Leveraging mobility data to analyze persistent SARS-CoV-2 mutations and inform targeted genomic surveillance.

Given the rapid cross-country spread of SARS-CoV-2 and the resulting difficulty in tracking lineage spread, we investigated the potential of combining mobile service data and fine-granular metadata (such as postal codes and genomic data) to advance integrated genomic surveillance of the pandemic in the federal state of Thuringia, Germany. We sequenced over 6500 SARS-CoV-2 Alpha genomes (B.1.

Association between gestational age and severe maternal morbidity in preterm delivery: A nationwide population-based cohort study.

Objective: This study investigates whether early gestational age (GA) at delivery is associated with an increased risk for severe maternal morbidity (SMM) in women with preterm delivery.

Methods: This retrospective national cohort study based on the Programme de Médicalisation des Systèmes d'Information database included mothers who gave birth between 22 and 37 weeks in metropolitan France in 2019 (in utero deaths and medical terminations of pregnancies were excluded). SMM was defined as a composite criterion consisting of the occurrence of at least one of the following events: death, severe preeclampsia, obstetric surgical complications, severe maternal diseases, and admission to the intensive care unit.

Hypospadias Associated With Fetal Growth Restriction: A Multicentric Descriptive and Prognostic Cohort Study.

Objective: To determine the prevalence of genetic and endocrine abnormalities and to assess fetal, neonatal and surgical outcomes in cases of hypospadias associated with fetal growth restriction.

Method: A multicentric retrospective study was conducted across five prenatal diagnosis centers in Paris. The cohort encompassed all fetuses diagnosed with the combination of fetal growth restriction < 10th percentile (FGR) and hypospadias from 2013 to 2021.

Accurate bacterial outbreak tracing with Oxford Nanopore sequencing and reduction of methylation-induced errors.

Our study investigates the effectiveness of Oxford Nanopore Technologies for accurate outbreak tracing by resequencing 33 isolates of a 3-year-long outbreak with Illumina short-read sequencing data as the point of reference. We detect considerable base errors through cgMLST and phylogenetic analysis of genomes sequenced with Oxford Nanopore Technologies, leading to the false exclusion of some outbreak-related strains from the outbreak cluster. Nearby methylation sites cause these errors and can also be found in other species besides Based on these data, we explore PCR-based sequencing and a masking strategy, which both successfully address these inaccuracies and ensure accurate outbreak tracing.

[Automated surveillance and risk prediction with the aim of risk-stratified infection control and prevention (RISK PRINCIPE)].

Healthcare-associated infections (HCAIs) represent an enormous burden for patients, healthcare workers, relatives and society worldwide, including Germany. The central tasks of infection prevention are recording and evaluating infections with the aim of identifying prevention potential and risk factors, taking appropriate measures and finally evaluating them. From an infection prevention perspective, it would be of great value if (i) the recording of infection cases was automated and (ii) if it were possible to identify particularly vulnerable patients and patient groups in advance, who would benefit from specific and/or additional interventions.

Nanopore-based enrichment of antimicrobial resistance genes - a case-based study.

Rapid screening of hospital admissions to detect asymptomatic carriers of resistant bacteria can prevent pathogen outbreaks. However, the resulting isolates rarely have their genome sequenced due to cost constraints and long turn-around times to get and process the data, limiting their usefulness to the practitioner. Here we used real-time, on-device target enrichment ("adaptive") sequencing as a highly multiplexed assay covering 1,147 antimicrobial resistance genes.

Does a physiology-based interpretation of cardiotocography allow to dispense with second-line methods? A cross-sectional online survey.

Context: Second line methods are used to help obstetricians to identify abnormalities that reflect foetal acidosis. Since the use of a new technique of cardiotocography (CTG) interpretation based on the pathophysiology of the foetal period, the use of second-line tests has been questioned.

Objective: To evaluate the impact of specific training in CTG physiology-based interpretation on professional attitudes towards the use of second-line methods.

The IgH -MAR regions promote UNG-dependent error-prone repair to optimize somatic hypermutation.

Intoduction: Two scaffold/matrix attachment regions (5'- and 3'- ) flank the intronic core enhancer (c) within the immunoglobulin heavy chain locus (). Besides their conservation in mice and humans, the physiological role of is still unclear and their involvement in somatic hypermutation (SHM) has never been deeply evaluated.

Methods: Our study analyzed SHM and its transcriptional control in a mouse model devoid of , further combined to relevant models deficient for base excision repair and mismatch repair.

[Reexpansion edema : complication of pleural effusion drainage].

Reexpansion pulmonary edema is a rare complication of pleural effusion drainage (liquid or gas). Its pathophysiology is not fully understood but it seems to be induced by an increase in the permeability of the alveolar-capillary membrane. The purpose of this case report is to present the clinic of reexpansion edema and also to provide practitioners with a management strategy.

What the Phage: a scalable workflow for the identification and analysis of phage sequences.

Phages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years.

The "Alzheimer Village": Assessment of Alzheimer's disease representations in the general population: A cross sectional phone survey.

Introduction: In most countries, the societal view of Alzheimer's disease (AD) is very negative. The initiatives that are part of the so-called "dementia-friendly approach" aim not only at promoting well-being and dignity of persons suffering from AD but also improving the way they are regarded and their inclusion in society. Unfortunately, scarce research has been conducted to assess whether such goals can be achieved.

Corrigendum: poreCov - An Easy to Use, Fast, and Robust Workflow for SARS CoV-2 Genome Reconstruction Nanopore Sequencing.

[This corrects the article DOI: 10.3389/fgene.2021.

Evaluation of microbiome enrichment and host DNA depletion in human vaginal samples using Oxford Nanopore's adaptive sequencing.

Metagenomic sequencing is promising for clinical applications to study microbial composition concerning disease or patient outcomes. Alterations of the vaginal microbiome are associated with adverse pregnancy outcomes, like preterm premature rupture of membranes and preterm birth. Methodologically these samples often have to deal with low relative amounts of prokaryotic DNA and high amounts of host DNA (> 90%), decreasing the overall microbial resolution.

Genotype distribution of cervical HPV among Caribbean women in a population-based study in Martinique: The DEPIPAPUFR study.

The Caribbean ranks seventh among the world regions most affected by cervical cancer. HPV-prevalence and genotype distributions also differ from regions. Knowledge of HPV genotype profiles is important for patients care and HPV vaccination implementation.

poreCov-An Easy to Use, Fast, and Robust Workflow for SARS-CoV-2 Genome Reconstruction Nanopore Sequencing.

In response to the SARS-CoV-2 pandemic, a highly increased sequencing effort has been established worldwide to track and trace ongoing viral evolution. Technologies, such as nanopore sequencing the ARTIC protocol are used to reliably generate genomes from raw sequencing data as a crucial base for molecular surveillance. However, for many labs that perform SARS-CoV-2 sequencing, bioinformatics is still a major bottleneck, especially if hundreds of samples need to be processed in a recurring fashion.

SARS-CoV-2 causes severe epithelial inflammation and barrier dysfunction.

Infections with SARS-CoV-2 can be asymptomatic, but they can also be accompanied by a variety of symptoms that result in mild to severe coronavirus disease-19 (COVID-19) and are sometimes associated with systemic symptoms. Although the viral infection originates in the respiratory system, it is unclear how the virus can overcome the alveolar barrier, which is observed in severe COVID-19 disease courses. To elucidate the viral effects on the barrier integrity and immune reactions, we used mono-cell culture systems and a complex human chip model composed of epithelial, endothelial, and mononuclear cells.

The International Virus Bioinformatics Meeting 2020.

The International Virus Bioinformatics Meeting 2020 was originally planned to take place in Bern, Switzerland, in March 2020. However, the COVID-19 pandemic put a spoke in the wheel of almost all conferences to be held in 2020. After moving the conference to 8-9 October 2020, we got hit by the second wave and finally decided at short notice to go fully online.

Older adults' lay theories of abilities predict their willingness to engage in preventive health behaviors.

Objectives: The present studies examined the linkages between older adults' lay theories regarding the modifiability of abilities and their intentions to perform preventive health behaviors. The 'entity theory' refers to the belief that traits are fixed. The 'incremental theory' is the belief that traits are malleable.

A Genotype-Phenotype Correlation Study of SHV β-Lactamases Offers New Insight into SHV Resistance Profiles.

The SHV β-lactamases (BLs) have undergone strong allele diversification that has changed their substrate specificities. Based on 147 NCBI entries for SHV alleles, mathematical models predicted 5 positions as relevant for the β-lactamase inhibitor (BLI)-resistant (2br) phenotype, 12 positions as relevant for the extended-spectrum BL (ESBL) (2be) phenotype, and 2 positions as related solely to the narrow-spectrum (2b) phenotype. These positions and six additional positions described in other studies (including one promoter mutation) were systematically substituted and investigated for their substrate specificities in a BL-free background, representing, to our knowledge, the most comprehensive substrate and substitution analysis for SHV alleles to date.

Subjective Age in the Oldest Old: What is the Association with Disability and Sensory Impairment?

Background And Purpose: Disability and sensory impairment are particularly pronounced among the oldest old population (80 years and older). Considering these specificities, we analyzed the association of such parameters with subjective age, a strong predictor of health-related outcomes. We assumed that greater disability and sensory impairment (hearing and visual) would be linked with an older subjective age.

Understanding the mechanisms underlying the effects of negative age stereotypes and perceived age discrimination on older adults' well-being.

Although numerous studies have documented that negative age stereotypes and perceived age discrimination are related to older adults' lower well-being, few studies have investigated the mechanisms underlying these relationships. In this study, we tested whether self-perceptions of aging and subjective age would help to account for the relation between stereotypes and discrimination and self-esteem. According to the internalization hypothesis, we expected that the effects of negative age stereotypes and greater perceived age discrimination would be driven by more negative self-perceptions of aging and older subjective age.

Does negative information about aging influence older adults' physical performance and subjective age?

This study investigated the way negative stereotypes influence older adults' physical performance and how old they feel mentally and physically. Sixty-four older adults aged 65 years and older performed different physical tasks using a 3D optoelectronic system under a low or high stereotype threat condition. Self-perceptions of aging were considered as a moderator of the effects of threat.