bluuebunny/crossref_metadata_2025 huggingface dataset:
An Unfolding Tabletop Simulation Training Exercise on Disaster Planning for Nursing Students
Authors: Johnson Clare , Badowski Donna Marie , Quandt Raegan
Published: June 2022

Background:

Disaster planning is an essential component for nursing students to learn.

Problem:

Clinical experiences of disasters are typically unavailable for nursing students. Increasing frequency of disaster events around the globe has made disaster planning knowledge and skills a critical component in nursing education and professional practice.

Approach:

An unfolding tabletop disaster planning exercise was created as a simulation training strategy meant to strengthen essential disaster response skills. The exercise involves 5 realistic scenarios related to a mass casualty event, taking students from the disaster site to the hospital-based disaster response.

Outcomes:

Implementation of a tabletop disaster planning simulation in one nursing program replaced the traditional lecture-based disaster content.

Conclusion:

An unfolding tabletop disaster planning simulation is a comprehensive, interactive, sustainable, and low-cost teaching strategy that draws on nursing students' fundamental knowledge. Students had the opportunity to practice clinical skills required during a disaster, such as communication, prioritization, teamwork, and delegation.
Haemophilus Influenzae-Induced Corneal Ulcer and Endophthalmitis Triggered by Hair Dye
Authors: Xie Tian , Jing Meng
Published: June 2022

The present report describes a 79-year-old woman developed eye pain in her right eye after accidental exposure to the hair dye when she dyed her hair. Her visual acuity was no light perception and intraocular ocular pressure was 10 mmHg in her right eye. Slit-lamp biomicroscopy revealed a huge corneal ulcer with the central cornea almost perforated and severe hypopyon in anterior chamber and moderate opacity in vitreous. Time-of-flight mass-spectrum of cornea scraping confirmed that the pathogen was haemophilus influenzae. Right-eye enucleation was performed. Topical chloramphenicol eye drops (0.25%) and ciprofloxacin (0.3%) and the ceftezole intravenous infusion were applied. The infection was controlled and the patient recovered well on 1 month follow-up. Doctors should be aware of the diagnosis and treatment of this complication associated with the application of hair dye as the popularity of this procedure increases.
Decompression of Odontogenic Keratocysts Before Enucleation Reduces the Rate of Recurrence
Authors: Stanbouly Dani , Lee Kevin C. , Fazzolari Justin R. , Philipone Elizabeth
Published: June 2022

Background:

The purpose of this study was to determine if 2-stage conservative treatment (decompression followed by enucleation) of odontogenic keratocysts reduced the rate of recurrence compared to single-stage conservative treatment.

Methods:

This was a pooled cohort study composed of both patients identified at our institution and cases reported in the literature. The primary predictor variable was treatment modality (single versus 2-staged conservative treatment). The outcome variable was the overall recurrence rate.

Results:

A total of 684 patient cases were included in the final pooled sample. The mean age was 39.80years (range: 7–80 years). The mandible (76.8%) was the most common site, with the rest of the lesions manifesting in the maxilla (23.0%). A total of 58.1% of the lesions were unilocular, whereas the remaining 41.9% were multilocular. Two-stage conservative treatment demonstrated a lower recurrence rate (14.5% versus 22.1%; P = 0.029).

Conclusions:

Decompression is known to reduce lesion size and optimize the favorability of conservative treatment. Furthermore, we propose that 2-staged treatment may also be associated with a lower recurrence rate.
Computed Tomography Assessment of Maxillary Sinus and Inferior Nasal Airway After Le Fort I Osteotomy
Authors: Ueki Koichiro , Takayama Akihiro , Moroi Akinori , Yoshizawa Kunio
Published: June 2022

Purpose:

This study aimed to evaluate and predict the factors that affect the postoperative maxillary sinus and inferior nasal cavity conditions after Le Fort I osteotomy.

Subjects and Methods:

The rate of aerated (healthy) sinus area and the inferior nasal airway area were calculated by preoperative computed tomography measurements and at 1 week and 1 year postoperatively. Factors predicting the rate of aerated sinus area and the ratio of the inferior nasal cavity area after 1-week were examined using these variables.

Results:

The subjects consisted of 112 patients (224 sides) who underwent Le Fort I osteotomy with sagittal split ramus osteotomy. The rate of aerated sinus area after 1 week was significantly correlated with sex, age, and amount of blood loss (P < 0.0001). The rate of the inferior nasal cavity area after 1 week was significantly correlated with the anterior impaction amount of the maxilla and the preoperative rate of the inferior nasal airway area (P= 0.0017).

Conclusions:

This study suggests that attention should be paid to females, older patients, and the amount of blood loss to prevent sinusitis, and larger maxillary impaction at the anterior site should be carefully planned to prevent severe nasal obstruction immediately after Le Fort I osteotomy.
Four Different Reasons of Subcutaneous Emphysema With or Without Pneumomediastinum and Pneumothorax After Facial Bone Surgery
Authors: Choung Han-Wool , Choi Young-Jun , Kang Hyun , Lee Ui-Lyong
Published: June 2022

In the present study, the authors report rare case series with subcutaneous emphysema with or without pneumomediastinum and pneumothorax after orthognathic and facial bone contouring surgery, compare their clinical and radiologic findings, and suggest precautions. Four patients who showed subcutaneous emphysema on follow up chest X-ray and computed tomography after orthognathic and facial bone contouring surgery were included in the study. In all cases post-op subcutaneous emphysema were detected, however, the aspect and mechanisms of post-op air spread were all different. After the conservative management with administering the O2 by nasal cannula or endotracheal tube, the symptoms were relieved except 1 patient who needed chest tube insertion and further supra-sternal incision. In conclusion, subcutaneous emphysema with or without pneumomediastinum and pneumothorax after orthognathic and facial bone contouring surgery can be occurred by cervical fascia injury or alveolar ruptures. To preventing those complications, traumatic naso-tracheal intubation, excessive positive pressure ventilation, intermaxillary fixation immediate after the surgery, and increase of intra-alveolar pressure of the patients should be avoided.
Preoperative Treatment of Severe Diabetes Mellitus and Hypertension Mitigates Healthcare Disparities and Prevents Adverse Postoperative Discharge to a Nursing Home
Authors: Wachtendorf Luca J. , Azimaraghi Omid , Rangasamy Valluvan , Sane Miheer , Subramaniam Balachundhar , Vazquez Rafael , Wongtangman Karuna , Houle Timothy T. , Bellin Eran Y. , Akeju Oluwaseun , Straker Tracey , Chambers Terry-Ann T. , Oriol Nancy E. , Eikermann Matthias ,   for the Health Outcomes and Perioperative Equity (H.O.P.E) group investigators writing committee
Published: June 2022

Objective:

To evaluate whether patients of Black race are at higher risk of adverse postoperative discharge to a nursing home, and if a higher prevalence of severe diabetes mellitus and hypertension are contributing.

Background:

It is unclear whether a patient’s race predicts adverse discharge to a nursing home after surgery, and if preexisting diseases are contributing.

Methods:

A total of 368,360 adults undergoing surgery between 2007 and 2020 across 2 academic healthcare networks in New England were included. Patients of self-identified Black or White race were compared. The primary outcome was postoperative discharge to a nursing facility. Mediation analysis was used to examine the impact of preexisting severe diabetes mellitus and hypertension on the primary association.

Results:

In all, 10.3% (38,010/368,360) of patients were Black and 26,434 (7.2%) patients were discharged to a nursing home. Black patients were at increased risk of postoperative discharge to a nursing facility (adjusted absolute risk difference: 1.9%; 95% confidence interval: 1.6%–2.2%; P<0.001). A higher prevalence of preexisting severe diabetes mellitus and hypertension in Black patients mediated 30.2% and 15.6% of this association. Preoperative medication-based treatment adherent to guidelines in patients with severe diabetes mellitus or hypertension mitigated the primary association (P-for-interaction <0.001). The same pattern of effect mitigation by pharmacotherapy was observed for the endpoint 30-day readmission.

Conclusions:

Black race was associated with postoperative discharge to a nursing facility compared to White race. Optimized preoperative assessment and treatment of diabetes mellitus and hypertension improves surgical outcomes and provides an opportunity to the surgeon to help eliminate healthcare disparities.
Foxm1 drives cardiomyocyte proliferation in adult zebrafish after cardiac injury
Authors: Zuppo Daniel A. , Missinato Maria A. , Santana-Santos Lucas , Li Guang , Benos Panayiotis V. , Tsang Michael
Published: June 2022

The regenerative capacity of the mammalian heart is poor with one potential reason being that adult cardiomyocytes cannot proliferate at sufficient levels to replace lost tissue. During development and early neonatal stages, cardiomyocytes can successfully divide under injury conditions; however, as these cells mature their ability to proliferate rapidly decreases. Therefore, understanding which regulatory programs are required to induce post-mitotic, mature cardiomyocytes into a proliferative state is essential in order to enhance cardiac regeneration. Unlike mammals, adult zebrafish cardiomyocytes in the injury border zone do proliferate. This model provides an opportunity to elucidate how these border zone cells respond to different stimuli post-injury and to study which regulatory programs are required for adult cardiomyocyte proliferation. Here we report the forkhead transcription factor,foxm1, is required for cardiomyocyte proliferation after cardiac injury through transcriptional regulation of cell cycle genes. Transcriptomic analysis of injured adult zebrafish hearts revealed thatfoxm1expression is increased after injury in border zone cardiomyocytes.foxm1mutants showed decreased cardiomyocyte proliferation after ventricular resection, resulting in larger fibrotic scars. Moreover, decreased expression of cell cycle progression genes suggests that Foxm1 is required for different cell cycle checkpoints during cardiomyocyte division. Subsequent analyses of Foxm1 targets revealed the microtubule and kinetochore binding protein,cenpf, is required for cardiac regeneration ascenpfmutants failed to regenerate due to increased cardiomyocyte binucleation. Thus,foxm1andcenpfare required for cardiomyocytes to complete mitosis during zebrafish cardiac regeneration.
Updated Variant Curation Expert Panel Criteria and Pathogenicity Classifications for 251 Variants for RYR1-related Malignant Hyperthermia Susceptibility
Authors: Johnston Jennifer J. , Dirksen Robert T. , Girard Thierry , Hopkins Phil M. , Kraeva Natalia , Ognoon Mungunsukh , Radenbaugh K. Bailey , Riazi Sheila , Robinson Rachel L. , Saddic Louis A. , Sambuughin Nyamkhishig , Saxena Richa , Shepherd Sarah , Stowell Kathryn , Weber James , Yoo Seeley , Rosenberg Henry , Biesecker Leslie G.
Published: June 2022

The ClinGen malignant hyperthermia susceptibility (MHS) variant curation expert panel specified the ACMG/AMP criteria for RYR1-related MHS and a pilot analysis of 84 variants was published. We have now classified an additional 251 variants for RYR1-related MHS according to current ClinGen standards and updated the criteria where necessary. Criterion PS4 was modified such that individuals with multiple RYR1 variants classified as pathogenic (P), likely pathogenic (LP) or variant of uncertain significance (VUS) were not considered as providing evidence for pathogenicity. Critera PS1 and PM5 were revised to consider LP variants at the same amino acid residue as providing evidence for pathogenicity at reduced strength. Finally, PM1 was revised such that if PS1 or PM5 are used PM1, if applicable, should be downgraded to supporting. Of the 251 RYR1 variants, 42 were classified as P/LP, 16 as B/LB, and 193 as VUS. The primary driver of 176 VUS classifications was insufficient evidence supporting pathogenicity, rather than evidence against pathogenicity. Functional data supporting PS3/BS3 was identified for only 13 variants. Based on the posterior probabilities of pathogenicity and variant frequencies in gnomAD, we estimated the prevalence of individuals with RYR1-related MHS pathogenic variants to be between 1/300 and 1/1,075, considerably higher than current estimates. We have updated ACMG/AMP criteria for RYR1-related MHS and classified 251 variants. We suggest that prioritization of functional studies is needed to resolve the large number of VUS classifications and allow for appropriate risk assessment. RYR1-related MHS pathogenic variants are likely to be more common than currently appreciated.
Hypomethylation of contracted D4Z4 repeats in facioscapulohumeral muscular dystrophy
Authors: Hiramuki Yosuke , Kure Yuriko , Saito Yoshihiko , Ogawa Megumu , Ishikawa Keiko , Mori-Yoshimura Madoka , Oya Yasushi , Takahashi Yuji , Kim Dae-Seong , Arai Noriko , Mori Chiaki , Matsumura Tsuyoshi , Hamano Tadanori , Nakamura Kenichiro , Ikezoe Koji , Hayashi Shinichiro , Goto Yuichi , Noguchi Satoru , Nishino Ichizo
Published: June 2022

Facioscapulohumeral muscular dystrophy (FSHD) can be subdivided into two types: FSHD1, caused by contraction of the D4Z4 repeat on chromosome 4q35, and FSHD2, caused by mild contraction of the D4Z4 repeat plus aberrant hypomethylation mediated by genetic variants in SMCHD1, DNMT3B, or LRIF1. Genetic diagnosis of FSHD is challenging because of the complex procedures required. Here, we applied Nanopore CRISPR/Cas9-targeted resequencing for the diagnosis of FSHD by simultaneous detection of D4Z4 repeat length and methylation status at nucleotide level in genetically-confirmed and suspected patients. We found significant hypomethylation of contracted D4Z4 repeats in FSHD1 and strong correlation between methylation rate and patient phenotype. This finding can explain how repeat contraction contributes to disease pathogenesis by activating DUX4 expression.
The slowly evolving genome of the xenacoelomorph wormXenoturbella bocki
Authors: Schiffer Philipp H. , Natsidis Paschalis , Leite Daniel J. , Robertson Helen E. , Lapraz François , Marlétaz Ferdinand , Fromm Bastian , Baudry Liam , Simpson Fraser , Høye Eirik , Zakrzewski Anne-C. , Kapli Paschalia , Hoff Katharina J. , Mueller Steven , Marbouty Martial , Marlow Heather , Copley Richard R. , Koszul Romain , Sarkies Peter , Telford Maximilian J.
Published: June 2022

The evolutionary origins of Bilateria remain enigmatic. One of the more enduring proposals highlights similarities between a cnidarian-like planula larva and simple acoel-like flatworms. This idea is based in part on the view of the Xenacoelomorpha as an outgroup to all other bilaterians which are themselves designated the Nephrozoa (protostomes and deuterostomes). Genome data can help to elucidate phylogenetic relationships and provide important comparative data. Here we assemble and analyse the genome of the simple, marine xenacoelomorphXenoturbella bocki, a key species for our understanding of early bilaterian and deuterostome evolution. Our highly contiguous genome assembly ofX. bockihas a size of ∼111 Mbp in 18 chromosome like scaffolds, with repeat content and intron, exon and intergenic space comparable to other bilaterian invertebrates. We findX. bockito have a similar number of genes to other bilaterians and to have retained ancestral metazoan synteny. Key bilaterian signalling pathways are also largely complete and most bilaterian miRNAs are present. We conclude thatX. bockihas a complex genome typical of bilaterians, in contrast to the apparent simplicity of its body plan. Overall, our data do not provide evidence supporting the idea that Xenacoelomorpha are a primitively simple outgroup to other bilaterians and gene presence/absence data support a relationship with Ambulacraria.
Desiccation resistance differences in Drosophila species can be largely explained by variations in cuticular hydrocarbons
Authors: Wang Zinan , Receveur Joseph P. , Pu Jian , Cong Haosu , Richards Cole , Liang Muxuan , Chung Henry
Published: June 2022

Maintaining water balance is a universal challenge for organisms living in terrestrial environments, especially for insects, which have essential roles in our ecosystem. Although the high surface area to volume ratio in insects makes them vulnerable to water loss, insects have evolved different levels of desiccation resistance to adapt to diverse environments. To withstand desiccation, insects use a lipid layer called cuticular hydrocarbons (CHCs) to reduce water evaporation from the body surface. It has long been hypothesized that the waterproofing capability of this CHC layer, which can confer different levels of desiccation resistance, depends on its chemical composition. However, it is unknown which CHC components are important contributors to desiccation resistance and how these components can determine differences in desiccation resistance. In this study, we used machine learning algorithms, correlation analyses, and synthetic CHCs to investigate how different CHC components affect desiccation resistance in 50 Drosophila and related species. We showed that desiccation resistance differences across these species can be largely explained by variation in cuticular hydrocarbons. In particular, length variation in a subset of CHCs, the methyl-branched CHCs (mbCHCs), is a key determinant of desiccation resistance. We also showed a significant correlation between the evolution of longer mbCHCs and higher desiccation resistance. Given the ubiquitous presence of mbCHCs in insects, the evolution of mbCHCs may be a general mechanism of how insects evolve desiccation resistance and adapt to diverse and changing environments.

Significance

As our planet is becoming more arid due to global warming, preventing dehydration is key to the survival of insects, an essential part of our ecosystem. However, factors that determine how insects may evolve resistance to desiccation are relatively unknown. Using Drosophila species from diverse habitats, we showed that variations in the composition of cuticular hydrocarbons (CHCs), a hydrophobic layer found on insects to prevent evaporative water loss, can largely explain desiccation resistance differences. In addition, the evolution of longer methyl-branched CHCs (mbCHCs), underlies the evolution of higher desiccation resistance in this genus. As mbCHCs are ubiquitously present in most insects, we suggest that evolutionary changes in mbCHCs may be a general determinant of desiccation resistance across insect species.
Within-hotel transmission of SARS-CoV-2 during on-arrival quarantine in Hong Kong
Authors: Adam Dillon C. , Martín-Sánchez Mario , Gu Haogao , Wu Peng , Lau Eric H. Y. , Leung Gabriel M. , Poon Leo L. M. , Cowling Benjamin J.
Published: June 2022

Background

On-arrival quarantine has been one of the primary measures used to prevent the introduction of COVID-19 into Hong Kong since the start of the pandemic. Most on-arrival quarantines have been done in hotels, with the duration of quarantine and testing frequency during quarantine varying throughout the pandemic for various reasons. However, hotels are not necessarily designed with infection control in mind. We aimed to study the potential risk of transmission between persons in on-arrival quarantine.

Methods

We examined data on each laboratory-confirmed COVID-19 case identified in on-arrival quarantine in a hotel in Hong Kong between 1 May 2020 and 31 January 2022. We sequenced the full genomes of viruses from cases that overlapped with other confirmed cases in terms of the hotel of stay, date of arrival and date of testing positive. A combination of epidemiological information and sequence information was then used to identify probable transmission events.

Findings

Among 221 imported cases that overlapped with other quarantined cases, phylogenetic analysis identified eight suspected clusters comprising 20 cases in total. Only three of these clusters had been recognised as hotel transmission events.

Interpretation

We have identified potential occurrences of COVID-19 transmission within hotel quarantine in Hong Kong demonstrating the underlying low but non-zero risk associated with sequestering arrivals within hotels. In future pandemics, on-arrival quarantine in hotels could be used to delay the introduction of infection, but the construction of purpose-built facilities for on-arrival quarantine might be necessary to minimize importation risk.

Funding

Health and Medical Research Fund, Hong Kong
The burden of respiratory conditions in the emergency department of Muhimbili National Hospital in Tanzania in the first two years of the COVID-19 pandemic
Authors: Ndumwa Harrieth P , Mboya Erick A , Amani Davis Elias , Mashoka Ramadhani , Nicholaus Paulina , Haniffa Rashan , Beane Abi , Mfinanga Juma , Sunguya Bruno , Sawe Hendry R. , Baker Tim
Published: June 2022

Background

Globally, respiratory diseases cause 10 million deaths every year. With the COVID-19 pandemic, the burden of respiratory illness increased and led to significant morbidity and mortality in both high- and low-income countries. This study assessed the burden and trend of respiratory conditions among patients presenting to the emergency department of Muhimbili National Hospital in Tanzania and compared with national COVID-19 data to determine if this knowledge may be useful for the surveillance of disease outbreaks in settings of limited specific diagnostic testing.

Methods

The study used routinely collected data from the electronic information system in the Emergency Medical Department (EMD) of Muhimbili National Hospital in Tanzania. All patients presenting to the EMD in a 2-year period, 2020 and 2021 with respiratory conditions were included. Descriptive statistics and graphical visualizations were used to describe the burden of respiratory conditions and the trends over time and to compare to national Tanzanian COVID-19 data during the same period.

Results

One in every four patients who presented to the EMD of the Muhimbili National Hospital had a respiratory condition – 1039 patients per month. Of the 24,942 patients, 52% were males, and the median age (IQR) was 34.7 (21.7, 53.7) years. The most common respiratory diagnoses were pneumonia (52%), upper respiratory tract infections (31%), asthma (4.8%) and suspected COVID-19 (2.5%). There were four peaks of respiratory conditions coinciding with the four waves in the national COVID-19 data.

Conclusions

There is a high burden of respiratory conditions among patients presenting to the EMD of Muhimbili National Hospital. The trend shows four peaks of respiratory conditions in 2020-2021 seen to coincide with the four waves in the national COVID-19 data. Real-time hospital-based surveillance tools may be useful for early detection of respiratory disease outbreaks and other public health emergencies in settings with limited diagnostic testing.
The influence of different exercise types on elderly depressed patients: protocol for an umbrella review
Authors: Liu Jie , Gao Shu-qing , Zhang Lian-cheng
Published: June 2022

Introduction

At present, there are a large number of studies confirming that exercise can improve the depression of the elderly, but there is no research to compare the effects of different exercise programs. Therefore, the purpose of this article is to compare the effects of different exercise programs on the mood improvement of elderly people with depression, and select suitable exercise programs., In order to provide guidance and suggestions for clinical practice.

Methods and analysis

Document retrieval was carried out in 7 databases including CNKI, ebsco, PsycARTICLES, PsycINFO, PubMed, Cochrane Library and Google Scholar. The retrieval time was from January 1, 2000 to May 1, 2022.

Results

Obtain the exact amount of effect of different exercise programs on the mood improvement of elderly depression patients. This study will provide more convincing evidence for the effect of physical exercise on improving the mood of the elderly with depression. In addition, by comparing the effects of different exercise programs, the best program for the depression of elderly people with depression can be obtained, and some specific exercise suggestions can be provided for clinical practice, so as to promote the successful aging of the elderly.

Ethics and dissemination

As this research is a systematic review of published literature, ethical approval is not required. The results will be reported according to the latest guidelines for Preferred Reporting Items for Systematic Reviews and Meta-Analyses 2020 statement, and will be submitted to a peer-reviewed journal.

PROSPERO registration number

CRD42021250602.

Strengths and limitations of this study

The planned systematic review will systematically report on the improvement of different types of exercise in elderly patients with depression.

This protocol describes a comprehensive search strategy and eligibility criteria, which have no geographical restriction.

The systematic review might be limited by the presence of selection and/or attrition bias inherent in some of the selected studies.

Find the best exercise prescription for older adults with depression

As with many reviews, the results may yield significant heterogeneity among the included studies.
Analysis of 16S rRNA gene sequence of nasopharyngeal exudate from healthy donors reveals changes in key microbial communities associated with aging
Authors: Candel Sergio , Pérez-Sanz Fernando , Tyrkalska Sylwia D. , Moreno-Docón Antonio , Esteban Ángel , L. Cayuela María , Mulero Victoriano
Published: June 2022

Background

Functional or compositional perturbations of the microbiome can occur at different sites of the body and this dysbiosis has been linked to various diseases. Changes in the nasopharyngeal microbiome are associated to patient’s susceptibility to multiple viral infections, including COVID-19, supporting the idea that the nasopharynx may be playing an important role in health and disease. Most studies on the nasopharyngeal microbiome have focused on a specific component in the lifespan, such as infanthood or the elderly, or have other limitations such as low sample sizes. Therefore, detailed studies analyzing the age- and sex-associated changes in the nasopharyngeal microbiome of healthy people across their whole life are essential to understand the relevance of the nasopharynx in the pathogenesis of multiple diseases, particularly viral infections such as COVID-19.

Results

120 nasopharyngeal samples from healthy subjects of all ages and both sexes were analyzed by 16s rRNA sequencing. Nasopharyngeal bacterial alpha diversity did not vary in any case between age or sex groups. Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes were the predominant phyla in all the age groups, with several sex-associated differences probably due to the different levels of sex hormones between both sexes. Acinetobacter, Brevundimonas, Dolosigranulum, Finegoldia, Haemophilus, Leptotrichia, Moraxella, Peptoniphilus, Pseudomonas, Rothia, and Staphylococcus were the only 11 bacterial genera that presented significant age-associated differences. Other bacterial genera such as Anaerococcus, Burkholderia, Campylobacter, Delftia, Prevotella, Neisseria, Propionibacterium, Streptococcus, Ralstonia, Sphingomonas, and Corynebacterium appeared in the population with a very high frequency, suggesting that their presence might be biologically relevant.

Conclusions

In contrast to other anatomical areas such as the gut, bacterial diversity in the nasopharynx of healthy subjects remains very stable and resistant to perturbations throughout the whole life and in both sexes. Age-associated changes in taxonomic composition were observed at phylum, family, and genus levels, as well as several sex-associated changes probably due to the different levels of sex hormones present in both sexes at certain ages. Our results provide a complete and valuable dataset that will be useful for future research aiming for studying the relationship between changes in the nasopharyngeal microbiome and susceptibility to or severity of multiple diseases, including COVID-19.
Population genomic insights into the evolution of the SARS-CoV-2 Omicron variant
Authors: Garg Kritika M. , Lamba Vinita , Chattopadhyay Balaji
Published: June 2022

A thorough understanding of the patterns of population subdivision of a pathogen can prevent disease spread. For SARS-CoV-2, the availability of millions of genomes makes this task analytically challenging. Our study used population genomic methods and identified subtle subdivisions within the Omicron variant, in addition to that captured by the Pango lineage. Further, some of the identified clusters of the Omicron variant revealed statistically significant signatures of selection or expansion revealing the role of microevolutionary processes in the spread of the virus. These are crucial information for policy makers as preventive measures can be designed to mitigate further spread based on a holistic understanding of the variability of the virus and evolutionary processes aiding its spread.
Screening for Pathogenic Variants in Cardiomyopathy Genes Predicts Mortality and Composite Outcomes in UK Biobank
Authors: Asatryan Babken , Shah Ravi A. , Dabbagh Ghaith Sharaf , Landstrom Andrew P. , Darbar Dawood , Khanji Mohammed Y , Lopes Luis R. , Duijvenboden Stefan van , Muser Daniele , Lee Aaron Mark , Haggerty Christopher M. , Arora Pankaj , Semsarian Christopher , Reichlin Tobias , Somers Virend K. , Owens Anjali T. , Petersen Steffen E. , Deo Rajat , Munroe Patricia B , Aung Nay , Chahal C. Anwar A.
Published: June 2022

Background

Inherited cardiomyopathies can present with broad variation of phenotype. Data are limited regarding genetic screening strategies and outcomes associated with putative pathogenic variants (PuPV) in cardiomyopathy-associated genes in the general population.

Objective

We aimed to determine the risk of mortality and cardiomyopathy-related outcomes associated with PuPV in cardiomyopathy-associated genes in UK Biobank.

Methods

Using whole exome sequencing data, variants in dilated, hypertrophic and arrhythmogenic cardiomyopathy-associated genes with at least limited evidence of disease causality according to ClinGen Expert Panel curations, were annotated using REVEL (≥0.65) and ANNOVAR (predicted loss of function) to identify PuPVs. Individuals with PuPV comprised the genotype-positive (G+) and those without PuPV the genotype-negative (G-) cohorts. Group comparisons were made using time-to-event analyses for the primary (all-cause mortality) and secondary outcomes (diagnosis of cardiomyopathy; composite outcome of diagnosis of cardiomyopathy, heart failure, arrhythmia, stroke, and death).

Results

Among 200,619 participants, 22,401 (11.2%) were found to host ≥1 PuPV in cardiomyopathy-associated genes (G+). After adjusting for age and sex, G+ individuals had increased all-cause mortality [HR 1.07 (95%CI 1.02-1.13; p=0.011)] and increased rates of diagnosis of cardiomyopathy later in life [HR 2.37 (95%CI 1.98-2.85; p<0.0001)], which further increased in those with PuPV in definitive/strong evidence ClinGen genes [3.25 (95%CI 2.63-4.00; p<0.0001)]. G+ individuals had a higher risk of developing the composite outcome [HR 1.11 (95%CI 1.06-1.15; p<0.0001)].

Conclusions

Adults with PuPV in cardiomyopathy-associated genes have higher all-cause mortality and increased risk of developing cardiomyopathy-associated features and complications, compared to genotype-negative controls.

Condensed Abstract

Leveraging the UK Biobank prospective cohort, we analyzed whole exome sequencing data in dilated, hypertrophic and arrhythmogenic cardiomyopathy-associated genes using a population screening ‘genotype-first’ approach. Individuals with putative pathogenic variants in genes implicated in cardiomyopathies showed an increased risk of all-cause mortality, higher risk of developing clinical cardiomyopathy later in life, and higher risk of a composite outcome (cardiomyopathy, heart failure, arrhythmia, stroke, and death) compared to genotype-negative controls. These findings highlight the potential role of ‘genotype-first’ approach in elevating personalized medicine into population level precision health in the future.
Sparse Parallel Independent Component Analysis and Its Application to Identify Stable and Replicable Imaging-genomic Association Patterns in UK Biobank
Authors: Duan Kuaikuai , Chen Jiayu , Fu Zening , Silva Rogers F. , Calhoun Vince D. , Dell’Orco Michela , Perrone-Bizzozero Nora I , Du Yuhui , Jiang Wenhao , Liu Jingyu
Published: June 2022

Data fusion analyses of brain imaging and genomics enable the linking of genomic factors to brain patterns. Due to the small to modest effect sizes of common genetic variants, it is usually challenging to reliably identify relevant genetic factors from the rest of the genome with the typical sample size in neuroimaging studies. To alleviate this problem, we propose sparse parallel independent component analysis (spICA) to leverage the sparsity of individual genomic sources, building upon the existing parallel independent component analysis (pICA) algorithm. Sparsity is enforced by performing Hoyer projection on the estimated independent sources. Simulation results demonstrate that spICA yields improved recovery of imaging-genomic associations and sources compared to pICA. We applied spICA to whole-brain gray matter volume (GMV) and whole-genome single nucleotide polymorphisms (SNPs) data of five different sets of 24,985 discovery samples in the UK Biobank. We identified three GMV sources significantly and stably associated with one SNP source and replicated these associations. GMV sources highlighted frontal, parietal, and temporal regions. Their corresponding loadings on individuals were related to multiple cognitive measures, and the temporal region interacts with age influencing cognition. The SNP component underscored SNPs in chromosome 17 that were enriched in the inflammation response pathway and in regulation effect in the prefrontal cortex via gene expression, methylation, transcription expression, and isoform percentage.
System-wide profiling by proteome integral solubility alteration assay of drug residence times for target characterization
Authors: Sabatier Pierre , Beusch Christian M. , Meng Zhaowei , Zubarev Roman A.
Published: June 2022

Most drugs used in the clinic and drug candidates target multiple proteins, and thus detailed characterization of their efficacy targets is required. While current methods rely on quantitative measurements at thermodynamic equilibrium, kinetic parameters such as the residence time of a drug on its target provide a better proxy for efficacy in vivo. Here, we present Residence Time Proteome Integral Solubility Alteration (ResT-PISA) assay which provides monitoring temporal protein solubility profiles after drug removal (“off-curve”) in cell lysate or intact cells, quantifying the lifetime of drug-target interaction. A compressed version of the assay measures the integral under the off-curve enabling the multiplexing of binding affinity and residence time assessments into a single proteomic analysis. We introduce a combined scoring system for three parametric dimensions to improve prioritization of targets. By providing complementary information to other characteristics of drug-target interaction, ResT-PISA approach will be useful in drug development and precision medicine.
The RNA demethylase FTO controls m6A marking on SARS-CoV-2 and classifies COVID-19 severity in patients
Authors: Malbec Lionel , Celerier Margot , Bizet Martin , Calonne Emilie , Hofmann-Winkler Heike , Boeckx Bram , Abdelnabi Rana , Putmans Pascale , Hassabi Bouchra , Naesens Lieve , Lambrechts Diether , Pöhlmann Stefan , Deplus Rachel , Delang Leen , Jeschke Jana , Fuks François
Published: June 2022

The RNA modification N6-methyladenosine (m6A) plays a key role in the life cycles of several RNA viruses. Whether this applies to SARS-CoV-2 and whether m6A affects the outcome of COVID-19 disease is still poorly explored. Here we report that the RNA demethylase FTO strongly affects both m6A marking of SARS-CoV-2 and COVID-19 severity. By m6A profiling of SARS-CoV-2, we confirmed in infected cultured cells and showed for the first time in vivo in hamsters that the regions encoding TRS_L and the nucleocapsid protein are multiply marked by m6A, preferentially within RRACH motifs that are specific to β-coronaviruses and well conserved across SARS-CoV-2 variants. In cells, downregulation of the m6A demethylase FTO, occurring upon SARS-CoV-2 infection, increased m6A marking of SARS-CoV-2 RNA and slightly promoted viral replication. In COVID-19 patients, a negative correlation was found between FTO expression and both SARS-CoV-2 expression and disease severity. FTO emerged as a classifier of disease severity and hence a potential stratifier of COVID-19 patients.
Constraints of vigilance-dependent noradrenergic signaling to mouse cerebellar Bergmann glia
Authors: Salinas-Birt Angelica , Zhu Xiangyu , Lim Eunice Y. , Santory Aryana J. Cruz , Ye Liang , Paukert Martin
Published: June 2022

Behavioral state plays an important role in determining astroglia Ca2+signaling. In particular, locomotion-mediated elevated vigilance has been found to trigger norepinephrine-dependent whole cell Ca2+elevations in astroglia throughout the brain. For cerebellar Bergmann glia it has recently been found that locomotion-induced transient Ca2+elevations depend on their α1A-adrenergic receptors. With increasing availability and implementation of locomotion as behavioral parameter it becomes important to understand the constraints of noradrenergic signaling to astroglia. Here we evaluated the effect of speed, duration and interval of locomotion on Ca2+signals in Bergmann glia as well as cerebellar noradrenergic axon terminals. We found almost no dependence on locomotion speed, but following the initial Ca2+transient prolonged locomotion events revealed a steady-state Ca2+elevation. Comparison of time course and recovery of transient Bergmann glia and noradrenergic terminal Ca2+dynamics suggested that noradrenergic terminal Ca2+activity determines Bergmann glia Ca2+activation and does not require noradrenergic receptor desensitization to account for attenuation during prolonged locomotion. Further, analyzing the correlation among Ca2+dynamics within regions within the field of observation we found that coordinated activity among noradrenergic terminals accounts for fluctuations of steady-state Bergmann glia Ca2+activity. Together, our findings will help to better understand astroglia Ca2+dynamics during less controlled awake behavior and may guide the identification of behavioral contexts preferably dependent on astroglia Ca2+signaling.
Ancient brainstem inhibitory neurons control selective spatial attention
Authors: Kothari Ninad B. , Banerjee Arunima , Zhang Qingcheng , You Wen-Kai , Mysore Shreesh P.
Published: June 2022

To behave adaptively in complex environments, animals must selectively process the most important information in space while ignoring distractors. Contrary to the dominant cortico-centric view, we report that an evolutionarily old group of inhibitory neurons in the brainstem, called PLTi, is critical for this function of selective spatial attention. In freely behaving mice performing a human-like spatial attention task, we found that bilateral silencing of PLTi severely disrupted target selection without causing perceptual or motor impairments. PLTi’s effects depended necessarily on goal-relevant, rather than just physical salience-based signals, together revealing it as a dedicated brain site for priority-driven attentional target selection. PLTi’s core computational function is its explicit implementation of the abstract cognitive decision boundary separating target from distracters: it controlled the accuracy and categorical precision of this decision boundary, doing so by shaping neural representations of competing stimuli in the superior colliculus, a major sensorimotor hub. PLTi may, therefore, be a conserved brainstem engine across vertebrates for winner-take-all-like spatial decisions in goal-driven behavior.
CROP-Seq: a single-cell CRISPRi platform for characterizing candidate genes relevant to metabolic disorders in human adipocytes
Authors: Bielczyk-Maczynska Ewa , Sharma Disha , Blencowe Montgomery , Gustafsson Peter Saliba , Gloudemans Michael J. , Yang Xia , Carcamo-Orive Ivan , Wabitsch Martin , Svensson Katrin J. , Park Chong Y. , Quertermous Thomas , Knowles Joshua W. , Li Jiehan
Published: June 2022

Objective

CROP-Seq combines gene silencing using CRISPR interference (CRISPRi) with single-cell RNA sequencing (scRNA-Seq) to conduct a functional reverse genetic screen of novel gene targets associated with adipocyte differentiation or function, with single-cell transcriptomes as the readout.

Methods

We created a human preadipocyte SGBS cell line with stable expression of KRAB-dCas9 for CRISPRi-mediated gene knock-down. This line was transduced with a lentiviral library of sgRNAs targeting 6 genes of interest (3 sgRNAs / gene, 18 sgRNAs), 6 positive control genes (3 sgRNAs / gene, 18 sgRNAs), and non-targeting control sgRNAs (4 sgRNAs). Transduced cells were selected and differentiated, and individual cells were captured using microfluidics at day 0, 4 and 8 of adipogenic differentiation. Next, expression and sgRNA libraries were created and sequenced. Bioinformatic analysis of resulting scRNA-Seq expression data was used to determine the effects of gene knock-down and the dysregulated pathways, and to predict cellular phenotypes.

Results

Single-cell transcriptomes obtained from SGBS cells following CRISPRi recapitulate different states of differentiation from preadipocytes to adipocytes. We confirmed successful knock-down of targeted genes. Transcriptome-wide changes were observed for all targeted genes, with over 400 differentially expressed genes identified per gene at least at one timepoint. Knock-down of known adipogenesis regulators PPARG and CEBPB inhibited adipogenesis. Gene set enrichment analyses revealed molecular processes for adipose tissue differentiation and function for novel genes. MAFF knock-down led to a downregulation of transcriptional response to proinflammatory cytokine TNF-α in preadipocytes. TIPARP knock-down resulted in an increase in the expression of a beiging marker UCP1 at D8 of adipogenesis.

Conclusions

The CROP-Seq system in SGBS cells can determine the consequences of target gene knock-down at the transcriptome level. This powerful, hypothesis-free tool can identify novel regulators of adipogenesis, preadipocyte and adipocyte function associated with metabolic disease.

Highlights

CRISPR interference screen coupled with single-cell RNA sequencing (CROP-Seq)

Parallel screening of 12 genes in human SGBS adipocytes and preadipocytes

Uncovered novel regulators of adipogenesis and adipocyte function

Graphical abstract
Structure-Uptake Relationship Studies of Oxazolidinones in Gram-negative ESKAPE Pathogens
Authors: Hu Ziwei , Leus Inga V. , Chandar Brinda , Sherborne Bradley , Avila Quentin P. , Rybenkov Valentin V. , Zgurskaya Helen I. , Duerfeldt Adam S.
Published: June 2022

To date, little is known about applicability and/or generality of molecular features and how they impact small molecule permeation into Gram-negative bacteria. Identifying motifs or structural trends that correlate with broad and/or species-specific permeation would enable the rational design of new antibacterials. The clinical success of linezolid for treating Gram-positive infections paired with the high conservation of bacterial ribosomes predicts that if oxazolidinones were engineered to accumulate in Gram-negative bacteria, then this pharmacological class would find broad utility in eradicating infections. Here we report an investigative study of a strategically designed library of oxazolidinones to determine the effects of molecular structure on accumulation and biological activity.E. coli, A. baumannii, andP. aeruginosastrains with varying degrees of compromise (in efflux and outer membrane) were used to identify motifs that hinder permeation across the outer-membrane and/or enhance efflux susceptibility broadly and specifically between species. The results of this study illustrate that small changes in molecular structure are enough to overcome the efflux and/or permeation issues of this scaffold. Three oxazolidinone analogs (3e,12f, and14) were identified from this study that exhibit activity against all three pathogens assessed, a biological profile not observed for linezolid.
Mex67 paralogs mediate division of labor in trypanosome RNA processing and export
Authors: Obado Samson O. , Stein Milana , Hegedűsová Eva , Zhang Wenzhu , Hutchinson Sebastian , Brillantes Marc , Glover Lucy , Paris Zdeněk , Chait Brian T. , Field Mark C. , Rout Michael P.
Published: June 2022

In opistokhonts (animals and fungi), mRNA export to the cytoplasm is mediated by the Mex67/Mtr2 (NXF1/NXT1) heterodimer via the nuclear pore complex (NPC). In contrast to most nucleocytoplasmic transport, mRNA export requires ATP-dependent remodeling machinery, and in animals and fungi is Ran-independent. While most eukaryotes possess one Mex67 gene, trypanosomes have three distinct Mex67 paralogs, while retaining a single Mtr2 gene. We show here that these paralogs, TbMex67, TbMex67b and TbMex67L, have differing and non-redundant roles in RNA export. Specifically, TbMex67 and TbMex67b retain a canonical role in mRNA export, albeit associating with specific mRNA cohorts, but in contrast, TbMex67L is primarily involved in ribosome biogenesis. Together with the association of all Mex67 paralogs with the Ran machinery, these findings indicate significant departures in RNA export mechanisms in these divergent organisms, with implications for evolutionary origins and diversity in control of gene expression.