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2015
Palma, A. S., Y. Liu, H. Zhang, Y. Zhang, B. V. McCleary, G. Yu, Q. Huang, L. S. Guidolin, A. E. Ciocchini, A. Torosantucci, D. Wang, AL Carvalho, C. M. Fontes, B. Mulloy, R. A. Childs, T. Feizi, and W. Chai. "Unravelling glucan recognition systems by glycome microarrays using the designer approach and mass spectrometry." Mol Cell Proteomics (2015). AbstractWebsite

Glucans are polymers of D-glucose with differing linkages in linear or branched sequences. They are constituents of microbial and plant cell-walls and involved in important bio-recognition processes including immunomodulation, anti-cancer activities, pathogen virulence and plant cell-wall biodegradation. Translational possibilities for these activities in medicine and biotechnology are considerable. High-throughput micro-methods are needed to screen proteins for recognition of specific glucan sequences as a lead to structure-function studies and their exploitation. We describe construction of a glucome microarray, the first sequence-defined glycome-scale microarray, using a designer approach from targeted ligand-bearing glucans in conjunction with a novel high-sensitivity mass spectrometric sequencing method, as a screening tool to assign glucan recognition motifs. The glucome microarray comprises 153 oligosaccharide probes with high purity, representing major sequences in glucans. The negative-ion electrospray tandem mass spectrometry with collision-induced dissociation was used for complete linkage analysis of gluco-oligosaccharides in linear homo and hetero and branched sequences. The system is validated using antibodies and carbohydrate-binding modules known to target α- or β-glucans in different biological contexts, extending knowledge on their specificities, and applied to reveal new information on glucan recognition by two signalling molecules of the immune system against pathogens: Dectin-1 and DC-SIGN. The sequencing of the glucan oligosaccharides by the MS method and their interrogation on the microarrays provides detailed information on linkage, sequence and chain length requirements of glucan-recognizing proteins, and are a sensitive means of revealing unsuspected sequences in the polysaccharides.

Palma, Angelina S., Yan Liu, Hongtao Zhang, Yibing Zhang, Barry V. McCleary, Guangli Yu, Qilin Huang, Leticia S. Guidolin, Andres E. Ciocchini, Antonella Torosantucci, Denong Wang, Ana Luisa Carvalho, Carlos M. G. A. Fontes, Barbara Mulloy, Robert A. Childs, Ten Feizi, and Wengang Chai. "Unravelling Glucan Recognition Systems by Glycome Microarrays Using the Designer Approach and Mass Spectrometry." Molecular & Cellular Proteomics. 14 (2015): 974-988. Abstract
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2014
Altstadt, S. G., et al. "{$^{13,14}$B(n, $\gamma$) via Coulomb Dissociation for Nucleosynthesis towards the r-Process}." Nuclear Data Sheets. 120 (2014): 197-200. AbstractWebsite
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Gameiro, J., Cardoso, T., and Rybarczyk Y. ". Kinect-Sign: teaching sign language to listeners through a game." Innovative and Creative Developments in Multimodal Interaction Systems . Eds. Y. Rybarczyk, T. Cardoso, J. Rosas, and L. Camarinha-Matos. Heidelberg: Springer, 2014. 141-159.
Coelho, T., De Oliveira, R., Cardoso, T., Rosas, J., and Rybarczyk Y. "Body ownership of virtual avatars: an affordance approach of telepresence." Innovative and Creative Developments in Multimodal Interaction Systems. Eds. Y. Rybarczyk, T. Cardoso, J. Rosas, and L. Camarinha-Matos. Heidelberg: Springer, 2014. 3-19.
Seabra, J., Rybarczyk, Y., Batista, A., Rybarczyk, P., Lebret, M.C., and Vernay D. "Development of a wearable monitoring system for service dogs." IEEE Roman’14, Workshop on Wearable Technology and Human-Wearable Robot Interaction. Edinburgh, UK 2014.
Rybarczyk, Y., Coelho, T., Cardoso, T., and De Oliveira R. "Effect of avatars and viewpoints on performance in virtual world: efficiency vs. telepresence." EAI Endorsed Transactions on Creative Technologies. 14.1 (2014): e4.Website
Cunha, Jácome, João Paulo Fernandes, Rui Pereira, and João Saraiva. "Graphical Querying of Model-Driven Spreadsheets." Human Interface and the Management of Information. Information and Knowledge Design and Evaluation. Ed. Sakae Yamamoto. Vol. 8521. Lecture Notes in Computer Science, 8521. Springer International Publishing, 2014. 419-430. Abstracthci14.pdf

This paper presents a graphical interface to query model-driven spreadsheets, based on experience with previous work and empirical studies in querying systems, to simplify query construction for typical end-users with little to no knowledge of SQL. We briefly show our previous text based model-driven querying system. Afterwards, we detail our graphical model-driven querying interface, explaining each part of the interface and showing an example. To validate our work, we executed an empirical study, comparing our graphical querying approach to an alternative querying tool, which produced positive results.

Rodrigues, F., Rybarczyk, Y., and Gonçalves M.J. "On the use of IT for treating aphasic patients: a 3D web-based solution." 13th International Conference on Applications of Computer Engineering. Lisbon, Portugal 2014. copy.pdf
Young, M. T., S. Hua, L. Steel, D. Foffa, S. L. Brusatte, S. Thüring, O. Mateus, J. Ignacio-Ruiz Omeñaca, Y. Lepage, P. Havilk, and M. B. Andrade. "Revision of the Late Jurassic teleosaurid genus Machimosaurus (Crocodylomorpha, Thalattosuchia)." Royal Society Open Science. 1.140222 (2014): 1-42.young_et_al_2014_machimosaurus_crocodylomorph_revision.pdf
Huisman, G., Bruijnes, M., Kolkmeier, J., Jung, M., Frederiks, A.D., and Rybarczyk Y. "Touching virtual agents: embodiment and mind." Innovative and Creative Developments in Multimodal Interaction Systems . Eds. Y. Rybarczyk, T. Cardoso, J. Rosas, and L. Camarinha-Matos. Heidelberg: Springer, 2014. 114-138.
Bernardino, A., Rybarczyk, Y., and Barata J. "Versatility of human body control through low-cost electromyographic interface." 13th International Conference on Applications of Computer Engineering. Lisbon, Portugal 2014. copy.pdf
Young, M. T., S. Hua, L. Steel, D. Foffa, S. L. Brusatte, S. Thüring, O. Mateus, J. I. Ruiz-Omeñaca, P. Havlik, Y. Lepage, and M. B. De Andrade. "Revision of the Late Jurassic teleosaurid genus Machimosaurus (Crocodylomorpha, Thalattosuchia)." Royal Society Open Science. 1 (2014). Abstract
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2013
R, Jardim-Goncalves, Grilo A, Agostinho C, Lampathaki F, and Charalabidis Y. "Systematisation of Interoperability Body of Knowledge: the foundation for Enterprise Interoperability as a science." ENTERPRISE INFORMATION SYSTEMS. 7 (2013): 7-32. Abstract
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Ghisolfi, A., C. Fliedel, V. Rosa, R. Pattacini, A. Thibon, K. Yu. Monakhov, and P. Braunstein. "Solvent-dependent reversible ligand exchange in nickel complexes of a monosulfide bis(diphenylphosphino)(N-thioether)amine." Chemistry - An Asian Journal. 8.8 (2013): 1795-1805. AbstractWebsite
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Vernay, D., Lebret M.C., Rybarczyk P., and Rybarczyk Y. "Collaboration hommes, chiens et robots : quels scenarios ?" Interactions et Intercompréhension : une Approche Comparative. Eds. M. Grandgeorge, B. LePevedic, and F. Pugniere. Fernelmont: E.M.E, 2013. 189-200.copy.pdf
Gameiro, J., Cardoso T., and Rybarczyk Y. "Kinect-Sign, teaching sign language to “listeners” through a game." Conference on Electronics, Telecommunications and Computers. Lisbon, Portugal 2013. copy.pdf
Carrasco, G., Rybarczyk Y., Cardoso T., and Martins I.P. "A serious game for multimodal training of physician novices." 6th International Conference of Education, Research and Innovation. Seville, Spain 2013. copy.pdfposter.pdf
Mendes, P., Rybarczyk Y., Rybarczyk P., and Vernay D. "A web-based platform for the therapeutic education of patients with physical disabilities." 6th International Conference of Education, Research and Innovation. Seville, Spain 2013. poster.pdf
Martí, Antonio, Elisa Antolín, Pablo {García Linares}, Iñigo Ramiro, Irene Artacho, Esther López, Estela Hernández, Manuel J. Mendes, Alex Mellor, Ignacio Tobías, David {Fuertes Marrón}, Cesar Tablero, Ana B. Cristóbal, Christopher G. Bailey, Maria Gonzalez, Michael Yakes, Mathew P. Lumb, Robert Walters, and Antonio Luque. "{Six not-so-easy pieces in intermediate band solar cell research}." Journal of Photonics for Energy. 3 (2013): 31299. AbstractWebsite

Abstract.  The concept of intermediate band solar cell (IBSC) is, apparently, simple to grasp. However, since the idea was proposed, our understanding has improved and some concepts can now be explained more clearly than when the concept was initially introduced. Clarifying these concepts is important, even if they are well known for the advanced researcher, so that research efforts can be driven in the right direction from the start. The six pieces of this work are: Does a miniband need to be formed when the IBSC is implemented with quantum dots? What are the problems for each of the main practical approaches that exist today? What are the simplest experimental techniques to demonstrate whether an IBSC is working as such or not? What is the issue with the absorption coefficient overlap and the Mott's transition? What would the best system be, if any?

2012
Paulino, Hervé, and Gilberto Camacho. "Enhancing Service-Oriented Computing with Software Mobility." Algorithms and Architectures for Parallel Processing - 12th International Conference, ICA3PP 2012, Fukuoka, Japan, September 4-7, 2012, Proceedings, Part I. Eds. Bernady Apduhan Guojun Wang Koji Nakano O. Yang Xiang, Ivan Stojmenovic, and Albert Zomaya. Lecture Notes in Computer Science. Springer-Verlag, 2012. 487-501. Abstract
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Zajega, F., Mancas M., Ben Mandhkour R., Leroy J., Riche N., Rocca F., Rybarczyk Y., and Dutoit T. "KinAct: the attentive social game demonstration." 11th Asian Conference on Computer Vision. Daejeon, Korea 2012. copy.pdf
de Calheiros Velozo, A., G. Lavareda, C. Nunes de Carvalho, and A. Amaral. "Thermal dehydrogenation of amorphous silicon deposited on c-Si: Effect of the substrate temperature during deposition." PHYSICA STATUS SOLIDI C: CURRENT TOPICS IN SOLID STATE PHYSICS, VOL 9, NO 10-11. Eds. S. Pizzini, G. Kissinger, H. YamadaKaneta, and J. Kang. Vol. 9. Physica Status Solidi C-Current Topics in Solid State Physics, 9. European Mat Res Soc (E-MRS), 2012. 2198-2202. Abstract

Samples of doped and undoped a-Si: H were deposited at temperatures ranging from 100 degrees C to 350 degrees C and then submitted to different dehydrogenation temperatures (from 350 degrees C to 550 degrees C) and times (from 1 h to 4 h). a-Si: H films were characterised after deposition through the measurements of specific material parameters such as: the optical gap, the conductivity at 25 degrees C, the thermal activation energy of conductivity and its hydrogen content. Hydrogen content was measured after each thermal treatment. Substrate dopant contamination from phosphorus-doped a-Si thin films was evaluated by SIMS after complete dehydrogenation and a junction depth of 0.1 mu m was obtained. Dehydrogenation results show a strong dependence of the hydrogen content of the as-deposited film on the deposition temperature. Nevertheless, the dehydrogenation temperature seems to determine the final H content in a way almost independent from the initial content in the sample. H richer films dehydrogenate faster than films with lower hydrogen concentration. (C) 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim

de Calheiros Velozo, A., G. Lavareda, C. Nunes de Carvalho, and A. Amaral. "Thermal dehydrogenation of amorphous silicon deposited on c-Si: Effect of the substrate temperature during deposition." PHYSICA STATUS SOLIDI C: CURRENT TOPICS IN SOLID STATE PHYSICS, VOL 9, NO 10-11. Eds. S. Pizzini, G. Kissinger, H. YamadaKaneta, and J. Kang. Vol. 9. Physica Status Solidi C-Current Topics in Solid State Physics, 9. European Mat Res Soc (E-MRS), 2012. 2198-2202. Abstract

Samples of doped and undoped a-Si: H were deposited at temperatures ranging from 100 degrees C to 350 degrees C and then submitted to different dehydrogenation temperatures (from 350 degrees C to 550 degrees C) and times (from 1 h to 4 h). a-Si: H films were characterised after deposition through the measurements of specific material parameters such as: the optical gap, the conductivity at 25 degrees C, the thermal activation energy of conductivity and its hydrogen content. Hydrogen content was measured after each thermal treatment. Substrate dopant contamination from phosphorus-doped a-Si thin films was evaluated by SIMS after complete dehydrogenation and a junction depth of 0.1 mu m was obtained. Dehydrogenation results show a strong dependence of the hydrogen content of the as-deposited film on the deposition temperature. Nevertheless, the dehydrogenation temperature seems to determine the final H content in a way almost independent from the initial content in the sample. H richer films dehydrogenate faster than films with lower hydrogen concentration. (C) 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim