cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh034419.07fu
title: SH034419.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh034420.07fu
title: SH034420.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh034421.07fu
title: SH034421.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5061/dryad.t75c4/1
title: bee visitation/floral density

description: Visitation rates of different bees (wild, honey, unique morphospecies) to apple trees of varying floral density
DOI: 10.5061/dryad.t75c4/2
title: fruitsetbees

description: Proportion fruit set, honey bee abundance, wild bee abundance, wild bee species richness and site characteristics at apple orchards in southern Wisconsin
DOI: 10.5061/dryad.t75c4/3
title: specieslist

description: List of all collected wild and honey bees identified to species
DOI: 10.5061/dryad.4387q/1
title: Nanostructural and color traits measured in dabbling ducks

description: Species means calculated from natural logarithms of raw nanostructural and color trait data. Data were collected from museum specimens and analyzed in R. 'Diameter_SD' is the standard deviation of natural-log transformed diameter values.
DOI: 10.5061/dryad.64313/1
title: Stress effects on mood, working memory, and physiological stress response

description: Mean values for mood (Profile of Mood States; POMS), heart rate (HR), cortisol (Cort), alpha-amylase (AA), and N-Back (NB) working memory, including hit rate, response time, and sensitivity, for each stress paradigm (TSST,SECPT, MAT, Control) and time point.
DOI: 10.5061/dryad.bv4tg/1
title: Data for female mate choice factor analysis

description: This is the dataset to calculate number of genetic factors for female mate choice
DOI: 10.5061/dryad.bv4tg/2
title: Data for color pattern factor analysis

description: This is the dataset to calculate number of genetic factors for male color pattern
DOI: 10.5061/dryad.bv4tg/3
title: F2 female behavior score

description: This is the dataset to evaluate time in association, male courting effort on female mate choice
DOI: 10.5061/dryad.bb460.2
title: Data from: Demographic properties shape tree size distribution in a Malaysian rain forest
DOI: 10.5061/dryad.bb460.2/1.2
title: Data for 370 species in actual community

description: Tree diameter data of 370 selected tree species in the Pasoh 50-ha plot in 1990 and 2000 census. Species names are kept unchanged (the "actual community"). The provided dataset is a processed subset of the original dataset for our demographic analysis of tree size distribution and demography of tree species populations demonstrated in the main paper. Readers interested in using the data for purposes other than testing our analysis are advised to obtain the raw data of tree inventories of the Pasoh 50-ha plot from the Forest Research Institute Malaysia (FRIM), the National Institute for Environmental Studies (NIES), Japan, and the Center for Tropical Forest Science (CTFS), Smithsonian Tropical Research Institute.
DOI: 10.5061/dryad.bb460.2/2.2
title: Data for 370 species in permuted community

description: Tree diameter data of 370 selected tree species in the Pasoh 50-ha plot in 1990 and 2000 census. In this data, species identity of each tree was shuffled to generate a fake, "permuted community". The provided dataset is a processed subset of the original dataset for our demographic analysis of tree size distribution and demography of tree species populations demonstrated in the main paper. Readers interested in using the data for purposes other than testing our analysis are advised to obtain the raw data of tree inventories of the Pasoh 50-ha plot from the Forest Research Institute Malaysia (FRIM), the National Institute for Environmental Studies (NIES), Japan, and the Center for Tropical Forest Science (CTFS), Smithsonian Tropical Research Institute.
DOI: 10.5061/dryad.bb460.2/3.2
title: Species names of 370 species

description: List of species codes and scientific species names for 370 selected tree species in the Pasoh 50-ha plot in 1990 and 2000 census. The provided dataset is a processed subset of the original dataset for our demographic analysis of tree size distribution and demography of tree species populations demonstrated in the main paper. Readers interested in using the data for purposes other than testing our analysis are advised to obtain the raw data of tree inventories of the Pasoh 50-ha plot from the Forest Research Institute Malaysia (FRIM), the National Institute for Environmental Studies (NIES), Japan, and the Center for Tropical Forest Science (CTFS), Smithsonian Tropical Research Institute.
DOI: 10.5061/dryad.bb460.1
title: Data from: Demographic properties shape tree size distribution in a Malaysian rain forest
DOI: 10.5061/dryad.bb460.2/4.2
title: R code for growth and mortality models

description: R code for parameter estimation of of size-growth function and mortality function, applied to the Bayesian analysis of tree dynamics in the Pasoh 50-ha plot.
DOI: 10.5061/dryad.ft7dj/1
title: CalMorph.pooled.raw.data.Rfile

description: This file contains an R object summarizing all data collected in this study.
DOI: 10.5061/dryad.n8c22/1
title: All syllables recorded and categorized from study

description: This file contains acoustic details of all syllables recorded from all Zosterops lateralis individuals and populations included in the current study. Data was gathered by DAP, all acoustic measurements were made in RavenPro 1.4 (Cornell Lab of Ornithology).
DOI: 10.5061/dryad.ff1r6/1
title: Raw data of centrifuge tests, contact sites, step durations

description: JMP spreadsheets with centrifuge force measurements, contact area and perimeter of attachment devices, measured step durations during locomotion.
DOI: 10.5061/dryad.40r32/1
title: Primary data on growth, maturation and survival

description: The data includes the cross-type, family and individual identifiers for all the 400 individual fish used in the experiment, as well as their size (standard length, in mm) at 15 different time points until day 510 after hatching when the experiments were terminated. Included is also information on day of maturation and survival. All the variables and their coding are described in second spread sheet of the file.
DOI: 10.5061/dryad.6f2j8/1
title: Code and Analyses

description: This zip contains the C code, R scripts, and simulation data files used to make all figures and quantitative comparisons.
DOI: 10.5061/dryad.db800/1
title: dryad_full dataset

description: genepop format of all individual genotypes at all 14 microsatellite loci
DOI: 10.5061/dryad.gv595/1
title: mix_bacteria

description: Files associated to the Figure 1.
DOI: 10.5061/dryad.gv595/2
title: mix_11yeasts

description: Files associated with the figure 2.
DOI: 10.5061/dryad.gv595/3
title: mix_environmental_sample

description: Files associated with the figure 3.
DOI: 10.5061/dryad.hd3st/1
title: Thermal limit and body mass data
DOI: 10.5061/dryad.vb855/1
title: Ribosome Profiling read coverage plots

description: Ribosome footprint read coverage plots (normalized by millions of reads sequenced). mRNA read coverage plots (normalized by millions of reads sequenced). Timepoints are referred to as 1-5 (Rings, Early Trophs, Late Trophs, Schizont, Merozoites, respectively)
DOI: 10.5061/dryad.r5954/1
title: Data from: Experiment 1 – protection against parasitoids conferred by different isolates of H. defensa
DOI: 10.5061/dryad.r5954/2
title: Data from: Experiment 2 - life history costs induced by different isolates of H. defensa
DOI: 10.5061/dryad.r5954/3
title: Data from: Experiment 3 - symbiont densities
DOI: 10.5061/dryad.p0bh4/1
title: Holopedium Survey Data

description: Holopedium abundance data from the Ontario paleolimnological survey, the Nova Scotia paleolimnogical survey and the two (1980s and 2000s) Ontario limnological surveys.
DOI: 10.5061/dryad.p0bh4/2
title: Longitudinal data from 8 Ontario lakes

description: We tested the mechanisms underlying increases in the relative and absolute abundance of Holopedium glacialis in the planktonic cladoceran assemblage of 8 central-Ontario, Canada lakes that were sampled monthly for 30 years.  Zooplankton were sampled during the ice-free season near the point of maximum depth by using a metered, 76 μm mesh, tow net. The net was deployed in 4 to 7 vertical hauls and its contents were combined to produce a composite that corrected for the diminution of lake stratum volume with depth. A minimum of 250 crustacean zooplankton were enumerated in each composite, subsampling to ensure that no taxon comprised more than 10% of the total count. Phytoplankton were sampled through the euphotic zone, and water chemistry samples were volume-weighted composites of all depths during isothermal periods, and of the mixed layers during periods of vernal and autumnal stratification. Dissolved oxygen profiles were generated at 1-2 m intervals from all depths. Finally, abundances of the zooplanktivore, Chaoborus spp. were quantified in samples from night-time vertical hauls at 10 stations visited during the autumn in all lakes in 1986 and in one lake from 1987-1994. In the laboratory, a minimum of 300 cells, colonies, or filaments of phytoplankton were counted within the Bacillariophyceae, Chlorophyceae, Cryptophyceae, Dinophyceae, and Euglenophyceae. Dimensions of all counted algae were measured, and summed to express values as an "edible" phytoplankton biovolume.
DOI: 10.5061/dryad.7s8h7/1
title: Truncated Opsin Alignment (including New Amphiura opsins)

description: Fasta file of the truncated opsin alignment used for phylogenetic analyses.
DOI: 10.5061/dryad.7s8h7/2
title: Bayesian tree of new Amphiura opsins

description: Tree files obtained in Bayesian analyses (modified with FigTree software, http://tree.bio.ed.ac.uk/software/figtree/)
DOI: 10.5061/dryad.7s8h7/3
title: ML tree of new Amphiura opsins

description: TREE files obtained in Maximum Likelihood Analyses (modified with FigTree software, http://tree.bio.ed.ac.uk/software/figtree/)
DOI: 10.5061/dryad.1t6s5.2
title: Data from: Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative
DOI: 10.5061/dryad.1t6s5.2/1.2
title: Plant data: sterilized field soil treatments

description: Plant pedigree information, phenotype data, and fitness data from greenhouse experiment investigating effects of 4 different sterilized field soils. "Block" = experimental block; "Genotype" = genotype code; "Subsp" = Subspecies code: W for west, E for east;  "Treatment" = origin of sterilized field soil; "FLT" = flowering time (days); "elong" = elongation rate (mm/day); "HAF" = height at flowering (mm); "Leafper" = number of leaves per mm stem; "NFr" = number of fruits
DOI: 10.5061/dryad.1t6s5.2/2.2
title: Plant data: microbial community treatments

description: Plant pedigree information, phenotype data, and fitness data from greenhouse experiment investigating effects of 4 different soil microbial communities. "Block" = experimental block; "Genotype" = genotype code; "Subsp" = Subspecies code: W for west, E for east; "Treatment" = origin of soil microbial community; "FLT" = flowering time (days); "elong" = elongation rate (mm/day); "HAF" = height at flowering (mm); "Leafper" = number of leaves per mm stem; "NFr" = number of fruits
DOI: 10.5061/dryad.1t6s5.1
title: Data from: Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative
DOI: 10.5061/dryad.1t6s5.2/3.2
title: Key to soil sample IDs

description: Soil sample-level metadata. "SampleID" = unique identifier for soil samples (JGI notation). "Plant_ID" = unique identifier for soil samples (Duke notation). "Site" = field site of origin. "oldPlate" = plate identifier (Duke notation). "newPlate" = plate identifier (JGI notation). "Year" = year of soil collection
DOI: 10.5061/dryad.1t6s5.2/4.2
title: 16S gene copy number estimates

description: 16S gene copy number estimates for OTUs generated using corrected bioinformatics pipeline. OTUs with no available estimates were assigned the mean copy number of 2.7175
DOI: 10.5061/dryad.1t6s5.2/5.2
title: soil OTU table (rarefied)

description: Soil OTU table rarefied to 40,000 reads per sample, used for all analyses in the publication (Wagner et al. 2014 Ecology Letters). This table contains only "reproducible" OTUs that had at least 25 reads in at least 5 samples BEFORE rarefaction (note that this thresholding step was performed on a larger dataset that included hundreds of samples, not yet published). First column contains unique identifiers of observed OTUs. Other columns contain the number of reads for each OTU in each soil sample after rarefaction.
DOI: 10.5061/dryad.1t6s5.2/6.2
title: soil OTU table

description: Unrarefied soil OTU table. This table contains only "reproducible" OTUs that had at least 25 reads in at least 5 samples (note that this thresholding step was performed on a larger dataset that included hundreds of samples, not yet published). First column contains unique identifiers of observed OTUs. Other columns contain the number of reads for each OTU in each soil sample. This file was the input leading to the rarefied dataset ('soil_otu_table_rare40k.txt') used for all downstream analyses in the publication.
DOI: 10.5061/dryad.1t6s5.2/7.2
title: OTU taxonomy

description: Contains taxonomic designations for OTUs
DOI: 10.5061/dryad.1t6s5.2/8.2
title: README
DOI: 10.5061/dryad.s677t/1
title: Baseline immune activity is associated with date rather than with moult stage in the Arctic-breeding barnacle goose (Branta leucopsis)
DOI: 10.5061/dryad.ph510/1
title: Membrane Protein Equilibration

description: These are MD trajectories to accompany the paper: "Lipid Binding and Force Transduction in MscL: A Continuum-Molecular Approach" by Juan M. Vanegas and Marino Arroyo. PLoS ONE 2014. All trajectories were generated with GROMACS version 4.5.5 (www.gromacs.org). All trajectoories can be read and analyzed by the standard GROMACS utilities. Trajectories (.xtc) can also be visualized by common molecular graphics programs such as UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) or VMD (http://www.ks.uiuc.edu/Research/vmd/). Topology files in text (.top) and binary (.tpr) form are included, as well as simulation parameters (.mdp). In some cases text files (.xvg) including coordinate information are also included. The file MscL_Equilibration.tar.gz contains the trajectory corresponding to the 500 ns equilibration period of the MscL Channel embedded in the POPE bilayer. The file Local_Stress_and_Traction.tar.gz contains the trajectories for the tensionless and tensioned simulations, as well as the files needed to visualize the traction on the surface of the protein. The stress tensor was calculated with a custom version of GROMACS (http://www.lacan.upc.edu/LocalStressFromMD) and the files can be visualized with the program ParaView. The file Arrhenius_Bell_unbinding.tar.gz contains the steered MD simulation trajectories used to estimate the strength of lipid binding to the MscL protein. The file Channel_Actuation.tar.gz contains the steered MD simulation trajectories used to actuate the MscL channel by pulling on protein-bound lipids. Finally, the file force_field_parameters.tar.gz contains the parameters used in all of the simulations. We used the G43A1-S3 lipid parameters in combination with the G54A7 protein parameters.
DOI: 10.5061/dryad.ph510/2
title: Steered Simulations to Estimate Lipid Binding Interaction

description: These are MD trajectories to accompany the paper: "Lipid Binding and Force Transduction in MscL: A Continuum-Molecular Approach" by Juan M. Vanegas and Marino Arroyo. PLoS ONE 2014. All trajectories were generated with GROMACS version 4.5.5 (www.gromacs.org). All trajectoories can be read and analyzed by the standard GROMACS utilities. Trajectories (.xtc) can also be visualized by common molecular graphics programs such as UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) or VMD (http://www.ks.uiuc.edu/Research/vmd/). Topology files in text (.top) and binary (.tpr) form are included, as well as simulation parameters (.mdp). In some cases text files (.xvg) including coordinate information are also included. The file MscL_Equilibration.tar.gz contains the trajectory corresponding to the 500 ns equilibration period of the MscL Channel embedded in the POPE bilayer. The file Local_Stress_and_Traction.tar.gz contains the trajectories for the tensionless and tensioned simulations, as well as the files needed to visualize the traction on the surface of the protein. The stress tensor was calculated with a custom version of GROMACS (http://www.lacan.upc.edu/LocalStressFromMD) and the files can be visualized with the program ParaView. The file Arrhenius_Bell_unbinding.tar.gz contains the steered MD simulation trajectories used to estimate the strength of lipid binding to the MscL protein. The file Channel_Actuation.tar.gz contains the steered MD simulation trajectories used to actuate the MscL channel by pulling on protein-bound lipids. Finally, the file force_field_parameters.tar.gz contains the parameters used in all of the simulations. We used the G43A1-S3 lipid parameters in combination with the G54A7 protein parameters.
DOI: 10.5061/dryad.ph510/3
title: Local Stress and Traction

description: These are MD trajectories to accompany the paper: "Lipid Binding and Force Transduction in MscL: A Continuum-Molecular Approach" by Juan M. Vanegas and Marino Arroyo. PLoS ONE 2014. All trajectories were generated with GROMACS version 4.5.5 (www.gromacs.org). All trajectoories can be read and analyzed by the standard GROMACS utilities. Trajectories (.xtc) can also be visualized by common molecular graphics programs such as UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) or VMD (http://www.ks.uiuc.edu/Research/vmd/). Topology files in text (.top) and binary (.tpr) form are included, as well as simulation parameters (.mdp). In some cases text files (.xvg) including coordinate information are also included. The file MscL_Equilibration.tar.gz contains the trajectory corresponding to the 500 ns equilibration period of the MscL Channel embedded in the POPE bilayer. The file Local_Stress_and_Traction.tar.gz contains the trajectories for the tensionless and tensioned simulations, as well as the files needed to visualize the traction on the surface of the protein. The stress tensor was calculated with a custom version of GROMACS (http://www.lacan.upc.edu/LocalStressFromMD) and the files can be visualized with the program ParaView. The file Arrhenius_Bell_unbinding.tar.gz contains the steered MD simulation trajectories used to estimate the strength of lipid binding to the MscL protein. The file Channel_Actuation.tar.gz contains the steered MD simulation trajectories used to actuate the MscL channel by pulling on protein-bound lipids. Finally, the file force_field_parameters.tar.gz contains the parameters used in all of the simulations. We used the G43A1-S3 lipid parameters in combination with the G54A7 protein parameters.
DOI: 10.5061/dryad.ph510/4
title: Steered Simulations to Actuate the Channel

description: These are MD trajectories to accompany the paper: "Lipid Binding and Force Transduction in MscL: A Continuum-Molecular Approach" by Juan M. Vanegas and Marino Arroyo. PLoS ONE 2014. All trajectories were generated with GROMACS version 4.5.5 (www.gromacs.org). All trajectoories can be read and analyzed by the standard GROMACS utilities. Trajectories (.xtc) can also be visualized by common molecular graphics programs such as UCSF Chimera (http://www.cgl.ucsf.edu/chimera/) or VMD (http://www.ks.uiuc.edu/Research/vmd/). Topology files in text (.top) and binary (.tpr) form are included, as well as simulation parameters (.mdp). In some cases text files (.xvg) including coordinate information are also included. The file MscL_Equilibration.tar.gz contains the trajectory corresponding to the 500 ns equilibration period of the MscL Channel embedded in the POPE bilayer. The file Local_Stress_and_Traction.tar.gz contains the trajectories for the tensionless and tensioned simulations, as well as the files needed to visualize the traction on the surface of the protein. The stress tensor was calculated with a custom version of GROMACS (http://www.lacan.upc.edu/LocalStressFromMD) and the files can be visualized with the program ParaView. The file Arrhenius_Bell_unbinding.tar.gz contains the steered MD simulation trajectories used to estimate the strength of lipid binding to the MscL protein. The file Channel_Actuation.tar.gz contains the steered MD simulation trajectories used to actuate the MscL channel by pulling on protein-bound lipids. Finally, the file force_field_parameters.tar.gz contains the parameters used in all of the simulations. We used the G43A1-S3 lipid parameters in combination with the G54A7 protein parameters.