cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.z08kprr96
title: Data from: Livestock overgrazing disrupts the positive associations between soil biodiversity and nitrogen availability

description: Livestock overgrazing influences both microbial communities and nutrient
 cycling in terrestrial ecosystems. However, the role of overgrazing in
 regulating the relationship between soil biodiversity and nitrogen
 availability remains largely unexplored. We performed long-term grazing
 exclusion experiments across eight sites along precipitation gradient
 covering three major types of grassland in northern China to compare the
 linkage between soil microbial diversity and N availability in overgrazed
 versus non-grazed conditions. We found a positive association between
 fungal diversity and soil available N in non-grazed grasslands. However,
 the positive association was absent in overgrazed environments. Bacterial
 diversity is not related to soil available N in either non-grazed or
 overgrazed grasslands. Moreover, in bacterial community, we found a
 positive link between the relative abundance of Actinobacteria with soil
 available N in non-grazed, but not overgrazed, grasslands. Instead we
 found the links between relative abundance of Bacteroidetes and
 Acidobacteria with soil available N in overgrazed grasslands, but not
 non-grazed, grasslands. Our work provides evidence that the relationships
 between microbial diversity and ecosystem functions are context-dependent,
 and so microbial community diversity is likely not the major driver of
 soil N mineralization in overgrazed grasslands. Our study suggests that
 high intensity anthropogenic activities in grasslands restrains the
 capacity of diverse soil microbial communities to sustain ecosystem
 function, and more broadly the capacity of entire ecosystems to maintain
 important ecosystem processes such as plant production. Our study also
 indicates that the fundamental microbial communities associated with N
 availability change with differing land management strategies (e.g.
 livestock grazing).
DOI: 10.5066/p1hupqg5
title: Gas and heat emission measurements at the Mud Volcano area, Yellowstone National Park

description: We measured soil CO2 fluxes on grids with the accumulation chamber method on July 15-17, 2021, September 10, 2022, and May 6-7, 2025, at Mud Volcano, an acid-sulfate, vapor-dominated area in Yellowstone National Park, WY. We also monitored variations in CO2, H2O and sensible and latent heat fluxes, air temperature and pressure, and wind speed and direction on a half-hourly basis from September 10 to November 9, 2022, using the eddy covariance approach. On July 16, 2021, and September 9, 2022, we collected gas samples from steaming ground for analysis of bulk chemical and carbon (d13C-CO2) and helium (Rc/Ra) isotope compositions. The soil CO2 flux, eddy covariance, and gas geochemical data sets were used to characterize baseline temporal and spatial variations in hydrothermal CO2 and heat emissions and gas sources for the study area. Data are saved in three spreadsheets in the *.csv format.
DOI: 10.25338/b8p60r
title: Equate SENAS and IVD cognitive measure: Summary of methods and results

description: Conceptually similar measures of episodic memory and executive function
 have been derived from different tests that compose the SENAS (Spanish and
 English Neuropsychological Assessment Scale) and IVD-PPG (ischemic
 vascular contributions to cognitive decline and dementia)
 neuropsychological test batteries. The purpose of this project was to
 create equated episodic memory and executive scores from these two
 batteries that are on the same measurement metric and can be combined in
 analyses using data from both projects. This will be particularly
 advantageous where the sample size from either project is small but a
 combined sample will improve statistical power. Analyses involving
 neuropathology cases and PIB-PET imaging are particular candidates.
DOI: 10.15468/dl.73ubx3
title: Occurrence Download

description: A dataset containing 1011 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((159.00094 -48.95058,200.03306 -48.95058,200.03306 -32.54476,159.00094 -32.54476,159.00094 -48.95058))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Thuidiopsis furfurosa"
 ]
}

 The dataset includes 1011 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002326-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.fxpnvx0nx
title: Data from: Body size correlates with discrete character morphological proxies

description: Principal coordinates analysis (PCoA) is a statistical ordination
 technique commonly applied to morphology-based cladistic matrices to study
 macroevolutionary patterns, morphospace occupation and disparity. However,
 PCoA-based morphospaces are dissociated from the original data; therefore,
 whether such morphospaces accurately reflect body plan disparity or
 extrinsic factors, such as body size, remains uncertain. We collated nine
 character-taxon matrices of dinosaurs together with body mass estimates
 for all taxa and tested for relationships between body size and both the
 principal ordinated axis of variation (PCo1) and the entire set of PCo
 scores. The possible effects of body size on macroevolutionary hypotheses
 derived from ordinated matrices were tested by re-evaluating evidence for
 the accelerated accumulation of avian-type traits indicated by a strong
 directional shift in PCo1 scores in hypothetical ancestors of modern
 birds. Body mass significantly accounted for, on average, approximately 50
 and 16 per cent of the phylogenetically corrected variance in PCo1 and all
 PCo scores, respectively. Along the avian stem lineage, approximately 30
 per cent of the morphological variation is attributed to the reconstructed
 body masses of each ancestor. When the effects of body size are adjusted,
 the period of accelerated trait accumulation is replaced by a more
 gradual, additive process. Our results indicate that even at low
 proportions of variance, body size can noticeably effect macroevolutionary
 hypotheses generated from ordinated morphospaces. Future studies should
 thoroughly explore the nature of their character data in association with
 PCoA-based morphospaces and use a residual/covariate approach to account
 for potential correlations with body size.
DOI: 10.5061/dryad.ngf1vhhqw
title: Distinct DNA methylation signatures in neuroendocrine tumors specific for primary site and inherited predisposition

description: Purpose: To compare the deoxyribonucleic acid (DNA) methylation signature
 of neuroendocrine tumors (NETs) by primary tumor site and inherited
 predisposition syndromes von Hippel–Lindau disease (VHL) and multiple
 endocrine neoplasia type 1 (MEN1). Methods Genome-wide DNA methylation
 (835 424 CpGs) of 96 NET samples. Principal components analysis (PCA) and
 unsupervised hierarchical clustering analyses were used to determine DNA
 methylome signatures. Results: Hypomethylated CpGs were significantly more
 common in VHL-related versus sporadic and MEN1-related NETs (P
 &lt; .001 for both comparisons). Small-intestinal NETs (SINETs)
 had the most differentially methylated CpGs, either hyper- or
 hypomethylated, followed by duodenal NETs (DNETs) and pancreatic NETs
 (PNETs, P &lt; .001 for all comparisons). There was complete
 separation of SINETs on PCA, and 3 NETs of unknown origin clustered with
 the SINET samples. Sporadic, VHL-related, and MEN1-related PNETs formed
 distinct groups on PCA, and VHL clustered separately, showing pronounced
 DNA hypomethylation, while sporadic and MEN1-related NETs clustered
 together. MEN1-related PNETs, DNETs, and gastric NETs each had a distinct
 DNA methylome signature, with complete separation by PCA and unsupervised
 clustering. Finally, we identified 12 hypermethylated CpGs in the 1A
 promoter of the APC (adenomatous polyposis coli) gene, with higher
 methylation levels in MEN1-related NETs versus VHL-related and sporadic
 NETs (P &lt; .001 for both comparisons). Conclusions: DNA CpG
 methylation profiles are unique in different primary NET types even when
 occurring in MEN1-related NETs. This tumor DNA methylome signature may be
 utilized for noninvasive molecular characterization of NETs, through DNA
 methylation profiling of biopsy samples or even circulating tumor DNA in
 the near future.
DOI: 10.5061/dryad.qz612jmbd
title: Data from: Experimental evidence for accelerated adaptation to desiccation through sexual selection on males

description: The impact of sexual selection on the adaptive process remains unclear. On
 the one hand, sexual selection might hinder adaptation by favouring costly
 traits and preferences that reduce nonsexual fitness. On the other hand,
 condition dependence of success in sexual selection may accelerate
 adaptation. Here, we used replicate populations of Drosophila melanogaster
 to artificially select on male desiccation resistance while manipulating
 the opportunity for precopulatory sexual selection in a factorial design.
 Following five generations of artificial selection, we measured the
 desiccation resistance of males and females to test whether the addition
 of sexual selection accelerated adaptation. We found a significant
 interaction between the effects of natural selection and sexual selection:
 desiccation resistance was highest in populations where sexual selection
 was allowed to operate. Despite only selecting on males, we also found a
 response in females. These results provide empirical support for the idea
 that sexual selection can accelerate the rate of adaptation.
description: Dataset was collected through observational and qualitative
 methods (see manuscript for details). It was processed through Excel and R
 Studio.
DOI: 10.5061/dryad.15dv41ntz
title: Screening and microsatellite data for Varroa infesting resistant honey bee pupae

description: We investigated how the evolution of host resistance could affect the
 infesting population of Varroa mites. We screened a Varroa-resistant honey
 bee population near Toulouse, France, for a Varroa resistance trait: the
 inhibition of Varroa's reproduction in drone pupae. We then genotyped
 Varroa which had co-infested a cell using microsatellites. Across all
 resistant honey bee colonies, Varroa's reproductive success was
 significantly higher in co-infested cells but the distribution of Varroa
 between singly and multiply infested cells was not different from random.
 While there was a trend for increased reproductive success when Varroa of
 differing haplotypes co-infested a cell, this was not significant. This
 dataset may be useful to anybody interested in the evolution of
 host-resistance on the parasitic mite Varroa destructor. There were no
 legal or ethical considerations associated with this study.
DOI: 10.5061/dryad.gmsbcc2jk
title: Differential ESR1 promoter Methylation in the peripheral blood of healthy middle-aged and older women- findings from the women 40+ healthy aging study

description: Background Estrogen receptor alpha (ERα) contributes to maintain
 biological processes preserving health during aging. DNA methylation
 changes of ERα gene (ESR1) were established as playing a direct role in
 the regulation of ERα levels. In this study, we hypothesized decreased DNA
 methylation of ESR1 associated with postmenopause, lower estradiol levels
 and increased age among healthy middle-aged and older women. Methods We
 assessed DNA methylation of ESR1 promoter region from dried blood spots
 and estradiol from saliva samples, among 130 healthy women aged 40-73
 years. Results We found that postmenopause and lower estradiol levels were
 associated with lower DNA methylation of a distal regulatory region, but
 not with DNA methylation of proximal promoters. Conclusion Our results
 indicate possible adaptive changes of ESR1 methylation in women healthy
 aging.
DOI: 10.5061/dryad.j3tx95x9m
title: Maintenance of variation in virulence and reproduction in populations of an agricultural plant pathogen

description: Genetic diversity within pathogen populations is critically important for
 predicting pathogen evolution, disease outcomes, and prevalence. However,
 we lack a good understanding of the processes maintaining genetic
 variation and constraints on pathogen life‐history
 evolution. Here, we analyzed interactions between 12
 wheat host genotypes and 145 strains of Zymoseptoria
 tritici from five global populations to investigate the evolution
 and maintenance of variation in pathogen virulence
 and reproduction. We found a strong positive correlation between
 virulence (amount of leaf necrosis) and reproduction (pycnidia density
 within lesions), with substantial variation in both traits maintained
 within populations. On average, highly virulent isolates exhibited higher
 reproduction, which might increase transmission potential in agricultural
 fields planted to homogeneous hosts at a high density. We further showed
 that pathogen strains with a narrow host range (i.e. specialists) for
 reproduction were on average less virulent, and those with a broader host
 range (i.e. generalists) were on average less fecund on a given specific
 host. These costs associated with adaptation to different host
 genotypes might constrain the emergence of generalists by disrupting the
 directional evolution of virulence and fecundity. We conclude that
 selection favoring pathogen strains that are virulent across diverse
 hosts, coupled with selection that maximizes fecundity on
 specific hosts, may explain the maintenance of these
 pathogenicity traits within and among populations.
DOI: 10.15468/dl.cc5mq5
title: Occurrence Download

description: A dataset containing 583 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Nototodarus sloanii",
 "HasCoordinate is true",
 "DecimalLatitude is greater than -90",
 "DecimalLatitude is less than 90",
 "DecimalLongitude is greater than -180",
 "OccurrenceStatus is Present",
 "Year is greater than or equal to 2015"
 ]
}

 The dataset includes 583 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002327-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.pzgmsbch2
title: Using real-time UV-visible spectrophotometer to assess an Al-Zn-Mg-Cu alloy’s dissolution in acidic solution

description: Applicability and limitations of using online non-destructive UV-vis
 spectrophotometer to monitor the dissolution of an Al-Zn-Mg-Cu alloy in
 HCl-containing solution were studied. ICP-AES results indicate that the
 spectrum absorbance at 252 nm is mainly attributed to Cu-containing
 complexes. Surprisingly, an hours-long “induction” period was observed
 from UV-vis results. This is not a real indicator of induction for Al
 dissolution as revealed by electrochemical impedance spectrum, actually it
 reflects the alloy's galvanic corrosion nature that Cu species are
 released after Al, Zn, Mg species.
DOI: 10.5061/dryad.qnk98sfcv
title: Patient or family perceived deterioration in functional status and outcome after Intensive Care admission: a retrospective cohort analysis of routinely collected data

description: Objective: To explore the association of patient or family reported
 functional deterioration (defined by a single question) in the preceding
 year, with mortality outcome for those admitted to the Intensive Care Unit
 (ICU).   Design: Retrospective observational analysis of a
 routinely collected data source.   Participants: Patients that
 were admitted to the ICU at Northwick Park Hospital, London North West
 University Healthcare NHS Trust between 1/10/2017 to 15/6/2019 were
 included. Patients were excluded if they had a prior ICU admission during
 the existing hospital episode or if information on functional
 deterioration could not be retrieved from either the patient or their
 advocate.   Primary Outcomes: Mortality at the point of hospital
 discharge and 1 year following admission to the ICU.   Results:
 Of the 1006 patients who were admitted to the ICU during the study period,
 information on functional deterioration was available for 621 patients who
 were included in the analysis. From these, 251 (40.4%) patients had
 patient or family reported functional deterioration in the preceding year,
 whilst 370 (59.6%) patients had a perceived stable functional baseline.
 Comparing the two groups, mortality was significantly higher in those who
 had functionally deteriorated compared to those with stable baseline
 function, at the point of hospital discharge (45.4% versus 25.9%;
 P&lt;0.0001) and at 1 year (59.4% versus 33.0%;
 P&lt;0.0001).    Conclusion: Patient or family
 reported functional deterioration was significantly associated with higher
 mortality at the point of hospital discharge and at 1 year. The concept of
 functional deterioration in the lead up to ICU admission warrants further
 exploration.
description: Data was collected from routine data sources that comprise of
 clinical records and local audit data submitted for the Intensive Care
 Audit and Research Centre (ICNARC) Case Mix Programme (CMP)
description: Routine data sources of all patients admitted to ICU during study
 time period. This data also includes those who were excluded from analysis
 (including patients where functional deteriroation wasn't known and
 patients who were ICU readmissions during the study period).
 We have removed identifiers from this dataset such as hospital
 admission dates, general demographic data, and other associated social
 data.
DOI: 10.5061/dryad.msbcc2fvh
title: Complex biotic interactions mediated by shrubs: revisiting the stress-gradient hypothesis and consequences for tree seedling survival

description: 1. Using nurse shrubs to improve tree seedling establishment in stressed
 environments is a common practice in forestry. Recent refinements of the
 stress-gradient hypothesis suggest that positive nurse effects occur under
 intermediate stress and decline in the harshest conditions. Additionally,
 indirect facilitation is expected in low-stressed/productive systems
 according to the initial stress-gradient hypothesis. However, there have
 been fewer investigations into the use of nurse shrubs to decrease
 herbivore impacts in stressed systems compared with the role of nurses on
 stress alleviation. This raises the need to clarify conditions in which
 the use of nurse shrubs would be most appropriate. 2. We conducted a field
 experiment in the sand dune forest of southwest France characterised by
 severe summer water shortages and the presence of different types of wild
 herbivores. In 2015 and 2016, Pinus pinaster seedlings were planted under
 shrubs (Arbutus unedo) or in shrub-removed locations, in fenced/unfenced
 areas. Survival, cause of mortality, and water stress were monitored for
 one year after plantation. 3. Summer drought was the main cause of
 mortality. Water stress increased in both years as summer progressed. We
 found direct facilitation only in July 2016 at intermediate water stress,
 due to a decrease in vapour pressure deficit under shrubs. These positive
 effects declined in late summer when stress was at a maximum. Rodent
 damage occurred under shrubs in spring whereas ungulate browsing was
 observed in open areas in autumn/winter. Overall seedling survival was
 equivalent under or outside shrubs during the first year, but was better
 under shrubs in the second one. 4. Synthesis and applications: Our results
 partially validate the refinement of the stress-gradient
 hypothesis, with a decline of positive interactions in the most
 water-stressed conditions. This draws attention to the difficulty of using
 shrubs as nurses to improve tree regeneration in the most xeric systems.
 In addition, we show that indirect associational effects, both positive
 and negative, could be as important as abiotic stress alleviation in a
 stressful ecosystem, and using shrubs to facilitate seedling survival
 could be efficient depending on the type of herbivore involved. This
 highlights the fact that considering plant-plant interactions can help in
 the design of management options, providing that up-to-date ecological
 theories are considered and that the different biotic and abiotic
 constraints are accurately evaluated.
DOI: 10.15468/dl.5yz8tb
title: Occurrence Download

description: A dataset containing 484 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Antopetitia abyssinica",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 484 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002328-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.2.31892.97926
title: Pearlman on DSS.pdf
DOI: 10.5061/dryad.1ns1rn8qt
title: Data from: Genome assembly of the ragweed leaf beetle, a step forward to better predict rapid evolution of a weed biocontrol agent to environmental novelties

description: Rapid evolution of weed biological control agents (BCAs) to new biotic and
 abiotic conditions is poorly understood and so far, only little considered
 both in pre-release and post-release studies, despite potential major
 negative or positive implications for risks of non-targeted attacks or for
 colonizing yet unsuitable habitats, respectively. Provision of genetic
 resources, such as assembled and annotated genomes, is essential to assess
 potential adaptive processes by identifying underlying genetic mechanisms.
 Here, we provide the first sequenced genome of a phytophagous insect used
 as a BCA, i.e. the leaf beetle Ophraella communa, a promising BCA of
 common ragweed, recently and accidentally introduced into Europe. A total
 33.98 Gb of raw DNA sequences, representing c. 43-fold coverage, were
 obtained using the PacBio SMRT-Cell sequencing approach. Among the five
 different assemblers tested, the SMARTdenovo assembly displaying the best
 scores was then corrected with Illumina short reads. A final genome of 774
 Mb containing 7,003 scaffolds was obtained. The reliability of the final
 assembly was then assessed by benchmarking universal single-copy
 orthologous genes (&gt; 96.0% of the 1,658 expected insect genes) and
 by remapping tests of Illumina short reads (average of 98.6% ± 0.7%
 without filtering). The number of protein-coding genes of 75,642,
 representing 82% of the published antennal transcriptome, and the
 phylogenetic analyses based on 825 orthologous genes placing O. communa in
 the monophyletic group of Chrysomelidae, confirm the relevance of our
 genome assembly. Overall, the genome provides a valuable resource for
 studying potential risks and benefits of this BCA facing environmental
 novelties.
description: Proteome and annotation
 files The
 "GenePrediction_Ophraella_communa_Augustus.aa" (fasta format)
 contains the 75,642 protein-coding genes predicted with Augustus (v3.2.3),
 using parameters “--gff3=on --species=tribolium2012”. The preliminary
 annotation of each 75,642 predicted proteins, performed with Pannzer2, is
 described in the "Annotation_Ophraella_communa.out" file (text
 format). Details of the meaning of columns are provided on the Pannzer2
 website (http://ekhidna2.biocenter.helsinki.fi/sanspanz/). An interactive
 html file can be generated using the command line below. <pre class="moz-quote-pre"> perl anno2html.pl &lt;
 Annotation_Ophraella_communa.out &gt;
 Annotation_Ophraella_communa.html </pre>