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2025
de Almeida, João M. G. C. F., Cândido Pinto Ricardo, and Carla Pinheiro. "Unveiling DIR proteins involved in cork formation: insights from transcriptome analysis and cis-element co-occurrence." Theoretical and Experimental Plant Physiology. 37 (2025). AbstractWebsite
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Coletti, Roberta, Orestes J. Cerdeira, Marcos Raydan, and Marta B. Lopes. "An unsupervised tool for biomarker discovery and cancer subtyping applied to glioblastoma." BioData Mining. 18.1 (2025): 85. AbstractWebsite

High-dimensional omics data often contain more variables than observations, which can lead to overfitting and negatively impact the results of classical data analysis methods. To address the issue, supervised variable selection methods are often used, incorporating penalty terms into the model. While effective for selecting task-specific variables, this approach may not preserve the overall dataset structure for multiple downstream analyses. This study aims to evaluate unsupervised variable selection approaches and introduce a novel tool that improves data interpretability while maintaining biological information.

2024
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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Rotatori, Filippo Maria, Lucrezia Ferrari, Cristina Sequero, Bruno Camilo, Octávio Mateus, and Miguel Moreno-Azanza. "An unexpected early-diverging iguanodontian dinosaur (Ornithischia, Ornithopoda) from the Upper Jurassic of Portugal." Journal of Vertebrate Paleontology (2024): e2310066. Abstractrotatori_et_al_2024_an_unexpected_iguanodontian_dinosaur__ornithischia__ornithopoda__portugal.pdfWebsite

Iguanodontia is a diverse clade of herbivorous ornithischian dinosaurs that were speciose and abundant during the Jurassic and Cretaceous. Although the monophyly of Iguanodontia is well supported, their internal relationships have sparked heated debate due to several phylogenetic paradigm shifts. Late Jurassic basally branching iguanodontians in particular are not well understood in terms of their systematic affinities and evolutionary relevance. Their fossil record in Europe is meager compared with North America, with only a few species currently recognized. Two taxa are currently known from the Upper Jurassic of England, the basally branching styracosternan Cumnoria prestwichii and the putative dryosaurid Callovosaurus leedsi. In the Upper Jurassic of Portugal, the styracosternan Draconyx loureiroi and the dryosaurid Eousdryosaurus nanohallucis are presently the only described basally branching iguanodontians. Here we report a new species of early diverging iguanodontian from the Upper Jurassic Lourinhã Formation of western-central Portugal. The new species is clearly distinguished from all other coeval taxa by an exclusive combination of characters that include a tibia with a cnemial crest that is directed craniolaterally and a fibular condyle that is angled at 90° with respect to the proximal epiphysis, a fibula with symmetrical proximal margins, and a reduced metatarsal I. The phylogenetic relationships of the Lourinhã iguanodontian were explored using maximum parsimony and Bayesian inference. The two analyses recover the Lourinhã iguanodontian as an indeterminate dryomorphan, with more precise affinities precluded due to the current available material. Body size is estimated between 3 and 4 meters for the holotype specimen, adding to the diversity of small ornithopods already recognized in the paleoichnological record of the Lourinhã Formation. http://zoobank.org/urn:lsid:zoobank.org:pub:5F4D52D0-0F0B-4809-8561-BE58C7C97D45

Rocha, H. The use of the TPACK framework on research about teachers’ knowledge to teach with digital technology. MEDA – Mathematics Education at the Digital Age. Bari, Italy: ERME, 2024. Abstract2024_meda_rocha.pdf

The potential of digital technologies for teaching and learning mathematics is widely recognized and teachers’ knowledge is one of the elements impacting their integration. Several authors have intended to characterize the teachers’ knowledge required and developed several models, being TPACK one of these models. In this study, we seek to conduct a systematic review of the research on the integration of digital technologies by mathematics teachers based on the TPACK model. Specifically, we intend to answer the following research questions: (1) What are the main methodological options adopted? (2) How is the framework operationalized/used in the studies? The review was based on a search in the Scopus database and resulted in the identification of 10 relevant documents. The analysis suggests a prevalence of qualitative approaches, but a strong use of questionnaires; and an integration of the model with other frameworks, namely the developmental model of TPACK.

Akalin, S. A., T. Mateus, G. Ribeiro, J. Deuermeier, T. Calmeiro, H. Águas, R. Martins, A. T. Vicente, MJ Mendes, and U. D. Yilmazer Menda. "Ultra-flexible, high-performing NAN transparent electrodes for bendable optoelectronic applications." Journal of Materials Science: Materials in Electronics. 35 (2024). AbstractWebsite
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Alexandre, M., H. Águas, E. Fortunato, R. Martins, and MJ Mendes. "Understanding the Potential of Light Absorption in Dots-in-Host Semiconductors." ACS Photonics (2024). AbstractWebsite
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Pereira, Maria Elias, Jonas Deuermeier, Rodrigo Martins, Pedro Barquinha, and Asal Kiazadeh. "Unlocking Neuromorphic Vision: Advancements in IGZO-Based Optoelectronic Memristors with Visible Range Sensitivity." ACS Applied Electronic Materials. 6 (2024): 5230-5243. AbstractWebsite
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2023
BARRULAS, RAQUEL ALEXANDRA VALADARES, DANIEL FERREIRA, VALENTINA CHIAPPARINO, MARCILEIA ZANATTA, CARLOS A. GARCÍA-GONZÁLEZ, João Paulo Miranda Ribeiro Borges, and MARTA CRISTINA PARRACHO CANÇADO CORVO. "Unlocking New Possibilities: The Synergy Between Ionic Liquids and Porous M0aterials." 2023. Abstract
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Silva, Ana B. P., Ana R. Jesus, Daniela A. S. Agostinho, José M. S. S. Esperança, Alexandre Paiva, Ana R. C. Duarte, and Patrícia M. Reis. "Using dicationic ionic liquids to upgrade the cytotoxicity and solubility of poorly water-soluble drugs." 3.1 (2023): 100052. AbstractWebsite

New dicationic ionic liquids (DcILs) based on carboxylic acid-derived, N-acetyl amino acid-derived or bromide anions, and ammonium cations were synthesized and characterized. DcILs were employed as co-solvents to improve the solubility of ibuprofen and ketoprofen belonging to BCS class II. These DcILs demonstrated to be less cytotoxic towards fibroblasts L929 cells and contributed to an augment in the solubility of both drugs when compared with monocationic ionic liquids (McILs). The cytotoxic profile of some of these ILs was established, and when the linker between two ammonium cations was an ether group or a short alkyl chain an IC50 higher than 200 mM for fibroblasts L929 cells was achieved. The anion structure showed to be a key factor in the solubility of both drugs, being the family of carboxylic acid-derived, the one that presented the most significant effect, followed by N-acetyl amino acid-derived and finally bromide. The two dimensional 1H1H– NOESY NMR spectra showed the interaction between the IL and the two oral drugs, responsible for the improvement of their solubility. The lipophilicity (logP) of ibuprofen and ketoprofen reduced in the presence of these new DcILs.

Santana, T., A. Antão, N. Guerra, and M. Vicente da Silva. "Upper bounds for the three-dimensional seismic active earth pressure coefficients." Géotechnique Letters. 13 (2023): 65-74. AbstractWebsite

A numerical implementation of the upper-bound theorem of limit analysis is applied to determine two-dimensional (2D) and three-dimensional (3D) active horizontal earth pressure coefficients considering seismic actions through a horizontal seismic coefficient. Results are obtained for vertical wall, horizontal soil, different friction angles of the soil, soil-to-wall friction ratios, horizontal seismic coefficients and wall width-to-height ratios. The few cases for which 3D active earth pressure coefficients are available in the literature using upper-bound methods were used for comparison with the corresponding earth pressure coefficients obtained in this study. This showed a general improvement of these results, which allows expecting a good accuracy for the set of cases studied. The ratios between the 3D and 2D horizontal active earth pressure coefficients are found to be practically independent of the soil-to-wall friction ratio. An equation is proposed for calculating these ratios. This equation can be easily used in the design of geotechnical structures requiring the determination of 3D active earth pressure coefficients.

2022
Caeiro, Frederico, L{\'ı}gia Henriques-Rodrigues, and Ivette M. Gomes. "The Use of Generalized Means in the Estimation of the Weibull Tail Coefficient." Computational and Mathematical Methods. 2022 (2022): 1-12. AbstractWebsite
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Jesus, Ana Rita, Ana Rita C. Duarte, and Alexandre Paiva. "Use of natural deep eutectic systems as new cryoprotectant agents in the vitrification of mammalian cells." 12.1 (2022): 8095. AbstractWebsite

In this work we present the potential of Natural Deep Eutectic Systems (NADES) as new vitrification media for the cryopreservation of mammalian cells. Several NADES composed of natural metabolites were prepared and tested as CPAs in two cell lines, L929 and HacaT cells. After the harvesting, cells were mixed with the eutectic systems, and frozen directly into liquid nitrogen to achieve a vitreous state. Then, the cells were thawed and it was observed that NADES were able to exert a significant cryoprotective effect in L929 cells, when compared with DMSO or in the absence of a CPA. For HacaT cells, only a eutectic system showed a slightly improvement in cell survival, while DMSO caused complete cell death. Moreover, the thermal behaviour of the best systems was studied for further understanding the protective properties of NADES as CPAs, and have shown a significant difference in terms of Tm and Tc when compared with DMSO and water. Additionally, the results obtained showed that NADES can be maintained in the growth media after the thawing step, without compromising cell viability. In summary, we have shown the great potential of NADES to be used as CPAs for the cryopreservation of different cell types, using the vitrification method.

Moreno-Azanza, Miguel, Blanca Balauz, Lope Ezquerro, Rute Coimbra, Octávio Mateus, and Carmen Nuñez-Lahuerta. "Unbroken dinosaur eggs accumulated together do not guarantee autochthony of the fossil assemblage." Journal of Taphonomy. 16.1-4 (2022): 129-130. Abstractmoreno-azanza_et_al_2020_unbroken_eggs.pdf

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Biscaia, H. C., J. Canejo, S. Zhang, and R. Almeida. "Using digital image correlation to evaluate the bond between carbon fibre-reinforced polymers and timber." Structural Health Monitoring. 21 (2022): 534-557. AbstractWebsite

The use of optic measurements such as digital image correlation to take strain measurements of fibre-reinforced polymers bonded to a substrate has been on the increase recently. This technique has proven to be useful to fully characterize the bond behaviour between two materials. Although modern digital cameras can take high-definition photos, this task is far from simple due to the tiny displacements that need to be measured. Consequently, digital image correlation measurements lead to relative errors that, at an initial stage of the debonding process, are higher than those calculated close to the debonding of the fibre-reinforced polymer from the substrate. This study aims to evaluate and analyse the use of the digital image correlation technique on the bond between carbon fibre-reinforced polymer laminates and timber when subjected to a pull-out load consistent with fracture Mode II. To allow the quantification of the relative errors obtained from the digital image correlation measurements during the full debonding process, several strain gauges were used to measure the strains in the carbon fibre-reinforced polymer composite. The accuracy of the digital image correlation measurements is analysed by comparing it with those obtained from the strain gauges, which is a very well-established measuring technique. Another contribution of this study is to check the versatility of the digital image correlation measurements on a broader range of situations. To that end, several timber prisms were bonded with seven different bonding techniques with and without the installation of a mechanical anchorage at the carbon fibre-reinforced polymer unpulled end. The results showed that the digital image correlation technique was able to track the slips calculated from the strain gauge measurements until the debonding load, but after that, some difficulties to measure the displacements of the anchored carbon fibre-reinforced polymer-to-timber joints were detected. The digital image correlation technique also over predicted bond stresses when compared with those taken from the strain gauges, which led to bond–slip relationships with higher bond stresses. © The Author(s) 2021.

2021
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.

2020
Rocha, H. "Using tasks to develop pre-service teachers’ knowledge for teaching mathematics with digital technology." ZDM Mathematics Education. 52.7 (2020): 1381-1396. AbstractWebsite

Teacher education is central to the development of the professional knowledge of pre-service teachers. The main goal of this paper is to refect on the development that the analysis (done by a group of pre-service secondary teachers) of a set of tasks, based on elements related to domains of KTMT—Knowledge for Teaching Mathematics with Technology—can bring to the knowledge of pre-service teachers of mathematics. Specifcally, the goal was to investigate the following questions: (1) What are the factors that guide the pre-service teachers’ task discussion? (2) Which KTMT domains are emphasized by pre-service teachers during task discussion? The elements taken into account are the characteristics of the tasks (focus on cognitive level, structuring level and technology role), the use of representations (focus on balance and articulation of representations), and the equilibrium between experimentation (focus on digital technology afordances) and justifcation (focus on argumentation and proof). The methodology of this case study involves a qualitative approach. The main conclusions suggest that infuences in the pre-service teachers’ discussion of tasks fell into the following categories: the potentialities of technology, the type of tasks, and the prospective teachers’ experience with a set of tasks, and analysis of some real students’ reports. With regard to KTMT, although it was possible to identify some global development, Teaching and Learning and Technology Knowledge was the domain in which stronger development took place.

Esgalhado, Filipa, Arnaldo Batista, Helena Mouriño, Sara Russo, Catarina Palma dos Reis, Fátima Serrano, Valentina Vassilenko, and Manuel Ortigueira. "Uterine contractions clustering based on electrohysterography." Computers in Biology and Medicine. 123.June (2020).
2019
Pacheco, J., J. de Brito, C. Chastre, and L. Evangelista. "Uncertainty models of reinforced concrete beams in bending: code comparison and recycled aggregate incorporation." Journal of Structural Engineering. 145 (2019): 04019013. AbstractWebsite

The bias factor of the Eurocode 2 [CEN (European Committee for Standardization) (2008). Eurocode 2: Design of ConcreteStructures–Part 1-1: General Rules and Rules for Buildings] and ACI 318 [ACI (American Concrete Institute) (2014). Building CodeRequirements for Structural Concrete and Commentary] flexural resistance models of reinforced concrete beams are compared withemphasis on the effect of the incorporation of coarse recycled aggregates sourced from concrete waste. The bias factor of the yielding momentcalculations according to both codes is also investigated, and the bias in the cracking moment when Eurocode 2 material clauses are used. Thedatabase was composed of 174 beams, and the criteria that led to its development are discussed. The effect of recycled aggregate incorporationon the statistical descriptors of the bias factor is evaluated and probabilistic modeling using lognormal distributions is argued for. Preliminarypartial safety factors for the bias factor of recycled aggregate concrete beams are proposed. No significant differences in the bias of theultimate moment were found between the two comparison vectors: Eurocode 2 versus ACI 318 specifications and recycled versus naturalcoarse aggregate. The bias of the cracking moment increased when coarse recycled aggregates were incorporated, most probably due to thehigher heterogeneity of recycled aggregates.

Gomes, Susana, Diana Querido, José Luís Ferreira, João Paulo Borges, Célia Henriques, and Jorge Carvalho Silva. "Using water to control electrospun Polycaprolactone fibre morphology for soft tissue engineering." 26.9 (2019): 222. Abstract
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Antão, Nunes A., N. M. C. Guerra, Vicente M. da Silva, and T. Santana Upper and lower bounds for the bearing apacity of foundations on soft soils with reinforcement columns. Proceedings of the 17 th European Conference on Soil Mechanics and Geotechnical Engineering. Reykjavik, Islândia, 2019.
2018
Maiti, B. K., L. B. Maia, AJ Moro, J. C. Lima, C. M. Cordas, I. Moura, and JJG Moura. "Unusual Reduction Mechanism of Copper in Cysteine-Rich Environment." Inorganic Chemistry. 57.14 (2018): 8078-8088. AbstractWebsite
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Lopes, João, João Falcão M. ª Silva, Fernando F. S. Pinho, and Paula Couto. "Utilização da metodologia BIM no apoio à reabilitação funcional de um edifício." 2º Congresso Português de Building Information Modelling. ISBN: 978-989-20-8396-4. DOI: https://doi.org/10.5281/zenodo.1226766. IST. Lisboa 2018.
Maiti, B. K., L. Maia, AJ Moro, J. C. Lima, C. M. Cordas, I. Moura, and JJG Moura. "Unusual reduction mechanism of copper in cysteine-rich environment." Inorg Chem. 57 (2018): 8078-8088. AbstractWebsite