bluuebunny/crossref_metadata_2025 huggingface dataset:
Meta-Analysis of Risk of Vaccine-Induced Immune Thrombotic Thrombocytopenia Following ChAdOx1-S Recombinant Vaccine
Authors: Chan Benjamin TB , Bobos Pavlos , Odutayo Ayodele , Pai Menaka
Published: May 2021

Context

Vaccine-induced immune thrombotic thrombocytopenia (VITT) has been reported after administering ChAdOx1-S recombinant COVID-19 vaccine (marketed as Vaxzevira™ by Astra-Zeneca, Covishield™). Estimates of incidence vary between countries, due to different age distributions chosen, case definitions and choice of denominator (persons vaccinated vs immunizations given). This study clarifies these estimates by pooling data from ten countries and examining differences by age group.

Methods

We examined case reports, press releases and immunization data and calculated pooled estimates of VITT incidence using random effects models. Sensitivity analyses considered different combinations of countries and varying assumptions on time between vaccination and reporting of cases.

Results

Pooling all countries, VITT incidence was 0.73 per 100,000 persons receiving first dose of Covishield/Vaxzevira [95% CI .43,1.23]. Incidence for age 65 and over was 0.11 per 100,000 persons [95% CI .05-.26], and significantly higher among those under age 55: 1.67 per 100,000 persons [95% CI 1.30-2.14] in the UK, 5.06 per 100,000 persons in Norway [95% CI 2.16, 11.86]. The latter had the best data on counts of persons vaccinated. Incidence for age 55 to 64 years was 0.34 [95% CI 0.13, 0.85] in the UK, lower than for under age 55.

Conclusion

VITT is a rare vaccine-associated adverse event. Incidence estimates vary between jurisdictions. However, even the highest reported incidence from Norway is low – and in settings with high community transmission, lower than risk of serious outcomes associated with Covid-19. Policymakers and individuals can use these data to calculate risk-benefit ratios and better target vaccine distribution.

Essentials

This paper measures risk of vaccine-induced immune thrombotic thrombocytopenia (VITT) after ChAdOx1-S recombinant COVID-19 vaccine

Pooled estimates of incidence were calculated with a random effects model based on data from 10 countries

Overall risk is 1 in 139,000; for age 65 and over, about 1 in 1,000,000; for age under 55, between 1 in 20,000 to 60,000

VITT risk is low and varies by age. These data can inform policies around vaccination distribution.
Benchmark of thirteen bioinformatic pipelines for metagenomic virus diagnostics using datasets from clinical samples
Authors: de Vries Jutte J.C. , Brown Julianne R. , Fischer Nicole , Sidorov Igor A. , Morfopoulou Sofia , Huang Jiabin , Oude Munnink Bas B. , Sayiner Arzu , Bulgurcu Alihan , Rodriguez Christophe , Gricourt Guillaume , Keyaerts Els , Beller Leen , Bachofen Claudia , Kubacki Jakub , Cordey Samuel , Laubscher Florian , Schmitz Dennis , Beer Martin , Hoeper Dirk , Huber Michael , Kufner Verena , Zaheri Maryam , Lebrand Aitana , Papa Anna , van Boheemen Sander , Kroes Aloys C.M. , Breuer Judith , Lopez-Labrador F. Xavier , Claas Eric C.J.
Published: May 2021

Metagenomic sequencing is increasingly being used in clinical settings for difficult to diagnose cases. The performance of viral metagenomic protocols relies to a large extent on the bioinformatic analysis. In this study, the European Society for Clinical Virology (ESCV) Network on NGS (ENNGS) initiated a benchmark of metagenomic pipelines currently used in clinical virological laboratories.

Methods

Metagenomic datasets from 13 clinical samples from patients with encephalitis or viral respiratory infections characterized by PCR were selected. The datasets were analysed with 13 different pipelines currently used in virological diagnostic laboratories of participating ENNGS members. The pipelines and classification tools were: Centrifuge, DAMIAN, DIAMOND, DNASTAR, FEVIR, Genome Detective, Jovian, MetaMIC, MetaMix, One Codex, RIEMS, VirMet, and Taxonomer. Performance, characteristics, clinical use, and user-friendliness of these pipelines were analysed.

Results

Overall, viral pathogens with high loads were detected by all the evaluated metagenomic pipelines. In contrast, lower abundance pathogens and mixed infections were only detected by 3/13 pipelines, namely DNASTAR, FEVIR, and MetaMix. Overall sensitivity ranged from 80% (10/13) to 100% (13/13 datasets). Overall positive predictive value ranged from 71-100%. The majority of the pipelines classified sequences based on nucleotide similarity (8/13), only a minority used amino acid similarity, and 6 of the 13 pipelines assembled sequences de novo. No clear differences in performance were detected that correlated with these classification approaches. Read counts of target viruses varied between the pipelines over a range of 2-3 log, indicating differences in limit of detection.

Conclusion

A wide variety of viral metagenomic pipelines is currently used in the participating clinical diagnostic laboratories. Detection of low abundant viral pathogens and mixed infections remains a challenge, implicating the need for standardization and validation of metagenomic analysis for clinical diagnostic use. Future studies should address the selective effects due to the choice of different reference viral databases.
LACK OF ASSOCIATION BETWEEN CONVALESCENT PLASMA ADMINISTRATION AND LENGTH OF HOSPITAL STAY: A HOSPITAL-DAY STRATIFIED MULTI-CENTER RETROSPECTIVE COHORT STUDY
Authors: Alamgir Joy , Abid M. Ruhul , Garibaldi Brian , Munir Naved , Setoguchi Soko , Hong Stephanie S. , Chen Xinci , Kocis Paul T. , Yajima Masanao , Alexander G. Caleb , Mehta Hemalkumar B. , Madhira Vithal , Ergas Rosa , O’Brien Thomas R. , Bozzette Sam
Published: May 2021

Background

Effects of timing of Convalescent plasma (CP) administration on hospitalized COVID-19 patients are not established.

Methods

We used the National COVID Cohort Collaborative data to perform a retrospective cohort study of hospitalized COVID-19 patients in the United States between 07-01-2020 and 12-19-2020. We stratified patients based on day of CP administration (Day 0, 1, 2, 3 and 4) from COVID-19 diagnosis. We used 35 predictors to frame matched cohorts accounting for clinical and sociodemographic characteristics. We used competing risk survival models to examine the association between CP administration and length of hospital stay with in-hospital death as a competing risk performing Gray’s test on the cumulative incidence function and Cox’s regression on cause specific hazard ratios.

Results

In a cohort of 4,003 hospitalized COVID-19 patients, 197 (4.9%) received CP within the first 5 days following COVID-19 diagnosis. After adjusting for potential confounding variables, there were no statistically significant associations between day of CP administration and length of hospital stay. Day 0 CP administration signallled lower mortality but was not statistically significant (HR 0.45 [0.19-1.03]).

Conclusions

We found no association between the timing of CP administration and length of stay among hospitalized COVID-19 patients.
Integrative lipidomics and metabolomics for system-level understanding of the metabolic syndrome in long-term treated HIV-infected individuals
Authors: Villumsen Sofie Olund , Benfeitas Rui , Dehlbæk Knudsen Andreas , Gelpi Marco , Høgh Julie , Thomsen Magda Teresa , Murray Daniel , Ullum Henrik , Neogi Ujjwal , Nielsen Susanne Dam
Published: May 2021

People living with HIV (PLWH) require life-long anti-retroviral treatment and often present with comorbidities such as metabolic syndrome (MetS). A systematic lipidomic characterization and its association with metabolism is currently missing. In this study, we included 100 PLWH with MetS and 100 without MetS from the Copenhagen comorbidity in HIV infection (COCOMO) cohort to examine whether and how lipidome profiles associated with MetS in PLWH. We combined several standard biostatistical, machine learning, and network analysis techniques to investigate the lipidome systematically and comprehensively. Our observations indicate an increased abundance of the glycerolipids and an association between structural composition patterns of glycerolipids in PLWH with MetS. Further integration of the key metabolites identified earlier in the same population and clinical data with lipidomics suggest disruption of the glutamate and fatty acid metabolism. suggest their involvement in pathogenesis of PLWH with MetS.
A prospective diagnostic study to measure the accuracy of detection of SARS-CoV-2 Variants Of Concern (VOC) utilising a novel RT-PCR GENotyping algorithm in an In silico Evaluation (VOC-GENIE)
Authors: Borley Daryl , Trevor R.A. , Richter Alex , Kidd Stephen , Cortes Nick , Moore Nathan , Goring Alice , Templeton Kate , Teltumbde Prachi , Grippon Seden , Oladimeji Paul , Sanchez-Bretano Aida , Dawson Andrew , Martin Joanne E
Published: May 2021

Background

SARS-CoV-2 variants of concern (VOCs) have been associated with higher rate of transmission, and evasion of immunisation and antibody therapeutics. Variant sequencing is widely utilized in the UK. However, only 0.5% (~650k) of the 133 million cumulative positive cases worldwide were sequenced (in GISAID) on 08 April 2021 with 97% from Europe and North America and only ~0.25% (~320k) were variant sequences. This may be due to the lack of availability, high cost, infrastructure and expert staff required for sequencing.

Public health decisions based on a non-randomised sample of 0.5% of the population may be insufficiently powered, and subject to sampling bias and systematic error. In addition, sequencing is rarely available in situ in a clinically relevant timeframe and thus, is not currently compatible with diagnosis and treatment patient care pathways. Therefore, we investigated an alternative approach using polymerase chain reaction (PCR) genotyping to detect the key single nucleotide polymorphisms (SNPs) associated with increased transmission and immune evasion in SARS-CoV-2 variants.

Methods

We investigated the utility of SARS-CoV-2 SNP detection with a panel of PCR-genotyping assays in a large data set of 640,482 SARS-CoV-2 high quality, full length sequences using a prospective in silico trial design and explored the potential impact of rapid in situ variant testing on the COVID-19 diagnosis and treatment patient pathway.

Results

Five SNPs were selected by screening the published literature for a reported association with increased transmission and / or immune evasion. 344881 sequences contained one or more of the five SNPs. This algorithm of SNPs was found to be able to identify the four variants of concern (VOCs) and sequences containing the E484K and L452R escape mutations.

Interpretation

The in silico analysis suggest that the key mutations and variants of SARS-CoV-2 may be reliably detected using a focused algorithm of biologically relevant SNPs. This highlights the potential for rapid in situ PCR genotyping to compliment or replace sequencing or to be utilized instead of sequences in settings where sequencing is not feasible, accessible or affordable. Rapid detection of variants with in situ PCR genotyping may facilitate a more effective COVID-19 diagnosis and treatment patient pathway.

Funding

The study was funded by Primer Design (UK), with kind contributions from all academic partners.
The impact of COVID-19 on the provision of respectful maternity care: findings from a global survey of health workers
Authors: Asefa Anteneh , Semaan Aline , Delvaux Therese , Huysmans Elise , Galle Anna , Sacks Emma , Bohren Meghan A. , Morgan Alison , Sadler Michelle , Vedam Saraswathi , Benova Lenka
Published: May 2021

Background

Significant adjustments to the provision of maternity care in response to the COVID-19 pandemic and the direct impacts of COVID-19 can compromise the quality of maternal and newborn care.

Aim

To explore how the COVID-19 pandemic affected frontline health workers’ ability to provide respectful maternity care globally.

Methods

We conducted a global online survey of health workers to assess the provision of maternal and newborn healthcare during the COVID-19 pandemic. We collected quantitative and qualitative data between July and December 2020 and conducted a qualitative content analysis to explore open-ended responses.

Findings

Health workers (n=1,127) from 71 countries participated; and 120 participants from 33 countries provided qualitative data. The COVID-19 pandemic negatively affected the provision of respectful maternity care in multiple ways. Six central themes were identified: less family involvement, reduced emotional and physical support for women, compromised standards of care, increased exposure to medically unjustified caesarean section, and staff overwhelmed by rapidly changing guidelines and enhanced infection prevention measures. Further, respectful care provided to women and newborns with suspected or confirmed COVID-19 infection was severely affected due to health workers’ fear of getting infected and measures taken to minimise COVID-19 transmission.

Discussion

Multidimensional and contextually-adapted actions are urgently needed to mitigate the impacts of the COVID-19 pandemic on the provision and continued promotion of respectful maternity care globally in the long-term.

Conclusions

The measures taken during the COVID-19 pandemic disrupted the quality of care provided to women during labour and childbirth generally, and respectful maternity care specifically.
COVID-19: Affect recognition through voice analysis during the winter lockdown in Scotland
Authors: de la Fuente Garcia Sofia , Haider Fasih , Luz Saturnino
Published: May 2021

The COVID-19 pandemic has led to unprecedented restrictions in people’s lifestyle which have affected their psychological wellbeing. In this context, this paper investigates the use of social signal processing techniques for remote assessment of emotions. It presents a machine learning method for affect recognition applied to recordings taken during the COVID-19 winter lockdown in Scotland (UK). This method is exclusively based on acoustic features extracted from voice recordings collected through home and mobile devices (i.e. phones, tablets), thus providing insight into the feasibility of monitoring people’s psychological wellbeing remotely, automatically and at scale. The proposed model is able to predict affect with a concordance correlation coefficient of 0.4230 (using Random Forest) and 0.3354 (using Decision Trees) for arousal and valence respectively.

Clinical relevance

In 2018/2019, 12% and 14% of Scottish adults reported depression and anxiety symptoms. Remote emotion recognition through home devices would support the detection of these difficulties, which are often underdiagnosed and, if untreated, may lead to temporal or chronic disability.
The evidence on transmission dynamics of COVID-19 from pre- and asymptomatic cases: protocol for a systematic review (Version 2)
Authors: Jefferson T , Plüddemann A , Spencer EA , Brassey J , Rosca EC , Onakpoya I , Evans DH , Conly JM , Heneghan C
Published: May 2021

Background

The role of forward transmission of infection from cases of SARS-CoV-2 who remain without symptoms and signs throughout the active phase of the disease (asymptomatic) and those who have not developed symptoms or signs when surveyed (presymptomatic) is at present unclear, despite the important role that they may play in transmission dynamics.

Methods

We will search LitCovid, medRxiv, Google Scholar and the WHO Covid-19 database using Covid-19, SARS-CoV-2, transmission, and appropriate synonyms as search terms. We will also search the reference lists of included studies for additional relevant studies. We will include studies of people exposed to SARS-CoV-2 within 2-14 days of close contact or suspected community or institutional exposure to index asymptomatic or pre-symptomatic infected individuals, as defined in each study along with secondary case(s) infected. We will include only studies that provide proof of transmission outcome using culturable virus and /or genetic sequencing. The inclusion of this higher-quality evidence aims to overcome the methodological shortcomings of lower quality studies. We will assess the microbiologic or genetic sequencing evidence in an effort to inform the quality of the chain of transmission evidence and adequacy of follow up of sign and symptom monitoring.

Expected results

We intend to present the evidence in three distinct packages: study description, methodological quality assessment and data extracted. We intend on summarising the evidence and drawing conclusions as to the quality of the evidence.
Development and validation of cost-effective one-step multiplex RT-PCR assay for detecting the SARS-CoV-2 infection using SYBR Green melting curve analysis
Authors: Sarkar Shovon Lal , Alam A. S. M. Rubayet Ul , Das Prosanto Kumar , Pramanik Md. Hasan Ali , Al-Emran Hassan M. , Jahid Iqbal Kabir , Hossain M. Anwar
Published: May 2021

TaqMan probe-based expensive commercial real-time (RT) PCR kits are being used in COVID-19 diagnosis. The unprecedented scale of SARS-CoV-2 infections has urgently needed to meet the challenge of testing more persons at a reasonable cost. This study developed a rapid, simple, and cost-effective alternative diagnostic method based on melting curve analysis of SYBR green multiplex assay with a host-specific internal control. A total of 90 randomly selected samples were used for comparing the assay with an available commercial kit to analyse the variation and validity of this in-house developed method. Our customized designed primers specifically detected the virus as similar to commercial kit manufactured by Sansure Biotech Inc. We optimized separately the N, E, S, and RdRp genes by SYBR Green RT-PCR method based on melting curve analysis. Afterwards, a multiplex COVID-19 diagnosis method targeting N and E genes of the virus along with the β-actin gene of the host as an internal control has been established. The total run-time of our proposed method was less than 90 minutes. The cost of each sample processing was less than $2. Overall, this one-step and one-tube method can revolutionize the COVID-19 diagnosis in developing countries.
Higher case fatality rate among obstetric patients with COVID-19 in the second year of pandemic in Brazil: do new genetic variants play a role?
Authors: Takemoto Maíra L S , Nakamura-Pereira Marcos , Menezes Mariane O , Katz Leila , Knobel Roxana , Amorim Melania M R , Andreucci Carla B
Published: May 2021

Background

In Brazil, a 20% increase in maternal mortality rate due to COVID-19 is projected for 2020. On January 4, 2021, the P.1 SARS-CoV-2 genetic variant was firstly identified in the country and recent data has indicated an association with higher hospitalization rates and mortality. The impact of P.1 variant in the obstetric population remains unclear.

Methods

We carried out a preliminary analysis of sociodemographic and clinical characteristics of COVID-19 confirmed maternal deaths (between 10-50 years old) comparing cases reported to the Brazilian official severe acute respiratory syndrome (SARS) surveillance system (SS) in 2020 with those from 2021 (until April 12, 2021). This preliminary analysis employed methods described in previous reports from our group.

Results

803 maternal deaths out of 8,248 COVID-19 maternal SARS cases with a recorded outcome were reported to the SARS-SS since March 2020. Case fatality rate was significantly higher in 2021 (15.6% vs 7.4%). The first three months of 2021 already account for 46.2% of all deaths occurred in the 13-months analysed period. COVID-19 fatal cases from 2021 had a lower proportion of at least one risk factor or comorbidity as compared to 2020 but had a higher frequency of obesity. There were no significant differences in terms of age, type of residence area (urban, rural, or peri-urban), type of funding of the notification unit (public vs. private), COVID-19 diagnostic criteria, pregnancy status (pregnancy or postpartum), cardiovascular disease or diabetes. The proportion of hospitalization, ICU admission, and respiratory support before death was also not significantly different.

Conclusion

Case fatality rate was increased in the three first months of 2021 when compared to 2020. Once variables related to health care access and demographics are not significantly different and women seem to be healthier in the 2021 sample, such difference may be related to the circulation of more aggressive genetic variants in the country.
Implementation of an interactive mobile application to pilot a rapid assay to detect HIV drug resistance mutations in Kenya
Authors: Vrana Justin D. , Panpradist Nuttada , Higa Nikki , Ko Daisy , Ruth Parker , Kanthula Ruth , Lai James J. , Yang Yaoyu , Sakr Samar R. , Chohan Bhavna , Chung Michael H. , Frenkel Lisa M. , Lutz Barry R. , Klavins Eric , Beck Ingrid A.
Published: May 2021

Introduction

Usability is an overlooked aspect of implementing lab-based assays, particularly novel assays in low-resource-settings. Esoteric instructions can lead to irreproducible test results and patient harm. To address these issues, we developed a software application based on “Aquarium”, a laboratory-operating system run on a computer tablet that provides step-by-step digital interactive instructions, protocol management, and sample tracking. Aquarium was paired with a near point-of-care HIV drug resistance test, “OLA-Simple”, that detects mutations associated with virologic failure. In this observational study we evaluated the performance of Aquarium in guiding untrained users through the multi-step laboratory protocol with little supervision.

Methods

A feasibility study was conducted in a laboratory at Coptic Hope Center in Nairobi, Kenya. To evaluate the training by Aquarium software, twelve volunteers who were unfamiliar with the kit performed the test on blinded samples (2 blood specimens; 5 codons/sample). Steps guided by Aquarium included: CD4+ T-Cell separation, PCR, ligation, detection, and interpretation of test results. Participants filled out a short survey regarding their demographics and experience with the software and kit.

Results and discussion

12/12 laboratory technicians had no prior experience performing CD4+ separation and 7/12 had no experience performing laboratory-based molecular assays. 12/12 isolated CD4+ T cells from whole blood with yields comparable to isolations performed by trained personnel. The OLA-Simple workflow was completed by all, with correct visual and software interpretation of results for 90% (108/120) and 97% (116/120) of codons, respectively. In the surveys, participants favorably assessed the use of software guidance.

Conclusions

Aquarium digital instructions enabled first-time users in Kenya to complete the OLA-simple kit workflow with minimal training. Aquarium could increase the accessibility of laboratory assays in low-resource-settings and potentially standardize implementation of clinical laboratory tests.
Looking beyond the obvious: a critical systematic review and meta-analyses of risk factors for fertility problems in a globalized world
Authors: Bayoumi R.R. , Boivin J. , Fatemi H.M. , Hurt L. , Serour G.I. , van der Poel S. , Venetis C.
Published: May 2021

Background

Well-established risk factors for fertility problems such as smoking have been included in fertility awareness efforts globally. However, these efforts neglect risks that women in low and middle-income countries (LMIC) face.

Objective

To address this gap, we identified eight risk factors affecting women in LMIC and the aim of the current review was to estimate the impact of these risks on fertility.

Methods

We conducted systematic reviews and where data was available meta-analyses. We searched Medline, Embase, Cochrane library, regional databases and key organizational websites (1946-June 2016, updated January 2018, latest update taking place in 2021). Two researchers screened and extracted data independently. We included all study designs that assessed exposure to risk in clinical or community-based samples and excluded studies without control groups. The outcome of interest was fertility problems (inability to achieve pregnancy or live birth and neonatal death). We calculated pooled effect estimates from reported effect sizes or raw data. We assessed study quality using the Newcastle-Ottawa Scale. We registered the review with PROSPERO, registration number CRD42016048497.

Results

We identified 2,418 studies and included 61 (57 in meta-analyses). Results revealed a nine-fold increased risk of inability to become pregnant in genital tuberculosis (OR 8.91, CI 1.89-42.12) and almost threefold in HIV (OR 2.93, CI 1.95-4.42) and bacterial vaginosis (OR 2.81, CI 1.85-4.27). A twofold increased risk of tubal-factor infertility in Female Genital Mutilation/Cutting–Type II/III (OR 2.06, CI 1.03-4.15) and increased post-natal mortality in consanguinity (stillbirth, OR 1.28, CI 1.04-1.57; neonatal death, OR 1.57, CI 1.22-2.02).

Strength and limitations

Reliability of results was bolstered by a rigorous systematic review methodology that is replicable but limited by methodological shortcomings of the available primary studies and the small number of studies in each meta-analysis.

Conclusions

The risk factors investigated appeared to impact the reproductive process through multiple biological, behavioural, and clinical pathways. Additionally, infection and pelvic inflammatory disease seemed to be common pathways for several risk factors. The complex multifactorial risk profile can be addressed by LMIC using a global health framework to determine which risk factors are significant to their populations and how to tackle them. The subsequent health promotion encompassing these relevant health indicators could translate into more prevention and effective early detection of fertility problems in LMIC. Finally, the findings of multifactorial risk reinforced the need to put fertility as an agenda in global health initiatives.
Hypomethylation of Monoamine Oxidase A promoter/exon 1 region is associated with temper outbursts in Prader-Willi syndrome
Authors: Deest Maximilian , Buchholz Vanessa , Jahn Kirsten , Eberlein Christian , Bleich Stefan , Frieling Helge
Published: May 2021

Background

Prader-Willi syndrome (PWS) is a rare neurodevelopmental disorder caused by the absence of paternally expressed and maternally imprinted genes on chromosome 15q 11.2-13. It is associated with a certain behavioural phenotype with repetitive and ritualistic behaviours, skin-picking and temper outbursts. Temper outbursts are characterized by verbal and physical aggression with screaming, destroying property, and/or physical aggression towards others. They drastically effect the quality of life of the individuals as well as the relatives and caregivers. Recent studies show a promising therapeutic effect of serotonin reuptake inhibitors like sertraline on frequency and intensity of outbursts. Monoamine oxidase A (MAOA) (X p11.23) plays a crucial role in the metabolism of monoamines such as serotonin, norepinephrine, and dopamine. Dysregulation in methylation of the CpG island spanning the promoter region and exon 1 of MAOA is implicated in impulsive and aggressive behaviour.

Methods

In the present study, methylation rates of CpG dinucleotides in the MAOA promoter and exon 1 region were determined from DNA derived from whole blood samples of PWS patients (n=32) and controls (n=14) matched for age, sex and BMI via bisulfite sequencing. PWS patients were grouped into those showing temper outbursts, and those who do not.

Results

Overall, PWS patients show a significant lower methylation rate at the promoter/exon 1 region than healthy controls in both sexes. Furthermore, PWS patients, male as well female with temper outbursts show a significant lower methylation rate than those without temper outbursts (p<0.001 and p=0.006)

Conclusion

The MAOA promoter/exon 1 region methylation seems to be dysregulated in PWS patients in sense of a hypomethylation, especially in those suffering from temper outbursts. As MAOA is involved in the metabolism of serotonin, we conclude that this dysregulation plays a crucial role in the pathophysiology of temper outbursts in PWS. Furthermore, our findings suggest, that dysregulation of certain genes outside the PWS locus contribute to the behavioural phenotype of PWS.
RT-qPCR-based tests for SARS-CoV-2 detection in pooled saliva samples for massive population screening to monitor epidemics
Authors: Różański Michał , Walczak-Drzewiecka Aurelia , Witaszewska Jolanta , Wójcik Ewelina , Guziński Arkadiusz , Zimoń Bogumił , Matusiak Rafał , Kazimierczak Joanna , Borowiec Maciej , Kania Katarzyna , Paradowska Edyta , Pawełczyk Jakub , Dziadek Jarosław , Dastych Jarosław
Published: May 2021

Swab, quantitative, reverse transcription polymerase chain reaction (RT-qPCR) tests remain the gold standard of diagnostics of SARS-CoV-2 infections. However, these tests are costly and time-consuming, and swabbing limits their throughput. We developed a 3-gene, seminested RT-qPCR test with SYBR green-based detection, optimized for testing pooled saliva samples for high-throughput diagnostics of epidemic-affected populations. The proposed two-tier approach depends on decentralized self-collection of saliva samples, pooling, 1st-tier testing with the mentioned highly sensitive screening test and subsequent 2nd-tier testing of individual samples from positive pools with the in vitro diagnostic (IVD) test. The screening test was able to detect 5 copies of the viral genome in 10 µl of isolated RNA with 50% probability and 18.8 copies with 95% probability and reached Ct values that were highly linearly RNA concentration-dependent. In the side-by-side comparison (testing artificial pooled samples), the screening test attained slightly better results than the commercially available IVD-certified RT-qPCR diagnostic test (100% specificity and 89.8% sensitivity vs. 100% and 73.5%, respectively). Testing of 1475 individual clinical samples pooled in 374 pools of 4 revealed 0.8% false positive pools and no false negative pools. In weekly prophylactic testing of 113 people within 6 months, a two-tier testing approach enabled the detection of 18 infected individuals, including several asymptomatic individuals, with a fraction of the costs of individual RT-PCR testing.
Phylogenomics of SAR116 clade reveals two subclades with different evolutionary trajectories and important role in the ocean sulfur cycle
Authors: Roda-Garcia Juan J. , Haro-Moreno Jose M. , Huschet Lukas A. , Rodriguez-Valera Francisco , López-Pérez Mario
Published: May 2021

The SAR116 clade within the class Alphaproteobacteria represents one of the most abundant groups of heterotrophic bacteria inhabiting the surface of the ocean. The small number of cultured representatives of SAR116 (only two to date) is a major bottleneck that has prevented an in-depth study at the genomic level to understand the relationship between genome diversity and its role in the marine environment. In this study, we use all publicly available genomes to provide a genomic overview of the phylogeny, metabolism and biogeography within the SAR116 clade. This increased genomic diversity revealed has led to the discovery of two subclades of SAR116 that, despite having similar genome size (ca. 2.4 Mb) and coexist in the same environment, display different properties in their genomic make up. One represents a novel subclade for which no pure cultures have been isolated and is composed mainly of single-amplified genomes (SAGs). Genomes within this subclade showed convergent evolutionary trajectories with more streamlining features, such as low GC content (ca. 30%), short intergenic spacers (<22 bp) and strong purifying selection (low dN/dS). Besides, they were more abundant in metagenomic databases recruiting also at the deep chlorophyll maximum. Less abundant and restricted to the upper photic layers of the global ocean, the other subclade of SAR116, enriched in MAGs, accommodated the only two pure cultures. Genomic analysis suggested that both clades have a significant role in the sulfur cycle with differences in the way in which both clades can metabolize the dimethylsulfoniopropionate (DMSP).

IMPORTANCE

SAR116 clade of Alphaproteobacteria is an ubiquitous group of heterotrophic bacteria inhabiting the surface of the ocean, but the information about their ecology and population genomic diversity is scarce due to the difficulty of getting pure culture isolates. The combination of single-cell genomics and metagenomics has become an alternative approach to study this kind of microbes. Our results expand the understanding of the genomic diversity, distribution, and lifestyles within this clade and provide evidence of different evolutionary trajectories in the genome make-up of the two subclades that could serve to understand how evolutionary pressure can drive different adaptations to the same environment. Therefore, the SAR116 clade represents an ideal model organism for the study of the evolutionary streamlining of genomes in microbes that have relatively close relatedness to each other.
Combinatorial Immunotherapies Overcome MYC-Driven Immune Evasion
Authors: Lee Joyce V. , Housley Filomena , Yau Christina , Van de Mark Daniel , Nakagawa Rachel , Hemmati Golzar , Hernandez Grace A. , Winkler Juliane , Zhang Yibing , Samson Susan , Baas Carole , Esserman Laura J. , Van ‘T Veer Laura J. , Rugo Hope S. , Matloubian Mehrdad , Goga Andrei
Published: May 2021

For many human cancers, including triple negative breast cancer (TNBC), a modest number of patients benefit from immune checkpoint inhibitors, and few experience cancer remission1. Expression of programed death-ligand 1 (PD-L1), tumor immune infiltration, or tumor mutation burden have been widely investigated for predicting cancer immunotherapy response1-5. Whether specific oncogenes diminish response to immunotherapy6-10and whether these effects are reversible remains poorly understood. We predicted thatMYC, an oncogene that is frequently overexpressed11,12and is associated with worse prognosis12, may predict immunotherapy response in patients with TNBC. Here, we report that MYC-elevated TNBCs are resistant to immune checkpoint inhibitors. Using mouse models of TNBC and patient data we report that MYC signaling is associated with low tumor cell PD-L1, low overall immune cell infiltration, and low tumor cell MHC-I expression. Restoring interferon signaling in the tumor reduces MYC expression and increases MHC-I expression. By combining a TLR9 agonist and an agonistic antibody against OX40 with anti-PD-L1, most mice experience complete tumor regression and are protected from new TNBC tumor outgrowth. Our findings demonstrate that MYC-dependent immune evasion is reversible and druggable, and if strategically targeted, may improve outcomes for patients treated with immune checkpoint inhibitors.
ARS2-directed alternative splicing mediates CD28 driven T cell glycolysis and effector function
Authors: Holling G. Aaron , Sharda Anand P. , Honikel Mackenzie M. , James Caitlin M. , Lightman Shivana M. , Qiao Guanxi , Singel Kelly L. , Emmons Tiffany R. , Giridharan Thejaswini , Hou Shengqi , Intlekofer Andrew M. , Higashi Richard M. , Fan Teresa W. M. , Lane Andrew N. , Eng Kevin H. , Segal Brahm H. , Repasky Elizabeth A. , Lee Kelvin P. , Olejniczak Scott H.
Published: May 2021

CD8 T cell activation prompts extensive transcriptome remodeling underlying effector differentiation and function. Regulation of transcriptome composition by the mitogen-inducible nuclear cap-binding complex (CBC) adaptor protein ARS2 has critical cell type-specific consequences, including thymic T cell survival. Here we show that ARS2 was upregulated by CD28 during activation of peripheral T cells, was essential for anti-tumor immunity, and facilitated T cell activation-induced alternative splicing. The novel splicing function of ARS2 was mediated at least in part by recruitment of splicing factors to nascent transcripts including the M2 isoform of pyruvate kinase (Pkm2), a key determinant of CD8 T cell effector properties. Notably, ARS2-directedPkm2splicing occurred days after stimulation of PI3K-indepdendent CD28 signaling and increased glycolysis beyond levels determined by PI3K signaling during T cell priming. Thus, ARS2-directedPkm2splicing represents a mechanism by which CD28 drives glycolytic metabolism, allowing for optimal effector cytokine production and T cell anti-tumor immunity.
Transcriptomes of peripheral blood mononuclear cells from juvenile dermatomyositis patients show elevated inflammation even when clinically inactive
Authors: Roberson Elisha D.O. , Mesa Rosana A. , Morgan Gabrielle A. , Cao Li , Marin Wilfredo , Pachman Lauren M.
Published: May 2021

In juvenile dermatomyositis (JDM), the most common pediatric inflammatory myopathy, weakness is accompanied by a characteristic rash that often becomes chronic, and is associated with vascular damage. We hoped to understand the molecular underpinnings of JDM, particularly in untreated disease, which would facilitate the identification of novel mechanisms and clinical targets that might disrupt disease progression. We studied the RNA-Seq data from untreated JDM peripheral blood mononuclear cells (PBMCs; n=11), PBMCs from a subset of the same patients when clinically inactive (n=8/11), and separate samples of untreated JDM skin and muscle (n=4 each). All JDM samples were compared to non-inflammatory control tissues. The untreated JDM PBMCs showed a strong signature for type1 interferon response, along with IL-1, IL-10, and NF-κB. Surprisingly, PBMCs from clinically inactive JDM individuals had persistent immune activation that was enriched for IL-1 signaling. JDM skin and muscle both showed evidence for type 1 interferon activation and genes related to antigen presentation, and decreased expression of genes related for cellular respiration. Additionally we found that PBMC gene expression correlates with disease activity scores (DAS; skin, muscle, and total domains) and with nailfold capillary end row loop number (an indicator of microvascular damage). This includedotoferlin, which was significantly increased in untreated JDM PBMCs and correlated with all 3 DAS domains. Overall, these data demonstrate that PBMC transcriptomes are informative of molecular disruptions in JDM and provide transcriptional evidence of chronic inflammation despite clinical quiescence.
Modelling the depth-dependent VASO and BOLD responses in human primary visual cortex
Authors: Akbari Atena , Bollmann Saskia , Ali Tonima S , Barth Markus
Published: May 2021

Functional magnetic resonance imaging (fMRI) using a blood-oxygenation-level-dependent (BOLD) contrast is a common method for studying human brain function non-invasively. Gradient-echo (GRE) BOLD is highly sensitive to the blood oxygenation change in blood vessels; however, the spatial signal specificity can be degraded due to signal leakage from activated lower layers to superficial layers in depth-dependent (also called laminar or layer-specific) fMRI. Alternatively, physiological variables such as cerebral blood volume using the VAscular-Space-Occupancy (VASO) contrast have shown higher spatial specificity compared to BOLD. To better understand the physiological mechanisms such as blood volume and oxygenation changes and to interpret the measured depth-dependent responses, models are needed which reflect vascular properties at this scale. For this purpose, we extended and modified the “cortical vascular model” previously developed to predict layer-specific BOLD signal changes in human primary visual cortex to also predict a layer-specific VASO response. To evaluate the model, we compared the predictions with experimental results of simultaneous VASO and BOLD measurements in a group of healthy participants. Fitting the model to our experimental data provided an estimate of CBV change in different vascular compartments upon neural activity. We found that stimulus-evoked CBV change mainly occurs in small arterioles, capillaries and intracortical arteries, and that the contribution from venules and ICVs is small. Our results confirm that VASO is less susceptible to large vessel effects compared to BOLD, as blood volume changes in intracortical arteries did not substantially affect the resulting depth-dependent VASO profiles, whereas depth-dependent BOLD profiles showed a bias towards signal contributions from intracortical veins.
Male differentiation in the marine copepodOithona nanareveals the development of a new nervous ganglion linked to Lin12-Notch-Repeat protein-associated proteolysis
Authors: Sugier Kevin , Laso-Jadart Romuald , Vacherie Benoit , Käfer Jos , Bertrand Laurie , Labadie Karine , Martins Nathalie , Orvain Céline , Petit Emmanuelle , Poulain Julie , Wincker Patrick , Jamet Jean-Louis , Alberti Adriana , Madoui Mohammed-Amin
Published: May 2021

Background

Copepods are among the most numerous animals, and play an essential role in the marine trophic web and biogeochemical cycles. The genusOithonais described as having the highest density of copepods, and as being the most cosmopolite copepods. TheOithonamale paradox describes the activity states of males, which are obliged to alternate between immobile and mobile phases for ambush feeding and mate searching, respectively, while the female is typically less mobile and often feeding. To characterize the molecular basis of this sexual dimorphism, we combined immunofluorescence, genomics, transcriptomics, and protein-protein interaction approaches.

Results

Immunofluorescence of β3- and α-tubulin revealed two male-specific nervous ganglia in the lateral first segment of theOithona nanamale’s prosome. In parallel, transcriptomic analysis showed male-specific enrichment for nervous system development-related transcripts. Twenty-seven Lin12-Notch Repeat domain-containing protein coding genes (LDPGs) of the 75 LDPGs identified in the genome were specifically expressed only in males. Furthermore, most of the LDPGs (27%) coded for proteins having predicted proteolytic activity, and non-LDPG proteolysis-associated transcripts showed a male-specific enrichment. Using yeast double–hybrid assays, we constructed a protein-protein interaction network involving two LDPs with proteases, extracellular matrix proteins, and neurogenesis-related proteins.

Conclusions

For the first time, our study describes the lateral nervous ganglia ofO. nanamales, unique to copepods. We also demonstrated a role of LDPGs and their associated proteolysis in male-specific physiology, and we hypothesize a role of the LDPGs in the development of the lateral ganglia through directed lysis of the extracellular matrix for the growth of neurites and genesis of synapses.
PKC-ε Regulates Vesicle Delivery and Focal Exocytosis for Efficient IgG-mediated Phagocytosis
Authors: D’Amico Anna E. , Wong Alexander C. , Zajd Cheryl M. , Murali Ananya , Lennartz Michelle R.
Published: May 2021

PKC-ε is required for membrane addition during IgG-mediated phagocytosis; its role in this process is ill-defined. High resolution imaging revealed that PKC-ε exits the Golgi and enters phagosomes on vesicles that then fuse. TNF-α and PKC-α colocalize at the Golgi and on vesicles that enter the phagosome. Loss of PKC-ε and TNF-α delivery upon nocodazole treatment confirmed vesicular transport on microtubules. That TNF-α+vesicles are not delivered in macrophages from PKC-ε null mice, or upon dissociation of the Golgi-associated pool of PKC-ε, implicates Golgi-tethered PKC-ε as a driver of Golgi-to-phagosome trafficking. Finally, we established that PKC-ε’s regulatory domain is sufficient for delivery of TNF-α+vesicles to the phagosome. These studies reveal a novel role for PKC-ε in focal exocytosis: its regulatory domain drives Golgi-derived vesicles to the phagosome while catalytic activity is required for their fusion. This is one of the first examples of a PKC requirement for vesicular trafficking and describes a novel function for a PKC regulatory domain.

Golgi-tethered PKC-ε regulates vesicle trafficking along phagosomally-directed microtubules and vesicle fusion into forming phagosomes. Unexpectedly, the regulatory domain is sufficient for vesicle delivery.

Graphical Abstract

PKC-ε is required for Golgi-to-phagosome trafficking. Golgi-tethered PKC-ε+vesicles carry TNF-α to IgG phagosomes. Dissociation of PKC-ε from the Golgi with PIK93 or expression of hSac1-K2A prevents vesicle delivery. The regulatory domain of PKC-ε (εRD) is sufficient for vesicle delivery, but not fusion. Created withBioRender.com
Evaluation ofin vitroandin vivotoxicity of pristine molybdenum disulphide nanosheets in Swiss albino mice
Authors: Yadav Umakant , Singh Vimal , Mishra Himanshu , Saxena Preeti S. , Srivastava Anchal
Published: May 2021

The Molybdenum disulfide nanosheets (MoS2-NSs) thin films has received increasing attention recently due to their versatile multi functionality including catalytic properties, photoluminescence and flexibility, which suggests their future, uses for biomedical applications. However, there are no studies in detail related with biocompatibility of MoS2thin sheets. Here, weevaluated the dose-dependent effects of MoS2-NSs on cell viability (MTT assay) and release of lactate dehydrogenase (LDH) into culture media using MG-63 cells, as well as haemolysis, hematological, serum biochemical, antioxidants and histopathological parameters inSwiss albinomice. The MoS2-NSs was synthesizedviafacile hydrothermal method and characterized using XRD, Raman, SEM, TEM and HRTEM. Thein vitrostudy results suggest that at lower concentration MoS2-NSs does not causes any toxicity. The lethal dose (LD50) was evaluated by intraperitoneal administration with different concentrations and estimated as ~1.0 mg kg-1. The higher dose (1.5 mg kg-1) of MoS2-NSs showed significant alteration in hematological markers and serum biochemical enzymes, as compared to control. Lipid peroxidation also shows significant alteration with respect to the control. Histopathological, hematological and biochemical examination, revealed no remarkable changes at lower concentration (less than 1.0 mg kg-1), however, higher concentration (1.5 mg kg-1) causes significant histopathological, antioxidants and biochemical alterations in tissues and serum, respectively. The results suggest that the lower concentration of MoS2-NSs can be used in future biomedical applications.
Heterogeneity in viral infections increases the rate of deleterious mutation accumulation
Authors: Allman Brent , Koelle Katia , Weissman Daniel
Published: May 2021

1

RNA viruses have high mutation rates, with the majority of mutations being deleterious. We examine patterns of deleterious mutation accumulation over multiple rounds of viral replication, with a focus on how cellular coinfection and heterogeneity in viral output affect these patterns. Specifically, using agentbased intercellular simulations we find, in agreement with previous studies, that coinfection of cells by viruses relaxes the strength of purifying selection, and thereby increases the rate of deleterious mutation accumulation. We further find that cellular heterogeneity in viral output exacerbates the rate of deleterious mutation accumulation, regardless of whether this heterogeneity in viral output is stochastic or is due to variation in cellular multiplicity of infection. These results highlight the need to consider the unique life histories of viruses and their population structure to better understand observed patterns of viral evolution.