cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2601h/25
title: CFD simulation file for Parvancorina sagitta from Russia, original relief, oriented at 90° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina sagitta from Russia with original relief was oriented at 90° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/26
title: CFD simulation file for Parvancorina sagitta from Russia, original relief, oriented at 180° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina sagitta from Russia with original relief was oriented at 180° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2bk07/1
title: Genotype data for workers
DOI: 10.5061/dryad.3t2d4/6
title: Jacobsen_Pool2_forward_reads_part2

description: Second half of the bzip-compressed fastq-file containing raw sequences (forward reads) from Illumina HiSeq of pooled fungal DNA extracted from 98 samples (Pool2) of wood-inhabiting insects. Split with HJSplit as recommended by Dryad (http://wiki.datadryad.org/Large_File_Transfer).
DOI: 10.5061/dryad.3t2d4/7
title: Jacobsen_Pool2_backward_reads_part1

description: First half of the bzip-compressed fastq-file containing raw sequences (backward reads) from Illumina HiSeq of pooled fungal DNA extracted from 98 samples (Pool2) of wood-inhabiting insects. Split with HJSplit as recommended by Dryad (http://wiki.datadryad.org/Large_File_Transfer).
DOI: 10.5061/dryad.3t2d4/8
title: Jacobsen_Pool2_backward_reads_part2

description: Second half of the bzip-compressed fastq-file containing raw sequences (backward reads) from Illumina HiSeq of pooled fungal DNA extracted from 98 samples (Pool2) of wood-inhabiting insects. Split with HJSplit as recommended by Dryad (http://wiki.datadryad.org/Large_File_Transfer).
DOI: 10.5061/dryad.3t2d4/9
title: Rep_seqs_OTUs_scata_10k

description: Representative sequences for OTUs as clustered by Scata (https://scata.mykopat.slu.se/) in subsampled dataset (max 10k sequences from each insect sample).
DOI: 10.5061/dryad.59433/1
title: Sulfur deposition and sulfate concentration

description: Estimated total deposition of S for Lake Skärshultsjön, including wet, dry and sea salt, and estimated sulfate concentration in the same lake. Data modeled as in Moldan, F., B J. Cosby, and R. F. Wright. 2013. Modeling past and future acidification of Swedish Lakes. Ambio 42: 577-586. doi:10.1007/s13280-012-0360-8 and provided by Swedish Environment Institute
DOI: 10.5061/dryad.59433/2
title: Water color between years

description: Water color for 50 lakes in the years 1935, 1982 and 2015 given in mg Pt/L.
DOI: 10.5061/dryad.59433/3
title: Long-term water color in 18 lakes

description: Lake names, years and water color in mg Pt/L for 18 lakes.
DOI: 10.5061/dryad.59433/4
title: Land-use and climate variables

description: Spruce coverage in percent, based on sediment pollen records from Lake Fiolen. The modeling of vegetation coverage is assumed to be representative for an area with a 500-kilometer radius from the lake. 10-running means of growing degree days, i.e. number of days each year where average temperature was above 5°C, in Jönköping. 10-year running means of discharge from Lake Allgunnen.
DOI: 10.5061/dryad.766cp.2
title: Data from: Crowds replicate performance of scientific experts scoring phylogenetic matrices of phenotypes
DOI: 10.5061/dryad.766cp.2/1.2
title: Appendix 1  - List of six matrices developed for this study.

description: Online Appendix 1.  List of six matrices developed for this study, including character names, types of characters, and assessment of character difficulty by experts.  See also Morphobank (www.morphobank.org) projects P950, P2463, P2502, P2490, P2491, and P2577.
DOI: 10.5061/dryad.766cp.2/2.2
title: Appendix 2 characterDifficultyMP_3-15-16_MAH edited

description: Online Appendix 2.  List of characters evaluated and their simplified anatomical descriptions used in the Evolution Project.  The latter were presented to non-experts in the crowd.
DOI: 10.5061/dryad.766cp.2/3.2
title: Appendix 3 Anemones-character-taxon-results

description: Online Appendix 3.  Sea anemones character scores.  For each character and taxon in the anemones matrix, we show the probability (“Estimate”) that a crowd member’s score would agree with the majority vote of the crowd.  We also show the lower confidence interval on this probability (ci.lower), which is the crowd confidence score.  Finally, we indicate whether the majority vote was correct, and compute an ROC curve for the crowd’s scores.  The Threshold Plot worksheet provides a visualization of this information.
DOI: 10.5061/dryad.766cp.2/4.2
title: Appendix 4 Anemones-user-results

description: Online Appendix 4.  Sea anemones user scores.  For each crowd member, we report the number of scores they provided and the number that were correct.  The “Estimate” column is the probability that this crowd member voted correctly, and the “ci.lower” column gives the 95% lower confidence bound on this probability.  These scores are for all characters (evaluation and test).
DOI: 10.5061/dryad.766cp.2/5.2
title: Appendix 5 Bats-character-taxon-results

description: Online Appendix 5.  Bats character scores.
DOI: 10.5061/dryad.766cp.2/6.2
title: Appendix 6 Bats-users-results

description: Online Appendix 6.  Bats user scores.
DOI: 10.5061/dryad.766cp.2/7.2
title: Appendix 7 Catfish-character-taxon-results

description: Online Appendix 7.  Catfish character scores.
DOI: 10.5061/dryad.766cp.2/8.2
title: Appendix 8 Catfish-user-results

description: Online Appendix 8.  Catfish user scores.
DOI: 10.5061/dryad.766cp.2/9.2
title: Appendix 9 Diatoms-character-taxon-results

description: Online Appendix 9.  Diatom character scores
DOI: 10.5061/dryad.93h33/1
title: AtlanticSalmon_93KGenepop

description: Genepop file containing 93,703 SNPs from Labrador Atlantic salmon, filtered from original 220K SNP chip.
DOI: 10.5061/dryad.93h33/2
title: format_dataframe_for_RF

description: R script to convert data in adjusted PLINK format to format suitable for RF analyses. Example run of RF included in script.
DOI: 10.5061/dryad.9k9n0/12
title: whisker-dynamic-response.zip

description: source code to elaborate videos and produce figures. it was cloned from github by "git clone -b shared4paper https://github.com/pgallir/whisker-dynamic-response".
DOI: 10.5061/dryad.9k9n0/13
title: camrec450_verFunc.zip

description: labview project for data acquisition. the folder camrec450_verFunc/stim/ contains the stimulus library that was used as input to the shaker, and the code to generate it.
DOI: 10.5061/dryad.9k9n0/14
title: compressData.sh

description: code used to compress and split data to produce this shared dataset.
DOI: 10.5061/dryad.9k9n0/15
title: unzipData.sh

description: code to merge data parts and  decompress from this shared dataset back to folders.
DOI: 10.5061/dryad.9k9n0/16
title: supplementary

description: images to produce supplementary figures are in folders: colorationprocess; photobleaching. updated code: updated-whisker-dynamic-response
DOI: 10.5061/dryad.9sm68/1
title: DATA_Zhang et al EcoLett

description: Data for Fig 4, 5, 6
DOI: 10.5061/dryad.bj5k0/12
title: panama_sp_list

description: List of species known from Panama
DOI: 10.5061/dryad.d47fm/1
title: PGM_DATA_MotileExperiment

description: This file contains raw PGM (Ion Torrent, Life technology) data for adaptors 1, 2 and 3. See file "PGM_SequencingRuns" for corresponding samples.
DOI: 10.5061/dryad.d47fm/2
title: PGM_DATA_SessileExperiment_Run2

description: This file contains raw PGM (Ion Torrent, Life technologies) data for adaptors 6, 13, 14 and 16. See file "PGM_SequencingRuns" for corresponding samples.
DOI: 10.5061/dryad.d47fm/3
title: PGM_DATA_SessileExperiment_Run3

description: This file contains raw PGM (Ion Torrent, Life technology) data for adaptors 10, 11, 12 and 15. See file "PGM_SequencingRuns" for corresponding samples.
DOI: 10.5061/dryad.d47fm/4
title: PGM_DATA_SessileExperiment_Run4

description: This file contains raw PGM (Ion Torrent, Life technology) data for adaptors 8 and 9. See file "PGM_SequencingRuns" for corresponding samples.
DOI: 10.5061/dryad.hc93j/1
title: HEL_Biomass_Data_2009_2015

description: Plant biomass data from experimental plots, XLS format
DOI: 10.5061/dryad.hc93j/2
title: HEL_Veg_PhotoQuadrat_Data_2011_2015

description: Plant community composition data, XLS format
DOI: 10.5061/dryad.hc93j/3
title: HEL_Nitrogen_Data_2008_2012

description: Soil Nitrogen data from resin bags, XLS format
DOI: 10.5061/dryad.hc93j/4
title: HEL_Biomass_Data_2009_2015

description: Plant biomass data from experimental plots, CSV format
DOI: 10.5061/dryad.hc93j/5
title: HEL_Nitrogen_Data_2008_2012

description: Soil Nitrogen data from resin bags, CSV format
DOI: 10.5061/dryad.j6j09/1
title: FID and threat status information of pairs of bird species

description: Flight initiation distance (FID) information of pairs of bird species, sample size (n), the identity of these pairs of species, their threat status and the difference in their FID.
DOI: 10.5061/dryad.k3b10.2
title: Data from: Malagasy cichlids differentially limit impacts of body shape evolution on oral jaw functional morphology
DOI: 10.5061/dryad.k3b10.2/1.2
title: species info

description: - Table of data and information for Malagasy cichlids. 
- “subfamily” is the corresponding subfamily that each species occurs in.
- “body_centroid_size” is the average centroid size from body shape coordinates in Malagasy cichlids.
- “jaw_centroid_size” is the average centroid size from oral jaw fourbar shape coordinates in Malagasy cichlids.
-  “MKT” is the maxillary kinematic transmission for species’ average oral jaw fourbar shapes.
DOI: 10.5061/dryad.k83g4/12
title: Dataset 1-genomics

description: Dataset containing files related to sequencing and annotation as a compressed .zip archive.
DOI: 10.5061/dryad.k83g4/13
title: Dataset 2-phenomics

description: Dataset containing files related to phenomic studies including GC-FID, GC/MS, HPLC, and phenotype microarrays.
DOI: 10.5061/dryad.k83g4/15
title: Dataset_3

description: Interactive Venn diagram displaying shared and unique protein families (Pfams) among 6 different algae. File can be uploaded to interactivenn.net.
DOI: 10.5061/dryad.kg686/1
title: bait-120-60-selection

description: Sequences used to design MYbaits kit.
DOI: 10.5061/dryad.kg686/2
title: Curated alignments and gene trees

description: Includes alignments and partition files, RAxML bootstrap and best tree files for curated nuclear loci.
DOI: 10.5061/dryad.kg686/3
title: aTRAM alignments and gene trees

description: Includes raw alignments for 48 nuclear loci obtained through aTRAM assembly. Also edited alignments and RAxML output files for 39 nuclear loci.
DOI: 10.5061/dryad.n572r/1
title: SPACECAP inputs used

description: Zip archive containing SPACECAP input files for 24 surveys of leopard population density in the Soutpansberg Mountains, South Africa from 2012 to 2016. For each survey (for dates see article) the archive contains a 
          - capture history file "capture_sXX.csv"
          - trap deployment file "deployment_sXX.csv"
          - potential home range centres file "HRC_s01.csv"
DOI: 10.5061/dryad.n572r/2
title: ANIMAL_ID coding in capture file

description: Details of coding used in SPACECAP input files. In input files ANIMAL_IDs must be represented as sequential numbers. This file shows which ANIMAL_IDs correspond to which individual animals.
DOI: 10.5061/dryad.n572r/4
title: densityInclExcl2008

description: Camera trap data analysed using "cameraTrapAnalysis.R".
DOI: 10.5061/dryad.ns5qs/1
title: Figure 1B Membrane ARHGAP10 and β-Arrestin1  [ADU]). Experiments in triplicate.

description: Data for Figure 1B in Excel file. Membrane ARHGAP10 and β-Arrestin1  [ADU]). Experiments in triplicate.
DOI: 10.5061/dryad.ns5qs/2
title: Figure 1D Membrane β-Arrestin1 intensity

description: Data for Fig 1D  in Excel file. Membrane β-Arrestin1 intensity (AI) in Caco-2 and Caco-2 ShPTEN cell monolayers after control or LPA treatment. Experiments in triplicate. In each replicate, signal intensity was assessed in 10 cells (C-L). Mean ± sem values were plotted.
DOI: 10.5061/dryad.ns5qs/3
title: Figure 1F β-Arrestin1  membrane (ADU) in Caco-2 and Caco-2 ShPTEN cells after control or LPA treatment

description: Data for Fig 1F in Excel file. β-Arrestin1  membrane (ADU) in Caco-2 and Caco-2 ShPTEN cells after control or LPA treatment. Experiments in triplicate.
DOI: 10.5061/dryad.ns5qs/4
title: Figure 1 supplement 2

description: Data for Fig 1 Supplement 2 in Excel file. Arbitrary intensity values for membrane β-Arrestin1 after LPA treatment in PTEN+/+ and PTEN-/- HCT116 cell monolayers. Confocal imaging conducted in 10 cells for each replicate (n=3) for each experimental condition.
DOI: 10.5061/dryad.ns5qs/5
title: Figure 1 supplement 4

description: Data for Figure 1 Supplement 4 in Excel file.  Membrane β-Arrestin1 ADU in PTEN+/+  and PTEN-/- HCT116 cells after LPA treatment. Experiments in triplicate
DOI: 10.5061/dryad.ns5qs/6
title: Figure 2B

description: Data for Figure 2B in Excel file. CDC42-GTP ADU in Caco-2 cells after β-Arrestin1 or NT SiRNA. Experiments in triplicate.
DOI: 10.5061/dryad.t5k6f/1
title: SNPs of Sahelian mosquito populations

description: The dataset used in the above publication contain genotypes at 738 SNPs loci in a total of 505 mosquitoes representing 13 samples. The variable PoD denotes locality, followed by year (the last two digits of years spanning 2008 to 2011), and month, each in 2 letter code (see paper for complete locality names, GPS coordinates and descriptions). MosID is the variable containing the mosquito unique identifier, followed by the variables listing the mosquito sex (Sex) and collection date (CollDate). The locus variable is defined by the chromosome arm e.g., '2R' and followed by the unique position of this SNP in the conventional genome sequence of Anopheles gambiae. The genotype of this mosquito at this locus is provided in the variable Geno. Undetermined genotypes are denoted by zeros.
DOI: 10.5061/dryad.vp3cc/1
title: Fish data
DOI: 10.5061/dryad.vp3cc/2
title: Environmental data
DOI: 10.5061/dryad.1gq66/1
title: Disturbance treatments

description: Cell counts of E. coli JM109 (prey) and Tetrahymena pyriformis (predator) in three experimental treatments: Undisturbed (control), press and pulse disturbance. All treatments were replicated three times.
DOI: 10.5061/dryad.1gq66/2
title: Growth Curves

description: Cell counts [cells/ml] of Escherichia coli  JM109 (prey) and Tetrahymena pyriformis (predator) within 24 hours in monocultures and in combination.
DOI: 10.5061/dryad.2601h/27
title: CFD simulation file for Parvancorina sagitta from Russia, relief increased by 15%, oriented at 0° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina sagitta from Russia with relief increased by 15% was oriented at 0° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/28
title: CFD simulation file for Parvancorina sagitta from Russia, relief increased by 15%, oriented at 90° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina sagitta from Russia with relief increased by 15% was oriented at 90° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/29
title: CFD simulation file for Parvancorina sagitta from Russia, relief increased by 15%, oriented at 180° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina sagitta from Russia with relief increased by 15% was oriented at 180° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/30
title: CFD simulation file for Parvancorina sagitta from Russia, relief increased by 30%, oriented at 0° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina sagitta from Russia with relief increased by 30% was oriented at 0° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/31
title: CFD simulation file for Parvancorina sagitta from Russia, relief increased by 30%, oriented at 90° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina sagitta from Russia with relief increased by 30% was oriented at 90° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/32
title: CFD simulation file for Parvancorina sagitta from Russia, relief increased by 30%, oriented at 180° to the current, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A model of Parvancorina sagitta from Russia with relief increased by 30% was oriented at 180° to the current and was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.2601h/33
title: CFD simulation file for null model of Parvancorina sagitta from Russia, MPH format

description: Computational fluid dynamics (CFD) simulations of water flow were performed in COMSOL. A null model of Parvancorina sagitta from Russia was fixed to the lower surface of a half-cylinder. Three-dimensional, incompressible flow of water was simulated with a normal inflow velocity inlet at the upstream end of the half-cylinder and a zero-pressure outlet at the downstream end. Slip boundary conditions were assigned to the top and sides of the half-cylinder, and no-slip boundary conditions were assigned to the Parvancorina model and the lower surface of the half-cylinder. The domain was meshed using free tetrahedral elements and the shear stress transport turbulence model was used to solve the Reynolds-averaged Navier–Stokes equations. A stationary solver was used to compute the steady-state flow patterns. Simulations were performed with an inlet velocity of 0.1, 0.2, and 0.5 m/s.
DOI: 10.5061/dryad.38t23/1
title: BAYES BSE file

description: Base file used in BAYES mixed-stock analysis
DOI: 10.5061/dryad.38t23/2
title: BAYES CTL1

description: CTL1 file used in BAYES mixed-stock analysis