cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.278q9/4
title: Cotinga_HighResolutionScansReplace

description: High Resolution CT scans of Cotinga cayana
DOI: 10.5061/dryad.278q9/5
title: Cleuchorrhea_HighResolutionScansReplace

description: High Resolution CT scans of Corapipo leucorrhoa
DOI: 10.5061/dryad.278q9/6
title: Clanceolata_HighResolutionScansReplace

description: High Resolution CT scans of Chiroxiphia lanceolata
DOI: 10.5061/dryad.3702g/1
title: Heliconia_Pollination

description: The file describes the number of pollinated Heliconia tortuosa styles as a function of the number of corridors connecting the forest fragment.
DOI: 10.5061/dryad.3702g/2
title: Phaguy_Occup

description: The file describes the number of detected Green Hermits P. Guy in small forest fragments as a function of the number of corridors connecting the forest fragment.
DOI: 10.5061/dryad.3702g/3
title: Amatza_Occup

description: The file describes the number of detected Amazilia tzacatl hummingbirds in small forest fragments as a function of the number of corridors connecting the forest fragment.
DOI: 10.5061/dryad.3702g/5
title: Powdertransfer

description: The file describes the number of fluorescent dye particles transferred between experimental feeders by hummingbirds, either along a corridor ("c"), through forest ("f") or through pasture ("p").
DOI: 10.5061/dryad.3t758/1
title: Phylogenic analysis of endophytic fungi isolated from the leaf, stem and petiole of E. jambolana.

description: Phylogenic analysis of endophytic fungi isolated from 3 different tissues the leaf, stem and petiole of E. jambolana. The phylogenic tree was constructed using Neighbor- Joining method. Bootstrap values above 50% from 1000 replicates are indicated at each node.
DOI: 10.5061/dryad.3t758/2
title: sequence
DOI: 10.5061/dryad.4tv57/44
title: README

description: This includes information about how the data was collected and with what methods
DOI: 10.5061/dryad.5ch0p/1
title: Parental microsatellite genotypes

description: Family ID, sex and multilocus genotypes (24 microsatellites) of the 52 S. gregaria parents used in the study.
DOI: 10.5061/dryad.7309c/1
title: Foley_Springer_Teeling_PRSB2016_Alignment

description: Alignment and data partitions used to generate the ML tree used for estimating divergence times in PAML.
DOI: 10.5061/dryad.73p72/1
title: main data file

description: IIEdata.tar.gz is a zip file that contains all of the simulation data files.
DOI: 10.5061/dryad.73p72/2
title: IIEdata

description: IIEdata.nb is a Mathematica notebook file containing the scripts for manipulating and graphing the raw data files contained in IIEdata.tar.gz.
DOI: 10.5061/dryad.76gg2/1
title: RSPB-2016-0164 Danilova Mollon Exp1 data

description: data obtained for experiment 1
DOI: 10.5061/dryad.76gg2/2
title: RSPB-2016-0164 Danilova Mollon control exp data

description: data used in the control experiment
DOI: 10.5061/dryad.76gg2/3
title: RSPB-2016-0164 Danilova Mollon Suppl exp data

description: data used for p.5: Hue and saturation thresholds very close to the white point
DOI: 10.5061/dryad.7fn47/1
title: Cossatot River Hybrid Zone SNPs

description: Genotyping by sequencing data for samples taken from the hybrid zone in the Cossatot River. Data are in hapmap format.
DOI: 10.5061/dryad.7fn47/2
title: Glover River Hybrid Zone SNPs

description: Genotyping by sequencing data for samples taken from the hybrid zone in the Glover River. Data are in hapmap format.
DOI: 10.5061/dryad.82nc3/1
title: DataForAssessingSeasonalEffectsOnElectricityAndWaterForRepository

description: This Excel file contains data used to conduct a seasonal analysis to assess whether seasonal patterns exist in electricity use in dorms and whether these patterns differ by latitude.  The first worksheet contains metadata.
DOI: 10.5061/dryad.82nc3/2
title: Fall 2010 Campus Conservation Nationals survey

description: This online survey was administered to students attending colleges who participated in the Fall 2010 Campus Conservation Nationals competition.  Not all schools who participated in the competition administered the survey.
DOI: 10.5061/dryad.82nc3/3
title: Spring 2012 Campus Conservation Nationals survey

description: This online survey was administered to students attending colleges who participated in the Spring 2012 Campus Conservation Nationals competition. Not all schools who participated in the competition administered the survey.
DOI: 10.5061/dryad.82nc3/4
title: Fall 10 Campus Conservation Nationals electricity, water, webhit, and commitment data

description: This data file contains data at the dorm level collected by Lucid before, during, and after the Fall 2010 CCN competition.  The first sheet contains metadata defining all variable names.
DOI: 10.5061/dryad.82nc3/5
title: Spring 2012 Campus Conservation Nationals electricity, water, and commitment data

description: This data file contains data at the dorm level collected by Lucid before, during, and after the Spring 2012 CCN competition. The first sheet contains metadata defining all variable names.
DOI: 10.5061/dryad.8b7k4/1
title: Collective Learning Data_Dryad

description: Data on individual training, collective learning of colony, and colony mass gained
DOI: 10.5061/dryad.8d8v4/1
title: Cryptosporidium deformability - data

description: The files within the ZIP archive are in CSV format and can be readily accessed by Microsoft Excel, MATLAB, and many other programs. CSV files were recorded by the CyUI software from Cytosurge AG (Glattbrug, Switzerland). "spec.fwd.csv" and "spec.bwd.csv" files refer to the approach or retraction phases of the force spectroscopy measurements, respectively. Only the "spec.fwd.csv" (approach) files were used in the data analysis. Cantilever spring constants, deflection sensitivities, and sampling frequencies are specified in the header of the csv files. The initial cantilever-substrate separation was 10 micron for the C. muris and 5.0-5.3 micron for the C. parvum measurements.
DOI: 10.5061/dryad.8t3nf/1
title: Data Regnier et al
DOI: 10.5061/dryad.c7366/1
title: Figure2_Source_data

description: High-resolution immunogold layers.High-resolution images (2.22 nm/pixel) showing the area of the VNC. The archive contains one image file for each antibody.
DOI: 10.5061/dryad.cv77f/2
title: Paul et al raw data file

description: The raw data for both the POC meat and biscuit experiments, as well as the beavioural data on suckling used for the analysis in Paul et al.
DOI: 10.5061/dryad.db6s4/1
title: Saipan bird, rainfall, and EVI data and analysis code

description: 7 data files and 3 R workspaces (for survival analyses) are included to reproduce results reported in the paper. Individual files and R code are included in the README.pdf file.
DOI: 10.5061/dryad.dh371/3
title: Supplementary file 3. List of the previously reported phosphosite with the related publications
DOI: 10.5061/dryad.gk1s2/1
title: Xylotitan cenosus size data

description: Measurements of fossil elements of Xylotitan cenosus
DOI: 10.5061/dryad.gn219/1
title: PMID list

description: list of PMIDs used to create concept profiles; gzipped file, one PMID per line
DOI: 10.5061/dryad.gn219/2
title: Medline concept index

description: Concept index of Medline articles as specified in http://dx.doi.org/10.5061/dryad.gn219/1
DOI: 10.5061/dryad.gn219/3
title: Overview of software packages

description: Software packages used for the various analyses and figures. Links are clickable and point to the repository for that code or data.
DOI: 10.5061/dryad.gn219/4
title: Explicit associations (co-occurrence) nanopublications

description: Set of 7,858,449 nanopublications, each of which asserts a single gene-disease co-occurrence and the PubMed ID of the abstract in which they co-occur
DOI: 10.5061/dryad.gn219/5
title: All associations as nanopublications

description: The complete set of all ~204 million associations (explicit and implicit) as nanopublications. Each nanopublication asserts an association between a gene and a disease concept and the percentile rank of the match score.
DOI: 10.5061/dryad.gn219/6
title: All associations as CSV

description: All ~204 million associations (explicit and implicit) listed as a CSV text file. Note that concept pairs are specified by concept ID and its first label according to our thesaurus.
DOI: 10.5061/dryad.gn219/7
title: Pre-compiled software dependencies

description: Collection of JAR files containing the dependencies for generating concept profiles and match scores. Source code is also available in our github repository.
DOI: 10.5061/dryad.h5fg1/3
title: Growth curves (OD_600) over 48 hours in BSA 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 BSA medium (casamino acids with BSA, which can only be degraded by elastase). 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. 2A.
DOI: 10.5061/dryad.mn36c/2
title: Mean individual-level scrounging probabilities and relative fitness

description: Mean probabilities of scrounging behaviour (column 8), amount of resource consumed (column 7), and relative fitness (see manuscript for definition) (column 6) for individuals of different social ranks (column 5) across different fixed values of N (column 1), a/F (column 2), c (column 3) and lambda (column 4). Data generated in R. Probabilities, consumption rates, and fitnesses are computational approximations of analytical solutions provided in manuscript.
DOI: 10.5061/dryad.nq8h7/1
title: Group home ranges, breeding and non-breeding

description: providing home range sizes of different groups, as well as potential explanatory variables
DOI: 10.5061/dryad.nq8h7/2
title: Insects abundance - light-trap samples
DOI: 10.5061/dryad.nq8h7/3
title: ranging behaviour_all year

description: group movement data over the entire year and potential predictors
DOI: 10.5061/dryad.s04bb/10
title: Adult Pituitary Trypsin Untreated Data2

description: GFP fluorescence measured from single cells in adult pituitary tissue. Control sample to compare to Adult Pituitary Trypsin Treated Data2.
DOI: 10.5061/dryad.s04bb/11
title: Adult Pituitary Trypsin Treated Data2

description: GFP fluorescence measured from single cells in adult pituitary tissue treated with trypsin for 2hrs prior to confocal imaging. Compare to Adult Pituitary Trypsin Untreated Data2.
DOI: 10.5061/dryad.s04bb/12
title: Adult Pituitary_Cx_AGA_Data1

description: GFP fluorescence measured from single cells in adult pituitary tissue treated with 18alpha-glycyrrhetinic acid (20uM) for 2hrs prior to confocal imaging. Compare to Adult Pituitary Data2.
DOI: 10.5061/dryad.s04bb/13
title: Adult Pituitary_Cx_AGA_Data2

description: GFP fluorescence measured from single cells in adult pituitary tissue treated with 18alpha-glycyrrhetinic acid (20uM) for 2hrs prior to confocal imaging. Compare to Adult Pituitary Data3.
DOI: 10.5061/dryad.s04bb/6
title: P1_5 Pituitary Data1

description: GFP fluorescence measured from single cells in post-natal day1.5 pituitary tissue and subsequent modelling of transcription activity using a stochastic switch model.
DOI: 10.5061/dryad.s04bb/7
title: P1_5 Pituitary Data2

description: GFP fluorescence measured from single cells in post-natal day1.5 pituitary tissue and subsequent modelling of transcription activity using a stochastic switch model.
DOI: 10.5061/dryad.s04bb/8
title: Adult Pituitary Trypsin Untreated Data1

description: GFP fluorescence measured from single cells in adult pituitary tissue. Control sample to compare to Adult Pituitary Trypsin Treated Data1.
DOI: 10.5061/dryad.s04bb/9
title: Adult Pituitary Trypsin Treated Data1

description: GFP fluorescence measured from single cells in adult pituitary tissue treated with trypsin for 2hrs prior to confocal imaging. Compare to Adult Pituitary Trypsin Untreated Data1.
DOI: 10.5061/dryad.vt0j1/1
title: Echinoderm TIMP Sequences

description: The file contains sequences that belong to the TIMP gene family (tissue inhibitors of metalloproteinases). Different alignments represent the results of successive culling procedures to remove possible non-homologues. The sequences were obtained from an echinoderm transcriptome data set.
DOI: 10.5061/dryad.085vq/3
title: copdur2_mating_latency2

description: The data file “copdur2_mating_latency2” includes females that remated and for which we recorded copulation duration of the 2nd mating. It also includes and the number of eggs they laid and the number of offspring that eclosed from eggs laid after the second mating.
DOI: 10.5061/dryad.085vq/4
title: Data used in P2 analysis

description: The file “Paternities no zero P2” includes females that were used in P2 analyses.
DOI: 10.5061/dryad.085vq/5
title: All_matings

description: The file “All matings” lists all females that mated in the first mating as well as their behaviour after it. This file should be used cautiously as it may not be exactly the same as the files above that have been used in statistical analysis (some wrongly typed numbers have been corrected in the above files). We give this file for the purpose of checking which females remated and which did not.
DOI: 10.5061/dryad.1b07d/1
title: Archaea sequence data

description: Primers used for PCR amplification of bacteria and archaea 16S rRNA genes, ciliate protozoa18S rRNA genes and anaerobic fungi ITS1 genes were designed in silico using ecoPrimers,the OBITools software suite (http://www.grenoble.prabi.fr/trac/OBITools) and adatabase created from sequences stored in GenBank. PCR amplicons were combined in equal volumes and purified (QIAquick PCR purificationkit, Qiagen, Germany). After library preparation using a standard protocol with only five PCRcycles, amplicons were sequenced using the MiSeq technology from Illumina (Fasteris, SA,Geneva, Switzerland), which produced 250-base paired-end reads for all markers, other thanfor archaea (100-base paired-end reads).Alignment of paired-end reads, sample assignment and removal of sequences with ambiguousnucleotides and sequences of lengths outside the empirical sequence length distribution wereperformed with the OBITools software suite. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx',that is also part of this Dryad data package.
DOI: 10.5061/dryad.1b07d/2
title: Bacteria sequence data

description: Primers used for PCR amplification of bacteria and archaea 16S rRNA genes, ciliate protozoa18S rRNA genes and anaerobic fungi ITS1 genes were designed in silico using ecoPrimers,the OBITools software suite (http://www.grenoble.prabi.fr/trac/OBITools) and adatabase created from sequences stored in GenBank. PCR amplicons were combined in equal volumes and purified (QIAquick PCR purificationkit, Qiagen, Germany). After library preparation using a standard protocol with only five PCRcycles, amplicons were sequenced using the MiSeq technology from Illumina (Fasteris, SA,Geneva, Switzerland), which produced 250-base paired-end reads for all markers, other thanfor archaea (100-base paired-end reads).Alignment of paired-end reads, sample assignment and removal of sequences with ambiguousnucleotides and sequences of lengths outside the empirical sequence length distribution wereperformed with the OBITools software suite. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx',that is also part of this Dryad data package.
DOI: 10.5061/dryad.1b07d/3
title: Fungi sequence data

description: Primers used for PCR amplification of bacteria and archaea 16S rRNA genes, ciliate protozoa18S rRNA genes and anaerobic fungi ITS1 genes were designed in silico using ecoPrimers,the OBITools software suite (http://www.grenoble.prabi.fr/trac/OBITools) and adatabase created from sequences stored in GenBank. PCR amplicons were combined in equal volumes and purified (QIAquick PCR purificationkit, Qiagen, Germany). After library preparation using a standard protocol with only five PCRcycles, amplicons were sequenced using the MiSeq technology from Illumina (Fasteris, SA,Geneva, Switzerland), which produced 250-base paired-end reads for all markers, other thanfor archaea (100-base paired-end reads).Alignment of paired-end reads, sample assignment and removal of sequences with ambiguousnucleotides and sequences of lengths outside the empirical sequence length distribution wereperformed with the OBITools software suite. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx',that is also part of this Dryad data package.
DOI: 10.5061/dryad.1b07d/4
title: Protozoa sequence data

description: Primers used for PCR amplification of bacteria and archaea 16S rRNA genes, ciliate protozoa18S rRNA genes and anaerobic fungi ITS1 genes were designed in silico using ecoPrimers,the OBITools software suite (http://www.grenoble.prabi.fr/trac/OBITools) and adatabase created from sequences stored in GenBank. PCR amplicons were combined in equal volumes and purified (QIAquick PCR purificationkit, Qiagen, Germany). After library preparation using a standard protocol with only five PCRcycles, amplicons were sequenced using the MiSeq technology from Illumina (Fasteris, SA,Geneva, Switzerland), which produced 250-base paired-end reads for all markers, other thanfor archaea (100-base paired-end reads).Alignment of paired-end reads, sample assignment and removal of sequences with ambiguousnucleotides and sequences of lengths outside the empirical sequence length distribution wereperformed with the OBITools software suite. Primer sequences and metadata for each sample are provided in the file 'Sequence metadata.xlsx',that is also part of this Dryad data package.
DOI: 10.5061/dryad.1b07d/5
title: Sequence metadata

description: This file contains information on animal ID's, primer sequences, sampling periods and diets.
DOI: 10.5061/dryad.2q3k2/1
title: MrBayes_Analyses

description: NEXUS input file for analyses in MrBayes. Three approaches to calibration are included: Tip Calibration; Node Calibration; Tip and Node Combined Calibration.
DOI: 10.5061/dryad.2q3k2/2
title: TED_Post_Full

description: Majority-rule consensus tree obtained from a sample from the posterior distribution in the total-evidence, tip-calibrated, divergence time analysis.The position of all fossil taxa are presented in this topology.
DOI: 10.5061/dryad.2q3k2/3
title: TipandNode_Post_Full

description: Majority-rule consensus tree obtained from a posterior sample of trees in the combined tip and node calibration analysis. The position of all fossil taxa are presented in this topology.
DOI: 10.5061/dryad.2q3k2/4
title: Supplementary_Methods

description: Justification for sampling the time-prior from a fixed consensus-tree topology and details of all divergence-time analyses performed.
DOI: 10.5061/dryad.313hd/1
title: Supplementary Table 1

description: Supplementary Table 1. List of bone specimens from Arch-2 Cave, Vancouver Island, Canada.
DOI: 10.5061/dryad.322vn/1
title: Alignment_Campanulaceae_all_genes_dataset
DOI: 10.5061/dryad.322vn/2
title: Alignment_Campanulaceae_coding_only_dataset
DOI: 10.5061/dryad.322vn/3
title: Alignment_Campanulaceae_plastid_only_dataset
DOI: 10.5061/dryad.322vn/4
title: FlwrSym_Matrix
DOI: 10.5061/dryad.322vn/5
title: PollenPresent_AntherArrangement_Matrix
DOI: 10.5061/dryad.322vn/6
title: PollenPresent_Invagination_Matrix
DOI: 10.5061/dryad.322vn/7
title: PollenPresent_Mechanism_Matrix
DOI: 10.5061/dryad.322vn/8
title: PollenPresent_StylarGrowth_Matrix
DOI: 10.5061/dryad.3702g/4
title: Titration

description: The file describes the number of observed hummingbirds at artificial feeders, with and without corridors. Feeders at distance "0" and "1" are at the forest edge, distance "2" corresponds to 10 meters distance to the edge, "3" to 20 meters distance, etc. up to "6" for 50 meters distance.
DOI: 10.5061/dryad.3703v/1
title: 2011 Pumpkinseed Summary

description: Stable isotope measurements of male and female pumpkinseed sunfish (Lepomis gibbosus) collected from littoral and pelagic habitats during 2011. Fish were collected over two time periods: May – June 2011 (Spring 2011) or August 2011 (Summer 2011). Isotopic compositions (δ13C and δ15N) of liver tissues are shown, as well as % Littoral resource estimates (see methods for details).
DOI: 10.5061/dryad.3703v/2
title: 2012 Male Pumpkinseed and Eggs Summary

description: Stable isotope measurements of nesting male pumpkinseed sunfish (Lepomis gibbosus) and eggs collected from the males’ nests in the littoral and pelagic habitats. Nesting males were collected during Spring 2012 (11 – 22 June). Isotopic compositions (δ13C and δ15N) of nesting male liver tissue and egg samples from the male’s nests are shown. Diet estimates of nesting males are shown based on % Littoral resource contributions to diet for each individual (see methods for details).
DOI: 10.5061/dryad.3cb25/1
title: Supplementary figures

description: Supplementary figures for Fujisawa et al. 2016
DOI: 10.5061/dryad.3cb25/2
title: Supplementary text S1

description: Online appendix for Fujisawa et al. 2016. Supplementary text S1.
DOI: 10.5061/dryad.3cb25/3
title: Alignments of Bacillus

description: Sequence alignments of seven house keeping genes of Bacillus isolates in Nexus format.
DOI: 10.5061/dryad.3cb25/4
title: Beast MCC trees of Bacillus

description: Beast MCC trees of seven house keeping genes of Bacillus isolates
DOI: 10.5061/dryad.3cb25/5
title: Clonalframe consensus tree of Bacillus

description: Clonalframe consensus tree build with seven house keeping genes of Bacillus isolates
DOI: 10.5061/dryad.3cb25/6
title: Three speices simulations

description: Simulated gene trees for three species simulations. Twenty five loci are interleaved as line1-locus1, line2-locus2, ... line26-locus1, ...
DOI: 10.5061/dryad.3cb25/7
title: Ten species simulation (Simulation A&B)

description: Simulated gene trees for ten species simulations. Forty loci are interleaved.
DOI: 10.5061/dryad.3cb25/8
title: Ten species simulation (simulation C)

description: Gene trees reconstructed from simulated sequences. Forty loci are interleaved.
DOI: 10.5061/dryad.5ht3n/3
title: A polymer dataset for accelerated property prediction and design

description: This tarball includes 1073 CIF files, each of them provides the optimized structure and the accompanied properties calculated with first-principles computations. The README.txt file provides details on the inputs of the runs used to calculate the properties reportes.
DOI: 10.5061/dryad.63bh4/1
title: RSOS-160032 RAW DATA

description: Raw Data of the figures shown in the manuscript on Excel file.
DOI: 10.5061/dryad.7nc75/1
title: Ziemba et al. 2016 Lab and Field Data

description: Laboratory and field data for experiments examining the interactions between invasive Asian earthworms and terrestrial salamanders in northeastern Ohio, USA.
DOI: 10.5061/dryad.80jh7/2
title: Potomac MSAP Matrices

description: Methylation susceptible (MS) and unmethylated (UM) matrices from six sampling locations in the Potomac River.
DOI: 10.5061/dryad.82nc3/6
title: Fall 10 CCN data aggregated at dorm level with psychological variables

description: This data file contains data at the dorm level collected from our online survey and merged with the resource use data. The first sheet contains metadata defining all variable names.
DOI: 10.5061/dryad.82nc3/7
title: Spring 2012 CCN data with psychological variables

description: This data file contains data at the dorm level collected from our online survey and merged with the resource use data. The first sheet contains metadata defining all variable names.
DOI: 10.5061/dryad.86922/1
title: TRiPS_Dryad_2016

description: R scripts, functions and data needed to perform TRiPS and reproduce analysis and figures in main article.