bluuebunny/crossref_metadata_2025 huggingface dataset:
Prevalence of RT-qPCR-detected SARS-CoV-2 infection at schools: First results from the Austrian School-SARS-CoV-2 prospective cohort study
Authors: Willeit Peter , Krause Robert , Lamprecht Bernd , Berghold Andrea , Hanson Buck , Stelzl Evelyn , Stoiber Heribert , Zuber Johannes , Heinen Robert , Köhler Alwin , Bernhard David , Borena Wegene , Doppler Christian , von Laer Dorothee , Schmidt Hannes , Pröll Johannes , Steinmetz Ivo , Wagner Michael
Published: January 2021

Background

The role of schools in the SARS-CoV-2 pandemic is much debated. We aimed to quantify reliably the prevalence of SARS-CoV-2 infections at schools detected with reverse-transcription quantitative polymerase-chain-reaction (RT-qPCR).

Methods

This nationwide prospective cohort study monitors a representative sample of pupils (grade 1-8) and teachers at Austrian schools throughout the school year 2020/2021. We repeatedly test participants for SARS-CoV-2 infection using a gargling solution and RT-qPCR. We herein report on the first two rounds of examinations. We used mixed-effect logistic regression to estimate odds ratios and robust 95% confidence intervals (95% CI).

Findings

We analysed data on 10734 participants from 245 schools (9465 pupils, 1269 teachers). Prevalence of SARS-CoV-2 infection increased from 0.39% at round 1 (95% CI 0.28-0·55%, 29 September-22 October 2020) to 1·39% at round 2 (95% CI 1·04-1·85%, 10-16 November). Odds ratios for SARS-CoV-2 infection were 2·26 (95% CI 1·25-4·12, P=0·007) in regions with >500 vs. ≤500 inhabitants/km2, 1·67 (95% CI 1·42-1·97, P<0·001) per two-fold higher regional 7-day incidence, and 2·78 (95% CI 1·73-4·48, P<0·001) in pupils at schools with high/very high vs. low/moderate social deprivation. Associations of community incidence and social deprivation persisted in a multivariable adjusted model. Prevalence did not differ by average number of pupils per class nor between age groups, sexes, pupils vs. teachers, or primary (grade 1-4) vs. secondary schools (grade 5-8).

Interpretation

This monitoring study in Austrian schools revealed SARS-CoV-2 infection in 0·39%-1·39% of participants and identified associations of regional community incidence and social deprivation with higher prevalence.

Funding

BMBWF Austria.
Ivermectin shows clinical benefits in mild to moderate COVID19: A randomised controlled double blind dose response study in Lagos
Authors: Babalola OE , Bode CO , Ajayi AA , Alakaloko FM , Akase IE , Otrofanowei E , Salu OB , Adeyemo WL , Ademuyiwa AO , Omilabu S
Published: January 2021

Introduction

In vitro studies have shown the efficacy of Ivermectin (IV) to inhibit the SARS - CoV-2 viral replication, but questions remained as to In-vivo applications. We set out to explore the efficacy and safety of Ivermectin in persons infected with COVID19.

Methods

We conducted a translational proof of concept (PoC) randomized, double blind placebo controlled, dose response, parallel group study of IV efficacy in RT - PCR proven COVID 19 positive patients. 62 patients were randomized to 3 treatment groups. (A) IV 6mg regime, (B)IV 12 mg regime (given Q84hrs for 2weeks) (C, control) Lopinavir/Ritonavir. All groups plus standard of Care.

Results

The Days to COVID negativity [DTN] was significantly and dose dependently reduced by IV (p = 0.0066). The DTN for Control were, = 9.1+/−5.2, for A 6.0 +/− 2.9, and for B 4.6 +/−3.2. 2 Way repeated measures ANOVA of ranked COVID 19 + / − scores at 0, 84, 168, 232 hours showed a significant IV treatment effect (p=0.035) and time effect (p <0.0001). IV also tended to increase SPO2 % compared to controls, p = 0.073, 95% CI - 0.39 to 2.59 and increased platelet count compared to C (p = 0.037) 95%CI 5.55 - 162.55 × 103/ml. The platelet count increase was inversely correlated to DTN (r = −0.52, p = 0.005). No SAE was reported.

Conclusions

12 mg IV regime may have superior efficacy. IV should be considered for use in clinical management of SARS-Cov-2, and may find applications in community prophylaxis in high-risk areas.
In Vivo Assessment of the Safety of Standard Fractionation Temporally Feathered Radiation Therapy (TFRT) for Head and Neck Squamous Cell Carcinoma: An R-IDEAL Stage 1/2a First-in-Humans/Feasibility Demonstration of New Technology Implementation
Authors: Parsai Shireen , Qiu Richard Lei J. , Qi Peng , Sedor Geoffrey , Fuller Clifton D. , Murray Eric , Majkszak David , Dorio Nicole , Koyfman Shlomo , Woody Neil , Joshi Nikhil , Scott Jacob G.
Published: January 2021

Introduction

Prior in silico simulations of studies of Temporally Feathered Radiation Therapy (TFRT) have demonstrated potential reduction in normal tissue toxicity. This R-IDEAL Stage 1/2A study seeks to demonstrate the first-in-human implementation of TFRT in treating patients with head and neck squamous cell carcinoma (HNSCC).

Materials and Methods

Patients with HNSCC treated with definitive radiation therapy were eligible (70 Gy in 35 fractions) were eligible. The primary endpoint was feasibility of TFRT planning as defined by radiation start within 15 days of CT simulation. Secondary endpoints included estimates of acute grade 3-5 toxicity.

Results

The study met its accrual goal of 5 patients. TFRT plans were generated in four of the five patients within 15 business days of CT simulation, therefore meeting the primary endpoint. One patient was not treated with TFRT at physician’s discretion, though the TFRT plan had been generated within sufficient time from the CT simulation. For patients who received TFRT, the median time from CT simulation to radiation start was 10 business days (range 8-15). The average time required for radiation planning was 6 days. In all patients receiving TFRT, each subplan and every daily fraction was delivered in the correct sequence without error. The OARs feathered included: oral cavity, each submandibular gland, each parotid gland, supraglottis, and posterior pharyngeal wall (OAR pharynx). Prescription dose PTV coverage (>95%) was ensured in each TFRT subplan and the composite TFRT plan. One of five patients developed an acute grade 3 toxicity.

Conclusions

This study demonstrates the first-in-human implementation of TFRT (R-IDEAL Stage 1), proving its feasibility in the modern clinical workflow. Additionally, assessments of acute toxicities and dosimetric comparisons to a standard radiotherapy plan were described (R-IDEAL Stage 2a).

Highlights

This prospective study is the first-in-human application for Temporally Feathered Radiation Therapy (TFRT).

In theory, TFRT may reduce radiation-induced toxicities by optimizing the time through which radiation is delivered and consequently improve normal tissue recovery.

In this study, patients with head and neck squamous cell carcinoma were treated with TFRT.

The primary endpoint of technical feasibility was met when patients were successfully treated with TFRT techniques without introducing delays in radiation commencement.
Representative Estimates of COVID-19 Infection Fatality Rates from Three Locations in India
Authors: Cai R. , Novosad P. , Tandel V. , Asher S. , Malani A.
Published: January 2021

There are very few estimates of the age-specific infection fatality rate (IFR) of SARS-CoV-2 in low- and middle-income countries. India reports the second highest number of SARS-CoV-2 infections in the world. We estimate age-specific IFR using data from seroprevalence surveys in Mumbai (population 12 million) and Karnataka (population 61 million), and a random sample of economically distressed migrants in Bihar with mortality followup. Among men aged 50–89, IFR is 0.12% in Karnataka (95% C.I. 0.09%–0.15%), 0.53% in Mumbai (0.52%–0.54%), and 5.64% among migrants in Bihar (0–11.16%). IFR in India is approximately twice as high for men as for women, is heterogeneous across contexts, and rises much less at older ages than in comparable studies from high income countries.
A novel age-informed approach for genetic association analysis in Alzheimer’s disease
Authors: Guen Yann Le , Belloy Michael E. , Napolioni Valerio , Eger Sarah J. , Kennedy Gabriel , Tao Ran , He Zihuai , Greicius Michael D. ,   for the Alzheimer’s Disease Neuroimaging Initiative
Published: January 2021

Introduction

Many Alzheimer’s disease (AD) genetic association studies disregard age or incorrectly account for it, hampering variant discovery.

Method

Using simulated data, we compared the statistical power of several models: logistic regression on AD diagnosis adjusted and not adjusted for age; linear regression on a score integrating case-control status and age; and multivariate Cox regression on age-at-onset. We applied these models to real exome-wide data of 11,127 sequenced individuals (54% cases) and replicated suggestive associations in 21,631 genotype-imputed individuals (51% cases).

Results

Modelling variable AD risk across age results in 10-20% statistical power gain compared to logistic regression without age adjustment, while incorrect age adjustment leads to critical power loss. Applying our novel AD-age score and/or Cox regression, we discovered and replicated novel variants associated with AD on KIF21B, USH2A, RAB10, RIN3 and TAOK2 genes.

Discussion

Our AD-age score provides a simple means for statistical power gain and is recommended for future AD studies.
Dopamine transporter in obesity: a meta-analysis
Authors: Pak Kyoungjune , Kim Keunyoung , Kim In Joo
Published: January 2021

The brain plays a major role in controlling the desire to eat. This meta-analysis aimed to assess the association between dopamine transporter (DAT) availability, and obesity. We performed a systematic search of MEDLINE (from inception to November 2020) and EMBASE (from inception to November 2020) for articles published in English using the keywords “dopamine transporter,” “obesity,” and “neuroimaging”. Data were plotted for each radiopharmaceutical, and linear regression was used to describe the relationship between DAT ratio, and body mass index (BMI), spline curves were adopted to fit data between DAT ratio and BMI. Five studies including 421 subjects were eligible for inclusion in this study. Two studies with 123I-FP-CIT, one with 99mTc-TRODAT, one with 123I-PE21, and one with 18F-FP-CIT were included. DAT availabilities from ENC-DAT project were higher than those from PPMI database both for caudate nucleus, and putamen. As there might be the inter-study variability, we calculated DAT ratio, after dividing DAT availabilities of subjects with overweight/obese BMI with mean DAT availabilities of subjects with normal BMI. In conclusion, we have shown that DAT availability of subjects with overweight/obesity was not different from those with normal BMI.
Plastid phylogenomics of theSansevieriaclade (Dracaena; Asparagaceae) resolves a rapid evolutionary radiation
Authors: van Kleinwee Iris , Larridon Isabel , Shah Toral , Bauters Kenneth , Asselman Pieter , Goetghebeur Paul , Leliaert Frederik , Veltjen Emily
Published: January 2021

Sansevierias are a diverse group of flowering plants native to Africa, Madagascar, the Arabian Peninsula and the Indian subcontinent, popular outside their native range as low maintenance houseplants. Traditionally recognized as a distinct genus,Sansevieriawas recently merged with the larger genusDracaenabased on molecular phylogenetic data. Within theSansevieriaclade, taxonomic uncertainties remain despite numerous attempts to classify the species. We aim to arrive at a robust phylogeny using a plastid phylogenomic approach, and estimate a time-frame of diversification to infer the evolutionary history of the group, including geographical and morphological evolution. Molecular data was obtained using genome skimming for 50Sansevieria, representing all informal groups previously instated based on morphology, and twoDracaena sensu strictospecies. The resulting Maximum Likelihood phylogenetic hypotheses are generally well supported, except for some very short branches along the backbone of the tree. The time-calibrated phylogeny indicates a recent rapid radiation with the main clades emerging in the Pliocene. Two well-supported clades align with previously defined informal groups, i.e.,SansevieriasectionDracomima, characterised by the Dracomima-type inflorescence, and theZeylanicagroup, native to the Indian subcontinent. Other morphologically defined informal groups are shown to be polyphyletic: a pattern due to convergent evolution of the identifying characters. Cylindrical leaves arose multiple times independently in the evolution of theSansevieriaclade and similarly, the Cephalantha-type inflorescence has originated multiple times from an ancestor with a Sansevieria-type inflorescence. To provide a more accessible tool for species identification and delimitation, genes and spacer regions were screened for variability and phylogenetic informativeness to investigate their potential as chloroplast DNA barcodes. Candidate chloroplast DNA barcodes include thetrnH-rpl12, ndhH-rps15, psbE-petL, psbT-psbN, rps18-rpl20intergenic spacers, the chloroplast generps8and the first intron ofycf3.
Genome Wide Association Study in the New Haven Lexinome Project IdentifiesGARRE1as a Novel Gene for Reading Performance
Authors: Adams Andrew K. , Guertin Emily L. , Truong Dongnhu T. , Atkinson Elizabeth G. , DeMille Mellissa M.C. , Bosson-Heenan Joan M. , Frijters Jan C. , Gruen Jeffrey R.
Published: January 2021

Despite high prevalence and high heritability, few candidate genes have been identified for reading disability. To identify novel genetic variants we performed a genome-wide association study (GWAS) using high-depth whole genome sequencing and predicated on reading performance in 407 subjects enrolled in a longitudinal study of response-to-intervention, called the New Haven Lexinome Project. The primary GWAS identified a single peak of 31 SNPs on chromosome 19 that achieved the threshold for genome-wide significance (rs2599553P=3.13×10−8) located over an expression quantitative trait locus (eQTL) forGARRE1(Granule Associated Rac And RHOG Effector 1). Little is known about the function ofGARRE1, except that it is highly and developmentally expressed in human cerebellum relative to cortex. Local ancestry regression showed the strongest association for the lead variant in African or Admixed American populations, who have been under-represented in previous genetic studies of reading. We replicated our chromosome 19 results in the Genes, Reading, and Dyslexia (GRaD) cohort and found a moderating effect of age with implications for the consideration of developmental effects in the design of future analyses. Growth curve modeling demonstrated that minor alleles of the lead SNP are related to reading longitudinally from Grade 1 to Grade 5, and that children with at least 1 minor allele of rs2599553 persistently underperformed relative to their peers by 0.33 to 0.5 standard deviations on standardized assessments of non-word decoding and reading fluency.

Significance Statement

To the best of our knowledge, this work represents the only GWAS predicated on longitudinal reading performance data. Starting with initial discovery, we replicate our association in a second cohort, address common causes of type I error, localize the signal to a single gene, implicate a region of the brain most likely to be affected by variation in our candidate, show a gene-by-age effect with implications for study design in this field, and demonstrate that minor alleles of our lead SNP are associated with significant and persistent clinical effects on reading development in children.
Respiratory and intestinal epithelial cells exhibit differential susceptibility and innate immune responses to contemporary EV-D68 isolates
Authors: Freeman Megan Culler , Wells Alexandra I. , Ciomperlik-Patton Jessica , Myerburg Michael M. , Anstadt Jennifer , Coyne Carolyn B.
Published: January 2021

Enterovirus D68 (EV-D68) has been implicated in outbreaks of severe respiratory illness and acute flaccid myelitis (AFM) and is detected in patient respiratory samples and from stool and wastewater, suggesting both respiratory and enteric routes of transmission. Here, we used a panel of EV-D68 isolates, including a historical isolate and multiple contemporary isolates from AFM outbreak years, to define the dynamics of viral replication and the host response to infection in primary human airway cells and stem cell-derived enteroids. We show that some recent EV-D68 isolates have decreased sensitivity to acid and temperature compared with an earlier isolate and that the respiratory, but not intestinal, epithelium induces a robust type III interferon (IFN) response that restricts infection. Our findings define the differential responses of the respiratory and intestinal epithelium to contemporary EV-D68 isolates and suggest that some isolates have the potential to target both the human airway and gastrointestinal tracts.
Inferring the basis of binaural detection with a modified autoencoder
Authors: Smith Samuel S. , Sollini Joseph , Akeroyd Michael A.
Published: January 2021

The binaural system utilizes interaural timing cues to improve the detection of auditory signals presented in noise. In humans, the binaural mechanisms underlying this phenomenon cannot be directly measured - and hence remain contentious. As an alternative, we trained modified autoencoder networks to mimic human-like behavior in a binaural detection task. The autoencoder architecture emphasizes interpretability and, hence, we “opened it up” to see if it could infer latent mechanisms underlying binaural detection. We found that the optimal network automatically developed artificial neurons with sensitivity to timing cues and with dynamics consistent with a cross-correlation mechanism. These computations were similar to neural dynamics reported in animal models. That these computations emerged to account for human hearing attests to their generality as a solution for binaural signal detection. Methodologically, the study examines the utility of explanatory-driven neural networks and how they may be used to infer mechanisms of audition.
Dinophyceae use exudates as weapons against the parasiteAmoebophryasp. (Syndiniales)
Authors: Marc Long , Dominique Marie , Jeremy Szymczak , Jordan Toullec , Estelle Bigeard , Marc Sourisseau , Mickael Le Gac , Laure Guillou , Cécile Jauzein
Published: January 2021

Parasites of the genusAmoebophryasp. are important contributors to marine ecosystems and can be determining factors in the demise of blooms of Dinophyceae, including microalgae commonly responsible for toxic red tides. Yet they rarely lead to the total collapse of Dinophyceae blooms. The addition of resistant Dinophyceae (Alexandrium minutumorScrippsiella donghaienis) or their exudate into a well-established host-parasite culture (Scrippsiella acuminata-Amoebophryasp.) mitigated the success of the parasite and increased the survival of the sensitive host. Effect were mediated via water-borne molecules without the need of a physical contact. Severity of the anti-parasitic defenses fluctuated depending on the species, the strain and its concentration, but never totally prevented the parasite transmission. The survival time ofAmoebophryasp. free-living stages (dinospores) decreased in presence ofA. minutumbut not ofS. donghaienis. The progeny drastically decreased with both species. Integrity of the membrane of dinospores was altered byA. minutumwhich provided a first indication on the mode of action of these anti-parasitic molecules. These results demonstrate that extracellular defenses are an effective strategy against parasites that does not only protect the resistant cells but also have the potential to affect the whole surrounding community.
Essential oil composition ofCallistemon citrinus(Curtis) and its protective assessment towardsTribolium castaneum(Herbst) (Coleoptera: Tenebrionidae)
Authors: Ramachandran Maduraiveeran , Baskar Kathirvelu , Hashem Abeer , Abd_Allah Elsayed Fathi , Jayakumar Manickkam
Published: January 2021

Essential oil (EO) was extracted fromCallistemon citrinusleaves by hydro-distillation. The extracted oil was analysed by GC and Mass Spectroscopy. Analysis report showed that the major constituent of the essential oil was eucalyptol (40.44%). The EO ofC. citrinusexhibited 100% fumigation toxicity (adult mortality) against adult and 95.8% larvicidal activity againstTribolium castaneumat 160 μL/L (12 hrs) and 320 μL/L (48 hrs), respectively. The effective concentration of 37.05 μL/L (adult) and 144.31 μL/L (larva) at 24 and 48 hrs respectively. A 100% repellent activity was observed at 20 μl for adult beetles and 93.3% for larvae ofT. castaneumat 20 μl after 24 h. Exposure toC. citrinusEO significantly reduced beetle fecundity, ovicidal activity, egg hatching, larvae survival, and emergence of adult. The effect of EO on detoxification enzymes ofT. castaneumadults was examined. Results indicated that the activity of detoxification enzymes drastically varied when compared with control. This EO had toxicant effects on all stages of the life ofT. castaneum. Hence it may be used as fumigant instead of the use of using synthetic chemical fumigants.
Covid19Risk.ai: An open source repository and online calculator of prediction models for early diagnosis and prognosis of Covid-19
Authors: Halilaj Iva , Chatterjee Avishek , van Wijk Yvonka , Wu Guangyao , van Eeckhout Brice , Oberije Cary , Lambin Philippe
Published: January 2021

Objective

The current pandemic has led to a proliferation of predictive models being developed to address various aspects of COVID-19 patient care. We aimed to develop an online platform that would serve as an open source repository for a curated subset of such models, and provide a simple interface for included models to allow for online calculation. This platform would support doctors during decision-making regarding diagnoses, prognoses, and follow-up of COVID-19 patients, expediting the models’ transition from research to clinical practice.

Methods

In this proof-of-principle study, we performed a literature search in PubMed and WHO database to find suitable models for implementation on our platform. All selected models were publicly available (peer reviewed publications or open source repository) and had been validated (TRIPOD type 3 or 2b). We created a method for obtaining the regression coefficients if only the nomogram was available in the original publication. All predictive models were transcribed on a practical graphical user interface using PHP 8.0.0, and published online together with supporting documentation and links to the associated articles.

Results

The open source websitehttps://covid19risk.ai/currently incorporates nine models from six different research groups, evaluated on datasets from different countries. The website will continue to be populated with other models related to COVID-19 prediction as these become available. This dynamic platform allows COVID-19 researchers to contact us to have their model curated and included on our website, thereby increasing the reach and real-world impact of their work.

Conclusion

We have successfully demonstrated in this proof-of-principle study that our website provides an inclusive platform for predictive models related to COVID-19. It enables doctors to supplement their judgment with patient-specific predictions from externally-validated models in a user-friendly format. Additionally, this platform supports researchers in showcasing their work, which will increase the visibility and use of their models.
How to attract and retain health workers in rural areas of a fragile state: findings from a labour market survey in Guinea
Authors: Witter Sophie , Herbst Christopher H. , Smitz Marc , Balde Mamadou Dioulde , Magazi Ibrahim , Zaman Rashid U.
Published: January 2021

Most countries face challenges attracting and retaining health staff in remote areas but this is especially acute in fragile and shock-prone contexts, like Guinea, where imbalances in staffing are high and financial and governance arrangements to address rural shortfalls are weak.

The objective of this study was to understand how health staff could be better motivated to work and remain in rural, under-served areas in Guinea. In order to inform the policy dialogue on strengthening human resources for health, we conducted three nationally representative cross-sectional surveys, adapted from tools used in other fragile contexts.

We found that the locational job preferences of health workers in Guinea are particularly influenced by opportunities for training, working conditions, and housing. Most staff are satisfied with their work and with supervision, however, financial aspects and working conditions are considered least satisfactory, and worrying findings include the high proportion of staff favouring emigration, their high tolerance of informal user payments, as well as their limited exposure to rural areas during training.

Based on our findings, we highlight measures which could improve rural recruitment and retention in Guinea and similar settings. These include offering upgrading and specialization in return for rural service; providing greater exposure to rural areas during training; increasing recruitment from rural areas; experimenting with fixed term contracts in rural areas; and improving working conditions in rural posts. The development of incentive packages should be accompanied by action to tackle wider issues, such as reforms to training and staff management.
The chromatin remodelling factor Chd7 protects auditory neurons and sensory hair cells from stress-induced degeneration
Authors: Ahmed Mohi , Moon Ruth , Prajapati Ravindra Singh , James Elysia , Basson M. Albert , Streit Andrea
Published: January 2021

Neurons and sensory cells are particularly vulnerable to oxidative stress due to their high oxygen demand during stimulus perception and transmission1-4. The mechanisms that protect them from stress-induced death and degeneration remain elusive. Here we show that embryonic deletion of the chromodomain helicase DNA-binding protein 7 (CHD7) in auditory neurons or hair cells leads to sensorineural hearing loss due to postnatal degeneration of both cell types. Mechanistically, we demonstrate thatCHD7controls the expression of major stress pathway components. In its absence, hair cells are hypersensitive, dying rapidly after brief exposure to stress inducers, suggesting that sound at the onset of hearing triggers their degeneration. In humans,CHD7haploinsufficiency causes CHARGE syndrome, a disorder affecting multiple organs including the ear5,6. Our findings suggest thatCHD7mutations cause developmentally silent phenotypes that predispose cells to postnatal degeneration due to a failure of protective mechanisms.
A nuclear pore sub-complex restricts the propagation of Ty retrotransposons by limiting their transcription
Authors: Bonnet Amandine , Chaput Carole , Palancade Benoit , Lesage Pascale
Published: January 2021

Beyond their canonical function in nucleocytoplasmic exchanges, nuclear pore complexes (NPCs) regulate the expression of protein-coding genes. Here, we have implemented transcriptomic and molecular methods to specifically address the impact of the NPC on retroelements, which are present in multiple copies in genomes. We report a novel function for the Nup84 complex, a core NPC building block, in specifically restricting the transcription of LTR-retrotransposons in yeast. Nup84 complex-dependent repression impacts bothCopiaandGypsyTy LTR-retrotransposons, all over theS. cerevisiaegenome. Mechanistically, the Nup84 complex restricts the transcription of Ty1, the most active yeast retrotransposon, through the tethering of the SUMO-deconjugating enzyme Ulp1 to NPCs. Strikingly, the modest accumulation of Ty1 RNAs caused by Nup84 complex loss-of-function is sufficient to trigger an important increase of Ty1 cDNA levels, resulting in massive Ty1 retrotransposition. Altogether, our studies expand our understanding of the complex interactions between retrotransposons and the NPC, and highlight the importance for the cells to keep retrotransposon under tight transcriptional control.

AUTHOR SUMMARY

Retroelements, which replicate by reverse transcription of their RNA into a cDNA that is integrated into the host genetic material, play an important role in the plasticity of eukaryotic genomes. The study of yeast retrotransposons has led to the identification of host factors that limit retroelement mobility, including components of the nuclear pore complex (NPC), most of them still awaiting mechanistic characterization. Here, we investigated the contribution of the Nup84 complex, a core NPC scaffold, to retrotransposon biology in budding yeast. Our findings uncover that the Nup84 complex restricts the transcription of phylogenetically-distinct Ty retroelements. By focusing on Ty1 retrotransposons, we provide evidence that repression by the Nup84 complex depends on the maintenance at the NPC of the SUMO-protease Ulp1, an essential enzyme of the SUMO pathway with multiple targets in the transcription machinery. We finally show that this transcriptional control is critical for genome dynamics, since a small increase in the accumulation of Ty1 RNAs leads to massive retrotransposition. Our data reveal that although relatively abundant, Ty transcripts are limiting for retrotransposition, underscoring the importance of a tight control of their expression. They also characterize a new non-canonical function of NPCs, confirming their connection with genome expression and stability.
MAVERICC: Efficient marker-free rescue of vaccinia virus recombinants byin vitroCRISPR-Cas9 engineering
Authors: Laudermilch Ethan , Chandran Kartik
Published: January 2021

Vaccinia virus (VACV)-based vectors are in extensive use as vaccines and cancer immunotherapies. VACV engineering has traditionally relied on homologous recombination between a parental viral genome and a transgene-bearing transfer plasmid, a highly inefficient process that necessitates the use of a selection or screening marker to isolate recombinants. Recent extensions of this approach have sought to enhance the recovery of transgene-bearing viruses through the use of CRISPR-Cas9 engineering to cleave the viral genome in infected cells. However, these methods do not completely eliminate the generation of WT viral progeny and thus continue to require multiple rounds of viral propagation and plaque purification. Here, we describe MAVERICC (marker-freevaccinia virusengineering of recombinants throughin vitroCRISPR/Cas9cleavage), a new strategy to engineer recombinant VACVs in a manner that overcomes current limitations. MAVERICC also leverages the CRISPR/Cas9 system but requires no markers and yields essentially pure preparations of the desired recombinants in a single step. We used this approach to rapidly introduce point mutations, insertions, and deletions at multiple locations in the VACV genome, both singly and in combination. The efficiency and versatility of MAVERICC make it an ideal choice for generating mutants and mutant libraries at arbitrarily selected locations in the viral genome to build complex VACV vectors, effect vector improvements, and facilitate the study of poxvirus biology.

Graphical Abstract

Overview of MAVERICC.Conceptual overview of the approach outlined in this manuscript. To make VACV recombinants, the parental virus is first purified and vDNA is isolated with phenol:chloroform extraction. This purified vDNA is then treated with Cas9 enzyme and sgRNAs that are directed to a specific locus in the VACV genome. The cleaved vDNA is then transfected into FWPV-infected BSC-40 cells along with a transfer amplicon containing an insertion or mutation of interest flanked by homologous sequences. Recombination is allowed to occur for 5-7 days, during which time the cleaved vDNA is healed by the transfer amplicon, thus editing the VACV genome, and packaged into infectious viral particles. Individual plaques are grown up and rVACVs are isolated after a single round of plaque purification. Image was created with Biorender.com.
A novel skeletal-specific adipogenesis pathway defines key origins and adaptations of bone marrow adipocytes with age and disease
Authors: Robles Hero , Zhang Xiao , Magee Kristann L. , Lorenz Madelyn R. , Wang Zhaohua , Harris Charles A. , Craft Clarissa S. , Scheller Erica L.
Published: January 2021

Bone marrow adipocytes (BMAs) accumulate with age and in diverse disease states. However, their age- and disease-specific origins and adaptations remain unclear, impairing our understanding of their context-specific endocrine functions and relationship with surrounding tissues. In this study, we identified a novel, bone marrow-specific adipogenesis pathway using theAdipoqCre+/DTA+‘fat free’ mouse (FF), a model in whichAdipoq-Cre drives diphtheria toxin-induced cell death in all adiponectin-expressing cells. Adiponectin is highly expressed by BMAs, peripheral adipocytes, and a subset of bone marrow stromal progenitor cells with preadipocyte-like characteristics. Consistent with this, FF mice presented with uniform depletion of peripheral white and brown adipose tissues, in addition to loss of BMAs in canonical locations such as the tail vertebrae. However, unexpectedly, a distinctly localized subset of BMAs accumulated with age in FF mice in regions such as the femoral and tibial diaphysis that are generally devoid of bone marrow adipose tissue (BMAT). Ectopic BMAs in FF mice were defined by increased lipid storage and decreased expression of cytokines including hematopoietic support factorCxcl12and adipokines adiponectin, resistin, and adipsin. FF BMAs also displayed resistance to lipolytic stimuli including cold stress and β3-adrenergic agonist CL316,243. This was associated with reduced expression of adrenergic receptors and monoacylglycerol lipase. Global ablation of adiponectin-expressing cells regulated bone accrual in an age- and sex-dependent manner. High bone mass was present early in life and this was more pronounced in females. However, with age, both male and female FF mice had decreased cortical thickness and mineral content. In addition, unlike BMAs in healthy mice, expansion of ectopic BMAs in FF mice was inversely correlated with cortical bone volume fraction. Subcutaneous fat transplant and normalization of systemic metabolic parameters was sufficient to prevent ectopic BMA expansion in FF mice but did not prevent the initial onset of the high bone mass phenotype. Altogether, this defines a novel, secondary adipogenesis pathway that relies on recruitment of adiponectin-negative stromal progenitors. This pathway is unique to the bone marrow and is activated with age and in states of metabolic stress, resulting in expansion of BMAs specialized for lipid storage with compromised lipid mobilization and endocrine function within regions traditionally devoted to hematopoiesis. Our findings further distinguish BMAT from peripheral adipose tissues and contribute to our understanding of BMA origins and adaptation with age and disease.
Training level reveals a dynamic dialogue between stress and memory systems in birds
Authors: Lormant Flore , Ferreira Vitor Hugo Bessa , Lemarchand Julie , Cornilleau Fabien , Constantin Paul , Parias Céline , Bertin Aline , Lansade Léa , Leterrier Christine , Lévy Frédéric , Calandreau Ludovic
Published: January 2021

It is now well-accepted that memory is a dynamic process, and that stress and training level may influence which memory system an individual engages when solving a task. In this work, we investigated whether and how chronic stress impacts spatial and cue-based memories according to training level. To that aim, control and chronically stressed Japanese quail were trained in a task that could be solved using spatial and cue-based memory and tested for their memory performances after 5 and 15 training days (initial training and overtraining, respectively) and following an emotional challenge (exposure to an open field). While chronic stress negatively impacted spatial memory in chronically stressed birds after initial training, this impact was lowered after overtraining compared to control quail. Interestingly, the emotional challenge reinstated the differences in performance between the two groups, revealing that chronic stress/overtraining did not eliminate spatial memory. Differences caused by previous stressors can re-emerge depending on the more immediate psychological state of the individual. Contrary to spatial memory, cue-based memory was not impaired in any test occasion, confirming that this form of memory is resistant to chronic stress. Altogether these findings reveal a dynamic dialogue between stress, training, and memory systems in birds.
Weight loss response following lifestyle intervention associated with baseline gut metagenomic signature in humans
Authors: Diener Christian , Qin Shizhen , Zhou Yong , Patwardhan Sushmita , Tang Li , Lovejoy Jennifer , Magis Andrew T. , Price Nathan D. , Hood Leroy , Gibbons Sean M.
Published: January 2021

We report a weight-loss response analysis on a small cohort of individuals (N=25) selected from a larger population (N∼5,000) enrolled in a commercial scientific wellness program, which included healthy lifestyle coaching. Each individual had baseline data on blood metabolomics, blood proteomics, clinical labs, lifestyle questionnaires, and stool metagenomes. A subset of these participants (N=15) lost at least 10% of their body weight within a 6-12 month period and saw significant improvement in metabolic health markers (‘weight loss’ group), while another subset of individuals (N=10) undergoing the same lifestyle intervention showed no change in BMI over the same timeframe (‘no weight loss’ group). Only a single baseline blood analyte, a metabolite linked to fried food consumption, was (negatively) associated with weight loss, but a large number of baseline stool metagenomic features, including complex polysaccharide and protein degradation genes, stress-response genes, respiration-related genes, cell wall synthesis genes, and gut bacterial replication rates, were significantly associated with weight loss after explicitly controlling for baseline BMI. Together, these results provide a set of baseline gut microbiome functional features that are associated with weight loss outcomes.
Generation of PathogenicTPP1Mutations in Human Stem Cells as a Model for CLN2 Disease
Authors: Ma Li , Prada Adriana , Schmidt Michael , Morrow Eric M.
Published: January 2021

Neuronal ceroid lipofuscinosis type 2 (CLN2 disease) is an autosomal recessive neurodegenerative disorder generally with onset at 2 to 4 years of age and characterized by seizures, loss of vision, progressive motor and mental decline, and premature death. CLN2 disease is caused by loss-of-function mutations in the tripeptidyl peptidase 1 (TPP1) gene leading to deficiency in TPP1 enzyme activity. Approximately 60% of patients have one of two pathogenic variants (c.509-1G>C or c.622C>T [p.(Arg208*)]). In order to generate a human stem cell model of CLN2 disease, we used CRISPR/Cas9-mediated knock-in technology to introduce these mutations in a homozygous state into H9 human embryonic stem cells. Heterozygous lines of the c.622C>T (p.(Arg208*)) mutation were also generated, which included a heterozygous mutant with a wild-type allele and different compound heterozygous coding mutants resulting from indels on one allele. We describe the methodology that led to the generation of the lines and provide data on the initial validation and characterization of these CLN2 disease models. Notably, both mutant lines (c.509-1G>C and c.622C>T [p.(Arg208*)]) in the homozygous state were shown to have reduced or absent protein, respectively, and deficiency of TPP1 enzyme activity. These models, which we are making available for wide-spread sharing, will be useful for future studies of molecular and cellular mechanisms underlying CLN2 disease and for therapeutic development.
Burden is in the eye of the beholder: Sensitivity of yellow fever disease burden estimates to modeling assumptions
Authors: Perkins T. Alex , Huber John H. , Minh Quan Tran , Oidtman Rachel J. , Walters Magdalene K. , Siraj Amir S. , Moore Sean M.
Published: January 2021

Geographically stratified estimates of disease burden play an important role in setting priorities for the management of different diseases and for targeting interventions against a single disease. Such estimates involve numerous assumptions, which uncertainty about is not always well accounted for. We developed a framework for estimating the burden of yellow fever in Africa and evaluated its sensitivity to assumptions about the interpretation of serological data and choice of regression model. We addressed the latter with an ensemble approach, and we found that the former resulted in a nearly twentyfold difference in burden estimates (range of central estimates: 8.4×104-1.5×106deaths in 2021-2030). Even so, statistical uncertainty made even greater contributions to variance in burden estimates (87%). Combined with estimates that most infections go unreported (range of 95% credible intervals: 99.65-99.99%), our results suggest that yellow fever’s burden will remain highly uncertain without major improvements in surveillance.
Impaired performance of SARS-CoV-2 antigen-detecting rapid tests at elevated temperatures
Authors: Haage Verena , de Oliveira-Filho Edmilson Ferreira , Moreira-Soto Andres , Kühne Arne , Fischer Carlo , Sacks Jilian , Corman Victor Max , Müller Marcel A. , Drosten Christian , Drexler Jan Felix
Published: January 2021

Rapid antigen-detecting tests (Ag-RDTs) can complement molecular diagnostics for COVID-19. The recommended temperature for storage of SARS-CoV-2 Ag-RDTs ranges between 5-30°C. In many countries that would benefit from SARS-CoV-2 Ag-RDTs, mean temperatures exceed 30°C. We assessed analytical sensitivity and specificity of eleven commercially available SARS-CoV-2 Ag-RDTs using different storage and operational temperatures, including (i) long-term storage and testing at recommended conditions, (ii) recommended storage conditions followed by 10 minutes exposure to 37°C and testing at 37°C and (iii) 3 weeks storage followed by testing at 37°C. The limits of detection of SARS-CoV-2 Ag-RDTs under recommended conditions ranged from 8.2×105-7.9×107genome copies/ml of infectious SARS-CoV-2 cell culture supernatant. Despite long-term storage at recommended conditions, 10 minutes pre-incubation of Ag-RDTs and testing at 37°C resulted in about ten-fold reduced sensitivity for 46% of SARS-CoV-2 Ag-RDTs, including both Ag-RDTs currently listed for emergency use by the World Health Organization. After 3 weeks of storage at 37°C, 73% of SARS-CoV-2 Ag-RDTs exhibited about ten-fold reduced sensitivity. Specificity of SARS-CoV-2 Ag-RDTs using cell culture-derived human coronaviruses HCoV-229E and HCoV-OC43 was not affected by storage and testing at 37°C. In summary, short- and long-term exposure to elevated temperatures likely impairs sensitivity of several SARS-CoV-2 Ag-RDTs that may translate to false-negative test results at clinically relevant virus concentrations compatible with inter-individual transmission. Ensuring appropriate transport and storage conditions, and development of tests that are more robust across temperature fluctuations will be important for accurate use of SARS-CoV-2 Ag-RDTs in tropical settings.
Stochastic model for COVID-19 in slums: interaction between biology and public policies
Authors: Solari Hernan G. , Natiello Mario A.
Published: January 2021

We present a mathematical model for the simulation of the development of an outbreak of COVID-19 in a slum area under different interventions. Instead of representing interventions as modulations of the parameters of a free running epidemic we introduce a model structure that accounts for the actions but does not assume the results. The disease is modelled in terms of the progression of viremia reported in scientific works. The emergence of symptoms in the model reflects the statistics of a nation-wide highly detailed database consisting of more than 62000 cases (about a half of the confirmed by RT-PCR tests) with recorded symptoms in Argentina. The stochastic model displays several of the characteristics of COVID-19 such as a high variability in the evolution of the outbreaks, including long periods in which they run undetected, spontaneous extinction followed by a late outbreak and unimodal as well as bimodal progressions of daily counts of cases (second waves without ad-hoc hypothesis). We show how the relation between undetected cases (including the 'asymptomatic' cases) and detected cases changes as a function of the public policies, the efficiency of the implementation and the timing with respect to the development of the outbreak. We show also that the relation between detected cases and total cases strongly depends on the implemented policies and that detected cases cannot be regarded as a measure of the outbreak, being the dependency between total cases and detected cases in general not monotonic as a function of the efficiency in the intervention method. According to the model, it is possible to control an outbreak with interventions based on the detection of symptoms only in the case when the presence of just one symptom prompts isolation and the detection efficiency reaches about 80% of the cases. Requesting two symptoms to trigger intervention can be enough to fail in the goals.
Massively parallel disruption of enhancers active during human corticogenesis
Authors: Geller Evan , Gockley Jake , Emera Deena , Uebbing Severin , Cotney Justin , Noonan James P.
Published: January 2021

Changes in gene regulation have been linked to the expansion of the human cerebral cortex and to neurodevelopmental disorders. However, the biological effects of genetic variation within developmental regulatory elements on human corticogenesis are not well understood. We used sgRNA-Cas9 genetic screens in human neural stem cells (hNSCs) to disrupt 10,674 expressed genes and 2,227 enhancers active in the developing human cortex and determine the resulting effects on cellular proliferation. Gene disruptions affecting proliferation were enriched for genes associated with risk for human neurodevelopmental phenotypes including primary microcephaly and autism spectrum disorder. Although disruptions in enhancers had overall weaker effects on proliferation than gene disruptions, we identified enhancer disruptions that severely perturbed hNSC self-renewal. Disruptions in Human Accelerated Regions and Human Gain Enhancers, regulatory elements implicated in the evolution of the human brain, also perturbed hNSC proliferation, establishing a role for these elements in human neurodevelopment. Integrating proliferation phenotypes with chromatin interaction maps revealed regulatory relationships between enhancers and target genes that contribute to neurogenesis and potentially to human cortical evolution.