bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimates of the global burden of Congenital Rubella Syndrome, 1996-2019
Authors: Vynnycky Emilia , Knapp Jennifer K , Papadopoulos Timos , Cutts Felicity T , Hachiya Masahiko , Miyano Shinsuke , Reef Susan E 
Published: April 2023

AbstractBackgroundMany countries introduced rubella-containing vaccination (RCV) after 2011, following changes in recommended World Health Organization (WHO) vaccination strategies and external support. The full impact of these introductions is unknown as previous estimates of the global burden of Congenital Rubella Syndrome (CRS) considered the period 1996-2010.MethodsWe updated a previously-published literature review to identify rubella seroprevalence studies among unvaccinated populations. These were used in an age-structured transmission model, including routine and campaign vaccination coverage to estimate the CRS incidence during 1996-2019 in each country, each region and globally.FindingsFor 2019, the highest CRS incidence was estimated for the WHO African (AFR) and Eastern Mediterranean (EMR) regions (64 (95% CI: 24-123) and 27 (95% CI: 4-67) per 100,000 live births respectively), where nearly half of births occur in countries that have introduced RCV.. In regions elsewhere, where over 95% of births occurred in countries which had introduced RCV, the estimated CRS incidence was low (<1 (95% CI: <1-8) and <1 (95% CI: <1-12) per 100,000 live births in the South East Asian (SEAR) and Western Pacific (WPR) regions respectively, and similarly in Europe and the Americas). The estimated number of CRS births globally declined by approximately two thirds from 100,000 (95% CI: 54,000-166,000) in 2010 to 32,000 (95% CI: 13,000-60,000) by 2019, with the biggest falls in SEAR and WPR.InterpretationThe introduction of RCV in SEAR and WPR led to dramatic regional and global reductions in the CRS incidence since 2010. Introducing RCV in the remaining countries and maintaining high RCV coverage can result in further reductions.FundingGavi the Vaccine Alliance via the Vaccine Impact Modelling Consortium (VIMC). VIMC is jointly funded by Gavi the Vaccine Alliance and the Bill and Melinda Gates Foundation (BMGF grant number: OPP1157270).
A comparative national-level analysis of government food system resilience activities in preparation for future food system disruptions
Authors: Lloyd Jane , Moore E.R.H. , Dowell Lyndsey , Neff Roni 
Published: April 2023

AbstractBackground:The COVID-19 pandemic, extreme weather events, and the Russian invasion of Ukraine have highlighted global food system vulnerabilities and a lack of preparedness and prospective planning for increasingly complex disruptions. This has spurred an interest in food system resilience. Despite the elevated interest in food system resilience, there is a lack of comparative analyses of national-level food system resilience efforts. An improved understanding of the food system resilience landscape can support and inform future policies, programs, and planning.Methods:We conducted a cross-country comparison of national-level food system resilience activities from Australia, Aotearoa (New Zealand), Sweden, and the United States. We developed upon and adapted the resilience framework proposed by Harris and Spiegel to compare actions derived from thirteen national food system resilience documents. We coded the documents based on how the governments determined actions by food system resilience attribute utilized, part of the food supply chain, specific shocks or stressors, implementation level, the temporal focus of action, and the expected impact on food security. We analyzed and compared countries’ coded categories, subcategories, and category combinations.Results:The results showed that countries are using multi-pronged policy actions to address food system resilience issues and are focused on both retrospective reviews and prospective models of disruptive events to inform their decisions. Some work has been done towards preparing for climate change and other natural disasters, but not as much for other shocks or stressors.Conclusions:The analysis identified potential gaps, concentrations, and themes in national food systems resilience. The framework can be applied to augment existing policy, create new policy, as well as to supplement and complement other existing frameworks.
Diagnostic Utility of Brain MRI in Spontaneous Intracerebral Hemorrhage: A Retrospective Cohort Study and Meta-Analysis
Authors: Wilson Mitch , Wang Jia-Yi , Andreev Alexander , Katsanos Aristeidis H. , Selim Magdy , Lioutas Vasileios-Arsenios 
Published: April 2023

ABSTRACTBackgroundThe diagnostic yield of brain Magnetic Resonance Imaging (MRI) in spontaneous intracerebral hemorrhage (ICH) is unclear. We performed both an independent single-center retrospective cohort study and a meta-analysis to assess the detection rate of secondary lesions on MRI in patients with spontaneous ICH.MethodsIn the retrospective cohort study, we examined 856 consecutive patients with spontaneous ICH. Brain MRI scans on admission and follow-up were assessed for secondary lesions. We also examined clinical and CT radiographic variables associated with secondary lesions in univariable analysis. In the meta-analysis we searched PubMed and EMBASE for articles investigating the secondary lesion detection rate on brain MRI in spontaneous ICH. Random-effects models were used to calculate the pooled estimate of secondary lesion detection rate. The meta-analysis used the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines.ResultsOf the 856 patients with ICH, 481 (56%) had at least one brain BRI performed [70±14 years, 270(56% male)]. 462(54%) had an admission MRI and 138(16%) had both admission and follow-up MRIs. The detection rate of secondary lesions on admission MRIs was 24/462(5.2%). 4/127(3.1%) patients with a negative admission MRI had a lesion identified on follow-up MRI. No clinical or radiographic variables were associated with a secondary lesion on MRI using univariable analysis. The meta-analysis included 5 studies total (4 identified in the PubMed and EMBASE searches as well as our own cohort study) comprising 1147 patients with spontaneous ICH who underwent brain MRI. The pooled detection rate of secondary lesions was 11% (95%CI: 7-16%).ConclusionsNo predictors of secondary lesion detection were identified in our cohort study. Prospective studies are required to better understand the diagnostic utility of MRI in spontaneous ICH.
AI-based histologic scoring enables automated and reproducible assessment of enrollment criteria and endpoints in NASH clinical trials
Authors: Iyer Janani S. , Pokkalla Harsha , Biddle-Snead Charles , Carrasco-Zevallos Oscar , Lin Mary , Shanis Zahil , Le Quang , Juyal Dinkar , Pouryahya Maryam , Pedawi Aryan , Hoffman Sara , Elliott Hunter , Leidal Kenneth , Myers Robert P. , Chung Chuhan , Billin Andrew N. , Watkins Timothy R. , Resnick Murray , Wack Katy , Glickman Jon , Burt Alastair D. , Loomba Rohit , Sanyal Arun J. , Montalto Michael C. , Beck Andrew H. , Taylor-Weiner Amaro , Wapinski Ilan 
Published: April 2023

ABSTRACTClinical trials in nonalcoholic steatohepatitis (NASH) require histologic scoring for assessment of inclusion criteria and endpoints. However, guidelines for scoring key features have led to variability in interpretation, impacting clinical trial outcomes. We developed an artificial intelligence (AI)-based measurement (AIM) tool for scoring NASH histology (AIM-NASH). AIM-NASH predictions for NASH Clinical Research Network (CRN) grades of necroinflammation and stages of fibrosis aligned with expert consensus scores and were reproducible. Continuous scores produced by AIM-NASH for key histological features of NASH correlated with mean pathologist scores and with noninvasive biomarkers and strongly predicted patient outcomes. In a retrospective analysis of the ATLAS trial, previously unmet pathological endpoints were met when scored by the AIM-NASH algorithm alone. Overall, these results suggest that AIM-NASH may assist pathologists in histologic review of NASH clinical trials, reducing inter-rater variability on trial outcomes and offering a more sensitive and reproducible measure of patient therapeutic response.
Bivalent COVID-19 mRNA booster vaccination (BA.1 or BA.4/BA.5) increases neutralization of matched Omicron variants
Authors: Springer David N. , Bauer Michael , Medits Iris , Camp Jeremy V. , Aberle Stephan W. , Burtscher Clemens , Höltl Eva , Weseslindtner Lukas , Stiasny Karin , Aberle Judith H. 
Published: April 2023

AbstractWe report SARS-CoV-2 neutralizing antibody titers in sera of triple-vaccinated individuals who received a booster dose of an original monovalent or a bivalent BA.1- or BA.4/BA.5-adapted vaccine, or had a breakthrough infection with Omicron variants BA.1, BA.2 or BA.4/BA.5. A bivalent BA.4/BA.5 booster or Omicron-breakthrough infection induced increased Omicron-neutralization titers compared with the monovalent booster. The XBB.1.5 variant effectively evaded neutralizing-antibody responses elicited by current vaccines and/or infection with previous variants.
A novel mutation in EROS (CYBC1) causes Chronic Granulomatous Disease
Authors: Mortimer Paige M , Nichols Esme , Thomas Joe , Shanbhag Rachna , Singh Neha , Coomber Eve L , Malik Talat H , Pickering Matthew C , Randzavola Lyra , Rae William , Bhattad Sagar , Thomas David C 
Published: April 2023

AbstractChronic Granulomatous Disease (CGD) is an inborn error of immunity characterised by opportunistic infection and sterile granulomatous inflammation. CGD is caused by a failure of reactive oxygen species (ROS) production by the phagocyte NADPH oxidase. Mutations in the genes encoding phagocyte NADPH oxidase subunits cause CGD. We and others have described a novel form of CGD (CGD5) secondary to lack of EROS (CYBC1), a highly selective chaperone for gp91phox. EROS-deficient cells express minimal levels of gp91phoxand its binding partner p22phox, but EROS also controls the expression of other proteins such as P2×7. The full nature of CGD5 is currently unknown. We describe a homozygous frameshift mutation inCYBC1leading to CGD. Individuals who are heterozygous for this mutation are found in South Asian populations (allele frequency = 0.00006545), thus it is not a private mutation. Therefore, it is likely to be the underlying cause of other cases of CGD.
A TNF-IL-1 circuit controlsYersiniawithin intestinal granulomas
Authors: Matsuda Rina , Daniel Sorobetea , Zhang Jenna , Peterson Stefan T. , Grayczyk James P. , Herrmann Beatrice , Yost Winslow , O’Neill Rosemary , Bohrer Andrea C. , Lanza Matthew , Assenmacher Charles-Antoine , Mayer-Barber Katrin D. , Shin Sunny , Brodsky Igor E. 
Published: April 2023

AbstractSummaryMonocytes restrictYersiniainfection within intestinal granulomas. Here, we report that monocyte-intrinsic TNF signaling drives production of IL-1 that signals to non-hematopoietic cells to control intestinalYersiniainfection within granulomas.Tumor necrosis factor (TNF) is a pleiotropic inflammatory cytokine that mediates antimicrobial defense and granuloma formation in response to infection by numerous pathogens.Yersinia pseudotuberculosiscolonizes the intestinal mucosa and induces recruitment of neutrophils and inflammatory monocytes into organized immune structures termed pyogranulomas that control the bacterial infection. Inflammatory monocytes are essential for control and clearance ofYersiniawithin intestinal pyogranulomas, but how monocytes mediateYersiniarestriction is poorly understood. Here, we demonstrate that TNF signaling in monocytes is required for bacterial containment following entericYersiniainfection. We further show that monocyte-intrinsic TNFR1 signaling drives production of monocyte-derived interleukin-1 (IL-1), which signals through IL-1 receptor on non-hematopoietic cells to enable pyogranuloma-mediated control ofYersiniainfection. Altogether, our work reveals a monocyte-intrinsic TNF-IL-1 collaborative circuit as a crucial driver of intestinal granuloma function, and defines the cellular target of TNF signaling that restricts intestinalYersiniainfection.
Two distinct stimulus-locked EEG signatures reliably encode domain-general confidence during decision formation
Authors: Kopčanová Martina , Ince Robin A. A. , Benwell Christopher S. Y. 
Published: April 2023

AbstractDecision confidence, an internal estimate of how accurate our choices are, is essential for metacognitive self-evaluation and guides behaviour. However, it can be suboptimal and hence understanding the underlying neurocomputational mechanisms is crucial. To do so, it is essential to establish the extent to which both behavioural and neurophysiological measures of metacognition are reliable over time and shared across cognitive domains. The evidence regarding domain-generality of metacognition has been mixed, while the test-retest reliability of the most widely used metacognitive measures has not been reported. Here, in human participants of both sexes, we examined behavioural and electroencephalographic (EEG) measures of metacognition across two tasks that engage distinct cognitive domains – visual perception and semantic memory. The test-retest reliability of all measures was additionally tested across two experimental sessions. The results revealed a dissociation between metacognitive bias and efficiency, whereby only metacognitive bias showed strong test-retest reliability and domain-generality whilst metacognitive efficiency (measured by M-ratio) was neither reliable nor domain-general. Hence, overall confidence calibration (i.e., metacognitive bias) is a stable trait-like characteristic underpinned by domain-general mechanisms whilst metacognitive efficiency may rely on more domain-specific computations. Additionally, we found two distinct stimulus-locked EEG signatures related to the trial-by-trial fluctuations in confidence ratings during decision formation. A late event-related potential was reliably linked to confidence across cognitive domains, while evoked spectral power predicted confidence most reliably in the semantic knowledge domain. Establishing the reliability and domain-generality of neural predictors of confidence represents an important step in advancing our understanding of the mechanisms underlying self-evaluation.Significance StatementUnderstanding the mechanisms underlying metacognition is essential for addressing deficits in self-evaluation. Open questions exist regarding the domain-generality and reliability of both behavioural and neural measures of metacognition. We show that metacognitive bias is reliable across cognitive domains and time, whereas the most adopted measure of metacognitive efficiency is domain-specific and shows poor test-retest reliability. Hence, more reliable measures of metacognition, tailored to specific domains, are needed. We further show that decision confidence is linked to two EEG signatures: late event-related potentials and evoked alpha/beta spectral power. While the former predicts confidence in both perception and semantic knowledge domains, the latter is only reliably linked to knowledge confidence. These findings provide crucial insights into the computations underlying metacognition across domains.
scDEED: a statistical method for detecting dubious 2D single-cell embeddings and optimizing t-SNE and UMAP hyperparameters
Authors: Xia Lucy , Lee Christy , Li Jingyi Jessica 
Published: April 2023

AbstractTwo-dimensional (2D) embedding methods are crucial for single-cell data visualization. Popular methods such as t-SNE and UMAP are commonly used for visualizing cell clusters; however, it is well known that t-SNE and UMAP’s 2D embedding might not reliably inform the similarities among cell clusters. Motivated by this challenge, we developed a statistical method, scDEED, for detecting dubious cell embeddings output by any 2D-embedding method. By calculating a reliability score for every cell embedding, scDEED identifies the cell embeddings with low reliability scores as dubious and those with high reliability scores as trustworthy. Moreover, by minimizing the number of dubious cell embeddings, scDEED provides intuitive guidance for optimizing the hyperparameters of an embedding method. Applied to multiple scRNA-seq datasets, scDEED demonstrates its effectiveness for detecting dubious cell embeddings and optimizing the hyperparameters of t-SNE and UMAP.
Immediate effects of light on circadian eclosion and locomotor activity depend on distinct sensory input pathways
Authors: Bidell Daniel , Feige Natalie-Danielle , Triphan Tilman , Müller Claudia , Pauls Dennis , Helfrich-Förster Charlotte , Selcho Mareike 
Published: April 2023

ABSTRACTAnimals need to be able to sharpen circadian behavioural output in the adaptation to the variable environment. Light is the main entraining signal of the circadian clock, but can also directly increase alertness, locomotor activity, body temperature and heart rate in diurnal animals including humans. Thus, immediate effects of light can enhance or even overwrite circadian output and thereby mask circadian behaviour.InDrosophila melanogaster, immediate light effects are most evident as a lights-on response in two well described behavioural rhythms of the fly – the emergence rhythm of the adult insect from the pupa, called eclosion, and the diurnal rhythm of locomotor activity. Here, we show that the immediate effect of light on rhythmic eclosion depends on the R8 photoreceptor cells of the compound eyes, while the light response of locomotor activity is triggered by different light detecting cells and organs, that seem to compensate for the loss of each other.
Development of genomic resources for cattails (Typha), a globally important macrophyte genus
Authors: Aleman Alberto , Dorken Marcel E. , Shafer Aaron B. A. , Patel Tulsi , Volkova Polina A. , Freeland Joanna R. 
Published: April 2023

Abstract1. BackgroundA critical knowledge gap in freshwater plants research is the lack of genetic tools necessary to answer fundamental questions about their demographic histories, adaptation, and phylogenetic relationships. One example of this isTypha, a global genus of freshwater plants foundational to wetlands that is also becoming an increasingly problematic biological invader in numerous regions worldwide; while important insights have been discovered for this genus, existing markers are insufficient to answer fundamental questions about their demographic histories, adaptation, and phylogenetic relationships, to identify introduced and hybrid lineages, and to examine patterns of hybridisation and introgression.2. MethodsWe optimised a library preparation and data processing protocol to develop genome–wide nuclear and plastid resources for studying the evolutionary history, genetic structure and diversity, hybridisation, local adaptation, invasiveness, and geographic expansion dynamics ofTypha.3. Main resultsWe sequenced 140Typhasamples and identified ∼120K nuclear SNPs that differentiateT. angustifolia,T. domingensisandT. latifoliaand retrieved their plastome sequences. We observed genetic introgression among the three species.4. ConclusionsFollowing a fast, straightforward, and cost–efficient genomic library preparation protocol, we produced a suite of genome–wide resources to facilitate investigations into the taxonomy and population genetics ofTyphaand to advance the genomic understanding of wetland plants.5. ContributionsThe protocol described, the updated chromosome–level genome assembly ofT. latifolia, the catalogue of species-specific SNPs, and the chloroplast sequences produced in this study comprise permanent resources that can be applied to study the genetic composition of multiple populations and hybrid zones and will be incorporated into future studies ofTypha,an ecologically important and globally invasive macrophyte.
The Healthcare Access and Delivery Survey: Turkiye Earthquake response
Authors: Rahman Najeeb , İnanç Balkan İlker 
Published: April 2023

AbstractBackgroundConducting rapid health assessments during large-scale disasters can present significant challenges. While responding to key humanitarian needs is a priority, assessing and understanding gaps and areas for strengthening are vital in ensuring a comprehensive and equitable response.AimTo utilise the perspectives of healthcare workers responding to the Turkiye earthquake 2023, as a means of assessing humanitarian health response gaps.Design and settingObservational, descriptive, prospective study design in Turkiye.MethodOnline survey tool using a Likert-type scale, aligned with minimum standards of humanitarian health response themes, in both English and Turkish distributed by healthcare organisations and academic networks to a convenience sample of health workers responding to the earthquake.Results45 respondents with perspectives demonstrating general limitations across all humanitarian health themes, with particular gaps in:Coordination and response timelinessReporting and surveillanceMental health, palliative care and sexual and reproductive healthConclusionUsing a survey tool to assess health worker perspective is feasible and provides rapid insights into humanitarian response efforts. Such data can be added to other assessment information to build a more comprehensive picture of needs while engaging with a key stakeholder group, and can support service providers to address gaps and strengthen response actions.
A major myna problem; invasive predator removal benefits female survival and population growth of a translocated island endemic
Authors: Brown Thomas J. , Hellicar Max , Accouche Wilna , van der Woude Jildou , Dugdale Hannah , Komdeur Jan , Richardson David S. 
Published: April 2023

AbstractInvasive predators are a major driver of extinctions and continue to threaten native populations worldwide. Island eradications of (mostly mammalian) invasive predators have facilitated the (re)establishment of numerous island-endemic populations. Other invasive taxa, such as some predatory birds, could pose a more persistent threat due to their ability to fly and actively re-invade even remote and isolated islands. However, the impact of invasive predatory birds has been largely overlooked. We report on a novel sex-specific impact of an invasive-nest predator, the common myna (Acridotheres tristis), on a reintroduced population of Seychelles warblers (Acrocephalus sechellensis); translocated from Cousin Island to Denis Island in 2004. Regular post-translocation monitoring revealed that female mortality was 20% higher than males, leading to a 60–70% male-biased population sex-ratio between 2005–2015. This was attributed to mynas inflicting severe injuries to incubating female warblers while attempting to prey upon eggs in their nests. These effects likely contributed to the slower-than-expected population growth observed (relative to previous translocations of Seychelles warblers to other islands) over the same period. An eradication programme beginning in 2011 removed all mynas from Denis by 2015. Subsequently, we observed a balancing of sex-specific survival and the population sex-ratio of Seychelles warblers and, consequently, accelerated population growth. This study demonstrates the importance of assessing the threat posed by all invasive taxa (not just mammals) to island conservation. Furthermore, we show how extended monitoring is needed to identify problems, and develop solutions, post-translocation.