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- The European reference genome atlas : piloting a decentralised approach to equitable biodiversity genomicsPublication . Mc Cartney, Ann M.; Formenti, Giulio; Mouton, Alice; Panis, Diego De; Marins, Luísa S.; Leitão, Henrique G.; Diedericks, Genevieve; Kirangwa, Joseph; Morselli, Marco; Salces-Ortiz, Judit; Escudero, Nuria; Iannucci, Alessio; Natali, Chiara; Svardal, Hannes; Fernández, Rosa; Pooter, Tim De; Joris, Geert; Strazisar, Mojca; Wood, Jonathan M. D.; Herron, Katie E.; Seehausen, Ole; Watts, Phillip C.; Shaw, Felix; Davey, Robert P.; Minotto, Alice; Fernández, José M.; Böhne, Astrid; Alegria, Carla; Alioto, Tyler; Alves, Paulo C.; Amorim, Isabel R.; Aury, Jean-Marc; Backstrom, Niclas; Baldrian, Petr; Baltrunaite, Laima; Barta, Endre; BedHom, Bertrand; Belser, Caroline; Bergsten, Johannes; Bertrand, Laurie; Bilandija, Helena; Binzer-Panchal, Mahesh; Bista, Iliana; Blaxter, Mark; Borges, Paulo A. V.; Dias, Guilherme Borges; Bosse, Mirte; Brown, Tom; Bruggmann, Rémy; Buena-Atienza, Elena; Burgin, Josephine; Buzan, Elena; Cariani, Alessia; Casadei, Nicolas; Chiara, Matteo; Chozas, Sergio; Čiampor Jr., Fedor; Crottini, Angelica; Cruaud, Corinne; Cruz, Fernando; Dalen, Love; Biase, Alessio De; Campo, Javier del; Delic, Teo; Dennis, Alice B.; Derks, Martijn F. L.; Diroma, Maria Angela; Djan, Mihajla; Duprat, Simone; Eleftheriadi, Klara; Feulner, Philine G. D.; Flot, Jean-François; Forni, Giobbe; Fosso, Bruno; Fournier, Pascal; Fournier-Chambrillon, Christine; Gabaldon, Toni; Garg, Shilpa; Gissi, Carmela; Giupponi, Luca; Gomez-Garrido, Jessica; González, Josefa; Grilo, Miguel L.; Grüning, Björn; Guerin, Thomas; Guiglielmoni, Nadege; Gut, Marta; Haesler, Marcel P.; Hahn, Christoph; Halpern, Balint; Harrison, Peter W.; Heintz, Julia; Hindrikson, Maris; Höglund, Jacob; Howe, Kerstin; Hughes, Graham M.; Istace, Benjamin; Cock, Mark J.; Janžekovič, Franc; Jonsson, Zophonias O.; Joye-Dind, Sagane; Koskimäki, Janne J.; Krystufek, Boris; Kubacka, Justyna; Kuhl, Heiner; Kusza, Szilvia; Labadie, Karine; Lähteenaro, Meri; Lantz, Henrik; Lavrinienko, Anton; Leclère, Lucas; Lopes, Ricardo Jorge; Madsen, Ole; Magdelenat, Ghislaine; Magoga, Giulia; Manousaki, Tereza; Mappes, Tapio; Marques, João Pedro; Redondo, Gemma I. Martinez; Maumus, Florian; McCarthy, Shane A.; Megens, Hendrik-Jan; Melo-Ferreira, José; Mendes, Sofia L.; Montagna, Matteo; Moreno, João; Mosbech, Mai-Britt; Moura, Mónica; Musilova, Zuzana; Myers, Eugene; Nash, Will J.; Nater, Alexander; Nicholson, Pamela; Niell, Manuel; Nijland, Reindert; Noel, Benjamin; Noren, Karin; Oliveira, Pedro H.; Olsen, Remi-Andre; Ometto, Lino; Oomen, Rebekah A.; Ossowski, Stephan; Palinauskas, Vaidas; Palsson, Snaebjorn; Panibe, Jerome P.; Pauperio, Joana; Pavlek, Martina; Payen, Emilie; Pawlowska, Julia; Pellicer, Jaume; Pesole, Graziano; Pimenta, João; Pippel, Martin; Pirttilä, Anna Maria; Poulakakis, Nikos; Rajan, Jeena; Rego, Rúben M. C.; Resendes, Roberto; Resl, Philipp; Riesgo, Ana; Rodin-Morch, Patrik; Soares, Andre E. R.; Fernandes, Carlos Rodriguez; Romeiras, Maria M.; Roxo, Guilherme; Rüber, Lukas; Ruiz-Lopez, Maria Jose; Saarma, Urmas; Silva, Luis P. da; Sim-Sim, Manuela; Soler, Lucile; Sousa, Vitor C.; Santos, Carla Sousa; Spada, Alberto; Stefanovic, Milomir; Steger, Viktor; Stiller, Josefin; Stöck, Matthias; Struck, Torsten H.; Sudasinghe, Hiranya; Tapanainen, Riikka; Tellgren-Roth, Christian; Trindade, Helena; Tukalenko, Yevhen; Urso, Ilenia; Vacherie, Benoit; Belleghem, Steven M. Van; Oers, Kees Van; Vargas-Chavez, Carlos; Velickovic, Nevena; Vella, Noel; Vella, Adriana; Vernesi, Cristiano; Vicente, Sara; Villa, Sara; Pettersson, Olga Vinnere; Volckaert, Filip A. M.; Voros, Judit; Wincker, Patrick; Winkler, Sylke; Ciofi, Claudio; Waterhouse, Robert M.; Mazzoni, Camila J.A genomic database of all Earth’s eukaryotic species could contribute to many scientific discoveries; however, only a tiny fraction of species have genomic information available. In 2018, scientists across the world united under the Earth BioGenome Project (EBP), aiming to produce a database of high-quality reference genomes containing all ~1.5 million recognized eukaryotic species. As the European node of the EBP, the European Reference Genome Atlas (ERGA) sought to implement a new decentralised, equitable and inclusive model for producing reference genomes. For this, ERGA launched a Pilot Project establishing the first distributed reference genome production infrastructure and testing it on 98 eukaryotic species from 33 European countries. Here we outline the infrastructure and explore its effectiveness for scaling high-quality reference genome production, whilst considering equity and inclusion. The outcomes and lessons learned provide a solid foundation for ERGA while offering key learnings to other transnational, national genomic resource projects and the EBP.
- The effects of the leg position on the Nordic hamstring exercise eccentric force : a randomized cross-over studyPublication . Ferreira, Ricardo Maia; Martins, Pedro Nunes; Nunes, Hugo; Fernandes, Luís Gonçalves; Amorim, César Ferreira; Ferreira, Luciana Maia AlvesGiven the posterior chain configuration, it is anticipated that tibial positioning influences hamstring recruitment; medial hamstrings should be more activated during medial rotation, while lateral hamstrings should be more activated during lateral rotation. However, most studies showing this pattern have focused on concentric or isometric strength, leaving the influence on eccentric strength fairly unknown. Therefore, the aim of this study was to investigate the electromyographic response of the hamstring muscles during Nordic hamstring exercises in three leg positions: internal rotation, external rotation, and neutral. This study encompassed a randomized crossover study and used surface electromyography to analyze the activity of the biceps femoris and semitendinosus muscles during the Nordic hamstring exercise, in the three positions. Results indicated no statistically significant differences in muscle activation between positions or sides (p > 0.05), though small effect sizes were observed for the biceps femoris in different positions (η2 = 0.01–0.03). Furthermore, the internal rotation position generally elicited the highest muscle activations. Notably, biceps femoris muscles exhibited higher activations compared to semitendinosus muscles, with the greatest differences seen in the internal rotation position. This suggests that tibial rotation influences hamstring recruitment patterns; however, it was lower than expected.
- The effects of activated carbon toothpastes on orthodontic elastomeric chains : an in vitro studyPublication . Pereira, Pedro Mariano; Bugiaghis, Iman; Carmo, Mariana Isidro Do; Proença, LuísObjectives: Using toothpaste with activated carbon might increase the decay of orthodontic elastomeric chains’ (ECs) tensile strength, thereby compromising orthodontic treatment. Therefore, this study aimed to evaluate the influence of activated charcoal toothpaste on orthodontic ECs. Materials and Methods: A total sample of 180 EC segments from 3M Unitek®, Ormco® and Ortho Classic® brands were equally divided into 12 groups, each comprising 15 specimens. These pieces were kept in artificial saliva at 37 °C and brushed twice daily for 28 days, with three distinct types of toothpaste: Colgate® Total, Colgate® Max White, and Dr Organic® Extra Whitening Charcoal Toothpaste. The latter two toothpastes contain activated charcoal. Tensile strength, resistance to rupture and colour variation were evaluated at time zero and day 28. Descriptive statistics, one-way ANOVA and Tukey HSD tests were performed at p ≤ 0.05. Results: Toothpaste with and without activated carbon significantly reduced the tensile strength and resistance to rupture of the ECs, and altered EC colour (p < 0.0001). There was inconsistency in the effect of the activated carbon on EC characteristics, most probably due to the different compositions of the ECs and percentages of whitening agents in the toothpastes. Conclusions: The material composition of ECs contributes to their tensile strength decay, resistance to rupture and colour change over time. The variable percentage of activated carbon in a toothpaste likely underlies the different effects observed, depending on the EC brand. Clinical Relevance: It might be reasonable to advise patients wearing ECs to avoid using toothpaste with activated carbon until further evidence becomes available.
- The effect of polyunsaturated fatty acid (PUFA) supplementation on clinical manifestations and inflammatory parameters in individuals with Sjögren’s syndrome : a literature review of randomized controlled clinical trialsPublication . Nave, Catarina Bento da; Pereira, Paula; Silva, Maria LeonorBackground: Sjögren’s syndrome is a chronic autoimmune disease that causes dry mouth and eyes and can lead to non-Hodgkin’s lymphoma in 5–10% of cases after 10 years. Clinical trials have shown that the oral administration of polyunsaturated fatty acids (PUFAs) seems to have a beneficial effect on Sjögren’s syndrome. Aim: This literature review provides an overview of the effects of PUFA supplementation on clinical manifestations and inflammatory parameters in Sjögren’s syndrome. Methodology: We conducted a literature review using the PubMed, Biomed Central, and Cochrane Library electronic databases and using search terms “Sjögren” AND “omega-3”; and “omega-6” AND “fatty acids” AND “oil”. This literature review followed the PRISMA guidelines and included randomized clinical trials in humans with or without a control group using the oral administration of PUFA. Results: From 26 articles found in the databases, a total of 6 articles were included. Of these six trials, five trials showed an effect on clinical manifestations and three trials on inflammatory parameters. Most of the studies did not show a significant effect on the parameters analyzed. One study showed a significant improvement in dry keratoconjunctivitis compared to the control group. The results suggest that PUFAs may improve inflammatory parameters in patients with Sjögren’s syndrome. Conclusions: This literature review supports the idea that the oral administration of PUFA may possess a potential effect on clinical manifestations. However, due to the limited number of studies and the heterogeneity of clinical trial methodology, further investigations should be employed. Understanding the potential mechanism of action of PUFAs on clinical biomarkers in Sjögren’s syndrome may clarify their importance in clinical practice for health professionals.
- The child oral health impact profile : short form 19 cross-cultural adaptation and validity for the Portuguese pediatric populationPublication . Laborne, Fanny; Machado, Vanessa; Botelho, João; Lopes, Luísa BandeiraBackground/Objectives: To better understand the impact of different oral conditions on children, several instruments are available to measure oral health-related quality of life (OHRQoL). To adapt and validate cross-culturally the Child Oral Health Impact Profile—Short Form 19 (COHIP-SF19) questionnaire to the Portuguese language. Methods: The COHIP SF-19 was translated and back-translated, and tested for its reliability and for psychometric properties in children who were aged between 8 and 17 years old. The COHIP-19-PT was tested for its internal consistency, construct validity, content validity, and test–retest reliability. Results: The COHIP-19-PT revealed good internal consistency (Cronbach’s alpha = 0.88) and test–retest reliability (interclass correlation = 0.78). The CFA analysis confirmed the structure of COHIP-19-PT. The first-order model showed an adequate fit: GFI = 0.878; CFI = 0.812; RMSEA = 0.083 (90% CI: 0.077–0.090). No invariance was found for the gender-based groups. The correlation between the sub-scales was also assessed, confirming significant correlations between all subdomains. Conclusions: The COHIP-19-PT is a valid and reliable scale for measuring children’s oral health-related quality of life.
- The anatomical bases of the 3D digital facial approximation of the Zlatý kůň 1 woman (ca. 43,000 BP)Publication . Moraes, Cicero; Galassi, Francesco Maria; Sineo, Luca; Šindelář, Jiří; Varotto, Elena; Mietlińska-Sauter, Joanna; Antunes-Ferreira, Nathalie; Habicht, Michael E.; Beaini, ThiagoIn 1950 on Mount Zlatý kůň (‘Golden Horse’) in modern-day Czech Republic a system of caves was discovered. During many years of research in this area, human and animal osteological remains have been excavated, among which the most interesting ones were nine fragments of a female skull, now dated to ca. 43,000 yrs BP which are one of the earliest known anatomically modern humans in Eurasia. The aim of this research was to use purely digital techniques to: (1) to reconstruct the skull based on the 3D data of preserved fragments, (2) to approximate the probable appearance of the female it belonged to, and (3) to analyze the calculated shape of the reconstructed mandible and volume of the neurocranium in the context of similarities and differences with other representatives of the genus Homo. Computer techniques used in this research constitute a new, original approach to the problem of 3D analyses and may be useful primarily in bioarchaeological sciences, where metric analyses of the most valuable bone artifacts are often severely limited due to the incompleteness of the material available for research. The digital techniques presented here may also contribute significantly to the field of surgery, with the possibility of being adapted for applications in cranial prosthetics and post-traumatic reconstructive surgery.
- Temporalis muscle changes following botulinum toxin A injections in masseter hypertrophy patients : a randomized triple-blinded trialPublication . Nobre, Bryanne B. de Souza; Machado, Luciana de Oliveira Resende; Poluha, Rodrigo Lorenzi; Câmara-Souza, Mariana Barbosa; Carbone, Ana Claudia; Almeida, Andre Mariz de; Grigoriadis, Anastasios; Kumar, Abhishek; Canales, Giancarlo De la TorreBackground: This study aimed to elucidate the effects of botulinum toxin A (BoNT-A) treatment for patients diagnosed with masseter hypertrophy on the temporalis muscle, with a particular focus on assessing alterations in muscle thickness, electromyographic (EMG) activity, and the development of muscle pain. Methods: The present randomized triple-blinded clinical trial enrolled 26 female participants aged between 25 and 50 years complaining about masseter hypertrophy. Participants received 75U of BoNT-A (abobotulinumtoxinA) in both masseter muscles and after three months were randomized to receive a second treatment session of saline solution (S-BoNT-A) or BoNT-A (M-BoNT-A). Longitudinal assessments included temporalis muscle thickness through ultrasound, EMG activity, subjective pain, and masseter prominence severity after one, three, and six months of the first injection session. Muscle thickness, EMG, and subjective pain were analysed using two-way ANOVA with repeated measures and post hoc Sidak test, and for masseter prominence severity, Friedman and Mann–Whitney tests were used. Results: Regarding inter-group comparisons, a higher muscle thickness (p < 0.02) and a higher EMG activity (p < 0.01) were found in the M-BoNT-A group at the 6-month follow-up. For subjective pain assessments, inter-group comparisons showed a higher prevalence of painful regions in M-BoNT-A group at the 6-month follow-up (p < 0.02). No significant differences were found in masseter prominence severity at the 6 months assessment between groups. Conclusion: BoNT-A treatment for masseter hypertrophy lead to structural and functional changes in the temporalis muscle, presenting higher changes after multiple injections of this treatment.
- Targeting vascular endothelial growth factor receptor 2 (VEGFR-2) : latest insights on synthetic strategiesPublication . Marques, Carolina S.; Brandão, Pedro; Burke, Anthony J.Vascular endothelial growth factor receptor 2 (VEGFR-2) is a crucial mediator of angiogenesis, playing a pivotal role in both normal physiological processes and cancer progression. Tumors harness VEGFR-2 signaling to promote abnormal blood vessel growth, which is a key step in the metastasis process, making it a valuable target for anticancer drug development. While there are VEGFR-2 inhibitors approved for therapeutic use, they face challenges like drug resistance, off-target effects, and adverse side effects, limiting their effectiveness. The quest for new drug candidates with VEGFR-2 inhibitory activity often starts with the selection of key structural motifs present in molecules currently used in clinical practice, expanding the chemical space by generating novel derivatives bearing one or more of these moieties. This review provides an overview of recent advances in the development of novel VEGFR-2 inhibitors, focusing on the synthesis of new drug candidates with promising antiproliferative and VEGFR-2 inhibition activities, organizing them by relevant structural features.
- Sustainable carbon dots loaded into carboxymethylcellulose based hydrogels for uterine cancer bioimagingPublication . Rodrigues, Jordane S.; Brandão, Pedro; Duarte, Sofia O. D.; Silveira, Izabela Boueri da; Leite, Maria de Fátima; Gonçalves, Max. P.; Borsagli, Fernanda G. L. Medeiros; Fonte, PedroBackground/Objectives: The development of innovative materials for disease diagnostics and therapeutics is a fast-growing area of scientific research. In this work, we report the development of innovative hydrogels incorporating carbon dots (Cdots) for bioimaging purposes. Methods: The Cdots were prepared using a sustainable and low-cost process, starting with an underused fiber from the Brazilian semiarid region. Spectroscopy analysis (Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, UV-visible spectroscopy), X-ray diffraction, photoluminescence, zeta potential, scanning electron microscopy, and transmission electron microscopy were used to characterize these hydrogels. In addition, biocompatibility using the resazurin assay and cellular uptake by confocal microscopy were evaluated. Results: Our results showed that the Cdots changed the structure and crystallinity of hydrogels, mainly due to heat treatment. In addition, hydrogels’ chemical groups suffer red and blue shifts following the Cdots incorporation. Moreover, the Cdots were homogeneously incorporated into the hydrogel matrix. Importantly, the cytotoxicity levels were maintained above 90% (p < 0.01), and cellular uptake studies using HeLa cells demonstrated intracellular fluorescence of both the Cdots and hydrogels after incubation. Additionally, the concentration of Cdots within hydrogels significantly affected fluorescence intensity, even compared with pure Cdots. Conclusions: These results showcase the potential for these hydrogels to be further developed as biomarkers and therapeutic biomaterials for women’s health.
- Susceptibility patterns of Candida species collected from intensive care units in Portugal : a prospective study in 2020–2022Publication . Nascimento, Teresa; Inácio, João; Guerreiro, Daniela; Diaz, Priscila; Patrício, Patrícia; Proença, Luís; Toscano, Cristina; Barroso, HelenaBackground: For Candida infections antifungal therapy is often empirical and mainly depends on locally antifungal surveillance data, which differs between geographic regions. Aims: To monitor the epidemiology and antifungal susceptibility of Candida spp. from combined axillar-groin samples in intensive care unit (ICU) patients on admission (day1, D1), day 5 (D5) and day 8 (D8). Methods: From 2020 to 2022, 675 patients from three ICUs were enrolled. Candida isolates were identified by MALDI-TOF MS and PCR. In vitro antifungals susceptibility tests (AFST) were performed for fluconazole, voriconazole, amphotericin B and anidulafungin, by concentration gradient Etest® strip technique. Results: Out of 988 swabs, 355 isolates were identified as Candida species from 232 patients, being 89 isolates retrieved from patients that remained colonised at D5 and D8. AFST was conducted for all Candida isolates. The overall rate of resistance to fluconazole was 2.7%, with 3 out of 133 C. albicans, 2 out of 89 C. parapsilosis and 2 out of 24 C. glabrata isolates identified as resistant. Voriconazole susceptibility was observed in 99.2% of the isolates, with only one C. albicans isolate identified as resistant to this triazole. All isolates were susceptible to amphotericin B and 98.5% to anidulafungin. Three Candida spp. exhibited resistance to anidulafungin, C. albicans, C. tropicalis, and C. parapsilosis. Conclusions: This study highlights the importance of C. albicans as a frequent coloniser and showed that antifungal resistance remains uncommon among Candida isolates from ICUs in Portugal. The results may contribute to better management within institutions to guide therapeutic decision making.