cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.1nm650h.1/3.1
title: Rscript_all_analyzes_pub

description: R script to reproduce all analyzes and plots reported in Vindstad et al. "Can novel pest outbreaks drive ecosystem transitions in northern-boreal birch forest?"
DOI: 10.5061/dryad.1nm650h.1/4.1
title: README. Explanation of variables

description: Explanation of the variables found in the datafiles forest_data_2010_pub.txt and forest_data_2016_pub.txt
DOI: 10.5061/dryad.1v3g322/4
title: sqrt sex NMDS diet and habitat RESCALED Primer

description: abiotic vectors used in NMDS analysis of sea otter foraging data across sex classes
DOI: 10.5061/dryad.21b52d0/2
title: Hillemann et al 2019 Parid diurnal patterns at feeder

description: Data and R code underlying the analysis of Parid diurnal patterns at feeders (number of individuals and number of calls recorded throughout the day)
DOI: 10.5061/dryad.21b52d0/3
title: Hillemann et al 2019 Parid playback

description: Data and R code underlying the analysis of the playback experiment
DOI: 10.5061/dryad.2ck7120/38
title: DNA12_ZFZR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA12
Marker: ZFZR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/39
title: DNA13_LFCR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA13
Marker: LFCR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/40
title: DNA13_MFZR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA13
Marker: MFZR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/41
title: DNA13_ZFZR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA13
Marker: ZFZR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/42
title: DNA14_LFCR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA14
Marker: LFCR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/43
title: DNA14_MFZR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA14
Marker: MFZR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/44
title: DNA14_ZFZR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA14
Marker: ZFZR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/45
title: DNA15_LFCR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA15
Marker: LFCR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/46
title: DNA15_MFZR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA15
Marker: MFZR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.39g63v2/1
title: Additional_file_1_ML_tree_alignment
DOI: 10.5061/dryad.39g63v2/2
title: Additional_file_2 Predicted ApoD genes across phylogeny
DOI: 10.5061/dryad.39g63v2/3
title: Additional_file_3 PDB files for cluster analyses
DOI: 10.5061/dryad.39g63v2/5
title: Additional_file_5_raw_transcriptomic_data_information_and_gene_expression_profiles
DOI: 10.5061/dryad.3d63vh5/1
title: Supporting Figures and Supplemental Tables

description: Supporting Figures with legend and supplemental tables. Note: These figures are also available in the file 'Supporting Figure 1 and 2.pptx', and the supplemental tables are available in the file 'Suppl Tables.docx'.
DOI: 10.5061/dryad.3d63vh5/2
title: Supporting Figure 1 and 2 (.pptx)

description: Supporting figures in pptx format. See 'Supporting Figure legend.docx' for a description of the figures.
DOI: 10.5061/dryad.3d63vh5/3
title: Supplmental Tables (.docx)

description: Supplemental tables in .docx format.
DOI: 10.5061/dryad.47sd969/1
title: Cheilodipterus artus_msat_genotypes_dryad data

description: Microsatellit genotypes in GenAlex format for Cheilodipterus artus from Scott Reef and Rowley Shoals inlcuding GPS coordinates and fork and tail lengths
DOI: 10.5061/dryad.4cv1421/13
title: Supporting Information 1

description: Formulae used to calculate the distances and disparity measures.
DOI: 10.5061/dryad.4cv1421/14
title: Supporting Information 2

description: References for the matrices employed.
DOI: 10.5061/dryad.4cv1421/15
title: Supporting Information 3

description: Characteristics of the matrices used in this study, along with information regarding the particular analyses in which each was used.
DOI: 10.5061/dryad.4cv1421/16
title: Supporting Information 4

description: Histograms for the 126 matrices with more than 5% of missing
data showing the distribution of the percentage of missing entries per taxon. The vertical dashed line
indicates the mean percentage of missing entries.
DOI: 10.5061/dryad.4cv1421/17
title: Supporting Information 5

description: Histograms showing the percentage of matrices with significant and negative (black), non-significant
(light grey), and significant and positive (dark grey) Spearman’s correlations for the GED and the
MORD, with α = 0.05. The distances are calculated based on the first 3 PCos and all the PCos. This are
the results without any kind of correction for negative eigenvalues.
Scatter plots for the 126 matrices with more than 5% of missing data showing the Euclidean distance to
the centroid for each taxon against its percentage of missing entries. The distance to the centroid is
scaled to 1 independently for each distance measure in order to fit them in the same plot. The red dots
correspond to the calculation with GED, while the blue dots refer to those made with MORD. A simple
regression line is fitted through each group in order to illustrate the tendency of the data. The number
of taxa indicated between brackets corresponds to the untrimmed matrices. The subtitle indicates
whether the Spearman’s correlation between the plotted variables is significant and negative (SN), nonsignificant
(NS), or significant and positive (SP) at α = 0.05.
DOI: 10.5061/dryad.55mc74q/1
title: GA Population Accession Experiment

description: This is a spreadsheet of the results from the greenhouse gibberellin experiment with population accessions and basis for the PC analysis in Figure 2 and Figure S2.
DOI: 10.5061/dryad.55mc74q/2
title: GA NIL Experiment

description: This is a spreadsheet of results of the gibberellin addition experiment with the near isogenic lines and parental lines. It is the basis of Figure 3.
DOI: 10.5061/dryad.55mc74q/3
title: NIL PPG Experiment

description: This spreadsheet contains the data from the experiment to evaluate the concentration of defensive phenylpropanoid glycoside (PPG) compounds in near isogenic and parental lines. It is the basis for Figure 4.
DOI: 10.5061/dryad.60c370d/1
title: z_ant_light

description: Site of dead ants monitored by the study
DOI: 10.5061/dryad.60c370d/2
title: light_sensor_z_ant

description: Light sensor collected by the study
DOI: 10.5061/dryad.60c370d/3
title: temp_rel_humid_z_ant

description: Relative-Humidity sensor collected by the study
DOI: 10.5061/dryad.617n11q/1
title: Raw_Dataset

description: This dataset is comprised of T2-weighted magnetic resonance images from 39 patients along with prostate masks that identify where the prostate is on each image. The data format is .tif. Included are 1235 total images. This folder contains the T2 images and masks.
DOI: 10.5061/dryad.617n11q/2
title: Data sorted for analysis

description: This dataset is comprised of T2-weighted magnetic resonance images from 39 patients along with prostate masks that identify where the prostate is on each image. The data format is .tif. Included are 1235 total images. This is the dataset from the paper analysis sorted into groups.
DOI: 10.5061/dryad.68pk1rv/1
title: Ttri_gff3.tar.gz

description: The gff3 file of horseshoe crab.
DOI: 10.5061/dryad.68pk1rv/3
title: Ttri_pep.tar.gz

description: The protein sequence file of horseshoe crab.
DOI: 10.5061/dryad.68pk1rv/4
title: Ttri_repeat_annotation.gff.tar.gz

description: The repeats annotation file of horseshoe crab.
DOI: 10.5061/dryad.68pk1rv/5
title: Ttri_genome.fa.tar.gz

description: The genome file of horseshoe crab.
DOI: 10.5061/dryad.68pk1rv/6
title: Ttri_genome.fa.sm.fa.tar.gz

description: The repeats-masked genome file of horseshoe crab.
DOI: 10.5061/dryad.6cc5h8f/1
title: Clinical reasoning: A 14-year-old girl with headache, seizures, and confusion.

description: Comparison of the sisters clinical characters. Primers used for mutation screening in CBS gene. Sequence results of CBS and MTHFR mutations. Mutations identified in this family with homocystinuria.The information of controls. Ethics Approval.
DOI: 10.5061/dryad.7np78gp/1
title: All data used in BEHECO-2018-0305

description: All data used for results presented with metadata and three data sheets.
DOI: 10.5061/dryad.9kj41f0/1
title: Kutzer et al data files

description: Data files are labelled according to the experiment and model number(s). Full details on the statistical models and model numbers can be found in Appendix 1, which is a supplementary file for the paper.
DOI: 10.5061/dryad.bt3m1p2/1
title: qPCR expression data and Locomotor activity data

description: Expression data for each analysed gene are located in the qPCR folder (raw and processed).Behavioural data (raw and processed) are in the RNAi data folder. Each folder contains a readme file.
DOI: 10.5061/dryad.c18qh26/1
title: Data_FM

description: Zip folder containing datasets and R code to reproduce the analysis of our paper.
DOI: 10.5061/dryad.c6d5m11/1
title: Sex specific behaviors in Ophryotrocha worms

description: Measurements of motility and parental care in hermaphroditic worms (Ophryotrocha diadema) exposed to different levels of mate competition. Measurements of motility and parental care in pairs of worms with separate sexes (Ophryotrocha labronica).
DOI: 10.5061/dryad.hv18jn6/1
title: nanoparticle-enhanced ionic liquids
DOI: 10.5061/dryad.m4t3rd5/1
title: Locations and genotypes scored in Nigritella miniata sampled at Sennes (Dolomites, South Tyrol, Italy).

description: Locations and genotypes scored in Nigritella miniata sampled at Sennes (Dolomites, South Tyrol, Italy). Data from other locatities in the Dolomites used as reference are also included. Columns Gc51-a through Gc77-d report simples sequence repeat (SSR) fragment sizes at loci Gc51 (first four columns) and Gc77 (last four columns). Nigritella miniata is a tetraploid species, and all four SSR fragments identified at a locus are usually of different size. Unique combinations of fragments are recognized as genotypes.
DOI: 10.5061/dryad.nm1189t.3/10.3
title: Count reads files for post-kseq populations

description: Text files pertaining to sequences present in post-kseq populations, from the kseq assay performed at the end of selection. A, B, C etc. pertain to replicates; 1-indicates 250uM BYO, 2-indicates 50uM, 3-indicates 10uM, 4-indicates 2uM. Each file contains round information in its header, followed by sequences and the number of times they appeared in that round.
DOI: 10.5061/dryad.nm1189t.3/3.3
title: k-seq Analysis - script

description: Python script to calculate catalytic kinetics for a population of sequences, using the k-Seq methodology.
DOI: 10.5061/dryad.nm1189t.3/4.3
title: k-seq Analysis - example input files

description: Input files for k-seq Analysis: kseq_rounds is example-rounds.txt, normalization_list is example-normalization.txt, substrate_concs is example-subst-concs.txt, rounds_to_average is example-rnds-to-avg.txt and rounds_to_error is example-rnds-to-err.txt.
DOI: 10.5061/dryad.nm1189t.3/5.3
title: Pathways between Peak Sequences - script

description: Python script to searche for the shortest pathway between two sequences along a fitness landscape.
DOI: 10.5061/dryad.nm1189t.3/6.3
title: Fastq files for original selection

description: Fastq files pertaining to sequences present in rounds of selection, from the original BYO aminoacylase ribozyme selection. Conserved primer regions have been removed; sequences correspond only to the randomized internal region of the library.
DOI: 10.5061/dryad.nm1189t.3/7.3
title: Count reads files for original selection

description: Text files pertaining to sequences present in rounds of selection, from the original BYO aminoacylase ribozyme selection. Each file contains round information in its header, followed by sequences and the number of times they appeared in that round.
DOI: 10.5061/dryad.nm1189t.3/8.3
title: Fastq files for second selection

description: Fastq files pertaining to sequences present in rounds of selection, from the second BYO aminoacylase ribozyme selection.
DOI: 10.5061/dryad.nm1189t.3/9.3
title: Count reads files for second selection

description: Text files pertaining to sequences present in rounds of selection, from the second BYO aminoacylase ribozyme selection. Each file contains round information in its header, followed by sequences and the number of times they appeared in that round.
DOI: 10.5061/dryad.ns790j4/1
title: Teske_NeutralLoci

description: Selectively neutral SNPs
DOI: 10.5061/dryad.p46k773/2
title: MicroClimate from Climate Change Experiments (doi:10.5063/F17P8WNT).

description: Database of daily microclimate data (above-ground and soil temperature, and soil moisture) from warming experiments, information on experimental sites included in database, and definitions of warming and precipitation treatments applied to each plot are available in Knowledge Network for Biocomplexity (KNB) at https://doi.org/10.5063/F17P8WNT
DOI: 10.5061/dryad.p46k773/4
title: R Code to create full database

description: Links expclim.csv and treats_detail.csv
DOI: 10.5061/dryad.q66s28s/1
title: TxR_data
DOI: 10.5061/dryad.t7r6kg5/1
title: lentago_collections_table

description: Table with individuals collected for this study. The state and county are listed for each individual
DOI: 10.5061/dryad.tm40gd8/1
title: SNPs from Flowers et al. (2019) in vcf format

description: This file contains SNPs used in Flowers et al. (2019) Cross-species hybridization and the origin of North African date palms in vcf format. Only SNPs passing filters are included in the file.
DOI: 10.5061/dryad.v9t58mk/1
title: DataS1

description: The DataS1 file contains all raw data and analyses associated with the publication including mixed effect models of plant traits, calculations associated with plasticity index and climate data of population origin.
DOI: 10.17632/6cmhnw59zz.1
title: Data for: 3315860

description: These 3 files are being used to write the Introductory part of the paper. More data about the success and failures of research programs will be added very soon.
DOI: 10.17632/nf554nbbhb.1
title: Data for: Supporting sustainable expansion of livestock production in South Asia and Sub-Saharan Africa: Scenario analysis of investment options

description: Technical notes on the Global Economic Model (IMPACT) and Investment Scenarios included in the Study, Supporting sustainable expansion of livestock production in South Asia and Sub-Saharan Africa:
DOI: 10.5061/dryad.1sd556t/1
title: dadi scripts

description: Python scripts to run dadi for the three models described in the paper
DOI: 10.5061/dryad.2ck7120/47
title: DNA15_ZFZR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA15
Marker: ZFZR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/48
title: DNA16_LFCR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA16
Marker: LFCR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/49
title: DNA16_MFZR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA16
Marker: MFZR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/50
title: DNA16_ZFZR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA16
Marker: ZFZR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/51
title: DNA17_LFCR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA17
Marker: LFCR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/52
title: DNA17_MFZR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA17
Marker: MFZR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/53
title: DNA17_ZFZR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA17
Marker: ZFZR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2ck7120/54
title: DNA18_LFCR.tar

description: Fastq file with raw data of Illumina reads
Plate: DNA18
Marker: LFCR
Tag combinations to identify the samples from each fastq files are found in the 'CSV file with metadata on fastq files'
DOI: 10.5061/dryad.2qh4k34/1
title: WGS_fastq_Deoxy_D_glucose

description: Fastq files obtained from whole genome sequencing of mutants growing on 2-Deoxy-D-glucose as sole carbon source. Each mutant was paired end sequenced using Illumina's Miseq. Thus there are two fastq files per mutant. Each file name has a DA number designating the strain, and description of the strain can be obtained from the supplementary table 3 of the manuscript.
DOI: 10.5061/dryad.2qh4k34/2
title: WGS_fastq_valine

description: Fastq files obtained from whole genome sequencing of mutants growing on valine as sole carbon source. Each mutant was paired end sequenced using Illumina's Miseq. Thus there are two fastq files per mutant. Each file name has a DA number designating the strain, and description of the strain can be obtained from the supplementary table 3 of the manuscript.
DOI: 10.5061/dryad.39g63v2/6
title: Additional_file_6_qPCR primer sequences
DOI: 10.5061/dryad.39g63v2/7
title: Additional_file_4_PAML_branch_site_model
DOI: 10.5061/dryad.3h7951k/1
title: Phenology data for tree and wildflower species in Concord

description: Raw phenology data for tree and wildflower species in Concord, MA, USA.
DOI: 10.5061/dryad.3h7951k/2
title: Daily carbon gain estimates

description: Daily carbon gain data used in carbon gain simulations under phenological mismatch. Data for 6 wildflower species were from field measurements taken in a common garden near Pittsburgh, PA (see Heberling, J.M., Cassidy, S.T., Fridley, J.D. & Kalisz, S. (2019) Carbon gain phenologies of spring-flowering perennials in a deciduous forest indicate a novel niche for a widespread invader. New Phytologist 221: 778-788).
DOI: 10.5061/dryad.3k5c0sh/1
title: Structure input file for the northern clade.

description: A Structure data file consisting of 131 individuals genotyped at 647 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.
DOI: 10.5061/dryad.3k5c0sh/2
title: Structure input file for E. chisholmensis and E. naufragia populations.

description: A Structure data file consisting of 53 E. chisholmensis and E. naufragia samples genotyped at 647 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.
DOI: 10.5061/dryad.3k5c0sh/3
title: Structure input file for E. tonkawae.

description: A Structure data file consisting of 78 E. tonkawae samples genotyped at 647 loci. See README file for MAINPARAMS and EXTRAPARAMS settings.
DOI: 10.5061/dryad.4cv1421/18
title: Supporting Information 6

description: Scatter plots for the 126 matrices with more than 5% of missing
data showing the Spearman’s correlation coefficient between the Euclidean distance to the centroid for
each taxon and its percentage of missing entries against the percentage of explained variance of the
PCos used to calculate the distance to the centroid.
DOI: 10.5061/dryad.4cv1421/19
title: Supporting Information 7

description: Histograms for the 33 matrices with less than 5% of missing data.
DOI: 10.5061/dryad.4cv1421/20
title: Supporting Information 8

description: Results from the 33 morphological matrices for the studied
disparity measures against the proportion of randomly-distributed missing entries added to
morphological matrices, calculated from distance matrices generated from the GED and the
MORD.
DOI: 10.5061/dryad.4cv1421/21
title: Supporting Information 9

description: Results of simulations with groups of taxa and different
distributions of missing entries for the nine matrices with more than 50 taxa and 50 characters, and
less than 5% of missing data.
DOI: 10.5061/dryad.4cv1421/22
title: Supporting Information 10

description: Description and results of the analysis performed to compare the results of this paper to those of Ciampaglio et al. (2001).
DOI: 10.5061/dryad.4cv1421/23
title: Matrices for Lehmann et al. (2019)

description: Matrices used in the analyses, saved in nexus format. Separated by folders for each different analysis.
DOI: 10.5061/dryad.4cv1421/24
title: Scripts for Lehmann et al. (2019)

description: Scripts used for the analyses and creation of figures and supplementary information.
DOI: 10.5061/dryad.4j36s87/1
title: North Dakota duck nesting dataset

description: These are survival data for duck nests in North Dakota.  Column headers are described in the publication.  Nest fate information follows that required by program MARK accessed through the package RMark (see description by Rotella on the CRAN site).
DOI: 10.5061/dryad.5b6r521/1
title: IR and XRD

description: The data of IR and XRD spectra.
DOI: 10.5061/dryad.6h5v2pv/1
title: Supplementary Information

description: Raw data underlying the analyses in the publication.
DOI: 10.5061/dryad.770nj18/6
title: Table S1. Analysis of axillary LN metastasis by immunohistochemistry for CK5 in DCIS tumor-bearing mice
DOI: 10.5061/dryad.770nj18/7
title: Toxicol Sciences_Kim H et al_Supple Fig1

description: Figure S1. Low dose BPA promotes the proliferation and migration capacities of DCIS.com, MCF-7 and MDA-MB-231 cells.
DOI: 10.5061/dryad.770nj18/8
title: Toxicol Sciences_Kim H et al_Supple Fig2

description: Figure S2. Low dose BPA promotes the migration capacities of RAW264.7 cells, also increases M1 and M2 polarization markers in a dose- and time-dependent manner.
DOI: 10.5061/dryad.791n66r/1
title: Absolute and relative volumes of neuropil types in generation 33

description: This file gives the absolute volumes in cubic micrometer of all neuropil types, except the lamina. A separate sheet gives the volumes relative to the total (except lamina) neuropil volume. This data set supports figs 3, 4 and 5.
DOI: 10.5061/dryad.791n66r/2
title: Memory data (gen 33)

description: The raw data supporting Fig 6
DOI: 10.5061/dryad.791n66r/3
title: Raw selection data

description: Dataset supporting Fig 1 and 2. For every generation that was used for selection there is a separate excel sheet, and every row represents one individual female wasp. The rows that have a background color represent the individuals selected to produce the next generation
DOI: 10.5061/dryad.84b178d/1
title: The Devil You Know datasets
DOI: 10.5061/dryad.8j5j72t/1
title: Cysteine supplementation - Dryad