bluuebunny/crossref_metadata_2025 huggingface dataset:
Development and validation of a prognostic model for COVID-19: a population-based cohort study in Iceland
Authors: Eythorsson Elias , Bjarnadottir Valgerdur , Runolfsdottir Hrafnhildur Linnet , Helgason Dadi , Ingvarsson Ragnar Freyr , Bjornsson Helgi K , Olafsdóttir Lovisa Bjork , Bjarnadottir Solveig , Agustsson Arnar Snaer , Oskarsdottir Kristin , Thorvaldsson Hrafn Hliddal , Kristjansdottir Guðrun , Bjornsson Aron Hjalti , Emilsdottir Arna R , Armannsdottir Brynja , Guðlaugsson Olafur , Hansdottir Sif , Gottfredsson Magnus , Bjarnason Agnar , Sigurdsson Martin I , Indridason Olafur S , Palsson Runolfur
Published: July 2021

Background

The severity of SARS-CoV-2 infection varies from asymptomatic state to severe respiratory failure and the clinical course is difficult to predict. The aim of the study was to develop a prognostic model to predict the severity of COVID-19 at the time of diagnosis and determine risk factors for severe disease.

Methods

All SARS-CoV-2-positive adults in Iceland were prospectively enrolled into a telehealth service at diagnosis. A multivariable proportional-odds logistic regression model was derived from information obtained during the enrollment interview with those diagnosed before May 1, 2020 and validated in those diagnosed between May 1 and December 31, 2020. Outcomes were defined on an ordinal scale; no need for escalation of care during follow-up, need for outpatient visit, hospitalization, and admission to intensive care unit (ICU) or death. Risk factors were summarized as odds ratios (OR) adjusted for confounders identified by a directed acyclic graph.

Results

The prognostic model was derived from and validated in 1,625 and 3,131 individuals, respectively. In total, 375 (7.9%) only required outpatient visits, 188 (4.0%) were hospitalized and 50 (1.1%) were either admitted to ICU or died due to complications of COVID-19. The model included age, sex, body mass index (BMI), current smoking, underlying conditions, and symptoms and clinical severity score at enrollment. Discrimination and calibration were excellent for outpatient visit or worse (C-statistic 0.75, calibration intercept 0.04 and slope 0.93) and hospitalization or worse (C-statistic 0.81, calibration intercept 0.16 and slope 1.03). Age was the strongest risk factor for adverse outcomes with OR of 75-compared to 45-year-olds, ranging from 5.29-17.3. Higher BMI consistently increased the risk and chronic obstructive pulmonary disease and chronic kidney disease correlated with worse outcomes.

Conclusion

Our prognostic model can accurately predict the outcome of SARS-CoV-2 infection using information that is available at the time of diagnosis.
Children with SARS-CoV-2 in the National COVID Cohort Collaborative (N3C)
Authors: Martin Blake , DeWitt Peter E. , Russell Seth , Anand Adit , Bradwell Katie R. , Bremer Carolyn , Gabriel Davera , Girvin Andrew T. , Hajagos Janos G. , McMurry Julie A. , Neumann Andrew J. , Pfaff Emily R. , Walden Anita , Wooldridge Jacob T. , Yoo Yun Jae , Saltz Joel , Gersing Ken R. , Chute Christopher G. , Haendel Melissa A. , Moffitt Richard , Bennett Tellen D.
Published: July 2021

Importance

SARS-CoV-2

Objective

To determine the characteristics, changes over time, outcomes, and severity risk factors of SARS-CoV-2 affected children within the National COVID Cohort Collaborative (N3C)

Design

Prospective cohort study of patient encounters with end dates before May 27th, 2021.

Setting

45 N3C institutions

Participants

Children <19-years-old at initial SARS-CoV-2 testing

Main Outcomes and Measures

Case incidence and severity over time, demographic and comorbidity severity risk factors, vital sign and laboratory trajectories, clinical outcomes, and acute COVID-19 vs MIS-C contrasts for children infected with SARS-CoV-2.

Results

728,047 children in the N3C were tested for SARS-CoV-2; of these, 91,865 (12.6%) were positive. Among the 5,213 (6%) hospitalized children, 685 (13%) met criteria for severe disease: mechanical ventilation (7%), vasopressor/inotropic support (7%), ECMO (0.6%), or death/discharge to hospice (1.1%). Male gender, African American race, older age, and several pediatric complex chronic condition (PCCC) subcategories were associated with higher clinical severity (p≤0.05). Vital signs (all p≤0.002) and many laboratory tests from the first day of hospitalization were predictive of peak disease severity. Children with severe (vs moderate) disease were more likely to receive antimicrobials (71% vs 32%, p<0.001) and immunomodulatory medications (53% vs 16%, p<0.001).

Compared to those with acute COVID-19, children with MIS-C were more likely to be male, Black/African American, 1-to-12-years-old, and less likely to have asthma, diabetes, or a PCCC (p<0.04). MIS-C cases demonstrated a more inflammatory laboratory profile and more severe clinical phenotype with higher rates of invasive ventilation (12% vs 6%) and need for vasoactive-inotropic support (31% vs 6%) compared to acute COVID-19 cases, respectively (p<0.03).

Conclusions

In the largest U.S. SARS-CoV-2-positive pediatric cohort to date, we observed differences in demographics, pre-existing comorbidities, and initial vital sign and laboratory test values between severity subgroups. Taken together, these results suggest that early identification of children likely to progress to severe disease could be achieved using readily available data elements from the day of admission. Further work is needed to translate this knowledge into improved outcomes.
Effectiveness of the ChAdOx1 vaccine in the elderly during SARS-CoV-2 Gamma variant transmission in Brazil
Authors: Hitchings Matt D.T. , Ranzani Otavio T. , Dorion Murilo , D’Agostini Tatiana Lang , de Paula Regiane Cardoso , de Paula Olivia Ferreira Pereira , de Moura Villela Edlaine Faria , Scaramuzzini Torres Mario Sergio , de Oliveira Silvano Barbosa , Schulz Wade , Almiron Maria , Said Rodrigo , de Oliveira Roberto Dias , da Silva Patricia Vieira , de Araújo Wildo Navegantes , Gorinchteyn Jean Carlo , Andrews Jason R. , Cummings Derek A.T. , Ko Albert I. , Croda Julio
Published: July 2021

Background

A two-dose regimen of ChAdOx1 coronavirus disease 19 (Covid-19) vaccine with an inter-dose interval of three months has been implemented in many countries with restricted vaccine supply. However, there is limited evidence for the effectiveness of ChAdOx1 by dose in elderly populations in countries with high prevalence of the Gamma variant of severe acute respiratory syndrome 2 (SARS-CoV-2).

Methods

We conducted a test-negative case-control study to estimate the effectiveness of ChAdOx1 vaccine in adults aged 60 years or older during a Gamma-variant-associated epidemic in São Paulo state, Brazil, between 17 January and 2 July 2021. Cases and matched test-negative controls were individuals, identified from surveillance databases, who experienced an acute respiratory illness and underwent SARS-CoV-2 RT-PCR testing. We used conditional logistic regression to estimate the effectiveness by dose against RT-PCR-confirmed Covid-19, Covid-19 hospitalization, and Covid-19-related death.

Results

61,164 individuals were selected into matched case-control pairs. Starting ≥28 days after the first dose, adjusted effectiveness of a single dose of ChAdOx1 was 33.4% (95% CI, 26.4 to 39.7) against Covid-19, 55.1% (95% CI, 46.6 to 62.2) against hospitalization, and 61.8% (95% CI, 48.9 to 71.4) against death. Starting ≥14 days after the second dose, the adjusted effectiveness of the two-dose schedule was 77.9% (95% CI, 69.2 to 84.2) against Covid-19, 87.6% (95% CI, 78.2 to 92.9) against hospitalization, and 93.6% (95% CI, 81.9 to 97.7) against death.

Conclusions

Completion of the ChAdOx1 vaccine schedule afforded significantly increased protection over a single dose against mild and severe Covid-19 outcomes in elderly individuals during widespread Gamma variant transmission.
Forward planning driven by context-dependent conflict processing in anterior cingulate cortex
Authors: Ott Florian , Legler Eric , Kiebel Stefan J.
Published: July 2021

Forward planning is often essential to achieve goals over extended time periods. However, forward planning is typically computationally costly for the brain and should only be employed when necessary. The explicit calculation of how necessary forward planning will be, is in itself computationally costly. We therefore assumed that the brain generates a mapping from a particular situation to a proxy of planning value to make fast decisions about whether to use forward planning, or not. Moreover, since the state space of real world decision problems can be large, we hypothesized that such a mapping will rely on mechanisms that generalize sets of situations based on shared demand for planning. We tested this hypothesis in an fMRI study using a novel complex sequential task. Our results indicate that participants abstracted from the set of task features to more generalized control contexts that govern the balancing between forward planning and a simple response strategy. Strikingly, we found that correlations of conflict with response time and with activity in the dorsal anterior cingulate cortex were dependent on context. This context-dependency might reflect that the cognitive control system draws on category-based cognition, harnessing regularities in control demand across task space to generate control contexts that help reduce the complexity of control allocation decisions.
The effect of singers’ masks on the impulse dispersion of aerosols during singing
Authors: Echternach Matthias , Herrmann Laila , Gantner Sophia , Tur Bogac , Peters Gregor , Westphalen Caroline , Benthaus Tobias , Köberlein Marie , Kuranova Liudmila , Döllinger Michael , Kniesburges Stefan
Published: July 2021

Background

During the Covid-19 pandemic, singing activities were restricted due to several super-spreading events that have been observed during rehearsals and vocal performances. However, it has not been clarified how the aerosol dispersion, which has been assumed to be the leading transmission factor, could be reduced by masks which are specially designed for singers.

Material and Methods

12 professional singers (10 of the Bavarian Radio-Chorus and two freelancers, 7 females and 5 males) were asked to sing the melody of the ode of joy of Beethoven’s 9thsymphony “Freude schöner Götterfunken, Tochter aus Elysium” in D-major without masks and afterwards with five different singers’ masks, all distinctive in their material and proportions. Every task was conducted after inhaling the basic liquid from an e-cigarette. The aerosol dispersion was recorded by three high-definition video cameras during and after the task. The cloud was segmented and the dispersion was analyzed for all three spatial dimensions. Further, the subjects were asked to rate the practicability of wearing the tested masks during singing activities using a questionnaire.

Results

Concerning the median distances of dispersion, all masks were able to decrease the impulse dispersion of the aerosols to the front. In contrast, the dispersion to the sides and to the top was increased. The evaluation revealed that most of the subjects would reject performing a concert with any of the masks.

Conclusion

Although, the results exhibit that the tested masks could be able to reduce the radius of aerosol expulsion for virus-laden aerosol particles, there are more improvements necessary to enable the practical implementations for professional singing.
Nonlinear Functional Network Connectivity in Resting Fmri Data
Authors: Motlaghian S. M. , Belger A. , Bustillo J. R. , Ford J. M. , Lim K. , Mathalon D. H. , Mueller B. A. , O’Leary D. , Pearlson G. , Potkin S. G. , Preda A. , van Erp T.G. , Calhoun V. D.
Published: July 2021

In this work, we focus on explicitly nonlinear relationships in functional networks. We introduce a technique using normalized mutual information (MI), that calculates the nonlinear correlation between different brain regions. We demonstrate our proposed approach using simulated data, then apply it to a dataset previously studied in (Damaraju et al., 2014). This resting-state fMRI data included 151 schizophrenia patients and 163 age- and gender-matched healthy controls. We first decomposed these data using group independent component analysis (ICA) and yielded 47 functionally relevant intrinsic connectivity networks. Our analysis showed a modularized nonlinear relationship among brain functional networks that was particularly noticeable in the sensory and visual cortex. Interestingly, the modularity appears both meaningful and distinct from that revealed by the linear approach. Group analysis identified significant differences in nonlinear dependencies between schizophrenia patients and healthy controls particularly in visual cortex, with controls showing more nonlinearity in most cases. Certain domains, including cognitive control, and default mode, appeared much less nonlinear, whereas links between the visual and other domains showed evidence of substantial nonlinear and modular properties. Overall, these results suggest that quantifying nonlinear dependencies of functional connectivity may provide a complementary and potentially important tool for studying brain function by exposing relevant variation that is typically ignored.

Further, we propose a method that captures both linear and nonlinear effects in a ‘boosted’ approach. This method increases the sensitivity to group differences in comparison to the standard linear approach, at the cost of being unable to separate linear and nonlinear effects.
Circulating osteopontin released by injured kidneys causes pulmonary inflammation and edema
Authors: Khamissi Fatima Zohra , Ning Liang , Kefaloyianni Eirini , Dun Hao , Arthanarisami Akshayakeerthi , Keller Amy , Atkinson Jeffrey J. , Li Wenjun , Wong Brian , Dietmann Sabine , Lavine Kory , Kreisel Daniel , Herrlich Andreas
Published: July 2021

Multiorgan failure is devastating, and its mechanisms and mediators are not clear. Tissue injury in one organ appears to trigger disease in remote organs. Kidney and lung are frequently affected, such as when acute kidney injury (AKI) causes acute lung injury (ALI), a frequent clinical condition with high mortality. Here we identify factors secreted from the injured kidney that cause acute lung injury. We developed a murine model mimicking the generation of respiratory failure following acute kidney injury. To identify interorgan crosstalk mediators involved, we performed scRNAseq of mouse kidneys and lungs after AKI. We then applied ligand-receptor (L-R) pairing analysis across cells residing in kidney (ligands) or lung (receptors) to identify kidney-released circulating osteopontin (OPN) as a novel mediator of AKI-induced ALI (AKI-ALI). OPN release very early after AKI largely from tubule cells triggered neutrophil and macrophage infiltration into lungs associated with endothelial leakage, interstitial edema, and functional impairment. Pharmacological or genetic inhibition of OPN prevented AKI-ALI. Transplantation of ischemicwtkidneys intowtmice caused AKI-ALI, while transplantation of ischemic OPN-global-knockout kidneys failed to induce lung endothelial leakage and AKI-ALI, identifying circulating kidney-released OPN as sufficient to cause AKI-ALIin vivo. We show that AKI in humans results in elevations in OPN levels in the serum. Increased serum OPN levels in patients with multiorgan failure have been shown to positively correlate with reduced kidney function, respiratory failure, and mortality. Thus, our results identifying OPN as a mediator of AKI-ALI may have important therapeutic implications in human AKI-ALI and multiorgan failure.
CoVizu: Rapid analysis and visualization of the global diversity of SARS-CoV-2 genomes
Authors: Ferreira Roux-Cil , Wong Emmanuel , Gugan Gopi , Wade Kaitlyn , Liu Molly , Baena Laura Muñoz , Chato Connor , Lu Bonnie , Olabode Abayomi S. , Poon Art F. Y.
Published: July 2021

Phylogenetics has played a pivotal role in the genomic epidemiology of SARS-CoV-2, such as tracking the emergence and global spread of variants, and scientific communication. However, the rapid accumulation of genomic data from around the world — with over two million genomes currently available in the GISAID database — is testing the limits of standard phylogenetic methods. Here, we describe a new approach to rapidly analyze and visualize large numbers of SARS-CoV-2 genomes. Using Python, genomes are filtered for problematic sites, incomplete coverage, and excessive divergence from a strict molecular clock. All differences from the reference genome, including indels, are extracted using minimap2, and compactly stored as a set of features for each genome. For each Pango lineage (https://cov-lineages.org), we collapse genomes with identical features into ‘variants’, generate 100 bootstrap samples of the feature set union to generate weights, and compute the symmetric differences between the weighted feature sets for every pair of variants. The resulting distance matrices are used to generate neigihbor-joining trees in RapidNJ and converted into a majority-rule consensus tree for the lineage. Branches with support values below 50% or mean lengths below 0.5 differences are collapsed, and tip labels on affected branches are mapped to internal nodes as directly-sampled ancestral variants. Currently, we process about million genomes in approximately nine hours on 34 cores. The resulting trees are visualized using the JavaScript framework D3.js as ‘beadplots’, in which variants are represented by horizontal line segments, annotated with beads representing samples by collection date. Variants are linked by vertical edges to represent branches in the consensus tree. These visualizations are published at https://filogeneti.ca/CoVizu. All source code was released under an MIT license at https://github.com/PoonLab/covizu.
Sex determination genetransformerregulates the male-female difference inDrosophilafat storage via the adipokinetic hormone pathway
Authors: Wat Lianna W. , Chowdhury Zahid S. , Millington Jason W. , Biswas Puja , Rideout Elizabeth J.
Published: July 2021

Sex differences in whole-body fat storage exist in many species. For example,Drosophilafemales store more fat than males. Yet, the mechanisms underlying this sex difference in fat storage remain incompletely understood. Here, we identify a key role for sex determination genetransformer(tra) in regulating the male-female difference in fat storage. Normally, a functional Tra protein is present only in females, where it promotes female sexual development. We show that loss of Tra in females reduced whole-body fat storage, whereas gain of Tra in males augmented fat storage. Tra’s role in promoting fat storage was largely due to its function in neurons, specifically the Adipokinetic hormone (Akh)-producing cells (APCs). Our analysis of Akh pathway regulation revealed a male bias in APC activity and Akh pathway function, where this sex-biased regulation influenced the sex difference in fat storage by limiting triglyceride accumulation in males. Importantly, Tra loss in females increased Akh pathway activity, and genetically manipulating the Akh pathway rescued Tra-dependent effects on fat storage. This identifies sex-specific regulation of Akh as one mechanism underlying the male-female difference in whole-body triglyceride levels, and provides important insight into the conserved mechanisms underlying sexual dimorphism in whole-body fat storage.
Measuring cystic fibrosis drug responses in organoids derived from 2D differentiated nasal epithelia
Authors: Amatngalim Gimano D. , Rodenburg Lisa W. , Aalbers Bente L. , Raeven Henriette H. M. , Aarts Ellen M. , Silva Iris A.L. , Nijenhuis Wilco , Vrendenbarg Sacha , Kruisselbrink Evelien , Brunsveld Jesse E. , van Drunen Cornelis M. , Michel Sabine , de Winter-de Groot Karin M. , Heijerman Harry G. , Kapitein Lukas C. , Amaral Magarida D. , van der Ent Cornelis K. , Beekman Jeffrey M.
Published: July 2021

Cystic Fibrosis (CF) is caused by genetic defects that impair the cystic fibrosis transmembrane conductance regulator (CFTR) channel in airway epithelial cells. These defects may be overcome by specific CFTR modulating drugs, for which the efficacy can be predicted in a personalized manner using 3D nasal-brushing-derived airway organoids in a forskolin-induced swelling assay. Despite of this, previously described application of 3D airway organoids in CFTR function assays have not been fully optimal. In this report we therefore describe an alternative method of culturing nasal brushing-derived airway organoids, which are created from an equally differentiated airway epithelial monolayer of a 2D air-liquid interface culture. In addition, we have defined organoid culture conditions, with the growth factor/cytokine combination neuregulin-1β and interleukine-1β, which enabled consistent detection of CFTR modulator responses in nasal airway organoids cultures from subjects with CF.
The interplay of additivity, dominance, and epistasis in a diploid yeast cross
Authors: Matsui Takeshi , Mullis Martin N. , Roy Kevin , Hale Joseph J. , Schell Rachel , Levy Sasha F. , Ehrenreich Ian M.
Published: July 2021

We used a double barcoding system to generate and phenotype a panel of ~200,000 diploid yeast segregants that can be partitioned into hundreds of interrelated families. This experimental design enabled the detection of thousands of genetic interactions and many loci whose effects vary across families. Traits were largely specified by a small number of hub loci with major additive and dominance effects, and pervasive epistasis. Genetic background commonly influenced both the additive and dominance effects of loci, with multiple modifiers typically involved. The most prominent dominance modifier was the mating locus, which had no effect on its own. Our findings show that the interplay between additivity, dominance, and epistasis underlies a complex genotype-to-phenotype map in diploids.

One sentence summary

In diploids, epistasis frequently modifies both additivity and dominance.
Distinct Colon Mucosa Microbiomes associated with Tubular Adenomas and Serrated Polyps
Authors: Avelar-Barragan Julio , DeDecker Lauren , Lu Zachary , Coppedge Bretton , Karnes William E. , Whiteson Katrine L.
Published: July 2021

Background

Colorectal cancer is the second most deadly and third most common cancer in the world. Its development is heterogenous, with multiple mechanisms of carcinogenesis. Two distinct mechanisms include the adenoma-carcinoma sequence and the serrated pathway. The gut microbiome has been identified as a key player in the adenoma-carcinoma sequence, but its role in serrated carcinogenesis is less clear. In this study, we characterized the gut microbiome of 140 polyp-free and polyp-bearing individuals using colon mucosa and fecal samples to determine if microbiome composition was associated with each of the two key pathways.

Results

We discovered significant differences between the microbiomes of colon mucosa and fecal samples, with sample type explaining 14% of the variation observed in the microbiome. Multiple mucosal samples were collected from each individual to investigate whether the gut microbiome differed between polyp and healthy intestinal tissue, but no differences were found. Colon mucosa sampling revealed that the microbiomes of individuals with tubular adenomas and serrated polyps were significantly different from each other and polyp-free individuals, explaining 2-10% of the variance in the microbiome. Further analysis revealed differential abundances of 6 microbes and 1,143 microbial genes across tubular adenoma, serrated polyp, and polyp-free cases.

Conclusion

By directly sampling the colon mucosa and distinguishing between the different developmental pathways of colorectal cancer, this study helps characterize potential mechanistic targets for serrated carcinogenesis. This research also provides insight into multiple microbiome sampling strategies by assessing each method’s practicality and effect on microbial community composition.
A Wastewater-based Epidemiology tool for COVID-19 Surveillance in Portugal
Authors: Monteiro Sílvia , Rente Daniela , Cunha Mónica V. , Gomes Manuel Carmo , Marques Tiago A. , Lourenço Artur B. , Cardoso Eugénia , Álvaro Pedro , Silva Marco , Coelho Norberta , Vilaça João , Meireles Fátima , Brôco Nuno , Carvalho Marta , Santos Ricardo
Published: July 2021

Shedding of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in the feces and urine of infected patients and subsequent presence in wastewater has produced interest on the use of this matrix for sentinel surveillance at a community level and as a complementary approach to syndromic surveillance. With this work, we set the foundations for wastewater-based epidemiology (WBE) in Portugal by monitoring the trends of SARS-CoV-2 RNA circulation in the community, on a nationwide perspective during different epidemiological phases of the pandemic. The Charité assays (E_Sarbecco, RdRP, and N_Sarbecco) were applied to monitor, over 32-weeks (April to December 2020), the dynamics of SARS-CoV-2 RNA at the inlet of five wastewater treatment plants (WWTP), which together serve more than two million people in Portugal. Raw wastewater from three COVID-19 reference hospitals was also analyzed during this period. In total, more than 600 samples were tested. Sampling started late April 2020, during lockdown, and, for the first weeks, detection of SARS-CoV-2 RNA was sporadic, with concentrations varying from 103 to 105 genome copies per liter (GC/L). Prevalence of SARS-CoV-2 RNA increased steeply by the end of May into late June, mainly in Lisboa e Vale do Tejo region (LVT), during the reopening phase. After the summer, with the reopening of schools in mid-September and return to partial face-to-face work, a pronounced increase of SARS-CoV-2 RNA in wastewater was detected. In the LVT area, SARS-CoV-2 RNA load agreed with reported trends in hotspots of infection. Synchrony between trends of SARS-CoV-2 RNA in raw wastewater and daily new COVID-19 cases highlights the value of WBE as a surveillance tool for this virus, particularly after the phasing out of the epidemiological curve and when hotspots of disease re-emerge in the population which might be difficult to spot based solely on syndromic surveillance and contact tracing.
The metabolic, virulence and antimicrobial resistance profiles of colonizing Streptococcus pneumoniae shift after pneumococcal vaccine introduction in urban Malawi
Authors: Gori Andrea , Obolski Uri , Swarthout Todd D. , Lourenço José , Weight Caroline M. , Cornick Jen , Kamng’ona Arox , Mwalukomo Thandie S. , Msefula Jacquline , Brown Comfort , Maiden Martin C. , French Neil , Gupta Sunetra , Heyderman Robert S.
Published: July 2021

Streptococcus pneumoniae accounts for at least 300,000 deaths from pneumonia, septicaemia and meningitis among children under 5-years-old worldwide. Protein–polysaccharide conjugate vaccines (PCVs) are highly effective at reducing vaccine serotype disease but emergence of non-vaccine serotypes and persistent nasopharyngeal carriage threaten to undermine this success. Here, we address the hypothesis that following vaccine introduction in high disease and carriage burden settings, adapted pneumococcal genotypes emerge with the potential to facilitate vaccine escape. We show that beyond serotype replacement, there are marked changes in S. pneumoniae carriage population genetics amongst 2804 isolates sampled 4-8 years after the 2011 introduction of PCV-13 in urban Malawi. These changes are characterised by metabolic genotypes with distinct virulence and antimicrobial resistance (AMR) profiles. This included exclusive genes responsible for metabolism and carbohydrate transport, and toxin-antitoxin systems located in an integrative-conjugative region suggestive of horizontal gene transfer. These emergent genotypes were found to have differential growth, haemolytic, or epithelial adhesion/invasion traits that may confer advantage in the nasopharyngeal niche. Together these data show that in the context of PCV13 introduction in a high burden population, there has been a shift in the pneumococcal population dynamics with the emergence of genotypes that have undergone multiple adaptations extending beyond simple serotype replacement, a process that could further undermine vaccine control and promote the spread of AMR.
Unlike Chloroquine, mefloquine inhibits SARS-CoV-2 infection in physiologically relevant cells and does not induce viral variants
Authors: Sacramento Carolina Q. , Fintelman-Rodrigues Natalia , Dias Suelen S. G. , Temerozo Jairo R. , Da Silva Aline de Paula D. , da Silva Carine S. , Ferreira André C. , Mattos Mayara , Soares Vinicius C. , Pereira-Dutra Filipe , Miranda Milene D. , Barreto-Vieira Debora F. , da Silva Marcos Alexandre N. , Santos Suzana S. , Torres Mateo , Rajoli Rajith K R , Paccanaro Alberto , Owen Andrew , Bou-Habib Dumith Chequer , Bozza Patrícia T. , Souza Thiago Moreno L.
Published: July 2021

Repositioning of clinical approved drugs could represent the fastest way to identify therapeutic options during public health emergencies, the majority of drugs explored for repurposing as antivirals for 2019 coronavirus disease (COVID-19) have failed to demonstrate clinical benefit. Without specific antivirals, the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic continues to cause major global mortality. Antimalarial drugs, such as chloroquine (CQ)/hydroxychloroquine (HCQ) and mefloquine have emerged as potential anti-SARS-CoV-2 antivirals. CQ/HCQ entered the Solidarity and RECOVERY clinical trials against COVID-19 and showed lack of efficacy. Importantly, mefloquine is not a 4-aminoquinoline like CQ and HCQ and has been previously repurposed for other respiratory diseases. Unlike the 4-aminoquinolines that accumulate in the high pH of intracellular lysosomes of the lung, the high respiratory tract penetration of mefloquine is driven by its high lipophilicity. While CQ and HCQ exhibit activity in Vero E6 cells, their activity is obviated in TMPRSS2-expressing cells, such as Calu-3 cells, which more accurately recapitulate in vivo entry mechanisms for SARS-CoV-2. Accordingly, here we report the anti-SARS-CoV-2 activity of mefloquine in Calu-3 type II pneumocytes and primary human monocytes. Mefloquine inhibited SARS-CoV-2 replication in Calu-3 cells with low cytotoxicity and EC50and EC90values of 1.2 and 5.3 µM, respectively. In addition, mefloquine reduced up to 68% the SARS-CoV-2 RNA levels in infected monocytes, reducing viral-induced inflammation. Mefloquine blocked early steps of the SARS-CoV-2 replicative cycle and was less prone than CQ to induce drug-associated viral mutations and synergized with RNA polymerase inhibitor. The pharmacological parameters of mefloquine are consistent with its plasma exposure in humans and its tissue-to-plasma predicted coefficient points that this drug may accumulate in the lungs. These data indicate that mefloquine could represent an orally available clinically approved drug option against COVID-19 and should not be neglected on the basis of the failure of CQ and HCQ.
Ultrastructure expansion microscopy of Plasmodium gametocytes reveals the molecular architecture of a microtubule organisation centre coordinating mitosis with axoneme assembly
Authors: Rashpa Ravish , Brochet Mathieu
Published: July 2021

The transmission of malaria-causing parasites to mosquitoes relies on the production of the gametocyte stages and their development into gametes upon a blood feed. These stages display various microtubule cytoskeletons and the architecture of the corresponding microtubule organisation centres (MTOC) remains elusive. Combining ultrastructure expansion microscopy (U-ExM) with bulk proteome labelling, we first reconstructed in 3D the subpellicular microtubule network and its associated actin cytoskeleton, which confer cell rigidity to Plasmodium falciparum gametocytes. Upon activation, as the microgametocyte undergoes three rounds of endomitosis, it simultaneously assembles axonemes to form eight flagellated microgametes. Here, U-ExM combined with Pan-ExM revealed the molecular architecture of a single bipartite MTOC coordinating mitosis with axoneme formation. This MTOC spans the nuclear membrane linking acentriolar mitotic plaques to cytoplasmic basal bodies by proteinaceous filaments. The eight basal bodies are concomitantly de novo assembled from a deuterosome-like structure, where centrin, γ-tubulin, SAS4/CPAP and SAS6 form distinct subdomains. Once assembled, the basal bodies show a fusion of the proximal and central cores where colocalised centrin and SAS6 are surrounded by a SAS4/CPAP-toroid in the lumen of the microtubule wall. Sequential nucleation of axonemes and mitotic spindles is associated with a dynamic movement of γ-tubulin from the basal bodies to the acentriolar plaques. We finally show that this atypical MTOC architecture relies on two non-canonical MTOC regulators, the calcium-dependent protein kinase 4 and the serine/arginine-protein kinase 1. Altogether, these results provide insights into the molecular organisation of a bipartite MTOC that may reflect a functional transition of a basal body to coordinate axoneme formation with mitosis.
Transgenesis in the acoel worm Hofstenia miamia
Authors: Ricci Lorenzo , Srivastava Mansi
Published: July 2021

The acoel worm Hofstenia miamia, which can replace tissue lost to injury via differentiation of a population of stem cells, has emerged as a new research organism for studying regeneration. To enhance the depth of mechanistic studies in this system, we devised a protocol for microinjection into embryonic cells that resulted in stable transgene integration into the genome and generated animals with tissue-specific fluorescent transgene expression in epidermis, gut, and muscle. We demonstrate that transgenic Hofstenia are amenable to the isolation of specific cell types, detailed investigations of regeneration, tracking of photoconverted molecules, and live imaging. Further, our stable transgenic lines revealed new insights into the biology of Hofstenia, unprecedented details of cell morphology and the organization of muscle as a cellular scaffold for other tissues. Our work positions Hofstenia as a powerful system with unparalleled tools for mechanistic investigations of development, whole-body regeneration, and stem cell biology.
Reduced protein kinase C delta association with a higher molecular weight complex in mitochondria of Barth Syndrome lymphoblasts
Authors: Mejia Edgard M. , Zegallai Hana M. , Sparagna Genevieve C. , Hatch Grant M.
Published: July 2021

The protein kinase C delta (PKCδ) signalosome exists as a high molecular weight complex in mitochondria and controls mitochondrial oxidative phosphorylation. Barth Syndrome (BTHS) is a rare X-linked genetic disease in which mitochondrial oxidative phosphorylation is impaired due to a mutation in the gene TAFAZZIN which results in reduction in the phospholipid cardiolipin and an accumulation of monolysocardiolipin. Here we examined if PKCδ association with a higher molecular weight complex was altered in mitochondria of BTHS lymphoblasts. Immunoblot analysis of blue native-polyacrylamide gel electrophoresis mitochondrial fractions revealed that PKCδ associated with a higher molecular weight complex in control lymphoblasts but this was markedly reduced in BTHS patient B lymphoblasts in spite of an increase in PKCδ protein expression. We hypothesize that the lack of PKCδ within this higher molecular weight complex may contribute to defective mitochondrial PKCδ signaling and thus to the bioenergetic defects observed in BTHS.
Lowland plant arrival in alpine ecosystems facilitates a decrease in soil carbon content under experimental climate warming
Authors: Walker Tom W. N. , Gavazov Konstantin , Guillaume Thomas , Lambert Thibault , Mariotte Pierre , Routh Devin , Signarbieux Constant , Block Sebastián , Münkemüller Tamara , Nomoto Hanna , Crowther Thomas W. , Richter Andreas , Buttler Alexandre , Alexander Jake M.
Published: July 2021

Climate warming is releasing carbon from soils around the world1–3, constituting a positive climate feedback. Warming is also causing species to expand their ranges into new ecosystems4–9. Yet, in most ecosystems, whether range expanding species will amplify or buffer expected soil carbon loss is unknown10. Here we used two whole-community transplant experiments and a follow-up glasshouse experiment to determine whether the establishment of herbaceous lowland plants in alpine ecosystems influences soil carbon content under warming. We found that warming (transplantation to low elevation) led to a negligible decrease in alpine soil carbon content, but its effects became significant and 52% ± 31% (mean ± 95% CIs) larger after lowland plants were introduced at low density into the ecosystem. We present evidence that decreases in soil carbon content likely occurred via lowland plants increasing rates of root exudation, soil microbial respiration and CO2 release under warming. Our findings suggest that warming-induced range expansions of herbaceous plants have the potential to alter climate feedbacks from this system, and that plant range expansions among herbaceous communities may be an overlooked mediator of warming effects on carbon dynamics.
Isolation of wild yeasts from Olympic National Park and Moniliella megachiliensis ONP131 physiological characterization for beer fermentation
Authors: Piraine Renan Eugênio Araujo , Nickens David Gerald , Sun David J. , Leite Fábio Pereira Leivas , Bochman Matthew L.
Published: July 2021

Thousands of yeasts have the potential for industrial application, though many were initially considered contaminants in the beer industry. However, these organisms are currently considered important components in beers because they contribute new flavors. Non-Saccharomyces wild yeasts can be important tools in the development of new products, and the objective of this work was to obtain and characterize novel yeast isolates for their ability to produce beer. Wild yeasts were isolated from environmental samples from Olympic National Park and analyzed for their ability to ferment malt extract medium and beer wort. Six different strains were isolated, of which Moniliella megachiliensis ONP131 displayed the highest levels of attenuation during fermentations. We found that M. megachiliensis could be propagated in common yeast media, tolerated incubation temperatures of 37°C and a pH of 2.5, and was able to grow in media containing maltose as the sole carbon source. Yeast cultivation was considerably impacted (p<0.05) by lactic acid, ethanol, and high concentrations of maltose, but ONP131 was tolerant to high salinity and hop acid concentrations. This is one of the first physiological characterizations of M. megachiliensis, which has potential for the production of beer and other fermented beverages.
Impaired developmental microglial pruning of excitatory synapses on CRH-expressing hypothalamic neurons exacerbates stress responses throughout life
Authors: Bolton Jessica L. , Short Annabel K. , Othy Shivashankar , Kooiker Cassandra L. , Shao Manlin , Gunn Benjamin G. , Beck Jaclyn , Bai Xinglong , Law Stephanie M. , Savage Julie C. , Lambert Jeremy J. , Belelli Delia , Tremblay Marie-Ève , Cahalan Michael D. , Baram Tallie Z.
Published: July 2021

The developmental origins of stress-related mental illnesses are well-established, and early-life stress/adversity (ELA) is an important risk factor. However, it is unclear how ELA impacts the maturation of salient brain circuits, provoking enduring vulnerability to stress and stress-related disorders. Here we find that ELA increases the number and function of excitatory synapses onto stress-sensitive hypothalamic corticotropin-releasing hormone (CRH)-expressing neurons, and implicate disrupted synapse pruning by microglia as a key mechanism. Microglial process dynamics on live imaging, and engulfment of synaptic elements by microglia, were both attenuated in ELA mice, associated with deficient signaling of the microglial phagocytic receptor Mer. Accordingly, selective chemogenetic activation of ELA microglia increased microglial process dynamics and reduced excitatory synapse density to control levels. Selective early-life microglial activation also mitigated the adrenal hypertrophy and prolonged stress responses in adult ELA mice, establishing microglial actions during development as powerful contributors to experience-dependent sculpting of stress-related brain circuits.
Impact of human airway epithelial cellular composition on SARS-CoV-2 infection biology
Authors: Wang Ying , Thaler Melissa , Ninaber Dennis K. , van der Does Anne M. , Ogando Natacha S. , Beckert Hendrik , Taube Christian , Salgado-Benvindo Clarisse , Snijder Eric J. , Bredenbeek Peter J. , Hiemstra Pieter S. , van Hemert Martijn J.
Published: July 2021

Infection biology and pathogenesis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the causative agent of the coronavirus disease 2019 (COVID-19), are incompletely understood. Here, we assessed the impact of airway epithelial cellular composition on infection in air-liquid interface (ALI) cultures of differentiated primary human tracheal (PTEC) and bronchial epithelial cells (PBEC). We first compared SARS-CoV-2 infection kinetics, related antiviral and inflammatory responses, and viral entry factors in PTEC and PBEC. Next, the contribution of differentiation time was investigated by differentiating ALI-PTEC/PBEC for 3-5 weeks and comparing dynamics of viral replication/spread, cellular composition and epithelial responses. We observed a gradual increase in viral load with prolonged culture duration. Ciliated and goblet cells were predominantly infected in both PTEC and PBEC. Immunofluorescence analysis and RT-qPCR showed that compared to other cell types mainly ciliated and goblet cell numbers were affected by increased culture duration. An increased proportion of these two target cell types was associated with increased viral load. Furthermore, modulation of cellular composition using IL-13 and the Notch signaling inhibitor DAPT, underlined the importance of both ciliated and goblet cells for infection. DAPT treatment resulted in a lower viral load and a relative increase in ciliated cells at the expense of goblet cells, compared to IL-13 treated cultures in which both cell types were present and viral load was higher.

In conclusion, our results identify cellular composition as a contributing factor to airway epithelial susceptibility to SARS-CoV-2.

IMPORTANCE

In this study, we determined an effect of culture duration and airway cellular composition of ALI-PBEC and ALI-PTEC cultures on SARS-CoV-2 infection. We found that SARS-CoV-2 infection was increased with prolonged cell culture time and the total percentage and proportion of ciliated and goblet cells played an important role in infection level, suggesting that airway epithelial differentiation/maturation levels may in part determine susceptibility of SARS-CoV-2 infection.

The development of effective therapies either targeting virus replication or pathogenesis against SARS-CoV-2 requires robust cell culture-based infection models to test small molecules and biologicals. Therefore, it is important to identify factors that are essential for reliably modeling SARS-CoV-2-airway epithelial cell interactions. This study sheds light on virus-airway epithelial cell interactions and adds to the complexity of SARS-CoV-2 cell tropism in the airways. In addition, the effect of IL-13 on viral infection hints at a causal connection between SARS-CoV-2 infection and (allergic) asthma.
The Pol II preinitiation complex (PIC) influences Mediator binding but not promoter–enhancer looping
Authors: Sun Fei , Sun Terrence , Kronenberg Michael , Tan Xianglong , Huang Chengyang , Carey Michael F.
Published: July 2021

Knowledge of how Mediator and TFIID cross-talk contributes to promoter–enhancer (P-E) communication is important for elucidating the mechanism of enhancer function. We conducted an shRNA knockdown screen in murine embryonic stem cells to identify the functional overlap between Mediator and TFIID subunits on gene expression. Auxin-inducible degrons were constructed for TAF12 and MED4, the subunits eliciting the greatest overlap. Degradation of TAF12 led to a dramatic genome-wide decrease in gene expression accompanied by destruction of TFIID, loss of Pol II preinitiation complex (PIC) at promoters, and significantly decreased Mediator binding to promoters and enhancers. Interestingly, loss of the PIC elicited only a mild effect on P-E looping by promoter capture Hi-C (PCHi-C). Degradation of MED4 had a minor effect on Mediator integrity but led to a consistent twofold loss in gene expression, decreased binding of Pol II to Mediator, and decreased recruitment of Pol II to the promoters, but had no effect on the other PIC components. PCHi-C revealed no consistent effect of MED4 degradation on P-E looping. Collectively, our data show that TAF12 and MED4 contribute mechanistically in different ways to P-E communication but neither factor appears to directly control P-E looping, thereby dissociating P-E communication from physical looping.
Load-bearing capacity and resonance stability of inelastic beams and plane trusses with initial defects
Authors: Milašinović Dragan D. , Kozarić Ljiljana , Bursać Smilja , Bešević Miroslav , Miličić Ilija , Varju Đerđ
Published: July 2021

Purpose

The purpose of this paper is to contribute to the solution of the buckling and resonance stability problems in inelastic beams and wooden plane trusses, taking into account geometric and material defects.

Design/methodology/approach

Two sources of non-linearity are analyzed, namely the geometrical non-linearity due to geometrical imperfections and material non-linearity due to material defects. The load-bearing capacity is obtained by the rheological-dynamical analogy (RDA). The RDA inelastic theory is used in conjunction with the damage mechanics to analyze the softening behavior with the scalar damage variable for stiffness reduction. Based on the assumed damages in the wooden truss, the corresponding external masses are calculated in order to obtain the corresponding fundamental frequencies, which are compared with the measured ones.

Findings

RDA theory uses rheology and dynamics to determine the structures' response, those results in the post-buckling branch can then be compared by fracture mechanics. The RDA method uses the measured P and S wave velocities, as well as fundamental frequencies to find material properties at the limit point. The verification examples confirmed that the RDA theory is more suitable than other non-linear theories, as those proved to be overly complex in terms of their application to the real structures with geometrical and material defects.

Originality/value

The paper presents a novel method of solving the buckling and resonance stability problems in inelastic beams and wooden plane trusses with initial defects. The method is efficient as it provides explanations highlighting that an inelastic beam made of ductile material can break in any stage from brittle to extremely ductile, depending on the value of initial imperfections. The characterization of the internal friction and structural damping via the damping ratio is original and effective.