cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0m625h4/7
title: MAGNOLIA_SSR_lacandonica23_CONVERT

description: This file includes SSR/microsatellite genotype data of 40 individuals of 2 populations of Magnolia lacandonica: 20 individuals per population. DNA of the 40 individuals was extracted from leaves using the CTAB method. The leaves were dried on silica-gel and collected from trees in the forests of Mexico. The 40 individuals were genotyped using 23 de novo developed microsatellites.
DOI: 10.5061/dryad.0m625h4/8
title: MAGNOLIA_SSR_pallescens20_CONVERT

description: This file includes SSR/microsatellite genotype data of 40 individuals of 2 populations of Magnolia pallescens: 20 individuals per population. DNA of the 40 individuals was extracted from leaves using the CTAB method. The leaves were dried on silica-gel and collected from trees in the forests of the Dominican Republic. The 40 individuals were genotyped using 20 de novo developed microsatellites.
DOI: 10.5061/dryad.0m625h4/9
title: MAGNOLIA_SSR_portoricensis29_CONVERT

description: This file includes SSR/microsatellite genotype data of 40 individuals of 2 populations of Magnolia portoricensis: 20 individuals per population. DNA of the 40 individuals was extracted from leaves using the CTAB method. The leaves were dried on silica-gel and collected from trees in the forests of Puerto Rico. The 40 individuals were genotyped using 29 de novo developed microsatellites.
DOI: 10.5061/dryad.1200vf4/2
title: Time budget

description: Dataset on time budget by focal subordinates.
DOI: 10.5061/dryad.21cj2vp/1
title: Eppinga and Pucko Dataset

description: Excel file containing the results of a post-hurricane tree survey on Saba and St. Eustatius. A description of the data is provided in the accompanying readme document.
DOI: 10.5061/dryad.24080nk/1
title: GAMS code

description: This file contains the 10 GAMS programs written for the contiguity and compactness models tested in the article, plus the one written for the modified Onal&Briers (2006) model.
DOI: 10.5061/dryad.2bg877b/3
title: PLCL_tensiletest_data
DOI: 10.5061/dryad.2bg877b/4
title: PLCL_Interconnectivity_data

description: PLCL scaffold interconnectivity data
DOI: 10.5061/dryad.2dp8877/1
title: Longitudinal growth

description: Longitudinal growth of roots in three treatments (control, stemflow diverted, and velamen removed). Growth is measured in centimeters after 22 months.
DOI: 10.5061/dryad.3695391/1
title: Sodium_data

description: Excel file containing the R code and the data used in the model.
DOI: 10.5061/dryad.3fb854n/1
title: Total haemoglobin content

description: Total haemoglobin content measured in µmol/L in the 30 genotypes of Daphnia magna studied here at the control temperature (20C) and after exposure to hyper-thermal stress (30C). Genotype ID, population ID, average Hb content across three replicates and log2 fold change of total Hb content between the two experimental temperatures are shown. The Hb data are From Cambronero et al. 2017.
DOI: 10.5061/dryad.3kf1913/2
title: R code for both dynamic optimization and simulations

description: This file contains the code for:
 Differential allocation of parental investment and the trade-off between size and number of offspring
 Proceeding of the Royal Society B. 2018. doi: 10.1098/rspb.2018.1074
 Ratikainen et al. 
 R Code for both stochastic dynamic optimisation figures and simulations. The entire model was created in R version 3.3.1, and the code uses the additional package abind.
DOI: 10.5061/dryad.53b6n5f/1
title: Antibiotic minimum inhibitory concentrations

description: Minimum inhibitory concentrations (µg/ml) for antibiotics from different classes (kanamycin, streptomycin, ampicillin, nalidixic acid, erythromycin, and rifampicin) for HMC33.1 synthetic bacterial community strains.
DOI: 10.5061/dryad.53b6n5f/2
title: Carbon source utilization phenotypes

description: Carbon source utilization phenotypes (1 able and 0 unable to grow on carbon source as sole carbon source) for HMC33.1 synthetic bacterial community strains (Biolog EcoPlate).
DOI: 10.5061/dryad.53b6n5f/3
title: Genomic features

description: Genomic feature data collated into a single data frame, displaying strain, contig, locus, and genomic feature information, for HMC33.1 synthetic bacterial community strains. The features include antibiotic resistance genes, virulence factors, plasmid or genomic island associated sequences, prophages, insertion sequences, and CRISPR loci. For each individual feature, the following information is provided: strain, contig, contig_number, length, start, end, type, subtype and tool. Annotated genome files where contig annotations correspond with the annotations in this table are available from the corresponding author upon request.
DOI: 10.5061/dryad.53b6n5f/4
title: Functional modules predicted from genome assemblies

description: Genomic predictions for functional modules (obtained using MAPLE 2.3.0) for HMC33.1 synthetic bacterial community strains. The numbers are module completion ratio (MCR) percentages.
DOI: 10.5061/dryad.62sm982/1
title: simulation_files

description: This is the Dryad data submission corresponding to 
"Sex chromosome turnovers and genetic drift: a simulation study"
by Saunders, Neuenschwander and Perrin, Journal of Evolutionary Biology


It contains two folders:

* a folder with the input files for the simulations with information on all parameters.

* a folder with the allelic value files, necessary to specify the type to turnover studied in a simulation (or set of simulations).


All informations and download links for quantiNemo executable and corresponding manual can be found at http://www2.unil.ch/popgen/softwares/quantinemo
DOI: 10.5061/dryad.6g33308/2
title: Average and maximum adult tick abundance by species, Santa Barbara County, CA
DOI: 10.5061/dryad.6g33308/3
title: Average and maximum nymphal tick abundance by species, Santa Barbara County, CA
DOI: 10.5061/dryad.6g33308/4
title: Average and maximum larval tick abundance by species, Santa Barbara County, CA
DOI: 10.5061/dryad.85hg502/2
title: Glas Maol vegetation survey 2009

description: File contains the data from the vegetation survey on all the experimental plots.
DOI: 10.5061/dryad.8rb517m/1
title: Transmission_models

description: All code (.R) and raw data necessary to run model selection analyses of 'Ca. Mycoplasma haemominutum' transmission among felids as described in Kellner et al. 2018.
DOI: 10.5061/dryad.8rb517m/2
title: Phylogenetics.zip

description: Sequence alignment (.fas) and information associated with phylogenetic analysis and ancestral state reconstruction in Kellner et al. 2018.
DOI: 10.5061/dryad.b9m61cg/11
title: NSP323_triloba_v3.working.gene_models.gff3

description: Working gene model annotation in GFF3 format.
DOI: 10.5061/dryad.b9m61cg/12
title: NSP323_triloba_v3.working.gene_models.pep.fa

description: Amino acid sequences corresponding to the working gene model coding sequences.
DOI: 10.5061/dryad.b9m61cg/13
title: NSP323_triloba_chr_v3.fa

description: Ipomoea triloba (NSP323) Genome Assembly (v3) - FASTA format
DOI: 10.5061/dryad.b9m61cg/14
title: NSP323_triloba_chr_v3.hm.fa

description: Ipomoea triloba (NSP323) Hard Masked Genome Assembly (v3) - FASTA format
DOI: 10.5061/dryad.b9m61cg/15
title: trilo_aln_8x8_parents_freebayes_mRNA_regions.vcf.gz

description: Quality-filtered variant calls for the MDP clones based on alignment of genomic reads to I. triloba.
DOI: 10.5061/dryad.b9m61cg/16
title: I_trifida_NSP306_stress_FPKM_expression_matrix_v3_anno.xlsx

description: FPKM values of v3 high confidence gene models for 15 I. trifida abiotic and biotic stress RNA-seq libraries. The libraries are described in the 'Library Key' worksheet.
DOI: 10.5061/dryad.b9m61cg/17
title: I_trifida_NSP306_FPKM_expression_matrix_v3_anno.xlsx

description: FPKM values of v3 high confidence gene models for 8 I. trifida RNA-seq libraries (callus_flower, callus_stem, flower, flowerbud, leaf, root1, root2, stem).
DOI: 10.5061/dryad.b9m61cg/18
title: NSP306_trifida_v3.hc.func_anno.txt

description: Putative functional annotation of high confidence gene models.
DOI: 10.5061/dryad.b9m61cg/19
title: NSP306_trifida_v3.hc.gene_models.cdna.fa

description: Nucleotide sequences of the high confidence gene model transcript sequences (cDNA).
DOI: 10.5061/dryad.bh84vs3/1
title: Data and code (zip file)

description: This file contains the data and code used to produce the figures and results.  The primary data file, all_data.csv, contains the fruit trait-related information (fruit color, fruit length, and plant habit, as well as taxonomic and geographic information).  The primary analysis file, Analyses_final.R, can be run to produce all figures and tables.  The remaining files and scripts are described in the README.txt file.
DOI: 10.60732/28f038f2
title: pure_magnesium_DFT_PRM2020

description: This dataset provides DFT (as implemented in VASP) calculations for pure magnesium. Configuration sets include bulk, generalized stacking fault energies, stable stacking fault, decohesion, relaxed surfaces, dimer, corner and rod, and vacancy configurations of Mg.
DOI: 10.60732/083a6253
title: sGDML_Aspirin_ccsd_NC2018_test

description: The test set of a train/test pair from the aspirin dataset from sGDML. To create the coupled cluster datasets, the data used for training the models were created by running abinitio MD in the NVT ensemble using the Nosé-Hoover thermostat at 500 K during a 200 ps simulation with a resolution of 0.5 fs. Energies and forces were recalculated by all-electron coupled cluster with single, double and perturbative triple excitations (CCSD(T)). The Dunning correlation-consistent basis set CCSD/cc-pVDZ was used for aspirin. All calculations were performed with the Psi4 software suite.
DOI: 10.60732/ced227e5
title: OC22-IS2RE-Validation-in-domain

description: In-domain validation configurations for the initial structure to relaxed total energy (IS2RE) task of OC22. Open Catalyst 2022 (OC22) is a database of training trajectories for predicting catalytic reactions on oxide surfaces meant to complement OC20, which did not contain oxide surfaces.
DOI: 10.60732/5ebf5a54
title: LiGePS_SSE_PBE

description: Approximately 6,500 configurations of Li10GeP2S12, based on crystal structures from the Materials Project database, material ID mp-696129. One of two LiGePS datasets from this source. The other uses the PBEsol functional, rather than the PBE functional.
DOI: 10.60732/2a29960c
title: vanadium_in_high_entropy_alloys_AM2020

description: Dataset created for "Vanadium is an optimal element for strengthening in both fcc and bcc high-entropy alloys", to explore the effect of V in the high-entropy systems fcc Co-Cr-Fe-Mn-Ni-V and bcc Cr-Mo-Nb-Ta-V-W-Hf-Ti-Zr. Structures include pure V, misfit volumes of V in Ni, and misfit volumes of Ni2V random alloys
DOI: 10.60732/8a437fac
title: JARVIS_DFT_2D_3_12_2021

description: The DFT-2D-3-12-2021 dataset is part of the joint automated repository for various integrated simulations (JARVIS) DFT database. This subset contains configurations of 2D materials. JARVIS is a set of tools and datasets built to meet current materials design challenges.
DOI: 10.60732/e05d99fd
title: NequIP_NC_2022

description: Approximately 57,000 configurations from the evaluation datasets for NequIP graph neural network model for interatomic potentials. Trajectories have been taken from LIPS, LIPO glass melt-quench simulation, and formate decomposition on Cu datasets.
DOI: 10.60732/74f33a37
title: CoCrFeNiPd_MRL2020

description: The dataset for "Origin of high strength in the CoCrFeNiPd high-entropy alloy", containing DFT-calculated values of the high-entropy alloy CoCrFeNiPd, created to explore the reasons behind experimental findings of the increased strength CoCrFeNiPd in comparison to CoCrFeNi.
DOI: 10.15468/dl.uxkvdu
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Macrosolen crassus Danser"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050751-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/54902e18
title: Zn_MTP_CMS2023

description: A training dataset of diverse atomic configurations of Zn, varying in aggregation states, crystal structures, defect types, and sizes. The aim was to derive a potential capable of accurately describing a broad spectrum of local atomic configurations in Zn.
DOI: 10.60732/31dbb6ee
title: Mo_PRM2019

description: This dataset was designed to enable machine learning of Mo elastic, thermal, and defect properties, as well as surface energetics, melting, and the structure of the liquid phase. The dataset was constructed by starting with the dataset from J. Byggmästar et al., Phys. Rev. B 100, 144105 (2019), then rescaling all of the configurations to the correct lattice spacing and adding in gamma surface configurations.
DOI: 10.15468/dl.z8w99b
title: Occurrence Download

description: A dataset containing 96 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ligularia liatroides (C.Winkl.) Hand.-Mazz."
 ]
}

 The dataset includes 96 records from 15 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050752-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/419ba77a
title: JARVIS_MEGNet2

description: The JARVIS-MEGNet2 dataset is part of the joint automated repository for various integrated simulations (JARVIS) database. This subset contains 133K materials with formation energy from the Materials Project, as used in the training of the MEGNet ML model. JARVIS is a set of tools and datasets built to meet current materials design challenges.
DOI: 10.60732/3cef7b09
title: Matbench_mp_e_form

description: Matbench v0.1 test dataset for predicting DFT formation energy from structure. Adapted from Materials Project database. Entries having formation energy more than 2.5eV and those containing noble gases are removed. Retrieved April 2, 2019. For benchmarking w/ nested cross validation, the order of the dataset must be identical to the retrieved data; refer to the Automatminer/Matbench publication for more details.Matbench is an automated leaderboard for benchmarking state of the art ML algorithms predicting a diverse range of solid materials' properties. It is hosted and maintained by the Materials Project.
DOI: 10.60732/20ba88af
title: Fe_nanoparticles_PRB_2023

description: This iron nanoparticles database contains dimers; trimers; bcc, fcc, hexagonal close-packed (hcp), simple cubic, and diamond crystalline structures. A wide range of cell parameters, as well as rattled structures, bcc-fcc and bcc-hcp transitional structures, surface slabs cleaved from relaxed bulk structures, nanoparticles and liquid configurations are included. The energy, forces and virials for the atomic structures were computed at the DFT level of theory using VASP with the PBE functional and standard PAW pseudopotentials for Fe (with 8 valence electrons, 4s^23d^6). The kinetic energy cutoff for plane waves was set to 400 eV and the energy threshold for convergence was 10-7 eV. All the DFT calculations were carried out with spin polarization.
DOI: 10.60732/82344f5c
title: AFF_JCP_2022

description: Approximately 145,000 configurations of alkane, aspirin, alpha-glucose and uracil, partly taken from the MD-17 dataset, used in training an 'Atomic Neural Net' model.
DOI: 10.60732/b6043e2b
title: OrbNet_Denali

description: All DFT single-point calculations for the OrbNet Denali training set were carried out in Entos Qcore version 0.8.17 at the ωB97X-D3/def2-TZVP level of theory using in-core density fitting with the neese=4 DFT integration grid.
DOI: 10.15468/dl.86xrm3
title: Occurrence Download

description: A dataset containing 27 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Mauloutchia heckelii Capuron"
 ]
}

 The dataset includes 27 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050754-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/1eaf36bf
title: SAIT_semiconductors_ACS_2023_SiN_validation

description: Validation configurations from the SAIT_semiconductors_ACS_2023_SiN dataset. This dataset contains SiN, Si and N configurations from the SAIT semiconductors datasets. SAIT semiconductors datasets comprise two rich datasets for the important semiconductor thin film materials silicon nitride (SiN) and hafnium oxide (HfO), gathered for the development of MLFFs. DFT simulations were conducted under various conditions that include differing initial structures, stoichiometry, temperature, strain, and defects.
DOI: 10.60732/8ad1a886
title: CGM-MLP_natcomm2023_screening_deposited-carbon@Cu_test

description: 468 structures uniformly selected from the MD/tfMC simulation, excluding any structures that are part of the training set. This dataset was one of the datasets used in testing screening parameters during the process of producing an active learning dataset for Cu-C interactions for the purposes of exploring substrate-catalyzed deposition as a means of controllable synthesis of carbon nanomaterials. The combined dataset includes structures from the Carbon_GAP_20 dataset and additional configurations of carbon clusters on a Cu(111) surface.
DOI: 10.15468/dl.putjs2
title: Occurrence Download

description: A dataset containing 973 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lygodium smithianum C.Presl ex Kuhn"
 ]
}

 The dataset includes 973 records from 43 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0050755-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.60732/dbe982a6
title: SAIT_semiconductors_ACS_2023_SiN_train

description: Training configurations from the SAIT_semiconductors_ACS_2023_SiN dataset. This dataset contains SiN, Si and N configurations from the SAIT semiconductors datasets. SAIT semiconductors datasets comprise two rich datasets for the important semiconductor thin film materials silicon nitride (SiN) and hafnium oxide (HfO), gathered for the development of MLFFs. DFT simulations were conducted under various conditions that include differing initial structures, stoichiometry, temperature, strain, and defects.
DOI: 10.5281/zenodo.10892291
title: Graph Neural Network vs. Large Language Model: A Comparative Analysis for Bug Report Priority and Severity Prediction
DOI: 10.5281/zenodo.10892292
title: Graph Neural Network vs. Large Language Model: A Comparative Analysis for Bug Report Priority and Severity Prediction
DOI: 10.60732/7239a192
title: BOTnet_ACAC_2022_train_600K_MD

description: 500 decorrelated geometries sampled from 600 K xTB MD run. Acetylacetone dataset generated from a long molecular dynamics simulation at 300 K using a Langevin thermostat at the semi-empirical GFN2-xTB level of theory. Configurations were sampled at an interval of 1 ps and the resulting set of configurations were recomputed with density functional theory using the PBE exchange-correlation functional with D3 dispersion correction and def2-SVP basis set and VeryTightSCF convergence settings using the ORCA electronic structure package.
DOI: 10.60732/b10d497c
title: JARVIS_Open_Catalyst_10K

description: The JARVIS_Open_Catalyst_10K dataset is part of the joint automated repository for various integrated simulations (JARVIS) DFT database. This subset contains configurations from the 10K training, rest validation and test dataset from the Open Catalyst Project (OCP). JARVIS is a set of tools and datasets built to meet current materials design challenges.
DOI: 10.60732/93adbc95
title: Ag-PBE_MSMSE_2021

description: Approximately 7,600 configurations of Ag used as part of a training dataset for a DP-GEN-based ML model for a Ag-Au nanoalloy potential.
DOI: 10.60732/fb4d895d
title: Matbench_mp_gap

description: The Matbench_mp_gap dataset is a Matbench v0.1 test dataset for predicting DFT PBE band gap from structure, adapted from the Materials Project database. Entries having a formation energy (or energy above the convex hull) greater than 150meV and those containing noble gases have been removed. Retrieved April 2, 2019. Refer to the Automatminer/Matbench publication for more details. This dataset contains band gap as calculated by PBE DFT from the Materials Project, in eV. Matbench is an automated leaderboard for benchmarking state of the art ML algorithms predicting a diverse range of solid materials' properties. It is hosted and maintained by the Materials Project.
DOI: 10.6084/m9.figshare.7375190.v1
title: Additional file 6: of The genome of the water strider Gerris buenoi reveals expansions of gene repertoires associated with adaptations to life on the water

description: List of annotated aquaporin genes in Gerris buenoi including gene names and closest identity. (XLSX 58 kb)
DOI: 10.6084/m9.figshare.14715164.v1
title: Additional file 5 of Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation

description: Additional file 5: Table S4. Protein data (LFQ intensities) for the discovery set of CIMP and non-CIMP cell lines.
DOI: 10.6084/m9.figshare.8948138
title: Additional file 4: of Effects of short-time exposure to atrazine on miRNA expression profiles in the gonad of common carp (Cyprinus carpio)

description: Differentially expressed mRNAs of PGC stage after exposed to atrazine for 24â h. (XLS 13978 kb)
DOI: 10.6084/m9.figshare.14715158.v2
title: Additional file 3 of Highly recurrent CBS epimutations in gastric cancer CpG island methylator phenotypes and inflammation

description: Additional file 3: Table S2. List of downregulated genes at RNA level in the discovery set of CIMP vs non-CIMP cell lines (P &lt; 0.05).
DOI: 10.6084/m9.figshare.13142366.v1
title: Additional file 3 of Metabolomics analysis reveals Embden Meyerhof Parnas pathway activation and flavonoids accumulation during dormancy transition in tree peony

description: Additional file 3: Table S3. DMs related to dormancy release, which were also involved in metabolic pathways.
DOI: 10.6084/m9.figshare.8948159
title: Additional file 6: of Effects of short-time exposure to atrazine on miRNA expression profiles in the gonad of common carp (Cyprinus carpio)

description: Differentially expressed mRNAs of juvenile ovary after exposed to atrazine for 24â h. (XLS 20271 kb)
DOI: 10.6084/m9.figshare.8948147
title: Additional file 5: of Effects of short-time exposure to atrazine on miRNA expression profiles in the gonad of common carp (Cyprinus carpio)

description: Differentially expressed mRNAs of juvenile ovary after exposed to atrazine for 8â h. (XLS 20365 kb)
DOI: 10.6084/m9.figshare.12618165.v1
title: Additional file 2 of Maternal obesity alters C19MC microRNAs expression profile in fetal umbilical cord blood

description: Additional file 2: Table S2. Characteristics of eight differentially expressed C19MC microRNAs. List of microRNAs’ ID, NCBI location in chromosome and their nucleotide sequence.
DOI: 10.6084/m9.figshare.8948156
title: Additional file 6: of ADAR1 promotes the epithelial-to-mesenchymal transition and stem-like cell phenotype of oral cancer by facilitating oncogenic microRNA maturation

description: Table S2. Clinicopathological profiles of 61 primary OSCC patients. OSCC, oral squamous cell carcinoma; P, P value; T, tumor size; N, lymph node; M, distant metastasis; TNM, tumor-node-metastases.Â (XLSX 26 kb)
DOI: 10.6084/m9.figshare.8948165.v1
title: Additional file 7: of Effects of short-time exposure to atrazine on miRNA expression profiles in the gonad of common carp (Cyprinus carpio)

description: Differentially expressed mRNAs of juvenile testis after exposed to atrazine for 8â h. (XLS 24312 kb)