cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.mf4h560/6
title: COLONY_Files

description: The zip folder contains text files with microsatellite data. The microsatellite data from the metamorphs (genetic_data_froglets_cleaned.txt), the microsatellites for four eggs per clutch (genetic_data_LB_froglets.txt) used as maternal sibs, the marker error rates to be used in Colony (MarkerTypeErrorRate.txt) and the known maternal relationship and offspring genotypes as output from Colony.
DOI: 10.5061/dryad.mf4h560/7
title: Code_analysis_figures_Dittrich_etal_2018_Ecology_Evolution

description: Contains R-source code to conduct all analysis descriped in the main manuscript and to reproduce the figures.
DOI: 10.5061/dryad.mf4h560/8
title: Code_supplement_Dittrich_etal_2018_Ecology_Evolution

description: Contains R-source code to conduct all analysis descriped in the supplement and to reproduce the figures.
DOI: 10.5061/dryad.n6s1dk1/1
title: Genotypes Clinus cottoides Parentage

description: Contains microsatellite genotypes of all adults and embryos used for parentage analyses
DOI: 10.5061/dryad.pv814j1/17
title: Specimen 6_2cut
DOI: 10.5061/dryad.pv814j1/18
title: Specimen 7 Control
DOI: 10.5061/dryad.pv814j1/19
title: Specimen 7_1cut
DOI: 10.5061/dryad.pv814j1/21
title: Specimen 8 Control
DOI: 10.5061/dryad.pv814j1/22
title: Specimen 8_1cut
DOI: 10.5061/dryad.pv814j1/23
title: Specimen 9 Control
DOI: 10.5061/dryad.pv814j1/24
title: Specimen 9_1cut
DOI: 10.5061/dryad.pv814j1/25
title: Specimen 10 Control
DOI: 10.5061/dryad.rg0n5t5/1
title: Reed_et_al_2019.zip

description: This .zip package contains data files for the article: Reed et al. 2019. Prairie plant phenology driven more by temperature than moisture in climate manipulations across a latitudinal gradient in the Pacific Northwest, USA. Ecology and Evolution. Please see the README.txt file for a description of each data file.
DOI: 10.5061/dryad.v511900/1
title: Optical density of zenk expression

description: Optical density of zenk expression in different brain regions.
DOI: 10.5061/dryad.v511900/2
title: Behavioural data

description: Behavioural data on male-male interactions.
DOI: 10.5061/dryad.v511900/3
title: Morphological data
DOI: 10.5061/dryad.vk24fr1/1
title: Length-mass regression data for arthropods from different geographic regions

description: This data includes data used in Sohlström et al. to estimate how live body mass of arthropods depends on body length and further co-variables.
Description of headers:
Order refers to taxonomic order.
Suborder refers to taxonomic suborder. 
Family refers to taxonomic family.
Live body mass [mg] refers to the body mass of the living organism, measured using a precision scale.
Body length [mm] refers to the maximum body length, measured without appendages.
Body width [mm] refers to the maximum body width, measured without appendages.
Geographic region refers to the location where the arthropods have been sampled. “tropical” refers to organisms collected near Jambi, Indonesia and “temperate” refers to organisms collected near Göttingen, Germany.
Groups for Table S1 refers to groups that have been further subset due to taxonomy, morphological or behavioural characteristics. The regressions of these groups are presented in the supporting information (Table S1).
Analysis refers to where the results of the order are presented in the publication (e.g. Main analysis, Supporting information). Results of 12 orders are presented in the main text only, results of 7 orders are presented in the main text at the order level and in the supporting information based on the Groups for Table S1 and results of 4 orders are presented in the supporting information only.
DOI: 10.17632/3984rjzbw6.1
title: Data for: Fast FEM Simulation of AC Transport Losses in Bi-2223 High Temperature Superconducting Tapes via Equivalent Filament Domain

description: The .xlsx files contain data not available in numerical format in the paper.
DOI: 10.17632/5vh6nz62k8.1
title: Data for: New Spectral-Induced Polarization Measurement with Low Cost and High Efficiency

description: '80092al.tss' is the raw data of the lawn test. '80099oah.tss' is the raw data of the field test. 'SIP2_128.b' is the 'Amp-Phase-Frequency Table' used in data processing in this paper.
DOI: 10.5061/dryad.003k4g0/1
title: Priority_Effects_Model_Oikos

description: This script runs the model described in equations 1-7, and which creates the data behind figures 2-5.
DOI: 10.5061/dryad.26c0m59/3
title: METADATA_pilosocereus_leucocephalus_seeds_per_fruit

description: METADATA or README file to interpret dataset
DOI: 10.5061/dryad.26c0m59/4
title: DATA_pilosocereus_leucocephalus_seeds_per_fruit

description: Seeds per fruit found in Pilosocereus leucocephalus
DOI: 10.5061/dryad.271f74f/1
title: TipperneData_a

description: This file contains data for wader species and environment at one out of two survey sites, 'Tipperne', Denmark, during 1928-2014.
DOI: 10.5061/dryad.271f74f/2
title: VejlerneData

description: This file contains data for wader species and environment at one out of two survey site 'Vejlerne', Denmark, during 1978-2014.
DOI: 10.5061/dryad.306sf0b/5
title: Supplementary Figures and Tables

description: PDF document with supplementary tables and figures: 
Supplementary Table S1. Yeast strains used in this work; 
Supplementary Fig. S1. Organ expression pattern of CsMTP6 in cucumber; Supplementary Fig. S2. ClustalW alignment of the CsMTP6 nucleic acid and CsMTP6 amino acid sequences;
Supplementary Fig. S3. Western blot analysis of mitochondria isolated from yeast expressing CsMTP6;
Supplementary Fig. S4. Localization of CsMTP6 in Δzrc1, K667 and Δsmf1 cells;
Supplementary Fig. S5. Effect of CsMTP6 expression on yeast sensitivity to Zn, Ni and Cd.
DOI: 10.5061/dryad.37qv5rd/1
title: Raw .fastq sequence files for PeerJ submission "Digging for DNA at depth: rapid universal metabarcoding surveys (RUMS) as a tool to detect coral reef biodiversity across a depth gradient"

description: Raw .fastq 18S rRNA sequences for sediment samples collected at two coral reefs in Okinawa, Japan.
DOI: 10.5061/dryad.4769955/1
title: Haverkamp et al_Benzyl acetone emissions at different distances

description: Benzyl acetone emission from flowers at different angles and distances
DOI: 10.5061/dryad.5h06vv2/1
title: turtle_image_metadata

description: This file contains all turtle detections along with relevant metadata such as the image the detection is in, that image's file location, aircraft information, and precise turtle location in each image in both GPS and pixel locations. Also included are many validated false positives with the same metadata but a label of 0 instead of certain or positive turtle.
DOI: 10.5061/dryad.5h06vv2/2
title: duke_turtles

description: This is the first subset of images for the paper. Image metadata as well as turtle locations can be found in turtle_image_metadata.csv.
DOI: 10.5061/dryad.5h06vv2/3
title: duke_turtles_r1

description: This is the second subset of images for the paper. Image metadata as well as turtle locations can be found in turtle_image_metadata.csv.
DOI: 10.5061/dryad.66h3627/1
title: Trilobite occurrence dataset

description: Trilobite presence-absence dataset of samples from the Cambro-Ordovician of the Argentine Cordillera Oriental with environmental assignation (shallow subtidal, deep subtidal, offshore).
DOI: 10.5061/dryad.66h3627/2
title: R code

description: R code for the diversity analyses
DOI: 10.5061/dryad.66h3627/3
title: List of genera

description: Names of the genera corresponding to the numbers that appear in the occupancy-rank plots depicted in figure 4.
DOI: 10.5061/dryad.7519042/18
title: Struthio_camelus_scan_data_b_16bit

description: Struthio camelus (second scan) CT scan data - 16 bit
DOI: 10.5061/dryad.76j14s5/1
title: aLRT SH-like trees paralogon 1

description: Phylogenetic aLRT SH-like trees of the neighboring gene families included in analysis of nAChR paralogon 1. There is one neighboring gene family per page in alphabetical order. Taxa ID and sequence information details are provided in the table below.
DOI: 10.5061/dryad.76j14s5/2
title: Table paralogon 1

description: Table containing information about the nAChR neighboring gene families included in the analysis of the nAChR paralogon 1. First, information about genome assembly versions used are listed, then the following information about the neighboring gene families is provided: species, HGNC/ZFIN/Flybase symbol name, chromosome or genomic scaffold position, Ensembl ID or NCBI accession number, taxa ID and additional comments regarding sequence update date on NCBI or if there has been manual edits of the original Ensembl or NCBI sequence. There is one page per family, presented in alphabetical order.
DOI: 10.5061/dryad.76j14s5/3
title: aLRT SH-like trees paralogon 3

description: Phylogenetic aLRT SH-like tree of the neighboring gene families included in analysis of nAChR paralogon 3. There is one neighboring gene family per page in alphabetical order. Taxa ID and sequence information details are provided in the table below.
DOI: 10.5061/dryad.82j677c/1
title: Herbaria records

description: Herbaria records used in analysis of flowering time.
DOI: 10.5061/dryad.82j677c/2
title: Budbreak in Nature

description: Data used to estimate live oak budbreak phenology
DOI: 10.5061/dryad.82j677c/3
title: Initial Budbreak Common Garden

description: Date of first budbreak in sapling live oaks reared in a common garden
DOI: 10.5061/dryad.8c40mb0/1
title: README

description: This file explains all the variables and provides full references for the data in each of the datasets that accompany: Portalier S., Fussmann G. F., Loreau M. & Cherif M., 2018ms, The mechanics of predator-prey interactions: first principles of physics predict predator-prey size ratios.
DOI: 10.5061/dryad.8c40mb0/2
title: Predator-prey species-based data

description: The file provides average body masses for predators and prey, across a wide range of sizes and different life media.
DOI: 10.5061/dryad.8c40mb0/3
title: Predator-prey individual-based data

description: The file provides individual body masses of predators and prey in marine food webs.
DOI: 10.5061/dryad.c392v5q/1
title: Quality of life

description: Quality of life based on the PROMIS® system
DOI: 10.5061/dryad.ct362tv/3
title: Supplementary File 3

description: List of loci identified as outliers, including allele frequencies, and BLAST results for each.
DOI: 10.5061/dryad.ct362tv/4
title: Supplementary File 4

description: RAD genotype data for the full set of 4,969 loci in genepop format.  Sample names correspond to the 'Alias' column in Supplementary File 2.
DOI: 10.5061/dryad.ct362tv/5
title: Supplementary File 5

description: RAD genotype data for 4,931 loci in genepop format.  This file is similar to Supplementary File 4, except that the outlier loci have been removed here.  Sample names correspond to the 'Alias' column in Supplementary File 2.
DOI: 10.5061/dryad.ct362tv/6
title: Supplementary File 6

description: Microsatellite genotype data in genepop format.  Names of individuals correspond to the 'Sample Name' field in Supplementary File 2.
DOI: 10.5061/dryad.ct362tv/7
title: STACKS catalog file

description: DNA sequences and metadata for consensus loci created using the scripts presented in Supplementary File 1.  This catalog file was generated using the cstacks script in STACKS.  Detailed information regarding the file format is available in the STACKS user manual (http://catchenlab.life.illinois.edu/stacks/manual/).
DOI: 10.5061/dryad.ct362tv/8
title: RAD genotype data in variant call format

description: RAD genotype data resulting from the pipeline presented in Supplementary File 1, in variant call format.  Locus names correspond to those listed in the catalog file (Data1_batch_1.catalog.tags.tsv).  This file was produced using the populations script in STACKS.
DOI: 10.5061/dryad.ft4sn88/10
title: Dryad_Supplementary_File_10_richness_modifier_10nov2016.28nov2016

description: Dryad Supplementary File 10. R script used to modify richness estimates of ant genera.
DOI: 10.5061/dryad.ft4sn88/11
title: Dryad Supplementary File 11. Higher-level taxonomy of vascular plant genera used in analyses.

description: Dryad Supplementary File 11. Higher-level taxonomy of vascular plant genera used in analyses.
DOI: 10.5061/dryad.ft4sn88/12
title: Dryad Supplementary File 12. Constraint tree derived from higher-level taxonomy which was used to infer vascular plant phylogeny.

description: Dryad Supplementary File 12. Constraint tree derived from higher-level taxonomy which was used to infer vascular plant phylogeny.
DOI: 10.5061/dryad.ft4sn88/13
title: Dryad Supplementary File 13. Partition file used to infer vascular plant phylogeny.

description: Dryad Supplementary File 13. Partition file used to infer vascular plant phylogeny.
DOI: 10.5061/dryad.ft4sn88/14
title: Dryad Supplementary File 14. Constrained ML phylogeny of vascular plants.

description: Dryad Supplementary File 14. Constrained ML phylogeny of vascular plants.
DOI: 10.5061/dryad.ft4sn88/15
title: Dryad Supplementary File 15. Genera dropped from the vascular plant ML phylogeny.

description: Dryad Supplementary File 15. Genera dropped from the vascular plant ML phylogeny.
DOI: 10.5061/dryad.ft4sn88/7
title: Dryad Supplementary File 7. Time-calibrated maximum-likelihood phylogeny of 1731 ant species and associated Aculeata outgroup taxa.

description: Dryad Supplementary File 7. Time-calibrated maximum-likelihood phylogeny of 1731 ant species and associated Aculeata outgroup taxa.
DOI: 10.5061/dryad.ft4sn88/8
title: Dryad Supplementary File 8. List of valid ant species derived from AntWiki.

description: Dryad Supplementary File 8. List of valid ant species derived from AntWiki.
DOI: 10.5061/dryad.ft4sn88/9
title: Dryad Supplementary File 9. List of valid ant species assigned to alternate genera.

description: Dryad Supplementary File 9. List of valid ant species assigned to alternate genera.
DOI: 10.5061/dryad.k3f951q/1
title: supplementary_file
DOI: 10.5061/dryad.kd1qt0p.1
title: Data from: High-molecular-weight polymers from dietary fiber drive aggregation of particulates in the murine small intestine
DOI: 10.5061/dryad.kd1qt0p.1/4.1
title: Figure 2 - Source Data 4

description: This zip archive contains the original z-stacks used for Figure 2, panels F-G. These are provided as TIF files, which are readable by FIJI. All imaging parameters are included in the image metadata. They are labeled by “Group#” (indicating which CDF they below to in the figure) and “Trial#” if multiple technical replicates were done for a given sample from a Group. The control done in Hanks’ Balanced Salt Solution (HBSS) is labeled as “HBSS”. 

Additionally, this file contains .csv files of all the statistics on particle sizes collected by the ImageJ macro. These are labeled in the format “Group#_trial#_automated_counting_statistics”. It also contains a .csv file of the particle # IDs of the singlet particles that were used to get the average singlet size, which was then used to normalize the ECDFs (as explained in detail in Materials and Methods). These are labeled in the format “Group#_trial#_singlet_IDs”. These .csv files were used in combination with the jupyter notebooks (also provided in this submission) to generate Figure 2, panels F-G. If multiple technical replicates were performed on a sample, the resulting ECDFs were combined to create one master ECDF for that sample.
DOI: 10.5061/dryad.kd1qt0p.1/7.1
title: Figure 3 - Source Data 2

description: This zip archive contains the original z-stacks used for Figure 3, panels E-F. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows (if multiple technical replicates were done it is indicated): A7PS263_s6_t1 = 30 µm-filtered, technical replicate #1; A7PS263_s7_t1 = 0.45 µm-filtered; A7PS263_s8_t1 = 100 kDa-filtered; A7PS263_s9_t1 = 30 kDa-filtered; A7PS263_s10_t1 = 3 kDa-filtered; A7PS284_s13_t1 = HBSS; A7PS285_s3_t1 = 30 µm-filtered, technical replicate #2; A7PS285_s4_t1 = 0.45 µm-filtered, technical replicate #2; A7PS285_s7_t1 = 30 µm-filtered, technical replicate #3; A7PS285_s8_t1 = 0.45 µm-filtered, technical replicate #3. 

Additionally, this file contains .csv files of all the statistics on particle sizes collected by the ImageJ macro. These are labeled in the format “zstackname_automated_counting_statistics”, where “zstackname” is the title of the associated z-stack. It also contains a .csv file of the particle # IDs of the singlet particles that were used to get the average singlet size, which was then used to normalize the ECDFs (as explained in detail in Materials and Methods). These are labeled in the format “zstackname_singlet_IDs”, where “zstackname” is the title of the associated z-stack. These .csv files were used in combination with the Jupyter notebooks (also provided with this submission) to generate Figure 3, panels E-F. If multiple technical replicates were performed on a sample, the resulting ECDFs were combined to create one master ECDF for that sample.
DOI: 10.5061/dryad.kd1qt0p.2/33.2
title: Bootstrap confidence intervals code

description: This zip folder contains the source code to generate 95% empirical bootstrap confidence intervals. The .html and .ipynb files are identical. The code was written with Python version 3.6.4. It has been verified to work with numpy version 1.13.3, pandas version 0.21.1, scipy version 1.0.0, bokeh version 0.12.15, holoviews version 1.9.1, and numba version 0.36.2. 

 

The test data folder provides data that can be used to verify that the code is working. Make sure to change the file paths to what is appropriate for your computer. The test data will reproduce Figure 7G from the main text. This data was also provided as part of “Figure 7 – source data 4”.
DOI: 10.5061/dryad.kd1qt0p.2/34.2
title: volume-weighted ECDF code

description: This zip folder contains the source code to generate 95% empirical bootstrap confidence intervals The .html and .ipynb file are identical. The code was written with Python version 3.6.4. It has been verified to work with numpy version 1.13.3, pandas version 0.21.1, scipy version 1.0.0, bokeh version 0.12.15, and holoviews version 1.9.1. 

 

The test data folder provides data that can be used to verify that the code is working. Make sure to change the file paths to what is appropriate for your computer. The test data will reproduce Figure 5, Panel A from the main text. This data was also provided as part of “Figure 5 – source data 1”.
DOI: 10.5061/dryad.kd1qt0p.2/35.2
title: Depletion Calculations Code

description: This zip folder contains the source code to generate the plots of the interparticle potential minima displayed in Figure 4H. The .html and .ipynb file are identical. The code was written with Python version 3.6.4. It has been verified to work with numpy version 1.13.3, pandas version 0.21.1, scipy version 1.0.0, bokeh version 0.12.15, sympy version 1.1.1, holoviews version 1.9.1, and numba version 0.36.2.
DOI: 10.5061/dryad.kd1qt0p.2/36.2
title: Diffusion coefficients Code

description: This zip folder contains the source code to generate the plots of the diffusion coefficients displayed in Figure 4I. The .html and .ipynb file are identical. The code was written with Python version 3.6.4. It has been verified to work with numpy version 1.13.3, pandas version 0.21.1, scipy version 1.0.0, bokeh version 0.12.15, sympy version 1.1.1, holoviews version 1.9.1, and numba version 0.36.2.
DOI: 10.5061/dryad.kd1qt0p.2/37.2
title: Figure 4 - figure supplement 2

description: This zip archive contains the original z-stacks used for the PEG 1 MDa data in Figure 4, figure supplement 2.. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows:   
A7PS362_s1_t1 = 6.52 mg/mL PEG 1 MDa
A7PS362_s2_t1 = 3.26 mg/mL PEG 1 MDa 
A7PS362_s3_t1 = 1.63 mg/mL PEG 1 MDa
A7PS362_s4_t1 = 0.815 mg/mL PEG 1 MDa
A7PS362_s5_t1 = 0.407 mg/mL PEG 1 MDa
A7PS362_s6_t1 = 0.204 mg/mL PEG 1 MDa
A7PS362_s7_t1 = 0.102 mg/mL PEG 1 MDa
A7PS362_s8_t1 = 0.0509 mg/mL PEG 1 MDa

Additionally, this file contains .csv files of all the statistics on particle sizes collected by the ImageJ macro. These are labeled in the format “zstackname_automated_counting_statistics”, where “zstackname” is the title of the associated z-stack. It also contains a .csv file of the particle # IDs of the singlet particles that were used to get the average singlet size, which was then used to normalize the ECDFs (as explained in detail in Materials and Methods). These are labeled in the format “zstackname_singlet_IDs”, where “zstackname” is the title of the associated z-stack. These .csv files were used in combination with the Jupyter notebooks provided as additional files to this paper to generate Figure 4, figure supplement 2.
DOI: 10.5061/dryad.n66q0nv/1
title: Table of urban metrics

description: The table lists 1,177 urban metrics and their specific categorizations, collected from a survey of urban wildlife studies published between 2012 and 2016. Column abbreviations: com_type = component type; com_s_type = component subtype; meth_cat_con = whether method was categorical or continuous; prop_hr = ratio of metric spatial scale to species' typical home range.
DOI: 10.5061/dryad.pr00820/1
title: Coyote Population Pedigree

description: This datafile contains pedigree information for all individual pups and parents included in the study. The 'pedantics' package was used on these data to determine pedigree specifications and summary statistics for the pedigree used in all Bayesian animal models. These data can be found in the Supporting Information Table S1.
DOI: 10.5061/dryad.pr00820/2
title: Coyote Risk-Taking Assays

description: This CSV file contains all foraging (i.e. risk-taking) assay data, for both pups and parents, over the 5-15 week study period. Each row represents a single observation for each individual in order to assess repeated measures in pups/parents. The "animal", "dam", and "sire" columns are synonymous to those found in the 'Coyote Pedigree' file attached; this was done as a requirement by the 'MCMCglmm' package, which needs all three columns to structure data around the pedigree. The column titled "Lit.ID" denotes the litter identity of each pup, the variable used to observe common environment effects using MCMCglmm. The "ID" column is identical to the "animal" column, but is necessary in order to partition additive genetic effects from permanent environment effects (see Wilson et al. 2010 - An Ecologist's Guide to the Animal Model). The column "Age" denotes the age of the pup/litter when the observation occurred, the "life.stage" partitions pup observations from adult observations, and the "Dev.Period" column partitions the weaning and post-weaning periods (i.e. 5-9 week observations and 10-14 week observations, which can be traced back to the "Age" column). The "risk.success" column represents whether an individual foraged or not during an observation (i.e. "0" for no, and "1" for yes), whereas the "risk.total" column is always equal to "1", denoting the total number of observations.  This column is only important insofar as the way in which you choose to analyze the data in the MCMCglmm package.  If using the distribution family argument "multinomial2", then the "risk.total" column is used as the second variable in that dependent variable form. Further - "Lit.size" denotes litter size of the pup/adult, "Year" (either 1st or 2nd) denotes the year of observation and the parity of the parent, "Sex" is self-explanatory, and "Trmt" indicates the PARENTAL odor treatment group, which occurred BEFORE the pups were born (see Schell et al. 2016 - Olfactory attractants and parity affect prenatal androgens and territoriality of coyote breeding pairs).