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2012
Bras, Joana L. A., Ana Luisa Carvalho, Aldino Viegas, Shabir Najmudin, Victor D. Alves, Jose A. M. Prates, Luis M. A. Ferreira, Maria J. Romao, Harry J. Gilbert, and Carlos M. G. A. Fontes. "Escherichia coli expression, purification, crystallization, and structure determination of bacterial cohesin-dockerin complexes." Methods in enzymology. Vol. 510. 2012. 395-415. Abstract

Cellulosomes are highly efficient nanomachines that play a fundamental role during the anaerobic deconstruction of complex plant cell wall carbohydrates. The assembly of these complex nanomachines results from the very tight binding of repetitive cohesin modules, located in a noncatalytic molecular scaffold, and dockerin domains located at the C-terminus of the enzyme components of the cellulosome. The number of enzymes found in a cellulosome varies but may reach more than 100 catalytic subunits if cellulosomes are further organized in polycellulosomes, through a second type of cohesin-dockerin interaction. Structural studies have revealed how the cohesin-dockerin interaction mediates cellulosome assembly and cell-surface attachment, while retaining the flexibility required to potentiate catalytic synergy within the complex. Methods that might be applied for the production, purification, and structure determination of cohesin-dockerin complexes are described here. Copyright 2012 Elsevier Inc. All rights reserved.

Barišić, Ankica, Vasco Amaral, Miguel Goulão, and Bruno Barroca. "Evaluating the Usability of Domain-Specific Languages." Formal and Practical Aspects of Domain-Specific Languages: Recent Developments. Ed. Marjan Mernik. IGI Global, 2012. Abstract

We can regard Domain-Specific Languages (DSLs) as User Interfaces (UIs) because they bridge the gap
between the domain experts and the computation platforms. Usability of DSLs by domain experts is a key
factor for their successful adoption. The few reports supporting improvement claims are persuasive, but
mostly anecdotal. Systematic literature reviews show that evidences on the effects of the introduction of
DSLs are actually very scarce. In particular, the evaluation of usability is often skipped, relaxed, or at
least omitted from papers reporting the development of DSLs. The few exceptions mostly take place at
the end of the development process, when fixing problems is already too expensive. A systematic
approach, based on techniques for the experimental evaluation of UIs, should be used to assess suitability
of new DSLs. This chapter presents a general experimental evaluation model, tailored for DSLs’
experimental evaluation, and instantiates it in several DSL’s evaluation examples.

Herrera, J., Rivera P. Salas, R. Vargas, I. Macia, R. Pinho, A. Garcia, J. Araújo, and K. Breitman An Exploraty Study of Aspect-Oriented Requirement Engineering Tools. 26º Simpósio Brasileiro de Engenharia de Software (SBES). Natal, Brazil: IEEE digital library, 2012.
Lucas, D., H. C. Biscaia, M. A. G. Silva, and C. Chastre Factores que influenciam o desempenho da ligação GFRP/betão. Betão Estrutural 2012. Porto: FEUP, 2012. Abstractlucas2012bisich_-_be2012.pdf

Os compósitos de FRP podem descolar prematuramente da superfíce de betão, isto é, antes de esgotada a sua resistência elástica. Esta situação é mais provável se não forem tidos em conta factores como o tipo de preparação da superfície, a exposição a acção ambiental severa, e a resistência do próprio betão. Com o objectivo de analisar a influência de parte destes factores no desempenho da ligação compósito de fibra de vidro (GFRP) e betão, empreendeu-se uma campanha experimental baseada em ensaios de corte duplo. Os resultados permitiram determinar e comparar as forças máximas transmitidas ao GFRP e tensões de aderência máxima para diferentes tratamentos de superfície e condições de envelhecimento. Foram também determinadas aproximações para curvas de tensão de aderência vs. deslizamento (bond-slip). Os resultados obtidos são contrastados com resultados obtidos por modelação numérica.

Mendes, Ana Sofia, Maria Amalia Botelho, Ana Luisa Papoila, João Viegas, Daniel Aelenei, Paixão, P. Paquete, Iolanda Caires, Susana Azevedo, Pedro Martins, J. Martins, C. Pedro, P. Neves, Nuno Neuparth, and João Teixeira. "Geria Project preliminary study on indoor air quality and health related quality of life in elderly care centers." CISE 2012, Conference. 2012. Abstract

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Guirgis, Bassem, Cláudia Sá e Cunha, Inês Gomes, Miguel Cavadas, Isabel Silva, Gonçalo Doria, Gregory Blatch, Pedro Baptista, Eulália Pereira, Hassan Azzazy, Maria Mota, Miguel Prudêncio, and Ricardo Franco. "Gold nanoparticle-based fluorescence immunoassay for malaria antigen detection." Analytical and Bioanalytical Chemistry. 402.3 (2012): 1019-1027.
Lapa, N., R. Barbosa, and B. Mendes. "Intrinsic properties of new materials for civil engineering works based on the reuse of MSWI bottom ashes: chemical and ecotoxicological assessment." Urban Mining: A global cycle approach to resource recovery from solid waste. Eds. R. Cossu, V. Salieri, and V. Bisinella. Padova: CISA Publisher, 2012. 298-307.
Brás, C. P., W. W. Hager, and J. J. Júdice. "An investigation of feasible descent algorithms for estimating the condition number of a matrix." TOP - Journal of the Spanish Society of Statistics and Operations Research. 20 (2012): 791-809. AbstractWebsite

Techniques for estimating the condition number of a nonsingular matrix are developed. It is shown that Hager's 1-norm condition number estimator is equivalent to the conditional gradient algorithm applied to the problem of maximizing the 1-norm of a matrix-vector product over the unit sphere in the 1-norm. By changing the constraint in this optimization problem from the unit sphere to the unit simplex, a new formulation is obtained which is the basis for both conditional gradient and projected gradient algorithms. In the test problems, the spectral projected gradient algorithm yields condition number estimates at least as good as those obtained by the previous approach. Moreover, in some cases, the spectral gradient projection algorithm, with a careful choice of the parameters, yields improved condition number estimates.

Guimarães, D., M. L. Carvalho, M. Becker, A. von Bohlen, V. Geraldes, I. Rocha, and J. P. Santos. "Lead concentration in feces and urine of exposed rats by x-ray fluorescence and electrothermal atomic absorption spectrometry." X-Ray Spectrom.. 41 (2012): 80. Abstract

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Ramos, Tania Rodrigues Pereira, Maria Isabel Gomes, and Ana Paula Barbosa-póvoa. "Minimizing CO2 Emissions in a Recyclable Waste Collection System with Multiple Depots." EUROMA/POMS Joint Conference. 2012. 1-11. Abstracteuroma_2012_fullpaper_final.pdf

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Cunha, Jácome, João Saraiva, and Joost Visser. "Model-Based Programming Environments for Spreadsheets." Programming Languages. Eds. Francisco de Carvalho Junior, and Luis Barbosa. Vol. 7554. Lecture Notes in Computer Science, 7554. Springer Berlin / Heidelberg, 2012. 117-133. Abstractsblp12.pdf

Although spreadsheets can be seen as a flexible programming environment, they lack some of the concepts of regular programming languages, such as structured data types. This can lead the user to edit the spreadsheet in a wrong way and perhaps cause corrupt or redundant data. We devised a method for extraction of a relational model from a spreadsheet and the subsequent embedding of the model back into the spreadsheet to create a model-based spreadsheet programming environment. The extraction algorithm is specific for spreadsheets since it considers particularities such as layout and column arrangement. The extracted model is used to generate formulas and visual elements that are then embedded in the spreadsheet helping the user to edit data in a correct way. We present preliminary experimental results from applying our approach to a sample of spreadsheets from the EUSES Spreadsheet Corpus.

Brazinha, C., A. P. Fonseca, H. Pereira, O. M. N. D. Teodoro, and J. G. C. Crespo. "Modelling gas permeation based on the morphology of a natural polymer material." Procedia Engineering. Vol. 44. 2012. 529-531. Abstract2012_modelling_gas_permeation.pdf

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Mouquinho, AI, K. T. Petrova, M. T. Barros, and J. C. Sotomayor. "New Polymer Networks for PDLC Films Application." New Polymers for Special Applications . Ed. A. De-Souza-Gomes. Rijeka: InTech, 2012. 139-164.
Zeballos, L. J., M. I. Gomes, A. P. Barbosa-Povoa, and A. Q. Novais. "Optimum Design and Planning of Resilient and Uncertain Closed-Loop Supply Chains." 22nd European Symposium on Computer Aided Process Engineering. Eds. Ian David Lockhart Bogle, and Michael Fairweather. Vol. 30. Computer Aided Chemical Engineering, 30. London: Elsevier, 2012. 407-411. Abstract

The design and planning of efficient supply chains (SC) is a major challenge that increases when the return of products has to be accounted for, the so-called closed-loop supply chains (CLSC). In the present work the effect of disruptions and modifications in the operating conditions of CLSCs are investigated on the basis of a 2-stage scenario based model previously developed by the authors. Metrics derived from graph theory are used, along with more conventional economic and operational indices. A discussion on the results obtained is presented to assess how the design and planning of the CLSC respond to these challenges and how these metrics may contribute to this objective.

Boavida, Nuno, António B. Moniz, Torsten Fleischer, Sophie Kuppler, Andreas Lösch, Jens Schippl, and Judith Simon. "Perspectives on Technology, Society and Innovation." TATuP - Zeitschrift für Technikfolgenabschätzung in Theorie und Praxis. 21.3 (2012): 92-95. AbstractWebsite

To focus on processes of scientific and technological design and on how newly designed objects are used in different ways than initially intended (“displaced”), the organizers (the Society for Social Studies on Science-4S and the European Association of Studies on Science and Technology-EASST) chose the conference theme “Design and Displacement”. The concept of design here referred to innovative processes in forming new ideas and material objects. This general idea was reflected in a multitude of sub-topics.

Bernardo, M., N. Lapa, M. Gonçalves, B. Mendes, F. Pinto, I. Fonseca, and H. Lopes. "Physico-chemical properties of chars obtained in the co-pyrolysis of waste mixtures." Journal of Hazardous Materials. 219-220 (2012): 196-202. AbstractWebsite

The present work aims to perform a multistep upgrading of chars obtained in the co-pyrolysis of PE, PP and PS plastic wastes, pine biomass and used tires. The quality of the upgraded chars was evaluated by measuring some of their physico-chemical properties in order to assess their valorisation as adsorbents’ precursors. The crude chars were submitted to a sequential solvent extraction with organic solvents of increasing polarity (hexane, mixture 1:1 v/v hexane:acetone and acetone) followed by an acidic demineralization procedure with 1 M HCl solution. The results obtained showed that the upgrading treatment allow the recovery of 63–81% of the pyrolysis oils trapped in the crude chars and a reduction in the char's ash content in the range of 64–86%. The textural and adsorption properties of the upgraded chars were evaluated and the results indicate that the chars are mainly mesoporous and macroporous materials, with adsorption capacities in the range of 3.59–22.2 mg/g for the methylene blue dye. The upgrading treatment allowed to obtain carbonaceous materials with quality to be reused as adsorbents or as precursors for activated carbon.

Peça, I. N., K. T. Petrova, M. M. Cardoso, and M. T. Barros. "Preparation and Characterization of Polymeric Nanoparticles Composed of Poly(DL-lactide-co-glycolide) and Poly(DL-lactide-co-glycolide)-co-poly(ethylene glycol) 10%Triblock end-capped with a galactose moiety." React. Funct. Polym. 72.10 (2012): 729-735. DOI: 10.1016/j.reactfunctpolym.2012.06.019.
Morgado, Carmen, and Fernanda Barbosa Presentation Problem in CS1 courses. Proc. of 17th Annual Conference on Innovation and Technology in Computer Science Education (ITICSE). Haifa, Israel, 2012.
Pimenta, J., FMV Dias, C. C. Marques, M. C. Baptista, M. I. Vasques, A. E. M. Horta, J. P. Barbas, R. Soares, P. Mesquita, E. Cabrita, CMGA Fontes, J. A. Prates, and R. M. Pereira. "The Prion-like Protein Doppel Enhances Ovine Spermatozoa Fertilizing Ability." Reproduction in Domestic Animals. 47.2 (2012): 196-202. Abstract

The function of prion-like protein Doppel was suggested to be related to male fertility. In this study, the importance of ovine Doppel polypeptide on spermatozoa capacitation and fertilization was evaluated. After refolding, recombinant Doppel (rDpl) was supplemented with different concentrations (40, 80 or 190 ng/ml) to ovine spermatozoa during the capacitation process. In experiment 1, post-thawed ovine spermatozoa were incubated with different concentrations of rDpl during 1 h for swim-up, and changes in sperm motility, concentration, vigour, viability and capacitation were monitored (10 replicates). In experiment 2, the fertilization ability of post-swim-up spermatozoa incubated as above was tested through heterologous fertilization of bovine in vitro matured oocytes (n = 423, three replicates). Regardless of dosage, rDpl improved (p = 0.03) spermatozoa viability. Sperm individual motility and vigour were the highest (p = 0.04) for the group receiving 190 ng/ml rDpl. Sperm supplemented with the highest doses of rDpl achieved higher (p = 0.02) fertilization rates (56.0 +/- 3.0%) than control (39.1 +/- 2.2%) and 40 ng/ml rDpl (39.8 +/- 2.7%). Preliminary data suggest that Doppel protein may enhance in vitro spermatozoa fertilizing ability.

Pinho, Fernando F. S., Válter J. G. Lúcio, and Manuel F. C. BAIÃO. "Rubble Stone Masonry Walls in Portugal Strengthened with Reinforced Micro-Concrete Layers." Bulletin of Earthquake Engineering. 10.ISSN 1570-761X. DOI 10.1007/s10518-011-9280-4 (2012): 161-180.
Morgado, Carmen, and Fernanda Barbosa A Structured Approach to Problem Solving in CS1. Proc. of 17th Annual Conference on Innovation and Technology in Computer Science Education (ITICSE). Haifa, Israel, 2012.
Bernardo, M., N. Lapa, M. Gonçalves, B. Mendes, and F. Pinto. "Study of the organic extraction and acid leaching of chars obtained in the pyrolysis of plastics, tire rubber and forestry biomass wastes." Procedia Engineering. 42 (2012): 1909-1916. AbstractWebsite

The present work aims to perform a characterization of chars obtained in the co-pyrolysis of waste mixtures composed by plastics, tires and pine biomass, to provide knowledge about the composition, leaching behavior and risk assessment of these materials in order to define strategies for their possible valorization or safe disposal. The chars were submitted to sequential solvent extractions with organic solvents of increasing polarity that allow the recovery of significant amounts of the pyrolysis oils trapped in the crude chars improving the yield of the pyrolysis liquids. An acidic demineralization procedure was successfully applied to the chars and high efficiency removals of the majority of the heavy metals were achieved. The demineralization study also demonstrated that hazardous heavy metals such as chromium, nickel and cadmium are significantly immobilized in the char matrix, and other heavy metals of concern such as zinc and lead will not represent a leaching problem if acidic conditions were not used. The obtained chars present sufficient quality and characteristics to be used as fuel or alternatively, to be used as adsorbents or precursors of activated carbon.

da Silva, Mara Soares, Raquel Viveiros, Ana Aguiar-Ricardo, Vasco D. B. Bonifacio, and Teresa Casimiro. "Supercritical fluid technology as a new strategy for the development of semi-covalent molecularly imprinted materials." RSC Adv.. 2 (2012): 5075-5079. AbstractPDFWebsite

Molecularly imprinted polymeric particles with molecular recognition towards Bisphenol A (BPA) were synthesized for the first time using the semi-covalent imprinting approach in supercritical carbon dioxide (scCO2). The material{'}s affinity to BPA was achieved by co-polymerizing ethylene glycol dimethacrylate (EGDMA) with a template-containing monomer{,} Bisphenol A dimethacrylate (BPADM) in scCO2. Bisphenol A is then cleaved from the polymeric matrix by hydrolysis with tetrabutylammonium hydroxide (n-Bu4OH) also in a supercritical environment{,} taking advantage of the high diffusivity of scCO2. The selectivity of the molecular imprinted polymer (MIP) was assessed by evaluating its capability to bind BPA in comparison with progesterone and [small alpha]-ethinylestradiol. In addition{,} the cross-linked particles were used to prepare a PMMA-based hybrid imprinted membrane by a scCO2-assisted phase inversion method. Results show that the incorporation of MIP particles was able to confer molecular affinity to BPA to the membrane and that at dynamic conditions of filtration{,} this imprinted porous structure was able to adsorb a higher amount of BPA than the corresponding non-imprinted hybrid membrane. Our work represents a valuable greener alternative to conventional methods{,} for the synthesis of affinity materials which are able to maintain molecular recognition properties in water.

Martins, R. M. S., F. Beckmann, R. Castanhinha, O. Mateus, R. Araújo, and P. K. Pranzas Synchrotron radiation-based micro-computed tomography applied to the characterization of dinosaur fossils from the Lourinhã Formation. 1 st . Meeting of Synchrotron Radiation Users from Portugal. Caparica, Portugal, 2012.martins_et_al_2012_tomography_enurs_martins-rui_dinosaurfossils.pdf
Faísca-Phillips, A. M., and M. T. Barros. "Synthesis of geminal bisphosphonates via organocatalyzed enantioselective Michael additions of cyclic ketones and 4-piperidones." Org. Biomol. Chem.. 10 (2012): 404-412.