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2024
Svedberg, Dennis, Rahel R. Winiger, Alexandra Berg, Himanshu Sharma, Christian Tellgren-Roth, Bettina A. Debrunner-Vossbrinck, Charles R. Vossbrinck, and Jonas Barandun. "Functional annotation of a divergent genome using sequence and structure-based similarity." BMC Genomics. 25 (2024). AbstractWebsite
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Tavares, Catarina, Tânia Vieira, Jorge C. Silva, João PMR Borges, and Carmo M. Lança. "Bioactive Hydroxyapatite Aerogels with Piezoelectric Particles." Biomimetics 2024, Vol. 9, Page 143. 9 (2024): 143. AbstractWebsite

Open-cell foams based on hydroxyapatite (HAp) can mimic the extracellular matrix (ECM) to better replace damaged hard tissues and assist in their regeneration processes. Aerogels of HAp nanowires (NW) with barium titanate (BT) particles were produced and characterized regarding their physical and chemical properties, bioactivity, and in vitro cytotoxicity. Considering the role of piezoelectricity (mainly due to collagen) and surface charges in bone remodeling, all BT particles, of size 280 nm and 2 and 3 µm, contained BaTiO3 in their piezoelectric tetragonal phase. The synthesized nanowires were verified to be AB-type carbonated hydroxyapatite. The aerogels showed high porosity and relatively homogeneous distribution of the BT particles. Barium titanate proved to be non-cytotoxic while all the aerogels produced were cytotoxic for an extract concentration of 1 mg/mL but became non-cytotoxic at concentrations of 0.5 mg/mL and below. It is possible that these results were affected by the higher surface area and quicker dissolution rate of the aerogels. In the bioactivity assays, SEM/EDS, it was not easy to differentiate between the apatite deposition and the surface of the HAp wires. However, a quantitative EDS analysis shows a possible CaP deposition/dissolution cycle taking place.

Sharma, Himanshu, Nathan Jespersen, Kai Ehrenbolger, Lars-Anders Carlson, and Jonas Barandun. "Ultrastructural insights into the microsporidian infection apparatus reveal the kinetics and morphological transitions of polar tube and cargo during host cell invasion." PLOS Biology. 22 (2024): e3002533. AbstractWebsite
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Shankar, Kasturika, Marie N. Sorin, Himanshu Sharma, Oskar Skoglund, Selma Dahmane, Josy Ter Beek, Solomon Tesfalidet, Louise Nenzén, and Lars-Anders Carlson. "In vitroreconstitution reveals membrane clustering and RNA recruitment by the enteroviral AAA+ ATPase 2C." PLOS Pathogens. 20(8): e10 (2024). AbstractWebsite
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Ribeiro, D. O., F. Bonnardel, A. S. Palma, A. L. M. Carvalho, and S. Perez. "CBMcarb-DB: interface of the three-dimensional landscape of carbohydrate-binding modules." Carbohydrate Chemistry: Chemical and Biological Approaches Volume 46. Eds. Amélia Pilar Rauter, Yves Queneau, and Angelina Sá Palma. Vol. 46. Royal Society of Chemistry, 2024. Abstract

Carbohydrate-binding-modules (CBMs) are discrete auxiliary protein modules with a non-catalytic carbohydrate-binding function and that exhibit a great diversity of binding specificities. CBMcarb-DB is a curated database that classifies the three-dimensional structures of CBM–carbohydrate complexes determined by single-crystal X-ray diffraction methods and solution NMR spectroscopy. We designed the database architecture and the navigation tools to query the database with the Protein Data Bank (PDB), UniProtKB, and GlyTouCan (universal glycan repository) identifiers. Special attention was devoted to describing the bound glycans using simple graphical representation and numerical format for cross-referencing to other glycosciences and functional data databases. CBMcarb-DB provides detailed information on CBMs and their bound oligosaccharides and features their interactions using several open-access applications. We also describe how the curated information provided by CBMcarb-DB can be integrated with AI algorithms of 3D structure prediction, facilitating structure–function studies. Also in this chapter, we discuss the exciting convergence of CBMcarb-DB with the glycan array repository, which serves as a valuable resource for investigating the specific binding interactions between glycans and various biomolecular targets. The interaction of the two fields represents a significant milestone in glycosciences. CBMcarb-DB is freely available at https://cbmdb.glycopedia.eu/ and https://cbmcarb.webhost.fct.unl.pt.

Azevedo, Afonso, Mariana P. Coelho, Jacinta O. Pinho, Paula I. P. Soares, Catarina P. Reis, João P. Borges, and Manuela M. Gaspar. "An alternative hybrid lipid nanosystem combining cytotoxic and magnetic properties as a tool to potentiate antitumor effect of 5-fluorouracil." (2024): 122558. Abstract
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Tavares, Catarina, Tânia Vieira, Jorge C. Silva, João PMR Borges, and Carmo M. Lança. "Bioactive Hydroxyapatite Aerogels with Piezoelectric Particles." 9.3 (2024): 143. Abstract
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Gonçalves, Adriana, Raquel Cabrita, Joana Matos, Inês Rodrigues, Tânia Vieira, João Paulo Borges, and Paula I. P. Soares. "Dual-stimuli-responsive poly (vinyl alcohol) nanofibers for localized cancer treatment: Magnetic hyperthermia and drug release studies." (2024): 105492. Abstract
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Vieira, Tânia, Ana Margarida Rebelo, João Paulo Borges, Célia Henriques, and Jorge Carvalho Silva. "Electrospun Polycaprolactone Membranes Expanded with Chitosan Granules for Cell Infiltration." 16.4 (2024): 527. Abstract
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Hammami, Imen, Manuel Pedro Fernandes Graça, Sílvia Rodrigues Gavinho, Suresh Kumar Jakka, João Paulo Borges, Jorge Carvalho Silva, and Luís Cadillon Costa. "Exploring the Impact of Copper Oxide Substitution on Structure, Morphology, Bioactivity, and Electrical Properties of 45S5 Bioglass®." 9.4 (2024): 213. Abstract
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Caseiro, Catarina, Nicholas G. S. McGregor, Victor Diogo Alves, Ana Luísa Carvalho, Maria João Romão, Gideon J. Davies, Carlos M. G. A. Fontes, and Pedro Bule. "Family GH157 enzyme exhibits broad linkage tolerance and a dual endo/exo- β -glucanase activity on β-glucans." (2024): 137402. AbstractWebsite

The structural and chemical diversity of β-glucans is reflected on the variety of essential biological roles tackled by these polysaccharides. This natural heterogeneity requires an elaborate assortment of enzymatic mechanisms to assemble, degrade or modify, as well as to extract their full biotechnological potential. Recent metagenomic efforts have provided an unprecedented growth in potential new biocatalysts, most of which remain unconfirmed or uncharacterized. Here we report the first biochemical and structural characterization of two bacterial β-glucanases from the recently created glycoside hydrolase family 157 (LaGH157 and BcGH157) and investigate their molecular basis for substrate hydrolysis. Structural analysis by X-ray crystallography revealed that GH157 enzymes belong to clan GH-A, possessing a (β/α)8-barrel fold catalytic domain, two β-sandwich accessory domains and two conserved catalytic glutamates residues, with relative positions compatible with a retaining mechanism of hydrolysis. Specificity screening and enzyme kinetics suggest that the enzymes prefer mixed-linkage glucans over β-1,3-glucans. Activity screening showed that both enzymes exhibit pH optimum at 6.5 and temperature optimum for LaGH157 and BcGH157 at 25 °C and 48 °C, respectively. Product analysis with HPAEC-PAD and LC-MS revealed that both enzymes are endo-1,3(4)-β-glucanases, capable of cleaving β-1,3 and β-1,4-linked glucoses, when preceded by a β-1,3 linkage. Moreover, BcGH157 needs a minimum of 4 subsites occupied for hydrolysis to occur, while LaGH157 only requires 3 subsites. Additionally, LaGH157 possesses exohydrolytic activity on β-1,3 and branching β-1,6 linkages. This unusual bifunctional endo-1,3(4)/exo-1,3–1,6 activity constitutes an expansion on our understanding of β-glucan deconstruction, with the potential to inspire future applications.

Gavinho, Sílvia Rodrigues, Imen Hammami, Suresh Kumar Jakka, Sílvia Soreto Teixeira, Jorge Carvalho Silva, João Paulo Borges, and Manuel Pedro Fernandes Graça. "Influence of the Addition of Zinc, Strontium, or Magnesium Oxides to the Bioglass 45S5 Network on Electrical Behavior." 17.2 (2024): 499. Abstract
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Boavida, Nuno, António B. Moniz, Maria Rosário do Jorge, Célia Costa da Cabral, and Marta Candeias 2º Relatório do Projeto Europeu CERP: Trabalho de Campo. Lisboa: CICS.NOVA, 2024. Abstract

Este relatório pretende descrever e analisar o trabalho de campo realizado no âmbito do projeto CERP. O projeto pretende compreender o estado da arte em Portugal da negociação coletiva portuguesa com referências à transição sustentável e justa no setor dos transportes e no setor público.

Boavida, Nuno, Maria Rosário do Jorge, Marta Candeias, António B. Moniz, and Célia Costa da Cabral A contratação coletiva portuguesa com referências à transição sustentável e justa no setor dos transportes e no setor público. Lisboa: CICS.NOVA, 2024. Abstract

Este relatório pretende fazer uma revisão da literatura sobre a negociação coletiva portuguesa com referências à transição sustentável e justa no setor dos transportes e no setor público.
Portugal tem sido dos países que iniciou já o seu caminho de transição e encerrou as centrais a carvão. Mas em países do Leste europeu, por exemplo, existe muita indústria associada à produção de electricidade a partir do carvão, e onde o encerramento levanta sérias questões sociais. Nestes casos, em particular, é necessário um processo gradual que inclua medidas de apoio à formação e reconversão dos trabalhadores envolvidos.

Burigo, André, and Octávio Mateus. "Allosaurus europaeus (Theropoda: Allosauroidea) Revisited and Taxonomy of the Genus." Diversity. 17.1 (2024): 29. Abstractburigo__mateus_2024_diversity-17-00029.pdfWebsite

Allosaurus is one of the most famous theropod dinosaurs, but the validity and relationships between the different species have been confusing and often questioned. Portugal is relevant to the understanding of the genus in light of the discovery of A. europaeus ML415 from the Early Tithonian of Lourinhã and Allosaurus MNHNUL/AND.001 from Andrés. However, the exact classification and validity of these two specimens has always been controversial. The presence of Allosaurus in Portugal is strong evidence for a North America–Europe Late Jurassic dispersal, later supported by other taxa. A detailed cranial description and specimen-based phylogeny were performed and resolved many of the open questions: (1) The diversity of Allosaurus is limited to three named species: A. fragilis, A. europaeus, and A. jimmadseni. (2) Nine autapomorphies were found in A. europaeus, confirming the validity of the species. (3) Phylogenetic analyses place both Portuguese specimens in the genus Allosaurus, based on the following synapomorphies: jugal bone lateral view, relative heights of quadratojugal prongs, the dorsal prong is equal in height, the jugal bone in lateral view shows shallow accessory pneumatization of the antorbital fossa, the palatine pneumatic recess shape is small, and lacrimal horn morphology has a triangular horn. (4) The Andrés specimen is placed with the A. europaeus and they are considered here to be the same species, which is paleo-geographically and biochronologically congruent. (5) A. europaeus and A. jimmadseni are sister taxa and closer to each other than to A. fragilis. The genus is distributed in occurrences from the United States, Germany, and Portugal, and from the Late Kimmeridgian to the Late Tithonian, while the Cenomanian report from Japan is reidentified as Segnosaurus.

Rotatori, Filippo Maria, Mattia Quaranta, Filippo Bertozzo, Tom Hübner, Bruno Camilo, Octávio Mateus, and Miguel Moreno-Azanza. "Hadrosaur-like vascularisation in the dentary of an early diverging iguanodontian dinosaur." Historical Biology. 36.10 (2024): 1979-1984. Abstractrotatori_et_al_2023_hadrosaur_like_vascularisation_in_the_dentary_of_an_early_diverging_iguanodontian_dinosaur.pdfWebsite

ABSTRACTVirtual palaeontology is a growing field, leading palaeontologists to better understand the microanatomy of many extinct species. The application of techniques such as CT and μCT-scanning allows the researchers to study micro-anatomical features in a non-invasive way and make inferences on the palaeobiology of animals. Dinosaurs have been extensively studied using these techniques, with particular focus on the microanatomy of the cranium, whereas relatively little is known of other cranial elements, such as the lower jaw. Here, we aim to fill this gap, describing the microanatomy of the specimen ML 768, an isolated dentary belonging to a dryosaurid iguanodontian dinosaur from the Upper Jurassic of Lourinhã Fm. The dentary ML 768 was subjected to μCT-scanning, and subsequently the data were segmented in Avizo and rendered in Blender. We identified functional and replacement teeth, recognising remnants of old replacement cycles. Furthermore, we mapped a rich neurovascular network present in the dentary and compared it with reference literature. We found that the high vascularisation is shared with other cerapodan dinosaurs with high tooth replacement rates, although homoeostasis may have also played a role in the development of this condition. Further evidence is needed to appreciate the macroevolutionary significance of these findings.

Pereira, Duarte, Carmen Morgado, and Fernanda Barbosa NextBlocks: An Interactive Block Programming Platform. ITiCSE 2024. Milan, Italy, 2024. Abstract

Since Seymour Papert's work with the Logo programming language in the 1960s, there has been a prevailing belief in the effectiveness of visual programming environments for teaching programming to children and novices. As these platforms evolved and became more prevalent, using block programming to teach children and beginners became increasingly more common. However, modern block programming platforms like Scratch and Code.org excessively restrict educators by not allowing them to create custom exercises in the platform. They also tend to make programming a solo activity, not allowing for collaboration and cooperation between learners (Scratch is an exception in this regard). Additionally, they are usually located in standalone websites instead of being implemented in locations that students already frequent regularly. Having identified these gaps in the field of block programming environments, this paper proposes NextBlocks, a new block programming platform implemented as a Moodle plugin. This platform enables educators to create custom exercises, emphasizing social perception and collaboration features. It supports features that are uncommon in block programming environments, contributing to a more interactive and engaging learning experience. Furthermore, being integrated into the Moodle Learning Management System makes NextBlocks more easily accessible within the educational framework. As an open-source platform, besides solving current challenges, it can also serve as a foundation for future expansion by the education community. This paper explores some of the unique features of NextBlocks, presents a case study on the platform, and discusses its potential contributions to enhancing programming education for beginners within a collaborative learning environment.

Burigo, André, and Octávio Mateus. "Notes on the type specimens of Allosaurus atrox and A. Ferox (Theropoda, Allosauridae)." Paleolusitana. 2 (2024): 18-20. Abstractaburigo__omateus_v2.pdf

Allosaurus Marsh, 1877 is one of the most iconic theropods of the Late Jurassic of USA and Portugal. However,
since the first description the genus was used as taxonomical wastebasket to which several species were
described. We revisit three type specimens, Allosaurus fragilis YPM 1930, A. atrox YPM 1890 and A. ferox USNM
2315. We interpret the vertebral material of A. atrox and support it as a junior synonym of A. fragilis, and A. ferox
as Allosaurus indet. rather than A. fragilis.

Botelho, M. C., and H. Rocha. "O conhecimento profissional do professor na mobilização de diferentes representações com diferentes tecnologias." Iberian Journal of Information Systems and Technologies. E71 (2024): 486-499.Website
Rocha, H., and A. Babo. "Problem-solving and mathematical competence: a look to the relation during the study of Linear Programming." Thinking Skills and Creativity. 51 (2024): 1-14. AbstractWebsite

This study seeks reflection on the approaches of 11th grade students to Linear Programming problems, discussing the approaches taken at different moments of the teaching process. It aims to analyze:
How is the students’ mathematical competence characterized in relation to problemsolving;
What differences can be identified in the resolutions at different moments of the teaching and learning process.
We adopt a qualitative and interpretative methodology, analyzing the approaches of two pairs of students with different mathematical backgrounds. The analysis is guided by P´olya’s stages of solving a problem and aspects of the understanding of mathematical competence. The results show different approaches to the problems depending on the teaching moment and different competences. The mathematical background impacts the students’ success when they implement routine procedures, however it does not seem to determine the students’ competence to reason about a problem.

Botelho, M. C., and H. Rocha The role of teachers’ knowledge and the use of different technologies in the classroom. MEDA – Mathematics Education at the Digital Age. Bari, Italy: ERME, 2024. Abstract2024_meda_botelho_rocha.pdf

The potential of technology to enhance the learning of mathematics is widely acknowledged. However, realizing this potential requires teachers to possess the knowledge to effectively integrate it into their teaching practices. This study aims to characterize the mathematics teacher's knowledge when using different technologies in teaching and learning. It also aims to study the existence of relationships between the specific domains of the Knowledge for Teaching Mathematics with Technology – KTMT and the integration of graphing calculator and Excel. The methodology adopted is qualitative with an interpretative approach, using a case study of Mathematics teacher in the 11th grade (16-17 years old) with extensive experience in the use of technology. This study shows that different KTMT knowledge is mobilized, according to the technology chosen and the specific characteristics of each of the technologies used influenced the teacher's pedagogical choices.

Pan, Xiaoxi, Khalid AbdulJabbar, Jose Coelho-Lima, Anca-Ioana Grapa, Hanyun Zhang, Alvin Ho Kwan Cheung, Juvenal Baena, and others. "The artificial intelligence-based model ANORAK improves histopathological grading of lung adenocarcinoma." Nature Cancer. 5 (2024): 347-363. AbstractWebsite
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Bento, Mariana, Hannah Cook, Virginia Marin Anaya, Esther Bär, Andrew Nisbet, Ana Lourenço, Mohammad Hussein, and Catarina Veiga. "Characterisation of 3D-printable thermoplastics to be used as tissue-equivalent materials in photon and proton beam radiotherapy end-to-end quality assurance devices." Biomedical Physics & Engineering Express (2024). AbstractWebsite
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Coutinho, Mathilda L., João Pedro Veiga, Andreia Ruivo, Teresa Pereira da Silva, Silvia Bottura-Scardina, Maria Margarida R. A. Lima, Carlos Pereira, Ana Carvalho Dias, Luis Dias, Peter Vandenabeele, and José C. Roseiro. "Characterization of Tableware from Fábrica de Loiça de Sacavém—Linking Analytical and Documental Research." Minerals. 14 (2024). AbstractWebsite

Fábrica de Loiça de Sacavém (ca. 1858–1994) was among the first to produce white earthenware in Portugal, becoming one of the country’s leading ceramic manufacturers during the late 19th to early 20th centuries. Research on white earthenware has accompanied the growing interest in post-industrial archaeology but is still poorly explored compared to more ancient ceramic productions. This study focused on the ceramic body, glazes, and colourants of tableware produced by Fábrica de Loiça de Sacavém during the first 50 years of its activity (1859–1910). A multi-analytical approach was selected to investigate the chemical and mineralogical composition of the ceramic body, glaze, and pigments using optical microscopy, variable-pressure scanning electron microscope energy-dispersive X-ray spectroscopy (VP-SEM-EDS), μ-Raman spectroscopy, μ-X-ray Diffraction (μ-XRD), and reflectance spectroscopy (hyperspectral image analysis). The studied tableware was produced with a Ca-poor siliceous–aluminous white earthenware ceramic body covered with transparent alkali lead or lead borosilicate glaze, and most colourants were complex Cr-based pigments. These results are in agreement with the little documental evidence from this period found in the manufacturer’s archives.