bluuebunny/crossref_metadata_2025_split huggingface dataset:
Temporal trends in primary care-recorded self-harm during and beyond the first year of the COVID-19 pandemic: time series analysis of electronic healthcare records for 2.8 million patients in the Greater Manchester Care Record
Authors: Steeg Sarah , Bojanić Lana , Tilston George , Williams Richard , Jenkins David A. , Carr Matthew J. , Peek Niels , Ashcroft Darren M. , Kapur Nav , Voorhees Jennifer , Webb Roger T. 
Published: June 2021

AbstractBackgroundSurveillance of clinically treated self-harm episode frequency is an important component of suicide prevention in the dynamic context of COVID-19. Studies published to date have investigated the initial months following the onset of the pandemic, despite national and regional restrictions persisting to Summer 2021.MethodsWe conducted a descriptive time series analysis utilising data from the Greater Manchester Care Record, which contains de-identified, primary care health records of 2.8 million patients. Counts of incident and all episodes of self-harm recorded between 1st January 2019 and 31st May 2021 were made for all patients, with stratification by sex, age group, ethnicity, and index of multiple deprivation (IMD) quintile and examination of overall differences by national and regional restriction phases.FindingsBetween 1st January 2019 and 31st May 2021, 33,444 episodes of self-harm by 13,148 individuals were recorded. Frequency ratios of incident and all episodes of self-harm were 0.59 (95% CI 0.51 to 0.69) and 0.69 (CI 0.63 to 0.75) respectively in April 2020 compared to February 2020. Between August 2020 and May 2021 frequency ratios were 0.92 (CI 0.88 to 0.96) for incident episodes and 0.86 (CI 0.84 to 0.88) for all episodes compared to the same months in 2019. Reductions were largest among men and people living in the most deprived neighbourhoods. An increase in all-episode self-harm (frequency ratio 1.09, CI 1.03 to 1.16) was observed for adolescents aged 10-17 between August 2020 and May 2021.InterpretationThe COVID-19 pandemic has had a sustained impact on help seeking for self-harm. Reductions in primary care recorded self-harm have implications for clinicians’ ability to assess the needs and risks of individuals. Some patients may be experiencing prolonged untreated deterioration in their mental health while other groups are presenting in higher numbers. Our findings have important implications for primary care and mental health services in manging ongoing demand.FundingUKRI COVID-19 Rapid Response Initiative (grant reference COV0499), University of Manchester Presidential Fellowship (SS), and NIHR Greater Manchester Patient Safety Translational Research Centre.
The Impact of COVID-19 Restrictions on Childhood Vaccination Uptake: A Rapid Review
Authors: Heneghan C , Brassey J , Jefferson T. 
Published: June 2021

AbstractBackgroundVaccines are highly effective for preventing a range of childhood infections. However, there have been concerns about an alarming decline in vaccinations in 2020 due to the COVID-19 pandemic.MethodsWe performed a rapid review for studies that assessed childhood vaccination uptake during restrictive phases of the COVID-19 pandemic.ResultsWe found 35 published studies that compared changes in the pattern of childhood vaccinations before and during the pandemic. Thirteen were surveys; two mixed-methods surveys and interviews, three modelling studies and 17 retrospective cohort studies with historical controls. We also included ten reports by national or international agencies that had original data on vaccination uptake. Significant global disruptions to vaccine services were reported in Africa, Asia, America (including Latin America and the Caribbean) and Europe. We also found evidence of significant disruption to vaccine uptake for diphtheria tetanus pertussis, BCG, measles and polio. Countries where vaccination rates were already suboptimal had greater drops in uptake and there was evidence of smaller declines in younger children compared to older children. Children born to women who could not read and write were more likely to be incompletely immunized. Various initiatives were used to drive up vaccination rates post restrictions.ConclusionsObstacles to the delivery of vaccination services during the Covid-19 pandemic drove down immunisation rates, especially in disadvantaged people and poorer countries.
A systematic review of persistent symptoms and residual abnormal functioning following acute COVID-19: Ongoing symptomatic phase vs. post-COVID-19 syndrome
Authors: Jennings Glenn , Monaghan Ann , Xue Feng , Mockler David , Romero-Ortuño Román 
Published: June 2021

ABSTRACTObjectiveTo compare the two phases of long COVID, namely ongoing symptomatic COVID-19 (OSC; signs and symptoms from 4 to 12 weeks from initial infection) and post-COVID-19 syndrome (PCS; signs and symptoms beyond 12 weeks) with respect to symptomatology, abnormal functioning, psychological burden, and quality of life.DesignSystematic review.Data SourcesElectronic search of EMBASE, MEDLINE, ProQuest Coronavirus Research Database, LitCOVID, and Google Scholar between January and April 2021, and manual search for relevant citations from review articles.Eligibility CriteriaCross-sectional studies, cohort studies, randomised control trials, and case-control studies with participant data concerning long COVID symptomatology or abnormal functioning.Data ExtractionStudies were screened and assessed for risk of bias by two independent reviewers, with conflicts resolved with a third reviewer. The AXIS tool was utilised to appraise the quality of the evidence. Data were extracted and collated using a data extraction tool in Microsoft Excel.ResultsOf the 1,145 studies screened, 39 were included, all describing adult cohorts with long COVID and sample sizes ranging from 32 to 1,733. Studies included data pertaining to symptomatology, pulmonary functioning, chest imaging, cognitive functioning, psychological disorder, and/or quality of life. Fatigue presented as the most prevalent symptom during both OSC and PCS at 43% and 44%, respectively. Sleep disorder (36%; 33%), dyspnoea (31%; 40%), and cough (26%; 22%) followed in prevalence. Abnormal spirometry (FEV1 <80% predicted) was observed in 15% and 11%, and abnormal chest imaging observed in 34% and 28%, respectively. Cognitive impairments were also evident (20%; 15%), as well as anxiety (28%; 34%) and depression (25%; 32%). Decreased quality of life was reported by 40% of patients with OSC and 57% by those with PCS.ConclusionsThe prevalences of OSC and PCS were highly variable. Reported symptoms covered a wide range of body systems, with general overlap in frequencies between the two phases. However, abnormalities in lung function and imaging seemed to be more common in OSC, whilst anxiety, depression, and poor quality of life seemed more frequent in PCS. In general, the quality of the evidence was moderate and further research is needed to better understand the complex interplay of somatic versus psychosocial drivers in long COVID.Systematic Review RegistrationRegistered with PROSPERO with ID #CRD42021247846.
Biophysical Models of PAR Cluster Transport by Cortical Flow in C. elegans Early Embryogenesis
Authors: Zmurchok Cole , Holmes William R. 
Published: June 2021

AbstractThe clustering of membrane-bound proteins facilitates their transport by cortical actin flow in early Caenorhabditis elegans embryo cell polarity. PAR-3 clustering is critical for this process, yet the bio-physical processes that couple protein clusters to cortical flow remain unknown. We develop a discrete, stochastic agent-based model of protein clustering and test four hypothetical models for how clusters may interact with the flow. Results show that the canonical way to assess transport characteristics from single particle tracking data used thus far in this area, the Péclet number, is insufficient to distinguish these hypotheses and that all models can account for transport characteristics quantified by this measure. However, using this model, we demonstrate that these different cluster-cortex interactions may be distinguished using a different metric, namely, the scalar projection of cluster displacement on to the flow displacement vector. Our results thus provide a testable way to use existing single particle tracking data to test how endogenous protein clusters may interact with the cortical flow to localize during polarity establishment. To facilitate this investigation, we also develop both improved simulation and semi-analytic methodologies to quantify motion summary statistics (e.g., Péclet number and scalar projection) for these stochastic models as a function of biophysical parameters.
HPLC Method to Resolve, Identify and Quantify Guanine Nucleotides Bound to the GTPase Ras
Authors: Hannan Jonathan P. , Hayden Swisher G. , Martyr Justin G. , Cordaro Nicholas J. , Erbse Annette H. , Falke Joseph J. 
Published: June 2021

AbstractThe Ras superfamily of small G proteins play central roles in diverse signaling pathways. Superfamily members act as molecular on-off switches defined by their occupancy with GTP or GDP, respectively. In vitro functional studies require loading with a hydrolysis-resistant GTP analogue to increase the on-state lifetime, as well as knowledge of fractional loading with activating and inactivating nucleotides. The present study describes a method combining elements of previous approaches with new, optimized features to analyze the bound nucleotide composition of a G protein loaded with activating (GMPPNP) or inactivating (GDP) nucleotide. After nucleotide loading, the complex is washed to remove unbound nucleotides then bound nucleotides are heat-extracted and subjected to ion-paired, reverse-phase HPLC-UV to resolve, identify and quantify the individual nucleotide components. These data enable back-calculation to the nucleotide composition and fractional activation of the original, washed G protein population prior to heat extraction. The method is highly reproducible. Application to multiple HRas preparations and mutants confirms its ability to fully extract and analyze bound nucleotides, and to resolve the fractional on- and off-state populations. Furthermore, the findings yield a novel hypothesis for the molecular disease mechanism of Ras mutations at the E63 and Y64 positions.
Complex basis of hybrid female sterility and Haldane’s rule inHeliconiusbutterflies: Z-linkage and epistasis
Authors: Rosser Neil , Edelman Nathaniel B. , Queste Lucie M. , Nelson Michaela , Seixas Fernando , Dasmahapatra Kanchon K. , Mallet James 
Published: June 2021

AbstractHybrids between diverging populations are often sterile or inviable. Hybrid unfitness usually evolves first in the heterogametic sex – a pattern known as Haldane’s rule. The genetics of Haldane’s Rule have been extensively studied in species where the male is the heterogametic (XX/XY) sex, but its basis in taxa where the female is heterogametic (ZW/ZZ), such as Lepidoptera and birds, is largely unknown. Here, we analyse a new case of female hybrid sterility between geographic subspecies ofHeliconius pardalinus. The two subspecies mate freely in captivity, but female F1 hybrids in both directions of cross are sterile. Sterility is due to arrested development of oocytes after they become differentiated from nurse cells, but before yolk deposition. We backcrossed fertile male F1 hybrids to parental females, and mapped quantitative trait loci (QTLs) for female sterility. We also identified genes differentially expressed in the ovary, and as a function of oocyte development. The Z chromosome has a major effect, similar to the “large X effect” inDrosophila, with strong epistatic interactions between loci at either end of the Z chromosome, and between the Z chromosome and autosomal loci on chromosomes 8 and 20. Among loci differentially expressed between females with arrested vs. non-arrested ovary development, we identified six candidate genes known also fromDrosophila melanogasterandParage aegeriaoogenesis. This study is the first to characterize hybrid sterility using genome mapping in the Lepidoptera. We demonstrate that sterility is produced by multiple complex epistastic interactions often involving the sex chromosome, as predicted by the dominance theory of Haldane’s Rule.
Strategies ofMycoplasma ovipneumoniaeto evade immune clearance by alveolar macrophages
Authors: Gao Liyang , Zhang Kai , Zhang Ying , Ma Chunji , Zhou Xiaoyu , Li Min 
Published: June 2021

AbstractChronic nonprogressive pneumonia is a prevalent disease that infects many young sheep.Mycoplasma ovipneumoniaewas isolated from the lungs of sheep with chronic nonprogressive pneumonia. Evidences showed that it might associate with the development and duration of chronic pneumonia, moreover, sheep infected withM. ovipneumoniaeare easily infected by other organisms, suggesting thatM. ovipneumoniaemay play an immunosuppressive role during infection. However, the mechanism is still poorly understood. The infection occurs in the airway, where resident alveolar macrophages first encounterM. ovipneumoniae. Therefore, primary alveolar macrophages (AMs) were collected from the lungs of healthy adult sheep, and the (iTRAQ) protein assay was used to investigate the immunosuppressive effects ofM. ovipneumoniaeon sheep AMs. The RAW264.7 cells were used to confirm the findings. The results showed thatM. ovipneumoniaepromoted higher expression of anti-apoptotic proteins and lower expression of apoptosis-related proteins in the infected AMs. Moreover, the number of infected AMs increased. However,M. ovipneumoniaereduced ATP levels in AMs and impaired late endosome maturation and phagolysosome fusion. Furthermore,M. ovipneumoniaeinhibited the autophagy pathway via the Akt-mTOR axis in AMs. These findings indicated thatM. ovipneumoniaehad distinctive strategies to evade elimination caused by the AMs. The findings might explain the chronic infection and co-infection in sheep infected byM. ovipneumoniae.
Natural isolate and recombinant SARS-CoV-2 rapidly evolve in vitro to higher infectivity through more efficient binding to heparan sulfate and reduced S1/S2 cleavage
Authors: Shiliaev Nikita , Lukash Tetyana , Palchevska Oksana , Crossman David K. , Green Todd J. , Crowley Michael R. , Frolova Elena I. , Frolov Ilya 
Published: June 2021

ABSTRACTOne of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virulence factors is the ability to interact with high affinity to the ACE2 receptor, which mediates viral entry into cells. The results of our study demonstrate that within a few passages in cell culture, both the natural isolate of SARS-CoV-2 and the recombinant, cDNA-derived variant acquire an additional ability to bind to heparan sulfate (HS). This promotes a primary attachment of viral particles to cells before their further interactions with the ACE2. Interaction with HS is acquired through multiple mechanisms. These include i) accumulation of point mutations in the N-terminal domain (NTD) of the S protein, which increase the positive charge of the surface of this domain, ii) insertions into NTD of heterologous peptides, containing positively charged amino acids, and iii) mutation of the first amino acid downstream of the furin cleavage site. This last mutation affects S protein processing, transforms the unprocessed furin cleavage site into the heparin-binding peptide and makes viruses less capable of syncytia formation. These viral adaptations result in higher affinity of viral particles to heparin sepharose, dramatic increase in plaque sizes, more efficient viral spread, higher infectious titers and two orders of magnitude lower GE:PFU ratios. The detected adaptations also suggest an active role of NTD in virus attachment and entry. As in the case of other RNA+ viruses, evolution to HS binding may result in virus attenuation in vivo.IMPORTANCEThe spike protein of SARS-CoV-2 is a major determinant of viral pathogenesis. It mediates binding to ACE2 receptor and later, fusion of viral envelope and cellular membranes. The results of our study demonstrate that SARS-CoV-2 rapidly evolves during propagation in cultured cells. Its spike protein acquires mutations in the N-terminal domain (NTD) and in P1‘ position of the furin cleavage site (FCS). The amino acid substitutions or insertions of short peptides in NTD are closely located on the protein surface and increase its positive charge. They strongly increase affinity of the virus to heparan sulfate, make it dramatically more infectious for the cultured cells and decrease GE:PFU ratio by orders of magnitude. The S686G mutation also transforms the FCS into the heparin-binding peptide. Thus, the evolved SARS-CoV-2 variants efficiently use glycosaminoglycans on the cell surface for primary attachment before the high affinity interaction of the spikes with the ACE2 receptor.
Chloride intracellular channel 4 (CLIC4) expression is transcriptionally regulated by crosstalk of the TGF-β, Wnt and Hedgehog signalling pathways
Authors: Wasson Christopher W. , Caballero-Ruiz Begoña , Mankouri Jamel , Canettieri Gianluca , Riobo-Del Galdo Natalia A. , Del Galdo Francesco 
Published: June 2021

AbstractChloride intracellular channel 4 (CLIC4) is a recently discovered driver of fibroblast activation in Scleroderma (SSc) and cancer-associated fibroblasts. CLIC4 expression and activity are regulated by TGF-β signalling through the SMAD3 transcription factor. In view of the aberrant activation of canonical Wnt and Hedgehog (Hh) signalling in fibrosis, we investigated their role in CLIC4 upregulation. Here, we show Wnt3a/β-catenin and Smoothened/GLI signalling cooperate with SMAD3 to regulate CLIC4 expression in normal dermal fibroblasts, and that inhibition of SMAD3 expression or activity abolishes Wnt and Hh-dependent CLIC4 induction. We further show that expression of the profibrotic marker α-smooth muscle actin strongly correlates with CLIC4 expression in dermal fibroblasts. Our data highlight novel mechanisms that regulate CLIC4 expression that present targetable pathways to prevent fibroblast activation in SSc and other fibrotic conditions.
Absolute quantitation of individual SARS-CoV-2 RNA molecules: a new paradigm for infection dynamics and variant differences
Authors: Lee Jeffrey Y , Wing Peter AC , Gala Dalia S , Noerenberg Marko , Järvelin Aino I , Titlow Josh , Zhuang Xiaodong , Palmalux Natasha , Iselin Louisa , Thompson Mary Kay , Parton Richard M , Wainman Alan , Agranoff Daniel , James William , Castello Alfredo , McKeating Jane A , Davis Ilan 
Published: June 2021

SummaryDespite an unprecedented global research effort on SARS-CoV-2, early replication events remain poorly understood. Given the clinical importance of emergent viral variants with increased transmission, there is an urgent need to understand the early stages of viral replication and transcription. We used single molecule fluorescence in situ hybridisation (smFISH) to quantify positive sense RNA genomes with 95% detection efficiency, while simultaneously visualising negative sense genomes, sub-genomic RNAs and viral proteins. Our absolute quantification of viral RNAs and replication factories revealed that SARS-CoV-2 genomic RNA is long-lived after entry, suggesting that it avoids degradation by cellular nucleases. Moreover, we observed that SARS-CoV-2 replication is highly variable between cells, with only a small cell population displaying high burden of viral RNA. Unexpectedly, the B.1.1.7 variant, first identified in the UK, exhibits significantly slower replication kinetics than the Victoria strain, suggesting a novel mechanism contributing to its higher transmissibility with important clinical implications.Graphical AbstractIn briefBy detecting nearly all individual SARS-CoV-2 RNA molecules, we quantified viral replication and defined cell susceptibility to infection. We discovered that a minority of cells show significantly elevated viral RNA levels and observed slower replication kinetics for the Alpha variant relative to the Victoria strain.HighlightsSingle molecule quantification of SARS-CoV-2 replication uncovers early infection kineticsThere is substantial heterogeneity between cells in rates of SARS-CoV-2 replicationGenomic RNA is stable and persistent during the initial stages of infectionB.1.1.7 variant replicates more slowly than the Victoria strain
Insulin-dependent and -independent dynamics of insulin receptor trafficking in muscle cells
Authors: Cen Haoning Howard , Rogalski Jason , Abraham Libin , Gold Michael R. , Foster Leonard J. , Johnson James D. 
Published: June 2021

AbstractInsulin resistance contributes to type 2 diabetes and can be driven by hyperinsulinemia. Insulin receptor (INSR) internalization and cell-surface dynamics at rest and during insulin exposure are incompletely understood in muscle cells. Using surfacing labeling and live-cell imaging, we observed robust basal internalization of INSR in C2C12 myoblasts, without a robust effect of added insulin. Mass-spectrometry analysis of INSR-binding proteins identified potential molecular mechanisms associated with internalization. We confirmed known interactors, including IGF1R, but also identified underappreciated INSR-binding factors such as ANXA2. Protein-protein interaction network mapping suggested links between INSR and caveolin-mediated endocytosis. INSR interacted with both caveolin and clathrin heavy chain (CLTC) in mouse skeletal muscle and C2C12 myoblasts. Whole cell 2D super-resolution imaging revealed that high levels of insulin (20 nM) increased INSR colocalization with CAV1 but decreased its colocalization with CLTC. Single particle tracking confirmed the colocalization of cell-surface INSR with both over-expressed CAV1-mRFP and CLTC-mRFP. INSR tracks that colocalized with CAV1 exhibited longer radii and lifetimes, regardless of insulin exposure, compared to non-colocalized tracks, whereas insulin further increased the lifetime of INSR/CLTC colocalized tracks. Overall, these data suggest that muscle cells utilize both CAV1 and CLTC-dependent pathways for INSR dynamics and internalization.
Lipid-mediated Association of the Slg1 Transmembrane Domains in Yeast Plasma Membranes
Authors: Alavizargar Azadeh , Elting Annegret , Wedlich-Söldner Roland , Heuer Andreas 
Published: June 2021

AbstractClustering of transmembrane proteins underlies a multitude of fundamental biological processes at the plasma membrane (PM) such as receptor activation, lateral domain formation and mechanotransduction. The self-association of the respective transmembrane domains (TMD) has also been suggested to be responsible for the micron-scaled patterns seen for integral membrane proteins in the budding yeast plasma membrane. However, the underlying interplay between local lipid composition and TMD identity is still not mechanistically understood. In this work we combined coarse-grained molecular dynamics (MD) simulations of simplified bilayer systems with high resolution live-cell microscopy to analyze the distribution of a representative helical yeast TMD from the PM sensor Slg1 within different lipid environments. In our simulations we specifically evaluated the effects of acyl chain saturation and anionic lipids head groups on the association of two TMDs. We found that weak lipid-protein interactions significantly affect the configuration of TMD dimers and the free energy of association. Increased amounts of unsaturated phospholipids strongly reduced helix-helix interaction, while the presence of anionic phosphatidylserine (PS) hardly affected dimer formation. We could experimentally confirm this surprising lack of effect of PS using the network factor, a mesoscopic measure of PM pattern formation in yeast cells. Simulations also showed that formation of TMD dimers in turn increased the order parameter of the surrounding lipids and induced long-range perturbations in lipid organization. In summary, our results shed new light on the mechanisms for lipid-mediated dimerization of TMDs in complex lipid mixtures.