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2023
Nóbrega, Cláudia S., Ana Luísa Carvalho, Maria João Romão, and Sofia R. Pauleta. "Structural Characterization of Neisseria gonorrhoeae Bacterial Peroxidase—Insights into the Catalytic Cycle of Bacterial Peroxidases." International Journal of Molecular Sciences. 24 (2023). AbstractWebsite

Neisseria gonorrhoeae is an obligate human pathogenic bacterium responsible for gonorrhea, a sexually transmitted disease. The bacterial peroxidase, an enzyme present in the periplasm of this bacterium, detoxifies the cells against hydrogen peroxide and constitutes one of the primary defenses against exogenous and endogenous oxidative stress in this organism. The 38 kDa heterologously produced bacterial peroxidase was crystallized in the mixed-valence state, the active state, at pH 6.0, and the crystals were soaked with azide, producing the first azide-inhibited structure of this family of enzymes. The enzyme binds exogenous ligands such as cyanide and azide, which also inhibit the catalytic activity by coordinating the P heme iron, the active site, and competing with its substrate, hydrogen peroxide. The inhibition constants were estimated to be 0.4 ± 0.1 µM and 41 ± 5 mM for cyanide and azide, respectively. Imidazole also binds and inhibits the enzyme in a more complex mechanism by binding to P and E hemes, which changes the reduction potential of the latest heme. Based on the structures now reported, the catalytic cycle of bacterial peroxidases is revisited. The inhibition studies and the crystal structure of the inhibited enzyme comprise the first platform to search and develop inhibitors that target this enzyme as a possible new strategy against N. gonorrhoeae.

Duarte, Marlene, Victor D. Alves, Márcia Correia, Catarina Caseiro, Luís M. A. Ferreira, Maria João Romão, Ana Luísa Carvalho, Shabir Najmudin, Edward A. Bayer, Carlos M. G. A. Fontes, and Pedro Bule. "Structure-function studies can improve binding affinity of cohesin-dockerin interactions for multi-protein assemblies." International Journal of Biological Macromolecules. 224 (2023): 55-67. AbstractWebsite

The cellulosome is an elaborate multi-enzyme structure secreted by many anaerobic microorganisms for the efficient degradation of lignocellulosic substrates. It is composed of multiple catalytic and non-catalytic components that are assembled through high-affinity protein-protein interactions between the enzyme-borne dockerin (Doc) modules and the repeated cohesin (Coh) modules present in primary scaffoldins. In some cellulosomes, primary scaffoldins can interact with adaptor and cell-anchoring scaffoldins to create structures of increasing complexity. The cellulosomal system of the ruminal bacterium, Ruminococcus flavefaciens, is one of the most intricate described to date. An unprecedent number of different Doc specificities results in an elaborate architecture, assembled exclusively through single-binding-mode type-III Coh-Doc interactions. However, a set of type-III Docs exhibits certain features associated with the classic dual-binding mode Coh-Doc interaction. Here, the structure of the adaptor scaffoldin-borne ScaH Doc in complex with the Coh from anchoring scaffoldin ScaE is described. This complex, unlike previously described type-III interactions in R. flavefaciens, was found to interact in a dual-binding mode. The key residues determining Coh recognition were also identified. This information was used to perform structure-informed protein engineering to change the electrostatic profile of the binding surface and to improve the affinity between the two modules. The results show that the nature of the residues in the ligand-binding surface plays a major role in Coh recognition and that Coh-Doc affinity can be manipulated through rational design, a key feature for the creation of designer cellulosomes or other affinity-based technologies using tailored Coh-Doc interactions.

Ribeiro, G., G. Ferreira, U. D. Menda, M. Alexandre, M. J. Brites, M. A. Barreiros, S. Jana, H. Águas, R. Martins, P. A. Fernandes, P. Salomé, and MJ Mendes. "Sub-Bandgap Sensitization of Perovskite Semiconductors via Colloidal Quantum Dots Incorporation." Nanomaterials. 13 (2023). AbstractWebsite
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2022
Querido, Diana, Tânia Vieira, José Luís Ferreira, Célia Henriques, João Paulo Borges, and Jorge Carvalho Silva. "Study on the Incorporation of Chitosan Flakes in Electrospun Polycaprolactone Scaffolds." 14.8 (2022): 1496. Abstract
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Costa, Lúcia AA, Marta Mateus, João Paulo Borges, Jorge Carvalho Silva, Susana Barreiros, and Paula I. P. Soares. "Superparamagnetic Iron Oxide Nanozymes for Synergistic Cancer Treatment." 8.1 (2022): 3. Abstract
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Neves-Silva, R., and L. M. Camarinha-Matos. "Simulation-Based Decision Support System for Energy Efficiency in Buildings Retrofitting." Sustainability. 14.12216 (2022).
de Miguel, Pablo Sanz, António B. Moniz, Nuno Boavida, Joan Antoni Serra, M. Pańków, G. Karoulas, Marina Peliz, and I. Papageorgiou Social partners’ involvement in dual vocational education and training (VET): a comparison of Greece, Spain, Poland and Portugal. Barcelona: Notus, 2022. Abstractsocial_partners_involvement_in_dual_vocatioanl_education_and_training_vet._a_comparison_of_greece_spain_poland_and_portugal.pdfWebsite

The research report presents the key findings from the INVOLVE project (VS/2020/0145). It contributes to the debates on the participation of social partners in dual VET governance under countries generally classified as state-centred, skills-formation regimes (Spain, Greece, Portugal and Poland). The research report analysed the actual role played by social partners in the dual VET systems in the selected countries at different governance levels and the extent to which trade unions and employer organisations are involved on an equal footing. It also formulates policy recommendations supporting collective responses to dual VET systems in the selected countries. Findings are based on desk research, fieldwork consisting of semi-structured interviews and mini-case studies and national scenarios developed by INVOLVE partners, on the basis of a scenario workshop methodology

Teixeira, P., C. Martins, and H. Rocha STE(A)M approach: Distinguishing and discussing meanings. EduLearn. Spain: IATED, 2022. Abstract

The STE(A)M approach has been recognized by several authors for its potential in assisting teaching and learning, and several curriculum standards already value its application in the classroom. This approach is based on the articulation between different areas, the clarification, and the deepening of the concepts being studied. Although there are different approaches, according to the fields involved, STEM and STEAM are two among the most often mentioned in the literature. STEM is based on learning that integrates the following areas of knowledge: Science, Technology, Engineering, and Mathematics. The conceptualization of the STE(A)M approach is not consensual and uniform. There are different models focusing on problem-solving based learning, project-based-learning, design-based learning, and engineering models. Still, different authors present different conceptualizations of this approach. In this paper, we relied on the existing literature to discuss the different understandings of the STE(A)M approach. We will also pay attention to mathematics and how different authors see the disciplines’ role within a STE(A)M approach and discuss the evolution of the mentioned authors’ positions throughout time. Thus, methodologically, we undertook the following steps: (i) literature search based on the selected keywords; (ii) selection of the texts, considering the authors and time gap, in order to analyze the evolution of the research and (iii) collection and organization of the relevant topics for the study. This study aims to present the meanings, conceptualizations, and possible influences present in different models and for understand the evolution of the STEM and STEAM approaches over time. The main findings suggest a focus on the interdisciplinary or transdisciplinary approach as opposed to the primeval years of investigations in STEM and STEAM when many authors advocated a multidisciplinary approach. This change in thinking is due to the need to train students in an integral and holistic manner, developing citizens with transversal knowledge and skills prepared for the current societal challenges.

Guillaume, A. R. D., F. Costa, and O. Mateus. "Stegosaur tracks from the Upper Jurassic of Portugal: new occurrences and perspectives." Ciências da Terra / Earth Sciences Journal. 20.1 (2022): 37-60. Abstractguillaumeetal.pdf

The record of Late Jurassic stegosaur tracks from the Lourinhã Formation (Kimmeridgian-Tithonian) is here revised. Thirty-eight dinosaur tracks, preserved as natural infill casts, are here reported, and thirty-two of them are attributed to the ichnogenus Deltapodus. Four of those present impressions of skin, with polygonal scales and random pattern. Deltapodus is the most common ichnogenus in the track record of the Lourinhã Formation. The sizes and shape suggest one single dacentrurine trackmaker, which could be Miragaia longicollum, also common in the same horizons.

Isufi, Brisid, André Almeida, Rui Marreiros, António Pinho Ramos, and Válter Lúcio. "Slab–column connection punching and ductility improvement methods for seismic response of buildings with flat slabs." Structural Concrete. 23 (2022): 1385-1398. AbstractWebsite
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Faghih, Amin, and Magda Rebelo. "A spectral approach to non-linear weakly singular fractional integro-differential equations." Fractional Calculus and Applied Analysis (2022): 1-29. Abstract
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Torabian, Ala, Brisid Isufi, Davood Mostofinejad, and António Pinho Ramos. "STRENGTHENING OF FLAT SLABS WITH FIBRE REINFORCED POLYMERS USING THE EXTERNALLY BONDED REINFORCEMENT ON GROOVES METHOD: A REVIEW." REHABEND. 2022. 1946-1953. Abstract
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Moreira, Inês P., Carina Esteves, Susana I. C. J. Palma, Efthymia Ramou, Ana L. M. Carvalho, and Ana C. A. Roque. "Synergy between silk fibroin and ionic liquids for active gas-sensing materials." Materials Today Bio (2022): 100290. AbstractWebsite

Silk fibroin is a biobased material with excellent biocompatibility and mechanical properties, but its use in bioelectronics is hampered by the difficult dissolution and low intrinsic conductivity. Some ionic liquids are known to dissolve fibroin but removed after fibroin processing. However, ionic liquids and fibroin can cooperatively give rise to functional materials, and there are untapped opportunities in this combination. The dissolution of fibroin, followed by gelation, in designer ionic liquids from the imidazolium chloride family with varied alkyl chain lengths (2–10 carbons) is shown here. The alkyl chain length of the anion has a large impact on fibroin secondary structure which adopts unconventional arrangements, yielding robust gels with distinct hierarchical organization. Furthermore, and due to their remarkable air-stability and ionic conductivity, fibroin ionogels are exploited as active electrical gas sensors in an electronic nose revealing the unravelled possibilities of fibroin in soft and flexible electronics.

2021
Amaro, P., J. P. Santos, S. Bhattacharyya, T. K. Mukherjee, and J. K. Saha. "Stabilization method with the relativistic configuration-interaction calculation applied to two-electron resonances." Physical Review A. 103 (2021). AbstractWebsite
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Nunes, M. J., C. M. Cordas, JJG Moura, J. P. Noronha, and L. C. Branco. "Screening of Potential Stress Biomarkers in Sweat Associated with Sports Training." Sports Medicine - Open. 7.1 (2021). AbstractWebsite
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Lima, Carlos D. L., Helena Coelho, Ana Gimeno, Filipa Trovão, Ana Diniz, Jorge S. Dias, Jesús Jiménez-Barbero, Francisco Corzana, Ana Luísa Carvalho, Eurico J. Cabrita, and Filipa Marcelo. "Structural insights into the molecular recognition mechanism of the cancer and pathogenic epitope, LacdiNAc by immune-related lectins." Chemistry – A European JournalChemistry – A European Journal. n/a.n/a (2021). AbstractWebsite

Interactions of glycan-specific epitopes to human lectin receptors represent novel immune checkpoints for investigating cancer and infection diseases. By employing a multidisciplinary approach that combines isothermal titration calorimetry, NMR spectroscopy, molecular dynamics simulations, and X-ray crystallography, we disclosed the molecular determinants that govern the recognition of the tumour and pathogenic glycobiomarker LacdiNAc (GalNAc?1-4GlcNAc, LDN), including their comparison with the ubiquitous LacNAc epitope (Gal?1-4GlcNAc, LN), by two human immune-related lectins, galectin-3 (hGal-3) and the macrophage galactose C-type lectin (hMGL). A different mechanism of binding and interactions is observed for the hGal-3/LDN and hMGL/LDN complexes, which explains the remarkable difference in the binding specificity of LDN and LN by these two lectins. The new structural clues reported herein are fundamental for the chemical design of mimetics targeting hGal-3/hMGL recognition process.

Cardoso, Joao O., Joao Paulo Borges, and Alexandre Velhinho. "Structural metamaterials with negative mechanical/thermomechanical indices: A review." (2021). Abstract
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El-Haouzi, Hind B., Etienne Valette, Bettina-Johanna Krings, and António B. Moniz. "Social Dimensions in CPS & IoT Based Automated Production Systems." Societies. 11.3 (2021): 98. AbstractWebsite

Since the 1970s, the application of microprocessor in industrial machinery and the development of computer systems have transformed the manufacturing landscape. The rapid integration and automation of production systems have outpaced the development of suitable human design criteria, creating a deepening gap between humans and systems in which human was seen as an important source of errors and disruptions. Today, the situation seems different: the scientific and public debate about the concept of Industry 4.0 has raised awareness about the central role humans have to play in manufacturing systems, the design of which must be considered from the very beginning. The future of industrial systems, as represented by Industry 4.0, will rely on the convergence of several research fields such as Intelligent Manufacturing Systems (IMS), Cyber-Physical Systems (CPS), Internet of Things (IoT), but also socio-technical fields such as social approaches within technical systems. This article deals with different human social dimensions associated with CPS and IoT and focuses on their conceptual evolution regarding automated production systems’ sociability, notably by bringing humans back in the loop. Hereby, this paper aims to take stock of current research trends to show the importance of integrating human operators as a part of a socio-technical system based autonomous and intelligent products or resources. Consequently, different models of sociability as a way to integrate humans in the broad sense and/or the develop future automated production systems have been identified from the literature and analysed.

Mota, P., M. L. Esquível, and NP Krasii. "Some Double Diffusion Models For Stock Prices." Global and Stochastic Analysis. 8.2 (2021). AbstractWebsite

Regime switching diffusion processes with one or two thresholds and regime switching occurring by a change in the diffusion drift and/or volatility functions parameters of a stochastic differential equation, whose solution defines a continuous time diffusion process, were defined in previous works; the change in regime occurring whenever the trajectory of the process crosses a threshold, possibly with some delay. In this paper we generalise the previous
results by allowing the underlying diffusion process to change from one family of diffusions in one regime to an entirely different one in the other regime; these families of diffusions are characterised by specific functional forms for drift and volatility coefficients depending on parameters. We propose an estimation procedure for all the parameters, namely the thresholds, the delay and, for both regimes, diffusion’s parameters and we apply the introduced estimation procedure to both simulated and real data.

Ribau, A. M., L. L. Ferrás, M. L. Morgado, M. Rebelo, M. A. Alves, F. T. Pinho, and A. M. Afonso. "A study on mixed electro-osmotic/pressure-driven microchannel flows of a generalised Phan-Thien–Tanner fluid." Journal of Engineering Mathematics . 127.7 (2021).
Rotatori, Filippo Maria, Bruno Camilo Silva, Miguel Moreno-Azanza, and Octávio Mateus A systematic overview of medium and large-sized iguanodontians (Dinosauria, Ornithopoda) from the Upper Jurassic Lourinhã Formation, Portugal. XIX Encontro de Jovens Investigadores em Paleontologia, .Livro de resumos., 2021. Abstractrotatoriet_l_2021_ejip.pdf

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Rossi, Mariana, Brisid Isufi, and António Pinho Ramos. "Seismic behavior of slab-column connections with varying flexural reinforcement ratio." fib Symposium. Vol. 2021-June. 2021. 987-994. Abstract
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Isufi, Brisid, Rui Marreiros, António Pinho Ramos, and Válter Lúcio. "Seismic behaviour of slab-column connections with various punching shear enhancement methods." fib Symposium. Vol. 2021-June. 2021. 978-986. Abstract
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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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