cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h9w0vt4tx
title: Structural basis for negative regulation of ABA signaling by ROP11 GTPase

description: Abscisic acid (ABA) is an essential plant hormone responsible for plant
 development and stress responses. Recent structural and biochemical
 studies have identified the key components involved in ABA signaling
 cascade, including PYR/PYL/RCAR receptors, protein phosphatases PP2C, and
 protein kinases SnRK2. The plant-specific, Roh-like (ROPs) small GTPases
 are negative regulators of ABA signal transduction by interacting with
 PP2C, which can shut off “leaky” ABA signal transduction caused by
 constitutive activity of monomeric PYR/PYL/RCAR receptors. However, the
 structural basis for negative regulation of ABA signaling by ROP GTPases
 remain elusive. In this study, we have utilized large-scale coarse-grained
 (10.05 milliseconds) and all-atom molecular dynamics simulations and
 standard protein-protein binding free energy calculations to predict the
 complex structure of AtROP11 and phosphatase AtABI1. In addition, we have
 elucidated the detailed complex association pathway and identified the
 critical residue pairs in AtROP11 and AtABI1 for complex stability.
 Overall, this study has established a powerful framework of using
 large-scale molecular simulations to predict unknown protein complex
 structures and elucidated the molecular mechanism of  negative
 regulation of ABA signal transduction by small GTPases.
description: # Structural basis for negative regulation of ABA signaling by ROP11
 GTPase Dataset DOI: [10.5061/dryad.h9w0vt4tx](10.5061/dryad.h9w0vt4tx) ##
 Description of the data and file structure ### Files and variables ####
 File: clustering\_tica\_600\_mapped.pkl **Description:** Pickle file
 containing time-lagged independent component analysis (tICA)
 representation of the normalized features. The clustering was performed
 with KMeans clustering with 600 clusters and 4 tICA dimensions. #### File:
 msm800.pkl **Description:** Pickle file containing the Markov state model
 (MSM) object, constructed from clustered tICA. The MSM was created with
 600 clusters, 4 tICA dimensions and a lag-time of 800ns. #### File:
 features\_normalized.npy **Description:** Numpy file containing normalized
 features used to construct tICA. #### File: features\_raw\.npy
 **Description:** Numpy file containing raw features consisting of 1
 centre-of-mass distance and 5 dihedral angles.
DOI: 10.15468/dl.yjrfk2
title: Occurrence Download

description: A dataset containing 1083515 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Engraulis ringens",
 "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 1083515 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004273-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g29t5a
title: Occurrence Download

description: A dataset containing 30 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Ecuador",
 "Geometry POLYGON((-80.52439 -2.80359,-77.562 -2.80359,-77.562 0.64173,-80.52439 0.64173,-80.52439 -2.80359))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Lemna"
 ]
}

 The dataset includes 30 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004292-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7h44j105w
title: Data from: A point mutation in an otherwise dispensable upstream Fshb enhancer moderately impairs fertility in female mice

description: Follicle-stimulating hormone (FSH) is necessary for fertility in both
 sexes as a regulator of gametogenesis and hormone synthesis. Humans with
 loss-of-function mutations within the gene encoding the FSH beta subunit
 (FSHB) are infertile. Similarly, female Fshb knock-out mice are infertile
 and fail to ovulate, and males are subfertile. We recently reported the
 discovery and characterization of an upstream enhancer of FSHB located 26
 Kb upstream of the transcriptional start site in humans (-17 Kb in mouse)
 that also amplifies activin and gonadotropin-releasing hormone induction
 of FSHB. Notably, the upstream enhancer contains a polymorphic,
 fertility-associated site in humans, rs11031006 (G/A), and the minor
 allele (A) increased enhancer activity in vitro as compared to the major
 allele (G), likely by increasing the affinity of an SF1 binding element.
 To investigate the role of the novel enhancer and rs11031006 variant in
 vivo, we created mouse models to assess deletion of the upstream enhancer
 and the impact of the G&gt;A point mutation at the
 rs11031006-equivalent base. A full characterization of the -17 Kb enhancer
 deletion model revealed no apparent differences in fertility or serum
 FSH/LH levels, nor did a larger deletion that also included an additional
 putative regulatory element. In contrast, female mice homozygous for the
 mutated A allele at the rs11031006-equivalent position had fewer litters
 over a 120-day fertility assay, abnormal estrous cycling at 10 months, and
 reduced pituitary Lhb transcript abundance. Overall, while the mouse -17
 Kb Fshb enhancer is dispensable for fertility, the rs11031006-equivalent
 G&gt;A mutation results in subfertility in females.
description: # Fertility is impaired by a point mutation in an upstream Fshb enhancer
 in female mice Dataset DOI:
 [10.5061/dryad.7h44j105w](10.5061/dryad.7h44j105w) ## Description of the
 data and file structure In this study, we created mouse models to evaluate
 the role of the -17 Kb *Fshb* enhancer and the rs11031006 variant.
 Overall, we evaluated reproduction in three mouselines: FshbeΔ777: 777 bp
 deletion encompassing the enhancer region located 17 Kb upstream of the
 *Fshb* TSS (chr2:107,076,836-107,077,614, mm10). FshbeΔ6kb: A 6 Kb
 deletion including the enhancer at 17 Kb and the C2 element at 12 Kb
 (deletion of chr2:107,071,698-107,078,356, mm10). SNP06_G&gt;A: G&gt;A
 point mutation at the genomic position equivalent to the human
 rs11031006(G/A) single nucleotide polymorphism (chr2:107,077,053, mm10).
 ### Files and variables #### File: Supplemental\_Dryad.pdf
 **Description:** Graphical representations of data. All data necessary to
 support the research findings in this supplement are included here. ##
 Code/software Any PDF viewer.
DOI: 10.5281/zenodo.18407741
title: SuperDARN data in netCDF format (2006-Dec)

description: 2006-Dec SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5281/zenodo.6631255
title: SuperDARN data in netCDF format (2006-Dec)

description: 2006-Dec SuperDARN radar data in netCDF format. These files were produced using version 3.0 of the public FitACF algorithm, using the AACGM v2 coordinate system. Cite this dataset if using our data in a publication.


The RST is available here: https://github.com/SuperDARN/rst



The research enabled by SuperDARN is due to the efforts of teams of scientists and engineers working in many countries to build and operate radars, process data and provide access, develop and improve data products, and assist users in interpretation.
Users of SuperDARN data and data products are asked to acknowledge this support in presentations and publications.
A brief statement on how to acknowledge use of SuperDARN data is provided below.




Users are also asked to consult with a SuperDARN PI prior to submission of work intended for publication.
A listing of radars and PIs with contact information can be found here:
(SuperDARN Radar Overview)



Recommended form of acknowledgement for the use of SuperDARN data:



'The authors acknowledge the use of SuperDARN data. SuperDARN is a collection of radars funded by national scientific funding agencies of Australia, Canada, China, France, Italy, Japan, Norway, South Africa, United Kingdom and the United States of America.'
DOI: 10.5061/dryad.59zw3r2kj
title: It’s not fur: newspaper article reporting of abandonment and relinquishment of pets exhibit taxonomic biases in framing and language use

description: Animal domestication and companionship hold cultural and economic
 significance, but there are downsides to the practice, too, including the
 relinquishment and/or abandonment of animals (cessation of ownership). As
 such, the topic attracts a great deal of media coverage. However, we
 expect biases exist in the amount and nature of coverage different animal
 species receive, informing our views on the relative scale and importance
 of ownership cessation in different taxa. We systematically searched
 English language newspaper articles about cessation of ownership of pets
 in the UK, to test whether major pet groups (cats and dogs; traditionally
 kept small mammals; reptiles and amphibians) differ in the number of
 newspaper article reports, framing, and language use. Significant
 variation was observed, with a greater number of articles focused on cats
 and dogs. Reptiles and amphibians received less coverage and were framed
 more negatively. Popular newspaper articles write about reptiles and
 amphibians in a way that is consistent with ‘othering,’ i.e., using words
 that insult, exclude, or dismiss another group. This trend may have
 important implications for public perceptions of the taxon, and any
 perceived lack of worth of a given taxon may feed into the support for
 interventions and policies aiming to optimise their welfare.
description: # It’s not fur: newspaper article reporting of abandonment and
 relinquishment of pets exhibit taxonomic biases in framing and language
 use Dataset DOI: [10.5061/dryad.59zw3r2kj](10.5061/dryad.59zw3r2kj) ##
 Description of the data and file structure Dataset underlying the
 presented analyses. ### Files and variables #### File:
 Supplementary_Info_File_1.docx **Description:** Example articles'
 framings. #### File: Supplementary_Info_File_2.csv
 **Description:** Dataset of articles included in analyses. This version
 does contain the main article text and is hosted on Zenodo.
 **Supplementary_Info_File_2.1_dryad.csv** This file does not contain the
 main text of the articles. This is so that it is compliant with
 Dryad's CC0 policy. ##### Variables General - dummy variable to score
 articles framed in a general (thematic) structure. Taxon focus - dummy
 variable to score articles framed in a taxon-focused (thematic) structure.
 Individual - dummy variable to score articles framed in an individual
 (episodic) structure. cat_dog - dummy variable coding for this taxon.
 small_furry - dummy variable coding for this taxon. herp - dummy variable
 coding for this taxon. pubdate - publication date of the article 
 DocumentURL - link to article ## Code/software N/A ## Access information
 Data was derived from the following sources: * Newspaper articles via
 Proquest.
DOI: 10.5061/dryad.mw6m9067k
title: Data for: Positive feedback on climate warming by stream microbial decomposers indicated by a global space-for-time substitution study

description: Decomposition of plant litter is a key ecological process in streams,
 whose contribution to the global carbon cycle is large relative to their
 extent on Earth. We examined the mechanisms underlying the temperature
 sensitivity (TS) of instream decomposition and forecast effects of climate
 warming on this process. Comparing data from 41 globally distributed
 sites, we assessed the TS of microbial and total decomposition using
 litter of nine plant species combined in six mixtures. Microbial
 decomposition con- formed to the metabolic theory of ecology and its TS
 was consistently higher than that of total decomposition, which was higher
 than found previously. Litter quality influenced the difference between
 microbial and total decomposition, with total decompo- sition of more
 recalcitrant litter being more sensitive to temperature. Our projections
 suggest that (i) warming will enhance the microbial contribution to
 decomposition, increasing CO2 outgassing and intensifying the warming
 trend, especially in colder regions; and (ii) riparian species composition
 will have a major influence on this process.
description: ## Dataset of Pérez Boyero et al. 2025 GCB article: Positive Feedback on
 Climate Warming by StreamMicrobial Decomposers Indicated by a
 GlobalSpace-For-Time Substitution Study Link to a read-only copy of the
 study:
 [https://onlinelibrary.wiley.com/share/author/ZMPU2PNUUHMSBCEMUS7P?target=10.1111/gcb.70171](https://onlinelibrary.wiley.com/share/author/ZMPU2PNUUHMSBCEMUS7P?target=10.1111/gcb.70171) Link to the online version of the study: [https://onlinelibrary.wiley.com/doi/full/10.1111/gcb.70171](https://onlinelibrary.wiley.com/doi/full/10.1111/gcb.70171) Link to the supplementary information: [https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111%2Fgcb.70171&file=gcb70171-sup-0001-Supinfo.pdf](https://onlinelibrary.wiley.com/action/downloadSupplement?doi=10.1111%2Fgcb.70171&file=gcb70171-sup-0001-Supinfo.pdf) [https://doi.org/10.5061/dryad.mw6m9067k](https://doi.org/10.5061/dryad.mw6m9067k) Main dataset of the mentioned GCB article ## Description of the data and file structure The dataset contains: * "raw decomposition data" (decomposition rates in terms of time, units: d-1 & in terms of accumulated heat, units dd-1) of each litterbag x litter specie combination in the 41 studied sites. * "mean decomposition data" includes mean values and standard errors of the raw decomposition rates. This dataset also provide some data transformation. * In both datasets there is some relevant environmental accompanying variables such as Latitude, mean water temperature... * "Codes" and "Region info" must be considered as legends in order to connect provided dataset with information on the referenced study. ## Sharing/Access information As stated in the original study, any other required information are available from the corresponding author upon reasonable request. ## Code/Software NA
DOI: 10.15468/dl.jg2mb2
title: Occurrence Download

description: A dataset containing 11 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Etrumeus whiteheadi",
 "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 11 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004295-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.2au3k8
title: Occurrence Download

description: A dataset containing 59 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Floridosentis mugilis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 59 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004296-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.05qfttfds
title: Data from: Loss of pigments in females is associated with sexual dichromatism in an ornamental trait

description: Sexual dichromatism is thought to evolve primarily as a function of sexual
 selection, especially female choice. However other forces, from
 sex-specific environmental conditions to social signaling in females, can
 also generate color differences between sexes. We studied dewlap
 dichromatism across 292 species of Anolis lizards. Dewlaps are colorful
 throat ornaments found on males of most anole species but are also present
 in females in many species. Although male and female dewlaps often have
 similar coloration, in some species they are strikingly dichromatic. We
 found that ornament color is labile and that dichromatism results from the
 loss of costly pigments in females. This pattern could indicate a shift
 towards signal loss in females; however, the secondary gains of female
 dewlaps across the phylogeny suggest a potential advantageous function.
 Possible mechanisms for female dewlap coloration include social selection,
 non-sexual signaling, or detectability in different microhabitats (e.g.,
 sensory drive). Female dewlap color overlap between co-occurring species
 is both less than expected by chance overall and reduced in species-rich
 communities, suggesting that dichromatism could be driven by competition.
 Our results highlight that selection on females drives the observed
 pattern of dichromatism, suggesting a potentially adaptive role for female
 ornaments and emphasizing the need for additional work to understand
 female ornament evolution.
description: # Loss of pigments in females is associated with sexual dichromatism in an
 ornamental trait Dataset DOI:
 [10.5061/dryad.05qfttfds](10.5061/dryad.05qfttfds) ## Description of the
 data and file structure Data relating to Westeen et al. Loss of
 pigmentation in females is associated with sexual dichromatism in an
 ornamental trait. Dewlap data for all species of anoles collected for this
 study (N = 339). Cells were left blank if values were not determined. ###
 Files and variables #### File: data.csv **Description:**  ##### Variables
 * Genus = genus - Species = species * Fauna = anole fauna to which the
 species belongs: GA = Greater Antillean, Dactyloa, and Draconura - mSVL =
 male snout-vent length in mm * fSVL = female snout-vent length in mm - SSD
 = sexual size dimorphism as ((male SVL /female SVL)-1) * mDewlap = male
 dewlap state: no, rudimentary, yes - fDewlap = female dewlap state: no,
 rudimentary, yes * mColor: colors present in male dewlap, categorical -
 mCarot: male dewlap contains carotenoid pigments, -1 = no dewlap, 0 = no
 carotenoids, 1 = carotentoids * fColor: colors present in female dewlap,
 categorical; NA = no female dewlap - fCarot: female dewlap contains
 carotenoid pigments, -1 = no dewlap, 0 = no carotenoids, 1 = carotentoids
 * ColorDimorphism: 1 = one sex missing dewlap (structurally dimorphic), 0
 = monochromatic, 1 = dichromatic
DOI: 10.5061/dryad.g1jwstr32
title: Mycorrhiza: Saprotroph interactions and carbon cycling in the rhizosphere

description: Labile carbon (C) inputs in soils are expected to increase in the future
 due to global change drivers such as elevated atmospheric
 CO2 concentrations or warming and potential increases in plant
 primary productivity. However, the role of mycorrhizal association in
 modulating microbial activity and soil organic matter (SOM)
 biogeochemistry responses to increasing below-ground C inputs remains
 unclear. We employed 18O–H2O quantitative stable isotope probing to
 investigate the effects of synthetic root exudate addition (0, 250, 500,
 and 1000 µg C g soil-1) on bacterial growth traits and SOM biogeochemistry
 in rhizosphere soils of trees associated with arbuscular mycorrhizal (AM)
 and ectomycorrhizal (ECM) fungi. Soil respiration increased proportionally
 to the amount of exudate addition in both AM and ECM soils. However,
 microbial biomass C (MBC) responses differed, increasing in AM and
 decreasing in ECM soils. In AM soils, exudate addition increased
 taxon-specific and community-wide relative growth rates of bacteria
 leading to enhanced biomass production. Conversely, in ECM soils, relative
 growth rates were less responsive to exudate addition, and estimates of
 MBC mortality increased with increasing exudate addition. In the AM soils,
 aggregated bacterial growth traits were predictive of soil respiration but
 this relationship was not observed in ECM soils, perhaps due to
 substantial MBC mortality. These findings highlight the distinct responses
 of bacterial communities in AM and ECM rhizosphere soils to exudate
 addition. Considering that microbial products contribute to the formation
 of stable soil organic carbon (SOC) pools, future increases in labile
 exudate release in response to global change may consequently lead to
 greater SOC gains in AM soils compared ECM soils.
description: # Mycorrhiza: Saprotroph interactions and carbon cycling in the
 rhizosphere Dataset DOI:
 [10.5061/dryad.g1jwstr32](10.5061/dryad.g1jwstr32) ## Description of the
 data and file structure The first sheet in 'Data.xlsx' presents
 taxon-specific mean weighted average density (WAD) of unlabeled samples
 (t₀ samples), WAD of labeled samples (¹⁸O-labeled t₅ samples), ¹⁸O excess
 atom fraction (EAF), relative growth rate (RGR, 5 days⁻¹), and new biomass
 production (NBi, mg C g⁻¹ soil 5 days⁻¹). The data are organized by
 taxonomy (at the genus level), sample, plot, mycorrhizal association
 (arbuscular mycorrhizal (AM) and ectomycorrhizal (ECM)), and exudate input
 levels (μg C g⁻¹ soil). The second sheet provides data on soil respiration
 (mmol CO₂ g⁻¹ day⁻¹), microbial biomass carbon (MBC, mg C g⁻¹ soil), and
 the community-weighted mean (CWM) of relative growth rates (5 days⁻¹) and
 new MBC production (mg C g⁻¹ soil), categorized by sample, plot,
 mycorrhizal association, and exudate input levels.
DOI: 10.15468/dl.437c3z
title: Occurrence Download

description: A dataset containing 108 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Cisthene conjuncta"
 ]
}

 The dataset includes 108 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0004297-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.