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2021
Alexandre, Leonardo, Rafael S. Costa, and Rui Henriques. "DI2: prior-free and multi-item discretization of biological data and its applications." BMC bioinformatics. 22 (2021): 1-19. Abstract
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Duarte, Marlene, Aldino Viegas, Victor D. Alves, José A. M. Prates, Luís M. A. Ferreira, Shabir Najmudin, Eurico J. Cabrita, Ana Luísa Carvalho, Carlos M. G. A. Fontes, and Pedro Bule. "A dual cohesin–dockerin complex binding mode in Bacteroides cellulosolvens contributes to the size and complexity of its cellulosome." Journal of Biological Chemistry. 296 (2021): 100552. AbstractWebsite

The Cellulosome is an intricate macromolecular protein complex that centralizes the cellulolytic efforts of many anaerobic microorganisms through the promotion of enzyme synergy and protein stability. The assembly of numerous carbohydrate processing enzymes into a macromolecular multiprotein structure results from the interaction of enzyme-borne dockerin modules with repeated cohesin modules present in noncatalytic scaffold proteins, termed scaffoldins. Cohesin–dockerin (Coh-Doc) modules are typically classified into different types, depending on structural conformation and cellulosome role. Thus, type I Coh-Doc complexes are usually responsible for enzyme integration into the cellulosome, while type II Coh-Doc complexes tether the cellulosome to the bacterial wall. In contrast to other known cellulosomes, cohesin types from Bacteroides cellulosolvens, a cellulosome-producing bacterium capable of utilizing cellulose and cellobiose as carbon sources, are reversed for all scaffoldins, i.e., the type II cohesins are located on the enzyme-integrating primary scaffoldin, whereas the type I cohesins are located on the anchoring scaffoldins. It has been previously shown that type I B. cellulosolvens interactions possess a dual-binding mode that adds flexibility to scaffoldin assembly. Herein, we report the structural mechanism of enzyme recruitment into B. cellulosolvens cellulosome and the identification of the molecular determinants of its type II cohesin–dockerin interactions. The results indicate that, unlike other type II complexes, these possess a dual-binding mode of interaction, akin to type I complexes. Therefore, the plasticity of dual-binding mode interactions seems to play a pivotal role in the assembly of B. cellulosolvens cellulosome, which is consistent with its unmatched complexity and size.

Alishah, H. M., F. P. G. Choi, U. D. Menda, C. Kahveci, M. C. Rodop, MJ Mendes, and S. Gunes. "Effect of Bathocuproine Concentration on the Photovoltaic Performance of NiOx-Based Perovskite Solar Cells." Journal of the Mexican Chemical Society. 65 (2021): 149-160. AbstractWebsite
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Araújo, João, Wolfram Bentz, and Peter J. Cameron. "The existential transversal property: a generalization of homogeneity and its impact on semigroups." Trans. Amer. Math. Soc.. 374 (2021): 1155-1195. AbstractWebsite
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Biscaia, H. C., R. Almeida, S. Zhang, and J. Canejo. "Experimental calibration of the bond-slip relationship of different CFRP-to-timber joints through digital image correlation measurements." Composites Part C: Open Access. 4 (2021). AbstractWebsite

Nowadays, the use of the Digital Image Correlation (DIC) technique has spread and it is being used in several engineering areas to measure displacements. The available data obtained from the DIC measurement to evaluate the bond performance between a Carbon fibre Reinforced Polymer (CFRP) externally bonded to a timber substrate is scarce. From the existing data obtained with other materials, this contactless technique revealed to be quite useful but its accuracy with other well-established techniques, such as the use of electric strain gauges is not well understood yet. Therefore, the current work aims to study the accuracy of 2D DIC measurements with the measurements obtained from the use of strain gauges within a low-cost perspective. To that end, several CFRP-to-timber bonded joints were tested under the single-lap shear test and different bonding techniques were considered as well. Some flaws intrinsically derived from the DIC measurements that complicate the bond assessment, such as the fluctuations in the generated displacements field, are identified, and to bypass this problem a new methodology is proposed. This new methodology is based on two different closed-form solutions that, after defining the local and global bond behaviours of different CFRP-to-timber bonded joints, allowed to eliminate the fluctuations found from the DIC measurements, facilitating the estimation and the comprehension of the full debonding process of the CFRP-to-timber joints, which was achieved with a good proximity to the homologous debonding process derived from the strain gauge measurements. © 2020

Azevedo, A., J. Firmo, J. Correia, C. Chastre, H. Biscaia, and N. Franco. "Fire behaviour of rc slab strips strengthened with advanced cfrp strengthening systems." fib Symposium. Vol. 2021-June. 2021. 1306-1315. Abstract

Carbon fibre reinforced polymer (CFRP) composite systems are widely used to strengthen reinforced concrete (RC) structures through bonding strips/sheets on the concrete surface – externally bonded reinforcement (EBR) technique, or through strips/rods bonded inside slits in the concrete cover – near-surface mounted (NSM) technique. Although both techniques provide high strength increases, it is usually not possible to use the CFRPs’ full strength due to premature debonding, especially with EBR. This limitation can be overcome when using CREatE (continuous reinforcement embedded at ends) technique (developed by the last three authors), which consists of (i) bonding the central part of the CFRP strip (as in EBR), or the CFRP rod (as in NSM), and (ii) anchoring both ends of the strip/rod inside the concrete section, after a transition curve, enhancing its anchorage capacity. However, all these techniques are susceptible to fire, due to the polymeric nature of CFRP materials and epoxy adhesives. This paper presents the results of an experimental study regarding the fire behaviour of RC slab strips strengthened with EBR, NSM and CREatE techniques, in which the influence of applying different fire protection systems was investigated. The specimens were strengthened with those systems and simultaneously subjected to a service load and the ISO 834 fire curve. The following main results were obtained: (i) without fire protection, the CREatE technique presented the highest fire resistance due to the better anchorage of the CFRP; (ii) when protected, the NSM technique presented higher fire resistance compared to EBR and CREatE techniques; and (iii) “critical” temperatures were proposed for each technique, 1.0Tg, 2.5Tg, and 3.0Tg for EBR, NSM and CREatE techniques, respectively. © Fédération Internationale du Béton (fib) – International Federation for Structural Concrete.

Santos, J. P., Mauro Guerra, Jorge M. Sampaio, Gonçalo R. Vília, César A. Godinho, Daniel Pinheiro, Pedro Amaro, José P. Marques, Jorge Machado, Paul Indelicato, Fernando Parente, and José Paulo Santos. "Fundamental Parameters Related to Selenium K\alpha and K\beta Emission X-ray Spectra." Atoms (2021). AbstractWebsite
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Abbate, V., E. Babilio, FA dos Santos, N. Singh, and F. Fraternali. "Geometric patterns and dynamics of foldable moduli for adaptive façades." COMPDYN Proceedings. Vol. 2021-June. 2021. Abstract
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Menda, U. D., G. Ribeiro, D. Nunes, T. Calmeiro, H. Águas, E. Fortunato, R. Martins, and MJ Mendes. "High-performance wide bandgap perovskite solar cells fabricated in ambient high-humidity conditions." Materials Advances. 2 (2021): 6344-6355. AbstractWebsite
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Alexandre, M., H. Águas, E. Fortunato, R. Martins, and MJ Mendes. "Light management with quantum nanostructured dots-in-host semiconductors." Light: Science and Applications. 10 (2021). AbstractWebsite
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Alexandre, Leonardo, Rafael S. Costa, Lúcio Lara Santos, and Rui Henriques. "Mining pre-surgical patterns able to discriminate post-surgical outcomes in the oncological domain." IEEE Journal of Biomedical and Health Informatics. 25 (2021): 2421-2434. Abstract
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Silva, Teresa P., João X. Matos, Daniel de Oliveira, Igor Morais, Pedro Gonçalves, Lu{\'ıs Albardeiro, Fernanda Carvalho, Ugur D. Menda, and João P. Veiga. "Orange Pickeringite from the Algares 30-Level Adit, Aljustrel Mine, Iberian Pyrite Belt, Portugal." Minerals. 11 (2021): 1115. Abstract
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Araújo, João, Wolfram Bentz, and Peter J. Cameron. "Primitive permutation groups and strongly factorizable transformation semigroups." J. Algebra. 565 (2021): 513-530. AbstractWebsite
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Santos, F., N. Singh, A. Amendola, F. Fraternali, and A. Micheletti. "Seismic metamaterials with tensegrity architecture." COMPDYN Proceedings. Vol. 2021-June. 2021. Abstract
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Boane, Jenny L. N., Pedro Centeno, Ana Mouquinho, Miguel Alexandre, Tomás Calmeiro, Elvira Fortunato, Rodrigo Martins, Manuel J. Mendes, and Hugo Águas. "Soft-Microstructured Transparent Electrodes for Photonic-Enhanced Flexible Solar Cells." Micro. 1 (2021): 215-227. AbstractWebsite

Microstructured transparent conductive oxides (TCOs) have shown great potential as photonic electrodes in photovoltaic (PV) applications, providing both optical and electrical improvements in the solar cells’ performance due to: (1) strong light trapping effects that enhance broadband light absorption in PV material and (2) the reduced sheet resistance of the front illuminated contact. This work developed a method for the fabrication and optimization of wavelength-sized indium zinc oxide (IZO) microstructures, which were soft-patterned on flexible indium tin oxide (ITO)-coated poly(ethylene terephthalate) (PET) substrates via a simple, low-cost, versatile, and highly scalable colloidal lithography process. Using this method, the ITO-coated PET substrates patterned with IZO micro-meshes provided improved transparent electrodes endowed with strong light interaction effects—namely, a pronounced light scattering performance (diffuse transmittance up to  50%). In addition, the photonic-structured IZO mesh allowed a higher volume of TCO material in the electrode while maintaining the desired transparency, which led to a sheet resistance reduction (by  30%), thereby providing further electrical benefits due to the improvement of the contact conductance. The results reported herein pave the way for a new class of photonic transparent electrodes endowed with mechanical flexibility that offer strong potential not only as advanced front contacts for thin-film bendable solar cells but also for a much broader range of optoelectronic applications.

Araújo, João, João Pedro Araújo, Wolfram Bentz, Peter J. Cameron, and Pablo Spiga. "A transversal property for permutation groups motivated by partial transformations." J. Algebra. 573 (2021): 741-759. AbstractWebsite
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Antão, A. N., M. Vicente da Silva, N. Monteiro, and N. Deusdado. "Upper and lower bounds for three-dimensional undrained stability of shallow tunnels." Transportation Geotechnics. 27 (2021): 100491. AbstractWebsite

This paper deals with the determination of upper and lower bounds for the three-dimensional undrained stability of shallow tunnels. The tunnel is circular and a distance between its face and its lining is considered. The soil shear strength is modeled using the Tresca criterion. Results of the upper and lower bounds of the stability number are presented, for several geometrical and resistance configurations and their comparison with previous results is made, showing the clear improvement obtained. Finally, equations approaching the stability number are proposed.

{Guerra, Mauro, Jorge Sampaio, Gon{\c c}alo V{\'ılia, César Godinho, Daniel Pinheiro, Pedro Amaro, José Marques, Jorge Machado, Paul Indelicato, Fernando Parente, and José Santos. "{Fundamental Parameters Related to Selenium K$\alpha$ and K$\beta$ Emission X-ray Spectra}." Atoms. 9 (2021): 8-10. AbstractWebsite

We present relativistic ab initio calculations of fundamental parameters for atomic selenium, based on the Multiconfiguration Dirac-Fock method. In detail, fluorescence yields and subshell linewidths, both of K shell, as well as K$\beta$ to K$\alpha$ intensity ratio are provided, showing overall agreement with previous theoretical calculations and experimental values. Relative intensities were evaluated assuming the same ionization cross-section for the K-shell hole states, leading to a statistical distribution of these initial states. A method for estimating theoretical linewidths of X-ray lines, where the lines are composed by a multiplet of fine-structure levels that are spread in energy, is proposed. This method provides results that are closer to K$\alpha$1,2 experimental width values than the usual method, although slightly higher discrepancies occur for the K$\beta$1,3 lines. This indicates some inaccuracies in the calculation of Auger rates that have a higher contribution for partial linewidths of the subshells involved in the K$\beta$1,3 profile. Apart from this, the calculated value of K$\beta$ to K$\alpha$ intensity ratio, which is less sensitive to Auger rates issues, is in excellent agreement with recommended values.

Boretzky, K., I. Gasparic, M. Heil, J. Mayer, A. Heinz, C. Caesar, D. Kresan, H. Simon, H. T. Törnqvist, D. Körper, G. Alkhazov, L. Atar, T. Aumann, D. Bemmerer, S. V. Bondarev, L. T. Bott, S. Chakraborty, M. I. Cherciu, L. V. Chulkov, M. Ciobanu, U. Datta, E. De Filippo, C. A. Douma, J. Dreyer, Z. Elekes, J. Enders, D. Galaviz, E. Geraci, B. Gnoffo, K. Göbel, V. L. Golovtsov, Gonzalez D. Diaz, N. Gruzinsky, T. Heftrich, H. Heggen, J. Hehner, T. Hensel, E. Hoemann, M. Holl, A. Horvat, Á. Horváth, G. Ickert, Jelavić D. Malenica, H. T. Johansson, B. Jonson, J. Kahlbow, N. Kalantar-Nayestanaki, A. Kelic-Heil, M. Kempe, K. Koch, N. G. Kozlenko, A. G. Krivshich, N. Kurz, V. Kuznetsov, C. Langer, Y. Leifels, I. Lihtar, B. Löher, J. Machado, N. S. Martorana, K. Miki, T. Nilsson, E. M. Orischin, E. V. Pagano, S. Pirrone, G. Politi, P. M. Potlog, A. Rahaman, R. Reifarth, C. Rigollet, M. Röder, D. M. Rossi, P. Russotto, D. Savran, H. Scheit, F. Schindler, D. Stach, E. Stan, Stomvall J. Gill, P. Teubig, M. Trimarchi, L. Uvarov, M. Volknandt, S. Volkov, A. Wagner, V. Wagner, S. Wranne, D. Yakorev, L. Zanetti, A. Zilges, K. Zuber, and R. 3B. collaboration. "{NeuLAND: The high-resolution neutron time-of-flight spectrometer for R3B at FAIR}." Nuclear Inst. and Methods in Physics Research, A. 1014 (2021): 165701. AbstractWebsite

Nuclear Inst. and Methods in Physics Research, A, 1014 (2021) 165701. doi:10.1016/j.nima.2021.165701

Goodfellow, Brian J., Filipe Freire, Ana Luísa Carvalho, Susana S. Aveiro, Peggy Charbonnier, Jean-Marc Moulis, Leonildo Delgado, Gloria C. Ferreira, João E. Rodrigues, Pierre Poussin-Courmontagne, Catherine Birck, Alastair McEwen, and Anjos L. Macedo. "{The SOUL family of heme-binding proteins: Structure and function 15 years later}." Coordination Chemistry Reviews. 448 (2021): 214189. AbstractWebsite

The SOUL, or heme-binding protein HBP/SOUL, family represents a group of evolutionary conserved putative heme-binding proteins that contains a number of members in animal, plant andbacterial species. The structures of the murine form of HEBP1, or p22HBP, and the human form of HEBP2, or SOUL, have been determined in 2006 and 2011 respectively. In this work we discuss the structures of HEBP1 and HEBP2 in light of new X-ray data for heme bound murine HEBP1. The interaction between tetrapyrroles and HEBP1, initially proven to be hydrophobic in nature, was thought to also involve electrostatic interactions between heme propionate groups and positively charged amino acid side chains. However, the new X-ray structure, and results from murine HEBP1 variants and human HEBP1, confirm the hydrophobic nature of the heme-HEBP1 interaction, resulting in Kd values in the low nanomolar range, and rules out any electrostatic stabilization. Results from NMR relaxation time measurements for human HEBP1 describe a rigid globular protein with no change in motional regime upon heme binding. X-ray structures deposited in the PDB for human HEBP2 are very similar to each other and to the new heme-bound murine HEBP1 X-ray structure (backbone rmsd ca. 1 {\AA}). Results from a HSQC spectrum centred on the histidine side chain N$δ$-proton region for HEBP2 confirm that HEBP2 does not bind heme via H42 as no chemical shift differences were observed upon heme addition for backbone NH and N$δ$ protons. A survey of the functions attributed to HEBP1 and HEBP2 over the last 20 years span a wide range of cellular pathways. Interestingly, many of them are specific to higher eukaryotes, particularly mammals and a potential link between heme release under oxidative stress and human HEBP1 is also examined using recent data. However, at the present moment, trying to relate function to the involvement of heme or tetrapyrrole binding, specifically, makes little sense with our current biological knowledge and can only be applied to HEBP1, as HEBP2 does not interact with heme. We suggest that it may not be justified to call this very small family of proteins, heme-binding proteins. The family may be more correctly called “the SOUL family of proteins related to cellular fate” as, even though only HEBP1 binds heme tightly, both proteins may be involved in cell survival and/or proliferation.

2020
Syndikus, I., M. Petri, A. O. Macchiavelli, S. Paschalis, C. A. Bertulani, T. Aumann, H. Alvarez-Pol, L. Atar, S. Beceiro-Novo, J. Benlliure, J. M. Boillos, K. Boretzky, M. J. G. Borge, B. A. Brown, M. Caamano, C. Caesar, E. Casarejos, W. Catford, J. Cederkäll, S. Chakraborty, L. V. Chulkov, D. Cortina-Gil, E. Cravo, R. Crespo, Datta U. Pramanik, I. Dillmann, Diaz P. Fernandez, Z. Elekes, J. Enders, F. Farinon, L. M. Fraile, D. Galaviz, H. Geissel, R. Gernhäuser, P. Golubev, K. Göbel, M. Heil, M. Heine, A. Heinz, A. Henriques, M. Holl, H. T. Johansson, B. Jonson, N. Kalantar-Nayestanaki, R. Kanungo, A. Kelic-Heil, T. Kröll, N. Kurz, C. Langer, T. Le Bleis, J. Machado, J. Marganiec-Gałązka, E. Nacher, T. Nilsson, C. Nociforo, V. Panin, A. Perea, S. B. Pietri, R. Plag, A. Rahaman, R. Reifarth, A. Revel, G. Ribeiro, C. Rigollet, D. M. Rossi, D. Savran, H. Scheit, H. Simon, O. Sorlin, O. Tengblad, Y. Togano, M. Vandebrouck, V. Volkov, F. Wamers, C. Wheldon, G. L. Wilson, J. S. Winfield, H. Weick, P. Woods, D. Yakorev, M. Zhukov, A. Zilges, K. Zuber, and R. 3B. collaboration. "{Probing the Z=6 spin-orbit shell gap with (p,2p) quasi-free scattering reactions}." Physics Letters B. 809 (2020): 135748. AbstractWebsite

Physics Letters B, 809 (2020) 135748. 10.1016/j.physletb.2020.135748

Togawa, M., S. Kühn, C. Shah, P. Amaro, R. Steinbrügge, J. Stierhof, N. Hell, M. Rosner, K. Fujii, M. Bissinger, R. Ballhausen, M. Hoesch, J. Seltmann, S. Park, F. Grilo, F. S. Porter, J. P. Santos, M. Chung, T. Stöhlker, J. Wilms, T. Pfeifer, G. V. Brown, M. A. Leutenegger, S. Bernitt, and Crespo J. R. López-Urrutia. "Observation of strong two-electron–one-photon transitions in few-electron ions." Physical Review A. 102 (2020). AbstractWebsite
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Duarte, Susana, {Maria Rosário} do Cabrita, and V. Cruz-Machado. "Business model, lean and green management and industry 4.0: A conceptual relationship." Proceedings of the 13th International Conference on Management Science and Engineering Management, 2019 - Volume 1. Eds. Jiuping Xu, Gheorghe Duca, {Fang Lee } Cooke, and {Syed Ejaz } Ahmed. Advances in Intelligent Systems and Computing. Germany: Springer Verlag, 2020. 359-372. Abstract

The Industry 4.0 addresses a radical change on business processes. Through communication technology, objects interact with each other; the physical and digital worlds merge. This makes an environment more flexible, allowing to respond faster to specific customer requirements. Therefore, businesses need to rapidly adapt to avoid being left behind. A business model is required to meet the new concepts of Industry 4.0. In addition, lean and green characteristics may align with business model elements. Understanding how these concepts interact is something that need clarification. Based on literature review, a conceptual relationship between Business Model (Canvas), Lean and green management approach and Industry 4.0 approach is presented. Lean and green management characteristics are identified to be aligned through a Business Model Canvas perspective. Also, the concepts of the Industry 4.0 can be applied in each element of the Business Model Canvas. Managers and entrepreneurs can create, design or redefine their business knowing the lean and green application and Industry 4.0 execution. This research aims to contribute to the discussion of the relationships between these concepts. To the authors’ knowledge, this work is one of the first to try to relate these concepts.

Martins, L., P. Amaro, S. Pessanha, M. Guerra, J. Machado, M. L. Carvalho, J. P. Santos, and P. Indelicato. "{Overview and calculation of X-ray K-shell transition yields for comprehensive data libraries}." X-Ray Spectrom.. 62 (2020): 63-26. AbstractWebsite

The simulation of atomic relaxation relies on data libraries with tabulated partial fluorescence yield values of radiative transitions, commonly derived from the Evaluated Atomic Data Library (EADL)....

Martins, Jorge, Asal Kiazadeh, Joana V. Pinto, Ana Rovisco, Tiago Gonçalves, Jonas Deuermeier, Eduardo Alves, Rodrigo Martins, Elvira Fortunato, and Pedro Barquinha. "{Ta2O5/SiO2 Multicomponent Dielectrics for Amorphous Oxide TFTs}." Electronic Materials. 2 (2020): 1-16. AbstractWebsite

Co-sputtering of SiO2 and high-$ąppa$ Ta2O5 was used to make multicomponent gate dielectric stacks for In-Ga-Zn-O thin-film transistors (IGZO TFTs) under an overall low thermal budget (T = 150 °C). Characterization of the multicomponent layers and of the TFTs working characteristics (employing them) was performed in terms of static performance, reliability, and stability to understand the role of the incorporation of the high-$ąppa$ material in the gate dielectric stack. It is shown that inherent disadvantages of the high-$ąppa$ material, such as poorer interface properties and poor gate insulation, can be counterbalanced by inclusion of SiO2 both mixed with Ta2O5 and as thin interfacial layers. A stack comprising a (Ta2O5)x(SiO2)100 − x film with x = 69 and a thin SiO2 film at the interface with IGZO resulted in the best performing TFTs, with field-effect mobility (µFE) ≈ 16 cm2·V−1·s−1, subthreshold slope (SS) ≈ 0.15 V/dec and on/off ratio exceeding 107. Anomalous Vth shifts were observed during positive gate bias stress (PGBS), followed by very slow recoveries (time constant exceeding 8 × 105 s), and analysis of the stress and recovery processes for the different gate dielectric stacks showed that the relevant mechanism is not dominated by the interfaces but seems to be related to the migration of charged species in the dielectric. The incorporation of additional SiO2 layers into the gate dielectric stack is shown to effectively counterbalance this anomalous shift. This multilayered gate dielectric stack approach is in line with both the large area and the flexible electronics needs, yielding reliable devices with performance suitable for successful integration on new electronic applications.