Dynamic clade transitions and the influence of vaccine rollout on the spatiotemporal circulation of SARS-CoV-2 variants in São Paulo, Brazil.

Since 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to the persistence of the disease. Due to limitations in the real-time genomic monitoring of new variants in some Brazilian states, we aimed to investigate whether genomic surveillance, coupled with epidemiological data and SARS-CoV-2 variants spatiotemporal spread in a smaller region, can reflect the pandemic progression at a national level. Our findings revealed three SARS-CoV-2 variant replacements from 2021 to early 2022, corresponding to the introduction and increase in the frequency of Gamma, Delta, and Omicron variants, as indicated by peaks of the Effective Reproductive Number (Reff). These distinct clade replacements triggered two waves of COVID-19 cases, influenced by the increasing vaccine uptake over time. Our results indicated that the effectiveness of vaccination in preventing new cases during the Delta and Omicron circulations was six and eleven times higher, respectively, than during the period when Gamma was predominant, and it was highly efficient in reducing the number of deaths. Furthermore, we demonstrated that genomic monitoring at a local level can reflect the national trends in the spread and evolution of SARS-CoV-2.

AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes.

Current genome sequencing technologies have made it possible to generate highly contiguous genome assemblies for non-model animal species. Despite advances in genome assembly methods, there is still room for improvement in the delineation of specific gene features in the genomes. Here we present genome visualization and annotation tools to support seven livestock species (bovine, chicken, goat, horse, pig, sheep, and water buffalo), available in a new resource called AgAnimalGenomes. In addition to supporting the manual refinement of gene models, these browsers provide visualization tracks for hundreds of RNAseq experiments, as well as data generated by the Functional Annotation of Animal Genomes (FAANG) Consortium. For species with predicted gene sets from both Ensembl and RefSeq, the browsers provide special tracks showing the thousands of protein-coding genes that disagree across the two gene sources, serving as a valuable resource to alert researchers to gene model issues that may affect data interpretation. We describe the data and search methods available in the new genome browsers and how to use the provided tools to edit and create new gene models.

Retrospective Insights of the COVID-19 Epidemic in the Major Latin American City, São Paulo, Southeastern Brazil.

São Paulo is the financial center of Brazil, with a population of over 12 million, that receives travelers from all over the world for business and tourism. It was the first city in Brazil to report a case of COVID-19 that rapidly spread across the city despite the implementation of the restriction measures. Despite many reports, much is still unknown regarding the genomic diversity and transmission dynamics of this virus in the city of São Paulo. Thus, in this study, we provide a retrospective overview of the COVID-19 epidemic in São Paulo City, Southeastern, Brazil, by generating a total of 9995 near-complete genome sequences from all the city's different macro-regions (North, West, Central, East, South, and Southeast). Our analysis revealed that multiple independent introduction events of different variants (mainly Gamma, Delta, and Omicron) occurred throughout time. Additionally, our estimates of viral movement within the different macro-regions further suggested that the East and the Southeast regions were the largest contributors to the Gamma and Delta viral exchanges to other regions. Meanwhile, the North region had a higher contribution to the dispersion of the Omicron variant. Together, our results reinforce the importance of increasing SARS-CoV-2 genomic monitoring within the city and the country to track the real-time evolution of the virus and to detect earlier any eventual emergency of new variants of concern that could undermine the fight against COVID-19 in Brazil and worldwide.

Multi-omic data integration for the study of production, carcass, and meat quality traits in Nellore cattle.

Data integration using hierarchical analysis based on the central dogma or common pathway enrichment analysis may not reveal non-obvious relationships among omic data. Here, we applied factor analysis (FA) and Bayesian network (BN) modeling to integrate different omic data and complex traits by latent variables (production, carcass, and meat quality traits). A total of 14 latent variables were identified: five for phenotype, three for miRNA, four for protein, and two for mRNA data. Pearson correlation coefficients showed negative correlations between latent variables miRNA 1 (mirna1) and miRNA 2 (mirna2) (-0.47), ribeye area (REA) and protein 4 (prot4) (-0.33), REA and protein 2 (prot2) (-0.3), carcass and prot4 (-0.31), carcass and prot2 (-0.28), and backfat thickness (BFT) and miRNA 3 (mirna3) (-0.25). Positive correlations were observed among the four protein factors (0.45-0.83): between meat quality and fat content (0.71), fat content and carcass (0.74), fat content and REA (0.76), and REA and carcass (0.99). BN presented arcs from the carcass, meat quality, prot2, and prot4 latent variables to REA; from meat quality, REA, mirna2, and gene expression mRNA1 to fat content; from protein 1 (prot1) and mirna2 to protein 5 (prot5); and from prot5 and carcass to prot2. The relations of protein latent variables suggest new hypotheses about the impact of these proteins on REA. The network also showed relationships among miRNAs and nebulin proteins. REA seems to be the central node in the network, influencing carcass, prot2, prot4, mRNA1, and meat quality, suggesting that REA is a good indicator of meat quality. The connection among miRNA latent variables, BFT, and fat content relates to the influence of miRNAs on lipid metabolism. The relationship between mirna1 and prot5 composed of isoforms of nebulin needs further investigation. The FA identified latent variables, decreasing the dimensionality and complexity of the data. The BN was capable of generating interrelationships among latent variables from different types of data, allowing the integration of omics and complex traits and identifying conditional independencies. Our framework based on FA and BN is capable of generating new hypotheses for molecular research, by integrating different types of data and exploring non-obvious relationships.

The Divergent Pattern of SARS-CoV-2 Variant Predominance and Transmission Dynamics in the Brazilian Island of Ilhabela.

Our effort in SARS-CoV-2 genomic surveillance in Brazil has detected the Alpha Variant of Concern with a predominance higher than 75% in the population of Ilhabela island (São Paulo State) at a time when the Gamma VOC was already predominating the mainland raised concerns for closer surveillance on this island. Therefore, we intensified the surveillance for 24 weeks by generating data from 34% of local positive cases. Our data show that the patterns of VOC predominance dynamics and infection rates were in general distinct from the mainland. We report here the first known case of Alpha predominance in a Brazilian population, a delay greater than 3 months for the Gamma to dominate the previous variants compared to the mainland, and a faster dispersion rate of Gamma and Delta VOCs compared to the mainland. Phylogenetic analysis revealed the SARS-CoV-2 transmission dynamics in Ilhabela were characterized by multiple independent introduction events of Gamma and Delta, with a few events of Alpha introduction, two of them followed by community transmission. This study evidenced the peculiar behavior of SARS-CoV-2 variants in an isolated population and brought to light the importance of specific programs for SARS-CoV-2 genomic surveillance in isolated populations.

SAP30 Gene Is a Probable Regulator of Muscle Hypertrophy in Chickens.

Animals with muscle hypertrophy phenotype are targeted by the broiler industry to increase the meat production and the quality of the final product. Studies characterizing the molecular machinery involved with these processes, such as quantitative trait loci studies, have been carried out identifying several candidate genes related to this trait; however, validation studies of these candidate genes in cell culture is scarce. The aim of this study was to evaluate SAP30 as a candidate gene for muscle development and to validate its function in cell culture in vitro. The SAP30 gene was downregulated in C2C12 muscle cell culture using siRNA technology to evaluate its impact on morphometric traits and gene expression by RNA-seq analysis. Modulation of SAP30 expression increased C2C12 myotube area, indicating a role in muscle hypertrophy. RNA-seq analysis identified several upregulated genes annotated in muscle development in treated cells (SAP30-knockdown), corroborating the role of SAP30 gene in muscle development regulation. Here, we provide experimental evidence of the involvement of SAP30 gene as a regulator of muscle cell hypertrophy.

Busca por assistência odontológica em Unidade de Pronto Atendimento: as perspectivas do usuário

Os serviços de urgência, incluindo a assistência pré-hospitalar das UPAs, por funcionarem ininterruptamente, podem atrair os usuários que não se vincularam à Atenção Básica (Caccia-bava, MCG et al.). Apesar de parecer mais resolutivo para os usuários, esse fato pode desencadear uma série de prejuízos para o sistema como filas, lentidão no atendimento, insatisfação, estresse na equipe e pacientes, diminuição na qualidade do atendimento e, ainda, aumento nos gastos públicos com saúde. Este estudo teve por objetivo identificar motivos que levaram usuários vinculados ao SSC do GHC a buscarem assistência odontológica de urgência na UPA Moacyr Scliar em horários de atendimentos regular das US durante o período de abril a julho no ano de 2017. A investigação foi realizada por meio de análise do sistema de informações e entrevista telefônica através de um questionário estruturado composto por 5 questões. Os resultados apontaram que, para essas condições, houve – em média – atendimento de 20 usuários/mês no período acompanhado, com maior procura às segundas-feiras (30%) e no turno da tarde (58,8%). O questionário foi aplicado a 50 usuários dentre aqueles atendidos no período; entre os entrevistados, a dor de dente foi o motivo mais frequente da procura (62%); 80% procuraram a urgência odontológica da UPA pela primeira vez, sendo que 98% tinham conhecimento da sua US de referência. O estudo indica que 26,7% dos usuários buscam a UPA por não conseguirem atendimento na sua US, enquanto 17,8% dos respondentes desconhecem a existência de dentista na sua US ou de atendimento a urgências; 15,6% dos participantes acreditam que a UPA é mais rápida ou mais perto de onde estavam e 11,1% relatam atendimento na US sem resolutividade. Para o período em questão, torna-se possível inferir que as US integrantes do SSC/GHC acolhem grande parte da demanda aguda/consultadia dos seus usuários, devido a esta procura corresponder a 0,02% do contingente populacional coberto...

Radiopacity Evaluation of Gutta-Percha Points in Thinner Samples than the ANSI/ADA Recommendation.

The aim of this study was to evaluate the radiopacity of different gutta-percha points (Endo Points®, Dentsply®, Tanari®, Meta®, Roeko® and Odous®) in samples of 1 mm thick as established by ANSI/ADA Specification #57 and ISO 6876/2001, in comparison with thinner samples. Twelve test specimens for each material, four for each thickness (0.3, 0.6, and 1 mm and diameter of 8 mm), were laminated and compressed between two polished glass plates until the desirable thickness. Digital radiographs were obtained along with a graduated aluminum stepwedge varying from 1 to 10 mm in thickness. The X-ray unit was set at 70 kVp, 10 mA and 0.4 s exposure time, at a focal distance of 36 cm. One calibrated observer quantified the average values of pixels with Adobe Photoshop® software. Data were analyzed using ANOVA and Tukey tests, at 5% significance level. At 0.6 and 1 mm thickness, all the tested materials showed radiopacity higher than 3 mm of aluminum (reference value). At 0.3 mm thickness, Odous and Tanari presented significantly less radiopacity than the reference, and the other materials showed similar radiopacity to the reference. The study concluded that the materials demonstrated different radiopacities and all had values above the minimum recommended by ANSI/ADA specification #57, being Odous and Tanari less radiopaque than the reference value in thinner samples (0.3mm).

Radiopacity Evaluation of Gutta-Percha Points in Thinner Samples than the ANSI/ADA Recommendation

Abstract The aim of this study was to evaluate the radiopacity of different gutta-percha points (Endo Points®, Dentsply®, Tanari®, Meta®, Roeko® and Odous®) in samples of 1 mm thick as established by ANSI/ADA Specification #57 and ISO 6876/2001, in comparison with thinner samples. Twelve test specimens for each material, four for each thickness (0.3, 0.6, and 1 mm and diameter of 8 mm), were laminated and compressed between two polished glass plates until the desirable thickness. Digital radiographs were obtained along with a graduated aluminum stepwedge varying from 1 to 10 mm in thickness. The X-ray unit was set at 70 kVp, 10 mA and 0.4 s exposure time, at a focal distance of 36 cm. One calibrated observer quantified the average values of pixels with Adobe Photoshop® software. Data were analyzed using ANOVA and Tukey tests, at 5% significance level. At 0.6 and 1 mm thickness, all the tested materials showed radiopacity higher than 3 mm of aluminum (reference value). At 0.3 mm thickness, Odous and Tanari presented significantly less radiopacity than the reference, and the other materials showed similar radiopacity to the reference. The study concluded that the materials demonstrated different radiopacities and all had values above the minimum recommended by ANSI/ADA specification #57, being Odous and Tanari less radiopaque than the reference value in thinner samples (0.3mm).

Resumo O objetivo deste estudo foi avaliar a radipacidade de diferentes pontas de guta-percha (Endo Points®, Dentsply®, Tanari®, Meta®, Roeko® e Odous®) em amostras de 1 mm de espessura, conforme estabelecido pela especificação #57 da ANSI/ADA e pela ISO 6876/2001, em comparação com amostras de menor espessura. Doze amostras de cada material, quatro para cada espessura (0,3, 0,6 e 1 mm; 8 mm de diâmetro), foram confeccionadas por meio de laminação e compressão entre duas lâminas de vidro polidas, até a espessura desejada. Radiografias digitais foram obtidas juntamente com uma escala de alumínio graduada, com espessuras variando de 1 a 10 mm. O aparelho de raios X foi ajustado para 70 kVp, 10 mA, 0,4s de tempo de exposição, com distância focal de 36 cm. Um observador calibrado quantificou a média dos valores de pixel no programa Adobe Photoshop®. Os dados foram analisados utilizando os testes ANOVA e Tukey, com nível de significância de 5%. Nas espessuras de 0,6 e 1 mm, todos os materiais testados apresentaram radiopacidade maior do que 3 mm de alumínio (valor de referência). Na espessura de 0,3 mm, Odous e Tanari apresentaram radiopacidade significativamente menor que a referência, e as outras marcas mostraram radiopacidade semelhante à referência. Conclui-se que os materiais apresentaram diferentes radiopacidades e todos mostraram valores acima do mínimo recomendado pela especificação #57 da ANSI/ADA, sendo Odous e Tanari menos radiopacos do que o valor de referência nas amostras mais finas (0.3 mm).

Dissolução de cimentos endodônticos resinosos por solventes orgânicos em diferentes intervalos de tempo / Dissolution of resin-based root canal sealers by organic solvents at different time intervals

Objetivo: O objetivo deste estudo foi investigar se o tempo deexposição dos cimentos endodônticos resinosos a solventesorgânicos afeta sua solubilidade. Materiais e métodos: Moldes desilicona de condensação circulares padronizados (4,47 mm de largurapor 1,5 mm de altura) foram preenchidos com quatro cimentosendodônticos resinosos recém-misturados (Acroseal®, Epiphany®, AHPlus® e Sealer26®) e armazenados a 37°C por duas semanas (n=08).Depois de inspecionado, cada corpo-de-prova foi pesado três vezes eindividualmente imerso em Citrol®, Endosolv R®, hipoclorito de sódio a2,5% ou água destilada (controle) por 10 minutos, 02 horas e 24horas. Nos intervalos testados, a perda média de cada materialobturador imerso nos solventes foi determinada. Os dados foramanalisados estatisticamente com ANOVA de duas vias, Bonferronipost hoc e teste de Pearson (α=0,05). Resultados: O Endosolv R® foisignificativamente mais eficiente na dissolução do Sealer26® do que aágua destilada (grupo controle), óleo de laranjas e hipoclorito desódio 2,5%. O Citrol® e o hipoclorito de sódio 2,5% demonstrarammaior potencial para dissolver o cimento Sealer26® no intervalo de 24horas, quando comparados ao grupo controle. As diferenças de peso entre os cimentos imersos em hipoclorito de sódio 2,5% não semostraram estatisticamente significantes. A solubilidade foisignificativamente correlacionada com o tempo de exposição somentequando o Endosolv R® (+0,829) ou a água destilada (+0,441) foramempregados. Conclusão: A dissolução de cimentos à base de resinafoi afetada pelo intervalo de exposição e tipo de solvente orgânicoutilizado. Endosolv R® e períodos mais longos de exposiçãopromoveram maior solubilização dos cimentos de base resinosa testados.

Aim: The aim of this study was to investigate whether time exposureof resin-based root canal sealers to organic solvents affects theirsolubility. Materials and methods: Standardized circular siliconmoulds (4.47mm wide and 1.5mm high) were filled with four freshlymixed resin-based root canal sealers (Acroseal®, Epiphany®, AHPlus® and Sealer 26®) and stored at 37° for two weeks (n=8). Afterinspection, each sample was weighted thrice and individuallyimmersed in Citrol®, Endosolv R®, 2.5% sodium hypochlorite ordistilled water for 10, 120 and 1440 min. In the tested intervals, themean weight loss of each filling material immersed in solvents wasdetermined. Data were statistically analyzed by Two-wayANOVA, Bonferroni post hoc and Pearson tests (α=0.05). Results:Endosolv ® R was significantly more effective in dissolving Sealer26 ®than distilled water (control group), orange oil and 2.5% sodiumhypochlorite. Citrol® and 2.5% sodium hypochlorite showed thegreatest potential to dissolve Sealer26 ® within 24 hours, compared tothe control group. The weight losses between sealers immersed insodium hypochlorite 2.5% were not statistically significant. Solubilitywas significantly correlated with exposure intervals only whenEndosolv R® (+0,829) or double-distilled water (+0,441) wereapplied. Conclusion: Dissolution of resin-based root canal sealerswas affected by exposure interval and type of organic solvent used.Endosolv R® and longer exposure intervals promoted greatersolubilization of the resin-based sealers tested.