bluuebunny/crossref_metadata_2025 huggingface dataset:
COVID-19 outcomes associated with clinical and demographic characteristics in patients hospitalized with severe and critical disease in Peshawar
Authors: Imran Muhammad , Azharuddin  , Yousaf Muhammad , Khan Sajjad , Khan Abdul Jalil , Iqbal Zafar , Jan RahmanUllah , Khan Shahid , Khan Muhammad Salman
Published: March 2022

Background

As a novel disease, understanding the relationship between the clinical and demographic characteristics of coronavirus disease 2019 (COVID-19) patients and their outcome is critical. We investigated this relationship in hospitalized patients in a tertiary healthcare setting.

Aims/objectives

To study COVID-19 severity and outcomes in relation to clinical and demographic characteristics of in admitted patients

Methodology

In this cross-sectional study, medical records for 1087 COVID-19 patients were reviewed to extract symptoms, comorbidities, demographic characteristics, and outcomes data. Statistical analyses included the post-stratification chi-square test, independent sample t-test, multivariate logistic regression, and time-to-event analysis.

Results

The majority of the study participants were >50 years old (67%) and male (59%) and had the following symptoms: fever (96%), cough (95%), shortness of breath (73%), loss of taste (77%), and loss of smell (77%). Regarding worst outcome, multivariate regression analysis showed that these characteristics were statistically significant: shortness of breath (adjusted odds ratio [aOR] 31.3; 95% CI, 11.87–82.53; p < 0.001), intensive care unit (ICU) admission (aOR 28.3; 95% CI,9.0–89.6; p < 0.001), diabetes mellitus (aOR 5.1; 95% CI;3.2–8.2; p < 0.001), ischemic heart disease (aOR 3.4; 95% CI,1.6–7; p = 0.001), nausea and vomiting (aOR 3.3; 95% CI, 1.7–6.6; p = 0.001), and prolonged hospital stay (aOR 1.04; 95% CI, 1.02–1.08; p = 0.001), while patients with rhinorrhea were significantly protected (aOR 0.3; 95% CI, 0.2–0.5; p < 0.001). A Kaplan–Meier curve showed that the symptoms of shortness of breath, ICU admission, fever, nausea and vomiting, and diarrhea increased the risk of mortality.

Conclusion

Increasing age, certain comorbidities and symptoms, and direct admission to the ICU increased the risk of worse outcomes. Further research is needed to determine risk factors that may increase disease severity and devise a proper risk-scoring system to initiate timely management.
Tracking population mental health before and across stages of the COVID-19 pandemic in young adults
Authors: Kwong Alex S. F. , Northstone Kate , Pearson Rebecca M. , McIntosh Andrew M. , Timpson Nicholas J.
Published: March 2022

The SARS-CoV-2 (COVID-19) pandemic has been associated with worsening mental health. Longitudinal studies have monitored changes in mental health from pre-pandemic levels, identifying critical points for mental health as COVID-19 restrictions evolve. Here we highlight changes in depression and anxiety in the UK from pre-pandemic across four pandemic occasions: April and June 2020, January, and July 2021 – corresponding to changes in COVID-19 restrictions. Data were from >5,000 27–29-year-olds from the Avon Longitudinal Study of Parents and Children (ALSPAC). We found that anxiety almost doubled throughout the pandemic compared to pre-pandemic levels and remained high until July 2021 when COVID-19 restrictions were fully lifted. Depression was lower than pre-pandemic levels in April 2020 but increased as the pandemic evolved until July 2021. Women, those with existing mental/physical health conditions and those with economic hardship were most at risk of sustained poorer mental health across the pandemic. Our results highlight the importance of longitudinal studies for tracking mental health during the COVID-19 pandemic and across virus suppression policy changes.
Impact of Vaccination, Prior Infection, and Therapy on Delta and Omicron Variants
Authors: Wang Xiaofeng , Zein Joe , Ji Xinge , Lin Dan-Yu
Published: March 2022

We studied 249,070 patients who were tested for SARS-CoV-2 in the Cleveland Clinic Health System between October 1, 2021 and January 31, 2022. We found that vaccination, especially with recent boosting, was more effective than prior infection and monoclonal antibody therapy against both the delta and omicron variants. Vaccination and prior infection were much less effective against infection with the omicron variant than with the delta variant, but the opposite was true of death after infection. Boosting greatly increased the effectiveness of the two mRNA vaccines against both infection and death, although its effects waned markedly after 6 months. In addition, monoclonal antibody therapy was notably less effective at preventing death from the omicron variant than from the delta variant. Finally, the relatively low mortality of the omicron variant was due to both the reduced lethality of this variant and the increased population immunity acquired from booster vaccination and previous infection.
Booster dose of BNT162b2 in a CoronaVac primary vaccination protocol improves neutralization of SARS-CoV-2 Omicron variant
Authors: Campos Guilherme R. F. , Almeida Nathalie Bonatti Franco , Filgueiras Priscilla Soares , Corsini Camila Amormino , Gomes Sarah Vieira Contin , de Miranda Daniel Alvim Pena , de Assis Jéssica Vieira , Silva Thaís Bárbara de Souza , Alves Pedro Augusto , Fernandes Gabriel da Rocha , de Oliveira Jaquelline Germano , Rahal Paula , Queiroz Rafaella Fortini Grenfelle , Nogueira Maurício L.
Published: March 2022

The emergence of the new SARS-CoV-2 Omicron variant, which is known to accumulate a huge number of mutations when compared to other variants, brought to light the concern about vaccine escape, especially from the neutralization by antibodies induced by vaccination. In this scenario, we evaluated the impact on antibody neutralization induction, against Omicron variant, by a booster dose of BNT162b2 mRNA vaccine after the CoronaVac primary vaccination scheme. The percentage of seroconverted individuals 30 and 60 days after CoronaVac scheme was 17% and 10%, respectively. After booster dose administration, the seroconvertion rate increased to 76.6%. The neutralization mean titer against Omicron in the CoronaVac protocol decreased over time, but after the booster dose, the mean titer increased 43.1 times, indicating a positive impact of this vaccine combination in the serological immune response.
Assessing Direct and Spillover Effects of Intervention Packages in Network-Randomized Studies
Authors: Buchanan Ashley L. , Hernández-Ramírez Raúl Ulises , Lok Judith J. , Vermund Sten H. , Friedman Samuel R. , Forastiere Laura , Spiegelman Donna
Published: March 2022

Intervention packages may result in a greater public health impact than single interventions. Understanding the separate impact of each component in the overall package effectiveness can improve intervention delivery. We adapted an approach to evaluate the effects of a time-varying intervention package in a network-randomized study. In some network-randomized studies, only a subset of participants in exposed networks receive the intervention themselves. The spillover effect contrasts average potential outcomes if a person was not exposed themselves under intervention in the network versus no intervention in a control network. We estimated effects of components of the intervention package in HIV Prevention Trials Network 037, a Phase III network-randomized HIV prevention trial among people who inject drugs and their risk networks using Marginal Structural Models to adjust for time-varying confounding. The index participant in an intervention network received a peer education intervention initially at baseline, then boosters at 6 and 12 months. All participants were followed to ascertain HIV risk behaviors. There were 560 participants with at least one follow-up visit, 48% of whom were randomized to the intervention, and 1,598 participant-visits were observed. The spillover effect of the boosters in the presence of initial peer education training was a 39% rate reduction (Rate Ratio = 0.61; 95% confidence interval= 0.43, 0.87). These methods will be useful to evaluate intervention packages in studies with network features.
Metabolic associations with stroke, dementia, and imaging markers of cerebral small vessel disease: a comprehensive metabolomics study
Authors: Harshfield Eric L , Markus Hugh S
Published: March 2022

Background

Cerebral small vessel disease is a major cause of ischemic stroke and vascular dementia, which are among the leading causes of death and disability worldwide. Metabolomics can help identify novel risk factors to better understand pathogenesis, predict disease progression and severity, and identify therapeutic targets.

Methods

We analyzed metabolomics profiles from 118,021 UK Biobank participants with baseline metabolomics measurements (baseline surveys, 2006-2010; latest follow-up, March 2022). We examined cross-sectional associations of 325 metabolites with clinical diagnoses of stroke and dementia and MRI markers of small vessel disease. We also evaluated relationships between metabolites and future risk of stroke and dementia and performed Mendelian randomization to ascertain causal relationships.

Results

Among 118,021 participants (54% women; mean recruitment age, 56.5 years), 2,477 stroke and 1,785 dementia events were recorded (median follow-up, 13.1 years). In cross-sectional analyses, lower levels of apolipoproteins, free cholesterol, cholesteryl esters, fatty acids, lipoprotein particle concentrations, phospholipids, and triglycerides were associated with increased white matter microstructural damage on diffusion tensor MRI. Lower levels of amino acids and fatty acids and higher levels of ketone bodies were associated with increased risk of dementia. In longitudinal analyses, lipoprotein subclasses of very large HDL were associated with increased risk of stroke, and acetate, 3-hydroxybutyrate, and relative lipoprotein lipid concentrations were associated with increased risk of dementia. Mendelian randomization analyses identified strong evidence supporting causal relationships for many associations.

Conclusions

biomarker profiling platform and experimentation In this large-scale metabolomics study, we found multiple metabolites associated with stroke, dementia, and MRI markers of small vessel disease. Further studies may help develop personalized prediction models for patients at increased risk of stroke and dementia and provide insights into mechanistic pathways and future treatment approaches.

Key Points

Question

Are metabolites associated with stroke, dementia, and MRI markers of cerebral small vessel disease?

Findings

In an analysis of individual-participant data from 118,021 participants, we identified 289 metabolites that were significantly associated with stroke, dementia, and MRI markers of small vessel disease.

Meaning

Metabolic markers were associated with risk of stroke, dementia, and MRI markers of small vessel disease, which could be used to develop personalized prediction models and novel treatment approaches for patients at increased risk of vascular-related conditions.
Birth history is associated with whole-blood and T-cell methylation patterns in relapse onset multiple sclerosis
Authors: Campagna Maria Pia , Xavier Alexandre , Stankovich Jim , Maltby Vicki , Slee Mark , Kilpatrick Trevor , Scott Rodney J , Butzkueven Helmut , Lechner-Scott Jeannette , Lea Rodney , Jokubaitis Vilija
Published: March 2022

Background

Pregnancy in women with multiple sclerosis (MS) is associated with a reduction of long-term disability progression. The mechanism that drives this effect is unknown, but converging evidence suggests a role for epigenetic mechanisms altering immune and/or central nervous system function.

Objectives

We aimed to identify whole blood and immune cell-specific DNA methylation patterns associated with parity in relapse-onset multiple sclerosis.

Methods

We compared whole-blood methylation patterns between 96 matched pairs of nulligravida and parous females with MS (n=192). Parity was defined as at least one term or pre-term birth, and nulligravida was defined as no prior pregnancies. Methylation was measured with Illumina EPIC arrays, and data was pre-processed and statistically analysed using theChAMPpackage. Cell-type proportions were estimated using theEpiDISHpackage, and cell-specific analysis conducted using linear regression. Gene-set enrichment analysis (GSEA) was performed with ToppGene API and GOmeth. Methylation age was calculated with themethyAgepackage. Methylation age acceleration (MAA) was calculated by regressing methylation age on chronological age. FDR<0.05 was used to assess significance.

Results

The median time from last pregnancy to blood collection was 16.66 years (range = 1.45 – 44.42 years). We identified 903 differentially methylated positions (DMPs) in whole blood; 365 were hypomethylated and 528 were hypermethylated in parous women. We further identified two differentially methylated regions (DMRs) inCRYGNon Chromosome 7 and an intergenic region on Chromosome 15. There were four and eight cell type specific DMPs in CD4+ and CD8+ cells, respectively. Differentially methylated genes were enriched in neuronal plasticity pathways. Parity was associated with reduced MAA by a mean of 1.44 to 2.27 years using the PhenoAge (p = 0.002) and GrimAge (p = 0.005) algorithms.

Conclusion

Whole-blood methylation patterns are associated with birth history in females with relapse-onset multiple sclerosis. We found enrichment of differentially methylated genes encoding neuronal processes and reduced MAA in parous women. These methylation changes could mediate the long-term benefit of pregnancy for disease progression in multiple sclerosis.
Temporal coordination between chromosome mobility and homologous recombination
Authors: Joseph Fraulin , Lee So Jung , Bryant Eric Edward , Reid Robert J. D. , Sunjevaric Ivana , Rothstein Rodney
Published: March 2022

Homologous recombination (HR), a principal cellular pathway for double-strand break (DSB) repair, is linked to changes in chromosome movement. Although increased chromosome mobility in response to a DSB has been observed in a variety of species, its precise role in HR remains controversial. Here, we find that end resection, the recruitment of recombination proteins, increased chromosome mobility, the pairing of homologs and gene conversion are temporally linked in response to a DSB. In mre11Δ mutant cells, which exhibit a delay in the initial processing of a DSB, chromosome mobility and all subsequent recombination events are also delayed. Overexpression of the Dna2 nuclease suppresses the mre11Δ delay in end resection and restores the original timing of chromosome mobility and all subsequent downstream HR events. Thus, changing the timing of chromosome mobility results in a corresponding change in essential downstream HR events, reinforcing its mechanistic role in the DNA repair process.
Distinct Neurexin-Cerebellin Complexes Control AMPA- and NMDA-Receptor Responses in a Circuit-Dependent Manner
Authors: Dai Jinye , Liakath-Ali Kif , Golf Samantha , Südhof Thomas C.
Published: March 2022

At mature CA1→subiculum synapses, alternatively spliced SS4+ variants of neurexin-1 (Nrxn1SS4+) and neurexin-3 (Nrxn3SS4+) enhance NMDA- and suppress AMPA-receptors, respectively. Both Nrxn1SS4+and Nrxn3SS4+act by binding to secreted cerebellin-2 (Cbln2) that in turn activates postsynaptic GluD1, which is homologous to AMPA- and NMDA-receptors. Whether neurexin-Cbln2-GluD1 signaling complexes have additional functions in synapse formation besides regulating NMDA- and AMPA-receptors, and whether they perform similar roles at other synapses, remains unknown. Using constitutiveCbln2deletions, we here demonstrate that at CA1→subiculum synapses,Cbln2performs no additional developmental functions besides regulating AMPA- and NMDA-receptors. Moreover, we show that low-level expression of Cbln1, which is functionally redundant with Cbln2, does not compensate for a synapse-formation function of Cbln2 at CA1→subiculum synapses. In exploring the generality of these findings, we found that in prefrontal cortex, Nrxn1SS4+-Cbln2 signaling selectively regulates NMDA-receptors, whereas Nrxn3SS4+-Cbln2 signaling has no apparent role. In contrast, in the cerebellum Nrxn3SS4+-Cbln1 signaling regulates AMPA-receptors, whereas now Nrxn1SS4+-Cbln1 signaling has no manifest effect. Thus, Nrxn1SS4+- and Nrxn3SS4+-Cbln1/2 signaling complexes generally control NMDA- and AMPA-receptors in different synapses without regulating synapse formation, but these signaling complexes are differentially active in diverse neural circuits.
A nuclear receptor facilitates differentiation of human PSCs into more mature hepatocytes
Authors: Ma Haiting , de Zwaan Esmée , Guo Yang Eric , Cejas Paloma , Thiru Prathapan , van de Bunt Martijn , Jeppesen Jacob F. , Syamala Sudeepa , Dall’Agnese Alessandra , Abraham Brian J. , Fu Dongdong , Garrett-Engele Carrie , Lee Tony , Long Henry W , Griffith Linda G. , Young Richard A. , Jaenisch Rudolf
Published: March 2022

The capacity to generate functional hepatocytes from renewable human pluripotent stem cells (hPSCs) could address limited supplies of primary human hepatocytes. However, hepatocytes differentiated from hPSCs in vitro are functionally immature. To understand mechanisms regulating maturation of in vitro derived hepatocytes, we developed a 3D spheroid differentiation system and compared gene regulatory elements in uncultured human primary hepatocytes with those in hepatocytes that were differentiated in 2D or 3D conditions from human PSCs by RNA-seq, ATAC-seq, and H3K27Ac ChIP-seq. Three-dimensional differentiation improved enhancer activity and expression of transcription factor ONECUT1, but was insufficient to upregulate human-specific mature hepatocytes marker gene CYP3A4 or super-enhancer regulated transcription factor gene NFIC. Regulome comparisons showed reduced enrichment of thyroid receptor THRB motifs in accessible chromatin and in active enhancers without reduced transcription of THRB, suggesting the regulation at the level of THRB ligands in PSC-differentiated hepatocytes. Addition of thyroid hormone T3 to the PSC-differentiated hepatocytes increased CYP3A4 expression. T3 increased binding of THRB to the CYP3A4 proximal enhancer and restored the super-enhancer status and gene expression of NFIC and reduced expression of AFP. The resultant hPSC-hepatocytes showed gene expression, epigenetic status and super-enhancer landscape closer to primary hepatocytes and activated regulatory regions including non-coding SNPs associated with liver-related diseases. Transplanting the 3D PSC-hepatocytes into immunocompromised mice resulted in engraftment of human hepatocytes in the mouse liver parenchyma without disrupting normal liver histology at 6 months after transplantation. This work provides insights into the functions of nuclear receptor THRB and highlights the importance of the environmental factors-nuclear receptors axis in regulating maturation of human PSC-differentiated cell types.
Neural responses to biological motion distinguish autistic and schizotypal traits in the general population
Authors: Hudson Matthew , Santavirta Severi , Putkinen Vesa , Seppälä Kerttu , Sun Lihua , Karjalainen Tomi , Karlsson Henry K. , Hirvonen Jussi , Nummenmaa Lauri
Published: March 2022

Difficulties in social interactions are common to both autism and schizophrenia, and contribute to correlated autistic and schizotypal traits in the neurotypical population. It remains unresolved whether this represents a shared etiology or a superficial phenotypic overlap. Both conditions are associated with atypical neural activity in response to the perception of social stimuli, and also decreased neural synchronization between individuals that may prohibit establishing shared experiences. This study sought to establish if neural activity and neural synchronization associated with biological motion perception are differentially associated with autistic and schizotypal traits in the neurotypical population. Participants watched an audiovisual montage of naturalistic social interactions whilst hemodynamic brain activity was measured with fMRI. A separate sample of participants provided a continuous measure of the extent of biological motion, which was used to predict hemodynamic activity. General Linear Model analysis revealed that biological motion perception was associated with neural activity across the action-observation network. However, inter-subject phase synchronization analysis revealed that neural activity synchronized between individuals in occipital and parietal areas, but de-synchronized in temporal and frontal regions. Autistic traits were associated with a decrease in neural activity (precuneus, middle cingulate gyrus) and schizotypal traits were associated with a decrease in neural synchronization (middle and inferior frontal gyri). Biological motion perception elicits convergent and divergent patterns of neural activity and neural synchronization, and are differentially associated with shared traits related with autism and schizophrenia in the general population, suggesting that they originate from different neural mechanisms.
A comparison of the genes and genesets identified by EWAS and GWAS of fourteen complex traits
Authors: Battram Thomas , Gaunt Tom R. , Relton Caroline L. , Timpson Nicholas J. , Hemani Gibran
Published: March 2022

Identifying the genes, properties of these genes and pathways to understand the underlying biology of complex traits responsible for differential health states in the population is a common goal of epigenome-wide and genome-wide association studies (EWAS and GWAS). GWAS identify genetic variants that effect the trait of interest or variants that are in linkage disequilibrium with the true causal variants. EWAS identify variation in DNA methylation, a complex molecular phenotype, associated with the trait of interest. Therefore, while GWAS in principle will only detect variants within or near causal genes, EWAS can also detect genes that confound the association between a trait and a DNA methylation site, or are reverse causal. Here we systematically compare association EWAS and GWAS results of 14 complex traits (N > 4500). A small fraction of detected genomic regions were shared by both EWAS and GWAS (0-9%). We evaluated if the genes or gene ontology terms flagged by GWAS and EWAS overlapped, and after a multiple testing correction, found substantial overlap for diastolic blood pressure (gene overlap P = 5.2×10−6, term overlap P = 0.001). We superimposed our empirical findings against simulated models of varying genetic and epigenetic architectures and observed that in a majority of cases EWAS and GWAS are likely capturing distinct genesets, implying that genes identified by EWAS are not generally causally upstream of the trait. Overall our results indicate that EWAS and GWAS are capturing different aspects of the biology of complex traits.
Multilevel Correlates of Abdominal Obesity in Adolescents and Youth Living with HIV in peri-urban Cape Town, South Africa.
Authors: Kamkuemah Monika , Gausi Blessings , Oni Tolu , Middelkoop Keren
Published: March 2022

Background

Chronic non-communicable disease comorbidities are a major problem faced by people living with HIV (PLHIV). Obesity is an important factor contributing to such comorbidities and PLHIV face an elevated risk of obesity. However, there is data paucity on the intersection of obesity and HIV in adolescents and youth living with HIV (AYLHIV) in sub-Saharan Africa. We therefore aimed to investigate the prevalence of abdominal obesity and associated multilevel factors in AYLHIV in peri-urban Cape Town, South Africa.Methods

We conducted a cross-sectional study enrolling AYLHIV aged 15 – 24 years attending primary healthcare facilities in peri-urban Cape Town in 2019. All measures, except for physical examination measures, were obtained via self-report using a self-administered electronic form. Our outcome of interest was abdominal obesity (waist-to-height ratio >= 0.5). We collected individual-level data and data on community, built and food environment factors. Data was summarized using descriptive statistics, stratified by sex. Multilevel logistic regression was conducted to investigate factors associated with abdominal obesity, adjusted for sex and age.Findings

A total of 87 participants were interviewed, 76% were female and the median age was 20.7 (IQR 18.9-23.0) years. More than two fifths had abdominal obesity (41%; 95% CI: 31.0- 51.7%), compared to published rates for young people in the general population (13.7- 22.1%). In multilevel models, skipping breakfast (aOR= 5.42; 95% CI: 1.32 – 22.25) was associated with higher odds of abdominal obesity, while daily wholegrain consumption (aOR= 0.20; 95% CI: 0.05 – 0.71) and weekly physical activity (aOR = 0.24; 95% CI: 0.06 – 0.92) were associated with lower odds of abdominal obesity. Higher anticipated stigma was associated with reduced odds of obesity (aOR= 0.58; 95% CI: 0.33 – 1.00). Land-use mix diversity (aOR= 0.52; 95% CI: 0.27 – 0.97), access to recreational places (aOR= 0.37; 95% CI: 0.18 – 0.74), higher perceived pedestrian and traffic safety (aOR= 0.20; 95% CI: 0.05 – 0.80) and having a non-fast-food restaurant within walking distance (aOR= 0.30; 95% CI: 0.10 – 0.93) were associated with reduced odds of abdominal obesity. The main limitations of the study were low statistical power and possible reporting bias from self-report measures.Conclusions

Our findings demonstrate a high prevalence of abdominal obesity and highlight multilevel correlates of obesity in AYLHIV in South Africa. An intersectoral approach to obesity prevention, intervening at multiple levels is necessary to intervene at this critical life stage.
Estimating time-dependent infectious contact: a multi-strain epidemiological model of SARS-CoV-2 on the island of Ireland
Authors: Kamiya Tsukushi , Alvarez-Iglesias Alberto , Ferguson John , Murphy Shane , Sofonea Mircea T. , Fitz-Simon Nicola
Published: March 2022

Mathematical modelling plays a key role in understanding and predicting the epidemiological dynamics of infectious diseases. We construct a flexible discrete-time model that incorporates multiple viral strains with different transmissibilities to estimate the changing infectious contact that generates new infections. Using a Bayesian approach, we fit the model to longitudinal data on hospitalisation with COVID-19 from the Republic of Ireland and Northern Ireland during the first year of the pandemic. We describe the estimated change in infectious contact in the context of governmentmandated non-pharmaceutical interventions in the two jurisdictions on the island of Ireland. We take advantage of the fitted model to conduct counterfactual analyses exploring the impact of lockdown timing and introducing a novel, more transmissible variant. We found substantial differences in infectious contact between the two jurisdictions during periods of varied restriction easing and December holidays. Our counterfactual analyses reveal that implementing lockdowns earlier would have decreased subsequent hospitalisation substantially in most, but not all cases, and that an introduction of a more transmissible variant - without necessarily being more severe - can cause a large impact on the health care burden.
Understanding the role of mask-wearing during COVID-19 on the island of Ireland
Authors: Fitz-Simon Nicola , Ferguson John , Alvarez-Iglesias Alberto , Sofonea Mircea T. , Kamiya Tsukushi
Published: March 2022

Background

Non-pharmaceutical interventions (NPI) play a key role in managing epidemics, yet it is challenging to evaluate their impacts on disease spread and outcomes.

Methods

To estimate the effect of a mask-wearing intervention to mitigate the spread of SARS-CoV-2 on the island of Ireland, we focused on the potential for interindividual infectious contact over time as the outcome. This is difficult to measure directly; in a companion paper we estimated it using a multi-strain epidemiological model. We used data on mask-wearing and mobility in both Northern Ireland (NI) and the Republic of Ireland (ROI) to predict independently the estimated infectious contact over time. We made counterfactual predictions of infectious contact rates and hospitalisations under a hypothetical intervention where 90% of the population were wearing masks during early 2020, when in reality few people were wearing masks in public; this was mandated in both jurisdictions on 10th August 2020.

Results

There were 1601 hospitalisations with COVID-19 in NI between 12th March and 10th August 2020, and 1521 in ROI between 3rd April and 10th August 2020. Under the counterfactual mask-wearing scenario, we estimated 512 (95% CI 400, 730) hospitalisations in NI, and 344 (95% CI 266, 526) in ROI, during the same periods.

Conclusions

We have estimated a large effect of population mask-wearing on COVID-19 hospitalisations. This could be partly due to other factors that were also changing over time.
Acute manipulation and real-time visualization of membrane trafficking and exocytosis inDrosophila
Authors: Glashauser Jade , Camelo Carolina , Hollmann Manuel , Backer Wilko , Jacobs Thea , Sanchez Jone Isasti , Schleutker Raphael , Förster Dominique , Berns Nicola , Riechmann Veit , Luschnig Stefan
Published: March 2022

Intracellular trafficking of secretory proteins plays key roles in animal development and physiology, but tools for investigating dynamics of membrane trafficking have been limited to cultured cells. Here we present a system that enables acute manipulation and real-time visualization of membrane trafficking through reversible retention of proteins in the endoplasmic reticulum (ER) in living multicellular organisms. By adapting the “retention using selective hooks” (RUSH) approach toDrosophila, we show that trafficking of GPI-linked, secreted, and transmembrane proteins can be controlled with high temporal precision in intact animals and cultured organs. We demonstrate the potential of this approach by analyzing the kinetics of ER exit and apical secretion and the spatiotemporal dynamics of tricellular junction assembly in epithelia of living embryos. Furthermore, we show that controllable ER-retention enables tissue-specific depletion of secretory protein function. The system is broadly applicable to visualize and manipulate membrane trafficking in diverse cell typesin vivo.
NAb-seq: an accurate, rapid and cost-effective method for antibody long-read sequencing in hybridoma cell lines and single B cells
Authors: Subas Satish Hema Preethi , Zeglinski Kathleen , Uren Rachel T. , Nutt Stephen L. , Ritchie Matthew E. , Gouil Quentin , Kluck Ruth M.
Published: March 2022

Despite their common use in research, monoclonal antibodies are currently not systematically sequenced. This can lead to issues with reproducibility and the occasional loss of antibodies with loss of cell lines. Hybridoma cell lines have been the primary means of generating monoclonal antibodies from immunized animals including mice, rats, rabbits and alpacas. Excluding therapeutic antibodies, few hybridoma-derived antibody sequences are known. Sanger sequencing has been “the gold standard” for antibody gene sequencing but relies on the availability of species-specific degenerate primer sets for amplification of light and heavy antibody genes, in addition to lengthy and expensive cDNA preparation. Here we leveraged recent improvements in long-read Oxford Nanopore Technologies (ONT) sequencing to develop NAb-seq: a three-day, species-independent, and cost-effective workflow to characterize paired full-length immunoglobulin light and heavy chain genes from hybridoma cell lines. When compared to Sanger sequencing of two hybridoma cell lines, long-read ONT sequencing was highly accurate, reliable, and amenable to high throughput. We further show that the method is applicable to single cells, allowing efficient antibody discovery in rare populations such as memory B cells. In summary, NAb-seq promises to accelerate identification and validation of hybridoma antibodies as well as antibodies from single B cells used in research, diagnostics and therapeutics.
Human neutrophils direct epithelial cell extrusion to enhance intestinal epithelial host defense duringSalmonellainfection
Authors: Lawrence Anna-Lisa E. , Berger Ryan P. , Hill David R. , Huang Sha , Yadagiri Veda K. , Bons Brooke , Fields Courtney , Sule Gautam J. , Knight Jason S. , Wobus Christiane E. , Spence Jason R. , Young Vincent B. , O’Riordan Mary X. , Abuaita Basel H.
Published: March 2022

Infection of the human gut bySalmonella entericaTyphimurium (STM) results in a localized inflammatory disease that is not mimicked in murine infections. To determine mechanisms by which neutrophils, as early responders to bacterial challenge, direct inflammatory programming of human intestinal epithelium, we established a multi-component human intestinal organoid (HIO) model of STM infection. HIOs were micro-injected with STM and then seeded with primary human polymorphonuclear leukocytes (PMN-HIOs), specifically neutrophils and analyzed for bacterial growth and host cell survival. Surprisingly, PMNs did not affect luminal colonization ofSalmonella,but their presence reduced intraepithelial bacterial burden. Adding PMNs to infected HIOs resulted in substantial accumulation of shed intestinal epithelial cells that could be blocked by Caspase-1 or Caspase-3 inhibition. Cleaved Caspase-3 was present in epithelial cells, but expression of the inflammasome adaptor, ASC, was only detected in PMNs. Caspase inhibition also increased bacterial burden in the epithelium of the PMN-HIO, suggesting PMNs enhance activation of cell death pathways in human intestinal epithelial cells as a protective response to infection. These data support a critical function for neutrophils beyond their antimicrobial role whereby they amplify cell death and extrusion of epithelial cells from theSalmonella-infected intestinal monolayer.

Significance statement

Neutrophils are early responders toSalmonellaintestinal infection, but how they influence infection progression and outcome is unknown. Here we use a co-culture model of human intestinal organoids and human primary neutrophils to study the contribution of human neutrophils toSalmonellainfection of the intestinal epithelium. We found that neutrophils markedly enhanced epithelial defenses, including enhancing cell extrusion to reduce intraepithelial burden ofSalmonellaand association with the epithelium, rather than directly killingSalmonellain the HIO lumen. These findings reveal a novel role for neutrophils in the gut beyond killing invading pathogens and illuminate how neutrophils can reprogram cells in the gut environment to enhance antimicrobial defenses.
Changes of urinary proteomic before and after QIV and COVID-19 vaccination
Authors: Pan Xuanzhen , Liu Yongtao , Bao Yijin , Wei Lilong , Gao Youhe
Published: March 2022

We first collected a young people’s urine samples cohort of quadrivalent influenza vaccine. Urine protein at 24 hours after vaccination was enriched in immune-related pathways, though the specific pathways varied. Perhaps because different people may be in a previous life encountered some of the viruses in the vaccine, the second immunization was triggered. Or everyone has a different constitution, exposure to the same virus triggering different immunity. We then collected urine samples from several uninfected SARS-CoV-2 young people before and after the first, second, and third doses of the COVID-19 vaccine. We found that the differential protein compared between after the second dose (24h) and before the second dose enriched pathways were involved in regulated exocytosis and immune-related pathways, indicating not first exposure to antigen. Surprisingly, the urine differential protein-enriched pathways before and after the first dose were similar to those before and after the second dose. We assume that although the volunteers have not been infected with SARS-CoV-2, they might have been exposed to other coimmunogenic coronaviruses. 2~4h after the third vaccination, the differentially expressed protein also enriched regulated exocytosis and immune-related pathways, indicating that the body has triggered the immune response in a very short time after vaccination, and urine proteome is a good window to monitor the changes of human immune function.
Neural Correlates of Linguistic Collocations During Continuous Speech Perception
Authors: Garibyan Armine , Schilling Achim , Boehm Claudia , Zankl Alexandra , Krauss Patrick
Published: March 2022

Language is fundamentally predictable, both on a higher schematic level as well as low-level lexical items. Regarding predictability on a lexical level, collocations are frequent co-occurrences of words that are often characterized by high strength of association. So far, psycho-and neurolin guistic studies have mostly employed highly artificial experimental paradigms in the investigation of collocations by focusing on the processing of single words or isolated sentences. In contrast, here we analyze EEG brain responses recorded during stimulation with continuous speech, i.e. audio books. We find that the N400 response to collocations is significantly different from that of non-collocations, whereas the effect varies with respect to cortical region (anterior/ posterior) and laterality (left/right). Our results are in line with studies using continuous speech, and they mostly contradict those using artificial paradigms and stimuli. To the best of our knowledge, this is the first neurolinguistic study on collocations using continuous speech stimulation.
Influence of residual microbial nucleic acid in instruments for hip joint arthroplasty on false-positive results of metagenomic sequencing
Authors: Yin Han , Wang Chengtan , Xu Duliang , Xu Mingtao , Ha Chengzhi , Li Wei , Pang Feng , Wang Dawei
Published: March 2022

The purpose of this study was to analyze the effect of residual microbial nucleic acid in instruments for hip joint arthroplasty on false-positive sequencing results. Samples were taken from 3 different acetabular reamer for hip arthroplasty in 7 different hospitals. The whole process was strictly aseptic, metagenomic next-generation sequencing (mNGS) was performed according to standard operating procedures. The sterility of instruments was confirmed by culture method. The sequencing results of specimens from different hospitals were compared to analyze the difference of background bacteria. Bioinformatics analysis and visualization were presented through R language. A total of 26 samples were processed by mNGS, including 24 instrument swab samples, 1 blank swab control, and 1 blank water control. 254,314,707 reads were sequenced in all samples. The results showed that 1.13% of Clean Reads can be matched to pathogenic microorganism genomes, of which bacterial sequences account for 87.48%, fungal sequences account for 11.18%, parasite sequences account for 1.26%, and virus sequences account for 0.06%. The results of PCA (Principal Component Analysis) demonstrated that the distribution of bacteria on the surface of instruments was significantly different between medical institutions. Through the Venn diagram, it was found that 465 species of bacteria in all region hospitals, Liaocheng People’s Hospital had a maximum of 340 species of bacteria, followed by Guanxian County People’s Hospital with 169 species. The clustering heat map illustrated that the distribution of bacterial groups in three different instrument samples in the same hospital was basically the same, and the bacterial genera varied significantly among hospitals. The residual microbial nucleic acid fragments are mainly bacterial DNA and represent differences in different medical institutions, The establishment of independent background bacterial libraries in different medical institutions can effectively improve the accuracy of mNGS diagnosis and help to exclude background microorganisms interference.
Dynamics in vertical transmission of viruses in naturally selected and traditionally managed honey bee colonies across Europe
Authors: Claeys Bouuaert David , De Smet Lina , Brunain Marleen , Dahle Bjørn , Blacquière Tjeerd , Dalmon Anne , Dezmirean Daniel , Elen Dylan , Filipi Janja , Giurgiu Alexandru , Gregorc Aleš , Kefuss John , Locke Barbara , de Miranda Joachim R. , Oddie Melissa , Panziera Delphine , Parejo Melanie , Pinto M. Alice , de Graaf Dirk C.
Published: March 2022

The ‘suppressed in-ovo virus infection’ trait (SOV) was the first trait applied in honey bee breeding programs aimed to increase resilience to virus infections, a major threat for colony survival. By screening drone eggs for viruses, the SOV trait scores the antiviral resistance of queens and its implications for vertical transmission. In this study, queens from both naturally surviving and traditionally managed colonies from across Europe were screened using a two-fold improved SOV phenotyping protocol. First, a gel-based RT-PCR was replaced by a RT-qPCR. This not only allowed quantification of the infection load but also increased the test sensitivity. Second, a genotype specific primer set was replaced by a primer set that covered all known deformed wing virus (DWV) genotypes, which resulted in higher virus loads and fewer false negative results. It was demonstrated that incidences of vertical transmission of DWV were more frequent in naturally surviving populations than in traditionally managed colonies, although the virus load in the eggs remained the same. Dynamics in vertical transmission were further emphasized when comparing virus infections with queen age. Interestingly, older queens showed significantly lower infection loads of DWV in both traditionally managed and naturally surviving colonies, as well as reduced DWV infection frequencies in traditionally managed colonies when compared with younger queens. Seasonal variation in vertical transmission was found with lower infection frequencies in spring compared to summer for DWV and black queen cell virus. Together, these patterns in vertical transmission suggest an adaptive antiviral response of queens aimed at reducing vertical transmission over time.
The effects of antibiotic combination treatments onPseudomonas aeruginosatolerance evolution and coexistence withStenotrophomonas maltophilia
Authors: Law Jack P. , Wood A. Jamie , Friman Ville-Petri
Published: March 2022

Pseudomonas aeruginosabacterium is a common pathogen of Cystic Fibrosis (CF) patients due to its ability to evolve resistance to antibiotics during treatments. WhileP. aeruginosaresistance evolution is well characterised in monocultures, it is less well understood in polymicrobial CF infections. Here, we investigated how exposure to ciprofloxacin, colistin, or tobramycin antibiotics, administered at sub-MIC doses alone and in combination, shaped the tolerance evolution ofP. aeruginosa(PAO1 lab and clinical CF LESB58 strains) in the absence and presence of a commonly co-occurring species,Stenotrophomonas maltophilia. Increases in antibiotic tolerances were primarily driven by the presence of that antibiotic in the treatment. We observed a reciprocal cross-tolerance between ciprofloxacin and tobramycin, and when combined these antibiotics selected increased MICs for all antibiotics. Though the presence ofS. maltophiliadid not affect the tolerance or the MIC evolution, it droveP. aeruginosainto extinction more frequently in the presence of tobramycin due to its relatively greater innate tobramycin tolerance. In contrast,P. aeruginosadominated and droveS. maltophiliaextinct in most other treatments. Together, our findings suggest that besides driving high-level antibiotic tolerance evolution, sub-MIC antibiotic exposure can alter competitive bacterial interactions, leading to target pathogen extinctions in multi-species communities.
Evidence for the role of music on the growth and signal response in duckweed
Authors: Ye Zi , Yang Rui , Xue Ying , Chen Xinglin , Xu Ziyi , Ren Qiuting , Sun Jinge , Ma Xu , Yang Lin
Published: March 2022

Sound vibration, an external mechanical force, has been proved to modulate plant growth and development like rain, wind, and vibration. However, the role of music on plants, especially on signal response, has been usually neglected in research. Herein, we investigated the growth state, gene expression, and signal response in duckweed treated with soft music. The protein content in duckweed after music treatment for 7 days was about 1.6 times that in duckweed without music treatment. Additionally, Fv/Fm in duckweed treated with music was 0.78, which was significantly higher in comparison with the control group (P < 0.01). Interestingly, music promoted the Glu and Ca signaling response. To further explore the global molecular mechanism, we performed transcriptome analysis. A total of 1296 DEGs were found for all these investigated genes in duckweed treated with music compared to the control group. Among these, up-regulation of the expression of metabolism-related genes related to glycolysis, cell wall biosynthesis, oxidative phosphorylation, and pentose phosphate pathways were found. Overall, these results provided a molecular basis to music-triggered signal response, transcriptomic, and growth changes in duckweed, which also highlighted the potential of music as an environmentally friendly stimulus to promote improved protein production in duckweed.
Cardio PyMEA: A user-friendly, open-source Python application for cardiomyocyte microelectrode array analysis
Authors: Dunham Christopher S. , Mackenzie Madelynn E. , Nakano Haruko , Kim Alexis R. , Nakano Atsushi , Stieg Adam Z. , Gimzewski James K.
Published: March 2022

Open source analytical software for the analysis of electrophysiological cardiomyocyte data offers a variety of new functionalities to complement closed-source, proprietary tools. Here, we present the Cardio PyMEA application, a free, modifiable, and open source program for the analysis of microelectrode array (MEA) data obtained from cardiomyocyte cultures. Cardio PyMEA was written entirely in Python 3 to provide an accessible, integrated workflow that possesses a user-friendly graphical user interface (GUI) written in PyQt5 to allow for performant, cross-platform utilization. This application makes use of object-oriented programming (OOP) principles to facilitate the relatively straightforward incorporation of custom functionalities, e.g. power law analysis, that suit the needs of the user. Cardio PyMEA is available as an open source application under the terms of the GNU General Public License (GPL). The source code for Cardio PyMEA can be downloaded from Github at the following repository: https://github.com/csdunhamUC/cardio_pymea.
Efficient rescue of a newly classified Ebinur lake orthobunyavirus with GFP reporter and its application in rapid antiviral screening
Authors: Ren Nanjie , Wang Fei , Zhao Lu , Wang Shunlong , Zhang Guilin , Li Jiaqi , Zhang Bo , Bergeron Eric , Yuan Zhiming , Xia Han
Published: March 2022

Orthobunyaviruses have been reported to cause severe diseases in humans or animals, posing a threat to human health and social economy. Ebinur lake virus (EBIV) is a newly classified orthobunyavirus, which needs further intensive study and therapies to cope with its potential infection risk to human and animals. Here, through the reverse genetics system, the recombinant EBIV of wild type (rEBIV/WT) and NP-conjugated-eGFP (rEBIV/eGFP/S) were rescued for the application of the rapid antiviral drug screening. The eGFP fluorescence signal of the rEBIV/eGFP/S was stable in the process of successive passage in BHK-21 cells (over 10 passages) and this recombinant virus could replicate in various cell lines. Compared to the wild type EBIV, the rEBIV/eGFP/S caused the smaller plaques and its peak titers were lower, suggesting attenuation due to the eGFP insertion. Through the high-content screening (HCS) system, ribavirin showed an inhibitory effect on the rEBIV/eGFP/S with an EC50 of 21.91 μM, while favipiravir did not inhibit, even at high concentrations. In addition, five of ninety-six natural compounds had antiviral against EBIV. The robust reverse genetics system for EBIV will facilitate investigation into replication and assembly mechanisms and assist drug and vaccine development.