bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effectiveness of ChAdOx1-S COVID-19 Booster Vaccination against the Omicron and Delta variants in England
Authors: Kirsebom Freja , Andrews Nick , Sachdeva Ruchira , Stowe Julia , Ramsay Mary , Bernal Jamie Lopez 
Published: May 2022

AbstractBackgroundDespite the potential widespread global use of the ChAdOx1-S booster, to date there are no published data on the real-world effectiveness. VE studies have found one and two doses of the ChAdOx1-S vaccine to be highly effective, and clinical trial data have demonstrated enhanced immunity following a ChAdOx1-S booster. In England, some individuals received a ChAdOx1-S booster where vaccination with mRNA vaccines was clinically contraindicated.MethodsThe demographic characteristics of those who received a ChAdOx1-S booster were compared to those who received a BNT162b2 booster. A test-negative case control design was used to estimate vaccine effectiveness of the ChAdOx1-S booster against symptomatic disease and hospitalisation in England.FindingsThose who received a ChAdOx1-S booster were more likely to be female (adjusted odds ratio (OR) 1.67 (1.64-1.71)), in a clinical risk group (adjusted OR 1.58 (1.54-1.63)), in the CEV group (adjusted OR 1.84 (1.79-1.89)) or severely immunosuppressed (adjusted OR 2.05 (1.96-2.13)).Protection against symptomatic disease in those aged 65 years and older peaked at 66.1% (16.6 to 86.3%) and 68.5% (65.7 to 71.2%) amongst those who received the ChAdOx1-S and BNT162b2 booster vaccines, respectively. Protection waned to 44.5% (22.4 to 60.2%) and 54.1% (50.5 to 57.5%) after 5-9 weeks. Protection against hospitalisation following Omicron infection peaked at 82.3% (64.2 to 91.3%) after receiving a ChAdOx1-S booster, as compared to 90.9% (88.7 to 92.7%) for those who received a BNT162b2 booster.InterpretationDifferences in the population boosted with ChAdOx1-S in England renders direct comparison of vaccine effectiveness by manufacturer challenging. Nonetheless, this study supports the use of the ChAdOx1-S booster for protection against severe disease with COVID-19 in settings that have not yet offered booster doses and suggests that those who received ChAdOx1-S as a booster in England do not require re-vaccination ahead of others.FundingUKHSA
Human behaviour, NPI and mobility reduction effects on COVID-19 transmission in different countries of the world
Authors: Mohammadi Zahra , Cojocaru Monica Gabriela , Thommes Edward Wolfgang 
Published: May 2022

AbstractBackgroundThe outbreak of Coronavirus disease, which originated in Wuhan, China in 2019, has affected the lives of billions of people globally. Throughout 2020, the reproduction number of COVID-19 was widely used by decision-makers to explain their strategies to control the pandemic.MethodsIn this work, we deduce and analyze both initial and effective reproduction numbers for 12 diverse world regions between February and December of 2020. We consider mobility reductions, mask wearing and compliance with masks, mask efficacy values alongside other non-pharmaceutical interventions (NPIs) in each region to get further insights in how each of the above factored into each region’s SARS-COV-2 transmission dynamic.ResultsWe quantify in each region the following reductions in the observed effective reproduction numbers of the pandemic: i) reduction due to decrease in mobility (as captured in Google mobility reports); ii) reduction due to mask wearing and mask compliance; iii) reduction due to other NPI’s, over and above the ones identified in i) and ii).ConclusionIn most cases mobility reduction coming from nationwide lockdown measures has helped stave off the initial wave in countries who took these types of measures. Beyond the first waves, mask mandates and compliance, together with social-distancing measures (which we refer to as other NPI’s) have allowed some control of subsequent disease spread. The methodology we propose here is novel and can be applied to other respiratory diseases such as influenza or RSV.
Clinicopathological and Imaging Features of Primary Biliary Cholangitis
Authors: Xie Mengdan , Nyabanga Custon Tafadzwa , Sehmbhi Mantej , Khalili Nour Al , Chon Christy , Kamath Amita , Dinani Amreen M. , Weisberg Ilan S. 
Published: May 2022

Abstract/KeywordsBackground and AimsPrimary biliary cholangitis (PBC) is a chronic inflammatory autoimmune disease of the biliary epithelial cells, causing slow progression of cholestasis and fibrosis. The aim of the study is to summarize the imaging features of PBC and examine the correlation between its clinicopathological and radiologic features, elucidating the specific clinicopathological and radiologic differences between male and female PBC patients, as well as between AMA-positive and AMA-negative PBC patients.MethodsDemographic, laboratory, radiologic and survival data were collected retrospectively for patients diagnosed and treated for PBC at the Mount Sinai Health System between 2016 and 2020 with at least one ultrasound, CT, or MRI of abdomen available for assessment. Biochemical and radiologic data were compared between male v.s. female groups, and AMA-positive v.s. AMA-negative group.ResultsA total of 273 patients diagnosed with PBC were included. Non-specific hepatic parenchymal disease, cirrhosis, cholelithiasis, splenomegaly, lymphadenopathy, benign liver masses/cysts were the most common features on abdominal images. 24% of PBC patients had biliary tree abnormalities on MRI. LAD was reported in 38-47% of PBC patients. There was no significant difference in age, race, or ethnicity between the sexes of patients with PBC, however imaging characteristics of portal hypertension were more frequently seen in men. AMA-negative PBC patients had similar distributions of age, race/ethnicity and survival to AMA-positive PBC patients.ConclusionOur study summarized the clinicopathological and imaging features of PBC and distinct subgroups. This would assist in the diagnosis of PBC and avoid over-testing in real-world practice.
Comparison of selective genotyping strategies in genomic selection programs for broilers using stochastic simulation
Authors: Alemu Setegn. W. , Sørensen Anders C. , Wang Lei , Henshall John , Hawken Rachel , Madsen Per , Jensen Just 
Published: May 2022

AbstractBreeding programs using genomic information have become common in broilers. In broilers, the main traits for selection are body weight and feed efficiency. These traits are measured in both sexes and before sexual maturity. Thus, increases in genetic gain in broiler breeding programs due to the use of genomic information are attributable primarily to the increased accuracy of predicted breeding values of potential parents. As not all birds can be genotyped due to economic constraints, an optimal genotyping strategy needs to be chosen. The objective of this study was to investigate the rates of genetic gain and inbreeding obtained by varying three factors: the percentage of birds genotyped (PG), the percentage of birds genotyped randomly (PRG) or selectively, and the percentage of males among genotyped birds (PMG). Stochastic computer simulation with a full factorial experimental design was used. Significant interaction among the factors (PG, PRG, and PMG) was observed for the rate of genetic gain in body weight and aggregate breeding value, but not for the gain in residual feed intake or the rate of inbreeding per generation. Our findings indicate that the PG, PRG, and PMG need to be considered when selecting a genotyping strategy for a broiler breeding program. If available resources allow only to genotype a small percentage (e.g., 2.5% or 5%) of all birds, the genotyping of 50–100% of male birds and selection of birds to be genotyped using phenotypic information is best. If resources allow to genotype more (e.g., ≥20%) candidates, genotyping of equal numbers of each sex, and low PRG level (i.e., preselection of the majority of candidate based on performance) is best. Provided that a proper genotyping strategy is chosen, we conclude that the incorporation of genomic information in broiler breeding programs can substantially increase the rate of genetic gain.
Reprogramming of cardiac phosphoproteome, proteome and transcriptome confers resilience to chronic adenylyl cyclase-driven stress
Authors: Qu Jia-Hua , Chakir Khalid , Tarasov Kirill V. , Riordon Daniel R. , Perino Maria Grazia , Silvester Allwin Jennifa , Lakatta Edward G. 
Published: May 2022

AbstractOur prior study (Tarasov, K. V. et al., 2022) discovered that numerous adaptive mechanisms emerge in response to cardiac-specific overexpression of adenylyl cyclase type 8 (TGAC8) which included overexpression of a large number of proteins. Here we conducted an unbiased phosphoproteomics analysis in order to determine the role of altered protein phosphorylation in the adaptive heart performance and protection profile of adult TGAC8 left ventricle (LV) at 3-4 months of age, and integrated the phosphoproteome with transcriptome and proteome. Based on differentially regulated phosphoproteins by genotype, numerous stress-response pathways within reprogrammed TGAC8 LV, including PKA, PI3K and AMPK signaling pathways, predicted upstream regulators (e.g., PDPK1, PAK1 and PTK2B), and downstream functions (e.g., cell viability, protein quality control), and metabolism were enriched. In addition to PKA, numerous other kinases and phosphatases were hyper-phosphorylated in TGAC8 vs. WT. Hyper-phosphorylated transcriptional factors in TGAC8 were associated with increased mRNA transcription, immune responses and metabolic pathways. Combination of the phosphoproteome with its proteome and with the previously published TGAC8 transcriptome enabled the elucidation of cardiac performance and adaptive protection profiles coordinately regulated at post-translational modification (PTM) (phosphorylation), translational and transcriptional levels. Many stress-response signaling pathways, i.e., PI3K/AKT, ERK/MAPK and ubiquitin labeling, were consistently enriched and activated in the TGAC8 LV at transcriptional, translational and PTM levels. Thus, reprogramming of the cardiac phosphoproteome, proteome and transcriptome confers resilience to chronic adenylyl cyclase-driven stress. We identified numerous pathways/function predictions via gene sets, phosphopeptides, and phosphoproteins, which may point to potential novel therapeutic targets to enhance heart adaptivity, maintaining heart performance while avoiding cardiac dysfunction.
Taxonomically Restricted Genes are Associated with Responses to Biotic and Abiotic Stresses in Sugarcane (Saccharum spp.)
Authors: Cardoso-Silva Claudio Benicio , Aono Alexandre Hild , Mancini Melina Cristina , Sforca Danilo Augusto , da Silva Carla Cristina , Pinto Luciana Rossini , Adams Keith L. , de Souza Anete Pereira 
Published: May 2022

ABSTRACTOrphan genes (OGs) are protein-coding genes that are restricted to particular clades or species and lack homology with genes from other organisms, making their biological function difficult to predict. OGs can rapidly originate and become functional; consequently, they may support rapid adaptation to environmental changes. Extensive spread of mobile elements, and whole genome duplication, occurred in the Saccharum group, which may have contributed to the origin and diversification of OGs in the sugarcane genome. Here, we identified and characterized OGs in sugarcane, examined their expression profiles across tissues and genotypes, and investigated their regulation under varying conditions. We identified 319 OGs in the Saccharum spontaneum genome without detected homology to protein-coding genes in green plants, except those belonging to Saccharinae. Transcriptomic analysis showed 288 sugarcane OGs with detectable expression levels in at least one tissue or genotype. We observed similar expression patterns of OGs in sugarcane genotypes originating from the closest geographical locations. We also observed tissue-specific expression of some OGs, possibly indicating a complex regulatory process for maintaining diverse functional activity of these genes across sugarcane tissues and genotypes. Sixty-six OGs were differentially expressed under stress conditions, especially cold and osmotic stresses. Gene co-expression network and functional enrichment analyses suggested that sugarcane OGs may be involved in several biological mechanisms, including stimulus response and defence mechanisms. These findings provide a valuable genomic resource for sugarcane researchers, especially those interested in selecting stress-responsive genes.
Human Neuronal Excitation/Inhibition Balance Explains and Predicts Neurostimulation Induced Learning Benefits
Authors: van Bueren Nienke E. R. , van der Ven Sanne H. G. , Hochman Shachar , Sella Francesco , Kadosh Roi Cohen 
Published: May 2022

AbstractPrevious research has highlighted the role of the excitation/inhibition ratio (E/I) for typical and atypical development, mental health, cognition, and learning. Other research has highlighted the benefits of high-frequency random noise stimulation (tRNS)—an excitatory form of neurostimulation—on learning. We examined the E/I as a potential mechanism and studied whether tRNS effect on learning depends on E/I as measured by the aperiodic exponent as its putative marker. In addition to manipulating E/I using tRNS, we also manipulated the level of learning (learning/overlearning) that has been shown to influence E/I. Participants (n=102) received either sham stimulation or 20 min tRNS over the dorsolateral prefrontal cortex (DLPFC) during a mathematical learning task. We showed that tRNS increased E/I, as reflected by the aperiodic exponent, and that lower E/I predicted greater benefit from tRNS specifically for the learning task. In contrast to previous Magnetic Resonance Spectroscopy-based E/I studies, we found no effect of the level of learning on E/I. A further analysis using a different data set suggest that both measures of E/I (EEG vs MRS) may reflect, at least partly, different biological mechanisms. Our results highlight the role of E/I as a marker for neurostimulation efficacy and learning. This mechanistic understanding provides better opportunities for augmented learning and personalized interventions.
Modelling mouse auditory response dynamics along a continuum of consciousness using a deep recurrent neural network
Authors: O’Reilly Jamie A. 
Published: May 2022

AbstractObjectiveUnderstanding neurophysiological changes that accompany transitions between anaesthetized and conscious states is a key objective of anesthesiology and consciousness science. This study aimed to characterize the dynamics of auditory-evoked potential morphology in mice along a continuum of consciousness.ApproachEpidural field potentials were recorded from above the primary auditory cortices of two groups of laboratory mice: urethane-anaesthetized (A, n = 14) and conscious (C, n = 17). Both groups received auditory stimulation in the form of a repeated pure-tone stimulus, before and after receiving 10 mg/kg i.p. ketamine (AK and CK). Evoked responses were then ordered by ascending sample entropy into AK, A, CK, and C, considered to reflect physiological correlates of awareness. These data were used to train a recurrent neural network (RNN) with an input parameter encoding state. Model outputs were compared with grand-average event-related potential (ERP) waveforms. Subsequently, the state parameter was varied to simulate changes in the ERP that occur during transitions between states, and relationships with dominant peak amplitudes were quantified.Main resultsThe RNN synthesized output waveforms that were in close agreement with grand-average ERPs for each group (r2 > 0.9, p < 0.0001). Varying the input state parameter generated model outputs reflecting changes in ERP morphology predicted to occur between states. Positive peak amplitudes within 25 to 50 ms, and negative peak amplitudes within 50 to 75 ms post-stimulus-onset, were found to display a sigmoidal characteristic during the transition from anaesthetized to conscious states. In contrast, negative peak amplitudes within 0 to 25 ms displayed greater linearity.SignificanceThis study demonstrates a method for modelling changes in ERP morphology that accompany transitions between states of consciousness using a RNN. In future studies, this approach may be applied to human data to support the clinical use of ERPs to predict transition to consciousness.
PanCircBase: An online resource for the exploration of circular RNAs in pancreatic islets
Authors: Sinha Tanvi , Mishra Smruti Sambhav , Singh Suman , Panda Amaresh Chandra 
Published: May 2022

AbstractCircular RNAs (circRNAs) are a novel class of covalently closed RNA molecules that recently emerged as a critical regulator of gene expression in development and diseases. Recent research has highlighted the importance of novel circRNAs in the biosynthesis and secretion of insulin from β-cells of pancreatic islets. However, all circRNAs expressed in pancreatic islets or β-cells are not readily available in the database. In this study, we analyzed publicly available RNA-sequencing datasets of the pancreatic islets to catalog all circRNAs expressed in pancreatic islets to construct the PanCircBase (www.pancircbase.net/) database that provides the following resources: (i) pancreatic islet circRNA annotation details (genomic position, host gene, exon information, splice length, sequence, other database IDs, cross-species conservation), (ii) divergent primers for PCR analysis of circRNAs, (iii) siRNAs for silencing of target circRNAs, (iv) miRNAs associated with circRNAs, (v) possible protein-coding circRNAs and their polypeptides. In summary, this is a comprehensive online resource for exploring circRNA expression and its possible function in pancreatic β-cells.
Concussive head trauma perturbs axon initial segment function in axotomized and intact layer 5 pyramidal neurons
Authors: Harris Alan C. , Sun Jianli , Jacobs Kimberle 
Published: May 2022

AbstractThe axon initial segment (AIS) is a critical locus of control of action potential (AP) generation and neuronal information synthesis. Concussive traumatic brain injury gives rise to diffuse axotomy, and the majority of neocortical axonal injury arises at the AIS. Consequently, concussive traumatic brain injury might profoundly disrupt the functional specialization of this region. To investigate this hypothesis, one and two days after mild central fluid percussion injury in Thy1-YFP-H mice, we recorded high-resolution APs from axotomized and adjacent intact layer 5 pyramidal neurons and applied a second derivative (2°) analysis to measure the AIS- and soma-regional contributions to the AP upstroke. All layer 5 pyramidal neurons recorded from sham animals manifested two stark 2° peaks separated by a negative intervening slope. In contrast, within injured mice, we discovered a subset of axotomized layer 5 pyramidal neurons in which the AIS-regional 2° peak was abolished, a functional perturbation associated with diminished excitability, axonal sprouting and distention of the AIS as assessed by staining for ankyrin-G. Our analysis revealed an additional subpopulation of both axotomized and intact layer 5 pyramidal neurons that manifested a melding together of the AIS- and soma-regional 2° peaks, suggesting a more subtle aberration of sodium channel function and/or translocation of the AIS initiation zone closer to the soma. When these experiments were repeated in animals in which cyclophilin-D was knocked out, these effects were ameliorated, suggesting that trauma-induced AIS functional perturbation is associated with mitochondrial calcium dysregulation.
Hybridization drives mitochondrial DNA degeneration and metabolic shift in a species with biparental mitochondrial inheritance
Authors: Hénault Mathieu , Marsit Souhir , Charron Guillaume , Landry Christian R. 
Published: May 2022

ABSTRACTMitochondrial DNA (mtDNA) is a cytoplasmic genome that is essential for respiratory metabolism. While uniparental mtDNA inheritance is most common in animals and plants, distinct mtDNA haplotypes can coexist in a state of heteroplasmy, either because of paternal leakage or de novo mutations. MtDNA integrity and the resolution of heteroplasmy have important implications, notably for mitochondrial genetic disorders, speciation and genome evolution in hybrids. However, the impact of genetic variation on the transition to homoplasmy from initially heteroplasmic backgrounds remains largely unknown. Here, we useSaccharomycesyeasts, fungi with constitutive biparental mtDNA inheritance, to investigate the resolution of mtDNA heteroplasmy in a variety of hybrid genotypes. We previously designed 11 crosses along a gradient of parental evolutionary divergence using undomesticated isolates ofSaccharomyces paradoxusandSaccharomyces cerevisiae. Each cross was independently replicated 48 to 96 times, and the resulting 864 hybrids were evolved under relaxed selection for mitochondrial function. Genome sequencing of 446 MA lines revealed extensive mtDNA recombination, but recombination rate was not predicted by parental divergence level. We found a strong positive relationship between parental divergence and the rate of large-scale mtDNA deletions, which lead to the loss of respiratory metabolism. We also uncovered associations between mtDNA recombination, mtDNA deletion, and genome instability that were genotype-specific. Our results show that hybridization in yeast induces mtDNA degeneration through large-scale deletion and loss of function, with deep consequences for mtDNA evolution, metabolism and the emergence of reproductive isolation.
Health-Related Quality of Life and Coping Strategies adopted by COVID-19 survivors: A nationwide cross-sectional study in Bangladesh
Authors: Hossain Mohammad Anwar , Shafin Rubayet , Ahmed Md. Shahoriar , Rana Md. Shohag , Walton Lori Maria , Raigangar Veena , Ara Tasnim , Rasel Md. Aminul Haque , Hossain Mohammad Sohrab , Kabir Md. Feroz , Islam Mir Raihanul , Hasan Md. Nazmul , Hossain Delowar , Rumana Farjana Sharmin , Jahid Iqbal Kabir 
Published: May 2022

AbstractThis study aims to investigate the health-related quality of life and coping strategies among COVID-19 survivors in Bangladesh.MethodsThis is a cross-sectional study of 2198 adult, COVID-19 survivors living in Bangladesh. Data were collected from previously diagnosed COVID-19 participants (confirmed by an RT-PCR test) via door-to-door interviews in the eight different divisions in Bangladesh. For data collection, Bengali translated Brief COPE inventory and WHO Brief Quality of Life (WHO-QOLBREF) questionnaires were used. The data collection period was from June 2020 to March 2021.ResultsMales 72.38% (1591) were more affected by COVID-19 than females 27.62% (607). Age showed significant correlations (p<0.005) with physical, psychological and social relationships; whereas, gender showed only significant correlation with physical health (p<0.001). Marital status, occupation, living area, and co-morbidities showed significant co-relation with all four domains of QoL (p<0.001). Education and affected family members showed significant correlation with physical and social relationship (p<0.001). However, smoking habit showed significant correlations with both social relationship and environment (p<0.001). Age and marital status showed a significant correlation with avoidant coping strategy (p<0.001); whereas gender and co-morbidities showed significant correlation with problem focused coping strategies (p<0.001). Educational qualification, occupation and living area showed significant correlation with all three coping strategies (p<0.001).ConclusionSurvivors of COVID-19 showed mixed types of coping strategies; however, the predominant coping strategy was avoidant coping, followed by problem focused coping, with emotion focused coping reported as the least prevalent. Marital status, occupation, living area and co-morbidities showed a greater effect on QoL in all participants. This study represents the real scenario of nationwide health associated quality of life and coping strategy during and beyond the Delta pandemic.