cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q8r53
title: Data from: Ecological impacts of invasive alien species along temperature gradients: testing the role of environmental matching

description: Invasive alien species (IAS) can cause substantive ecological impacts, and
 the role of temperature in mediating these impacts may become increasingly
 significant in a changing climate. Habitat conditions and physiological
 optima offer predictive information for IAS impacts in novel environments.
 Here, using meta-analysis and laboratory experiments, we tested the
 hypothesis that the impacts of IAS in the field are inversely correlated
 with the difference in their ambient and optimal temperatures. A
 meta-analysis of 29 studies of consumptive impacts of IAS in inland waters
 revealed that the impacts of fishes and crustaceans are higher at
 temperatures that more closely match their thermal growth optima. In
 particular, the maximum impact potential was constrained by increased
 differences between ambient and optimal temperatures, as indicated by the
 steeper slope of a quantile regression on the upper 25th percentile of
 impact data compared to that of a weighted linear regression on all data
 with measured variances. We complemented this study with an experimental
 analysis of the functional response - the relationship between predation
 rate and prey supply - of two invasive predators (freshwater mysid shrimp,
 Hemimysis anomala and Mysis diluviana) across relevant temperature
 gradients; both of these species have previously been found to exert
 strong community-level impacts that are corroborated by their functional
 responses to different prey items. The functional response experiments
 showed that maximum feeding rates of H. anomala and M. diluviana have
 distinct peaks near their respective thermal optima. Although variation in
 impacts may be caused by numerous abiotic or biotic habitat
 characteristics, both our analyses point to temperature as a key mediator
 of IAS impact levels in inland waters and suggest that IAS management
 should prioritize habitats in the invaded range that more closely match
 the thermal optima of targeted invaders.
description: Appendix B - Iacarella
 et alRaw data (experimental
 results) for Figures 2 & 3 in Iacarella et al. Ecol
 Appl.
DOI: 10.5061/dryad.m074c
title: Data from: Beyond biomass: soil feedbacks are transient over plant life-stages and alter fitness

description: 1. Plants influence associated soil biotic communities that in turn can
 alter the performance of the subsequently growing plants. Although such
 ‘plant-soil feedbacks’ (PSFs) are considered as important drivers of plant
 community assembly, past PSF studies have mainly addressed plant biomass
 production. However, plant performance is not only the production of
 biomass, but comprises a sequence of different life-stages: from seed
 germination over vegetative growth up to the production of a viable
 progeny. 2. Here we assessed the effects of soil biotic communities that
 were previously conditioned for three years by a focal plant species
 monoculture or species mixtures on key plant life-stages from germination
 and vegetative growth to flowering and the production of viable seeds. We
 used three common grassland herb species that were grown in a sterile
 substrate and inoculated with a sterile control soil, or with living
 soils. Living soils were conditioned either by the focal species in
 monoculture, or a four- or eight-species mixture that included the focal
 species to represent a decrease in the target plants’ conspecific
 influence on the soil communities. 3. We show that the effect of soil
 biota changed from positive at the plants’ juvenile life-stages to neutral
 or negative at the plants’ adult life-stages, and ultimately decreased
 plant fitness. A higher conspecific influence on the soil communities
 pronounced the positive effects at the juvenile life-stage, but also the
 negative effects at adult life-stages. Further, we observed direct soil
 biotic effects on flower production and plant fitness that were not
 mediated by adult biomass production. This suggests that soil biotic
 effects may alter plant resource allocation and even may have
 trans-generational effects on plant fitness. 4. Synthesis. We conclude
 that there is no overarching effect of soil biota that remains consistent
 at all the life-stages of a plant. Thus, our results highlight the
 importance to consider plant life-stage and ultimately plant fitness
 especially when plant soil interactions are used to explain plant
 community dynamics.
description: Plant responses to soil
 inoculation treatments at different life-stagesdata_dudenhoeffer_et_al.xlsx
DOI: 10.5061/dryad.mj3cd
title: Data from: Genetic variation for outcrossing among Caenorhabditis elegans isolates

description: The evolution of breeding systems results from the existence of genetic
 variation and selective forces favoring different outcrossing rates. In
 this study we determine the extent of genetic variation for characters
 directly related to outcrossing, such as male frequency, male mating
 ability, and male reproductive success, in several wild isolates of the
 nematode Caenorhabditis elegans. This species is characterized by an
 androdioecious breeding system in which males occur with hermaphrodites
 that can either self-fertilize or outcross with males. We find genetic
 variation for all characters measured, but also find that environmental
 variation is a large fraction of the total phenotypic variance. We further
 determine the existence of substantial genetic variation for population
 competitive performance in several laboratory environments. However, these
 measures are uncorrelated with outcrossing characters. The data presented
 here contribute to an understanding of male maintenance in natural
 populations through their role in outcrossing.
description: data_teotonioetal.2006the excel files contains the data from Teotonio et al. 2006 Evolution, regarding male proportions, population performance, etc. in separate sheets. Details on the methods can be found in the original MS. Please contact teotonio@biologie.ens.fr if you have questions about experimental design or data coding
DOI: 10.5061/dryad.498j63f
title: Data from: CSF1R-related leukoencephalopathy: a major player in primary microgliopathies

description: Since the discovery of CSF1R gene mutations in families with hereditary
 diffuse leukoencephalopathy with spheroids in 2012, more than 70 different
 mutations have been identified around the world. Through the analyses of
 mutation carriers, CSF1R-related leukoencephalopathy has been distinctly
 characterized clinically, radiologically, and pathologically. Typically,
 patients present with frontotemporal dementia–like phenotype in their
 40s–50s, accompanied by motor symptoms, including pyramidal and
 extrapyramidal signs. Women tend to develop the clinical symptoms at a
 younger age than men. On brain imaging, in addition to white matter
 abnormalities, thinning of the corpus callosum, diffusion-restricted
 lesions in the white matter, and brain calcifications are hallmarks.
 Primary axonopathy followed by demyelination was suggested by pathology.
 Haploinsufficiency of colony-stimulating factor-1 receptor (CSF1R) is
 evident in a patient with a frameshift mutation, facilitating the
 establishment of Csf1r haploinsufficient mouse model. These mice develop
 clinical, radiologic, and pathologic phenotypes consistent with those of
 human patients with CSF1R mutations. In vitro, perturbation of CSF1R
 signaling is shown in cultured cells expressing mutant CSF1R. However, the
 underlying mechanisms by which CSF1R mutations selectively lead to white
 matter degeneration remains to be elucidated. Given that CSF1R mainly
 expresses in microglia, CSF1R-related leukoencephalopathy is
 representative of primary microgliopathies, of which microglia have a
 pivotal and primary role in pathogenesis. In this review, we address the
 current knowledge of CSF1R-related leukoencephalopathy and discuss the
 putative pathophysiology, with a focus on microglia, as well as future
 research directions.
description: e-References
DOI: 10.5061/dryad.jt2sm
title: Data from: Carpal tunnel syndrome sssessment with ultrasonography: value of inlet-to-outlet median nerve area ratio in patients versus healthy volunteers

description: Objective: To evaluate the diagnostic value of the Inlet-to-outlet median
 nerve area ratio (IOR) in patients with clinically and
 electrophysiologically confirmed carpal tunnel syndrome (CTS). Methods:
 Forty-six wrists in 46 consecutive patients with clinical and
 electrodiagnostic evidence of CTS and forty-four wrists in 44 healthy
 volunteers were examined with ultrasonography. The cross-sectional area
 (CSA) of the median nerve was measured at the carpal tunnel inlet (the
 level of scaphoid-pisiform) and outlet (the level of the hook of the
 hamate), and the IOR was calculated for each wrist. Ultrasonography and
 electrodiagnostic tests were performed under blinded conditions.
 Electrodiagnostic testing combined with clinical symptoms were considered
 to be the gold standard test. Receiver operating characteristic (ROC)
 curves were used to evaluate the diagnostic value between the inlet CSA
 and IOR. Results: The study population included 16 men and 30 women (mean
 age, 45.3 years; range, 18–83 years). The control population included 18
 men and 26 women (mean age, 50.4 years; range, 18–79 years). The mean
 inlet CSA was 8.7 mm2 in healthy controls and 14.6mm2 in CTS group
 (P&lt;0.001). The mean IOR in healthy volunteers (1.0) was smaller
 than that in patients (1.6, P&lt;0.001). Receiver operating
 characteristic analysis revealed a diagnostic advantage to using the IOR
 rather than the inlet CSA (P&lt;0.01). An IOR cutoff value of ≥ 1.3
 would yield 93% specificity and 91% sensitivity in the diagnosis of CTS.
 Conclusion: The IOR of median nerve area promises to be an effective means
 in the diagnosis of CTS. A large-scale, randomized controlled trial is
 required to determine how and when this parameter will be used.
description: Inlet-to-outlet area
 ratio study dataInlet-to-outlet area ratio
 data.xlsx
DOI: 10.15468/dl.2dge9p
title: Occurrence Download

description: A dataset containing 156 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Enkianthus perulatus",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 156 records from 46 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001295-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.36j49h1
title: Data from: Antibacterial effect of (2E,2E)-4,4-Trisulfanediylbis(but-2-enoic acid) against Staphylococcus aureus

description: A new highly active molecule, (2E, 2E)-4,4-trisulfanediylbis(but-2-enoic
 acid) (TSDB), was designed and synthesized through comparative molecular
 field analysis with the diallyl trisulfide structure of garlic. TSDB
 exerted a strong inhibitory effect against Staphylococcus aureus, with
 minimal inhibitory and minimal bactericidal concentrations of 16 and 128
 μg/mL, respectively. TSDB destructed the integrity of the S. aureus cell
 membrane but weakly damaged the bacterial cell wall. TSDB also increased
 the conductivity and protein expression in microbial broth but minimally
 influenced the level of extracellular alkaline phosphatase. TSDB could be
 a novel food preservative.
description: TSDB (2E,
 2E)-4,4-trisulfanediylbis(but-2-enoic acid)PLOS ONE
 DATA.xlsx
DOI: 10.15468/dl.htry89
title: Occurrence Download

description: A dataset containing 434 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is China",
 "TaxonKey is Eucommia ulmoides",
 "Year 1975-2026"
 ]
}

 The dataset includes 434 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001296-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.43j74d0
title: Data from: Estimating population density of the white-tailed deer in Finland using non-invasive genetic sampling and spatial capture–recapture

description: The white-tailed deer is an important game species in Finland. We
 evaluated the potential of estimating the white-tailed deer pre-harvest
 density using non-invasive DNA collection within a spatial
 capture–recapture (SCR) framework. We sampled faeces during three weekly
 visits in autumn 2015 from 180, 20 x 20 m plots clustered in groups of
 four. Individual identification was based on 12–14 microsatellites. Of the
 245 faecal samples collected, an individual could be identified from only
 36 (15%). We identified 27 white-tailed deer individuals of which seven
 were recaptured. The SCR model produced a plausible density estimate (3.5
 indiv. km–2) which was similar to estimates based on dung count and
 large-scale national estimates, although a posteriori simulation showed
 the SCR estimate was likely positive biased. Although we found that SCR
 based on faecal DNA can provide pre-harvest density estimates of the
 white-tailed deer, the approach is not without challenges and we discuss
 these suggesting possible solutions.
description: trap data file
 (tdf)Comma separated file
 with header in first line. Information is on Spatial-Capture-Recaptures
 sampling plots. Each plot is 20mx20m. Each plot was visited once per week
 (=occasion) during three weeks. Plots were cleaned of feces prior data
 collecttion. Fecal samples were taken and analysed. File contains an
 identifier (ID) for each trap, its spatial location (X and Y; unit in
 meter) and whether it was operational (1) or not (0) during each of three
 occasions (occ1, occ2, occ3).tdf.txtencounter data file (edf)Comma separated file with header in first line. File contains spatial capture recapture data on individuals which were identified using DNA extracted from fecal pellets sampled in plots (see tdf file) for which 12-14 microsatellite markers could be amplified. Each individual is a unique genotype based on these markers. The information contains Session (always 1), identifier for each individual (ID), during which week it was encountered (occasion), and in which sample plot (TrapID; coded as in the tdf file), as well as the sex of the individual (Sex; F-female; M-male)edf.txtScript in program RR script to conduct spatial capture recapture analyses as well as the simulation reported in our paperRscriptAnalyses.txt
DOI: 10.5061/dryad.858j5m7
title: Data from: Broad thermal tolerance is negatively correlated with virulence in an opportunistic bacterial pathogen

description: Predicting the effects of global increase in temperatures on disease
 virulence is challenging, especially for environmental opportunistic
 bacteria, because pathogen fitness may be differentially affected by
 temperature within and outside host environment. So far, there is very
 little empirical evidence on the connections between optimal temperature
 range and virulence in environmentally growing pathogens. Here we explored
 if the virulence of an environmentally growing opportunistic fish
 pathogen, Flavobacterium columnare, is malleable to evolutionary changes
 via correlated selection on thermal tolerance. To this end, we
 experimentally quantified the thermal performance curves (TPCs) for
 maximum biomass of 49 F. columnare isolates from eight different
 geographic locations in Finland over ten years (2003-2012). We also
 characterized virulence profiles of these strains in a zebra-fish (Danio
 rerio) infection model. We show that virulence among the strains increased
 over the years, but tolerance to higher temperatures was negatively
 associated with virulence. Our data suggest that temperature has a strong
 effect on the pathogen genetic diversity, and therefore presumably also on
 disease dynamics. However, the observed increase in frequency and severity
 of F. columnare epidemics over the last decade cannot be directly linked
 to bacterial evolution due to increased mean temperature, but is most
 likely associated with factors related to increased length of growing
 season, or other time dependent change in environment. Our study
 demonstrates that complex interactions between the host, the pathogen and
 the environment influence disease virulence of environmentally growing
 opportunistic pathogen.
description: Growth data (biomass
 yields)Maximum biomass yields
 (measured in optical density units) at several experimental temperatures
 for Flavobacterium columnare strains. Two replicates are usually available
 for each strain at each temperature.ashrafi-2018-growth-data.tsvMaster table used for statistical analysesMaster table containing the final, curated data used in the statistical analyses of the articleashrafi-2018-master-table.tsvREADMEREADME file describing the content of each column of the tab-separated data files of this data package
DOI: 10.5061/dryad.d8fj8s3
title: Data from: Inducible defense destabilizes predator–prey dynamics: the importance of multiple predators

description: Phenotypic plasticity in prey can have a dramatic impact on predator–prey
 dynamics, e.g. by inducible defense against temporally varying levels of
 predation. Previous work has overwhelmingly shown that this effect is
 stabilizing: inducible defenses dampen the amplitudes of population
 oscillations or eliminate them altogether. However, such studies have
 neglected scenarios where being protected against one predator increases
 vulnerability to another (incompatible defense). Here we develop a model
 for such a scenario, using two distinct prey phenotypes and two predator
 species. Each prey phenotype is defended against one of the predators, and
 vulnerable to the other. In strong contrast with previous studies on the
 dynamic effects of plasticity involving a single predator, we find that
 increasing the level of plasticity consistently destabilizes the system,
 as measured by the amplitude of oscillations and the coefficients of
 variation of both total prey and total predator biomasses. We explain this
 unexpected and seemingly counterintuitive result by showing that
 plasticity causes synchronization between the two prey phenotypes (and,
 through this, between the predators), thus increasing the temporal
 variability in biomass dynamics. These results challenge the common view
 that plasticity should always have a stabilizing effect on biomass
 dynamics: adding a single predator–prey interaction to an established
 model structure gives rise to a system where different mechanisms may be
 at play, leading to dramatically different outcomes.
description: Simulation code in
 Wolfram MathematicaModel definitions and
 simulation codes for the main contourplots (Fig. 3, 5, 6, 8) and time
 series generation for the bifurcation plots (Appendix
 B).vanVelzen_etal_Oikos2018_SimulationCode.zip
DOI: 10.15468/dl.sud4tm
title: Occurrence Download

description: A dataset containing 65058 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Euphorbia paralias"
 ]
}

 The dataset includes 65058 records from 514 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001268-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7k78dg0
title: Data from: Effects of grasshoppers on prairies: herbivore composition matters more than richness in three grassland ecosystems

description: 1. Understanding how biodiversity affects ecosystem processes is a key
 question in ecology. Previous research has found that increasing plant
 diversity often enhances many ecosystem processes, but less is known about
 the role of consumer diversity to ecosystem processes, especially in
 terrestrial ecosystems. Furthermore, we do not know how general
 biodiversity responses are among ecosystem types. 2. We examined the role
 of insect herbivore (Orthoptera) diversity on plant production using
 parallel field experiments in three grassland ecosystems (mixed grass
 prairie, tallgrass prairie, and coastal tallgrass prairie) to determine if
 the effects of grasshopper diversity were consistent among sites. 3. Using
 mesocosms, we manipulated Orthopteran species richness (0, 1, 2, 3, or 4
 species), functional richness (number of functional feeding groups
 present; 0, 1, or 2 functional groups), and functional composition
 (composition of functional groups present; mixed feeders only, grass
 feeders only, both mixed feeders and grass feeders). Diversity treatments
 were maintained throughout the experiment by replacing dead individuals.
 Plant biomass was destructively sampled at the end of the experiment. 4.
 We found no effect of species richness or functional richness on plant
 biomass. However, herbivore functional composition was important, and
 effects were qualitatively similar across sites: the presence of only
 grass feeding species reduced plant biomass more than either mixed feeding
 species alone or both groups together. Orthopterans had consistent effects
 across a range of abiotic conditions, as well as different plant community
 and orthopteran community compositions. 5. Our results suggest that
 functional composition of insect herbivores affects plant communities in
 grasslands more than herbivore species richness or functional richness,
 and this pattern was robust among grassland types.
description: README_Laws_etal_grasshoppers_prairieReadme file for: Effects of grasshoppers on prairies: herbivore composition matters more than richness in three grassland ecosystems, Laws, Angela, Prather, Chelse, Branson, David, Pennings, Stevenplant_biomassPlant biomass data from each of the three field sites (Montana, Kansas, Texas). These data are from surveys at each site, not the experiment.plant_richnessPlant species richness for each of the three study sites (Montana, Kansas, Texas). Data are for surveys at each site, not the experiment.orthoptera_densitySurvey data from each site (Montana, Kansas, Texas) measuring grasshopper density.orthoptera_richnessGrasshopper community composition data for each site (Montana, Kansas, Texas). Data were collected from sweep net samples. Each Orthopteran species collected is listed, as well as the number of each species caught.experimental_dataPlant biomass data from the experiment, examining how Orthopteran species richness and functional richness affect plant biomass in three grasslands located in Montana, Kansas, and Texas.