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2018
Pereira, F. A. M., M. F. S. F. de Moura, N. Dourado, J. J. L. Morais, J. Xavier, and M. I. R. Dias. "Determination of mode II cohesive law of bovine cortical bone using direct and inverse methods." International Journal of Mechanical Sciences. 138-139 (2018): 448-456. AbstractWebsite

This study presents two alternative methods to determine the cohesive law of bovine cortical bone under mode II loading, employing the End Notched Flexure (ENF) test. The direct method results from the combination of the progress of the mode II strain energy release rate with the crack tip shear displacement, obtained by digital image correlation. The resulting cohesive law is determined by differentiation of this relation relatively to the crack shear displacement. The inverse method employs finite element analyses with cohesive zone modelling, in association with an optimization procedure. The resulting strategy enables determining the cohesive law without establishing a pre-defined shape. The significant conclusion that comes out of this work is that both methods offer consistent results regarding the estimation of the cohesive law in bone. Given that the inverse method dispenses the use of sophisticated equipment to obtain the cohesive law in bone, it can be used as a more convenient procedure to accomplish efficient studies in the context of bone fracture characterization under mode II loading.

Kumar, Krishan, Márcia Correia, Virgínia R. Pires, Arun Dhillon, Kedar Sharma, Vikky Rajulapati, Carlos M. G. A. Fontes, Ana Luísa Carvalho, and Arun Goyal. "Novel insights into the degradation of β-1,3-glucans by the cellulosome of Clostridium thermocellum revealed by structure and function studies of a family 81 glycoside hydrolase." International Journal of Biological Macromolecules (2018): -. AbstractWebsite

Abstract The family 81 glycoside hydrolase (GH81) from Clostridium thermocellum is a β-1,3-glucanase belonging to cellulosomal complex. The gene encoding \{GH81\} from Clostridium thermocellum (CtLam81A) was cloned and expressed displaying a molecular mass of  82 kDa. CtLam81A showed maximum activity against laminarin (100 U/mg), followed by curdlan (65 U/mg), at pH 7.0 and 75 °C. CtLam81A displayed Km, 2.1 ± 0.12 mg/ml and Vmax, 109 ± 1.8 U/mg, against laminarin under optimized conditions. CtLam81A activity was significantly enhanced by Ca2+ or Mg2+ ions. Melting curve analysis of CtLam81A showed an increase in melting temperature from 91 °C to 96 °C by Ca2+ or Mg2+ ions and decreased to 82 °C by EDTA, indicating that Ca2+ and Mg2+ ions may be involved in catalysis and in maintaining structural integrity. \{TLC\} and MALDI-TOF analysis of β-1,3-glucan hydrolysed products released initially, showed β-1,3-glucan-oligosaccharides degree of polymerization (DP) from \{DP2\} to DP7, confirming an endo-mode of action. The catalytically inactive mutant CtLam81A-E515A generated by site-directed mutagenesis was co-crystallized and tetragonal crystals diffracting up to 1.4 Å resolution were obtained. CtLam81A-E515A contained 15 α-helices and 38 β-strands forming a four-domain structure viz. a β-sandwich domain I at N-terminal, an α/β-domain II, an (α/α)6 barrel domain III, and a small 5-stranded β-sandwich domain IV.

Monteiro, C. M. B., F. D. Amaro, M. S. Sousa, M. Abdou-Ahmed, P. Amaro, F. Biraben, T. Chen, D. S. Covita, A. J. Dax, M. Diepold, L. M. P. Fernandes, B. Franke, S. Galtier, A. L. Gouvêa, J. Götzfried, T. Graf, T. W. Hansch, M. Hildebrandt, P. Indelicato, L. Julien, K. Kirch, A. Knecht, F. Kottmann, J. J. Krauth, Y. Liu, J. Machado, F. Mulhauser, B. Naar, T. Nebel, F. Nez, R. Pohl, J. P. Santos, J. M. F. dos Santos, K. Schuhmann, C. I. Szabo, D. Taqqu, J. F. C. A. Veloso, and A. Antognini. "{On the double peak structure of avalanche photodiode response to monoenergetic x-rays at various temperatures and bias voltages}." J. Inst.. 13 (2018): C01033. Abstract
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Diaz Fernandez, P., et al. "{Quasifree ( p,pN) scattering of light neutron-rich nuclei near N=14}." Physical Review C. 97 (2018): 1459. Abstract
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2017
Mateus, O., J. and Dinis, P. P. Cunha, and and. "The Lourinhã Formation: the Upper Jurassic to lower most Cretaceous of the Lusitanian Basin, Portugal – landscapes where dinosaurs walked." Ciências da Terra - Earth Sciences Journal. 19 (2017): 75-97. AbstractWebsite
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Kryshtafovych, Andriy, Reinhard Albrecht, Arnaud Baslé, Pedro Bule, Alessandro T. Caputo, Ana Luisa Carvalho, Kinlin L. Chao, Ron Diskin, Krzysztof Fidelis, Carlos M. G. A. Fontes, Folmer Fredslund, Harry J. Gilbert, Celia W. Goulding, Marcus D. Hartmann, Christopher S. Hayes, Osnat Herzberg, Johan C. Hill, Andrzej Joachimiak, Gert-Wieland Kohring, Roman I. Koning, Leila {Lo Leggio}, Marco Mangiagalli, Karolina Michalska, John Moult, Shabir Najmudin, Marco Nardini, Valentina Nardone, Didier Ndeh, Thanh H. Nguyen, Guido Pintacuda, Sandra Postel, Mark J. van Raaij, Pietro Roversi, Amir Shimon, Abhimanyu K. Singh, Eric J. Sundberg, Kaspars Tars, Nicole Zitzmann, and Torsten Schwede. "Target highlights from the first post-PSI CASP experiment (CASP12, May-August 2016)." Proteins: Structure, Function, and Bioinformatics (2017). AbstractWebsite

The functional and biological significance of the selected CASP12 targets are described by the authors of the structures. The crystallographers discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP12 experiment. This article is protected by copyright. All rights reserved.

Pohl, Randolf, François Nez, Luis M. P. Fernandes, Marwan Abdou Ahmed, Fernando D. Amaro, Pedro Amaro, François Biraben, João M. R. Cardoso, Daniel S. Covita, Andreas Dax, Satish Dhawan, Marc Diepold, Beatrice Franke, Sandrine Galtier, Adolf Giesen, Andrea L. Gouvea, Johannes Götzfried, Thomas Graf, Theodor W. Hänsch, Malte Hildebrandt, Paul Indelicato, Lucile Julien, Klaus Kirch, Andreas Knecht, Paul Knowles, Franz Kottmann, Julian J. Krauth, Eric-Olivier Le Bigot, Yi-Wei Liu, José A. M. Lopes, Livia Ludhova, Jorge Machado, Cristina M. B. Monteiro, Françoise Mulhauser, Tobias Nebel, Paul Rabinowitz, Joaquim M. F. dos Santos, Jose Paulo Santos, Lukas A. Schaller, Karsten Schuhmann, Catherine Schwob, Csilla I. Szabo, David Taqqu, João F. C. A. Veloso, Andreas Voss, Birgit Weichelt, and Aldo Antognini. "Laser Spectroscopy of Muonic Atoms and Ions." Proceedings of the 12th International Conference on Low Energy Antiproton Physics (LEAP2016). Journal of the Physical Society of Japan, 2017. 1-12. Abstract
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Hussain, Abid, Ana T. S. Semeano, Susana I. C. J. Palma, Ana S. Pina, José Almeida, Bárbara F. Medrado, Ana C. C. S. Pádua, Ana L. Carvalho, Madalena Dionísio, Rosamaria W. C. Li, Hugo Gamboa, Rein V. Ulijn, Jonas Gruber, and Ana C. A. Roque. "Tunable gas sensing gels by cooperative assembly." Advanced Functional Materials. just accep (2017): xx. AbstractWebsite

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Nóbrega, C. S., M. Raposo, G. Van Driessche, B. Devreese, and S. R. Pauleta. "Biochemical characterization of the bacterial peroxidase from the human pathogen Neisseria gonorrhoeae." Journal of Inorganic Biochemistry. 171 (2017): 108-119. AbstractWebsite
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Mendes, Jorge, Jácome Cunha, Francisco Duarte, Gregor Engels, João Saraiva, and Stefan Sauer. "Systematic Spreadsheet Construction Processes." IEEE Symposium on Visual Languages and Human-Centric Computing (VL/HCC). Raleigh, North Carolina, USA: IEEE, 2017. paper.pdf
Cain, Alan J., and António Malheiro. "Combinatorics of Cyclic Shifts in Plactic, Hypoplactic, Sylvester, and Related Monoids." Combinatorics on Words: 11th International Conference, WORDS 2017, Montréal, QC, Canada, September 11-15, 2017, Proceedings. Eds. Srečko Brlek, Francesco Dolce, Christophe Reutenauer, and Élise Vandomme. Cham: Springer International Publishing, 2017. 190-202. Abstract

The cyclic shift graph of a monoid is the graph whose vertices are elements of the monoid and whose edges link elements that differ by a cyclic shift. For certain monoids connected with combinatorics, such as the plactic monoid (the monoid of Young tableaux) and the sylvester monoid (the monoid of binary search trees), connected components consist of elements that have the same evaluation (that is, contain the same number of each generating symbol). This paper discusses new results on the diameters of connected components of the cyclic shift graphs of the finite-rank analogues of these monoids, showing that the maximum diameter of a connected component is dependent only on the rank. The proof techniques are explained in the case of the sylvester monoid.

Rybarczyk, Y., Kleine Deters, J., Aladro Gonzalvo, A., Gonzalez, M., Villarreal, S., and Esparza D. "ePHoRt project: a web-based platform for home motor rehabilitation." 5th World Conference on Information Systems and Technologies. Madeira, Portugal 2017.
Paiva, Luís, Pedro Pereira, Bruno Almeida, Pedro Maló, Juha Hyvärinen, Krzysztof Klobut, Vanda Dimitriou, and Tarek Hassan Interoperability: A Data Conversion Framework to Support Energy Simulation. Vol. 1. Sustainable Places 2017, 1., 2017. Abstract

In this paper an interoperability solution is proposed, aiming to go from (building) construction models to energy simulation. Moreover, the energy simulation results will feed the KPI’s analysis of a designed building. The proposed solution will be used to translate different data formats allowing the communication between different systems in an automated environment. The solution presented in this paper exploits the concept of Plug’n’Interoperate (PnI), that is supported by the principle of self-configuration as to automate, as much as possible, the configuration and participation of systems into a shared interoperability environment. In order to validate this approach two different scenarios were taken into account, translating from a CAD (Computer- Aided Design) model data format to an energy simulation data format.

Deters, J.K., Zalakeviciute, R., Gonzalez, M., and Rybarczyk Y. "Modeling PM2.5 urban pollution using machine learning and selected meteorological parameters." Journal of Electrical and Computer Engineering. 2017 (2017): 1-14.copy.pdf
Dimitrova, I., Vítor H. Fernandes, and J. Koppitz. "A note on generators of the endomorphism semigroup of an infinite countable chain." Journal of Algebra and its Applications (DOI: 10.1142/S0219498817500311). 16 (2017): 1750031 (9 pages). AbstractWebsite

In this note, we consider the semigroup $O(X)$ of all order endomorphisms of an infinite chain $X$ and the subset $J$ of $O(X)$ of all transformations $\alpha$ such that $|Im(\alpha)|=|X|$. For an infinite countable chain $X$, we give a necessary and sufficient condition on $X$ for $O(X) = < J >$ to hold. We also present a sufficient condition on $X$ for $O(X) = < J >$ to hold, for an arbitrary infinite chain $X$.

Dias, J. P., and F. Oliveira. "On a quasilinear non-local Benney system." Journal of Hyperbolic Differential Equations. 14.1 (2017): 135-156.Website
Rybarczyk, Y., Kleine Deters, J., Aladro, A., Esparza, D., Gonzalez, M., Villarreal, S., and Nunes I. "Recognition of physiotherapeutic exercises through DTW and low-cost vision-based motion capture." 8th International Conference on Applied Human Factors and Ergonomics. Los Angeles, USA 2017.
Rybarczyk, Y., Kleine Deters, J., Cointe, C., Aladro, A., and Esparza D. "Telerehabilitation platform for hip surgery recovery." IEEE ETCM. Salinas, Ecuador 2017.
Mendes, Jorge, Jácome Cunha, Francisco Duarte, Gregor Engels, João Saraiva, and Stefan Sauer. "Towards Systematic Spreadsheet Construction Processes (Abstract/Poster)." Proceedings of the 39th International Conference on Software Engineering (ICSE 2017). Buenos Aires, Argentina: ACM and IEEE CS, 2017. paper.pdfposter.pdf
Almeida, R. M., S. Dell'acqua, I. Moura, S. R. Pauleta, and JJG Moura CHAPTER 11: Electron Transfer and Molecular Recognition in Denitrification and Nitrate Dissimilatory Pathways. Eds. I. Moura, JJG Moura, L. B. Maia, C. D. Garner, and S. R. Pauleta. Vol. 2017-January. RSC Metallobiology, 2017-January. Royal Society of Chemistry, 2017. Abstract

The electron transfer pathways for the enzymes involved in the four sequential steps of the denitrification pathway are reviewed. In addition, brief information on the electron transfer events is also provided on two enzymes that participate in the dissimilatory nitrate reduction to ammonia. The two main aspects discussed are the intra- and inter-molecular electron transfer pathways and the molecular recognition processes involving the redox partners. When available, information on the residues that are involved in these pathways is given, and their role in electron transfer and/or the formation of the transient electron transfer complexes is discussed. © The Royal Society of Chemistry 2017.

Pereira, F. A. M., M. F. S. F. de Moura, N. Dourado, J. J. L. Morais, J. Xavier, and M. I. R. Dias. "Direct and inverse methods applied to the determination of mode I cohesive law of bovine cortical bone using the DCB test." International Journal of Solids and Structures. 128 (2017): 210-220. AbstractWebsite

Abstract This work addresses the determination of the cohesive law under mode I loading of bovine cortical bone tissue using the Double Cantilever Beam (DCB) test. Direct and inverse methods were proposed to assess the cohesive laws representative of bone fracture under mode I loading. The direct method combines the evolution of the strain energy release rate under mode I loading with the crack tip opening displacement that is monitored by digital image correlation technique. According to this method, the cohesive law is obtained by differentiation of such relation with respect to the crack opening. The inverse procedure is performed through a finite element analysis including cohesive zone modelling, conjointly with a developed optimization algorithm. This identification strategy does not require a pre-established shape of the cohesive law as with the conventional inverse based procedures, which is viewed as a novelty of this work. It was concluded that both methods provide consistent results, being appellative tools concerning systematic and methodical studies dedicated to bone fracture characterization.