Computational Tools for the Analysis of Uncultivated Phage Genomes

Over a century of bacteriophage research has uncovered a plethora of fundamental aspects of their biology, ecology, and evolution. Furthermore, the introduction of community-level studies through metagenomics has revealed unprecedented insights on the impact that phages have on a range of ecological and physiological processes. It was not until the introduction of viral metagenomics that we began to grasp the astonishing breadth of genetic diversity encompassed by phage genomes. Novel phage genomes have been reported from a diverse range of biomes at an increasing rate, which has prompted the development of computational tools that support the multilevel characterization of these novel phages based solely on their genome sequences. The impact of these technologies has been so large that, together with MAGs (Metagenomic Assembled Genomes), we now have UViGs (Uncultivated Viral Genomes), which are now officially recognized by the International Committee for the Taxonomy of Viruses (ICTV), and new taxonomic groups can now be created based exclusively on genomic sequence information. Even though the available tools have immensely contributed to our knowledge of phage diversity and ecology, the ongoing surge in software programs makes it challenging to keep up with them and the purpose each one is designed for. Therefore, in this review, we describe a comprehensive set of currently available computational tools designed for the characterization of phage genome sequences, focusing on five specific analyses: (i) assembly and identification of phage and prophage sequences, (ii) phage genome annotation, (iii) phage taxonomic classification, (iv) phage-host interaction analysis, and (v) phage microdiversity

In vivo evaluation of the sealing ability of two endodontic sealers in root canals exposed to the oral environment for 45 and 90 days Avaliação, in vivo, da capacidade de selamento de dois cimentos endodônticos em canais radiculares expostos ao meio bucal por 45 e 90 dias

This in vivo study evaluated the sealing ability of a resin-based sealer (AH Plus) and a zinc oxide-eugenol sealer (Endofill) in dogs' teeth, exposed to the oral environment for 45 and 90 days. Forty eight lower incisors from 8 dogs were endodonticaly treated. A stratified randomization determined the sealer use in each root canal. All canals were filled using the lateral condensation technique. The excess filling material at the cervical portion of the root canal was sectioned, leaving a 10-mm obturation length inside the canal. Teeth were provisionally sealed with glass ionomer cement for 24 h and the canals were exposed to the oral environment for either 45 or 90 days. Therefore, the experimental groups were as follows: A45- AH Plus for 45 days; A90- AH Plus for 90 days; E45- Endofill for 45 days; and E90- Endofill for 90 days (n=12). After the experimental period, the dogs were killed and the lower jaw was removed. The incisors were extracted and the roots were covered with two coats of nail varnish. The teeth were immersed in India ink for 96 h and submitted to diaphanization. Dye leakage (in mm) was measured using stereomicroscopy (10x magnification). The results were statistically analyzed using two-way ANOVA and Tukey test for multiple comparisons (á = 0.05). Group E90 (2.03&plusmn;0.94) showed significantly higher mean leakage value than all other groups (p<0.001). None of the sealers, in both study conditions, were able to prevent dye leakage.<br>Este estudo in vivo avaliou a capacidade de selamento de um cimento endodôntico resinoso (AH Plus) e um a base de óxido de zinco eugenol (Endofill), em dentes de cães, expostos ao meio bucal, por 45 e 90 dias. Foi realizado o tratamento endodôntico de 48 incisivos inferiores de 8 cães. Uma randomização estratificada determinou o tipo de cimento a ser usado em cada canal que foram tratados pela técnica de condensação lateral. Após a obturação, o excesso de material obturador, na porção cervical do canal radicular foi seccionado, restando o comprimento de 10 mm no interior do canal radicular. Os dentes foram selados, provisoriamente, com cimento de ionômero de vidro por 24 h. A seguir, o selamento coronário foi removido e os canais ficaram expostos ao meio bucal. Desta forma, delineou-se os seguintes grupos experimentais: A45- AH Plus por 45 dias; A90- AH Plus por 90 dias; E45- Endofill por 45 dias; e E90- Endofill por 90 dias (n=12). Passado o período experimental, os cães foram mortos e as mandíbulas removidas. Realizou-se a exodontia dos incisivos e as suas raízes foram impermeabilizadas com duas camadas de esmalte para unhas. Os dentes foram imersos em tinta nanquim por 96 h. Após realizou-se a diafanização dos espécimes e a infiltração de corante foi medida (em mm) com auxílio de uma lupa esteroscópica, em aumento de 10x. Os resultados foram analisados estatisticamente através da Análise de Variância de dois fatores e Teste de Comparações Múltiplas de Tukey (á = 0.05). O grupo E90 (2.03&plusmn;0.94) apresentou uma infiltração média significativamente maior do que a ocorrida nos demais grupos (p<0.001). Os cimentos avaliados, nos dois períodos experimentais, não foram capazes de impedir a infiltração de corante

Patients awaiting surgery for neurosurgical diseases during the first wave of the COVID-19 pandemic in Spain: a multicentre cohort study.

The large number of infected patients requiring mechanical ventilation has led to the postponement of scheduled neurosurgical procedures during the first wave of the COVID-19 pandemic. The aims of this study were to investigate the factors that influence the decision to postpone scheduled neurosurgical procedures and to evaluate the effect of the restriction in scheduled surgery adopted to deal with the first outbreak of the COVID-19 pandemic in Spain on the outcome of patients awaiting surgery. This was an observational retrospective study. A tertiary-level multicentre study of neurosurgery activity between 1 March and 30 June 2020. A total of 680 patients awaiting any scheduled neurosurgical procedure were enrolled. 470 patients (69.1%) were awaiting surgery because of spine degenerative disease, 86 patients (12.6%) due to functional disorders, 58 patients (8.5%) due to brain or spine tumours, 25 patients (3.7%) due to cerebrospinal fluid (CSF) disorders and 17 patients (2.5%) due to cerebrovascular disease. The primary outcome was mortality due to any reason and any deterioration of the specific neurosurgical condition. Second, we analysed the rate of confirmed SARS-CoV-2 infection. More than one-quarter of patients experienced clinical or radiological deterioration. The rate of worsening was higher among patients with functional (39.5%) or CSF disorders (40%). Two patients died (0.4%) during the waiting period, both because of a concurrent disease. We performed a multivariate logistic regression analysis to determine independent covariates associated with maintaining the surgical indication. We found that community SARS-CoV-2 incidence (OR=1.011, p Patients awaiting neurosurgery experienced significant collateral damage even when they were considered for scheduled procedures