The Bayesian Phylogenetic Bootstrap and its Application to Short Trees and Branches.

Felsenstein's bootstrap is the most commonly used method to measure branch support in phylogenetics. Current sequencing technologies can result in massive sampling of taxa (e.g.

BioFlow-Insight: facilitating reuse of Nextflow workflows with structure reconstruction and visualization.

Bioinformatics workflows are increasingly used for sharing analyses, serving as a cornerstone for enhancing the reproducibility and shareability of bioinformatics analyses. In particular, Nextflow is a commonly used workflow system, permitting the creation of large workflows while offering substantial flexibility. An increasing number of Nextflow workflows are being shared on repositories such as GitHub.

Analysis during chest compressions in out-of-hospital cardiac arrest patients, a cross/sectional study: The DEFI 2022 study.

Aims: During out-of-hospital cardiac arrest (OHCA), an automatic external defibrillator (AED) analyzes the cardiac rhythm every two minutes; however, 80% of refibrillations occur within the first minute post-shock. We have implemented an algorithm for Analyzing cardiac rhythm While performing chest Compression (AWC). When AWC detects a shockable rhythm, it shortens the time between analyses to one minute.

Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion.

The unceasing circulation of SARS-CoV-2 leads to the continuous emergence of novel viral sublineages. Here, we isolate and characterize XBB.1, XBB.

Accurate Detection of Convergent Mutations in Large Protein Alignments With ConDor.

Evolutionary convergences are observed at all levels, from phenotype to DNA and protein sequences, and changes at these different levels tend to be correlated. Notably, convergent mutations can lead to convergent changes in phenotype, such as changes in metabolism, drug resistance, and other adaptations to changing environments. We propose a two-component approach to detect mutations subject to convergent evolution in protein alignments.

Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites.

Integrons are genetic elements involved in bacterial adaptation which capture, shuffle and express genes encoding adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination between attC and attI integron sites. Using computational and molecular genetic approaches, here we demonstrate that the integrase also catalyses cassette integration into bacterial genomes outside of its known att sites.

Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion.

The unceasing circulation of SARS-CoV-2 leads to the continuous emergence of novel viral sublineages. Here, we isolated and characterized XBB.1, XBB.

Trends in survival from out-of-hospital cardiac arrest with a shockable rhythm and its association with bystander resuscitation: a retrospective study.

Objective: Over 300 000 cases of out-of-hospital cardiac arrests (OHCAs) occur each year in the USA and Europe. Despite decades of investment and research, survival remains disappointingly low. We report the trends in survival after a ventricular fibrillation/pulseless ventricular tachycardia OHCA, over a 13-year period, in a French urban region, and describe the simultaneous evolution of the rescue system.

BioConvert: a comprehensive format converter for life sciences.

Bioinformatics is a field known for the numerous standards and formats that have been developed over the years. This plethora of formats, sometimes complementary, and often redundant, poses many challenges to bioinformatics data analysts. They constantly need to find the best tool to convert their data into the suitable format, which is often a complex, technical and time consuming task.

Reprohackathons: promoting reproducibility in bioinformatics through training.

Motivation: The reproducibility crisis has highlighted the importance of improving the way bioinformatics data analyses are implemented, executed, and shared. To address this, various tools such as content versioning systems, workflow management systems, and software environment management systems have been developed. While these tools are becoming more widely used, there is still much work to be done to increase their adoption.

APOBEC3F Is a Mutational Driver of the Human Monkeypox Virus Identified in the 2022 Outbreak.

Background: On May 6, 2022, a powerful outbreak of monkeypox virus (MPXV) had been reported outside of Africa, with many continuing new cases being reported around the world. Analysis of mutations among the 2 different lineages present in the 2021 and 2022 outbreaks revealed the presence of G->A mutations occurring in the 5'GpA context, indicative of APOBEC3 cytidine deaminase activity.

Methods: By using a sensitive polymerase chain reaction (differential DNA denaturation PCR) method allowing differential amplification of AT-rich DNA, we analyzed the level of APOBEC3-induced MPXV editing in infected cells and in patients.

Enhanced neutralization escape to therapeutic monoclonal antibodies by SARS-CoV-2 omicron sub-lineages.

The landscape of SARS-CoV-2 variants dramatically diversified with the simultaneous appearance of multiple subvariants originating from BA.2, BA.4, and BA.

Developing and reusing bioinformatics data analysis pipelines using scientific workflow systems.

Data analysis pipelines are now established as an effective means for specifying and executing bioinformatics data analysis and experiments. While scripting languages, particularly Python, R and notebooks, are popular and sufficient for developing small-scale pipelines that are often intended for a single user, it is now widely recognized that they are by no means enough to support the development of large-scale, shareable, maintainable and reusable pipelines capable of handling large volumes of data and running on high performance computing clusters. This review outlines the key requirements for building large-scale data pipelines and provides a mapping of existing solutions that fulfill them.

In-Depth Characterization of Full-Length Archived Viral Genomes after Nine Years of Posttreatment HIV Control.

In the search for control of human immunodeficiency virus type 1 (HIV-1) infection without antiretroviral therapy, posttreatment controllers (PTCs) are models of HIV remission. To better understand their mechanisms of control, we characterized the HIV blood reservoirs of 8 PTCs (median of 9.4 years after treatment interruption) in comparison with those of 13 natural HIV infection controllers (HICs) (median of 18 years of infection) and with those of individuals receiving efficient antiretroviral therapy initiated during either primary HIV infection (PHIs;  = 8) or chronic HIV infection (CHIs;  = 6).

Deciphering RNA G-quadruplex function during the early steps of HIV-1 infection.

G-quadruplexes (G4s) are four-stranded nucleic acid structures formed by the stacking of G-tetrads. Here we investigated their formation and function during HIV-1 infection. Using bioinformatics and biophysics analyses we first searched for evolutionary conserved G4-forming sequences in HIV-1 genome.

Prehospital Lyophilized Plasma Transfusion for Trauma-Induced Coagulopathy in Patients at Risk for Hemorrhagic Shock: A Randomized Clinical Trial.

Importance: Blood transfusion is a mainstay of therapy for trauma-induced coagulopathy, but the optimal modalities for plasma transfusion in the prehospital setting remain to be defined.

Objective: To determine whether lyophilized plasma transfusion can reduce the incidence of trauma-induced coagulopathy compared with standard care consisting of normal saline infusion.

Design, Setting, And Participants: This randomized clinical trial was performed at multiple centers in France involving prehospital medical teams.

Considerable escape of SARS-CoV-2 Omicron to antibody neutralization.

The SARS-CoV-2 Omicron variant was first identified in November 2021 in Botswana and South Africa. It has since spread to many countries and is expected to rapidly become dominant worldwide. The lineage is characterized by the presence of around 32 mutations in spike-located mostly in the N-terminal domain and the receptor-binding domain-that may enhance viral fitness and enable antibody evasion.

Correction to 'Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows'.

[This corrects the article DOI: 10.1093/nargab/lqab075.].

Gotree/Goalign: toolkit and Go API to facilitate the development of phylogenetic workflows.

Phylogenetics is nowadays at the center of numerous studies in many fields, ranging from comparative genomics to molecular epidemiology. However, phylogenetic analysis workflows are usually complex and difficult to implement, as they are often composed of many small, reccuring, but important data manipulations steps. Among these, we can find file reformatting, sequence renaming, tree re-rooting, tree comparison, bootstrap support computation, etc.

Maternal and neonatal outcomes related to Zika virus in pregnant women in Southern Vietnam: An epidemiological and virological prospective analysis.

Background: In 2016-2017, 68 women in Southern Vietnam had RT-PCR confirmed Zika virus (ZIKV) infection during pregnancy. We report here the outcomes of the pregnancies and the virological analyses related to this outbreak.

Methods: We collected clinical and epidemiological information from the women who were enrolled in the study.

Automatic external defibrillator provided by unmanned aerial vehicle (drone) in Greater Paris: A real world-based simulation.

Aim: To reduce the delay in defibrillation of out-of-hospital cardiac arrest (OHCA) patients, recent publications have shown that drones equipped with an automatic external defibrillator (AED) appear to be effective in sparsely populated areas. To study the effectiveness of AED-drones in high-density urban areas, we developed an algorithm based on emergency dispatch parameters for the rate and detection speed of cardiac arrests and technical and meteorological parameters.

Methods: We ran a numerical simulation to compare the actual time required by the Basic Life Support team (BLSt) for OHCA patients in Greater Paris in 2017 to the time required by an AED-drone.