cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2rbnzs7sk
title: Script and results of the Bayesian analyses of environmental and phylogenetic effects of leaf composition

description: These are the script and results of the Bayesian analysis of an article
 published in Ecology. In this study, we tested the suitability of
 biogeochemical niche hypothesis in a set of forestal tree rainforest
 species in a French Guiana forest. Biogeochemical niche
 hypothesis (BN) aims to relate species/genotype elemental composition with
 its niche based on the fact that different elements are involved
 differentially in distinct plant functions. These are the results of the
 models that allow us to analyze the effects of experimental independent
 variables (season, site and topography) on dependent variables (foliar
 traits) taking into account as random factors phylogeny of the distinct
 studied species and also taxonomy effects not linked to phylogeny such as
 convergence and divergence evolutive processes. This script provides all
 the necessary information to conduct this type of analyses including the
 R-packages necessaries to conduct it. We observed strong legacy
 (phylogenic+species) signals in the species-specific foliar elemental
 composition (elementome) and, for the first time, provide empirical
 evidence for a relationship between species-specific foliar elementome and
 functional traits. Our study thus supports the BN hypothesis and confirms
 the general niche segregation process through which the species-specific
 use of bio-elements drives the high levels of a-diversity in this tropical
 forest.
DOI: 10.5068/d1cq47
title: The effects of the upper atmosphere and corona on the solar wind interaction with Venus

description: Since Venus has no substantial planetary magnetic field, the fast-flowing
 solar wind plasma interacts directly with its ionosphere, upper
 atmosphere, and corona. The thermal atmosphere and hot oxygen corona of
 Venus are expected to play essential roles in the interaction process. To
 quantify their effects, we combine three major state-of-the-art
 three-dimensional numerical models, including (1) The Venus Thermosphere
 General Circulation model (VTGCM), (2) The Adaptive Mesh Particle
 Simulator (AMPS), and (3) A multi-species MHD model of Venus based on
 Block Adaptive Tree Solar-wind Roe Upwind Scheme (BATSRUS). The global
 multi-species MHD model is used to simulate the planet’s interaction with
 the ambient solar wind, where the background neutral densities are
 provided by VTGCM and AMPS. Using the above-mentioned numerical models,
 the effect of the upper atmosphere and corona on solar-wind-driven ion
 escape rates are examined for three typical solar cycle conditions,
 including solar maximum, solar median, and solar minimum conditions. The
 model results suggest that even though the hot oxygen corona only has a
 minor effect on the ion density profiles in the ionosphere, it
 can enhance ion loss rate up to ~25% for high solar activity. 
description: Numerical simulation results using a multi-species single-fluid
 MHD model.
description: The data is provided in ASCII files and should work with any
 plotting software. In addition, binary data is provided for some cases
 which can be opened with TECPLOT.
DOI: 10.5061/dryad.j6q573njp
title: Natural history data for Nicrophorus orbicollis

description: Burying beetles of the genus Nicrophorus have become a model for studying
 the evolution of complex parental care in a laboratory. Nicrophorus
 species depend on small vertebrate carcasses to breed, which they process
 and provision to their begging offspring. However, vertebrate carcasses
 are highly sought after by a wide variety of species and so competition is
 expected to be critical to the evolution of parental care. Despite this,
 the competitive environment for Nicrophorus is rarely characterized in the
 wild and remains a missing factor in laboratory studies. Here, we
 performed a systematic sampling of Nicrophorus orbicollis living near the
 southern extent of their range at Whitehall Forest in Clarke County,
 Georgia, USA. We determined the density of N. orbicollis and other
 necrophilous species that may affect the availability of this breeding
 resource through interference or exploitation competition. In addition, we
 characterize body size, a key trait involved in competitive ability, for
 all Nicrophorus species at Whitehall Forest throughout the season.
 Finally, we compare our findings to other published natural history data
 for Nicrophorines. We document a significantly longer active season than
 was observed twenty years previously at Whitehall Forest for both N.
 orbicollis and Nicrophorus tomentosus, potentially due to climate change.
 As expected, the adult body size of N. orbicollis was larger than N.
 tomentosus, the only other Nicrophorus species that was captured in 2022
 at Whitehall Forest. The other most prevalent insects captured included
 species in the families Staphylinidae, Histeridae, Scarabaeidae, and
 Elateridae, which may act as competitors or predators of Nicrophorus
 young. Together, our results indicate significant variation in intra- and
 interspecific competition relative to populations within the N. orbicollis
 range. These findings suggest that the competitive environment shows
 extensive spatiotemporal variation, providing the basis to make
 predictions for how ecology may influence parenting in this species.
DOI: 10.5061/dryad.n2z34tn1p
title: The histone demethylase Kdm3 prevents auto-immune piRNAs production in Drosophila

description: Genome integrity of the animal germline is protected from transposable
 element activity by PIWI-interacting RNAs (piRNAs). While piRNA biogenesis
 is intensively explored, little is known about the genetical determination
 of piRNA clusters, the genomic sources of piRNAs. Using a bimodal
 epigenetic state piRNA cluster (BX2), we identified the histone
 demethylase Kdm3 as being able to prevent a cryptic piRNA production. In
 the absence of Kdm3, dozens of coding gene-containing regions become
 genuine germline dual-strand piRNA clusters. Eggs laid by Kdm3 mutant
 females show developmental defects phenocopying loss of function of genes
 embedded into the additional piRNA clusters, suggesting an inheritance of
 functional ovarian “auto-immune” piRNAs. Antagonizing piRNA cluster
 determination through chromatin modifications appears crucial to prevent
 auto-immune genic piRNAs production.
DOI: 10.15468/dl.93chja
title: Occurrence Download

description: A dataset containing 152 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Gentiana macrophylla",
 "Year 1975-2026"
 ]
}

 The dataset includes 152 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003484-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.18931zd2g
title: Information transfer in mammalian glycan-based communication

description: Glycan-binding proteins, so-called lectins, are exposed on mammalian cell
 surfaces and decipher the information encoded within glycans translating
 it into biochemical signal transduction pathways in the cell. These
 glycan-lectin communication pathways are complex and difficult to analyze.
 However, quantitative data with single -cell resolution provide means to
 disentangle the associated signaling cascades. We chose C-type lectin
 receptors (CTLs) expressed on immune cells as a model system to study
 their capacity to transmit information encoded in glycans of incoming
 particles. In particular, we used NF-κBnuclear factor kappa-B-reporter
 cell lines expressing DC-specific ICAM-3–grabbing nonintegrin
 (DC-SIGN)DC-SIGN, macrophage C-type lectin (MCL), dectin-1, dectin-2, and
 minclemacrophage-inducible C-type lectin (MINCLE), as well as TNFαR and
 TLR-1&2 in monocytic cell lines and compared their transmission of
 glycan-encoded information. All receptors did transmit information with
 similar signaling capacity, except dectin-2. This lectin was identified to
 be less efficient in information transmission compared to the other CTLs,
 and even while en the sensitivity of the dectin-2 pathway was enhanced by
 overexpression of its co-receptor FcRγ, its transmitted information was
 not. Next, we expanded our investigation towards the integration of
 multiple signal transduction pathways including synergistic lectins, which
 is crucial during pathogen recognition. We show how the signaling capacity
 of lectin receptors using a similar signal transduction pathway (dectin-1
 and dectin-2) areis being integrated by compromising between the lectins.
 In contrast, co-expression of MCL synergistically enhanced the dectin-2
 signaling capacity, particularly at low -glycan stimulant concentration.
 By using dectin-2 and other lectins as examples, we demonstrate how
 signaling capacity of dectin-2 is modulated in the presence of other
 lectins, and therefore, the findings provide insight into how immune cells
 translate glycan information using
description: The
 data consist of a flow cytometry raw data file and excel sheets locating
 the experimental conditions of the flow cytometry
 files. The
 data include all the experimental data used for every figure set of the
 paper.
description: We used FlowCal library to import fcs. Please
 see: https://taborlab.github.io/FlowCal/python_tutorial/index.html The fcs files are already gated, but if it is not, use this gating method: gated = FlowCal.gate.ellipse(s_g1, channels=['FSC-A', 'SSC-A'], log=True, center=(5.6, 5.3), a=0.3, b=0.25, theta=60/180.*np.pi) The GFP channel is "BL1-A" and the labelled zymosan signal is 'FL7-A'.
DOI: 10.15468/dl.vejgc3
title: Occurrence Download

description: A dataset containing 1320 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Cheritra freja"
 ]
}

 The dataset includes 1320 records from 36 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003481-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.z612jm6gr
title: Assessing the Immunization Information System and Electronic Health Record interface accuracy for COVID-19 vaccinations

description: Objective Our objective is to assess the accuracy of the COVID-19
 vaccination status within the Electronic Health Record for a panel of
 patients in a primary care practice when manual queries of the state
 immunization databases are required to access outside immunization
 records. Results A manual query of the local Immunization Information
 Systems for 4,114 adult patients with “unknown” vaccination status showed
 44% of the patients were previously vaccinated. Attempts to assess the
 comprehensiveness of the Immunization Information Systems were hampered by
 incomplete documentation in the chart and poor response to patient
 outreach. Conclusions  When the interface between the patient
 chart and the local Immunization Information System depends on a manual
 query for the transfer of data, the COVID-19 vaccination status for a
 panel of patients is often inaccurate. This study was reviewed by the
 University of Kansas Medical Center Institutional Review Board and was
 designated as a quality improvement project.
description: This study evaluated COVID-19 vaccination status of adult primary
 care patients within a university-based health system electronic health
 record by manually querying the Kansas and Missouri Immunization
 Information Systems.
DOI: 10.5061/dryad.8sf7m0ct5
title: Sexual selection does not drive hindwing tail elaboration in a moon moth, Actias luna

description: The most emblematic animal traits are often attributed to sexual
 selection. While this pressure is an important force, elaborated traits
 that have been driven solely by natural selection are less enumerated.
 Here, we test an elaborate trait that has been studied in an anti-predator
 context, but that remains unstudied for its role in mating. We gave female
 Actias luna (Saturniidae) moths a choice between two males of differing
 hindwing tail treatments. In our primary experiment, males with intact
 tails garnered more matings than males with tails removed, but this
 difference appears to result from damage incurred by tail removal. We
 verified this with a series of additional experiments: we created a
 tail/no-tail dyad where we removed tails from both males, then reglued
 tails to one and applied glue to the hindwings of the other. We found no
 difference in mating success. To ensure that this no-difference result was
 not due to the glue itself, we offered females two intact males, with glue
 added to the wings of one. This dyad also had equal mating success. We
 therefore find no evidence that tails play a role in sexual selection.
 These results, in combination with previous research on bat-moth battles
 using A. luna, leads us to conclude that hindwing tail elaboration was
 likely driven by natural selection alone. We suggest that future research
 testing multiple selective forces on animal traits is needed to reveal the
 prevalence of natural versus sexual selection as the primary force driving
 trait elaboration in diverse animal taxa.
DOI: 10.5061/dryad.j3tx95xkn
title: Impacts of ecological restoration on the genetic diversity of plant species: A global meta-analysis

description: 1. In contrast to the depth of knowledge available for the enhancement of
 plant species diversity and ecosystem services through ecological
 restoration, our understanding of how ecological restoration impacts
 genetic diversity (GD) of plant species has not yet been synthesized. 2.
 We performed a global meta-analysis to examine whether ecological
 restoration improved GD of plant species in restored populations. First,
 we compared the GD of restored populations with reference or degraded
 populations. Second, we explored whether the influence of ecological
 restoration on plant GD varies between species with different
 characteristics (life form and threat status), between different
 restoration strategies (active/passive, seeding/planting,
 mixture/non-mixture) or between different restoration times (&lt;50
 and ≥50 years; with an average of 29.3 years). 3. The GD of restored
 populations was significantly lower (HE, 1.06%; PPB, 5.10%, and SWI,
 4.95%) than in reference populations but was comparable to degraded
 populations. The inbreeding coefficient (FIS, the proportion by which the
 heterozygosity of an individual is reduced by inbreeding) was consistently
 comparable between restored populations and reference or degraded
 populations. 4. Woody species but not herbs had significantly lower GD in
 restored populations than in reference populations. Forest but not
 grassland ecosystem had significantly lower GD in restored populations
 than in reference populations. Passive but not active restoration, seeding
 rather than planting, and mixing materials from different sources rather
 than using a single source, all significantly increased the GD of restored
 populations. When the restoration time was ≥50 years, in contrast to
 &lt;50 years, GD was comparable between the restored and reference
 populations. 5. Synthesis and applications. In general, ecological
 restoration did not significantly improve the GD of plant species compared
 to reference or degraded populations. This might be due in part to the
 relatively short restoration time. Using passive restoration, seeding, and
 mixed sources could significantly increase the GD of restored populations.
 We emphasize that GD should not be treated as a minor cobenefit of
 ecological restoration for other purposes and that the recovery of GD
 should be listed as a vital goal in future ecological restoration with
 plant species.
DOI: 10.5061/dryad.18931zd2h
title: Perovskite modified catalysts with improved coke resistance for steam reforming of glycerol to renewable hydrogen fuel

description: Catalytic steam reforming of renewable feedstock to renewable energy or
 chemicals always goes with intense coking activities that produce
 carbonaceous products leading to low performance and eventual catalyst
 deactivation. A supported metal catalyst such as Ni/Al2O3 is
 known to catalyse gasification and decomposition of biomass feedstock
 largely for renewable fuel production with promising results. Catalyst
 deactivation from high carbon deposition, agglomeration, and phase
 transformations resulting in rapid deactivation are some of the issues
 identified with the use of the catalyst. In this work, improvement on the
 coke resistance and catalytic properties of the Ni/Al2O3 catalyst is
 sought via the use of a thermally stable and coke-resistant perovskite
 La0.75Sr0.25Cr0.5Mn0.5O3-δ (LSCM) as catalyst promoter/modifier and
 involving Zirconia-doped Ceria (Ce-Zr) as alternative support in steam
 reforming of pure and by-product glycerol. The stabilizing influence of
 the LSCM on the Ni catalyst has improved stability against agents of
 deactivation with a significant improvement of catalytic activity of
 Ni/Al2O3 in H2 production and robust suppression of carbon
 deposition. Particularly, the synergy between the LSCM promoter and
 alternative Ce0.75Zr0.25O2 support enhanced the basic and redox properties
 known for Ce0.75Zr0.25O2 support in contrast to the weak acid
 centres in the γ-Al2O3 support which further improved nickel stability,
 catalyst-support interaction with a resultant high catalytic activity, and
 robust coke suppression as a result of enhanced oxygen mobility. There is
 a correlation between the product distribution, nature of coke deposited,
 and reforming temperature, as well as the type of support and structural
 modification. Hence, the integration of a robust perovskite material as a
 catalyst promoter and choice of support could be tailored in the design
 and development of robust catalyst systems to improve the performance of
 supported metal catalysts particularly the suppression of carbon
 deposition for hydrocarbon and biomass conversion to renewable fuel or
 chemicals.
description: The dataset is from material synthesis, characterisation, and
 catalyst testing.
description: Origin software
DOI: 10.5061/dryad.vx0k6djx6
title: Environment and genotype influence on Populus tremuloides condensed tannin composition

description: This dataset contains concentration and molecular structural information
 (mean degree of polymerization, procyanidin:prodelphinidin ratios,
 stereochemistry) describing condensed tannins in Populus tremuloides
 (aspen) tree foliage in different genotypes and in response to altered
 environmental conditions (warming, freeze damage, ozone exposure, elevated
 carbon dioxide, elevated soil nutrients, altered soil microbiome, mammal
 browsing, and insect herbivory).
description: Condensed tannins were analyzed by extraction from vacuum-dried,
 finely ground foliage into methanol, followed by thiolysis and
 quantification by ultra high performance liquid chromatography with
 negative electrospray ionization mass spectrometry. Missing values (due to
 failure of analytical method or quality assurance criteria) were coded as
 'null.' The individual field and glasshouse-based experiments
 from which the specimens used in creation of these data were sourced,
 along with the full analytical method, are cited below:
 Bennett AE, Rubert-Nason KF, Lindroth RL (2020) Response of aspen
 genotypes to browsing damage is not influenced by soil community
 diversity. Plant Soil 452:153-170.
 https://doi.org/10.1007/s11104-020-04466-8 Couture JJ,
 Meehan TD, Rubert-Nason KF, Lindroth RL (2017) Effects of elevated
 atmospheric carbon dioxide and tropospheric ozone on phytochemical
 composition of trembling aspen (Populus tremuloides) and paper birch
 (Betula papyrifera). J Chem Ecol 43:26-38. https://doi.org/
 10.1007/s10886-016-0798-4 Li Z, Rubert-Nason KF,
 Jamieson MA, Raffa KF, Lindroth RL (2021) Root secondary metabolites in
 Populus tremuloides: Effects of simulated climate warming, defoliation,
 and genotype. J Chem Ecol 47:313-321. https://doi.org/10.1007/s10886-021-01259-w Rubert-Nason KF, Couture JJ, Gryzmala EA, Townsend PA, Lindroth RL (2017) Vernal freeze damage and genetic variation alter tree growth, chemistry, and insect interactions. Plant Cell Environ 40:743-2753. https://doi.org/10.1111/pce.13042 Rubert-Nason KF, Keefover-Ring KM, Lindroth RL (2012) Genotype and environment modulate the response of trembling aspen to simulated ungulate browsing. Ecological Society of America National Meeting, Portland, Oregon. Aug. 5-10, 2012. Session 7683. https://eco.confex.com/eco/2012/webprogram/Session7683.html. Accessed 2 Jan 2023 Rubert-Nason KF, Lindroth RL (2019) Analysis of condensed tannins in Populus spp. using reversed phase UPLC-PDA-(-)esiMS following thiolytic depolymerization. Phytochem Anal 30:257-267. https://doi.org/10.1002/pca.2810
description: Datasets corresponding to each experiment including relevant
 citations are indexed by tab in Microsoft Excel (*.xlsx) format; a
 metadata tab defines abbreviations used in column headings.
DOI: 10.5061/dryad.rr4xgxdd8
title: Data from: Long-term capture data uncover shifts in the daily activity patterns of Amazonian birds

description: Although the duration of biological rhythms varies from milliseconds to
 decades, daily cycles are especially widespread for individual organisms.
 These circadian rhythms are synchronized by light-dark cycles, which
 govern predictable changes in other microclimate variables. Despite the
 fixed, regular nature of these abiotic cycles at low latitudes, little is
 known about how different animals structure activity along these
 gradients. We used 25 years of capture-recapture data and ~25,000 unique
 captures to characterize ‘activity’ (time of capture) for 65 species of
 Amazonian birds in the lowest forest stratum (0–2.5 m). To quantify
 vertical niche breadths, we also measured foraging heights for these same
 species in the field. Activity peaked within the first two hours after
 sunrise for most species (71%), while others peaked 1–3 hours later (29%).
 This difference was associated with an apparent preference for specific
 vertical strata, as terrestrial and near-ground birds peaked ~1 hour after
 sunrise, while birds from higher strata delayed their first bouts of
 activity in the lower understory (by an average of 40 to 100 minutes).
 Peak capture times also correlated with long-term abundance trends, as
 only species with the earliest capture times showed strong declines,
 suggesting that associations with mid- or late-morning microclimates may
 contribute to resiliency in birds typical of higher strata. Because
 arboreal species largely avoid the lower understory in the early morning,
 when terrestrial birds are active, we infer that they are poorly adapted
 to low-light environments. However, with their broad vertical niches and
 reliance on brighter microhabitats, we suggest that an arboreal lifestyle
 diminishes specialization and may increase the capacity to cope with a
 wider range of daily microclimate conditions. We predict that subtle, but
 important, shifts in daily activity patterns would materialize if other
 biodiversity-monitoring programs could analyze similar temporal datasets.