bluuebunny/crossref_metadata_2025_split huggingface dataset:
Review article: Scoping review of the characteristics and outcomes of adults presenting to the emergency department during heatwaves
Authors: Wu Wendy Jingyi , Hutton Jennie , Zordan Rachel , Ranse Jamie , Crilly Julia , Tutticci Naomi , English Timothy , Currie Jane 
Published: October 2023

AbstractAs a result of climate change heatwaves are expected to increase in frequency and intensity and will have detrimental impacts on human health globally. EDs are often the critical point of care for acute heat illnesses and other conditions associated with heat exposure. Existing literature has focused on heatwave‐related hospitalisation and mortality. This scoping review aimed to identify, evaluate and summarise current literature regarding patient characteristics and outcomes of ED admissions from heatwaves. A scoping review of the literature was conducted using six databases: Medline, EMBASE, EMCARE, CINAHL, PsycINFO, and Scopus, using MeSH terms and keywords related to ‘heatwave’ and ‘Emergency Department’. Articles were included if they were: published in English from January 2000 to August 2021, related to ED, and examined high temperature periods consistent with heatwave criteria. Articles were appraised using the Mixed Methods Appraisal Tool (MMAT). Thirty‐one studies were included, mostly from the United States, Australia, and France. The study designs include retrospective case analysis, case–control, and time‐series analysis. Eight studies examined known heatwaves, 21 used different criteria to identify heatwave occurrence, and two focused on heat‐related illness. The selected articles display a moderate‐high quality on MMAT. ED admissions for both heat‐related illnesses and other conditions increased during heatwaves, with up to 18.5 times risk increase. The risk was elevated for all population groups, and substantially in the elderly, male patients with certain comorbidities, medications, or lower socioeconomic status. Outcomes including hospitalisation and mortality rates after ED admissions showed positive associations with heatwaves. The heatwaves resulting from climate change will place increasing demands on EDs providing care for increasingly susceptible populations. Significant public heatwave planning across multiple sectors is required to reduce the risk of overwhelming EDs with these patients.
Prokaryote communities associated with different types of tissue formed and substrates inhabited by Serpula lacrymans
Authors: Embacher Julia , Zeilinger Susanne , Kirchmair Martin , Neuhauser Sigrid 
Published: October 2023

AbstractThe basidiomycete Serpula lacrymans is responsible for major timber devastation in houses. Basidiomycetes are known to harbour a diverse but poorly understood microbial community of bacteria, archaea, yeasts and filamentous fungi. In this study, we used amplicon‐sequencing to analyse the abundance and composition of prokaryotic communities associated with fruiting bodies of S. lacrymans and compared them to communities of surrounding material to access the ‘background’ community structure. Our findings indicate that bacterial genera cluster depended on sample type and that the main driver for microbial diversity is specimen, followed by sample origin. The most abundant bacterial phylum identified in the fruiting bodies was Pseudomonadota, followed by Actinomycetota and Bacteroidota. The prokaryote community of the mycelium was dominated by Actinomycetota, Halobacterota and Pseudomonadota. Actinomycetota was the most abundant phylum in both environment samples (infested timber and underground scree), followed by Bacillota in wood and Pseudomonadota in underground samples. Nocardioides, Pseudomonas, Pseudonochardia, Streptomyces and Rubrobacter spp. were among others found to comprise the core microbiome of S. lacrymans basidiocarps. This research contributes to the understanding of the holobiont S. lacrymans and gives hints to potential bacterial phyla important for its development and lifestyle.
rphylopic: An R package for fetching, transforming, and visualising PhyloPic silhouettes
Authors: Gearty William , Jones Lewis A. 
Published: October 2023

Abstract

Effective data visualisation is vital for data exploration, analysis and communication in research. In ecology and evolutionary biology, data are often associated with various taxonomic entities. Graphics of organisms associated with these taxa are valuable for framing results within a broader biological context. However, acquiring and using such resources can be challenging due to availability and licensing constraints. The PhyloPic database solves many of these issues by making organism silhouettes freely available. Tools that integrate this database with existing research workflows are needed to remove hurdles associated with data visualisation in the biological sciences.

Here, we introduce rphylopic, an R package for fetching, transforming and visualising silhouettes of organisms from the PhyloPic database. In addition to making over 8000 organism silhouettes available within the R programming language, rphylopic empowers users to modify the appearance of these silhouettes for ultimate customisability when coding production–quality visualisations in both base R and ggplot2 workflows.

In this work, we provide details about how the package can be installed, its implementation and potential use cases. For the latter, we showcase three examples across the ecology and evolutionary biology spectrum.

Our hope is that rphylopic will make it easier for biologists to develop more accessible and engaging data visualisations by making external resources readily accessible, customisable and usable within R. In turn, by integrating into existing workflows, rphylopic helps to ensure that science is reproducible and accessible.
PoolDilutionR: An R package for easy optimization of isotope pool dilution calculations
Authors: Morris Kendalynn A. , Bond‐Lamberty Ben P. , Day Donnie J. , Patel Kaizad F. , Pennington Stephanie C. , Ward Nicholas D. , von Fischer Joseph C. 
Published: October 2023

Abstract

Isotopic pool dilution is a powerful approach to quantify gross biogeochemical transformation rates, but remains seldom used despite its potential.

To facilitate broader implementation of pool dilution methods, we present a user‐friendly R package that optimizes gross production and consumption rates (and optionally fractionation constants as well) based on standard pool dilution time series data.

This package features extensive documentation and example analyses, and is easily integrated into analytical pipelines.

With this open‐source tool, the biogeochemistry community will be able to readily apply isotope pool dilution to a wide range of processes.
Prevalence of tree nut allergy in Europe: A systematic review and meta‐analysis
Authors: Spolidoro Giulia C. I. , Lisik Daniil , Nyassi Sungkutu , Ioannidou Athina , Ali Mohamed Mustafa , Amera Yohannes Tesfaye , Rovner Graciela , Khaleva Ekaterina , Venter Carina , van Ree Ronald , Worm Margitta , Vlieg‐Boerstra Berber , Sheikh Aziz , Muraro Antonella , Roberts Graham , Nwaru Bright I. 
Published: October 2023

AbstractIn 2014, the European Academy of Allergy and Clinical Immunology (EAACI) published the first systematic review that summarized the prevalence of food allergy (FA) and food sensitization in Europe for studies published 2000–2012. However, only summary estimates for tree nut allergy (TNA) were feasible in that work. In the current update of that systematic review, we summarized the prevalence of tree nut allergy/sensitization to individual tree nuts. Six databases were searched for relevant papers published 2012–2021 and 17 eligible studies were added to the 15 studies already identified between 2000 and 2012, giving a total of 32 studies. Of the investigated tree nuts, meta‐analysis was possible for hazelnut, walnut, almond, and in few cases, for cashew, and Brazil nut. The lifetime self‐reported prevalence was 0.8% (95% CI 0.5–1.1) for hazelnut and 0.4% (0.2–0.9) for walnut. The point self‐reported prevalence was 4.0% (2.9–5.2) for hazelnut, 3.4% (2.0–4.9) for Brazil nut, 2.0% (1.1–2.9) for almond, and 1.8% (1.1–2.5) for walnut. Point prevalence of food challenge‐confirmed TNA was 0.04% (0.0–0.1) for hazelnut and 0.02% (0.01–0.1) for walnut. Due to paucity of data, we could not identify any meaningful and consistent differences across age groups and European regions.
Blood CD62Llow inflammatory eosinophils are related to the severity of asthma and reduced by mepolizumab
Authors: Vultaggio Alessandra , Accinno Matteo , Vivarelli Emanuele , Mecheri Valentina , Maggiore Giandomenico , Cosmi Lorenzo , Parronchi Paola , Rossi Olivero , Maggi Enrico , Gallo Oreste , Matucci Andrea 
Published: October 2023

AbstractBackgroundEosinophils have been divided into different subpopulations with distinct phenotypes based on CD62L expression. No data are available regarding the correlation between eosinophils subphenotypes and clinical severity of asthma, as well as the effect of anti‐IL‐5 therapy on these cells. The study investigates the correlation between blood CD62Llow inflammatory eosinophils (iEos) and clinical severity of severe eosinophilic asthma (SEA) and evaluates the impact of mepolizumab on iEos.Methods112 patients were screened and were divided in two groups: biological‐naive (n = 51) and biological‐treated patients (n = 61). The Biological‐naive patients were analyzed before treatment (Group A) and 19 out of 51 patients, were longitudinally analyzed before and after treatment with mepolizumab 100 mg s.c/4 weeks (Group B); 32 patients were excluded because they were being treated with other biological therapies. Blood eosinophils were analyzed by FACS and correlated with clinical scores. In vitro effect of IL‐5 and mepolizumab on CD62L expression was assessed.ResultsA significant correlation between blood CD62Llow cells and clinical scores of asthma and nasal polyps, as well as the number of asthma exacerbations in the last year was shown in untreated patients. In longitudinally studied patients we observed a marked reduction of CD62Llow cells paralleled by an increase in the proportion of CD62Lbright cells, associated with clinical improvement of asthma control. In vitro, CD62L expression on eosinophils is modulated by IL‐5 and anti‐IL‐5.ConclusionA positive correlation between CD62Llow iEos and the baseline clinical features of SEA with CRSwNP was shown. Furthermore mepolizumab restores the healthy balance among eosinophils sub‐phenotypes in SEA patients.
Understanding the immune profile of sudden infant death syndrome – proteomic perspectives
Authors: Ferrante Linda , Opdal Siri H. , Byard Roger W. 
Published: October 2023

AbstractAimThe aim of this study was to investigate a panel of immune proteins in cases of sudden infant death syndrome (SIDS). It was hypothesised that, in at least a subset of SIDS, a dysregulated immune response may be a contributing factor leading to death.MethodsThe subjects included 46 SIDS cases and 41 controls autopsied at the Department of Forensic Sciences, Norway. The causes of death in the controls were accidents/trauma. Samples of cerebrospinal fluid (CSF) were analysed quantitatively by Proximity Extension Assay (PEA).ResultsInitial results revealed that normalised protein expression differed in 35 proteins. For the purposes of this report five proteins that are involved in immune system were selected for analysis: IFNLR1 (p = 0.003), IL10 (p = 0.007), IRAK4 (p < 0.001) and IL6 (p = 0.035); all had lower protein concentrations in SIDS cases compared to controls except for CD28 (p = 0.024) which had higher protein concentrations in SIDS cases.ConclusionThe results confirm previous studies indicating that a dysregulation of the immune system may be a predisposing factor for SIDS. The results may indicate that these aberrant protein concentrations could lead to an inadequate response to immune triggers and uncontrolled defence mechanisms towards the common cold or other non‐fatal infections.
The CD4/CD8 ratio of infused CD19‐CAR‐T is a prognostic factor for efficacy and toxicity
Authors: Galli Eugenio , Bellesi Silvia , Pansini Ilaria , Di Cesare Giacomo , Iacovelli Camilla , Malafronte Rosalia , Maiolo Elena , Chiusolo Patrizia , Sica Simona , Sorà Federica , Hohaus Stefan 
Published: October 2023

SummaryCD4+ and CD8+ chimeric antigen receptor T cells (CAR‐T) play different roles in the in vivo anti‐tumour response, but the role of the CD4+/CD8+ ratio among infused CAR‐T has not been clearly defined yet. We analysed leftovers from infused anti‐CD19 CAR‐T bags of 31 patients with aggressive B‐cell lymphomas. The median ratio was 1.44, lower for brexu‐cel compared to tisa‐cel and axi‐cel. The CAR+CD4+/CD8+ ratio was influenced by lactate dehydrogenase levels at apheresis, not by age, previous treatments or the CD4+/CD8+ ratio in peripheral blood. Patients with a response at 3 months after CAR‐T (M3) had a lower CAR+CD4+/CD8+ ratio in the infused products compared to non‐responders (ratio 0.74 vs. 2.47, p = 0.011). A CAR+CD4+/CD8+ ratio higher than the cut point of 1.12 was associated with an increased risk of treatment failure at M3 (OR 23.3, p = 0.012) and M6 (OR 10, p = 0.028). The median 6‐month PFS was 76% for patients with a ratio lower than 1.12% vs. 31% for the others. The prognostic role of the CAR+CD4+/CD8+ ratio was independent of the costimulatory domain (CD28 vs. 4‐1BB) of the product (OR 16.41, p = 0.041). Our data indicate a crucial role for CD8+ CAR‐T and the CAR+CD4+/CD8+ ratio in predicting CAR‐T efficacy.
Large‐scale genomic data reveal the phylogeny and evolution of owlet moths (Noctuoidea)
Authors: Li Xuankun , Breinholt Jesse W. , Martinez Jose I. , Keegan Kevin , Ellis Emily A. , Homziak Nicholas T. , Zwick Andreas , Storer Caroline G. , McKenna Duane , Kawahara Akito Y. 
Published: October 2023

AbstractThe owlet moths (Noctuoidea; ~43–45K described species) are one of the most ecologically diverse and speciose superfamilies of animals. Moreover, they comprise some of the world's most notorious pests of agriculture and forestry. Despite their contributions to terrestrial biodiversity and impacts on ecosystems and economies, the evolutionary history of Noctuoidea remains unclear because the superfamily lacks a statistically robust phylogenetic and temporal framework. We reconstructed the phylogeny of Noctuoidea using data from 1234 genes (946.4 kb nucleotides) obtained from the genome and transcriptome sequences of 76 species. The relationships among the six families of Noctuoidea were well resolved and consistently recovered based on both concatenation and gene coalescence approaches, supporting the following relationships: Oenosandridae + (Notodontidae + (Erebidae + (Nolidae + (Euteliidae + Noctuidae)))). A Yule tree prior with three unlinked molecular clocks was identified as the preferred BEAST analysis using marginal‐likelihood estimations. The crown age of Noctuoidea was estimated at 74.5 Ma, with most families originating before the end of the Paleogene (23 Ma). Our study provides the first statistically robust phylogenetic and temporal framework for Noctuoidea, including all families of owlet moths, based on large‐scale genomic data.
Integrated transcriptomic and proteomic profiling reveals the key molecular signatures of brain endothelial reperfusion injury
Authors: Ji Yabin , Chen Yiman , Tan Xixi , Huang Xiaowen , Gao Qiang , Ma Yinzhong , Yang Shilun , Yin Meifang , Yu Min , Fang Cheng , Wang Yu , Shi Zhu , Chang Junlei 
Published: October 2023

AbstractBackgroundReperfusion therapy after ischemic stroke often causes brain microvascular injury. However, the underlying mechanisms are unclear.MethodsTranscriptomic and proteomic analyses were performed on human cerebral microvascular endothelial cells following oxygen–glucose deprivation (OGD) or OGD plus recovery (OGD/R) to identify molecules and signaling pathways dysregulated by reperfusion. Major findings were further validated in a mouse model of cerebral ischemia and reperfusion.ResultsTranscriptomic analysis identified 390 differentially expressed genes (DEGs) between the OGD/R and OGD group. Pathway analysis indicated that these genes were mostly associated with inflammation, including the TNF signaling pathway, TGF‐β signaling pathway, cytokine–cytokine receptor interaction, NOD‐like receptor signaling pathway, and NF‐κB signaling pathway. Proteomic analysis identified 201 differentially expressed proteins (DEPs), which were primarily associated with extracellular matrix destruction and remodeling, impairment of endothelial transport function, and inflammatory responses. Six genes (DUSP1, JUNB, NFKBIA, NR4A1, SERPINE1, and THBS1) were upregulated by OGD/R at both the mRNA and protein levels. In mice with cerebral ischemia and reperfusion, brain TNF signaling pathway was activated by reperfusion, and inhibiting TNF‐α with adalimumab significantly attenuated reperfusion‐induced brain endothelial inflammation. In addition, the protein level of THBS1 was substantially upregulated upon reperfusion in brain endothelial cells and the peri‐endothelial area in mice receiving cerebral ischemia.ConclusionOur study reveals the key molecular signatures of brain endothelial reperfusion injury and provides potential therapeutic targets for the treatment of brain microvascular injury after reperfusion therapy in ischemic stroke.
Do Democracy Vouchers help democracy?
Authors: Papich Sarah 
Published: October 2023

AbstractSeattle's Democracy Vouchers program provides a unique form of public financing for political campaigns in which voters decide how to allocate public funding across candidates. This paper is the first to study the effects of public financing for political campaigns on political participation. I estimate that the Democracy Vouchers program increases voter turnout by 4.9 percentage points, suggesting that public financing programs can increase political participation. I also find that campaigns become more reliant on small contributions. For city council candidates, dollars from small contributions under $100 increase by 156% while dollars from large contributions over $250 decrease by 93%.
Cognitive Orientation to daily Occupational Performance to improve occupational performance goals for children with executive function deficits after acquired brain injury
Authors: Lebrault Hélène , Martini Rose , Manolov Rumen , Chavanne Céline , Krasny‐Pacini Agata , Chevignard Mathilde 
Published: October 2023

AbstractAimTo determine the effectiveness of the Cognitive Orientation to daily Occupational Performance (CO‐OP) approach in improving the occupational performance goals of children and young people with executive function deficits after acquired brain injury (ABI) (e.g. etiologies such as stroke, encephalitis, brain tumor, and traumatic brain injury).MethodA replicated single‐case experimental study using a randomized multiple baseline design across participants and goals was used. Three clusters of four participants (12 participants, nine males and three females, aged 8–16 years) were included. The intervention consisted of 14 individual CO‐OP sessions. Each participant chose four goals; three goals were trained during the intervention sessions and a fourth goal served as the control. The Goal Attainment Scale (GAS) was used as a repeated measure to determine goal achievement while the Canadian Occupational Performance Measure (COPM) was used to identify the perceived goal achievement of children, young people, and their parents.ResultsFor 26 of the 35 trained goals, the intervention led to statistically significant improvements in the GAS. Perceived occupational performance and satisfaction improved significantly for the trained goals (30 out of 35 goals for the COPM performance and satisfaction of participants; 26 out 31 goals for the COPM performance of parents; 24 out of 31 goals for the COPM satisfaction of parents) and were maintained at the follow‐up. Almost all COPM control goal results were significant, but these changes were not supported by the GAS measures or the statistical analysis.InterpretationThe generally positive results of this study provide evidence of the benefits of using the CO‐OP approach with this population.
Freshwater fish as hosts for parasites in Australia: How much do we really know?
Authors: Barton Diane P. , Shamsi Shokoofeh 
Published: October 2023

AbstractAustralia has a highly endemic freshwater fish fauna, but basic biological knowledge for most is lacking. This includes an understanding, and description, of their parasite fauna. Additionally, the impacts of introduced fish species, and their parasites which have transferred across to native species, are also mostly unknown. This review provides the current level of knowledge of parasitic infection of the freshwater fish in Australia, both introduced and native. Only about a third of the native freshwater fish, but almost two‐thirds of introduced fish, have been reported as a host for a parasite. The majority of records occur along the eastern coastline of Australia and throughout the Murray Darling Basin; two drainage regions were yet to record any parasite infections. Of the 124 fish species, across 43 families, found as hosts in Australia, only 11 species had more than 10 reports of infection, with 31% of fish species only having single reports. A total of 13 different types of parasites were reported, with digeneans, protozoans, nematodes and monogeneans the most commonly reported. Significant gaps in the knowledge of parasites, and their potential impacts, of Australian freshwater fish still exist, and the need for fish biologists and fish parasitologists to work together is highlighted to ensure that as much information about each group can be obtained.
Deterministic assembly processes shaping habitat‐specific glycoside hydrolase composition
Authors: Li Dan‐dan , Zhang Zheng , Zhang Peng , Wang Jia‐ning , Liu Ya , Li Yue‐zhong 
Published: October 2023

AbstractAimGlycoside hydrolases (GHs) encoded by prokaryotes play a crucial role in the degradation of carbohydrates, which is a key step in the carbon cycle. However, their global distribution remains poorly understood. Here, we conducted a comprehensive investigation of the global biogeographic patterns of prokaryotic‐encoded GHs.LocationGlobal.Time periodPresent.Major taxa studiedProkaryotes.MethodsWe conducted a global survey of GH distribution based on 10,000 samples from the Earth Microbiome Project (EMP) and 17,923 completely sequenced prokaryotic genomes. The samples were retrieved from seven continents, covering all 17 EMP Ontology environments. We evaluated the assembly process and influencing factors of GH functional genes within prokaryotic communities, and analysed the rank abundance distributions (RADs), occupancy frequency distributions (OFDs), and taxonomic sources of GH families across various environments.ResultsThe median number of GH genes per thousand genes encoded by global prokaryotic communities was 9.11 (7.16–11.58), with a higher GH abundance in host‐associated communities than in free‐living communities. The median number of GH families in prokaryotic communities was 105 (86–121), with fewer families but tighter functional connections between families in host‐associated communities compared to free‐living communities. In any environment, the RAD of GH families followed a lognormal model, and their OFD was bimodal, with a strong positive correlation between the two. In addition, most GH families had complex and diverse taxonomic sources across different environments.Main conclusionsThis study provides a panoramic view of the functional potentials for carbohydrate degradation across prokaryotic communities under diverse environmental conditions. The composition of GHs encoded by prokaryotic communities exhibits clear habitat specificity, which is driven by a combination of biotic and abiotic factors and generated through highly deterministic assembly processes.