Genome-wide analysis of differential transcriptional and epigenetic variability across human immune cell types

Abstract Background A healthy immune system requires immune cells that adapt rapidly to environmental challenges. This phenotypic plasticity can be mediated by transcriptional and epigenetic variability. Results We apply a novel analytical approach to measure and compare transcriptional and epigenetic variability genome-wide across CD14+CD16− monocytes, CD66b+CD16+ neutrophils, and CD4+CD45RA+ naïve T cells from the same 125 healthy individuals. We discover substantially increased variability in neutrophils compared to monocytes and T cells. In neutrophils, genes with hypervariable expression are found to be implicated in key immune pathways and are associated with cellular properties and environmental exposure. We also observe increased sex-specific gene expression differences in neutrophils. Neutrophil-specific DNA methylation hypervariable sites are enriched at dynamic chromatin regions and active enhancers. Conclusions Our data highlight the importance of transcriptional and epigenetic variability for the key role of neutrophils as the first responders to inflammatory stimuli. We provide a resource to enable further functional studies into the plasticity of immune cells, which can be accessed from: http://blueprint-dev.bioinfo.cnio.es/WP10/hypervariability

Single-dose BNT162b2 vaccine protects against asymptomatic SARS-CoV-2 infection

The BNT162b2 mRNA COVID-19 vaccine (Pfizer-BioNTech) is being utilised internationally for mass COVID-19 vaccination. Evidence of single-dose protection against symptomatic disease has encouraged some countries to opt for delayed booster doses of BNT162b2, but the effect of this strategy on rates of asymptomatic SARS-CoV-2 infection remains unknown. We previously demonstrated frequent pauci- and asymptomatic SARS-CoV-2 infection amongst healthcare workers (HCWs) during the UK’s first wave of the COVID-19 pandemic, using a comprehensive PCR-based HCW screening programme (Rivett et al., 2020; Jones et al., 2020). Here, we evaluate the effect of first-dose BNT162b2 vaccination on test positivity rates and find a fourfold reduction in asymptomatic infection amongst HCWs ≥12 days post-vaccination. These data provide real-world evidence of short-term protection against asymptomatic SARS-CoV-2 infection following a single dose of BNT162b2 vaccine, suggesting that mass first-dose vaccination will reduce SARS-CoV-2 transmission, as well as the burden of COVID-19 disease

Genomic epidemiology of SARS-CoV-2 in a UK university identifies dynamics of transmission

AbstractUnderstanding SARS-CoV-2 transmission in higher education settings is important to limit spread between students, and into at-risk populations. In this study, we sequenced 482 SARS-CoV-2 isolates from the University of Cambridge from 5 October to 6 December 2020. We perform a detailed phylogenetic comparison with 972 isolates from the surrounding community, complemented with epidemiological and contact tracing data, to determine transmission dynamics. We observe limited viral introductions into the university; the majority of student cases were linked to a single genetic cluster, likely following social gatherings at a venue outside the university. We identify considerable onward transmission associated with student accommodation and courses; this was effectively contained using local infection control measures and following a national lockdown. Transmission clusters were largely segregated within the university or the community. Our study highlights key determinants of SARS-CoV-2 transmission and effective interventions in a higher education setting that will inform public health policy during pandemics.</jats:p

PANC Study (Pancreatitis: A National Cohort Study): national cohort study examining the first 30 days from presentation of acute pancreatitis in the UK

Abstract Background Acute pancreatitis is a common, yet complex, emergency surgical presentation. Multiple guidelines exist and management can vary significantly. The aim of this first UK, multicentre, prospective cohort study was to assess the variation in management of acute pancreatitis to guide resource planning and optimize treatment. Methods All patients aged greater than or equal to 18 years presenting with acute pancreatitis, as per the Atlanta criteria, from March to April 2021 were eligible for inclusion and followed up for 30 days. Anonymized data were uploaded to a secure electronic database in line with local governance approvals. Results A total of 113 hospitals contributed data on 2580 patients, with an equal sex distribution and a mean age of 57 years. The aetiology was gallstones in 50.6 per cent, with idiopathic the next most common (22.4 per cent). In addition to the 7.6 per cent with a diagnosis of chronic pancreatitis, 20.1 per cent of patients had a previous episode of acute pancreatitis. One in 20 patients were classed as having severe pancreatitis, as per the Atlanta criteria. The overall mortality rate was 2.3 per cent at 30 days, but rose to one in three in the severe group. Predictors of death included male sex, increased age, and frailty; previous acute pancreatitis and gallstones as aetiologies were protective. Smoking status and body mass index did not affect death. Conclusion Most patients presenting with acute pancreatitis have a mild, self-limiting disease. Rates of patients with idiopathic pancreatitis are high. Recurrent attacks of pancreatitis are common, but are likely to have reduced risk of death on subsequent admissions. </jats:sec

Viktor Krivulin. Concerto a richiesta e altre poesie, a cura di Marco Sabbatini

Prima raccolta antologica in italiano di Viktor Krivulin, con saggio introduttivo, nota bio-bibliografica, note ai testi e traduzioni a cura di Marco Sabbatin

Supplementary information files for Influence of Guideline Operationalization on Youth Activity Prevalence in the International Children’s Accelerometry Database

Supplementary files for article Influence of Guideline Operationalization on Youth Activity Prevalence in the International Children’s Accelerometry Database Introduction The United Kingdom and World Health Organization recently changed their youth physical activity (PA) guidelines from 60 min of moderate- to vigorous-intensity PA (MVPA) every day, to an average of 60 min of MVPA per day, over a week. The changes are based on expert opinion due to insufficient evidence comparing health outcomes associated with different guideline definitions. This study used the International Children’s Accelerometry Database to compare approaches to calculating youth PA compliance and associations with health indicators. Methods Cross-sectional accelerometer data (n = 21,612, 5–18 yr) were used to examine compliance with four guideline definitions: daily method (DM; ≥60 min MVPA every day), average method (AM; average of ≥60 min MVPA per day), AM5 (AM compliance and ≥5 min of vigorous PA [VPA] on ≥3 d), and AM15 (AM compliance and ≥15 min VPA on ≥3 d). Associations between compliance and health indicators were examined for all definitions. Results Compliance varied from 5.3% (DM) to 29.9% (AM). Associations between compliance and health indicators were similar for AM, AM5, and AM15. For example, compliance with AM, AM5, and AM15 was associated with a lower BMI z-score (statistics are coefficient [95% CI]): AM (−0.28 [−0.33 to −0.23]), AM5 (−0.28 [−0.33 to −0.23], and AM15 (−0.30 [−0.35 to −0.25]). Associations between compliance and health indicators for DM were similar/weaker, possibly reflecting fewer DM-compliant participants with health data and lower variability in exposure/outcome data. Conclusions Youth completing 60 min of MVPA every day do not experience superior health benefits to youth completing an average of 60 min of MVPA per day. Guidelines should encourage youth to achieve an average of 60 min of MVPA per day. Different guideline definitions affect inactivity prevalence estimates; this must be considered when analyzing data and comparing studies

Supplementary information files for Influence of Guideline Operationalization on Youth Activity Prevalence in the International Children’s Accelerometry Database

Supplementary files for article Influence of Guideline Operationalization on Youth Activity Prevalence in the International Children’s Accelerometry Database Introduction The United Kingdom and World Health Organization recently changed their youth physical activity (PA) guidelines from 60 min of moderate- to vigorous-intensity PA (MVPA) every day, to an average of 60 min of MVPA per day, over a week. The changes are based on expert opinion due to insufficient evidence comparing health outcomes associated with different guideline definitions. This study used the International Children’s Accelerometry Database to compare approaches to calculating youth PA compliance and associations with health indicators. Methods Cross-sectional accelerometer data (n = 21,612, 5–18 yr) were used to examine compliance with four guideline definitions: daily method (DM; ≥60 min MVPA every day), average method (AM; average of ≥60 min MVPA per day), AM5 (AM compliance and ≥5 min of vigorous PA [VPA] on ≥3 d), and AM15 (AM compliance and ≥15 min VPA on ≥3 d). Associations between compliance and health indicators were examined for all definitions. Results Compliance varied from 5.3% (DM) to 29.9% (AM). Associations between compliance and health indicators were similar for AM, AM5, and AM15. For example, compliance with AM, AM5, and AM15 was associated with a lower BMI z-score (statistics are coefficient [95% CI]): AM (−0.28 [−0.33 to −0.23]), AM5 (−0.28 [−0.33 to −0.23], and AM15 (−0.30 [−0.35 to −0.25]). Associations between compliance and health indicators for DM were similar/weaker, possibly reflecting fewer DM-compliant participants with health data and lower variability in exposure/outcome data. Conclusions Youth completing 60 min of MVPA every day do not experience superior health benefits to youth completing an average of 60 min of MVPA per day. Guidelines should encourage youth to achieve an average of 60 min of MVPA per day. Different guideline definitions affect inactivity prevalence estimates; this must be considered when analyzing data and comparing studies