coli in complex media. BMC biotechnology. 13(1):44. AbstractWebsite

Background
In situ magnetic separation (ISMS) has emerged as a powerful tool to overcome process constraints such as product degradation or inhibition of target production. In the present work, an integrated ISMS process was established for the production of his-tagged single chain fragment variable (scFv) D1.3 antibodies (?D1.3?) produced by E. coli in complex media. This study investigates the impact of ISMS on the overall product yield as well as its biocompatibility with the bioprocess when metal-chelate and triazine-functionalized magnetic beads were used.

Results
Both particle systems are well suited for separation of D1.3 during cultivation. While the triazine beads did not negatively impact the bioprocess, the application of metal-chelate particles caused leakage of divalent copper ions in the medium. After the ISMS step, elevated copper concentrations above 120?mg/L in the medium negatively influenced D1.3 production. Due to the stable nature of the model protein scFv D1.3 in the biosuspension, the application of ISMS could not increase the overall D1.3 yield as was shown by simulation and experiments.

Conclusions
We could demonstrate that triazine-functionalized beads are a suitable low-cost alternative to selectively adsorb D1.3 fragments, and measured maximum loads of 0.08?g D1.3 per g of beads. Although copper-loaded metal-chelate beads did adsorb his-tagged D1.3 well during cultivation, this particle system must be optimized by minimizing metal leakage from the beads in order to avoid negative inhibitory effects on growth of the microorganisms and target production. Hereby, other types of metal chelate complexes should be tested to demonstrate biocompatibility. Such optimized particle systems can be regarded as ISMS platform technology, especially for the production of antibodies and their fragments with low stability in the medium. The proposed model can be applied to design future ISMS experiments in order to maximize the overall product yield while the amount of particles being used is minimized as well as the number of required ISMS steps.

Coelho, C, Marangon J, Rodrigues D, Moura JJG, Romão MJ, Paes de Sousa PM, Correia dos Santos MM.  2013.  Induced peroxidase activity of haem containing nitrate reductases revealed by protein film electrochemistry. J Electroanal Chem. 693:105-113.
Paes de Sousa, PM, Grazina R, Barbosa ADS, de Castro B, Moura JJG, Cunha-Silva L, Salete S.  2013.  Insights into the electrochemical behaviour of composite materials: Monovacant polyoxometalates porous metal-organic framework. Electrochim Acta. 87:853-859.
Gromicho, M, Magalhaes M, Torres F, Dinis J, Fernandes AR, Rendeiro P, Tavares P, Laires A, Rueff J, Rodrigues AS.  2013.  Instability of mRNA expression signatures of drug transporters in chronic myeloid leukemia patients resistant to imatinib. Oncol Rep. 29(2):741-50.13gromichoor.pdf
Merino, EG, Danéde F, Derrollez P, Dias CJ, Viciosa TM, Correia NT, Dionísio M.  2013.  Investigating the influence of morphology in the dynamical behavior of semicrystalline Triton X100: insights in the detection/nondetection of the α′-Process. The Journal of Physical Chemistry B. 17:9793-9805.Website
Grazina, R, Pauleta S, Moura JJG, Moura I.  2013.  Iron-sulfur centers: New roles for ancient metal sites. Comprehensive Inorganic Chemistry II, Vol. 3: Bioinorganic Fundamentals and Applications: Metals in Natural Living Systems and Metals in Toxicology and Medicine. :103-148., Oxford: Elsevier
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