cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.29886080
title: Epidemiology, management, and outcomes of patients hospitalized with community-acquired infection in a resource-limited setting in Southeast Asia: a prospective observational study.

description: We conducted a prospective, observational study from May 2022-August 2023 at two hospitals in northeast Thailand. Adults hospitalized with community-acquired infection were enrolled within 24 hours of hospital admission. Patient information including demographics as well as clinical, laboratory and microbiological data were recorded. Patients were followed, including after discharge, for the primary outcome of 28-day mortality. We identified patients meeting Sepsis-3 criteria and assessed related epidemiology, management, and mortality risk factors.
DOI: 10.6084/m9.figshare.29886080.v1
title: Epidemiology, management, and outcomes of patients hospitalized with community-acquired infection in a resource-limited setting in Southeast Asia: a prospective observational study.

description: We conducted a prospective, observational study from May 2022-August 2023 at two hospitals in northeast Thailand. Adults hospitalized with community-acquired infection were enrolled within 24 hours of hospital admission. Patient information including demographics as well as clinical, laboratory and microbiological data were recorded. Patients were followed, including after discharge, for the primary outcome of 28-day mortality. We identified patients meeting Sepsis-3 criteria and assessed related epidemiology, management, and mortality risk factors.
DOI: 10.5061/dryad.dc8nn
title: Data from: Data sources for trait databases: comparing the phenomic content of monographs and evolutionary matrices

description: Databases of organismal traits that aggregate information from one or
 multiple sources can be leveraged for large-scale analyses in biology. Yet
 the differences among these data streams and how well they capture trait
 diversity have never been explored. We present the first analysis of the
 differences between phenotypes captured in free text of descriptive
 publications (‘monographs’) and those used in phylogenetic analyses
 (‘matrices’). We focus our analysis on osteological phenotypes of the
 limbs of four extinct vertebrate taxa critical to our understanding of the
 fin-to-limb transition. We find that there is low overlap between the
 anatomical entities used in these two sources of phenotype data,
 indicating that phenotypes represented in matrices are not simply a subset
 of those found in monographic descriptions. Perhaps as expected, compared
 to characters found in matrices, phenotypes in monographs tend to
 emphasize descriptive and positional morphology, be somewhat more complex,
 and relate to fewer additional taxa. While based on a small set of focal
 taxa, these qualitative and quantitative data suggest that either source
 of phenotypes alone will result in incomplete knowledge of variation for a
 given taxon. As a broader community develops to use and expand databases
 characterizing organismal trait diversity, it is important to recognize
 the limitations of the data sources and develop strategies to more fully
 characterize variation both within species and across the tree of life.
description: Supplemental
 MaterialsThe following reports
 were generated for each taxa based on the curated matrices and
 ‘monographs’ from the Phenoscape Knowledgebase. These reports list the
 entities and qualities used in each EQ statement from these works. These
 data were used to (1) compare the overlap of entities (E) and phenotypes
 (EQs) for monographs and matrices for each of the four taxa, and (2)
 calculate the anatomical entities (E), qualities (Q), and phenotypes (EQ)
 that were unique to monographs and matrices.SupplementalMaterials_Dechecchi_et_al.pdfSupplementary Table 1Relative proportions of different character types in datasets derived from monographs and matrices.Supplementary Table 2Breakdown of EQ complexity scores across EQ statements from matrices (A) and ‘monographs’ (B).
DOI: 10.5061/dryad.8792
title: Data from: Shifting functional roles and the evolution of conifer pollen-producing and seed-producing cones

description: Exploring patterns in the evolution of seed plant reproductive morphology
 within a functional context offers a framework in which to identify and
 evaluate factors that potentially drive reproductive evolution. Conifers
 are a particularly useful group for studies of this kind because they have
 a long geologic history and their reproductive organs are borne on
 separate structures with discrete functions. Multivariate analysis of
 morphological data collected from pollen-producing and seed-producing
 cones of Paleozoic, Mesozoic, and extant conifer species shows that seed
 cones underwent a significant expansion of morphological diversity that
 began during the Early–Middle Jurassic and has continued into the present
 day. In contrast, pollen cones show significantly lower levels of
 morphological diversity and exhibit similar basic morphologies throughout
 conifer evolutionary history. The increase in seed cone diversity through
 time is primarily the result of two novel structural and organizational
 features that evolved independently in different conifer families during
 the Mesozoic: robust, tightly packed cones in members of Araucariaceae,
 Cupressaceae sensu lato, and Pinaceae, and highly reduced, fleshy cones or
 solitary seeds in Podocarpaceae, Taxaceae, and some members of
 Cupressaceae sensu stricto. In extant conifers, these cone morphologies
 are associated with species that have strong interactions with vertebrate
 seed predators, seed dispersers, or a combination of both. This suggests
 that increases in the strength and complexity of biotic interactions in
 the Jurassic and Cretaceous were a primary driver of conifer reproductive
 evolution, and that patterns of character evolution relate to the
 increasing importance of cone tissue in seed protection and seed dispersal
 through time.
description: Leslie_Paleobiology_Supplemental MaterialThis file includes the full character data from the combined pollen cone and seed cone multivariate analysis as well as the full character data from the pollen cone-specific and seed cone-specific multivariate analyses. It also includes a list and description of the pollen cone-specific and seed cone-specific characters and a full list of the sources used to compile the morphological information for fossil and living conifers.
DOI: 10.5061/dryad.35q1p98
title: Data from: Long-term outcome in neuroZika: when biological diagnosis matters

description: Objectives: To characterize the full spectrum, relative frequency and
 prognosis of the neurological manifestations in Zika virus (ZIKV)
 postnatal infection. Methods: We conducted an observational study in
 consecutive ZIKV-infected patients presenting with neurological
 manifestations during the French West Indies 2016 outbreak. Results:
 Eighty-seven patients, including 6 children, were enrolled. Ninety-five
 percent of all cases required hospitalization. Guillain-Barré syndrome was
 the most frequent manifestation (46.0%) followed by encephalitis or
 encephalomyelitis (20.7%), isolated single or multiple cranial nerve
 palsies (9.2%), other peripheral manifestations (6.9%), and stroke (1.1%).
 Fourteen patients (16.1%) including one child, developed a mixed disorder
 involving both the central and peripheral nervous system. Mechanical
 ventilation was required in 21 cases all of whom had ZIKV RNA in at least
 one biological fluid. Two adult patients died due to neuroZika. Clinical
 follow-up (median 14 months; interquartile range, 13-17) was available for
 76 patients. Residual disability (modified Rankin scale ≥2) was identified
 in 19 (25.0%) patients, in 6 cases (7.9%), disability was severe (modified
 Rankin scale ≥4). Amongst patients with ZIKV RNA detected in one
 biological fluid, the risk of residual disability or death was higher (odd
 ratio 9.19; CI 1.12-75.22; p = 0.039). Conclusions: NeuroZika spectrum
 represents a heterogenous group of clinical neurological manifestations.
 During an outbreak, clinicians should consider neuroZika in patients
 presenting with cranial nerve palsies and a mixed neurological disorder.
 Long-term sequelae are frequent in NeuroZika. ZIKV reverse-transcription
 PCR status at admission can inform prognosis and should therefore be taken
 into consideration in the management of hospitalised patients.
description: NeuroZika study,
 Lannuzel et al.Supplementary figure S1
 and supplementary Tables S1-5
DOI: 10.5061/dryad.j4d15
title: Data from: Toward a better understanding of Apis mellifera and Varroa destructor microbiomes: introducing PhyloH as a novel phylogenetic diversity analysis tool

description: The study of diversity in biological communities is an intriguing field.
 Huge amount of data are nowadays available (provided by the innovative DNA
 sequencing techniques), and management, analysis and display of results
 are not trivial. Here, we propose for the first time the use of
 phylogenetic entropy as a measure of bacterial diversity in studies of
 microbial community structure. We then compared our new method (i.e. the
 web tool phyloh) for partitioning phylogenetic diversity with the
 traditional approach in diversity analyses of bacteria communities. We
 tested phyloh to characterize microbiome in the honeybee (Apis mellifera,
 Insecta: Hymenoptera) and its parasitic mite varroa (Varroa destructor,
 Arachnida: Parasitiformes). The rationale is that the comparative analysis
 of honeybee and varroa microbiomes could open new perspectives concerning
 the role of the parasites on honeybee colonies health. Our results showed
 a dramatic change of the honeybee microbiome when varroa occurs,
 suggesting that this parasite is able to influence host microbiome. Among
 the different approaches used, only the entropy method, in conjunction
 with phylogenetic constraint as implemented in phyloh, was able to
 discriminate varroa microbiome from that of parasitized honeybees. In
 conclusion, we foresee that the use of phylogenetic entropy could become a
 new standard in the analyses of community structure, in particular to
 prove the contribution of each biological entity to the overall diversity.
description: Supplementary_material_MER-14-0280.R1Supplementary material MER-14-0280.R1
DOI: 10.5061/dryad.6h88s
title: Data from: Starting a DNA barcode reference library for shallow water polychaetes from the southern European Atlantic coast

description: Annelid polychaetes have been seldom the focus of dedicated DNA barcoding
 studies, despite their ecological relevance and often dominance,
 particularly in soft-bottom estuarine and coastal marine ecosystems. Here,
 we report the first assessment of the performance of DNA barcodes in the
 discrimination of shallow water polychaete species from the southern
 European Atlantic coast, focusing on specimens collected in estuaries and
 coastal ecosystems of Portugal. We analysed cytochrome oxidase I DNA
 barcodes (COI-5P) from 164 specimens, which were assigned to 51
 morphospecies. To our data set from Portugal, we added available published
 sequences selected from the same species, genus or family, to inspect for
 taxonomic congruence among studies and collection location. The final data
 set comprised 290 specimens and 79 morphospecies, which generated 99
 Barcode Index Numbers (BINs) within Barcode of Life Data Systems (BOLD).
 Among these, 22 BINs were singletons, 47 other BINs were concordant,
 confirming the initial identification based on morphological characters,
 and 30 were discordant, most of which consisted on multiple BINs found for
 the same morphospecies. Some of the most prominent cases in the latter
 category include Hediste diversicolor (O.F. Müller, 1776) (7), Eulalia
 viridis (Linnaeus, 1767) (2) and Owenia fusiformis (delle Chiaje, 1844)
 (5), all of them reported from Portugal and frequently used in ecological
 studies as environmental quality indicators. Our results for these species
 showed discordance between molecular lineages and morphospecies, or added
 additional relatively divergent lineages. The potential inaccuracies in
 environmental assessments, where underpinning polychaete species diversity
 is poorly resolved or clarified, demand additional and extensive
 investigation of the DNA barcode diversity in this group, in parallel with
 alpha taxonomy efforts.
description: Global nucleotide
 treeGlobal sequence
 alignmentHediste diversicolor
 nucleotide treeHediste diversicolor
 sequence alignment
DOI: 10.5061/dryad.01f10
title: Data from: Organic farming increases richness of fungal taxa in the wheat phyllosphere

description: Organic farming is often advocated as an approach to mitigate biodiversity
 loss on agricultural land. The phyllosphere provides a habitat for diverse
 fungal communities that are important for plant health and productivity.
 However, it is still unknown how organic farming affects the diversity of
 phyllosphere fungi in major crops. We sampled wheat leaves from 22
 organically and conventionally cultivated fields in Sweden, paired based
 on their geographical location and wheat cultivar. Fungal communities were
 described using amplicon sequencing and real-time PCR. Species richness
 was higher on wheat leaves from organically managed fields, with a mean of
 54 OTUs compared with 40 OTUs for conventionally managed fields. The main
 components of the fungal community were similar throughout the 350 km long
 sampling area and seven operational taxonomic units (OTUs) were present in
 all fields: Zymoseptoria, Dioszegia fristingensis, Cladosporium, Dioszegia
 hungarica, Cryptococcus, Ascochyta and Dioszegia. Fungal abundance was
 highly variable between fields, 103-105 internal transcribed spacer (ITS)
 copies per ng wheat DNA, but did not differ between cropping systems.
 Further analyses showed that weed biomass was the strongest explanatory
 variable for fungal community composition and OTU richness. These findings
 help provide a more comprehensive understanding of the effect of organic
 farming on the diversity of organism groups in different habitats within
 the agroecosystem.
description: R codeThe R code for
 reproducing the statistical analyses and figures in the paper. The data
 are available in the 'SuppInfo_TablesS1-S6.xlsx' file and the R
 script reads from this file. Alternatively, the data are also available in
 .csv format.SuppInfo-Rcode.rFigure S1-S3Figure S1 Richness of fungal OTUs at different clustering dissimilarity cut-offs. Figure S2 Fungal OTUs significantly affected by cropping system. Figure S3 Comparison of potential pathogens between cropping systems.SuppInfo_FigureS1-S3.pdfTable S1-S6 (xlsx)Table S1 Sample identifying barcodes. Table S2 Species identification for fungal operational taxonomic units (OTUs). Table S3 Characteristics of organically and conventionally managed wheat fields (explanatory variables). Table S4 OTU table. Abundance of fungal OTUs (no. of ITS copies/ng wheat DNA) across 22 wheat fields. Table S5 Real-time PCR data per extraction replicate. Table S6 OTU table. Read counts per extraction replicate.SuppInfo_TablesS1-S6.xlsxTable S1-S6 (csv)Supplementary data files in csv format.SuppInfo_TablesS1-S6.zipFungal OTU sequencesDNA sequence of the most abundant sequence in each OTU in fasta format (284 OTUs).Fungal_OTUs.fasta
DOI: 10.5061/dryad.46kv1
title: Data from: Linking life-history traits, ecology and niche breadth evolution in North American eriogonoids (Polygonaceae)

description: Macroevolutionary and microevolutionary studies provide complementary
 explanations of the processes shaping the evolution of niche breadth.
 Macroevolutionary approaches scrutinize factors such as the temporal and
 spatial environmental heterogeneities that drive differentiation among
 species. Microevolutionary studies, in contrast, focus on the processes
 that affect intraspecific variability. We combine these perspectives by
 using macroevolutionary models in a comparative study of intraspecific
 variability. We address potential differences in rates of evolution of
 niche breadth and position in annual and perennial plants of the
 Eriogonoideae subfamily of the Polygonaceae. We anticipated higher rates
 of evolution in annuals than in perennials owing to differences in
 generation time that are paralleled by rates of molecular evolution.
 Instead, we find that perennial eriogonoid species present greater
 environmental tolerance (wider climate niche) than annual species. Niche
 breadth of perennial species has evolved two to four times faster than in
 annuals, while niche optimum has diversified more rapidly among annual
 species than among perennials. Niche breadth and average elevation of
 species are correlated. Moreover, niche breadth increases more rapidly
 with mean species elevation in perennials than in annuals. Our results
 suggest that both environmental gradients and life history strategy
 influence rates and patterns of niche breadth evolution.
description: Supplementary
 InformationNumber of occurrences
 for each species and species sampling; Fossil calibration; AUC and CI for
 niche models; Relative input of variables into niche models; Test for
 normality of PC variances; Kurtosis for PC scores distributions;
 Geographical range for each species; Mean latitude and centroid-based
 latitude estimates for each species; Evolutionary models comparison for
 niche position and breadthSI.doc
DOI: 10.5061/dryad.3530j
title: Data from: Transcriptomes of parents identify parenting strategies and sexual conflict in a subsocial beetle

description: Parenting in the burying beetle Nicrophorus vespilloides is complex and,
 unusually, the sex and number of parents that can be present is flexible.
 Such flexibility is expected to involve specialized behaviour by the two
 sexes under biparental conditions. Here, we show that offspring fare
 equally well regardless of the sex or number of parents present. Comparing
 transcriptomes, we find a largely overlapping set of differentially
 expressed genes in both uniparental and biparental females and in
 uniparental males including vitellogenin, associated with reproduction,
 and takeout, influencing sex-specific mating and feeding behaviour. Gene
 expression in biparental males is similar to that in non-caring states.
 Thus, being ‘biparental’ in N. vespilloides describes the family social
 organization rather than the number of directly parenting individuals.
 There was no specialization; instead, in biparental families, direct male
 parental care appears to be limited with female behaviour unchanged. This
 should lead to strong sexual conflict.
description: qPCR data for
 β-glucosidases in femalesBeta-gluc-Female.xlsqPCR data for β-glucosidases in malesBeta-gluc-Males.xlsqPCR data for peptidoglycan recognition protein in femalesPGRP3-Females.xlsqPCR data for peptidoglycan recognition protein in malesPGRP3-Males.xlsqPCR data for vitellogenin 1 and vitellogenin 2 in males and femalesqRT verification Vg male & females.xlsqPCR data for Serine Protease in femalesSerine_Protease_Females.xlsqPCR data for Serine Protease in malesSerine_Protease_Males.xlsqPCR data for Takeout in femalesTakeout_RNA-seq_validation_Females.xlsqPCR data for Takeout in malesTakeout_RNA-seq_validation_Males.xlsqPCR data for Thaumatin in femalesThaumatin-Females.xlsqPCR data for Thaumatin in malesThaumatin-Males.xls
DOI: 10.5061/dryad.rv0k6
title: Data from: Inferring skeletal production from time-averaged assemblages: skeletal loss pulls the timing of production pulses towards the modern period

description: Age-frequency distributions of dead skeletal material on the landscape or
 seabed—information on the time that has elapsed since the death of
 individuals—provide decadal- to millennial-scale perspectives both on the
 history of production and on the processes that lead to skeletal
 disintegration and burial. So far, however, models quantifying the
 dynamics of skeletal loss have assumed that skeletal production is
 constant during time-averaged accumulation. Here, to improve inferences in
 conservation paleobiology and historical ecology, we evaluate the joint
 effects of temporally variable production and skeletal loss on postmortem
 age-frequency distributions (AFDs) to determine how to detect fluctuations
 in production over the recent past from AFDs. We show that, relative to
 the true timing of past production pulses, the modes of AFDs will be
 shifted to younger age cohorts, causing the true age of past pulses to be
 underestimated. This shift in the apparent timing of a past pulse in
 production will be stronger where loss rates are high and/or the rate of
 decline in production is slow; also, a single pulse coupled with a
 declining loss rate can, under some circumstances, generate a bimodal
 distribution. We apply these models to death assemblages of the bivalve
 Nuculana taphria from the Southern California continental shelf, finding
 that: (1) an onshore-offshore gradient in time averaging is dominated by a
 gradient in the timing of production, reflecting the tracking of
 shallow-water habitats under a sea-level rise, rather than by a gradient
 in disintegration and sequestration rates, which remain constant with
 water depth; and (2) loss-corrected model-based estimates of the timing of
 past production are in good agreement with likely past changes in local
 production based on an independent sea-level curve.
description: Supplement table 3 with
 age dataSupplement table 3 -
 Amino acid racemization data and estimated calendar ages based on
 radiocarbon calibration.Supplement table 3 with
 data.xlsSupplementary tables and
 figuresSupplementary file with
 2 supplementary tables and 2 supplementary figuresTomasovych et al. supplementary
 tables and figures.pdfTomasovych et al.
 supplement R codeSource code for model
 likelihoods and figures written in R language. Six density functions for
 fitting parameters of models with optimizing likelihoods are followed by
 age data of four depth assemblages. Fitting of age data with models occurs
 within the loop, followed by (1) figures showing the relation between the
 observed medians and IQRs and the values expected under different models,
 (2) likelihood surfaces for the Weibull and two-phase model, (3)
 simulations showing the effect of loss rate on the shape of AFD under
 one-phase and two-phase models, and (4) simulations showing the effects of
 sample size and fluctuating sinusoidal production on loss-rate
 parameters.