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.

Autoimmune Condition Diagnosis Following Recurrent Pregnancy Loss.

Problem: Research has suggested a link between recurrent pregnancy loss (RPL) and cell-mediated immunity dysregulation. We aimed to determine if a history of RPL is associated with diagnosis of a cell-mediated autoimmune condition (AIC).

Method Of Study: A retrospective cohort study was conducted using the TriNetX research network.

Neonatal birthweight prediction using two- and three-dimensional estimated fetal weight among borderline small fetuses.

Purpose: This study aimed (1) to determine the degree of correlation between 2D and 3D estimated fetal weight (EFW) and neonatal birth weight (BW) among borderline small fetuses and (2) to compare the accuracy and precision of 2D and 3D EFW in BW prediction.

Methods: A retrospective cohort study evaluated fetuses who had an ultrasound performed between January 2017 and September 2021 at a tertiary maternal center. All singleton pregnancies with 3D EFW within 4 weeks of delivery were included.

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.

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.

Defining biomarkers in oral cancer according to smoking and drinking status.

Introduction: Oral Squamous Cell Carcinomas (OSCC) are mostly related to tobacco consumption eventually associated to alcohol (Smoker/Drinker patients: SD), but 25-30% of the patients have no identified risk factors (Non-Smoker/Non-Drinker patients: NSND). We hypothesized that these patients have distinguishable immune profiles that could be useful for prognosis.

Materials And Methods: Cells present in immune tumor microenvironment (TME) and blood from 87 OSCC HPV-negative patients were analyzed using a multiparameter flow cytometry assay, in a prospective case-control study.

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).

Molecular dynamics simulation of thermal transport across a solid/liquid interface created by a meniscus.

Understandings heat transfer across a solid/liquid interface is crucial for establishing novel thermal control pathways in a range of energy applications. One of the major problems raised in this context is the impact of the three-phase contact line between solid, liquid, and gas on heat flux perturbations at the nanoscale. The focus of this research is the thermal transport nanosized meniscus restricted between two solid walls.

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.

Factors Attributed to Breastfeeding Success in a Tertiary Obstetric Hospital.

Introduction: Increasing breastfeeding rates is a national health objective, however substantial barriers and disparities continue to exist in breastfeeding initiation and continuation. Our study aim is to identify factors associated with birthing persons' breastfeeding "success" (patients admitted to Labor & Delivery desiring to breastfeed and discharged breastfeeding) and breastfeeding "failure" (patients admitted to Labor & Delivery desiring to breastfeed and discharged exclusively formula feeding).

Materials And Methods: We conducted a retrospective cohort study between July 2015 and June 2016.