cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0h82m/3
title: Fig. 1 Position of the eleven Danish strains within the B. anthracis phylogenetic tree based on whole-genome SNP analysis.

description: Figure 1. Position of the eleven Danish strains from cattle within the B. anthracis phylogenetic tree based on whole-genome SNP analysis. Minimum spanning tree based on 6596 chromosomal SNPs (A), 222 pXO1 SNPs (B) and 166 pXO2 SNPs (C). The 13 different canSNP groups are color-coded: C.Br.A1055 in white, B.Br.CNEVA in yellow, B.Br.001/002 and B.Br.Kruger in orange, A.Br.011/009 in light blue, A.Br.008/011 in blue, A.Br.WNA in dark blue, A.Br.005/006 in pink, A.Br.003/004 in red, A.Br.001/002 in green, A.Br.WNA in dark green, A.Br.Aust94 in brown and A.Br.Vollum in purple. The position of the 11 Danish isolates (in bold and underligned), the African IEMVT89 and 40 available whole genome-sequenced strains is marked. The length of each branch is proportional (logarithmic scale) to the number of SNPs identified between strains. Indicated in red are the position and name of some new or published SNPs specific to various canSNP groups: A05 (A.Br.005/006 group); A.Br.008 (A.Br.008/009 group); A08/D and A08/D1 (A.Br.008/011); A.Br.011 (A.Br.011/009); A.Br.009 (A.Br.WNA); A.Br.002 and A01 (A.Br.001/002 and A.Br.Ames); A02, A02/A, A02/B, A02/B1 (A.Br.001/002 subgroup A02); A.Br.001 and A01/A-DK (A.Br.Ames); A.Br.013,  A.Br.015a, A.Br.15b, A.Br.026 (A.Br.Aust94). Based on a parsimony approach, the trees sizes are, respectively, 6730 (A), 227 (B) and 168 SNPs (C), i.e. containing approximately 1.9 (A), 2.2 (B) or 1.2 (C) % of homoplasia.The minimum spanning tree was drawn in BioNumerics version 6.6 (Applied Maths) using default settings.
DOI: 10.5061/dryad.103h8/1
title: Feeding, mating, and fecundity data and analysis for T. eriodictyonis

description: Original data collected by Katherine Gould. Excel 2013 file (.xlsx). Clarifying notes can be found withing the spreadsheets. In general, Et refers to Eriodictyon trichocalyx and Ec refers to Eriodictyon crassifolium. Mating treatments (e.g. Et-Ec) use male's plant then female's plant code.
DOI: 10.5061/dryad.1168f/1
title: tooth_fossil
DOI: 10.5061/dryad.13qh4/1
title: data

description: Please see the Readme.txt file for a description of the data.
DOI: 10.5061/dryad.143sp/1
title: Data

description: Data used for analysis and graphs
DOI: 10.5061/dryad.37hr9/1
title: Data and Analysis Scripts

description: Contains raw and filtered data sets used in analyses (MNAK, MGK, etc), and scripts for performing the analyses in the paper. The scripts are in R and require perspectev to be in installed (see https://cran.r-project.org/web/packages/perspectev/). Further information about using perspectev can be found here: http://evolve.zoo.ox.ac.uk/Evolve/Perspectev.html
DOI: 10.5061/dryad.3n2j5/1
title: 2 yrs data for PCA on reproductive success
DOI: 10.5061/dryad.3n2j5/2
title: 4 yrs data for PCA on reproductive success
DOI: 10.5061/dryad.3n2j5/3
title: 2 years data for PCA on survival
DOI: 10.5061/dryad.469vn/1
title: song data

description: Raw data for song analysis
DOI: 10.5061/dryad.5p6vv/1
title: DRYAD_Supplemental Data
DOI: 10.5061/dryad.61f4v/1
title: II Levin Encounternet methods paper calibration and field test files

description: The following CSV files are contained in the zipped folder: BarnFieldTest.csv: data for comparison of tag-tag RSSI in field vs. barn. BrokenLogComparison.csv: data to compare broken logs to unbroken logs of comparable length from Encounternet tag deployment. Brokenlogs.csv: Data containing all broken log files. Dyads.csv: Data for all dyadic logs collected from Encounternet tag deployment. DyadsforLogistcReg.csv: Data for logistic regression on dyadic logs. RangeTestforDummyMount.csv: Data for comparison of tag mount dummy for field testing. TagBaseTest.csv: Data for tests of inter-receiver station variability. TagTagDistCat.csv: Data for tests of inter-tag variability. TagTagTest.csv: Data for tests of inter-tag variability
DOI: 10.5061/dryad.67n7n/20
title: Location Samples

description: Details on the river samples location. All rivers are located in New Zealand.
DOI: 10.5061/dryad.6t5n0/1
title: Oppold et al. 2015_Figure 2_methylation data

description: Raw data and statistics of global DNA methylation levels in Aedes albopictus.
DOI: 10.5061/dryad.6t5n0/2
title: Oppold et al. 2015_Figure 3_toxicity data

description: Raw data and statistics of imidacloprid insecticide sensitivity of Aedes albopictus.
DOI: 10.5061/dryad.72dk5/2
title: Original and pre-processed data, and analysis results

description: Data acquired from infants at risk of Postoperative Apnea (in MATLAB *.mat format). Also, results of the analysis of these data by 4 scorers using the RIPScore manual scoring tool.
DOI: 10.5061/dryad.74ms0/10
title: mussel750_001

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/11
title: mussel750_002

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/12
title: mussel750_003

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/5
title: mussel380_004

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/6
title: mussel550_001

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/7
title: mussel550_002

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/8
title: mussel550_003

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/9
title: mussel550_004

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.8n2c0/1
title: Random buffer habitat diversity

description: This file contains the Shannon diversity index on habitat categories in buffers around random points.
DOI: 10.5061/dryad.8n2c0/2
title: Plant species richness

description: This file contains the plant species richness and the habitat diversity of buffers around plant sampling points.
DOI: 10.5061/dryad.8n2c0/3
title: Pollinator species richness

description: This file contains the bumblebee, butterfly and solitary bee species richness and the habitat diversity of buffers around pollinator sampling points.
DOI: 10.5061/dryad.8n2c0/4
title: Summer bird species richness

description: This file contains the summer bird species richness and the habitat diversity of buffers around summer bird sampling points.
DOI: 10.5061/dryad.8n2c0/5
title: Winter bird species richness

description: This file contains the winter bird species richness and the habitat diversity of buffers around winter bird sampling points.
DOI: 10.5061/dryad.8n2c0/6
title: Farm level species richness all taxa

description: This file contains the species richness of all taxa sampled at each of the 12 farms, summed at the farm level.
DOI: 10.5061/dryad.c1sd4/1
title: Matrix.for.RAxML.Analysis

description: A NEXUS file written for Mesquite with a concatenated alignment and for all haplotypes which was used to reconstruct phylogenetic relationships (in RAxML) of populations of Pteronarcella badia and its sister species across western North America.
DOI: 10.5061/dryad.c1sd4/2
title: BEAST.Divergence.Dating

description: The input file for BEAST containing all haplotypes which was used to infer divergence among populations of Pteronarcella badia across western North America.
DOI: 10.5061/dryad.c1sd4/3
title: BEAST.BSP

description: A BEAST input file used to infer recent demographic history via Bayesian Skyline analysis of Pteronarcella badia populations in western North America.
DOI: 10.5061/dryad.c1sd4/4
title: Migrate.Infiles

description: Three input files used to infer migration rates of Pteronarcella badia across, and within several major drainage basin boundaries in Western North America.
DOI: 10.5061/dryad.c1sd4/5
title: TCS.mtConcat

description: The input file used to generate a haplotype network of Pteronarcella badia in TCS using a concatenated dataset of mitochondrial genes.
DOI: 10.5061/dryad.c1sd4/6
title: TCS.28S

description: The input file used to generate a haplotype network of Pteronarcella badia in TCS using a portion of 28S rRNA.
DOI: 10.5061/dryad.c1sd4/7
title: IBD.Infiles

description: Input files for IBD (Isolation-by-Distance) web server (http://ibdws.sdsu.edu/~ibdws/distances.html) used to test for isolation-by-distance as a determinant of population structure within each major clade of Pteronarcella badia sequences.
DOI: 10.5061/dryad.ch206/1
title: mosquito mortality data

description: Mortality data for mosquitoes exposed to Beauveria bassiana fungus. 'Experiment' indicates the experiment and block, with A1 and A2 representing the constant temperature Anopheles stephensi experiments (block 1: 20, 22, 24, 26, 28, 30 and 34 °C; block 2: 10, 14, 18, 26 and 32 °C), B representing the Anopheles gambiae experiment, C representing the blood feeding experiment and D representing the diurnal temperature variation experiment. 'Temperature' indicates the mean experimental temperature.  'AR' indicates fungal application rate. 'Diet' indicates whether mosquitoes were allowed to feed on blood (1) or fed exclusively on glucose-PABA solution (0). 'DTR' indicates the diurnal temperature range in degrees Celsius, with '0' indicating constant temperatures. 'Cup' indicates replicate experimental cups. 'Day' indicates time in days since fungal exposure. 'Event' indicates whether mosquitoes died (1) or were censored (0), i.e. they survived to the end of the experiment. 'Count' indicates the number of individual mosquitoes associated with the 'Event' column for each treatment and time point.
DOI: 10.5061/dryad.ck4h0/1
title: Coda interclick interval data from Gero et al Individual, unit, and vocal clan level identity cues in sperm whale codas in RSOS

description: Eastern Caribbean sperm whale coda inter-click interval dataset from Gero et al. Individual, unit, and vocal clan level identity cues in sperm whale codas in RSOS
DOI: 10.5061/dryad.d5j06/1
title: Embryonic lethality data

description: This is a tab-delimited text file with one header row, 27,360 data rows, and 19 columns. Each data row corresponds to a unique image taken of a well in a 96-well plate, in which there are (potentially) adult worms, dead embryos, and living larvae. The column headers are: adults_man (the number of adults in the image, manually counted by a human); eggs_man (the score of the abundance of dead embryos in the image, from 0 to 9, scored manually by a human); larvae_man (the score of the abundance of living larvae in the image, from 0 to 9, scored manually by a human); strain (the worm strain); vector (the gene targeted by RNAi, or in the case of "empty," the negative control RNAi clone); date (the one of three date batches in which the experiments were conducted); well_row (the row, from A to H, in a 96-well plate, in which the well was located); well_col (the column, from 1 to 12, in a 96-well plate, in which the well was located); fol_strain (the grouping, from a to c, to which the worm strain in this image belonged when it was dispensed into the 96-well plates; strains were dispensed in sets of 8, as each plate has 8 rows); fol_lib (the RNAi library, from 1 to 4, to which the bacteria in this well belonged when it was dispensed); fol_bac_rep (the batch of bacterial culture, either "car," "gre," or "roy" that was dispensed into this well; from a single bacterial library, three replicate culture batches were grown in three deep-well 96-well plates, from which the RNAi bacteria were dispensed into the experimental plates); fol_plate_rep (the replicate plate number, from 1 to 8; each experimental condition of worm strain and RNAi vector was replicated 8 times, across the three replicate batches of bacterial culture); image (the image number, from 1 to 96, in a 96-well plate, assigned by the image capture software); adult_area (the number of pixels assigned to the "adult" category by the DevStaR algorithm); larva_area (the number of pixels assigned to the "larva" category by the DevStaR algorithm); egg_area (the number of pixels assigned to the "embryo" category by the DevStaR algorithm); adults (the count of adults in the image by the DevStaR algorithm); larvae (the count of living larvae in the image by the DevStaR algorithm); eggs (the count of dead embryos in the image, determined by dividing egg_area by 70). NA values in the manually scored columns (adults_man, eggs_man, larvae_man) indicate that the well failed to grow a mature culture of worms. This is often due to somatic lethality of the targeted gene (e.g. the somatic control vector tba-2), or to fungal contamination. Because these images were checked by a human eye, rows with NAs in the manual columns should be excluded from most analyses.
DOI: 10.5061/dryad.gq883/12
title: Enrichment Assemblies

description: These are all 63 assemblies, in bam format with the resulting consensus sequences as fasta. All sequences are labelled by capture pool ID in table 2.
DOI: 10.5061/dryad.j5nd1/1
title: Matrix proviverrinae

description: Matrix dealing with the relationships among Proviverrinae
DOI: 10.5061/dryad.j5nd1/2
title: Reference material and literature

description: List of material and literature used for the coding
DOI: 10.5061/dryad.j5nd1/3
title: Characters

description: List of characters
DOI: 10.5061/dryad.j5r51/10
title: Simulated laminar recordings for excitatory synapses only in the lower dendritic bush

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper when excitatory synapses are located only in the lower dendritic bush, computed from LFPy. Each row is a different depth. Input intensity is 1.5 sp/ms.
DOI: 10.5061/dryad.j5r51/11
title: Simulated laminar recordings for cortical excitatory synapses only in the upper dendritic bush

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper when cortical excitatory synapses are located only in the upper bush and thalamic excitatory synapses are distributed homogeneneously over the whole neuron surface, computed from LFPy. Each row is a different depth. Input intensity is 1.5 sp/ms.
DOI: 10.5061/dryad.j5r51/12
title: LIF network output variables for input 1.5 sp/ms

description: Outputs of Leaky Integrate and Fire Network described in the paper for input intensity 1.5 sp/ms. Simulation lasts for 10100 ms sampled at 20kHz. Columns are 1) Membrane potential 2-5) local AMPA, thalamic AMPA, long range cortical AMPA, local GABA over excitatory neurons, 6-9) same as 2-5) but computed over inhibitory neurons, 10) input firing rate, 11-12) firing rate of inhibitory neurons and excitatory neurons
DOI: 10.5061/dryad.j5r51/13
title: LIF network output variables for input 0.5 sp/ms

description: LIF network output variables for input 0.5 sp/msOutputs of Leaky Integrate and Fire Network described in the paper for input intensity 1.5 sp/ms. Simulation lasts for 10100 ms sampled at 20kHz. Columns are 1) Membrane potential 2-5) local AMPA, thalamic AMPA, long range cortical AMPA, local GABA over excitatory neurons, 6-9) same as 2-5) but computed over inhibitory neurons, 10) input firing rate, 11-12) firing rate of inhibitory neurons and excitatory neurons
DOI: 10.5061/dryad.j5r51/8
title: Simulated laminar recordings for homogeneous synaptic distribution

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper when both inhibitory and excitatory synapses are distributed homogeneously over the whole neuron surface, computed from LFPy. Each row is a different depth. Input intensity is 1.5 sp/ms.
DOI: 10.5061/dryad.j5r51/9
title: Simulated laminar recordings for excitatory synapses only in the upper dendritic bush

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper when excitatory synapses located only in the upper dendritic bush, computed from LFPy. Each row is a different depth. Input intensity is 1.5 sp/ms.
DOI: 10.5061/dryad.ms046/1
title: Data plotted in figures 3 and 4

description: Data are numerically obtained by a code developed in Mathematica 9.1.
DOI: 10.5061/dryad.pm86c/1
title: Blue Tits data set from 2008 to 2013

description: Please see the README.txt file
DOI: 10.5061/dryad.q6ds5/1
title: Raw data from the HARM experiment

description: Data collected in laboratory experiment conducted in 2014. See README file for list of variables.
DOI: 10.5061/dryad.q6ds5/2
title: Raw data from the FOREIGN male experiment

description: Data collected in laboratory at Queen's University, Kingston, Ontario, Canada in 2014
DOI: 10.5061/dryad.q86q0/1
title: Context-dependent effects of Y chromosome and mitochondrial haplotype on male locomotive activity in Drosophila melanogaster

description: ID: Identifies Mito_Y_Dup_Diet where C=yeast and S=agar. Sample and Run: ID is split up into Sample and Run. Plate: Two different plates were used in the experiment. Hour: Broadly defines the time the assay was run. MinsAftLight: More specifically defines the time the assay was run. SocialEnviro: Describes the two different social contexts the assays were run under. Block: Describes the different sets of grandparental flies which the focal males descended from. ParentalAge: Describes the age of the parents when laying the eggs that grew into the focal males. Distmm: Distance travelled by flies in the 30 mins assay, in mm. emptyTime: Time when the software did not track the movement of the flies (checking the video images manually suggested this was because the flies were stationary). Mt = Mitochondrial haplotype, D = Dahomey, M = Madang.Y = Y chromosome genotype. Dup: The lines were maintained as two duplicates of each Mt and Y substitution. Diet: Focal males were assigned to one of two diets after emergence as adults - standard yeast diet (nutrient-rich) and a diet of just agar with no added nutrients (nutrient-deprived). Block.ParentalAge: Parental age nested within block. MtYDup: Identifies the MitoYDuplicate combination.
DOI: 10.5061/dryad.qb6b5/1
title: ABC estimator - equilibrium population

description: R script for running the ABC estimator assuming an equilibrium population