bluuebunny/crossref_metadata_2025 huggingface dataset:
Teaching Microbial Genomics in the COVID-19 age: principles, theory, and practice
Authors: Stach Jem , Marles-Wright Jon , Montero-Calasanz Maria del Carmen
Published: May 2022

The importance of genomics in the COVID-19 age cannot be overstated and genomics has a key place in the advanced undergraduate microbiology curriculum. The COVID-19 pandemic, and its attendant lockdowns, have necessitated a change in the delivery of our microbial genomics module. The key challenges for delivering a remote computer-based genomics module, are ensuring student engagement and learning; and supporting the technical aspects of remote computer work.

In the absence of in-person classes, we have adapted our material covering the principles and theory of microbial genomics, to asynchronous videos and synchronous online workshops. Practical training for all undergraduate microbiologists in the UK has been severely reduced, which has forced us to focus skills training towards computational aspects of genome assembly, analysis, and interpretation. The set up and implementation of a robust and scalable Linux-based genome analysis pipeline for students presents many challenges: from organising remote access to computer clusters; software support; and managing hardware.

Assessment for the module is based on the demonstrating learning and skills development through the analysis of SARS-CoV2 genomes to identify spike protein variation and mapping this to published structures. Terminal assessment is through the analysis of newly sequenced bacterial genomes and the preparation of a genome report suitable for publication.

We will outline the implementation and management of our Microbial Genomics module as a model for computer-based skills training for undergraduate microbiologists. Furthermore, we will discuss the impact of the COVID-19 pandemic on the module and the opportunities it has presented.
A Campylobacter integrative conjugative element with a CRISPR-Cas9 system targeting competing plasmids: a history of plasmid warfare?
Authors: Vliet Arnoud van , Charity Oliver , Reuter Mark
Published: May 2022

Microbial genomes are highly adaptable, with mobile genetic elements such as integrative conjugative elements (ICE) mediating the dissemination of new genetic information throughout bacterial populations. This is countered by defence mechanism such as CRISPR-Cas systems, which limit invading mobile elements by targetting specific sequences on these elements. Here we have studied the distribution the pVir, pTet and PCC42 plasmids and a new 70-129 kb ICE (CampyICE1) in the foodborne microbial pathogens Campylobacter jejuni and Campylobacter coli. CampyICE1 contains a degenerated Type II-C CRISPR system consisting of a sole Cas9 protein, which is distinct from the previously described Cas9 proteins from C. jejuni andC. coli. CampyICE1 is highly conserved in structure and gene order, containing blocks of genes predicted to be involved in recombination, regulation and conjugation. CampyICE1 was detected in 134/5,829 (2.3%) C. jejunigenomes and 92/1,347 (6.8%) C. coligenomes. Similar ICE were detected in a number ofnon-jejuni/coli Campylobacter species, which lacked a CRISPR-Cas system. Finally, CampyICE1 contained 3 separate short CRISPR spacer arrays, and a total of 124 unique spacers were identified, of which 67 are predicted to target the Campylobacterplasmids pVir, pTet, and pCC42, and 12 predicted to target other Campylobacter plasmids (63.7%). The presence of a functional CampyICE1 Cas9 protein and matching anti-plasmid spacers was associated with the absence of these plasmids (186/214 genomes), implicating that the CampyICE1-encoded CRISPR-Cas has contributed the exclusion of competing plasmids. Hence the CampyICE1 CRISPR-Cas system may be a part of ongoing plasmid warfare in Campylobacter spp.
Recombination, and Then What? How Zika Virus Hybrids Improve Their Fitness
Authors: Dermendjieva Michaela , Donald Claire , Kohl Alain , Evans David
Published: May 2022

Zika virus (ZIKV) is an emerging flavivirus primarily transmitted through the bite of Aedesmosquitoes. It spread explosively around the tropics in the 21st century, and still presents a threat to human health. There is a need to better understand the drivers of emergence of ZIKV and likely consequences of its future evolution. RNA recombination is a process of genetic exchange which occurs in positive-sense RNA viruses and contributes to virus evolution. We have developed a recombinant-specific PCR assay for detection of ZIKV recombinants in mammalian and insect cell co-infections. Using this system, we demonstrated the ability of distinct geographic and genetic isolates to recombine and tested their viability in tissue culture. Initial ZIKV recombinants produce plaques with a significantly smaller diameter than either parental strain. Recombinant large-plaque variants were isolated through serial passage and plaque purification, and the genome analysed for adaptive mutations. A single nucleotide coding mutation in NS1 was detected in several independent large-plaque variants. The role of this mutation in virus replication was investigated through reverse genetics to assess whether it gave the recombinant a replicative advantage. Understanding the genetic changes that arise during, and following recombination is important in the context of virus evolution. It is particularly relevant for ZIKV, as co-circulation of the African and Asian strains of ZIKV in nature has already occurred in parts of Latin America and Africa. Current and future studies will focus on the phenotype of recombinant ZIKV, their replication in mammalian and insect cell lines, and in mosquitoes.
Understanding the Role of Norovirus VP1 in Viral Infectivity and Persistence
Authors: Mills Jake , Snowden Joseph , Herod Morgan
Published: May 2022

Human noroviruses (HNV) are a prevalent cause of gastroenteritis that contribute to >200,000 deaths each year and cost >£40 billion worldwide per annum. There is currently no approved vaccine or therapy, and a greater understanding of the virus life-cycle could help develop new approaches towards disease control. Although HNV infection is usually self-limiting, persistent infections can establish in immunocompromised people - however the underlying mechanisms are poorly understood. Our studies use the murine norovirus (MNV) model system to investigate fundamental virus biology, and several strains of MNV can also persist in the murine host. The primary receptor for MNV, CD300lf, interacts with a network of amino acids (AAs) on the protruding domain of the virus major capsid protein (VP1). We hypothesised that genetic variations leading to changes within this network of AAs could influence the VP1-CD300lf interaction and viral persistence.

Bioinformatic analysis of the VP1-receptor interface highlighted variation in just a single AA that correlates with persistent MNV strains. To confirm this AA is important for receptor interactions we conducted in vitro evolution experiments on suspension or adherent grown cells. Passage through suspension cells resulted in the selection of hydrophobic residues at this position co-incidental with a 1.5-fold increase in viral titre. In contrast, small polar residues were maintained at this position during passage on adherent cells. Furthermore, infectivity assays with infectious clones suggest that hydrophobic residues favour infection of suspension cells over adherent cells. Work is ongoing to understand the importance of this AA on viral infectivity and persistence.
Control Of Hepatitis E Virus Polyprotein Processing By Cellular Proteases
Authors: Pierce Danielle M. , Buchanan Frazer J. T. , Cox Abigail , Stonehouse Nicola J. , Herod Morgan R.
Published: May 2022

Hepatitis E Virus (HEV) is one of the leading causes of acute viral hepatitis, with ~20 million HEV infections worldwide per annum, and mortality rates up to 25% in pregnant women. However, many aspects of the biology of the virus are poorly understood. HEV has a positive-sense single-stranded RNA genome. ORF1 encodes the non-structural polyprotein required for viral RNA replication. This polyprotein (sometimes termed pORF1) is predicted to contain seven domains based on sequence homology to related viruses and it is hypothesised that this polyprotein must undergo proteolysis to generate functional protein units. However, it is unknown if the pORF1 polyprotein undergoes full proteolysis, the potential locations of any cleavage boundaries and whether a viral or host cell protease is responsible.

We have adapted our in vitro-based proteolysis assays to investigate cleavage of HEV pORF1. In comparison to related RNA viruses, our data suggest that pORF1 has no auto-catalytic activity. Previous studies have shown that the liver-produced protease, thrombin, is essential for replication. In the presence of thrombin, we have shown that the ORF1 polyprotein undergoes specific proteolysis to produce eight distinct protein products. Combining bioinformatics with pORF1 truncations/mutagenesis, we have located the position of the pORF1 thrombin cleavage sites. Interestingly, these cleavage sites correspond to the junctions between the predicted pORF1 protein domains. Our data suggests that thrombin is an important cellular protease for controlling pORF1 proteolysis. Work is ongoing to understand the importance of each thrombin cleavage site in viral replication.
Identification of Residues within Flavivirus Non-Structural Protein Associated with Mosquito Transmission
Authors: Vamos Boglarka , Cheung Yin , Maringer Kevin
Published: May 2022

Flavivirus non-structural protein 1 (NS1) is present at high levels in patient blood and has been previously implicated in increasing virus acquisition by mosquito vectors, which may facilitate increased transmission. Therefore, flaviviruses transmitted by Aedes aegypti mosquitoes were hypothesised to have similarities within NS1, and potentially other NS proteins, that may correlate with mosquito-borne (rather than tick-borne or no vector) transmission. Representative flavivirus amino acid sequences were downloaded from the NCBI Protein database, aligned using viprbrc.org and then manually analysed to identify residues correlating with arthropod vector tropism. All available sequences for individual clinically important flaviviruses were then analysed on viprbrc.org to determine sequence conservation within viral species for those residues correlating with vector tropism. Overall, we found five residues in NS1 that were highly correlated with transmission by mosquitoes, had functionally relevant differences in amino acid side chain properties between mosquito- and tick-borne viruses and had conservation within viral species. Additionally, a further nine residues in NS3 and four residues in NS4A were identified using the same methodology. Importantly, for NS1, for which more data is available regarding its role in influencing transmission, the residues we identified have not been implicated in increased transmission thus far. Hence, future work would aim to test the impact of mutating these NS1 residues to elucidate whether they modulate NS1 secretion into the blood stream, virus replication and/or transmission. Gaining an understanding of the molecular determinants underpinning vector tropism could be useful in the creation of transmission-incompetent vectors.
Comparison of lentiviral and vesicular stomatitis virus core SARS-CoV-2 pseudotypes and generation of a stable cell line for use in antibody neutralisation assays
Authors: Neto Martin Mayora , Cantoni Diego , Genova Cecilia di , Scott Simon , Derveni Mariliza , Wright Edward , Temperton Nigel
Published: May 2022

Betacoronavirus SARS-CoV-2, the causative agent of COVID19, is a single stranded positive sense RNA virus. Since its emergence there has been great efforts to identify correlates of protection,which is crucial for vaccine evaluation studies. However, handling SARS-CoV-2 requires BSL-3 containment facilities slowing research efforts. Pseudotype viruses (PV) are a safe alternative to authentic virus that can be handled at low containment. PVs are chimeric viruses containing the core of a virus where its genome has been completely or partially replaced by a reporter gene, displaying a correctly folded SARS-CoV-2 spike on its surface. We developed lentiviral and vesicular stomatitis virus (VSV) core PVs alongside a stable A549 cell line expressing receptor ACE2 and protease TMPRSS2 responsible for S protein priming, for use in neutralization assays. Lentiviral PVs were generated by transfection with plasmids encoding the spike, HIV-1 gag-pol and a luciferase reporter. For VSV PVs, producer cells pre-transfected with the spike were infected with recombinant VSV expressing luciferase,before harvesting. The stable A549 cell line was generated by sequential infection of VSV-G PVs bearing lentiviral vectors encoding ACE2 and TMPRSS2 genes followed by antibiotic selection, before being tested in neutralization assays. We compared lentiviral and VSV PV platforms using monoclonal antibodies and convalescent sera with our stable A549 cells or HEK293T cells pre-transfected with plasmids encoding ACE2 and TMPRSS2. Antibody titres showed equivalence however VSV had the advantage of a shorter incubation therefore enabling a higher throughput. PVs offer a robust platform for future seroepidemiology and vaccine evaluation studies.
SARS-CoV-2 Spike has broad tropism for mammalian ACE2 proteins yet exhibits a distinct pattern of receptor usage when compared to other β-coronavirus Spike proteins
Authors: Conceicao* Carina , Thakur* Nazia , Human Stacey , Kelly James T , Logan Leanne , Bialy Dagmara , Bhat Sushant , Stevenson-Leggett Phoebe , Zagrajek Adrian K , Hollinghurst Philippa , Varga Michal , Tsirigoti Christina , Tully Matthew , Chiu Chris , Moffat Katy , Silesian Adrian Paul , Hammond John A , Maier Helena J , Bickerton Erica , Shelton Holly , Dietrich Isabelle , Graham Stephen C , Bailey Dalan
Published: May 2022

The Coronavirus Disease 2019 (COVID-19) pandemic, caused by SARS Coronavirus 2 (SARS-CoV-2), continues to cause significant mortality in human populations worldwide. SARS-CoV-2 has high sequence similarity to SARS-CoV and other related coronaviruses circulating in bats. It is still unclear whether transmission occurred directly from bats to humans, or through an intermediate host, bringing into question the broader host range of SARS-CoV-2. Using a combination of low biocontainment entry assays as well as live virus, we explored the receptor usage of SARS-CoV-2 using angiotensin-converting enzyme 2 (ACE2) receptors from 22 different species. We demonstrated that in addition to human ACE2, the Spike of SARS-CoV-2 has broad tropism for other mammalian ACE2s, including dog, cat and cattle. However, comparison of SARS-CoV-2 receptor usage to the related SARS-CoV and bat coronavirus, RaTG13, identified distinct patterns of receptor usage, with the two human viruses being more closely aligned. Finally, using bioinformatics, structure analysis and targeted mutagenesis, we identified key residues at the Spike-ACE2 interface which may have played a pivotal role in the emergence of SARS-CoV-2 in humans, some of which are also mutated in newly circulating variants of the virus. To summarise, the broad tropism of SARS-CoV-2 at the point of viral entry identifies the potential risk of infection of a wide range of companion animals, livestock and wildlife.
Genomic and Phenotypic Characterisation of Multi-Drug ResistantEscherichia coli carried by meat handlers and slaughterhouse meat from North-Western Tanzania
Authors: MacFadyen Alison , Seni Jeremiah , Moremi Nyambura , Silago Vitus , Mshana Stephen E. , Oravcová Katarina
Published: May 2022

Our research is part of a larger project Supporting the National Action Plan on Antimicrobial Resistance (SNAP-AMR) in Tanzania. The aspect of this work is to determine the AMR carriage and associated mobile genetic elements of extended spectrum β-lactamase (ESBL) producing Escherichia coli within the community of Mwanza, in North-Western Tanzania. From 54 slaughterhouses a total of 322 E. coli isolates were obtained from raw meat, with 210 originating from meat handlers. Initial antimicrobial susceptibility testing identified 71 (22%) and 27 (13%) of the meat and meat handler isolates, respectively, as being ESBL E. coli. ST2852 was the most abundant MLST, followed by globally disseminated and ESBL associated ST38. Whole genome sequencing and phenotypic analysis revealed 88% of our isolates were resistant to three or more antimicrobial classes. On average, our isolates carried at least 10 different AMR associated genes, with 80% having one or more AMR conferring chromosomal mutation. In relation to ESBL, 88 out of 98 of the isolates carried the globally disseminated allotype blaCTX-M-15, with over 55% of the isolates encoding blaCTX-M-15on multi-drug resistant (MDR) plasmids. The remaining strains encoded one of three different blaCTX-Mallotypes. Our data highlights high prevalence of MDR ESBL E. coli within the community and its potential risk of transmission through the food chain. In our future work, we will combine these community carriage data with our work on ESBL Enterobacteriaceae carriage and infection within healthcare settings, to evaluate the genomic epidemiology of ESBL organisms in this region.
KNOWLEDGE AND AWARENESS OF OSTEOPOROSIS AMONG 144 YOUNG WOMEN AT CALMETTE HOSPITAL
Authors: Satha SUM , Putthimundul UY
Published: May 2022

Objectives

To evaluate the level of knowledge and awareness about osteoporosis of young women at Calmette hospital.

Methods

We conveniently selected 144 women based on the selecting criteria. They were interviewed in Khmer language, face-to-face using structured-questionnaire which include demographic characteristic, lifestyle information, knowledge of osteoporosis and interest in an osteoporosis prevention.

Results

The average age of the participants was 28.43 (±4.42) years. Self-employed represented a large proportion. The study showed that only one fourth of participants went to a higher education. Most of the participants stated that they have known about osteoporosis while friends or family was the most common source of information. Only 16.67% have known osteoporotic patient. Most of them have a moderately bone-friendly lifestyle. Their calcium source depended largely on green vegetable. The average mean score of knowledge was 9.34 (±3.08) (range from 0 to 20). However, a half of them worried about suffering of osteoporosis in their later years of life. Around two thirds wanted to undergo an osteoporosis screening test. A majority was interested in osteoporosis prevention. Social media and community outreach were recommended as sensitizing measures. The osteoporosis knowledge was only correlated significantly (P-value: 0.007) with educational level.

Conclusion

Despite of low level of knowledge of osteoporosis, young Cambodian women was interested in osteoporosis screening and prevention. Educational intervention, such as public awareness programs regarding a bone-friendly lifestyle and osteoporosis screening, is crucial in sensitizing the general population about osteoporosis and its complication.
Fast and Accurate Species Trees from Weighted Internode Distances
Authors: Liu Baqiao , Warnow Tandy
Published: May 2022

Species tree estimation is a basic step in many biological research projects, but is complicated by the fact that gene trees can differ from the species tree due to processes such as incomplete lineage sorting (ILS), gene duplication and loss (GDL), and horizontal gene transfer (HGT), which can cause different regions within the genome to have different evolutionary histories (i.e., “gene tree heterogeneity”). One approach to estimating species trees in the presence of gene tree heterogeneity resulting from ILS operates by computing trees on each genomic region (i.e., computing “gene trees”) and then using these gene trees to define a matrix of average internode distances, where the internode distance in a tree T between two species x and y is the number of nodes in T between the leaves corresponding to x and y. Given such a matrix, a tree can then be computed using methods such as neighbor joining. Methods such as ASTRID and NJst (which use this basic approach) are provably statistically consistent, very fast (low degree polynomial time) and have had high accuracy under many conditions that makes them competitive with other popular species tree estimation methods. In this study, inspired by the very recent work of weighted ASTRAL, we present weighted ASTRID, a variant of ASTRID that takes the branch uncertainty on the gene trees into account in the internode distance. Our experimental study evaluating weighted ASTRID shows improvements in accuracy compared to the original (unweighted) ASTRID while remaining fast. Moreover, weighted ASTRID shows competitive accuracy against weighted ASTRAL, the state of the art. Thus, this study provides a new and very fast method for species tree estimation that improves upon ASTRID, has comparable accuracy with the state of the art while remaining much faster. Weighted ASTRID is available at https://github.com/RuneBlaze/internode.
Overuse in US Medicare during the COVID-19 pandemic: 2020 versus 2019
Authors: Chalmers Kelsey , Brownlee Shannon , Gopinath Valérie , Saini Vikas
Published: May 2022

Background

The COVID-19 pandemic and March 2020 shutdown in the US reduced the volume of healthcare services, but the impact on overuse has not been investigated.

Objective

To examine the change in overuse rates and volumes through 2020.

Design

A retrospective cohort study using Medicare fee-for-service claims.

Setting

Outpatient and inpatient claims.

Participants

Patients who met the criteria for one of 10 overuse measures with a claim between January 1 2019 to December 31 2020.

Measurements

Overuse volumes were reported as patients with claims meeting overuse metric criteria per 100,000 Medicare beneficiaries. Overuse rates were measured by the same overuse cohort per 100 patients meeting the denominator criteria of the metric. Rates in 2020 were compared to the same date period in 2019 using incidence rate ratios (IRRs) estimated from Poisson regressions.

Results

In 2019, 302,379 patients had an overuse claim (14.72% of 2,053,792 patients in the cohort) versus 234,481 (13.79% of 1,699,807) in 2020. The overall cohort included 2,112,904 (61.0%) women and a mean (SD) age of 76.5 (8.1) years. There was a 52.3% decrease in overall cohort volume during the COVID-19 shutdown; 2,341,017 patients in 2020 versus 4,912,453 in 2019. There was a 72.57% decrease in patients with an overuse procedure between April 2019 (N = 11,794) and 2020 (N = 3,220) (IRR 0.27 (95% CI 0.25 to 0.3; p <0.001)), including spinal fusion/laminectomy, carotid endarterectomy, knee arthroscopy, hysterectomy and vertebroplasty.

Limitations

This study uses claim-based measures of overuse and is limited to the first ten months of the COVID-19 pandemic.

Conclusions

The shutdown period during March through May in 2020 had a drastic impact on both the overuse volume and rates for these 10 overuse metrics.
Limited induction of lung-resident memory T cell responses against SARS-CoV-2 by mRNA vaccination
Authors: Pieren Daan K.J. , Kuguel Sebastián G. , Rosado Joel , Robles Alba G. , Rey-Cano Joan , Mancebo Cristina , Esperalba Juliana , Falcó Vicenç , Buzón María J. , Genescà Meritxell
Published: May 2022

Resident memory T cells (TRM) present at the respiratory tract may be essential to enhance early SARS-CoV-2 viral clearance, thus limiting viral infection and disease. While long-term antigen (Ag)-specific TRMare detectable beyond 11 months in the lung of convalescent COVID-19 patients after mild and severe infection, it is unknown if mRNA vaccination encoding for the SARS-CoV-2 S-protein can induce this frontline protection. We found that the frequency of CD4+T cells secreting interferon (IFN)γ in response to S-peptides was variable but overall similar in the lung of mRNA-vaccinated patients compared to convalescent-infected patients. However, in vaccinated patients, lung responses presented less frequently a TRMphenotype compared to convalescent infected individuals and polyfunctional CD107a+IFNγ+TRMwere virtually absent. Thus, a robust and broad TRMresponse established in convalescent-infected individuals may be advantageous in limiting disease if the virus is not blocked by initial mechanisms of protection, such as neutralization. Still, mRNA vaccines might induce responses within the lung parenchyma, potentially contributing to the overall disease control.
Effects of Sensorimotor Voice Training on Event-Related Potentials to Pitch-Shifted Auditory Feedback
Authors: Patel Sona , Hebert Karen , Korzyukov Oleg , Larson Charles R.
Published: May 2022

The pitch perturbation technique is a validated technique that has been used for over 30 years to understand how people control their voice. This technique involves altering a person’s voice pitch in real-time while they produce a vowel (commonly, a prolonged /a/ sound). Although post-task changes in the voice have been observed in several studies (e.g., a change in mean F0 across the duration of the experiment), the potential for using the pitch perturbation technique as a training tool for voice pitch regulation and/or modification has not been explored. The present study examined changes in event related potentials (ERPs) and voice pitch in three groups of subjects due to altered voice auditory feedback following a brief, four-day training period. Participants in the opposing group were trained to change their voice F0 in the opposite direction of a pitch perturbation stimulus. Participants in the following group were trained to change their voice F0 in the same direction as the pitch perturbation stimulus. Participants in the non-varying group did not voluntarily change their pitch, but instead were asked to hold their voice constant when they heard pitch perturbations. Results showed that all three types of training affected the ERPs (N1 peak latency, P2 peak latency, and P2 peak amplitude) and the response latency and magnitude of the voice pitch shift response in the baseline, “hold your voice pitch steady” task (an indicator of voice pitch regulation). These results demonstrate that participation in pitch-shifted auditory feedback tasks even for brief periods of time can modulate the automatic tendency to compensate for alterations in voice pitch feedback and has therapeutic potential.
Airborne Pathogen Detection in Fine Aerosol Exhaled Breath Condensates
Authors: Henderson John , Mantso Theodora , Ali Saqib , Groß Rüdiger , Müller Janis A. , Wilkinson Amie , Shah Kavit , Usher Louise , Auld Beth , Nelson Andrew , Cheung William , Namdeo Anil , Combrinck Madeleine , Hackney Phil , Turgul Volkan , Jahaj Edison , Athanasiou Nikolaos , Nikolouzakis Taxiarchis , Almeida Pedro J. , Rokka Chrysa , Queiroz Daniel C. , Wright Edward , Zafiropoulos Alexandros , Kale Izzet , Smith Darren , Kofteridis Diamantis P. , Tsatsakis Aristides , Münch Jan , Katsaounou Paraskevi A. , Kotanidou Anastasia , Lagiou Pagona , Magiorkinis Gkikas , Aquiar Renato S , Teixeira Mauro M. , Moschos Sterghios A.
Published: May 2022

Rationale

Exhaled breath condensate (EBC) promises a valuable, non-invasive, and easy to obtain clinical sample. However, it’s not currently used diagnostically due to poor reproducibility, sample contamination, and sample loss.

Objective

We evaluated whether a new, hand-held EBC collector (PBM-HALETM) that separates inertially impacted large droplets (LD) before condensing fine aerosols (FA) in distinct, self-sealing containers, overcomes current limitations.

Methods

Sampling consistency was determined in healthy volunteers by microbial culture, 16S phylogenetics, spectrophotometry, RT-PCR, and HILIC-MS. Capture of aerosolised polystyrene beads, liposomes, virus-like particles, or pseudotyped virus was analysed by nanoparticle tracking analysis, reporter expression assays, and flow cytometry. Acute symptomatic COVID-19 case tidal FA EBC viral load was quantified by RT-qPCR. Exhaled particles were counted by laser light scattering.

Measurements and Main Results

Salivary amylase-free FA EBC capture was linear (R2=0.9992; 0.25-30 min) yielding RNA (6.03 μg/mL) containing eukaryotic 18S rRNA (RT-qPCR; p<0.001) but not human GAPDH, RNase P, or beta actin mRNA;141 non-volatile metabolites included eukaryotic cell membrane components, and cuscohygrine 3 days after cocaine abuse. Culturable aerobe viability was condensation temperature-dependent. Breath fraction-specific microbiota were stable, identifying Streptococcus enrichment in a mild dry cough case. Nebulized pseudotyped virus infectivity loss <67% depended on condensation temperature, and particle charge-driven aggregation. SARS-CoV-2 RNA genomes were detected only by forced expiration FA EBC capture, in 100% of acute COVID-19 patients.

Conclusions

High purity, distal airway FA EBC can reproducibly and robustly inform contamination-free infectious agent emission sources, and be quantitatively assayed for multiple host, microbial, and lifestyle biomarker classes.
Impact of ‘Black Race’ coefficient in eGFR on Our Community and Medical Education
Authors: Kanungo Shibani , Lorber Amy R. , Schmitt Christine , VanRiper Kaitlyn , Billian Joseph
Published: May 2022

A critical national conversation over the use of race in estimation of glomerular filtration rate (eGFR) was stimulated by medical students at the University of Washington over the past few years. They explored, with overdue scrutiny, the ways race is portrayed and used in medical education and practice. Questions were raised about the inclusion of the multiplicative factor for Black race in eGFR calculation, with implications for differential clinical management, and the possibility of disadvantaging patients, solely based on race. Their call for investigation and action, among the rising voices of many, started a reexamination of eGFR and the numerous other areas of medicine touched by racism. As a result, national groups of physicians, scientists, specialists, and patients (including the American Society of Nephrology and National Kidney Foundation) have called for removal of race from calculation of eGFR. We scrutinized use of ‘Black race’ coefficient in eGFR calculation and consequence of its use on our local community in SW Michigan. A cross-sectional analysis of electronic health record (EHR) data from local hospital systems demonstrates the impact removal of race from eGFR calculation could have on our community. Our work may serve as a prototype for ongoing and thorough examination of questions of race in medicine. Truly eradicating racism from medicine may require continuous critical evaluation of current established norms of medical education and care. As similar issues arise in medical education, we can identify how such changes shape healthcare on a local level and integrate this knowledge into our education.

Key points

Question

Can use of Black race in eGFR equation affects our local community?

Findings

Cross sectional study of a community population accessing local health care system for assessment of kidney function, found significant association between self-identified ‘Black’ population advance to CKD Stage 3 or higher upon removal of “black race” coefficient in eGFR MDRD calculation.

Meaning

Race use in medical practice and medical education further perpetuates systemic racism and widens health care access inequity.
The International Concussion and Head Injury Research Foundation Brain health in Retired athletes Study of Ageing and Impact-Related Neurodegenerative Disease (ICHIRF-BRAIN Study)
Authors: Turner Michael , Beirne Cliff , Belli Antonio , Blennow Kaj , Zetterberg Henrik , Dewar Bonnie Kate , di Pietro Valentina , Gissane Conor , Heslegrave Amanda , Laverse Etienne , McEneaney Victoria , McGoldrick Adrian , Murray James , O’Halloran Patrick , Pearson Ben , Pitsiladis Yannis , Toffoli Marco , Williams Huw , McCrory Paul
Published: May 2022

Introduction and aims

Traumatic brain injury (TBI) is a leading cause of death and disability worldwide. Large registry studies have demonstrated a dose–response relationship between TBI and neurodegenerative disease ; however, disentangling the direct effects of TBI from ageing and/or a progressive neurodegenerative process is problematic. This study is a prospective long-term cohort study to examine a population of retired elite athletes at high risk of concussion and mTBI during their sporting careers compared to age- and sex-matched controls with no history of TBI. The aim is to determine the incidence and risk factors for neurodegenerative disease and/or age-related effects on brain health in this population.

Methods and analysis

A population of retired male and female elite athletes and controls aged 40-85 years, will be assessed at baseline and serial time points over 10 years during life using a multi-dimensional assessment including: Questionnaire; SCAT3/5; Neurological and physical examination; Instrumented balance assessment; Computerised neurocognitive screen; Neuropsychological assessment; Advanced MR brain neuroimaging; Visual saccades; Blood workup; Fluid biomarkers; Gut metabolomics; Salivary MicroRNA analysis; Genetic analysis; and where available Brain banking and neuropathology

Ethics and dissemination

Ethics approval was granted by St Mary’s University SMEC as well as at the various satellite trial sites. The trial is registered with ISRCTN (BioMed Central) with ID number: 11312093. In addition to the usual dissemination process, this phenotypically well-characterised dataset will reside in a publicly accessible infrastructure of integrated databases, imaging repositories, and biosample repositories and de-identified data will be made available to collaborating researchers.
African Ancestry GWAS of Dementia in a Large Military Cohort Identifies Significant Risk Loci
Authors: Sherva Richard , Zhang Rui , Sahelijo Nathan , Jun Gyungah , Anglin Tori , Chanfreau Catherine , Cho Kelly , Fonda Jennifer R. , Gaziano J. Michael , Harrington Kelly M. , Ho Yuk-Lam , Kremen William , Litkowski Elizabeth , Lynch Julie , Neale Zoe , Roussos Panos , Marra David , Mez Jesse , Miller Mark W. , Salat David H. , Tsuang Debby , Wolf Erika , Zeng Qing , Panizzon Matthew S. , Merritt Victoria C. , Farrer Lindsay A. , Hauger Richard L. , Logue Mark W.
Published: May 2022

We conducted the largest genome-wide association study (GWAS) of Alzheimer’s disease and related dementia (ADRD) in individuals of African-ancestry (AFR) to date using participants from the Million Veteran Program (MVP; 4,012 ADRD cases and 18,435 controls). A proxy GWAS based on survey-reported parental dementia (n=6,641 proxy cases, 45,970 controls) was also performed. The MVP AFR ADRD GWAS and proxy GWAS results were meta-analyzed and combined with the Alzheimer’s Disease Genetics Consortium’s (ADGC) AFR AD GWAS results. The MVP meta-analysis yielded genome-wide significant associations in or near APOE, ROBO1, and RP11-340A13.2. The MVP/ADGC meta-analysis yielded additional genome-wide significant variants near known risk genes TREM2, CD2AP, and ABCA7. We examined differences in expression of the implicated genes in a cohort of AD case and control brains. This study provides insight into dementia pathophysiology in historically understudied individuals of AFR and may help to address health disparities.
Latent anxiety and depression dimensions differ among eating disorders: a Swedish nationwide investigation
Authors: Hübel Christopher , Birgegård Andreas , Johansson Therese , Petersen Liselotte V. , Isomaa Rasmus , Herle Moritz
Published: May 2022

Objective

Anxiety and depression symptoms are common in eating disorders. To study these, we need high-quality self-report questionnaires. The 19-item self-rated Comprehensive Psychopathological Rating Scale for Affective Syndromes (CPRS-S-A) is not validated in eating disorders. We tested its factor structure, invariance, and differences its latent dimensions.

Method

Patients were registered by 45 treatment units in the Swedish nationwide Stepwise quality assurance database for specialised eating disorder care (n= 9,509). Patients self-reported their anxiety and depression symptoms on the CPRS-S-A. Analyses included exploratory and confirmatory factor analysis in a split samples and invariance difference testing in subscales across eating disorders.

Results

Results suggested a four-factor solution: Depression, Somatic & fear symptoms, Disinterest, and Worry. Multigroup confirmatory factor analysis indicated an invariant factor structure. We detected the following differences: Patients with anorexia nervosa binge-eating/purging subtype scored the highest and patients with unspecified feeding and eating disorders the lowest on all subscales. Patients with anorexia nervosa or purging disorder show more somatic & fear symptoms than individuals with either bulimia nervosa or binge-eating disorder.

Conclusion

Our four-factor solution of the CPRS-S-A is suitable for patients with eating disorders and may help to identify differences in anxiety and depression dimensions amongst eating disorders.

Significant Outcomes

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Symptoms of anxiety and depression in eating disorder patients load on four dimensions: Depression, Somatic & fear symptoms, Disinterest, and Worry.

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Patients with anorexia nervosa binge-eating/purging subtype show the largest depression and anxiety symptom burden while patients with subsyndromal forms of eating disorders show the lowest.

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Instead of calculating total scores of anxiety and depression, a dimensional approach delivers more fine-grained association results.

Limitations

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Our sample consisted of eating disorder patients only and there was no healthy control group or data from patients with other psychiatric disorders for comparison.

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The sample consisted predominantly of women which limits the ability to identify sex differences.

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The sample included Swedish treatment seeking patients of mostly white European ancestry limiting the generalisability of our findings.
A repeat pattern of founder events for SARS-CoV-2 variants in Alaska
Authors: Haan Tracie J. , Smith Lisa K. , DeRonde Stephanie , House Elva , Zidek Jacob , Puhak Diana , Mullen Logan , Redlinger Matthew , Parker Jayme , Barnes Brian M. , Burkhead Jason L. , Knall Cindy , Bortz Eric , Chen Jack , Drown Devin M.
Published: May 2022

Alaska is a unique US state because of its large size, geographically disparate population density, and physical distance from the contiguous United States. Here, we describe a pattern of SARS-CoV-2 variant emergence across Alaska reflective of these differences. Using genomic data, we found that in Alaska the Omicron sublineage BA.2.3 overtook BA.1.1 by the week of 2022-02-27, reaching 48.5% of sequenced cases. On the contrary in the contiguous United States, BA.1.1 dominated cases for longer, eventually being displaced by BA.2 sublineages other than BA.2.3. BA.2.3 only reached a prevalence of 10.9% in the contiguous United States. Using phylogenetics, we found evidence of potential origins of the two major clades of BA.2.3 in Alaska and with logistic regression estimated how it emerged and spread throughout the state. The combined evidence is suggestive of founder events in Alaska and is reflective of how Alaska’s unique dynamics influence the emergence of SARS-CoV-2 variants.
Genetic diversity of Staphylococcus aureus wall teichoic acid glycosyltransferases affects immune recognition
Authors: Tamminga Sara M. , Völpel Simon L. , Schipper Kim , Stehle Thilo , Pannekoek Yvonne , van Sorge Nina M.
Published: May 2022

Staphylococcus aureus (S. aureus) is a leading cause of skin and soft tissue infections and (hospital-acquired) systemic infections. Wall teichoic acids (WTAs) are cell wall-anchored glycopolymers that are important for S. aureus nasal colonization, endocarditis, and antibiotic resistance. WTAs consist of a polymerized ribitol phosphate (RboP) chain that can be glycosylated with N-acetylglucosamine (GlcNAc) by three glycosyltransferases: TarS, TarM, and TarP. TarS and TarP modify WTA with β-linked GlcNAc on the C-4 (β1,4-GlcNAc) and the C-3 position (β1,3-GlcNAc) of the RboP subunit, respectively, whereas TarM modifies WTA with α-linked GlcNAc at the C-4 position (α1,4-GlcNAc). Importantly, these WTA glycosylation patterns impact immune recognition and clearance of S. aureus. Previous studies suggest that tarS is near-universally expressed within the S. aureus population, whereas a smaller proportion co-express either tarM or tarP. To gain more insight in the presence and genetic variation of tarS, tarM, and tarP in the S. aureus population, we analyzed a collection of 25,652 S. aureus genomes within the PubMLST database. Over 99% of isolates contained tarS. Co-expression of tarS/tarM or tarS/tarP occurred in 37% and 7% of isolates, respectively, and was associated to specific S. aureus clonal complexes. We also identified 26 isolates (0.1%) that contained all three glycosyltransferase genes. At sequence level, we identified tar alleles with amino acid substitutions in critical enzymatic residues or with premature stop codons. Several tar variants were expressed in a S. aureus tar-negative strain. Analysis using specific monoclonal antibodies and human langerin showed that WTA glycosylation was severely attenuated or absent. Overall, our data provide a broad overview of the genetic diversity of the three WTA glycosyltransferases in the S. aureus population and the functional consequences for immune recognition.
A generalizable brain extraction net (BEN) for multimodal MRI data from rodents, nonhuman primates, and humans
Authors: Yu Ziqi , Han Xiaoyang , Xu Wenjing , Zhang Jie , Marr Carsten , Shen Dinggang , Peng Tingying , Zhang Xiao-Yong , Feng Jianfeng
Published: May 2022

Accurate brain tissue extraction on magnetic resonance imaging (MRI) data is crucial for analyzing brain structure and function. While several conventional tools have been optimized to handle human brain data, there have been no generalizable methods to extract brain tissues for multimodal MRI data from rodents, nonhuman primates, and humans. Therefore, developing a flexible and generalizable method for extracting whole brain tissue across species would allow researchers to analyze and compare experiment results more efficiently. Here, we propose a domain-adaptive and semi-supervised deep neural network, named the Brain Extraction Net (BEN), to extract brain tissues across species, MRI modalities, and MR scanners. We have evaluated BEN on 18 independent datasets, including 783 rodent MRI scans, 246 nonhuman primate MRI scans, and 4,601 human MRI scans, covering five species, four modalities, and six MR scanners with various magnetic field strengths. Compared to conventional toolboxes, the superiority of BEN is illustrated by its robustness, accuracy, and generalizability. Our proposed method not only provides a generalized solution for extracting brain tissue across species but also significantly improves the accuracy of atlas registration, thereby benefiting the downstream processing tasks. As a novel fully automated deep-learning method, BEN is designed as an open-source software to enable high-throughput processing of neuroimaging data across species in preclinical and clinical applications.
Programmable RNA Sensing for Cell Monitoring and Manipulation
Authors: Qian Yongjun , Li Jiayun , Zhao Shengli , Matthews Elizabeth , Adoff Michael , Zhong Weixin , An Xu , Yeo Michele , Park Christine , Wang Bor-Shuen , Southwell Derek , Huang Z. Josh
Published: May 2022

RNAs are the central and universal mediator of genetic information underlying the diversity of cell types and cell states, which together shape tissue organization and organismal function across species and life spans. Despite advances in RNA sequencing and massive accumulation of transcriptome datasets across life sciences, the dearth of technologies that leverage RNAs to observe and manipulate cell types remains a prohibitive bottleneck in biology and medicine. Here, we describe CellREADR (Cell access through RNA sensing by Endogenous ADAR), a programmable RNA sensing technology that leverages RNA editing mediated by ADAR (adenosine deaminase acting on RNA) for coupling the detection of cell-defining RNAs with translation of effector proteins. Viral delivery of CellREADR conferred specific cell type access in mouse and rat brains and in ex vivo human brain tissues. Furthermore, CellREADR enabled recording and control of neuron types in behaving mice. CellREADR thus highlights the potential for RNA-based monitoring and editing of animal cells in ways that are specific, versatile, easy, and generalizable across organ systems and species, with broad applications in biology, biotechnology, and programmable RNA medicine.
Integration of imaging modalities with lipidomic characterization to investigate MSCs potency metrics
Authors: Priyadarshani Priyanka , Van Grouw Alexandria , Liversage Adrian Ross , Nikitina Arina , Tehrani Kayvan Forouhesh , Kemp Melissa , Fernandez Facundo , Mortensen Luke J.
Published: May 2022

Mesenchymal stem cells (MSCs) are widely used as therapeutics targets for numerous autoimmune diseases. However, MSC therapies have had limited success so far in clinical trials, mainly being heterogenous population it is difficult to determine MSCs efficiencies. It is critical to understand internal signaling of individual MSCs population that directly affect the cell phenotype. Lipid signaling is closely associated with cell shape so, a holistic approach to understand how changes in lipid metabolites trickles all the way to single cell phenotype could reveal deeper understanding of MSCs functional regulation. So, we aim to evaluate lipid metabolic profiles of single cell MSCs with known variability in immune regulation and explore the phenotypic changes that occur because of differences in lipid signaling. We use longitudinal label free phase imaging strategies to obtain cell phenotypic features which are directly correlated with single cell lipid metabolome obtained using advanced MALDI-MSI technique. Correlation maps indicate associations between lipid signaling and phenotypic changes in MSCs.

Moreover, a novel machine learning clustering approach detects the heterogeneity in the MSCs subpopulation then methodically see how each heterogenous population is being impacted by the changes in lipid profiles which could be linked to the functional behaviors of the cell.
Fast and accurate out-of-core PCA framework for large scale biobank data
Authors: Li Zilong , Meisner Jonas , Albrechtsen Anders
Published: May 2022

Principal Component Analysis (PCA) is widely utilized in statistics, machine learning, and genomics for dimensionality reduction and uncovering low-dimensional latent structure. To address the challenges posed by ever-growing data size, fast and memory-efficient PCA methods have gained prominence. In this paper, we propose a novel Randomized Singular Value Decomposition (RSVD) algorithm implemented in PCAone, featuring a window-based optimization scheme that enables accelerated convergence while improving the accuracy. Additionally, PCAone incorporates out-of-core and multithreaded implementations for the existing Implicitly Restarted Arnoldi Method (IRAM) and RSVD. Through comprehensive evaluations using multiple large-scale real-world datasets in different fields, we demonstrate the advantage of PCAone over existing methods. The new algorithm achieves significantly faster computation time while maintaining accuracy comparable to the slower IRAM method. Notably, our analyses of UK Biobank, comprising around 0.5 million individuals and 6.1 million common SNPs, demonstrate that PCAone accurately computes the top 40 principal components within a 9 hours. This analysis effectively captures population structure, signals of selection, structural variants, and low recombination regions, utilizing less than 20 GB of memory and 20 CPU threads. Furthermore, when applied to single-cell RNA sequencing data featuring 1.3 million cells, PCAone, accurately capturing the top 40 principal components in 49 minutes. This performance represents a 10-fold improvement over state-of-the-art tools.