cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.61691/1
title: SNP genotypic data from American pika in North Cascades National Park

description: Excel file including genotypes at 9825 SNPs for 67 American pika sampled in North Cascades National Park, Washington, USA. The first column is contig name. The second column is SNP position within the contig. Every two columns after is an individual. Each row is a locus. Sample names include the transect identifier (PP=Pyramid Peak; TL=Thornton Lake), site name (ex. 1A), and individual number (ex. 20a). Allele calls are as follows: 1=A, 2=C, 3=G, 4=T.
DOI: 10.5061/dryad.6h7nt/1
title: Readme

description: Readme file.
DOI: 10.5061/dryad.6h7nt/2
title: Acapella_Scripts_Parameters

description: This zipped file contains the Acapella script used to analyze all the image datasets and the Acapella parameters files for each analysis session. The parameters files are named according to the relative image dataset analyzed.
DOI: 10.5061/dryad.6h7nt/3
title: R_Analysis_Fig3_6

description: This zipped file contains the The the .txt single-object level image analysis results files generated by Acapella, the .Rmd R script used for the analysis and the .html R output file. This .Rmd R script was used to generate  Fig. 3 - 6 of the article.
DOI: 10.5061/dryad.6td18/1
title: Simulations

description: The code for the simulations used in the article to test the statistical method.
DOI: 10.5061/dryad.6td18/2
title: Simulation_analysis

description: Code for compiling and analyzing the output of the simulations in Simulations.r, and plot the figures in the article.
DOI: 10.5061/dryad.6td18/3
title: Functions

description: This source file includes functions used for the analysis of the datasets in the file examples.r
DOI: 10.5061/dryad.6td18/4
title: examples

description: This file includes a tutored example of analysis using a simulation, followed by the analysis of the case study on Hoge Veluwe great tits.
DOI: 10.5061/dryad.6td18/5
title: data

description: This R workspace includes the data of the case study on Hoge Veluwe great tits, to be used in the source file examples.r, which also includes a description of the data.
DOI: 10.5061/dryad.6v5tn/1
title: Anemia and Related Nutrient Deficiencies after Roux-en-Y Gastric Bypass Surgery

description: Study characteristics; Proportion of study participants with anemia before and after RYGB surgery; Proportion of study participants with low ferritin/ serum iron/ vitamin B12/ folate level before and after RYGB surgery; Hemoglobin/Hematocrit level among study participants; Ferritin/ serum Iron/ vitamin B12/ folate level among study participants before and after RYGB surgery before and after RYGB surgery; Literature search and study selection; Forest plot for proportion of study participants with anemia before RYGB and 12 months after RYGB; Forest plot for proportion of study participants with (A) ferritin (B) serum iron (C) vitamin B12 and (D) folate deficiencies before RYGB and 12 months after RYGB; Funnel plot comparing log(mean) and s.e. of log(mean) for proportion of study participants with anemia 12 months after RYGB; MEDLINE (via PubMed) search query with ‘All Fields’; Cochrane Library search query with ‘Search All Text’
DOI: 10.5061/dryad.b4d70/1
title: Behavioral data

description: The .xlsx file contains raw data of behavioral parameters for individual mice as well as treatment and genotypes.
DOI: 10.5061/dryad.b5837/1
title: Data for capture-recapture analyses

description: This dataset contains individual encounter histories (2002-2012) starting the year of first photography, with covariates: sex, raw bib size measurements and their squared values (taken the year of first photography), standardized bib size measurements and their squared values (taken the year of first photography, and standardized within this year), mean adjusted bib sizes and their squared values, and individual identities (band numbers). The file format is "headed" (i.e. containing explicit label for each column) with "txt" extension, which is compatible with E-SURGE and easily convertible with EXCEL (or equivalent) or R for any other use.
DOI: 10.5061/dryad.b5837/2
title: Data for variability analyses

description: This dataset contains all bib size measurements obtained from photographies taken at captures and recaptures events in the field (without any transformation). The dataset also contains covariates used to model bib size variation with mixed models: sex, year, colony size, age, body mass, tarsus length, colony identity and individual identity. The file format is "csv" which can be easily opened with EXCEL (or equivalent) and R for processing.
DOI: 10.5061/dryad.c2n5j/1
title: MEC-15-690-Dryad

description: This zip file extracts data used in Roy et al MEC-15-0690. The ".txt" file is the raw microsatellite scores in number of repeats formatted for the Convert.exe program. The different forlders contain the data and results (Lositan and Bayescan) for various tests and analyses performed in the MS cited above. ".in" files are for structurama 2.0 input (Mac format), ".u" files are for IMa2 input (also accompanied by ".priors" files), while structure inputs list only "Project_data" files (and should be renamed as such prior to use).
DOI: 10.5061/dryad.d4752/1
title: Mus climbing for PLoS One

description: csv file
DOI: 10.5061/dryad.d5n0d/1
title: Genotype data

description: Microsatellite genotypes for 15 loci in six charr populations
DOI: 10.5061/dryad.hn40n/1
title: Evolution literature review data
DOI: 10.5061/dryad.md0vg/1
title: Immune raw data
DOI: 10.5061/dryad.mf3rb/1
title: Raw data
DOI: 10.5061/dryad.n0432/1
title: Genotype data

description: Genotype data used in the manuscript "Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae". The file contains data for each sample with the locality and microsatellite genotypes for all individuals.
DOI: 10.5061/dryad.n0432/2
title: R Script Linear Regressions

description: R Script for Linear Regression analyses (Latitudinal gradients) from the manuscript "Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae"
DOI: 10.5061/dryad.n0432/3
title: Geographic coordinates Geneland

description: Geographic coordinates used for Geneland analysis in the manuscript "Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae"
DOI: 10.5061/dryad.n0432/4
title: Input file Structure analysis

description: Input file used for Structure analysis in the manuscript "Emerging patterns of genetic variation in the New Zealand endemic scallop Pecten novaezelandiae"
DOI: 10.5061/dryad.n1cg7/1
title: Sequence alignments and tree files

description: The file contains sequence alignments of sequences generated using Sanger sequencing and next generation sequencing.  The NJ tree files associated with Figures 3 and 4 are also included in this file.
DOI: 10.5061/dryad.nq648/1
title: STEM_probability-of-occurrence

description: Weekly estimates of probability of occurrence for 142 migratory species within 37.5 km radius circles centered on 12 weather surveillance radar stations located in the northeastern USA . Estimates are derived from spatiotemporal exploratory models (STEM) with occurrence information from the eBird citizen science dataset for the combined period 2004 to 2011.
DOI: 10.5061/dryad.nq648/2
title: WSR_station_reflectivity

description: Daily total effective scattering area (reflectivity) of birds (square centimeters) per unit volume (cubic km) estimated at 12 weather surveillance radar (WSR) stations in the northeastern USA during the autumn of 2010 and 2011 within 37.5 km radius of each WSR station and within 100-m altitudinal bins.
DOI: 10.5061/dryad.nv5d2/2
title: CCPDD Predator Prey Link Data

description: This file includes the data from the California Current Predator Diet Database (CCPDD) that was used for the analysis of forage species in predator diet in our publication. Each record (row) includes data for predator and prey taxonomy, citation info, location, date, observation type, sample size and units for measuring amount of prey consumed.
DOI: 10.5061/dryad.ps80f/1
title: Mass prediction tool and modern Oxford mammal skeleton data
DOI: 10.5061/dryad.sq41r/1
title: forest regeneration data

description: see readMe.txt
DOI: 10.5061/dryad.t741c/4
title: Raw_tracks_predator_trials

description: Raw ctrax output (after manual correction) for predator model trials.
DOI: 10.5061/dryad.t741c/5
title: Processed_tracks

description: Location and orientation data (video tracking) for both predator and control trials, after processing.
DOI: 10.5061/dryad.t741c/6
title: Video_snapshots

description: Screen grabs that may be used to process the raw tracking data.
DOI: 10.5061/dryad.vf2jk8n5.2
title: Data from: A national geographic framework for guiding conservation on a landscape scale
DOI: 10.5061/dryad.vf2jk8n5.2/1.2
title: National_Fish_Habitat_Action_Plan

description: National Fish Habitat Action Plan. 2006. http://fishhabitat.org/documents/plan/National_Fish_Habitat_Action_Plan.pdf
DOI: 10.5061/dryad.vf2jk8n5.2/2.2
title: NEAT_FinalRpt

description: National Ecological Assessment Team. 2006. Strategic Habitat Conservation. Final Report of the National Ecological Assessment Team. United States Geological Survey and the United States Fish and Wildlife Service report. http://training.fws.gov/CSP/Resources/SHC/shc_finalrpt.pdf
DOI: 10.5061/dryad.vf2jk8n5.2/3.2
title: NAWMP ImplementationFramework 2004

description: North American Waterfowl Management Plan, Plan Committee. 2004. North American Waterfowl Management Plan 2004. Implementation Framework: Strengthening the Biological Foundation. Canadian Wildlife Service, U.S. Fish and Wildlife Service, Secretaria de Medio Ambiente y Recursos Naturales, 106 pp. http://www.fws.gov/birdhabitat/NAWMP/files/ImplementationFramework.pdf
DOI: 10.5061/dryad.vf2jk8n5.2/4.2
title: FWS memo on LCC boundary change guidance (Final)

description: U.S. Fish and Wildlife Service. 2006. Landscape Conservation Cooperatives. Operational Memo for Addressing Requests for Consideration of LCC Geographic Boundary Changes. Office of the Science Advisor, Dec. 2011.
DOI: 10.5061/dryad.10278/18
title: Bumble bee foraging model

description: R script for a simple mathematical model modified from Essenberg 2012 to predict foraging efficiency of generalist and specialist bees given variation in flight speed, flower density, handling time, and the proportion of shallow vs. deep flowers in the community. The output of the model describes the relative advantage of being a generalist. The generalist is favored when its relative advantage is greater than 1.
DOI: 10.5061/dryad.128p6/2
title: Appendix S2. Full serial sections of Fasciculatia striatoparadoxa
DOI: 10.5061/dryad.23h4q/1
title: Barson_et_al_candidate_region_sequences_and_QTN_table
DOI: 10.5061/dryad.23h4q/2
title: Barson_et_al_GenABEL

description: File in GenABEL format containing SNP genotype and individual phenotype information
DOI: 10.5061/dryad.2qg54/4
title: Data files and scripts

description: Archive of all data files and scripts needed to reproduce population genetic results, as well as our mitogenome tree and aligned mitogenomes. BAM files can be found in the NCBI SRA, accession PRJNA298405. Files in this archive can also be found on github, DOI: http://dx.doi.org/10.5281/zenodo.32936
DOI: 10.5061/dryad.44372/10
title: Align_NE.SW_NKTR_230.phased.sequences

description: This file contains NKTR aligned sequences used in most phylogeographic analyses: population assignment, haplotype genealogy, species tree estimation, migration estimate, species validation, and model based approach. Northeast (NE) sequences cluster was used separately in phylogeographic reconstruction.
DOI: 10.5061/dryad.44372/11
title: Align_NE.SW_R35_268.phased.sequeces

description: This file contains R35 aligned sequences used in most phylogeographic analyses: population assignment, haplotype genealogy, species tree estimation, migration estimate, species validation, and model based approach. Northeast (NE) sequences cluster was used separately in phylogeographic reconstruction.
DOI: 10.5061/dryad.44372/12
title: Align_NE.SW_RP40_264.phased.sequences

description: This file contains RP40 aligned sequences used in most phylogeographic analyses: population assignment, haplotype genealogy, species tree estimation, migration estimate, species validation, and model based approach. Northeast (NE) sequences cluster was used separately in phylogeographic reconstruction.
DOI: 10.5061/dryad.44372/13
title: Tree_12S_62samples_substitution.rate
DOI: 10.5061/dryad.44372/14
title: Tree_12S_137samples.outgroup_gblock
DOI: 10.5061/dryad.44372/9
title: Align_NE.SW_ATPSB_252.phased.sequences_gblock

description: This file contains ATPSB aligned sequences used in most phylogeographic analyses: population assignment, haplotype genealogy, species tree estimation, migration estimate, species validation, and model based approach. Northeast (NE) sequences cluster was used separately in phylogeographic reconstruction.
DOI: 10.5061/dryad.50r1b/1
title: Data on radiation tolerance in Hypsibius dujardini

description: This file contains all data used in the study on radiation tolerance in Hypsibius dujardini, by Beltran-Pardo et al.
DOI: 10.5061/dryad.6g06h/2
title: raw dominance interaction data 2009_2013

description: data that informed Elo scores.
DOI: 10.5061/dryad.6h7nt/10
title: BC_140819_M2A_GFP_NPM_UN

description: This zipped file contains the image dataset relative to Untreated Mac2A cells stained with the hiBA-NPM1 probe set. This dataset was used to generate Fig. 3 - 6 of the article.
DOI: 10.5061/dryad.6h7nt/11
title: BC_150527_K299_ZERO_ALK_UN

description: This zipped file contains the image dataset relative to 0% Untreated K299 cells (100% Mac2A cells) stained with the hiBA-ALK probe set. This dataset was used to generate Fig. S1 of the article.
DOI: 10.5061/dryad.6h7nt/12
title: BC_150527_K299_POINTONE_ALK_UN

description: This zipped file contains the image dataset relative to 0.1% Untreated K299 cells stained with the hiBA-ALK probe set. This dataset was used to generate Fig. S1 of the article.
DOI: 10.5061/dryad.6h7nt/13
title: BC_150527_K299_POINTFIVE_ALK_UN

description: This zipped file contains the image dataset relative to 0.5% Untreated K299 cells stained with the hiBA-ALK probe set. This dataset was used to generate Fig. S1 of the article.
DOI: 10.5061/dryad.6h7nt/4
title: R_Analysis_FigS1

description: This zipped file contains the The the .txt single-object level image analysis results files generated by Acapella, the .Rmd R script used for the analysis and the .html R output file. This .Rmd R script was used to generate  Fig. S1 of the article.
DOI: 10.5061/dryad.6h7nt/5
title: BC_140819_M2A_GFP_ALK_UN

description: This zipped file contains the image dataset relative to Untreated Mac2A cells stained with the hiBA-ALK probe set. This dataset was used to generate Fig. 3 - 6 of the article.
DOI: 10.5061/dryad.6h7nt/6
title: BC_140713_K299_K299_ALK_UN

description: This zipped file contains the image dataset relative to Untreated K299 cells stained with the hiBA-ALK probe set. This dataset was used to generate Fig. 3 - 6 of the article.
DOI: 10.5061/dryad.6h7nt/7
title: BC_140713_K299_K299_NPM_UN

description: This zipped file contains the image dataset relative to Untreated K299 cells stained with the hiBA-NPM1 probe set. This dataset was used to generate Fig. 3 - 6 of the article.
DOI: 10.5061/dryad.6h7nt/8
title: BC_140815_M2A_GFP_ALK_IR

description: This zipped file contains the image dataset relative to Irradiated (25 Gy) Mac2A cells stained with the hiBA-ALK probe set. This dataset was used to generate Fig. 3 - 6 of the article.
DOI: 10.5061/dryad.6h7nt/9
title: BC_140815_M2A_GFP_NPM_IR

description: This zipped file contains the image dataset relative to Irradiated (25 Gy) Mac2A cells stained with the hiBA-NPM1 probe set. This dataset was used to generate Fig. 3 - 6 of the article.
DOI: 10.5061/dryad.7g4c9/1
title: Supplemental_methods_Kasimatis_Riginos_Dryad

description: Supplementary methods
DOI: 10.5061/dryad.7g4c9/2
title: Supplemental_tables_Kasimatis_Riginos_Oct2015_Dryad

description: Supplementary Tables (ESM Tables 1-5)
DOI: 10.5061/dryad.7g4c9/3
title: Data_source_appendix_Kasimatis_Riginos_Oct2015_dryad

description: Appendix - includes references for original data sources and raw data (ESM Table 6)
DOI: 10.5061/dryad.7g4c9/4
title: SuppFig1_sppnumb

description: ESM Figure S1
DOI: 10.5061/dryad.7g4c9/5
title: Supp_fig2_chrongram

description: ESM Figure S2
DOI: 10.5061/dryad.7g4c9/6
title: Kasimatis_Riginos_data_Oct2015

description: Excel worksheet containing all raw data for analyses.
DOI: 10.5061/dryad.7g4c9/7
title: volume_Oct2015

description: CSV formatted infile with egg volume data. (Also represented in the excel file.)
DOI: 10.5061/dryad.9v9d3.1
title: Data from: Camouflaged or tanned: plasticity in freshwater snail pigmentation
DOI: 10.5061/dryad.9v9d3.2
title: Data from: Camouflaged or tanned: plasticity in freshwater snail pigmentation
DOI: 10.5061/dryad.9v9d3.2/1.2
title: Pigmentation and index of roundness measurements
DOI: 10.5061/dryad.b26q1/1
title: 1_US_acquisitions_in-vivo_liver_motions

description: Ultrasound images (B-mode) of in-vivo liver tissues during respiration and apnea (porcine model); data of liver motion magnitudes obtained with an ultrasound speckle tracking method; statistical analyses
DOI: 10.5061/dryad.b26q1/2
title: 2_Fusion_Modeling_In-vivo_Liver_Motion

description: Fusion modeling data of HIFU treatment in moving liver tissues (porcine model) for 2 HIFU focusing strategies: a spherical and a toroidal focusing. Simulated pressure fields, temperature and thermal dose maps, motion data, statistical analyses
DOI: 10.5061/dryad.b26q1/3
title: 3_Preliminary_In-vivo_validation_of_Fusion_Modeling

description: In-vivo validation in the porcine model of the fusion modeling method, for 2 differents HIFU focusing strategies: spherical and toroidal. In each subfolder are stored: photos of the in-vivo set-up, ultrasound images of in-vivo liver tissues during respiration (pictures and movies, B-mode), photos of macroscopic analyses on liver gross samples, fusion modeling data for each in-vivo experiment (including simulated ultrasound pressure fields, temperature and thermal dose maps after the end of the HIFU treatment, and in-vivo liver motion data accounted for the fusion modeling)
DOI: 10.5061/dryad.bv8j6/1
title: RIAT Restoring Study 329 data files

description: Zip file containing: Original SKB CSR (both Appendix D & Appendix G); ii) RIAT Excel spreadsheet for Harms/Adverse Event data; RIAT Excel spreadsheet for Withdrawals/dropouts from the study. R code used to analyse Efficacy data; Original SKB Study 329 Trial protocol which was followed in Restoring Study 329 (RIAT).
DOI: 10.5061/dryad.dp2f7/2
title: "all.ITS.2014.08.21"

description: Sequences used to conduct the ITS analysis
DOI: 10.5061/dryad.g4590/1
title: Spatiotemporal data on multiple ecosystem services

description: The file provides the data for 7 ecosystem services, quantified from 1971 to 2006 (with a time step of 5 years) and across 131 municipalities of the Monteregie, a region located in Southern Quebec, Canada. Data on population density, distance from Montreal and soil capability for agriculture are provided at the same spatio-temporal scales. Missing data are coded as "NA" in the data file. For pork production, certain number are protected by a Licence agreement with Ministries (see the material and methods section of the article for more information). Those data are coded as "*" in this column.
DOI: 10.5061/dryad.gs340.1
title: Data from: The skull and endocranium of a Lower Jurassic ichthyosaur based on digital reconstructions
DOI: 10.5061/dryad.gs340.2
title: Data from: The skull and endocranium of a Lower Jurassic ichthyosaur based on digital reconstructions
DOI: 10.5061/dryad.gs340.2/1.2
title: Phylogenetic details

description: Overview of methods of phylogenetic analysis, character choice, and results of the analysis.
DOI: 10.5061/dryad.hn40n/10
title: readme

description: Description of the contents of all the other files in this Dryad submission.
DOI: 10.5061/dryad.hn40n/11
title: R script to statistically analyse the p value data

description: R script detailing the statistical analyses we performed on the p value datasets.
DOI: 10.5061/dryad.hn40n/2
title: Exact p value dataset
DOI: 10.5061/dryad.hn40n/3
title: journal_categories
DOI: 10.5061/dryad.hn40n/4
title: p values data 24 Sept
DOI: 10.5061/dryad.hn40n/5
title: Proportion of significant p values per paper
DOI: 10.5061/dryad.hn40n/6
title: R script to filter and classify the p value data
DOI: 10.5061/dryad.hn40n/9
title: Quiz answers - guessing effect size from abstracts

description: The answers provided by the 9 evolutionary biologists to quiz we designed, which aimed to test whether trained specialists are able to infer the relative size/direction of effect size from a paper's title and abstract.
DOI: 10.5061/dryad.kc33b/1
title: Lifespan Data for Y-lines from Griffin et al 2015

description: Data contains lifespan (variable: Age) data for 33 Y chromosome substitution lines (variable: Line), measured in 13560 flies, across three experimental blocks (variable: Block) and 456 vials (variable: Vial).
DOI: 10.5061/dryad.m0jk7/1
title: NimbleGen Capture Probe Sequences

description: NimbleGen capture probe sequences designed against assemblies obtained from sequencing fosmids created from Aspidoscelis inornata and Sceloporus cowlesi DNA.
DOI: 10.5061/dryad.m6f93/1
title: genotypic data of seven strains of Xenopus tropicalis

description: data in genepop format.
DOI: 10.5061/dryad.m6f93/2
title: Genotypicdata of eleven strains for sixty SSLP markers

description: Genepop format
DOI: 10.5061/dryad.nr716/1
title: SNPdata

description: This spreadsheet contains the genomic data used to demonstrate the feasability of using intact portions of a mosquito's leg as sources of template DNA for whole genome amplifcation. The "Data" tab contains sample and genotype information on 292 Anopheles gambiae sensu latu samples collected in Uganda.
DOI: 10.5061/dryad.nv5d2/1
title: CCPDD Location GIS files for polygons and points

description: These files can be used to link data from the CCPDD to GIS shape files using the field LocatNum.
DOI: 10.5061/dryad.pb0dn.2
title: Data from: Comparison of population-genetic structuring in congeneric kelp- versus rock-associated snails: a test of a dispersal-by-rafting hypothesis
DOI: 10.5061/dryad.pb0dn.2/2.2
title: NikulaSpencerWaters2011_msatdata_updated31072012
DOI: 10.5061/dryad.q771r.1
title: Data from: RAD-genotyping reveals fine-scale genetic structuring and provides powerful population assignment in a widely distributed marine species; the American lobster (Homarus americanus).
DOI: 10.5061/dryad.qn82p/1
title: 1850_2012_elite_winners

description: Speeds (yard/sec) of winners of elite thoroughbred horse races run in Great Britain on the turf (flat only) between 1850 and 2012. Data were sourced from Ruff’s Guide to the Turf (1850-1951 annual editions), the Raceform Flat Annual (1949-1994) and Raceform Interactive (1996-2012; www.raceform.co.uk).
DOI: 10.5061/dryad.qn82p/2
title: 1997_2012

description: Speed of horses in GB flat races run on the turf between 1997 and 20012. Data were sourced from Raceform Interactive ( www.raceform.co.uk).
DOI: 10.5061/dryad.vf2jk8n5.1
title: Data from: A national geographic framework for guiding conservation on a landscape scale
DOI: 10.5061/dryad.vf2jk8n5.2/10.2
title: NABCI BCR descriptions

description: U.S. North American Bird Conservation Initiative Committee. 2000. North American Bird Conservation Initiative (NABCI) Bird Conservation Region Descriptions: A Supplement to the North American Bird Conservation Initiative Bird Conservation Regions Map. U.S. Fish & Wildlife Service, Migratory Birds, Arlington VA USA. http://www.nabci-us.org/aboutnabci/bcrdescrip.pdf .