cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh105770.07fu
title: SH105770.07FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5061/dryad.8d2t65n/8
title: reproduction unmated parents N2

description: Daily reproduction of unmated parents (N2) subjected to daf-2 RNAi or empty vector.
DOI: 10.5061/dryad.98gp587/1
title: Predation of California Red Scale

description: Four datasheets are included: 1) California red scale mortality studies with exclusion techniques, 2) abundance of predators through stem tap sampling, 3) proportion of predators testing positive using PCR for pest DNA detection, 4) estimation of predation rates using predator abundance and PCR results.
DOI: 10.5061/dryad.98sp59j/2
title: SNP_flanking_sequences_and_alleles_from_gadMor2_alignment

description: SNP flanking sequences and alleles from alignment with gadMor2 annotated genome assembly by Tørresen et al. 2017 (https://doi.org/10.6084/m9.figshare.3408247.v3).
DOI: 10.5061/dryad.bq25514/1
title: ExtendedData_Dineen

description: Trait matrices, abundance data, and references for Permian and Triassic paleocommunities
DOI: 10.5061/dryad.dv44mg0/1
title: Diversifying livestock promotes multidiversity and multifunctionality in managed grasslands

description: Diversifying livestock promotes multidiversity and
multifunctionality in managed grasslands
DOI: 10.5061/dryad.fb88292/11
title: S_2b_Reduced_dataset

description: S2. Molecular matrix for the reduced dataset (S2b).
DOI: 10.5061/dryad.fb88292/12
title: S_2c_Dataset_with_COI

description: S2. Molecular matrix for the dataset with a mitochondrial fragment (S2c).
DOI: 10.5061/dryad.fb88292/13
title: S_3a_core analysis_RAxML_topology

description: S3. RAxML topology (S3a) obtained from the core analysis. Numbers at the nodes indicate rapid-bootstrap support values.
DOI: 10.5061/dryad.fb88292/14
title: S_3b_core_analysis_median_ages

description: S3. Time-calibrated tree (S3b) obtained from the core analysis. Node ages are the median of node age posterior distributions.
DOI: 10.5061/dryad.fb88292/15
title: S_4_deep_Level_fossils_median_ages

description: S4. Tree obtained when using only deep-level fossil calibrations. Node ages are the median of node age posterior distributions.
DOI: 10.5061/dryad.fb88292/16
title: S_5_shallow_Level_fossils_median_ages

description: S5. Tree obtained when using only shallow-level fossil calibrations. Node ages are the median of node age posterior distributions.
DOI: 10.5061/dryad.fb88292/17
title: S_6_reduced_dataset_median_ages

description: S6. Tree obtained from the reduced dataset. Node ages are the median of node age posterior distributions.
DOI: 10.5061/dryad.fb88292/18
title: S_7_exponential_priors_median_ages

description: S7. Tree obtained when using exponential fossil calibration priors. Node ages are the median of node age posterior distributions.
DOI: 10.5061/dryad.h517t14/1
title: Main data
DOI: 10.5061/dryad.h517t14/2
title: R Scripts
DOI: 10.5061/dryad.h517t14/3
title: Phylogenetic trees
DOI: 10.5061/dryad.h517t14/4
title: Results from the BayesTraits analysis
DOI: 10.5061/dryad.kd1qt0p/28
title: Table 5 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table 5. “WT_LSI_raw_data.xlsx” contains the data for the wild-type lower small intestine, “Rag1KO_LSI_raw_data.xlsx” contains the data for the immunoglobulin-deficient (Rag1KO) lower small intestine. In both the excel files, RI = refractive index, RALS = Right-angle light scattering, LALS = low-angle light scattering, DP = differential pressure (the viscometer). All values are measured in millivolts except for retention volume, which is measured in milliliters (mL). 
The file “Table S4 – source data 1.OmnisecArchive” contains all this data, along with the data for the pullulan and dextran standard that were used to calibrate the instrument. This can be used in conjunction with Malvern OMNISEC v10.20 software to reproduce the calculations displayed in the table. LALS data was not used for these calculations because of the noisiness of the signal from the detector.
DOI: 10.5061/dryad.kd1qt0p/31
title: Table 8 - source data 1

description: This zip archive contains the chromatography data that was used to calculate the values displayed in Table 8. “pectin_LSI_raw_data.xlsx” contains the data for the lower small intestine of pectin-fed mice, “Fibersol-2_LSI_raw_data.xlsx” contains the data for the lower small intestine of Fibersol-2-fed mice. In both the excel files, RI = refractive index, RALS = Right-angle light scattering, LALS = low-angle light scattering, DP = differential pressure (the viscometer). All values are measured in millivolts except for retention volume, which is measured in milliliters (mL). 
The file “Table S7 – source data 1” contains all the data, along with the data for the pullulan and dextran standard that were used to calibrate the instrument. This can be used in conjunction with Malvern OMNISEC v10.20 software to reproduce the calculations displayed in the table. LALS data was not used for these calculations because of the noisiness of the signal from the detector.
DOI: 10.5061/dryad.kd1qt0p/32
title: Aggregate Image Analysis Code

description: These FIJI ImageJ macros were used to determine volumes of aggregates of particles in z-stacks.

"Aggregate_Counting_Macro_1.2.4_for_publication.ijm" takes in a z-stack and generates various statistics about aggregates including volume, surface area, and position. Results for Test_dataset_08_01_18 are located in the Results folder.

"Average_Singlet_Size_Macro_1.0.0_for_publication.ijm" takes the object map output from the Aggregate_Counting_Macro and prompts the user to record the ID number associated with 10 single particles. The singlets can then be used to convert aggregate volumes from the Aggregate_Counting_Macro into particle counts.
Written in the ImageJ macro language.

Test dataset was run in FIJI version 2.00-rc-68/1.52e, Build:bad6864e55 using macOS Version 10.13.4.
DOI: 10.5061/dryad.kd1qt0p/33
title: Bootstrap confidence intervals code

description: This zip folder contains the source code to generate 95% empirical bootstrap confidence intervals. The .html and .ipynb files are identical. The code was written with Python version 3.6.4. It has been verified to work with numpy version 1.13.3, pandas version 0.21.1, scipy version 1.0.0, bokeh version 0.12.15, holoviews version 1.9.1, and numba version 0.36.2. 

 

The test data folder provides data that can be used to verify that the code is working. Make sure to change the file paths to what is appropriate for your computer. The test data will reproduce Figure 7G from the main text. This data was also provided as part of “Figure 7 – source data 4”.
DOI: 10.5061/dryad.kd1qt0p/34
title: volume-weighted ECDF code

description: This zip folder contains the source code to generate 95% empirical bootstrap confidence intervals The .html and .ipynb file are identical. The code was written with Python version 3.6.4. It has been verified to work with numpy version 1.13.3, pandas version 0.21.1, scipy version 1.0.0, bokeh version 0.12.15, and holoviews version 1.9.1. 

 

The test data folder provides data that can be used to verify that the code is working. Make sure to change the file paths to what is appropriate for your computer. The test data will reproduce Figure 5, Panel A from the main text. This data was also provided as part of “Figure 5 – source data 1”.
DOI: 10.5061/dryad.kd1qt0p/35
title: Depletion Calculations Code

description: This zip folder contains the source code to generate the plots of the interparticle potential minima displayed in Figure 4H. The .html and .ipynb file are identical. The code was written with Python version 3.6.4. It has been verified to work with numpy version 1.13.3, pandas version 0.21.1, scipy version 1.0.0, bokeh version 0.12.15, sympy version 1.1.1, holoviews version 1.9.1, and numba version 0.36.2.
DOI: 10.5061/dryad.kd1qt0p/36
title: Diffusion coefficients Code

description: This zip folder contains the source code to generate the plots of the diffusion coefficients displayed in Figure 4I. The .html and .ipynb file are identical. The code was written with Python version 3.6.4. It has been verified to work with numpy version 1.13.3, pandas version 0.21.1, scipy version 1.0.0, bokeh version 0.12.15, sympy version 1.1.1, holoviews version 1.9.1, and numba version 0.36.2.
DOI: 10.5061/dryad.kd1qt0p/37
title: Figure 4 - figure supplement 2

description: This zip archive contains the original z-stacks used for the PEG 1 MDa data in Figure 4, figure supplement 2.. These are provided as TIF files. All imaging parameters are included in the image metadata. They are labeled as follows:   
A7PS362_s1_t1 = 6.52 mg/mL PEG 1 MDa
A7PS362_s2_t1 = 3.26 mg/mL PEG 1 MDa 
A7PS362_s3_t1 = 1.63 mg/mL PEG 1 MDa
A7PS362_s4_t1 = 0.815 mg/mL PEG 1 MDa
A7PS362_s5_t1 = 0.407 mg/mL PEG 1 MDa
A7PS362_s6_t1 = 0.204 mg/mL PEG 1 MDa
A7PS362_s7_t1 = 0.102 mg/mL PEG 1 MDa
A7PS362_s8_t1 = 0.0509 mg/mL PEG 1 MDa

Additionally, this file contains .csv files of all the statistics on particle sizes collected by the ImageJ macro. These are labeled in the format “zstackname_automated_counting_statistics”, where “zstackname” is the title of the associated z-stack. It also contains a .csv file of the particle # IDs of the singlet particles that were used to get the average singlet size, which was then used to normalize the ECDFs (as explained in detail in Materials and Methods). These are labeled in the format “zstackname_singlet_IDs”, where “zstackname” is the title of the associated z-stack. These .csv files were used in combination with the Jupyter notebooks provided as additional files to this paper to generate Figure 4, figure supplement 2.
DOI: 10.5061/dryad.n7s0g10/1
title: Dwarf brooder versus giant broadcaster: combining genetic and reproductive data to unravel cryptic diversity in an Antarctic brittle star

description: Bayesian Tree file, Outputs from GMYC and mPTP analyses (TXT), COI haplotypes (FASTA), Metadata for each specimen (EXCEL)
DOI: 10.5061/dryad.pv40d2r/4
title: Egg Dataset

description: A tab delimited dataset of insect egg shape and size from the published literature, including additional variables (e.g. volume, aspect ratio) calculated from data in egg_dataset_raw_values.tsv. See publication methods for details on how final values were calculated.
DOI: 10.5061/dryad.pv40d2r/5
title: Egg Dataset (Raw Values)

description: A tab delimited dataset of insect egg shape and size from the published literature, reporting the values as recorded (e.g. original published taxonomic name, text description of maximum and minimum egg length). See publication for details and on how data was collected.
DOI: 10.5061/dryad.pv40d2r/6
title: Bibliography Egg Dataset (BibTeX format)

description: A bibtex file of sources cited in the egg dataset. References listed here can be matched to entries in the egg dataset by their unique bibliographic identifier (e.g. Iwata1958).
DOI: 10.5061/dryad.pv40d2r/7
title: Bibliography Egg Dataset (PDF format)

description: A formatted bibliography of sources cited in the egg dataset.
DOI: 10.5061/dryad.rt400df/1
title: LfremontiiAdaptivePotential

description: The zip file "L.fremontiiAdaptivePotential" contains the input data, outputs and SAS codes implemented to estimate the adaptive potential of L.fremontii in response to ENSO events. All associated climate data is also contained within this file (see README)
DOI: 10.5061/dryad.sg4m5h0/4
title: experiment 2 - data
DOI: 10.5061/dryad.sg4m5h0/5
title: field prevalence - analysis
DOI: 10.5061/dryad.sg4m5h0/6
title: field prevalence - data
DOI: 10.5061/dryad.sg4m5h0/7
title: ReadMe
DOI: 10.5061/dryad.t4r1n64/1
title: Neurology2018941971R_Supplemental data

description: Supplemental data
DOI: 10.5061/dryad.th757vg/2
title: Nuclear genes with populations

description: Zip file with nuclear gene alignments
DOI: 10.17632/4cpv86ry35.1
title: Data for: Transforming screening uptake in low-resource and under-informed populations: a preliminary study of factors influencing women’s decisions to uptake screening
DOI: 10.17632/8bk3v63dh5.1
title: Data for: Long-term Changes in Married Couples’ Labor Supply and Taxes: Evidence from the US and Europe Since the 1980s

description: The zip-file "Tax Codes" contains tax codes for the 8 sample countries from 1983 to 2016. Facts_intro contains the data presented in Section 2 of the paper.
DOI: 10.17632/cv2y964xbd.1
title: Data for: KLF4 sensitizes the colon cancer cell HCT-15 to cisplatin by altering the expression of HMGB1 and hTERT

description: Raw data of Western blot
DOI: 10.17632/nt2s36d6k3.1
title: Data for: Preferential settling at sites with higher conspecific density does not protect Yellow Warblers (Setophaga petechia) from brood parasitism.

description: These data for Acta Oecologica manuscript submission ACTOEC_2018_318, short communication manuscript titled, "Preferential settling at sites with higher conspecific density does not protect Yellow Warblers (Setophaga petechia) from brood parasitism."
DOI: 10.17632/pwvsjjkpnj.1
title: Data for: Construction of 3D boron nitride nanosheets/silver networks in epoxy-based composites with high thermal conductivity via in-situ sintering of silver nanoparticles

description: 1: AFM data of BNNS-NH2; 2: Complex viscosity of epoxy compopsites; 3: DSC curves of epoxy composites; 4: Dynamic rheological properties of EP/BNNS@AgNPs composites; 5: EDX spectrum of BNNS@AgNPs; 6: TGA curves for neat epoxy, EP/h-BN and EP/BNNS@AgNPs composites with various filler contents.
DOI: 10.17632/x3c7y8dyw5.1
title: Data for: Trace element systematics and ore-forming processes in mafic VMS deposits: Evidence from the Troodos ophiolite, Cyprus

description: Trace element geochemistry from Troodos VMS analysed via LA-ICP-MS
DOI: 10.5061/dryad.3310h18/1
title: X-ray diffraction raw data for β-FeSe, g-C3N4, and 3wt% β-FeSe/g-C3N4 composites.

description: X-ray diffraction (XRD) data were measured by a PANalytical X’pert Pro diffractometer using Cu target radiation.
DOI: 10.5061/dryad.3310h18/2
title: The X-ray photoelectron spectroscopy raw data for 3wt% β-FeSe/g-C3N4 composites

description: The X-ray photoelectron spectroscopy (XPS) data were collected on a Thermo ESCALAB 250 Xi system.
DOI: 10.5061/dryad.3310h18/4
title: Electrochemical impedance spectroscopy for g-C3N4  and 3wt% β-FeSe/g-C3N4 composites

description: The EIS measurements were conducted on a CHI 660C electrochemical workstation.
DOI: 10.5061/dryad.3pf2cb4/1
title: Datasets

description: This file contains all data supporting the publication, including qualitative scores for signature, trait*environment scores, quantitative comparison data (mean trait data), and location data for all populations and gardens. A "data dictionary" tab is also provided to explain the contents.
DOI: 10.5061/dryad.3pf2cb4/2
title: R Code for Quantitative Analysis

description: R Code supporting the quantitative analysis. Data called for by this code are in the "quantitative analysis" tab of the "GBLA_forDryad_datasets" excel file.
DOI: 10.5061/dryad.3rf15cg/1
title: Freq_and_temp_overlap_weight

description: spectral and temporal overlap for focal species (Fig 3)
DOI: 10.5061/dryad.3rf15cg/2
title: Jaccard_indice_3min_period
DOI: 10.5061/dryad.3rf15cg/3
title: Number_bird_species_detected_3min_period
DOI: 10.5061/dryad.4c963s4/1
title: DataforEE
DOI: 10.5061/dryad.510dt0g/7
title: Species richness, frequency and abundance

description: Number of individuals per species sampled in cushion plants of Acaena integerrrima with and without Embothrium, and in bare ground plots.
DOI: 10.5061/dryad.56r4rv4/2
title: Testing phase

description: Results of the four unconditioned tests conducted.
DOI: 10.5061/dryad.5vb1601/1
title: Raw Illumina R1 reads for lower Waitangi parchment
DOI: 10.5061/dryad.5vb1601/2
title: Raw Illumina R2 reads for lower Waitangi parchment
DOI: 10.5061/dryad.61tc3hd/1
title: Age-structured serology data for Madagascar fruit bats

description: The attached .xls file contains all raw data used in the associated publication, "Disentangling serology to elucidate henipa- and filovirus transmission in Madagascar." The dataset identifies all individual bats by a unique sampleID. Each bat is listed multiple times in the dataset, corresponding to different antigens which were serologically surveyed. Each unique sampleID is associated with relevant ecological metadata: site and date of sampling, species, sex, age class (adult vs. juvenile), age in years from cementum annuli tooth analysis, mass in grams, and forearm length in mm. The "kin" column lists the sampleID of dam-pup pairs, such that a dam with a unique sampleID will have her pup's ID listed under the kin column and vice-versa; all animals for which this pairing is not relevant (most) receive an "NA" value in this column. The "recap" column indicates whether an animal was recaptured ("Y" or "N") during our sampling. Seventeen animals in this data subset were recaptured (recap="Y"), and the date of capture can be used to determine which capture event is indicated by a given row in the dataset. Finally, "antigen" givens the antigen tested for a given row in the dataset and "titer" indicates the corresponding MFI value for that Luminex test. Most of the data correspond to researcher = "Brook_et_al" (our research team), though we have also included researcher = "IPM" data used in some of the seasonal analyses. In these cases, no raw serotiter was available, and we list only the result ("seropositive" vs. "seronegative") of the corresponding test (ELISA or SNT).
DOI: 10.5061/dryad.6jr886q/2
title: Data file

description: The file includes the data set used to reach the conclusions drawn in the manuscript. They are formatted as a zip archive.
DOI: 10.5061/dryad.6p65fh1/1
title: Teodoro et al. 2019

description: 1. Carboxylate concentrations during vellozioid root development in Barbacenia tomentosa: immature (2-4 days), mature (6-12 days) and senescent (more than 15 days); 2. Mineral element concentration (mg g-1) in quartzite rock in campos rupestres. The rock samples were collected in Itutinga, Diamantina and Serra do Cipó National Park (n=9), Minas Gerais, Brazil; 3. Solubilized phosphorus (P) from quartzite rock collected in campos rupestres as affected by the addition of carboxylates (malate).
DOI: 10.5061/dryad.6qf743b/1
title: Data from: Increases in local richness (alpha-diversity) following invasion are offset by biotic homogenization in a biodiversity hotspot
DOI: 10.5061/dryad.70bs72s/1
title: genetic data

description: Genotypes of molecular markers in guppies F1 families
DOI: 10.5061/dryad.71568mt/1
title: JSMBAP_Caterpillars

description: Details of all individual caterpillars collected (by branch beating) and identified along our Scottish transect of 40 woodland field sites 2014-16.
DOI: 10.5061/dryad.71568mt/2
title: JSMBAP_Branch_Beating

description: Details on each branch beating and whether or not a caterpillar was captured. From our Scottish transect 2014-16.
DOI: 10.5061/dryad.71568mt/3
title: JSMBAP_Habitat

description: Habitat data of each of the 40 field sites along our Scottish transect.
DOI: 10.5061/dryad.71568mt/4
title: JSMBAP_Nestbox_Details

description: Geographic details of each bird nestbox (and site) on our 40-site Scottish transect 2014-16.
DOI: 10.5061/dryad.8hh028v/1
title: ESM_R Data

description: Raw data for eye preferences in relation to mate guarding behaviour, contest escalation, contest success, female approach side and mating success.
DOI: 10.5061/dryad.93481g3.2
title: Data from: Patterns of genetic differentiation in Colorado potato beetle correlate with contemporary, not historic, potato land cover
DOI: 10.5061/dryad.93481g3.2/1.2
title: shapefile - Oregon/Washington

description: Potato land cover data at the county level for Oregon and Washington (1840-2012), generated from the Census of Agriculture. Values of potato land cover are represented as a proportion of total county area.
DOI: 10.5061/dryad.9hg52sm/1
title: Tiff stack of CT slices of CCNHM 1000

description: Zipped tiff stack of leveled CT slices of close-up of the bony labyrinth based on microCT scan of CCNHM-1000 petrosal. Files generated in VGStudioMax 2.2 from original CT data volume.
DOI: 10.5061/dryad.9hg52sm/2
title: CCNHM–1000 inner ear endocast model

description: Digital endocast of the bony labyrinth (inner ear) of CCNHM-1000; 3D model in STL format. STL generated in VGStudioMax 2.2.
DOI: 10.5061/dryad.9hg52sm/3
title: Part 1 of the NSI Volume data files

description: Zipped section of 3D volume files of original CT data of CCNHM 1000 close-up scan of the inner ear. All files of this series should be extracted and used together.
DOI: 10.5061/dryad.9hg52sm/4
title: Part 2 of NSI Volume data files

description: Compressed section of 3D volume files of original CT data of CCNHM 1000 close-up scan of the inner ear. All files of this series should be extracted and used together.
DOI: 10.5061/dryad.9n94b60/1
title: Effect of mites and beetle body temperature on contests between rival females
DOI: 10.5061/dryad.9n94b60/2
title: Are mites a source of heat
DOI: 10.5061/dryad.9n94b60/3
title: Effect of mite density on beetle body temperature
DOI: 10.5061/dryad.9n94b60/4
title: Treadmill experiment
DOI: 10.5061/dryad.9n94b60/5
title: Beetle surface area covered and surface area volume ratio
DOI: 10.5061/dryad.9n94b60/6
title: Effect of mites on contests between beetles differed in size
DOI: 10.5061/dryad.9n94b60/7
title: Effect of mites on burying beetle reproductive success with respect to beetle body size
DOI: 10.5061/dryad.b41j15h/1
title: NOR011

description: This folder contains data for participant NOR011, including the full-size montage (.tiff) of the retinal pigment epithelium (RPE) cell mosaic, and individual regions of interest (ROIs) used for analysis in the study. High resolution retinal images were acquired in the living human eye using an adaptive optics scanning light ophthalmoscope.
DOI: 10.5061/dryad.b41j15h/2
title: NOR025

description: This folder contains data for participant NOR011, including the full-size montage (.tiff) of the retinal pigment epithelium (RPE) cell mosaic, and individual regions of interest (ROIs) used for analysis in the study. High resolution retinal images were acquired in the living human eye using an adaptive optics scanning light ophthalmoscope.
DOI: 10.5061/dryad.cg10jn5/1
title: Svedäng et al 2018 Cod samples

description: Genotype list.
DOI: 10.5061/dryad.cq11s60/1
title: MD_Microsat2019.xlsx

description: Genotypes based on 10 microsatellite loci for 224 pond bats representing Germany, Denmark and Russia
DOI: 10.5061/dryad.cv6j89s/1
title: Stark et al._SI_Final_2018

description: Raw data