bluuebunny/crossref_metadata_2025_split huggingface dataset:
Risk of death following SARS-CoV-2 infection or COVID-19 vaccination in young people in England: a self-controlled case series study
Authors: Nafilyan Vahé , Bermingham Charlotte , Ward Isobel L. , Morgan Jasper , Zaccardi Francesco , Khunti Kamlesh , Stanborough Julie , Banerjee Amitava 
Published: March 2022

AbstractObjectivesTo assess whether there is a change in the incidence of cardiac and all-cause death in young people following COVID-19 vaccination or SARS-CoV-2 infection in unvaccinated individuals.DesignSelf-controlled case series.SettingNational, linked electronic health record data in England.Study populationIndividuals aged 12-29 who had received at least one dose of COVID-19 vaccination and died between 8 December 2020 and 2 February 2022 and registered by 16 February 2022 within 12 weeks of COVID-19 vaccination; Individuals aged 12-29 who died within 12 weeks of testing positive for SARS-CoV-2.Main outcome measuresCardiac and all-cause deaths occurring within 12 weeks of vaccination or SARS-CoV-2 infection.ResultsCompared to the baseline period, there was no evidence of a change in the incidence of cardiac death in the six weeks after vaccination, whether for each of weeks 1 to 6 or the whole six-week period. There was a decrease in the risk of all-cause death in the first week after vaccination and no change in each of weeks 2 to 6 after vaccination or whole six-week period after vaccination. Subgroup analyses by sex, age, vaccine type, and last dose also showed no change in the risk of death in the first six weeks after vaccination. There was a large increase in the incidence of cardiac and all-cause death in the overall risk period after SARS-CoV-2 infection among the unvaccinated.ConclusionThere is no evidence of an association between COVID-19 vaccination and an increased risk of death in young people. By contrast, SARS-CoV-2 infection was associated with substantially higher risk of cardiac related death and all-cause death.What is already known on this topicSeveral studies have highlighted the association between COVID-19 vaccination and the risk of myocarditis, myopericarditis, and other cardiac problems, especially in young people, but associated risk of mortality is unclear. Since younger people have lower risk of COVID-19 hospitalisation and mortality, the mortality risk associated with vaccination is potentially more important to them in balancing the risk and benefit of vaccination.What this study addsAlthough there is a risk of myocarditis or myopericarditis with COVID-19, there is no evidence of increased risk of cardiac or all-cause mortality following COVID-19 vaccination in young people aged 12 to 29. Given the increased risk of mortality following SARS-CoV-2 infection in this group, the risk-benefit analysis favours COVID-19 vaccination for this age group.
Systematic Review and Meta-analysis of Mental Health Impact on BAME Populations with Preterm Birth
Authors: Delanerolle G , Zeng Y , Phiri P , Phan T , Tempest N , Busuulwa P , Shetty A , Raymont V , Rathod S , Shi JQ , Hapangama DK 
Published: March 2022

AbstractBackgroundPreterm birth (PTB) is one of the main causes of neonatal deaths globally, with approximately 15 million infants are born preterm. Therefore, the mental health (MH) impact experienced by mothers experiencing a PTB is important, especially within the Black, Asian and Minority Ethnic (BAME) populations.AimThe aims of the study were to determine the prevalence of MH conditions among BAME women with PTB as well as the MH assessments used to characterise the MH outcomes.MethodsA systematic methodology was developed and published as a protocol in PROSPERO (CRD42020210863). Multiple databases were used to extract relevant data. I2 and Egger’s tests were used to detect the heterogeneity and publication bias. A Trim and fill method was used to demonstrate the influence of publication bias and the credibility of conclusions.ResultsThirty-nine studies met the eligibility criteria from a possible 3526. The prevalence rates of depression among PTB-BAME mothers were significantly higher than full-term mothers with a standard median deviation (SMD) of 1.5 and a 95% confidence interval (CI) 29-74%. The subgroup analysis indicated, depressive symptoms to be time sensitive. Women within the very PTB category demonstrated a significantly higher prevalence of depression than those categorised as non-very PTB. The prevalence rates of anxiety and stress among PTB-BAME mothers were significantly higher than full-term mothers (OR of 88% and 60% with a CI of 42%-149% and 24-106%, respectively).ConclusionBAME women with PTB suffers with MH conditions. Many studies did not report on BAME population specific MH outcomes. Therefore, the impact of PTB is not accurately represented in this population, and thus could negatively influence the quality of maternity services.Core TipThis study demonstrates the mental health impact due to preterm birth among the Black, Asian and Ethnic minority women. There is minimal research available at present around this subject matter, and potential disease sequalae.
The World Health Organization’s Disease Outbreak News: a retrospective database
Authors: Carlson Colin J. , Boyce Matthew R. , Dunne Margaret , Graeden Ellie , Lin Jessica , Abdellatif Yasser Omar , Palys Max A. , Pavez Munir , Phelan Alexandra L. , Katz Rebecca 
Published: March 2022

AbstractThe World Health Organization (WHO) notifies the global community about disease outbreaks through the Disease Outbreak News (DON). These online reports tell important stories about both outbreaks themselves and the high-level decision making that governs information sharing during public health emergencies. However, they have been used only minimally in global health scholarship to date. Here, we collate all 2,789 of these reports from their first use through the start of the Covid-19 pandemic (January 1996 to December 2019), and develop an annotated database of the subjective and often inconsistent information they contain. We find that these reports are dominated by a mix of persistent worldwide threats (particularly influenza and cholera) and persistent epidemics (like Ebola virus disease in Africa or MERS-CoV in the Middle East), but also document important periods in history like the anthrax bioterrorist attacks at the turn of the century, the spread of chikungunya and Zika virus to the Americas, or even recent lapses in progress towards polio elimination. We present three simple vignettes that show how researchers can use these data to answer both qualitative and quantitative questions about global outbreak dynamics and public health response. However, we also find that the retrospective value of these reports is visibly limited by inconsistent reporting (e.g., of disease names, case totals, mortality, and actions taken to curtail spread). We conclude that sharing a transparent rubric for which outbreaks are considered reportable, and adopting more standardized formats for sharing epidemiological metadata, might help make the DON more useful to researchers and policymakers.
TheVenturia inaequaliseffector repertoire is expressed in waves and is dominated by expanded families with predicted structural similarity to avirulence proteins from other plant-pathogenic fungi
Authors: Rocafort Mercedes , Bowen Joanna K. , Hassing Berit , Cox Murray P. , McGreal Brogan , de la Rosa Silvia , Plummer Kim M. , Bradshaw Rosie E. , Mesarich Carl H. 
Published: March 2022

AbstractBackgroundScab, caused by the biotrophic fungusVenturia inaequalis, is the most economically important disease of apples worldwide. During infection,V. inaequalisoccupies the subcuticular environment, where it secretes virulence factors, termed effectors, to promote host colonization. Consistent with other plant-pathogenic fungi, many of these effectors are expected to be non-enzymatic proteins, some of which can be recognized by corresponding host resistance proteins to activate plant defences, thus acting as avirulence determinants. To develop durable control strategies against scab, a better understanding of the roles that these effector proteins play in promoting subcuticular growth byV. inaequalis, as well as in activating, suppressing or circumventing resistance protein-mediated defences in apple, is required.ResultsWe generated the first comprehensive RNA-seq transcriptome ofV. inaequalisduring colonization of apple. Analysis of this transcriptome revealed five temporal waves of gene expression that peaked during early, mid or mid-late infection. While the number of genes encoding secreted, non-enzymatic proteinaceous effector candidates (ECs) varied in each wave, most belonged to waves that peaked in expression during mid-late infection. Spectral clustering based on sequence similarity determined that the majority of ECs belonged to expanded protein families. To gain insights into function, the tertiary structures of ECs were predicted using AlphaFold2. Strikingly, despite an absence of sequence similarity, many ECs were predicted to have structural similarity to avirulence proteins from other plant-pathogenic fungi, including members of the MAX, LARS, ToxA and FOLD effector families. In addition, several other ECs, including an EC family with sequence similarity to the AvrLm6 avirulence effector fromLeptosphaeria maculans, were predicted to adopt a KP6-like fold. Thus, proteins with a KP6-like fold represent another structural family of effectors shared among plant-pathogenic fungi.ConclusionsOur study reveals the transcriptomic profile underpinning subcuticular growth byV. inaequalisand provides an enriched list of ECs that can be investigated for roles in virulence and avirulence. Furthermore, our study supports the idea that numerous sequence-unrelated effectors across plant-pathogenic fungi share common structural folds. In doing so, our study gives weight to the hypothesis that many fungal effectors evolved from ancestral genes through duplication, followed by sequence diversification, to produce sequence-unrelated but structurally similar proteins.
Classifying the activity states of small vertebrates using automated VHF telemetry
Authors: Gottwald Jannis , Royauté Raphaël , Becker Marcel , Geitz Tobias , Höchst Jonas , Lampe Patrick , Leister Lea , Lindner Kim , Maier Julia , Rösner Sascha , Schabo Dana G. , Freisleben Bernd , Brandl Roland , Müller Thomas , Farwig Nina , Nauss Thomas 
Published: March 2022

AbstractThe most basic behavioural states of animals can be described as active or passive. However, while high-resolution observations of activity patterns can provide insights into the ecology of animal species, few methods are able to measure the activity of individuals of small taxa in their natural environment. We present a novel approach in which the automated VHF radio-tracking of small vertebrates fitted with lightweight transmitters (< 0.2 g) is used to distinguish between active and passive behavioural states.A dataset containing > 3 million VHF signals was used to train and test a random forest model in the assignment of either active or passive behaviour to individuals from two forest-dwelling bat species (Myotis bechsteinii(n = 50) andNyctalus leisleri(n = 20)). The applicability of the model to other taxonomic groups was demonstrated by recording and classifying the behaviour of a tagged bird and by simulating the effect of different types of vertebrate activity with the help of humans carrying transmitters. The random forest model successfully classified the activity states of bats as well as those of birds and humans, although the latter were not included in model training (F-score 0.96–0.98).The utility of the model in tackling ecologically relevant questions was demonstrated in a study of the differences in the daily activity patterns of the two bat species. The analysis showed a pronounced bimodal activity distribution ofN. leisleriover the course of the night while the night-time activity ofM. bechsteiniiwas relatively constant. These results show that significant differences in the timing of species activity according to ecological preferences or seasonality can be distinguished using our method.Our approach enables the assignment of VHF signal patterns to fundamental behavioural states with high precision and is applicable to different terrestrial and flying vertebrates. To encourage the broader use of our radio-tracking method, we provide the trained random forest models together with an R-package that includes all necessary data-processing functionalities. In combination with state-of-the-art open-source automated radio-tracking, this toolset can be used by the scientific community to investigate the activity patterns of small vertebrates with high temporal resolution, even in dense vegetation.
Targeted delivery of galunisertib attenuates fibrogenesis in an integratedex vivorenal transplant and fibrosis model
Authors: van Leeuwen L. Leonie , Leuvenink Henri G.D. , Kessler Benedikt M. , Olinga Peter , Ruigrok Mitchel J.R. 
Published: March 2022

AbstractNormothermic machine perfusion is an emerging preservation technique for kidney allografts to reduce post-transplant complications, including interstitial fibrosis and tubular atrophy. This technique, however, could be improved by adding antifibrotic molecules to perfusion solutions. We established Machine perfusion and Organ slices as a Platform for Ex vivo Drug delivery (MOPED), to explore fibrogenesis suppression strategies. We perfused porcine kidneysex vivowith galunisertib—a potent inhibitor of the transforming growth factor beta signaling pathway. To determine whether effects persisted, we also cultured precision-cut tissue slices prepared from the respective kidneys. Galunisertib supplementation improved the general viability, without negatively affecting renal function or elevating levels of injury markers or byproducts of oxidative stress. Galunisertib also reduced inflammation and more importantly, strongly suppressed the onset of fibrosis, especially when the treatment was continued in slices. Our results illustrate the value of targeted drug delivery, using isolated organ perfusion, for reducing post-transplant complications.One Sentence SummaryGalunisertib supplementation during normothermic machine perfusion attenuates fibrogenesis without compromising renal function.
Information maximization explains state-dependent synaptic plasticity and memory reorganization during non-rapid eye movement sleep
Authors: Yoshida Kensuke , Toyoizumi Taro 
Published: March 2022

AbstractSlow waves during the non-rapid eye movement (NREM) sleep reflect the alternating up and down states of cortical neurons; global and local slow waves promote memory consolidation and forgetting, respectively. Furthermore, distinct spike-timing-dependent plasticity (STDP) operates in these up and down states. The contribution of different plasticity rules to neural information coding and memory reorganization remains unknown. Here, we show that optimal synaptic plasticity for information maximization in a cortical neuron model provides a unified explanation for these phenomena. The model indicates that the optimal synaptic plasticity is biased towards depression as the baseline firing rate increases. This property explains the distinct STDP observed in the up and down states. Furthermore, it explains how global and local slow waves predominantly potentiate and depress synapses, respectively, if the background firing rate of excitatory neurons declines with the spatial scale of waves as the model predicts. The model provides a unifying account of the role of NREM sleep, bridging neural information coding, synaptic plasticity, and memory reorganization.
XY sex determination in a cnidarian
Authors: Chen Ruoxu , Sanders Steven M. , Ma Zhiwei , Paschall Justin , Chang E. Sally , Riscoe Brooke M. , Schnitzler Christine E. , Baxevanis Andreas D. , Nicotra Matthew L. 
Published: March 2022

AbstractSex determination occurs across animal species, but most of our knowledge about the mechanisms of sex determination comes from only a handful of bilaterian taxa. This limits our ability to infer the evolutionary history of sex determination within animals. In this study, we generated a linkage map of the genome of the colonial cnidarian Hydractinia symbiolongicarpus and used this map to determine that this species has an XX/XY sex determination system. We delineate the pseudoautosomal and non-recombining regions of the Y chromosome and show that the latter encodes a number of genes with male gonad-specific expression. These findings establish Hydractinia as a tractable non-bilaterian model system for the study of sex determination.Significance StatementWhat determines whether an animal is male or female? The answer depends on the species. Some rely on signals from their environment, while others take cues from their genome. Most of what we understand about sex determination comes from traditional model organisms (such as mice, flies, and worms) or groups of well-studied vertebrates and insects. Studying sex determination in other animals, especially those from phyla that diverged early in animal evolution, would allow us to better understand how sex has evolved across the animal kingdom and could reveal pathways present in the eumetazoan ancestor >600 million years ago. In this study, we show that the cnidarian Hydractinia symbiolongicarpus has XY sex determination, establishing this species as a model system for sex determination in an understudied group of animals.
Comparative analysis of genome-wide protein-DNA interactions across domains of life reveals unique binding patterns for hypersaline archaeal histones
Authors: Sakrikar Saaz , Hackley Rylee K. , Martinez-Pastor Mar , Darnell Cynthia L. , Vreugdenhil Angie , Schmid Amy K. 
Published: March 2022

ABSTRACTDNA-binding proteins with roles in chromatin architecture and transcriptional regulation are present in all three domains of life. Histones package DNA and regulate gene expression in eukaryotes, and find their evolutionary origin in the domain of life Archaea. Previously characterised archaeal histones have a somewhat conserved functional role in nucleosome formation and DNA packaging. However, previous research has indicated that the histone-like proteins of high salt-adapted archaea, or halophiles, appear to function differently. The sole histone protein encoded by the model halophilic species Halobacterium salinarum is non-essential, is involved in direct and indirect transcriptional regulation, and does not appear to package DNA. Here we use protein-DNA binding assays, computational analysis, and quantitative phenotyping to compare DNA binding patterns across halophilic histone proteins, bacterial and archaeal TFs, NAPs, and eukaryotic histones. Like TFs, halophilic histones bind the genome too sparsely to compact the genome. However, unlike TFs, binding occurs in both coding and intergenic regions. Unlike histones, halophilic histone occupancy is not depleted at the start sites of genes, and halophilic genomes lack the dinucleotide periodicity known to facilitate histone binding. We detect unique sequence preferences for histone binding in halophiles. Together these data suggest that the non-essentiality and genome-wide binding features of halophilic histone-like proteins are conserved across halophiles; they bind DNA in ways resembling both TFs and chromatin proteins, but do not appear to play a role in forming chromatin.IMPORTANCEMost cells in eukaryotic species – from yeast to humans– possess histone proteins that pack and unpack DNA in response to environmental cues. These essential proteins regulate the genes necessary for important cellular processes, including development and stress protection. The domain of life Archaea represent the evolutionary progenitors of eukaryotes. The universal conservation of the primary sequences of histone proteins across archaeal lineages suggests that eukaryotic histones originated in the Archaea. However, archaeal histones lack N-terminal tails and, in some species, package DNA in a continuous helix with no linker DNA between nucleosomes. We recently discovered that histones in hypersaline adapted archaeal species do not package DNA, and can act like transcription factors (TFs) to regulate stress response gene expression. Here we compare hypersaline histone function to a variety of DNA binding proteins across the tree of life, revealing a mosaic of functions for hypersaline-adapted histones.
Computer-assisted analysis of polysomnographic recordings improves inter-scorer associated agreement and scoring times
Authors: Alvarez-Estevez Diego , Rijsman Roselyne M. 
Published: March 2022

ABSTRACTStudy ObjectivesTo investigate inter-scorer agreement and scoring time differences associated with visual and computer-assisted analysis of polysomnographic (PSG) recordings.MethodsA group of 12 expert scorers reviewed 5 PSGs that were independently selected in the context of each of the following tasks: (i) sleep stating, (ii) detection of EEG arousals, (iii) analysis of the respiratory activity, and (iv) identification of leg movements. All scorers independently reviewed the same recordings, hence resulting in 20 scoring exercises from an equal amount of different subjects. The procedure was repeated, separately, using the classical visual manual approach and a computer-assisted (semi-automatic) procedure. Resulting inter-scorer agreement and scoring times were examined and compared among the two methods.ResultsComputer-assisted sleep scoring showed a consistent and statistically relevant effect toward less time required for the completion of each of the PSG scoring tasks. Gain factors ranged from 1.26 (EEG arousals) to 2.41 (limb movements). Inter-scorer kappa agreement was also consistently increased with the use of supervised semi-automatic scoring. Specifically, agreement increased from K=0.76 to K=0.80 (sleep stages), K=0.72 to K=0.91 (limb movements), K=0.55 to K=0.66 (respiratory activity), and K=0.58 to K=0.65 (EEG arousals). Inter-scorer agreement on the examined set of diagnostic indices did also show a trend toward higher Interclass Correlation Coefficient scores when using the semi-automatic scoring approach.ConclusionsComputer-assisted analysis can improve inter-scorer agreement and scoring times associated with the review of PSG studies resulting in higher efficiency and overall quality in the diagnosis sleep disorders.
CNV-ClinViewer: Enhancing the clinical interpretation of large copy-number variants online
Authors: Macnee Marie , Pérez-Palma Eduardo , Brünger Tobias , Klöckner Chiara , Platzer Konrad , Stefanski Arthur , Montanucci Ludovica , Bayat Allan , Radtke Maximilian , Collins Ryan L , Talkowski Michael , Blankenberg Daniel , Møller Rikke S , Lemke Johannes R , Nothnagel Michael , May Patrick , Lal Dennis 
Published: March 2022

ABSTRACTPurposeLarge copy number variants (CNVs) can cause a heterogeneous spectrum of rare and severe disorders. However, most CNVs are benign and are part of natural variation in human genomes. CNV pathogenicity classification, genotype-phenotype analyses, and therapeutic target identification are challenging and time-consuming tasks that require the integration and analysis of information from multiple scattered sources by experts.MethodsWe developed a web-application combining >250,000 patient and population CNVs together with a large set of biomedical annotations and provide tools for CNV classification based on ACMG/ClinGen guidelines and gene-set enrichment analyses.ResultsHere, we introduce the CNV-ClinViewer (https://cnv-ClinViewer.broadinstitute.org), an open-source web-application for clinical evaluation and visual exploration of CNVs. The application enables real-time interactive exploration of large CNV datasets in a user-friendly designed interface.ConclusionOverall, this resource facilitates semi-automated clinical CNV interpretation and genomic loci exploration and, in combination with clinical judgment, enables clinicians and researchers to formulate novel hypotheses and guide their decision-making process. Subsequently, the CNV-ClinViewer enhances for clinical investigators patient care and for basic scientists translational genomic research.