Impact of Lifting Mask Mandates on COVID-19 Incidence and Mortality in Portugal: An Ecological Study.

INTRODUCTION: The use of face masks in public was one of several COVID-19 non-pharmaceutical interventions adopted to mitigate the pandemic in Portugal. The aim of this study was to evaluate the impact of lifting the mask mandate on the April 22, 2022 on COVID-19 incidence and mortality in mainland Portugal and in the Azores. As a secondary objective, we aimed to evaluate the evolution of COVID-19 cases in a setting without a mask mandate (Azores islands) and in a setting with a mask mandate (Madeira islands). MATERIAL AND METHODS: Surveillance data on laboratory-confirmed COVID-19 cases and COVID-19 deaths were used to conduct an interrupted time series analysis to estimate changes in daily incidence and deaths during a mask mandate period (28th March - 21st April 2022) and during a post-mask mandate period (22nd April - 15th May 2022), in mainland Portugal and the Azores. In a second phase, for each group of islands, we fitted a negative binomial regression model, with daily COVID-19 incident cases as the primary outcome of interest, and relative frequency of Omicron BA.5 lineage as explanatory variable. RESULTS: Significant changes in trends were observed for the overall incidence rate and COVID-19 deaths; increasing trends were observed for COVID-19 incidence and deaths in the post mandate period [5.3% per day; incidence rate ratio (IRR): 1.053; 95% confidence interval (CI): 1.029 - 1.078] and [3.2% per day; mortality rate ratio (MRR): 1.032; 95% CI: 1.003 - 1.062], respectively. For every unit increase in the percentage of Omicron BA.5 lineage there was a 1.5% increase per day (IRR: 1.015; 95% CI: 1.006 - 1.024) in COVID-19 incidence rate in the Azores islands, while for Madeira islands an increase of 0.05% COVID-19 cases per day was observed (IRR: 1.005; 95% CI: 1.000 - 1.010). CONCLUSION: Lifting the mask mandate in Portugal was associated with an increase in COVID-19 incidence and deaths, thus highlighting the positive effect of face mask policies in preventing respiratory virus transmission and saving lives.

CFD simulation and PIV validation of the gas/liquid behavior in an UASB reactor / Simulação CFD e validação PIV do comportamento gás/líquido em um reator UASB

ABSTRACT As the world population increases, the need to develop more efficient wastewater treatment systems requires the use of new technologies. Software aided project and optimization of bioreactors and bioprocesses have become a matter of interest in recent years, especially due to the advance in the state-of-the-art of computational resources. This work aimed to perform gas/liquid numerical simulations using the Fluent 16.2 software and to validate this model through Particle Image Velocimetry (PIV) and shadow imaging techniques. Eulerian-Eulerian, laminar, tridimensional and transient simulations were carried out. The results for the mass imbalance for the gas and liquid phases, gas volumetric fraction, gas velocity, bubble size, liquid magnitude and upflow velocity and the velocity profiles for the liquid phase were successfully validated against experimental data. Concerning the dispersed phase, it was found a difference of 4.37% for the gas volumetric fraction between experiments and simulations. Simulated results showed a difference for the bubble mean velocity of 1.73% when compared with shadow imaging results. No coalescence was observed along the experiments, and the flow regime was characterized as dispersed bubble flow. Regarding the liquid phase, it was found a difference of 3.2% for the mean velocity, between simulated and PIV results. Simulated and experimental velocity profiles showed a better agreement at the center of the reactor. Some differences were observed in those profiles, due to geometry simplifications assumed in order to get a better mesh. Considering the good agreement between simulation and experiments, the model was considered validated.

RESUMO Conforme a população mundial aumenta, a necessidade de desenvolvimento de sistemas de tratamento de efluentes mais eficientes requer o uso de novas tecnologias. O projeto e otimização de biorreatores e bioprocessos auxiliados por softwares têm se tornado uma questão de interesse, em especial devido ao avanço no estado da arte quando se trata de recursos computacionais. O objetivo deste trabalho foi realizar simulações numéricas gás/liquido, utilizando o software Fluent 16.2, e validar experimentalmente o modelo computacional através de técnicas de PIV e Shadow Imaging. Foram realizadas simulações laminares, tridimensionais, transientes adotando uma abordagem Euleriana-Euleriana. Os resultados para o desequilíbrio de massa para as fases gasosa e líquida, a fração volumétrica de gás, a velocidade do gás, o tamanho da bolha, a magnitude e a velocidade ascensional do líquido e os perfis de escoamento do líquido foram validados experimentalmente com êxito. Foi verificada uma diferença de 4,37% entre resultados numéricos e experimentais para a fração volumétrica de gás no reator. Quando comparados os resultados das simulações com os resultados obtidos através de Shadow Imaging, foi encontrada uma diferença de 1,73% para a velocidade média da bolha. Não foi verificada coalescência ao longo dos experimentos realizados, e o escoamento foi caracterizado como fluxo de bolhas dispersas. Em relação à fase líquida, foi encontrada uma diferença de 3,2% para a velocidade média, entre os resultados simulados e de PIV. Os perfis de velocidade simulada e experimental mostraram uma melhor concordância no centro do reator. Algumas diferenças foram observadas nesses perfis, devido às simplificações geométricas assumidas para obter uma malha melhor. Considerando a boa concordância entre resultados numéricos e experimentais, o modelo foi considerado validado.

Seasonal variation of the organic and inorganic composition of sugarcane vinasse: main implications for its environmental uses.

Sugarcane vinasse is the main waste stream of the Brazilian agroindustry. The typical composition of sugarcane vinasse gives it a high polluting potential that implies the necessity to define sustainable strategies for managing this waste. Knowledge of the inorganic and organic composition of vinasse and its seasonal variation is extremely important to conduct scientific research to define alternative managements for vinasse disposal other than fertigation. This study evaluated the variability of vinasse composition throughout the same harvesting season and among three harvesting seasons of one Brazilian annexed biorefinery (2015-2017). The contents of chemical oxygen demand (COD), biochemical oxygen demand (BOD5), total solids (TS), suspended solids (SS), salinity (K+, Na+, Ca2+, Mg2+, Cl-, F-), nutrients (N, P, S), trace metals (Al3+, As2+, Ba2+, Cd2+, Cr3+, Co2+, Cu2+, Fe2+, Pb2+, Mn2+, Hg2+, Mo2+, Ni2+, Se2+, Zn2+), and specific soluble organic compounds (sugars, alcohols, and organic acids), as well as pH and conductivity, were monitored in 13 samples. The results indicated that sugarcane vinasse is a suitable feedstock for biological treatments, such as anaerobic digestion processes for energy recovery, as well as substrate for biomass (e.g., microalgae, energy crops, lignocellulosic biomass) growth. The application of a previous treatment makes vinasse a more environmentally friendly natural fertilizer for land fertigation.

O processo e a prática do aconselhamento genético no Brasil: uma revisão de escopo / The process and practice of genetic counseling in Brazil: a scope review

Nessa dissertação foi realizada uma scoping review (SR) com objetivo de buscar na literatura o que existe, até o presente momento, para verificar as principais evidências científicas referentes ao processo e à prática do aconselhamento genético (AG) no Brasil. O método apresentado nessa revisão, scoping review, é utilizado para investigar conceitos-chave subjacentes a uma nova área de pesquisa, explorar de forma sistematizada os conceitos, teorias, evidências e lacunas referentes a um tema específico. O estudo propôs como questão de pesquisa: "Quais são as evidências científicas referentes ao processo e à prática do AG no Brasil?" Os descritores e palavras-chave prioritariamente utilizados para realizar a busca nas bases de dados foram: genetic counseling OR genetic service, Latin America OR South America OR Brazil OR Brazilian. Após utilizar a estratégia de busca, específica para cada uma das seis bases de dados (PubMed, EMBASE, SCOPUS e Web of Science, CINAHL e LILACS), foram encontrados 1028 artigos, os quais foram exportados para o software Rayyan QCRI e removidos aqueles que se encontravam em duplicata. Foram excluídos artigos em duplicata entre as bases supracitadas; trabalhos que se referiam a modelos animais, relatos de casos, editoriais, cartas, revisões de literatura, resumos e dissertações e teses; literatura cinzenta; e que não haviam sido produzidos no Brasil. Por meio desse software, dois revisores executaram, de forma independente, a leitura dos títulos e resumos de 609 artigos e 62 foram selecionados para a leitura na íntegra. Dentre esses últimos, apenas 25 de fato respondiam à questão de pesquisa. De acordo com os estudos que compuseram a amostra final desta revisão, percebe-se que ainda não há um consenso sobre os modelos de prática de AG utilizados no Brasil e nem clareza sobre as ações que compôem o processo de aconselhamento. O AG, marjoritariamente é realizado por médicos, embora esteja evidenciado na literatura a importância da equipe multiprofissional. Vale salientar, que se trata de uma área de estudo em ascenção, pois possui uma grande demanda e apresenta um número de publicações crescente a cada ano

In the present dissertation, the author carries out a scoping review (SR) to analyse the main scientific evidences concerning the process and the practice of Genetic Counselling (GR) in Brazil. The scoping review method is used to investigate key-concepts present in a new area of research and to explore, in a systematized way, the concepts, theories, evidences and omissions regarding a specific subject. This study proposes as its subject of research the following question: "what are the scientific evidences regarding the process and the practice of GR in Brazil?". The descriptors and key-words primarily used in the research in databases were: genetic counselling OR genetic service, Latin America OR South America OR Brazil OR Brazilian. Research strategies tailored to each one of the six databases (PubMed, EMBASE, SCOPUS, y Web of Science, CINAHL y LILACS) led to 1028 articles, which were exported to the Rayyan QCRI software. Articles that were published in more than on database, works regarding animal models, case reports, editorials, letters, literature reviews, summaries, dissertations, theses, grey literature, and works that were not published in Brazil were all excluded. Making use of this software, two independent reviewers read the titles and summaries of 609 articles, from among which 62 were selected to be fully read. Only 25 of these 62 articles effectively answered the question proposed in the dissertation. The studies present in the final sample of this revision show that there is not a consensus regarding the models of practice of GR used in Brazil, as well as that there is a lack of clarity concerning the actions that are part of the counselling process. RG is mainly performed by doctors, in spite of the fact that the specialized literature shows the importance of multiprofessional teams. It is important to highlight the importance of this area of research, as shown by an increasing demand and by a growing number of studies published every year

Integrated diversity analysis of the microbial community in a reverse osmosis system from a Brazilian oil refinery.

Oil refineries are known for the large volume of water used in their processes, as well as the amount of wastewater generated at the end of the production chain. Due to strict environmental regulations, the recycling of water has now become a viable alternative for refineries. Among the many methods available to treat wastewater for reuse, the use of membranes in reverse osmosis systems stands out due to several economic and environmental benefits. However, these systems are vulnerable to contamination and deposition of microorganisms, mainly because of the feedwater quality. In this study, the microbial diversity of feedwater and reverse osmosis membranes was investigated using a combination of culture-dependent and culture-independent methods in order to characterize the microorganisms colonizing and deteriorating the membranes. In total, 37 bacterial isolates, 17 filamentous fungi and approximately 400 clones were obtained and analyzed. Among the bacterial genera identified, the most represented were Sphingobium, Acidovorax, Microbacterium, Rhizobium and Shinella. The results revealed genera that acted as candidate key players in initial biofilm formation in membrane systems, and provided important information concerning the microbial ecology of oligotrophic aquatic systems.

Ammonium removal from high-salinity oilfield-produced water: assessing the microbial community dynamics at increasing salt concentrations.

Water generated during oil exploration is chemically complex and contains high concentrations of ammonium and, in some cases, high salinity. The most common way to remove ammonium from effluent is a biological process, which can be performed by different routes and different groups of microorganisms. However, the presence of salts in the effluents could be an inhibiting factor for biological processes, interfering directly with treatment. This study aimed to evaluate changes in the profile of a microbial community involved in the process of ammonium removal when subjected to a gradual increase of salt (NaCl), in which the complete inhibition of the ammonium removal process occurred at 125 g L-1 NaCl. During the sludge acclimatization process, samples were collected and submitted to denaturing gradient gel electrophoresis (DGGE) and massive sequencing of the 16S ribosomal RNA (rRNA) genes. As the salt concentration increased in the reactor, a change in the microbial community was observed by the DGGE band profiles. As a result, there was a reduction in the presence of bacterial populations, and an increase in archaeal populations was found. The sequencing data suggested that ammonium removal in the reactor was carried out by different metabolic routes by autotrophic nitrifying bacteria, such as Nitrosococcus, Nitrosomonas, Nitrosovibrio, Nitrospira, and Nitrococcus; ammonium-oxidizing archaea Candidatus nitrosoarchaeum; ANAMMOX microorganisms, such as Candidatus brocadia, Candidatus kuenenia, and Candidatus scalindua; and microorganisms with the potential to be heterotrophic nitrifying, such as Paracoccus spp., Pseudomonas spp., Bacillus spp., Marinobacter sp., and Alcaligenes spp.

Triple-negative and luminal A breast tumors: differential expression of miR-18a-5p, miR-17-5p, and miR-20a-5p.

New concepts in epigenetics, microRNAs, and gene expression analysis have significantly enhanced knowledge of cancer pathogenesis over the last decade. MicroRNAs (miRNAs) are a class of non-coding RNAs that regulate gene expression by base pairing with target messenger RNAs (mRNAs), resulting in the repression of translation or the degradation of mRNA. To compare the carcinogenic process in tumors with different prognoses, we used real-time RT-PCR to evaluate the miRNA expression profiles of 24 triple-negative breast invasive ductal carcinoma, 20 luminal A breast invasive ductal carcinoma, and 13 normal breast parenchyma controls. We extracted total RNA from tissues fixed in formol and embedded in paraffin (FFPE). Results revealed the upregulation of miR-96-5p (9.35-fold; p = 0.000115), miR-182-5p (7.75-fold; p = 0.000033), miR-7-5p (6.71-fold; p = 0.015626), and miR-21-5p (6.10-fold; p = 0.000000) in tumors group. In addition, the expression of miR-125b-5p (4.49-fold; p = 0.000000) and miR-205-5p (4.36-fold; p = 0.006098) was downregulated. When the expression profiles of triple-negative and luminal A tumors were compared, there was enhanced expression of miR-17-5p (4.27-fold; p = 0.000664), miR-18a-5p (9.68-fold; p = 0.000545), and miR-20a-5 (4.07-fold; p = 0.001487) in the triple-negative tumors compared with luminal A. These data suggest that there is a similar regulation of certain miRNAs in triple-negative and luminal A tumors. However, it is possible that differences in the expression of miR-17-92 cluster will explain the phenotypic differences between these molecular tumor subtypes.

Identification of genes and pathways related to phenol degradation in metagenomic libraries from petroleum refinery wastewater.

Two fosmid libraries, totaling 13,200 clones, were obtained from bioreactor sludge of petroleum refinery wastewater treatment system. The library screening based on PCR and biological activity assays revealed more than 400 positive clones for phenol degradation. From these, 100 clones were randomly selected for pyrosequencing in order to evaluate the genetic potential of the microorganisms present in wastewater treatment plant for biodegradation, focusing mainly on novel genes and pathways of phenol and aromatic compound degradation. The sequence analysis of selected clones yielded 129,635 reads at an estimated 17-fold coverage. The phylogenetic analysis showed Burkholderiales and Rhodocyclales as the most abundant orders among the selected fosmid clones. The MG-RAST analysis revealed a broad metabolic profile with important functions for wastewater treatment, including metabolism of aromatic compounds, nitrogen, sulphur and phosphorus. The predicted 2,276 proteins included phenol hydroxylases and cathecol 2,3- dioxygenases, involved in the catabolism of aromatic compounds, such as phenol, byphenol, benzoate and phenylpropanoid. The sequencing of one fosmid insert of 33 kb unraveled the gene that permitted the host, Escherichia coli EPI300, to grow in the presence of aromatic compounds. Additionally, the comparison of the whole fosmid sequence against bacterial genomes deposited in GenBank showed that about 90% of sequence showed no identity to known sequences of Proteobacteria deposited in the NCBI database. This study surveyed the functional potential of fosmid clones for aromatic compound degradation and contributed to our knowledge of the biodegradative capacity and pathways of microbial assemblages present in refinery wastewater treatment system.

Phylogenetic and functional diversity of metagenomic libraries of phenol degrading sludge from petroleum refinery wastewater treatment system.

In petrochemical refinery wastewater treatment plants (WWTP), different concentrations of pollutant compounds are received daily in the influent stream, including significant amounts of phenolic compounds, creating propitious conditions for the development of particular microorganisms that can rapidly adapt to such environment. In the present work, the microbial sludge from a refinery WWTP was enriched for phenol, cloned into fosmid vectors and pyrosequenced. The fosmid libraries yielded 13,200 clones and a comprehensive bioinformatic analysis of the sequence data set revealed a complex and diverse bacterial community in the phenol degrading sludge. The phylogenetic analyses using MEGAN in combination with RDP classifier showed a massive predominance of Proteobacteria, represented mostly by the genera Diaphorobacter, Pseudomonas, Thauera and Comamonas. The functional classification of phenol degrading sludge sequence data set generated by MG-RAST showed the wide metabolic diversity of the microbial sludge, with a high percentage of genes involved in the aerobic and anaerobic degradation of phenol and derivatives. In addition, genes related to the metabolism of many other organic and xenobiotic compounds, such as toluene, biphenyl, naphthalene and benzoate, were found. Results gathered herein demonstrated that the phenol degrading sludge has complex phylogenetic and functional diversities, showing the potential of such community to degrade several pollutant compounds. This microbiota is likely to represent a rich resource of versatile and unknown enzymes which may be exploited for biotechnological processes such as bioremediation.

MammaGene: ensaio quantitativo de 21 genes para prognóstico do câncer de mama receptor de estrogênio positivo / MammaGene®: a quantitative 21-gene assay for prognostic of breast cancer estrogen receptor-positive

Objetivos: Padronizar em nosso meio um ensaio que analisa, por RT-PCR, 21 genes e descrever a experiência inicial com 95 casos consecutivos de carcinoma inicial de mama receptor de estrogênio positivo. Métodos: O teste foi desenvolvido a partir dos relatos publicados por Cronin et al. (2004) e Paik et al. (2004) para a avaliação da expressão de genes em tecido fixado em formalina e incluído em parafina. O teste foi aplicado em uma coorte consecutiva de 95 amostras de câncer de mama receptor de estrogênio positivo e os escores finais foram comparados com a idade da paciente, O tamanho do tumor, o tipo e o grau histológico, expressão imunoistoquímica do receptor de estrogênio, índice de Ki67 e subtipo molecular. Resultados: Os escores finais variaram de 3 a 90 e as categorias de risco de recorrência em dez anos foram: baixa (34 casos), intermediária (38 casos) e alta (23 casos). Não houve associação das categorias de risco com idade, comprometimento linfonodal e tipo histológico. A media do tamanho dos tumores foi maior no grupo de alto escore (2,0 versus 1,2 cm). Observou-se associação entre o escore obtido pelo teste e grau histológico, Ki-67, nível de expressão de receptor de estrogênio e subtipo molecular. Conclusão: A realização do teste de 21 genes foi factível em nosso meio. Alem disso, os dados preliminares, aliados aos dados da literatura, sugerem que tal teste pode ser uma ferramenta útil na avaliação do risco de recorrência a distância em câncer de mama receptor de estrogênio positivo. No entanto, estudos adicionais são necessários para comparar os resultados deste trabalho com séries amplas publicadas na literatura.

Objectives: To standardize a homemade RT-PCR-based 21-gene assay and to describe the preliminary experience with 95 early positive estrogen receptor breast cancer consecutive cases. Methods: The test was developed using the reports described by Cronin et al. (2004) and Paik et al. (2004) for the evaluation of gene expression in fixed, paraffin-embedded tumor tissue. The test was performed in a consecutive cohort of 95 positive estrogen receptor breast carcinomas, and the final scores were compared with the patient's age, tumor size, histological type, histological degree, estrogen receptor immunohistochemical expression, Ki-67 expression, and molecular luminal subtype. Results: Final scores ranged from 3 to 90 and risk categories of recurrence in ten years were: low (34 cases), intermediate (38 cases), and high (23 cases). There was no association between score categorical distribution and age, lymph node status, or histological type. Mean tumor size was higher in the high score group (2.0 versus 1.2 cm). We have observed an overall concordance between the score obtained by the test, and the histological degree, Ki-67, estrogen receptor level, and molecular subtype. Conclusion: The developed 21-gene assay is a feasible test to be performed in a homemade setting. Besides, the preliminary data from this study suggest, in comparison with data from the literature, that this test has the potential to be a useful tool to evaluate the risk of breast cancer distant recurrence. However, further data are necessary in order to compare this paper's results with larger series published in the literature.

Monitoring the bacterial community dynamics in a petroleum refinery wastewater membrane bioreactor fed with a high phenolic load.

The phenolic compounds are a major contaminant class often found in industrial wastewaters and the biological treatment is an alternative tool commonly employed for their removal. In this sense, monitoring microbial community dynamics is crucial for a successful wastewater treatment. This work aimed to monitor the structure and activity of the bacterial community during the operation of a laboratory-scale continuous submerged membrane bioreactor (SMBR), using PCR and RT-PCR followed by Denaturing Gradient Gel Electrophoresis (DGGE) and 16S rRNA libraries. Multivariate analyses carried out using DGGE profiles showed significant changes in the total and metabolically active dominant community members during the 4-week treatment period, explained mainly by phenol and ammonium input. Gene libraries were assembled using 16S rDNA and 16S rRNA PCR products from the fourth week of treatment. Sequencing and phylogenetic analyses of clones from 16S rDNA library revealed a high diversity of taxa for the total bacterial community, with predominance of Thauera genus (ca. 50%). On the other hand, a lower diversity was found for metabolically active bacteria, which were mostly represented by members of Betaproteobacteria (Thauera and Comamonas), suggesting that these groups have a relevant role in the phenol degradation during the final phase of the SMBR operation.

Comparison of electrophoretic protein profiles of campylobacter jejuni subsp. jejuni isolated from different animal species

Electrophoretic protein profiles of Campylobacter jejuni subsp. jejuni strains isolated from feces of seven animal species, including man, were compared. Fourteen strains (two from each species) plus two human strains and the reference one, were ruptured by ultrasound and their total soluble proteins were analyzed by SDS-PAGE technique in a 12(per cent) polyacrylamide gel with computerized densitometric reading by the molecular analyst software. All the strains had bands in common that correspond to 45 and 66 Kda molecular weight. The disagreement corresponded to a 97 to 200 Kda molecular weight region. From the 17 strains, 13 (76.5 per cent), were classified as biotype I, three (17.6 per cent) as biotype II and one (5.8 per cent) as biotype III. Since protein extracts were obtained from cells grown under identical conditions, and thus, able to express the same phenotype, this disagreement region could be related to different genotypes or serotypes.