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2022
Pinto, José, João Antunes, João Ramos, Rafael S. Costa, and Rui Oliveira. "Modeling and optimization of bioreactor processes." Current Developments in Biotechnology and Bioengineering. Elsevier, 2022. 89-115. Abstract
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Carvalho, Fernanda, Pedro Sousa, Nuno Leal, Joaquim Simão, Elissavet Kavoulaki, Maria Margarida Lima, Teresa Pereira da Silva, Hugo Águas, Giuseppina Padeletti, and João Pedro Veiga. "Mortars from the Palace of Knossos in Crete, Greece: A Multi-Analytical Approach." Minerals. 12 (2022): 30. Abstract
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2021
Krauth, Julian J., Karsten Schuhmann, Marwan Abdou Ahmed, Fernando D. Amaro, Pedro Amaro, François Biraben, Tzu-Ling Chen, Daniel S. Covita, Andreas J. Dax, Marc Diepold, Luis M. P. Fernandes, Beatrice Franke, Sandrine Galtier, Andrea L. Gouvea, Johannes Götzfried, Thomas Graf, Theodor W. Hänsch, Jens Hartmann, Malte Hildebrandt, Paul Indelicato, Lucile Julien, Klaus Kirch, Andreas Knecht, Yi-Wei Liu, Jorge Machado, Cristina M. B. Monteiro, Françoise Mulhauser, Boris Naar, Tobias Nebel, François Nez, Joaquim M. F. dos Santos, José Paulo Santos, Csilla I. Szabo, David Taqqu, João F. C. A. Veloso, Jan Vogelsang, Andreas Voss, Birgit Weichelt, Randolf Pohl, Aldo Antognini, and Franz Kottmann. "Measuring the $\upalpha$-particle charge radius with muonic helium-4 ions." Nature. 589 (2021): 527-531. AbstractWebsite
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Conti, Simone, Emanuel Tschopp, G. Sala, and Octavio Mateus. "Multibody simulations of diplodocid tail motion." Annual conference of the European Association of Vertebrate Palaeontologists. European Association of Vertebrate Palaeontologists, 2021. conti_et_al_2021_diplodocid_tail._eavp_abstract.pdf
Conti, Simone, Octávio Mateus, and G. Sala. "Mechanical characterization of tibial bone material of an ostrich." Rossi V., Fanti F., Barbieri G., Cavalazzi B. & Scarponi D. (Editors) 2021. Paleodays 2021. Abstract Book del XXI Convegno della Società Paleontologica Italiana, live virtual edition: 127 pp. Bologna (Italy): University of Bologna, 2021. conti_et_al_2021_ostrich_bone.pdf
G., Correia Viviana, Trovão Filipa, Pinheiro Benedita A., Brás Joana L. A., Silva Lisete M., Nunes Cláudia, Coimbra Manuel A., Liu Yan, Feizi Ten, Fontes Carlos M. G. A., Mulloy Barbara, Chai Wengang, Carvalho Ana Luísa, and Palma Angelina S. "Mapping Molecular Recognition of β1,3-1,4-Glucans by a Surface Glycan-Binding Protein from the Human Gut Symbiont Bacteroides ovatus." Microbiology SpectrumMicrobiology Spectrum (2021): e01826-21. AbstractWebsite

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Rocha, H. "Mathematical knowledge for teaching with technology: episodes of one teacher’s practice - Conhecimento matemático para ensinar com tecnologia: episódios da prática de uma professora." Educação Matemática Debate. 5.11 (2021): 1-22. AbstractWebsite

Research has highlighted the potential of technology to transform the teaching of Mathematics, but also the relevance of teachers and their professional knowledge. In this article, a qualitative methodology is adopted and two episodes of the practice of one teacher are analyzed in the scope of the study of functions in the 10th grade, based on the model of Knowledge for Teaching Mathematics with Technology (KTMT). The goal is to characterize the teacher's knowledge from her practice, simultaneously understanding how this contributes to promoting the development of the teacher's knowledge. The conclusions reached show the importance of including in the KTMT conception aspects highlighted by the research on technology integration. These aspects are determinant to characterize the teacher's knowledge. They also show the relevance of the practice for the development of the teacher's knowledge and the dynamic character of the vision of knowledge offered by KTMT.

Caetano, Constantino, Maria Luisa Morgado, Paula Patrício, João F. Pereira, and Baltazar Nunes. "Mathematical Modelling of the Impact of Non-Pharmacological Strategies to Control the COVID-19 Epidemic in Portugal." Mathematics. 9.10 (2021).
Anjos, Miguel F., and Manuel V. C. Vieira. "Mathematical optimization approach for facility layout on several rows." Optimization Letters. 15.1 (2021): 9-23.
Esquível, Manuel L., Nadezhda P. Krasii, Gracinda R. Guerreiro, and Paula Patrício. "The Multi-Compartment SI (RD) Model with Regime Switching: An Application to COVID-19 Pandemic." Symmetry. 13 (2021): 2427. Abstract

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Canarias, Tiago, Alexei Karlovich, and Eugene Shargorodsky. "Multiplication Is an open bilinear mapping in the Banach algebra of functions of bounded Wiener $p$-variation." Real Analysis Exchange. 46.1 (2021): 121-148.Website
dos Santos, Raquel, Maria João Romão, Ana Cecília A. Roque, and Ana Luísa Carvalho. "Magnetic particles used in a new approach for designed protein crystallization." CrystEngComm. 23 (2021): 1083-1090. AbstractWebsite

After more than one hundred and thirty thousand protein structures determined by X-ray crystallography{,} the challenge of protein crystallization for 3D structure determination remains. In the quest for additives for efficient protein crystallization{,} inorganic materials emerge as an alternative. Magnetic particles (MPs) are versatile inorganic materials{,} easy to use{,} modify and manipulate in a wide range of biological assays. The potential of using functionalised MPs as crystallization chaperones for protein crystallization was shown in this work. MPs with distinct coatings were rationally designed to promote protein crystallization by affinity-triggered heterogeneous nucleation. Hen egg white lysozyme (HEWL) and trypsin{,} were crystallized in the presence of MPs either bare or coated with a polysaccharide (chitin) or a protein (casein){,} respectively. The addition of MPs was characterized in terms of bound protein to the MPs{,} crystal morphology{,} time-lapse of crystal emergence{,} crystallization yield fold change and crystal diffraction quality for structure determination. The MPs additives have shown to bind to the respective target protein{,} and to promote nucleation and crystal growth without compromising crystal morphology. On the other hand{,} MPs addition led to faster detectable crystal emergence and up to 13 times higher crystallization yield{,} addressing some the challenges in protein crystallization{,} the main bottleneck of macromolecular crystallography. Structure determination of the protein crystallized in the presence of MPs revealed that the structural characteristics of the protein remained unchanged{,} as shown by the superposition with PDB annotated proteins. Moreover{,} and unlike most reported cases{,} it was possible to exclude the inhibitor benzamidine during trypsin crystallisation{,} which is a remarkable result opening new prospects in enzyme engineering and drug design. Our results show that MPs coated with affinity ligands to target proteins can be used as controlled and tailor-made crystallization inducers.

del Sanjuán Sánchez, Ursula Pilar, Juan Herrera Herbert, Joao Pedro Veiga, Alicia López Mederos, Maria Muñiz Fernandez, Alicia Calvo Paz, Carlos Carrión Isaacs, Lu{\'ıs Vela Bárez, and Guillermo Pérez de Gracia D{\'ıaz. "MINEHERITAGE: An innovative education project linking European mining history with the modern European society development." (2021). Abstract
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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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2020
Caeiro, Frederico, L{\'ı}gia Henriques-Rodrigues, Ivette M. Gomes, and Ivanilda Cabral. "Minimum-variance reduced-bias estimation of the extreme value index: A theoretical and empirical study." Computational and Mathematical Methods (2020). AbstractWebsite
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Ribeiro, Diana O., Aldino Viegas, Virgínia M. R. Pires, João Medeiros-Silva, Pedro Bule, Wengang Chai, Filipa Marcelo, Carlos M. G. A. Fontes, Eurico J. Cabrita, Angelina S. Palma, and Ana Luísa Carvalho. "Molecular basis for the preferential recognition of beta 1,3-1,4-glucans by the family 11 carbohydrate-binding module from Clostridium thermocellum." The FEBS journal. 287 (2020): 2723-2743. Abstract

Understanding the specific molecular interactions between proteins and $\beta$1,3-1,4-mixed-linked d-glucans is fundamental to harvest the full biological and biotechnological potential of these carbohydrates and of proteins that specifically recognize them. The family 11 carbohydrate-binding module from Clostridium thermocellum (CtCBM11) is known for its binding preference for $\beta$1,3-1,4-mixed-linked over $\beta$1,4-linked glucans. Despite the growing industrial interest of this protein for the biotransformation of lignocellulosic biomass, the molecular determinants of its ligand specificity are not well defined. In this report, a combined approach of methodologies was used to unravel, at a molecular level, the ligand recognition of CtCBM11. The analysis of the interaction by carbohydrate microarrays and NMR and the crystal structures of CtCBM11 bound to $\beta$1,3-1,4-linked glucose oligosaccharides showed that both the chain length and the position of the $\beta$1,3-linkage are important for recognition, and identified the tetrasaccharide Glc$\beta$1,4Glc$\beta$1,4Glc$\beta$1,3Glc sequence as a minimum epitope required for binding. The structural data, along with site-directed mutagenesis and ITC studies, demonstrated the specificity of CtCBM11 for the twisted conformation of $\beta$1,3-1,4-mixed-linked glucans. This is mediated by a conformation-selection mechanism of the ligand in the binding cleft through CH-$π$ stacking and a hydrogen bonding network, which is dependent not only on ligand chain length, but also on the presence of a $\beta$1,3-linkage at the reducing end and at specific positions along the $\beta$1,4-linked glucan chain. The understanding of the detailed mechanism by which CtCBM11 can distinguish between linear and mixed-linked $\beta$-glucans strengthens its exploitation for the design of new biomolecules with improved capabilities and applications in health and agriculture. DATABASE: Structural data are available in the Protein Data Bank under the accession codes 6R3M and 6R31.

Barcelos, João, Maria João Falcão Silva, Paula Couto, and Fernando Pinho. "Multicriteria analysis to support decision in public buildings rehabilitation interventions." REHABEND 2020 - Euro-American Congress on Construction Pathology, Rehabilitation Technology and Heritage Management. ISBN: 978-84-09-17873-5. University of Cantabria, Spain 2020.
dos Santos, Raquel, Inês Iria, Ana M. Manuel, Ana P. Leandro, Catarina A. C. Madeira, Joao Goncalves, Ana Luísa Carvalho, and Ana Cecília Roque. "Magnetic Precipitation: A New Platform for Protein Purification." Biotechnology JournalBiotechnology Journal. n/a.n/a (2020): 2000151. AbstractWebsite

One of the trends in downstream processing comprises the use of ?anything-but-chromatography? methods to overcome the current downfalls of standard packed-bed chromatography. Precipitation and magnetic separation are two techniques already proven to accomplish protein purification from complex media, yet never used in synergy. With the aim to capture antibodies directly from crude extracts, a new approach combining precipitation and magnetic separation was developed and named as affinity magnetic precipitation. A precipitation screening, based on the Hofmeister series, and a commercial precipitation kit were tested with affinity magnetic particles to assess the best condition for antibody capture from human serum plasma and clarified cell supernatant. The best conditions were obtained when using PEG3350 as precipitant at 4°C for 1h, reaching 80% purity and 50% recovery of polyclonal antibodies from plasma, and 99% purity with 97% recovery yield of anti-TNFα mAb from cell supernatants. These results show that the synergetic use of precipitation and magnetic separation can represent an alternative for the efficient capture of antibodies. This article is protected by copyright. All rights reserved

Teixeira, L. R., C. M. Cordas, M. P. Fonseca, N. E. C. Duke, P. R. Pokkuluri, and C. A. Salgueiro. "Modulation of the Redox Potential and Electron/Proton Transfer Mechanisms in the Outer Membrane Cytochrome OmcF From Geobacter sulfurreducens." Frontiers in Microbiology. 10 (2020). AbstractWebsite
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Tekinerdogan, Bedir, Dominique Blouin, Hans Vangheluwe, Miguel Goulão, Paulo Carreira, and Vasco Amaral Multi-Paradigm Modelling Approaches for Cyber-Physical Systems. Elsevier, 2020.
Singh, N., A. Amendola, F. Santos, G. Benzoni, and F. Fraternali. "Mechanical response of tensegrity dissipative devices incorporating shape memory alloys." IOP Conference Series: Materials Science and Engineering. Vol. 999. 2020. Abstract
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Miranda, R., E. Babilio, N. Singh, D. P. Villamil, F. Santos, and F. Fraternali. "Mechanics of energy harvesters based on tensegrity solar facades." IOP Conference Series: Materials Science and Engineering. Vol. 999. 2020. Abstract
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Miranda, R., E. Babilio, N. Singh, F. Santos, and F. Fraternali. "Mechanics of smart origami sunscreens with energy harvesting ability." Mechanics Research Communications. 105 (2020). AbstractWebsite
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Reboredo, {Fernando Henrique}, A. Barbosa, {Maria Manuela} Silva, {Maria Luisa} Carvalho, {José Paulo} Santos, {Maria Fernanda} Pessoa, Fernando Lidon, {José C. } Ramalho, and Mauro Guerra. "Mineral Content of Food Supplements of Plant Origin, by Energy Dispersive X-ray Fluorescence: A Risk Assessment." Exposure and Health. 12 (2020): 917-927. Abstract

The aim of this study is to evaluate the elemental composition of six food supplements of plant origin, commonly sold in the Portuguese market, by energy dispersive X-ray fluorescence. The presence of arsenic in all the Maca, Ashwagandha, Camu-Camu and Hemp protein samples (except the generic form) is a reason of concern due to the long-term effects of As mainly in its inorganic form. Thus, great caution must be taken on some food supplements, particularly the cases of Moringa from Egypt and Yellow/Xpresso Maca, whose inorganic As concentrations are in line with the upper bound concentration for the 95th dietary exposure according to the European Food Safety Authority which is 0.64 μg/kg bw/day. In what regards Hemp protein, if the supplier’s daily intake recommendation (30 g) is followed, values as high as 1.75 μg/kg bw/day of inorganic As will be consumed, which are dangerously above the upper bound. In this case this specific supplement lot should be removed from the market. Also the consumption of Hemp protein leads to a daily intake of Mn above the Daily Reference Intake (DRI) and Adequate Intakes (AIs) for adults. The contamination of Goji berries by Pb is a reason for concern—organic berries contained 11.3 μg/g while berries derived from conventional agriculture 11.6 μg/g, leading to daily intake doses of 315.3 μg and 324.8 μg, respectively, if the recommended daily intake of 28 g is followed. Our findings point out to an inadequacy of the recommended intakes by the supplier vis a vis the concentrations observed, greatly increasing the risk for public health.