cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d40s45p
title: Data from: Fast formation of a supramolecular ion gel/solvoplastic elastomer with excellent stretchability

description: This study describes a simple yet efficient approach for the preparation
 of an ionic gel that is also elastomeric in its solid state bulk form. A
 series of poly(2-(Diethylamino)ethyl methacrylate-co-Lauryl methacrylate)
 P(DMAEMA-co-LMA) copolymer were synthesized first by radical
 polymerization. Quaternization of the PDMAEMA component in THF enables the
 formation of supramolecular network, gave rise to an ion gel. An elastomer
 with an elongation at break of over 600 % was obtained from the gel. The
 elastomer, connected by supramolecular ionic crosslinks, is solvoplastic
 in certain solvent. The simple yet efficient approach of the formation of
 ion-gel and the dried elastomer allows fast preparation of both gel-like
 and solid-state elastic materials for various applications where
 recyclability are required.
description: Raw data of GPC, IR and
 Tensile
DOI: 10.5061/dryad.1f2c124
title: Data from: Mutualists stabilize coexistence of congeneric legumes

description: Coexistence requires that stabilizing niche differences, which cause
 species to limit themselves more than others, outweigh relative fitness
 differences that cause competitive exclusion. Interactions with shared
 mutualists, which can differentially affect host fitness and change in
 magnitude with host frequency, can satisfy these conditions for
 coexistence, yet empirical tests of mutualist effects on relative fitness
 and stabilizing niche differences are largely lacking within the framework
 of coexistence theory. Here, we show that N-fixing rhizobial mutualists
 mediate coexistence in four naturally co-occurring, congeneric legume
 (Trifolium) species. Using experimental greenhouse communities, we
 quantified relative fitness and stabilizing niche differences for each
 species in the presence of rhizobia originating from conspecific or
 congeneric hosts. Rhizobia stabilized coexistence by increasing
 self-limitation of Trifolium species grown with conspecific rhizobia, thus
 allowing congeners to increase when rare. Greenhouse-measured invasion
 growth rates predicted natural, unmanipulated coexistence dynamics of
 Trifolium species over two years in our field sites. Our results
 demonstrate that interactions with shared mutualists can stabilize
 coexistence of closely related species.
description: Greenhouse experiment
 community biomass datacommunity_data_v2.csvGreenhouse experiment neighborhood dataIndividual biomass, trait, and neighborhood composition for Trifolium greenhouse experimentneighborhood_data_seed2.csvField survey dataEstimate density (individuals per square meter) of Trifolium species in 2x2-m field plots at Bodega Marine Reserve, CA, 2015-20162015_2016_plot_tri_density.csv
DOI: 10.5061/dryad.1176k
title: Data from: Integrating viscoelastic mass spring dampers into position-based dynamics to simulate soft tissue deformation in real time

description: We propose a novel method to simulate soft tissue deformation for virtual
 surgery applications. The method considers the mechanical properties of
 soft tissue, such as its viscoelasticity, nonlinearity, and
 incompressibility; its speed, stability, and accuracy also meet the
 requirements for a surgery simulator. Modifying the traditional equation
 for mass spring dampers introduces nonlinearity and viscoelasticity into
 the calculation of elastic force. Then, the elastic force is used in the
 constraint projection step for naturally reducing constraint potential.
 The node position is enforced by the combined spring force and constraint
 conservative force through Newton’s second law. We conduct a comparison
 study of conventional mass spring dampers and position based dynamics
 (PBD) for our new integrating method. Our approach enables stable, fast,
 and large step simulation by freely controlling visual effects based on
 nonlinearity, viscoelasticity and incompressibility. We implement a
 laparoscopic cholecystectomy simulator to demonstrate the practicality of
 our method, in which liver and gallbladder deformation can be simulated in
 real time. Our method is an appropriate choice for the development of
 real-time virtual surgery applications.
description: OpenDataThe Physic and Render Model of Liver Organ and Gallbladder Organ. Also, the program script run on the Unity3D 2017 Platform
DOI: 10.5061/dryad.b5c1f
title: Data from: How chimpanzees solve collective action problems

description: We presented small groups of chimpanzees with two collective action
 situations, in which action was necessary for reward but there was a
 disincentive for individuals to act due to the possibility of free-riding
 on the efforts of others. We found that in simpler scenarios (Experiment
 1) in which group size was small, there was a positive relationship
 between rank and action with more dominant individuals volunteering to act
 more often, particularly when the reward was less dispersed. Social
 tolerance also seemed to mediate action whereby higher tolerance levels
 within a group resulted in individuals of lower ranks sometimes acting and
 appropriating more of the reward. In more complex scenarios when group
 size was larger and cooperation was necessary (Experiment 2), overcoming
 the problem was more challenging. There was highly significant variability
 in the action rates of different individuals as well as between dyads
 suggesting success was more greatly influenced by the individual
 personalities and personal relationships present in the group.
description: Experiment1_CAP_resultsExperiment1_CAP__results.xlsxExperiment2_CAP__results
DOI: 10.5061/dryad.d96q7
title: Data from: Using genomic data to revisit a classic example of reproductive character displacement in Haitian Anolis lizards

description: The pattern of reproductive character displacement (RCD)—in which traits
 associated with reproductive isolation are more different where two
 species occur together than where they occur in isolation—is frequently
 attributed to reinforcement, a process during which natural selection
 acting against maladaptive mating events leads to enhanced prezygotic
 isolation between species or incipient species. One of the first studies
 of RCD to include molecular genetic data was described 40 years ago in a
 complex of Haitian trunk anole lizards using a small number of allozyme
 loci. In this example, Anolis caudalis appears to experience divergence in
 the color and pattern of an extensible throat fan, or dewlap, in areas of
 contact with closely related species at the northern and southern limits
 of its range. However, this case study has been largely overlooked for
 decades; meanwhile, explanations for geographic variation in dewlap color
 and pattern have focused primarily on adaptation to local signalling
 environments. We reinvestigate this example using amplified fragment
 length polymorphism (AFLP) genome scans, mtDNA sequence data, information
 on dewlap phenotypes and GIS data on environmental variation to test the
 hypothesis of RCD generated by reinforcement in Haitian trunk anoles.
 Together, our phenotypic and genetic results are consistent with RCD at
 the southern and northern limits of the range of A. caudalis. We evaluate
 the evidence for reinforcement as the explanation for RCD in Haitian trunk
 anoles, consider alternative explanations and provide suggestions for
 future work on the relationship between dewlap variation and speciation in
 Haitian trunk anoles.
description: 210LocusAFLP_with_outgroup821AFLP_MtDNA_combined_4part821LocusAFLP_with_outgroupgeoreferenced_climateClimate data extracted from BIOCLIM layers using geo-referenced locality data
DOI: 10.5061/dryad.ps8kr80
title: Data from: Genome-wide SNP analysis unveils genetic structure and phylogeographic history of snow sheep (Ovis nivicola) populations inhabiting the Verkhoyansk Mountains and Momsky Ridge (northeastern Siberia)

description: Insights into the genetic characteristics of a species provide important
 information for wildlife conservation programs. Here, we used the
 OvineSNP50 BeadChip developed for domestic sheep to examine population
 structure and evaluate genetic diversity of snow sheep (Ovis nivicola)
 inhabiting Verkhoyansk Range and Momsky Ridge. A total of 1121 polymorphic
 SNPs were used to test 80 specimens representing five populations,
 including four populations of the Verkhoyansk Mountain chain: Kharaulakh
 Ridge–Tiksi Bay (TIK, n = 22), Orulgan Ridge (ORU, n = 22), the central
 part of Verkhoyansk Range (VER, n = 15), Suntar-Khayata Ridge (SKH, n =
 13), and Momsky Ridge (MOM, n = 8). We showed that the studied populations
 were genetically structured according to a geographical pattern. Pairwise
 FST values ranged from 0.044 to 0.205. Admixture analysis identified K = 2
 as the most likely number of ancestral populations. A Neighbor-Net tree
 showed that TIK was an isolated group related to the main network through
 ORU. TreeMix analysis revealed that TIK and MOM originated from two
 different ancestral populations and detected gene flow from MOM to ORU.
 This was supported by the f3 statistic, which showed that ORU is an
 admixed population with TIK and MOM/SKH heritage. Genetic diversity in the
 studied groups was increasing southward. Minimum values of observed (Ho)
 and expected (He) heterozygosity and allelic richness (Ar) were observed
 in the most northern population–TIK, and maximum values were observed in
 the most southern population–SKH. Thus, our results revealed clear genetic
 structure in the studied populations of snow sheep and showed that TIK has
 a different origin from MOM, SKH and VER even though they are
 conventionally considered a single subspecies known as Yakut snow sheep
 (Ovis nivicola lydekkeri). Most likely, TIK was an isolated group during
 the late Pleistocene glaciations of Verkhoyansk Range.
description: Dotsev_et_al_Ovis_nivicola_SNPs_2018PLINK .ped file for Ovis nivicola SNP GenotypesDotsev_et_al_Ovis_nivicola_SNPs_2018_mapPLINK .map file for Ovis nivicola SNP GenotypesDotsev_et_al_Ovis_nivicola_SNPs_2018.mapSampling_sites_coordinatesExcel file with Ovis niviola sampling sites coordinates.
DOI: 10.5061/dryad.8c5n1
title: Data from: Costs of resistance and correlational selection in the multiple-herbivore community of Solanum carolinense

description: Although a central assumption of most plant-defense theories is that
 resistance is costly, fitness costs have proven difficult to detect in the
 field. One useful, though labor-intensive, method to detect costs is to
 quantify stabilizing selection acting on resistance in field populations.
 Here, we report on an experimental field study of Solanum carolinense in
 which we employed a quadratic phenotypic-selection analysis on 12 types of
 resistance (defined operationally as one minus the proportion of tissue
 damaged) involving nine species of herbivores. For seven types of
 resistance, we found significant stabilizing selection and intermediate
 optimum levels, indicating the existence of fitness costs. These costs
 were greatest for resistance against frugivores, moderate for florivores,
 and lowest for folivores. In addition, significant correlational selection
 gradients were found for ten pairs of resistance measures, which we
 interpret as evidence that the fitness impacts of these pairs of
 herbivores combined non-additively. When the herbivores fed on the same
 type of tissue, their impact was synergistic (greater than additive), and
 when they fed on different tissues, their impact was antagonistic (less
 than additive). We suggest this may be a general pattern for correlational
 selection on resistance to different herbivores.
description: Data used in quadratic
 selection analysisThis is an amended
 version of the data that were used to conduct the phenotypic selection
 analyses in this paper. It is an Excel file with columns not germane to
 these analyses removed.Data for
 Dryad.xlsx
DOI: 10.5061/dryad.mp0d5
title: Data from: Quantifying "apparent" impact and distinguishing impact from invasiveness in multispecies plant invasions

description: The quantification of invader impacts remains a major hurdle to
 understanding and managing invasions. Here, we demonstrate a method for
 quantifying the community-level impact of multiple plant invaders by
 applying Parker et al.'s (1999) equation (impact = range x local
 abundance x per capita effect or per unit effect) using data from 620
 survey plots from 31 grasslands across west-central Montana, USA. In
 testing for interactive effects of multiple invaders on native plant
 abundance (percent cover), we found no evidence for invasional meltdown or
 synergistic interactions for the 25 exotics tested. While much concern
 exists regarding impact thresholds, we also found little evidence for
 non-linear relationships between invader abundance and impacts. These
 results suggest that management actions that reduce invader abundance
 should reduce invader impacts monotonically in this system. Eleven of 25
 invaders had significant per unit impacts (negative local-scale
 relationships between invader and native cover). In decomposing the
 components of impact, we found that local invader abundance had a
 significant influence on the likelihood of impact but range (number of
 plots occupied) did not. This analysis helped to differentiate measures of
 invasiveness (local abundance and range) from impact to distinguish high
 impact invaders from invaders which exhibit negligible impacts, even when
 widespread. Distinguishing between high and low impact invaders should
 help refine trait-based prediction of problem species. Despite the unique
 information derived from evaluation of per unit effects of invaders,
 invasiveness scores based on range and local abundance produced similar
 rankings to impact scores that incorporated estimates of per unit effects.
 Hence, information on range and local abundance alone was sufficient to
 identify problematic plant invaders at the regional scale. In comparing
 empirical data on invader impacts to the state noxious weed list, we found
 that the noxious weed list captured 45% of the high-impact invaders but
 missed 55% and assigned the lowest risk category to the highest impact
 invader. While such subjective weed lists help to guide invasive species
 management, empirical data are needed to develop more comprehensive
 rankings of ecological impacts. Using weed lists to classify invaders for
 testing invasion theory is not well supported.
description: IMPACT
 DATAPlot level data from
 grassland surveys used for impact analyses.
DOI: 10.5281/zenodo.17429139
title: Merged E3SMv3 PPE, surrogate predictions, and coarsened reference data

description: E3SMv3 Autocalibration data including E3SMv3 simulations, E3SMv3 parameter values, surrogate model predictions, and observational/reanalysis data. The data are climatologies for four seasons (DJF, MAM, JJA, SON), or sometimes annual means (ANN). Surface field are defined on a lat x lon grid, while fields with a vertical dimension (lev) are zonally-averaged (lat x lev). Data are filled with "nan" if they are not defined for a given season or product. 

Variables include: 

RESTOM, dnet_cld_dir, SWCF, LWCF, PRECT, TREFHT, PSL, Z500, U850, U200, RELHUM, T, U, SWCRE_ano_grd_adj, LWCRE_ano_grd_adj, params.

Descriptions and units are found in the variable attributes. 

Data can be indexed by:

time = ["ANN", "DJF", "JJA", "MAM", "SON"], 

product = ["mod", "obs", "sur"]*,

*sur is shorthand for surrogate model,

input_param = ['clubb_c1', 'clubb_gamma_coef', 'zmconv_tau', 'zmconv_dmpdz',       'zmconv_micro_dcs', 'nucleate_ice_subgrid', 'p3_nc_autocon_expon',       'p3_qc_accret_expon', 'zmconv_auto_fac', 'zmconv_accr_fac', 'zmconv_ke',       'cldfrc_dp1', 'p3_embryonic_rain_size', 'p3_mincdnc'], 

and lat, lon, and lev. 

Model and surrogate data can also be indexed by the "workdir", i.e. a string name assigned to each simulation in the PPE:

workdir[ens_idx]: [..."ens/workdir.399/20230802.v3alpha02.F2010.pmcpu.intel.8N",     "ens/workdir.400/20230802.v3alpha02.F2010.pmcpu.intel.8N", "ctrl",     "L001", "L002", "L003", "H001", "H002", "H003"]

SWCRE_ano_grd_adj and LWCRE_ano_grd_adj are gridded shortwave cloud feedback and gridded longwave cloud feedback, respectively).

Upload version "v2" (January 26, 2026) is identical data to v1, but includes coordinates, units, and variable descriptions. 

Any errors or misrepresentations of the observational data as they were remapped from their native grids to the merged grid are the fault of the author. See references. 

This research used computing resources of the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility located at Lawrence Berkeley National Laboratory, operated under Contract No. DE-AC02-05CH11231, using the NERSC award to project E3SM.
DOI: 10.5281/zenodo.18381651
title: Merged E3SMv3 PPE, surrogate predictions, and coarsened reference data

description: E3SMv3 Autocalibration data including E3SMv3 simulations, E3SMv3 parameter values, surrogate model predictions, and observational/reanalysis data. The data are climatologies for four seasons (DJF, MAM, JJA, SON), or sometimes annual means (ANN). Surface field are defined on a lat x lon grid, while fields with a vertical dimension (lev) are zonally-averaged (lat x lev). Data are filled with "nan" if they are not defined for a given season or product. 

Variables include: 

RESTOM, dnet_cld_dir, SWCF, LWCF, PRECT, TREFHT, PSL, Z500, U850, U200, RELHUM, T, U, SWCRE_ano_grd_adj, LWCRE_ano_grd_adj, params.

Descriptions and units are found in the variable attributes. 

Data can be indexed by:

time = ["ANN", "DJF", "JJA", "MAM", "SON"], 

product = ["mod", "obs", "sur"]*,

*sur is shorthand for surrogate model,

input_param = ['clubb_c1', 'clubb_gamma_coef', 'zmconv_tau', 'zmconv_dmpdz',       'zmconv_micro_dcs', 'nucleate_ice_subgrid', 'p3_nc_autocon_expon',       'p3_qc_accret_expon', 'zmconv_auto_fac', 'zmconv_accr_fac', 'zmconv_ke',       'cldfrc_dp1', 'p3_embryonic_rain_size', 'p3_mincdnc'], 

and lat, lon, and lev. 

Model and surrogate data can also be indexed by the "workdir", i.e. a string name assigned to each simulation in the PPE:

workdir[ens_idx]: [..."ens/workdir.399/20230802.v3alpha02.F2010.pmcpu.intel.8N",     "ens/workdir.400/20230802.v3alpha02.F2010.pmcpu.intel.8N", "ctrl",     "L001", "L002", "L003", "H001", "H002", "H003"]

SWCRE_ano_grd_adj and LWCRE_ano_grd_adj are gridded shortwave cloud feedback and gridded longwave cloud feedback, respectively).

Upload version "v2" (January 26, 2026) is identical data to v1, but includes coordinates, units, and variable descriptions. 

Any errors or misrepresentations of the observational data as they were remapped from their native grids to the merged grid are the fault of the author. See references. 

This research used computing resources of the National Energy Research Scientific Computing Center (NERSC), a U.S. Department of Energy Office of Science User Facility located at Lawrence Berkeley National Laboratory, operated under Contract No. DE-AC02-05CH11231, using the NERSC award to project E3SM.
DOI: 10.5061/dryad.n378d
title: Data from: A spatiotemporal analysis of acoustic interactions between great reed warblers (Acrocephalus arundinaceus) using microphone arrays and robot audition software HARK

description: Acoustic interactions are important for understanding intra- and
 interspecific communication in songbird communities from the viewpoint of
 soundscape ecology. It has been suggested that birds may divide up sound
 space to increase communication efficiency in such a manner that they tend
 to avoid overlap with other birds when they sing. We are interested in
 clarifying the dynamics underlying the process as an example of complex
 systems based on short-term behavioral plasticity. However, it is very
 problematic to manually collect spatiotemporal patterns of acoustic events
 in natural habitats using data derived from a standard single-channel
 recording of several species singing simultaneously. Our purpose here is
 to investigate fine-scale spatiotemporal acoustic interactions of the
 great reed warbler. We surveyed spatial and temporal patterns of several
 vocalizing color-banded great reed warblers (Acrocephalus arundinaceus)
 using an open source software for robot audition HARK (Honda Research
 Institute Japan Audition for Robots with Kyoto University) and three new
 16-channel, stand-alone, and water-resistant microphone arrays, named
 DACHO spread out in the bird's habitat. We first show that our system
 estimated the location of two color-banded individuals' song posts
 with mean error distance of 5.5 ± 4.5 m from the location of observed song
 posts. We then evaluated the interdigitation of the temporal pattern of
 localized songs by comparing the duration of localized songs with those
 annotated by human observers, with an accuracy score of average 0.89% for
 one bird that stayed at one song post. We found significant temporal
 overlap avoidance and an asymmetric relationship between songs of the two
 singing individuals, using transfer entropy. We believe that our system
 and analytical approach contribute to a better understanding of fine-scale
 acoustic interactions in time and space in bird communities.
description: The results of the
 spatial localization of great reed warblers using three microphone
 arraysspatial_localization_of_GRWA_using_microphone_arrays.zip
DOI: 10.5061/dryad.mr7q2t9
title: Data from: Consumption of carotenoids not increased by bacterial infection in brown trout embryos (Salmo trutta)

description: Carotenoids are organic pigment molecules that play important roles in
 signalling, control of oxidative stress, and immunity. Fish allocate
 carotenoids to their eggs, which gives them the typical yellow to red
 colouration and supports their resistance against microbial infections.
 However, it is still unclear whether carotenoids act mainly as a shield
 against infection or are used up during the embryos' immune defence.
 We investigated this question with experimental families produced from
 wild-caught brown trout (Salmo trutta). Singly raised embryos were either
 exposed to the bacterial pathogen Pseudomonas fluorescens or sham-treated
 at one of two stages during their development. A previous study on these
 experimental families reported positive effects of egg carotenoids on
 embryo growth and resistance against the infection. Here, we quantified
 carotenoid consumption, i.e. the active metabolization of carotenoids into
 compounds that are not other carotenoid types, in these infected and
 sham-infected maternal sib groups. We found that carotenoid contents
 mostly decreased during embryogenesis. However, these decreases were
 neither linked to the virulence induced by the pathogen nor dependent on
 the time point of infection. We conclude that egg carotenoids are not
 significantly used up by the embryos' immune defence.
description: Parental
 traitsSee
 README.xlsxParents.txtEmbyro traits while in 24-well platesSee README.xlsxdata24_carots.txtEmbryo traits while in 12-well platesSee README.xlsxdata12_carots.txt