cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.b6gp8/2
title: bark_thickness_analysis

description: This R script produces summary statistics, model fits, and figures for the bark_thickness_data.csv file.
DOI: 10.5061/dryad.5d079/1
title: Abs spectra of A millepora

description: Absorption spectra of clarified tissue extracts of the HR and LR A. millepora morphs. The absorption spectrum of purified recombinant amilFP597 normalised to the peak value of the HR spectrum is included for comparison.
DOI: 10.5061/dryad.5d079/2
title: amilFP597 copies

description: Copy numbers of amilFP597 variant genes determined by semi-quantitative PCR amplification of a conserved genomic exon 3 fragment and by diagnostic restriction analysis with ApeK1.
DOI: 10.5061/dryad.5d079/3
title: amilFP597 indel (+) and indel (-) promoter variants

description: Sequences of all promoter clones of amilFP597 coding sequence.
DOI: 10.5061/dryad.5d079/4
title: amilFP597 exon 3 sequences

description: The chromophore coding sequences of RFP-related genes of A. millepora were amplified using genomic DNAof LR, MR and HR morphs as the template with primers designed to conserved regions within exon 3 .
DOI: 10.5061/dryad.5d079/5
title: amilFP597 promoter

description: Analysis of the amilFP597 promoter copy ratios in six A. millepora morphs with different levels of redness.
DOI: 10.5061/dryad.5d079/6
title: Sequences RFP full length genes

description: All raw sequences used to reconstruct the amilFP597 gene in A. millepora.Full-length sequences of indel (-) and indel (+) promoter variants of the amilFP597 gene were obtained for the MR morph. These sequences, extending from the promoter region to the 3’UTR, were produced by joining thesequences of two overlapping PCR products covering the 5’ region [promoter to exon 3 amplified using primerspRFPlargeF (+) or pRFPsmallF (-) and RFP SP1] and the 3’ region (intron 2 to 3’UTR amplified using primersRFP_I2-3’U_F and RFP_I2-3’U_R2). Sequence differences in the overlap between the 5’ and 3’ regionfragments were used to assign the latter to either the indel (+) or indel (-) promoter variant genes. Thepromoter-exon 3 and intron 2-3’UTR fragments were cloned and sequenced on both strands using vectorprimers and by primer walking. The assembled sequences have been submitted to GenBank as accessionsKC818413 [indel (-) gene] and KC818414 [indel (+) gene].
DOI: 10.5061/dryad.5d079/7
title: Spectroscopic characteristics of GFP-like proteins

description: All spectroscopic data utilised for the characterisation of amilFP597, amilCP506, amilCP564 and amilFP605
DOI: 10.5061/dryad.1jt86/1
title: Master_all_nests_DS_Dryad

description: Laying date and temperature data
DOI: 10.5061/dryad.256kh/1
title: Read Me

description: Contents of files submitted to DataDryad
DOI: 10.5061/dryad.256kh/2
title: geminata_msats_dataset

description: microsatellite data in Genepop format
DOI: 10.5061/dryad.256kh/10
title: ABC_AnalysisB_header

description: Header file for DIY ABC analysis B.
DOI: 10.5061/dryad.256kh/11
title: ABC_AnalysisC_header

description: Header file for DIY ABC analysis C.
DOI: 10.5061/dryad.256kh/3
title: geminata_mtDNA_dataset

description: mitochondrial COI data in NEXUS format
DOI: 10.5061/dryad.256kh/4
title: BEAST1.7.5

description: BEAST XML file for Bayesian analysis of COI data
DOI: 10.5061/dryad.256kh/5
title: Structurama2.0_input

description: Structurama2 msat input file for Bayesian clustering
DOI: 10.5061/dryad.256kh/6
title: DAPC R code

description: R commands for DAPC analyses in the adegenet1.3-8 package.
DOI: 10.5061/dryad.256kh/7
title: msat_20regions

description: Regional assignments for DAPC analyses.
DOI: 10.5061/dryad.256kh/8
title: msat_coordinates

description: Collection coordinates for DAPC analyses.
DOI: 10.5061/dryad.256kh/9
title: ABC_AnalysisA_header

description: Header file for DIY ABC analysis A.
DOI: 10.5061/dryad.256kh/12
title: ABC_AnalysisD_header

description: Header file for DIY ABC analysis D.
DOI: 10.5061/dryad.2vr4c/1
title: NewtBdRepeatedMeasuresData

description: This file contains Bd qPCR data from the chytridiomycosis infection experiment in Raffel et al. (2015), Proc Roy Soc B.
DOI: 10.5061/dryad.2vr4c/2
title: NewtMortalityData

description: This file contains newt survival data from the chytridiomycosis infection experiment in Raffel et al. (2015), Proc Roy Soc B.
DOI: 10.5061/dryad.177g0/1
title: Bees-Field beans data
DOI: 10.5061/dryad.177g0/2
title: Metadata
DOI: 10.5061/dryad.177g0/3
title: Bees-Oilseed rape data
DOI: 10.5061/dryad.177g0/4
title: Bees-Strawberries data
DOI: 10.5061/dryad.177g0/5
title: Nematodes data
DOI: 10.5061/dryad.177g0/6
title: Earthworms data
DOI: 10.5061/dryad.177g0/14
title: Carabids seed As data
DOI: 10.5061/dryad.177g0/15
title: Carabids seed Ca data
DOI: 10.5061/dryad.177g0/16
title: Carabids seed Ga data
DOI: 10.5061/dryad.177g0/7
title: Dung beetles dung removal data
DOI: 10.5061/dryad.177g0/8
title: Dung beetles seed removal data
DOI: 10.5061/dryad.177g0/9
title: Carabids aphid biocontrol data
DOI: 10.5061/dryad.177g0/17
title: Carabids seed Pt data
DOI: 10.5061/dryad.7154q/1
title: cowbird responses to virtual vehicle approach

description: These data were collected in a video laboratory in 2012.  Brown-headed cowbirds were exposed to video playback of an approaching vehicle with two sizes and eight vehicle speeds.  Alert responses (alert distance and alert time to collision) and flight responses (flight initiation distance and flight time to collision) were recorded based on the median of a group of three cowbirds.
DOI: 10.5061/dryad.5tt50/1
title: Transect_Data

description: The data file consists of microsatellite allele lengths for the 13 loci described in the paper. The data file has individuals organized in rows, with the each ID in the first column. The subsequent 26 columns correspond to microsatellite data (two columns per locus). Missing data are coded as zeros.
DOI: 10.5061/dryad.8f1m3/1
title: Morphological mesherments of Tadpoles of atukorali
DOI: 10.5061/dryad.64b5p/1
title: Genbank-derived ITS2 reference library

description: This is a reference library of 2628 plant ribosomal sequences downloaded from Genbank on March 11, 2014. This library represents approximately half of the 4918 plant species potentially present in Ohio and surrounding states (USDA PLANTS database; http://plants.usda.gov/). This file is in FASTA format.
DOI: 10.5061/dryad.68t78/1
title: Outcome of Sperm Competition Trials
DOI: 10.5061/dryad.68t78/2
title: Sperm concentration and velocity measurements
DOI: 10.5061/dryad.hf305/2
title: DataForSubmitting

description: Meta-dataset of studies comparing organic and conventional yields.
DOI: 10.5061/dryad.2vg05/1
title: Figure2Dat1

description: Genotype data for between strain pedigree.
DOI: 10.5061/dryad.2vg05/2
title: Figure2Dat2

description: Genotype data for within strain pedigree
DOI: 10.5061/dryad.2vg05/3
title: Figure3Dat

description: Genotype and phenotype data for between strain pedigree.
DOI: 10.5061/dryad.2vg05/4
title: 2071

description: Aligned sequence data for locus BGIBMGA002071.
DOI: 10.5061/dryad.2vg05/5
title: 2076

description: Aligned sequence file for locus BGIBMGA002076
DOI: 10.5061/dryad.2vg05/6
title: 2032

description: Aligned sequence data for locus BGIBMGA002032
DOI: 10.5061/dryad.2vg05/7
title: 2104

description: Aligned sequence data for locus BGIBMGA002104
DOI: 10.5061/dryad.2vg05/8
title: 2005

description: Aligned sequence data for locus BGIBMGA002005
DOI: 10.5061/dryad.2vg05/9
title: 622

description: Aligned sequence data for locus BGIBMGA000622
DOI: 10.5061/dryad.2vg05/10
title: 643

description: Aligned sequence data for locus BGIBMGA000643
DOI: 10.5061/dryad.2vg05/11
title: 647

description: Aligned sequence data for locus BGIBMGA000647
DOI: 10.5061/dryad.2vg05/12
title: 563

description: Aligned sequence data for locus BGIBMGA000563
DOI: 10.5061/dryad.2vg05/13
title: 559

description: Aligned sequence data for locus BGIBMGA000559
DOI: 10.5061/dryad.2vg05/14
title: 680

description: Aligned sequence data for locus BGIBMGA000680
DOI: 10.5061/dryad.2vg05/15
title: 683

description: Aligned sequence data for locus BGIBMGA000683
DOI: 10.5061/dryad.2vg05/16
title: My537

description: Aligned sequence data for locus BGIBMGA000537
DOI: 10.5061/dryad.2vg05/17
title: 532

description: Aligned sequence data for locus BGIBMGA000532
DOI: 10.5061/dryad.2vg05/18
title: 524short

description: Aligned sequence data for locus BGIBMGA000524
DOI: 10.5061/dryad.2vg05/19
title: 710

description: Aligned sequence data for locus BGIBMGA000710
DOI: 10.5061/dryad.2vg05/20
title: 1368

description: Aligned sequence data for locus BGIBMGA000494
DOI: 10.5061/dryad.2vg05/21
title: 9691

description: Aligned sequence data for locus BGIBMGA000480
DOI: 10.5061/dryad.2vg05/22
title: 13318

description: Aligned sequence data for locus BGIBMGA013318
DOI: 10.5061/dryad.2vg05/23
title: 13333

description: Aligned sequence data for locus BGIBMGA013333
DOI: 10.5061/dryad.2vg05/24
title: 8010

description: Aligned sequence data for locus BGIBMGA012295
DOI: 10.5061/dryad.2vg05/25
title: 12292

description: Aligned sequence data for locus BGIBMGA012292
DOI: 10.5061/dryad.2vg05/26
title: 13832

description: Aligned sequence data for locus BGIBMGA012249
DOI: 10.5061/dryad.2vg05/27
title: 2623

description: Aligned sequence data for locus BGIBMGA012238
DOI: 10.5061/dryad.61m2s/1
title: Anopheles coluzzii & gambiae georeferenced frequencies
DOI: 10.5061/dryad.61m2s/2
title: Larval Salinity Tolerance Bioassays Global Dataset
DOI: 10.5061/dryad.61m2s/3
title: Larval Salinity Tolerance Bioassays Rural Coastal Dataset
DOI: 10.5061/dryad.h5h3c/1
title: SnailShedDataforDryad

description: Laboratory-raised Helisoma trivolvis snails were held at one of 5 acclimation temperatures (13-25 deg C) for 11 days prior to being moved to one of 5 performance temperatures (16-28 deg C) for 7 days.  Some snails were exposed in the laboratory to Ribeiroia ondatrae, and parasite release was measured at several time-points before and after the temperature shift.  Please see paper methods for more details.
DOI: 10.5061/dryad.ng64q/1
title: Histology images

description: Zipped folder containing photomicrographs of mouse brain sections. Sections are from MPS I mice and IDUA heterozygotes, and are stained with the black gold stain. Images have been resized and converted to grayscale. Images are scaled to 173 pixels per millimeter unless noted otherwise in the filename (“..._NotToScale”). Files are titled "histology_[mouse identifier]_[tissue section identifier].tif". Mice 13021, 13224, 13255, N3, N4, and N5 are mice with MPS I; mice 13257, 13258, N1, N2, and N6 are heterozygotes.
DOI: 10.5061/dryad.ng64q/2
title: Histology analysis_for Dryad

description: Excel spreadsheet containing analyzed histological data. The “Optical density” tab contains raw optical density values for each tissue section, normalized values, normalized means for each animal, and normalized means for each genotype. The “Outliers” tab contains analysis of each animal for outlying values (see the publication in PLOS ONE for details). The “cc thickness” tab contains raw data for corpus callosum thickness, comparison with atlas values for each section, animal means, and genotype means. Mice 13021, 13224, 13255, N3, N4, and N5 are mice with MPS I; mice 13257, 13258, N1, N2, and N6 are heterozygotes.
DOI: 10.5061/dryad.ng64q/3
title: MRI analysis_for Dryad

description: Excel spreadsheet containing analyzed MRI data. The “MRI ROI comparison” tab contains mean relaxation time constants for each ROI in each animal for each sequence, as well as means for each genotype. The “MRI vs histology” tab contains correlation of tissue section-derived normalized optical density with MRI relaxation time constants for each MRI sequence. The “Outliers” tab contains analysis of each animal for outlying values (see the publication in PLOS ONE for details). Mice 13021, 13224, 13255, N3, N4, and N5 are mice with MPS I; mice 13257, 13258, N1, N2, and N6 are heterozygotes.
DOI: 10.5061/dryad.ng64q/4
title: MRI relaxation time constant maps

description: Zipped folder containing MRI relaxation time constant maps. Files are meant to be opened and analyzed using the Aedes toolbox for MATLAB. See the publication in PLOS ONE for more details. Files are titled "MRI	_[mouse identifier]_[MRI sequence].t1r [or .t1]". Mice 13021, 13224, 13255, N3, N4, and N5 are mice with MPS I; mice 13257, 13258, N1, N2, and N6 are heterozygotes.
DOI: 10.5061/dryad.g00qr/1
title: BJLS Predation risk in spiders

description: Number of spider individuals in relation to hunting strategy on spruce branches (bird predation-free and control)
DOI: 10.5061/dryad.d0p8h/1
title: Mukherjee_Appendix S1.R1

description: Appendix S1. Available skeletal elements of Hyperodapedon used for bone histology. The alphabets ‘a, b’ denote elements from the same individual. Single (*) and double (**) asterisks denote measured diameter and width, respectively.
DOI: 10.5061/dryad.vv7c8/1
title: Leaf N, P and N:P ratios and measurements of environmental factors in an temperate steppe, Xilin River Basin, Inner Mongolia, China

description: Include leaf N, P and N:P ratios of 80 species in 1979 and 2006, soil traits of the sampling sites, the comparison of the two leaf N determination methods (Kjeldahl N determination and elemental analyzer), the precipitation of Xilin River Basin from 1953 to 2011.
DOI: 10.6084/m9.figshare.6171563.v1
title: Model Fit and Item Factor Analysis: Overfactoring, Underfactoring, and a Program to Guide Interpretation

description: In exploratory item factor analysis (IFA), researchers may use model fit statistics and commonly invoked fit thresholds to help determine the dimensionality of an assessment. However, these indices and thresholds may mislead as they were developed in a confirmatory framework for models with continuous, not categorical, indicators. The present study used Monte Carlo simulation methods to investigate the ability of popular model fit statistics (chi-square, root mean square error of approximation, the comparative fit index, and the Tucker–Lewis index) and their standard cutoff values to detect the optimal number of latent dimensions underlying sets of dichotomous items. Models were fit to data generated from three-factor population structures that varied in factor loading magnitude, factor intercorrelation magnitude, number of indicators, and whether cross loadings or minor factors were included. The effectiveness of the thresholds varied across fit statistics, and was conditional on many features of the underlying model. Together, results suggest that conventional fit thresholds offer questionable utility in the context of IFA.
DOI: 10.6084/m9.figshare.6171509
title: Figure 2c from Foliage motion under wind, from leaf flutter to branch buffeting

description: Matlab code generating figure 2c with raw data
DOI: 10.6084/m9.figshare.6171506
title: Figure 4a from Foliage motion under wind, from leaf flutter to branch buffeting

description: Matlab code generating figure 4a with raw data
DOI: 10.6084/m9.figshare.6171494
title: Figure 4b from Foliage motion under wind, from leaf flutter to branch buffeting

description: Matlab code generating figure 4b with raw data
DOI: 10.6084/m9.figshare.6171494.v1
title: Figure 4b from Foliage motion under wind, from leaf flutter to branch buffeting

description: Matlab code generating figure 4b with raw data
DOI: 10.6084/m9.figshare.6171491
title: Microsatellites File S3 from Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of <i>Fundulus heteroclitus</i>

description: Microsatellite file 3
DOI: 10.6084/m9.figshare.6171491.v1
title: Microsatellites File S3 from Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of <i>Fundulus heteroclitus</i>

description: Microsatellite file 3
DOI: 10.6084/m9.figshare.6171488
title: Figure 2a from Foliage motion under wind, from leaf flutter to branch buffeting

description: Matlab code generating figure 2a with raw data
DOI: 10.6084/m9.figshare.6171485
title: Microsatellites File S2 from Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of <i>Fundulus heteroclitus</i>

description: Microsatellite file 2
DOI: 10.6084/m9.figshare.6171485.v1
title: Microsatellites File S2 from Stable genetic structure and connectivity in pollution-adapted and nearby pollution-sensitive populations of <i>Fundulus heteroclitus</i>

description: Microsatellite file 2
DOI: 10.6084/m9.figshare.6171482
title: Figure 3 from Foliage motion under wind, from leaf flutter to branch buffeting

description: Matlab code generating figure 3 with raw data
DOI: 10.6084/m9.figshare.6171482.v1
title: Figure 3 from Foliage motion under wind, from leaf flutter to branch buffeting

description: Matlab code generating figure 3 with raw data
DOI: 10.6084/m9.figshare.6171479
title: Figure 2b from Foliage motion under wind, from leaf flutter to branch buffeting

description: Matlab code generating figure 2b with raw data
DOI: 10.6084/m9.figshare.6171479.v1
title: Figure 2b from Foliage motion under wind, from leaf flutter to branch buffeting

description: Matlab code generating figure 2b with raw data
DOI: 10.6084/m9.figshare.6171473
title: Figure 4c from Foliage motion under wind, from leaf flutter to branch buffeting

description: Matlab code generating figure 4c with raw data
DOI: 10.6084/m9.figshare.6171383
title: Supplementary Materials

description: A pdf file containing supplemental information, tables, figures, and datasets associated with the manuscript titled, "Phylogenomics reveals the dynamic evolution of fungal nitric oxide reductases and their relationship to secondary metabolism".<br>
DOI: 10.6084/m9.figshare.6171383.v2
title: Supplemental Information

description: A pdf file containing supplemental information, tables, and figures associated with the manuscript titled, "Phylogenomics reveals the dynamic evolution of fungal nitric oxide reductases and their relationship to secondary metabolism" submitted to the mBio journal for publication. There are also six Dataset files associated with the main manuscript text included here as well. <br>
DOI: 10.6084/m9.figshare.6171383.v4
title: Supplementary Materials

description: A pdf file containing supplemental information, tables, figures, and datasets associated with the manuscript titled, "Phylogenomics reveals the dynamic evolution of fungal nitric oxide reductases and their relationship to secondary metabolism".<br>
DOI: 10.6084/m9.figshare.6171383.v3
title: Supplementary Materials

description: A pdf file containing supplemental information, tables, and figures associated with the manuscript titled, "Phylogenomics reveals the dynamic evolution of fungal nitric oxide reductases and their relationship to secondary metabolism". There are also six dataset files associated with the main manuscript text included here as well. <br>
DOI: 10.6084/m9.figshare.6171281
title: Korda Lake 15/04/2018 TQ 04590 88480 part 2

description: Korda Lake 15/04/2018 TQ 04590 88480 part 2<br>
DOI: 10.6084/m9.figshare.6171281.v1
title: Korda Lake 15/04/2018 TQ 04590 88480 part 2

description: Korda Lake 15/04/2018 TQ 04590 88480 part 2<br>
DOI: 10.6084/m9.figshare.6171248
title: Pseudopaludicola ameghini reproduction

description: The characteristics of the reproductive site, amplexus, spawn, eggs, and tadpoles of <i>P. ameghini</i>, based on material and observations partly collected in the vicinities of the presumed type-locality.<br>
DOI: 10.6084/m9.figshare.6171248.v1
title: Pseudopaludicola ameghini reproduction

description: The characteristics of the reproductive site, amplexus, spawn, eggs, and tadpoles of <i>P. ameghini</i>, based on material and observations partly collected in the vicinities of the presumed type-locality.<br>
DOI: 10.6084/m9.figshare.6171185
title: The macroecological dynamics of species coexistence in birds

description: A .zip file containing the code and data used in the analysis of Pigot et al. '<i>The macroecological dynamics of species coexistence in birds</i>' Nature Ecology and Evolution, DOI: 10.1038/s41559-018-0572-9. The data contains information on the divergence times, functional traits and environmental contexts for a global sample of avian sister species pairs (n = 1115).
DOI: 10.6084/m9.figshare.6171185.v1
title: The macroecological dynamics of species coexistence in birds

description: A .zip file containing the code and data used in the analysis of Pigot et al. '<i>The macroecological dynamics of species coexistence in birds</i>' Nature Ecology and Evolution, DOI: 10.1038/s41559-018-0572-9. The data contains information on the divergence times, functional traits and environmental contexts for a global sample of avian sister species pairs (n = 1115).
DOI: 10.6084/m9.figshare.6171161
title: Molecular characterization of fowl aviadenoviruses species D and E associated with inclusion body hepatitis in chickens and falcons indicates possible cross-species transmission

description: During the period from 2015 to 2017, frequent outbreaks of inclusion body hepatitis (IBH) were observed in broiler chickens and falcons in Saudi Arabia. Fifty samples were collected from both species. The histopathological examination and polymerase chain reaction confirmed the IBH infection in eight samples (five samples from chickens and three samples from falcons). The genomic sequence and phylogenetic analysis based on nucleotide and amino acid sequences of Saudi strains, reference fowl aviadenoviruses (FAdVs) and field viruses available in Genbank revealed that all investigated FAdVs clustered into FAdV-2 (species D) and FAdV-6 (species E). The host-dependent characterization revealed that falcon origin strains showed low identity (∼35%) with falcon adenoviruses isolated from USA, which clustered into a separate group. The identification of FAdV-D and FAdV-E in diseased falcons and chickens indicates cross-species transmission although falcons and chickens are phylogenetically different. The control of IBH infection in falcons and chickens should be based on the separation of carriers and susceptible chickens as well as falcons to prevent cross-species contact. Vaccination is an important method for prevention of IBH. The characterization of newly emerging FAdV strains provides valuable information for the development of an efficacious control strategy based on the molecular structure of current circulating FAdV strains in different species of birds.