cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.19221527
title: One-on-one comparison between qCSI and NEWS scores for mortality risk assessment in patients with COVID-19

description: To compare the predictive value of the quick COVID-19 Severity Index (qCSI) and the National Early Warning Score (NEWS) for 90-day mortality amongst COVID-19 patients. Multicenter retrospective cohort study conducted in adult patients transferred by ambulance to an emergency department (ED) with suspected COVID-19 infection subsequently confirmed by a SARS-CoV-2 test (polymerase chain reaction). We collected epidemiological data, clinical covariates (respiratory rate, oxygen saturation, systolic blood pressure, heart rate, temperature, level of consciousness and use of supplemental oxygen) and hospital variables. The primary outcome was cumulative all-cause mortality during a 90-day follow-up, with mortality assessment monitoring time points at 1, 2, 7, 14, 30 and 90 days from ED attendance. Comparison of performances for 90-day mortality between both scores was carried out by univariate analysis. From March to November 2020, we included 2,961 SARS-CoV-2 positive patients (median age 79 years, IQR 66–88), with 49.2% females. The qCSI score provided an AUC ranging from 0.769 (1-day mortality) to 0.749 (90-day mortality), whereas AUCs for NEWS ranging from 0.825 for 1-day mortality to 0.777 for 90-day mortality. At all-time points studied, differences between both scores were statistically significant (<i>p</i> &lt; .001). Patients with SARS-CoV-2 can rapidly develop bilateral pneumonias with multiorgan disease; in these cases, in which an evacuation by the EMS is required, reliable scores for an early identification of patients with risk of clinical deterioration are critical. The NEWS score provides not only better prognostic results than those offered by qCSI at all the analyzed time points, but it is also better suited for COVID-19 patients.KEY MESSAGESThis work aims to determine whether NEWS is the best score for mortality risk assessment in patients with COVID-19.AUCs for NEWS ranged from 0.825 for 1-day mortality to 0.777 for 90-day mortality and were significantly higher than those for qCSI in these same outcomes.NEWS provides a better prognostic capacity than the qCSI score and allows for long-term (90 days) mortality risk assessment of COVID-19 patients. This work aims to determine whether NEWS is the best score for mortality risk assessment in patients with COVID-19. AUCs for NEWS ranged from 0.825 for 1-day mortality to 0.777 for 90-day mortality and were significantly higher than those for qCSI in these same outcomes. NEWS provides a better prognostic capacity than the qCSI score and allows for long-term (90 days) mortality risk assessment of COVID-19 patients.
DOI: 10.6084/m9.figshare.19221527.v1
title: One-on-one comparison between qCSI and NEWS scores for mortality risk assessment in patients with COVID-19

description: To compare the predictive value of the quick COVID-19 Severity Index (qCSI) and the National Early Warning Score (NEWS) for 90-day mortality amongst COVID-19 patients. Multicenter retrospective cohort study conducted in adult patients transferred by ambulance to an emergency department (ED) with suspected COVID-19 infection subsequently confirmed by a SARS-CoV-2 test (polymerase chain reaction). We collected epidemiological data, clinical covariates (respiratory rate, oxygen saturation, systolic blood pressure, heart rate, temperature, level of consciousness and use of supplemental oxygen) and hospital variables. The primary outcome was cumulative all-cause mortality during a 90-day follow-up, with mortality assessment monitoring time points at 1, 2, 7, 14, 30 and 90 days from ED attendance. Comparison of performances for 90-day mortality between both scores was carried out by univariate analysis. From March to November 2020, we included 2,961 SARS-CoV-2 positive patients (median age 79 years, IQR 66–88), with 49.2% females. The qCSI score provided an AUC ranging from 0.769 (1-day mortality) to 0.749 (90-day mortality), whereas AUCs for NEWS ranging from 0.825 for 1-day mortality to 0.777 for 90-day mortality. At all-time points studied, differences between both scores were statistically significant (<i>p</i> &lt; .001). Patients with SARS-CoV-2 can rapidly develop bilateral pneumonias with multiorgan disease; in these cases, in which an evacuation by the EMS is required, reliable scores for an early identification of patients with risk of clinical deterioration are critical. The NEWS score provides not only better prognostic results than those offered by qCSI at all the analyzed time points, but it is also better suited for COVID-19 patients.KEY MESSAGESThis work aims to determine whether NEWS is the best score for mortality risk assessment in patients with COVID-19.AUCs for NEWS ranged from 0.825 for 1-day mortality to 0.777 for 90-day mortality and were significantly higher than those for qCSI in these same outcomes.NEWS provides a better prognostic capacity than the qCSI score and allows for long-term (90 days) mortality risk assessment of COVID-19 patients. This work aims to determine whether NEWS is the best score for mortality risk assessment in patients with COVID-19. AUCs for NEWS ranged from 0.825 for 1-day mortality to 0.777 for 90-day mortality and were significantly higher than those for qCSI in these same outcomes. NEWS provides a better prognostic capacity than the qCSI score and allows for long-term (90 days) mortality risk assessment of COVID-19 patients.
DOI: 10.5061/dryad.674
title: Data from: Combining and Comparing Morphometric Shape Descriptors with a Molecular Phylogeny: The Case of Fruit Type Evolution in Bornean Lithocarpus (Fagaceae)

description: Fruit type in the genus Lithocarpus (Fagaceae) includes both classic oak
 acorns and novel modifications. Bornean taxa with modified fruits can be
 separated into two sections (Synaedrys and Lithocarpus) based on subtle
 shape differences. Following strict criteria for homology and
 representation, this variation in shape can be captured and the sections
 distinguished using elliptic Fourier or eigenshape analysis. Phenograms of
 fruit shape, constructed using restricted maximum likelihood techniques
 and these morphometric descriptors, were incorporated into combined and
 comparative analyses with molecular sequence data from the internal
 transcribed spacer (ITS) region of the nuclear rDNA using branch-weighted
 matrix representation. The combined analysis strongly suggested
 independent derivation of the novel fruit type in the two sections from
 different acorn-like ancestors, while the comparative analysis indicated
 frequent decoupling between the molecular and morphological change as
 inferred at well-supported nodes. The acorn fruit type has undergone
 little modification between ingroup and outgroup, despite large molecular
 distance. Greater morphological than molecular change was inferred at
 critical transitions between acorn and novel fruit types, particularly for
 section Lithocarpus. The combination of these two different types of data
 improved our understanding of the macroevolution of fruit type in this
 difficult group and the comparative analysis highlighted the significant
 incongruities in evolutionary pattern between the two datasets.
description: Cannon and Manos Data
 SetCannon.nexus
DOI: 10.5061/dryad.43v0t
title: Data from: Transfer of maternal antibodies against avian influenza virus in mallards (Anas platyrhynchos)

description: Maternal antibodies protect chicks from infection with pathogens early in
 life and may impact pathogen dynamics due to the alteration of the
 proportion of susceptible individuals in a population. We investigated the
 transfer of maternal antibodies against avian influenza virus (AIV) in a
 key AIV host species, the mallard (Anas platyrhynchos). Combining
 observations in both the field and in mallards kept in captivity, we
 connected maternal AIV antibody concentrations in eggs to (i) female body
 condition, (ii) female AIV antibody concentration, (iii) egg laying order,
 (iv) egg size and (v) embryo sex. We applied maternity analysis to the
 eggs collected in the field to account for intraspecific nest parasitism,
 which is reportedly high in Anseriformes, detecting parasitic eggs in one
 out of eight clutches. AIV antibody prevalence in free-living and captive
 females was respectively 48% and 56%, with 43% and 24% of the eggs
 receiving these antibodies maternally. In both field and captive study,
 maternal AIV antibody concentrations in egg yolk correlated positively
 with circulating AIV antibody concentrations in females. In the captive
 study, yolk AIV antibody concentrations correlated positively with egg
 laying order. Female body mass and egg size from the field and captive
 study, and embryos sex from the field study were not associated with
 maternal AIV antibody concentrations in eggs. Our study indicates that
 maternal AIV antibody transfer may potentially play an important role in
 shaping AIV infection dynamics in mallards.
description: Maternal antibody
 transfer in free-living and captive mallardsFrom April until June
 2010, free-living female mallards were caught from their nest in a
 woodland area in the Alblasserwaard, the Netherlands. Each captured female
 was marked with a metal ring, aged and several measurements were collected
 (tarsus length, head+bill length, wing length, body mass). Blood samples
 were collected for detection of antibodies to avian influenza virus (AIV).
 Per clutch two eggs were collected, of which the length and breadth was
 measured to assess egg volume. Egg yolks were separated to assess maternal
 antibodies to AIV, embryo size was measured and sex of embryos determined.
 In the same period, blood samples and several measurements (tarsus length,
 head+bill length, body mass) were collected from captured females in an
 outdoor aviary in Heteren, the Netherlands. Four eggs per clutch were
 collected (one per egg stage), of which the length and breadth was
 measured. Egg laying order was assessed. Egg yolks were separated and
 embryo size was measured. Serial dilution was applied to validate the use
 of OD-values of egg yolk and female serum as a quantitative estimate of
 antibody concentration.Data van Dijk et al. Maternal
 antibodies.xlsx
DOI: 10.5061/dryad.g8n25
title: Data from: The potential for adaptive maintenance of diversity in antimicrobial peptides

description: Genes involved in immune defence are among the fastest evolving in the
 genomes of many species. Interestingly, however, genes encoding
 antimicrobial peptides (AMPs) have shown little evidence for adaptive
 divergence in arthropods, despite the centrality of these peptides in
 direct killing of microbial pathogens. This observation, coupled with a
 failure to detect phenotypic consequence of genetic variation in AMPs, has
 led to the hypothesis that individual AMPs make minor contributions to
 overall immune defence and that AMPs instead act as a collective cocktail.
 Recent data, however, have suggested an alternative explanation for the
 apparent lack of adaptive divergence in AMP genes. Molecular evolutionary
 and phenotypic data have begun to suggest that variant AMP alleles may be
 maintained through balancing selection in invertebrates, a pattern similar
 to that observed in several vertebrate AMPs. Signatures of balancing
 selection include high rates of non-synonymous polymorphism, trans-species
 amino acid polymorphisms, and convergence of amino acid states across the
 phylogeny. In this review, we revisit published literature on insect AMP
 genes and analyse newly available population genomic datasets in
 Drosophila, finding enrichment for patterns consistent with adaptive
 maintenance of polymorphism.
description: Tarball of fasta files
 from studyTarball contains fastas
 of 4 species alignments from studyunckless2016PhilTrans.tar.gz
DOI: 10.6084/m9.figshare.18537795
title: Effect of pulmonary rehabilitation in patients with chronic obstructive pulmonary disease: a systematic review and meta-analysis of randomized controlled trials

description: The present systematic review and meta-analysis of randomized clinical trials (RCTs) aimed to investigate the effects of pulmonary rehabilitation in individuals with chronic obstructive pulmonary disease (COPD). The RCTs of pulmonary rehabilitation programs published between 1999 and 2021 were retrieved from electronic databases (PubMed, Cochrane Library, and Embase). Two reviewers independently assessed the topical relevance and trial quality and extracted data for meta-analysis using the Stata software version 14.0. A total of 39 trials involving 2,397 participants with COPD were evaluated. We found that patients who received pulmonary rehabilitation program had significant improvement in the 6-min walk test (6MWT), St. George Respiratory Questionnaire score, and the modified British Medical Research Council score as compared to those who received usual care. Yoga and Tai Chi showed significant improvement in the forced expiratory volume (FEV1)% in 1 s predicted value. However, no significant difference was detected in the modified Borg score, forced vital capacity (FVC), and FEV1/FVC predicted value between the pulmonary rehabilitation and usual care groups. Yoga and Tai Chi showed a significant improvement in the FEV1% predicted value. Also, pulmonary rehabilitation program improved the exercise capacity, the quality of life, and dyspnoea in patients with COPD.Key messagesA total of 39 trials involving 2,397 participants with COPD were evaluated.We found that patients who received pulmonary rehabilitation program had significant improvement in the 6MWT, St. George Respiratory Questionnaire score, and the modified British Medical Research Council score as compared to those who received usual care.Yoga and Tai Chi showed significant improvement in the FEV1% predicted value.No significant difference was detected in the modified Borg score, FVC, and FEV1/FVC predicted value between the pulmonary rehabilitation and usual care groups. A total of 39 trials involving 2,397 participants with COPD were evaluated. We found that patients who received pulmonary rehabilitation program had significant improvement in the 6MWT, St. George Respiratory Questionnaire score, and the modified British Medical Research Council score as compared to those who received usual care. Yoga and Tai Chi showed significant improvement in the FEV1% predicted value. No significant difference was detected in the modified Borg score, FVC, and FEV1/FVC predicted value between the pulmonary rehabilitation and usual care groups.
DOI: 10.6084/m9.figshare.18537795.v1
title: Effect of pulmonary rehabilitation in patients with chronic obstructive pulmonary disease: a systematic review and meta-analysis of randomized controlled trials

description: The present systematic review and meta-analysis of randomized clinical trials (RCTs) aimed to investigate the effects of pulmonary rehabilitation in individuals with chronic obstructive pulmonary disease (COPD). The RCTs of pulmonary rehabilitation programs published between 1999 and 2021 were retrieved from electronic databases (PubMed, Cochrane Library, and Embase). Two reviewers independently assessed the topical relevance and trial quality and extracted data for meta-analysis using the Stata software version 14.0. A total of 39 trials involving 2,397 participants with COPD were evaluated. We found that patients who received pulmonary rehabilitation program had significant improvement in the 6-min walk test (6MWT), St. George Respiratory Questionnaire score, and the modified British Medical Research Council score as compared to those who received usual care. Yoga and Tai Chi showed significant improvement in the forced expiratory volume (FEV1)% in 1 s predicted value. However, no significant difference was detected in the modified Borg score, forced vital capacity (FVC), and FEV1/FVC predicted value between the pulmonary rehabilitation and usual care groups. Yoga and Tai Chi showed a significant improvement in the FEV1% predicted value. Also, pulmonary rehabilitation program improved the exercise capacity, the quality of life, and dyspnoea in patients with COPD.Key messagesA total of 39 trials involving 2,397 participants with COPD were evaluated.We found that patients who received pulmonary rehabilitation program had significant improvement in the 6MWT, St. George Respiratory Questionnaire score, and the modified British Medical Research Council score as compared to those who received usual care.Yoga and Tai Chi showed significant improvement in the FEV1% predicted value.No significant difference was detected in the modified Borg score, FVC, and FEV1/FVC predicted value between the pulmonary rehabilitation and usual care groups. A total of 39 trials involving 2,397 participants with COPD were evaluated. We found that patients who received pulmonary rehabilitation program had significant improvement in the 6MWT, St. George Respiratory Questionnaire score, and the modified British Medical Research Council score as compared to those who received usual care. Yoga and Tai Chi showed significant improvement in the FEV1% predicted value. No significant difference was detected in the modified Borg score, FVC, and FEV1/FVC predicted value between the pulmonary rehabilitation and usual care groups.
DOI: 10.5061/dryad.8217n76
title: Data from: Artificial light at night causes top-down and bottom-up trophic effects on invertebrate populations

description: 1. Globally, many ecosystems are exposed to artificial light at night.
 Nighttime lighting has direct biological impacts on species at all trophic
 levels. However, the effects of artificial light on biotic interactions
 largely remain to be determined. 2. We exposed experimental mesocosms
 containing combinations of grassland plants and invertebrate herbivores
 and predators to illumination at night over a three-year period to
 simulate conditions under different common forms of street lighting. 3. We
 demonstrate both top-down (predation controlled) and bottom-up (resource
 controlled) impacts of artificial light at night in grassland communities.
 The impacts on invertebrate herbivore abundance were wavelength dependent
 and mediated via other trophic levels. 4. White LED lighting decreased the
 abundance of a generalist herbivore mollusc by 55% in the presence of a
 visual predator, but not in its absence, while monochromatic amber light
 (with a peak wavelength similar to low pressure sodium lighting) decreased
 abundance of a specialist herbivore aphid (by 17%) by reducing the cover
 and flower abundance of its main food plant in the system. Artificial
 white light also significantly increased the food plant’s foliar carbon to
 nitrogen ratio. 5. We conclude that exposure to artificial light at night
 can trigger ecological effects spanning trophic levels, and that the
 nature of such impacts depends on the wavelengths emitted by the lighting
 technology employed. 6. Policy implications Our results confirm that
 artificial light at night, at illuminance levels similar to roadside
 vegetation, can have population effects mediated by both top-down and
 bottom-up effects on ecosystems. Given the increasing ubiquity of light
 pollution at night, these impacts may be widespread in the environment.
 These results underlines the importance of minimising disruption of
 natural ecosystems by reducing light pollution into natural and
 semi-natural ecosystems.26-Jun-2018
description: CNratioFoliar carbon and nitrogen content of Lotus pedunculatus leavespoint_quadrat_110713Point quadrat data for July 2013point_quadrat_240714POint quadrat data from July 2014point_quadrat_220715Point quadrat data form July 2015lotus_p_2013Lotus pedunculatus flower counts 2013lotus_p_2014Lotus pedunculatus flower counts 2014lotus_p_2015Lotus pedunculatus 2015PeaAphid2013Aphid (Acyrthosiphon pisum) counts 2013PeaAphid2014Aphid (Acyrthosiphon pisum) counts 2014PeaAphid2015Aphid (Acyrthosiphon pisum) counts 2015slugs2013Slug (Deroceras reticulatum) counts 2013slugs2014Slug (Deroceras reticulatum) counts 2014slugs2015Sulg (Deroceras reticulatum) counts 2015
DOI: 10.5061/dryad.2q6bm
title: Data from: Hidden diversity and phylogeographic history provide conservation insights for the edible seaweed Sargassum fusiforme in the Northwest Pacific

description: Understanding the evolutionary processes that have created diversity and
 the genetic potential of species to adapt to environmental change is an
 important premise for biodiversity conservation. Herein, we used
 mitochondrial trnW-L and cox3 and plastid rbcL-S data sets to analyze
 population genetic variation and phylogeographic history of the brown alga
 Sargassum fusiforme, whose natural resource has been largely exterminated
 in the Asia-Northwest Pacific in the past decades. Phylogenetic trees and
 network analysis consistently revealed three major haplotype-groups (A, B
 and C) in S. fusiforme, with A and B distributed in the Japan-Pacific
 coast. Group C consisted of three sub-groups (C1, C2 and C3) which were
 distributed in the Sea of Japan, the Yellow-Bohai Sea and East China Sea,
 respectively. Isolation-with-migration (IMa) analysis revealed that the
 three groups diverged approximately during the mid-Pleistocene (c.
 756–1,224 ka). Extended Bayesian skyline plots (EBSP) showed that groups A
 and B underwent relatively long-term stable population size despite a
 subsequent rapid demographic expansion, while sub-groups C2 and C3
 underwent a sudden expansion at c. 260 ka. FST and AMOVA analysis detected
 low population-level genetic variation and high degrees of divergence
 between groups. The cryptic diversity and phylogeographic patterns found
 in S. fusiforme not only are essential to understand how environmental
 shifts and evolutionary processes shaped diversity and distribution of
 coastal seaweeds but also provide additional insights for conserving and
 managing seaweed resources and facilitate predictions of their responses
 to future climate change and habitat loss.
description: Detailed sampling
 information and DNA sequences for genetic analysesThere are three files in
 the compressed file folder.One Excel file has listed detailed sampling
 information for each population of Sargassum fusiforme. The second file in
 fasta format consists of the concatenated sequences of 560 mitochondrial
 trnW-L spacer and cox3 gene. The last file in fasta format includes 592
 sequences of chloroplast rbcL-S spacer.MEC-16-0703.zip
DOI: 10.15468/dl.papzx7
title: Occurrence Download

description: A dataset containing 210 species occurrences available in GBIF matching the query:
{
 "and" : [
 "CoordinateUncertaintyInMeters 0.0-5000.0",
 "TaxonKey is Crateva adansonii"
 ]
}

 The dataset includes 210 records from 12 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001146-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.