cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.8sc52/5
title: CRM image scan of 6 day old biofilm, cosmic ray corrected, exported in ASCII format

description: WiTec Project file of a CRM image scan of the 6 day old Shewanella oneidensis biofilm. From M&M: The measurement was performed on a WITec alpha300 confocal Raman microscope, using a 50 µm pinhole and a Zeiss LD plan-NEOFLUAR 20×/0.4 corr air objective with coverslip correction. 20× magnification was used in order to keep as many bacteria as possible in the focal plane while still resolving individual bacteria. The excitation wavelength was 532 nm, with laser power of 3 mW at the focal plane. The Raman detector was a newton EMCCD camera cooled to -60o C with a 600 g/mm grating. Integration time was 1 second and lateral resolution 2 pixel/µm. The file was exported in ASCII format.
DOI: 10.5061/dryad.8sc52/6
title: CRM image scan of 9 day old biofilm, cosmic ray corrected, exported in ASCII format

description: WiTec Project file of a CRM image scan of the 9 day old Shewanella oneidensis biofilm. From M&M: The measurement was performed on a WITec alpha300 confocal Raman microscope, using a 50 µm pinhole and a Zeiss LD plan-NEOFLUAR 20×/0.4 corr air objective with coverslip correction. 20× magnification was used in order to keep as many bacteria as possible in the focal plane while still resolving individual bacteria. The excitation wavelength was 532 nm, with laser power of 3 mW at the focal plane. The Raman detector was a newton EMCCD camera cooled to -60o C with a 600 g/mm grating. Integration time was 1 second and lateral resolution 2 pixel/µm. The file was exported in ASCII format.
DOI: 10.5061/dryad.8sc52/7
title: CRM image scan of 35 day old biofilm, cosmic ray corrected, exported in ASCII format

description: WiTec Project file of a CRM image scan of the 35 day old Shewanella oneidensis biofilm. From M&M: The measurement was performed on a WITec alpha300 confocal Raman microscope, using a 50 µm pinhole and a Zeiss LD plan-NEOFLUAR 20×/0.4 corr air objective with coverslip correction. 20× magnification was used in order to keep as many bacteria as possible in the focal plane while still resolving individual bacteria. The excitation wavelength was 532 nm, with laser power of 3 mW at the focal plane. The Raman detector was a newton EMCCD camera cooled to -60o C with a 600 g/mm grating. Integration time was 1 second and lateral resolution 2 pixel/µm. The file was exported in ASCII format.
DOI: 10.5061/dryad.b3604/1
title: Analysis and simulation code

description: Zip file includes three directories.  (1) Mathematica code to derive the main results. (2) R code to generate the figures. (3) C code to run the simulations.
DOI: 10.5061/dryad.br874/1
title: island_habitat

description: Habitat features of each island
DOI: 10.5061/dryad.br874/2
title: Landmark configurations of specimens

description: Rough landmark configurations of all specimens
DOI: 10.5061/dryad.br874/3
title: dorso_covariate
DOI: 10.5061/dryad.cf6nh/1
title: Retrospective assessment of postnatal depression Myers Burger Johns

description: The data provided are sufficient to replicate the analysis of the effect of postnatal depression on completed fertility and parity progression presented in Myers, S., Burger, O., and Johns, S.E. (in press) Postnatal depression and reproductive success in modern, low-fertility contexts. Evolution, Medicine, and Public Health. To preserve participant anonymity the data are provided in processed form and country in which child rearing occurred has been omitted. For a full description of the measures included please consult the aforementioned paper.
DOI: 10.5061/dryad.db005/1
title: Squamata Tree, Methods, and Data

description: The tree, methods, and data used to create the fully-sampled PASTIS phylogenies and the estimates of ED for all species.
DOI: 10.5061/dryad.db005/2
title: squam_shl_new_Posterior_9755.1000

description: First 1000 fully-sampled squamate trees.
DOI: 10.5061/dryad.db005/3
title: squam_shl_new_Posterior_9755.2000

description: Second 1000 fully-sampled squamate trees.
DOI: 10.5061/dryad.db005/4
title: squam_shl_new_Posterior_9755.3000

description: Third 1000 fully-sampled squamate trees.
DOI: 10.5061/dryad.db005/5
title: squam_shl_new_Posterior_9755.4000

description: Fourth 1000 fully-sampled squamate trees.
DOI: 10.5061/dryad.db005/6
title: squam_shl_new_Posterior_9755.5000

description: Fifth 1000 fully-sampled squamate trees.
DOI: 10.5061/dryad.db005/7
title: squam_shl_new_Posterior_9755.6000

description: Sixth 1000 fully-sampled squamate trees.
DOI: 10.5061/dryad.db005/8
title: squam_shl_new_Posterior_9755.7000

description: Seventh 1000 fully-sampled squamate trees.
DOI: 10.5061/dryad.df264/1
title: Supplementary data
DOI: 10.5061/dryad.gp545/1
title: Jack Stanley - NPS Audit. Age, gender, Employment and Diagnosis edited for anonymisation purposes

description: The original data set contained 388 cases. 5 were removed to preserve anonymity. These were numbers 12, 160, 232, 387 and 459. Interested parties can contact Jack Stanley at s1004557@sms.ed.ac.uk if they would be interested in seeing the full data set. Furthermore age has been included as a range, uncommon diagnoses grouped as 'other' and data for students and self employed individuals has all been grouped as 'employed' for the purposes of coding. The frequencies of each of the latter two variables remain included in the results section for interest.
DOI: 10.5061/dryad.h468f/1
title: Rainbowfish positional and feeding data and Matlab scripts

description: Rainbowfish positional and feeding data and Matlab scripts
DOI: 10.5061/dryad.hr069/11
title: HCT data files

description: data files for hypoxia Challenge tests
DOI: 10.5061/dryad.hr069/9
title: 20th dec fish 10 hypoxia
DOI: 10.5061/dryad.j0036/1
title: S. punctum heat shock experiment

description: Responses to heat shock (15 minutes at 42C) in thermal experimental evolution lines of Sepsis punctum (originating from Zurich, Switzerland)
DOI: 10.5061/dryad.nk25m/1
title: Buczek et al_MHC, parasites and antlers
DOI: 10.5061/dryad.pr078/10
title: reference.maf.005_bayescan

description: Input file for BayeScan - reference dataset
DOI: 10.5061/dryad.pr078/12
title: EnvVar_phase3

description: Values of the environmental variables used as input for Bayenv
DOI: 10.5061/dryad.pr078/14
title: reference.maf.005_bayenv

description: Input file for Bayenv - reference dataset
DOI: 10.5061/dryad.pr078/4
title: reference.maf.005_ped

description: plink ped file for Bayescan and Bayenv - reference dataset
DOI: 10.5061/dryad.pr078/5
title: reference_thinned_map

description: plink map file for Arlequin - reference dataset
DOI: 10.5061/dryad.pr078/6
title: reference_thinned_ped

description: plink ped file for Arlequin - reference dataset
DOI: 10.5061/dryad.pr078/7
title: candidate_005_arp

description: Input file for Arlequin - candidate dataset
DOI: 10.5061/dryad.pr078/8
title: reference_thinned_arp

description: Input file for Arlequin - reference dataset
DOI: 10.5061/dryad.pr078/9
title: candidate.maf.005_bayescan

description: Input file for BayeScan - candidate dataset
DOI: 10.5061/dryad.q1j71/1
title: tolerance and resistance

description: Tolerance and resistance measures collected from 9 genotypes of S. altissima grown across and nutrient gradient within the greenhouse. Resistance was estimated using the relative growth rates of herbivores placed on previously fed on (induced) vs. control (constitutive) plants. Tolerance of herbivory of each genotype is estimated by dividing the fitness of a damaged plant by the fitness of an undamaged plant
DOI: 10.5061/dryad.q1j71/2
title: Plant trait data

description: Trait from plant individuals of 9 genotypes of S. altissima grown across a nutrient gradient (4 levels: 0ppm=lowest to 400ppm highest) and herbivory gradient (3 levels: 0= no herbivory, 1= 1 week of herbivory, 2=2 weeks of herbivory) within a greenhouse experiment. Column abbreviations are in metadata sheet.
DOI: 10.5061/dryad.qg269/1
title: waxmothF2data

description: The file contains the backcross progeny phenotypes and genotypes. The cross was the hybrid male progeny of a Kansas female with a Florida male crossed to a Kansas male. Included are the phenotypic and genotypic values for all individuals.
DOI: 10.5061/dryad.qg269/2
title: waxmoth_parentals_hybrids

description: This file contains the phenotypic data for males of the Kansas line, the Florida line, and their hybrid males (Kansas female crossed with a Florida male).  The data includes two life history variables and three acoustic calling song variables.
DOI: 10.5061/dryad.18v4b/1
title: Behavioral and morphological data and responses to alarm calls

description: This file combines data from Jullien and Thiollay 1998 with our data for estimations of flocking propensity (field data collected in 2011).  Data on morphological and behavioral traits were either derived from the literature (foraging strategy, body mass) or collected from our observations in 2011 (Foraging height, Density, Distance to Alarm Calls). The columns in the data set are the following: Species=Name of species Fyes=Number of times seen with a flock Fno=Number of times not seen with a flock Ntrials=Total number of trials Propensity=Flocking propensity of each species based on proportion of observations in which species was observed flockingMass=Body Mass in gramsHeight= Mean Height derived from observations across all individuals of species from alarm trials (data from 2011 only).  Density=Mean Density derived from observations across all individuals of species from alarm trials (data from 2011 only).Fstrategy= Foraging strategies of each speciesDistance=Mean distance across all individuals of a species from alarm playback trials (data from 2011 only).Ayes=Number of positive responses of a species to alarm playback trials (data from 2011 only).Ano=Number of negative responses of a species to alarm playback trials (data from 2011 only).AlarmTrials=Total number of alarm playback trials per species (data from 2011 only).ProbAlarm=Proportion of positive responses to alarms (data from 2011 only).A.response= Characterizes a binomial response for each species where a species is classified as responding to alarm calls if it responds at least once irrespective of the number of trials.
DOI: 10.5061/dryad.18v4b/2
title: phy_dryad

description: The phylogenetic tree used in the analysis derived from Jetz et al. (2012).
DOI: 10.5061/dryad.28631/1
title: R code for topological noise removal through decimation and smoothing

description: This file contains the code written in R for removing topological noise from a mesh, by applying decimation and smoothing procedures. The code makes use of the tool described in the main text of the paper.
DOI: 10.5061/dryad.28631/2
title: Surface smoothing procedure for applications of Geometric Morphometrics

description: R code for the tool described in the main text of the paper. The tool performs an estimation of the smoothing settings providing the highest recovery or lowest loss of topological information in a Geometric Morphometric context.
DOI: 10.5061/dryad.28631/3
title: venus.mesh

description: The 3D model used in the example shown in the supplementary information of the paper (used with the code in Sup1.R).
DOI: 10.5061/dryad.28631/4
title: SCP1.mesh

description: The 3D model of the neanderthal cranium of Saccopastore 1 used in the example shown in the supplementary information of the paper (used with the code in Sup2.R).
DOI: 10.5061/dryad.28631/5
title: SCP1.Lset

description: The 3D landmark set recorded on the neanderthal cranium of Saccopastore 1 and used in the example shown in the supplementary information of the paper (used with the code in Sup2.R).
DOI: 10.5061/dryad.28631/6
title: SCP1.SLset

description: The 3D semi-landmark set built on the neanderthal cranium of Saccopastore 1 and used in the example shown in the supplementary information of the paper (used with the code in Sup2.R).
DOI: 10.5061/dryad.31v06/11
title: Supplemental Table 9 -  supplement of Figure 4. qRT_PCR primer list
DOI: 10.5061/dryad.31v06/12
title: Supplemental Table 10-  supplement of Figure 6S2. Bacterial qPCR primers
DOI: 10.5061/dryad.31v06/13
title: Supplemental Table 4 - supplement of Figure 6S2. Shared Operational Taxonomic Units (OTUs) in mice displaying a decreased social behavior (NOD_vehicle and C57BL:6 transplanted with NOD microbiota)

description: Shared Operational Taxonomic Units (OTUs) in mice displaying a decreased social behavior (NOD_vehicle and C57BL:6 transplanted with NOD microbiota). GreenGenes v13-8 OTU IDs and taxonomy for OTUs present in NOD mice gavaged with vehicle for 14 days not found in the same animals at baseline (n= 3 samples per time-point).
DOI: 10.5061/dryad.4fp90/1
title: experiments_phyto_12_26_15

description: cell densities of phytoplankton taxa in initial lake water and in each experimental replicate. column definitions are provided in ReadMe.txt.
DOI: 10.5061/dryad.4fp90/2
title: Chla

description: chlorophyll a concentrations in initial lake water and in experimental replicates. column definitions are provided in ReadMe.txt
DOI: 10.5061/dryad.4fp90/3
title: park_lakes_db

description: 675 dissolved inorganic nitrogen (NO3-N and NH3-N) observations from lakes above 1,200 m sampled between 1988 and 2014 across Mount Rainier, North Cascades, and Olympic National Parks. The database was compiled by Jason Williams. Column definitions and information about data origins and compilation are provided in ReadMe.txt
DOI: 10.5061/dryad.4jd39/1
title: bisection_data

description: Behavioral response data was aquired with custom made Python software and written into text files. For details see ReadMe file.
DOI: 10.5061/dryad.4tv57/35
title: NE_Wobble
DOI: 10.5061/dryad.4tv57/36
title: RR_MVC
DOI: 10.5061/dryad.4tv57/37
title: RR_Seated
DOI: 10.5061/dryad.4tv57/38
title: RR_Standing
DOI: 10.5061/dryad.4tv57/39
title: RR_Wobble
DOI: 10.5061/dryad.4tv57/40
title: WO_MVC
DOI: 10.5061/dryad.4tv57/41
title: WO_Seated
DOI: 10.5061/dryad.4tv57/42
title: WO_Standing
DOI: 10.5061/dryad.4tv57/43
title: WO_Wobble
DOI: 10.5061/dryad.4v2s0/1
title: Functional Response and Behavioural raw data

description: Sheet 1 presents all the raw functional response data for each of the 3 species as well as each of the 3 multi-species combinations. Each row represents a feeding trial and includes the number of prey supplied and eaten during the trial and the number of prey alive at the end of the trial. Sheet 2 presents raw data from the behavioural experiment. In this regard, for each multi-predator combination, counts of each behavioural category are presented, along with the descriptions of each category.
DOI: 10.5061/dryad.5k7f1/1
title: Summary table of all data Excel

description: Excel spreadsheet with labeled columns of data, including: sample name, life stage (mother, established colony, larva), origin in study site (main/ outside quadrat, maternal colony), colony size, spatial coordinates, genotypes (2 columns per locus)
DOI: 10.5061/dryad.5k7f1/2
title: Summary table of all data CSV

description: CSV table with labeled columns of data, including: sample name, life stage (mother, established colony, larva), origin in study site (main/ outside quadrat, maternal colony), colony size, spatial coordinates, genotypes (2 columns per locus)
DOI: 10.5061/dryad.6g53s/1
title: eDNA DATA_ALR et al. JAppEcol2015

description: The environmental DNA (eDNA) concentration (pg/L) of each sample is provided, including replicate measurements. For each site, the latitude, longitude and site depth (m) are also provided.
DOI: 10.5061/dryad.6rv61/1
title: GIS results

description: Contains a mix of shapefiles and georeferenced TIFF files of the results shown in the paper's figures.
DOI: 10.5061/dryad.7rf84/1
title: Data file
DOI: 10.5061/dryad.db005/10
title: squam_shl_new_Posterior_9755.9000

description: Ninth 1000 fully-sampled squamate trees.
DOI: 10.5061/dryad.db005/11
title: squam_shl_new_Posterior_9755.10000

description: Tenth 1000 fully-sampled squamate trees.
DOI: 10.5061/dryad.db005/9
title: squam_shl_new_Posterior_9755.8000

description: Eighth 1000 fully-sampled squamate trees.
DOI: 10.5061/dryad.dh371/1
title: Supplementary file 1. Complete List of identified Proteins in Proteome Study
DOI: 10.5061/dryad.dh371/2
title: Supplementary file 2. Complete list of phosphosites quantified in the three stimulation comparisons
DOI: 10.5061/dryad.g8d5k/1
title: M_fissipes_phyml

description: Phylogeny of mitochondrial COI lineages from 11 populations of Microhyla fissipes in Taiwan. This tree was constructed by using PhyML 3.0 with 1000 bootstrap replicates.
DOI: 10.5061/dryad.h5fg1/1
title: CFUs of mixes of strains in CAA and BSA at 0 and 48 hours

description: Population sizes of each of the strains (wildtype WT, lasB mutants DLB and lasR mutants DLR) were quantified in monoculture and in coculture at different ratios of WT to mutant (9:1, 1:1 or 1:9). Experiments were conducted in two growth media: CAA (casamino acids + M9), which all strains could take up and BSA (casamino acids + M9 + BSA, which could only be digested using elastase). To distinguish the strains in cocultures, fluorescently-labelled strains (YFP or DsRed) were used and mixed in all possible combinations to test for labelling effects. We quantified population sizes by plating out dilution series and counting colony-forming units. These are listed in the file for t=0h and t=48h. This shows how the ratio of the strains and the total population size change throughout the experiment. These data were used to generate Fig. 1B, 2B and 3.
DOI: 10.5061/dryad.h5fg1/2
title: Growth curves (OD_600) over 48 hours in CAA medium

description: Population sizes of each of all experimental treatments (monocultures of wildtype WT, lasB mutants DLB and lasR mutants DLR) and cocultures of WT and one of the mutants at different ratios (9:1, 1:1 or 1:9) growing in CAA medium (casamino acids, which all strains should be able to take up). We quantified population sizes using a Tecan plate reader measuring OD_600. These are listed in the file every hour for 48 hours. These data were used to generate Fig. 1A.
DOI: 10.5061/dryad.j62n1/1
title: Microarray data; chronic and pulsed stimulations of TNFalpha

description: GFP-p65 MEFs were either chronically or periodically stimulated (90' and 180' forcing periods) with TNF-alpha. RNA samples were extracted at selected timepoints using the Illustra RNAspin Mini kit (GE Healthcare). Following extraction, RIN (RNA Integrity Number) was &gt;9 (BioAnalyser, Agilent RNA Nano Kit). RNA samples (500 ng) were reverse transcribed with the Illumina TotalPrep RNA Amplification Kit (Ambion) and copy RNA (cRNA) was generated with 14 hour in vitro transcription reactions and checked at the BioAnalyser. Washing, staining, and hybridization were performed according to standard Illumina protocols. cRNA samples were then hybridized to Illumina BeadChip Array MouseRefSeq-8 v2. BeadChips were scanned with BeadArray™ Reader in channel 2. The .zip file contains the following files:  Quality control files: "Zambrano_90MIN_ControlProbe.csv", "Zambrano_180MIN_ControlProbe.csv", "Zambrano_Chronic_ControlProbe.csv". Raw data files: "ZambranoMicroarray_90MIN.csv", "ZambranoMicroarray_180MIN.csv", "ZambranoMicroarray_Chronic.csv".
DOI: 10.5061/dryad.kh6f7/1
title: Great Tit Distribution Map All Data

description: This excel file contains all the data used in the following paper: "Distribution and abundance of glucocorticoid and mineralocorticoid receptors throughout the brain of the great tit (Parus major)." by Rebecca A. Senft, Simone L. Meddle and Alexander T. BaughThe sheets have titles describing their contents. The first is the distribution map for glucocorticoid and mineralocorticoid receptor expression in all regions of the brain in one female great tit, color-coded for expression level. The second contains the information for mineralocorticoid and glucocorticoid expression in the hippocampus and paraventricular nucleus of the hypothalamus across our population of 25 individual great tits. Tables to the right break this information down by individual bird (instead of by image). The third sheet includes mean expression for the population, as well as some demographic variables.
DOI: 10.5061/dryad.kr8kk/1
title: gelsemium_velvet_assembly

description: gelsemium_velvet_assembly.fasta
DOI: 10.5061/dryad.kr8kk/2
title: gelsemium_sspace_assembly

description: gelsemium_sspace_assembly.fasta
DOI: 10.5061/dryad.m3987/1
title: PilakoutaSieberSmisethJEB2016.csv

description: Raw data on the joint effects of brood size and inbreeding status on offspring fitness in the burying beetle Nicrophorus vespilloides.
DOI: 10.5061/dryad.mn36c/1
title: Mean group-level scrounging probabilities

description: Mean group-level scrounging probabilities (column 5) for different, fixed values of N (column 1), a/F (column 2), c (column 3), and lambda (column 4). Data generated in R, representing numerical approximations of analytical solutions provided in manuscript.
DOI: 10.5061/dryad.p6d88/1
title: evolution experiment
DOI: 10.5061/dryad.p6d88/2
title: FDS competition assays
DOI: 10.5061/dryad.p6d88/3
title: host ratio shift competition assays
DOI: 10.5061/dryad.p6d88/4
title: tradeoff AP competition assays
DOI: 10.5061/dryad.p6d88/5
title: Variable name definitions
DOI: 10.5061/dryad.pr078/11
title: EnvironmentalVariables_phase3.xls

description: Details of the environmental variabes used in Bayenv
DOI: 10.5061/dryad.pr078/13
title: candidate.maf.005_bayenv

description: Input file for Bayenv - candidate dataset
DOI: 10.5061/dryad.s04bb/1
title: Adult Pituitary Data1

description: GFP fluorescence measured from single cells in adult pituitary tissue and subsequent modelling of transcription activity using a stochastic switch model.
DOI: 10.5061/dryad.s04bb/2
title: Adult Pituitary Data2

description: GFP fluorescence measured from single cells in adult pituitary tissue and subsequent modelling of transcription activity using a stochastic switch model.
DOI: 10.5061/dryad.s04bb/3
title: Adult Pituitary Data3

description: GFP fluorescence measured from single cells in adult pituitary tissue and subsequent modelling of transcription activity using a stochastic switch model.
DOI: 10.5061/dryad.s04bb/4
title: E18_5 Pituitary Data1

description: GFP fluorescence measured from single cells in embryonic day18.5 pituitary tissue and subsequent modelling of transcription activity using a stochastic switch model.
DOI: 10.5061/dryad.s04bb/5
title: E18_5 Pituitary Data2

description: GFP fluorescence measured from single cells in embryonic day18.5 pituitary tissue and subsequent modelling of transcription activity using a stochastic switch model.
DOI: 10.5061/dryad.tm508/1
title: Morphological data for male crickets

description: The pronotum length and body mass for sexually attractive and unattractive males that were immune-challenged with lipopolysaccharide or injected with saline.
DOI: 10.5061/dryad.tm508/2
title: Sexual signalling data for male crickets

description: Calling rate of sexually attractive and unattractive males that were immune-challenged with lipopolysaccharide or injected with saline.
DOI: 10.5061/dryad.085vq/1
title: Used SNP markers

description: The columns correspond to marker name, usage in parentage analysis (parents and offspring), usage in population analysis, the Drosophila virilis gene the marker maps to, the relevant D. virilis chromosome and the top blast hit of the marker by using Blast2GO
DOI: 10.5061/dryad.085vq/2
title: Data on females' first mating

description: The data file “First mating” includes all females that mated in the first mating and the number of eggs they laid and the number of offspring that eclosed from eggs laid after the first mating.
DOI: 10.5061/dryad.278q9/1
title: Pmentalis_HighResolutionScansReplace

description: High Resolution CT scans of Pipra mentalis
DOI: 10.5061/dryad.278q9/2
title: Mvitellinus_HighResolutionScansReplace

description: High Resolution CT scans of Manacus vitellinus
DOI: 10.5061/dryad.278q9/3
title: Mcandei_HighResolutionScansReplace

description: High Resolution CT scans of Manacus candei