cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.258nm86/5
title: RESAMPLED_DATA

description: A zipped folder with data sets (structure format) of 292 individuals resampled from the main dataset used to investigate male-bias patterns in the results.
DOI: 10.5061/dryad.258nm86/7
title: RESULTS_5_METHODS

description: Results of the five clustering methods.
DOI: 10.5061/dryad.258nm86/9
title: SIMULATED_DATA_22_LOCI

description: This zipped folder includes 100 simulated datasets (22 loci).
DOI: 10.5061/dryad.2sf02m1/1
title: R scripts and input data
DOI: 10.5061/dryad.3dv23p2/1
title: High_latitude_origin_of_sea_chubs_Knudsen_etal_2019_J_Biogeogr

description: The tar.gz file holds multiple directories with bash codes for unix and R-codes for analysis of time calibrated phylogenetic trees and xml-files to be used with BEAST v1.8.4. The tar.gz file can be uncompressed in a unix terminal, and can also be git cloned from this bitbucket repository: https://xanthic_Rudderfish@bitbucket.org/xanthic_Rudderfish/high_latitude_origin_of_sea_chubs_suppl_info_knudsen_etal_2019.git . The README file has instructions and guides on how the different files and directories can be used to rerun the analysis and reproduce the phylogenetic trees presented in the publication. The supporting information associated with this publication also holds information and instructions to how the analysis were done.
DOI: 10.5061/dryad.3p9h20r/1
title: Tripod gait example data.

description: MATLAB version 7.3 .mat file, created using MATLAB 9.4.
DOI: 10.5061/dryad.3p9h20r/2
title: Limb coordination model data
DOI: 10.5061/dryad.3p9h20r/3
title: Canonical gait model data

description: MATLAB version 7.3 .mat file, created using MATLAB 9.4.
DOI: 10.5061/dryad.3p9h20r/4
title: Dataset of responses of freely-walking flies to translating random dot visual stimuli.

description: MATLAB version 7.3 .mat file, created using MATLAB 9.4.
DOI: 10.5061/dryad.3p9h20r/5
title: Dataset of wild-type spontaneous behavior.

description: MATLAB version 7.3 .mat file, created using MATLAB 9.4.
DOI: 10.5061/dryad.406jj88/4
title: Survival data/analyses 2013

description: See Read Me
DOI: 10.5061/dryad.406jj88/5
title: Read Me Mautz, Rode et al 2019

description: Read Me of the different zip folders
DOI: 10.5061/dryad.406jj88/6
title: AICc functions

description: Script with AICc functions used for the analyses
DOI: 10.5061/dryad.4cs9573/5
title: Oophaga sylvatica Thermal Proteome Profiling

description: This assay was performed to identify proteins that bind to alkaloids. The assay relies on thermodynamic principles of protein-ligand binding, where a protein that has bound its small molecule target has increased thermal stability, a shift detectable by tandem mass spectrometry. A single laboratory reared frog was used for this analysis.
DOI: 10.5061/dryad.4gk50rc/1
title: AcroBSIA

description: Bulk Stable Isotopes (13C, 15N) of shallow (&lt;5m) and deep (30-40m) corals from the genus Acropora and with Hispidose morphology.
DOI: 10.5061/dryad.4gk50rc/2
title: AcroLipidR

description: Percent weight of lipids from coral tissues of the genus Acropora, collected along a depth gradients from 0-40m in Kimbe Bay, Papua New Guinea.
DOI: 10.5061/dryad.4gk50rc/3
title: ChaetAcroSelec

description: Feeding selectivity data along a depth gradient from 0-30m for two obligate coral feeding butterflyfishes (Chaetodon baronessa and Chetodon octofasciatus) in Kimbe Bay, PNG.
DOI: 10.5061/dryad.4gk50rc/4
title: ChaetDietOverlapChristines

description: Data on the among depth diet overlap of two obligate coral feeding butterflyfish species (Chaetodon baronessa and Chaetodon octofasciatus) on Christines Reef in Kimbe Bay, Papua New Guinea.
DOI: 10.5061/dryad.4gk50rc/5
title: ChristinesPreyCoralCover2015

description: The percent cover of coral genera along a depth gradient from 0-30m on Christines Reef, Kimbe Bay, PNG.
DOI: 10.5061/dryad.4gk50rc/6
title: KimbeBayDepthCoralCover2013

description: The percent cover of all hard corals and corals of the genus Acropora along a depth gradient from 0-40m and across nine reefs in Kimbe Bay, PNG.
DOI: 10.5061/dryad.4gk50rc/7
title: CSIAAAMixingModelData

description: Data for mixing models of baseline carbon contributions to Acropora corals and Chaetodon baronessa in shallow (&lt;5m) and deep (20-40m) depths in Kimbe Bay, PNG. Compound Specific Stable Isotope Analyises of Amino Acids.
DOI: 10.5061/dryad.5d69g86/2
title: Fish kairomone

description: The file includes data from small-scale bioassays identifying a fish-borne kairomone responsible for the induction of diel vertical migration in Daphnia magna.
DOI: 10.5061/dryad.6d2h8bp.2
title: Data from: Phylogeny, ancestors, and anagenesis in the hominin fossil record
DOI: 10.5061/dryad.6d2h8bp.2/1.2
title: scripts

description: Python scripts used to test direct ancestor arrangements
DOI: 10.5061/dryad.73k278d/1
title: MHC sequence & micorsatellite diversity of bottlenose dolphins

description: This supplementary data file contains the following: MHC class II DQB sequence alignment (Fig. A1); Microsatellite primer sequences and information on multiplexing and microsatellite alleles detected in dolphin populations (Table A1); Sampling information for conservative sampling approach (Table A2); Microsatellite and MHC II DQB diversity measures for East and West Shark Bay (Table A3); MHC II DQB sequence variants and BLASTN hits (GenBank) (Table A4); ANOVA test results, comparing microsatellite diversity measures between subsamples of the Shark Bay population (Table A5).
DOI: 10.5061/dryad.cv803rv/3
title: ABR_RESOURCE_Annotation
DOI: 10.5061/dryad.cv803rv/4
title: _M00013165_to_M00145618

description: Data zip-file 1 of 19
DOI: 10.5061/dryad.cv803rv/5
title: _M00145660_to_M00218577

description: Data zip-file 2 of 19
DOI: 10.5061/dryad.cv803rv/6
title: _M00218786_to_M00286920

description: Data zip-file 3 of 19
DOI: 10.5061/dryad.cv803rv/7
title: _M00286927_to_M00370330

description: Data zip-file 4 of 19
DOI: 10.5061/dryad.cv803rv/8
title: _M00371702_to_M00491851

description: Data zip-file 5 of 19
DOI: 10.5061/dryad.cv803rv/9
title: _M00491852_to_M00617707

description: Data zip-file 6 of 19
DOI: 10.5061/dryad.d76v3p1/1
title: Supplementary data for Phylogenomics of Aplacophora (Mollusca, Aculifera) and a solenogaster without a foot

description: This archive contains assemblies for all transcriptomes sequenced for this project ("Assembled_transcriptomes" folder), input and output files of all phylogenetic analyses ("Phylogenetic_analysis_results" folder), the custom Solenogastres HaMStR core ortholog set produced for this study ("Solenogastres_hmmer3_core_ortholog_set_for_HaMStR" folder), a file with all COI sequences extracted from the newly sequenced transcriptomes ("COI_mined_from_transcriptomes.fas"), and the script used to process the HaMStR output and generate the datasets analyzed in this study ("Dataset_assembly_script.sh").
DOI: 10.5061/dryad.dm97908/1
title: Aquaculture footprint on genetic variation

description: This data package includes the microsatellite genotype datasets as well as the files and the scripts needed to reproduce the analyses and the figures of the paper that were obtained using the R 3.5.2 statistical environment
DOI: 10.5061/dryad.h15c4sp/1
title: Koivula et al. Urban forest fragment carabids and plants

description: Data contain ground beetle and vascular plant data collected from 10 urban forest stands, at three edge distances in each stand: 0, 10 and 20 m from the edge toward interior. Half of the stands had been treated with undergrowth removal. Beetle data are numbers of individuals, and plants are average percent covers, per distance x stand. Data contain numbers of individuals and numbers of species of forest, open-habitat and generalist species, and species-level numbers; column names show species with 4+4 letter abbreviations of their scientific names. Please consult Appendix and Readme file for details.
DOI: 10.5061/dryad.h7g27vc/1
title: Periodic closure bioeconomic model

description: This zip file contains Matlab code for running bioeconomic fisheries models of periodically harvested closures. Use the file "Main_Script.m" to set initial parameter values and run the models. The file "Fishery_eval.m" contains the population model for each management scenario (i.e. non-spatial management, no-take closure, and periodically harvested closures). Other code files in this folder include: dispersal kernal (fish movement between patches), logistic growth function, optimization functions, and functions for saving model data.
DOI: 10.5061/dryad.h7g27vc/2
title: Load and Plot

description: "Load and Plot" contains Matlab code for loading model data, plotting figures, and an excel file with periodic closure sizes.
DOI: 10.5061/dryad.h7g27vc/3
title: bioeconomic_model_data

description: Model data for all bioeconomic model scenarios. File names include the level of fish movement between patches (S), size of the closure (c), level of overfishing (of) and the fish population growth rate (r) for the particular simulation.
DOI: 10.5061/dryad.kb401ch/1
title: Hrubra total SNP dataset

description: Total genomic dataset consisting of 5,239 SNP loci. Individual and population codes correspond with those provided in Table 1 of the manuscript
DOI: 10.5061/dryad.mq427sp/1
title: Rufous-and-white Wren Song Matching Data

description: Male and female wren responses to playback of shared and unshared songs.
DOI: 10.5061/dryad.mv06pv1/1
title: data_females

description: The female dataset includes all data on females (each female per line) of the two species and for each year of experiment. The table also gives the females' identification (mother ID), their affiliated hydric treatment and reproductive timing as described in the manuscript. For each mother, the number of offspring females and males at birth are available to calculate secondary sex ratio.
DOI: 10.5061/dryad.mv06pv1/2
title: data_juveniles

description: The juvenile dataset includes all data on juveniles (each juvenile per line) of the two species and for each year of experiment. Each juvenile is identified with a number (juvenile ID) and affiliated to its mother (mother ID) and relevant maternal hydric treatment. Each juvenile has been sexed and measured for body growth rate as described in the manuscript. In lizard analyses, we also accounted for outdoor enclosure in analyses, so the table also includes this information.
DOI: 10.5061/dryad.p7q9359/1
title: BD_Plos_One
DOI: 10.17632/7byjhd7fp5.1
title: Data for: MATHEMATICAL MODELLING OF THERMAL DYNAMIC STRESSES ON THE BASIS OF A DUAL – PHASE LAG MODEL

description: Supplementary material to the article containing the problem’s solution file with the solution algorithm, the final formula for the desired function, graphical results, and an assessment of the basic equation and uniqueness conditions discrepancies
DOI: 10.17632/9nvjkn3fv2.1
title: Data for: EFFECT OF TEMPERATURE, pH, β- AND HP-β-CDs ON THE SOLUBILITY AND STABILITY OF FLAVANONES: NARINGENIN AND HESPERETIN
DOI: 10.17632/m82vhzkkbd.1
title: Data for: A new reverse transcription-insulated isothermal polymerase chain reaction (RT-iiPCR) assay for DHAV-3 detection based on the POCKIT™ system

description: These documents contain some important dates about the development and evaluation of this RT-iiPCR of DHAV-3. And we listed as follows: Fig 1 The linear relation of every dilution detected by rRT-PCR. Table 1 Reference strains and isolates used in this study for specificity testing of RT-iiPCR. Table 2 Primer information rRT-PCR assay. Table 3 Evaluation of the sensitivity of the rRT-PCR and RT-iiPCR assays to DHAV-3. Table 4 Performance evaluations of the PetNADTM and TRizol RNA extraction methods for the detection of DHAV-3 by rRT-PCR and RT-iiPCR, respectively. Table 5 The Contingency table for analysis of the level of agreement between the rRT-PCR and the RT-iiPCR assays for the detection of DHAV-3 in liver samples.
DOI: 10.17632/r3djxj7vdb.1
title: Data for: Differentiating Conscientious from Indiscriminate Responders in Existing NEO-Five Factor Inventory-3 Data

description: these three data sets were used for the paper: Differentiating Conscientious from Indiscriminate Responders in Existing NEO-Five Factor Inventory-3 Data by Zdravko Marjanovic and Ronald R. Holden
DOI: 10.17632/tx3rxdcxwt.1
title: Data for: 3362908

description: Financial Data
DOI: 10.5061/dryad.003vg7g/1
title: Neonatal brain transcriptome profiles

description: C57BL/6J neonates were exposed in utero, through maternal dietary exposure to control, BAC C12 (120 mg/kg/day), or BAC C16 (120 mg/kg/day). At postnatal day 0, neonates were sacrificed and brains were collected. This excel sheet contains 14 columns. Four biological replicates per treatment were used for transcriptomics analyses. Rows contain FPKM values of each transcript, signified by Ensembl IDs and Gene Names.
DOI: 10.5061/dryad.1jv12nj/1
title: MaleAdultFitnessData_Dryad

description: Data from 'male reproductive fitness assay' - a reciprocal transplant in which males from all 21 experimental populations from within a given larval adaptation set, and the ancestor, were all assayed in each of the three mating environments (i.e. the mating environment in which they had been evolving as well as the other two mating environments). Rows are individual (ancestral) females and 'DsRed_offspring' and 'wildtype_offspring' denote the number of offspring of the given phenotype produced by this female. Mating treatments and mating environments are as described in the publication.
DOI: 10.5061/dryad.1jv12nj/2
title: FemaleAdultFitnessData_Dryad

description: Data from the 'Female Reproductive Fitness Assay' - a reciprocal transplant in which females from all 21 populations (i.e. seven from each of the three evolutionary mating treatments) and the ancestral population were all assayed in each of the three assay mating environments. In all cases males in these assays came from the ancestral population. 'No.egg' indicates the total number of eggs produced by a single female in a given assay. 'Average fecundity' is the average of all females in a given replicate. Mating treatments and assay environments are as described in the publication.
DOI: 10.5061/dryad.1jv12nj/3
title: MatingRateData_Dryad

description: Data from the preliminary Assay on the 'Effect of mating environment on mating rate', as described in the Supplemental materials of the publication. The assay was performed over three days (1-3) with hourly observations (time; 24h clock) in which the number of observed matings was recorded ('Number_of_matings').
DOI: 10.5061/dryad.38fh0mc/1
title: Castro_etal_Biotropica_Data

description: This file contains the data of aquatic invertebrates abundance (family and genera) collected in each site used in this study. The file also contains the environmental metrics and metadata describing each one.
DOI: 10.5061/dryad.3p9h20r/7
title: Dataset of responses to transient activation of moonwalker neurons

description: MATLAB version 7.3 .mat file, created using MATLAB 9.4.
DOI: 10.5061/dryad.3q80581/1
title: Rüber_et_al_Channidae_rRNA_befor_Gblocks

description: rRNA alignment of 246 taxa before Gblocks
DOI: 10.5061/dryad.3q80581/2
title: Rüber_et_al_Channidae

description: Final alignment of rRNA, cytb and rag1 of 246 taxa used for analysis
DOI: 10.5061/dryad.56qq231/1
title: Morphometric Data and Scripts for Analysis

description: This .zip file contains the following folders, with the following contents: "Raw Data" - TPS files containing raw landmark data collected from photographs of specimens; "Morphometric Data" - .TPS files containing shape data used in our analyses by the scripts in the "Scripts" folder; "Time Data" - Phylogenies and stratigraphic occurrence data for all species in our analyses; "Scripts" - R scripts used to analyze our datasets.
DOI: 10.5061/dryad.653q97g/1
title: 2019Beck-ArcticCharrEmbryonicGeneExpression_data

description: All data collected for this study can be found in this file
DOI: 10.5061/dryad.6d2h8bp.1
title: Data from: Phylogeny, ancestors, and anagenesis in the hominin fossil record
DOI: 10.5061/dryad.6d2h8bp.1/1.1
title: scripts

description: Python scripts used to test direct ancestor arrangements
DOI: 10.5061/dryad.6d2h8bp.1/2.1
title: ranges

description: stratigraphic ranges of hominin taxa
DOI: 10.5061/dryad.6d2h8bp.1/3.1
title: clade_best_strat.jitter

description: final hominin tree inferred from stratophylogenetic rearrangements and AIC comparisons
DOI: 10.5061/dryad.6d2h8bp.2/2.2
title: ranges

description: stratigraphic ranges of hominin taxa
DOI: 10.5061/dryad.6d2h8bp.2/3.2
title: clade_best_strat.jitter

description: final hominin tree inferred from stratophylogenetic rearrangements and AIC comparisons
DOI: 10.5061/dryad.6d2h8bp.2/4.2
title: hominin_temporal_ranges

description: Spreadsheet with the temporal ranges used for each hominin taxon in the analysis.
DOI: 10.5061/dryad.6d2h8bp.2/5.2
title: hominin_temporal_ranges_citations

description: Comprehensive list of citations supporting the temporal ranges used in the analyses.
DOI: 10.5061/dryad.74bf15t/1
title: uncertainty data 12-7-17

description: Data for uncertainty experiment 1
DOI: 10.5061/dryad.74bf15t/2
title: raw num Q US

description: Raw data for disease uncertainty experiment 2
DOI: 10.5061/dryad.7fp676d.1
title: Data from: Feeding strategies of brown howler monkeys in response to variations in food availability
DOI: 10.5061/dryad.7fp676d.1/1.1
title: database_feeding_behavior

description: Here we provided a single database on the feeding behavior and other activities of six wild groups of brown howler monkeys (Alouatta guariba clamitans). This research was conducted during a 36-month period in three small (&lt;10 ha: S1, S2, and S3) and three large (&gt;90 ha: L1,L2, and L3) Atlantic forest fragments in Rio Grande do Sul State, southern Brazil.
DOI: 10.5061/dryad.7fp676d.2
title: Data from: Feeding strategies of brown howler monkeys in response to variations in food availability
DOI: 10.5061/dryad.7fp676d.2/1.2
title: database_feeding_behavior

description: Here we provided a single database on the feeding behavior and other activities of six wild groups of brown howler monkeys (Alouatta guariba clamitans). This research was conducted during a 36-month period in three small (&lt;10 ha: S1, S2, and S3) and three large (&gt;90 ha: L1,L2, and L3) Atlantic forest fragments in Rio Grande do Sul State, southern Brazil.
DOI: 10.5061/dryad.7fp676d.2/2.2
title: dataset_plant_phenology

description: Dataset on the phenology of food plant species exploited by brown howlers during the study period.
DOI: 10.5061/dryad.7g5b162/1
title: Reproductive mode data file
DOI: 10.5061/dryad.7g5b162/2
title: Poeciliinae traits data file
DOI: 10.5061/dryad.7g5b162/8
title: README
DOI: 10.5061/dryad.7rv4ct1/1
title: Bortot et al Biol Letters Excel Data
DOI: 10.5061/dryad.813nj25/1
title: Patient Cohort Topics for Clinical Information Retrieval

description: This file contains the topics in plain text for evaluating clinical information retrieval systems. A total of 56 topics, each illustrating a patient cohort, were developed through a collaboration between Mayo Clinic and Oregon Health & Science University (OHSU). Initially there were 29 topics generated from OHSU and 30 from Mayo Clinic. Three topics with similar characteristics from both sides were merged during topic development to avoid redundancy. Clinical study data requests, as submitted by researchers to the Oregon Clinical and Translational Research Institute (OCTRI), OHSU’s Research Data Warehouse (RDW), provided the basis for 26 topics at OHSU. The 30 topics from Mayo Clinic were modeled after cohorts from the Phenotype KnowledgeBase (PheKB) (7 topics), Rochester Epidemiology Project (REP) (9 topics), National Quality Forum (NQF) (12 topics), and Mayo RDW (2 topics).
DOI: 10.5061/dryad.85g65v8/1
title: SUP2

description: A .biom file containing the raw sequencing data used in the analysis.
DOI: 10.5061/dryad.b412jp5/1
title: Script_S1

description: This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": DESeq2 analysis of T. americanus, Transcriptome constructed using Trinity and filtered for those contigs that contain an open reading frame, Expected read counts created using RSEM
DOI: 10.5061/dryad.b412jp5/2
title: Script_S2

description: This is code to replicate the analysis from Alleman et al. "Tandem-Running and Scouting Behavior is Characterized by Up-Regulation of Learning and Memory formation genes within the Ant Brain": DESeq2 analysis of T. longispinosus, Transcriptome constructed using Trinity and filtered for those contigs that contain an open reading frame, Expected read counts created using RSEM.
DOI: 10.5061/dryad.cv803rv/10
title: _M00617709_to_M00754249

description: Data zip-file 7 of 19
DOI: 10.5061/dryad.cv803rv/11
title: _M00754250_to_M00889693

description: Data zip-file 8 of 19
DOI: 10.5061/dryad.cv803rv/12
title: _M00889694_to_M01025210

description: Data zip-file 9 of 19
DOI: 10.5061/dryad.cv803rv/13
title: _M01025211_to_M01164518

description: Data zip-file 10 of 19
DOI: 10.5061/dryad.cv803rv/14
title: _M01164520_to_M01328136

description: Data zip-file 11 of 19
DOI: 10.5061/dryad.cv803rv/15
title: _M01328137_to_M01470166

description: Data zip-file 12 of 19
DOI: 10.5061/dryad.cv803rv/16
title: _M01470167_to_M01623523

description: Data zip-file 13 of 19
DOI: 10.5061/dryad.cv803rv/17
title: _M01623527_to_M01745797

description: Data zip-file 14 of 19
DOI: 10.5061/dryad.cv803rv/18
title: _M01745798_to_M01867451

description: Data zip-file 15 of 19
DOI: 10.5061/dryad.jm843d8/1
title: Mathematica code for the simulations and figures

description: Mathematica code for all simulations and figures in a *.cdf, open file format, by Wolfram. It is arranged into five chapters and SI -- the respective cells need to be expanded to reveal their content.
DOI: 10.5061/dryad.kh2gv5f/1
title: Test set

description: Micrographs used for testing neural network
DOI: 10.5061/dryad.kh2gv5f/2
title: Training set

description: Micrographs used for the training data set for neural networks.
DOI: 10.5061/dryad.kh2gv5f/3
title: Caffe model weights and model structure

description: Zip file contains the caffe model weights (sc_feb2019.caffemodel) and caffe model structure definition file (sc_feb2019.prototxt)
DOI: 10.5061/dryad.kn92b41/1
title: Dataset_Yang_et al_2019

description: The file contains all the original data including soil heterotrophic respiration, litter layer residence time, species diversity, soil properties, community level plant chemical composition and microbial community composition.
DOI: 10.17632/3ctdn8hckf.1
title: Data for: Organic geochemistry, distribution and hydrocarbon potential of source rocks in the Paleocene, Lishui Sag, East China Sea Shelf Basin
DOI: 10.17632/5gzjmpjmrj.1
title: Data for: Effects of tea polyphenols and Ca(OH)2 on the intermolecular forces and mechanical, rheological, and microstructural characteristics of whole duck egg white gel

description: FTIR, pH, surface hydrophobicity, protein fractions, rheology
DOI: 10.17632/5jzy94jpp9.1
title: Data for: Slums in Brazil: Where are They Located, Who Lives in Them,}{and Do They `Squeeze' the Formal Housing Market?

description: STATA data file